rem stringlengths 0 477k | add stringlengths 0 313k | context stringlengths 6 599k |
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JMenuItem propsItem = new JMenuItem( "Properties" ); propsItem.addActionListener( this ); propsItem.setActionCommand( PHOTO_PROPS_CMD ); JMenuItem showItem = new JMenuItem( "Show image" ); showItem.addActionListener( this ); showItem.setActionCommand( PHOTO_SHOW_CMD ); JMenuItem rotateCW = new JMenuItem( "Rotate 90 deg... | editSelectionPropsAction = new EditSelectionPropsAction( this, "Properties...", null, "Edit properties of the selected photos", KeyEvent.VK_P ); JMenuItem propsItem = new JMenuItem( editSelectionPropsAction ); showSelectedPhotoAction = new ShowSelectedPhotoAction( this, "Show image", null, "Show the selected phot(s)", ... | void createUI() { photoTransferHandler = new PhotoCollectionTransferHandler( this ); setTransferHandler( photoTransferHandler ); addMouseListener( this ); addMouseMotionListener( this ); // Create the popup menu popup = new JPopupMenu(); JMenuItem props... |
Rectangle r = new Rectangle(e.getX(), e.getY(), 1, 1); scrollRectToVisible(r); | public void mouseDragged(MouseEvent e ) { switch ( dragType ) { case DRAG_TYPE_SELECT: handleSelectionDragEvent( e ); break; case DRAG_TYPE_DND: handleDnDDragEvent( e ); break; default: log.error( "Invalid drag type" ); } } | |
Thumbnail thumbnail = photo.getThumbnail(); if ( thumbnail != null ) { BufferedImage img = thumbnail.getImage(); int x = startx + (columnWidth - img.getWidth())/(int)2; int y = starty + (rowHeight - img.getHeight())/(int)2; g2.drawImage( img, new AffineTransform( 1f, 0f, 0f, 1f, x, y ), null ); if ( isSelected ) { ... | Thumbnail thumbnail = null; if ( photo.hasThumbnail() ) { thumbnail = photo.getThumbnail(); } else { thumbnail = Thumbnail.getDefaultThumbnail(); if ( !thumbCreatorThread.isBusy() ) { thumbCreatorThread.createThumbnail( photo ); } } BufferedImage img = thumbnail.getImage(); int x = startx + (columnWidth - img.getWidt... | 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 = photo.getThumbnail(); if (... |
Color prevBkg = g2.getBackground(); if ( isSelected ) { g2.setBackground( Color.BLUE ); } Font attrFont = new Font( "Arial", Font.PLAIN, 10 ); FontRenderContext frc = g2.getFontRenderContext(); if ( showDate && photo.getShootTime() != null ) { DateFormat df = new SimpleDateFormat( "dd.MM.yyyy k:mm" ); String dateStr = ... | g2.drawImage( img, new AffineTransform( 1f, 0f, 0f, 1f, x, y ), null ); if ( isSelected ) { Stroke prevStroke = g2.getStroke(); Color prevColor = g2.getColor(); g2.setStroke( new BasicStroke( 3.0f) ); g2.setColor( Color.BLUE ); g2.drawRect( x, y, img.getWidth(), img.getHeight() ); g2.setColor( prevColor ); g2.setStroke... | 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 = photo.getThumbnail(); if (... |
logger.debug(toString()); | logger.debug("posting report: "+toString()); | public void postReport() { logger.debug(toString()); if (numReportsThisRun++ > MAX_REPORT_TRIES) { logger.info( String.format( "Not logging this error, threshold of %d exceeded", MAX_REPORT_TRIES)); return; } exception.printStackTra... |
BufferedReader in = new BufferedReader(new InputStreamReader(dest.getInputStream())); | InputStreamReader inputStreamReader = new InputStreamReader(dest.getInputStream()); BufferedReader in = new BufferedReader(inputStreamReader); | public void postReport() { logger.debug(toString()); if (numReportsThisRun++ > MAX_REPORT_TRIES) { logger.info( String.format( "Not logging this error, threshold of %d exceeded", MAX_REPORT_TRIES)); return; } exception.printStackTra... |
logger.debug("Finished posting report"); | public void postReport() { logger.debug(toString()); if (numReportsThisRun++ > MAX_REPORT_TRIES) { logger.info( String.format( "Not logging this error, threshold of %d exceeded", MAX_REPORT_TRIES)); return; } exception.printStackTra... | |
T.add((getSubscribersLink(topicID,String.valueOf(emailCount))),4,row); | T.add((getSubscribersLink(topic.getListId(),String.valueOf(emailCount))),4,row); | public PresentationObject getTopicsOverView(IWContext iwc){ Table T = new Table(); int row = 1; T.add(getTopicLink(-1,iwrb.getLocalizedString("new_topic","New topic")),1,row); row++; T.add(tf.format(iwrb.getLocalizedString("name","Name"),tf.HEADER),1,row); T.add(tf.format(iwrb.getLocalizedString("category",... |
pairwiseButton.setSelected(true); | tripleButton.setSelected(true); | public void refreshTable(){ this.removeAll(); snpsByName = new Hashtable(); this.setLayout(new BoxLayout(this,BoxLayout.Y_AXIS)); Vector columnNames = new Vector(); Vector tableData = new Vector(); columnNames.add("#"); columnNames.add("Name"); columnNames.add... |
Vector results = pedFile.getResults(); | Vector results = null; if (pedFile != null){ results = pedFile.getResults(); } | void prepareMarkerInput(File infile, String[][] hapmapGoodies) throws IOException, HaploViewException{ //this method is called to gather data about the markers used. //It is assumed that the input file is two columns, the first being //the name and the second the absolute position. the maxdist ... |
