JoaoJunior/formatted-java-preprocessed-code-APR

private MarkerResult checkMarker(int loc)throws PedFileException{ MarkerResult result = new MarkerResult(); Individual currentInd; int missing=0, founderHetCount=0, mendErrNum=0; int allele1=0, allele2=0, hom=0, het=0, haploid = 0; Hashtable founderGenoCount = new Hashtable(); ...

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private MarkerResult checkMarker(int loc)throws PedFileException{ MarkerResult result = new MarkerResult(); Individual currentInd; int missing=0, founderHetCount=0, mendErrNum=0; int allele1=0, allele2=0, hom=0, het=0, haploid = 0; Hashtable founderGenoCount = new Hashtable(); ...

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protected void createUI() { setLayout(new BorderLayout()); setBorder(BorderFactory.createEmptyBorder(10, 10, 10, 10)); tabPane = new JTabbedPane(); add( tabPane, BorderLayout.CENTER ); // General pane JPanel generalPane = new JPanel(); tabPane.addTab( "General", generalPane ); // Create the fields & their labels /...

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public void doTag(XMLOutput output) throws Exception { Task task = getTask(); String text = getBodyText(); // if the task has an addText() Method method = MethodUtils.getAccessibleMethod( taskType, "addText", addTaskParamTypes ); if (method != null) { ...

public void doTag(XMLOutput output) throws Exception { Task task = getTask(); // if the task has an addText() Method method = MethodUtils.getAccessibleMethod( taskType, "addText", addTaskParamTypes ); if (method != null) { Object[] args = { text }; ...

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public void doTag(XMLOutput output) throws Exception { Task task = getTask(); String text = getBodyText(); // if the task has an addText() Method method = MethodUtils.getAccessibleMethod( taskType, "addText", addTaskParamTypes ); if (method != null) { ...

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public Task getTask() throws Exception { if ( task == null ) { task = (Task) taskType.newInstance(); task.setProject(project); task.setTaskName(taskName); task.init(); setDynaBean( new ConvertingWrapDynaBean(task) ); } return task; }

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public Task getTask() throws Exception { if ( task == null ) { task = (Task) taskType.newInstance(); task.setProject(project); task.setTaskName(taskName); task.init(); setDynaBean( new ConvertingWrapDynaBean(task) ); } return task; }

public Task getTask() throws Exception { if ( task == null ) { task = (Task) taskType.newInstance(); task.setProject(project); task.setTaskName(taskName); task.init(); setDynaBean( new ConvertingWrapDynaBean(task) ); } return this.task; ...

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public void setTask(Task task) { this.task = task; setDynaBean( new ConvertingWrapDynaBean(task) ); }

public void setTask(Task task) { this.task = task; setDynaBean( new ConvertingWrapDynaBean( this.task ) ); }

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public ServerConnection getServerConnection(ApplicationConfig config) throws ConnectionFailedException { try { /* Create an RMI connector client */ HashMap env = new HashMap(); String[] credentials = new String[] {config.getUsername(), ...

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public void testDatabaseInsert()throws ArchitectException { // setup a playpen like database SQLDatabase db = new SQLDatabase(); UndoManager undoManager = new UndoManager(db); db.setIgnoreReset(true); SQLTable table1 = new SQLTable(db,"table1","remark1","TABLE",true); SQLTable table2 = new SQLTable(db,"table2"...

public void testDatabaseInsert()throws ArchitectException { // setup a playpen like database SQLDatabase db = new SQLDatabase(); UndoManager undoManager = new UndoManager(db); db.setPlayPenDatabase(true); SQLTable table1 = new SQLTable(db,"table1","remark1","TABLE",true); SQLTable table2 = new SQLTable(db,"tab...

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public void testPhotoAddition() { String testImgDir = "c:\\java\\photovault\\testfiles"; String fname = "test1.jpg"; File f = new File( testImgDir, fname ); PhotoInfo photo = null; try { photo = PhotoInfo.addToDB( f ); } catch ( PhotoNotFoundException e ) { fail( "Could not find photo: " + e.getMessage() );...

