JoaoJunior/formatted-java-preprocessed-code-APR

public static Vector calcCCTDT(Vector chromosomes){ Vector results = new Vector(); int numMarkers = Chromosome.getSize(); for (int i = 0; i < numMarkers; i++){ TDTResult thisResult = new TDTResult(Chromosome.getMarker(i)); for (int j = 0; j < chromosomes.size()-1; j++){ Chromosome theChrom = (Chromosome)chromosomes.get(j); j++; Chromosome nextChrom = (Chromosome)chromosomes.get(j); if (theChrom.getAffected()){ thisResult.tallyCCInd(theChrom.getGenotype(i), nextChrom.getGenotype(i), 0); }else{ thisResult.tallyCCInd(theChrom.getGenotype(i), nextChrom.getGenotype(i), 1); } } results.add(thisResult); } return results; }

public static Vector calcCCTDT(Vector chromosomes){ Vector results = new Vector(); int numMarkers = Chromosome.getSize(); for (int i = 0; i < numMarkers; i++){ TDTResult thisResult = new TDTResult(Chromosome.getMarker(i)); for (int j = 0; j < chromosomes.size()-1; j++){ Chromosome theChrom = (Chromosome)chromosomes.get(j); j++; Chromosome nextChrom = (Chromosome)chromosomes.get(j); if (theChrom.getAffected()){ thisResult.tallyCCInd(theChrom.getFilteredGenotype(i), nextChrom.getFilteredGenotype(i), 0); }else{ thisResult.tallyCCInd(theChrom.getGenotype(i), nextChrom.getGenotype(i), 1); } } results.add(thisResult); } return results; }

1,110,172

public static Vector calcCCTDT(Vector chromosomes){ Vector results = new Vector(); int numMarkers = Chromosome.getSize(); for (int i = 0; i < numMarkers; i++){ TDTResult thisResult = new TDTResult(Chromosome.getMarker(i)); for (int j = 0; j < chromosomes.size()-1; j++){ Chromosome theChrom = (Chromosome)chromosomes.get(j); j++; Chromosome nextChrom = (Chromosome)chromosomes.get(j); if (theChrom.getAffected()){ thisResult.tallyCCInd(theChrom.getGenotype(i), nextChrom.getGenotype(i), 0); }else{ thisResult.tallyCCInd(theChrom.getGenotype(i), nextChrom.getGenotype(i), 1); } } results.add(thisResult); } return results; }

public static Vector calcCCTDT(Vector chromosomes){ Vector results = new Vector(); int numMarkers = Chromosome.getSize(); for (int i = 0; i < numMarkers; i++){ TDTResult thisResult = new TDTResult(Chromosome.getMarker(i)); for (int j = 0; j < chromosomes.size()-1; j++){ Chromosome theChrom = (Chromosome)chromosomes.get(j); j++; Chromosome nextChrom = (Chromosome)chromosomes.get(j); if (theChrom.getAffected()){ thisResult.tallyCCInd(theChrom.getGenotype(i), nextChrom.getGenotype(i), 0); }else{ thisResult.tallyCCInd(theChrom.getFilteredGenotype(i), nextChrom.getFilteredGenotype(i), 1); } } results.add(thisResult); } return results; }

1,110,173

public static Vector calcTrioTDT(Vector chromosomes) { Vector results = new Vector(); int numMarkers = Chromosome.getSize(); for(int k=0;k<numMarkers;k++){ results.add(new TDTResult(Chromosome.getMarker(k))); } for(int i=0;i<chromosomes.size()-3;i++){ Chromosome chrom1T = (Chromosome)chromosomes.get(i); i++; Chromosome chrom1U = (Chromosome)chromosomes.get(i); i++; Chromosome chrom2T = (Chromosome)chromosomes.get(i); i++; Chromosome chrom2U = (Chromosome)chromosomes.get(i); //System.out.println("ind1T: " + chrom1T.getPed() + "\t" + chrom1T.getIndividual() ); //System.out.println("ind1U: " + chrom1U.getPed() + "\t" + chrom1U.getIndividual() ); //System.out.println("ind2T: " + chrom2T.getPed() + "\t" + chrom2T.getIndividual() ); //System.out.println("ind2U: " + chrom2U.getPed() + "\t" + chrom2U.getIndividual() ); for(int j=0;j<numMarkers;j++){ if(!chrom1T.kidMissing[j] && !chrom2T.kidMissing[j]) { byte allele1T = chrom1T.getGenotype(j); byte allele1U = chrom1U.getGenotype(j); byte allele2T = chrom2T.getGenotype(j); byte allele2U = chrom2U.getGenotype(j); if( !(allele1T == 0 || allele1U == 0 || allele2T == 0 || allele2U == 0) ){ TDTResult curRes = (TDTResult)results.get(j); curRes.tallyTrioInd(allele1T,allele1U); curRes.tallyTrioInd(allele2T,allele2U); } } } } return results; }

public static Vector calcTrioTDT(Vector chromosomes) { Vector results = new Vector(); int numMarkers = Chromosome.getFilteredSize(); for(int k=0;k<numMarkers;k++){ results.add(new TDTResult(Chromosome.getMarker(k))); } for(int i=0;i<chromosomes.size()-3;i++){ Chromosome chrom1T = (Chromosome)chromosomes.get(i); i++; Chromosome chrom1U = (Chromosome)chromosomes.get(i); i++; Chromosome chrom2T = (Chromosome)chromosomes.get(i); i++; Chromosome chrom2U = (Chromosome)chromosomes.get(i); //System.out.println("ind1T: " + chrom1T.getPed() + "\t" + chrom1T.getIndividual() ); //System.out.println("ind1U: " + chrom1U.getPed() + "\t" + chrom1U.getIndividual() ); //System.out.println("ind2T: " + chrom2T.getPed() + "\t" + chrom2T.getIndividual() ); //System.out.println("ind2U: " + chrom2U.getPed() + "\t" + chrom2U.getIndividual() ); for(int j=0;j<numMarkers;j++){ if(!chrom1T.kidMissing[j] && !chrom2T.kidMissing[j]) { byte allele1T = chrom1T.getGenotype(j); byte allele1U = chrom1U.getGenotype(j); byte allele2T = chrom2T.getGenotype(j); byte allele2U = chrom2U.getGenotype(j); if( !(allele1T == 0 || allele1U == 0 || allele2T == 0 || allele2U == 0) ){ TDTResult curRes = (TDTResult)results.get(j); curRes.tallyTrioInd(allele1T,allele1U); curRes.tallyTrioInd(allele2T,allele2U); } } } } return results; }

1,110,174

public static Vector calcTrioTDT(Vector chromosomes) { Vector results = new Vector(); int numMarkers = Chromosome.getSize(); for(int k=0;k<numMarkers;k++){ results.add(new TDTResult(Chromosome.getMarker(k))); } for(int i=0;i<chromosomes.size()-3;i++){ Chromosome chrom1T = (Chromosome)chromosomes.get(i); i++; Chromosome chrom1U = (Chromosome)chromosomes.get(i); i++; Chromosome chrom2T = (Chromosome)chromosomes.get(i); i++; Chromosome chrom2U = (Chromosome)chromosomes.get(i); //System.out.println("ind1T: " + chrom1T.getPed() + "\t" + chrom1T.getIndividual() ); //System.out.println("ind1U: " + chrom1U.getPed() + "\t" + chrom1U.getIndividual() ); //System.out.println("ind2T: " + chrom2T.getPed() + "\t" + chrom2T.getIndividual() ); //System.out.println("ind2U: " + chrom2U.getPed() + "\t" + chrom2U.getIndividual() ); for(int j=0;j<numMarkers;j++){ if(!chrom1T.kidMissing[j] && !chrom2T.kidMissing[j]) { byte allele1T = chrom1T.getGenotype(j); byte allele1U = chrom1U.getGenotype(j); byte allele2T = chrom2T.getGenotype(j); byte allele2U = chrom2U.getGenotype(j); if( !(allele1T == 0 || allele1U == 0 || allele2T == 0 || allele2U == 0) ){ TDTResult curRes = (TDTResult)results.get(j); curRes.tallyTrioInd(allele1T,allele1U); curRes.tallyTrioInd(allele2T,allele2U); } } } } return results; }

1,110,175

public void sendMail(MailAddress sender, Collection recipients, MimeMessage message) throws MessagingException { //log.info("start processing incoming mail having id = " + msg.getMessageID()); MailProcessingRecord mailProcessingRecord = new MailProcessingRecord(); mailProcessingRecord.setReceivingQueue("smtpOutbound"); mailProcessingRecord.setTimeFetchStart(System.currentTimeMillis()); mailProcessingRecord.setByteReceivedTotal(message.getSize()); try { if (!MailMatchingUtils.isMatchCandidate(message)) return; String id = MailMatchingUtils.getMailIdHeader(message); mailProcessingRecord.setMailId(id); String[] subjectHeader = message.getHeader("Subject"); if (subjectHeader != null && subjectHeader.length > 0) { mailProcessingRecord.setSubject(subjectHeader[0]); } // TODO mailProcessingRecord.setByteReceivedText(); // TODO mailProcessingRecord.setByteReceivedBinary(); mailProcessingRecord.setTimeFetchEnd(System.currentTimeMillis()); } catch(MessagingException e) { log.error("error processing incoming mail: " + e.getMessage()); throw e; // rethrow after logging } finally{ MailProcessingRecord matchedAndMergedRecord = m_results.matchMailRecord(mailProcessingRecord); if (matchedAndMergedRecord == null) { if (mailProcessingRecord.getMailId() == null) mailProcessingRecord.setMailId(MailProcessingRecord.getNextId()); m_results.addNewMailRecord(mailProcessingRecord); } else { MailMatchingUtils.validateMail(message, matchedAndMergedRecord); } } }

1,110,177

public void doTag(XMLOutput output) throws Exception { Project project = getAntProject(); String tagName = getTagName(); Object parentObject = null; // must be a datatype. TaskSource ancestor = (TaskSource) findAncestorWithClass( TaskSource.class ); if ( ancestor != null ) { parentObject = ancestor.getTaskObject(); } // lets assume that Task instances are not nested inside other Task instances // for example <manifest> inside a <jar> should be a nested object, where as // if the parent is not a Task the <manifest> should create a ManifestTask if ( ! ( parentObject instanceof Task ) && project.getTaskDefinitions().containsKey( tagName ) ) { if ( log.isDebugEnabled() ) { log.debug( "Creating an ant Task for name: " + tagName ); } // the following algorithm follows the lifetime of a tag // http://jakarta.apache.org/ant/manual/develop.html#writingowntask // kindly recommended by Stefan Bodewig // create and set its project reference task = createTask( tagName ); if ( task instanceof TaskAdapter ) { setObject( ((TaskAdapter)task).getProxy() ); } else { setObject( task ); } // set the task ID if one is given Object id = getAttributes().remove( "id" ); if ( id != null ) { project.addReference( (String) id, task ); } // ### we might want to spoof a Target setting here // now lets initialize task.init(); // now lets invoke the body to call all the createXXX() or addXXX() methods String body = getBodyText(); // now lets set any attributes of this tag... setBeanProperties(); // now lets set the addText() of the body content, if its applicaable Method method = MethodUtils.getAccessibleMethod( task.getClass(), "addText", addTaskParamTypes ); if (method != null) { String text = getBodyText(); Object[] args = { text }; method.invoke(this.task, args); } // now lets set all the attributes of the child elements // XXXX: to do! // now we're ready to invoke the task // XXX: should we call execute() or perform()? task.perform(); } else { if ( log.isDebugEnabled() ) { log.debug( "Creating a nested object name: " + tagName ); } if ( parentObject == null ) { parentObject = findBeanAncestor(); } Object nested = createNestedObject( parentObject, tagName ); if ( nested == null ) { nested = createDataType( tagName ); } if ( nested != null ) { setObject( nested ); // set the task ID if one is given Object id = getAttributes().remove( "id" ); if ( id != null ) { project.addReference( (String) id, nested ); } try{ PropertyUtils.setProperty( nested, "name", tagName ); } catch (Exception e) { } // now lets invoke the body String body = getBodyText(); // now lets set any attributes of this tag... setBeanProperties(); // now lets add it to its parent if ( parentObject != null ) { IntrospectionHelper ih = IntrospectionHelper.getHelper( parentObject.getClass() ); try { ih.storeElement( project, parentObject, nested, tagName ); } catch (Exception e) { //log.warn( "Caught exception setting nested: " + tagName, e ); } } } else { // lets treat this tag as static XML... StaticTag tag = new StaticTag("", tagName, tagName); tag.setParent( getParent() ); tag.setBody( getBody() ); tag.setContext(context); for (Iterator iter = getAttributes().entrySet().iterator(); iter.hasNext();) { Map.Entry entry = (Map.Entry) iter.next(); String name = (String) entry.getKey(); Object value = entry.getValue(); tag.setAttribute(name, value); } tag.doTag(output); } } }

1,110,178

public void doTag(XMLOutput output) throws Exception { Project project = getAntProject(); String tagName = getTagName(); Object parentObject = null; // must be a datatype. TaskSource ancestor = (TaskSource) findAncestorWithClass( TaskSource.class ); if ( ancestor != null ) { parentObject = ancestor.getTaskObject(); } // lets assume that Task instances are not nested inside other Task instances // for example <manifest> inside a <jar> should be a nested object, where as // if the parent is not a Task the <manifest> should create a ManifestTask if ( ! ( parentObject instanceof Task ) && project.getTaskDefinitions().containsKey( tagName ) ) { if ( log.isDebugEnabled() ) { log.debug( "Creating an ant Task for name: " + tagName ); } // the following algorithm follows the lifetime of a tag // http://jakarta.apache.org/ant/manual/develop.html#writingowntask // kindly recommended by Stefan Bodewig // create and set its project reference task = createTask( tagName ); if ( task instanceof TaskAdapter ) { setObject( ((TaskAdapter)task).getProxy() ); } else { setObject( task ); } // set the task ID if one is given Object id = getAttributes().remove( "id" ); if ( id != null ) { project.addReference( (String) id, task ); } // ### we might want to spoof a Target setting here // now lets initialize task.init(); // now lets invoke the body to call all the createXXX() or addXXX() methods String body = getBodyText(); // now lets set any attributes of this tag... setBeanProperties(); // now lets set the addText() of the body content, if its applicaable Method method = MethodUtils.getAccessibleMethod( task.getClass(), "addText", addTaskParamTypes ); if (method != null) { String text = getBodyText(); Object[] args = { text }; method.invoke(this.task, args); } // now lets set all the attributes of the child elements // XXXX: to do! // now we're ready to invoke the task // XXX: should we call execute() or perform()? task.perform(); } else { if ( log.isDebugEnabled() ) { log.debug( "Creating a nested object name: " + tagName ); } if ( parentObject == null ) { parentObject = findBeanAncestor(); } Object nested = createNestedObject( parentObject, tagName ); if ( nested == null ) { nested = createDataType( tagName ); } if ( nested != null ) { setObject( nested ); // set the task ID if one is given Object id = getAttributes().remove( "id" ); if ( id != null ) { project.addReference( (String) id, nested ); } try{ PropertyUtils.setProperty( nested, "name", tagName ); } catch (Exception e) { } // now lets invoke the body String body = getBodyText(); // now lets set any attributes of this tag... setBeanProperties(); // now lets add it to its parent if ( parentObject != null ) { IntrospectionHelper ih = IntrospectionHelper.getHelper( parentObject.getClass() ); try { ih.storeElement( project, parentObject, nested, tagName ); } catch (Exception e) { //log.warn( "Caught exception setting nested: " + tagName, e ); } } } else { // lets treat this tag as static XML... StaticTag tag = new StaticTag("", tagName, tagName); tag.setParent( getParent() ); tag.setBody( getBody() ); tag.setContext(context); for (Iterator iter = getAttributes().entrySet().iterator(); iter.hasNext();) { Map.Entry entry = (Map.Entry) iter.next(); String name = (String) entry.getKey(); Object value = entry.getValue(); tag.setAttribute(name, value); } tag.doTag(output); } } }

1,110,179

protected Object findBeanAncestor() throws Exception { Tag tag = getParent(); if (tag != null) { if (tag instanceof BeanSource) { BeanSource beanSource = (BeanSource) tag; return beanSource.getBean(); } } return tag; }

protected Object findBeanAncestor() throws Exception { Tag tag = getParent(); while (tag != null) { if (tag instanceof BeanSource) { BeanSource beanSource = (BeanSource) tag; return beanSource.getBean(); } } return tag; }

1,110,181

protected Object findBeanAncestor() throws Exception { Tag tag = getParent(); if (tag != null) { if (tag instanceof BeanSource) { BeanSource beanSource = (BeanSource) tag; return beanSource.getBean(); } } return tag; }

protected Object findBeanAncestor() throws Exception { Tag tag = getParent(); if (tag != null) { if (tag instanceof BeanSource) { BeanSource beanSource = (BeanSource) tag; return beanSource.getBean(); } } return getParent(); }

1,110,182

public void actionPerformed( ActionEvent e ) { importFile(); }

public void actionPerformed( ActionEvent e ) { BrowserWindow br = new BrowserWindow(); br.setVisible( true ); }

1,110,184

public void actionPerformed( ActionEvent e ) { System.exit( 0 ); }

public void actionPerformed( ActionEvent e ) { importFile(); }

1,110,185

protected TagScript createTag( String namespaceURI, String localName, Attributes list) throws SAXException { try { // use the URI to load a taglib TagLibrary taglib = context.getTagLibrary(namespaceURI); if (taglib == null) { if (namespaceURI != null && namespaceURI.startsWith("jelly:")) { String uri = namespaceURI.substring(6); // try to find the class on the claspath try { Class taglibClass = getClassLoader().loadClass(uri); taglib = (TagLibrary) taglibClass.newInstance(); context.registerTagLibrary(namespaceURI, taglib); } catch (ClassNotFoundException e) { log.warn("Could not load class: " + uri + " so disabling the taglib", e); } catch (IllegalAccessException e) { log.warn("Constructor for class is not accessible: " + uri + " so disabling the taglib", e); } catch (InstantiationException e) { log.warn("Class could not be instantiated: " + uri + " so disabling the taglib", e); } catch (ClassCastException e) { log.warn("Class is not a TagLibrary: " + uri + " so disabling the taglib", e); } } } if (taglib != null) { TagScript script = taglib.createTagScript(localName, list); if ( script != null ) { configureTagScript(script); // clone the attributes to keep them around after this parse script.setSaxAttributes(new AttributesImpl(list)); // now iterate through through the expressions int size = list.getLength(); for (int i = 0; i < size; i++) { String attributeName = list.getLocalName(i); String attributeValue = list.getValue(i); Expression expression = taglib.createExpression( getExpressionFactory(), script, attributeName, attributeValue); if (expression == null) { expression = createConstantExpression(localName, attributeName, attributeValue); } script.addAttribute(attributeName, expression); } } return script; } return null; } catch (Exception e) { log.warn( "Could not create taglib or URI: " + namespaceURI + " tag name: " + localName, e); throw createSAXException(e); } }

protected TagScript createTag( String namespaceURI, String localName, Attributes list) throws SAXException { try { // use the URI to load a taglib TagLibrary taglib = context.getTagLibrary(namespaceURI); if (taglib == null) { if (namespaceURI != null && namespaceURI.startsWith("jelly:")) { String uri = namespaceURI.substring(6); // try to find the class on the claspath try { Class taglibClass = getClassLoader().loadClass(uri); taglib = (TagLibrary) taglibClass.newInstance(); context.registerTagLibrary(namespaceURI, taglib); } catch (ClassNotFoundException e) { throw createSAXException("Could not load class: " + uri + " so taglib instantiation failed", e); } catch (IllegalAccessException e) { log.warn("Constructor for class is not accessible: " + uri + " so disabling the taglib", e); } catch (InstantiationException e) { log.warn("Class could not be instantiated: " + uri + " so disabling the taglib", e); } catch (ClassCastException e) { log.warn("Class is not a TagLibrary: " + uri + " so disabling the taglib", e); } } } if (taglib != null) { TagScript script = taglib.createTagScript(localName, list); if ( script != null ) { configureTagScript(script); // clone the attributes to keep them around after this parse script.setSaxAttributes(new AttributesImpl(list)); // now iterate through through the expressions int size = list.getLength(); for (int i = 0; i < size; i++) { String attributeName = list.getLocalName(i); String attributeValue = list.getValue(i); Expression expression = taglib.createExpression( getExpressionFactory(), script, attributeName, attributeValue); if (expression == null) { expression = createConstantExpression(localName, attributeName, attributeValue); } script.addAttribute(attributeName, expression); } } return script; } return null; } catch (Exception e) { log.warn( "Could not create taglib or URI: " + namespaceURI + " tag name: " + localName, e); throw createSAXException(e); } }

1,110,186

protected TagScript createTag( String namespaceURI, String localName, Attributes list) throws SAXException { try { // use the URI to load a taglib TagLibrary taglib = context.getTagLibrary(namespaceURI); if (taglib == null) { if (namespaceURI != null && namespaceURI.startsWith("jelly:")) { String uri = namespaceURI.substring(6); // try to find the class on the claspath try { Class taglibClass = getClassLoader().loadClass(uri); taglib = (TagLibrary) taglibClass.newInstance(); context.registerTagLibrary(namespaceURI, taglib); } catch (ClassNotFoundException e) { log.warn("Could not load class: " + uri + " so disabling the taglib", e); } catch (IllegalAccessException e) { log.warn("Constructor for class is not accessible: " + uri + " so disabling the taglib", e); } catch (InstantiationException e) { log.warn("Class could not be instantiated: " + uri + " so disabling the taglib", e); } catch (ClassCastException e) { log.warn("Class is not a TagLibrary: " + uri + " so disabling the taglib", e); } } } if (taglib != null) { TagScript script = taglib.createTagScript(localName, list); if ( script != null ) { configureTagScript(script); // clone the attributes to keep them around after this parse script.setSaxAttributes(new AttributesImpl(list)); // now iterate through through the expressions int size = list.getLength(); for (int i = 0; i < size; i++) { String attributeName = list.getLocalName(i); String attributeValue = list.getValue(i); Expression expression = taglib.createExpression( getExpressionFactory(), script, attributeName, attributeValue); if (expression == null) { expression = createConstantExpression(localName, attributeName, attributeValue); } script.addAttribute(attributeName, expression); } } return script; } return null; } catch (Exception e) { log.warn( "Could not create taglib or URI: " + namespaceURI + " tag name: " + localName, e); throw createSAXException(e); } }

protected TagScript createTag( String namespaceURI, String localName, Attributes list) throws SAXException { try { // use the URI to load a taglib TagLibrary taglib = context.getTagLibrary(namespaceURI); if (taglib == null) { if (namespaceURI != null && namespaceURI.startsWith("jelly:")) { String uri = namespaceURI.substring(6); // try to find the class on the claspath try { Class taglibClass = getClassLoader().loadClass(uri); taglib = (TagLibrary) taglibClass.newInstance(); context.registerTagLibrary(namespaceURI, taglib); } catch (ClassNotFoundException e) { log.warn("Could not load class: " + uri + " so disabling the taglib", e); } catch (IllegalAccessException e) { throw createSAXException("Constructor for class is not accessible: " + uri + " so taglib instantiation failed",e); } catch (InstantiationException e) { log.warn("Class could not be instantiated: " + uri + " so disabling the taglib", e); } catch (ClassCastException e) { log.warn("Class is not a TagLibrary: " + uri + " so disabling the taglib", e); } } } if (taglib != null) { TagScript script = taglib.createTagScript(localName, list); if ( script != null ) { configureTagScript(script); // clone the attributes to keep them around after this parse script.setSaxAttributes(new AttributesImpl(list)); // now iterate through through the expressions int size = list.getLength(); for (int i = 0; i < size; i++) { String attributeName = list.getLocalName(i); String attributeValue = list.getValue(i); Expression expression = taglib.createExpression( getExpressionFactory(), script, attributeName, attributeValue); if (expression == null) { expression = createConstantExpression(localName, attributeName, attributeValue); } script.addAttribute(attributeName, expression); } } return script; } return null; } catch (Exception e) { log.warn( "Could not create taglib or URI: " + namespaceURI + " tag name: " + localName, e); throw createSAXException(e); } }

1,110,187

protected TagScript createTag( String namespaceURI, String localName, Attributes list) throws SAXException { try { // use the URI to load a taglib TagLibrary taglib = context.getTagLibrary(namespaceURI); if (taglib == null) { if (namespaceURI != null && namespaceURI.startsWith("jelly:")) { String uri = namespaceURI.substring(6); // try to find the class on the claspath try { Class taglibClass = getClassLoader().loadClass(uri); taglib = (TagLibrary) taglibClass.newInstance(); context.registerTagLibrary(namespaceURI, taglib); } catch (ClassNotFoundException e) { log.warn("Could not load class: " + uri + " so disabling the taglib", e); } catch (IllegalAccessException e) { log.warn("Constructor for class is not accessible: " + uri + " so disabling the taglib", e); } catch (InstantiationException e) { log.warn("Class could not be instantiated: " + uri + " so disabling the taglib", e); } catch (ClassCastException e) { log.warn("Class is not a TagLibrary: " + uri + " so disabling the taglib", e); } } } if (taglib != null) { TagScript script = taglib.createTagScript(localName, list); if ( script != null ) { configureTagScript(script); // clone the attributes to keep them around after this parse script.setSaxAttributes(new AttributesImpl(list)); // now iterate through through the expressions int size = list.getLength(); for (int i = 0; i < size; i++) { String attributeName = list.getLocalName(i); String attributeValue = list.getValue(i); Expression expression = taglib.createExpression( getExpressionFactory(), script, attributeName, attributeValue); if (expression == null) { expression = createConstantExpression(localName, attributeName, attributeValue); } script.addAttribute(attributeName, expression); } } return script; } return null; } catch (Exception e) { log.warn( "Could not create taglib or URI: " + namespaceURI + " tag name: " + localName, e); throw createSAXException(e); } }

protected TagScript createTag( String namespaceURI, String localName, Attributes list) throws SAXException { try { // use the URI to load a taglib TagLibrary taglib = context.getTagLibrary(namespaceURI); if (taglib == null) { if (namespaceURI != null && namespaceURI.startsWith("jelly:")) { String uri = namespaceURI.substring(6); // try to find the class on the claspath try { Class taglibClass = getClassLoader().loadClass(uri); taglib = (TagLibrary) taglibClass.newInstance(); context.registerTagLibrary(namespaceURI, taglib); } catch (ClassNotFoundException e) { log.warn("Could not load class: " + uri + " so disabling the taglib", e); } catch (IllegalAccessException e) { log.warn("Constructor for class is not accessible: " + uri + " so disabling the taglib", e); } catch (InstantiationException e) { throw createSAXException("Class could not be instantiated: " + uri + " so taglib instantiation failed",e); } catch (ClassCastException e) { log.warn("Class is not a TagLibrary: " + uri + " so disabling the taglib", e); } } } if (taglib != null) { TagScript script = taglib.createTagScript(localName, list); if ( script != null ) { configureTagScript(script); // clone the attributes to keep them around after this parse script.setSaxAttributes(new AttributesImpl(list)); // now iterate through through the expressions int size = list.getLength(); for (int i = 0; i < size; i++) { String attributeName = list.getLocalName(i); String attributeValue = list.getValue(i); Expression expression = taglib.createExpression( getExpressionFactory(), script, attributeName, attributeValue); if (expression == null) { expression = createConstantExpression(localName, attributeName, attributeValue); } script.addAttribute(attributeName, expression); } } return script; } return null; } catch (Exception e) { log.warn( "Could not create taglib or URI: " + namespaceURI + " tag name: " + localName, e); throw createSAXException(e); } }

1,110,188

protected TagScript createTag( String namespaceURI, String localName, Attributes list) throws SAXException { try { // use the URI to load a taglib TagLibrary taglib = context.getTagLibrary(namespaceURI); if (taglib == null) { if (namespaceURI != null && namespaceURI.startsWith("jelly:")) { String uri = namespaceURI.substring(6); // try to find the class on the claspath try { Class taglibClass = getClassLoader().loadClass(uri); taglib = (TagLibrary) taglibClass.newInstance(); context.registerTagLibrary(namespaceURI, taglib); } catch (ClassNotFoundException e) { log.warn("Could not load class: " + uri + " so disabling the taglib", e); } catch (IllegalAccessException e) { log.warn("Constructor for class is not accessible: " + uri + " so disabling the taglib", e); } catch (InstantiationException e) { log.warn("Class could not be instantiated: " + uri + " so disabling the taglib", e); } catch (ClassCastException e) { log.warn("Class is not a TagLibrary: " + uri + " so disabling the taglib", e); } } } if (taglib != null) { TagScript script = taglib.createTagScript(localName, list); if ( script != null ) { configureTagScript(script); // clone the attributes to keep them around after this parse script.setSaxAttributes(new AttributesImpl(list)); // now iterate through through the expressions int size = list.getLength(); for (int i = 0; i < size; i++) { String attributeName = list.getLocalName(i); String attributeValue = list.getValue(i); Expression expression = taglib.createExpression( getExpressionFactory(), script, attributeName, attributeValue); if (expression == null) { expression = createConstantExpression(localName, attributeName, attributeValue); } script.addAttribute(attributeName, expression); } } return script; } return null; } catch (Exception e) { log.warn( "Could not create taglib or URI: " + namespaceURI + " tag name: " + localName, e); throw createSAXException(e); } }

protected TagScript createTag( String namespaceURI, String localName, Attributes list) throws SAXException { try { // use the URI to load a taglib TagLibrary taglib = context.getTagLibrary(namespaceURI); if (taglib == null) { if (namespaceURI != null && namespaceURI.startsWith("jelly:")) { String uri = namespaceURI.substring(6); // try to find the class on the claspath try { Class taglibClass = getClassLoader().loadClass(uri); taglib = (TagLibrary) taglibClass.newInstance(); context.registerTagLibrary(namespaceURI, taglib); } catch (ClassNotFoundException e) { log.warn("Could not load class: " + uri + " so disabling the taglib", e); } catch (IllegalAccessException e) { log.warn("Constructor for class is not accessible: " + uri + " so disabling the taglib", e); } catch (InstantiationException e) { log.warn("Class could not be instantiated: " + uri + " so disabling the taglib", e); } catch (ClassCastException e) { throw createSAXException("Class is not a TagLibrary: " + uri + " so taglib instantiation failed",e); } } } if (taglib != null) { TagScript script = taglib.createTagScript(localName, list); if ( script != null ) { configureTagScript(script); // clone the attributes to keep them around after this parse script.setSaxAttributes(new AttributesImpl(list)); // now iterate through through the expressions int size = list.getLength(); for (int i = 0; i < size; i++) { String attributeName = list.getLocalName(i); String attributeValue = list.getValue(i); Expression expression = taglib.createExpression( getExpressionFactory(), script, attributeName, attributeValue); if (expression == null) { expression = createConstantExpression(localName, attributeName, attributeValue); } script.addAttribute(attributeName, expression); } } return script; } return null; } catch (Exception e) { log.warn( "Could not create taglib or URI: " + namespaceURI + " tag name: " + localName, e); throw createSAXException(e); } }

1,110,189

public AntTag(Project project, String tagName) { this.project = project; this.tagName = tagName; }

1,110,190

public Object createDataType(String name) throws Exception { Object dataType = null; Class type = (Class) getAntProject().getDataTypeDefinitions().get(name); if ( type != null ) { try { Constructor ctor = null; boolean noArg = false; // DataType can have a "no arg" constructor or take a single // Project argument. try { ctor = type.getConstructor(new Class[0]); noArg = true; } catch (NoSuchMethodException nse) { ctor = type.getConstructor(new Class[] { Project.class }); noArg = false; } if (noArg) { dataType = (DataType) ctor.newInstance(new Object[0]); } else { dataType = (DataType) ctor.newInstance(new Object[] {project}); } ((DataType)dataType).setProject( project ); } catch (Throwable t) { // ignore log.error(t); } } return dataType; }

public Object createDataType(String name) throws Exception { Object dataType = null; Class type = (Class) getAntProject().getDataTypeDefinitions().get(name); if ( type != null ) { try { Constructor ctor = null; boolean noArg = false; // DataType can have a "no arg" constructor or take a single // Project argument. try { ctor = type.getConstructor(new Class[0]); noArg = true; } catch (NoSuchMethodException nse) { ctor = type.getConstructor(new Class[] { Project.class }); noArg = false; } if (noArg) { dataType = (DataType) ctor.newInstance(new Object[0]); } else { dataType = (DataType) ctor.newInstance(new Object[] { getAntProject() }); } ((DataType)dataType).setProject( project ); } catch (Throwable t) { // ignore log.error(t); } } return dataType; }

1,110,191

public Object createDataType(String name) throws Exception { Object dataType = null; Class type = (Class) getAntProject().getDataTypeDefinitions().get(name); if ( type != null ) { try { Constructor ctor = null; boolean noArg = false; // DataType can have a "no arg" constructor or take a single // Project argument. try { ctor = type.getConstructor(new Class[0]); noArg = true; } catch (NoSuchMethodException nse) { ctor = type.getConstructor(new Class[] { Project.class }); noArg = false; } if (noArg) { dataType = (DataType) ctor.newInstance(new Object[0]); } else { dataType = (DataType) ctor.newInstance(new Object[] {project}); } ((DataType)dataType).setProject( project ); } catch (Throwable t) { // ignore log.error(t); } } return dataType; }

public Object createDataType(String name) throws Exception { Object dataType = null; Class type = (Class) getAntProject().getDataTypeDefinitions().get(name); if ( type != null ) { try { Constructor ctor = null; boolean noArg = false; // DataType can have a "no arg" constructor or take a single // Project argument. try { ctor = type.getConstructor(new Class[0]); noArg = true; } catch (NoSuchMethodException nse) { ctor = type.getConstructor(new Class[] { Project.class }); noArg = false; } if (noArg) { dataType = (DataType) ctor.newInstance(new Object[0]); } else { dataType = (DataType) ctor.newInstance(new Object[] {project}); } ((DataType)dataType).setProject( getAntProject() ); } catch (Throwable t) { // ignore log.error(t); } } return dataType; }

1,110,192

public Project getAntProject() { return this.project; }

public Project getAntProject() { return AntTagLibrary.getProject(context); }

1,110,193

public void doTag(XMLOutput output) throws Exception { getBody().run(context, output); }

public void doTag(XMLOutput output) throws Exception { invokeBody(output); }

1,110,195

public ActionForward execute(WebContext context, ActionMapping mapping, ActionForm actionForm, HttpServletRequest request, HttpServletResponse response) throws Exception { Map users = UserManager.getInstance().getAllUsers(); request.setAttribute(RequestAttributes.USERS, users); return mapping.findForward(Forwards.SUCCESS); }

public ActionForward execute(WebContext context, ActionMapping mapping, ActionForm actionForm, HttpServletRequest request, HttpServletResponse response) throws Exception { Map users = UserManager.getInstance().getAllUsers(); Map orderedUsers = new TreeMap(users); request.setAttribute(RequestAttributes.USERS, orderedUsers); return mapping.findForward(Forwards.SUCCESS); }

1,110,199

public String makeDropForeignKeySQL(String fkCatalog, String fkSchema, String fkTable, String fkName) { return "\n ALTER TABLE ONLY " +DDLUtils.toQualifiedName(fkCatalog, fkSchema, fkTable) +" DROP CONSTRAINT " +fkName; }

public String makeDropForeignKeySQL(String fkTable, String fkName) { return "\n ALTER TABLE ONLY " +DDLUtils.toQualifiedName(fkCatalog, fkSchema, fkTable) +" DROP CONSTRAINT " +fkName; }

1,110,200

public String makeDropForeignKeySQL(String fkCatalog, String fkSchema, String fkTable, String fkName) { return "\n ALTER TABLE ONLY " +DDLUtils.toQualifiedName(fkCatalog, fkSchema, fkTable) +" DROP CONSTRAINT " +fkName; }

1,110,201

public void modifyColumn(SQLColumn c) throws ArchitectDiffException { Map colNameMap = new HashMap(); SQLTable t = c.getParentTable(); print("\n ALTER TABLE ONLY "); print( toQualifiedName(t) ); print(" ALTER COLUMN "); // Column name String columnPhysName = createPhysicalName(colNameMap,c); print(columnPhysName); print(" TYPE "); print(columnType(c)); // Column nullability print(", ALTER COLUMN "); print(columnPhysName); print(" "); print(c.isDefinitelyNullable() ? "DROP" : "SET"); print(" NOT NULL"); endStatement(DDLStatement.StatementType.MODIFY, c); }

public void modifyColumn(SQLColumn c) { Map colNameMap = new HashMap(); SQLTable t = c.getParentTable(); print("\n ALTER TABLE ONLY "); print( toQualifiedName(t) ); print(" ALTER COLUMN "); // Column name String columnPhysName = createPhysicalName(colNameMap,c); print(columnPhysName); print(" TYPE "); print(columnType(c)); // Column nullability print(", ALTER COLUMN "); print(columnPhysName); print(" "); print(c.isDefinitelyNullable() ? "DROP" : "SET"); print(" NOT NULL"); endStatement(DDLStatement.StatementType.MODIFY, c); }

1,110,202

public String toIdentifier(String logicalName, String physicalName) { // replace spaces with underscores if (logicalName == null) return null; if (logger.isDebugEnabled()) logger.debug("getting physical name for: " + logicalName); String ident = logicalName.replace(' ','_').toLowerCase(); if (logger.isDebugEnabled()) logger.debug("after replace of spaces: " + ident); // make sure first character is alpha Pattern p = Pattern.compile("^[^a-zA-Z]+"); Matcher m = p.matcher(ident); if (m.find()) { // just add something alpha to the front for now ident = "X" + ident; if (logger.isDebugEnabled()) logger.debug("identifiers must start with letter; prepending X: " + ident); } // see if it's a reserved word, and add something alpha to front if it is... if (isReservedWord(ident)) { ident = "X" + ident; if (logger.isDebugEnabled()) logger.debug("identifier was reserved word, prepending X: " + ident); } // replace anything that is not a letter, character, or underscore with an underscore... ident = ident.replaceAll("[^a-zA-Z0-9_$]", "_"); // first time through // XXX clean this up if (physicalName == null) { // length is ok if (ident.length() <= 63) { return ident; } else { // length is too big if (logger.isDebugEnabled()) logger.debug("truncating identifier: " + ident); String base = ident.substring(0, 60); int tiebreaker = ((ident.hashCode() % 1000) + 1000) % 1000; if (logger.isDebugEnabled()) logger.debug("new identifier: " + base + tiebreaker); return (base + tiebreaker); } } else { // back for more, which means that we probably // had a namespace conflict. Hack the ident down // to size if it's too big, and then generate // a hash tiebreaker using the ident and the // passed value physicalName if (logger.isDebugEnabled()) logger.debug("physical identifier is not unique, regenerating: " + physicalName); String base = ident; if (ident.length() > 63) { base = ident.substring(0, 60); } int tiebreaker = (((ident + physicalName).hashCode() % 1000) + 1000) % 1000; if (logger.isDebugEnabled()) logger.debug("regenerated identifier is: " + (base + tiebreaker)); return (base + tiebreaker); } }

private String toIdentifier(String logicalName, String physicalName) { // replace spaces with underscores if (logicalName == null) return null; if (logger.isDebugEnabled()) logger.debug("getting physical name for: " + logicalName); String ident = logicalName.replace(' ','_').toLowerCase(); if (logger.isDebugEnabled()) logger.debug("after replace of spaces: " + ident); // make sure first character is alpha Pattern p = Pattern.compile("^[^a-zA-Z]+"); Matcher m = p.matcher(ident); if (m.find()) { // just add something alpha to the front for now ident = "X" + ident; if (logger.isDebugEnabled()) logger.debug("identifiers must start with letter; prepending X: " + ident); } // see if it's a reserved word, and add something alpha to front if it is... if (isReservedWord(ident)) { ident = "X" + ident; if (logger.isDebugEnabled()) logger.debug("identifier was reserved word, prepending X: " + ident); } // replace anything that is not a letter, character, or underscore with an underscore... ident = ident.replaceAll("[^a-zA-Z0-9_$]", "_"); // first time through // XXX clean this up if (physicalName == null) { // length is ok if (ident.length() <= 63) { return ident; } else { // length is too big if (logger.isDebugEnabled()) logger.debug("truncating identifier: " + ident); String base = ident.substring(0, 60); int tiebreaker = ((ident.hashCode() % 1000) + 1000) % 1000; if (logger.isDebugEnabled()) logger.debug("new identifier: " + base + tiebreaker); return (base + tiebreaker); } } else { // back for more, which means that we probably // had a namespace conflict. Hack the ident down // to size if it's too big, and then generate // a hash tiebreaker using the ident and the // passed value physicalName if (logger.isDebugEnabled()) logger.debug("physical identifier is not unique, regenerating: " + physicalName); String base = ident; if (ident.length() > 63) { base = ident.substring(0, 60); } int tiebreaker = (((ident + physicalName).hashCode() % 1000) + 1000) % 1000; if (logger.isDebugEnabled()) logger.debug("regenerated identifier is: " + (base + tiebreaker)); return (base + tiebreaker); } }

1,110,203

private MarkerResult checkMarker(int loc)throws PedFileException{ MarkerResult result = new MarkerResult(); Individual currentInd; //int indivgeno=0, int missing=0, parenthet=0, mendErrNum=0; int allele1=0, allele2=0, hom=0, het=0; //Hashtable allgenos = new Hashtable(); Hashtable numindivs=new Hashtable(); Hashtable parentgeno = new Hashtable(); Hashtable kidgeno = new Hashtable(); //Hashtable parenthom = new Hashtable(); int[] parentHom = new int[5]; //Hashtable count = new Hashtable(); int[] count = new int[5]; for(int i=0;i<5;i++) { parentHom[i] =0; count[i]=0; } //String allele1_string, allele2_string; //loop through each family, check data for marker loc Enumeration famList = _pedFile.getFamList(); while(famList.hasMoreElements()){ Family currentFamily = _pedFile.getFamily((String)famList.nextElement()); Enumeration indList = currentFamily.getMemberList(); //loop through each individual in the current Family while(indList.hasMoreElements()){ currentInd = currentFamily.getMember((String)indList.nextElement()); if (currentInd.getIsTyped()){ byte[] markers = currentInd.getMarker(loc); allele1 = markers[0]; //allele1_string = Integer.toString(allele1); allele2 = markers[1]; //allele2_string = Integer.toString(allele2); String familyID = currentInd.getFamilyID(); if(numindivs.containsKey(familyID)){ int value = ((Integer)numindivs.get(familyID)).intValue() +1; numindivs.put(familyID, new Integer(value)); } else{ numindivs.put(familyID, new Integer(1)); } //no allele data missing if(allele1 > 0 && allele2 >0){ //make sure entry has parents if(!(currentInd.getMomID().equals("0") || currentInd.getDadID().equals("0"))){ //do mendel check //byte[] marker = ((Individual)pedFileHash.get(familyID + " " + currentInd.getMomID())).getUnfilteredMarker(loc); byte[] marker = (currentFamily.getMember(currentInd.getMomID())).getMarker(loc); int momAllele1 = marker[0]; int momAllele2 = marker[1]; //marker = ((Individual)pedFileHash.get(familyID + " " + currentInd.getDadID())).getUnfilteredMarker(loc); marker = (currentFamily.getMember(currentInd.getDadID())).getMarker(loc); int dadAllele1 = marker[0]; int dadAllele2 = marker[1]; //don't check if parents are missing any data if (!(momAllele1 == 0 || momAllele2 == 0 || dadAllele1 == 0 || dadAllele2 ==0)){ //mom hom if(momAllele1 == momAllele2){ //both parents hom if (dadAllele1 == dadAllele2){ //both parents hom same allele if (momAllele1 == dadAllele1){ //kid must be hom same allele if (allele1 != momAllele1 || allele2 != momAllele1) { mendErrNum ++; currentInd.zeroOutMarker(loc); currentFamily.getMember(currentInd.getMomID()).zeroOutMarker(loc); currentFamily.getMember(currentInd.getDadID()).zeroOutMarker(loc); } //parents hom diff allele }else{ //kid must be het if (allele1 == allele2) { mendErrNum++; currentInd.zeroOutMarker(loc); currentFamily.getMember(currentInd.getMomID()).zeroOutMarker(loc); currentFamily.getMember(currentInd.getDadID()).zeroOutMarker(loc); } } //mom hom dad het }else{ //kid can't be hom for non-momallele if (allele1 != momAllele1 && allele2 != momAllele1){ mendErrNum++; currentInd.zeroOutMarker(loc); currentFamily.getMember(currentInd.getMomID()).zeroOutMarker(loc); currentFamily.getMember(currentInd.getDadID()).zeroOutMarker(loc); } } //mom het }else{ //dad hom if (dadAllele1 == dadAllele2){ //kid can't be hom for non-dadallele if(allele1 != dadAllele1 && allele2 != dadAllele1){ mendErrNum++; currentInd.zeroOutMarker(loc); currentFamily.getMember(currentInd.getMomID()).zeroOutMarker(loc); currentFamily.getMember(currentInd.getDadID()).zeroOutMarker(loc); } } //both parents het no mend err poss } } } //end mendel check } } } indList = currentFamily.getMemberList(); //loop through each individual in the current Family while(indList.hasMoreElements()){ currentInd = currentFamily.getMember((String)indList.nextElement()); if (currentInd.getIsTyped()){ byte[] markers; byte[] zeroArray = {0,0}; if (currentInd.getZeroed(loc)){ markers = zeroArray; }else{ markers = currentInd.getMarker(loc); } allele1 = markers[0]; //allele1_string = Integer.toString(allele1); allele2 = markers[1]; //allele2_string = Integer.toString(allele2); String familyID = currentInd.getFamilyID(); if(numindivs.containsKey(familyID)){ int value = ((Integer)numindivs.get(familyID)).intValue() +1; numindivs.put(familyID, new Integer(value)); } else{ numindivs.put(familyID, new Integer(1)); } //no allele data missing if(allele1 > 0 && allele2 >0){ //indiv has no parents -- i.e. is a founder if(currentInd.getMomID().compareTo(Individual.DATA_MISSING)==0 && currentInd.getDadID().compareTo(Individual.DATA_MISSING)==0){ //$parentgeno{$ped}++ //set parentgeno if(parentgeno.containsKey(familyID)){ int value = ((Integer)parentgeno.get(familyID)).intValue() +1; parentgeno.put(familyID, new Integer(value)); } else{ parentgeno.put(familyID, new Integer(1)); } if(allele1 != allele2) { parenthet++; } else{ //incOrSetOne(parenthom,allele1_string); parentHom[allele1]++; } count[allele1]++; count[allele2]++; } else{//$kidgeno{$ped}++ if(kidgeno.containsKey(familyID)){ int value = ((Integer)kidgeno.get(familyID)).intValue() +1; kidgeno.put(familyID, new Integer(value)); } else{ kidgeno.put(familyID, new Integer(1)); } } if(allele1 == allele2) { hom++; } else { het++; } } //missing data else missing++; } } } double obsHET = getObsHET(het, hom); double[] freqStuff = getFreqStuff(count); double preHET = freqStuff[0]; double maf = freqStuff[1]; //HW p value double pvalue = getPValue(parentHom, parenthet); //geno percent double genopct = getGenoPercent(het, hom, missing); // num of families with a fully genotyped trio //int famTrio =0; int famTrio = getNumOfFamTrio(numindivs, parentgeno, kidgeno); //rating int rating = this.getRating(genopct, pvalue, obsHET, mendErrNum,maf); result.setObsHet(obsHET); result.setPredHet(preHET); result.setMAF(maf); result.setHWpvalue(pvalue); result.setGenoPercent(genopct); result.setFamTrioNum(famTrio); result.setMendErrNum(mendErrNum); result.setRating(rating); return result; }

1,110,204

private MarkerResult checkMarker(int loc)throws PedFileException{ MarkerResult result = new MarkerResult(); Individual currentInd; //int indivgeno=0, int missing=0, parenthet=0, mendErrNum=0; int allele1=0, allele2=0, hom=0, het=0; //Hashtable allgenos = new Hashtable(); Hashtable numindivs=new Hashtable(); Hashtable parentgeno = new Hashtable(); Hashtable kidgeno = new Hashtable(); //Hashtable parenthom = new Hashtable(); int[] parentHom = new int[5]; //Hashtable count = new Hashtable(); int[] count = new int[5]; for(int i=0;i<5;i++) { parentHom[i] =0; count[i]=0; } //String allele1_string, allele2_string; //loop through each family, check data for marker loc Enumeration famList = _pedFile.getFamList(); while(famList.hasMoreElements()){ Family currentFamily = _pedFile.getFamily((String)famList.nextElement()); Enumeration indList = currentFamily.getMemberList(); //loop through each individual in the current Family while(indList.hasMoreElements()){ currentInd = currentFamily.getMember((String)indList.nextElement()); if (currentInd.getIsTyped()){ byte[] markers = currentInd.getMarker(loc); allele1 = markers[0]; //allele1_string = Integer.toString(allele1); allele2 = markers[1]; //allele2_string = Integer.toString(allele2); String familyID = currentInd.getFamilyID(); if(numindivs.containsKey(familyID)){ int value = ((Integer)numindivs.get(familyID)).intValue() +1; numindivs.put(familyID, new Integer(value)); } else{ numindivs.put(familyID, new Integer(1)); } //no allele data missing if(allele1 > 0 && allele2 >0){ //make sure entry has parents if(!(currentInd.getMomID().equals("0") || currentInd.getDadID().equals("0"))){ //do mendel check //byte[] marker = ((Individual)pedFileHash.get(familyID + " " + currentInd.getMomID())).getUnfilteredMarker(loc); byte[] marker = (currentFamily.getMember(currentInd.getMomID())).getMarker(loc); int momAllele1 = marker[0]; int momAllele2 = marker[1]; //marker = ((Individual)pedFileHash.get(familyID + " " + currentInd.getDadID())).getUnfilteredMarker(loc); marker = (currentFamily.getMember(currentInd.getDadID())).getMarker(loc); int dadAllele1 = marker[0]; int dadAllele2 = marker[1]; //don't check if parents are missing any data if (!(momAllele1 == 0 || momAllele2 == 0 || dadAllele1 == 0 || dadAllele2 ==0)){ //mom hom if(momAllele1 == momAllele2){ //both parents hom if (dadAllele1 == dadAllele2){ //both parents hom same allele if (momAllele1 == dadAllele1){ //kid must be hom same allele if (allele1 != momAllele1 || allele2 != momAllele1) { mendErrNum ++; currentInd.zeroOutMarker(loc); currentFamily.getMember(currentInd.getMomID()).zeroOutMarker(loc); currentFamily.getMember(currentInd.getDadID()).zeroOutMarker(loc); } //parents hom diff allele }else{ //kid must be het if (allele1 == allele2) { mendErrNum++; currentInd.zeroOutMarker(loc); currentFamily.getMember(currentInd.getMomID()).zeroOutMarker(loc); currentFamily.getMember(currentInd.getDadID()).zeroOutMarker(loc); } } //mom hom dad het }else{ //kid can't be hom for non-momallele if (allele1 != momAllele1 && allele2 != momAllele1){ mendErrNum++; currentInd.zeroOutMarker(loc); currentFamily.getMember(currentInd.getMomID()).zeroOutMarker(loc); currentFamily.getMember(currentInd.getDadID()).zeroOutMarker(loc); } } //mom het }else{ //dad hom if (dadAllele1 == dadAllele2){ //kid can't be hom for non-dadallele if(allele1 != dadAllele1 && allele2 != dadAllele1){ mendErrNum++; currentInd.zeroOutMarker(loc); currentFamily.getMember(currentInd.getMomID()).zeroOutMarker(loc); currentFamily.getMember(currentInd.getDadID()).zeroOutMarker(loc); } } //both parents het no mend err poss } } } //end mendel check } } } indList = currentFamily.getMemberList(); //loop through each individual in the current Family while(indList.hasMoreElements()){ currentInd = currentFamily.getMember((String)indList.nextElement()); if (currentInd.getIsTyped()){ byte[] markers; byte[] zeroArray = {0,0}; if (currentInd.getZeroed(loc)){ markers = zeroArray; }else{ markers = currentInd.getMarker(loc); } allele1 = markers[0]; //allele1_string = Integer.toString(allele1); allele2 = markers[1]; //allele2_string = Integer.toString(allele2); String familyID = currentInd.getFamilyID(); if(numindivs.containsKey(familyID)){ int value = ((Integer)numindivs.get(familyID)).intValue() +1; numindivs.put(familyID, new Integer(value)); } else{ numindivs.put(familyID, new Integer(1)); } //no allele data missing if(allele1 > 0 && allele2 >0){ //indiv has no parents -- i.e. is a founder if(currentInd.getMomID().compareTo(Individual.DATA_MISSING)==0 && currentInd.getDadID().compareTo(Individual.DATA_MISSING)==0){ //$parentgeno{$ped}++ //set parentgeno if(parentgeno.containsKey(familyID)){ int value = ((Integer)parentgeno.get(familyID)).intValue() +1; parentgeno.put(familyID, new Integer(value)); } else{ parentgeno.put(familyID, new Integer(1)); } if(allele1 != allele2) { parenthet++; } else{ //incOrSetOne(parenthom,allele1_string); parentHom[allele1]++; } count[allele1]++; count[allele2]++; } else{//$kidgeno{$ped}++ if(kidgeno.containsKey(familyID)){ int value = ((Integer)kidgeno.get(familyID)).intValue() +1; kidgeno.put(familyID, new Integer(value)); } else{ kidgeno.put(familyID, new Integer(1)); } } if(allele1 == allele2) { hom++; } else { het++; } } //missing data else missing++; } } } double obsHET = getObsHET(het, hom); double[] freqStuff = getFreqStuff(count); double preHET = freqStuff[0]; double maf = freqStuff[1]; //HW p value double pvalue = getPValue(parentHom, parenthet); //geno percent double genopct = getGenoPercent(het, hom, missing); // num of families with a fully genotyped trio //int famTrio =0; int famTrio = getNumOfFamTrio(numindivs, parentgeno, kidgeno); //rating int rating = this.getRating(genopct, pvalue, obsHET, mendErrNum,maf); result.setObsHet(obsHET); result.setPredHet(preHET); result.setMAF(maf); result.setHWpvalue(pvalue); result.setGenoPercent(genopct); result.setFamTrioNum(famTrio); result.setMendErrNum(mendErrNum); result.setRating(rating); return result; }

private MarkerResult checkMarker(int loc)throws PedFileException{ MarkerResult result = new MarkerResult(); Individual currentInd; //int indivgeno=0, int missing=0, parenthet=0, mendErrNum=0; int allele1=0, allele2=0, hom=0, het=0; //Hashtable allgenos = new Hashtable(); Hashtable numindivs=new Hashtable(); Hashtable parentgeno = new Hashtable(); Hashtable kidgeno = new Hashtable(); //Hashtable parenthom = new Hashtable(); int[] parentHom = new int[5]; //Hashtable count = new Hashtable(); int[] count = new int[5]; for(int i=0;i<5;i++) { parentHom[i] =0; count[i]=0; } //String allele1_string, allele2_string; //loop through each family, check data for marker loc Enumeration famList = _pedFile.getFamList(); while(famList.hasMoreElements()){ Family currentFamily = _pedFile.getFamily((String)famList.nextElement()); Enumeration indList = currentFamily.getMemberList(); //loop through each individual in the current Family while(indList.hasMoreElements()){ currentInd = currentFamily.getMember((String)indList.nextElement()); if (currentInd.getIsTyped()){ byte[] markers = currentInd.getMarker(loc); allele1 = markers[0]; //allele1_string = Integer.toString(allele1); allele2 = markers[1]; //allele2_string = Integer.toString(allele2); String familyID = currentInd.getFamilyID(); if(numindivs.containsKey(familyID)){ int value = ((Integer)numindivs.get(familyID)).intValue() +1; numindivs.put(familyID, new Integer(value)); } else{ numindivs.put(familyID, new Integer(1)); } //no allele data missing if(allele1 > 0 && allele2 >0){ //make sure entry has parents if(!(currentInd.getMomID().equals("0") || currentInd.getDadID().equals("0"))){ //do mendel check //byte[] marker = ((Individual)pedFileHash.get(familyID + " " + currentInd.getMomID())).getUnfilteredMarker(loc); byte[] marker = (currentFamily.getMember(currentInd.getMomID())).getMarker(loc); int momAllele1 = marker[0]; int momAllele2 = marker[1]; //marker = ((Individual)pedFileHash.get(familyID + " " + currentInd.getDadID())).getUnfilteredMarker(loc); marker = (currentFamily.getMember(currentInd.getDadID())).getMarker(loc); int dadAllele1 = marker[0]; int dadAllele2 = marker[1]; //don't check if parents are missing any data if (!(momAllele1 == 0 || momAllele2 == 0 || dadAllele1 == 0 || dadAllele2 ==0)){ //mom hom if(momAllele1 == momAllele2){ //both parents hom if (dadAllele1 == dadAllele2){ //both parents hom same allele if (momAllele1 == dadAllele1){ //kid must be hom same allele if (allele1 != momAllele1 || allele2 != momAllele1) { mendErrNum ++; currentInd.zeroOutMarker(loc); currentFamily.getMember(currentInd.getMomID()).zeroOutMarker(loc); currentFamily.getMember(currentInd.getDadID()).zeroOutMarker(loc); } //parents hom diff allele }else{ //kid must be het if (allele1 == allele2) { mendErrNum++; currentInd.zeroOutMarker(loc); currentFamily.getMember(currentInd.getMomID()).zeroOutMarker(loc); currentFamily.getMember(currentInd.getDadID()).zeroOutMarker(loc); } } //mom hom dad het }else{ //kid can't be hom for non-momallele if (allele1 == allele2) { mendErrNum++; currentInd.zeroOutMarker(loc); currentFamily.getMember(currentInd.getMomID()).zeroOutMarker(loc); currentFamily.getMember(currentInd.getDadID()).zeroOutMarker(loc); } } //mom het }else{ //dad hom if (dadAllele1 == dadAllele2){ //kid can't be hom for non-dadallele if(allele1 != dadAllele1 && allele2 != dadAllele1){ mendErrNum++; currentInd.zeroOutMarker(loc); currentFamily.getMember(currentInd.getMomID()).zeroOutMarker(loc); currentFamily.getMember(currentInd.getDadID()).zeroOutMarker(loc); } } //both parents het no mend err poss } } } //end mendel check } } } indList = currentFamily.getMemberList(); //loop through each individual in the current Family while(indList.hasMoreElements()){ currentInd = currentFamily.getMember((String)indList.nextElement()); if (currentInd.getIsTyped()){ byte[] markers; byte[] zeroArray = {0,0}; if (currentInd.getZeroed(loc)){ markers = zeroArray; }else{ markers = currentInd.getMarker(loc); } allele1 = markers[0]; //allele1_string = Integer.toString(allele1); allele2 = markers[1]; //allele2_string = Integer.toString(allele2); String familyID = currentInd.getFamilyID(); if(numindivs.containsKey(familyID)){ int value = ((Integer)numindivs.get(familyID)).intValue() +1; numindivs.put(familyID, new Integer(value)); } else{ numindivs.put(familyID, new Integer(1)); } //no allele data missing if(allele1 > 0 && allele2 >0){ //indiv has no parents -- i.e. is a founder if(currentInd.getMomID().compareTo(Individual.DATA_MISSING)==0 && currentInd.getDadID().compareTo(Individual.DATA_MISSING)==0){ //$parentgeno{$ped}++ //set parentgeno if(parentgeno.containsKey(familyID)){ int value = ((Integer)parentgeno.get(familyID)).intValue() +1; parentgeno.put(familyID, new Integer(value)); } else{ parentgeno.put(familyID, new Integer(1)); } if(allele1 != allele2) { parenthet++; } else{ //incOrSetOne(parenthom,allele1_string); parentHom[allele1]++; } count[allele1]++; count[allele2]++; } else{//$kidgeno{$ped}++ if(kidgeno.containsKey(familyID)){ int value = ((Integer)kidgeno.get(familyID)).intValue() +1; kidgeno.put(familyID, new Integer(value)); } else{ kidgeno.put(familyID, new Integer(1)); } } if(allele1 == allele2) { hom++; } else { het++; } } //missing data else missing++; } } } double obsHET = getObsHET(het, hom); double[] freqStuff = getFreqStuff(count); double preHET = freqStuff[0]; double maf = freqStuff[1]; //HW p value double pvalue = getPValue(parentHom, parenthet); //geno percent double genopct = getGenoPercent(het, hom, missing); // num of families with a fully genotyped trio //int famTrio =0; int famTrio = getNumOfFamTrio(numindivs, parentgeno, kidgeno); //rating int rating = this.getRating(genopct, pvalue, obsHET, mendErrNum,maf); result.setObsHet(obsHET); result.setPredHet(preHET); result.setMAF(maf); result.setHWpvalue(pvalue); result.setGenoPercent(genopct); result.setFamTrioNum(famTrio); result.setMendErrNum(mendErrNum); result.setRating(rating); return result; }

