bugged stringlengths 6 599k | fixed stringlengths 10 599k | __index_level_0__ int64 0 1.13M |
|---|---|---|
protected void configure() { // load the properties file of libraries available InputStream in = null; URL url = getClassLoader().getResource("org/apache/commons/jelly/jelly.properties"); if (url != null) { log.debug("Loading Jelly default tag libraries from: " + ur... | protected void configure() { // load the properties file of libraries available InputStream in = null; URL url = getClassLoader().getResource("org/apache/commons/jelly/jelly.properties"); if (url != null) { log.debug("Loading Jelly default tag libraries from: " + ur... | 1,109,690 |
public String getElementName(); | String getElementName(); | 1,109,691 |
public void setColumnNumber(int columnNumber); | void setColumnNumber(int columnNumber); | 1,109,692 |
public void setElementName(String elementName); | void setElementName(String elementName); | 1,109,693 |
public void setFileName(String fileName); | void setFileName(String fileName); | 1,109,694 |
public void setLineNumber(int lineNumber); | void setLineNumber(int lineNumber); | 1,109,695 |
public String getMessage() { return super.getMessage() + " At line: " + lineNumber + " column: " + columnNumber; } | public String getMessage() { return super.getMessage() + " File: " + fileName + " At tag <" + elementName + ">: line: " + lineNumber + " column: " + columnNumber; } | 1,109,696 |
private void argHandler(String[] args){ argHandlerMessages = new Vector(); int maxDistance = -1; //this means that user didn't specify any output type if it doesn't get changed below blockOutputType = -1; double hapThresh = -1; double minimumMAF=-1; double spacingThr... | private void argHandler(String[] args){ argHandlerMessages = new Vector(); int maxDistance = -1; //this means that user didn't specify any output type if it doesn't get changed below blockOutputType = -1; double hapThresh = -1; double minimumMAF=-1; double spacingThr... | 1,109,698 |
public void setAttribute(String name, Object value) { super.setAttribute( name, value.toString() ); } | public void setAttribute(String name, Object value) { super.setAttribute( name, value.toString() ); } | 1,109,700 |
public void testParserCache2() throws Exception { // no default namespace setUp("nsFilterTest.jelly"); Script script = jelly.compileScript(); script.run(context,xmlOutput); assertTrue("should have no var when default namspace is not set", context.getVariable("use... | public void testParserCache2() throws Exception { // no default namespace setUp("nsFilterTest.jelly"); Script script = jelly.compileScript(); script.run(context,xmlOutput); assertTrue("should have no var when default namspace is not set", context.getVariable("use... | 1,109,701 |
void prepareHapsInput(File infile) throws IOException, HaploViewException{ //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]; ... | public Vector prepareHapsInput(File infile) throws IOException, HaploViewException, PedFileException { //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[... | 1,109,702 |
void prepareHapsInput(File infile) throws IOException, HaploViewException{ //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]; ... | void prepareHapsInput(File infile) throws IOException, HaploViewException{ //this method is called to suck in data from a file (its only argument) //of genotypes and sets up the Chromosome objects. isHaps = true; Vector chroms = new Vector(); byte[] genos = new byte[0]; Str... | 1,109,703 |
void prepareHapsInput(File infile) throws IOException, HaploViewException{ //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]; ... | void prepareHapsInput(File infile) throws IOException, HaploViewException{ //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]; ... | 1,109,704 |
void prepareHapsInput(File infile) throws IOException, HaploViewException{ //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]; ... | void prepareHapsInput(File infile) throws IOException, HaploViewException{ //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]; ... | 1,109,705 |
void prepareHapsInput(File infile) throws IOException, HaploViewException{ //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]; ... | void prepareHapsInput(File infile) throws IOException, HaploViewException{ //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]; ... | 1,109,706 |
void prepareHapsInput(File infile) throws IOException, HaploViewException{ //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]; ... | void prepareHapsInput(File infile) throws IOException, HaploViewException{ //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]; ... | 1,109,707 |
public void doTag(final XMLOutput output) throws Exception { String name = getName(); if ( name == null ) { name = toString(); } // #### we need to redirect the output to a TestListener // or something? TestCase testCase = new TestCase(name) { ... | public void doTag(final XMLOutput output) throws Exception { String name = getName(); if ( name == null ) { name = toString(); } // #### we need to redirect the output to a TestListener // or something? TestCase testCase = new TestCase(name) { ... | 1,109,709 |