MarkerResult mr = (MarkerResult)results.elementAt(i); | MarkerResult mr = null; if (results != null){ mr = (MarkerResult)results.elementAt(i); } | void prepareMarkerInput(File infile, String[][] hapmapGoodies) throws IOException, HaploViewException{ //this method is called to gather data about the markers used. //It is assumed that the input file is two columns, the first being //the name and the second the absolute position. the maxdist ... |
pos, Math.rint(mr.getMAF()*100.0)/100.0, a1, a2, | pos, maf, a1, a2, | void prepareMarkerInput(File infile, String[][] hapmapGoodies) throws IOException, HaploViewException{ //this method is called to gather data about the markers used. //It is assumed that the input file is two columns, the first being //the name and the second the absolute position. the maxdist ... |
double genoPC = mr.getGenoPercent(); if (prevPosition != Long.MIN_VALUE){ if (pos == prevPosition){ dupsToBeFlagged = true; if (genoPC >= mr.getGenoPercent()){ thisMarker.setDup(1); prevMarker.setDup(2); }else{ thisMarker.setDup(2); prevMarker.setDup(1); | if (mr != null){ double genoPC = mr.getGenoPercent(); if (prevPosition != Long.MIN_VALUE){ if (pos == prevPosition){ dupsToBeFlagged = true; if (genoPC >= mr.getGenoPercent()){ thisMarker.setDup(1); prevMarker.setDup(2); }else{ thisMarker.setDup(2); prevMarker.setDup(1); } | void prepareMarkerInput(File infile, String[][] hapmapGoodies) throws IOException, HaploViewException{ //this method is called to gather data about the markers used. //It is assumed that the input file is two columns, the first being //the name and the second the absolute position. the maxdist ... |
} prevPosition = pos; prevMarker = thisMarker; | prevPosition = pos; prevMarker = thisMarker; } | void prepareMarkerInput(File infile, String[][] hapmapGoodies) throws IOException, HaploViewException{ //this method is called to gather data about the markers used. //It is assumed that the input file is two columns, the first being //the name and the second the absolute position. the maxdist ... |
markerInfo.add(new SNP("Marker " + String.valueOf(i+1), (i*4000), Math.rint(mr.getMAF()*100.0)/100.0,a1,a2)); | markerInfo.add(new SNP("Marker " + String.valueOf(i+1), (i*4000), maf,a1,a2)); | void prepareMarkerInput(File infile, String[][] hapmapGoodies) throws IOException, HaploViewException{ //this method is called to gather data about the markers used. //It is assumed that the input file is two columns, the first being //the name and the second the absolute position. the maxdist ... |
service.addApplication(Utils.getServiceContext(context), appConfigData); | service.addAppWithDashboard(Utils.getServiceContext(context), appConfigData); | public ActionForward execute(WebContext context, ActionMapping mapping, ActionForm actionForm, HttpServletRequest request, HttpServletResponse response) throws Exception{ ... |
public UserList(int count, String namePrefix, String domain, String password) { this(count, namePrefix, domain); m_password = password; | public UserList(int count, String namePrefix, String domain) { m_count = count; m_namePrefix = namePrefix; m_domain = domain; | public UserList(int count, String namePrefix, String domain, String password) { this(count, namePrefix, domain); m_password = password; } |
p.add(filename = new JTextField((ddlg.getFile() == null ? "" : ddlg.getFile().getPath()), 35)); | File outFile = ddlg.getFile(); if (outFile == null) { outFile = new File(System.getProperty("user.dir"), project.getName()+".ddl"); } p.add(filename = new JTextField((outFile.getPath()), 35)); | protected void setup() { GenericDDLGenerator ddlg = project.getDDLGenerator(); setLayout(new FormLayout()); add(new JLabel("Allow Connection?")); add(allowConnection = new JCheckBox()); allowConnection.setSelected(ddlg.getAllowConnection()); add(new JLabel("Output File")); JPanel p = new JPanel(new FlowLayout()... |
registerTag("setTimeZone", SetTimeZoneTag.class); registerTag("timeZone", TimeZoneTag.class); | public FmtTagLibrary() { registerTag("bundle", BundleTag.class); registerTag("message", MessageTag.class); registerTag("param", ParamTag.class); registerTag("setLocale", SetLocaleTag.class); } | |
System.out.println("SQLObject: firing dbChildrenInserted event"); | System.out.println(getClass().getName()+": firing dbChildrenInserted event"); | protected void fireDbChildrenInserted(int[] newIndices, List newChildren) { System.out.println("SQLObject: firing dbChildrenInserted event"); SQLObjectEvent e = new SQLObjectEvent (this, newIndices, (SQLObject[]) newChildren.toArray(new SQLObject[newChildren.size()])); Iterator it = getSqlObjectListeners().... |
System.out.println("SQLObject: notified "+count+" listeners"); | System.out.println(getClass().getName()+": notified "+count+" listeners"); | protected void fireDbChildrenInserted(int[] newIndices, List newChildren) { System.out.println("SQLObject: firing dbChildrenInserted event"); SQLObjectEvent e = new SQLObjectEvent (this, newIndices, (SQLObject[]) newChildren.toArray(new SQLObject[newChildren.size()])); Iterator it = getSqlObjectListeners().... |
expression = createExpression( localName, attributeName, attributeValue ); | expression = createConstantExpression( localName, attributeName, attributeValue ); | protected TagScript createStaticTag( String namespaceURI, String localName, Attributes list ) throws SAXException { try { Tag tag = new StaticTag( namespaceURI, localName ); TagScript script = new TagScript( tag ); // now iterate through through th... |