1,110,205

private MarkerResult checkMarker(int loc)throws PedFileException{ MarkerResult result = new MarkerResult(); Individual currentInd; //int indivgeno=0, int missing=0, parenthet=0, mendErrNum=0; int allele1=0, allele2=0, hom=0, het=0; //Hashtable allgenos = new Hashtable(); Hashtable numindivs=new Hashtable(); Hashtable parentgeno = new Hashtable(); Hashtable kidgeno = new Hashtable(); //Hashtable parenthom = new Hashtable(); int[] parentHom = new int[5]; //Hashtable count = new Hashtable(); int[] count = new int[5]; for(int i=0;i<5;i++) { parentHom[i] =0; count[i]=0; } //String allele1_string, allele2_string; //loop through each family, check data for marker loc Enumeration famList = _pedFile.getFamList(); while(famList.hasMoreElements()){ Family currentFamily = _pedFile.getFamily((String)famList.nextElement()); Enumeration indList = currentFamily.getMemberList(); //loop through each individual in the current Family while(indList.hasMoreElements()){ currentInd = currentFamily.getMember((String)indList.nextElement()); if (currentInd.getIsTyped()){ byte[] markers = currentInd.getMarker(loc); allele1 = markers[0]; //allele1_string = Integer.toString(allele1); allele2 = markers[1]; //allele2_string = Integer.toString(allele2); String familyID = currentInd.getFamilyID(); if(numindivs.containsKey(familyID)){ int value = ((Integer)numindivs.get(familyID)).intValue() +1; numindivs.put(familyID, new Integer(value)); } else{ numindivs.put(familyID, new Integer(1)); } //no allele data missing if(allele1 > 0 && allele2 >0){ //make sure entry has parents if(!(currentInd.getMomID().equals("0") || currentInd.getDadID().equals("0"))){ //do mendel check //byte[] marker = ((Individual)pedFileHash.get(familyID + " " + currentInd.getMomID())).getUnfilteredMarker(loc); byte[] marker = (currentFamily.getMember(currentInd.getMomID())).getMarker(loc); int momAllele1 = marker[0]; int momAllele2 = marker[1]; //marker = ((Individual)pedFileHash.get(familyID + " " + currentInd.getDadID())).getUnfilteredMarker(loc); marker = (currentFamily.getMember(currentInd.getDadID())).getMarker(loc); int dadAllele1 = marker[0]; int dadAllele2 = marker[1]; //don't check if parents are missing any data if (!(momAllele1 == 0 || momAllele2 == 0 || dadAllele1 == 0 || dadAllele2 ==0)){ //mom hom if(momAllele1 == momAllele2){ //both parents hom if (dadAllele1 == dadAllele2){ //both parents hom same allele if (momAllele1 == dadAllele1){ //kid must be hom same allele if (allele1 != momAllele1 || allele2 != momAllele1) { mendErrNum ++; currentInd.zeroOutMarker(loc); currentFamily.getMember(currentInd.getMomID()).zeroOutMarker(loc); currentFamily.getMember(currentInd.getDadID()).zeroOutMarker(loc); } //parents hom diff allele }else{ //kid must be het if (allele1 == allele2) { mendErrNum++; currentInd.zeroOutMarker(loc); currentFamily.getMember(currentInd.getMomID()).zeroOutMarker(loc); currentFamily.getMember(currentInd.getDadID()).zeroOutMarker(loc); } } //mom hom dad het }else{ //kid can't be hom for non-momallele if (allele1 != momAllele1 && allele2 != momAllele1){ mendErrNum++; currentInd.zeroOutMarker(loc); currentFamily.getMember(currentInd.getMomID()).zeroOutMarker(loc); currentFamily.getMember(currentInd.getDadID()).zeroOutMarker(loc); } } //mom het }else{ //dad hom if (dadAllele1 == dadAllele2){ //kid can't be hom for non-dadallele if(allele1 != dadAllele1 && allele2 != dadAllele1){ mendErrNum++; currentInd.zeroOutMarker(loc); currentFamily.getMember(currentInd.getMomID()).zeroOutMarker(loc); currentFamily.getMember(currentInd.getDadID()).zeroOutMarker(loc); } } //both parents het no mend err poss } } } //end mendel check } } } indList = currentFamily.getMemberList(); //loop through each individual in the current Family while(indList.hasMoreElements()){ currentInd = currentFamily.getMember((String)indList.nextElement()); if (currentInd.getIsTyped()){ byte[] markers; byte[] zeroArray = {0,0}; if (currentInd.getZeroed(loc)){ markers = zeroArray; }else{ markers = currentInd.getMarker(loc); } allele1 = markers[0]; //allele1_string = Integer.toString(allele1); allele2 = markers[1]; //allele2_string = Integer.toString(allele2); String familyID = currentInd.getFamilyID(); if(numindivs.containsKey(familyID)){ int value = ((Integer)numindivs.get(familyID)).intValue() +1; numindivs.put(familyID, new Integer(value)); } else{ numindivs.put(familyID, new Integer(1)); } //no allele data missing if(allele1 > 0 && allele2 >0){ //indiv has no parents -- i.e. is a founder if(currentInd.getMomID().compareTo(Individual.DATA_MISSING)==0 && currentInd.getDadID().compareTo(Individual.DATA_MISSING)==0){ //$parentgeno{$ped}++ //set parentgeno if(parentgeno.containsKey(familyID)){ int value = ((Integer)parentgeno.get(familyID)).intValue() +1; parentgeno.put(familyID, new Integer(value)); } else{ parentgeno.put(familyID, new Integer(1)); } if(allele1 != allele2) { parenthet++; } else{ //incOrSetOne(parenthom,allele1_string); parentHom[allele1]++; } count[allele1]++; count[allele2]++; } else{//$kidgeno{$ped}++ if(kidgeno.containsKey(familyID)){ int value = ((Integer)kidgeno.get(familyID)).intValue() +1; kidgeno.put(familyID, new Integer(value)); } else{ kidgeno.put(familyID, new Integer(1)); } } if(allele1 == allele2) { hom++; } else { het++; } } //missing data else missing++; } } } double obsHET = getObsHET(het, hom); double[] freqStuff = getFreqStuff(count); double preHET = freqStuff[0]; double maf = freqStuff[1]; //HW p value double pvalue = getPValue(parentHom, parenthet); //geno percent double genopct = getGenoPercent(het, hom, missing); // num of families with a fully genotyped trio //int famTrio =0; int famTrio = getNumOfFamTrio(numindivs, parentgeno, kidgeno); //rating int rating = this.getRating(genopct, pvalue, obsHET, mendErrNum,maf); result.setObsHet(obsHET); result.setPredHet(preHET); result.setMAF(maf); result.setHWpvalue(pvalue); result.setGenoPercent(genopct); result.setFamTrioNum(famTrio); result.setMendErrNum(mendErrNum); result.setRating(rating); return result; }

1,110,206

private MarkerResult checkMarker(int loc)throws PedFileException{ MarkerResult result = new MarkerResult(); Individual currentInd; //int indivgeno=0, int missing=0, parenthet=0, mendErrNum=0; int allele1=0, allele2=0, hom=0, het=0; //Hashtable allgenos = new Hashtable(); Hashtable numindivs=new Hashtable(); Hashtable parentgeno = new Hashtable(); Hashtable kidgeno = new Hashtable(); //Hashtable parenthom = new Hashtable(); int[] parentHom = new int[5]; //Hashtable count = new Hashtable(); int[] count = new int[5]; for(int i=0;i<5;i++) { parentHom[i] =0; count[i]=0; } //String allele1_string, allele2_string; //loop through each family, check data for marker loc Enumeration famList = _pedFile.getFamList(); while(famList.hasMoreElements()){ Family currentFamily = _pedFile.getFamily((String)famList.nextElement()); Enumeration indList = currentFamily.getMemberList(); //loop through each individual in the current Family while(indList.hasMoreElements()){ currentInd = currentFamily.getMember((String)indList.nextElement()); if (currentInd.getIsTyped()){ byte[] markers = currentInd.getMarker(loc); allele1 = markers[0]; //allele1_string = Integer.toString(allele1); allele2 = markers[1]; //allele2_string = Integer.toString(allele2); String familyID = currentInd.getFamilyID(); if(numindivs.containsKey(familyID)){ int value = ((Integer)numindivs.get(familyID)).intValue() +1; numindivs.put(familyID, new Integer(value)); } else{ numindivs.put(familyID, new Integer(1)); } //no allele data missing if(allele1 > 0 && allele2 >0){ //make sure entry has parents if(!(currentInd.getMomID().equals("0") || currentInd.getDadID().equals("0"))){ //do mendel check //byte[] marker = ((Individual)pedFileHash.get(familyID + " " + currentInd.getMomID())).getUnfilteredMarker(loc); byte[] marker = (currentFamily.getMember(currentInd.getMomID())).getMarker(loc); int momAllele1 = marker[0]; int momAllele2 = marker[1]; //marker = ((Individual)pedFileHash.get(familyID + " " + currentInd.getDadID())).getUnfilteredMarker(loc); marker = (currentFamily.getMember(currentInd.getDadID())).getMarker(loc); int dadAllele1 = marker[0]; int dadAllele2 = marker[1]; //don't check if parents are missing any data if (!(momAllele1 == 0 || momAllele2 == 0 || dadAllele1 == 0 || dadAllele2 ==0)){ //mom hom if(momAllele1 == momAllele2){ //both parents hom if (dadAllele1 == dadAllele2){ //both parents hom same allele if (momAllele1 == dadAllele1){ //kid must be hom same allele if (allele1 != momAllele1 || allele2 != momAllele1) { mendErrNum ++; currentInd.zeroOutMarker(loc); currentFamily.getMember(currentInd.getMomID()).zeroOutMarker(loc); currentFamily.getMember(currentInd.getDadID()).zeroOutMarker(loc); } //parents hom diff allele }else{ //kid must be het if (allele1 == allele2) { mendErrNum++; currentInd.zeroOutMarker(loc); currentFamily.getMember(currentInd.getMomID()).zeroOutMarker(loc); currentFamily.getMember(currentInd.getDadID()).zeroOutMarker(loc); } } //mom hom dad het }else{ //kid can't be hom for non-momallele if (allele1 != momAllele1 && allele2 != momAllele1){ mendErrNum++; currentInd.zeroOutMarker(loc); currentFamily.getMember(currentInd.getMomID()).zeroOutMarker(loc); currentFamily.getMember(currentInd.getDadID()).zeroOutMarker(loc); } } //mom het }else{ //dad hom if (dadAllele1 == dadAllele2){ //kid can't be hom for non-dadallele if(allele1 != dadAllele1 && allele2 != dadAllele1){ mendErrNum++; currentInd.zeroOutMarker(loc); currentFamily.getMember(currentInd.getMomID()).zeroOutMarker(loc); currentFamily.getMember(currentInd.getDadID()).zeroOutMarker(loc); } } //both parents het no mend err poss } } } //end mendel check } } } indList = currentFamily.getMemberList(); //loop through each individual in the current Family while(indList.hasMoreElements()){ currentInd = currentFamily.getMember((String)indList.nextElement()); if (currentInd.getIsTyped()){ byte[] markers; byte[] zeroArray = {0,0}; if (currentInd.getZeroed(loc)){ markers = zeroArray; }else{ markers = currentInd.getMarker(loc); } allele1 = markers[0]; //allele1_string = Integer.toString(allele1); allele2 = markers[1]; //allele2_string = Integer.toString(allele2); String familyID = currentInd.getFamilyID(); if(numindivs.containsKey(familyID)){ int value = ((Integer)numindivs.get(familyID)).intValue() +1; numindivs.put(familyID, new Integer(value)); } else{ numindivs.put(familyID, new Integer(1)); } //no allele data missing if(allele1 > 0 && allele2 >0){ //indiv has no parents -- i.e. is a founder if(currentInd.getMomID().compareTo(Individual.DATA_MISSING)==0 && currentInd.getDadID().compareTo(Individual.DATA_MISSING)==0){ //$parentgeno{$ped}++ //set parentgeno if(parentgeno.containsKey(familyID)){ int value = ((Integer)parentgeno.get(familyID)).intValue() +1; parentgeno.put(familyID, new Integer(value)); } else{ parentgeno.put(familyID, new Integer(1)); } if(allele1 != allele2) { parenthet++; } else{ //incOrSetOne(parenthom,allele1_string); parentHom[allele1]++; } count[allele1]++; count[allele2]++; } else{//$kidgeno{$ped}++ if(kidgeno.containsKey(familyID)){ int value = ((Integer)kidgeno.get(familyID)).intValue() +1; kidgeno.put(familyID, new Integer(value)); } else{ kidgeno.put(familyID, new Integer(1)); } } if(allele1 == allele2) { hom++; } else { het++; } } //missing data else missing++; } } } double obsHET = getObsHET(het, hom); double[] freqStuff = getFreqStuff(count); double preHET = freqStuff[0]; double maf = freqStuff[1]; //HW p value double pvalue = getPValue(parentHom, parenthet); //geno percent double genopct = getGenoPercent(het, hom, missing); // num of families with a fully genotyped trio //int famTrio =0; int famTrio = getNumOfFamTrio(numindivs, parentgeno, kidgeno); //rating int rating = this.getRating(genopct, pvalue, obsHET, mendErrNum,maf); result.setObsHet(obsHET); result.setPredHet(preHET); result.setMAF(maf); result.setHWpvalue(pvalue); result.setGenoPercent(genopct); result.setFamTrioNum(famTrio); result.setMendErrNum(mendErrNum); result.setRating(rating); return result; }

1,110,207

public CheckDataTableModel(Vector c, Vector d, int[] r, int[] dups){ super(c,d); ratings = r; this.dups = dups; }

public CheckDataTableModel(Vector c, Vector d, int[] r, int[] dups){ columnNames=c; data=d; ratings = r; this.dups = dups; }

1,110,208

public void compile() throws Exception { TaskTag tag = (TaskTag) findAncestorWithClass( TaskTag.class ); if ( tag == null ) { throw new JellyException( "You should only use Ant DataType tags within an Ant Task" ); } Task task = tag.getTask(); Class taskClass = task.getClass(); String methodName = "create" + name.substring(0,1).toUpperCase() + name.substring(1); Method method = taskClass.getMethod( methodName, emptyParameterTypes ); if ( method == null ) { throw new JellyException( "Cannot create Task property: " + name + " of Ant task: " + task + " as no method called: " + methodName + " could be found" ); } Object propertyBean = method.invoke( task, emptyParameters ); if ( propertyBean == null ) { throw new JellyException( "No property: " + name + " of task: " + task + " was returned." ); } setDynaBean( new ConvertingWrapDynaBean(propertyBean) ); }

public void compile() throws Exception { TaskTag tag = (TaskTag) findAncestorWithClass( TaskTag.class ); if ( tag == null ) { throw new JellyException( "You should only use Ant DataType tags within an Ant Task" ); } Task task = tag.getTask(); Class taskClass = task.getClass(); String methodName = "create" + name.substring(0,1).toUpperCase() + name.substring(1); Method method = MethodUtils.getAccessibleMethod( taskClass, methodName, emptyParameterTypes ); if ( method == null ) { throw new JellyException( "Cannot create Task property: " + name + " of Ant task: " + task + " as no method called: " + methodName + " could be found" ); } Object propertyBean = method.invoke( task, emptyParameters ); if ( propertyBean == null ) { throw new JellyException( "No property: " + name + " of task: " + task + " was returned." ); } setDynaBean( new ConvertingWrapDynaBean(propertyBean) ); }

1,110,209

public static void main(String[] args) { int exitValue = 0; String dir = System.getProperty("user.dir"); String sep = System.getProperty("file.separator"); String ver = System.getProperty("java.version"); System.out.println(ver); String jarfile = System.getProperty("java.class.path"); String argsToBePassed = new String(); boolean headless = false; for (int a = 0; a < args.length; a++){ argsToBePassed = argsToBePassed.concat(" " + args[a]); if (args[a].equals("-n")){ headless=true; } } try { //if the nogui flag is present we force it into headless mode String runString = "java -Xmx650m -classpath " + jarfile; if (headless){ runString += " -Djava.awt.headless=true"; } runString += " edu.mit.wi.haploview.HaploView"+argsToBePassed; Process child = Runtime.getRuntime().exec(runString); //start up a thread to simply pump out all messages to stdout StreamGobbler isg = new StreamGobbler(child.getInputStream()); isg.start(); //while the child is alive we wait for error messages boolean dead = false; StringBuffer errorMsg = new StringBuffer("Fatal Error:\n"); BufferedReader besr = new BufferedReader(new InputStreamReader(child.getErrorStream())); String line = null; if ((line = besr.readLine()) != null) { errorMsg.append(line); //if the child generated an error message, kill it child.destroy(); dead = true; } //if the child died painfully throw up R.I.P. dialog if (dead){ if (headless){ System.out.println(errorMsg); }else{ JFrame jf = new JFrame(); JOptionPane.showMessageDialog(jf, errorMsg, null, JOptionPane.ERROR_MESSAGE); } exitValue = -1; } } catch (Exception e) { if (headless){ System.out.println("Error:\nUnable to launch Haploview.\n"+e.getMessage()); }else{ JFrame jf = new JFrame(); JOptionPane.showMessageDialog(jf, "Error:\nUnable to launch Haploview.\n"+e.getMessage(), null, JOptionPane.ERROR_MESSAGE); } } System.exit(exitValue); }

public static void main(String[] args) { int exitValue = 0; String dir = System.getProperty("user.dir"); String sep = System.getProperty("file.separator"); String ver = System.getProperty("java.version"); System.out.println(ver); String jarfile = System.getProperty("java.class.path"); String argsToBePassed = new String(); boolean headless = false; for (int a = 0; a < args.length; a++){ argsToBePassed = argsToBePassed.concat(" " + args[a]); if (args[a].equals("-n") || args[a].equalsIgnoreCase("-nogui")){ headless=true; } } try { //if the nogui flag is present we force it into headless mode String runString = "java -Xmx650m -classpath " + jarfile; if (headless){ runString += " -Djava.awt.headless=true"; } runString += " edu.mit.wi.haploview.HaploView"+argsToBePassed; Process child = Runtime.getRuntime().exec(runString); //start up a thread to simply pump out all messages to stdout StreamGobbler isg = new StreamGobbler(child.getInputStream()); isg.start(); //while the child is alive we wait for error messages boolean dead = false; StringBuffer errorMsg = new StringBuffer("Fatal Error:\n"); BufferedReader besr = new BufferedReader(new InputStreamReader(child.getErrorStream())); String line = null; if ((line = besr.readLine()) != null) { errorMsg.append(line); //if the child generated an error message, kill it child.destroy(); dead = true; } //if the child died painfully throw up R.I.P. dialog if (dead){ if (headless){ System.out.println(errorMsg); }else{ JFrame jf = new JFrame(); JOptionPane.showMessageDialog(jf, errorMsg, null, JOptionPane.ERROR_MESSAGE); } exitValue = -1; } } catch (Exception e) { if (headless){ System.out.println("Error:\nUnable to launch Haploview.\n"+e.getMessage()); }else{ JFrame jf = new JFrame(); JOptionPane.showMessageDialog(jf, "Error:\nUnable to launch Haploview.\n"+e.getMessage(), null, JOptionPane.ERROR_MESSAGE); } } System.exit(exitValue); }

1,110,211

public void mousePressed (MouseEvent e) { //if users right clicks & holds, pop up the info if ((e.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK){ PairwiseLinkage[][] dPrimeTable = theData.getFilteredTable(); final int clickX = e.getX(); final int clickY = e.getY(); double dboxX = (double)(clickX - clickXShift - (clickY-clickYShift))/boxSize; double dboxY = (double)(clickX - clickXShift + (clickY-clickYShift))/boxSize; final int boxX, boxY; if (dboxX < 0){ boxX = (int)(dboxX - 0.5); } else{ boxX = (int)(dboxX + 0.5); } if (dboxY < 0){ boxY = (int)(dboxY - 0.5); }else{ boxY = (int)(dboxY + 0.5); } if ((boxX >= lowX && boxX <= highX) && (boxY > boxX && boxY < highY) && !(worldmapRect.contains(clickX,clickY))){ if (dPrimeTable[boxX][boxY] != null){ if (theData.infoKnown){ displayStrings[0] = new String ("(" +Chromosome.getFilteredMarker(boxX).getName() + ", " + Chromosome.getFilteredMarker(boxY).getName() + ")"); }else{ displayStrings[0] = new String("(" + (Chromosome.realIndex[boxX]+1) + ", " + (Chromosome.realIndex[boxY]+1) + ")"); } displayStrings[1] = new String ("D': " + dPrimeTable[boxX][boxY].getDPrime()); displayStrings[2] = new String ("LOD: " + dPrimeTable[boxX][boxY].getLOD()); displayStrings[3] = new String ("r^2: " + dPrimeTable[boxX][boxY].getRSquared()); displayStrings[4] = new String ("D' conf. bounds: " + dPrimeTable[boxX][boxY].getConfidenceLow() + "-" + dPrimeTable[boxX][boxY].getConfidenceHigh()); Graphics g = getGraphics(); g.setFont(boxFont); FontMetrics metrics = g.getFontMetrics(); int strlen = 0; for (int x = 0; x < 5; x++){ if (strlen < metrics.stringWidth(displayStrings[x])){ strlen = metrics.stringWidth(displayStrings[x]); } } //edge shifts prevent window from popping up partially offscreen int visRightBound = (int)(getVisibleRect().getWidth() + getVisibleRect().getX()); int visBotBound = (int)(getVisibleRect().getHeight() + getVisibleRect().getY()); int rightEdgeShift = 0; if (clickX + strlen + popupLeftMargin +5 > visRightBound){ rightEdgeShift = clickX + strlen + popupLeftMargin + 10 - visRightBound; } int botEdgeShift = 0; if (clickY + 5*metrics.getHeight()+10 > visBotBound){ botEdgeShift = clickY + 5*metrics.getHeight()+15 - visBotBound; } popupDrawRect = new Rectangle(clickX-rightEdgeShift, clickY-botEdgeShift, strlen+popupLeftMargin+5, 5*metrics.getHeight()+10); popupExists = true; repaint(); } } } }

public void mousePressed (MouseEvent e) { //if users right clicks & holds, pop up the info if ((e.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK){ PairwiseLinkage[][] dPrimeTable = theData.filteredDPrimeTable; final int clickX = e.getX(); final int clickY = e.getY(); double dboxX = (double)(clickX - clickXShift - (clickY-clickYShift))/boxSize; double dboxY = (double)(clickX - clickXShift + (clickY-clickYShift))/boxSize; final int boxX, boxY; if (dboxX < 0){ boxX = (int)(dboxX - 0.5); } else{ boxX = (int)(dboxX + 0.5); } if (dboxY < 0){ boxY = (int)(dboxY - 0.5); }else{ boxY = (int)(dboxY + 0.5); } if ((boxX >= lowX && boxX <= highX) && (boxY > boxX && boxY < highY) && !(worldmapRect.contains(clickX,clickY))){ if (dPrimeTable[boxX][boxY] != null){ if (theData.infoKnown){ displayStrings[0] = new String ("(" +Chromosome.getFilteredMarker(boxX).getName() + ", " + Chromosome.getFilteredMarker(boxY).getName() + ")"); }else{ displayStrings[0] = new String("(" + (Chromosome.realIndex[boxX]+1) + ", " + (Chromosome.realIndex[boxY]+1) + ")"); } displayStrings[1] = new String ("D': " + dPrimeTable[boxX][boxY].getDPrime()); displayStrings[2] = new String ("LOD: " + dPrimeTable[boxX][boxY].getLOD()); displayStrings[3] = new String ("r^2: " + dPrimeTable[boxX][boxY].getRSquared()); displayStrings[4] = new String ("D' conf. bounds: " + dPrimeTable[boxX][boxY].getConfidenceLow() + "-" + dPrimeTable[boxX][boxY].getConfidenceHigh()); Graphics g = getGraphics(); g.setFont(boxFont); FontMetrics metrics = g.getFontMetrics(); int strlen = 0; for (int x = 0; x < 5; x++){ if (strlen < metrics.stringWidth(displayStrings[x])){ strlen = metrics.stringWidth(displayStrings[x]); } } //edge shifts prevent window from popping up partially offscreen int visRightBound = (int)(getVisibleRect().getWidth() + getVisibleRect().getX()); int visBotBound = (int)(getVisibleRect().getHeight() + getVisibleRect().getY()); int rightEdgeShift = 0; if (clickX + strlen + popupLeftMargin +5 > visRightBound){ rightEdgeShift = clickX + strlen + popupLeftMargin + 10 - visRightBound; } int botEdgeShift = 0; if (clickY + 5*metrics.getHeight()+10 > visBotBound){ botEdgeShift = clickY + 5*metrics.getHeight()+15 - visBotBound; } popupDrawRect = new Rectangle(clickX-rightEdgeShift, clickY-botEdgeShift, strlen+popupLeftMargin+5, 5*metrics.getHeight()+10); popupExists = true; repaint(); } } } }

1,110,212

public void doTag(XMLOutput output) throws Exception { value = false; if ( test != null ) { if ( test.evaluateAsBoolean( context ) ) { value = true; getBody().run(context, output); } } }

public void doTag(XMLOutput output) throws Exception { value = false; if ( test != null ) { if ( test.evaluateAsBoolean( context ) ) { value = true; invokeBody(output); } } }

1,110,215

public int doStartTag() throws JspException{ HttpServletRequest request = (HttpServletRequest)pageContext.getRequest(); WebContext context = null; try{ context = WebContext.get(request); ApplicationConfig appConfig = context.getApplicationConfig(); // Graphs at cluster level are not supported yet assert !appConfig.isCluster(); String dashboardId = request.getParameter("dashBID"); DashboardConfig currentDashboardConfig = DashboardRepository.getInstance().get(dashboardId); assert currentDashboardConfig != null : "Error retrieving dashboard details"; DashboardComponent component = currentDashboardConfig.getComponents().get(getId()); String componentDisplay = component.draw(new DashboardContextImpl(context, currentDashboardConfig, (HttpServletRequest)pageContext.getRequest())); componentDisplay = MessageFormat.format(componentDisplay, getWidth(), getHeight(), Utils.getCookieValue(request, "JSESSIONID")); pageContext.getOut().println("<div id=\""+getId()+"\">"+componentDisplay+""); }catch(Throwable e){ logger.log(Level.SEVERE, "Error displaying component", e); }finally{ if(context != null) context.releaseResources(); } return SKIP_BODY; }

public int doStartTag() throws JspException{ HttpServletRequest request = (HttpServletRequest)pageContext.getRequest(); WebContext context = null; try{ context = WebContext.get(request); ApplicationConfig appConfig = context.getApplicationConfig(); // Graphs at cluster level are not supported yet assert !appConfig.isCluster(); String dashboardId = request.getParameter("dashBID"); DashboardConfig currentDashboardConfig = DashboardRepository.getInstance().get(dashboardId); assert currentDashboardConfig != null : "Error retrieving dashboard details"; DashboardComponent component = currentDashboardConfig.getComponents().get(getId()); String componentDisplay = component.draw(new DashboardContextImpl(context, currentDashboardConfig, (HttpServletRequest)pageContext.getRequest())); componentDisplay = MessageFormat.format(componentDisplay, getWidth(), getHeight(), Utils.getCookieValue(request, "JSESSIONID")); pageContext.getOut().println(componentDisplay); }catch(Throwable e){ logger.log(Level.SEVERE, "Error displaying component", e); }finally{ if(context != null) context.releaseResources(); } return SKIP_BODY; }

1,110,218

public DashboardContextImpl(WebContext webContext, DashboardConfig dashboardConfig, HttpServletRequest request){ this.webContext = webContext; this.dashboardConfig = dashboardConfig; this.request = request; }

public DashboardContextImpl(WebContext webContext, DashboardConfig dashboardConfig, HttpServletRequest request){ this.webContext = webContext; this.dashboardConfig = dashboardConfig; this.request = request; setServerPath(); }

1,110,219

public void setUrl(String jdbcURL) { log.info( "Setting url to: "+ jdbcURL ); this.jdbcURL = jdbcURL; }

public void setUrl(String jdbcURL) { this.jdbcURL = jdbcURL; }

1,110,220

public JeezTagLibrary(org.apache.tools.ant.Project antProject) { this.coreTagLib = new CoreTagLibrary(); this.antTagLib = new AntTagLibrary( antProject ); this.werkzTagLib = new WerkzTagLibrary(); registerTag( "target", TargetTag.class ); }

1,110,222

public TagScript createTagScript(String name, Attributes attrs) throws Exception { TagScript script = super.createTagScript( name, attrs ); if ( script == null ) { script = this.coreTagLib.createTagScript( name, attrs ); if ( script == null ) { script = this.werkzTagLib.createTagScript( name, attrs ); if ( script == null ) { script = this.antTagLib.createTagScript( name, attrs ); } } } return script; }

public TagScript createTagScript(String name, Attributes attrs) throws Exception { TagScript script = super.createTagScript( name, attrs ); if ( script == null ) { if ( script == null ) { script = this.werkzTagLib.createTagScript( name, attrs ); if ( script == null ) { script = this.antTagLib.createTagScript( name, attrs ); } } } return script; }

1,110,223

public TagScript createTagScript(String name, Attributes attrs) throws Exception { TagScript script = super.createTagScript( name, attrs ); if ( script == null ) { script = this.coreTagLib.createTagScript( name, attrs ); if ( script == null ) { script = this.werkzTagLib.createTagScript( name, attrs ); if ( script == null ) { script = this.antTagLib.createTagScript( name, attrs ); } } } return script; }

public TagScript createTagScript(String name, Attributes attrs) throws Exception { TagScript script = super.createTagScript( name, attrs ); if ( script == null ) { script = this.coreTagLib.createTagScript( name, attrs ); if ( script == null ) { script = this.werkzTagLib.createTagScript( name, attrs ); if ( script == null ) { if ( isRuntimeTask( name ) ) { if ( ! project.getTaskDefinitions().containsKey( name ) ) { script = this.antTagLib.createRuntimeTaskTagScript( name, attrs ); } else { this.runtimeTasks.remove( name ); } } if ( script == null ) { script = this.antTagLib.createTagScript( name, attrs ); } if ( name.equals( "taskdef" ) ) { addRuntimeTask( attrs.getValue( "name" ) ); } } } } return script; }

1,110,224

public ActionForward execute(WebContext context, ActionMapping mapping, ActionForm actionForm, HttpServletRequest request, HttpServletResponse response) throws Exception { makeResponseNotCacheable(response); final ObjectName objectName = context.getObjectName(); final ApplicationConfig config = context.getApplicationConfig(); final MBeanConfig configuredMBean = config.findMBeanByObjectName(objectName.getCanonicalName()); AccessController.checkAccess(context.getServiceContext(), ACL_VIEW_APPLICATIONS); if(configuredMBean != null) AccessController.checkAccess(context.getServiceContext(), ACL_VIEW_MBEANS); List applications = null; if(config.isCluster()){ applications = config.getApplications(); }else{ applications = new ArrayList(1); applications.add(config); } /* the ObjectInfo for the mbean that is being viewed */ ObjectInfo objInfo = null; /* array that will be initialized with all attribute names for this mbean */ String[] attributeNames = null; /* a Map which constains list of attribute values for each application in the cluster. ApplicationConfig is the key and attribute List is the value*/ final Map appConfigToAttrListMap = new HashMap(applications.size()); for(Iterator it=applications.iterator(); it.hasNext(); ){ ApplicationConfig childAppConfig = (ApplicationConfig)it.next(); try { ServerConnection serverConnection = ServerConnector.getServerConnection(childAppConfig); /* assuming that all servers in this cluster have exact same object info, we will get the ObjectInfo from the first server in the list */ if(objInfo == null){ objInfo = serverConnection.getObjectInfo(objectName); assert objInfo != null; ObjectAttributeInfo[] attributes = objInfo.getAttributes(); attributeNames = new String[attributes.length]; for (int i = 0; i < attributes.length; i++) { // TODO: we should only add the readable attributes here attributeNames[i] = attributes[i].getName(); } } /* add attribute values of this application to the map*/ appConfigToAttrListMap.put(childAppConfig, serverConnection.getAttributes(objectName, attributeNames)); } catch (ConnectionFailedException e){ logger.log(Level.FINE, "Error retrieving attributes for:" + childAppConfig.getName(), e); /* add null, indicating that the server is down */ appConfigToAttrListMap.put(childAppConfig, null); } } request.setAttribute("objInfo", objInfo); request.setAttribute("appConfigToAttrListMap", appConfigToAttrListMap); /* setup the form to be used in the html form */ MBeanConfigForm mbeanConfigForm = (MBeanConfigForm)actionForm; mbeanConfigForm.setObjectName(objectName.getCanonicalName()); ApplicationConfig appConfig = context.getApplicationConfig(); MBeanConfig mbeanConfig = appConfig.findMBeanByObjectName(objectName.getCanonicalName()); if(mbeanConfig != null){ if(appConfig.isCluster()){ request.setAttribute("mbeanIncludedIn", "cluster"); }else{ request.setAttribute("mbeanIncludedIn", "application"); } request.setAttribute("mbeanConfig", mbeanConfig); }else{ ApplicationConfig clusterConfig = appConfig.getClusterConfig(); if(clusterConfig != null){ mbeanConfig = clusterConfig.findMBeanByObjectName(objectName.getCanonicalName()); } if(mbeanConfig != null){ request.setAttribute("mbeanIncludedIn", "cluster"); request.setAttribute("mbeanConfig", mbeanConfig); } } return mapping.findForward(Forwards.SUCCESS); }

public ActionForward execute(WebContext context, ActionMapping mapping, ActionForm actionForm, HttpServletRequest request, HttpServletResponse response) throws Exception { makeResponseNotCacheable(response); final ObjectName objectName = context.getObjectName(); final ApplicationConfig config = context.getApplicationConfig(); final MBeanConfig configuredMBean = config.findMBeanByObjectName(objectName.getCanonicalName()); AccessController.checkAccess(context.getServiceContext(), ACL_VIEW_APPLICATIONS); if(configuredMBean != null) AccessController.checkAccess(context.getServiceContext(), ACL_VIEW_MBEANS); List applications = null; if(config.isCluster()){ applications = config.getApplications(); }else{ applications = new ArrayList(1); applications.add(config); } /* the ObjectInfo for the mbean that is being viewed */ ObjectInfo objInfo = null; /* array that will be initialized with all attribute names for this mbean */ String[] attributeNames = null; /* a Map which constains list of attribute values for each application in the cluster. ApplicationConfig is the key and attribute List is the value*/ final Map appConfigToAttrListMap = new HashMap(applications.size()); for(Iterator it=applications.iterator(); it.hasNext(); ){ ApplicationConfig childAppConfig = (ApplicationConfig)it.next(); try { ServerConnection serverConnection = ServerConnector.getServerConnection(childAppConfig); /* assuming that all servers in this cluster have exact same object info, we will get the ObjectInfo from the first server in the list (could be further down in the list, if the first server(s) is down */ if(objInfo == null){ objInfo = serverConnection.getObjectInfo(objectName); assert objInfo != null; ObjectAttributeInfo[] attributes = objInfo.getAttributes(); attributeNames = new String[attributes.length]; for (int i = 0; i < attributes.length; i++) { // TODO: we should only add the readable attributes here attributeNames[i] = attributes[i].getName(); } } /* add attribute values of this application to the map*/ appConfigToAttrListMap.put(childAppConfig, serverConnection.getAttributes(objectName, attributeNames)); } catch (ConnectionFailedException e){ logger.log(Level.FINE, "Error retrieving attributes for:" + childAppConfig.getName(), e); /* add null, indicating that the server is down */ appConfigToAttrListMap.put(childAppConfig, null); } } request.setAttribute("objInfo", objInfo); request.setAttribute("appConfigToAttrListMap", appConfigToAttrListMap); /* setup the form to be used in the html form */ MBeanConfigForm mbeanConfigForm = (MBeanConfigForm)actionForm; mbeanConfigForm.setObjectName(objectName.getCanonicalName()); ApplicationConfig appConfig = context.getApplicationConfig(); MBeanConfig mbeanConfig = appConfig.findMBeanByObjectName(objectName.getCanonicalName()); if(mbeanConfig != null){ if(appConfig.isCluster()){ request.setAttribute("mbeanIncludedIn", "cluster"); }else{ request.setAttribute("mbeanIncludedIn", "application"); } request.setAttribute("mbeanConfig", mbeanConfig); }else{ ApplicationConfig clusterConfig = appConfig.getClusterConfig(); if(clusterConfig != null){ mbeanConfig = clusterConfig.findMBeanByObjectName(objectName.getCanonicalName()); } if(mbeanConfig != null){ request.setAttribute("mbeanIncludedIn", "cluster"); request.setAttribute("mbeanConfig", mbeanConfig); } } return mapping.findForward(Forwards.SUCCESS); }

1,110,225

public ReadDataDialog(String title, HaploView h){ caller = h; setTitle(title); JPanel contents = new JPanel(); JButton hapmapButton = new JButton(HAPMAP_DATA); hapmapButton.addActionListener(this); //hapmap isn't ready yet hapmapButton.setEnabled(false); JButton rawdataButton = new JButton(RAW_DATA); rawdataButton.addActionListener(this); JButton phaseddataButton = new JButton(PHASED_DATA); phaseddataButton.addActionListener(this); contents.add(Box.createRigidArea(new Dimension(10,10))); contents.add(rawdataButton); contents.add(Box.createRigidArea(new Dimension(10,10))); contents.add(phaseddataButton); contents.add(Box.createRigidArea(new Dimension(10,10))); contents.add(hapmapButton); contents.add(Box.createRigidArea(new Dimension(10,10))); contents.setLayout(new BoxLayout(contents, BoxLayout.Y_AXIS)); this.setContentPane(contents); this.setLocation(caller.getX() + 100, caller.getY() + 100); //this.setLocation((getParent().getWidth() - this.getWidth()) / 2, // (getParent().getHeight() - this.getHeight()) / 2); this.setModal(true); }

1,110,227

public ReadDataDialog(String title, HaploView h){ caller = h; setTitle(title); JPanel contents = new JPanel(); JButton hapmapButton = new JButton(HAPMAP_DATA); hapmapButton.addActionListener(this); //hapmap isn't ready yet hapmapButton.setEnabled(false); JButton rawdataButton = new JButton(RAW_DATA); rawdataButton.addActionListener(this); JButton phaseddataButton = new JButton(PHASED_DATA); phaseddataButton.addActionListener(this); contents.add(Box.createRigidArea(new Dimension(10,10))); contents.add(rawdataButton); contents.add(Box.createRigidArea(new Dimension(10,10))); contents.add(phaseddataButton); contents.add(Box.createRigidArea(new Dimension(10,10))); contents.add(hapmapButton); contents.add(Box.createRigidArea(new Dimension(10,10))); contents.setLayout(new BoxLayout(contents, BoxLayout.Y_AXIS)); this.setContentPane(contents); this.setLocation(caller.getX() + 100, caller.getY() + 100); //this.setLocation((getParent().getWidth() - this.getWidth()) / 2, // (getParent().getHeight() - this.getHeight()) / 2); this.setModal(true); }

1,110,228

void load(int ft){ fileType = ft; JPanel contents = new JPanel(); contents.setLayout(new BoxLayout(contents, BoxLayout.Y_AXIS)); JPanel filePanel = new JPanel(); filePanel.setLayout(new BoxLayout(filePanel, BoxLayout.Y_AXIS)); JPanel topFilePanel = new JPanel(); JPanel botFilePanel = new JPanel(); genoFileField = new JTextField("",20); //workaround for dumb Swing can't requestfocus until shown bug genoFileField.requestFocus(); genoFileField.dispatchEvent( new FocusEvent( genoFileField, FocusEvent.FOCUS_GAINED, false ) ); infoFileField = new JTextField("",20); JButton browseGenoButton = new JButton("Browse"); browseGenoButton.setActionCommand(BROWSE_GENO); browseGenoButton.addActionListener(this); JButton browseInfoButton = new JButton("Browse"); browseInfoButton.setActionCommand(BROWSE_INFO); browseInfoButton.addActionListener(this); topFilePanel.add(new JLabel("Genotype file: ")); topFilePanel.add(genoFileField); topFilePanel.add(browseGenoButton); botFilePanel.add(new JLabel("Locus information file: ")); botFilePanel.add(infoFileField); botFilePanel.add(browseInfoButton); filePanel.add(topFilePanel); filePanel.add(botFilePanel); filePanel.setBorder(BorderFactory.createEmptyBorder(10,10,10,10)); contents.add(filePanel); JPanel prefsPanel = new JPanel(); maxComparisonDistField = new NumberTextField("500",4); prefsPanel.add(new JLabel("Ignore pairwise comparisons of markers >")); prefsPanel.add(maxComparisonDistField); prefsPanel.add(new JLabel("kb apart.")); contents.add(prefsPanel); doTDT = new JCheckBox(); doTDT.setSelected(false); if (ft == PED){ JPanel tdtPanel = new JPanel(); tdtPanel.add(new JLabel("Run family trio TDT? ")); tdtPanel.add(doTDT); contents.add(tdtPanel); } JPanel choicePanel = new JPanel(); JButton okButton = new JButton("OK"); this.getRootPane().setDefaultButton(okButton); okButton.addActionListener(this); JButton cancelButton = new JButton("Cancel"); cancelButton.addActionListener(this); choicePanel.add(okButton); choicePanel.add(cancelButton); contents.add(choicePanel); this.setContentPane(contents); this.pack(); }

1,110,230

void load(int ft){ fileType = ft; JPanel contents = new JPanel(); contents.setLayout(new BoxLayout(contents, BoxLayout.Y_AXIS)); JPanel filePanel = new JPanel(); filePanel.setLayout(new BoxLayout(filePanel, BoxLayout.Y_AXIS)); JPanel topFilePanel = new JPanel(); JPanel botFilePanel = new JPanel(); genoFileField = new JTextField("",20); //workaround for dumb Swing can't requestfocus until shown bug genoFileField.requestFocus(); genoFileField.dispatchEvent( new FocusEvent( genoFileField, FocusEvent.FOCUS_GAINED, false ) ); infoFileField = new JTextField("",20); JButton browseGenoButton = new JButton("Browse"); browseGenoButton.setActionCommand(BROWSE_GENO); browseGenoButton.addActionListener(this); JButton browseInfoButton = new JButton("Browse"); browseInfoButton.setActionCommand(BROWSE_INFO); browseInfoButton.addActionListener(this); topFilePanel.add(new JLabel("Genotype file: ")); topFilePanel.add(genoFileField); topFilePanel.add(browseGenoButton); botFilePanel.add(new JLabel("Locus information file: ")); botFilePanel.add(infoFileField); botFilePanel.add(browseInfoButton); filePanel.add(topFilePanel); filePanel.add(botFilePanel); filePanel.setBorder(BorderFactory.createEmptyBorder(10,10,10,10)); contents.add(filePanel); JPanel prefsPanel = new JPanel(); maxComparisonDistField = new NumberTextField("500",4); prefsPanel.add(new JLabel("Ignore pairwise comparisons of markers >")); prefsPanel.add(maxComparisonDistField); prefsPanel.add(new JLabel("kb apart.")); contents.add(prefsPanel); doTDT = new JCheckBox(); doTDT.setSelected(false); if (ft == PED){ JPanel tdtPanel = new JPanel(); tdtPanel.add(new JLabel("Run family trio TDT? ")); tdtPanel.add(doTDT); contents.add(tdtPanel); } JPanel choicePanel = new JPanel(); JButton okButton = new JButton("OK"); this.getRootPane().setDefaultButton(okButton); okButton.addActionListener(this); JButton cancelButton = new JButton("Cancel"); cancelButton.addActionListener(this); choicePanel.add(okButton); choicePanel.add(cancelButton); contents.add(choicePanel); this.setContentPane(contents); this.pack(); }

void load(int ft){ fileType = ft; JPanel contents = new JPanel();*/ contents.setLayout(new BoxLayout(contents, BoxLayout.Y_AXIS));*/ JPanel filePanel = new JPanel();*/ filePanel.setLayout(new BoxLayout(filePanel, BoxLayout.Y_AXIS));*/ JPanel topFilePanel = new JPanel();*/ JPanel botFilePanel = new JPanel();*/ genoFileField = new JTextField("",20);*/ //workaround for dumb Swing can't requestfocus until shown bug genoFileField.requestFocus();*/ genoFileField.dispatchEvent( new FocusEvent( genoFileField, FocusEvent.FOCUS_GAINED, false ) );*/ infoFileField = new JTextField("",20);*/ JButton browseGenoButton = new JButton("Browse");*/ browseGenoButton.setActionCommand(BROWSE_GENO);*/ browseGenoButton.addActionListener(this);*/ JButton browseInfoButton = new JButton("Browse");*/ browseInfoButton.setActionCommand(BROWSE_INFO);*/ browseInfoButton.addActionListener(this);*/ topFilePanel.add(new JLabel("Genotype file: "));*/ topFilePanel.add(genoFileField);*/ topFilePanel.add(browseGenoButton);*/ botFilePanel.add(new JLabel("Locus information file: "));*/ botFilePanel.add(infoFileField);*/ botFilePanel.add(browseInfoButton);*/ filePanel.add(topFilePanel);*/ filePanel.add(botFilePanel);*/ filePanel.setBorder(BorderFactory.createEmptyBorder(10,10,10,10));*/ contents.add(filePanel);*/ JPanel prefsPanel = new JPanel();*/ maxComparisonDistField = new NumberTextField("500",4);*/ prefsPanel.add(new JLabel("Ignore pairwise comparisons of markers >"));*/ prefsPanel.add(maxComparisonDistField);*/ prefsPanel.add(new JLabel("kb apart."));*/ contents.add(prefsPanel);*/ doTDT = new JCheckBox();*/ doTDT.setSelected(false);*/ if (ft == PED){ JPanel tdtPanel = new JPanel();*/ tdtPanel.add(new JLabel("Run family trio TDT? "));*/ tdtPanel.add(doTDT);*/ contents.add(tdtPanel);*/ } JPanel choicePanel = new JPanel();*/ JButton okButton = new JButton("OK");*/ this.getRootPane().setDefaultButton(okButton);*/ okButton.addActionListener(this);*/ JButton cancelButton = new JButton("Cancel");*/ cancelButton.addActionListener(this);*/ choicePanel.add(okButton);*/ choicePanel.add(cancelButton);*/ contents.add(choicePanel);*/ this.setContentPane(contents);*/ this.pack();*/ }