protected void runTest() throws Throwable { invokeBody(output); } | protected void runTest() throws Throwable { JellyContext newContext = new JellyContext( context ); getBody().run(newContext, output); } | 1,109,710 |
private void processFile(String fileName, int fileType, String infoFileName){ try { int outputType; long maxDistance; HaploData textData; File OutputFile; File inputFile; if(!arg_quiet && fileName != null){ System.out.println("U... | private void processFile(String fileName, int fileType, String infoFileName){ try { int outputType; long maxDistance; HaploData textData; File OutputFile; File inputFile; if(!arg_quiet && fileName != null){ System.out.println("U... | 1,109,712 |
void saveDprimeToText(){ fc.setSelectedFile(null); try{ fc.setSelectedFile(null); int returnVal = fc.showSaveDialog(this); if (returnVal == JFileChooser.APPROVE_OPTION) { new TextMethods().saveDprimeToText(theData.getFilteredTable(theData.dPrimeTable), f... | void saveDprimeToText(){ fc.setSelectedFile(null); try{ fc.setSelectedFile(null); int returnVal = fc.showSaveDialog(this); if (returnVal == JFileChooser.APPROVE_OPTION) { theData.saveDprimeToText(theData.getFilteredTable(theData.dPrimeTable), fc.getSelec... | 1,109,713 |
public int skipNext(int amount) throws FetchException { if (amount <= 0) { if (amount < 0) { throw new IllegalArgumentException("Cannot skip negative amount: " + amount); } return 0; } ResultSet rs = mResultSet; if (rs == null) { ... | public int skipNext(int amount) throws FetchException { if (amount <= 0) { if (amount < 0) { throw new IllegalArgumentException("Cannot skip negative amount: " + amount); } return 0; } ResultSet rs = mResultSet; if (rs == null) { ... | 1,109,714 |
public int skipNext(int amount) throws FetchException { if (amount <= 0) { if (amount < 0) { throw new IllegalArgumentException("Cannot skip negative amount: " + amount); } return 0; } ResultSet rs = mResultSet; if (rs == null) { ... | public int skipNext(int amount) throws FetchException { if (amount <= 0) { if (amount < 0) { throw new IllegalArgumentException("Cannot skip negative amount: " + amount); } return 0; } ResultSet rs = mResultSet; if (rs == null) { ... | 1,109,715 |
double max() default Double.MAX_VALUE; | double max() default Double.POSITIVE_INFINITY; | 1,109,717 |
double min() default Double.MIN_VALUE; | double min() default Double.NEGATIVE_INFINITY; | 1,109,718 |
public static boolean initODMG( String user, String passwd, PVDatabase dbDesc ) { getODMGImplementation(); // Find the connection repository info ConnectionRepository cr = MetadataManager.getInstance().connectionRepository(); PBKey connKey = cr.getStandardPBKeyForJcdAlias( "pv" ); JdbcCo... | public static void initODMG( String user, String passwd, PVDatabase dbDesc ) throws PhotovaultException { getODMGImplementation(); // Find the connection repository info ConnectionRepository cr = MetadataManager.getInstance().connectionRepository(); PBKey connKey = cr.getStandardPBKeyForJcdAlia... | 1,109,719 |
public static boolean initODMG( String user, String passwd, PVDatabase dbDesc ) { getODMGImplementation(); // Find the connection repository info ConnectionRepository cr = MetadataManager.getInstance().connectionRepository(); PBKey connKey = cr.getStandardPBKeyForJcdAlias( "pv" ); JdbcCo... | public static boolean initODMG( String user, String passwd, PVDatabase dbDesc ) { getODMGImplementation(); // Find the connection repository info ConnectionRepository cr = MetadataManager.getInstance().connectionRepository(); PBKey connKey = cr.getStandardPBKeyForJcdAlias( "pv" ); JdbcCo... | 1,109,720 |
public static boolean initODMG( String user, String passwd, PVDatabase dbDesc ) { getODMGImplementation(); // Find the connection repository info ConnectionRepository cr = MetadataManager.getInstance().connectionRepository(); PBKey connKey = cr.getStandardPBKeyForJcdAlias( "pv" ); JdbcCo... | public static boolean initODMG( String user, String passwd, PVDatabase dbDesc ) { getODMGImplementation(); // Find the connection repository info ConnectionRepository cr = MetadataManager.getInstance().connectionRepository(); PBKey connKey = cr.getStandardPBKeyForJcdAlias( "pv" ); JdbcCo... | 1,109,721 |
public static boolean initODMG( String user, String passwd, PVDatabase dbDesc ) { getODMGImplementation(); // Find the connection repository info ConnectionRepository cr = MetadataManager.getInstance().connectionRepository(); PBKey connKey = cr.getStandardPBKeyForJcdAlias( "pv" ); JdbcCo... | public static boolean initODMG( String user, String passwd, PVDatabase dbDesc ) { getODMGImplementation(); // Find the connection repository info ConnectionRepository cr = MetadataManager.getInstance().connectionRepository(); PBKey connKey = cr.getStandardPBKeyForJcdAlias( "pv" ); JdbcCo... | 1,109,722 |
public static boolean initODMG( String user, String passwd, PVDatabase dbDesc ) { getODMGImplementation(); // Find the connection repository info ConnectionRepository cr = MetadataManager.getInstance().connectionRepository(); PBKey connKey = cr.getStandardPBKeyForJcdAlias( "pv" ); JdbcCo... | public static boolean initODMG( String user, String passwd, PVDatabase dbDesc ) { getODMGImplementation(); // Find the connection repository info ConnectionRepository cr = MetadataManager.getInstance().connectionRepository(); PBKey connKey = cr.getStandardPBKeyForJcdAlias( "pv" ); JdbcCo... | 1,109,723 |