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public void testRetrieve() { DList folders = null; Transaction tx = odmg.newTransaction(); tx.begin(); try { OQLQuery query = odmg.newOQLQuery(); query.create( "select folders from " + PhotoFolder.class.getName() + " where name = \"Top\"" ); folders = (DList) query.execute(); tx.commit(); } catch ( ...

public void testRetrieve() { DList folders = null; Transaction tx = odmg.newTransaction(); tx.begin(); try { OQLQuery query = odmg.newOQLQuery(); query.create( "select folders from " + PhotoFolder.class.getName() + " where folderId = 1" ); folders = (DList) query.execute(); tx.commit(); } catch ( Ex...

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public void testRetrieve() { DList folders = null; Transaction tx = odmg.newTransaction(); tx.begin(); try { OQLQuery query = odmg.newOQLQuery(); query.create( "select folders from " + PhotoFolder.class.getName() + " where name = \"Top\"" ); folders = (DList) query.execute(); tx.commit(); } catch ( ...

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public void setUp() { // Create several photos with different shooting dates // Add them to a collection so that they are easy to delete afterwards Calendar cal = Calendar.getInstance(); photos = new Vector(); uids = new Vector(); cal.set( 2002, 11, 23 ); makePhoto( cal, "Katsokaa kun Lassi ui" ); cal.set( 2002, 11...

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protected void fireDbChildrenRemoved(int[] oldIndices, List oldChildren) { if (logger.isDebugEnabled()) { logger.debug(getClass().getName()+" "+toString()+": " + "firing dbChildrenRemoved event " + "(secondary = "+isSecondaryChangeMode()+")"); } SQLObjectEvent e = new SQLObjectEvent (this, oldIndices...

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protected void fireDbObjectChanged(String propertyName, Object oldValue, Object newValue) { SQLObjectEvent e = new SQLObjectEvent( this, propertyName, oldValue, newValue, isSecondaryChangeMode()); boolean same = (oldValue == null ? oldValue == newValue : oldValue.equals(newValue)); if (same) { logg...

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protected void fireDbObjectChanged(String propertyName, Object oldValue, Object newValue) { SQLObjectEvent e = new SQLObjectEvent( this, propertyName, oldValue, newValue, isSecondaryChangeMode()); boolean same = (oldValue == null ? oldValue == newValue : oldValue.equals(newValue)); if (same) { logg...

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public void fireDbStructureChanged() { if (logger.isDebugEnabled()) { logger.debug(getClass().getName()+" "+toString()+": " + "firing dbStructureChanged event " + "(secondary = "+isSecondaryChangeMode()+")"); } SQLObjectEvent e = new SQLObjectEvent( this, null, isSecondaryChangeMode()); int coun...

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public void fireDbStructureChanged() { if (logger.isDebugEnabled()) { logger.debug(getClass().getName()+" "+toString()+": " + "firing dbStructureChanged event " + "(secondary = "+isSecondaryChangeMode()+")"); } SQLObjectEvent e = new SQLObjectEvent( this, null, isSecondaryChangeMode()); int coun...

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protected void fireUndoCompoundEvent(UndoCompoundEvent e) { Iterator it = undoEventListeners.iterator(); if (e.getType().isStartEvent()) { while (it.hasNext()) { ((UndoCompoundEventListener) it.next()).compoundEditStart(e); } } else { while (it.hasNext()) { ((UndoCompoundEventListener) it.next()).compou...

protected void fireUndoCompoundEvent(UndoCompoundEvent e) { UndoCompoundEventListener[] listeners = sqlObjectListeners.toArray(new UndoCompoundEventListener[0]); if (e.getType().isStartEvent()) { while (it.hasNext()) { ((UndoCompoundEventListener) it.next()).compoundEditStart(e); } } else { while (it.hasNe...