1,110,231

public PedFile(){ //hardcoded hapmap info this.families = new Hashtable(); hapMapTranslate = new Hashtable(90,1); hapMapTranslate.put("NA10846", "1334 NA10846 NA12144 NA12145 1 0" ); hapMapTranslate.put("NA12144", "1334 NA12144 0 0 1 0"); hapMapTranslate.put("NA12145", "1334 NA12145 0 0 2 0"); hapMapTranslate.put("NA10847", "1334 NA10847 NA12146 NA12239 2 0" ); hapMapTranslate.put("NA12146", "1334 NA12146 0 0 1 0"); hapMapTranslate.put("NA12239", "1334 NA12239 0 0 2 0"); hapMapTranslate.put("NA07029", "1340 NA07029 NA06994 NA07000 1 0" ); hapMapTranslate.put("NA06994", "1340 NA06994 0 0 1 0"); hapMapTranslate.put("NA07000", "1340 NA07000 0 0 2 0"); hapMapTranslate.put("NA07019", "1340 NA07019 NA07022 NA07056 2 0" ); hapMapTranslate.put("NA07022", "1340 NA07022 0 0 1 0"); hapMapTranslate.put("NA07056", "1340 NA07056 0 0 2 0"); hapMapTranslate.put("NA07048", "1341 NA07048 NA07034 NA07055 1 0" ); hapMapTranslate.put("NA07034", "1341 NA07034 0 0 1 0"); hapMapTranslate.put("NA07055", "1341 NA07055 0 0 2 0"); hapMapTranslate.put("NA06991", "1341 NA06991 NA06993 NA06985 2 0" ); hapMapTranslate.put("NA06993", "1341 NA06993 0 0 1 0"); hapMapTranslate.put("NA06993.dup", "dup NA06993.dup 0 0 1 0"); hapMapTranslate.put("NA06985", "1341 NA06985 0 0 2 0"); hapMapTranslate.put("NA10851", "1344 NA10851 NA12056 NA12057 1 0" ); hapMapTranslate.put("NA12056", "1344 NA12056 0 0 1 0"); hapMapTranslate.put("NA12057", "1344 NA12057 0 0 2 0"); hapMapTranslate.put("NA07348", "1345 NA07348 NA07357 NA07345 2 0" ); hapMapTranslate.put("NA07357", "1345 NA07357 0 0 1 0"); hapMapTranslate.put("NA07345", "1345 NA07345 0 0 2 0"); hapMapTranslate.put("NA10857", "1346 NA10857 NA12043 NA12044 1 0" ); hapMapTranslate.put("NA12043", "1346 NA12043 0 0 1 0"); hapMapTranslate.put("NA12044", "1346 NA12044 0 0 2 0"); hapMapTranslate.put("NA10859", "1347 NA10859 NA11881 NA11882 2 0" ); hapMapTranslate.put("NA11881", "1347 NA11881 0 0 1 0"); hapMapTranslate.put("NA11882", "1347 NA11882 0 0 2 0"); hapMapTranslate.put("NA10854", "1349 NA10854 NA11839 NA11840 2 0" ); hapMapTranslate.put("NA11839", "1349 NA11839 0 0 1 0"); hapMapTranslate.put("NA11840", "1349 NA11840 0 0 2 0"); hapMapTranslate.put("NA10856", "1350 NA10856 NA11829 NA11830 1 0" ); hapMapTranslate.put("NA11829", "1350 NA11829 0 0 1 0"); hapMapTranslate.put("NA11830", "1350 NA11830 0 0 2 0"); hapMapTranslate.put("NA10855", "1350 NA10855 NA11831 NA11832 2 0" ); hapMapTranslate.put("NA11831", "1350 NA11831 0 0 1 0"); hapMapTranslate.put("NA11832", "1350 NA11832 0 0 2 0"); hapMapTranslate.put("NA12707", "1358 NA12707 NA12716 NA12717 1 0" ); hapMapTranslate.put("NA12716", "1358 NA12716 0 0 1 0"); hapMapTranslate.put("NA12717", "1358 NA12717 0 0 2 0"); hapMapTranslate.put("NA10860", "1362 NA10860 NA11992 NA11993 1 0" ); hapMapTranslate.put("NA11992", "1362 NA11992 0 0 1 0"); hapMapTranslate.put("NA11993", "1362 NA11993 0 0 2 0"); hapMapTranslate.put("NA11993.dup", "dup NA11993.dup 0 0 2 0"); hapMapTranslate.put("NA10861", "1362 NA10861 NA11994 NA11995 2 0" ); hapMapTranslate.put("NA11994", "1362 NA11994 0 0 1 0"); hapMapTranslate.put("NA11995", "1362 NA11995 0 0 2 0"); hapMapTranslate.put("NA10863", "1375 NA10863 NA12264 NA12234 2 0" ); hapMapTranslate.put("NA12264", "1375 NA12264 0 0 1 0"); hapMapTranslate.put("NA12234", "1375 NA12234 0 0 2 0"); hapMapTranslate.put("NA10830", "1408 NA10830 NA12154 NA12236 1 0" ); hapMapTranslate.put("NA12154", "1408 NA12154 0 0 1 0"); hapMapTranslate.put("NA12236", "1408 NA12236 0 0 2 0"); hapMapTranslate.put("NA10831", "1408 NA10831 NA12155 NA12156 2 0" ); hapMapTranslate.put("NA12155", "1408 NA12155 0 0 1 0"); hapMapTranslate.put("NA12156", "1408 NA12156 0 0 2 0"); hapMapTranslate.put("NA12156.dup", "dup NA12156.dup 0 0 2 0"); hapMapTranslate.put("NA10835", "1416 NA10835 NA12248 NA12249 1 0" ); hapMapTranslate.put("NA12248", "1416 NA12248 0 0 1 0"); hapMapTranslate.put("NA12248.dup", "dup NA1248.dup 0 0 1 0"); hapMapTranslate.put("NA12249", "1416 NA12249 0 0 2 0"); hapMapTranslate.put("NA10838", "1420 NA10838 NA12003 NA12004 1 0" ); hapMapTranslate.put("NA12003", "1420 NA12003 0 0 1 0"); hapMapTranslate.put("NA12003.dup", "dup NA12003.dup 0 0 1 0"); hapMapTranslate.put("NA12004", "1420 NA12004 0 0 2 0"); hapMapTranslate.put("NA10839", "1420 NA10839 NA12005 NA12006 2 0" ); hapMapTranslate.put("NA12005", "1420 NA12005 0 0 1 0"); hapMapTranslate.put("NA12006", "1420 NA12006 0 0 2 0"); hapMapTranslate.put("NA12740", "1444 NA12740 NA12750 NA12751 2 0" ); hapMapTranslate.put("NA12750", "1444 NA12750 0 0 1 0"); hapMapTranslate.put("NA12751", "1444 NA12751 0 0 2 0"); hapMapTranslate.put("NA12752", "1447 NA12752 NA12760 NA12761 1 0" ); hapMapTranslate.put("NA12760", "1447 NA12760 0 0 1 0"); hapMapTranslate.put("NA12761", "1447 NA12761 0 0 2 0"); hapMapTranslate.put("NA12753", "1447 NA12753 NA12762 NA12763 2 0" ); hapMapTranslate.put("NA12762", "1447 NA12762 0 0 1 0"); hapMapTranslate.put("NA12763", "1447 NA12763 0 0 2 0"); hapMapTranslate.put("NA12801", "1454 NA12801 NA12812 NA12813 1 0" ); hapMapTranslate.put("NA12812", "1454 NA12812 0 0 1 0"); hapMapTranslate.put("NA12813", "1454 NA12813 0 0 2 0"); hapMapTranslate.put("NA12802", "1454 NA12802 NA12814 NA12815 2 0" ); hapMapTranslate.put("NA12814", "1454 NA12814 0 0 1 0"); hapMapTranslate.put("NA12815", "1454 NA12815 0 0 2 0"); hapMapTranslate.put("NA12864", "1459 NA12864 NA12872 NA12873 1 0" ); hapMapTranslate.put("NA12872", "1459 NA12872 0 0 1 0"); hapMapTranslate.put("NA12873", "1459 NA12873 0 0 2 0"); hapMapTranslate.put("NA12865", "1459 NA12865 NA12874 NA12875 2 0" ); hapMapTranslate.put("NA12874", "1459 NA12874 0 0 1 0"); hapMapTranslate.put("NA12875", "1459 NA12875 0 0 2 0"); hapMapTranslate.put("NA12878", "1463 NA12878 NA12891 NA12892 2 0" ); hapMapTranslate.put("NA12891", "1463 NA12891 0 0 1 0"); hapMapTranslate.put("NA12892", "1463 NA12892 0 0 2 0"); hapMapTranslate.put("NA18526", "chi1 NA18526 0 0 2 0"); hapMapTranslate.put("NA18524", "chi2 NA18524 0 0 1 0"); hapMapTranslate.put("NA18529", "chi3 NA18529 0 0 2 0"); hapMapTranslate.put("NA18558", "chi4 NA18558 0 0 1 0"); hapMapTranslate.put("NA18532", "chi5 NA18532 0 0 2 0"); hapMapTranslate.put("NA18561", "chi6 NA18561 0 0 1 0"); hapMapTranslate.put("NA18942", "jap1 NA18942 0 0 2 0"); hapMapTranslate.put("NA18940", "jap2 NA18940 0 0 1 0"); hapMapTranslate.put("NA18951", "jap3 NA18951 0 0 2 0"); hapMapTranslate.put("NA18943", "jap4 NA18943 0 0 1 0"); hapMapTranslate.put("NA18947", "jap5 NA18947 0 0 2 0"); hapMapTranslate.put("NA18944", "jap6 NA18944 0 0 1 0"); hapMapTranslate.put("NA18562", "chi7 NA18562 0 0 1 0"); hapMapTranslate.put("NA18537", "chi8 NA18537 0 0 2 0"); hapMapTranslate.put("NA18603", "chi9 NA18603 0 0 1 0"); hapMapTranslate.put("NA18540", "chi10 NA18540 0 0 2 0"); hapMapTranslate.put("NA18605", "chi11 NA18605 0 0 1 0"); hapMapTranslate.put("NA18542", "chi12 NA18542 0 0 2 0"); hapMapTranslate.put("NA18945", "jap7 NA18945 0 0 1 0"); hapMapTranslate.put("NA18949", "jap8 NA18949 0 0 2 0"); hapMapTranslate.put("NA18948", "jap9 NA18948 0 0 1 0"); hapMapTranslate.put("NA18952", "jap10 NA18952 0 0 1 0"); hapMapTranslate.put("NA18956", "jap11 NA18956 0 0 2 0"); hapMapTranslate.put("NA18545", "chi13 NA18545 0 0 2 0"); hapMapTranslate.put("NA18572", "chi46 NA18572 0 0 1 0"); hapMapTranslate.put("NA18547", "chi15 NA18547 0 0 2 0"); hapMapTranslate.put("NA18609", "chi16 NA18609 0 0 1 0"); hapMapTranslate.put("NA18550", "chi17 NA18550 0 0 2 0"); hapMapTranslate.put("NA18608", "chi18 NA18608 0 0 1 0"); hapMapTranslate.put("NA18964", "jap12 NA18964 0 0 2 0"); hapMapTranslate.put("NA18953", "jap13 NA18953 0 0 1 0"); hapMapTranslate.put("NA18968", "jap14 NA18968 0 0 2 0"); hapMapTranslate.put("NA18959", "jap15 NA18959 0 0 1 0"); hapMapTranslate.put("NA18969", "jap16 NA18969 0 0 2 0"); hapMapTranslate.put("NA18960", "jap17 NA18960 0 0 1 0"); hapMapTranslate.put("NA18552", "chi19 NA18552 0 0 2 0"); hapMapTranslate.put("NA18611", "chi20 NA18611 0 0 1 0"); hapMapTranslate.put("NA18555", "chi21 NA18555 0 0 2 0"); hapMapTranslate.put("NA18564", "chi22 NA18564 0 0 2 0"); hapMapTranslate.put("NA18961", "jap18 NA18961 0 0 1 0"); hapMapTranslate.put("NA18972", "jap19 NA18972 0 0 2 0"); hapMapTranslate.put("NA18965", "jap20 NA18965 0 0 1 0"); hapMapTranslate.put("NA18973", "jap21 NA18973 0 0 2 0"); hapMapTranslate.put("NA18966", "jap22 NA18966 0 0 1 0"); hapMapTranslate.put("NA18975", "jap23 NA18975 0 0 2 0"); hapMapTranslate.put("NA18566", "chi23 NA18566 0 0 2 0"); hapMapTranslate.put("NA18563", "chi24 NA18563 0 0 1 0"); hapMapTranslate.put("NA18570", "chi25 NA18570 0 0 2 0"); hapMapTranslate.put("NA18612", "chi26 NA18612 0 0 1 0"); hapMapTranslate.put("NA18571", "chi27 NA18571 0 0 2 0"); hapMapTranslate.put("NA18620", "chi28 NA18620 0 0 1 0"); hapMapTranslate.put("NA18976", "jap24 NA18976 0 0 2 0"); hapMapTranslate.put("NA18967", "jap25 NA18967 0 0 1 0"); hapMapTranslate.put("NA18978", "jap26 NA18978 0 0 2 0"); hapMapTranslate.put("NA18970", "jap27 NA18970 0 0 1 0"); hapMapTranslate.put("NA18980", "jap28 NA18980 0 0 2 0"); hapMapTranslate.put("NA18995", "jap29 NA18995 0 0 1 0"); hapMapTranslate.put("NA18621", "chi29 NA18621 0 0 1 0"); hapMapTranslate.put("NA18594", "chi30 NA18594 0 0 2 0"); hapMapTranslate.put("NA18622", "chi31 NA18622 0 0 1 0"); hapMapTranslate.put("NA18573", "chi32 NA18573 0 0 2 0"); hapMapTranslate.put("NA18623", "chi33 NA18623 0 0 1 0"); hapMapTranslate.put("NA18576", "chi34 NA18576 0 0 2 0"); hapMapTranslate.put("NA18971", "jap30 NA18971 0 0 1 0"); hapMapTranslate.put("NA18981", "jap31 NA18981 0 0 2 0"); hapMapTranslate.put("NA18974", "jap32 NA18974 0 0 1 0"); hapMapTranslate.put("NA18987", "jap33 NA18987 0 0 2 0"); hapMapTranslate.put("NA18990", "jap34 NA18990 0 0 1 0"); hapMapTranslate.put("NA18991", "jap35 NA18991 0 0 2 0"); hapMapTranslate.put("NA18577", "chi35 NA18577 0 0 2 0"); hapMapTranslate.put("NA18624", "chi36 NA18624 0 0 1 0"); hapMapTranslate.put("NA18579", "chi37 NA18579 0 0 2 0"); hapMapTranslate.put("NA18632", "chi38 NA18632 0 0 1 0"); hapMapTranslate.put("NA18582", "chi39 NA18582 0 0 2 0"); hapMapTranslate.put("NA18633", "chi40 NA18633 0 0 1 0"); hapMapTranslate.put("NA18994", "jap36 NA18994 0 0 1 0"); hapMapTranslate.put("NA18992", "jap37 NA18992 0 0 2 0"); hapMapTranslate.put("NA18997", "jap38 NA18997 0 0 2 0"); hapMapTranslate.put("NA18996", "jap39 NA18996 0 0 1 0"); hapMapTranslate.put("NA18635", "chi41 NA18635 0 0 1 0"); hapMapTranslate.put("NA18592", "chi42 NA18592 0 0 2 0"); hapMapTranslate.put("NA18636", "chi43 NA18636 0 0 1 0"); hapMapTranslate.put("NA18593", "chi44 NA18593 0 0 2 0"); hapMapTranslate.put("NA18637", "chi45 NA18637 0 0 1 0"); hapMapTranslate.put("NA19000", "jap40 NA19000 0 0 1 0"); hapMapTranslate.put("NA18998", "jap41 NA18998 0 0 2 0"); hapMapTranslate.put("NA19005", "jap42 NA19005 0 0 1 0"); hapMapTranslate.put("NA18999", "jap43 NA18999 0 0 2 0"); hapMapTranslate.put("NA19007", "jap44 NA19007 0 0 1 0"); hapMapTranslate.put("NA19003", "jap45 NA19003 0 0 2 0"); hapMapTranslate.put("NA18500", "Yoruba004 NA18500 NA18501 NA18502 1 0"); hapMapTranslate.put("NA18501", "Yoruba004 NA18501 0 0 1 0"); hapMapTranslate.put("NA18502", "Yoruba004 NA18502 0 0 2 0"); hapMapTranslate.put("NA18503", "Yoruba005 NA18503 NA18504 NA18505 1 0"); hapMapTranslate.put("NA18504", "Yoruba005 NA18504 0 0 1 0"); hapMapTranslate.put("NA18505", "Yoruba005 NA18505 0 0 2 0"); hapMapTranslate.put("NA18506", "Yoruba009 NA18506 NA18507 NA18508 1 0"); hapMapTranslate.put("NA18507", "Yoruba009 NA18507 0 0 1 0"); hapMapTranslate.put("NA18508", "Yoruba009 NA18508 0 0 2 0"); hapMapTranslate.put("NA18860", "Yoruba012 NA18860 NA18859 NA18858 1 0"); hapMapTranslate.put("NA18859", "Yoruba012 NA18859 0 0 1 0"); hapMapTranslate.put("NA18858", "Yoruba012 NA18858 0 0 2 0"); hapMapTranslate.put("NA18515", "Yoruba013 NA18515 NA18516 NA18517 1 0"); hapMapTranslate.put("NA18516", "Yoruba013 NA18516 0 0 1 0"); hapMapTranslate.put("NA18517", "Yoruba013 NA18517 0 0 2 0"); hapMapTranslate.put("NA18521", "Yoruba016 NA18521 NA18522 NA18523 1 0"); hapMapTranslate.put("NA18522", "Yoruba016 NA18522 0 0 1 0"); hapMapTranslate.put("NA18523", "Yoruba016 NA18523 0 0 2 0"); hapMapTranslate.put("NA18872", "Yoruba017 NA18872 NA18871 NA18870 1 0"); hapMapTranslate.put("NA18871", "Yoruba017 NA18871 0 0 1 0"); hapMapTranslate.put("NA18870", "Yoruba017 NA18870 0 0 2 0"); hapMapTranslate.put("NA18854", "Yoruba018 NA18854 NA18853 NA18852 1 0"); hapMapTranslate.put("NA18853", "Yoruba018 NA18853 0 0 1 0"); hapMapTranslate.put("NA18852", "Yoruba018 NA18852 0 0 2 0"); hapMapTranslate.put("NA18857", "Yoruba023 NA18857 NA18856 NA18855 1 0"); hapMapTranslate.put("NA18856", "Yoruba023 NA18856 0 0 1 0"); hapMapTranslate.put("NA18855", "Yoruba023 NA18855 0 0 2 0"); hapMapTranslate.put("NA18863", "Yoruba024 NA18863 NA18862 NA18861 1 0"); hapMapTranslate.put("NA18862", "Yoruba024 NA18862 0 0 1 0"); hapMapTranslate.put("NA18861", "Yoruba024 NA18861 0 0 2 0"); hapMapTranslate.put("NA18914", "Yoruba028 NA18914 NA18913 NA18912 1 0"); hapMapTranslate.put("NA18913", "Yoruba028 NA18913 0 0 1 0"); hapMapTranslate.put("NA18912", "Yoruba028 NA18912 0 0 2 0"); hapMapTranslate.put("NA19094", "Yoruba040 NA19094 NA19092 NA19093 2 0"); hapMapTranslate.put("NA19092", "Yoruba040 NA19092 0 0 1 0"); hapMapTranslate.put("NA19093", "Yoruba040 NA19093 0 0 2 0"); hapMapTranslate.put("NA19103", "Yoruba042 NA19103 NA19101 NA19102 1 0"); hapMapTranslate.put("NA19101", "Yoruba042 NA19101 0 0 1 0"); hapMapTranslate.put("NA19102", "Yoruba042 NA19102 0 0 2 0"); hapMapTranslate.put("NA19139", "Yoruba043 NA19139 NA19138 NA19137 1 0"); hapMapTranslate.put("NA19138", "Yoruba043 NA19138 0 0 1 0"); hapMapTranslate.put("NA19137", "Yoruba043 NA19137 0 0 2 0"); hapMapTranslate.put("NA19202", "Yoruba045 NA19202 NA19200 NA19201 2 0"); hapMapTranslate.put("NA19200", "Yoruba045 NA19200 0 0 1 0"); hapMapTranslate.put("NA19201", "Yoruba045 NA19201 0 0 2 0"); hapMapTranslate.put("NA19173", "Yoruba047 NA19173 NA19171 NA19172 1 0"); hapMapTranslate.put("NA19171", "Yoruba047 NA19171 0 0 1 0"); hapMapTranslate.put("NA19172", "Yoruba047 NA19172 0 0 2 0"); hapMapTranslate.put("NA19205", "Yoruba048 NA19205 NA19203 NA19204 1 0"); hapMapTranslate.put("NA19203", "Yoruba048 NA19203 0 0 1 0"); hapMapTranslate.put("NA19204", "Yoruba048 NA19204 0 0 2 0"); hapMapTranslate.put("NA19211", "Yoruba050 NA19211 NA19210 NA19209 1 0"); hapMapTranslate.put("NA19210", "Yoruba050 NA19210 0 0 1 0"); hapMapTranslate.put("NA19209", "Yoruba050 NA19209 0 0 2 0"); hapMapTranslate.put("NA19208", "Yoruba051 NA19208 NA19207 NA19206 1 0"); hapMapTranslate.put("NA19207", "Yoruba051 NA19207 0 0 1 0"); hapMapTranslate.put("NA19206", "Yoruba051 NA19206 0 0 2 0"); hapMapTranslate.put("NA19161", "Yoruba056 NA19161 NA19160 NA19159 1 0"); hapMapTranslate.put("NA19160", "Yoruba056 NA19160 0 0 1 0"); hapMapTranslate.put("NA19159", "Yoruba056 NA19159 0 0 2 0"); hapMapTranslate.put("NA19221", "Yoruba058 NA19221 NA19223 NA19222 2 0"); hapMapTranslate.put("NA19223", "Yoruba058 NA19223 0 0 1 0"); hapMapTranslate.put("NA19222", "Yoruba058 NA19222 0 0 2 0"); hapMapTranslate.put("NA19120", "Yoruba060 NA19120 NA19119 NA19116 1 0"); hapMapTranslate.put("NA19119", "Yoruba060 NA19119 0 0 1 0"); hapMapTranslate.put("NA19116", "Yoruba060 NA19116 0 0 2 0"); hapMapTranslate.put("NA19142", "Yoruba071 NA19142 NA19141 NA19140 1 0"); hapMapTranslate.put("NA19141", "Yoruba071 NA19141 0 0 1 0"); hapMapTranslate.put("NA19140", "Yoruba071 NA19140 0 0 2 0"); hapMapTranslate.put("NA19154", "Yoruba072 NA19154 NA19153 NA19152 1 0"); hapMapTranslate.put("NA19153", "Yoruba072 NA19153 0 0 1 0"); hapMapTranslate.put("NA19152", "Yoruba072 NA19152 0 0 2 0"); hapMapTranslate.put("NA19145", "Yoruba074 NA19145 NA19144 NA19143 1 0"); hapMapTranslate.put("NA19144", "Yoruba074 NA19144 0 0 1 0"); hapMapTranslate.put("NA19143", "Yoruba074 NA19143 0 0 2 0"); hapMapTranslate.put("NA19129", "Yoruba077 NA19129 NA19128 NA19127 2 0"); hapMapTranslate.put("NA19128", "Yoruba077 NA19128 0 0 1 0"); hapMapTranslate.put("NA19127", "Yoruba077 NA19127 0 0 2 0"); hapMapTranslate.put("NA19132", "Yoruba101 NA19132 NA19130 NA19131 2 0"); hapMapTranslate.put("NA19130", "Yoruba101 NA19130 0 0 1 0"); hapMapTranslate.put("NA19131", "Yoruba101 NA19131 0 0 2 0"); hapMapTranslate.put("NA19100", "Yoruba105 NA19100 NA19098 NA19099 2 0"); hapMapTranslate.put("NA19098", "Yoruba105 NA19098 0 0 1 0"); hapMapTranslate.put("NA19099", "Yoruba105 NA19099 0 0 2 0"); hapMapTranslate.put("NA19194", "Yoruba112 NA19194 NA19192 NA19193 1 0"); hapMapTranslate.put("NA19192", "Yoruba112 NA19192 0 0 1 0"); hapMapTranslate.put("NA19193", "Yoruba112 NA19193 0 0 2 0"); hapMapTranslate.put("NA19240", "Yoruba117 NA19240 NA19239 NA19238 2 0"); hapMapTranslate.put("NA19239", "Yoruba117 NA19239 0 0 1 0"); hapMapTranslate.put("NA19238", "Yoruba117 NA19238 0 0 2 0"); }

public PedFile(){ //hardcoded hapmap info this.families = new Hashtable(); hapMapTranslate = new Hashtable(90,1); hapMapTranslate.put("NA10846", "1334 NA10846 NA12144 NA12145 1 0" ); hapMapTranslate.put("NA12144", "1334 NA12144 0 0 1 0"); hapMapTranslate.put("NA12145", "1334 NA12145 0 0 2 0"); hapMapTranslate.put("NA10847", "1334 NA10847 NA12146 NA12239 2 0" ); hapMapTranslate.put("NA12146", "1334 NA12146 0 0 1 0"); hapMapTranslate.put("NA12239", "1334 NA12239 0 0 2 0"); hapMapTranslate.put("NA07029", "1340 NA07029 NA06994 NA07000 1 0" ); hapMapTranslate.put("NA06994", "1340 NA06994 0 0 1 0"); hapMapTranslate.put("NA07000", "1340 NA07000 0 0 2 0"); hapMapTranslate.put("NA07019", "1340 NA07019 NA07022 NA07056 2 0" ); hapMapTranslate.put("NA07022", "1340 NA07022 0 0 1 0"); hapMapTranslate.put("NA07056", "1340 NA07056 0 0 2 0"); hapMapTranslate.put("NA07048", "1341 NA07048 NA07034 NA07055 1 0" ); hapMapTranslate.put("NA07034", "1341 NA07034 0 0 1 0"); hapMapTranslate.put("NA07055", "1341 NA07055 0 0 2 0"); hapMapTranslate.put("NA06991", "1341 NA06991 NA06993 NA06985 2 0" ); hapMapTranslate.put("NA06993", "1341 NA06993 0 0 1 0"); hapMapTranslate.put("NA06985", "1341 NA06985 0 0 2 0"); hapMapTranslate.put("NA10851", "1344 NA10851 NA12056 NA12057 1 0" ); hapMapTranslate.put("NA12056", "1344 NA12056 0 0 1 0"); hapMapTranslate.put("NA12057", "1344 NA12057 0 0 2 0"); hapMapTranslate.put("NA07348", "1345 NA07348 NA07357 NA07345 2 0" ); hapMapTranslate.put("NA07357", "1345 NA07357 0 0 1 0"); hapMapTranslate.put("NA07345", "1345 NA07345 0 0 2 0"); hapMapTranslate.put("NA10857", "1346 NA10857 NA12043 NA12044 1 0" ); hapMapTranslate.put("NA12043", "1346 NA12043 0 0 1 0"); hapMapTranslate.put("NA12044", "1346 NA12044 0 0 2 0"); hapMapTranslate.put("NA10859", "1347 NA10859 NA11881 NA11882 2 0" ); hapMapTranslate.put("NA11881", "1347 NA11881 0 0 1 0"); hapMapTranslate.put("NA11882", "1347 NA11882 0 0 2 0"); hapMapTranslate.put("NA10854", "1349 NA10854 NA11839 NA11840 2 0" ); hapMapTranslate.put("NA11839", "1349 NA11839 0 0 1 0"); hapMapTranslate.put("NA11840", "1349 NA11840 0 0 2 0"); hapMapTranslate.put("NA10856", "1350 NA10856 NA11829 NA11830 1 0" ); hapMapTranslate.put("NA11829", "1350 NA11829 0 0 1 0"); hapMapTranslate.put("NA11830", "1350 NA11830 0 0 2 0"); hapMapTranslate.put("NA10855", "1350 NA10855 NA11831 NA11832 2 0" ); hapMapTranslate.put("NA11831", "1350 NA11831 0 0 1 0"); hapMapTranslate.put("NA11832", "1350 NA11832 0 0 2 0"); hapMapTranslate.put("NA12707", "1358 NA12707 NA12716 NA12717 1 0" ); hapMapTranslate.put("NA12716", "1358 NA12716 0 0 1 0"); hapMapTranslate.put("NA12717", "1358 NA12717 0 0 2 0"); hapMapTranslate.put("NA10860", "1362 NA10860 NA11992 NA11993 1 0" ); hapMapTranslate.put("NA11992", "1362 NA11992 0 0 1 0"); hapMapTranslate.put("NA11993", "1362 NA11993 0 0 2 0"); hapMapTranslate.put("NA11993.dup", "dup NA11993.dup 0 0 2 0"); hapMapTranslate.put("NA10861", "1362 NA10861 NA11994 NA11995 2 0" ); hapMapTranslate.put("NA11994", "1362 NA11994 0 0 1 0"); hapMapTranslate.put("NA11995", "1362 NA11995 0 0 2 0"); hapMapTranslate.put("NA10863", "1375 NA10863 NA12264 NA12234 2 0" ); hapMapTranslate.put("NA12264", "1375 NA12264 0 0 1 0"); hapMapTranslate.put("NA12234", "1375 NA12234 0 0 2 0"); hapMapTranslate.put("NA10830", "1408 NA10830 NA12154 NA12236 1 0" ); hapMapTranslate.put("NA12154", "1408 NA12154 0 0 1 0"); hapMapTranslate.put("NA12236", "1408 NA12236 0 0 2 0"); hapMapTranslate.put("NA10831", "1408 NA10831 NA12155 NA12156 2 0" ); hapMapTranslate.put("NA12155", "1408 NA12155 0 0 1 0"); hapMapTranslate.put("NA12156", "1408 NA12156 0 0 2 0"); hapMapTranslate.put("NA12156.dup", "dup NA12156.dup 0 0 2 0"); hapMapTranslate.put("NA10835", "1416 NA10835 NA12248 NA12249 1 0" ); hapMapTranslate.put("NA12248", "1416 NA12248 0 0 1 0"); hapMapTranslate.put("NA12248.dup", "dup NA1248.dup 0 0 1 0"); hapMapTranslate.put("NA12249", "1416 NA12249 0 0 2 0"); hapMapTranslate.put("NA10838", "1420 NA10838 NA12003 NA12004 1 0" ); hapMapTranslate.put("NA12003", "1420 NA12003 0 0 1 0"); hapMapTranslate.put("NA12003.dup", "dup NA12003.dup 0 0 1 0"); hapMapTranslate.put("NA12004", "1420 NA12004 0 0 2 0"); hapMapTranslate.put("NA10839", "1420 NA10839 NA12005 NA12006 2 0" ); hapMapTranslate.put("NA12005", "1420 NA12005 0 0 1 0"); hapMapTranslate.put("NA12006", "1420 NA12006 0 0 2 0"); hapMapTranslate.put("NA12740", "1444 NA12740 NA12750 NA12751 2 0" ); hapMapTranslate.put("NA12750", "1444 NA12750 0 0 1 0"); hapMapTranslate.put("NA12751", "1444 NA12751 0 0 2 0"); hapMapTranslate.put("NA12752", "1447 NA12752 NA12760 NA12761 1 0" ); hapMapTranslate.put("NA12760", "1447 NA12760 0 0 1 0"); hapMapTranslate.put("NA12761", "1447 NA12761 0 0 2 0"); hapMapTranslate.put("NA12753", "1447 NA12753 NA12762 NA12763 2 0" ); hapMapTranslate.put("NA12762", "1447 NA12762 0 0 1 0"); hapMapTranslate.put("NA12763", "1447 NA12763 0 0 2 0"); hapMapTranslate.put("NA12801", "1454 NA12801 NA12812 NA12813 1 0" ); hapMapTranslate.put("NA12812", "1454 NA12812 0 0 1 0"); hapMapTranslate.put("NA12813", "1454 NA12813 0 0 2 0"); hapMapTranslate.put("NA12802", "1454 NA12802 NA12814 NA12815 2 0" ); hapMapTranslate.put("NA12814", "1454 NA12814 0 0 1 0"); hapMapTranslate.put("NA12815", "1454 NA12815 0 0 2 0"); hapMapTranslate.put("NA12864", "1459 NA12864 NA12872 NA12873 1 0" ); hapMapTranslate.put("NA12872", "1459 NA12872 0 0 1 0"); hapMapTranslate.put("NA12873", "1459 NA12873 0 0 2 0"); hapMapTranslate.put("NA12865", "1459 NA12865 NA12874 NA12875 2 0" ); hapMapTranslate.put("NA12874", "1459 NA12874 0 0 1 0"); hapMapTranslate.put("NA12875", "1459 NA12875 0 0 2 0"); hapMapTranslate.put("NA12878", "1463 NA12878 NA12891 NA12892 2 0" ); hapMapTranslate.put("NA12891", "1463 NA12891 0 0 1 0"); hapMapTranslate.put("NA12892", "1463 NA12892 0 0 2 0"); hapMapTranslate.put("NA18526", "chi1 NA18526 0 0 2 0"); hapMapTranslate.put("NA18524", "chi2 NA18524 0 0 1 0"); hapMapTranslate.put("NA18529", "chi3 NA18529 0 0 2 0"); hapMapTranslate.put("NA18558", "chi4 NA18558 0 0 1 0"); hapMapTranslate.put("NA18532", "chi5 NA18532 0 0 2 0"); hapMapTranslate.put("NA18561", "chi6 NA18561 0 0 1 0"); hapMapTranslate.put("NA18942", "jap1 NA18942 0 0 2 0"); hapMapTranslate.put("NA18940", "jap2 NA18940 0 0 1 0"); hapMapTranslate.put("NA18951", "jap3 NA18951 0 0 2 0"); hapMapTranslate.put("NA18943", "jap4 NA18943 0 0 1 0"); hapMapTranslate.put("NA18947", "jap5 NA18947 0 0 2 0"); hapMapTranslate.put("NA18944", "jap6 NA18944 0 0 1 0"); hapMapTranslate.put("NA18562", "chi7 NA18562 0 0 1 0"); hapMapTranslate.put("NA18537", "chi8 NA18537 0 0 2 0"); hapMapTranslate.put("NA18603", "chi9 NA18603 0 0 1 0"); hapMapTranslate.put("NA18540", "chi10 NA18540 0 0 2 0"); hapMapTranslate.put("NA18605", "chi11 NA18605 0 0 1 0"); hapMapTranslate.put("NA18542", "chi12 NA18542 0 0 2 0"); hapMapTranslate.put("NA18945", "jap7 NA18945 0 0 1 0"); hapMapTranslate.put("NA18949", "jap8 NA18949 0 0 2 0"); hapMapTranslate.put("NA18948", "jap9 NA18948 0 0 1 0"); hapMapTranslate.put("NA18952", "jap10 NA18952 0 0 1 0"); hapMapTranslate.put("NA18956", "jap11 NA18956 0 0 2 0"); hapMapTranslate.put("NA18545", "chi13 NA18545 0 0 2 0"); hapMapTranslate.put("NA18572", "chi46 NA18572 0 0 1 0"); hapMapTranslate.put("NA18547", "chi15 NA18547 0 0 2 0"); hapMapTranslate.put("NA18609", "chi16 NA18609 0 0 1 0"); hapMapTranslate.put("NA18550", "chi17 NA18550 0 0 2 0"); hapMapTranslate.put("NA18608", "chi18 NA18608 0 0 1 0"); hapMapTranslate.put("NA18964", "jap12 NA18964 0 0 2 0"); hapMapTranslate.put("NA18953", "jap13 NA18953 0 0 1 0"); hapMapTranslate.put("NA18968", "jap14 NA18968 0 0 2 0"); hapMapTranslate.put("NA18959", "jap15 NA18959 0 0 1 0"); hapMapTranslate.put("NA18969", "jap16 NA18969 0 0 2 0"); hapMapTranslate.put("NA18960", "jap17 NA18960 0 0 1 0"); hapMapTranslate.put("NA18552", "chi19 NA18552 0 0 2 0"); hapMapTranslate.put("NA18611", "chi20 NA18611 0 0 1 0"); hapMapTranslate.put("NA18555", "chi21 NA18555 0 0 2 0"); hapMapTranslate.put("NA18564", "chi22 NA18564 0 0 2 0"); hapMapTranslate.put("NA18961", "jap18 NA18961 0 0 1 0"); hapMapTranslate.put("NA18972", "jap19 NA18972 0 0 2 0"); hapMapTranslate.put("NA18965", "jap20 NA18965 0 0 1 0"); hapMapTranslate.put("NA18973", "jap21 NA18973 0 0 2 0"); hapMapTranslate.put("NA18966", "jap22 NA18966 0 0 1 0"); hapMapTranslate.put("NA18975", "jap23 NA18975 0 0 2 0"); hapMapTranslate.put("NA18566", "chi23 NA18566 0 0 2 0"); hapMapTranslate.put("NA18563", "chi24 NA18563 0 0 1 0"); hapMapTranslate.put("NA18570", "chi25 NA18570 0 0 2 0"); hapMapTranslate.put("NA18612", "chi26 NA18612 0 0 1 0"); hapMapTranslate.put("NA18571", "chi27 NA18571 0 0 2 0"); hapMapTranslate.put("NA18620", "chi28 NA18620 0 0 1 0"); hapMapTranslate.put("NA18976", "jap24 NA18976 0 0 2 0"); hapMapTranslate.put("NA18967", "jap25 NA18967 0 0 1 0"); hapMapTranslate.put("NA18978", "jap26 NA18978 0 0 2 0"); hapMapTranslate.put("NA18970", "jap27 NA18970 0 0 1 0"); hapMapTranslate.put("NA18980", "jap28 NA18980 0 0 2 0"); hapMapTranslate.put("NA18995", "jap29 NA18995 0 0 1 0"); hapMapTranslate.put("NA18621", "chi29 NA18621 0 0 1 0"); hapMapTranslate.put("NA18594", "chi30 NA18594 0 0 2 0"); hapMapTranslate.put("NA18622", "chi31 NA18622 0 0 1 0"); hapMapTranslate.put("NA18573", "chi32 NA18573 0 0 2 0"); hapMapTranslate.put("NA18623", "chi33 NA18623 0 0 1 0"); hapMapTranslate.put("NA18576", "chi34 NA18576 0 0 2 0"); hapMapTranslate.put("NA18971", "jap30 NA18971 0 0 1 0"); hapMapTranslate.put("NA18981", "jap31 NA18981 0 0 2 0"); hapMapTranslate.put("NA18974", "jap32 NA18974 0 0 1 0"); hapMapTranslate.put("NA18987", "jap33 NA18987 0 0 2 0"); hapMapTranslate.put("NA18990", "jap34 NA18990 0 0 1 0"); hapMapTranslate.put("NA18991", "jap35 NA18991 0 0 2 0"); hapMapTranslate.put("NA18577", "chi35 NA18577 0 0 2 0"); hapMapTranslate.put("NA18624", "chi36 NA18624 0 0 1 0"); hapMapTranslate.put("NA18579", "chi37 NA18579 0 0 2 0"); hapMapTranslate.put("NA18632", "chi38 NA18632 0 0 1 0"); hapMapTranslate.put("NA18582", "chi39 NA18582 0 0 2 0"); hapMapTranslate.put("NA18633", "chi40 NA18633 0 0 1 0"); hapMapTranslate.put("NA18994", "jap36 NA18994 0 0 1 0"); hapMapTranslate.put("NA18992", "jap37 NA18992 0 0 2 0"); hapMapTranslate.put("NA18997", "jap38 NA18997 0 0 2 0"); hapMapTranslate.put("NA18996", "jap39 NA18996 0 0 1 0"); hapMapTranslate.put("NA18635", "chi41 NA18635 0 0 1 0"); hapMapTranslate.put("NA18592", "chi42 NA18592 0 0 2 0"); hapMapTranslate.put("NA18636", "chi43 NA18636 0 0 1 0"); hapMapTranslate.put("NA18593", "chi44 NA18593 0 0 2 0"); hapMapTranslate.put("NA18637", "chi45 NA18637 0 0 1 0"); hapMapTranslate.put("NA19000", "jap40 NA19000 0 0 1 0"); hapMapTranslate.put("NA18998", "jap41 NA18998 0 0 2 0"); hapMapTranslate.put("NA19005", "jap42 NA19005 0 0 1 0"); hapMapTranslate.put("NA18999", "jap43 NA18999 0 0 2 0"); hapMapTranslate.put("NA19007", "jap44 NA19007 0 0 1 0"); hapMapTranslate.put("NA19003", "jap45 NA19003 0 0 2 0"); hapMapTranslate.put("NA18500", "Yoruba004 NA18500 NA18501 NA18502 1 0"); hapMapTranslate.put("NA18501", "Yoruba004 NA18501 0 0 1 0"); hapMapTranslate.put("NA18502", "Yoruba004 NA18502 0 0 2 0"); hapMapTranslate.put("NA18503", "Yoruba005 NA18503 NA18504 NA18505 1 0"); hapMapTranslate.put("NA18504", "Yoruba005 NA18504 0 0 1 0"); hapMapTranslate.put("NA18505", "Yoruba005 NA18505 0 0 2 0"); hapMapTranslate.put("NA18506", "Yoruba009 NA18506 NA18507 NA18508 1 0"); hapMapTranslate.put("NA18507", "Yoruba009 NA18507 0 0 1 0"); hapMapTranslate.put("NA18508", "Yoruba009 NA18508 0 0 2 0"); hapMapTranslate.put("NA18860", "Yoruba012 NA18860 NA18859 NA18858 1 0"); hapMapTranslate.put("NA18859", "Yoruba012 NA18859 0 0 1 0"); hapMapTranslate.put("NA18858", "Yoruba012 NA18858 0 0 2 0"); hapMapTranslate.put("NA18515", "Yoruba013 NA18515 NA18516 NA18517 1 0"); hapMapTranslate.put("NA18516", "Yoruba013 NA18516 0 0 1 0"); hapMapTranslate.put("NA18517", "Yoruba013 NA18517 0 0 2 0"); hapMapTranslate.put("NA18521", "Yoruba016 NA18521 NA18522 NA18523 1 0"); hapMapTranslate.put("NA18522", "Yoruba016 NA18522 0 0 1 0"); hapMapTranslate.put("NA18523", "Yoruba016 NA18523 0 0 2 0"); hapMapTranslate.put("NA18872", "Yoruba017 NA18872 NA18871 NA18870 1 0"); hapMapTranslate.put("NA18871", "Yoruba017 NA18871 0 0 1 0"); hapMapTranslate.put("NA18870", "Yoruba017 NA18870 0 0 2 0"); hapMapTranslate.put("NA18854", "Yoruba018 NA18854 NA18853 NA18852 1 0"); hapMapTranslate.put("NA18853", "Yoruba018 NA18853 0 0 1 0"); hapMapTranslate.put("NA18852", "Yoruba018 NA18852 0 0 2 0"); hapMapTranslate.put("NA18857", "Yoruba023 NA18857 NA18856 NA18855 1 0"); hapMapTranslate.put("NA18856", "Yoruba023 NA18856 0 0 1 0"); hapMapTranslate.put("NA18855", "Yoruba023 NA18855 0 0 2 0"); hapMapTranslate.put("NA18863", "Yoruba024 NA18863 NA18862 NA18861 1 0"); hapMapTranslate.put("NA18862", "Yoruba024 NA18862 0 0 1 0"); hapMapTranslate.put("NA18861", "Yoruba024 NA18861 0 0 2 0"); hapMapTranslate.put("NA18914", "Yoruba028 NA18914 NA18913 NA18912 1 0"); hapMapTranslate.put("NA18913", "Yoruba028 NA18913 0 0 1 0"); hapMapTranslate.put("NA18912", "Yoruba028 NA18912 0 0 2 0"); hapMapTranslate.put("NA19094", "Yoruba040 NA19094 NA19092 NA19093 2 0"); hapMapTranslate.put("NA19092", "Yoruba040 NA19092 0 0 1 0"); hapMapTranslate.put("NA19093", "Yoruba040 NA19093 0 0 2 0"); hapMapTranslate.put("NA19103", "Yoruba042 NA19103 NA19101 NA19102 1 0"); hapMapTranslate.put("NA19101", "Yoruba042 NA19101 0 0 1 0"); hapMapTranslate.put("NA19102", "Yoruba042 NA19102 0 0 2 0"); hapMapTranslate.put("NA19139", "Yoruba043 NA19139 NA19138 NA19137 1 0"); hapMapTranslate.put("NA19138", "Yoruba043 NA19138 0 0 1 0"); hapMapTranslate.put("NA19137", "Yoruba043 NA19137 0 0 2 0"); hapMapTranslate.put("NA19202", "Yoruba045 NA19202 NA19200 NA19201 2 0"); hapMapTranslate.put("NA19200", "Yoruba045 NA19200 0 0 1 0"); hapMapTranslate.put("NA19201", "Yoruba045 NA19201 0 0 2 0"); hapMapTranslate.put("NA19173", "Yoruba047 NA19173 NA19171 NA19172 1 0"); hapMapTranslate.put("NA19171", "Yoruba047 NA19171 0 0 1 0"); hapMapTranslate.put("NA19172", "Yoruba047 NA19172 0 0 2 0"); hapMapTranslate.put("NA19205", "Yoruba048 NA19205 NA19203 NA19204 1 0"); hapMapTranslate.put("NA19203", "Yoruba048 NA19203 0 0 1 0"); hapMapTranslate.put("NA19204", "Yoruba048 NA19204 0 0 2 0"); hapMapTranslate.put("NA19211", "Yoruba050 NA19211 NA19210 NA19209 1 0"); hapMapTranslate.put("NA19210", "Yoruba050 NA19210 0 0 1 0"); hapMapTranslate.put("NA19209", "Yoruba050 NA19209 0 0 2 0"); hapMapTranslate.put("NA19208", "Yoruba051 NA19208 NA19207 NA19206 1 0"); hapMapTranslate.put("NA19207", "Yoruba051 NA19207 0 0 1 0"); hapMapTranslate.put("NA19206", "Yoruba051 NA19206 0 0 2 0"); hapMapTranslate.put("NA19161", "Yoruba056 NA19161 NA19160 NA19159 1 0"); hapMapTranslate.put("NA19160", "Yoruba056 NA19160 0 0 1 0"); hapMapTranslate.put("NA19159", "Yoruba056 NA19159 0 0 2 0"); hapMapTranslate.put("NA19221", "Yoruba058 NA19221 NA19223 NA19222 2 0"); hapMapTranslate.put("NA19223", "Yoruba058 NA19223 0 0 1 0"); hapMapTranslate.put("NA19222", "Yoruba058 NA19222 0 0 2 0"); hapMapTranslate.put("NA19120", "Yoruba060 NA19120 NA19119 NA19116 1 0"); hapMapTranslate.put("NA19119", "Yoruba060 NA19119 0 0 1 0"); hapMapTranslate.put("NA19116", "Yoruba060 NA19116 0 0 2 0"); hapMapTranslate.put("NA19142", "Yoruba071 NA19142 NA19141 NA19140 1 0"); hapMapTranslate.put("NA19141", "Yoruba071 NA19141 0 0 1 0"); hapMapTranslate.put("NA19140", "Yoruba071 NA19140 0 0 2 0"); hapMapTranslate.put("NA19154", "Yoruba072 NA19154 NA19153 NA19152 1 0"); hapMapTranslate.put("NA19153", "Yoruba072 NA19153 0 0 1 0"); hapMapTranslate.put("NA19152", "Yoruba072 NA19152 0 0 2 0"); hapMapTranslate.put("NA19145", "Yoruba074 NA19145 NA19144 NA19143 1 0"); hapMapTranslate.put("NA19144", "Yoruba074 NA19144 0 0 1 0"); hapMapTranslate.put("NA19143", "Yoruba074 NA19143 0 0 2 0"); hapMapTranslate.put("NA19129", "Yoruba077 NA19129 NA19128 NA19127 2 0"); hapMapTranslate.put("NA19128", "Yoruba077 NA19128 0 0 1 0"); hapMapTranslate.put("NA19127", "Yoruba077 NA19127 0 0 2 0"); hapMapTranslate.put("NA19132", "Yoruba101 NA19132 NA19130 NA19131 2 0"); hapMapTranslate.put("NA19130", "Yoruba101 NA19130 0 0 1 0"); hapMapTranslate.put("NA19131", "Yoruba101 NA19131 0 0 2 0"); hapMapTranslate.put("NA19100", "Yoruba105 NA19100 NA19098 NA19099 2 0"); hapMapTranslate.put("NA19098", "Yoruba105 NA19098 0 0 1 0"); hapMapTranslate.put("NA19099", "Yoruba105 NA19099 0 0 2 0"); hapMapTranslate.put("NA19194", "Yoruba112 NA19194 NA19192 NA19193 1 0"); hapMapTranslate.put("NA19192", "Yoruba112 NA19192 0 0 1 0"); hapMapTranslate.put("NA19193", "Yoruba112 NA19193 0 0 2 0"); hapMapTranslate.put("NA19240", "Yoruba117 NA19240 NA19239 NA19238 2 0"); hapMapTranslate.put("NA19239", "Yoruba117 NA19239 0 0 1 0"); hapMapTranslate.put("NA19238", "Yoruba117 NA19238 0 0 2 0"); }

1,110,232

public PedFile(){ //hardcoded hapmap info this.families = new Hashtable(); hapMapTranslate = new Hashtable(90,1); hapMapTranslate.put("NA10846", "1334 NA10846 NA12144 NA12145 1 0" ); hapMapTranslate.put("NA12144", "1334 NA12144 0 0 1 0"); hapMapTranslate.put("NA12145", "1334 NA12145 0 0 2 0"); hapMapTranslate.put("NA10847", "1334 NA10847 NA12146 NA12239 2 0" ); hapMapTranslate.put("NA12146", "1334 NA12146 0 0 1 0"); hapMapTranslate.put("NA12239", "1334 NA12239 0 0 2 0"); hapMapTranslate.put("NA07029", "1340 NA07029 NA06994 NA07000 1 0" ); hapMapTranslate.put("NA06994", "1340 NA06994 0 0 1 0"); hapMapTranslate.put("NA07000", "1340 NA07000 0 0 2 0"); hapMapTranslate.put("NA07019", "1340 NA07019 NA07022 NA07056 2 0" ); hapMapTranslate.put("NA07022", "1340 NA07022 0 0 1 0"); hapMapTranslate.put("NA07056", "1340 NA07056 0 0 2 0"); hapMapTranslate.put("NA07048", "1341 NA07048 NA07034 NA07055 1 0" ); hapMapTranslate.put("NA07034", "1341 NA07034 0 0 1 0"); hapMapTranslate.put("NA07055", "1341 NA07055 0 0 2 0"); hapMapTranslate.put("NA06991", "1341 NA06991 NA06993 NA06985 2 0" ); hapMapTranslate.put("NA06993", "1341 NA06993 0 0 1 0"); hapMapTranslate.put("NA06993.dup", "dup NA06993.dup 0 0 1 0"); hapMapTranslate.put("NA06985", "1341 NA06985 0 0 2 0"); hapMapTranslate.put("NA10851", "1344 NA10851 NA12056 NA12057 1 0" ); hapMapTranslate.put("NA12056", "1344 NA12056 0 0 1 0"); hapMapTranslate.put("NA12057", "1344 NA12057 0 0 2 0"); hapMapTranslate.put("NA07348", "1345 NA07348 NA07357 NA07345 2 0" ); hapMapTranslate.put("NA07357", "1345 NA07357 0 0 1 0"); hapMapTranslate.put("NA07345", "1345 NA07345 0 0 2 0"); hapMapTranslate.put("NA10857", "1346 NA10857 NA12043 NA12044 1 0" ); hapMapTranslate.put("NA12043", "1346 NA12043 0 0 1 0"); hapMapTranslate.put("NA12044", "1346 NA12044 0 0 2 0"); hapMapTranslate.put("NA10859", "1347 NA10859 NA11881 NA11882 2 0" ); hapMapTranslate.put("NA11881", "1347 NA11881 0 0 1 0"); hapMapTranslate.put("NA11882", "1347 NA11882 0 0 2 0"); hapMapTranslate.put("NA10854", "1349 NA10854 NA11839 NA11840 2 0" ); hapMapTranslate.put("NA11839", "1349 NA11839 0 0 1 0"); hapMapTranslate.put("NA11840", "1349 NA11840 0 0 2 0"); hapMapTranslate.put("NA10856", "1350 NA10856 NA11829 NA11830 1 0" ); hapMapTranslate.put("NA11829", "1350 NA11829 0 0 1 0"); hapMapTranslate.put("NA11830", "1350 NA11830 0 0 2 0"); hapMapTranslate.put("NA10855", "1350 NA10855 NA11831 NA11832 2 0" ); hapMapTranslate.put("NA11831", "1350 NA11831 0 0 1 0"); hapMapTranslate.put("NA11832", "1350 NA11832 0 0 2 0"); hapMapTranslate.put("NA12707", "1358 NA12707 NA12716 NA12717 1 0" ); hapMapTranslate.put("NA12716", "1358 NA12716 0 0 1 0"); hapMapTranslate.put("NA12717", "1358 NA12717 0 0 2 0"); hapMapTranslate.put("NA10860", "1362 NA10860 NA11992 NA11993 1 0" ); hapMapTranslate.put("NA11992", "1362 NA11992 0 0 1 0"); hapMapTranslate.put("NA11993", "1362 NA11993 0 0 2 0"); hapMapTranslate.put("NA11993.dup", "dup NA11993.dup 0 0 2 0"); hapMapTranslate.put("NA10861", "1362 NA10861 NA11994 NA11995 2 0" ); hapMapTranslate.put("NA11994", "1362 NA11994 0 0 1 0"); hapMapTranslate.put("NA11995", "1362 NA11995 0 0 2 0"); hapMapTranslate.put("NA10863", "1375 NA10863 NA12264 NA12234 2 0" ); hapMapTranslate.put("NA12264", "1375 NA12264 0 0 1 0"); hapMapTranslate.put("NA12234", "1375 NA12234 0 0 2 0"); hapMapTranslate.put("NA10830", "1408 NA10830 NA12154 NA12236 1 0" ); hapMapTranslate.put("NA12154", "1408 NA12154 0 0 1 0"); hapMapTranslate.put("NA12236", "1408 NA12236 0 0 2 0"); hapMapTranslate.put("NA10831", "1408 NA10831 NA12155 NA12156 2 0" ); hapMapTranslate.put("NA12155", "1408 NA12155 0 0 1 0"); hapMapTranslate.put("NA12156", "1408 NA12156 0 0 2 0"); hapMapTranslate.put("NA12156.dup", "dup NA12156.dup 0 0 2 0"); hapMapTranslate.put("NA10835", "1416 NA10835 NA12248 NA12249 1 0" ); hapMapTranslate.put("NA12248", "1416 NA12248 0 0 1 0"); hapMapTranslate.put("NA12248.dup", "dup NA1248.dup 0 0 1 0"); hapMapTranslate.put("NA12249", "1416 NA12249 0 0 2 0"); hapMapTranslate.put("NA10838", "1420 NA10838 NA12003 NA12004 1 0" ); hapMapTranslate.put("NA12003", "1420 NA12003 0 0 1 0"); hapMapTranslate.put("NA12003.dup", "dup NA12003.dup 0 0 1 0"); hapMapTranslate.put("NA12004", "1420 NA12004 0 0 2 0"); hapMapTranslate.put("NA10839", "1420 NA10839 NA12005 NA12006 2 0" ); hapMapTranslate.put("NA12005", "1420 NA12005 0 0 1 0"); hapMapTranslate.put("NA12006", "1420 NA12006 0 0 2 0"); hapMapTranslate.put("NA12740", "1444 NA12740 NA12750 NA12751 2 0" ); hapMapTranslate.put("NA12750", "1444 NA12750 0 0 1 0"); hapMapTranslate.put("NA12751", "1444 NA12751 0 0 2 0"); hapMapTranslate.put("NA12752", "1447 NA12752 NA12760 NA12761 1 0" ); hapMapTranslate.put("NA12760", "1447 NA12760 0 0 1 0"); hapMapTranslate.put("NA12761", "1447 NA12761 0 0 2 0"); hapMapTranslate.put("NA12753", "1447 NA12753 NA12762 NA12763 2 0" ); hapMapTranslate.put("NA12762", "1447 NA12762 0 0 1 0"); hapMapTranslate.put("NA12763", "1447 NA12763 0 0 2 0"); hapMapTranslate.put("NA12801", "1454 NA12801 NA12812 NA12813 1 0" ); hapMapTranslate.put("NA12812", "1454 NA12812 0 0 1 0"); hapMapTranslate.put("NA12813", "1454 NA12813 0 0 2 0"); hapMapTranslate.put("NA12802", "1454 NA12802 NA12814 NA12815 2 0" ); hapMapTranslate.put("NA12814", "1454 NA12814 0 0 1 0"); hapMapTranslate.put("NA12815", "1454 NA12815 0 0 2 0"); hapMapTranslate.put("NA12864", "1459 NA12864 NA12872 NA12873 1 0" ); hapMapTranslate.put("NA12872", "1459 NA12872 0 0 1 0"); hapMapTranslate.put("NA12873", "1459 NA12873 0 0 2 0"); hapMapTranslate.put("NA12865", "1459 NA12865 NA12874 NA12875 2 0" ); hapMapTranslate.put("NA12874", "1459 NA12874 0 0 1 0"); hapMapTranslate.put("NA12875", "1459 NA12875 0 0 2 0"); hapMapTranslate.put("NA12878", "1463 NA12878 NA12891 NA12892 2 0" ); hapMapTranslate.put("NA12891", "1463 NA12891 0 0 1 0"); hapMapTranslate.put("NA12892", "1463 NA12892 0 0 2 0"); hapMapTranslate.put("NA18526", "chi1 NA18526 0 0 2 0"); hapMapTranslate.put("NA18524", "chi2 NA18524 0 0 1 0"); hapMapTranslate.put("NA18529", "chi3 NA18529 0 0 2 0"); hapMapTranslate.put("NA18558", "chi4 NA18558 0 0 1 0"); hapMapTranslate.put("NA18532", "chi5 NA18532 0 0 2 0"); hapMapTranslate.put("NA18561", "chi6 NA18561 0 0 1 0"); hapMapTranslate.put("NA18942", "jap1 NA18942 0 0 2 0"); hapMapTranslate.put("NA18940", "jap2 NA18940 0 0 1 0"); hapMapTranslate.put("NA18951", "jap3 NA18951 0 0 2 0"); hapMapTranslate.put("NA18943", "jap4 NA18943 0 0 1 0"); hapMapTranslate.put("NA18947", "jap5 NA18947 0 0 2 0"); hapMapTranslate.put("NA18944", "jap6 NA18944 0 0 1 0"); hapMapTranslate.put("NA18562", "chi7 NA18562 0 0 1 0"); hapMapTranslate.put("NA18537", "chi8 NA18537 0 0 2 0"); hapMapTranslate.put("NA18603", "chi9 NA18603 0 0 1 0"); hapMapTranslate.put("NA18540", "chi10 NA18540 0 0 2 0"); hapMapTranslate.put("NA18605", "chi11 NA18605 0 0 1 0"); hapMapTranslate.put("NA18542", "chi12 NA18542 0 0 2 0"); hapMapTranslate.put("NA18945", "jap7 NA18945 0 0 1 0"); hapMapTranslate.put("NA18949", "jap8 NA18949 0 0 2 0"); hapMapTranslate.put("NA18948", "jap9 NA18948 0 0 1 0"); hapMapTranslate.put("NA18952", "jap10 NA18952 0 0 1 0"); hapMapTranslate.put("NA18956", "jap11 NA18956 0 0 2 0"); hapMapTranslate.put("NA18545", "chi13 NA18545 0 0 2 0"); hapMapTranslate.put("NA18572", "chi46 NA18572 0 0 1 0"); hapMapTranslate.put("NA18547", "chi15 NA18547 0 0 2 0"); hapMapTranslate.put("NA18609", "chi16 NA18609 0 0 1 0"); hapMapTranslate.put("NA18550", "chi17 NA18550 0 0 2 0"); hapMapTranslate.put("NA18608", "chi18 NA18608 0 0 1 0"); hapMapTranslate.put("NA18964", "jap12 NA18964 0 0 2 0"); hapMapTranslate.put("NA18953", "jap13 NA18953 0 0 1 0"); hapMapTranslate.put("NA18968", "jap14 NA18968 0 0 2 0"); hapMapTranslate.put("NA18959", "jap15 NA18959 0 0 1 0"); hapMapTranslate.put("NA18969", "jap16 NA18969 0 0 2 0"); hapMapTranslate.put("NA18960", "jap17 NA18960 0 0 1 0"); hapMapTranslate.put("NA18552", "chi19 NA18552 0 0 2 0"); hapMapTranslate.put("NA18611", "chi20 NA18611 0 0 1 0"); hapMapTranslate.put("NA18555", "chi21 NA18555 0 0 2 0"); hapMapTranslate.put("NA18564", "chi22 NA18564 0 0 2 0"); hapMapTranslate.put("NA18961", "jap18 NA18961 0 0 1 0"); hapMapTranslate.put("NA18972", "jap19 NA18972 0 0 2 0"); hapMapTranslate.put("NA18965", "jap20 NA18965 0 0 1 0"); hapMapTranslate.put("NA18973", "jap21 NA18973 0 0 2 0"); hapMapTranslate.put("NA18966", "jap22 NA18966 0 0 1 0"); hapMapTranslate.put("NA18975", "jap23 NA18975 0 0 2 0"); hapMapTranslate.put("NA18566", "chi23 NA18566 0 0 2 0"); hapMapTranslate.put("NA18563", "chi24 NA18563 0 0 1 0"); hapMapTranslate.put("NA18570", "chi25 NA18570 0 0 2 0"); hapMapTranslate.put("NA18612", "chi26 NA18612 0 0 1 0"); hapMapTranslate.put("NA18571", "chi27 NA18571 0 0 2 0"); hapMapTranslate.put("NA18620", "chi28 NA18620 0 0 1 0"); hapMapTranslate.put("NA18976", "jap24 NA18976 0 0 2 0"); hapMapTranslate.put("NA18967", "jap25 NA18967 0 0 1 0"); hapMapTranslate.put("NA18978", "jap26 NA18978 0 0 2 0"); hapMapTranslate.put("NA18970", "jap27 NA18970 0 0 1 0"); hapMapTranslate.put("NA18980", "jap28 NA18980 0 0 2 0"); hapMapTranslate.put("NA18995", "jap29 NA18995 0 0 1 0"); hapMapTranslate.put("NA18621", "chi29 NA18621 0 0 1 0"); hapMapTranslate.put("NA18594", "chi30 NA18594 0 0 2 0"); hapMapTranslate.put("NA18622", "chi31 NA18622 0 0 1 0"); hapMapTranslate.put("NA18573", "chi32 NA18573 0 0 2 0"); hapMapTranslate.put("NA18623", "chi33 NA18623 0 0 1 0"); hapMapTranslate.put("NA18576", "chi34 NA18576 0 0 2 0"); hapMapTranslate.put("NA18971", "jap30 NA18971 0 0 1 0"); hapMapTranslate.put("NA18981", "jap31 NA18981 0 0 2 0"); hapMapTranslate.put("NA18974", "jap32 NA18974 0 0 1 0"); hapMapTranslate.put("NA18987", "jap33 NA18987 0 0 2 0"); hapMapTranslate.put("NA18990", "jap34 NA18990 0 0 1 0"); hapMapTranslate.put("NA18991", "jap35 NA18991 0 0 2 0"); hapMapTranslate.put("NA18577", "chi35 NA18577 0 0 2 0"); hapMapTranslate.put("NA18624", "chi36 NA18624 0 0 1 0"); hapMapTranslate.put("NA18579", "chi37 NA18579 0 0 2 0"); hapMapTranslate.put("NA18632", "chi38 NA18632 0 0 1 0"); hapMapTranslate.put("NA18582", "chi39 NA18582 0 0 2 0"); hapMapTranslate.put("NA18633", "chi40 NA18633 0 0 1 0"); hapMapTranslate.put("NA18994", "jap36 NA18994 0 0 1 0"); hapMapTranslate.put("NA18992", "jap37 NA18992 0 0 2 0"); hapMapTranslate.put("NA18997", "jap38 NA18997 0 0 2 0"); hapMapTranslate.put("NA18996", "jap39 NA18996 0 0 1 0"); hapMapTranslate.put("NA18635", "chi41 NA18635 0 0 1 0"); hapMapTranslate.put("NA18592", "chi42 NA18592 0 0 2 0"); hapMapTranslate.put("NA18636", "chi43 NA18636 0 0 1 0"); hapMapTranslate.put("NA18593", "chi44 NA18593 0 0 2 0"); hapMapTranslate.put("NA18637", "chi45 NA18637 0 0 1 0"); hapMapTranslate.put("NA19000", "jap40 NA19000 0 0 1 0"); hapMapTranslate.put("NA18998", "jap41 NA18998 0 0 2 0"); hapMapTranslate.put("NA19005", "jap42 NA19005 0 0 1 0"); hapMapTranslate.put("NA18999", "jap43 NA18999 0 0 2 0"); hapMapTranslate.put("NA19007", "jap44 NA19007 0 0 1 0"); hapMapTranslate.put("NA19003", "jap45 NA19003 0 0 2 0"); hapMapTranslate.put("NA18500", "Yoruba004 NA18500 NA18501 NA18502 1 0"); hapMapTranslate.put("NA18501", "Yoruba004 NA18501 0 0 1 0"); hapMapTranslate.put("NA18502", "Yoruba004 NA18502 0 0 2 0"); hapMapTranslate.put("NA18503", "Yoruba005 NA18503 NA18504 NA18505 1 0"); hapMapTranslate.put("NA18504", "Yoruba005 NA18504 0 0 1 0"); hapMapTranslate.put("NA18505", "Yoruba005 NA18505 0 0 2 0"); hapMapTranslate.put("NA18506", "Yoruba009 NA18506 NA18507 NA18508 1 0"); hapMapTranslate.put("NA18507", "Yoruba009 NA18507 0 0 1 0"); hapMapTranslate.put("NA18508", "Yoruba009 NA18508 0 0 2 0"); hapMapTranslate.put("NA18860", "Yoruba012 NA18860 NA18859 NA18858 1 0"); hapMapTranslate.put("NA18859", "Yoruba012 NA18859 0 0 1 0"); hapMapTranslate.put("NA18858", "Yoruba012 NA18858 0 0 2 0"); hapMapTranslate.put("NA18515", "Yoruba013 NA18515 NA18516 NA18517 1 0"); hapMapTranslate.put("NA18516", "Yoruba013 NA18516 0 0 1 0"); hapMapTranslate.put("NA18517", "Yoruba013 NA18517 0 0 2 0"); hapMapTranslate.put("NA18521", "Yoruba016 NA18521 NA18522 NA18523 1 0"); hapMapTranslate.put("NA18522", "Yoruba016 NA18522 0 0 1 0"); hapMapTranslate.put("NA18523", "Yoruba016 NA18523 0 0 2 0"); hapMapTranslate.put("NA18872", "Yoruba017 NA18872 NA18871 NA18870 1 0"); hapMapTranslate.put("NA18871", "Yoruba017 NA18871 0 0 1 0"); hapMapTranslate.put("NA18870", "Yoruba017 NA18870 0 0 2 0"); hapMapTranslate.put("NA18854", "Yoruba018 NA18854 NA18853 NA18852 1 0"); hapMapTranslate.put("NA18853", "Yoruba018 NA18853 0 0 1 0"); hapMapTranslate.put("NA18852", "Yoruba018 NA18852 0 0 2 0"); hapMapTranslate.put("NA18857", "Yoruba023 NA18857 NA18856 NA18855 1 0"); hapMapTranslate.put("NA18856", "Yoruba023 NA18856 0 0 1 0"); hapMapTranslate.put("NA18855", "Yoruba023 NA18855 0 0 2 0"); hapMapTranslate.put("NA18863", "Yoruba024 NA18863 NA18862 NA18861 1 0"); hapMapTranslate.put("NA18862", "Yoruba024 NA18862 0 0 1 0"); hapMapTranslate.put("NA18861", "Yoruba024 NA18861 0 0 2 0"); hapMapTranslate.put("NA18914", "Yoruba028 NA18914 NA18913 NA18912 1 0"); hapMapTranslate.put("NA18913", "Yoruba028 NA18913 0 0 1 0"); hapMapTranslate.put("NA18912", "Yoruba028 NA18912 0 0 2 0"); hapMapTranslate.put("NA19094", "Yoruba040 NA19094 NA19092 NA19093 2 0"); hapMapTranslate.put("NA19092", "Yoruba040 NA19092 0 0 1 0"); hapMapTranslate.put("NA19093", "Yoruba040 NA19093 0 0 2 0"); hapMapTranslate.put("NA19103", "Yoruba042 NA19103 NA19101 NA19102 1 0"); hapMapTranslate.put("NA19101", "Yoruba042 NA19101 0 0 1 0"); hapMapTranslate.put("NA19102", "Yoruba042 NA19102 0 0 2 0"); hapMapTranslate.put("NA19139", "Yoruba043 NA19139 NA19138 NA19137 1 0"); hapMapTranslate.put("NA19138", "Yoruba043 NA19138 0 0 1 0"); hapMapTranslate.put("NA19137", "Yoruba043 NA19137 0 0 2 0"); hapMapTranslate.put("NA19202", "Yoruba045 NA19202 NA19200 NA19201 2 0"); hapMapTranslate.put("NA19200", "Yoruba045 NA19200 0 0 1 0"); hapMapTranslate.put("NA19201", "Yoruba045 NA19201 0 0 2 0"); hapMapTranslate.put("NA19173", "Yoruba047 NA19173 NA19171 NA19172 1 0"); hapMapTranslate.put("NA19171", "Yoruba047 NA19171 0 0 1 0"); hapMapTranslate.put("NA19172", "Yoruba047 NA19172 0 0 2 0"); hapMapTranslate.put("NA19205", "Yoruba048 NA19205 NA19203 NA19204 1 0"); hapMapTranslate.put("NA19203", "Yoruba048 NA19203 0 0 1 0"); hapMapTranslate.put("NA19204", "Yoruba048 NA19204 0 0 2 0"); hapMapTranslate.put("NA19211", "Yoruba050 NA19211 NA19210 NA19209 1 0"); hapMapTranslate.put("NA19210", "Yoruba050 NA19210 0 0 1 0"); hapMapTranslate.put("NA19209", "Yoruba050 NA19209 0 0 2 0"); hapMapTranslate.put("NA19208", "Yoruba051 NA19208 NA19207 NA19206 1 0"); hapMapTranslate.put("NA19207", "Yoruba051 NA19207 0 0 1 0"); hapMapTranslate.put("NA19206", "Yoruba051 NA19206 0 0 2 0"); hapMapTranslate.put("NA19161", "Yoruba056 NA19161 NA19160 NA19159 1 0"); hapMapTranslate.put("NA19160", "Yoruba056 NA19160 0 0 1 0"); hapMapTranslate.put("NA19159", "Yoruba056 NA19159 0 0 2 0"); hapMapTranslate.put("NA19221", "Yoruba058 NA19221 NA19223 NA19222 2 0"); hapMapTranslate.put("NA19223", "Yoruba058 NA19223 0 0 1 0"); hapMapTranslate.put("NA19222", "Yoruba058 NA19222 0 0 2 0"); hapMapTranslate.put("NA19120", "Yoruba060 NA19120 NA19119 NA19116 1 0"); hapMapTranslate.put("NA19119", "Yoruba060 NA19119 0 0 1 0"); hapMapTranslate.put("NA19116", "Yoruba060 NA19116 0 0 2 0"); hapMapTranslate.put("NA19142", "Yoruba071 NA19142 NA19141 NA19140 1 0"); hapMapTranslate.put("NA19141", "Yoruba071 NA19141 0 0 1 0"); hapMapTranslate.put("NA19140", "Yoruba071 NA19140 0 0 2 0"); hapMapTranslate.put("NA19154", "Yoruba072 NA19154 NA19153 NA19152 1 0"); hapMapTranslate.put("NA19153", "Yoruba072 NA19153 0 0 1 0"); hapMapTranslate.put("NA19152", "Yoruba072 NA19152 0 0 2 0"); hapMapTranslate.put("NA19145", "Yoruba074 NA19145 NA19144 NA19143 1 0"); hapMapTranslate.put("NA19144", "Yoruba074 NA19144 0 0 1 0"); hapMapTranslate.put("NA19143", "Yoruba074 NA19143 0 0 2 0"); hapMapTranslate.put("NA19129", "Yoruba077 NA19129 NA19128 NA19127 2 0"); hapMapTranslate.put("NA19128", "Yoruba077 NA19128 0 0 1 0"); hapMapTranslate.put("NA19127", "Yoruba077 NA19127 0 0 2 0"); hapMapTranslate.put("NA19132", "Yoruba101 NA19132 NA19130 NA19131 2 0"); hapMapTranslate.put("NA19130", "Yoruba101 NA19130 0 0 1 0"); hapMapTranslate.put("NA19131", "Yoruba101 NA19131 0 0 2 0"); hapMapTranslate.put("NA19100", "Yoruba105 NA19100 NA19098 NA19099 2 0"); hapMapTranslate.put("NA19098", "Yoruba105 NA19098 0 0 1 0"); hapMapTranslate.put("NA19099", "Yoruba105 NA19099 0 0 2 0"); hapMapTranslate.put("NA19194", "Yoruba112 NA19194 NA19192 NA19193 1 0"); hapMapTranslate.put("NA19192", "Yoruba112 NA19192 0 0 1 0"); hapMapTranslate.put("NA19193", "Yoruba112 NA19193 0 0 2 0"); hapMapTranslate.put("NA19240", "Yoruba117 NA19240 NA19239 NA19238 2 0"); hapMapTranslate.put("NA19239", "Yoruba117 NA19239 0 0 1 0"); hapMapTranslate.put("NA19238", "Yoruba117 NA19238 0 0 2 0"); }