public java.util.Date getEndDate() { return endDate; } | public java.util.Date getEndDate() { return endDate != null ? (java.util.Date) endDate.clone() : null; } | 1,109,724 |
public java.util.Date getStartDate() { return startDate; } | public java.util.Date getStartDate() { return startDate != null ? (java.util.Date)startDate.clone() : null; } | 1,109,725 |
public void setEndDate( java.util.Date date ) { endDate = date; modified(); } | public void setEndDate( java.util.Date date ) { endDate = (date != null) ? (java.util.Date) date.clone() : null; modified(); } | 1,109,726 |
public void setStartDate( java.util.Date date ) { startDate = date; modified(); } | public void setStartDate( java.util.Date date ) { startDate = (date != null) ? (java.util.Date)date.clone() : null; modified(); } | 1,109,727 |
public void stateChanged(ChangeEvent e) { int tabNum = tabs.getSelectedIndex(); if (tabNum == VIEW_D_NUM || tabNum == VIEW_HAP_NUM){ exportMenuItems[0].setEnabled(true); exportMenuItems[1].setEnabled(true); }else if (tabNum == VIEW_TDT_NUM || tabNum... | public void stateChanged(ChangeEvent e) { int tabNum = tabs.getSelectedIndex(); if (tabNum == VIEW_D_NUM || tabNum == VIEW_HAP_NUM){ exportMenuItems[0].setEnabled(true); exportMenuItems[1].setEnabled(true); }else if (tabNum == VIEW_TDT_NUM || tabNum... | 1,109,728 |
public void stateChanged(ChangeEvent e) { int tabNum = tabs.getSelectedIndex(); if (tabNum == VIEW_D_NUM || tabNum == VIEW_HAP_NUM){ exportMenuItems[0].setEnabled(true); exportMenuItems[1].setEnabled(true); }else if (tabNum == VIEW_TDT_NUM || tabNum... | public void stateChanged(ChangeEvent e) { int tabNum = tabs.getSelectedIndex(); if (tabNum == VIEW_D_NUM || tabNum == VIEW_HAP_NUM){ exportMenuItems[0].setEnabled(true); exportMenuItems[1].setEnabled(true); }else if (tabNum == VIEW_TDT_NUM || tabNum... | 1,109,729 |
public void doAssociationTests(Vector affStatus, Vector permuteInd, Vector kidAffStatus) { if(fullProbMap == null || superdata == null || realAffectedStatus == null) { return; } if(affStatus == null){ affStatus = realAffectedStatus; } if(permuteInd == null) {... | public void doAssociationTests(Vector affStatus, Vector permuteInd, Vector kidAffStatus) { if(fullProbMap == null || superdata == null || realAffectedStatus == null || realKidAffectedStatus == null) { return; } if(affStatus == null){ affStatus = realAffectedStatus; ... | 1,109,732 |
public void doTag(XMLOutput output) throws Exception { String localName = null; int idx = name.indexOf(':'); if (idx >= 0) { localName = name.substring(idx + 1); } else { localName = name; } output.startElement(namespace, localName, name, attrib... | public void doTag(XMLOutput output) throws Exception { String localName = null; int idx = name.indexOf(':'); if (idx >= 0) { localName = name.substring(idx + 1); } else { localName = name; } output.startElement(namespace, localName, name, attrib... | 1,109,735 |
public void actionPerformed( ActionEvent e ) { returnReason = RETURN_REASON_APPROVE; setVisible( false ); } | public void actionPerformed( ActionEvent e ) { returnReason = RETURN_REASON_APPROVE; setVisible( false ); } | 1,109,737 |
public void actionPerformed( ActionEvent e ) { returnReason = RETURN_REASON_CANCEL; setVisible( false ); } | public void actionPerformed( ActionEvent e ) { returnReason = RETURN_REASON_APPROVE; setVisible( false ); } | 1,109,738 |
public static void main(String[] args) throws Exception { UserManager userManager = UserManager.getInstance(); User user = null; char[] password = null; int invalidAttempts = 0; do{ if(invalidAttempts > 0){ System.out.println("Invalid Admin Pas... | public static void main(String[] args) throws Exception { UserManager userManager = UserManager.getInstance(); User user = null; char[] password = null; int invalidAttempts = 0; if(args.length == 1){ password = args[0].toCharArray(); user = userManager.verifyUsernamePas... | 1,109,740 |
public static void main(String[] args) throws Exception { UserManager userManager = UserManager.getInstance(); User user = null; char[] password = null; int invalidAttempts = 0; do{ if(invalidAttempts > 0){ System.out.println("Invalid Admin Pas... | public static void main(String[] args) throws Exception { UserManager userManager = UserManager.getInstance(); User user = null; char[] password = null; int invalidAttempts = 0; do{ if(invalidAttempts > 0){ System.out.println("Invalid Admin Pas... | 1,109,741 |
public void mouseClicked(MouseEvent e) { if ((e.getModifiers() & InputEvent.BUTTON1_MASK) == InputEvent.BUTTON1_MASK) { int clickX = e.getX(); int clickY = e.getY(); if (showWM && wmInteriorRect.contains(clickX,clickY)){ //convert a click on the ... | public void mouseClicked(MouseEvent e) { if ((e.getModifiers() & InputEvent.BUTTON1_MASK) == InputEvent.BUTTON1_MASK) { int clickX = e.getX(); int clickY = e.getY(); if (showWM && wmInteriorRect.contains(clickX,clickY)){ //convert a click on the ... | 1,109,743 |
public void mouseClicked(MouseEvent e) { if ((e.getModifiers() & InputEvent.BUTTON1_MASK) == InputEvent.BUTTON1_MASK) { int clickX = e.getX(); int clickY = e.getY(); if (showWM && wmInteriorRect.contains(clickX,clickY)){ //convert a click on the ... | public void mouseClicked(MouseEvent e) { if ((e.getModifiers() & InputEvent.BUTTON1_MASK) == InputEvent.BUTTON1_MASK) { int clickX = e.getX(); int clickY = e.getY(); if (showWM && wmInteriorRect.contains(clickX,clickY)){ //convert a click on the ... | 1,109,744 |