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protected void fireUndoCompoundEvent(UndoCompoundEvent e) { Iterator it = undoEventListeners.iterator(); if (e.getType().isStartEvent()) { while (it.hasNext()) { ((UndoCompoundEventListener) it.next()).compoundEditStart(e); } } else { while (it.hasNext()) { ((UndoCompoundEventListener) it.next()).compou...

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protected void fireUndoCompoundEvent(UndoCompoundEvent e) { Iterator it = undoEventListeners.iterator(); if (e.getType().isStartEvent()) { while (it.hasNext()) { ((UndoCompoundEventListener) it.next()).compoundEditStart(e); } } else { while (it.hasNext()) { ((UndoCompoundEventListener) it.next()).compou...

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protected SAXException createSAXException(String message, Exception e) { log.warn("Underlying exception: " + e); e.printStackTrace(); if (locator != null) { String error = "Error at (" + locator.getLineNumber() + ", " ...

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public boolean evaluateAsBoolean(JellyContext context) { Object value = evaluateAsValue(context); if ( value instanceof Boolean ) { Boolean b = (Boolean) value; return b.booleanValue(); } else if ( value instanceof String ) { // return Boolean.getBoolean(...

public boolean evaluateAsBoolean(JellyContext context) { Object value = evaluateRecurse(context); if ( value instanceof Boolean ) { Boolean b = (Boolean) value; return b.booleanValue(); } else if ( value instanceof String ) { // return Boolean.getBoolean(...

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public Iterator evaluateAsIterator(JellyContext context) { Object value = evaluateAsValue(context); if ( value == null ) { return EMPTY_ITERATOR; } else if ( value instanceof Iterator ) { return (Iterator) value; } else if ( value instanceof Lis...

public Iterator evaluateAsIterator(JellyContext context) { Object value = evaluateRecurse(context); if ( value == null ) { return EMPTY_ITERATOR; } else if ( value instanceof Iterator ) { return (Iterator) value; } else if ( value instanceof Lis...

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public String evaluateAsString(JellyContext context) { Object value = evaluateAsValue(context); // sometimes when Jelly is used inside Maven the value // of an expression can actually be an expression. // e.g. ${foo.bar} can lookup "foo.bar" in a Maven context // which could actua...

public String evaluateAsString(JellyContext context) { Object value = evaluateRecurse(context); // sometimes when Jelly is used inside Maven the value // of an expression can actually be an expression. // e.g. ${foo.bar} can lookup "foo.bar" in a Maven context // which could actua...

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public static int getMimePartSize(MimeMultipart parts, String mimeType) { if (parts != null) { try { for (int i = 0; i < parts.getCount(); i++) { BodyPart bodyPart = parts.getBodyPart(i); if (bodyPart.getContentType().startsWith(mimeType)) { ...

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public void initSingleColumnSize(int colIndex) { TableUtils.fitColumnWidth(table, colIndex); }

public void initSingleColumnSize(int colIndex) { TableUtils.fitColumnWidth(table, colIndex, 0); }

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public static void main(String[] args) { JFrame jf = new JFrame(); 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("...

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.cl...

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public static void main(String[] args) { JFrame jf = new JFrame(); 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("...

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public static void main(String[] args) { JFrame jf = new JFrame(); 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("...

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public static void main(String[] args) { JFrame jf = new JFrame(); 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("...

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public static void main(String[] args) { JFrame jf = new JFrame(); 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("...

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public static void main(String[] args) { JFrame jf = new JFrame(); 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("...

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public static void main(String[] args) { JFrame jf = new JFrame(); 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("...

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public void doTag(XMLOutput output) throws Exception { for (int i = 0, size = whenTags.length; i < size; i++) { TagScript script = whenTags[i]; script.run(context, output); WhenTag tag = (WhenTag) script.getTag(); if (tag.getValue()) { return; ...

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public void doTag(XMLOutput output) throws Exception { try { conn = getConnection(); } catch (SQLException e) { throw new JellyException(sql + ": " + e.getMessage(), e); } /* * Use the SQL statement specified by the sql attribute, if any, * ot...