public PedFile(){ //hardcoded hapmap info this.families = new Hashtable(); hapMapTranslate = new Hashtable(90,1); hapMapTranslate.put("NA10846", "1334 NA10846 NA12144 NA12145 1 0" ); hapMapTranslate.put("NA12144", "1334 NA12144 0 0 1 0"); hapMapTranslate.put("NA12145", "1334 NA12145 0 0 2 0"); hapMapTranslate.put("NA10847", "1334 NA10847 NA12146 NA12239 2 0" ); hapMapTranslate.put("NA12146", "1334 NA12146 0 0 1 0"); hapMapTranslate.put("NA12239", "1334 NA12239 0 0 2 0"); hapMapTranslate.put("NA07029", "1340 NA07029 NA06994 NA07000 1 0" ); hapMapTranslate.put("NA06994", "1340 NA06994 0 0 1 0"); hapMapTranslate.put("NA07000", "1340 NA07000 0 0 2 0"); hapMapTranslate.put("NA07019", "1340 NA07019 NA07022 NA07056 2 0" ); hapMapTranslate.put("NA07022", "1340 NA07022 0 0 1 0"); hapMapTranslate.put("NA07056", "1340 NA07056 0 0 2 0"); hapMapTranslate.put("NA07048", "1341 NA07048 NA07034 NA07055 1 0" ); hapMapTranslate.put("NA07034", "1341 NA07034 0 0 1 0"); hapMapTranslate.put("NA07055", "1341 NA07055 0 0 2 0"); hapMapTranslate.put("NA06991", "1341 NA06991 NA06993 NA06985 2 0" ); hapMapTranslate.put("NA06993", "1341 NA06993 0 0 1 0"); hapMapTranslate.put("NA06993.dup", "dup NA06993.dup 0 0 1 0"); hapMapTranslate.put("NA06985", "1341 NA06985 0 0 2 0"); hapMapTranslate.put("NA10851", "1344 NA10851 NA12056 NA12057 1 0" ); hapMapTranslate.put("NA12056", "1344 NA12056 0 0 1 0"); hapMapTranslate.put("NA12057", "1344 NA12057 0 0 2 0"); hapMapTranslate.put("NA07348", "1345 NA07348 NA07357 NA07345 2 0" ); hapMapTranslate.put("NA07357", "1345 NA07357 0 0 1 0"); hapMapTranslate.put("NA07345", "1345 NA07345 0 0 2 0"); hapMapTranslate.put("NA10857", "1346 NA10857 NA12043 NA12044 1 0" ); hapMapTranslate.put("NA12043", "1346 NA12043 0 0 1 0"); hapMapTranslate.put("NA12044", "1346 NA12044 0 0 2 0"); hapMapTranslate.put("NA10859", "1347 NA10859 NA11881 NA11882 2 0" ); hapMapTranslate.put("NA11881", "1347 NA11881 0 0 1 0"); hapMapTranslate.put("NA11882", "1347 NA11882 0 0 2 0"); hapMapTranslate.put("NA10854", "1349 NA10854 NA11839 NA11840 2 0" ); hapMapTranslate.put("NA11839", "1349 NA11839 0 0 1 0"); hapMapTranslate.put("NA11840", "1349 NA11840 0 0 2 0"); hapMapTranslate.put("NA10856", "1350 NA10856 NA11829 NA11830 1 0" ); hapMapTranslate.put("NA11829", "1350 NA11829 0 0 1 0"); hapMapTranslate.put("NA11830", "1350 NA11830 0 0 2 0"); hapMapTranslate.put("NA10855", "1350 NA10855 NA11831 NA11832 2 0" ); hapMapTranslate.put("NA11831", "1350 NA11831 0 0 1 0"); hapMapTranslate.put("NA11832", "1350 NA11832 0 0 2 0"); hapMapTranslate.put("NA12707", "1358 NA12707 NA12716 NA12717 1 0" ); hapMapTranslate.put("NA12716", "1358 NA12716 0 0 1 0"); hapMapTranslate.put("NA12717", "1358 NA12717 0 0 2 0"); hapMapTranslate.put("NA10860", "1362 NA10860 NA11992 NA11993 1 0" ); hapMapTranslate.put("NA11992", "1362 NA11992 0 0 1 0"); hapMapTranslate.put("NA11993", "1362 NA11993 0 0 2 0"); hapMapTranslate.put("NA10861", "1362 NA10861 NA11994 NA11995 2 0" ); hapMapTranslate.put("NA11994", "1362 NA11994 0 0 1 0"); hapMapTranslate.put("NA11995", "1362 NA11995 0 0 2 0"); hapMapTranslate.put("NA10863", "1375 NA10863 NA12264 NA12234 2 0" ); hapMapTranslate.put("NA12264", "1375 NA12264 0 0 1 0"); hapMapTranslate.put("NA12234", "1375 NA12234 0 0 2 0"); hapMapTranslate.put("NA10830", "1408 NA10830 NA12154 NA12236 1 0" ); hapMapTranslate.put("NA12154", "1408 NA12154 0 0 1 0"); hapMapTranslate.put("NA12236", "1408 NA12236 0 0 2 0"); hapMapTranslate.put("NA10831", "1408 NA10831 NA12155 NA12156 2 0" ); hapMapTranslate.put("NA12155", "1408 NA12155 0 0 1 0"); hapMapTranslate.put("NA12156", "1408 NA12156 0 0 2 0"); hapMapTranslate.put("NA12156.dup", "dup NA12156.dup 0 0 2 0"); hapMapTranslate.put("NA10835", "1416 NA10835 NA12248 NA12249 1 0" ); hapMapTranslate.put("NA12248", "1416 NA12248 0 0 1 0"); hapMapTranslate.put("NA12248.dup", "dup NA1248.dup 0 0 1 0"); hapMapTranslate.put("NA12249", "1416 NA12249 0 0 2 0"); hapMapTranslate.put("NA10838", "1420 NA10838 NA12003 NA12004 1 0" ); hapMapTranslate.put("NA12003", "1420 NA12003 0 0 1 0"); hapMapTranslate.put("NA12003.dup", "dup NA12003.dup 0 0 1 0"); hapMapTranslate.put("NA12004", "1420 NA12004 0 0 2 0"); hapMapTranslate.put("NA10839", "1420 NA10839 NA12005 NA12006 2 0" ); hapMapTranslate.put("NA12005", "1420 NA12005 0 0 1 0"); hapMapTranslate.put("NA12006", "1420 NA12006 0 0 2 0"); hapMapTranslate.put("NA12740", "1444 NA12740 NA12750 NA12751 2 0" ); hapMapTranslate.put("NA12750", "1444 NA12750 0 0 1 0"); hapMapTranslate.put("NA12751", "1444 NA12751 0 0 2 0"); hapMapTranslate.put("NA12752", "1447 NA12752 NA12760 NA12761 1 0" ); hapMapTranslate.put("NA12760", "1447 NA12760 0 0 1 0"); hapMapTranslate.put("NA12761", "1447 NA12761 0 0 2 0"); hapMapTranslate.put("NA12753", "1447 NA12753 NA12762 NA12763 2 0" ); hapMapTranslate.put("NA12762", "1447 NA12762 0 0 1 0"); hapMapTranslate.put("NA12763", "1447 NA12763 0 0 2 0"); hapMapTranslate.put("NA12801", "1454 NA12801 NA12812 NA12813 1 0" ); hapMapTranslate.put("NA12812", "1454 NA12812 0 0 1 0"); hapMapTranslate.put("NA12813", "1454 NA12813 0 0 2 0"); hapMapTranslate.put("NA12802", "1454 NA12802 NA12814 NA12815 2 0" ); hapMapTranslate.put("NA12814", "1454 NA12814 0 0 1 0"); hapMapTranslate.put("NA12815", "1454 NA12815 0 0 2 0"); hapMapTranslate.put("NA12864", "1459 NA12864 NA12872 NA12873 1 0" ); hapMapTranslate.put("NA12872", "1459 NA12872 0 0 1 0"); hapMapTranslate.put("NA12873", "1459 NA12873 0 0 2 0"); hapMapTranslate.put("NA12865", "1459 NA12865 NA12874 NA12875 2 0" ); hapMapTranslate.put("NA12874", "1459 NA12874 0 0 1 0"); hapMapTranslate.put("NA12875", "1459 NA12875 0 0 2 0"); hapMapTranslate.put("NA12878", "1463 NA12878 NA12891 NA12892 2 0" ); hapMapTranslate.put("NA12891", "1463 NA12891 0 0 1 0"); hapMapTranslate.put("NA12892", "1463 NA12892 0 0 2 0"); hapMapTranslate.put("NA18526", "chi1 NA18526 0 0 2 0"); hapMapTranslate.put("NA18524", "chi2 NA18524 0 0 1 0"); hapMapTranslate.put("NA18529", "chi3 NA18529 0 0 2 0"); hapMapTranslate.put("NA18558", "chi4 NA18558 0 0 1 0"); hapMapTranslate.put("NA18532", "chi5 NA18532 0 0 2 0"); hapMapTranslate.put("NA18561", "chi6 NA18561 0 0 1 0"); hapMapTranslate.put("NA18942", "jap1 NA18942 0 0 2 0"); hapMapTranslate.put("NA18940", "jap2 NA18940 0 0 1 0"); hapMapTranslate.put("NA18951", "jap3 NA18951 0 0 2 0"); hapMapTranslate.put("NA18943", "jap4 NA18943 0 0 1 0"); hapMapTranslate.put("NA18947", "jap5 NA18947 0 0 2 0"); hapMapTranslate.put("NA18944", "jap6 NA18944 0 0 1 0"); hapMapTranslate.put("NA18562", "chi7 NA18562 0 0 1 0"); hapMapTranslate.put("NA18537", "chi8 NA18537 0 0 2 0"); hapMapTranslate.put("NA18603", "chi9 NA18603 0 0 1 0"); hapMapTranslate.put("NA18540", "chi10 NA18540 0 0 2 0"); hapMapTranslate.put("NA18605", "chi11 NA18605 0 0 1 0"); hapMapTranslate.put("NA18542", "chi12 NA18542 0 0 2 0"); hapMapTranslate.put("NA18945", "jap7 NA18945 0 0 1 0"); hapMapTranslate.put("NA18949", "jap8 NA18949 0 0 2 0"); hapMapTranslate.put("NA18948", "jap9 NA18948 0 0 1 0"); hapMapTranslate.put("NA18952", "jap10 NA18952 0 0 1 0"); hapMapTranslate.put("NA18956", "jap11 NA18956 0 0 2 0"); hapMapTranslate.put("NA18545", "chi13 NA18545 0 0 2 0"); hapMapTranslate.put("NA18572", "chi46 NA18572 0 0 1 0"); hapMapTranslate.put("NA18547", "chi15 NA18547 0 0 2 0"); hapMapTranslate.put("NA18609", "chi16 NA18609 0 0 1 0"); hapMapTranslate.put("NA18550", "chi17 NA18550 0 0 2 0"); hapMapTranslate.put("NA18608", "chi18 NA18608 0 0 1 0"); hapMapTranslate.put("NA18964", "jap12 NA18964 0 0 2 0"); hapMapTranslate.put("NA18953", "jap13 NA18953 0 0 1 0"); hapMapTranslate.put("NA18968", "jap14 NA18968 0 0 2 0"); hapMapTranslate.put("NA18959", "jap15 NA18959 0 0 1 0"); hapMapTranslate.put("NA18969", "jap16 NA18969 0 0 2 0"); hapMapTranslate.put("NA18960", "jap17 NA18960 0 0 1 0"); hapMapTranslate.put("NA18552", "chi19 NA18552 0 0 2 0"); hapMapTranslate.put("NA18611", "chi20 NA18611 0 0 1 0"); hapMapTranslate.put("NA18555", "chi21 NA18555 0 0 2 0"); hapMapTranslate.put("NA18564", "chi22 NA18564 0 0 2 0"); hapMapTranslate.put("NA18961", "jap18 NA18961 0 0 1 0"); hapMapTranslate.put("NA18972", "jap19 NA18972 0 0 2 0"); hapMapTranslate.put("NA18965", "jap20 NA18965 0 0 1 0"); hapMapTranslate.put("NA18973", "jap21 NA18973 0 0 2 0"); hapMapTranslate.put("NA18966", "jap22 NA18966 0 0 1 0"); hapMapTranslate.put("NA18975", "jap23 NA18975 0 0 2 0"); hapMapTranslate.put("NA18566", "chi23 NA18566 0 0 2 0"); hapMapTranslate.put("NA18563", "chi24 NA18563 0 0 1 0"); hapMapTranslate.put("NA18570", "chi25 NA18570 0 0 2 0"); hapMapTranslate.put("NA18612", "chi26 NA18612 0 0 1 0"); hapMapTranslate.put("NA18571", "chi27 NA18571 0 0 2 0"); hapMapTranslate.put("NA18620", "chi28 NA18620 0 0 1 0"); hapMapTranslate.put("NA18976", "jap24 NA18976 0 0 2 0"); hapMapTranslate.put("NA18967", "jap25 NA18967 0 0 1 0"); hapMapTranslate.put("NA18978", "jap26 NA18978 0 0 2 0"); hapMapTranslate.put("NA18970", "jap27 NA18970 0 0 1 0"); hapMapTranslate.put("NA18980", "jap28 NA18980 0 0 2 0"); hapMapTranslate.put("NA18995", "jap29 NA18995 0 0 1 0"); hapMapTranslate.put("NA18621", "chi29 NA18621 0 0 1 0"); hapMapTranslate.put("NA18594", "chi30 NA18594 0 0 2 0"); hapMapTranslate.put("NA18622", "chi31 NA18622 0 0 1 0"); hapMapTranslate.put("NA18573", "chi32 NA18573 0 0 2 0"); hapMapTranslate.put("NA18623", "chi33 NA18623 0 0 1 0"); hapMapTranslate.put("NA18576", "chi34 NA18576 0 0 2 0"); hapMapTranslate.put("NA18971", "jap30 NA18971 0 0 1 0"); hapMapTranslate.put("NA18981", "jap31 NA18981 0 0 2 0"); hapMapTranslate.put("NA18974", "jap32 NA18974 0 0 1 0"); hapMapTranslate.put("NA18987", "jap33 NA18987 0 0 2 0"); hapMapTranslate.put("NA18990", "jap34 NA18990 0 0 1 0"); hapMapTranslate.put("NA18991", "jap35 NA18991 0 0 2 0"); hapMapTranslate.put("NA18577", "chi35 NA18577 0 0 2 0"); hapMapTranslate.put("NA18624", "chi36 NA18624 0 0 1 0"); hapMapTranslate.put("NA18579", "chi37 NA18579 0 0 2 0"); hapMapTranslate.put("NA18632", "chi38 NA18632 0 0 1 0"); hapMapTranslate.put("NA18582", "chi39 NA18582 0 0 2 0"); hapMapTranslate.put("NA18633", "chi40 NA18633 0 0 1 0"); hapMapTranslate.put("NA18994", "jap36 NA18994 0 0 1 0"); hapMapTranslate.put("NA18992", "jap37 NA18992 0 0 2 0"); hapMapTranslate.put("NA18997", "jap38 NA18997 0 0 2 0"); hapMapTranslate.put("NA18996", "jap39 NA18996 0 0 1 0"); hapMapTranslate.put("NA18635", "chi41 NA18635 0 0 1 0"); hapMapTranslate.put("NA18592", "chi42 NA18592 0 0 2 0"); hapMapTranslate.put("NA18636", "chi43 NA18636 0 0 1 0"); hapMapTranslate.put("NA18593", "chi44 NA18593 0 0 2 0"); hapMapTranslate.put("NA18637", "chi45 NA18637 0 0 1 0"); hapMapTranslate.put("NA19000", "jap40 NA19000 0 0 1 0"); hapMapTranslate.put("NA18998", "jap41 NA18998 0 0 2 0"); hapMapTranslate.put("NA19005", "jap42 NA19005 0 0 1 0"); hapMapTranslate.put("NA18999", "jap43 NA18999 0 0 2 0"); hapMapTranslate.put("NA19007", "jap44 NA19007 0 0 1 0"); hapMapTranslate.put("NA19003", "jap45 NA19003 0 0 2 0"); hapMapTranslate.put("NA18500", "Yoruba004 NA18500 NA18501 NA18502 1 0"); hapMapTranslate.put("NA18501", "Yoruba004 NA18501 0 0 1 0"); hapMapTranslate.put("NA18502", "Yoruba004 NA18502 0 0 2 0"); hapMapTranslate.put("NA18503", "Yoruba005 NA18503 NA18504 NA18505 1 0"); hapMapTranslate.put("NA18504", "Yoruba005 NA18504 0 0 1 0"); hapMapTranslate.put("NA18505", "Yoruba005 NA18505 0 0 2 0"); hapMapTranslate.put("NA18506", "Yoruba009 NA18506 NA18507 NA18508 1 0"); hapMapTranslate.put("NA18507", "Yoruba009 NA18507 0 0 1 0"); hapMapTranslate.put("NA18508", "Yoruba009 NA18508 0 0 2 0"); hapMapTranslate.put("NA18860", "Yoruba012 NA18860 NA18859 NA18858 1 0"); hapMapTranslate.put("NA18859", "Yoruba012 NA18859 0 0 1 0"); hapMapTranslate.put("NA18858", "Yoruba012 NA18858 0 0 2 0"); hapMapTranslate.put("NA18515", "Yoruba013 NA18515 NA18516 NA18517 1 0"); hapMapTranslate.put("NA18516", "Yoruba013 NA18516 0 0 1 0"); hapMapTranslate.put("NA18517", "Yoruba013 NA18517 0 0 2 0"); hapMapTranslate.put("NA18521", "Yoruba016 NA18521 NA18522 NA18523 1 0"); hapMapTranslate.put("NA18522", "Yoruba016 NA18522 0 0 1 0"); hapMapTranslate.put("NA18523", "Yoruba016 NA18523 0 0 2 0"); hapMapTranslate.put("NA18872", "Yoruba017 NA18872 NA18871 NA18870 1 0"); hapMapTranslate.put("NA18871", "Yoruba017 NA18871 0 0 1 0"); hapMapTranslate.put("NA18870", "Yoruba017 NA18870 0 0 2 0"); hapMapTranslate.put("NA18854", "Yoruba018 NA18854 NA18853 NA18852 1 0"); hapMapTranslate.put("NA18853", "Yoruba018 NA18853 0 0 1 0"); hapMapTranslate.put("NA18852", "Yoruba018 NA18852 0 0 2 0"); hapMapTranslate.put("NA18857", "Yoruba023 NA18857 NA18856 NA18855 1 0"); hapMapTranslate.put("NA18856", "Yoruba023 NA18856 0 0 1 0"); hapMapTranslate.put("NA18855", "Yoruba023 NA18855 0 0 2 0"); hapMapTranslate.put("NA18863", "Yoruba024 NA18863 NA18862 NA18861 1 0"); hapMapTranslate.put("NA18862", "Yoruba024 NA18862 0 0 1 0"); hapMapTranslate.put("NA18861", "Yoruba024 NA18861 0 0 2 0"); hapMapTranslate.put("NA18914", "Yoruba028 NA18914 NA18913 NA18912 1 0"); hapMapTranslate.put("NA18913", "Yoruba028 NA18913 0 0 1 0"); hapMapTranslate.put("NA18912", "Yoruba028 NA18912 0 0 2 0"); hapMapTranslate.put("NA19094", "Yoruba040 NA19094 NA19092 NA19093 2 0"); hapMapTranslate.put("NA19092", "Yoruba040 NA19092 0 0 1 0"); hapMapTranslate.put("NA19093", "Yoruba040 NA19093 0 0 2 0"); hapMapTranslate.put("NA19103", "Yoruba042 NA19103 NA19101 NA19102 1 0"); hapMapTranslate.put("NA19101", "Yoruba042 NA19101 0 0 1 0"); hapMapTranslate.put("NA19102", "Yoruba042 NA19102 0 0 2 0"); hapMapTranslate.put("NA19139", "Yoruba043 NA19139 NA19138 NA19137 1 0"); hapMapTranslate.put("NA19138", "Yoruba043 NA19138 0 0 1 0"); hapMapTranslate.put("NA19137", "Yoruba043 NA19137 0 0 2 0"); hapMapTranslate.put("NA19202", "Yoruba045 NA19202 NA19200 NA19201 2 0"); hapMapTranslate.put("NA19200", "Yoruba045 NA19200 0 0 1 0"); hapMapTranslate.put("NA19201", "Yoruba045 NA19201 0 0 2 0"); hapMapTranslate.put("NA19173", "Yoruba047 NA19173 NA19171 NA19172 1 0"); hapMapTranslate.put("NA19171", "Yoruba047 NA19171 0 0 1 0"); hapMapTranslate.put("NA19172", "Yoruba047 NA19172 0 0 2 0"); hapMapTranslate.put("NA19205", "Yoruba048 NA19205 NA19203 NA19204 1 0"); hapMapTranslate.put("NA19203", "Yoruba048 NA19203 0 0 1 0"); hapMapTranslate.put("NA19204", "Yoruba048 NA19204 0 0 2 0"); hapMapTranslate.put("NA19211", "Yoruba050 NA19211 NA19210 NA19209 1 0"); hapMapTranslate.put("NA19210", "Yoruba050 NA19210 0 0 1 0"); hapMapTranslate.put("NA19209", "Yoruba050 NA19209 0 0 2 0"); hapMapTranslate.put("NA19208", "Yoruba051 NA19208 NA19207 NA19206 1 0"); hapMapTranslate.put("NA19207", "Yoruba051 NA19207 0 0 1 0"); hapMapTranslate.put("NA19206", "Yoruba051 NA19206 0 0 2 0"); hapMapTranslate.put("NA19161", "Yoruba056 NA19161 NA19160 NA19159 1 0"); hapMapTranslate.put("NA19160", "Yoruba056 NA19160 0 0 1 0"); hapMapTranslate.put("NA19159", "Yoruba056 NA19159 0 0 2 0"); hapMapTranslate.put("NA19221", "Yoruba058 NA19221 NA19223 NA19222 2 0"); hapMapTranslate.put("NA19223", "Yoruba058 NA19223 0 0 1 0"); hapMapTranslate.put("NA19222", "Yoruba058 NA19222 0 0 2 0"); hapMapTranslate.put("NA19120", "Yoruba060 NA19120 NA19119 NA19116 1 0"); hapMapTranslate.put("NA19119", "Yoruba060 NA19119 0 0 1 0"); hapMapTranslate.put("NA19116", "Yoruba060 NA19116 0 0 2 0"); hapMapTranslate.put("NA19142", "Yoruba071 NA19142 NA19141 NA19140 1 0"); hapMapTranslate.put("NA19141", "Yoruba071 NA19141 0 0 1 0"); hapMapTranslate.put("NA19140", "Yoruba071 NA19140 0 0 2 0"); hapMapTranslate.put("NA19154", "Yoruba072 NA19154 NA19153 NA19152 1 0"); hapMapTranslate.put("NA19153", "Yoruba072 NA19153 0 0 1 0"); hapMapTranslate.put("NA19152", "Yoruba072 NA19152 0 0 2 0"); hapMapTranslate.put("NA19145", "Yoruba074 NA19145 NA19144 NA19143 1 0"); hapMapTranslate.put("NA19144", "Yoruba074 NA19144 0 0 1 0"); hapMapTranslate.put("NA19143", "Yoruba074 NA19143 0 0 2 0"); hapMapTranslate.put("NA19129", "Yoruba077 NA19129 NA19128 NA19127 2 0"); hapMapTranslate.put("NA19128", "Yoruba077 NA19128 0 0 1 0"); hapMapTranslate.put("NA19127", "Yoruba077 NA19127 0 0 2 0"); hapMapTranslate.put("NA19132", "Yoruba101 NA19132 NA19130 NA19131 2 0"); hapMapTranslate.put("NA19130", "Yoruba101 NA19130 0 0 1 0"); hapMapTranslate.put("NA19131", "Yoruba101 NA19131 0 0 2 0"); hapMapTranslate.put("NA19100", "Yoruba105 NA19100 NA19098 NA19099 2 0"); hapMapTranslate.put("NA19098", "Yoruba105 NA19098 0 0 1 0"); hapMapTranslate.put("NA19099", "Yoruba105 NA19099 0 0 2 0"); hapMapTranslate.put("NA19194", "Yoruba112 NA19194 NA19192 NA19193 1 0"); hapMapTranslate.put("NA19192", "Yoruba112 NA19192 0 0 1 0"); hapMapTranslate.put("NA19193", "Yoruba112 NA19193 0 0 2 0"); hapMapTranslate.put("NA19240", "Yoruba117 NA19240 NA19239 NA19238 2 0"); hapMapTranslate.put("NA19239", "Yoruba117 NA19239 0 0 1 0"); hapMapTranslate.put("NA19238", "Yoruba117 NA19238 0 0 2 0"); }

1,110,233

public PedFile(){ //hardcoded hapmap info this.families = new Hashtable(); hapMapTranslate = new Hashtable(90,1); hapMapTranslate.put("NA10846", "1334 NA10846 NA12144 NA12145 1 0" ); hapMapTranslate.put("NA12144", "1334 NA12144 0 0 1 0"); hapMapTranslate.put("NA12145", "1334 NA12145 0 0 2 0"); hapMapTranslate.put("NA10847", "1334 NA10847 NA12146 NA12239 2 0" ); hapMapTranslate.put("NA12146", "1334 NA12146 0 0 1 0"); hapMapTranslate.put("NA12239", "1334 NA12239 0 0 2 0"); hapMapTranslate.put("NA07029", "1340 NA07029 NA06994 NA07000 1 0" ); hapMapTranslate.put("NA06994", "1340 NA06994 0 0 1 0"); hapMapTranslate.put("NA07000", "1340 NA07000 0 0 2 0"); hapMapTranslate.put("NA07019", "1340 NA07019 NA07022 NA07056 2 0" ); hapMapTranslate.put("NA07022", "1340 NA07022 0 0 1 0"); hapMapTranslate.put("NA07056", "1340 NA07056 0 0 2 0"); hapMapTranslate.put("NA07048", "1341 NA07048 NA07034 NA07055 1 0" ); hapMapTranslate.put("NA07034", "1341 NA07034 0 0 1 0"); hapMapTranslate.put("NA07055", "1341 NA07055 0 0 2 0"); hapMapTranslate.put("NA06991", "1341 NA06991 NA06993 NA06985 2 0" ); hapMapTranslate.put("NA06993", "1341 NA06993 0 0 1 0"); hapMapTranslate.put("NA06993.dup", "dup NA06993.dup 0 0 1 0"); hapMapTranslate.put("NA06985", "1341 NA06985 0 0 2 0"); hapMapTranslate.put("NA10851", "1344 NA10851 NA12056 NA12057 1 0" ); hapMapTranslate.put("NA12056", "1344 NA12056 0 0 1 0"); hapMapTranslate.put("NA12057", "1344 NA12057 0 0 2 0"); hapMapTranslate.put("NA07348", "1345 NA07348 NA07357 NA07345 2 0" ); hapMapTranslate.put("NA07357", "1345 NA07357 0 0 1 0"); hapMapTranslate.put("NA07345", "1345 NA07345 0 0 2 0"); hapMapTranslate.put("NA10857", "1346 NA10857 NA12043 NA12044 1 0" ); hapMapTranslate.put("NA12043", "1346 NA12043 0 0 1 0"); hapMapTranslate.put("NA12044", "1346 NA12044 0 0 2 0"); hapMapTranslate.put("NA10859", "1347 NA10859 NA11881 NA11882 2 0" ); hapMapTranslate.put("NA11881", "1347 NA11881 0 0 1 0"); hapMapTranslate.put("NA11882", "1347 NA11882 0 0 2 0"); hapMapTranslate.put("NA10854", "1349 NA10854 NA11839 NA11840 2 0" ); hapMapTranslate.put("NA11839", "1349 NA11839 0 0 1 0"); hapMapTranslate.put("NA11840", "1349 NA11840 0 0 2 0"); hapMapTranslate.put("NA10856", "1350 NA10856 NA11829 NA11830 1 0" ); hapMapTranslate.put("NA11829", "1350 NA11829 0 0 1 0"); hapMapTranslate.put("NA11830", "1350 NA11830 0 0 2 0"); hapMapTranslate.put("NA10855", "1350 NA10855 NA11831 NA11832 2 0" ); hapMapTranslate.put("NA11831", "1350 NA11831 0 0 1 0"); hapMapTranslate.put("NA11832", "1350 NA11832 0 0 2 0"); hapMapTranslate.put("NA12707", "1358 NA12707 NA12716 NA12717 1 0" ); hapMapTranslate.put("NA12716", "1358 NA12716 0 0 1 0"); hapMapTranslate.put("NA12717", "1358 NA12717 0 0 2 0"); hapMapTranslate.put("NA10860", "1362 NA10860 NA11992 NA11993 1 0" ); hapMapTranslate.put("NA11992", "1362 NA11992 0 0 1 0"); hapMapTranslate.put("NA11993", "1362 NA11993 0 0 2 0"); hapMapTranslate.put("NA11993.dup", "dup NA11993.dup 0 0 2 0"); hapMapTranslate.put("NA10861", "1362 NA10861 NA11994 NA11995 2 0" ); hapMapTranslate.put("NA11994", "1362 NA11994 0 0 1 0"); hapMapTranslate.put("NA11995", "1362 NA11995 0 0 2 0"); hapMapTranslate.put("NA10863", "1375 NA10863 NA12264 NA12234 2 0" ); hapMapTranslate.put("NA12264", "1375 NA12264 0 0 1 0"); hapMapTranslate.put("NA12234", "1375 NA12234 0 0 2 0"); hapMapTranslate.put("NA10830", "1408 NA10830 NA12154 NA12236 1 0" ); hapMapTranslate.put("NA12154", "1408 NA12154 0 0 1 0"); hapMapTranslate.put("NA12236", "1408 NA12236 0 0 2 0"); hapMapTranslate.put("NA10831", "1408 NA10831 NA12155 NA12156 2 0" ); hapMapTranslate.put("NA12155", "1408 NA12155 0 0 1 0"); hapMapTranslate.put("NA12156", "1408 NA12156 0 0 2 0"); hapMapTranslate.put("NA12156.dup", "dup NA12156.dup 0 0 2 0"); hapMapTranslate.put("NA10835", "1416 NA10835 NA12248 NA12249 1 0" ); hapMapTranslate.put("NA12248", "1416 NA12248 0 0 1 0"); hapMapTranslate.put("NA12248.dup", "dup NA1248.dup 0 0 1 0"); hapMapTranslate.put("NA12249", "1416 NA12249 0 0 2 0"); hapMapTranslate.put("NA10838", "1420 NA10838 NA12003 NA12004 1 0" ); hapMapTranslate.put("NA12003", "1420 NA12003 0 0 1 0"); hapMapTranslate.put("NA12003.dup", "dup NA12003.dup 0 0 1 0"); hapMapTranslate.put("NA12004", "1420 NA12004 0 0 2 0"); hapMapTranslate.put("NA10839", "1420 NA10839 NA12005 NA12006 2 0" ); hapMapTranslate.put("NA12005", "1420 NA12005 0 0 1 0"); hapMapTranslate.put("NA12006", "1420 NA12006 0 0 2 0"); hapMapTranslate.put("NA12740", "1444 NA12740 NA12750 NA12751 2 0" ); hapMapTranslate.put("NA12750", "1444 NA12750 0 0 1 0"); hapMapTranslate.put("NA12751", "1444 NA12751 0 0 2 0"); hapMapTranslate.put("NA12752", "1447 NA12752 NA12760 NA12761 1 0" ); hapMapTranslate.put("NA12760", "1447 NA12760 0 0 1 0"); hapMapTranslate.put("NA12761", "1447 NA12761 0 0 2 0"); hapMapTranslate.put("NA12753", "1447 NA12753 NA12762 NA12763 2 0" ); hapMapTranslate.put("NA12762", "1447 NA12762 0 0 1 0"); hapMapTranslate.put("NA12763", "1447 NA12763 0 0 2 0"); hapMapTranslate.put("NA12801", "1454 NA12801 NA12812 NA12813 1 0" ); hapMapTranslate.put("NA12812", "1454 NA12812 0 0 1 0"); hapMapTranslate.put("NA12813", "1454 NA12813 0 0 2 0"); hapMapTranslate.put("NA12802", "1454 NA12802 NA12814 NA12815 2 0" ); hapMapTranslate.put("NA12814", "1454 NA12814 0 0 1 0"); hapMapTranslate.put("NA12815", "1454 NA12815 0 0 2 0"); hapMapTranslate.put("NA12864", "1459 NA12864 NA12872 NA12873 1 0" ); hapMapTranslate.put("NA12872", "1459 NA12872 0 0 1 0"); hapMapTranslate.put("NA12873", "1459 NA12873 0 0 2 0"); hapMapTranslate.put("NA12865", "1459 NA12865 NA12874 NA12875 2 0" ); hapMapTranslate.put("NA12874", "1459 NA12874 0 0 1 0"); hapMapTranslate.put("NA12875", "1459 NA12875 0 0 2 0"); hapMapTranslate.put("NA12878", "1463 NA12878 NA12891 NA12892 2 0" ); hapMapTranslate.put("NA12891", "1463 NA12891 0 0 1 0"); hapMapTranslate.put("NA12892", "1463 NA12892 0 0 2 0"); hapMapTranslate.put("NA18526", "chi1 NA18526 0 0 2 0"); hapMapTranslate.put("NA18524", "chi2 NA18524 0 0 1 0"); hapMapTranslate.put("NA18529", "chi3 NA18529 0 0 2 0"); hapMapTranslate.put("NA18558", "chi4 NA18558 0 0 1 0"); hapMapTranslate.put("NA18532", "chi5 NA18532 0 0 2 0"); hapMapTranslate.put("NA18561", "chi6 NA18561 0 0 1 0"); hapMapTranslate.put("NA18942", "jap1 NA18942 0 0 2 0"); hapMapTranslate.put("NA18940", "jap2 NA18940 0 0 1 0"); hapMapTranslate.put("NA18951", "jap3 NA18951 0 0 2 0"); hapMapTranslate.put("NA18943", "jap4 NA18943 0 0 1 0"); hapMapTranslate.put("NA18947", "jap5 NA18947 0 0 2 0"); hapMapTranslate.put("NA18944", "jap6 NA18944 0 0 1 0"); hapMapTranslate.put("NA18562", "chi7 NA18562 0 0 1 0"); hapMapTranslate.put("NA18537", "chi8 NA18537 0 0 2 0"); hapMapTranslate.put("NA18603", "chi9 NA18603 0 0 1 0"); hapMapTranslate.put("NA18540", "chi10 NA18540 0 0 2 0"); hapMapTranslate.put("NA18605", "chi11 NA18605 0 0 1 0"); hapMapTranslate.put("NA18542", "chi12 NA18542 0 0 2 0"); hapMapTranslate.put("NA18945", "jap7 NA18945 0 0 1 0"); hapMapTranslate.put("NA18949", "jap8 NA18949 0 0 2 0"); hapMapTranslate.put("NA18948", "jap9 NA18948 0 0 1 0"); hapMapTranslate.put("NA18952", "jap10 NA18952 0 0 1 0"); hapMapTranslate.put("NA18956", "jap11 NA18956 0 0 2 0"); hapMapTranslate.put("NA18545", "chi13 NA18545 0 0 2 0"); hapMapTranslate.put("NA18572", "chi46 NA18572 0 0 1 0"); hapMapTranslate.put("NA18547", "chi15 NA18547 0 0 2 0"); hapMapTranslate.put("NA18609", "chi16 NA18609 0 0 1 0"); hapMapTranslate.put("NA18550", "chi17 NA18550 0 0 2 0"); hapMapTranslate.put("NA18608", "chi18 NA18608 0 0 1 0"); hapMapTranslate.put("NA18964", "jap12 NA18964 0 0 2 0"); hapMapTranslate.put("NA18953", "jap13 NA18953 0 0 1 0"); hapMapTranslate.put("NA18968", "jap14 NA18968 0 0 2 0"); hapMapTranslate.put("NA18959", "jap15 NA18959 0 0 1 0"); hapMapTranslate.put("NA18969", "jap16 NA18969 0 0 2 0"); hapMapTranslate.put("NA18960", "jap17 NA18960 0 0 1 0"); hapMapTranslate.put("NA18552", "chi19 NA18552 0 0 2 0"); hapMapTranslate.put("NA18611", "chi20 NA18611 0 0 1 0"); hapMapTranslate.put("NA18555", "chi21 NA18555 0 0 2 0"); hapMapTranslate.put("NA18564", "chi22 NA18564 0 0 2 0"); hapMapTranslate.put("NA18961", "jap18 NA18961 0 0 1 0"); hapMapTranslate.put("NA18972", "jap19 NA18972 0 0 2 0"); hapMapTranslate.put("NA18965", "jap20 NA18965 0 0 1 0"); hapMapTranslate.put("NA18973", "jap21 NA18973 0 0 2 0"); hapMapTranslate.put("NA18966", "jap22 NA18966 0 0 1 0"); hapMapTranslate.put("NA18975", "jap23 NA18975 0 0 2 0"); hapMapTranslate.put("NA18566", "chi23 NA18566 0 0 2 0"); hapMapTranslate.put("NA18563", "chi24 NA18563 0 0 1 0"); hapMapTranslate.put("NA18570", "chi25 NA18570 0 0 2 0"); hapMapTranslate.put("NA18612", "chi26 NA18612 0 0 1 0"); hapMapTranslate.put("NA18571", "chi27 NA18571 0 0 2 0"); hapMapTranslate.put("NA18620", "chi28 NA18620 0 0 1 0"); hapMapTranslate.put("NA18976", "jap24 NA18976 0 0 2 0"); hapMapTranslate.put("NA18967", "jap25 NA18967 0 0 1 0"); hapMapTranslate.put("NA18978", "jap26 NA18978 0 0 2 0"); hapMapTranslate.put("NA18970", "jap27 NA18970 0 0 1 0"); hapMapTranslate.put("NA18980", "jap28 NA18980 0 0 2 0"); hapMapTranslate.put("NA18995", "jap29 NA18995 0 0 1 0"); hapMapTranslate.put("NA18621", "chi29 NA18621 0 0 1 0"); hapMapTranslate.put("NA18594", "chi30 NA18594 0 0 2 0"); hapMapTranslate.put("NA18622", "chi31 NA18622 0 0 1 0"); hapMapTranslate.put("NA18573", "chi32 NA18573 0 0 2 0"); hapMapTranslate.put("NA18623", "chi33 NA18623 0 0 1 0"); hapMapTranslate.put("NA18576", "chi34 NA18576 0 0 2 0"); hapMapTranslate.put("NA18971", "jap30 NA18971 0 0 1 0"); hapMapTranslate.put("NA18981", "jap31 NA18981 0 0 2 0"); hapMapTranslate.put("NA18974", "jap32 NA18974 0 0 1 0"); hapMapTranslate.put("NA18987", "jap33 NA18987 0 0 2 0"); hapMapTranslate.put("NA18990", "jap34 NA18990 0 0 1 0"); hapMapTranslate.put("NA18991", "jap35 NA18991 0 0 2 0"); hapMapTranslate.put("NA18577", "chi35 NA18577 0 0 2 0"); hapMapTranslate.put("NA18624", "chi36 NA18624 0 0 1 0"); hapMapTranslate.put("NA18579", "chi37 NA18579 0 0 2 0"); hapMapTranslate.put("NA18632", "chi38 NA18632 0 0 1 0"); hapMapTranslate.put("NA18582", "chi39 NA18582 0 0 2 0"); hapMapTranslate.put("NA18633", "chi40 NA18633 0 0 1 0"); hapMapTranslate.put("NA18994", "jap36 NA18994 0 0 1 0"); hapMapTranslate.put("NA18992", "jap37 NA18992 0 0 2 0"); hapMapTranslate.put("NA18997", "jap38 NA18997 0 0 2 0"); hapMapTranslate.put("NA18996", "jap39 NA18996 0 0 1 0"); hapMapTranslate.put("NA18635", "chi41 NA18635 0 0 1 0"); hapMapTranslate.put("NA18592", "chi42 NA18592 0 0 2 0"); hapMapTranslate.put("NA18636", "chi43 NA18636 0 0 1 0"); hapMapTranslate.put("NA18593", "chi44 NA18593 0 0 2 0"); hapMapTranslate.put("NA18637", "chi45 NA18637 0 0 1 0"); hapMapTranslate.put("NA19000", "jap40 NA19000 0 0 1 0"); hapMapTranslate.put("NA18998", "jap41 NA18998 0 0 2 0"); hapMapTranslate.put("NA19005", "jap42 NA19005 0 0 1 0"); hapMapTranslate.put("NA18999", "jap43 NA18999 0 0 2 0"); hapMapTranslate.put("NA19007", "jap44 NA19007 0 0 1 0"); hapMapTranslate.put("NA19003", "jap45 NA19003 0 0 2 0"); hapMapTranslate.put("NA18500", "Yoruba004 NA18500 NA18501 NA18502 1 0"); hapMapTranslate.put("NA18501", "Yoruba004 NA18501 0 0 1 0"); hapMapTranslate.put("NA18502", "Yoruba004 NA18502 0 0 2 0"); hapMapTranslate.put("NA18503", "Yoruba005 NA18503 NA18504 NA18505 1 0"); hapMapTranslate.put("NA18504", "Yoruba005 NA18504 0 0 1 0"); hapMapTranslate.put("NA18505", "Yoruba005 NA18505 0 0 2 0"); hapMapTranslate.put("NA18506", "Yoruba009 NA18506 NA18507 NA18508 1 0"); hapMapTranslate.put("NA18507", "Yoruba009 NA18507 0 0 1 0"); hapMapTranslate.put("NA18508", "Yoruba009 NA18508 0 0 2 0"); hapMapTranslate.put("NA18860", "Yoruba012 NA18860 NA18859 NA18858 1 0"); hapMapTranslate.put("NA18859", "Yoruba012 NA18859 0 0 1 0"); hapMapTranslate.put("NA18858", "Yoruba012 NA18858 0 0 2 0"); hapMapTranslate.put("NA18515", "Yoruba013 NA18515 NA18516 NA18517 1 0"); hapMapTranslate.put("NA18516", "Yoruba013 NA18516 0 0 1 0"); hapMapTranslate.put("NA18517", "Yoruba013 NA18517 0 0 2 0"); hapMapTranslate.put("NA18521", "Yoruba016 NA18521 NA18522 NA18523 1 0"); hapMapTranslate.put("NA18522", "Yoruba016 NA18522 0 0 1 0"); hapMapTranslate.put("NA18523", "Yoruba016 NA18523 0 0 2 0"); hapMapTranslate.put("NA18872", "Yoruba017 NA18872 NA18871 NA18870 1 0"); hapMapTranslate.put("NA18871", "Yoruba017 NA18871 0 0 1 0"); hapMapTranslate.put("NA18870", "Yoruba017 NA18870 0 0 2 0"); hapMapTranslate.put("NA18854", "Yoruba018 NA18854 NA18853 NA18852 1 0"); hapMapTranslate.put("NA18853", "Yoruba018 NA18853 0 0 1 0"); hapMapTranslate.put("NA18852", "Yoruba018 NA18852 0 0 2 0"); hapMapTranslate.put("NA18857", "Yoruba023 NA18857 NA18856 NA18855 1 0"); hapMapTranslate.put("NA18856", "Yoruba023 NA18856 0 0 1 0"); hapMapTranslate.put("NA18855", "Yoruba023 NA18855 0 0 2 0"); hapMapTranslate.put("NA18863", "Yoruba024 NA18863 NA18862 NA18861 1 0"); hapMapTranslate.put("NA18862", "Yoruba024 NA18862 0 0 1 0"); hapMapTranslate.put("NA18861", "Yoruba024 NA18861 0 0 2 0"); hapMapTranslate.put("NA18914", "Yoruba028 NA18914 NA18913 NA18912 1 0"); hapMapTranslate.put("NA18913", "Yoruba028 NA18913 0 0 1 0"); hapMapTranslate.put("NA18912", "Yoruba028 NA18912 0 0 2 0"); hapMapTranslate.put("NA19094", "Yoruba040 NA19094 NA19092 NA19093 2 0"); hapMapTranslate.put("NA19092", "Yoruba040 NA19092 0 0 1 0"); hapMapTranslate.put("NA19093", "Yoruba040 NA19093 0 0 2 0"); hapMapTranslate.put("NA19103", "Yoruba042 NA19103 NA19101 NA19102 1 0"); hapMapTranslate.put("NA19101", "Yoruba042 NA19101 0 0 1 0"); hapMapTranslate.put("NA19102", "Yoruba042 NA19102 0 0 2 0"); hapMapTranslate.put("NA19139", "Yoruba043 NA19139 NA19138 NA19137 1 0"); hapMapTranslate.put("NA19138", "Yoruba043 NA19138 0 0 1 0"); hapMapTranslate.put("NA19137", "Yoruba043 NA19137 0 0 2 0"); hapMapTranslate.put("NA19202", "Yoruba045 NA19202 NA19200 NA19201 2 0"); hapMapTranslate.put("NA19200", "Yoruba045 NA19200 0 0 1 0"); hapMapTranslate.put("NA19201", "Yoruba045 NA19201 0 0 2 0"); hapMapTranslate.put("NA19173", "Yoruba047 NA19173 NA19171 NA19172 1 0"); hapMapTranslate.put("NA19171", "Yoruba047 NA19171 0 0 1 0"); hapMapTranslate.put("NA19172", "Yoruba047 NA19172 0 0 2 0"); hapMapTranslate.put("NA19205", "Yoruba048 NA19205 NA19203 NA19204 1 0"); hapMapTranslate.put("NA19203", "Yoruba048 NA19203 0 0 1 0"); hapMapTranslate.put("NA19204", "Yoruba048 NA19204 0 0 2 0"); hapMapTranslate.put("NA19211", "Yoruba050 NA19211 NA19210 NA19209 1 0"); hapMapTranslate.put("NA19210", "Yoruba050 NA19210 0 0 1 0"); hapMapTranslate.put("NA19209", "Yoruba050 NA19209 0 0 2 0"); hapMapTranslate.put("NA19208", "Yoruba051 NA19208 NA19207 NA19206 1 0"); hapMapTranslate.put("NA19207", "Yoruba051 NA19207 0 0 1 0"); hapMapTranslate.put("NA19206", "Yoruba051 NA19206 0 0 2 0"); hapMapTranslate.put("NA19161", "Yoruba056 NA19161 NA19160 NA19159 1 0"); hapMapTranslate.put("NA19160", "Yoruba056 NA19160 0 0 1 0"); hapMapTranslate.put("NA19159", "Yoruba056 NA19159 0 0 2 0"); hapMapTranslate.put("NA19221", "Yoruba058 NA19221 NA19223 NA19222 2 0"); hapMapTranslate.put("NA19223", "Yoruba058 NA19223 0 0 1 0"); hapMapTranslate.put("NA19222", "Yoruba058 NA19222 0 0 2 0"); hapMapTranslate.put("NA19120", "Yoruba060 NA19120 NA19119 NA19116 1 0"); hapMapTranslate.put("NA19119", "Yoruba060 NA19119 0 0 1 0"); hapMapTranslate.put("NA19116", "Yoruba060 NA19116 0 0 2 0"); hapMapTranslate.put("NA19142", "Yoruba071 NA19142 NA19141 NA19140 1 0"); hapMapTranslate.put("NA19141", "Yoruba071 NA19141 0 0 1 0"); hapMapTranslate.put("NA19140", "Yoruba071 NA19140 0 0 2 0"); hapMapTranslate.put("NA19154", "Yoruba072 NA19154 NA19153 NA19152 1 0"); hapMapTranslate.put("NA19153", "Yoruba072 NA19153 0 0 1 0"); hapMapTranslate.put("NA19152", "Yoruba072 NA19152 0 0 2 0"); hapMapTranslate.put("NA19145", "Yoruba074 NA19145 NA19144 NA19143 1 0"); hapMapTranslate.put("NA19144", "Yoruba074 NA19144 0 0 1 0"); hapMapTranslate.put("NA19143", "Yoruba074 NA19143 0 0 2 0"); hapMapTranslate.put("NA19129", "Yoruba077 NA19129 NA19128 NA19127 2 0"); hapMapTranslate.put("NA19128", "Yoruba077 NA19128 0 0 1 0"); hapMapTranslate.put("NA19127", "Yoruba077 NA19127 0 0 2 0"); hapMapTranslate.put("NA19132", "Yoruba101 NA19132 NA19130 NA19131 2 0"); hapMapTranslate.put("NA19130", "Yoruba101 NA19130 0 0 1 0"); hapMapTranslate.put("NA19131", "Yoruba101 NA19131 0 0 2 0"); hapMapTranslate.put("NA19100", "Yoruba105 NA19100 NA19098 NA19099 2 0"); hapMapTranslate.put("NA19098", "Yoruba105 NA19098 0 0 1 0"); hapMapTranslate.put("NA19099", "Yoruba105 NA19099 0 0 2 0"); hapMapTranslate.put("NA19194", "Yoruba112 NA19194 NA19192 NA19193 1 0"); hapMapTranslate.put("NA19192", "Yoruba112 NA19192 0 0 1 0"); hapMapTranslate.put("NA19193", "Yoruba112 NA19193 0 0 2 0"); hapMapTranslate.put("NA19240", "Yoruba117 NA19240 NA19239 NA19238 2 0"); hapMapTranslate.put("NA19239", "Yoruba117 NA19239 0 0 1 0"); hapMapTranslate.put("NA19238", "Yoruba117 NA19238 0 0 2 0"); }