expression = createExpression( localName, attributeName, attributeValue ); | expression = createConstantExpression( localName, attributeName, attributeValue ); | protected TagScript createTag( String namespaceURI, String localName, Attributes list ) throws SAXException { try { // use the URI to load a taglib TagLibrary taglib = (TagLibrary) taglibs.get( namespaceURI ); if ( taglib == null ) { if ( namespaceURI != null &... |
XMLParser parser = new XMLParser(); parser.setContext( getContext() ); Script script = parser.parse( getUrl().openStream() ); script = script.compile(); if ( log.isDebugEnabled() ) { log.debug( "Compiled script: " + getUrl() ); } return script; } | XMLParser parser = new XMLParser(); parser.setJellyContext(getJellyContext()); Script script = parser.parse(getUrl().openStream()); script = script.compile(); if (log.isDebugEnabled()) { log.debug("Compiled script: " + getUrl()); } return script; } | public Script compileScript() throws Exception { XMLParser parser = new XMLParser(); parser.setContext( getContext() ); Script script = parser.parse( getUrl().openStream() ); script = script.compile(); if ( log.isDebugEnabled() ) { log.debug( "Compiled script: "... |
if ( args.length <= 0 ) { System.out.println( "Usage: Jelly scriptFile [outputFile]" ); return; } Jelly jelly = new Jelly(); jelly.setScript( args[0] ); Writer writer = new BufferedWriter( new OutputStreamWriter( System.out ) ); Script script = jelly.compileScript(); XMLOutput output = XMLOutput.createXMLOutput( w... | if (args.length <= 0) { System.out.println("Usage: Jelly scriptFile [outputFile]"); return; } Jelly jelly = new Jelly(); jelly.setScript(args[0]); Writer writer = new BufferedWriter(new OutputStreamWriter(System.out)); Script script = jelly.compileScript(); XMLOutput output = XMLOutput.createXMLOutput(writer); Jell... | public static void main(String[] args) throws Exception { if ( args.length <= 0 ) { System.out.println( "Usage: Jelly scriptFile [outputFile]" ); return; } Jelly jelly = new Jelly(); jelly.setScript( args[0] ); /* // later we might wann... |
oldThumbnail = null; | protected void createThumbnail( VolumeBase volume ) { log.debug( "Creating thumbnail for " + uid ); ODMGXAWrapper txw = new ODMGXAWrapper(); txw.lock( this, Transaction.WRITE ); // Maximum size of the thumbnail int maxThumbWidth = 100; int maxThumbHeight = 1... | |
oldThumbnail = null; | public Thumbnail getExistingThumbnail() { if ( thumbnail == null ) { log.debug( "Finding thumbnail from database" ); // First try to find an instance from existing instances ImageInstance original = null; for ( int n = 0; n < instances.size(); n++ ) { ... | |
oldThumbnail = null; | public Thumbnail getThumbnail() { log.debug( "getThumbnail: entry, Finding thumbnail for " + uid ); if ( thumbnail == null ) { thumbnail = getExistingThumbnail(); if ( thumbnail == null ) { // Next try to create a new thumbnail instance log.debug( "N... | |
thumbnail = null; | invalidateThumbnail(); | public void setCropBounds( Rectangle2D cropBounds ) { ODMGXAWrapper txw = new ODMGXAWrapper(); txw.lock( this, Transaction.WRITE ); if ( !cropBounds.equals( getCropBounds() ) ) { // Rotation changes, invalidate the thumbnail thumbnail = null; } cropMinX = cro... |
thumbnail = null; | invalidateThumbnail(); | public void setPrefRotation(double v) { ODMGXAWrapper txw = new ODMGXAWrapper(); txw.lock( this, Transaction.WRITE ); if ( v != prefRotation ) { // Rotation changes, invalidate the thumbnail thumbnail = null; } this.prefRotation = v; modified(); ... |
String newPhotographer = "New photographer"; ctrl.setField( PhotoInfoController.PHOTOGRAPHER, newPhotographer ); try { ctrl.save(); } catch ( Exception e ) { fail( "Exception while saving: " + e.getMessage() ); } assertEquals( "PhotoInfo fields should match ctrl", newPhotographer, photo.getPhotographer() ); try { Photo... | public void testNewPhotoCreation() { File testFile = new File( "c:\\java\\photovault\\testfiles\\test1.jpg" ); ctrl.createNewPhoto( testFile ); String photographer = "Test photographer"; ctrl.setField( PhotoInfoController.PHOTOGRAPHER, photographer ); assertEquals( photographer, ctrl.getField( PhotoInfoCont... | |
Expression expression = (Expression) entry.getValue(); | if(name.indexOf(':')!=-1) name = name.substring(name.indexOf(':')+1); ExpressionAttribute expat = (ExpressionAttribute) entry.getValue(); Expression expression = expat.exp; | public void run(JellyContext context, XMLOutput output) throws JellyTagException { try { startNamespacePrefixes(output); } catch (SAXException e) { throw new JellyTagException("could not start namespace prefixes",e); } Tag tag = null; try { tag = g... |
dynaTag.setAttribute(name, value); | if(expat.prefix!=null || expat.prefix.length()>0 && tag instanceof StaticTag) ((StaticTag) dynaTag).setAttribute(name,expat.prefix, expat.nsURI,value); else dynaTag.setAttribute(name, value); | public void run(JellyContext context, XMLOutput output) throws JellyTagException { try { startNamespacePrefixes(output); } catch (SAXException e) { throw new JellyTagException("could not start namespace prefixes",e); } Tag tag = null; try { tag = g... |