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protected void setUp() throws Exception { super.setUp(); pp = ArchitectFrame.getMainInstance().getProject().getPlayPen(); SQLTable t1 = new SQLTable(pp.getDatabase(), true); pp.getDatabase().addChild(t1); pp.addTablePane(new TablePane(t1, pp), new Point(0,0)); SQLTable t2 = new SQLTable(pp.getDatabase(), true); ...

protected void setUp() throws Exception { super.setUp(); pp = ArchitectFrame.getMainInstance().getProject().getPlayPen(); SQLTable t1 = new SQLTable(pp.getDatabase(), true); pp.getDatabase().addChild(t1); pp.addTablePane(tp1 = new TablePane(t1, pp), new Point(0,0)); SQLTable t2 = new SQLTable(pp.getDatabase(), t...

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protected void setUp() throws Exception { super.setUp(); pp = ArchitectFrame.getMainInstance().getProject().getPlayPen(); SQLTable t1 = new SQLTable(pp.getDatabase(), true); pp.getDatabase().addChild(t1); pp.addTablePane(new TablePane(t1, pp), new Point(0,0)); SQLTable t2 = new SQLTable(pp.getDatabase(), true); ...

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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(); DList folders = null; ...

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public void setTags(TaggerController t) { tc = t; removeAll(); setLayout(new BoxLayout(this,BoxLayout.X_AXIS)); Vector colNames = new Vector(); Vector tableData = new Vector(); colNames.add("Allele"); colNames.add("Test"); colNames.add("r\u00b2"); for (...

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public BrowserWindow() { super( "Photovault Browser"); SwingUtilities.invokeLater(new java.lang.Runnable() { public void run() { createUI(); } }); addWindowListener(new WindowAdapter() { public void windowClosing(WindowEvent e) { System.exit(0); } } ); }

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

public void actionPerformed( ActionEvent e ) { importFile(); // br.setVisible( true ); }

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

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

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public synchronized void setupDialog() { logger.debug("running setupDialog()"); if (plexp == null) { throw new NullPointerException("setupDialog: plexp was null"); } // always refresh Target Database (it might have changed) plexp.setTargetDataSource(ArchitectFrame.getMainInstance().getProject().getTargetDatabas...

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public void actionPerformed(ActionEvent e) { String command = e.getActionCommand(); if (command.equals(RAW_DATA)){ load(PED); }else if (command.equals(PHASED_DATA)){ load(HAPS); }else if (command.equals(HAPMAP_DATA)){ load(HMP); }else if (command.e...

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public void actionPerformed(ActionEvent e) { String command = e.getActionCommand(); if (command.equals(RAW_DATA)){ load(PED); }else if (command.equals(PHASED_DATA)){ load(HAPS); }else if (command.equals(HAPMAP_DATA)){ load(HMP); }else if (command.e...

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public void actionPerformed(ActionEvent e) { String command = e.getActionCommand(); if (command.equals(RAW_DATA)){ load(PED); }else if (command.equals(PHASED_DATA)){ load(HAPS); }else if (command.equals(HAPMAP_DATA)){ load(HMP); }else if (command.e...

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public void actionPerformed(ActionEvent e) { String command = e.getActionCommand(); if (command.equals(RAW_DATA)){ load(PED); }else if (command.equals(PHASED_DATA)){ load(HAPS); }else if (command.equals(HAPMAP_DATA)){ load(HMP); }else if (command.e...

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protected void initTree() { folderNodes = new HashMap(); topNode = null; if ( model == null ) { return; } // Add all photos in the model to folder tree for ( int n = 0; n < model.length; n++ ) { addPhotoToTree( (PhotoInfo) model[n] ); } treeModel.nodeStructureChanged(topNode); }

protected void initTree() { folderNodes = new HashMap(); topNode = null; if ( model == null ) { return; } // Add all photos in the model to folder tree for ( int n = 0; n < model.length; n++ ) { if ( model[n] != null ) { addPhotoToTree( (PhotoInfo) model[n] ); } } treeModel.nodeStructureChanged(topN...