public void paintComponent(Graphics g){ DPrimeTable dPrimeTable = theData.dpTable; if (Chromosome.getSize() == 0){ //if there are no valid markers return; } Vector blocks = theData.blocks; Rectangle visRect = getVisibleRect(); //deal with zooming ... | public void paintComponent(Graphics g){ DPrimeTable dPrimeTable = theData.dpTable; if (Chromosome.getSize() == 0){ //if there are no valid markers return; } Vector blocks = theData.blocks; Rectangle visRect = getVisibleRect(); //deal with zooming ... | 1,109,745 |
public void paintComponent(Graphics g){ DPrimeTable dPrimeTable = theData.dpTable; if (Chromosome.getSize() == 0){ //if there are no valid markers return; } Vector blocks = theData.blocks; Rectangle visRect = getVisibleRect(); //deal with zooming ... | public void paintComponent(Graphics g){ DPrimeTable dPrimeTable = theData.dpTable; if (Chromosome.getSize() == 0){ //if there are no valid markers return; } Vector blocks = theData.blocks; Rectangle visRect = getVisibleRect(); //deal with zooming ... | 1,109,746 |
public void paintComponent(Graphics g){ DPrimeTable dPrimeTable = theData.dpTable; if (Chromosome.getSize() == 0){ //if there are no valid markers return; } Vector blocks = theData.blocks; Rectangle visRect = getVisibleRect(); //deal with zooming ... | public void paintComponent(Graphics g){ DPrimeTable dPrimeTable = theData.dpTable; if (Chromosome.getSize() == 0){ //if there are no valid markers return; } Vector blocks = theData.blocks; Rectangle visRect = getVisibleRect(); //deal with zooming ... | 1,109,747 |
public void paintComponent(Graphics g){ DPrimeTable dPrimeTable = theData.dpTable; if (Chromosome.getSize() == 0){ //if there are no valid markers return; } Vector blocks = theData.blocks; Rectangle visRect = getVisibleRect(); //deal with zooming ... | public void paintComponent(Graphics g){ DPrimeTable dPrimeTable = theData.dpTable; if (Chromosome.getSize() == 0){ //if there are no valid markers return; } Vector blocks = theData.blocks; Rectangle visRect = getVisibleRect(); //deal with zooming ... | 1,109,748 |
public void parsePhasedDownload(String[] info) throws IOException, PedFileException{ String targetChrom = "chr" + info[4]; Chromosome.setDataChrom(targetChrom); Chromosome.setDataBuild("ncbi_b35"); Vector legendMarkers = new Vector(); Vector legendPositions = new Vector(); ... | public void parsePhasedDownload(String[] info) throws IOException, PedFileException{ String targetChrom = "chr" + info[4]; Chromosome.setDataChrom(targetChrom); Chromosome.setDataBuild("ncbi_b35"); Vector legendMarkers = new Vector(); Vector legendPositions = new Vector(); ... | 1,109,749 |
public void parsePhasedDownload(String[] info) throws IOException, PedFileException{ String targetChrom = "chr" + info[4]; Chromosome.setDataChrom(targetChrom); Chromosome.setDataBuild("ncbi_b35"); Vector legendMarkers = new Vector(); Vector legendPositions = new Vector(); ... | public void parsePhasedDownload(String[] info) throws IOException, PedFileException{ String targetChrom = "chr" + info[4]; Chromosome.setDataChrom(targetChrom); Chromosome.setDataBuild("ncbi_b35"); Vector legendMarkers = new Vector(); Vector legendPositions = new Vector(); ... | 1,109,750 |
public void parsePhasedDownload(String[] info) throws IOException, PedFileException{ String targetChrom = "chr" + info[4]; Chromosome.setDataChrom(targetChrom); Chromosome.setDataBuild("ncbi_b35"); Vector legendMarkers = new Vector(); Vector legendPositions = new Vector(); ... | public void parsePhasedDownload(String[] info) throws IOException, PedFileException{ String targetChrom = "chr" + info[4]; Chromosome.setDataChrom(targetChrom); Chromosome.setDataBuild("ncbi_b35"); Vector legendMarkers = new Vector(); Vector legendPositions = new Vector(); ... | 1,109,751 |
public CheckDataPanel(File file) throws IOException{ //okay, for now we're going to assume the ped file has no header Vector pedFileStrings = new Vector(); BufferedReader reader = new BufferedReader(new FileReader(file)); String line; while((line = reader.readLine())!=null){ ... | public CheckDataPanel(File file) throws IOException{ //okay, for now we're going to assume the ped file has no header Vector pedFileStrings = new Vector(); BufferedReader reader = new BufferedReader(new FileReader(file)); String line; while((line = reader.readLine())!=null){ ... | 1,109,752 |
public void parsePhasedDownload(String[] info) throws IOException, PedFileException{ String targetChrom = "chr" + info[4]; Chromosome.setDataChrom(targetChrom); Chromosome.setDataBuild("ncbi_b35"); Vector legendMarkers = new Vector(); Vector legendPositions = new Vector(); ... | public void parsePhasedDownload(String[] info) throws IOException, PedFileException{ String targetChrom = "chr" + info[4]; Chromosome.setDataChrom(targetChrom); Chromosome.setDataBuild("ncbi_b35"); Vector legendMarkers = new Vector(); Vector legendPositions = new Vector(); ... | 1,109,753 |