public PedFile(){ //hardcoded hapmap info this.families = new Hashtable(); hapMapTranslate = new Hashtable(90,1); hapMapTranslate.put("NA10846", "1334 NA10846 NA12144 NA12145 1 0" ); hapMapTranslate.put("NA12144", "1334 NA12144 0 0 1 0"); hapMapTranslate.put("NA12145", "1334 NA12145 0 0 2 0"); hapMapTranslate.put("NA10847", "1334 NA10847 NA12146 NA12239 2 0" ); hapMapTranslate.put("NA12146", "1334 NA12146 0 0 1 0"); hapMapTranslate.put("NA12239", "1334 NA12239 0 0 2 0"); hapMapTranslate.put("NA07029", "1340 NA07029 NA06994 NA07000 1 0" ); hapMapTranslate.put("NA06994", "1340 NA06994 0 0 1 0"); hapMapTranslate.put("NA07000", "1340 NA07000 0 0 2 0"); hapMapTranslate.put("NA07019", "1340 NA07019 NA07022 NA07056 2 0" ); hapMapTranslate.put("NA07022", "1340 NA07022 0 0 1 0"); hapMapTranslate.put("NA07056", "1340 NA07056 0 0 2 0"); hapMapTranslate.put("NA07048", "1341 NA07048 NA07034 NA07055 1 0" ); hapMapTranslate.put("NA07034", "1341 NA07034 0 0 1 0"); hapMapTranslate.put("NA07055", "1341 NA07055 0 0 2 0"); hapMapTranslate.put("NA06991", "1341 NA06991 NA06993 NA06985 2 0" ); hapMapTranslate.put("NA06993", "1341 NA06993 0 0 1 0"); hapMapTranslate.put("NA06993.dup", "dup NA06993.dup 0 0 1 0"); hapMapTranslate.put("NA06985", "1341 NA06985 0 0 2 0"); hapMapTranslate.put("NA10851", "1344 NA10851 NA12056 NA12057 1 0" ); hapMapTranslate.put("NA12056", "1344 NA12056 0 0 1 0"); hapMapTranslate.put("NA12057", "1344 NA12057 0 0 2 0"); hapMapTranslate.put("NA07348", "1345 NA07348 NA07357 NA07345 2 0" ); hapMapTranslate.put("NA07357", "1345 NA07357 0 0 1 0"); hapMapTranslate.put("NA07345", "1345 NA07345 0 0 2 0"); hapMapTranslate.put("NA10857", "1346 NA10857 NA12043 NA12044 1 0" ); hapMapTranslate.put("NA12043", "1346 NA12043 0 0 1 0"); hapMapTranslate.put("NA12044", "1346 NA12044 0 0 2 0"); hapMapTranslate.put("NA10859", "1347 NA10859 NA11881 NA11882 2 0" ); hapMapTranslate.put("NA11881", "1347 NA11881 0 0 1 0"); hapMapTranslate.put("NA11882", "1347 NA11882 0 0 2 0"); hapMapTranslate.put("NA10854", "1349 NA10854 NA11839 NA11840 2 0" ); hapMapTranslate.put("NA11839", "1349 NA11839 0 0 1 0"); hapMapTranslate.put("NA11840", "1349 NA11840 0 0 2 0"); hapMapTranslate.put("NA10856", "1350 NA10856 NA11829 NA11830 1 0" ); hapMapTranslate.put("NA11829", "1350 NA11829 0 0 1 0"); hapMapTranslate.put("NA11830", "1350 NA11830 0 0 2 0"); hapMapTranslate.put("NA10855", "1350 NA10855 NA11831 NA11832 2 0" ); hapMapTranslate.put("NA11831", "1350 NA11831 0 0 1 0"); hapMapTranslate.put("NA11832", "1350 NA11832 0 0 2 0"); hapMapTranslate.put("NA12707", "1358 NA12707 NA12716 NA12717 1 0" ); hapMapTranslate.put("NA12716", "1358 NA12716 0 0 1 0"); hapMapTranslate.put("NA12717", "1358 NA12717 0 0 2 0"); hapMapTranslate.put("NA10860", "1362 NA10860 NA11992 NA11993 1 0" ); hapMapTranslate.put("NA11992", "1362 NA11992 0 0 1 0"); hapMapTranslate.put("NA11993", "1362 NA11993 0 0 2 0"); hapMapTranslate.put("NA11993.dup", "dup NA11993.dup 0 0 2 0"); hapMapTranslate.put("NA10861", "1362 NA10861 NA11994 NA11995 2 0" ); hapMapTranslate.put("NA11994", "1362 NA11994 0 0 1 0"); hapMapTranslate.put("NA11995", "1362 NA11995 0 0 2 0"); hapMapTranslate.put("NA10863", "1375 NA10863 NA12264 NA12234 2 0" ); hapMapTranslate.put("NA12264", "1375 NA12264 0 0 1 0"); hapMapTranslate.put("NA12234", "1375 NA12234 0 0 2 0"); hapMapTranslate.put("NA10830", "1408 NA10830 NA12154 NA12236 1 0" ); hapMapTranslate.put("NA12154", "1408 NA12154 0 0 1 0"); hapMapTranslate.put("NA12236", "1408 NA12236 0 0 2 0"); hapMapTranslate.put("NA10831", "1408 NA10831 NA12155 NA12156 2 0" ); hapMapTranslate.put("NA12155", "1408 NA12155 0 0 1 0"); hapMapTranslate.put("NA12156", "1408 NA12156 0 0 2 0"); hapMapTranslate.put("NA10835", "1416 NA10835 NA12248 NA12249 1 0" ); hapMapTranslate.put("NA12248", "1416 NA12248 0 0 1 0"); hapMapTranslate.put("NA12248.dup", "dup NA1248.dup 0 0 1 0"); hapMapTranslate.put("NA12249", "1416 NA12249 0 0 2 0"); hapMapTranslate.put("NA10838", "1420 NA10838 NA12003 NA12004 1 0" ); hapMapTranslate.put("NA12003", "1420 NA12003 0 0 1 0"); hapMapTranslate.put("NA12003.dup", "dup NA12003.dup 0 0 1 0"); hapMapTranslate.put("NA12004", "1420 NA12004 0 0 2 0"); hapMapTranslate.put("NA10839", "1420 NA10839 NA12005 NA12006 2 0" ); hapMapTranslate.put("NA12005", "1420 NA12005 0 0 1 0"); hapMapTranslate.put("NA12006", "1420 NA12006 0 0 2 0"); hapMapTranslate.put("NA12740", "1444 NA12740 NA12750 NA12751 2 0" ); hapMapTranslate.put("NA12750", "1444 NA12750 0 0 1 0"); hapMapTranslate.put("NA12751", "1444 NA12751 0 0 2 0"); hapMapTranslate.put("NA12752", "1447 NA12752 NA12760 NA12761 1 0" ); hapMapTranslate.put("NA12760", "1447 NA12760 0 0 1 0"); hapMapTranslate.put("NA12761", "1447 NA12761 0 0 2 0"); hapMapTranslate.put("NA12753", "1447 NA12753 NA12762 NA12763 2 0" ); hapMapTranslate.put("NA12762", "1447 NA12762 0 0 1 0"); hapMapTranslate.put("NA12763", "1447 NA12763 0 0 2 0"); hapMapTranslate.put("NA12801", "1454 NA12801 NA12812 NA12813 1 0" ); hapMapTranslate.put("NA12812", "1454 NA12812 0 0 1 0"); hapMapTranslate.put("NA12813", "1454 NA12813 0 0 2 0"); hapMapTranslate.put("NA12802", "1454 NA12802 NA12814 NA12815 2 0" ); hapMapTranslate.put("NA12814", "1454 NA12814 0 0 1 0"); hapMapTranslate.put("NA12815", "1454 NA12815 0 0 2 0"); hapMapTranslate.put("NA12864", "1459 NA12864 NA12872 NA12873 1 0" ); hapMapTranslate.put("NA12872", "1459 NA12872 0 0 1 0"); hapMapTranslate.put("NA12873", "1459 NA12873 0 0 2 0"); hapMapTranslate.put("NA12865", "1459 NA12865 NA12874 NA12875 2 0" ); hapMapTranslate.put("NA12874", "1459 NA12874 0 0 1 0"); hapMapTranslate.put("NA12875", "1459 NA12875 0 0 2 0"); hapMapTranslate.put("NA12878", "1463 NA12878 NA12891 NA12892 2 0" ); hapMapTranslate.put("NA12891", "1463 NA12891 0 0 1 0"); hapMapTranslate.put("NA12892", "1463 NA12892 0 0 2 0"); hapMapTranslate.put("NA18526", "chi1 NA18526 0 0 2 0"); hapMapTranslate.put("NA18524", "chi2 NA18524 0 0 1 0"); hapMapTranslate.put("NA18529", "chi3 NA18529 0 0 2 0"); hapMapTranslate.put("NA18558", "chi4 NA18558 0 0 1 0"); hapMapTranslate.put("NA18532", "chi5 NA18532 0 0 2 0"); hapMapTranslate.put("NA18561", "chi6 NA18561 0 0 1 0"); hapMapTranslate.put("NA18942", "jap1 NA18942 0 0 2 0"); hapMapTranslate.put("NA18940", "jap2 NA18940 0 0 1 0"); hapMapTranslate.put("NA18951", "jap3 NA18951 0 0 2 0"); hapMapTranslate.put("NA18943", "jap4 NA18943 0 0 1 0"); hapMapTranslate.put("NA18947", "jap5 NA18947 0 0 2 0"); hapMapTranslate.put("NA18944", "jap6 NA18944 0 0 1 0"); hapMapTranslate.put("NA18562", "chi7 NA18562 0 0 1 0"); hapMapTranslate.put("NA18537", "chi8 NA18537 0 0 2 0"); hapMapTranslate.put("NA18603", "chi9 NA18603 0 0 1 0"); hapMapTranslate.put("NA18540", "chi10 NA18540 0 0 2 0"); hapMapTranslate.put("NA18605", "chi11 NA18605 0 0 1 0"); hapMapTranslate.put("NA18542", "chi12 NA18542 0 0 2 0"); hapMapTranslate.put("NA18945", "jap7 NA18945 0 0 1 0"); hapMapTranslate.put("NA18949", "jap8 NA18949 0 0 2 0"); hapMapTranslate.put("NA18948", "jap9 NA18948 0 0 1 0"); hapMapTranslate.put("NA18952", "jap10 NA18952 0 0 1 0"); hapMapTranslate.put("NA18956", "jap11 NA18956 0 0 2 0"); hapMapTranslate.put("NA18545", "chi13 NA18545 0 0 2 0"); hapMapTranslate.put("NA18572", "chi46 NA18572 0 0 1 0"); hapMapTranslate.put("NA18547", "chi15 NA18547 0 0 2 0"); hapMapTranslate.put("NA18609", "chi16 NA18609 0 0 1 0"); hapMapTranslate.put("NA18550", "chi17 NA18550 0 0 2 0"); hapMapTranslate.put("NA18608", "chi18 NA18608 0 0 1 0"); hapMapTranslate.put("NA18964", "jap12 NA18964 0 0 2 0"); hapMapTranslate.put("NA18953", "jap13 NA18953 0 0 1 0"); hapMapTranslate.put("NA18968", "jap14 NA18968 0 0 2 0"); hapMapTranslate.put("NA18959", "jap15 NA18959 0 0 1 0"); hapMapTranslate.put("NA18969", "jap16 NA18969 0 0 2 0"); hapMapTranslate.put("NA18960", "jap17 NA18960 0 0 1 0"); hapMapTranslate.put("NA18552", "chi19 NA18552 0 0 2 0"); hapMapTranslate.put("NA18611", "chi20 NA18611 0 0 1 0"); hapMapTranslate.put("NA18555", "chi21 NA18555 0 0 2 0"); hapMapTranslate.put("NA18564", "chi22 NA18564 0 0 2 0"); hapMapTranslate.put("NA18961", "jap18 NA18961 0 0 1 0"); hapMapTranslate.put("NA18972", "jap19 NA18972 0 0 2 0"); hapMapTranslate.put("NA18965", "jap20 NA18965 0 0 1 0"); hapMapTranslate.put("NA18973", "jap21 NA18973 0 0 2 0"); hapMapTranslate.put("NA18966", "jap22 NA18966 0 0 1 0"); hapMapTranslate.put("NA18975", "jap23 NA18975 0 0 2 0"); hapMapTranslate.put("NA18566", "chi23 NA18566 0 0 2 0"); hapMapTranslate.put("NA18563", "chi24 NA18563 0 0 1 0"); hapMapTranslate.put("NA18570", "chi25 NA18570 0 0 2 0"); hapMapTranslate.put("NA18612", "chi26 NA18612 0 0 1 0"); hapMapTranslate.put("NA18571", "chi27 NA18571 0 0 2 0"); hapMapTranslate.put("NA18620", "chi28 NA18620 0 0 1 0"); hapMapTranslate.put("NA18976", "jap24 NA18976 0 0 2 0"); hapMapTranslate.put("NA18967", "jap25 NA18967 0 0 1 0"); hapMapTranslate.put("NA18978", "jap26 NA18978 0 0 2 0"); hapMapTranslate.put("NA18970", "jap27 NA18970 0 0 1 0"); hapMapTranslate.put("NA18980", "jap28 NA18980 0 0 2 0"); hapMapTranslate.put("NA18995", "jap29 NA18995 0 0 1 0"); hapMapTranslate.put("NA18621", "chi29 NA18621 0 0 1 0"); hapMapTranslate.put("NA18594", "chi30 NA18594 0 0 2 0"); hapMapTranslate.put("NA18622", "chi31 NA18622 0 0 1 0"); hapMapTranslate.put("NA18573", "chi32 NA18573 0 0 2 0"); hapMapTranslate.put("NA18623", "chi33 NA18623 0 0 1 0"); hapMapTranslate.put("NA18576", "chi34 NA18576 0 0 2 0"); hapMapTranslate.put("NA18971", "jap30 NA18971 0 0 1 0"); hapMapTranslate.put("NA18981", "jap31 NA18981 0 0 2 0"); hapMapTranslate.put("NA18974", "jap32 NA18974 0 0 1 0"); hapMapTranslate.put("NA18987", "jap33 NA18987 0 0 2 0"); hapMapTranslate.put("NA18990", "jap34 NA18990 0 0 1 0"); hapMapTranslate.put("NA18991", "jap35 NA18991 0 0 2 0"); hapMapTranslate.put("NA18577", "chi35 NA18577 0 0 2 0"); hapMapTranslate.put("NA18624", "chi36 NA18624 0 0 1 0"); hapMapTranslate.put("NA18579", "chi37 NA18579 0 0 2 0"); hapMapTranslate.put("NA18632", "chi38 NA18632 0 0 1 0"); hapMapTranslate.put("NA18582", "chi39 NA18582 0 0 2 0"); hapMapTranslate.put("NA18633", "chi40 NA18633 0 0 1 0"); hapMapTranslate.put("NA18994", "jap36 NA18994 0 0 1 0"); hapMapTranslate.put("NA18992", "jap37 NA18992 0 0 2 0"); hapMapTranslate.put("NA18997", "jap38 NA18997 0 0 2 0"); hapMapTranslate.put("NA18996", "jap39 NA18996 0 0 1 0"); hapMapTranslate.put("NA18635", "chi41 NA18635 0 0 1 0"); hapMapTranslate.put("NA18592", "chi42 NA18592 0 0 2 0"); hapMapTranslate.put("NA18636", "chi43 NA18636 0 0 1 0"); hapMapTranslate.put("NA18593", "chi44 NA18593 0 0 2 0"); hapMapTranslate.put("NA18637", "chi45 NA18637 0 0 1 0"); hapMapTranslate.put("NA19000", "jap40 NA19000 0 0 1 0"); hapMapTranslate.put("NA18998", "jap41 NA18998 0 0 2 0"); hapMapTranslate.put("NA19005", "jap42 NA19005 0 0 1 0"); hapMapTranslate.put("NA18999", "jap43 NA18999 0 0 2 0"); hapMapTranslate.put("NA19007", "jap44 NA19007 0 0 1 0"); hapMapTranslate.put("NA19003", "jap45 NA19003 0 0 2 0"); hapMapTranslate.put("NA18500", "Yoruba004 NA18500 NA18501 NA18502 1 0"); hapMapTranslate.put("NA18501", "Yoruba004 NA18501 0 0 1 0"); hapMapTranslate.put("NA18502", "Yoruba004 NA18502 0 0 2 0"); hapMapTranslate.put("NA18503", "Yoruba005 NA18503 NA18504 NA18505 1 0"); hapMapTranslate.put("NA18504", "Yoruba005 NA18504 0 0 1 0"); hapMapTranslate.put("NA18505", "Yoruba005 NA18505 0 0 2 0"); hapMapTranslate.put("NA18506", "Yoruba009 NA18506 NA18507 NA18508 1 0"); hapMapTranslate.put("NA18507", "Yoruba009 NA18507 0 0 1 0"); hapMapTranslate.put("NA18508", "Yoruba009 NA18508 0 0 2 0"); hapMapTranslate.put("NA18860", "Yoruba012 NA18860 NA18859 NA18858 1 0"); hapMapTranslate.put("NA18859", "Yoruba012 NA18859 0 0 1 0"); hapMapTranslate.put("NA18858", "Yoruba012 NA18858 0 0 2 0"); hapMapTranslate.put("NA18515", "Yoruba013 NA18515 NA18516 NA18517 1 0"); hapMapTranslate.put("NA18516", "Yoruba013 NA18516 0 0 1 0"); hapMapTranslate.put("NA18517", "Yoruba013 NA18517 0 0 2 0"); hapMapTranslate.put("NA18521", "Yoruba016 NA18521 NA18522 NA18523 1 0"); hapMapTranslate.put("NA18522", "Yoruba016 NA18522 0 0 1 0"); hapMapTranslate.put("NA18523", "Yoruba016 NA18523 0 0 2 0"); hapMapTranslate.put("NA18872", "Yoruba017 NA18872 NA18871 NA18870 1 0"); hapMapTranslate.put("NA18871", "Yoruba017 NA18871 0 0 1 0"); hapMapTranslate.put("NA18870", "Yoruba017 NA18870 0 0 2 0"); hapMapTranslate.put("NA18854", "Yoruba018 NA18854 NA18853 NA18852 1 0"); hapMapTranslate.put("NA18853", "Yoruba018 NA18853 0 0 1 0"); hapMapTranslate.put("NA18852", "Yoruba018 NA18852 0 0 2 0"); hapMapTranslate.put("NA18857", "Yoruba023 NA18857 NA18856 NA18855 1 0"); hapMapTranslate.put("NA18856", "Yoruba023 NA18856 0 0 1 0"); hapMapTranslate.put("NA18855", "Yoruba023 NA18855 0 0 2 0"); hapMapTranslate.put("NA18863", "Yoruba024 NA18863 NA18862 NA18861 1 0"); hapMapTranslate.put("NA18862", "Yoruba024 NA18862 0 0 1 0"); hapMapTranslate.put("NA18861", "Yoruba024 NA18861 0 0 2 0"); hapMapTranslate.put("NA18914", "Yoruba028 NA18914 NA18913 NA18912 1 0"); hapMapTranslate.put("NA18913", "Yoruba028 NA18913 0 0 1 0"); hapMapTranslate.put("NA18912", "Yoruba028 NA18912 0 0 2 0"); hapMapTranslate.put("NA19094", "Yoruba040 NA19094 NA19092 NA19093 2 0"); hapMapTranslate.put("NA19092", "Yoruba040 NA19092 0 0 1 0"); hapMapTranslate.put("NA19093", "Yoruba040 NA19093 0 0 2 0"); hapMapTranslate.put("NA19103", "Yoruba042 NA19103 NA19101 NA19102 1 0"); hapMapTranslate.put("NA19101", "Yoruba042 NA19101 0 0 1 0"); hapMapTranslate.put("NA19102", "Yoruba042 NA19102 0 0 2 0"); hapMapTranslate.put("NA19139", "Yoruba043 NA19139 NA19138 NA19137 1 0"); hapMapTranslate.put("NA19138", "Yoruba043 NA19138 0 0 1 0"); hapMapTranslate.put("NA19137", "Yoruba043 NA19137 0 0 2 0"); hapMapTranslate.put("NA19202", "Yoruba045 NA19202 NA19200 NA19201 2 0"); hapMapTranslate.put("NA19200", "Yoruba045 NA19200 0 0 1 0"); hapMapTranslate.put("NA19201", "Yoruba045 NA19201 0 0 2 0"); hapMapTranslate.put("NA19173", "Yoruba047 NA19173 NA19171 NA19172 1 0"); hapMapTranslate.put("NA19171", "Yoruba047 NA19171 0 0 1 0"); hapMapTranslate.put("NA19172", "Yoruba047 NA19172 0 0 2 0"); hapMapTranslate.put("NA19205", "Yoruba048 NA19205 NA19203 NA19204 1 0"); hapMapTranslate.put("NA19203", "Yoruba048 NA19203 0 0 1 0"); hapMapTranslate.put("NA19204", "Yoruba048 NA19204 0 0 2 0"); hapMapTranslate.put("NA19211", "Yoruba050 NA19211 NA19210 NA19209 1 0"); hapMapTranslate.put("NA19210", "Yoruba050 NA19210 0 0 1 0"); hapMapTranslate.put("NA19209", "Yoruba050 NA19209 0 0 2 0"); hapMapTranslate.put("NA19208", "Yoruba051 NA19208 NA19207 NA19206 1 0"); hapMapTranslate.put("NA19207", "Yoruba051 NA19207 0 0 1 0"); hapMapTranslate.put("NA19206", "Yoruba051 NA19206 0 0 2 0"); hapMapTranslate.put("NA19161", "Yoruba056 NA19161 NA19160 NA19159 1 0"); hapMapTranslate.put("NA19160", "Yoruba056 NA19160 0 0 1 0"); hapMapTranslate.put("NA19159", "Yoruba056 NA19159 0 0 2 0"); hapMapTranslate.put("NA19221", "Yoruba058 NA19221 NA19223 NA19222 2 0"); hapMapTranslate.put("NA19223", "Yoruba058 NA19223 0 0 1 0"); hapMapTranslate.put("NA19222", "Yoruba058 NA19222 0 0 2 0"); hapMapTranslate.put("NA19120", "Yoruba060 NA19120 NA19119 NA19116 1 0"); hapMapTranslate.put("NA19119", "Yoruba060 NA19119 0 0 1 0"); hapMapTranslate.put("NA19116", "Yoruba060 NA19116 0 0 2 0"); hapMapTranslate.put("NA19142", "Yoruba071 NA19142 NA19141 NA19140 1 0"); hapMapTranslate.put("NA19141", "Yoruba071 NA19141 0 0 1 0"); hapMapTranslate.put("NA19140", "Yoruba071 NA19140 0 0 2 0"); hapMapTranslate.put("NA19154", "Yoruba072 NA19154 NA19153 NA19152 1 0"); hapMapTranslate.put("NA19153", "Yoruba072 NA19153 0 0 1 0"); hapMapTranslate.put("NA19152", "Yoruba072 NA19152 0 0 2 0"); hapMapTranslate.put("NA19145", "Yoruba074 NA19145 NA19144 NA19143 1 0"); hapMapTranslate.put("NA19144", "Yoruba074 NA19144 0 0 1 0"); hapMapTranslate.put("NA19143", "Yoruba074 NA19143 0 0 2 0"); hapMapTranslate.put("NA19129", "Yoruba077 NA19129 NA19128 NA19127 2 0"); hapMapTranslate.put("NA19128", "Yoruba077 NA19128 0 0 1 0"); hapMapTranslate.put("NA19127", "Yoruba077 NA19127 0 0 2 0"); hapMapTranslate.put("NA19132", "Yoruba101 NA19132 NA19130 NA19131 2 0"); hapMapTranslate.put("NA19130", "Yoruba101 NA19130 0 0 1 0"); hapMapTranslate.put("NA19131", "Yoruba101 NA19131 0 0 2 0"); hapMapTranslate.put("NA19100", "Yoruba105 NA19100 NA19098 NA19099 2 0"); hapMapTranslate.put("NA19098", "Yoruba105 NA19098 0 0 1 0"); hapMapTranslate.put("NA19099", "Yoruba105 NA19099 0 0 2 0"); hapMapTranslate.put("NA19194", "Yoruba112 NA19194 NA19192 NA19193 1 0"); hapMapTranslate.put("NA19192", "Yoruba112 NA19192 0 0 1 0"); hapMapTranslate.put("NA19193", "Yoruba112 NA19193 0 0 2 0"); hapMapTranslate.put("NA19240", "Yoruba117 NA19240 NA19239 NA19238 2 0"); hapMapTranslate.put("NA19239", "Yoruba117 NA19239 0 0 1 0"); hapMapTranslate.put("NA19238", "Yoruba117 NA19238 0 0 2 0"); }

1,110,234

public PedFile(){ //hardcoded hapmap info this.families = new Hashtable(); hapMapTranslate = new Hashtable(90,1); hapMapTranslate.put("NA10846", "1334 NA10846 NA12144 NA12145 1 0" ); hapMapTranslate.put("NA12144", "1334 NA12144 0 0 1 0"); hapMapTranslate.put("NA12145", "1334 NA12145 0 0 2 0"); hapMapTranslate.put("NA10847", "1334 NA10847 NA12146 NA12239 2 0" ); hapMapTranslate.put("NA12146", "1334 NA12146 0 0 1 0"); hapMapTranslate.put("NA12239", "1334 NA12239 0 0 2 0"); hapMapTranslate.put("NA07029", "1340 NA07029 NA06994 NA07000 1 0" ); hapMapTranslate.put("NA06994", "1340 NA06994 0 0 1 0"); hapMapTranslate.put("NA07000", "1340 NA07000 0 0 2 0"); hapMapTranslate.put("NA07019", "1340 NA07019 NA07022 NA07056 2 0" ); hapMapTranslate.put("NA07022", "1340 NA07022 0 0 1 0"); hapMapTranslate.put("NA07056", "1340 NA07056 0 0 2 0"); hapMapTranslate.put("NA07048", "1341 NA07048 NA07034 NA07055 1 0" ); hapMapTranslate.put("NA07034", "1341 NA07034 0 0 1 0"); hapMapTranslate.put("NA07055", "1341 NA07055 0 0 2 0"); hapMapTranslate.put("NA06991", "1341 NA06991 NA06993 NA06985 2 0" ); hapMapTranslate.put("NA06993", "1341 NA06993 0 0 1 0"); hapMapTranslate.put("NA06993.dup", "dup NA06993.dup 0 0 1 0"); hapMapTranslate.put("NA06985", "1341 NA06985 0 0 2 0"); hapMapTranslate.put("NA10851", "1344 NA10851 NA12056 NA12057 1 0" ); hapMapTranslate.put("NA12056", "1344 NA12056 0 0 1 0"); hapMapTranslate.put("NA12057", "1344 NA12057 0 0 2 0"); hapMapTranslate.put("NA07348", "1345 NA07348 NA07357 NA07345 2 0" ); hapMapTranslate.put("NA07357", "1345 NA07357 0 0 1 0"); hapMapTranslate.put("NA07345", "1345 NA07345 0 0 2 0"); hapMapTranslate.put("NA10857", "1346 NA10857 NA12043 NA12044 1 0" ); hapMapTranslate.put("NA12043", "1346 NA12043 0 0 1 0"); hapMapTranslate.put("NA12044", "1346 NA12044 0 0 2 0"); hapMapTranslate.put("NA10859", "1347 NA10859 NA11881 NA11882 2 0" ); hapMapTranslate.put("NA11881", "1347 NA11881 0 0 1 0"); hapMapTranslate.put("NA11882", "1347 NA11882 0 0 2 0"); hapMapTranslate.put("NA10854", "1349 NA10854 NA11839 NA11840 2 0" ); hapMapTranslate.put("NA11839", "1349 NA11839 0 0 1 0"); hapMapTranslate.put("NA11840", "1349 NA11840 0 0 2 0"); hapMapTranslate.put("NA10856", "1350 NA10856 NA11829 NA11830 1 0" ); hapMapTranslate.put("NA11829", "1350 NA11829 0 0 1 0"); hapMapTranslate.put("NA11830", "1350 NA11830 0 0 2 0"); hapMapTranslate.put("NA10855", "1350 NA10855 NA11831 NA11832 2 0" ); hapMapTranslate.put("NA11831", "1350 NA11831 0 0 1 0"); hapMapTranslate.put("NA11832", "1350 NA11832 0 0 2 0"); hapMapTranslate.put("NA12707", "1358 NA12707 NA12716 NA12717 1 0" ); hapMapTranslate.put("NA12716", "1358 NA12716 0 0 1 0"); hapMapTranslate.put("NA12717", "1358 NA12717 0 0 2 0"); hapMapTranslate.put("NA10860", "1362 NA10860 NA11992 NA11993 1 0" ); hapMapTranslate.put("NA11992", "1362 NA11992 0 0 1 0"); hapMapTranslate.put("NA11993", "1362 NA11993 0 0 2 0"); hapMapTranslate.put("NA11993.dup", "dup NA11993.dup 0 0 2 0"); hapMapTranslate.put("NA10861", "1362 NA10861 NA11994 NA11995 2 0" ); hapMapTranslate.put("NA11994", "1362 NA11994 0 0 1 0"); hapMapTranslate.put("NA11995", "1362 NA11995 0 0 2 0"); hapMapTranslate.put("NA10863", "1375 NA10863 NA12264 NA12234 2 0" ); hapMapTranslate.put("NA12264", "1375 NA12264 0 0 1 0"); hapMapTranslate.put("NA12234", "1375 NA12234 0 0 2 0"); hapMapTranslate.put("NA10830", "1408 NA10830 NA12154 NA12236 1 0" ); hapMapTranslate.put("NA12154", "1408 NA12154 0 0 1 0"); hapMapTranslate.put("NA12236", "1408 NA12236 0 0 2 0"); hapMapTranslate.put("NA10831", "1408 NA10831 NA12155 NA12156 2 0" ); hapMapTranslate.put("NA12155", "1408 NA12155 0 0 1 0"); hapMapTranslate.put("NA12156", "1408 NA12156 0 0 2 0"); hapMapTranslate.put("NA12156.dup", "dup NA12156.dup 0 0 2 0"); hapMapTranslate.put("NA10835", "1416 NA10835 NA12248 NA12249 1 0" ); hapMapTranslate.put("NA12248", "1416 NA12248 0 0 1 0"); hapMapTranslate.put("NA12248.dup", "dup NA1248.dup 0 0 1 0"); hapMapTranslate.put("NA12249", "1416 NA12249 0 0 2 0"); hapMapTranslate.put("NA10838", "1420 NA10838 NA12003 NA12004 1 0" ); hapMapTranslate.put("NA12003", "1420 NA12003 0 0 1 0"); hapMapTranslate.put("NA12003.dup", "dup NA12003.dup 0 0 1 0"); hapMapTranslate.put("NA12004", "1420 NA12004 0 0 2 0"); hapMapTranslate.put("NA10839", "1420 NA10839 NA12005 NA12006 2 0" ); hapMapTranslate.put("NA12005", "1420 NA12005 0 0 1 0"); hapMapTranslate.put("NA12006", "1420 NA12006 0 0 2 0"); hapMapTranslate.put("NA12740", "1444 NA12740 NA12750 NA12751 2 0" ); hapMapTranslate.put("NA12750", "1444 NA12750 0 0 1 0"); hapMapTranslate.put("NA12751", "1444 NA12751 0 0 2 0"); hapMapTranslate.put("NA12752", "1447 NA12752 NA12760 NA12761 1 0" ); hapMapTranslate.put("NA12760", "1447 NA12760 0 0 1 0"); hapMapTranslate.put("NA12761", "1447 NA12761 0 0 2 0"); hapMapTranslate.put("NA12753", "1447 NA12753 NA12762 NA12763 2 0" ); hapMapTranslate.put("NA12762", "1447 NA12762 0 0 1 0"); hapMapTranslate.put("NA12763", "1447 NA12763 0 0 2 0"); hapMapTranslate.put("NA12801", "1454 NA12801 NA12812 NA12813 1 0" ); hapMapTranslate.put("NA12812", "1454 NA12812 0 0 1 0"); hapMapTranslate.put("NA12813", "1454 NA12813 0 0 2 0"); hapMapTranslate.put("NA12802", "1454 NA12802 NA12814 NA12815 2 0" ); hapMapTranslate.put("NA12814", "1454 NA12814 0 0 1 0"); hapMapTranslate.put("NA12815", "1454 NA12815 0 0 2 0"); hapMapTranslate.put("NA12864", "1459 NA12864 NA12872 NA12873 1 0" ); hapMapTranslate.put("NA12872", "1459 NA12872 0 0 1 0"); hapMapTranslate.put("NA12873", "1459 NA12873 0 0 2 0"); hapMapTranslate.put("NA12865", "1459 NA12865 NA12874 NA12875 2 0" ); hapMapTranslate.put("NA12874", "1459 NA12874 0 0 1 0"); hapMapTranslate.put("NA12875", "1459 NA12875 0 0 2 0"); hapMapTranslate.put("NA12878", "1463 NA12878 NA12891 NA12892 2 0" ); hapMapTranslate.put("NA12891", "1463 NA12891 0 0 1 0"); hapMapTranslate.put("NA12892", "1463 NA12892 0 0 2 0"); hapMapTranslate.put("NA18526", "chi1 NA18526 0 0 2 0"); hapMapTranslate.put("NA18524", "chi2 NA18524 0 0 1 0"); hapMapTranslate.put("NA18529", "chi3 NA18529 0 0 2 0"); hapMapTranslate.put("NA18558", "chi4 NA18558 0 0 1 0"); hapMapTranslate.put("NA18532", "chi5 NA18532 0 0 2 0"); hapMapTranslate.put("NA18561", "chi6 NA18561 0 0 1 0"); hapMapTranslate.put("NA18942", "jap1 NA18942 0 0 2 0"); hapMapTranslate.put("NA18940", "jap2 NA18940 0 0 1 0"); hapMapTranslate.put("NA18951", "jap3 NA18951 0 0 2 0"); hapMapTranslate.put("NA18943", "jap4 NA18943 0 0 1 0"); hapMapTranslate.put("NA18947", "jap5 NA18947 0 0 2 0"); hapMapTranslate.put("NA18944", "jap6 NA18944 0 0 1 0"); hapMapTranslate.put("NA18562", "chi7 NA18562 0 0 1 0"); hapMapTranslate.put("NA18537", "chi8 NA18537 0 0 2 0"); hapMapTranslate.put("NA18603", "chi9 NA18603 0 0 1 0"); hapMapTranslate.put("NA18540", "chi10 NA18540 0 0 2 0"); hapMapTranslate.put("NA18605", "chi11 NA18605 0 0 1 0"); hapMapTranslate.put("NA18542", "chi12 NA18542 0 0 2 0"); hapMapTranslate.put("NA18945", "jap7 NA18945 0 0 1 0"); hapMapTranslate.put("NA18949", "jap8 NA18949 0 0 2 0"); hapMapTranslate.put("NA18948", "jap9 NA18948 0 0 1 0"); hapMapTranslate.put("NA18952", "jap10 NA18952 0 0 1 0"); hapMapTranslate.put("NA18956", "jap11 NA18956 0 0 2 0"); hapMapTranslate.put("NA18545", "chi13 NA18545 0 0 2 0"); hapMapTranslate.put("NA18572", "chi46 NA18572 0 0 1 0"); hapMapTranslate.put("NA18547", "chi15 NA18547 0 0 2 0"); hapMapTranslate.put("NA18609", "chi16 NA18609 0 0 1 0"); hapMapTranslate.put("NA18550", "chi17 NA18550 0 0 2 0"); hapMapTranslate.put("NA18608", "chi18 NA18608 0 0 1 0"); hapMapTranslate.put("NA18964", "jap12 NA18964 0 0 2 0"); hapMapTranslate.put("NA18953", "jap13 NA18953 0 0 1 0"); hapMapTranslate.put("NA18968", "jap14 NA18968 0 0 2 0"); hapMapTranslate.put("NA18959", "jap15 NA18959 0 0 1 0"); hapMapTranslate.put("NA18969", "jap16 NA18969 0 0 2 0"); hapMapTranslate.put("NA18960", "jap17 NA18960 0 0 1 0"); hapMapTranslate.put("NA18552", "chi19 NA18552 0 0 2 0"); hapMapTranslate.put("NA18611", "chi20 NA18611 0 0 1 0"); hapMapTranslate.put("NA18555", "chi21 NA18555 0 0 2 0"); hapMapTranslate.put("NA18564", "chi22 NA18564 0 0 2 0"); hapMapTranslate.put("NA18961", "jap18 NA18961 0 0 1 0"); hapMapTranslate.put("NA18972", "jap19 NA18972 0 0 2 0"); hapMapTranslate.put("NA18965", "jap20 NA18965 0 0 1 0"); hapMapTranslate.put("NA18973", "jap21 NA18973 0 0 2 0"); hapMapTranslate.put("NA18966", "jap22 NA18966 0 0 1 0"); hapMapTranslate.put("NA18975", "jap23 NA18975 0 0 2 0"); hapMapTranslate.put("NA18566", "chi23 NA18566 0 0 2 0"); hapMapTranslate.put("NA18563", "chi24 NA18563 0 0 1 0"); hapMapTranslate.put("NA18570", "chi25 NA18570 0 0 2 0"); hapMapTranslate.put("NA18612", "chi26 NA18612 0 0 1 0"); hapMapTranslate.put("NA18571", "chi27 NA18571 0 0 2 0"); hapMapTranslate.put("NA18620", "chi28 NA18620 0 0 1 0"); hapMapTranslate.put("NA18976", "jap24 NA18976 0 0 2 0"); hapMapTranslate.put("NA18967", "jap25 NA18967 0 0 1 0"); hapMapTranslate.put("NA18978", "jap26 NA18978 0 0 2 0"); hapMapTranslate.put("NA18970", "jap27 NA18970 0 0 1 0"); hapMapTranslate.put("NA18980", "jap28 NA18980 0 0 2 0"); hapMapTranslate.put("NA18995", "jap29 NA18995 0 0 1 0"); hapMapTranslate.put("NA18621", "chi29 NA18621 0 0 1 0"); hapMapTranslate.put("NA18594", "chi30 NA18594 0 0 2 0"); hapMapTranslate.put("NA18622", "chi31 NA18622 0 0 1 0"); hapMapTranslate.put("NA18573", "chi32 NA18573 0 0 2 0"); hapMapTranslate.put("NA18623", "chi33 NA18623 0 0 1 0"); hapMapTranslate.put("NA18576", "chi34 NA18576 0 0 2 0"); hapMapTranslate.put("NA18971", "jap30 NA18971 0 0 1 0"); hapMapTranslate.put("NA18981", "jap31 NA18981 0 0 2 0"); hapMapTranslate.put("NA18974", "jap32 NA18974 0 0 1 0"); hapMapTranslate.put("NA18987", "jap33 NA18987 0 0 2 0"); hapMapTranslate.put("NA18990", "jap34 NA18990 0 0 1 0"); hapMapTranslate.put("NA18991", "jap35 NA18991 0 0 2 0"); hapMapTranslate.put("NA18577", "chi35 NA18577 0 0 2 0"); hapMapTranslate.put("NA18624", "chi36 NA18624 0 0 1 0"); hapMapTranslate.put("NA18579", "chi37 NA18579 0 0 2 0"); hapMapTranslate.put("NA18632", "chi38 NA18632 0 0 1 0"); hapMapTranslate.put("NA18582", "chi39 NA18582 0 0 2 0"); hapMapTranslate.put("NA18633", "chi40 NA18633 0 0 1 0"); hapMapTranslate.put("NA18994", "jap36 NA18994 0 0 1 0"); hapMapTranslate.put("NA18992", "jap37 NA18992 0 0 2 0"); hapMapTranslate.put("NA18997", "jap38 NA18997 0 0 2 0"); hapMapTranslate.put("NA18996", "jap39 NA18996 0 0 1 0"); hapMapTranslate.put("NA18635", "chi41 NA18635 0 0 1 0"); hapMapTranslate.put("NA18592", "chi42 NA18592 0 0 2 0"); hapMapTranslate.put("NA18636", "chi43 NA18636 0 0 1 0"); hapMapTranslate.put("NA18593", "chi44 NA18593 0 0 2 0"); hapMapTranslate.put("NA18637", "chi45 NA18637 0 0 1 0"); hapMapTranslate.put("NA19000", "jap40 NA19000 0 0 1 0"); hapMapTranslate.put("NA18998", "jap41 NA18998 0 0 2 0"); hapMapTranslate.put("NA19005", "jap42 NA19005 0 0 1 0"); hapMapTranslate.put("NA18999", "jap43 NA18999 0 0 2 0"); hapMapTranslate.put("NA19007", "jap44 NA19007 0 0 1 0"); hapMapTranslate.put("NA19003", "jap45 NA19003 0 0 2 0"); hapMapTranslate.put("NA18500", "Yoruba004 NA18500 NA18501 NA18502 1 0"); hapMapTranslate.put("NA18501", "Yoruba004 NA18501 0 0 1 0"); hapMapTranslate.put("NA18502", "Yoruba004 NA18502 0 0 2 0"); hapMapTranslate.put("NA18503", "Yoruba005 NA18503 NA18504 NA18505 1 0"); hapMapTranslate.put("NA18504", "Yoruba005 NA18504 0 0 1 0"); hapMapTranslate.put("NA18505", "Yoruba005 NA18505 0 0 2 0"); hapMapTranslate.put("NA18506", "Yoruba009 NA18506 NA18507 NA18508 1 0"); hapMapTranslate.put("NA18507", "Yoruba009 NA18507 0 0 1 0"); hapMapTranslate.put("NA18508", "Yoruba009 NA18508 0 0 2 0"); hapMapTranslate.put("NA18860", "Yoruba012 NA18860 NA18859 NA18858 1 0"); hapMapTranslate.put("NA18859", "Yoruba012 NA18859 0 0 1 0"); hapMapTranslate.put("NA18858", "Yoruba012 NA18858 0 0 2 0"); hapMapTranslate.put("NA18515", "Yoruba013 NA18515 NA18516 NA18517 1 0"); hapMapTranslate.put("NA18516", "Yoruba013 NA18516 0 0 1 0"); hapMapTranslate.put("NA18517", "Yoruba013 NA18517 0 0 2 0"); hapMapTranslate.put("NA18521", "Yoruba016 NA18521 NA18522 NA18523 1 0"); hapMapTranslate.put("NA18522", "Yoruba016 NA18522 0 0 1 0"); hapMapTranslate.put("NA18523", "Yoruba016 NA18523 0 0 2 0"); hapMapTranslate.put("NA18872", "Yoruba017 NA18872 NA18871 NA18870 1 0"); hapMapTranslate.put("NA18871", "Yoruba017 NA18871 0 0 1 0"); hapMapTranslate.put("NA18870", "Yoruba017 NA18870 0 0 2 0"); hapMapTranslate.put("NA18854", "Yoruba018 NA18854 NA18853 NA18852 1 0"); hapMapTranslate.put("NA18853", "Yoruba018 NA18853 0 0 1 0"); hapMapTranslate.put("NA18852", "Yoruba018 NA18852 0 0 2 0"); hapMapTranslate.put("NA18857", "Yoruba023 NA18857 NA18856 NA18855 1 0"); hapMapTranslate.put("NA18856", "Yoruba023 NA18856 0 0 1 0"); hapMapTranslate.put("NA18855", "Yoruba023 NA18855 0 0 2 0"); hapMapTranslate.put("NA18863", "Yoruba024 NA18863 NA18862 NA18861 1 0"); hapMapTranslate.put("NA18862", "Yoruba024 NA18862 0 0 1 0"); hapMapTranslate.put("NA18861", "Yoruba024 NA18861 0 0 2 0"); hapMapTranslate.put("NA18914", "Yoruba028 NA18914 NA18913 NA18912 1 0"); hapMapTranslate.put("NA18913", "Yoruba028 NA18913 0 0 1 0"); hapMapTranslate.put("NA18912", "Yoruba028 NA18912 0 0 2 0"); hapMapTranslate.put("NA19094", "Yoruba040 NA19094 NA19092 NA19093 2 0"); hapMapTranslate.put("NA19092", "Yoruba040 NA19092 0 0 1 0"); hapMapTranslate.put("NA19093", "Yoruba040 NA19093 0 0 2 0"); hapMapTranslate.put("NA19103", "Yoruba042 NA19103 NA19101 NA19102 1 0"); hapMapTranslate.put("NA19101", "Yoruba042 NA19101 0 0 1 0"); hapMapTranslate.put("NA19102", "Yoruba042 NA19102 0 0 2 0"); hapMapTranslate.put("NA19139", "Yoruba043 NA19139 NA19138 NA19137 1 0"); hapMapTranslate.put("NA19138", "Yoruba043 NA19138 0 0 1 0"); hapMapTranslate.put("NA19137", "Yoruba043 NA19137 0 0 2 0"); hapMapTranslate.put("NA19202", "Yoruba045 NA19202 NA19200 NA19201 2 0"); hapMapTranslate.put("NA19200", "Yoruba045 NA19200 0 0 1 0"); hapMapTranslate.put("NA19201", "Yoruba045 NA19201 0 0 2 0"); hapMapTranslate.put("NA19173", "Yoruba047 NA19173 NA19171 NA19172 1 0"); hapMapTranslate.put("NA19171", "Yoruba047 NA19171 0 0 1 0"); hapMapTranslate.put("NA19172", "Yoruba047 NA19172 0 0 2 0"); hapMapTranslate.put("NA19205", "Yoruba048 NA19205 NA19203 NA19204 1 0"); hapMapTranslate.put("NA19203", "Yoruba048 NA19203 0 0 1 0"); hapMapTranslate.put("NA19204", "Yoruba048 NA19204 0 0 2 0"); hapMapTranslate.put("NA19211", "Yoruba050 NA19211 NA19210 NA19209 1 0"); hapMapTranslate.put("NA19210", "Yoruba050 NA19210 0 0 1 0"); hapMapTranslate.put("NA19209", "Yoruba050 NA19209 0 0 2 0"); hapMapTranslate.put("NA19208", "Yoruba051 NA19208 NA19207 NA19206 1 0"); hapMapTranslate.put("NA19207", "Yoruba051 NA19207 0 0 1 0"); hapMapTranslate.put("NA19206", "Yoruba051 NA19206 0 0 2 0"); hapMapTranslate.put("NA19161", "Yoruba056 NA19161 NA19160 NA19159 1 0"); hapMapTranslate.put("NA19160", "Yoruba056 NA19160 0 0 1 0"); hapMapTranslate.put("NA19159", "Yoruba056 NA19159 0 0 2 0"); hapMapTranslate.put("NA19221", "Yoruba058 NA19221 NA19223 NA19222 2 0"); hapMapTranslate.put("NA19223", "Yoruba058 NA19223 0 0 1 0"); hapMapTranslate.put("NA19222", "Yoruba058 NA19222 0 0 2 0"); hapMapTranslate.put("NA19120", "Yoruba060 NA19120 NA19119 NA19116 1 0"); hapMapTranslate.put("NA19119", "Yoruba060 NA19119 0 0 1 0"); hapMapTranslate.put("NA19116", "Yoruba060 NA19116 0 0 2 0"); hapMapTranslate.put("NA19142", "Yoruba071 NA19142 NA19141 NA19140 1 0"); hapMapTranslate.put("NA19141", "Yoruba071 NA19141 0 0 1 0"); hapMapTranslate.put("NA19140", "Yoruba071 NA19140 0 0 2 0"); hapMapTranslate.put("NA19154", "Yoruba072 NA19154 NA19153 NA19152 1 0"); hapMapTranslate.put("NA19153", "Yoruba072 NA19153 0 0 1 0"); hapMapTranslate.put("NA19152", "Yoruba072 NA19152 0 0 2 0"); hapMapTranslate.put("NA19145", "Yoruba074 NA19145 NA19144 NA19143 1 0"); hapMapTranslate.put("NA19144", "Yoruba074 NA19144 0 0 1 0"); hapMapTranslate.put("NA19143", "Yoruba074 NA19143 0 0 2 0"); hapMapTranslate.put("NA19129", "Yoruba077 NA19129 NA19128 NA19127 2 0"); hapMapTranslate.put("NA19128", "Yoruba077 NA19128 0 0 1 0"); hapMapTranslate.put("NA19127", "Yoruba077 NA19127 0 0 2 0"); hapMapTranslate.put("NA19132", "Yoruba101 NA19132 NA19130 NA19131 2 0"); hapMapTranslate.put("NA19130", "Yoruba101 NA19130 0 0 1 0"); hapMapTranslate.put("NA19131", "Yoruba101 NA19131 0 0 2 0"); hapMapTranslate.put("NA19100", "Yoruba105 NA19100 NA19098 NA19099 2 0"); hapMapTranslate.put("NA19098", "Yoruba105 NA19098 0 0 1 0"); hapMapTranslate.put("NA19099", "Yoruba105 NA19099 0 0 2 0"); hapMapTranslate.put("NA19194", "Yoruba112 NA19194 NA19192 NA19193 1 0"); hapMapTranslate.put("NA19192", "Yoruba112 NA19192 0 0 1 0"); hapMapTranslate.put("NA19193", "Yoruba112 NA19193 0 0 2 0"); hapMapTranslate.put("NA19240", "Yoruba117 NA19240 NA19239 NA19238 2 0"); hapMapTranslate.put("NA19239", "Yoruba117 NA19239 0 0 1 0"); hapMapTranslate.put("NA19238", "Yoruba117 NA19238 0 0 2 0"); }