System.out.println("The current Name is the same as the old name"); | logger.debug("The current Name is the same as the old name"); | public void actionPerformed(ActionEvent e) { logger.debug("DBCS Action invoked"); ArchitectDataSource newDS = dbcsPanel.getDbcs(); String curName = null; for (Component c : ((TextPanel)dbcsPanel.getComponents()[0]).getComponents()) { if ("dbNameField".equals(c.getName())){ curName = ((JTextField) c).getText(... |
} else { this.shouldExport = false; | public void setExport(String export) { if ("true".equals(export)) { this.shouldExport = true; } } | |
} else { this.shouldInherit = false; | public void setInherit(String inherit) { if ("true".equals(inherit)) { this.shouldInherit = true; } } | |
public void characters(char ch[], int start, int length) throws SAXException { | public void characters(char[] ch, int start, int length) throws SAXException { | public void characters(char ch[], int start, int length) throws SAXException { contentHandler.characters(ch, start, length); } |
if (log.isDebugEnabled()) log.debug("error setting lexical handler properties", e); | if (log.isDebugEnabled()) { log.debug("error setting lexical handler properties", e); } | public static XMLOutput createXMLOutput(XMLReader xmlReader) { XMLOutput output = new XMLOutput(xmlReader.getContentHandler()); // isn't it lovely what we've got to do to find the LexicalHandler... ;-) for (int i = 0; i < LEXICAL_HANDLER_NAMES.length; i++) { try { Obje... |
contentHandler.endPrefixMapping(prefix); | namespaceStack.popNamespace(prefix); | public void endPrefixMapping(String prefix) throws SAXException { contentHandler.endPrefixMapping(prefix); } |
} else if (contentHandler instanceof XMLOutput) { ((XMLOutput)contentHandler).flush(); | public void flush() throws IOException { if( contentHandler instanceof XMLWriter ) { ((XMLWriter)contentHandler).flush(); } } | |
public void ignorableWhitespace(char ch[], int start, int length) | public void ignorableWhitespace(char[] ch, int start, int length) | public void ignorableWhitespace(char ch[], int start, int length) throws SAXException { contentHandler.ignorableWhitespace(ch, start, length); } |
contentHandler.startPrefixMapping(prefix, uri); | namespaceStack.pushNamespace(prefix, uri); | public void startPrefixMapping(String prefix, String uri) throws SAXException { contentHandler.startPrefixMapping(prefix, uri); } |
if (Options.getAssocTest() == 2) { | if (Options.getAssocTest() == ASSOC_TRIO) { | private void full_em_breakup( byte[][] input_haplos, int[] block_size, int numTrios, Vector affStatus) throws HaploViewException{ int num_poss, iter;//, maxk, numk; double total;//, maxprob; int block, start_locus, end_locus, biggest_block_size; int poss_full;//, best, h1, h2; int... |
if (Options.getAssocTest() == 1){ | if (Options.getAssocTest() == ASSOC_CC){ | private void full_em_breakup( byte[][] input_haplos, int[] block_size, int numTrios, Vector affStatus) throws HaploViewException{ int num_poss, iter;//, maxk, numk; double total;//, maxprob; int block, start_locus, end_locus, biggest_block_size; int poss_full;//, best, h1, h2; int... |
if(Options.getAssocTest() == 2) | if(Options.getAssocTest() == ASSOC_TRIO) | private void full_em_breakup( byte[][] input_haplos, int[] block_size, int numTrios, Vector affStatus) throws HaploViewException{ int num_poss, iter;//, maxk, numk; double total;//, maxprob; int block, start_locus, end_locus, biggest_block_size; int poss_full;//, best, h1, h2; int... |
} else if (Options.getAssocTest() == 1){ | } else if (Options.getAssocTest() == ASSOC_CC){ | private void full_em_breakup( byte[][] input_haplos, int[] block_size, int numTrios, Vector affStatus) throws HaploViewException{ int num_poss, iter;//, maxk, numk; double total;//, maxprob; int block, start_locus, end_locus, biggest_block_size; int poss_full;//, best, h1, h2; int... |
parent = new SQLTable(); | protected void setUp() throws Exception { parent.addChild(child); } | |
public void run(Context context, XMLOutput output) throws Exception { | public void run(JellyContext context, XMLOutput output) throws Exception { | public void run(Context context, XMLOutput output) throws Exception { getBody().run( context, output ); } |
double genoPct = 100.0*(het+hom)/(het+hom+missing); return genoPct; | if (het+hom+missing == 0){ return 0; }else{ return 100.0*(het+hom)/(het+hom+missing); } | private double getGenoPercent(int het, int hom, int missing){ double genoPct = 100.0*(het+hom)/(het+hom+missing); return genoPct; } |
clickY-botEdgeShift, | clickY-botEdgeShift+smallDataVertSlop, | public void mousePressed (MouseEvent e) { Rectangle blockselector = new Rectangle(clickXShift-boxRadius,clickYShift - boxRadius, (Chromosome.getFilteredSize()*boxSize), boxSize); //if users right clicks & holds, pop up the info if ((e.getModifiers() & InputEvent.BUTTON3_MASK) == ... |
public void run(Context context, XMLOutput output) throws Exception { | public void run(JellyContext context, XMLOutput output) throws Exception { | public void run(Context context, XMLOutput output) throws Exception { DynaTag dynaTag = (DynaTag) tag; // ### probably compiling this to 2 arrays might be quicker and smaller for ( Iterator iter = attributes.entrySet().iterator(); iter.hasNext(); ) { Map.Entry entry =... |