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public void addRelationship(SQLRelationship r) throws ArchitectDiffException { print("\n ALTER TABLE "); printQualified(r.getFkTable().getPhysicalName()); print(" ADD FOREIGN KEY "); print(r.getName()); print(" ( "); Map<String, SQLColumn> colNameMap = new HashMap<String, SQLColumn> (); boolean firstColumn =...

public void addRelationship(SQLRelationship r) throws ArchitectDiffException { print("\n ALTER TABLE "); printQualified(r.getFkTable().getPhysicalName()); print(" ADD CONSTRAINT "); print(r.getName()); print(" ( "); Map<String, SQLColumn> colNameMap = new HashMap<String, SQLColumn> (); boolean firstColumn = ...

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public void addRelationship(SQLRelationship r) throws ArchitectDiffException { print("\n ALTER TABLE "); printQualified(r.getFkTable().getPhysicalName()); print(" ADD FOREIGN KEY "); print(r.getName()); print(" ( "); Map<String, SQLColumn> colNameMap = new HashMap<String, SQLColumn> (); boolean firstColumn =...

public void addRelationship(SQLRelationship r) throws ArchitectDiffException { print("\n ALTER TABLE "); printQualified(r.getFkTable().getPhysicalName()); print(" ADD FOREIGN KEY "); print(r.getName()); print(" FOREIGN KEY ( "); Map<String, SQLColumn> colNameMap = new HashMap<String, SQLColumn> (); boolean f...

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private String columnDefinition(SQLColumn c, Map colNameMap) throws ArchitectDiffException { StringBuffer def = new StringBuffer(); getPhysicalName(colNameMap,c); // also adds generated physical name to the map GenericTypeDescriptor td = (GenericTypeDescriptor) typeMap.get(new Integer(c.getType())); if (td == nul...

protected String columnDefinition(SQLColumn c, Map colNameMap) throws ArchitectDiffException { StringBuffer def = new StringBuffer(); getPhysicalName(colNameMap,c); // also adds generated physical name to the map GenericTypeDescriptor td = (GenericTypeDescriptor) typeMap.get(new Integer(c.getType())); if (td == n...

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public void dropRelationship(SQLRelationship r) { print("\n ALTER TABLE "); printQualified(r.getFkTable().getPhysicalName()); print(" DROP FOREIGN KEY "); print(r.getName()); endStatement(DDLStatement.StatementType.DROP, r); }

public void dropRelationship(SQLRelationship r) { print("\n ALTER TABLE "); printQualified(r.getFkTable().getPhysicalName()); print(" DROP CONSTRAINT "); print(r.getName()); endStatement(DDLStatement.StatementType.DROP, r); }

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public void run(Context context, XMLOutput output) throws Exception { log.info( "Invoking dynamic tag with attributes: " + attributes ); attributes.put( "org.apache.commons.jelly.body", getBody() ); // create new context based on current attributes Context newContext = context.ne...

public void run(JellyContext context, XMLOutput output) throws Exception { log.info( "Invoking dynamic tag with attributes: " + attributes ); attributes.put( "org.apache.commons.jelly.body", getBody() ); // create new context based on current attributes Context newContext = conte...

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public void run(Context context, XMLOutput output) throws Exception { log.info( "Invoking dynamic tag with attributes: " + attributes ); attributes.put( "org.apache.commons.jelly.body", getBody() ); // create new context based on current attributes Context newContext = context.ne...

public void run(Context context, XMLOutput output) throws Exception { log.info( "Invoking dynamic tag with attributes: " + attributes ); attributes.put( "org.apache.commons.jelly.body", getBody() ); // create new context based on current attributes JellyContext newJellyContext = ...

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public void run(Context context, XMLOutput output) throws Exception { log.info( "Invoking dynamic tag with attributes: " + attributes ); attributes.put( "org.apache.commons.jelly.body", getBody() ); // create new context based on current attributes Context newContext = context.ne...