public ApplicationConfigData addApplication(ServiceContext context, ApplicationConfigData data){ AccessController.checkAccess(context, ACLConstants.ACL_ADD_APPLICATIONS); /* do the operation */ String appId = ApplicationConfig.getNextApplicationId(... | public ApplicationConfigData addApplication(ServiceContext context, ApplicationConfigData data){ AccessController.checkAccess(context, ACLConstants.ACL_ADD_APPLICATIONS); /* do the operation */ String appId = ApplicationConfig.getNextApplicationId(... | 1,109,754 |
public static void addDashboard(DashboardConfig config){ assert config != null; dashboardConfigs.add(config); saveConfig(); } | public static void addDashboard(DashboardConfig config){ assert config != null; dashboardConfigs.add(config); saveConfig(); } | 1,109,755 |
public static DashboardConfig getDashboard(String dashboardId){ for(Iterator it=dashboardConfigs.iterator(); it.hasNext();){ DashboardConfig config = (DashboardConfig)it.next(); if(config.getDashboardId().equals(dashboardId)){ return config; } } r... | public static DashboardConfig getDashboard(String dashboardId){ for(Iterator it=dashboardConfigs.iterator(); it.hasNext();){ DashboardConfig config = (DashboardConfig)it.next(); if(config.getDashboardId().equals(dashboardId)){ return config; } } r... | 1,109,756 |
public static void updateDashboard(DashboardConfig config){ assert config != null: "application config is null"; synchronized(writeLock){ int index = dashboardConfigs.indexOf(config); assert index != -1; dashboardConfigs.remove(index); dashboardConfigs.add(i... | public static void updateDashboard(DashboardConfig config){ assert config != null: "application config is null"; synchronized(writeLock){ int index = dashboardConfigs.indexOf(config); assert index != -1; dashboardConfigs.remove(index); dashboardConfigs.add(i... | 1,109,757 |
public void showDbcsDialog() { final DBCSPanel dbcsPanel = new DBCSPanel(); dbcsPanel.setDbcs(db.getDataSource()); DBCS_OkAction okAction = new DBCS_OkAction(dbcsPanel, true); Action cancelAction = new AbstractAction() { public void actionPerformed(ActionEvent e) { dbcsPanel.discardChanges(); } }; ... | public void showDbcsDialog() { final DBCSPanel dbcsPanel = new DBCSPanel(); dbcsPanel.setDbcs(db.getDataSource()); Action cancelAction = new AbstractAction() { public void actionPerformed(ActionEvent e) { dbcsPanel.discardChanges(); } }; JDialog d = ArchitectPanelBuilder.createArchitectPanelDialog... | 1,109,758 |
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... | public void doTag(XMLOutput output) throws Exception { try { conn = getConnection(); log.error("Caught exception while closing statement: " + e, e); } catch (SQLException e) { throw new JellyException(sql + ": " + e.getMessage(), e); log.error("Caught exception whil... | 1,109,759 |
public ObjectName getObjectName() { try { final String objectNameString = request.getParameter(RequestParams.OBJECT_NAME); if(objectNameString != null){ return new ObjectName(objectNameString); }else{ return null; } ... | public ObjectName getObjectName() { try { final String objectNameString = request.getParameter(RequestParams.OBJECT_NAME); if(objectNameString != null){ return new ObjectName(objectNameString); }else{ return null; } ... | 1,109,762 |
public ActionForward execute(WebContext context, ActionMapping mapping, ActionForm actionForm, HttpServletRequest request, HttpServletResponse response) { ApplicationForm appForm = ... | public ActionForward execute(WebContext context, ActionMapping mapping, ActionForm actionForm, HttpServletRequest request, HttpServletResponse response) { ApplicationForm appForm = ... | 1,109,763 |
public HaploAssocPanel(Haplotype[][] haps){ initialHaplotypeDisplayThreshold = Options.getHaplotypeDisplayThreshold(); Vector colNames = new Vector(); colNames.add("Haplotype"); colNames.add("Freq."); if (Options.getAssocTest() == ASSOC_TRIO){ colNames.add("T:U"); ... | public HaploAssocPanel(Haplotype[][] haps){ initialHaplotypeDisplayThreshold = Options.getHaplotypeDisplayThreshold(); Vector colNames = new Vector(); colNames.add("Haplotype"); colNames.add("Freq."); if (Options.getAssocTest() == ASSOC_TRIO){ colNames.add("T:U"); ... | 1,109,764 |
public BufferedImage export(int start, int stop, boolean compress) throws HaploViewException { forExport = true; exportStart = -1; if (start < 0){ start = 0; } while (true){ //if the marker we want has been filtered walk up until we find a valid one ... | public BufferedImage export(int start, int stop, boolean compress) throws HaploViewException { forExport = true; exportStart = -1; if (start < 0){ start = 0; } while (true){ //if the marker we want has been filtered walk up until we find a valid one ... | 1,109,765 |
private int drawSourceTargetCluster(Graphics2D g, Map<SQLTable, TablePane> panes, int maxSourceWidth, int maxTargetWidth, int sy, SQLTable st, Collection<SQLTable> targets) { int sx = 0; int tx = maxSourceWidth + sourceTargetGap; int ty = sy; for (SQLTable targetTable : targets) { ... | private int drawSourceTargetCluster(Graphics2D g, Map<SQLTable, TablePane> panes, int maxSourceWidth, int maxTargetWidth, int sy, SQLTable st, Collection<SQLTable> targets) { int sx = 0; int tx = maxSourceWidth + sourceTargetGap; int ty = sy; for (SQLTable targetTable : targets) { ... | 1,109,766 |