mouseMode = mouseModeType.SELECT_TABLE; | mouseMode = MouseModeType.SELECT_TABLE; | protected void cleanup() { if(addToPP) { pp.unzoomPoint(p); logger.debug("Placing table at: "+p); pp.addImpl(tp,p,pp.getPPComponentCount()); try { pp.db.addChild(tp.getModel()); pp.selectNone(); tp.setSelected(true); mouseMode = mouseModeType.SELECT_TABLE; } catch (ArchitectExceptio... |
mouseMode = mouseModeType.RUBBERBAND_MOVE; | mouseMode = MouseModeType.RUBBERBAND_MOVE; | public void mouseMoved(MouseEvent evt) { if (rubberBand != null) { // repaint old region in case of shrinkage Rectangle dirtyRegion = zoomRect(new Rectangle(rubberBand)); Point p = unzoomPoint(evt.getPoint()); rubberBand.setBounds(rubberBandOrigin.x, rubberBandOrigin.y, 0, 0); rubberBand.add(p); ... |
if ( mouseMode == mouseModeType.CREATING_RELATIONSHIP ) { } else { | if ( mouseMode == MouseModeType.CREATING_RELATIONSHIP ) { } else { | public void mousePressed(MouseEvent evt) { requestFocus(); maybeShowPopup(evt); Point p = evt.getPoint(); unzoomPoint(p); PlayPenComponent c = contentPane.getComponentAt(p); if (c != null) p.translate(-c.getX(), -c.getY()); if (c instanceof Relationship) { Relationship r = (Relationship) c; ... |
mouseMode = mouseModeType.MULTI_SELECT; } else { mouseMode = mouseModeType.SELECT_RELATIONSHIP; | mouseMode = MouseModeType.MULTI_SELECT; } else { mouseMode = MouseModeType.SELECT_RELATIONSHIP; | public void mousePressed(MouseEvent evt) { requestFocus(); maybeShowPopup(evt); Point p = evt.getPoint(); unzoomPoint(p); PlayPenComponent c = contentPane.getComponentAt(p); if (c != null) p.translate(-c.getX(), -c.getY()); if (c instanceof Relationship) { Relationship r = (Relationship) c; ... |
if ( mouseMode == mouseModeType.CREATING_TABLE ) { | if ( mouseMode == MouseModeType.CREATING_TABLE ) { | public void mousePressed(MouseEvent evt) { requestFocus(); maybeShowPopup(evt); Point p = evt.getPoint(); unzoomPoint(p); PlayPenComponent c = contentPane.getComponentAt(p); if (c != null) p.translate(-c.getX(), -c.getY()); if (c instanceof Relationship) { Relationship r = (Relationship) c; ... |
if ( !tp.isSelected() || mouseMode == mouseModeType.IDLE ) { mouseMode = mouseModeType.SELECT_TABLE; | if ( !tp.isSelected() || mouseMode == MouseModeType.IDLE ) { mouseMode = MouseModeType.SELECT_TABLE; | public void mousePressed(MouseEvent evt) { requestFocus(); maybeShowPopup(evt); Point p = evt.getPoint(); unzoomPoint(p); PlayPenComponent c = contentPane.getComponentAt(p); if (c != null) p.translate(-c.getX(), -c.getY()); if (c instanceof Relationship) { Relationship r = (Relationship) c; ... |
mouseMode = mouseModeType.MULTI_SELECT; | mouseMode = MouseModeType.MULTI_SELECT; | public void mousePressed(MouseEvent evt) { requestFocus(); maybeShowPopup(evt); Point p = evt.getPoint(); unzoomPoint(p); PlayPenComponent c = contentPane.getComponentAt(p); if (c != null) p.translate(-c.getX(), -c.getY()); if (c instanceof Relationship) { Relationship r = (Relationship) c; ... |
mouseMode = mouseModeType.SELECT_COLUMN; | mouseMode = MouseModeType.SELECT_COLUMN; | public void mousePressed(MouseEvent evt) { requestFocus(); maybeShowPopup(evt); Point p = evt.getPoint(); unzoomPoint(p); PlayPenComponent c = contentPane.getComponentAt(p); if (c != null) p.translate(-c.getX(), -c.getY()); if (c instanceof Relationship) { Relationship r = (Relationship) c; ... |
mouseMode = mouseModeType.IDLE; | mouseMode = MouseModeType.IDLE; | public void mousePressed(MouseEvent evt) { requestFocus(); maybeShowPopup(evt); Point p = evt.getPoint(); unzoomPoint(p); PlayPenComponent c = contentPane.getComponentAt(p); if (c != null) p.translate(-c.getX(), -c.getY()); if (c instanceof Relationship) { Relationship r = (Relationship) c; ... |
mouseMode = mouseModeType.MULTI_SELECT; | mouseMode = MouseModeType.MULTI_SELECT; | public void mouseReleased(MouseEvent evt) { draggingTablePanes = false; if (rubberBand != null) { if (evt.getButton() == MouseEvent.BUTTON1) { Rectangle dirtyRegion = rubberBand; rubberBandOrigin = null; rubberBand = null; zoomRect(dirtyRegion); repaintRubberBandRegion(dirtyRegion... |
mouseMode = mouseModeType.IDLE; | mouseMode = MouseModeType.IDLE; | public void mouseReleased(MouseEvent evt) { draggingTablePanes = false; if (rubberBand != null) { if (evt.getButton() == MouseEvent.BUTTON1) { Rectangle dirtyRegion = rubberBand; rubberBandOrigin = null; rubberBand = null; zoomRect(dirtyRegion); repaintRubberBandRegion(dirtyRegion... |
mouseMode = MouseModeType.MULTI_SELECT; | public void selectAll() { for (int i = 0, n = contentPane.getComponentCount(); i < n; i++) { if (contentPane.getComponent(i) instanceof Selectable) { Selectable s = (Selectable) contentPane.getComponent(i); s.setSelected(true); } } } | |
public static void setMouseMode(mouseModeType mouseMode) { | public static void setMouseMode(MouseModeType mouseMode) { | public static void setMouseMode(mouseModeType mouseMode) { PlayPen.mouseMode = mouseMode; } |
noImage = true; | public void loadMarkers(){ markersLoaded = true; repaint(); } | |
System.out.println(System.currentTimeMillis()); | public void paintComponent(Graphics g){ Graphics2D g2 = (Graphics2D) g; Dimension size = getSize(); Dimension pref = getPreferredSize(); Rectangle visRect = getVisibleRect(); /* boxSize = ((clipRect.width-2*H_BORDER)/dPrimeTable.length-1); if (boxSize... | |