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static public void init() { // Determine the property file name String propFname = System.getProperty( "photovault.propFname", defaultPropFname ); File propFile = new File( propFname ); props = new Properties(); try { InputStream is = new FileInputStream( propFile ); props.load( is ); } catch ( FileNotFound...

static public void init() { // Determine the property file name String propFname = System.getProperty( "photovault.propFname", defaultPropFname ); log.debug( "Using property file " + propFname ); File propFile = new File( propFname ); props = new Properties(); try { InputStream is = new FileInputStream( propFil...

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private void paintThumbnail( Graphics2D g2, PhotoInfo photo, int startx, int starty, boolean isSelected ) { // Current position in which attributes can be drawn int ypos = starty + rowHeight/2; if ( photo != null ) { Thumbnail thumbnail = null; if ( photo.hasThumbnail() ) { log.debug( ...

private void paintThumbnail( Graphics2D g2, PhotoInfo photo, int startx, int starty, boolean isSelected ) { // Current position in which attributes can be drawn int ypos = starty + rowHeight/2; if ( photo != null ) { Thumbnail thumbnail = null; log.debug( "finding thumb" ); boolean hasT...

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protected void setUp() throws Exception { super.setUp(); SQLDatabase mydb = new SQLDatabase(db.getDataSource()); Connection con = mydb.getConnection(); /* * Setting up a clean db for each of the tests */ Statement stmt = con.createStatement(); try { stmt.executeUpdate("DROP TABLE REGRESSION...

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public void testInherit() throws ArchitectException { SQLTable table1; SQLTable table2; table1 = db.getTableByName("REGRESSION_TEST1"); table2 = db.getTableByName("REGRESSION_TEST2"); table2.inherit(table1); assertEquals("The wrong 1st column was inherited",table2.getColumn(0).toString(),table1.getColu...

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public void testInherit() throws ArchitectException { SQLTable table1; SQLTable table2; table1 = db.getTableByName("REGRESSION_TEST1"); table2 = db.getTableByName("REGRESSION_TEST2"); table2.inherit(table1); assertEquals("The wrong 1st column was inherited",table2.getColumn(0).toString(),table1.getColu...

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public void testRemoveColumn() throws ArchitectException { SQLTable table1; SQLColumn col1; SQLColumn col2; table1 = db.getTableByName("REGRESSION_TEST1"); col1 = table1.getColumn(0); col2 = table1.getColumn(1); assertEquals("We removed a column when we shouldn't have",table1.getColumns().size(),2)...

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public void testRemoveColumn() throws ArchitectException { SQLTable table1; SQLColumn col1; SQLColumn col2; table1 = db.getTableByName("REGRESSION_TEST1"); col1 = table1.getColumn(0); col2 = table1.getColumn(1); assertEquals("We removed a column when we shouldn't have",table1.getColumns().size(),2)...

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public void testRemoveColumn() throws ArchitectException { SQLTable table1; SQLColumn col1; SQLColumn col2; table1 = db.getTableByName("REGRESSION_TEST1"); col1 = table1.getColumn(0); col2 = table1.getColumn(1); assertEquals("We removed a column when we shouldn't have",table1.getColumns().size(),2)...

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public void testRemoveColumnOutBounds() throws ArchitectException { SQLTable table1; SQLColumn col1; SQLColumn col2; table1 = db.getTableByName("REGRESSION_TEST1"); Exception exc = null; try { table1.removeColumn(16); } catch (IndexOutOfBoundsException e) { System.out.println("Method throws p...

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private void processFile(String fileName, int fileType, String infoFileName){ try { HaploData textData; File OutputFile; File inputFile; if(!quietMode && fileName != null){ System.out.println("Using data file " + fileName); } in...

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private File validateOutputFile(String fn){ File f = new File(fn); if (f.canWrite()){ System.out.println("File " + f.getName() + " can not be written."); System.exit(1); } if (f.exists() && !quietMode){ System.out.println("File " + f.getName() + " already...

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