public PedFile(){ //hardcoded hapmap info this.families = new Hashtable(); hapMapTranslate = new Hashtable(90,1); hapMapTranslate.put("NA10846", "1334 NA10846 NA12144 NA12145 1 0" ); hapMapTranslate.put("NA12144", "1334 NA12144 0 0 1 0"); hapMapTranslate.put("NA12145", "1334 NA12145 0 0 2 0"); hapMapTranslate.put("NA10847", "1334 NA10847 NA12146 NA12239 2 0" ); hapMapTranslate.put("NA12146", "1334 NA12146 0 0 1 0"); hapMapTranslate.put("NA12239", "1334 NA12239 0 0 2 0"); hapMapTranslate.put("NA07029", "1340 NA07029 NA06994 NA07000 1 0" ); hapMapTranslate.put("NA06994", "1340 NA06994 0 0 1 0"); hapMapTranslate.put("NA07000", "1340 NA07000 0 0 2 0"); hapMapTranslate.put("NA07019", "1340 NA07019 NA07022 NA07056 2 0" ); hapMapTranslate.put("NA07022", "1340 NA07022 0 0 1 0"); hapMapTranslate.put("NA07056", "1340 NA07056 0 0 2 0"); hapMapTranslate.put("NA07048", "1341 NA07048 NA07034 NA07055 1 0" ); hapMapTranslate.put("NA07034", "1341 NA07034 0 0 1 0"); hapMapTranslate.put("NA07055", "1341 NA07055 0 0 2 0"); hapMapTranslate.put("NA06991", "1341 NA06991 NA06993 NA06985 2 0" ); hapMapTranslate.put("NA06993", "1341 NA06993 0 0 1 0"); hapMapTranslate.put("NA06993.dup", "dup NA06993.dup 0 0 1 0"); hapMapTranslate.put("NA06985", "1341 NA06985 0 0 2 0"); hapMapTranslate.put("NA10851", "1344 NA10851 NA12056 NA12057 1 0" ); hapMapTranslate.put("NA12056", "1344 NA12056 0 0 1 0"); hapMapTranslate.put("NA12057", "1344 NA12057 0 0 2 0"); hapMapTranslate.put("NA07348", "1345 NA07348 NA07357 NA07345 2 0" ); hapMapTranslate.put("NA07357", "1345 NA07357 0 0 1 0"); hapMapTranslate.put("NA07345", "1345 NA07345 0 0 2 0"); hapMapTranslate.put("NA10857", "1346 NA10857 NA12043 NA12044 1 0" ); hapMapTranslate.put("NA12043", "1346 NA12043 0 0 1 0"); hapMapTranslate.put("NA12044", "1346 NA12044 0 0 2 0"); hapMapTranslate.put("NA10859", "1347 NA10859 NA11881 NA11882 2 0" ); hapMapTranslate.put("NA11881", "1347 NA11881 0 0 1 0"); hapMapTranslate.put("NA11882", "1347 NA11882 0 0 2 0"); hapMapTranslate.put("NA10854", "1349 NA10854 NA11839 NA11840 2 0" ); hapMapTranslate.put("NA11839", "1349 NA11839 0 0 1 0"); hapMapTranslate.put("NA11840", "1349 NA11840 0 0 2 0"); hapMapTranslate.put("NA10856", "1350 NA10856 NA11829 NA11830 1 0" ); hapMapTranslate.put("NA11829", "1350 NA11829 0 0 1 0"); hapMapTranslate.put("NA11830", "1350 NA11830 0 0 2 0"); hapMapTranslate.put("NA10855", "1350 NA10855 NA11831 NA11832 2 0" ); hapMapTranslate.put("NA11831", "1350 NA11831 0 0 1 0"); hapMapTranslate.put("NA11832", "1350 NA11832 0 0 2 0"); hapMapTranslate.put("NA12707", "1358 NA12707 NA12716 NA12717 1 0" ); hapMapTranslate.put("NA12716", "1358 NA12716 0 0 1 0"); hapMapTranslate.put("NA12717", "1358 NA12717 0 0 2 0"); hapMapTranslate.put("NA10860", "1362 NA10860 NA11992 NA11993 1 0" ); hapMapTranslate.put("NA11992", "1362 NA11992 0 0 1 0"); hapMapTranslate.put("NA11993", "1362 NA11993 0 0 2 0"); hapMapTranslate.put("NA11993.dup", "dup NA11993.dup 0 0 2 0"); hapMapTranslate.put("NA10861", "1362 NA10861 NA11994 NA11995 2 0" ); hapMapTranslate.put("NA11994", "1362 NA11994 0 0 1 0"); hapMapTranslate.put("NA11995", "1362 NA11995 0 0 2 0"); hapMapTranslate.put("NA10863", "1375 NA10863 NA12264 NA12234 2 0" ); hapMapTranslate.put("NA12264", "1375 NA12264 0 0 1 0"); hapMapTranslate.put("NA12234", "1375 NA12234 0 0 2 0"); hapMapTranslate.put("NA10830", "1408 NA10830 NA12154 NA12236 1 0" ); hapMapTranslate.put("NA12154", "1408 NA12154 0 0 1 0"); hapMapTranslate.put("NA12236", "1408 NA12236 0 0 2 0"); hapMapTranslate.put("NA10831", "1408 NA10831 NA12155 NA12156 2 0" ); hapMapTranslate.put("NA12155", "1408 NA12155 0 0 1 0"); hapMapTranslate.put("NA12156", "1408 NA12156 0 0 2 0"); hapMapTranslate.put("NA12156.dup", "dup NA12156.dup 0 0 2 0"); hapMapTranslate.put("NA10835", "1416 NA10835 NA12248 NA12249 1 0" ); hapMapTranslate.put("NA12248", "1416 NA12248 0 0 1 0"); hapMapTranslate.put("NA12249", "1416 NA12249 0 0 2 0"); hapMapTranslate.put("NA10838", "1420 NA10838 NA12003 NA12004 1 0" ); hapMapTranslate.put("NA12003", "1420 NA12003 0 0 1 0"); hapMapTranslate.put("NA12003.dup", "dup NA12003.dup 0 0 1 0"); hapMapTranslate.put("NA12004", "1420 NA12004 0 0 2 0"); hapMapTranslate.put("NA10839", "1420 NA10839 NA12005 NA12006 2 0" ); hapMapTranslate.put("NA12005", "1420 NA12005 0 0 1 0"); hapMapTranslate.put("NA12006", "1420 NA12006 0 0 2 0"); hapMapTranslate.put("NA12740", "1444 NA12740 NA12750 NA12751 2 0" ); hapMapTranslate.put("NA12750", "1444 NA12750 0 0 1 0"); hapMapTranslate.put("NA12751", "1444 NA12751 0 0 2 0"); hapMapTranslate.put("NA12752", "1447 NA12752 NA12760 NA12761 1 0" ); hapMapTranslate.put("NA12760", "1447 NA12760 0 0 1 0"); hapMapTranslate.put("NA12761", "1447 NA12761 0 0 2 0"); hapMapTranslate.put("NA12753", "1447 NA12753 NA12762 NA12763 2 0" ); hapMapTranslate.put("NA12762", "1447 NA12762 0 0 1 0"); hapMapTranslate.put("NA12763", "1447 NA12763 0 0 2 0"); hapMapTranslate.put("NA12801", "1454 NA12801 NA12812 NA12813 1 0" ); hapMapTranslate.put("NA12812", "1454 NA12812 0 0 1 0"); hapMapTranslate.put("NA12813", "1454 NA12813 0 0 2 0"); hapMapTranslate.put("NA12802", "1454 NA12802 NA12814 NA12815 2 0" ); hapMapTranslate.put("NA12814", "1454 NA12814 0 0 1 0"); hapMapTranslate.put("NA12815", "1454 NA12815 0 0 2 0"); hapMapTranslate.put("NA12864", "1459 NA12864 NA12872 NA12873 1 0" ); hapMapTranslate.put("NA12872", "1459 NA12872 0 0 1 0"); hapMapTranslate.put("NA12873", "1459 NA12873 0 0 2 0"); hapMapTranslate.put("NA12865", "1459 NA12865 NA12874 NA12875 2 0" ); hapMapTranslate.put("NA12874", "1459 NA12874 0 0 1 0"); hapMapTranslate.put("NA12875", "1459 NA12875 0 0 2 0"); hapMapTranslate.put("NA12878", "1463 NA12878 NA12891 NA12892 2 0" ); hapMapTranslate.put("NA12891", "1463 NA12891 0 0 1 0"); hapMapTranslate.put("NA12892", "1463 NA12892 0 0 2 0"); hapMapTranslate.put("NA18526", "chi1 NA18526 0 0 2 0"); hapMapTranslate.put("NA18524", "chi2 NA18524 0 0 1 0"); hapMapTranslate.put("NA18529", "chi3 NA18529 0 0 2 0"); hapMapTranslate.put("NA18558", "chi4 NA18558 0 0 1 0"); hapMapTranslate.put("NA18532", "chi5 NA18532 0 0 2 0"); hapMapTranslate.put("NA18561", "chi6 NA18561 0 0 1 0"); hapMapTranslate.put("NA18942", "jap1 NA18942 0 0 2 0"); hapMapTranslate.put("NA18940", "jap2 NA18940 0 0 1 0"); hapMapTranslate.put("NA18951", "jap3 NA18951 0 0 2 0"); hapMapTranslate.put("NA18943", "jap4 NA18943 0 0 1 0"); hapMapTranslate.put("NA18947", "jap5 NA18947 0 0 2 0"); hapMapTranslate.put("NA18944", "jap6 NA18944 0 0 1 0"); hapMapTranslate.put("NA18562", "chi7 NA18562 0 0 1 0"); hapMapTranslate.put("NA18537", "chi8 NA18537 0 0 2 0"); hapMapTranslate.put("NA18603", "chi9 NA18603 0 0 1 0"); hapMapTranslate.put("NA18540", "chi10 NA18540 0 0 2 0"); hapMapTranslate.put("NA18605", "chi11 NA18605 0 0 1 0"); hapMapTranslate.put("NA18542", "chi12 NA18542 0 0 2 0"); hapMapTranslate.put("NA18945", "jap7 NA18945 0 0 1 0"); hapMapTranslate.put("NA18949", "jap8 NA18949 0 0 2 0"); hapMapTranslate.put("NA18948", "jap9 NA18948 0 0 1 0"); hapMapTranslate.put("NA18952", "jap10 NA18952 0 0 1 0"); hapMapTranslate.put("NA18956", "jap11 NA18956 0 0 2 0"); hapMapTranslate.put("NA18545", "chi13 NA18545 0 0 2 0"); hapMapTranslate.put("NA18572", "chi46 NA18572 0 0 1 0"); hapMapTranslate.put("NA18547", "chi15 NA18547 0 0 2 0"); hapMapTranslate.put("NA18609", "chi16 NA18609 0 0 1 0"); hapMapTranslate.put("NA18550", "chi17 NA18550 0 0 2 0"); hapMapTranslate.put("NA18608", "chi18 NA18608 0 0 1 0"); hapMapTranslate.put("NA18964", "jap12 NA18964 0 0 2 0"); hapMapTranslate.put("NA18953", "jap13 NA18953 0 0 1 0"); hapMapTranslate.put("NA18968", "jap14 NA18968 0 0 2 0"); hapMapTranslate.put("NA18959", "jap15 NA18959 0 0 1 0"); hapMapTranslate.put("NA18969", "jap16 NA18969 0 0 2 0"); hapMapTranslate.put("NA18960", "jap17 NA18960 0 0 1 0"); hapMapTranslate.put("NA18552", "chi19 NA18552 0 0 2 0"); hapMapTranslate.put("NA18611", "chi20 NA18611 0 0 1 0"); hapMapTranslate.put("NA18555", "chi21 NA18555 0 0 2 0"); hapMapTranslate.put("NA18564", "chi22 NA18564 0 0 2 0"); hapMapTranslate.put("NA18961", "jap18 NA18961 0 0 1 0"); hapMapTranslate.put("NA18972", "jap19 NA18972 0 0 2 0"); hapMapTranslate.put("NA18965", "jap20 NA18965 0 0 1 0"); hapMapTranslate.put("NA18973", "jap21 NA18973 0 0 2 0"); hapMapTranslate.put("NA18966", "jap22 NA18966 0 0 1 0"); hapMapTranslate.put("NA18975", "jap23 NA18975 0 0 2 0"); hapMapTranslate.put("NA18566", "chi23 NA18566 0 0 2 0"); hapMapTranslate.put("NA18563", "chi24 NA18563 0 0 1 0"); hapMapTranslate.put("NA18570", "chi25 NA18570 0 0 2 0"); hapMapTranslate.put("NA18612", "chi26 NA18612 0 0 1 0"); hapMapTranslate.put("NA18571", "chi27 NA18571 0 0 2 0"); hapMapTranslate.put("NA18620", "chi28 NA18620 0 0 1 0"); hapMapTranslate.put("NA18976", "jap24 NA18976 0 0 2 0"); hapMapTranslate.put("NA18967", "jap25 NA18967 0 0 1 0"); hapMapTranslate.put("NA18978", "jap26 NA18978 0 0 2 0"); hapMapTranslate.put("NA18970", "jap27 NA18970 0 0 1 0"); hapMapTranslate.put("NA18980", "jap28 NA18980 0 0 2 0"); hapMapTranslate.put("NA18995", "jap29 NA18995 0 0 1 0"); hapMapTranslate.put("NA18621", "chi29 NA18621 0 0 1 0"); hapMapTranslate.put("NA18594", "chi30 NA18594 0 0 2 0"); hapMapTranslate.put("NA18622", "chi31 NA18622 0 0 1 0"); hapMapTranslate.put("NA18573", "chi32 NA18573 0 0 2 0"); hapMapTranslate.put("NA18623", "chi33 NA18623 0 0 1 0"); hapMapTranslate.put("NA18576", "chi34 NA18576 0 0 2 0"); hapMapTranslate.put("NA18971", "jap30 NA18971 0 0 1 0"); hapMapTranslate.put("NA18981", "jap31 NA18981 0 0 2 0"); hapMapTranslate.put("NA18974", "jap32 NA18974 0 0 1 0"); hapMapTranslate.put("NA18987", "jap33 NA18987 0 0 2 0"); hapMapTranslate.put("NA18990", "jap34 NA18990 0 0 1 0"); hapMapTranslate.put("NA18991", "jap35 NA18991 0 0 2 0"); hapMapTranslate.put("NA18577", "chi35 NA18577 0 0 2 0"); hapMapTranslate.put("NA18624", "chi36 NA18624 0 0 1 0"); hapMapTranslate.put("NA18579", "chi37 NA18579 0 0 2 0"); hapMapTranslate.put("NA18632", "chi38 NA18632 0 0 1 0"); hapMapTranslate.put("NA18582", "chi39 NA18582 0 0 2 0"); hapMapTranslate.put("NA18633", "chi40 NA18633 0 0 1 0"); hapMapTranslate.put("NA18994", "jap36 NA18994 0 0 1 0"); hapMapTranslate.put("NA18992", "jap37 NA18992 0 0 2 0"); hapMapTranslate.put("NA18997", "jap38 NA18997 0 0 2 0"); hapMapTranslate.put("NA18996", "jap39 NA18996 0 0 1 0"); hapMapTranslate.put("NA18635", "chi41 NA18635 0 0 1 0"); hapMapTranslate.put("NA18592", "chi42 NA18592 0 0 2 0"); hapMapTranslate.put("NA18636", "chi43 NA18636 0 0 1 0"); hapMapTranslate.put("NA18593", "chi44 NA18593 0 0 2 0"); hapMapTranslate.put("NA18637", "chi45 NA18637 0 0 1 0"); hapMapTranslate.put("NA19000", "jap40 NA19000 0 0 1 0"); hapMapTranslate.put("NA18998", "jap41 NA18998 0 0 2 0"); hapMapTranslate.put("NA19005", "jap42 NA19005 0 0 1 0"); hapMapTranslate.put("NA18999", "jap43 NA18999 0 0 2 0"); hapMapTranslate.put("NA19007", "jap44 NA19007 0 0 1 0"); hapMapTranslate.put("NA19003", "jap45 NA19003 0 0 2 0"); hapMapTranslate.put("NA18500", "Yoruba004 NA18500 NA18501 NA18502 1 0"); hapMapTranslate.put("NA18501", "Yoruba004 NA18501 0 0 1 0"); hapMapTranslate.put("NA18502", "Yoruba004 NA18502 0 0 2 0"); hapMapTranslate.put("NA18503", "Yoruba005 NA18503 NA18504 NA18505 1 0"); hapMapTranslate.put("NA18504", "Yoruba005 NA18504 0 0 1 0"); hapMapTranslate.put("NA18505", "Yoruba005 NA18505 0 0 2 0"); hapMapTranslate.put("NA18506", "Yoruba009 NA18506 NA18507 NA18508 1 0"); hapMapTranslate.put("NA18507", "Yoruba009 NA18507 0 0 1 0"); hapMapTranslate.put("NA18508", "Yoruba009 NA18508 0 0 2 0"); hapMapTranslate.put("NA18860", "Yoruba012 NA18860 NA18859 NA18858 1 0"); hapMapTranslate.put("NA18859", "Yoruba012 NA18859 0 0 1 0"); hapMapTranslate.put("NA18858", "Yoruba012 NA18858 0 0 2 0"); hapMapTranslate.put("NA18515", "Yoruba013 NA18515 NA18516 NA18517 1 0"); hapMapTranslate.put("NA18516", "Yoruba013 NA18516 0 0 1 0"); hapMapTranslate.put("NA18517", "Yoruba013 NA18517 0 0 2 0"); hapMapTranslate.put("NA18521", "Yoruba016 NA18521 NA18522 NA18523 1 0"); hapMapTranslate.put("NA18522", "Yoruba016 NA18522 0 0 1 0"); hapMapTranslate.put("NA18523", "Yoruba016 NA18523 0 0 2 0"); hapMapTranslate.put("NA18872", "Yoruba017 NA18872 NA18871 NA18870 1 0"); hapMapTranslate.put("NA18871", "Yoruba017 NA18871 0 0 1 0"); hapMapTranslate.put("NA18870", "Yoruba017 NA18870 0 0 2 0"); hapMapTranslate.put("NA18854", "Yoruba018 NA18854 NA18853 NA18852 1 0"); hapMapTranslate.put("NA18853", "Yoruba018 NA18853 0 0 1 0"); hapMapTranslate.put("NA18852", "Yoruba018 NA18852 0 0 2 0"); hapMapTranslate.put("NA18857", "Yoruba023 NA18857 NA18856 NA18855 1 0"); hapMapTranslate.put("NA18856", "Yoruba023 NA18856 0 0 1 0"); hapMapTranslate.put("NA18855", "Yoruba023 NA18855 0 0 2 0"); hapMapTranslate.put("NA18863", "Yoruba024 NA18863 NA18862 NA18861 1 0"); hapMapTranslate.put("NA18862", "Yoruba024 NA18862 0 0 1 0"); hapMapTranslate.put("NA18861", "Yoruba024 NA18861 0 0 2 0"); hapMapTranslate.put("NA18914", "Yoruba028 NA18914 NA18913 NA18912 1 0"); hapMapTranslate.put("NA18913", "Yoruba028 NA18913 0 0 1 0"); hapMapTranslate.put("NA18912", "Yoruba028 NA18912 0 0 2 0"); hapMapTranslate.put("NA19094", "Yoruba040 NA19094 NA19092 NA19093 2 0"); hapMapTranslate.put("NA19092", "Yoruba040 NA19092 0 0 1 0"); hapMapTranslate.put("NA19093", "Yoruba040 NA19093 0 0 2 0"); hapMapTranslate.put("NA19103", "Yoruba042 NA19103 NA19101 NA19102 1 0"); hapMapTranslate.put("NA19101", "Yoruba042 NA19101 0 0 1 0"); hapMapTranslate.put("NA19102", "Yoruba042 NA19102 0 0 2 0"); hapMapTranslate.put("NA19139", "Yoruba043 NA19139 NA19138 NA19137 1 0"); hapMapTranslate.put("NA19138", "Yoruba043 NA19138 0 0 1 0"); hapMapTranslate.put("NA19137", "Yoruba043 NA19137 0 0 2 0"); hapMapTranslate.put("NA19202", "Yoruba045 NA19202 NA19200 NA19201 2 0"); hapMapTranslate.put("NA19200", "Yoruba045 NA19200 0 0 1 0"); hapMapTranslate.put("NA19201", "Yoruba045 NA19201 0 0 2 0"); hapMapTranslate.put("NA19173", "Yoruba047 NA19173 NA19171 NA19172 1 0"); hapMapTranslate.put("NA19171", "Yoruba047 NA19171 0 0 1 0"); hapMapTranslate.put("NA19172", "Yoruba047 NA19172 0 0 2 0"); hapMapTranslate.put("NA19205", "Yoruba048 NA19205 NA19203 NA19204 1 0"); hapMapTranslate.put("NA19203", "Yoruba048 NA19203 0 0 1 0"); hapMapTranslate.put("NA19204", "Yoruba048 NA19204 0 0 2 0"); hapMapTranslate.put("NA19211", "Yoruba050 NA19211 NA19210 NA19209 1 0"); hapMapTranslate.put("NA19210", "Yoruba050 NA19210 0 0 1 0"); hapMapTranslate.put("NA19209", "Yoruba050 NA19209 0 0 2 0"); hapMapTranslate.put("NA19208", "Yoruba051 NA19208 NA19207 NA19206 1 0"); hapMapTranslate.put("NA19207", "Yoruba051 NA19207 0 0 1 0"); hapMapTranslate.put("NA19206", "Yoruba051 NA19206 0 0 2 0"); hapMapTranslate.put("NA19161", "Yoruba056 NA19161 NA19160 NA19159 1 0"); hapMapTranslate.put("NA19160", "Yoruba056 NA19160 0 0 1 0"); hapMapTranslate.put("NA19159", "Yoruba056 NA19159 0 0 2 0"); hapMapTranslate.put("NA19221", "Yoruba058 NA19221 NA19223 NA19222 2 0"); hapMapTranslate.put("NA19223", "Yoruba058 NA19223 0 0 1 0"); hapMapTranslate.put("NA19222", "Yoruba058 NA19222 0 0 2 0"); hapMapTranslate.put("NA19120", "Yoruba060 NA19120 NA19119 NA19116 1 0"); hapMapTranslate.put("NA19119", "Yoruba060 NA19119 0 0 1 0"); hapMapTranslate.put("NA19116", "Yoruba060 NA19116 0 0 2 0"); hapMapTranslate.put("NA19142", "Yoruba071 NA19142 NA19141 NA19140 1 0"); hapMapTranslate.put("NA19141", "Yoruba071 NA19141 0 0 1 0"); hapMapTranslate.put("NA19140", "Yoruba071 NA19140 0 0 2 0"); hapMapTranslate.put("NA19154", "Yoruba072 NA19154 NA19153 NA19152 1 0"); hapMapTranslate.put("NA19153", "Yoruba072 NA19153 0 0 1 0"); hapMapTranslate.put("NA19152", "Yoruba072 NA19152 0 0 2 0"); hapMapTranslate.put("NA19145", "Yoruba074 NA19145 NA19144 NA19143 1 0"); hapMapTranslate.put("NA19144", "Yoruba074 NA19144 0 0 1 0"); hapMapTranslate.put("NA19143", "Yoruba074 NA19143 0 0 2 0"); hapMapTranslate.put("NA19129", "Yoruba077 NA19129 NA19128 NA19127 2 0"); hapMapTranslate.put("NA19128", "Yoruba077 NA19128 0 0 1 0"); hapMapTranslate.put("NA19127", "Yoruba077 NA19127 0 0 2 0"); hapMapTranslate.put("NA19132", "Yoruba101 NA19132 NA19130 NA19131 2 0"); hapMapTranslate.put("NA19130", "Yoruba101 NA19130 0 0 1 0"); hapMapTranslate.put("NA19131", "Yoruba101 NA19131 0 0 2 0"); hapMapTranslate.put("NA19100", "Yoruba105 NA19100 NA19098 NA19099 2 0"); hapMapTranslate.put("NA19098", "Yoruba105 NA19098 0 0 1 0"); hapMapTranslate.put("NA19099", "Yoruba105 NA19099 0 0 2 0"); hapMapTranslate.put("NA19194", "Yoruba112 NA19194 NA19192 NA19193 1 0"); hapMapTranslate.put("NA19192", "Yoruba112 NA19192 0 0 1 0"); hapMapTranslate.put("NA19193", "Yoruba112 NA19193 0 0 2 0"); hapMapTranslate.put("NA19240", "Yoruba117 NA19240 NA19239 NA19238 2 0"); hapMapTranslate.put("NA19239", "Yoruba117 NA19239 0 0 1 0"); hapMapTranslate.put("NA19238", "Yoruba117 NA19238 0 0 2 0"); }

1,110,235

public PedFile(){ //hardcoded hapmap info this.families = new Hashtable(); hapMapTranslate = new Hashtable(90,1); hapMapTranslate.put("NA10846", "1334 NA10846 NA12144 NA12145 1 0" ); hapMapTranslate.put("NA12144", "1334 NA12144 0 0 1 0"); hapMapTranslate.put("NA12145", "1334 NA12145 0 0 2 0"); hapMapTranslate.put("NA10847", "1334 NA10847 NA12146 NA12239 2 0" ); hapMapTranslate.put("NA12146", "1334 NA12146 0 0 1 0"); hapMapTranslate.put("NA12239", "1334 NA12239 0 0 2 0"); hapMapTranslate.put("NA07029", "1340 NA07029 NA06994 NA07000 1 0" ); hapMapTranslate.put("NA06994", "1340 NA06994 0 0 1 0"); hapMapTranslate.put("NA07000", "1340 NA07000 0 0 2 0"); hapMapTranslate.put("NA07019", "1340 NA07019 NA07022 NA07056 2 0" ); hapMapTranslate.put("NA07022", "1340 NA07022 0 0 1 0"); hapMapTranslate.put("NA07056", "1340 NA07056 0 0 2 0"); hapMapTranslate.put("NA07048", "1341 NA07048 NA07034 NA07055 1 0" ); hapMapTranslate.put("NA07034", "1341 NA07034 0 0 1 0"); hapMapTranslate.put("NA07055", "1341 NA07055 0 0 2 0"); hapMapTranslate.put("NA06991", "1341 NA06991 NA06993 NA06985 2 0" ); hapMapTranslate.put("NA06993", "1341 NA06993 0 0 1 0"); hapMapTranslate.put("NA06993.dup", "dup NA06993.dup 0 0 1 0"); hapMapTranslate.put("NA06985", "1341 NA06985 0 0 2 0"); hapMapTranslate.put("NA10851", "1344 NA10851 NA12056 NA12057 1 0" ); hapMapTranslate.put("NA12056", "1344 NA12056 0 0 1 0"); hapMapTranslate.put("NA12057", "1344 NA12057 0 0 2 0"); hapMapTranslate.put("NA07348", "1345 NA07348 NA07357 NA07345 2 0" ); hapMapTranslate.put("NA07357", "1345 NA07357 0 0 1 0"); hapMapTranslate.put("NA07345", "1345 NA07345 0 0 2 0"); hapMapTranslate.put("NA10857", "1346 NA10857 NA12043 NA12044 1 0" ); hapMapTranslate.put("NA12043", "1346 NA12043 0 0 1 0"); hapMapTranslate.put("NA12044", "1346 NA12044 0 0 2 0"); hapMapTranslate.put("NA10859", "1347 NA10859 NA11881 NA11882 2 0" ); hapMapTranslate.put("NA11881", "1347 NA11881 0 0 1 0"); hapMapTranslate.put("NA11882", "1347 NA11882 0 0 2 0"); hapMapTranslate.put("NA10854", "1349 NA10854 NA11839 NA11840 2 0" ); hapMapTranslate.put("NA11839", "1349 NA11839 0 0 1 0"); hapMapTranslate.put("NA11840", "1349 NA11840 0 0 2 0"); hapMapTranslate.put("NA10856", "1350 NA10856 NA11829 NA11830 1 0" ); hapMapTranslate.put("NA11829", "1350 NA11829 0 0 1 0"); hapMapTranslate.put("NA11830", "1350 NA11830 0 0 2 0"); hapMapTranslate.put("NA10855", "1350 NA10855 NA11831 NA11832 2 0" ); hapMapTranslate.put("NA11831", "1350 NA11831 0 0 1 0"); hapMapTranslate.put("NA11832", "1350 NA11832 0 0 2 0"); hapMapTranslate.put("NA12707", "1358 NA12707 NA12716 NA12717 1 0" ); hapMapTranslate.put("NA12716", "1358 NA12716 0 0 1 0"); hapMapTranslate.put("NA12717", "1358 NA12717 0 0 2 0"); hapMapTranslate.put("NA10860", "1362 NA10860 NA11992 NA11993 1 0" ); hapMapTranslate.put("NA11992", "1362 NA11992 0 0 1 0"); hapMapTranslate.put("NA11993", "1362 NA11993 0 0 2 0"); hapMapTranslate.put("NA11993.dup", "dup NA11993.dup 0 0 2 0"); hapMapTranslate.put("NA10861", "1362 NA10861 NA11994 NA11995 2 0" ); hapMapTranslate.put("NA11994", "1362 NA11994 0 0 1 0"); hapMapTranslate.put("NA11995", "1362 NA11995 0 0 2 0"); hapMapTranslate.put("NA10863", "1375 NA10863 NA12264 NA12234 2 0" ); hapMapTranslate.put("NA12264", "1375 NA12264 0 0 1 0"); hapMapTranslate.put("NA12234", "1375 NA12234 0 0 2 0"); hapMapTranslate.put("NA10830", "1408 NA10830 NA12154 NA12236 1 0" ); hapMapTranslate.put("NA12154", "1408 NA12154 0 0 1 0"); hapMapTranslate.put("NA12236", "1408 NA12236 0 0 2 0"); hapMapTranslate.put("NA10831", "1408 NA10831 NA12155 NA12156 2 0" ); hapMapTranslate.put("NA12155", "1408 NA12155 0 0 1 0"); hapMapTranslate.put("NA12156", "1408 NA12156 0 0 2 0"); hapMapTranslate.put("NA12156.dup", "dup NA12156.dup 0 0 2 0"); hapMapTranslate.put("NA10835", "1416 NA10835 NA12248 NA12249 1 0" ); hapMapTranslate.put("NA12248", "1416 NA12248 0 0 1 0"); hapMapTranslate.put("NA12248.dup", "dup NA1248.dup 0 0 1 0"); hapMapTranslate.put("NA12249", "1416 NA12249 0 0 2 0"); hapMapTranslate.put("NA10838", "1420 NA10838 NA12003 NA12004 1 0" ); hapMapTranslate.put("NA12003", "1420 NA12003 0 0 1 0"); hapMapTranslate.put("NA12003.dup", "dup NA12003.dup 0 0 1 0"); hapMapTranslate.put("NA12004", "1420 NA12004 0 0 2 0"); hapMapTranslate.put("NA10839", "1420 NA10839 NA12005 NA12006 2 0" ); hapMapTranslate.put("NA12005", "1420 NA12005 0 0 1 0"); hapMapTranslate.put("NA12006", "1420 NA12006 0 0 2 0"); hapMapTranslate.put("NA12740", "1444 NA12740 NA12750 NA12751 2 0" ); hapMapTranslate.put("NA12750", "1444 NA12750 0 0 1 0"); hapMapTranslate.put("NA12751", "1444 NA12751 0 0 2 0"); hapMapTranslate.put("NA12752", "1447 NA12752 NA12760 NA12761 1 0" ); hapMapTranslate.put("NA12760", "1447 NA12760 0 0 1 0"); hapMapTranslate.put("NA12761", "1447 NA12761 0 0 2 0"); hapMapTranslate.put("NA12753", "1447 NA12753 NA12762 NA12763 2 0" ); hapMapTranslate.put("NA12762", "1447 NA12762 0 0 1 0"); hapMapTranslate.put("NA12763", "1447 NA12763 0 0 2 0"); hapMapTranslate.put("NA12801", "1454 NA12801 NA12812 NA12813 1 0" ); hapMapTranslate.put("NA12812", "1454 NA12812 0 0 1 0"); hapMapTranslate.put("NA12813", "1454 NA12813 0 0 2 0"); hapMapTranslate.put("NA12802", "1454 NA12802 NA12814 NA12815 2 0" ); hapMapTranslate.put("NA12814", "1454 NA12814 0 0 1 0"); hapMapTranslate.put("NA12815", "1454 NA12815 0 0 2 0"); hapMapTranslate.put("NA12864", "1459 NA12864 NA12872 NA12873 1 0" ); hapMapTranslate.put("NA12872", "1459 NA12872 0 0 1 0"); hapMapTranslate.put("NA12873", "1459 NA12873 0 0 2 0"); hapMapTranslate.put("NA12865", "1459 NA12865 NA12874 NA12875 2 0" ); hapMapTranslate.put("NA12874", "1459 NA12874 0 0 1 0"); hapMapTranslate.put("NA12875", "1459 NA12875 0 0 2 0"); hapMapTranslate.put("NA12878", "1463 NA12878 NA12891 NA12892 2 0" ); hapMapTranslate.put("NA12891", "1463 NA12891 0 0 1 0"); hapMapTranslate.put("NA12892", "1463 NA12892 0 0 2 0"); hapMapTranslate.put("NA18526", "chi1 NA18526 0 0 2 0"); hapMapTranslate.put("NA18524", "chi2 NA18524 0 0 1 0"); hapMapTranslate.put("NA18529", "chi3 NA18529 0 0 2 0"); hapMapTranslate.put("NA18558", "chi4 NA18558 0 0 1 0"); hapMapTranslate.put("NA18532", "chi5 NA18532 0 0 2 0"); hapMapTranslate.put("NA18561", "chi6 NA18561 0 0 1 0"); hapMapTranslate.put("NA18942", "jap1 NA18942 0 0 2 0"); hapMapTranslate.put("NA18940", "jap2 NA18940 0 0 1 0"); hapMapTranslate.put("NA18951", "jap3 NA18951 0 0 2 0"); hapMapTranslate.put("NA18943", "jap4 NA18943 0 0 1 0"); hapMapTranslate.put("NA18947", "jap5 NA18947 0 0 2 0"); hapMapTranslate.put("NA18944", "jap6 NA18944 0 0 1 0"); hapMapTranslate.put("NA18562", "chi7 NA18562 0 0 1 0"); hapMapTranslate.put("NA18537", "chi8 NA18537 0 0 2 0"); hapMapTranslate.put("NA18603", "chi9 NA18603 0 0 1 0"); hapMapTranslate.put("NA18540", "chi10 NA18540 0 0 2 0"); hapMapTranslate.put("NA18605", "chi11 NA18605 0 0 1 0"); hapMapTranslate.put("NA18542", "chi12 NA18542 0 0 2 0"); hapMapTranslate.put("NA18945", "jap7 NA18945 0 0 1 0"); hapMapTranslate.put("NA18949", "jap8 NA18949 0 0 2 0"); hapMapTranslate.put("NA18948", "jap9 NA18948 0 0 1 0"); hapMapTranslate.put("NA18952", "jap10 NA18952 0 0 1 0"); hapMapTranslate.put("NA18956", "jap11 NA18956 0 0 2 0"); hapMapTranslate.put("NA18545", "chi13 NA18545 0 0 2 0"); hapMapTranslate.put("NA18572", "chi46 NA18572 0 0 1 0"); hapMapTranslate.put("NA18547", "chi15 NA18547 0 0 2 0"); hapMapTranslate.put("NA18609", "chi16 NA18609 0 0 1 0"); hapMapTranslate.put("NA18550", "chi17 NA18550 0 0 2 0"); hapMapTranslate.put("NA18608", "chi18 NA18608 0 0 1 0"); hapMapTranslate.put("NA18964", "jap12 NA18964 0 0 2 0"); hapMapTranslate.put("NA18953", "jap13 NA18953 0 0 1 0"); hapMapTranslate.put("NA18968", "jap14 NA18968 0 0 2 0"); hapMapTranslate.put("NA18959", "jap15 NA18959 0 0 1 0"); hapMapTranslate.put("NA18969", "jap16 NA18969 0 0 2 0"); hapMapTranslate.put("NA18960", "jap17 NA18960 0 0 1 0"); hapMapTranslate.put("NA18552", "chi19 NA18552 0 0 2 0"); hapMapTranslate.put("NA18611", "chi20 NA18611 0 0 1 0"); hapMapTranslate.put("NA18555", "chi21 NA18555 0 0 2 0"); hapMapTranslate.put("NA18564", "chi22 NA18564 0 0 2 0"); hapMapTranslate.put("NA18961", "jap18 NA18961 0 0 1 0"); hapMapTranslate.put("NA18972", "jap19 NA18972 0 0 2 0"); hapMapTranslate.put("NA18965", "jap20 NA18965 0 0 1 0"); hapMapTranslate.put("NA18973", "jap21 NA18973 0 0 2 0"); hapMapTranslate.put("NA18966", "jap22 NA18966 0 0 1 0"); hapMapTranslate.put("NA18975", "jap23 NA18975 0 0 2 0"); hapMapTranslate.put("NA18566", "chi23 NA18566 0 0 2 0"); hapMapTranslate.put("NA18563", "chi24 NA18563 0 0 1 0"); hapMapTranslate.put("NA18570", "chi25 NA18570 0 0 2 0"); hapMapTranslate.put("NA18612", "chi26 NA18612 0 0 1 0"); hapMapTranslate.put("NA18571", "chi27 NA18571 0 0 2 0"); hapMapTranslate.put("NA18620", "chi28 NA18620 0 0 1 0"); hapMapTranslate.put("NA18976", "jap24 NA18976 0 0 2 0"); hapMapTranslate.put("NA18967", "jap25 NA18967 0 0 1 0"); hapMapTranslate.put("NA18978", "jap26 NA18978 0 0 2 0"); hapMapTranslate.put("NA18970", "jap27 NA18970 0 0 1 0"); hapMapTranslate.put("NA18980", "jap28 NA18980 0 0 2 0"); hapMapTranslate.put("NA18995", "jap29 NA18995 0 0 1 0"); hapMapTranslate.put("NA18621", "chi29 NA18621 0 0 1 0"); hapMapTranslate.put("NA18594", "chi30 NA18594 0 0 2 0"); hapMapTranslate.put("NA18622", "chi31 NA18622 0 0 1 0"); hapMapTranslate.put("NA18573", "chi32 NA18573 0 0 2 0"); hapMapTranslate.put("NA18623", "chi33 NA18623 0 0 1 0"); hapMapTranslate.put("NA18576", "chi34 NA18576 0 0 2 0"); hapMapTranslate.put("NA18971", "jap30 NA18971 0 0 1 0"); hapMapTranslate.put("NA18981", "jap31 NA18981 0 0 2 0"); hapMapTranslate.put("NA18974", "jap32 NA18974 0 0 1 0"); hapMapTranslate.put("NA18987", "jap33 NA18987 0 0 2 0"); hapMapTranslate.put("NA18990", "jap34 NA18990 0 0 1 0"); hapMapTranslate.put("NA18991", "jap35 NA18991 0 0 2 0"); hapMapTranslate.put("NA18577", "chi35 NA18577 0 0 2 0"); hapMapTranslate.put("NA18624", "chi36 NA18624 0 0 1 0"); hapMapTranslate.put("NA18579", "chi37 NA18579 0 0 2 0"); hapMapTranslate.put("NA18632", "chi38 NA18632 0 0 1 0"); hapMapTranslate.put("NA18582", "chi39 NA18582 0 0 2 0"); hapMapTranslate.put("NA18633", "chi40 NA18633 0 0 1 0"); hapMapTranslate.put("NA18994", "jap36 NA18994 0 0 1 0"); hapMapTranslate.put("NA18992", "jap37 NA18992 0 0 2 0"); hapMapTranslate.put("NA18997", "jap38 NA18997 0 0 2 0"); hapMapTranslate.put("NA18996", "jap39 NA18996 0 0 1 0"); hapMapTranslate.put("NA18635", "chi41 NA18635 0 0 1 0"); hapMapTranslate.put("NA18592", "chi42 NA18592 0 0 2 0"); hapMapTranslate.put("NA18636", "chi43 NA18636 0 0 1 0"); hapMapTranslate.put("NA18593", "chi44 NA18593 0 0 2 0"); hapMapTranslate.put("NA18637", "chi45 NA18637 0 0 1 0"); hapMapTranslate.put("NA19000", "jap40 NA19000 0 0 1 0"); hapMapTranslate.put("NA18998", "jap41 NA18998 0 0 2 0"); hapMapTranslate.put("NA19005", "jap42 NA19005 0 0 1 0"); hapMapTranslate.put("NA18999", "jap43 NA18999 0 0 2 0"); hapMapTranslate.put("NA19007", "jap44 NA19007 0 0 1 0"); hapMapTranslate.put("NA19003", "jap45 NA19003 0 0 2 0"); hapMapTranslate.put("NA18500", "Yoruba004 NA18500 NA18501 NA18502 1 0"); hapMapTranslate.put("NA18501", "Yoruba004 NA18501 0 0 1 0"); hapMapTranslate.put("NA18502", "Yoruba004 NA18502 0 0 2 0"); hapMapTranslate.put("NA18503", "Yoruba005 NA18503 NA18504 NA18505 1 0"); hapMapTranslate.put("NA18504", "Yoruba005 NA18504 0 0 1 0"); hapMapTranslate.put("NA18505", "Yoruba005 NA18505 0 0 2 0"); hapMapTranslate.put("NA18506", "Yoruba009 NA18506 NA18507 NA18508 1 0"); hapMapTranslate.put("NA18507", "Yoruba009 NA18507 0 0 1 0"); hapMapTranslate.put("NA18508", "Yoruba009 NA18508 0 0 2 0"); hapMapTranslate.put("NA18860", "Yoruba012 NA18860 NA18859 NA18858 1 0"); hapMapTranslate.put("NA18859", "Yoruba012 NA18859 0 0 1 0"); hapMapTranslate.put("NA18858", "Yoruba012 NA18858 0 0 2 0"); hapMapTranslate.put("NA18515", "Yoruba013 NA18515 NA18516 NA18517 1 0"); hapMapTranslate.put("NA18516", "Yoruba013 NA18516 0 0 1 0"); hapMapTranslate.put("NA18517", "Yoruba013 NA18517 0 0 2 0"); hapMapTranslate.put("NA18521", "Yoruba016 NA18521 NA18522 NA18523 1 0"); hapMapTranslate.put("NA18522", "Yoruba016 NA18522 0 0 1 0"); hapMapTranslate.put("NA18523", "Yoruba016 NA18523 0 0 2 0"); hapMapTranslate.put("NA18872", "Yoruba017 NA18872 NA18871 NA18870 1 0"); hapMapTranslate.put("NA18871", "Yoruba017 NA18871 0 0 1 0"); hapMapTranslate.put("NA18870", "Yoruba017 NA18870 0 0 2 0"); hapMapTranslate.put("NA18854", "Yoruba018 NA18854 NA18853 NA18852 1 0"); hapMapTranslate.put("NA18853", "Yoruba018 NA18853 0 0 1 0"); hapMapTranslate.put("NA18852", "Yoruba018 NA18852 0 0 2 0"); hapMapTranslate.put("NA18857", "Yoruba023 NA18857 NA18856 NA18855 1 0"); hapMapTranslate.put("NA18856", "Yoruba023 NA18856 0 0 1 0"); hapMapTranslate.put("NA18855", "Yoruba023 NA18855 0 0 2 0"); hapMapTranslate.put("NA18863", "Yoruba024 NA18863 NA18862 NA18861 1 0"); hapMapTranslate.put("NA18862", "Yoruba024 NA18862 0 0 1 0"); hapMapTranslate.put("NA18861", "Yoruba024 NA18861 0 0 2 0"); hapMapTranslate.put("NA18914", "Yoruba028 NA18914 NA18913 NA18912 1 0"); hapMapTranslate.put("NA18913", "Yoruba028 NA18913 0 0 1 0"); hapMapTranslate.put("NA18912", "Yoruba028 NA18912 0 0 2 0"); hapMapTranslate.put("NA19094", "Yoruba040 NA19094 NA19092 NA19093 2 0"); hapMapTranslate.put("NA19092", "Yoruba040 NA19092 0 0 1 0"); hapMapTranslate.put("NA19093", "Yoruba040 NA19093 0 0 2 0"); hapMapTranslate.put("NA19103", "Yoruba042 NA19103 NA19101 NA19102 1 0"); hapMapTranslate.put("NA19101", "Yoruba042 NA19101 0 0 1 0"); hapMapTranslate.put("NA19102", "Yoruba042 NA19102 0 0 2 0"); hapMapTranslate.put("NA19139", "Yoruba043 NA19139 NA19138 NA19137 1 0"); hapMapTranslate.put("NA19138", "Yoruba043 NA19138 0 0 1 0"); hapMapTranslate.put("NA19137", "Yoruba043 NA19137 0 0 2 0"); hapMapTranslate.put("NA19202", "Yoruba045 NA19202 NA19200 NA19201 2 0"); hapMapTranslate.put("NA19200", "Yoruba045 NA19200 0 0 1 0"); hapMapTranslate.put("NA19201", "Yoruba045 NA19201 0 0 2 0"); hapMapTranslate.put("NA19173", "Yoruba047 NA19173 NA19171 NA19172 1 0"); hapMapTranslate.put("NA19171", "Yoruba047 NA19171 0 0 1 0"); hapMapTranslate.put("NA19172", "Yoruba047 NA19172 0 0 2 0"); hapMapTranslate.put("NA19205", "Yoruba048 NA19205 NA19203 NA19204 1 0"); hapMapTranslate.put("NA19203", "Yoruba048 NA19203 0 0 1 0"); hapMapTranslate.put("NA19204", "Yoruba048 NA19204 0 0 2 0"); hapMapTranslate.put("NA19211", "Yoruba050 NA19211 NA19210 NA19209 1 0"); hapMapTranslate.put("NA19210", "Yoruba050 NA19210 0 0 1 0"); hapMapTranslate.put("NA19209", "Yoruba050 NA19209 0 0 2 0"); hapMapTranslate.put("NA19208", "Yoruba051 NA19208 NA19207 NA19206 1 0"); hapMapTranslate.put("NA19207", "Yoruba051 NA19207 0 0 1 0"); hapMapTranslate.put("NA19206", "Yoruba051 NA19206 0 0 2 0"); hapMapTranslate.put("NA19161", "Yoruba056 NA19161 NA19160 NA19159 1 0"); hapMapTranslate.put("NA19160", "Yoruba056 NA19160 0 0 1 0"); hapMapTranslate.put("NA19159", "Yoruba056 NA19159 0 0 2 0"); hapMapTranslate.put("NA19221", "Yoruba058 NA19221 NA19223 NA19222 2 0"); hapMapTranslate.put("NA19223", "Yoruba058 NA19223 0 0 1 0"); hapMapTranslate.put("NA19222", "Yoruba058 NA19222 0 0 2 0"); hapMapTranslate.put("NA19120", "Yoruba060 NA19120 NA19119 NA19116 1 0"); hapMapTranslate.put("NA19119", "Yoruba060 NA19119 0 0 1 0"); hapMapTranslate.put("NA19116", "Yoruba060 NA19116 0 0 2 0"); hapMapTranslate.put("NA19142", "Yoruba071 NA19142 NA19141 NA19140 1 0"); hapMapTranslate.put("NA19141", "Yoruba071 NA19141 0 0 1 0"); hapMapTranslate.put("NA19140", "Yoruba071 NA19140 0 0 2 0"); hapMapTranslate.put("NA19154", "Yoruba072 NA19154 NA19153 NA19152 1 0"); hapMapTranslate.put("NA19153", "Yoruba072 NA19153 0 0 1 0"); hapMapTranslate.put("NA19152", "Yoruba072 NA19152 0 0 2 0"); hapMapTranslate.put("NA19145", "Yoruba074 NA19145 NA19144 NA19143 1 0"); hapMapTranslate.put("NA19144", "Yoruba074 NA19144 0 0 1 0"); hapMapTranslate.put("NA19143", "Yoruba074 NA19143 0 0 2 0"); hapMapTranslate.put("NA19129", "Yoruba077 NA19129 NA19128 NA19127 2 0"); hapMapTranslate.put("NA19128", "Yoruba077 NA19128 0 0 1 0"); hapMapTranslate.put("NA19127", "Yoruba077 NA19127 0 0 2 0"); hapMapTranslate.put("NA19132", "Yoruba101 NA19132 NA19130 NA19131 2 0"); hapMapTranslate.put("NA19130", "Yoruba101 NA19130 0 0 1 0"); hapMapTranslate.put("NA19131", "Yoruba101 NA19131 0 0 2 0"); hapMapTranslate.put("NA19100", "Yoruba105 NA19100 NA19098 NA19099 2 0"); hapMapTranslate.put("NA19098", "Yoruba105 NA19098 0 0 1 0"); hapMapTranslate.put("NA19099", "Yoruba105 NA19099 0 0 2 0"); hapMapTranslate.put("NA19194", "Yoruba112 NA19194 NA19192 NA19193 1 0"); hapMapTranslate.put("NA19192", "Yoruba112 NA19192 0 0 1 0"); hapMapTranslate.put("NA19193", "Yoruba112 NA19193 0 0 2 0"); hapMapTranslate.put("NA19240", "Yoruba117 NA19240 NA19239 NA19238 2 0"); hapMapTranslate.put("NA19239", "Yoruba117 NA19239 0 0 1 0"); hapMapTranslate.put("NA19238", "Yoruba117 NA19238 0 0 2 0"); }

public PedFile(){ //hardcoded hapmap info this.families = new Hashtable(); hapMapTranslate = new Hashtable(90,1); hapMapTranslate.put("NA10846", "1334 NA10846 NA12144 NA12145 1 0" ); hapMapTranslate.put("NA12144", "1334 NA12144 0 0 1 0"); hapMapTranslate.put("NA12145", "1334 NA12145 0 0 2 0"); hapMapTranslate.put("NA10847", "1334 NA10847 NA12146 NA12239 2 0" ); hapMapTranslate.put("NA12146", "1334 NA12146 0 0 1 0"); hapMapTranslate.put("NA12239", "1334 NA12239 0 0 2 0"); hapMapTranslate.put("NA07029", "1340 NA07029 NA06994 NA07000 1 0" ); hapMapTranslate.put("NA06994", "1340 NA06994 0 0 1 0"); hapMapTranslate.put("NA07000", "1340 NA07000 0 0 2 0"); hapMapTranslate.put("NA07019", "1340 NA07019 NA07022 NA07056 2 0" ); hapMapTranslate.put("NA07022", "1340 NA07022 0 0 1 0"); hapMapTranslate.put("NA07056", "1340 NA07056 0 0 2 0"); hapMapTranslate.put("NA07048", "1341 NA07048 NA07034 NA07055 1 0" ); hapMapTranslate.put("NA07034", "1341 NA07034 0 0 1 0"); hapMapTranslate.put("NA07055", "1341 NA07055 0 0 2 0"); hapMapTranslate.put("NA06991", "1341 NA06991 NA06993 NA06985 2 0" ); hapMapTranslate.put("NA06993", "1341 NA06993 0 0 1 0"); hapMapTranslate.put("NA06993.dup", "dup NA06993.dup 0 0 1 0"); hapMapTranslate.put("NA06985", "1341 NA06985 0 0 2 0"); hapMapTranslate.put("NA10851", "1344 NA10851 NA12056 NA12057 1 0" ); hapMapTranslate.put("NA12056", "1344 NA12056 0 0 1 0"); hapMapTranslate.put("NA12057", "1344 NA12057 0 0 2 0"); hapMapTranslate.put("NA07348", "1345 NA07348 NA07357 NA07345 2 0" ); hapMapTranslate.put("NA07357", "1345 NA07357 0 0 1 0"); hapMapTranslate.put("NA07345", "1345 NA07345 0 0 2 0"); hapMapTranslate.put("NA10857", "1346 NA10857 NA12043 NA12044 1 0" ); hapMapTranslate.put("NA12043", "1346 NA12043 0 0 1 0"); hapMapTranslate.put("NA12044", "1346 NA12044 0 0 2 0"); hapMapTranslate.put("NA10859", "1347 NA10859 NA11881 NA11882 2 0" ); hapMapTranslate.put("NA11881", "1347 NA11881 0 0 1 0"); hapMapTranslate.put("NA11882", "1347 NA11882 0 0 2 0"); hapMapTranslate.put("NA10854", "1349 NA10854 NA11839 NA11840 2 0" ); hapMapTranslate.put("NA11839", "1349 NA11839 0 0 1 0"); hapMapTranslate.put("NA11840", "1349 NA11840 0 0 2 0"); hapMapTranslate.put("NA10856", "1350 NA10856 NA11829 NA11830 1 0" ); hapMapTranslate.put("NA11829", "1350 NA11829 0 0 1 0"); hapMapTranslate.put("NA11830", "1350 NA11830 0 0 2 0"); hapMapTranslate.put("NA10855", "1350 NA10855 NA11831 NA11832 2 0" ); hapMapTranslate.put("NA11831", "1350 NA11831 0 0 1 0"); hapMapTranslate.put("NA11832", "1350 NA11832 0 0 2 0"); hapMapTranslate.put("NA12707", "1358 NA12707 NA12716 NA12717 1 0" ); hapMapTranslate.put("NA12716", "1358 NA12716 0 0 1 0"); hapMapTranslate.put("NA12717", "1358 NA12717 0 0 2 0"); hapMapTranslate.put("NA10860", "1362 NA10860 NA11992 NA11993 1 0" ); hapMapTranslate.put("NA11992", "1362 NA11992 0 0 1 0"); hapMapTranslate.put("NA11993", "1362 NA11993 0 0 2 0"); hapMapTranslate.put("NA11993.dup", "dup NA11993.dup 0 0 2 0"); hapMapTranslate.put("NA10861", "1362 NA10861 NA11994 NA11995 2 0" ); hapMapTranslate.put("NA11994", "1362 NA11994 0 0 1 0"); hapMapTranslate.put("NA11995", "1362 NA11995 0 0 2 0"); hapMapTranslate.put("NA10863", "1375 NA10863 NA12264 NA12234 2 0" ); hapMapTranslate.put("NA12264", "1375 NA12264 0 0 1 0"); hapMapTranslate.put("NA12234", "1375 NA12234 0 0 2 0"); hapMapTranslate.put("NA10830", "1408 NA10830 NA12154 NA12236 1 0" ); hapMapTranslate.put("NA12154", "1408 NA12154 0 0 1 0"); hapMapTranslate.put("NA12236", "1408 NA12236 0 0 2 0"); hapMapTranslate.put("NA10831", "1408 NA10831 NA12155 NA12156 2 0" ); hapMapTranslate.put("NA12155", "1408 NA12155 0 0 1 0"); hapMapTranslate.put("NA12156", "1408 NA12156 0 0 2 0"); hapMapTranslate.put("NA12156.dup", "dup NA12156.dup 0 0 2 0"); hapMapTranslate.put("NA10835", "1416 NA10835 NA12248 NA12249 1 0" ); hapMapTranslate.put("NA12248", "1416 NA12248 0 0 1 0"); hapMapTranslate.put("NA12248.dup", "dup NA1248.dup 0 0 1 0"); hapMapTranslate.put("NA12249", "1416 NA12249 0 0 2 0"); hapMapTranslate.put("NA10838", "1420 NA10838 NA12003 NA12004 1 0" ); hapMapTranslate.put("NA12003", "1420 NA12003 0 0 1 0"); hapMapTranslate.put("NA12004", "1420 NA12004 0 0 2 0"); hapMapTranslate.put("NA10839", "1420 NA10839 NA12005 NA12006 2 0" ); hapMapTranslate.put("NA12005", "1420 NA12005 0 0 1 0"); hapMapTranslate.put("NA12006", "1420 NA12006 0 0 2 0"); hapMapTranslate.put("NA12740", "1444 NA12740 NA12750 NA12751 2 0" ); hapMapTranslate.put("NA12750", "1444 NA12750 0 0 1 0"); hapMapTranslate.put("NA12751", "1444 NA12751 0 0 2 0"); hapMapTranslate.put("NA12752", "1447 NA12752 NA12760 NA12761 1 0" ); hapMapTranslate.put("NA12760", "1447 NA12760 0 0 1 0"); hapMapTranslate.put("NA12761", "1447 NA12761 0 0 2 0"); hapMapTranslate.put("NA12753", "1447 NA12753 NA12762 NA12763 2 0" ); hapMapTranslate.put("NA12762", "1447 NA12762 0 0 1 0"); hapMapTranslate.put("NA12763", "1447 NA12763 0 0 2 0"); hapMapTranslate.put("NA12801", "1454 NA12801 NA12812 NA12813 1 0" ); hapMapTranslate.put("NA12812", "1454 NA12812 0 0 1 0"); hapMapTranslate.put("NA12813", "1454 NA12813 0 0 2 0"); hapMapTranslate.put("NA12802", "1454 NA12802 NA12814 NA12815 2 0" ); hapMapTranslate.put("NA12814", "1454 NA12814 0 0 1 0"); hapMapTranslate.put("NA12815", "1454 NA12815 0 0 2 0"); hapMapTranslate.put("NA12864", "1459 NA12864 NA12872 NA12873 1 0" ); hapMapTranslate.put("NA12872", "1459 NA12872 0 0 1 0"); hapMapTranslate.put("NA12873", "1459 NA12873 0 0 2 0"); hapMapTranslate.put("NA12865", "1459 NA12865 NA12874 NA12875 2 0" ); hapMapTranslate.put("NA12874", "1459 NA12874 0 0 1 0"); hapMapTranslate.put("NA12875", "1459 NA12875 0 0 2 0"); hapMapTranslate.put("NA12878", "1463 NA12878 NA12891 NA12892 2 0" ); hapMapTranslate.put("NA12891", "1463 NA12891 0 0 1 0"); hapMapTranslate.put("NA12892", "1463 NA12892 0 0 2 0"); hapMapTranslate.put("NA18526", "chi1 NA18526 0 0 2 0"); hapMapTranslate.put("NA18524", "chi2 NA18524 0 0 1 0"); hapMapTranslate.put("NA18529", "chi3 NA18529 0 0 2 0"); hapMapTranslate.put("NA18558", "chi4 NA18558 0 0 1 0"); hapMapTranslate.put("NA18532", "chi5 NA18532 0 0 2 0"); hapMapTranslate.put("NA18561", "chi6 NA18561 0 0 1 0"); hapMapTranslate.put("NA18942", "jap1 NA18942 0 0 2 0"); hapMapTranslate.put("NA18940", "jap2 NA18940 0 0 1 0"); hapMapTranslate.put("NA18951", "jap3 NA18951 0 0 2 0"); hapMapTranslate.put("NA18943", "jap4 NA18943 0 0 1 0"); hapMapTranslate.put("NA18947", "jap5 NA18947 0 0 2 0"); hapMapTranslate.put("NA18944", "jap6 NA18944 0 0 1 0"); hapMapTranslate.put("NA18562", "chi7 NA18562 0 0 1 0"); hapMapTranslate.put("NA18537", "chi8 NA18537 0 0 2 0"); hapMapTranslate.put("NA18603", "chi9 NA18603 0 0 1 0"); hapMapTranslate.put("NA18540", "chi10 NA18540 0 0 2 0"); hapMapTranslate.put("NA18605", "chi11 NA18605 0 0 1 0"); hapMapTranslate.put("NA18542", "chi12 NA18542 0 0 2 0"); hapMapTranslate.put("NA18945", "jap7 NA18945 0 0 1 0"); hapMapTranslate.put("NA18949", "jap8 NA18949 0 0 2 0"); hapMapTranslate.put("NA18948", "jap9 NA18948 0 0 1 0"); hapMapTranslate.put("NA18952", "jap10 NA18952 0 0 1 0"); hapMapTranslate.put("NA18956", "jap11 NA18956 0 0 2 0"); hapMapTranslate.put("NA18545", "chi13 NA18545 0 0 2 0"); hapMapTranslate.put("NA18572", "chi46 NA18572 0 0 1 0"); hapMapTranslate.put("NA18547", "chi15 NA18547 0 0 2 0"); hapMapTranslate.put("NA18609", "chi16 NA18609 0 0 1 0"); hapMapTranslate.put("NA18550", "chi17 NA18550 0 0 2 0"); hapMapTranslate.put("NA18608", "chi18 NA18608 0 0 1 0"); hapMapTranslate.put("NA18964", "jap12 NA18964 0 0 2 0"); hapMapTranslate.put("NA18953", "jap13 NA18953 0 0 1 0"); hapMapTranslate.put("NA18968", "jap14 NA18968 0 0 2 0"); hapMapTranslate.put("NA18959", "jap15 NA18959 0 0 1 0"); hapMapTranslate.put("NA18969", "jap16 NA18969 0 0 2 0"); hapMapTranslate.put("NA18960", "jap17 NA18960 0 0 1 0"); hapMapTranslate.put("NA18552", "chi19 NA18552 0 0 2 0"); hapMapTranslate.put("NA18611", "chi20 NA18611 0 0 1 0"); hapMapTranslate.put("NA18555", "chi21 NA18555 0 0 2 0"); hapMapTranslate.put("NA18564", "chi22 NA18564 0 0 2 0"); hapMapTranslate.put("NA18961", "jap18 NA18961 0 0 1 0"); hapMapTranslate.put("NA18972", "jap19 NA18972 0 0 2 0"); hapMapTranslate.put("NA18965", "jap20 NA18965 0 0 1 0"); hapMapTranslate.put("NA18973", "jap21 NA18973 0 0 2 0"); hapMapTranslate.put("NA18966", "jap22 NA18966 0 0 1 0"); hapMapTranslate.put("NA18975", "jap23 NA18975 0 0 2 0"); hapMapTranslate.put("NA18566", "chi23 NA18566 0 0 2 0"); hapMapTranslate.put("NA18563", "chi24 NA18563 0 0 1 0"); hapMapTranslate.put("NA18570", "chi25 NA18570 0 0 2 0"); hapMapTranslate.put("NA18612", "chi26 NA18612 0 0 1 0"); hapMapTranslate.put("NA18571", "chi27 NA18571 0 0 2 0"); hapMapTranslate.put("NA18620", "chi28 NA18620 0 0 1 0"); hapMapTranslate.put("NA18976", "jap24 NA18976 0 0 2 0"); hapMapTranslate.put("NA18967", "jap25 NA18967 0 0 1 0"); hapMapTranslate.put("NA18978", "jap26 NA18978 0 0 2 0"); hapMapTranslate.put("NA18970", "jap27 NA18970 0 0 1 0"); hapMapTranslate.put("NA18980", "jap28 NA18980 0 0 2 0"); hapMapTranslate.put("NA18995", "jap29 NA18995 0 0 1 0"); hapMapTranslate.put("NA18621", "chi29 NA18621 0 0 1 0"); hapMapTranslate.put("NA18594", "chi30 NA18594 0 0 2 0"); hapMapTranslate.put("NA18622", "chi31 NA18622 0 0 1 0"); hapMapTranslate.put("NA18573", "chi32 NA18573 0 0 2 0"); hapMapTranslate.put("NA18623", "chi33 NA18623 0 0 1 0"); hapMapTranslate.put("NA18576", "chi34 NA18576 0 0 2 0"); hapMapTranslate.put("NA18971", "jap30 NA18971 0 0 1 0"); hapMapTranslate.put("NA18981", "jap31 NA18981 0 0 2 0"); hapMapTranslate.put("NA18974", "jap32 NA18974 0 0 1 0"); hapMapTranslate.put("NA18987", "jap33 NA18987 0 0 2 0"); hapMapTranslate.put("NA18990", "jap34 NA18990 0 0 1 0"); hapMapTranslate.put("NA18991", "jap35 NA18991 0 0 2 0"); hapMapTranslate.put("NA18577", "chi35 NA18577 0 0 2 0"); hapMapTranslate.put("NA18624", "chi36 NA18624 0 0 1 0"); hapMapTranslate.put("NA18579", "chi37 NA18579 0 0 2 0"); hapMapTranslate.put("NA18632", "chi38 NA18632 0 0 1 0"); hapMapTranslate.put("NA18582", "chi39 NA18582 0 0 2 0"); hapMapTranslate.put("NA18633", "chi40 NA18633 0 0 1 0"); hapMapTranslate.put("NA18994", "jap36 NA18994 0 0 1 0"); hapMapTranslate.put("NA18992", "jap37 NA18992 0 0 2 0"); hapMapTranslate.put("NA18997", "jap38 NA18997 0 0 2 0"); hapMapTranslate.put("NA18996", "jap39 NA18996 0 0 1 0"); hapMapTranslate.put("NA18635", "chi41 NA18635 0 0 1 0"); hapMapTranslate.put("NA18592", "chi42 NA18592 0 0 2 0"); hapMapTranslate.put("NA18636", "chi43 NA18636 0 0 1 0"); hapMapTranslate.put("NA18593", "chi44 NA18593 0 0 2 0"); hapMapTranslate.put("NA18637", "chi45 NA18637 0 0 1 0"); hapMapTranslate.put("NA19000", "jap40 NA19000 0 0 1 0"); hapMapTranslate.put("NA18998", "jap41 NA18998 0 0 2 0"); hapMapTranslate.put("NA19005", "jap42 NA19005 0 0 1 0"); hapMapTranslate.put("NA18999", "jap43 NA18999 0 0 2 0"); hapMapTranslate.put("NA19007", "jap44 NA19007 0 0 1 0"); hapMapTranslate.put("NA19003", "jap45 NA19003 0 0 2 0"); hapMapTranslate.put("NA18500", "Yoruba004 NA18500 NA18501 NA18502 1 0"); hapMapTranslate.put("NA18501", "Yoruba004 NA18501 0 0 1 0"); hapMapTranslate.put("NA18502", "Yoruba004 NA18502 0 0 2 0"); hapMapTranslate.put("NA18503", "Yoruba005 NA18503 NA18504 NA18505 1 0"); hapMapTranslate.put("NA18504", "Yoruba005 NA18504 0 0 1 0"); hapMapTranslate.put("NA18505", "Yoruba005 NA18505 0 0 2 0"); hapMapTranslate.put("NA18506", "Yoruba009 NA18506 NA18507 NA18508 1 0"); hapMapTranslate.put("NA18507", "Yoruba009 NA18507 0 0 1 0"); hapMapTranslate.put("NA18508", "Yoruba009 NA18508 0 0 2 0"); hapMapTranslate.put("NA18860", "Yoruba012 NA18860 NA18859 NA18858 1 0"); hapMapTranslate.put("NA18859", "Yoruba012 NA18859 0 0 1 0"); hapMapTranslate.put("NA18858", "Yoruba012 NA18858 0 0 2 0"); hapMapTranslate.put("NA18515", "Yoruba013 NA18515 NA18516 NA18517 1 0"); hapMapTranslate.put("NA18516", "Yoruba013 NA18516 0 0 1 0"); hapMapTranslate.put("NA18517", "Yoruba013 NA18517 0 0 2 0"); hapMapTranslate.put("NA18521", "Yoruba016 NA18521 NA18522 NA18523 1 0"); hapMapTranslate.put("NA18522", "Yoruba016 NA18522 0 0 1 0"); hapMapTranslate.put("NA18523", "Yoruba016 NA18523 0 0 2 0"); hapMapTranslate.put("NA18872", "Yoruba017 NA18872 NA18871 NA18870 1 0"); hapMapTranslate.put("NA18871", "Yoruba017 NA18871 0 0 1 0"); hapMapTranslate.put("NA18870", "Yoruba017 NA18870 0 0 2 0"); hapMapTranslate.put("NA18854", "Yoruba018 NA18854 NA18853 NA18852 1 0"); hapMapTranslate.put("NA18853", "Yoruba018 NA18853 0 0 1 0"); hapMapTranslate.put("NA18852", "Yoruba018 NA18852 0 0 2 0"); hapMapTranslate.put("NA18857", "Yoruba023 NA18857 NA18856 NA18855 1 0"); hapMapTranslate.put("NA18856", "Yoruba023 NA18856 0 0 1 0"); hapMapTranslate.put("NA18855", "Yoruba023 NA18855 0 0 2 0"); hapMapTranslate.put("NA18863", "Yoruba024 NA18863 NA18862 NA18861 1 0"); hapMapTranslate.put("NA18862", "Yoruba024 NA18862 0 0 1 0"); hapMapTranslate.put("NA18861", "Yoruba024 NA18861 0 0 2 0"); hapMapTranslate.put("NA18914", "Yoruba028 NA18914 NA18913 NA18912 1 0"); hapMapTranslate.put("NA18913", "Yoruba028 NA18913 0 0 1 0"); hapMapTranslate.put("NA18912", "Yoruba028 NA18912 0 0 2 0"); hapMapTranslate.put("NA19094", "Yoruba040 NA19094 NA19092 NA19093 2 0"); hapMapTranslate.put("NA19092", "Yoruba040 NA19092 0 0 1 0"); hapMapTranslate.put("NA19093", "Yoruba040 NA19093 0 0 2 0"); hapMapTranslate.put("NA19103", "Yoruba042 NA19103 NA19101 NA19102 1 0"); hapMapTranslate.put("NA19101", "Yoruba042 NA19101 0 0 1 0"); hapMapTranslate.put("NA19102", "Yoruba042 NA19102 0 0 2 0"); hapMapTranslate.put("NA19139", "Yoruba043 NA19139 NA19138 NA19137 1 0"); hapMapTranslate.put("NA19138", "Yoruba043 NA19138 0 0 1 0"); hapMapTranslate.put("NA19137", "Yoruba043 NA19137 0 0 2 0"); hapMapTranslate.put("NA19202", "Yoruba045 NA19202 NA19200 NA19201 2 0"); hapMapTranslate.put("NA19200", "Yoruba045 NA19200 0 0 1 0"); hapMapTranslate.put("NA19201", "Yoruba045 NA19201 0 0 2 0"); hapMapTranslate.put("NA19173", "Yoruba047 NA19173 NA19171 NA19172 1 0"); hapMapTranslate.put("NA19171", "Yoruba047 NA19171 0 0 1 0"); hapMapTranslate.put("NA19172", "Yoruba047 NA19172 0 0 2 0"); hapMapTranslate.put("NA19205", "Yoruba048 NA19205 NA19203 NA19204 1 0"); hapMapTranslate.put("NA19203", "Yoruba048 NA19203 0 0 1 0"); hapMapTranslate.put("NA19204", "Yoruba048 NA19204 0 0 2 0"); hapMapTranslate.put("NA19211", "Yoruba050 NA19211 NA19210 NA19209 1 0"); hapMapTranslate.put("NA19210", "Yoruba050 NA19210 0 0 1 0"); hapMapTranslate.put("NA19209", "Yoruba050 NA19209 0 0 2 0"); hapMapTranslate.put("NA19208", "Yoruba051 NA19208 NA19207 NA19206 1 0"); hapMapTranslate.put("NA19207", "Yoruba051 NA19207 0 0 1 0"); hapMapTranslate.put("NA19206", "Yoruba051 NA19206 0 0 2 0"); hapMapTranslate.put("NA19161", "Yoruba056 NA19161 NA19160 NA19159 1 0"); hapMapTranslate.put("NA19160", "Yoruba056 NA19160 0 0 1 0"); hapMapTranslate.put("NA19159", "Yoruba056 NA19159 0 0 2 0"); hapMapTranslate.put("NA19221", "Yoruba058 NA19221 NA19223 NA19222 2 0"); hapMapTranslate.put("NA19223", "Yoruba058 NA19223 0 0 1 0"); hapMapTranslate.put("NA19222", "Yoruba058 NA19222 0 0 2 0"); hapMapTranslate.put("NA19120", "Yoruba060 NA19120 NA19119 NA19116 1 0"); hapMapTranslate.put("NA19119", "Yoruba060 NA19119 0 0 1 0"); hapMapTranslate.put("NA19116", "Yoruba060 NA19116 0 0 2 0"); hapMapTranslate.put("NA19142", "Yoruba071 NA19142 NA19141 NA19140 1 0"); hapMapTranslate.put("NA19141", "Yoruba071 NA19141 0 0 1 0"); hapMapTranslate.put("NA19140", "Yoruba071 NA19140 0 0 2 0"); hapMapTranslate.put("NA19154", "Yoruba072 NA19154 NA19153 NA19152 1 0"); hapMapTranslate.put("NA19153", "Yoruba072 NA19153 0 0 1 0"); hapMapTranslate.put("NA19152", "Yoruba072 NA19152 0 0 2 0"); hapMapTranslate.put("NA19145", "Yoruba074 NA19145 NA19144 NA19143 1 0"); hapMapTranslate.put("NA19144", "Yoruba074 NA19144 0 0 1 0"); hapMapTranslate.put("NA19143", "Yoruba074 NA19143 0 0 2 0"); hapMapTranslate.put("NA19129", "Yoruba077 NA19129 NA19128 NA19127 2 0"); hapMapTranslate.put("NA19128", "Yoruba077 NA19128 0 0 1 0"); hapMapTranslate.put("NA19127", "Yoruba077 NA19127 0 0 2 0"); hapMapTranslate.put("NA19132", "Yoruba101 NA19132 NA19130 NA19131 2 0"); hapMapTranslate.put("NA19130", "Yoruba101 NA19130 0 0 1 0"); hapMapTranslate.put("NA19131", "Yoruba101 NA19131 0 0 2 0"); hapMapTranslate.put("NA19100", "Yoruba105 NA19100 NA19098 NA19099 2 0"); hapMapTranslate.put("NA19098", "Yoruba105 NA19098 0 0 1 0"); hapMapTranslate.put("NA19099", "Yoruba105 NA19099 0 0 2 0"); hapMapTranslate.put("NA19194", "Yoruba112 NA19194 NA19192 NA19193 1 0"); hapMapTranslate.put("NA19192", "Yoruba112 NA19192 0 0 1 0"); hapMapTranslate.put("NA19193", "Yoruba112 NA19193 0 0 2 0"); hapMapTranslate.put("NA19240", "Yoruba117 NA19240 NA19239 NA19238 2 0"); hapMapTranslate.put("NA19239", "Yoruba117 NA19239 0 0 1 0"); hapMapTranslate.put("NA19238", "Yoruba117 NA19238 0 0 2 0"); }