textData = new HaploData(); | textData = new HaploData(0); | private void processFile(String fileName,int fileType,String infoFileName){ try { int outputType; long maxDistance; long negMaxDistance; HaploData textData; File OutputFile; File inputFile; inputFile = new File(fileName); ... |
loginContext = new LoginContext(AuthConstants.AUTH_CONFIG_INDEX, callbackHandler); | final LoginContext loginContext = new LoginContext(AuthConstants.AUTH_CONFIG_INDEX, callbackHandler); | public void login(ServiceContext context, String username, String password) throws ServiceException{ LoginCallbackHandler callbackHandler = new LoginCallbackHandler(username, password); User user = null; UserManager userManager = UserMana... |
try{ loginContext.logout(); UserActivityLogger.getInstance().logActivity(user.getName(), "logged out successfully"); }catch(LoginException lex){ throw new ServiceException(ErrorCodes.UNKNOWN_ERROR); } | UserActivityLogger.getInstance().logActivity(user.getName(), "logged out successfully"); | public void logout(ServiceContext context, User user)throws ServiceException{ try{ loginContext.logout(); UserActivityLogger.getInstance().logActivity(user.getName(), "logged out successfully"); }catch(LoginException lex){ throw new ServiceException(... |
Point bcp = new Point(Math.max(0, Math.min(tpsize.width, p.x)), Math.max(0, Math.min(tpsize.height, p.y))); boolean adjustX = bcp.y != 0 && bcp.y != tpsize.height; boolean adjustY = bcp.x != 0 && bcp.x != tpsize.width; | if (tp == relationship.getPkTable()) { if ((orientation & PARENT_FACES_LEFT) != 0) ep = new Point(0, Math.max(0, Math.min(tpsize.height, p.y))); else if ((orientation & PARENT_FACES_RIGHT) != 0) ep = new Point(tpsize.width, Math.max(0, Math.min(tpsize.height, p.y))); else if ((orientation & PARENT_FACES_TOP) != 0) ep... | public Point closestEdgePoint(TablePane tp, Point p) { Dimension tpsize = tp.getSize(); // clip point p to inside of tp Point bcp = new Point(Math.max(0, Math.min(tpsize.width, p.x)), Math.max(0, Math.min(tpsize.height, p.y))); boolean adjustX = bcp.y != 0 && bcp.y != tpsize.height; boolean adjustY = bc... |
if (adjustX) { if (bcp.x < (tpsize.width/2)) { bcp.x = 0; } else { bcp.x = tpsize.width; | ep = new Point(Math.max(0, Math.min(tpsize.width, p.x)), Math.max(0, Math.min(tpsize.height, p.y))); boolean adjustX = ep.y != 0 && ep.y != tpsize.height; boolean adjustY = ep.x != 0 && ep.x != tpsize.width; if (adjustX) { if (ep.x < (tpsize.width/2)) { ep.x = 0; } else { ep.x = tpsize.width; } | public Point closestEdgePoint(TablePane tp, Point p) { Dimension tpsize = tp.getSize(); // clip point p to inside of tp Point bcp = new Point(Math.max(0, Math.min(tpsize.width, p.x)), Math.max(0, Math.min(tpsize.height, p.y))); boolean adjustX = bcp.y != 0 && bcp.y != tpsize.height; boolean adjustY = bc... |
} if (adjustY) { if (bcp.y < (tpsize.height/2)) { bcp.y = 0; } else { bcp.y = tpsize.height; | if (adjustY) { if (ep.y < (tpsize.height/2)) { ep.y = 0; } else { ep.y = tpsize.height; } | public Point closestEdgePoint(TablePane tp, Point p) { Dimension tpsize = tp.getSize(); // clip point p to inside of tp Point bcp = new Point(Math.max(0, Math.min(tpsize.width, p.x)), Math.max(0, Math.min(tpsize.height, p.y))); boolean adjustX = bcp.y != 0 && bcp.y != tpsize.height; boolean adjustY = bc... |
return bcp; | return ep; | public Point closestEdgePoint(TablePane tp, Point p) { Dimension tpsize = tp.getSize(); // clip point p to inside of tp Point bcp = new Point(Math.max(0, Math.min(tpsize.width, p.x)), Math.max(0, Math.min(tpsize.height, p.y))); boolean adjustX = bcp.y != 0 && bcp.y != tpsize.height; boolean adjustY = bc... |
this.getRootPane().setDefaultButton(okButton); | 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(); JPan... | |
if ( selected != null ) { String newName = (String) JOptionPane.showInputDialog( this, "Enter name for new folder", "New folder", JOptionPane.PLAIN_MESSAGE, null, null, "New folder" ); if ( newName != null ) { PhotoFolder newFolder = PhotoFolder.create( newName, selected ); } } | if ( selected != null ) { boolean ready = false; while ( !ready ) { String newName = (String) JOptionPane.showInputDialog( this, "Enter name for new folder", "New folder", JOptionPane.PLAIN_MESSAGE, null, null, "New folder" ); if ( newName != null ) { if ( newName.length() > PhotoFolder.NAME_LENGTH ) { JOptionPane.show... | void createNewFolder() { if ( selected != null ) { String newName = (String) JOptionPane.showInputDialog( this, "Enter name for new folder", "New folder", JOptionPane.PLAIN_MESSAGE, null, null, "New folder" ); if ( newName != null ) { PhotoFolder newFolder = PhotoFolder.create( new... |
String newName = (String) JOptionPane.showInputDialog( this, "Enter new name", "Rename folder", JOptionPane.PLAIN_MESSAGE, null, null, origName ); if ( newName != null ) { PhotoFolder f = selected; f.setName( newName ); log.debug( "Changed name to " + newName ); } } | boolean ready = false; while ( !ready ) { String newName = (String) JOptionPane.showInputDialog( this, "Enter new name", "Rename folder", JOptionPane.PLAIN_MESSAGE, null, null, origName ); if ( newName != null ) { PhotoFolder f = selected; try { f.setName( newName ); ready = true; } catch ( IllegalArgumentException e )... | void renameSelectedFolder() { if ( selected != null ) { String origName = selected.getName(); String newName = (String) JOptionPane.showInputDialog( this, "Enter new name", "Rename folder", JOptionPane.PLAIN_MESSAGE, null, null, origName ); if ( newName != null ) { PhotoFolder f = s... |