private int drawSourceTargetCluster(Graphics2D g, Map<SQLTable, TablePane> panes, int maxSourceWidth, int maxTargetWidth, int sy, SQLTable st, Collection<SQLTable> targets) { int sx = 0; int tx = maxSourceWidth + sourceTargetGap; int ty = sy; for (SQLTable targetTable : targets) { ... | private int drawSourceTargetCluster(Graphics2D g, Map<SQLTable, TablePane> panes, int maxSourceWidth, int maxTargetWidth, int sy, SQLTable st, Collection<SQLTable> targets) { int sx = 0; int tx = maxSourceWidth + sourceTargetGap; int ty = sy; for (SQLTable targetTable : targets) { ... | 1,109,767 |
public void fitToRect( double width, double height ) { // System.err.println( "Fitting to " + width + ", " + height ); fitSize = true; maxWidth = width; maxHeight = height; // Revalidate the geometry & image size xformImage = null; revalidate(); } | public void fitToRect( double width, double height ) { // System.err.println( "Fitting to " + width + ", " + height ); fitSize = true; maxWidth = width; maxHeight = height; // Revalidate the geometry & image size xformImage = null; revalidate(); repaint(); } | 1,109,768 |
public void itemDeselected(SelectionEvent e) { changeToolTip(pp.getSelectedItems()); } | public void itemDeselected(SelectionEvent e) { setupAction(pp.getSelectedItems()); } | 1,109,769 |
public void itemSelected(SelectionEvent e) { changeToolTip(pp.getSelectedItems()); } | public void itemSelected(SelectionEvent e) { setupAction(pp.getSelectedItems()); } | 1,109,770 |
public static Project createProject() { Project project = new Project(); BuildLogger logger = new NoBannerLogger(); logger.setMessageOutputLevel( org.apache.tools.ant.Project.MSG_INFO ); logger.setOutputPrintStream( System.out ); logger.setErrorPrintStream( System.err); pro... | public static Project createProject() { Project project = new Project(); BuildLogger logger = new NoBannerLogger(); logger.setMessageOutputLevel( org.apache.tools.ant.Project.MSG_INFO ); logger.setOutputPrintStream( System.out ); logger.setErrorPrintStream( System.err); pro... | 1,109,772 |
public TagScript createRuntimeTaskTagScript(String taskName, Attributes attributes) throws Exception { TaskTag tag = new TaskTag( project, taskName ); return TagScript.newInstance( tag ); } | public TagScript createRuntimeTaskTagScript(String taskName, Attributes attributes) throws Exception { AntTag tag = new AntTag( project, taskName ); return TagScript.newInstance( tag ); } | 1,109,773 |
public void doTag(final XMLOutput output) throws Exception { boolean available = false; if (file != null) { available = file.exists(); } else if (uri != null) { URL url = context.getResource(uri); String fileName = url.getFile(); File file = new File(fileName); availabl... | public void doTag(final XMLOutput output) throws Exception { boolean available = false; if (file != null) { available = file.exists(); } else if (uri != null) { URL url = context.getResource(uri); String fileName = url.getFile(); File file = new File(fileName); availabl... | 1,109,776 |
public void addColumn(SQLColumn c, SQLTable t) throws ArchitectDiffException; | public void addColumn(SQLColumn c); | 1,109,777 |
public abstract void addPrimaryKey(SQLTable t, String primaryKeyName) throws ArchitectException; | public abstract void addPrimaryKey(SQLTable t) throws ArchitectException; | 1,109,778 |
public void addRelationship(SQLRelationship r) throws ArchitectDiffException; | public void addRelationship(SQLRelationship r); | 1,109,779 |
public void dropColumn(SQLColumn c, SQLTable t) throws ArchitectDiffException; | public void dropColumn(SQLColumn c); | 1,109,780 |
public abstract void dropPrimaryKey(SQLTable t, String primaryKeyName); | public abstract void dropPrimaryKey(SQLTable t); | 1,109,781 |
public abstract List generateDDLStatements(SQLDatabase source) throws SQLException, ArchitectException; | public abstract List<DDLStatement> generateDDLStatements(SQLDatabase source) throws SQLException, ArchitectException; | 1,109,782 |
public abstract String makeDropForeignKeySQL(String fkCatalog, String fkSchema, String fkTable, String fkName); | public abstract String makeDropForeignKeySQL(String fkTable, String fkName); | 1,109,783 |
public abstract String makeDropTableSQL(String catalog, String schema, String table); | public abstract String makeDropTableSQL(String table); | 1,109,784 |
public void modifyColumn(SQLColumn c) throws ArchitectDiffException ; | public void modifyColumn(SQLColumn c); | 1,109,785 |
private void saveUser(){ try { Document doc = new Document(); Element rootElement = new Element(AuthConstants.JM_USERS); for(Iterator it=users.values().iterator(); it.hasNext();){ User user = (User)it.next(); /* create a user element */ ... | private void saveUser(){ try { Document doc = new Document(); Element rootElement = new Element(AuthConstants.JM_USERS); for(Iterator it=users.values().iterator(); it.hasNext();){ User user = (User)it.next(); /* create a user element */ ... | 1,109,786 |
public User verifyUsernamePassword(String username, char[] password){ User user = (User)users.get(username); if(user != null){ final String hashedPassword = Crypto.hash(password); user = hashedPassword.equals(user.getPassword()) && "A".equals(user.getStatus()) ... | public User verifyUsernamePassword(String username, char[] password){ User user = (User)users.get(username); if(user != null){ final String hashedPassword = Crypto.hash(password); user = hashedPassword.equals(user.getPassword()) && User.STATUS_ACTIVE.equals(use... | 1,109,787 |