1,110,236

public void parseHapMap(Vector rawLines) throws PedFileException { int colNum = -1; int numLines = rawLines.size(); Individual ind; this.order = new Vector(); //sort first Vector lines = new Vector(); Hashtable sortHelp = new Hashtable(numLines-1,1.0f); long[] pos = new long[numLines-1]; lines.add(rawLines.get(0)); for (int k = 1; k < numLines; k++){ StringTokenizer st = new StringTokenizer((String) rawLines.get(k)); //strip off 1st 3 cols st.nextToken();st.nextToken();st.nextToken(); pos[k-1] = new Long(st.nextToken()).longValue(); sortHelp.put(new Long(pos[k-1]),rawLines.get(k)); } Arrays.sort(pos); for (int i = 0; i < pos.length; i++){ lines.add(sortHelp.get(new Long(pos[i]))); } //enumerate indivs StringTokenizer st = new StringTokenizer((String)lines.get(0), "\n\t\" \""); int numMetaColumns = 0; boolean doneMeta = false; while(!doneMeta && st.hasMoreTokens()){ String thisfield = st.nextToken(); numMetaColumns++; //so currently the first person ID always starts with NA (Coriell ID) but //todo: will this be true with AA samples etc? if (thisfield.startsWith("NA")){ doneMeta = true; } } numMetaColumns--; st = new StringTokenizer((String)lines.get(0), "\n\t\" \""); for (int i = 0; i < numMetaColumns; i++){ st.nextToken(); } StringTokenizer dt; while (st.hasMoreTokens()){ ind = new Individual(numLines); String name = st.nextToken(); String details = (String)hapMapTranslate.get(name); if (details == null){ throw new PedFileException("Hapmap data format error: " + name); } dt = new StringTokenizer(details, "\n\t\" \""); ind.setFamilyID(dt.nextToken().trim()); ind.setIndividualID(dt.nextToken().trim()); ind.setDadID(dt.nextToken().trim()); ind.setMomID(dt.nextToken().trim()); try { ind.setGender(Integer.parseInt(dt.nextToken().trim())); ind.setAffectedStatus(Integer.parseInt(dt.nextToken().trim())); }catch(NumberFormatException nfe) { throw new PedFileException("File error: invalid gender or affected status for indiv " + name); } //check if the family exists already in the Hashtable Family fam = (Family)this.families.get(ind.getFamilyID()); if(fam == null){ //it doesnt exist, so create a new Family object fam = new Family(ind.getFamilyID()); } fam.addMember(ind); this.families.put(ind.getFamilyID(),fam); String[] indFamID = new String[2]; indFamID[0] = ind.getFamilyID(); indFamID[1] = ind.getIndividualID(); this.order.add(ind); } //start at k=1 to skip header which we just processed above. hminfo = new String[numLines-1][]; for(int k=1;k<numLines;k++){ StringTokenizer tokenizer = new StringTokenizer((String)lines.get(k)); //reading the first line if(colNum < 0){ //only check column number count for the first line colNum = tokenizer.countTokens(); } if(colNum != tokenizer.countTokens()) { //this line has a different number of columns //should send some sort of error message //TODO: add something which stores number of markers for all lines and checks that they're consistent throw new PedFileException("Line number mismatch in input file. line " + (k+1)); } if(tokenizer.hasMoreTokens()){ hminfo[k-1] = new String[2]; for (int skip = 0; skip < numMetaColumns; skip++){ //meta-data crap String s = tokenizer.nextToken().trim(); //get marker name, chrom and pos if (skip == 0){ hminfo[k-1][0] = s; } if (skip == 2){ if (Chromosome.dataChrom != null){ if (!Chromosome.dataChrom.equals(s)){ throw new PedFileException("Hapmap file format error on line " + (k+1)+ ":\n There appear to be multiple chromosomes in the file."); } }else{ Chromosome.dataChrom = s; } } if (skip == 3){ hminfo[k-1][1] = s; } } int index = 0; while(tokenizer.hasMoreTokens()){ ind = (Individual)order.elementAt(index); String alleles = tokenizer.nextToken(); int allele1=0, allele2=0; if (alleles.substring(0,1).equals("A")){ allele1 = 1; }else if (alleles.substring(0,1).equals("C")){ allele1 = 2; }else if (alleles.substring(0,1).equals("G")){ allele1 = 3; }else if (alleles.substring(0,1).equals("T")){ allele1 = 4; } if (alleles.substring(1,2).equals("A")){ allele2 = 1; }else if (alleles.substring(1,2).equals("C")){ allele2 = 2; }else if (alleles.substring(1,2).equals("G")){ allele2 = 3; }else if (alleles.substring(1,2).equals("T")){ allele2 = 4; } byte[] markers = new byte[2]; markers[0] = (byte)allele1; markers[1]= (byte)allele2; ind.addMarker(markers); index++; } } } }

public void parseHapMap(Vector rawLines) throws PedFileException { int colNum = -1; int numLines = rawLines.size(); Individual ind; this.order = new Vector(); //sort first Vector lines = new Vector(); Hashtable sortHelp = new Hashtable(numLines-1,1.0f); long[] pos = new long[numLines-1]; lines.add(rawLines.get(0)); for (int k = 1; k < numLines; k++){ StringTokenizer st = new StringTokenizer((String) rawLines.get(k)); //strip off 1st 3 cols st.nextToken();st.nextToken();st.nextToken(); pos[k-1] = new Long(st.nextToken()).longValue(); sortHelp.put(new Long(pos[k-1]),rawLines.get(k)); } Arrays.sort(pos); for (int i = 0; i < pos.length; i++){ lines.add(sortHelp.get(new Long(pos[i]))); } //enumerate indivs StringTokenizer st = new StringTokenizer((String)lines.get(0), "\n\t\" \""); int numMetaColumns = 0; boolean doneMeta = false; while(!doneMeta && st.hasMoreTokens()){ String thisfield = st.nextToken(); numMetaColumns++; //so currently the first person ID always starts with NA (Coriell ID) but //todo: will this be true with AA samples etc? if (thisfield.startsWith("NA")){ doneMeta = true; } } numMetaColumns--; st = new StringTokenizer((String)lines.get(0), "\n\t\" \""); for (int i = 0; i < numMetaColumns; i++){ st.nextToken(); } StringTokenizer dt; while (st.hasMoreTokens()){ ind = new Individual(numLines); String name = st.nextToken(); String details = (String)hapMapTranslate.get(name); if (details == null){ throw new PedFileException("Hapmap data format error: " + name); } dt = new StringTokenizer(details, "\n\t\" \""); ind.setFamilyID(dt.nextToken().trim()); ind.setIndividualID(dt.nextToken().trim()); ind.setDadID(dt.nextToken().trim()); ind.setMomID(dt.nextToken().trim()); try { ind.setGender(Integer.parseInt(dt.nextToken().trim())); ind.setAffectedStatus(Integer.parseInt(dt.nextToken().trim())); }catch(NumberFormatException nfe) { throw new PedFileException("File error: invalid gender or affected status for indiv " + name); } //check if the family exists already in the Hashtable Family fam = (Family)this.families.get(ind.getFamilyID()); if(fam == null){ //it doesnt exist, so create a new Family object fam = new Family(ind.getFamilyID()); } fam.addMember(ind); this.families.put(ind.getFamilyID(),fam); String[] indFamID = new String[2]; indFamID[0] = ind.getFamilyID(); indFamID[1] = ind.getIndividualID(); this.order.add(ind); } //start at k=1 to skip header which we just processed above. hminfo = new String[numLines-1][]; for(int k=1;k<numLines;k++){ StringTokenizer tokenizer = new StringTokenizer((String)lines.get(k)); //reading the first line if(colNum < 0){ //only check column number count for the first line colNum = tokenizer.countTokens(); } if(colNum != tokenizer.countTokens()) { //this line has a different number of columns //should send some sort of error message //TODO: add something which stores number of markers for all lines and checks that they're consistent throw new PedFileException("Line number mismatch in input file. line " + (k+1)); } if(tokenizer.hasMoreTokens()){ hminfo[k-1] = new String[2]; for (int skip = 0; skip < numMetaColumns; skip++){ //meta-data crap String s = tokenizer.nextToken().trim(); //get marker name, chrom and pos if (skip == 0){ hminfo[k-1][0] = s; } if (skip == 2){ if (Chromosome.dataChrom != null){ if (!Chromosome.dataChrom.equals(s)){ throw new PedFileException("Hapmap file format error on line " + (k+1)+ ":\n There appear to be multiple chromosomes in the file."); } }else{ Chromosome.dataChrom = s; } } if (skip == 3){ hminfo[k-1][1] = s; } } int index = 0; while(tokenizer.hasMoreTokens()){ ind = (Individual)order.elementAt(index); int allele1=0, allele2=0; if (alleles.substring(0,1).equals("A")){ allele1 = 1; }else if (alleles.substring(0,1).equals("C")){ allele1 = 2; }else if (alleles.substring(0,1).equals("G")){ allele1 = 3; }else if (alleles.substring(0,1).equals("T")){ allele1 = 4; } if (alleles.substring(1,2).equals("A")){ allele2 = 1; }else if (alleles.substring(1,2).equals("C")){ allele2 = 2; }else if (alleles.substring(1,2).equals("G")){ allele2 = 3; }else if (alleles.substring(1,2).equals("T")){ allele2 = 4; } byte[] markers = new byte[2]; markers[0] = (byte)allele1; markers[1]= (byte)allele2; ind.addMarker(markers); index++; } } } }

1,110,238

public AddObjectsTask(List sqlObjects, Point preferredLocation, ProgressMonitor pm, JDialog parentDialog) { this.sqlObjects = sqlObjects; this.preferredLocation = preferredLocation; this.parentDialog = parentDialog; finished = false; new ProgressWatcher(pm, this); }

public AddObjectsTask(List<SQLObject> sqlObjects, Point preferredLocation, ProgressMonitor pm, JDialog parentDialog) { this.sqlObjects = sqlObjects; this.preferredLocation = preferredLocation; this.parentDialog = parentDialog; finished = false; new ProgressWatcher(pm, this); }

1,110,239

public void cleanup() { if (errorMessage != null) { Component c = ArchitectFrame.getMainInstance(); if (parentDialog != null) { c = parentDialog; } JOptionPane.showMessageDialog(c, errorMessage, "Error Dropping Tables into Playpen", JOptionPane.ERROR_MESSAGE); if (getNextProcess() != null) { setCancelled(true); } } }

1,110,240

public void doStuff () { ArchitectFrame.getMainInstance().getProject().getPlayPen().fireUndoCompoundEvent(new UndoCompoundEvent(this,EventTypes.MULTI_SELECT_START,"Starting multi-select")); if ( !isCancelled()){ hasStarted = true; logger.info("AddObjectsTask starting on thread "+Thread.currentThread().getName()); try { int pmMax = 0; Iterator soIt = sqlObjects.iterator(); // first pass: figure out how much work we need to do... while (soIt.hasNext()) { pmMax += ArchitectUtils.countTablesSnapshot((SQLObject)soIt.next()); } jobSize = new Integer(pmMax); // reset iterator soIt = sqlObjects.iterator(); while (soIt.hasNext() && !isCancelled()) { Object someData = soIt.next(); if (someData instanceof SQLTable) { TablePane tp = importTableCopy((SQLTable) someData, preferredLocation); message = ArchitectUtils.truncateString(((SQLTable)someData).getName()); preferredLocation.x += tp.getPreferredSize().width + 5; progress++; } else if (someData instanceof SQLSchema) { SQLSchema sourceSchema = (SQLSchema) someData; Iterator it = sourceSchema.getChildren().iterator(); while (it.hasNext() && !isCancelled()) { SQLTable sourceTable = (SQLTable) it.next(); message = ArchitectUtils.truncateString(sourceTable.getName()); TablePane tp = importTableCopy(sourceTable, preferredLocation); preferredLocation.x += tp.getPreferredSize().width + 5; progress++; } } else if (someData instanceof SQLCatalog) { SQLCatalog sourceCatalog = (SQLCatalog) someData; Iterator cit = sourceCatalog.getChildren().iterator(); if (sourceCatalog.isSchemaContainer()) { while (cit.hasNext() && !isCancelled()) { SQLSchema sourceSchema = (SQLSchema) cit.next(); Iterator it = sourceSchema.getChildren().iterator(); while (it.hasNext() && !isCancelled()) { SQLTable sourceTable = (SQLTable) it.next(); message = ArchitectUtils.truncateString(sourceTable.getName()); TablePane tp = importTableCopy(sourceTable, preferredLocation); preferredLocation.x += tp.getPreferredSize().width + 5; progress++; } } } else { while (cit.hasNext() && !isCancelled()) { SQLTable sourceTable = (SQLTable) cit.next(); message = ArchitectUtils.truncateString(sourceTable.getName()); TablePane tp = importTableCopy(sourceTable, preferredLocation); preferredLocation.x += tp.getPreferredSize().width + 5; progress++; } } } else if (someData instanceof SQLColumn) { SQLColumn column = (SQLColumn) someData; JLabel colName = new JLabel(column.getName()); colName.setSize(colName.getPreferredSize()); add(colName, preferredLocation); logger.debug("Added "+column.getName()+" to playpen (temporary, only for testing)"); colName.revalidate(); } else { logger.error("Unknown object dropped in PlayPen: "+someData); } } } catch (ArchitectException e) { e.printStackTrace(); } finally { finished = true; hasStarted = false; ArchitectFrame.getMainInstance().getProject().getPlayPen().fireUndoCompoundEvent(new UndoCompoundEvent(this,EventTypes.MULTI_SELECT_END,"Ending multi-select")); } logger.info("AddObjectsTask done"); } }

1,110,242

public void doStuff () { ArchitectFrame.getMainInstance().getProject().getPlayPen().fireUndoCompoundEvent(new UndoCompoundEvent(this,EventTypes.MULTI_SELECT_START,"Starting multi-select")); if ( !isCancelled()){ hasStarted = true; logger.info("AddObjectsTask starting on thread "+Thread.currentThread().getName()); try { int pmMax = 0; Iterator soIt = sqlObjects.iterator(); // first pass: figure out how much work we need to do... while (soIt.hasNext()) { pmMax += ArchitectUtils.countTablesSnapshot((SQLObject)soIt.next()); } jobSize = new Integer(pmMax); // reset iterator soIt = sqlObjects.iterator(); while (soIt.hasNext() && !isCancelled()) { Object someData = soIt.next(); if (someData instanceof SQLTable) { TablePane tp = importTableCopy((SQLTable) someData, preferredLocation); message = ArchitectUtils.truncateString(((SQLTable)someData).getName()); preferredLocation.x += tp.getPreferredSize().width + 5; progress++; } else if (someData instanceof SQLSchema) { SQLSchema sourceSchema = (SQLSchema) someData; Iterator it = sourceSchema.getChildren().iterator(); while (it.hasNext() && !isCancelled()) { SQLTable sourceTable = (SQLTable) it.next(); message = ArchitectUtils.truncateString(sourceTable.getName()); TablePane tp = importTableCopy(sourceTable, preferredLocation); preferredLocation.x += tp.getPreferredSize().width + 5; progress++; } } else if (someData instanceof SQLCatalog) { SQLCatalog sourceCatalog = (SQLCatalog) someData; Iterator cit = sourceCatalog.getChildren().iterator(); if (sourceCatalog.isSchemaContainer()) { while (cit.hasNext() && !isCancelled()) { SQLSchema sourceSchema = (SQLSchema) cit.next(); Iterator it = sourceSchema.getChildren().iterator(); while (it.hasNext() && !isCancelled()) { SQLTable sourceTable = (SQLTable) it.next(); message = ArchitectUtils.truncateString(sourceTable.getName()); TablePane tp = importTableCopy(sourceTable, preferredLocation); preferredLocation.x += tp.getPreferredSize().width + 5; progress++; } } } else { while (cit.hasNext() && !isCancelled()) { SQLTable sourceTable = (SQLTable) cit.next(); message = ArchitectUtils.truncateString(sourceTable.getName()); TablePane tp = importTableCopy(sourceTable, preferredLocation); preferredLocation.x += tp.getPreferredSize().width + 5; progress++; } } } else if (someData instanceof SQLColumn) { SQLColumn column = (SQLColumn) someData; JLabel colName = new JLabel(column.getName()); colName.setSize(colName.getPreferredSize()); add(colName, preferredLocation); logger.debug("Added "+column.getName()+" to playpen (temporary, only for testing)"); colName.revalidate(); } else { logger.error("Unknown object dropped in PlayPen: "+someData); } } } catch (ArchitectException e) { e.printStackTrace(); } finally { finished = true; hasStarted = false; ArchitectFrame.getMainInstance().getProject().getPlayPen().fireUndoCompoundEvent(new UndoCompoundEvent(this,EventTypes.MULTI_SELECT_END,"Ending multi-select")); } logger.info("AddObjectsTask done"); } }

public void doStuff () { ArchitectFrame.getMainInstance().getProject().getPlayPen().fireUndoCompoundEvent(new UndoCompoundEvent(this,EventTypes.MULTI_SELECT_START,"Starting multi-select")); if ( !isCancelled()){ hasStarted = true; int pmMax = 0; try { int pmMax = 0; Iterator soIt = sqlObjects.iterator(); // first pass: figure out how much work we need to do... while (soIt.hasNext()) { pmMax += ArchitectUtils.countTablesSnapshot((SQLObject)soIt.next()); } jobSize = new Integer(pmMax); // reset iterator soIt = sqlObjects.iterator(); while (soIt.hasNext() && !isCancelled()) { Object someData = soIt.next(); if (someData instanceof SQLTable) { TablePane tp = importTableCopy((SQLTable) someData, preferredLocation); message = ArchitectUtils.truncateString(((SQLTable)someData).getName()); preferredLocation.x += tp.getPreferredSize().width + 5; progress++; } else if (someData instanceof SQLSchema) { SQLSchema sourceSchema = (SQLSchema) someData; Iterator it = sourceSchema.getChildren().iterator(); while (it.hasNext() && !isCancelled()) { SQLTable sourceTable = (SQLTable) it.next(); message = ArchitectUtils.truncateString(sourceTable.getName()); TablePane tp = importTableCopy(sourceTable, preferredLocation); preferredLocation.x += tp.getPreferredSize().width + 5; progress++; } } else if (someData instanceof SQLCatalog) { SQLCatalog sourceCatalog = (SQLCatalog) someData; Iterator cit = sourceCatalog.getChildren().iterator(); if (sourceCatalog.isSchemaContainer()) { while (cit.hasNext() && !isCancelled()) { SQLSchema sourceSchema = (SQLSchema) cit.next(); Iterator it = sourceSchema.getChildren().iterator(); while (it.hasNext() && !isCancelled()) { SQLTable sourceTable = (SQLTable) it.next(); message = ArchitectUtils.truncateString(sourceTable.getName()); TablePane tp = importTableCopy(sourceTable, preferredLocation); preferredLocation.x += tp.getPreferredSize().width + 5; progress++; } } } else { while (cit.hasNext() && !isCancelled()) { SQLTable sourceTable = (SQLTable) cit.next(); message = ArchitectUtils.truncateString(sourceTable.getName()); TablePane tp = importTableCopy(sourceTable, preferredLocation); preferredLocation.x += tp.getPreferredSize().width + 5; progress++; } } } else if (someData instanceof SQLColumn) { SQLColumn column = (SQLColumn) someData; JLabel colName = new JLabel(column.getName()); colName.setSize(colName.getPreferredSize()); add(colName, preferredLocation); logger.debug("Added "+column.getName()+" to playpen (temporary, only for testing)"); colName.revalidate(); } else { logger.error("Unknown object dropped in PlayPen: "+someData); } } } catch (ArchitectException e) { e.printStackTrace(); } finally { finished = true; hasStarted = false; ArchitectFrame.getMainInstance().getProject().getPlayPen().fireUndoCompoundEvent(new UndoCompoundEvent(this,EventTypes.MULTI_SELECT_END,"Ending multi-select")); } logger.info("AddObjectsTask done"); } }

1,110,243

public void doStuff () { ArchitectFrame.getMainInstance().getProject().getPlayPen().fireUndoCompoundEvent(new UndoCompoundEvent(this,EventTypes.MULTI_SELECT_START,"Starting multi-select")); if ( !isCancelled()){ hasStarted = true; logger.info("AddObjectsTask starting on thread "+Thread.currentThread().getName()); try { int pmMax = 0; Iterator soIt = sqlObjects.iterator(); // first pass: figure out how much work we need to do... while (soIt.hasNext()) { pmMax += ArchitectUtils.countTablesSnapshot((SQLObject)soIt.next()); } jobSize = new Integer(pmMax); // reset iterator soIt = sqlObjects.iterator(); while (soIt.hasNext() && !isCancelled()) { Object someData = soIt.next(); if (someData instanceof SQLTable) { TablePane tp = importTableCopy((SQLTable) someData, preferredLocation); message = ArchitectUtils.truncateString(((SQLTable)someData).getName()); preferredLocation.x += tp.getPreferredSize().width + 5; progress++; } else if (someData instanceof SQLSchema) { SQLSchema sourceSchema = (SQLSchema) someData; Iterator it = sourceSchema.getChildren().iterator(); while (it.hasNext() && !isCancelled()) { SQLTable sourceTable = (SQLTable) it.next(); message = ArchitectUtils.truncateString(sourceTable.getName()); TablePane tp = importTableCopy(sourceTable, preferredLocation); preferredLocation.x += tp.getPreferredSize().width + 5; progress++; } } else if (someData instanceof SQLCatalog) { SQLCatalog sourceCatalog = (SQLCatalog) someData; Iterator cit = sourceCatalog.getChildren().iterator(); if (sourceCatalog.isSchemaContainer()) { while (cit.hasNext() && !isCancelled()) { SQLSchema sourceSchema = (SQLSchema) cit.next(); Iterator it = sourceSchema.getChildren().iterator(); while (it.hasNext() && !isCancelled()) { SQLTable sourceTable = (SQLTable) it.next(); message = ArchitectUtils.truncateString(sourceTable.getName()); TablePane tp = importTableCopy(sourceTable, preferredLocation); preferredLocation.x += tp.getPreferredSize().width + 5; progress++; } } } else { while (cit.hasNext() && !isCancelled()) { SQLTable sourceTable = (SQLTable) cit.next(); message = ArchitectUtils.truncateString(sourceTable.getName()); TablePane tp = importTableCopy(sourceTable, preferredLocation); preferredLocation.x += tp.getPreferredSize().width + 5; progress++; } } } else if (someData instanceof SQLColumn) { SQLColumn column = (SQLColumn) someData; JLabel colName = new JLabel(column.getName()); colName.setSize(colName.getPreferredSize()); add(colName, preferredLocation); logger.debug("Added "+column.getName()+" to playpen (temporary, only for testing)"); colName.revalidate(); } else { logger.error("Unknown object dropped in PlayPen: "+someData); } } } catch (ArchitectException e) { e.printStackTrace(); } finally { finished = true; hasStarted = false; ArchitectFrame.getMainInstance().getProject().getPlayPen().fireUndoCompoundEvent(new UndoCompoundEvent(this,EventTypes.MULTI_SELECT_END,"Ending multi-select")); } logger.info("AddObjectsTask done"); } }

1,110,244

DPrimeDisplay(PairwiseLinkage[][] t, boolean b, Vector v){ markersLoaded = b; dPrimeTable = t; markers = v; this.setDoubleBuffered(true); addMouseListener(new popMouseListener(this)); }

DPrimeDisplay(PairwiseLinkage[][] t, boolean b, Vector v){ markersLoaded = b; dPrimeTable = t; markers = v; this.setDoubleBuffered(true); addMouseListener(new PopMouseListener(this)); }

1,110,247

public double getPValue() { double pval = 0; try { pval= MathUtil.gammq(.5,.5*getChiSq()); } catch(CheckDataException e) {} return Math.rint(pval*10000.0)/10000.0; }

1,110,248

public void run(Context context, XMLOutput output) { if ( var == null ) { throw new IllegalArgumentException( "The var attribute cannot be null" ); } if ( select != null ) { Object value = select.evaluate( null ); context.setVariable( var, value ); } }

public void run(JellyContext context, XMLOutput output) { if ( var == null ) { throw new IllegalArgumentException( "The var attribute cannot be null" ); } if ( select != null ) { Object value = select.evaluate( null ); context.setVariable( var, value ); } }

1,110,249

public DashboardContextImpl(WebContext webContext, HttpServletRequest request){ this.webContext = webContext; this.request = request; }

public DashboardContextImpl(WebContext webContext, DashboardConfig dashboardConfig, HttpServletRequest request){ this.webContext = webContext; this.request = request; }

1,110,250

public DashboardContextImpl(WebContext webContext, HttpServletRequest request){ this.webContext = webContext; this.request = request; }

public DashboardContextImpl(WebContext webContext, HttpServletRequest request){ this.webContext = webContext; this.dashboardConfig = dashboardConfig; this.request = request; }

1,110,251

void readGenotypes(String[] inputOptions, int type){ //input is a 3 element array with //inputOptions[0] = ped file //inputOptions[1] = info file ("" if none) //inputOptions[2] = max comparison distance (don't compute d' if markers are greater than this dist apart) //type is either 3 or 4 for ped and hapmap files respectively final File inFile = new File(inputOptions[0]); //deal with max comparison distance if (inputOptions[2].equals("")){ inputOptions[2] = "0"; } maxCompDist = Long.parseLong(inputOptions[2])*1000; try { if (inFile.length() < 1){ throw new HaploViewException("Genotype file is empty or nonexistent: " + inFile.getName()); } if (type == HAPS){ //these are not available for non ped files viewMenuItems[VIEW_CHECK_NUM].setEnabled(false); viewMenuItems[VIEW_TDT_NUM].setEnabled(false); assocTest = 0; } theData = new HaploData(); if (type == HAPS){ theData.prepareHapsInput(new File(inputOptions[0])); }else{ theData.linkageToChrom(inFile, type); } //deal with marker information theData.infoKnown = false; File markerFile; if (inputOptions[1].equals("")){ markerFile = null; }else{ markerFile = new File(inputOptions[1]); } checkPanel = null; if (type == HAPS){ readMarkers(markerFile, null); }else{ readMarkers(markerFile, theData.getPedFile().getHMInfo()); checkPanel = new CheckDataPanel(theData, true); checkPanel.setAlignmentX(Component.CENTER_ALIGNMENT); } //let's start the math this.setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR)); final SwingWorker worker = new SwingWorker(){ public Object construct(){ dPrimeDisplay=null; changeKey(1); theData.generateDPrimeTable(); theData.guessBlocks(BLOX_GABRIEL); //theData.guessBlocks(BLOX_NONE); //for debugging, doesn't call blocks at first colorMenuItems[0].setSelected(true); blockMenuItems[0].setSelected(true); zoomMenuItems[0].setSelected(true); theData.blocksChanged = false; Container contents = getContentPane(); contents.removeAll(); int currentTab = VIEW_D_NUM; /*if (!(tabs == null)){ currentTab = tabs.getSelectedIndex(); } */ tabs = new JTabbedPane(); tabs.addChangeListener(new TabChangeListener()); //first, draw the D' picture JPanel panel = new JPanel(); panel.setLayout(new BoxLayout(panel, BoxLayout.Y_AXIS)); dPrimeDisplay = new DPrimeDisplay(window); JScrollPane dPrimeScroller = new JScrollPane(dPrimeDisplay); dPrimeScroller.getViewport().setScrollMode(JViewport.BLIT_SCROLL_MODE); dPrimeScroller.getVerticalScrollBar().setUnitIncrement(60); dPrimeScroller.getHorizontalScrollBar().setUnitIncrement(60); panel.add(dPrimeScroller); tabs.addTab(viewItems[VIEW_D_NUM], panel); viewMenuItems[VIEW_D_NUM].setEnabled(true); //compute and show haps on next tab panel = new JPanel(); panel.setLayout(new BoxLayout(panel, BoxLayout.Y_AXIS)); try { hapDisplay = new HaplotypeDisplay(theData); } catch(HaploViewException e) { JOptionPane.showMessageDialog(window, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE); } HaplotypeDisplayController hdc = new HaplotypeDisplayController(hapDisplay); hapScroller = new JScrollPane(hapDisplay); hapScroller.getVerticalScrollBar().setUnitIncrement(60); hapScroller.getHorizontalScrollBar().setUnitIncrement(60); panel.add(hapScroller); panel.add(hdc); tabs.addTab(viewItems[VIEW_HAP_NUM], panel); viewMenuItems[VIEW_HAP_NUM].setEnabled(true); //LOD panel /*panel = new JPanel(); panel.setLayout(new BoxLayout(panel, BoxLayout.Y_AXIS)); LODDisplay ld = new LODDisplay(theData); JScrollPane lodScroller = new JScrollPane(ld); panel.add(lodScroller); tabs.addTab(viewItems[VIEW_LOD_NUM], panel); viewMenuItems[VIEW_LOD_NUM].setEnabled(true);*/ //int optionalTabCount = 1; //check data panel if (checkPanel != null){ //optionalTabCount++; //VIEW_CHECK_NUM = optionalTabCount; //viewItems[VIEW_CHECK_NUM] = VIEW_CHECK_PANEL; JPanel metaCheckPanel = new JPanel(); metaCheckPanel.setLayout(new BoxLayout(metaCheckPanel, BoxLayout.Y_AXIS)); JLabel countsLabel = new JLabel("Using " + theData.numSingletons + " singletons and " + theData.numTrios + " trios from " + theData.numPeds + " families."); if (theData.numTrios + theData.numSingletons == 0){ countsLabel.setForeground(Color.red); } countsLabel.setAlignmentX(Component.CENTER_ALIGNMENT); metaCheckPanel.add(countsLabel); metaCheckPanel.add(checkPanel); cdc = new CheckDataController(window); metaCheckPanel.add(cdc); tabs.addTab(viewItems[VIEW_CHECK_NUM], metaCheckPanel); viewMenuItems[VIEW_CHECK_NUM].setEnabled(true); currentTab=VIEW_CHECK_NUM; } //TDT panel if(assocTest > 0) { //optionalTabCount++; //VIEW_TDT_NUM = optionalTabCount; //viewItems[VIEW_TDT_NUM] = VIEW_TDT; tdtPanel = new TDTPanel(theData.getPedFile(), assocTest); tabs.addTab(viewItems[VIEW_TDT_NUM], tdtPanel); viewMenuItems[VIEW_TDT_NUM].setEnabled(true); } tabs.setSelectedIndex(currentTab); contents.add(tabs); repaint(); setVisible(true); theData.finished = true; setTitle(TITLE_STRING + " -- " + inFile.getName()); return null; } }; timer = new javax.swing.Timer(50, new ActionListener(){ public void actionPerformed(ActionEvent evt){ if (theData.finished){ timer.stop(); for (int i = 0; i < blockMenuItems.length; i++){ blockMenuItems[i].setEnabled(true); } clearBlocksItem.setEnabled(true); readMarkerItem.setEnabled(true); blocksItem.setEnabled(true); exportMenuItems[2].setEnabled(true); setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR)); } } }); worker.start(); timer.start(); }catch(IOException ioexec) { JOptionPane.showMessageDialog(this, ioexec.getMessage(), "File Error", JOptionPane.ERROR_MESSAGE); } catch(PedFileException pfe){ JOptionPane.showMessageDialog(this, pfe.getMessage(), "File Error", JOptionPane.ERROR_MESSAGE); }catch (HaploViewException hve){ JOptionPane.showMessageDialog(this, hve.getMessage(), "File Error", JOptionPane.ERROR_MESSAGE); } }

void readGenotypes(String[] inputOptions, int type){ //input is a 3 element array with //inputOptions[0] = ped file //inputOptions[1] = info file ("" if none) //inputOptions[2] = max comparison distance (don't compute d' if markers are greater than this dist apart) //type is either 3 or 4 for ped and hapmap files respectively final File inFile = new File(inputOptions[0]); //deal with max comparison distance if (inputOptions[2].equals("")){ inputOptions[2] = "0"; } maxCompDist = Long.parseLong(inputOptions[2])*1000; try { if (inFile.length() < 1){ throw new HaploViewException("Genotype file is empty or nonexistent: " + inFile.getName()); } if (type == HAPS){ //these are not available for non ped files viewMenuItems[VIEW_CHECK_NUM].setEnabled(false); viewMenuItems[VIEW_TDT_NUM].setEnabled(false); assocTest = 0; } theData = new HaploData(); if (type == HAPS){ theData.prepareHapsInput(new File(inputOptions[0])); }else{ theData.linkageToChrom(inFile, type); } //deal with marker information theData.infoKnown = false; File markerFile; if (inputOptions[1].equals("")){ markerFile = null; }else{ markerFile = new File(inputOptions[1]); } checkPanel = null; if (type == HAPS){ readMarkers(markerFile, null); }else{ readMarkers(markerFile, theData.getPedFile().getHMInfo()); checkPanel = new CheckDataPanel(theData, true); checkPanel.setAlignmentX(Component.CENTER_ALIGNMENT); } //let's start the math this.setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR)); final SwingWorker worker = new SwingWorker(){ public Object construct(){ dPrimeDisplay=null; changeKey(1); theData.generateDPrimeTable(); theData.guessBlocks(BLOX_GABRIEL); //theData.guessBlocks(BLOX_NONE); //for debugging, doesn't call blocks at first colorMenuItems[0].setSelected(true); blockMenuItems[0].setSelected(true); zoomMenuItems[0].setSelected(true); theData.blocksChanged = false; Container contents = getContentPane(); contents.removeAll(); int currentTab = VIEW_D_NUM; /*if (!(tabs == null)){ currentTab = tabs.getSelectedIndex(); } */ tabs = new JTabbedPane(); tabs.addChangeListener(new TabChangeListener()); //first, draw the D' picture JPanel panel = new JPanel(); panel.setLayout(new BoxLayout(panel, BoxLayout.Y_AXIS)); dPrimeDisplay = new DPrimeDisplay(window); JScrollPane dPrimeScroller = new JScrollPane(dPrimeDisplay); dPrimeScroller.getViewport().setScrollMode(JViewport.BLIT_SCROLL_MODE); dPrimeScroller.getVerticalScrollBar().setUnitIncrement(60); dPrimeScroller.getHorizontalScrollBar().setUnitIncrement(60); panel.add(dPrimeScroller); tabs.addTab(viewItems[VIEW_D_NUM], panel); viewMenuItems[VIEW_D_NUM].setEnabled(true); //compute and show haps on next tab panel = new JPanel(); panel.setLayout(new BoxLayout(panel, BoxLayout.Y_AXIS)); try { hapDisplay = new HaplotypeDisplay(theData); } catch(HaploViewException e) { JOptionPane.showMessageDialog(window, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE); } HaplotypeDisplayController hdc = new HaplotypeDisplayController(hapDisplay); hapScroller = new JScrollPane(hapDisplay); hapScroller.getVerticalScrollBar().setUnitIncrement(60); hapScroller.getHorizontalScrollBar().setUnitIncrement(60); panel.add(hapScroller); panel.add(hdc); tabs.addTab(viewItems[VIEW_HAP_NUM], panel); viewMenuItems[VIEW_HAP_NUM].setEnabled(true); //LOD panel /*panel = new JPanel(); panel.setLayout(new BoxLayout(panel, BoxLayout.Y_AXIS)); LODDisplay ld = new LODDisplay(theData); JScrollPane lodScroller = new JScrollPane(ld); panel.add(lodScroller); tabs.addTab(viewItems[VIEW_LOD_NUM], panel); viewMenuItems[VIEW_LOD_NUM].setEnabled(true);*/ //int optionalTabCount = 1; //check data panel if (checkPanel != null){ //optionalTabCount++; //VIEW_CHECK_NUM = optionalTabCount; //viewItems[VIEW_CHECK_NUM] = VIEW_CHECK_PANEL; JPanel metaCheckPanel = new JPanel(); metaCheckPanel.setLayout(new BoxLayout(metaCheckPanel, BoxLayout.Y_AXIS)); JLabel countsLabel = new JLabel("Using " + theData.numSingletons + " singletons and " + theData.numTrios + " trios from " + theData.numPeds + " families."); if (theData.numTrios + theData.numSingletons == 0){ countsLabel.setForeground(Color.red); } countsLabel.setAlignmentX(Component.CENTER_ALIGNMENT); metaCheckPanel.add(countsLabel); metaCheckPanel.add(checkPanel); cdc = new CheckDataController(window); metaCheckPanel.add(cdc); tabs.addTab(viewItems[VIEW_CHECK_NUM], metaCheckPanel); viewMenuItems[VIEW_CHECK_NUM].setEnabled(true); currentTab=VIEW_CHECK_NUM; } //TDT panel if(assocTest > 0) { //optionalTabCount++; //VIEW_TDT_NUM = optionalTabCount; //viewItems[VIEW_TDT_NUM] = VIEW_TDT; try{ tdtPanel = new TDTPanel(theData.getPedFile(), assocTest); } catch(PedFileException e) { JOptionPane.showMessageDialog(window, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE); } tabs.addTab(viewItems[VIEW_TDT_NUM], tdtPanel); viewMenuItems[VIEW_TDT_NUM].setEnabled(true); } tabs.setSelectedIndex(currentTab); contents.add(tabs); repaint(); setVisible(true); theData.finished = true; setTitle(TITLE_STRING + " -- " + inFile.getName()); return null; } }; timer = new javax.swing.Timer(50, new ActionListener(){ public void actionPerformed(ActionEvent evt){ if (theData.finished){ timer.stop(); for (int i = 0; i < blockMenuItems.length; i++){ blockMenuItems[i].setEnabled(true); } clearBlocksItem.setEnabled(true); readMarkerItem.setEnabled(true); blocksItem.setEnabled(true); exportMenuItems[2].setEnabled(true); setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR)); } } }); worker.start(); timer.start(); }catch(IOException ioexec) { JOptionPane.showMessageDialog(this, ioexec.getMessage(), "File Error", JOptionPane.ERROR_MESSAGE); } catch(PedFileException pfe){ JOptionPane.showMessageDialog(this, pfe.getMessage(), "File Error", JOptionPane.ERROR_MESSAGE); }catch (HaploViewException hve){ JOptionPane.showMessageDialog(this, hve.getMessage(), "File Error", JOptionPane.ERROR_MESSAGE); } }

1,110,252

public Object construct(){ dPrimeDisplay=null; changeKey(1); theData.generateDPrimeTable(); theData.guessBlocks(BLOX_GABRIEL); //theData.guessBlocks(BLOX_NONE); //for debugging, doesn't call blocks at first colorMenuItems[0].setSelected(true); blockMenuItems[0].setSelected(true); zoomMenuItems[0].setSelected(true); theData.blocksChanged = false; Container contents = getContentPane(); contents.removeAll(); int currentTab = VIEW_D_NUM; /*if (!(tabs == null)){ currentTab = tabs.getSelectedIndex(); } */ tabs = new JTabbedPane(); tabs.addChangeListener(new TabChangeListener()); //first, draw the D' picture JPanel panel = new JPanel(); panel.setLayout(new BoxLayout(panel, BoxLayout.Y_AXIS)); dPrimeDisplay = new DPrimeDisplay(window); JScrollPane dPrimeScroller = new JScrollPane(dPrimeDisplay); dPrimeScroller.getViewport().setScrollMode(JViewport.BLIT_SCROLL_MODE); dPrimeScroller.getVerticalScrollBar().setUnitIncrement(60); dPrimeScroller.getHorizontalScrollBar().setUnitIncrement(60); panel.add(dPrimeScroller); tabs.addTab(viewItems[VIEW_D_NUM], panel); viewMenuItems[VIEW_D_NUM].setEnabled(true); //compute and show haps on next tab panel = new JPanel(); panel.setLayout(new BoxLayout(panel, BoxLayout.Y_AXIS)); try { hapDisplay = new HaplotypeDisplay(theData); } catch(HaploViewException e) { JOptionPane.showMessageDialog(window, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE); } HaplotypeDisplayController hdc = new HaplotypeDisplayController(hapDisplay); hapScroller = new JScrollPane(hapDisplay); hapScroller.getVerticalScrollBar().setUnitIncrement(60); hapScroller.getHorizontalScrollBar().setUnitIncrement(60); panel.add(hapScroller); panel.add(hdc); tabs.addTab(viewItems[VIEW_HAP_NUM], panel); viewMenuItems[VIEW_HAP_NUM].setEnabled(true); //LOD panel /*panel = new JPanel(); panel.setLayout(new BoxLayout(panel, BoxLayout.Y_AXIS)); LODDisplay ld = new LODDisplay(theData); JScrollPane lodScroller = new JScrollPane(ld); panel.add(lodScroller); tabs.addTab(viewItems[VIEW_LOD_NUM], panel); viewMenuItems[VIEW_LOD_NUM].setEnabled(true);*/ //int optionalTabCount = 1; //check data panel if (checkPanel != null){ //optionalTabCount++; //VIEW_CHECK_NUM = optionalTabCount; //viewItems[VIEW_CHECK_NUM] = VIEW_CHECK_PANEL; JPanel metaCheckPanel = new JPanel(); metaCheckPanel.setLayout(new BoxLayout(metaCheckPanel, BoxLayout.Y_AXIS)); JLabel countsLabel = new JLabel("Using " + theData.numSingletons + " singletons and " + theData.numTrios + " trios from " + theData.numPeds + " families."); if (theData.numTrios + theData.numSingletons == 0){ countsLabel.setForeground(Color.red); } countsLabel.setAlignmentX(Component.CENTER_ALIGNMENT); metaCheckPanel.add(countsLabel); metaCheckPanel.add(checkPanel); cdc = new CheckDataController(window); metaCheckPanel.add(cdc); tabs.addTab(viewItems[VIEW_CHECK_NUM], metaCheckPanel); viewMenuItems[VIEW_CHECK_NUM].setEnabled(true); currentTab=VIEW_CHECK_NUM; } //TDT panel if(assocTest > 0) { //optionalTabCount++; //VIEW_TDT_NUM = optionalTabCount; //viewItems[VIEW_TDT_NUM] = VIEW_TDT; tdtPanel = new TDTPanel(theData.getPedFile(), assocTest); tabs.addTab(viewItems[VIEW_TDT_NUM], tdtPanel); viewMenuItems[VIEW_TDT_NUM].setEnabled(true); } tabs.setSelectedIndex(currentTab); contents.add(tabs); repaint(); setVisible(true); theData.finished = true; setTitle(TITLE_STRING + " -- " + inFile.getName()); return null; }

public Object construct(){ dPrimeDisplay=null; changeKey(1); theData.generateDPrimeTable(); theData.guessBlocks(BLOX_GABRIEL); //theData.guessBlocks(BLOX_NONE); //for debugging, doesn't call blocks at first colorMenuItems[0].setSelected(true); blockMenuItems[0].setSelected(true); zoomMenuItems[0].setSelected(true); theData.blocksChanged = false; Container contents = getContentPane(); contents.removeAll(); int currentTab = VIEW_D_NUM; /*if (!(tabs == null)){ currentTab = tabs.getSelectedIndex(); } */ tabs = new JTabbedPane(); tabs.addChangeListener(new TabChangeListener()); //first, draw the D' picture JPanel panel = new JPanel(); panel.setLayout(new BoxLayout(panel, BoxLayout.Y_AXIS)); dPrimeDisplay = new DPrimeDisplay(window); JScrollPane dPrimeScroller = new JScrollPane(dPrimeDisplay); dPrimeScroller.getViewport().setScrollMode(JViewport.BLIT_SCROLL_MODE); dPrimeScroller.getVerticalScrollBar().setUnitIncrement(60); dPrimeScroller.getHorizontalScrollBar().setUnitIncrement(60); panel.add(dPrimeScroller); tabs.addTab(viewItems[VIEW_D_NUM], panel); viewMenuItems[VIEW_D_NUM].setEnabled(true); //compute and show haps on next tab panel = new JPanel(); panel.setLayout(new BoxLayout(panel, BoxLayout.Y_AXIS)); try { hapDisplay = new HaplotypeDisplay(theData); } catch(HaploViewException e) { JOptionPane.showMessageDialog(window, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE); } HaplotypeDisplayController hdc = new HaplotypeDisplayController(hapDisplay); hapScroller = new JScrollPane(hapDisplay); hapScroller.getVerticalScrollBar().setUnitIncrement(60); hapScroller.getHorizontalScrollBar().setUnitIncrement(60); panel.add(hapScroller); panel.add(hdc); tabs.addTab(viewItems[VIEW_HAP_NUM], panel); viewMenuItems[VIEW_HAP_NUM].setEnabled(true); //LOD panel /*panel = new JPanel(); panel.setLayout(new BoxLayout(panel, BoxLayout.Y_AXIS)); LODDisplay ld = new LODDisplay(theData); JScrollPane lodScroller = new JScrollPane(ld); panel.add(lodScroller); tabs.addTab(viewItems[VIEW_LOD_NUM], panel); viewMenuItems[VIEW_LOD_NUM].setEnabled(true);*/ //int optionalTabCount = 1; //check data panel if (checkPanel != null){ //optionalTabCount++; //VIEW_CHECK_NUM = optionalTabCount; //viewItems[VIEW_CHECK_NUM] = VIEW_CHECK_PANEL; JPanel metaCheckPanel = new JPanel(); metaCheckPanel.setLayout(new BoxLayout(metaCheckPanel, BoxLayout.Y_AXIS)); JLabel countsLabel = new JLabel("Using " + theData.numSingletons + " singletons and " + theData.numTrios + " trios from " + theData.numPeds + " families."); if (theData.numTrios + theData.numSingletons == 0){ countsLabel.setForeground(Color.red); } countsLabel.setAlignmentX(Component.CENTER_ALIGNMENT); metaCheckPanel.add(countsLabel); metaCheckPanel.add(checkPanel); cdc = new CheckDataController(window); metaCheckPanel.add(cdc); tabs.addTab(viewItems[VIEW_CHECK_NUM], metaCheckPanel); viewMenuItems[VIEW_CHECK_NUM].setEnabled(true); currentTab=VIEW_CHECK_NUM; } //TDT panel if(assocTest > 0) { //optionalTabCount++; //VIEW_TDT_NUM = optionalTabCount; //viewItems[VIEW_TDT_NUM] = VIEW_TDT; try{ tdtPanel = new TDTPanel(theData.getPedFile(), assocTest); } catch(PedFileException e) { JOptionPane.showMessageDialog(window, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE); } tabs.addTab(viewItems[VIEW_TDT_NUM], tdtPanel); viewMenuItems[VIEW_TDT_NUM].setEnabled(true); } tabs.setSelectedIndex(currentTab); contents.add(tabs); repaint(); setVisible(true); theData.finished = true; setTitle(TITLE_STRING + " -- " + inFile.getName()); return null; }

1,110,253

public static PhotoInfo addToDB( File imgFile ) throws PhotoNotFoundException { VolumeBase vol = null; try { vol = VolumeBase.getVolumeOfFile( imgFile ); } catch (IOException ex) { throw new PhotoNotFoundException(); } // Determine the fle that will be added as an instance File instanceFile = null; if ( vol == null ) { /* The "normal" case: we are adding a photo that is not part of any volume. Copy the file to the archive. */ vol = VolumeBase.getDefaultVolume(); instanceFile = vol.getFilingFname( imgFile ); try { FileUtils.copyFile( imgFile, instanceFile ); } catch (IOException ex) { log.warn( "Error copying file: " + ex.getMessage() ); throw new PhotoNotFoundException(); } } else if ( vol instanceof ExternalVolume ) { // Thisfile is in an external volume so we do not need a copy instanceFile = imgFile; } else if ( vol instanceof Volume ) { // Adding file from normal volume is not permitted throw new PhotoNotFoundException(); } else { throw new java.lang.Error( "Unknown subclass of VolumeBase: " + vol.getClass().getName() ); } // Create the image ODMGXAWrapper txw = new ODMGXAWrapper(); PhotoInfo photo = PhotoInfo.create(); txw.lock( photo, Transaction.WRITE ); photo.addInstance( vol, instanceFile, ImageInstance.INSTANCE_TYPE_ORIGINAL ); photo.setOrigFname( imgFile.getName() ); java.util.Date shootTime = new java.util.Date( imgFile.lastModified() ); photo.setShootTime( shootTime ); photo.setCropBounds( new Rectangle2D.Float( 0.0F, 0.0F, 1.0F, 1.0F ) ); photo.updateFromFileMetadata( instanceFile ); txw.commit(); return photo; }

public static PhotoInfo addToDB( File imgFile ) throws PhotoNotFoundException { VolumeBase vol = null; try { vol = VolumeBase.getVolumeOfFile( imgFile ); } catch (IOException ex) { throw new PhotoNotFoundException(); } // Determine the fle that will be added as an instance File instanceFile = null; if ( vol == null ) { /* The "normal" case: we are adding a photo that is not part of any volume. Copy the file to the archive. */ vol = VolumeBase.getDefaultVolume(); instanceFile = vol.getFilingFname( imgFile ); try { FileUtils.copyFile( imgFile, instanceFile ); } catch (IOException ex) { log.warn( "Error copying file: " + ex.getMessage() ); throw new PhotoNotFoundException(); } } else if ( vol instanceof ExternalVolume ) { // Thisfile is in an external volume so we do not need a copy instanceFile = imgFile; } else if ( vol instanceof Volume ) { // Adding file from normal volume is not permitted throw new PhotoNotFoundException(); } else { throw new java.lang.Error( "Unknown subclass of VolumeBase: " + vol.getClass().getName() ); } // Create the image ODMGXAWrapper txw = new ODMGXAWrapper(); PhotoInfo photo = PhotoInfo.create(); txw.lock( photo, Transaction.WRITE ); photo.addInstance( vol, instanceFile, ImageInstance.INSTANCE_TYPE_ORIGINAL ); String fname = imgFile.getName(); if ( fname.length() > ORIG_FNAME_LENGTH ) { fname = fname.substring( 0, ORIG_FNAME_LENGTH ); } photo.setOrigFname( fname ); java.util.Date shootTime = new java.util.Date( imgFile.lastModified() ); photo.setShootTime( shootTime ); photo.setCropBounds( new Rectangle2D.Float( 0.0F, 0.0F, 1.0F, 1.0F ) ); photo.updateFromFileMetadata( instanceFile ); txw.commit(); return photo; }

1,110,254

void updateFromFileMetadata( File f ) { ExifDirectory exif = null; try { Metadata metadata = JpegMetadataReader.readMetadata(f); if ( metadata.containsDirectory( ExifDirectory.class ) ) { try { exif = (ExifDirectory) metadata.getDirectory( ExifDirectory.class ); } catch ( MetadataException e ) { } } else { // No known directory was found no reason to continue return; } } catch (FileNotFoundException e) { // If error, just return - this is just an additional 'nice-if-succesful' operation. // If there is no metadata this will happen... return; } // Shooting date try { java.util.Date origDate = exif.getDate( exif.TAG_DATETIME_ORIGINAL ); setShootTime( origDate ); log.debug( "TAG_DATETIME_ORIGINAL: " + origDate.toString() ); } catch ( MetadataException e ) { log.info( "Error reading origDate: " + e.getMessage() ); } // Exposure try { double fstop = exif.getDouble( exif.TAG_FNUMBER ); log.debug( "TAG_FNUMBER: " + fstop ); setFStop( fstop ); } catch ( MetadataException e ) { log.info( "Error reading origDate: " + e.getMessage() ); } try { double sspeed = exif.getDouble( exif.TAG_EXPOSURE_TIME ); setShutterSpeed( sspeed ); log.debug( "TAG_EXPOSURE_TIME: " + sspeed ); } catch ( MetadataException e ) { log.info( "Error reading origDate: " + e.getMessage() ); } try { double flen = exif.getDouble( exif.TAG_FOCAL_LENGTH ); setFocalLength( flen ); } catch ( MetadataException e ) { log.info( "Error reading origDate: " + e.getMessage() ); } try { int filmSpeed = exif.getInt( exif.TAG_ISO_EQUIVALENT ); setFilmSpeed( filmSpeed ); } catch ( MetadataException e ) { log.info( "Error reading origDate: " + e.getMessage() ); } // Camera name. Put here both camera manufacturer and model String maker = exif.getString( exif.TAG_MAKE ); String model = exif.getString( exif.TAG_MODEL ); setCamera( maker + " " + model ); }

void updateFromFileMetadata( File f ) { ExifDirectory exif = null; try { Metadata metadata = JpegMetadataReader.readMetadata(f); if ( metadata.containsDirectory( ExifDirectory.class ) ) { try { exif = (ExifDirectory) metadata.getDirectory( ExifDirectory.class ); } catch ( MetadataException e ) { } } else { // No known directory was found no reason to continue return; } } catch (FileNotFoundException e) { // If error, just return - this is just an additional 'nice-if-succesful' operation. // If there is no metadata this will happen... return; } // Shooting date try { java.util.Date origDate = exif.getDate( exif.TAG_DATETIME_ORIGINAL ); setShootTime( origDate ); log.debug( "TAG_DATETIME_ORIGINAL: " + origDate.toString() ); } catch ( MetadataException e ) { log.info( "Error reading origDate: " + e.getMessage() ); } // Exposure try { double fstop = exif.getDouble( exif.TAG_FNUMBER ); log.debug( "TAG_FNUMBER: " + fstop ); setFStop( fstop ); } catch ( MetadataException e ) { log.info( "Error reading origDate: " + e.getMessage() ); } try { double sspeed = exif.getDouble( exif.TAG_EXPOSURE_TIME ); setShutterSpeed( sspeed ); log.debug( "TAG_EXPOSURE_TIME: " + sspeed ); } catch ( MetadataException e ) { log.info( "Error reading origDate: " + e.getMessage() ); } try { double flen = exif.getDouble( exif.TAG_FOCAL_LENGTH ); setFocalLength( flen ); } catch ( MetadataException e ) { log.info( "Error reading origDate: " + e.getMessage() ); } try { int filmSpeed = exif.getInt( exif.TAG_ISO_EQUIVALENT ); setFilmSpeed( filmSpeed ); } catch ( MetadataException e ) { log.info( "Error reading origDate: " + e.getMessage() ); } // Camera name. Put here both camera manufacturer and model String maker = exif.getString( exif.TAG_MAKE ); String model = exif.getString( exif.TAG_MODEL ); StringBuffer cameraBuf = new StringBuffer( maker ); cameraBuf.append( " "). append( model ); String camera = cameraBuf.toString(); if ( cameraBuf.length() > CAMERA_LENGTH ) { camera = cameraBuf.substring( 0, CAMERA_LENGTH ); } setCamera( camera ); }