markerInfo.add(new SNP(String.valueOf(i), (i*4000), maf)); | markerInfo.add(new SNP(String.valueOf(i), (i*3000), maf)); | public void linkageToChrom(boolean[] markerResults, PedFile pedFile){ Vector indList = pedFile.getOrder(); int numMarkers = 0; Vector usedParents = new Vector(); Individual currentInd; Family currentFamily; Vector chrom = new Vector(); for(int x=0; x < indList.size()... |
markerInfo.add(new SNP(String.valueOf(i), (i*4000), maf)); | markerInfo.add(new SNP(String.valueOf(i), (i*3000), maf)); | void prepareHapsInput(File infile) throws IOException{ //this method is called to suck in data from a file (its only argument) //of genotypes and sets up the Chromosome objects. String currentLine; Vector chroms = new Vector(); byte[] genos = new byte[0]; String ped, indiv;... |
int prepareMarkerInput(File infile) throws IOException{ | int prepareMarkerInput(File infile, long maxdist) throws IOException{ | int prepareMarkerInput(File infile) throws IOException{ //this method is called to gather data about the markers used. //It is assumed that the input file is two columns, the first being //the name and the second the absolute position String currentLine; Vector markers = new Vecto... |
for (int pos2 = 1; pos2 < dPrimeTable.length; pos2++){ for (int pos1 = 0; pos1 < pos2; pos1++){ long sep = Chromosome.getMarker(pos1).getPosition() - Chromosome.getMarker(pos2).getPosition(); if (maxdist > 0){ if ((sep > maxdist || sep < negMaxdist)){ dPrimeTable[pos1][pos2] = null; continue; } } } } | int prepareMarkerInput(File infile) throws IOException{ //this method is called to gather data about the markers used. //It is assumed that the input file is two columns, the first being //the name and the second the absolute position String currentLine; Vector markers = new Vecto... | |
public CreateRelationshipAction(PlayPen pp) { | public CreateRelationshipAction() { | public CreateRelationshipAction(PlayPen pp) { super("Create Relationship"); this.pp = pp; pp.addSelectionListener(this); } |
this.pp = pp; pp.addSelectionListener(this); | setEnabled(false); | public CreateRelationshipAction(PlayPen pp) { super("Create Relationship"); this.pp = pp; pp.addSelectionListener(this); } |
setShoresMixedCaseIdentifier(dbmd.storesMixedCaseIdentifiers()); setShoresUpperCaseIdentifier(dbmd.storesMixedCaseIdentifiers()); setShoresLowerCaseIdentifier(dbmd.storesMixedCaseIdentifiers()); | public synchronized void populate() throws ArchitectException { if (populated) return; int oldSize = children.size(); logger.debug("SQLDatabase: populate starting"); Connection con = null; ResultSet rs = null; try { con = getConnection(); DatabaseMetaData dbmd = con.getMetaData(); rs = dbmd.getCatalogs... | |
EM(){ | EM(Vector chromosomes, int numTrios){ | EM(){ //an old-school speedup courtesy of mjdaly two_n[0]=1; for (int i=1; i<31; i++){ two_n[i]=2*two_n[i-1]; } } |
this.chromosomes = chromosomes; this.numTrios = numTrios; | EM(){ //an old-school speedup courtesy of mjdaly two_n[0]=1; for (int i=1; i<31; i++){ two_n[i]=2*two_n[i-1]; } } | |
public EMReturn full_em_breakup( byte[][] input_haplos, int max_missing, int[] block_size, int dump_phased_haplos, int numTrios) throws HaploViewException{ | private void full_em_breakup( byte[][] input_haplos, int[] block_size, int numTrios, Vector affStatus) throws HaploViewException{ | public EMReturn full_em_breakup( byte[][] input_haplos, int max_missing, int[] block_size, int dump_phased_haplos, int numTrios) throws HaploViewException{ int num_poss, iter;//, maxk, numk; double total;//, maxprob; int block, start_locus, end_locus, biggest_block_size; int poss_full;//... |
boolean trioPhasing = true; | public EMReturn full_em_breakup( byte[][] input_haplos, int max_missing, int[] block_size, int dump_phased_haplos, int numTrios) throws HaploViewException{ int num_poss, iter;//, maxk, numk; double total;//, maxprob; int block, start_locus, end_locus, biggest_block_size; int poss_full;//... | |
if (trioPhasing) { | if (Options.getAssocTest() == 2) { | public EMReturn full_em_breakup( byte[][] input_haplos, int max_missing, int[] block_size, int dump_phased_haplos, int numTrios) throws HaploViewException{ int num_poss, iter;//, maxk, numk; double total;//, maxprob; int block, start_locus, end_locus, biggest_block_size; int poss_full;//... |
tempHap = (String)theHaplos.nextElement(); System.out.println(tempHap); } */ | tempHap = (String)theHaplos.nextElement(); System.out.println(tempHap); } */ Vector caseFreqs = new Vector(); Vector controlFreqs = new Vector(); double[] tempCase, tempControl, totalCase, totalControl; if (Options.getAssocTest() == 1){ tempCase = new double[poss_full]; tempControl = new double[poss_full]; totalCase =... | public EMReturn full_em_breakup( byte[][] input_haplos, int max_missing, int[] block_size, int dump_phased_haplos, int numTrios) throws HaploViewException{ int num_poss, iter;//, maxk, numk; double total;//, maxprob; int block, start_locus, end_locus, biggest_block_size; int poss_full;//... |