private Result buildResult(Filter<S> filter, OrderingList<S> ordering) throws SupportException, RepositoryException { List<IndexedQueryAnalyzer<S>.Result> subResults; if (filter == null) { subResults = Collections.singletonList(mIndexAnalyzer.analyze(filter, ordering)); } e... | private Result buildResult(Filter<S> filter, OrderingList<S> ordering) throws SupportException, RepositoryException { List<IndexedQueryAnalyzer<S>.Result> subResults; if (filter == null) { subResults = Collections.singletonList(mIndexAnalyzer.analyze(filter, ordering)); } e... | 1,109,788 |
private List<Set<ChainedProperty<S>>> getKeys() throws SupportException, RepositoryException { StorableInfo<S> info = StorableIntrospector.examine(mIndexAnalyzer.getStorableType()); List<Set<ChainedProperty<S>>> keys = new ArrayList<Set<ChainedProperty<S>>>(); keys.add(stripOrdering(i... | private List<Set<ChainedProperty<S>>> getKeys() throws SupportException, RepositoryException { StorableInfo<S> info = StorableIntrospector.examine(mIndexAnalyzer.getStorableType()); List<Set<ChainedProperty<S>>> keys = new ArrayList<Set<ChainedProperty<S>>>(); keys.add(stripOrdering(i... | 1,109,789 |
private Set<ChainedProperty<S>> stripOrdering(Set<? extends OrderedProperty<S>> orderedProps) { Set<ChainedProperty<S>> props = new HashSet<ChainedProperty<S>>(orderedProps.size()); for (OrderedProperty<S> ordering : orderedProps) { props.add(ordering.getChainedProperty()); } ... | private Set<ChainedProperty<S>> stripOrdering(Set<? extends OrderedProperty<S>> orderedProps) { Set<ChainedProperty<S>> props = new LinkedHashSet<ChainedProperty<S>>(orderedProps.size()); for (OrderedProperty<S> ordering : orderedProps) { props.add(ordering.getChainedProperty()); } ... | 1,109,790 |
public ActionForward execute(Exception exception, ExceptionConfig exConfig, ActionMapping mapping, ActionForm form, HttpServletRequest request, HttpServletResponse response) throws ServletException { Ac... | public ActionForward execute(Exception exception, ExceptionConfig exConfig, ActionMapping mapping, ActionForm form, HttpServletRequest request, HttpServletResponse response) throws ServletException { Ac... | 1,109,791 |
public DataFlavor bestImportFlavor(JComponent c, DataFlavor[] flavors) { System.out.println("PlayPenTransferHandler: can I import "+Arrays.asList(flavors)); for (int i = 0; i < flavors.length; i++) { String cls = flavors[i].getDefaultRepresentationClassAsString(); System.out.println("representation class =... | public DataFlavor bestImportFlavor(JComponent c, DataFlavor[] flavors) { logger.debug("PlayPenTransferHandler: can I import "+Arrays.asList(flavors)); for (int i = 0; i < flavors.length; i++) { String cls = flavors[i].getDefaultRepresentationClassAsString(); System.out.println("representation class = "+cls... | 1,109,792 |
public DataFlavor bestImportFlavor(JComponent c, DataFlavor[] flavors) { System.out.println("PlayPenTransferHandler: can I import "+Arrays.asList(flavors)); for (int i = 0; i < flavors.length; i++) { String cls = flavors[i].getDefaultRepresentationClassAsString(); System.out.println("representation class =... | public DataFlavor bestImportFlavor(JComponent c, DataFlavor[] flavors) { System.out.println("PlayPenTransferHandler: can I import "+Arrays.asList(flavors)); for (int i = 0; i < flavors.length; i++) { String cls = flavors[i].getDefaultRepresentationClassAsString(); System.out.println("representation class =... | 1,109,793 |
public DataFlavor bestImportFlavor(JComponent c, DataFlavor[] flavors) { System.out.println("PlayPenTransferHandler: can I import "+Arrays.asList(flavors)); for (int i = 0; i < flavors.length; i++) { String cls = flavors[i].getDefaultRepresentationClassAsString(); System.out.println("representation class =... | public DataFlavor bestImportFlavor(JComponent c, DataFlavor[] flavors) { System.out.println("PlayPenTransferHandler: can I import "+Arrays.asList(flavors)); for (int i = 0; i < flavors.length; i++) { String cls = flavors[i].getDefaultRepresentationClassAsString(); System.out.println("representation class =... | 1,109,794 |
public DataFlavor bestImportFlavor(JComponent c, DataFlavor[] flavors) { System.out.println("PlayPenTransferHandler: can I import "+Arrays.asList(flavors)); for (int i = 0; i < flavors.length; i++) { String cls = flavors[i].getDefaultRepresentationClassAsString(); System.out.println("representation class =... | public DataFlavor bestImportFlavor(JComponent c, DataFlavor[] flavors) { System.out.println("PlayPenTransferHandler: can I import "+Arrays.asList(flavors)); for (int i = 0; i < flavors.length; i++) { String cls = flavors[i].getDefaultRepresentationClassAsString(); System.out.println("representation class =... | 1,109,795 |
public void dragOver(DropTargetDragEvent dtde) { System.out.println("PlayPenDropTarget.dragOver()"); dtde.acceptDrag(DnDConstants.ACTION_COPY); } | public void dragOver(DropTargetDragEvent dtde) { dtde.acceptDrag(DnDConstants.ACTION_COPY); } | 1,109,796 |