1,110,261

public ScriptTag(BSFEngine engine) { this.engine = engine; }

public ScriptTag(BSFEngine engine, BSFManager manager) { this.engine = engine; }

1,110,262

public void doTag(XMLOutput output) throws MissingAttributeException, JellyTagException { String text = getBodyText(); log.debug(text); try { engine.eval(fileName, lineNumber, columnNumber, text); } catch (BSFException e) { throw new JellyTagException("Error occurred with script: " + e, e); } }

1,110,264

public void doTag(XMLOutput output) throws MissingAttributeException, JellyTagException { String text = getBodyText(); log.debug(text); try { engine.eval(fileName, lineNumber, columnNumber, text); } catch (BSFException e) { throw new JellyTagException("Error occurred with script: " + e, e); } }

1,110,265

public Thingy createDing() { System.out.println("addCreateDing: " + messages[i++]); return new Thingy(); }

public Thingy createDing() { System.out.println("createDing: " + messages[i++]); return new Thingy(); }

1,110,266

public boolean applyChanges() { // make a list of SQLTable objects and put them into // the wizard TreePath [] paths = dbTree.getSelectionPaths(); if (paths == null || paths.length == 0) { JOptionPane.showMessageDialog(getPanel(), "You must select at least one table or view.", "Error", JOptionPane.ERROR_MESSAGE); return false; } List list = new ArrayList(); Iterator it = Arrays.asList(paths).iterator(); while (it.hasNext()) { TreePath tp = (TreePath) it.next(); Object lastObj = tp.getLastPathComponent(); if (lastObj instanceof SQLTable) { logger.error("adding table: " + ((SQLTable)lastObj).getName()); list.add(lastObj); } } wizard.setSourceTables(list); return true; }

public boolean applyChanges() { // make a list of SQLTable objects and put them into // the wizard TreePath [] paths = dbTree.getSelectionPaths(); if (paths == null || paths.length == 0) { JOptionPane.showMessageDialog(getPanel(), "You must select at least one table or view.", "Error", JOptionPane.ERROR_MESSAGE); return false; } List list = new ArrayList(); Iterator it = Arrays.asList(paths).iterator(); while (it.hasNext()) { TreePath tp = (TreePath) it.next(); Object lastObj = tp.getLastPathComponent(); if (lastObj instanceof SQLTable) { logger.debug("adding table: " + ((SQLTable)lastObj).getName()); list.add(lastObj); } } wizard.setSourceTables(list); return true; }

1,110,267

public void run(Context context, XMLOutput output) throws Exception { if ( var == null ) { throw new JellyException( "<define:script> must have a var attribute" ); } context.setVariable( var, getBody() ); }

public void run(JellyContext context, XMLOutput output) throws Exception { if ( var == null ) { throw new JellyException( "<define:script> must have a var attribute" ); } context.setVariable( var, getBody() ); }

1,110,268

public void doTag(XMLOutput output) throws Exception { // ### should probably use HttpClient instead/* HttpClient client = getHttpClient(); client.startSession( getUrl() ); try { // must use inner tags to extract the output.... getBody().run(context, output) } finally { client.endSession(); } */ HttpConnection connection = getConnection(); if ( connection == null ) { throw new JellyException( "No HTTP connection available. " + "This tag should have a 'uri' attribute or be nested inside " + "a <http:connection> tag" ); } HttpMethod method = getMethod(); if ( method == null ) { throw new JellyException( "No HTTP Method available for this tag to execute" ); } int result = method.execute(getState(), connection); if ( var != null ) { context.setVariable(var, method); } }

public void doTag(XMLOutput output) throws Exception { // ### should probably use HttpClient instead/* HttpClient client = getHttpClient(); client.startSession( getUrl() ); try { // must use inner tags to extract the output.... invokeBody(output) } finally { client.endSession(); } */ HttpConnection connection = getConnection(); if ( connection == null ) { throw new JellyException( "No HTTP connection available. " + "This tag should have a 'uri' attribute or be nested inside " + "a <http:connection> tag" ); } HttpMethod method = getMethod(); if ( method == null ) { throw new JellyException( "No HTTP Method available for this tag to execute" ); } int result = method.execute(getState(), connection); if ( var != null ) { context.setVariable(var, method); } }

1,110,269

private boolean execute0(HandlerContext context) throws InvalidCommandException { String[] args = context.getCommand().getArgs(); if(args.length == 1){ /* print long help for given command */ CommandHandler handler = null; try { handler = CommandHandlerFactory.getHandler(args[0]); handler.help(); return true; } catch (InvalidCommandException e) { Out.println(e.getMessage()); Out.println(); } } /* print help about using jmanage command */ Out.println("jmanage [-username <username>] [-password <password>] " + "[-verbose[=<level>]] [command] [command args]"); /* print short help for all commands */ Out.println(); Out.println("Commands:"); Table table = new Table(2); Collection commandNames = CommandHandlerFactory.getCommandNames(); for(Iterator it=commandNames.iterator(); it.hasNext();){ String commandName = (String)it.next(); CommandHandler handler = CommandHandlerFactory.getHandler(commandName); table.add(commandName, handler.getShortHelp()); } table.print(); Out.println(); Out.println("Type \"help <command>\" for detailed command help."); return true; }

private boolean execute0(HandlerContext context) throws InvalidCommandException { String[] args = context.getCommand().getArgs(); if(args.length == 1){ /* print long help for given command */ CommandHandler handler; try { handler = CommandHandlerFactory.getHandler(args[0]); handler.help(); return true; } catch (InvalidCommandException e) { Out.println(e.getMessage()); Out.println(); } } /* print help about using jmanage command */ Out.println("jmanage [-username <username>] [-password <password>] " + "[-verbose[=<level>]] [command] [command args]"); /* print short help for all commands */ Out.println(); Out.println("Commands:"); Table table = new Table(2); Collection commandNames = CommandHandlerFactory.getCommandNames(); for(Iterator it=commandNames.iterator(); it.hasNext();){ String commandName = (String)it.next(); CommandHandler handler = CommandHandlerFactory.getHandler(commandName); table.add(commandName, handler.getShortHelp()); } table.print(); Out.println(); Out.println("Type \"help <command>\" for detailed command help."); return true; }

1,110,270

private boolean execute0(HandlerContext context) throws InvalidCommandException { String[] args = context.getCommand().getArgs(); if(args.length == 1){ /* print long help for given command */ CommandHandler handler = null; try { handler = CommandHandlerFactory.getHandler(args[0]); handler.help(); return true; } catch (InvalidCommandException e) { Out.println(e.getMessage()); Out.println(); } } /* print help about using jmanage command */ Out.println("jmanage [-username <username>] [-password <password>] " + "[-verbose[=<level>]] [command] [command args]"); /* print short help for all commands */ Out.println(); Out.println("Commands:"); Table table = new Table(2); Collection commandNames = CommandHandlerFactory.getCommandNames(); for(Iterator it=commandNames.iterator(); it.hasNext();){ String commandName = (String)it.next(); CommandHandler handler = CommandHandlerFactory.getHandler(commandName); table.add(commandName, handler.getShortHelp()); } table.print(); Out.println(); Out.println("Type \"help <command>\" for detailed command help."); return true; }

1,110,271

public void componentResized(ComponentEvent e) { logger.debug("Component "+e.getComponent().getName()+" changed size"); if (e.getComponent() == pkTable || e.getComponent() == fkTable) { revalidate(); } }

1,110,273

public void testChangeSFifthColumnIdxToSecond() throws ArchitectException{ table.changeColumnIndex(4, 1, true); assertEquals(4, table.getPkSize()); assertEquals(0, table.getColumnIndex(table.getColumnByName("one"))); assertEquals(1, table.getColumnIndex(table.getColumnByName("five"))); assertEquals(2, table.getColumnIndex(table.getColumnByName("two"))); assertEquals(3, table.getColumnIndex(table.getColumnByName("three"))); assertEquals(4, table.getColumnIndex(table.getColumnByName("four"))); assertEquals(5, table.getColumnIndex(table.getColumnByName("six"))); }

public void testChangeSFifthColumnIdxToSecond() throws Exception { EventLogger l = new EventLogger(); TableSnapshot original = l.makeTableSnapshot(table); ArchitectUtils.listenToHierarchy(l, table); table.changeColumnIndex(4, 1, true); assertEquals(4, table.getPkSize()); assertEquals(0, table.getColumnIndex(table.getColumnByName("one"))); assertEquals(1, table.getColumnIndex(table.getColumnByName("five"))); assertEquals(2, table.getColumnIndex(table.getColumnByName("two"))); assertEquals(3, table.getColumnIndex(table.getColumnByName("three"))); assertEquals(4, table.getColumnIndex(table.getColumnByName("four"))); assertEquals(5, table.getColumnIndex(table.getColumnByName("six"))); }

1,110,275

public TagScript createTagScript(String name, Attributes attributes) throws Exception { TagScript answer = super.createTagScript(name, attributes); if ( answer == null ) { Factory factory = getFactory( name ); if ( factory != null ) { ComponentTag tag = new ComponentTag(factory); answer = TagScript.newInstance(tag); } } return answer; }

public TagScript createTagScript(String name, Attributes attributes) throws Exception { TagScript answer = super.createTagScript(name, attributes); if ( answer == null ) { final Factory factory = getFactory( name ); if ( factory != null ) { ComponentTag tag = new ComponentTag(factory); answer = TagScript.newInstance(tag); } } return answer; }

1,110,278

public TagScript createTagScript(String name, Attributes attributes) throws Exception { TagScript answer = super.createTagScript(name, attributes); if ( answer == null ) { Factory factory = getFactory( name ); if ( factory != null ) { ComponentTag tag = new ComponentTag(factory); answer = TagScript.newInstance(tag); } } return answer; }

1,110,279

void createUI() { setLayout(new GridBagLayout()); folderTree = new JTree( ); folderTree.setRootVisible( true ); folderTree.setShowsRootHandles( false ); folderTree.setEditable( true ); folderTree.setCellEditor( new FolderNodeEditor( this ) ); folderTree.setCellRenderer( new FolderNodeEditor( this ) ); JScrollPane scrollPane = new JScrollPane( folderTree ); scrollPane.setPreferredSize( new Dimension( 300, 300 ) ); GridBagConstraints c = new GridBagConstraints(); c.gridx = 0; c.gridy = 0; c.gridheight = GridBagConstraints.REMAINDER; c.fill = GridBagConstraints.BOTH; add( scrollPane, c ); JButton addFolderBtn = new JButton( "Add to folder..." ); addFolderBtn.setActionCommand( ADD_ALL_TO_FOLDER_CMD ); addFolderBtn.addActionListener( this ); c = new GridBagConstraints(); c.gridx = 1; c.gridy = 0; add( addFolderBtn, c ); popup = new JPopupMenu(); JMenuItem addAllItem = new JMenuItem( "Add photos" ); addAllItem.addActionListener( this ); addAllItem.setActionCommand( ADD_ALL_TO_THIS_FOLDER_CMD ); JMenuItem removeAllItem = new JMenuItem( "Remove photos" ); removeAllItem.addActionListener( this ); removeAllItem.setActionCommand( REMOVE_ALL_FROM_THIS_FOLDER_CMD ); popup.add( addAllItem ); popup.add( removeAllItem ); MouseListener popupListener = new PopupListener(); folderTree.addMouseListener( popupListener ); }

1,110,280

void createUI() { setLayout(new GridBagLayout()); folderTree = new JTree( ); folderTree.setRootVisible( true ); folderTree.setShowsRootHandles( false ); folderTree.setEditable( true ); folderTree.setCellEditor( new FolderNodeEditor( this ) ); folderTree.setCellRenderer( new FolderNodeEditor( this ) ); JScrollPane scrollPane = new JScrollPane( folderTree ); scrollPane.setPreferredSize( new Dimension( 300, 300 ) ); GridBagConstraints c = new GridBagConstraints(); c.gridx = 0; c.gridy = 0; c.gridheight = GridBagConstraints.REMAINDER; c.fill = GridBagConstraints.BOTH; add( scrollPane, c ); JButton addFolderBtn = new JButton( "Add to folder..." ); addFolderBtn.setActionCommand( ADD_ALL_TO_FOLDER_CMD ); addFolderBtn.addActionListener( this ); c = new GridBagConstraints(); c.gridx = 1; c.gridy = 0; add( addFolderBtn, c ); popup = new JPopupMenu(); JMenuItem addAllItem = new JMenuItem( "Add photos" ); addAllItem.addActionListener( this ); addAllItem.setActionCommand( ADD_ALL_TO_THIS_FOLDER_CMD ); JMenuItem removeAllItem = new JMenuItem( "Remove photos" ); removeAllItem.addActionListener( this ); removeAllItem.setActionCommand( REMOVE_ALL_FROM_THIS_FOLDER_CMD ); popup.add( addAllItem ); popup.add( removeAllItem ); MouseListener popupListener = new PopupListener(); folderTree.addMouseListener( popupListener ); }

1,110,281

public void addAllToFolder( PhotoFolder f ) { addedToFolders.add( f ); removedFromFolders.remove( f ); FolderNode fn = (FolderNode)nodeMapper.mapFolderToNode( f ); fn.addAllPhotos(); // Notify the tree model that representation of this node may // be changed; PhotoCollectionChangeEvent e = new PhotoCollectionChangeEvent( f ); treeModel.photoCollectionChanged( e ); }

1,110,282

public void removeAllFromFolder( PhotoFolder f ) { addedToFolders.remove( f ); removedFromFolders.add( f ); FolderNode fn = (FolderNode) nodeMapper.mapFolderToNode( f ); fn.removeAllPhotos(); PhotoCollectionChangeEvent e = new PhotoCollectionChangeEvent( f ); treeModel.photoCollectionChanged( e ); }

1,110,283

public String toIdentifier(String logicalName, String physicalName) { // replace spaces with underscores if (logicalName == null) return null; logger.debug("getting physical name for: " + logicalName); String ident = logicalName.replace(' ','_').toUpperCase(); logger.debug("after replace of spaces: " + ident); // make sure first character is alpha Pattern p = Pattern.compile("^[^a-zA-Z]+"); Matcher m = p.matcher(ident); if (m.find()) { // just add something alpha to the front for now ident = "X" + ident; logger.debug("identifiers must start with letter, appending X: " + ident); } // see if it's a reserved word, and add something alpha to front if it is... if (isReservedWord(ident)) { ident = "X" + ident; logger.debug("identifier was reserved word, appending X: " + ident); } // replace anything that is not a letter, character, or underscore with an underscore... String tempString = ident; Pattern p2 = Pattern.compile("[^a-xA-Z0-9_]"); Matcher m2 = p2.matcher(ident); while (m2.find()) { tempString = tempString.replace(m2.group(),"_"); } ident = tempString; // first time through if (physicalName == null) { // length is ok if (ident.length() < 31) { return ident; } else { // length is too big logger.debug("truncating identifier: " + ident); String base = ident.substring(0,27); int tiebreaker = ((ident.hashCode() % 1000) + 1000) % 1000; logger.debug("new identifier: " + base + tiebreaker); return (base + tiebreaker); } } else { // back for more, which means that we had a // namespace conflict. Hack the ident down // to size if it's too big, and then generate // a hash tiebreaker using the ident and the // current value of physicalName logger.debug("physical idenfier is not unique, regenerating: " + physicalName); String base = ident; if (ident.length() > 27) { base = ident.substring(0,27); } int tiebreaker = (((ident + physicalName).hashCode() % 1000) + 1000) % 1000; logger.debug("regenerated identifier is: " + (base + tiebreaker)); return (base + tiebreaker); } }

public String toIdentifier(String logicalName, String physicalName) { // replace spaces with underscores if (logicalName == null) return null; if (logger.isDebugEnabled()) logger.debug("getting physical name for: " + logicalName); String ident = logicalName.replace(' ','_').toUpperCase(); logger.debug("after replace of spaces: " + ident); // make sure first character is alpha Pattern p = Pattern.compile("^[^a-zA-Z]+"); Matcher m = p.matcher(ident); if (m.find()) { // just add something alpha to the front for now ident = "X" + ident; logger.debug("identifiers must start with letter, appending X: " + ident); } // see if it's a reserved word, and add something alpha to front if it is... if (isReservedWord(ident)) { ident = "X" + ident; logger.debug("identifier was reserved word, appending X: " + ident); } // replace anything that is not a letter, character, or underscore with an underscore... String tempString = ident; Pattern p2 = Pattern.compile("[^a-xA-Z0-9_]"); Matcher m2 = p2.matcher(ident); while (m2.find()) { tempString = tempString.replace(m2.group(),"_"); } ident = tempString; // first time through if (physicalName == null) { // length is ok if (ident.length() < 31) { return ident; } else { // length is too big logger.debug("truncating identifier: " + ident); String base = ident.substring(0,27); int tiebreaker = ((ident.hashCode() % 1000) + 1000) % 1000; logger.debug("new identifier: " + base + tiebreaker); return (base + tiebreaker); } } else { // back for more, which means that we had a // namespace conflict. Hack the ident down // to size if it's too big, and then generate // a hash tiebreaker using the ident and the // current value of physicalName logger.debug("physical idenfier is not unique, regenerating: " + physicalName); String base = ident; if (ident.length() > 27) { base = ident.substring(0,27); } int tiebreaker = (((ident + physicalName).hashCode() % 1000) + 1000) % 1000; logger.debug("regenerated identifier is: " + (base + tiebreaker)); return (base + tiebreaker); } }

1,110,284

public String toIdentifier(String logicalName, String physicalName) { // replace spaces with underscores if (logicalName == null) return null; logger.debug("getting physical name for: " + logicalName); String ident = logicalName.replace(' ','_').toUpperCase(); logger.debug("after replace of spaces: " + ident); // make sure first character is alpha Pattern p = Pattern.compile("^[^a-zA-Z]+"); Matcher m = p.matcher(ident); if (m.find()) { // just add something alpha to the front for now ident = "X" + ident; logger.debug("identifiers must start with letter, appending X: " + ident); } // see if it's a reserved word, and add something alpha to front if it is... if (isReservedWord(ident)) { ident = "X" + ident; logger.debug("identifier was reserved word, appending X: " + ident); } // replace anything that is not a letter, character, or underscore with an underscore... String tempString = ident; Pattern p2 = Pattern.compile("[^a-xA-Z0-9_]"); Matcher m2 = p2.matcher(ident); while (m2.find()) { tempString = tempString.replace(m2.group(),"_"); } ident = tempString; // first time through if (physicalName == null) { // length is ok if (ident.length() < 31) { return ident; } else { // length is too big logger.debug("truncating identifier: " + ident); String base = ident.substring(0,27); int tiebreaker = ((ident.hashCode() % 1000) + 1000) % 1000; logger.debug("new identifier: " + base + tiebreaker); return (base + tiebreaker); } } else { // back for more, which means that we had a // namespace conflict. Hack the ident down // to size if it's too big, and then generate // a hash tiebreaker using the ident and the // current value of physicalName logger.debug("physical idenfier is not unique, regenerating: " + physicalName); String base = ident; if (ident.length() > 27) { base = ident.substring(0,27); } int tiebreaker = (((ident + physicalName).hashCode() % 1000) + 1000) % 1000; logger.debug("regenerated identifier is: " + (base + tiebreaker)); return (base + tiebreaker); } }

public String toIdentifier(String logicalName, String physicalName) { // replace spaces with underscores if (logicalName == null) return null; logger.debug("getting physical name for: " + logicalName); String ident = logicalName.replace(' ','_').toUpperCase(); if (logger.isDebugEnabled()) logger.debug("after replace of spaces: " + ident); // make sure first character is alpha Pattern p = Pattern.compile("^[^a-zA-Z]+"); Matcher m = p.matcher(ident); if (m.find()) { // just add something alpha to the front for now ident = "X" + ident; logger.debug("identifiers must start with letter, appending X: " + ident); } // see if it's a reserved word, and add something alpha to front if it is... if (isReservedWord(ident)) { ident = "X" + ident; logger.debug("identifier was reserved word, appending X: " + ident); } // replace anything that is not a letter, character, or underscore with an underscore... String tempString = ident; Pattern p2 = Pattern.compile("[^a-xA-Z0-9_]"); Matcher m2 = p2.matcher(ident); while (m2.find()) { tempString = tempString.replace(m2.group(),"_"); } ident = tempString; // first time through if (physicalName == null) { // length is ok if (ident.length() < 31) { return ident; } else { // length is too big logger.debug("truncating identifier: " + ident); String base = ident.substring(0,27); int tiebreaker = ((ident.hashCode() % 1000) + 1000) % 1000; logger.debug("new identifier: " + base + tiebreaker); return (base + tiebreaker); } } else { // back for more, which means that we had a // namespace conflict. Hack the ident down // to size if it's too big, and then generate // a hash tiebreaker using the ident and the // current value of physicalName logger.debug("physical idenfier is not unique, regenerating: " + physicalName); String base = ident; if (ident.length() > 27) { base = ident.substring(0,27); } int tiebreaker = (((ident + physicalName).hashCode() % 1000) + 1000) % 1000; logger.debug("regenerated identifier is: " + (base + tiebreaker)); return (base + tiebreaker); } }

1,110,285

public String toIdentifier(String logicalName, String physicalName) { // replace spaces with underscores if (logicalName == null) return null; logger.debug("getting physical name for: " + logicalName); String ident = logicalName.replace(' ','_').toUpperCase(); logger.debug("after replace of spaces: " + ident); // make sure first character is alpha Pattern p = Pattern.compile("^[^a-zA-Z]+"); Matcher m = p.matcher(ident); if (m.find()) { // just add something alpha to the front for now ident = "X" + ident; logger.debug("identifiers must start with letter, appending X: " + ident); } // see if it's a reserved word, and add something alpha to front if it is... if (isReservedWord(ident)) { ident = "X" + ident; logger.debug("identifier was reserved word, appending X: " + ident); } // replace anything that is not a letter, character, or underscore with an underscore... String tempString = ident; Pattern p2 = Pattern.compile("[^a-xA-Z0-9_]"); Matcher m2 = p2.matcher(ident); while (m2.find()) { tempString = tempString.replace(m2.group(),"_"); } ident = tempString; // first time through if (physicalName == null) { // length is ok if (ident.length() < 31) { return ident; } else { // length is too big logger.debug("truncating identifier: " + ident); String base = ident.substring(0,27); int tiebreaker = ((ident.hashCode() % 1000) + 1000) % 1000; logger.debug("new identifier: " + base + tiebreaker); return (base + tiebreaker); } } else { // back for more, which means that we had a // namespace conflict. Hack the ident down // to size if it's too big, and then generate // a hash tiebreaker using the ident and the // current value of physicalName logger.debug("physical idenfier is not unique, regenerating: " + physicalName); String base = ident; if (ident.length() > 27) { base = ident.substring(0,27); } int tiebreaker = (((ident + physicalName).hashCode() % 1000) + 1000) % 1000; logger.debug("regenerated identifier is: " + (base + tiebreaker)); return (base + tiebreaker); } }

public String toIdentifier(String logicalName, String physicalName) { // replace spaces with underscores if (logicalName == null) return null; logger.debug("getting physical name for: " + logicalName); String ident = logicalName.replace(' ','_').toUpperCase(); logger.debug("after replace of spaces: " + ident); // make sure first character is alpha Pattern p = Pattern.compile("^[^a-zA-Z]+"); Matcher m = p.matcher(ident); if (m.find()) { // just add something alpha to the front for now ident = "X" + ident; if (logger.isDebugEnabled()) logger.debug("identifiers must start with letter, appending X: " + ident); } // see if it's a reserved word, and add something alpha to front if it is... if (isReservedWord(ident)) { ident = "X" + ident; logger.debug("identifier was reserved word, appending X: " + ident); } // replace anything that is not a letter, character, or underscore with an underscore... String tempString = ident; Pattern p2 = Pattern.compile("[^a-xA-Z0-9_]"); Matcher m2 = p2.matcher(ident); while (m2.find()) { tempString = tempString.replace(m2.group(),"_"); } ident = tempString; // first time through if (physicalName == null) { // length is ok if (ident.length() < 31) { return ident; } else { // length is too big logger.debug("truncating identifier: " + ident); String base = ident.substring(0,27); int tiebreaker = ((ident.hashCode() % 1000) + 1000) % 1000; logger.debug("new identifier: " + base + tiebreaker); return (base + tiebreaker); } } else { // back for more, which means that we had a // namespace conflict. Hack the ident down // to size if it's too big, and then generate // a hash tiebreaker using the ident and the // current value of physicalName logger.debug("physical idenfier is not unique, regenerating: " + physicalName); String base = ident; if (ident.length() > 27) { base = ident.substring(0,27); } int tiebreaker = (((ident + physicalName).hashCode() % 1000) + 1000) % 1000; logger.debug("regenerated identifier is: " + (base + tiebreaker)); return (base + tiebreaker); } }

1,110,286

public String toIdentifier(String logicalName, String physicalName) { // replace spaces with underscores if (logicalName == null) return null; logger.debug("getting physical name for: " + logicalName); String ident = logicalName.replace(' ','_').toUpperCase(); logger.debug("after replace of spaces: " + ident); // make sure first character is alpha Pattern p = Pattern.compile("^[^a-zA-Z]+"); Matcher m = p.matcher(ident); if (m.find()) { // just add something alpha to the front for now ident = "X" + ident; logger.debug("identifiers must start with letter, appending X: " + ident); } // see if it's a reserved word, and add something alpha to front if it is... if (isReservedWord(ident)) { ident = "X" + ident; logger.debug("identifier was reserved word, appending X: " + ident); } // replace anything that is not a letter, character, or underscore with an underscore... String tempString = ident; Pattern p2 = Pattern.compile("[^a-xA-Z0-9_]"); Matcher m2 = p2.matcher(ident); while (m2.find()) { tempString = tempString.replace(m2.group(),"_"); } ident = tempString; // first time through if (physicalName == null) { // length is ok if (ident.length() < 31) { return ident; } else { // length is too big logger.debug("truncating identifier: " + ident); String base = ident.substring(0,27); int tiebreaker = ((ident.hashCode() % 1000) + 1000) % 1000; logger.debug("new identifier: " + base + tiebreaker); return (base + tiebreaker); } } else { // back for more, which means that we had a // namespace conflict. Hack the ident down // to size if it's too big, and then generate // a hash tiebreaker using the ident and the // current value of physicalName logger.debug("physical idenfier is not unique, regenerating: " + physicalName); String base = ident; if (ident.length() > 27) { base = ident.substring(0,27); } int tiebreaker = (((ident + physicalName).hashCode() % 1000) + 1000) % 1000; logger.debug("regenerated identifier is: " + (base + tiebreaker)); return (base + tiebreaker); } }

public String toIdentifier(String logicalName, String physicalName) { // replace spaces with underscores if (logicalName == null) return null; logger.debug("getting physical name for: " + logicalName); String ident = logicalName.replace(' ','_').toUpperCase(); logger.debug("after replace of spaces: " + ident); // make sure first character is alpha Pattern p = Pattern.compile("^[^a-zA-Z]+"); Matcher m = p.matcher(ident); if (m.find()) { // just add something alpha to the front for now ident = "X" + ident; logger.debug("identifiers must start with letter, appending X: " + ident); } // see if it's a reserved word, and add something alpha to front if it is... if (isReservedWord(ident)) { ident = "X" + ident; if (logger.isDebugEnabled()) logger.debug("identifier was reserved word, appending X: " + ident); } // replace anything that is not a letter, character, or underscore with an underscore... String tempString = ident; Pattern p2 = Pattern.compile("[^a-xA-Z0-9_]"); Matcher m2 = p2.matcher(ident); while (m2.find()) { tempString = tempString.replace(m2.group(),"_"); } ident = tempString; // first time through if (physicalName == null) { // length is ok if (ident.length() < 31) { return ident; } else { // length is too big logger.debug("truncating identifier: " + ident); String base = ident.substring(0,27); int tiebreaker = ((ident.hashCode() % 1000) + 1000) % 1000; logger.debug("new identifier: " + base + tiebreaker); return (base + tiebreaker); } } else { // back for more, which means that we had a // namespace conflict. Hack the ident down // to size if it's too big, and then generate // a hash tiebreaker using the ident and the // current value of physicalName logger.debug("physical idenfier is not unique, regenerating: " + physicalName); String base = ident; if (ident.length() > 27) { base = ident.substring(0,27); } int tiebreaker = (((ident + physicalName).hashCode() % 1000) + 1000) % 1000; logger.debug("regenerated identifier is: " + (base + tiebreaker)); return (base + tiebreaker); } }

1,110,287

public String toIdentifier(String logicalName, String physicalName) { // replace spaces with underscores if (logicalName == null) return null; logger.debug("getting physical name for: " + logicalName); String ident = logicalName.replace(' ','_').toUpperCase(); logger.debug("after replace of spaces: " + ident); // make sure first character is alpha Pattern p = Pattern.compile("^[^a-zA-Z]+"); Matcher m = p.matcher(ident); if (m.find()) { // just add something alpha to the front for now ident = "X" + ident; logger.debug("identifiers must start with letter, appending X: " + ident); } // see if it's a reserved word, and add something alpha to front if it is... if (isReservedWord(ident)) { ident = "X" + ident; logger.debug("identifier was reserved word, appending X: " + ident); } // replace anything that is not a letter, character, or underscore with an underscore... String tempString = ident; Pattern p2 = Pattern.compile("[^a-xA-Z0-9_]"); Matcher m2 = p2.matcher(ident); while (m2.find()) { tempString = tempString.replace(m2.group(),"_"); } ident = tempString; // first time through if (physicalName == null) { // length is ok if (ident.length() < 31) { return ident; } else { // length is too big logger.debug("truncating identifier: " + ident); String base = ident.substring(0,27); int tiebreaker = ((ident.hashCode() % 1000) + 1000) % 1000; logger.debug("new identifier: " + base + tiebreaker); return (base + tiebreaker); } } else { // back for more, which means that we had a // namespace conflict. Hack the ident down // to size if it's too big, and then generate // a hash tiebreaker using the ident and the // current value of physicalName logger.debug("physical idenfier is not unique, regenerating: " + physicalName); String base = ident; if (ident.length() > 27) { base = ident.substring(0,27); } int tiebreaker = (((ident + physicalName).hashCode() % 1000) + 1000) % 1000; logger.debug("regenerated identifier is: " + (base + tiebreaker)); return (base + tiebreaker); } }

1,110,288

public String toIdentifier(String logicalName, String physicalName) { // replace spaces with underscores if (logicalName == null) return null; logger.debug("getting physical name for: " + logicalName); String ident = logicalName.replace(' ','_').toUpperCase(); logger.debug("after replace of spaces: " + ident); // make sure first character is alpha Pattern p = Pattern.compile("^[^a-zA-Z]+"); Matcher m = p.matcher(ident); if (m.find()) { // just add something alpha to the front for now ident = "X" + ident; logger.debug("identifiers must start with letter, appending X: " + ident); } // see if it's a reserved word, and add something alpha to front if it is... if (isReservedWord(ident)) { ident = "X" + ident; logger.debug("identifier was reserved word, appending X: " + ident); } // replace anything that is not a letter, character, or underscore with an underscore... String tempString = ident; Pattern p2 = Pattern.compile("[^a-xA-Z0-9_]"); Matcher m2 = p2.matcher(ident); while (m2.find()) { tempString = tempString.replace(m2.group(),"_"); } ident = tempString; // first time through if (physicalName == null) { // length is ok if (ident.length() < 31) { return ident; } else { // length is too big logger.debug("truncating identifier: " + ident); String base = ident.substring(0,27); int tiebreaker = ((ident.hashCode() % 1000) + 1000) % 1000; logger.debug("new identifier: " + base + tiebreaker); return (base + tiebreaker); } } else { // back for more, which means that we had a // namespace conflict. Hack the ident down // to size if it's too big, and then generate // a hash tiebreaker using the ident and the // current value of physicalName logger.debug("physical idenfier is not unique, regenerating: " + physicalName); String base = ident; if (ident.length() > 27) { base = ident.substring(0,27); } int tiebreaker = (((ident + physicalName).hashCode() % 1000) + 1000) % 1000; logger.debug("regenerated identifier is: " + (base + tiebreaker)); return (base + tiebreaker); } }

public String toIdentifier(String logicalName, String physicalName) { // replace spaces with underscores if (logicalName == null) return null; logger.debug("getting physical name for: " + logicalName); String ident = logicalName.replace(' ','_').toUpperCase(); logger.debug("after replace of spaces: " + ident); // make sure first character is alpha Pattern p = Pattern.compile("^[^a-zA-Z]+"); Matcher m = p.matcher(ident); if (m.find()) { // just add something alpha to the front for now ident = "X" + ident; logger.debug("identifiers must start with letter, appending X: " + ident); } // see if it's a reserved word, and add something alpha to front if it is... if (isReservedWord(ident)) { ident = "X" + ident; logger.debug("identifier was reserved word, appending X: " + ident); } // replace anything that is not a letter, character, or underscore with an underscore... String tempString = ident; Pattern p2 = Pattern.compile("[^a-xA-Z0-9_]"); Matcher m2 = p2.matcher(ident); while (m2.find()) { tempString = tempString.replace(m2.group(),"_"); } ident = tempString; // first time through if (physicalName == null) { // length is ok if (ident.length() < 31) { return ident; } else { // length is too big if (logger.isDebugEnabled()) logger.debug("truncating identifier: " + ident); String base = ident.substring(0,27); int tiebreaker = ((ident.hashCode() % 1000) + 1000) % 1000; logger.debug("new identifier: " + base + tiebreaker); return (base + tiebreaker); } } else { // back for more, which means that we had a // namespace conflict. Hack the ident down // to size if it's too big, and then generate // a hash tiebreaker using the ident and the // current value of physicalName logger.debug("physical idenfier is not unique, regenerating: " + physicalName); String base = ident; if (ident.length() > 27) { base = ident.substring(0,27); } int tiebreaker = (((ident + physicalName).hashCode() % 1000) + 1000) % 1000; logger.debug("regenerated identifier is: " + (base + tiebreaker)); return (base + tiebreaker); } }

1,110,289

public String toIdentifier(String logicalName, String physicalName) { // replace spaces with underscores if (logicalName == null) return null; logger.debug("getting physical name for: " + logicalName); String ident = logicalName.replace(' ','_').toUpperCase(); logger.debug("after replace of spaces: " + ident); // make sure first character is alpha Pattern p = Pattern.compile("^[^a-zA-Z]+"); Matcher m = p.matcher(ident); if (m.find()) { // just add something alpha to the front for now ident = "X" + ident; logger.debug("identifiers must start with letter, appending X: " + ident); } // see if it's a reserved word, and add something alpha to front if it is... if (isReservedWord(ident)) { ident = "X" + ident; logger.debug("identifier was reserved word, appending X: " + ident); } // replace anything that is not a letter, character, or underscore with an underscore... String tempString = ident; Pattern p2 = Pattern.compile("[^a-xA-Z0-9_]"); Matcher m2 = p2.matcher(ident); while (m2.find()) { tempString = tempString.replace(m2.group(),"_"); } ident = tempString; // first time through if (physicalName == null) { // length is ok if (ident.length() < 31) { return ident; } else { // length is too big logger.debug("truncating identifier: " + ident); String base = ident.substring(0,27); int tiebreaker = ((ident.hashCode() % 1000) + 1000) % 1000; logger.debug("new identifier: " + base + tiebreaker); return (base + tiebreaker); } } else { // back for more, which means that we had a // namespace conflict. Hack the ident down // to size if it's too big, and then generate // a hash tiebreaker using the ident and the // current value of physicalName logger.debug("physical idenfier is not unique, regenerating: " + physicalName); String base = ident; if (ident.length() > 27) { base = ident.substring(0,27); } int tiebreaker = (((ident + physicalName).hashCode() % 1000) + 1000) % 1000; logger.debug("regenerated identifier is: " + (base + tiebreaker)); return (base + tiebreaker); } }

public String toIdentifier(String logicalName, String physicalName) { // replace spaces with underscores if (logicalName == null) return null; logger.debug("getting physical name for: " + logicalName); String ident = logicalName.replace(' ','_').toUpperCase(); logger.debug("after replace of spaces: " + ident); // make sure first character is alpha Pattern p = Pattern.compile("^[^a-zA-Z]+"); Matcher m = p.matcher(ident); if (m.find()) { // just add something alpha to the front for now ident = "X" + ident; logger.debug("identifiers must start with letter, appending X: " + ident); } // see if it's a reserved word, and add something alpha to front if it is... if (isReservedWord(ident)) { ident = "X" + ident; logger.debug("identifier was reserved word, appending X: " + ident); } // replace anything that is not a letter, character, or underscore with an underscore... String tempString = ident; Pattern p2 = Pattern.compile("[^a-xA-Z0-9_]"); Matcher m2 = p2.matcher(ident); while (m2.find()) { tempString = tempString.replace(m2.group(),"_"); } ident = tempString; // first time through if (physicalName == null) { // length is ok if (ident.length() < 31) { return ident; } else { // length is too big logger.debug("truncating identifier: " + ident); String base = ident.substring(0,27); int tiebreaker = ((ident.hashCode() % 1000) + 1000) % 1000; if (logger.isDebugEnabled()) logger.debug("new identifier: " + base + tiebreaker); return (base + tiebreaker); } } else { // back for more, which means that we had a // namespace conflict. Hack the ident down // to size if it's too big, and then generate // a hash tiebreaker using the ident and the // current value of physicalName logger.debug("physical idenfier is not unique, regenerating: " + physicalName); String base = ident; if (ident.length() > 27) { base = ident.substring(0,27); } int tiebreaker = (((ident + physicalName).hashCode() % 1000) + 1000) % 1000; logger.debug("regenerated identifier is: " + (base + tiebreaker)); return (base + tiebreaker); } }

1,110,290

public String toIdentifier(String logicalName, String physicalName) { // replace spaces with underscores if (logicalName == null) return null; logger.debug("getting physical name for: " + logicalName); String ident = logicalName.replace(' ','_').toUpperCase(); logger.debug("after replace of spaces: " + ident); // make sure first character is alpha Pattern p = Pattern.compile("^[^a-zA-Z]+"); Matcher m = p.matcher(ident); if (m.find()) { // just add something alpha to the front for now ident = "X" + ident; logger.debug("identifiers must start with letter, appending X: " + ident); } // see if it's a reserved word, and add something alpha to front if it is... if (isReservedWord(ident)) { ident = "X" + ident; logger.debug("identifier was reserved word, appending X: " + ident); } // replace anything that is not a letter, character, or underscore with an underscore... String tempString = ident; Pattern p2 = Pattern.compile("[^a-xA-Z0-9_]"); Matcher m2 = p2.matcher(ident); while (m2.find()) { tempString = tempString.replace(m2.group(),"_"); } ident = tempString; // first time through if (physicalName == null) { // length is ok if (ident.length() < 31) { return ident; } else { // length is too big logger.debug("truncating identifier: " + ident); String base = ident.substring(0,27); int tiebreaker = ((ident.hashCode() % 1000) + 1000) % 1000; logger.debug("new identifier: " + base + tiebreaker); return (base + tiebreaker); } } else { // back for more, which means that we had a // namespace conflict. Hack the ident down // to size if it's too big, and then generate // a hash tiebreaker using the ident and the // current value of physicalName logger.debug("physical idenfier is not unique, regenerating: " + physicalName); String base = ident; if (ident.length() > 27) { base = ident.substring(0,27); } int tiebreaker = (((ident + physicalName).hashCode() % 1000) + 1000) % 1000; logger.debug("regenerated identifier is: " + (base + tiebreaker)); return (base + tiebreaker); } }

public String toIdentifier(String logicalName, String physicalName) { // replace spaces with underscores if (logicalName == null) return null; logger.debug("getting physical name for: " + logicalName); String ident = logicalName.replace(' ','_').toUpperCase(); logger.debug("after replace of spaces: " + ident); // make sure first character is alpha Pattern p = Pattern.compile("^[^a-zA-Z]+"); Matcher m = p.matcher(ident); if (m.find()) { // just add something alpha to the front for now ident = "X" + ident; logger.debug("identifiers must start with letter, appending X: " + ident); } // see if it's a reserved word, and add something alpha to front if it is... if (isReservedWord(ident)) { ident = "X" + ident; logger.debug("identifier was reserved word, appending X: " + ident); } // replace anything that is not a letter, character, or underscore with an underscore... String tempString = ident; Pattern p2 = Pattern.compile("[^a-xA-Z0-9_]"); Matcher m2 = p2.matcher(ident); while (m2.find()) { tempString = tempString.replace(m2.group(),"_"); } ident = tempString; // first time through if (physicalName == null) { // length is ok if (ident.length() < 31) { return ident; } else { // length is too big logger.debug("truncating identifier: " + ident); String base = ident.substring(0,27); int tiebreaker = ((ident.hashCode() % 1000) + 1000) % 1000; logger.debug("new identifier: " + base + tiebreaker); return (base + tiebreaker); } } else { // back for more, which means that we had a // namespace conflict. Hack the ident down // to size if it's too big, and then generate // a hash tiebreaker using the ident and the // current value of physicalName if (logger.isDebugEnabled()) logger.debug("physical idenfier is not unique, regenerating: " + physicalName); String base = ident; if (ident.length() > 27) { base = ident.substring(0,27); } int tiebreaker = (((ident + physicalName).hashCode() % 1000) + 1000) % 1000; logger.debug("regenerated identifier is: " + (base + tiebreaker)); return (base + tiebreaker); } }

1,110,291

public String toIdentifier(String logicalName, String physicalName) { // replace spaces with underscores if (logicalName == null) return null; logger.debug("getting physical name for: " + logicalName); String ident = logicalName.replace(' ','_').toUpperCase(); logger.debug("after replace of spaces: " + ident); // make sure first character is alpha Pattern p = Pattern.compile("^[^a-zA-Z]+"); Matcher m = p.matcher(ident); if (m.find()) { // just add something alpha to the front for now ident = "X" + ident; logger.debug("identifiers must start with letter, appending X: " + ident); } // see if it's a reserved word, and add something alpha to front if it is... if (isReservedWord(ident)) { ident = "X" + ident; logger.debug("identifier was reserved word, appending X: " + ident); } // replace anything that is not a letter, character, or underscore with an underscore... String tempString = ident; Pattern p2 = Pattern.compile("[^a-xA-Z0-9_]"); Matcher m2 = p2.matcher(ident); while (m2.find()) { tempString = tempString.replace(m2.group(),"_"); } ident = tempString; // first time through if (physicalName == null) { // length is ok if (ident.length() < 31) { return ident; } else { // length is too big logger.debug("truncating identifier: " + ident); String base = ident.substring(0,27); int tiebreaker = ((ident.hashCode() % 1000) + 1000) % 1000; logger.debug("new identifier: " + base + tiebreaker); return (base + tiebreaker); } } else { // back for more, which means that we had a // namespace conflict. Hack the ident down // to size if it's too big, and then generate // a hash tiebreaker using the ident and the // current value of physicalName logger.debug("physical idenfier is not unique, regenerating: " + physicalName); String base = ident; if (ident.length() > 27) { base = ident.substring(0,27); } int tiebreaker = (((ident + physicalName).hashCode() % 1000) + 1000) % 1000; logger.debug("regenerated identifier is: " + (base + tiebreaker)); return (base + tiebreaker); } }

public String toIdentifier(String logicalName, String physicalName) { // replace spaces with underscores if (logicalName == null) return null; logger.debug("getting physical name for: " + logicalName); String ident = logicalName.replace(' ','_').toUpperCase(); logger.debug("after replace of spaces: " + ident); // make sure first character is alpha Pattern p = Pattern.compile("^[^a-zA-Z]+"); Matcher m = p.matcher(ident); if (m.find()) { // just add something alpha to the front for now ident = "X" + ident; logger.debug("identifiers must start with letter, appending X: " + ident); } // see if it's a reserved word, and add something alpha to front if it is... if (isReservedWord(ident)) { ident = "X" + ident; logger.debug("identifier was reserved word, appending X: " + ident); } // replace anything that is not a letter, character, or underscore with an underscore... String tempString = ident; Pattern p2 = Pattern.compile("[^a-xA-Z0-9_]"); Matcher m2 = p2.matcher(ident); while (m2.find()) { tempString = tempString.replace(m2.group(),"_"); } ident = tempString; // first time through if (physicalName == null) { // length is ok if (ident.length() < 31) { return ident; } else { // length is too big logger.debug("truncating identifier: " + ident); String base = ident.substring(0,27); int tiebreaker = ((ident.hashCode() % 1000) + 1000) % 1000; logger.debug("new identifier: " + base + tiebreaker); return (base + tiebreaker); } } else { // back for more, which means that we had a // namespace conflict. Hack the ident down // to size if it's too big, and then generate // a hash tiebreaker using the ident and the // current value of physicalName logger.debug("physical idenfier is not unique, regenerating: " + physicalName); String base = ident; if (ident.length() > 27) { base = ident.substring(0,27); } int tiebreaker = (((ident + physicalName).hashCode() % 1000) + 1000) % 1000; if (logger.isDebugEnabled()) logger.debug("regenerated identifier is: " + (base + tiebreaker)); return (base + tiebreaker); } }

1,110,292

public List getAttributes(ObjectName objectName, String[] attributeNames) { final ClassLoader contextClassLoader = Thread.currentThread().getContextClassLoader(); try { /* temporarily change the thread context classloader */ Thread.currentThread().setContextClassLoader(classLoader); /* invoke the method on the wrapped ServerConnection */ return connection.getAttributes(objectName, attributeNames); } finally { /* change the thread context classloader back to the original classloader*/ Thread.currentThread().setContextClassLoader(contextClassLoader); } }

public List getAttributes(ObjectName objectName, String[] attributeNames) { final ClassLoader contextClassLoader = Thread.currentThread().getContextClassLoader(); try { /* temporarily change the thread context classloader */ Thread.currentThread().setContextClassLoader(classLoader); /* invoke the method on the wrapped ServerConnection */ List attributeList = new LinkedList(); for(int i=0; i<attributeNames.length; i++){ attributeList.add(getAttribute(objectName, attributeNames[i])); } return attributeList; } finally { /* change the thread context classloader back to the original classloader*/ Thread.currentThread().setContextClassLoader(contextClassLoader); } }

1,110,293

public SQLObject[] getPathToNode(SQLObject node) { LinkedList path = new LinkedList(); while (node != null) { path.add(0, node); node = node.getParent(); } path.add(0, root); return (SQLObject[]) path.toArray(new SQLObject[path.size()]); }

1,110,297

private void buildPartialUI(DefaultFormBuilder builder, boolean defaultPlayPen) { String prefix; if (defaultPlayPen == true) { prefix = "source"; } else { prefix = "target"; } CellConstraints cc = new CellConstraints(); ArchitectFrame af = ArchitectFrame.getMainInstance(); SwingUIProject project = af.getProject(); playPenRadio = new JRadioButton(); playPenRadio.setName(prefix + "PlayPenRadio"); physicalRadio = new JRadioButton(); physicalRadio.setName(prefix + "PhysicalRadio"); loadRadio = new JRadioButton(); loadRadio.setName(prefix + "LoadRadio"); buttonGroup.add(playPenRadio); buttonGroup.add(physicalRadio); buttonGroup.add(loadRadio); schemaDropdown = new JComboBox(); schemaDropdown.setEnabled(false); schemaDropdown.setName(prefix + "SchemaDropdown"); catalogDropdown = new JComboBox(); catalogDropdown.setEnabled(false); catalogDropdown.setName(prefix + "CatalogDropdown"); databaseDropdown = new JComboBox(); databaseDropdown.setName(prefix + "DatabaseDropdown"); databaseDropdown.addItem(null); // the non-selection selection for (ArchitectDataSource ds : af.getUserSettings().getConnections()) { databaseDropdown.addItem(ds); } databaseDropdown.setEnabled(false); databaseDropdown.setRenderer(dataSourceRenderer); newConnButton = new JButton(); newConnButton.setName(prefix + "NewConnButton"); newConnButton.setAction(newConnectionAction); newConnectionAction.setEnabled(false); loadFilePath = new JTextField(); loadFilePath.setName(prefix + "LoadFilePath"); loadFilePath.setEnabled(false); loadFilePath.getDocument().addDocumentListener( new DocumentListener() { public void insertUpdate(DocumentEvent e) { startCompareAction.setEnabled(isStartable()); } public void removeUpdate(DocumentEvent e) { startCompareAction.setEnabled(isStartable()); } public void changedUpdate(DocumentEvent e) { startCompareAction.setEnabled(isStartable()); } }); loadFileButton = new JButton(); loadFileButton.setName(prefix + "LoadFileButton"); loadFileButton.setAction(chooseFileAction); chooseFileAction.setEnabled(false); catalogDropdown.addActionListener(new SchemaPopulator()); databaseDropdown.addActionListener(new CatalogPopulator()); ActionListener listener = new OptionGroupListener(); playPenRadio.addActionListener(listener); physicalRadio.addActionListener(listener); loadRadio.addActionListener(listener); if (defaultPlayPen) { playPenRadio.doClick(); } else { physicalRadio.doClick(); } // now give all our shiny new components to the builder builder.append(playPenRadio); builder.append("Current Project [" + project.getName() + "]"); builder.nextLine(); builder.append(""); // takes up blank space builder.append(physicalRadio); builder.append("Physical Database"); // builder.nextColumn(2); builder.append("Catalog"); builder.append("Schema"); builder.appendRow(builder.getLineGapSpec()); builder.appendRow("pref"); builder.nextLine(2); builder.nextColumn(4); builder.append(databaseDropdown); builder.append(catalogDropdown, schemaDropdown, newConnButton); builder.nextLine(); builder.append(""); builder.append(loadRadio); builder.append("From File:"); builder.nextLine(); builder.append(""); // takes up blank space builder.add(loadFilePath, cc.xyw(5, builder.getRow(), 5)); builder.nextColumn(8); builder.append(loadFileButton); builder.nextLine(); }

1,110,302

public Expression createExpression( ExpressionFactory factory, String tagName, String attributeName, String attributeValue) { if (attributeName.equals("select")) { return new XPathExpression(attributeValue); } // will use the default expression instead return null; }

public Expression createExpression( ExpressionFactory factory, String tagName, String attributeName, String attributeValue) throws JellyException { if (attributeName.equals("select")) { return new XPathExpression(attributeValue); } // will use the default expression instead return null; }

1,110,304

public Expression createExpression( ExpressionFactory factory, String tagName, String attributeName, String attributeValue) { if (attributeName.equals("select")) { return new XPathExpression(attributeValue); } // will use the default expression instead return null; }

1,110,305

public void handle() throws Exception { MailProcessingRecord mailProcessingRecord = prepareRecord(); MimeMessage message = loadMessage(); // do we _really_ have to handle this? if (!MailMatchingUtils.isMatchCandidate(message)) return; String id = MailMatchingUtils.getMailIdHeader(message); try { mailProcessingRecord.setByteReceivedTotal(message.getSize()); mailProcessingRecord.setMailId(id); mailProcessingRecord.setSubject(message.getSubject()); mailProcessingRecord.setTimeFetchEnd(System.currentTimeMillis()); } catch (MessagingException e) { log.info(queue + ": failed to process mail. remains on server"); return; } finally { MailProcessingRecord matchedAndMergedRecord = results.matchMailRecord(mailProcessingRecord); if (matchedAndMergedRecord != null) { MailMatchingUtils.validateMail(message, matchedAndMergedRecord); results.recordValidatedMatch(matchedAndMergedRecord); } } dismissMessage(); }

1,110,306

public void handle() throws Exception { MailProcessingRecord mailProcessingRecord = prepareRecord(); MimeMessage message = loadMessage(); // do we _really_ have to handle this? if (!MailMatchingUtils.isMatchCandidate(message)) return; String id = MailMatchingUtils.getMailIdHeader(message); try { mailProcessingRecord.setByteReceivedTotal(message.getSize()); mailProcessingRecord.setMailId(id); mailProcessingRecord.setSubject(message.getSubject()); mailProcessingRecord.setTimeFetchEnd(System.currentTimeMillis()); } catch (MessagingException e) { log.info(queue + ": failed to process mail. remains on server"); return; } finally { MailProcessingRecord matchedAndMergedRecord = results.matchMailRecord(mailProcessingRecord); if (matchedAndMergedRecord != null) { MailMatchingUtils.validateMail(message, matchedAndMergedRecord); results.recordValidatedMatch(matchedAndMergedRecord); } } dismissMessage(); }

public void handle() throws Exception { MailProcessingRecord mailProcessingRecord = prepareRecord(); MimeMessage message = loadMessage(); // do we _really_ have to handle this? if (!MailMatchingUtils.isMatchCandidate(message)) return; String id = MailMatchingUtils.getMailIdHeader(message); try { mailProcessingRecord.setByteReceivedTotal(message.getSize()); mailProcessingRecord.setMailId(id); mailProcessingRecord.setSubject(message.getSubject()); mailProcessingRecord.setTimeFetchEnd(System.currentTimeMillis()); } catch (MessagingException e) { log.info(queue + ": failed to process mail. remains on server"); return; } finally { MailProcessingRecord matchedAndMergedRecord = results.matchMailRecord(mailProcessingRecord); if (matchedAndMergedRecord != null) { MailMatchingUtils.validateMail(message, matchedAndMergedRecord); results.recordValidatedMatch(matchedAndMergedRecord); } } mailProcessingRecord.setMailId(id); mailProcessingRecord.setSubject(message.getSubject()); mailProcessingRecord.setTimeFetchEnd(System.currentTimeMillis()); } catch (MessagingException e) { log.info(queue + ": failed to process mail. remains on server"); return; } finally { MailProcessingRecord matchedAndMergedRecord = results.matchMailRecord(mailProcessingRecord); if (matchedAndMergedRecord != null) { MailMatchingUtils.validateMail(message, matchedAndMergedRecord); results.recordValidatedMatch(matchedAndMergedRecord); } } dismissMessage(); }

1,110,307

public void setUp() { odmg = OJB.getInstance(); db = odmg.newDatabase(); try { db.open( "repository.xml", Database.OPEN_READ_WRITE ); } catch ( ODMGException e ) { // log.warn( "Could not open database: " + e.getMessage() ); db = null; }// tx = odmg.newTransaction();// tx.begin(); }

1,110,308

public void doTag(XMLOutput output) throws Exception { Project project = getAntProject(); String tagName = getTagName(); Object parentObject = null; // must be a datatype. TaskSource ancestor = (TaskSource) findAncestorWithClass( TaskSource.class ); if ( ancestor != null ) { parentObject = ancestor.getTaskObject(); } // lets assume that Task instances are not nested inside other Task instances // for example <manifest> inside a <jar> should be a nested object, where as // if the parent is not a Task the <manifest> should create a ManifestTask if ( ! ( parentObject instanceof Task ) && project.getTaskDefinitions().containsKey( tagName ) ) { if ( log.isDebugEnabled() ) { log.debug( "Creating an ant Task for name: " + tagName ); } // the following algorithm follows the lifetime of a tag // http://jakarta.apache.org/ant/manual/develop.html#writingowntask // kindly recommended by Stefan Bodewig // create and set its project reference task = createTask( tagName ); if ( task instanceof TaskAdapter ) { setObject( ((TaskAdapter)task).getProxy() ); } else { setObject( task ); } // set the task ID if one is given Object id = getAttributes().remove( "id" ); if ( id != null ) { project.addReference( (String) id, task ); } // ### we might want to spoof a Target setting here // now lets initialize task.init(); // now lets invoke the body to call all the createXXX() or addXXX() methods String body = getBodyText(); // now lets set any attributes of this tag... setBeanProperties(); // now lets set the addText() of the body content, if its applicaable Method method = MethodUtils.getAccessibleMethod( task.getClass(), "addText", addTaskParamTypes ); if (method != null) { String text = getBodyText(); Object[] args = { text }; method.invoke(this.task, args); } // now lets set all the attributes of the child elements // XXXX: to do! // now we're ready to invoke the task // XXX: should we call execute() or perform()? task.perform(); } else { if ( log.isDebugEnabled() ) { log.debug( "Creating a nested object name: " + tagName ); } Object nested = createNestedObject( parentObject, tagName ); if ( nested == null ) { nested = createDataType( tagName ); } if ( nested != null ) { setObject( nested ); // set the task ID if one is given Object id = getAttributes().remove( "id" ); if ( id != null ) { project.addReference( (String) id, nested ); } try{ PropertyUtils.setProperty( nested, "name", tagName ); } catch (Exception e) { } } // now lets invoke the body String body = getBodyText(); // now lets set any attributes of this tag... setBeanProperties(); // now lets add it to its parent if ( parentObject != null ) { IntrospectionHelper ih = IntrospectionHelper.getHelper( parentObject.getClass() ); try { ih.storeElement( project, parentObject, nested, tagName ); } catch (Exception e) { //log.warn( "Caught exception setting nested: " + tagName, e ); } } } }

1,110,309