if(trioPhasing) | if(Options.getAssocTest() == 2) | public EMReturn full_em_breakup( byte[][] input_haplos, int max_missing, int[] block_size, int dump_phased_haplos, int numTrios) throws HaploViewException{ int num_poss, iter;//, maxk, numk; double total;//, maxprob; int block, start_locus, end_locus, biggest_block_size; int poss_full;//... |
int best1=0,best2=0,h1,h2; double tempnorm=0,product,bestProduct=0; | double tempnorm=0,product; | public EMReturn full_em_breakup( byte[][] input_haplos, int max_missing, int[] block_size, int dump_phased_haplos, int numTrios) throws HaploViewException{ int num_poss, iter;//, maxk, numk; double total;//, maxprob; int block, start_locus, end_locus, biggest_block_size; int poss_full;//... |
best1=0; best2=0; bestProduct=-999.999; tempnorm=0.00; for (int n=0; n<superdata[i].nsuper; n++) { for (int m=0; m<superdata[i+1].nsuper; m++) { if (kid_consistent(superdata[i].superposs[n].h1, superdata[i+1].superposs[m].h1,num_blocks, block_size,hlist,num_hlist,i/2,num_loci)) { product=superdata[i].superposs[n].p... | if (((Integer)affStatus.elementAt(i)).intValue() == 2){ tempnorm=0.00; for (int n=0; n<superdata[i].nsuper; n++) { for (int m=0; m<superdata[i+1].nsuper; m++) { if (kid_consistent(superdata[i].superposs[n].h1, superdata[i+1].superposs[m].h1,num_blocks, block_size,hlist,num_hlist,i/2,num_loci)) { product=superdata[i].... | public EMReturn full_em_breakup( byte[][] input_haplos, int max_missing, int[] block_size, int dump_phased_haplos, int numTrios) throws HaploViewException{ int num_poss, iter;//, maxk, numk; double total;//, maxprob; int block, start_locus, end_locus, biggest_block_size; int poss_full;//... |
if (superdata[i].superposs[n].h1 != superdata[i].superposs[n].h2) { tempT[superdata[i].superposs[n].h1]+=product; tempU[superdata[i].superposs[n].h2]+=product; | } } if (tempnorm > 0.00) { for (int j=0; j<poss_full; j++) { if (tempT[j] > 0.0000 || tempU[j] > 0.0000) { totalT[j] += (tempT[j]/tempnorm); totalU[j] += (tempU[j]/tempnorm); tempT[j]=tempU[j]=0.0000; | public EMReturn full_em_breakup( byte[][] input_haplos, int max_missing, int[] block_size, int dump_phased_haplos, int numTrios) throws HaploViewException{ int num_poss, iter;//, maxk, numk; double total;//, maxprob; int block, start_locus, end_locus, biggest_block_size; int poss_full;//... |
if (superdata[i+1].superposs[m].h1 != superdata[i+1].superposs[m].h2) { tempT[superdata[i+1].superposs[m].h1]+=product; tempU[superdata[i+1].superposs[m].h2]+=product; } tempnorm+=product; | public EMReturn full_em_breakup( byte[][] input_haplos, int max_missing, int[] block_size, int dump_phased_haplos, int numTrios) throws HaploViewException{ int num_poss, iter;//, maxk, numk; double total;//, maxprob; int block, start_locus, end_locus, biggest_block_size; int poss_full;//... | |
} } if (tempnorm > 0.00) { for (int j=0; j<poss_full; j++) { if (tempT[j] > 0.0000 || tempU[j] > 0.0000) { totalT[j] += (tempT[j]/tempnorm); totalU[j] += (tempU[j]/tempnorm); tempT[j]=tempU[j]=0.0000; } } tempnorm=0.00; | tempnorm=0.00; } | public EMReturn full_em_breakup( byte[][] input_haplos, int max_missing, int[] block_size, int dump_phased_haplos, int numTrios) throws HaploViewException{ int num_poss, iter;//, maxk, numk; double total;//, maxprob; int block, start_locus, end_locus, biggest_block_size; int poss_full;//... |
EMReturn results; | public EMReturn full_em_breakup( byte[][] input_haplos, int max_missing, int[] block_size, int dump_phased_haplos, int numTrios) throws HaploViewException{ int num_poss, iter;//, maxk, numk; double total;//, maxprob; int block, start_locus, end_locus, biggest_block_size; int poss_full;//... | |
if (trioPhasing){ results = new EMReturn((int[][])haplos_present.toArray(new int[0][0]), freqs, obsT, obsU); }else{ results = new EMReturn((int[][])haplos_present.toArray(new int[0][0]), freqs); } return results; | this.haplotypes = (int[][])haplos_present.toArray(new int[0][0]); this.frequencies = freqs; if (Options.getAssocTest() == 2){ this.obsT = obsT; this.obsU = obsU; } else if (Options.getAssocTest() == 1){ this.caseFreqs = caseFreqs; this.controlFreqs = controlFreqs; } | public EMReturn full_em_breakup( byte[][] input_haplos, int max_missing, int[] block_size, int dump_phased_haplos, int numTrios) throws HaploViewException{ int num_poss, iter;//, maxk, numk; double total;//, maxprob; int block, start_locus, end_locus, biggest_block_size; int poss_full;//... |
suite.addTestSuite(TestRelationship.class); | public static Test suite() { TestSuite suite = new TestSuite("Test for Architect's Swing GUI"); //$JUnit-BEGIN$ suite.addTestSuite(TestSwingUIProject.class); suite.addTestSuite(TestArchitectFrame.class); suite.addTestSuite(TestAutoLayoutAction.class); suite.addTestSuite(TestPlayPen.class); suite.addTestSuite(... | |
public float getFStop() { | public double getFStop() { | public float getFStop() { return FStop; } |
public float getFocalLength() { | public double getFocalLength() { | public float getFocalLength() { return focalLength; } |
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