public void drop(DropTargetDropEvent dtde) { Transferable t = dtde.getTransferable(); JComponent c = (JComponent) dtde.getDropTargetContext().getComponent(); DataFlavor importFlavor = bestImportFlavor(c, t.getTransferDataFlavors()); if (importFlavor == null) { dtde.rejectDrop(); } else { try { Obj... | public void drop(DropTargetDropEvent dtde) { Transferable t = dtde.getTransferable(); PlayPen c = (PlayPen) dtde.getDropTargetContext().getComponent(); DataFlavor importFlavor = bestImportFlavor(c, t.getTransferDataFlavors()); if (importFlavor == null) { dtde.rejectDrop(); } else { try { Object so... | 1,109,797 |
public void drop(DropTargetDropEvent dtde) { Transferable t = dtde.getTransferable(); JComponent c = (JComponent) dtde.getDropTargetContext().getComponent(); DataFlavor importFlavor = bestImportFlavor(c, t.getTransferDataFlavors()); if (importFlavor == null) { dtde.rejectDrop(); } else { try { Obj... | public void drop(DropTargetDropEvent dtde) { Transferable t = dtde.getTransferable(); JComponent c = (JComponent) dtde.getDropTargetContext().getComponent(); DataFlavor importFlavor = bestImportFlavor(c, t.getTransferDataFlavors()); if (importFlavor == null) { dtde.rejectDrop(); } else { try { Obj... | 1,109,798 |
public void drop(DropTargetDropEvent dtde) { Transferable t = dtde.getTransferable(); JComponent c = (JComponent) dtde.getDropTargetContext().getComponent(); DataFlavor importFlavor = bestImportFlavor(c, t.getTransferDataFlavors()); if (importFlavor == null) { dtde.rejectDrop(); } else { try { Obj... | public void drop(DropTargetDropEvent dtde) { Transferable t = dtde.getTransferable(); JComponent c = (JComponent) dtde.getDropTargetContext().getComponent(); DataFlavor importFlavor = bestImportFlavor(c, t.getTransferDataFlavors()); if (importFlavor == null) { dtde.rejectDrop(); } else { try { Obj... | 1,109,799 |
public void drop(DropTargetDropEvent dtde) { Transferable t = dtde.getTransferable(); JComponent c = (JComponent) dtde.getDropTargetContext().getComponent(); DataFlavor importFlavor = bestImportFlavor(c, t.getTransferDataFlavors()); if (importFlavor == null) { dtde.rejectDrop(); } else { try { Obj... | public void drop(DropTargetDropEvent dtde) { Transferable t = dtde.getTransferable(); JComponent c = (JComponent) dtde.getDropTargetContext().getComponent(); DataFlavor importFlavor = bestImportFlavor(c, t.getTransferDataFlavors()); if (importFlavor == null) { dtde.rejectDrop(); } else { try { Obj... | 1,109,800 |
public void blockOut(int start, int length) { Block block = new Block(start, length); System.out.println("blockOut "+block+": before "+blocks); ListIterator it = blocks.listIterator(); while (it.hasNext()) { Block nextBlock = (Block) it.next(); if (nextBlock.start > start) { it.previous(); ... | public void blockOut(int start, int length) { Block block = new Block(start, length); ListIterator it = blocks.listIterator(); while (it.hasNext()) { Block nextBlock = (Block) it.next(); if (nextBlock.start > start) { it.previous(); it.add(block); break; } } System.out.p... | 1,109,802 |
public void blockOut(int start, int length) { Block block = new Block(start, length); System.out.println("blockOut "+block+": before "+blocks); ListIterator it = blocks.listIterator(); while (it.hasNext()) { Block nextBlock = (Block) it.next(); if (nextBlock.start > start) { it.previous(); ... | public void blockOut(int start, int length) { Block block = new Block(start, length); System.out.println("blockOut "+block+": before "+blocks); ListIterator it = blocks.listIterator(); while (it.hasNext()) { Block nextBlock = (Block) it.next(); if (nextBlock.start > start) { it.previous(); ... | 1,109,803 |
public int findGapToLeft(int start, int length) { int closestLeftGap = Integer.MIN_VALUE; int prevBlockEnd = Integer.MIN_VALUE; Iterator it = blocks.iterator(); while (it.hasNext()) { Block block = (Block) it.next(); if ( (prevBlockEnd < block.start - length) && (block.start - length <= sta... | public int findGapToLeft(int start, int length) { int closestLeftGap = Integer.MIN_VALUE; int prevBlockEnd = Integer.MIN_VALUE; Iterator it = blocks.iterator(); while (it.hasNext()) { Block block = (Block) it.next(); if ( (prevBlockEnd < block.start - length) && (block.start - length <= sta... | 1,109,804 |
public int findGapToRight(int start, int length) { Iterator it = blocks.iterator(); while (it.hasNext()) { Block block = (Block) it.next(); if ( (start + length) < block.start ) { // current gap fits at right-hand side.. done! return start; } else { start = block.start + block.length... | public int findGapToRight(int start, int length) { Iterator it = blocks.iterator(); while (it.hasNext()) { Block block = (Block) it.next(); if ( (start + length) < block.start ) { // current gap fits at right-hand side.. done! return start; } else { start = Math.max(block.start + blo... | 1,109,805 |
public void layoutContainer(Container parent) { System.out.println("PlayPenLayout.layoutContainer"); } | public void layoutContainer(Container parent) { logger.debug("PlayPenLayout.layoutContainer"); } | 1,109,806 |
public void removeLayoutComponent(Component comp) { System.out.println("PlayPenLayout.removeLayoutComponent"); } | public void removeLayoutComponent(Component comp) { logger.debug("PlayPenLayout.removeLayoutComponent"); } | 1,109,807 |
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