List of usage examples for java.awt.event MouseMotionListener MouseMotionListener
MouseMotionListener
From source file:edu.ku.brc.specify.tasks.subpane.LocalityMapperSubPane.java
/** * *//*from www .ja v a2 s .c o m*/ protected void createUI() { kmlGen = new CollectingEventLocalityKMLGenerator(); this.collectingEvents = new ArrayList<CollectingEvent>(); CollectingEvent startCE = null; CollectingEvent endCE = null; Vector<Locality> localities = new Vector<Locality>(); Vector<String> labels = new Vector<String>(); for (Object obj : colEvents) { CollectingEvent collectingEvent = (CollectingEvent) obj; Locality locality = collectingEvent.getLocality(); if (locality == null || locality.getLatitude1() == null || locality.getLongitude1() == null) { continue; } collectingEvents.add(collectingEvent); kmlGen.addDataObj(collectingEvent, ""); if (collectingEvents.size() == 1) { startCE = collectingEvent; endCE = collectingEvent; } // XXX TODO FIX ME! if (startCE == null || endCE == null) { return; } // There may be an End Date that is further out than than the End Date of the last item // with the latest Start Date if (startCE.getStartDate().compareTo(collectingEvent.getStartDate()) > 1) { startCE = collectingEvent; } Calendar leftCal = endCE.getEndDate() != null ? endCE.getEndDate() : endCE.getStartDate(); Calendar rightCal = collectingEvent.getEndDate() != null ? collectingEvent.getEndDate() : collectingEvent.getStartDate(); if (leftCal.compareTo(rightCal) < 0) { endCE = collectingEvent; } Hashtable<String, Object> map = new Hashtable<String, Object>(); Set<CollectionObject> colObjs = collectingEvent.getCollectionObjects(); map.put("startDate", collectingEvent.getStartDate()); map.put("endDate", collectingEvent.getEndDate()); Set<Object> taxonNames = new HashSet<Object>(); for (CollectionObject co : colObjs) { for (Determination d : co.getDeterminations()) { if (d.isCurrentDet()) { //System.out.println(d.getTaxon().getName() + "("+co.getCountAmt()+")"); Taxon taxon = d.getPreferredTaxon(); if (taxon != null) { taxonNames.add(taxon.getName() + (co.getCountAmt() != null ? " (" + co.getCountAmt() + ")" : "")); if (taxon.getRankId() == 220) { Taxon genus = taxon.getParent(); if (genus.getRankId() == 180) { ImageGetter imgGetter = new ImageGetter(imageGetterList, imageMap, imageURLs, genus.getName(), taxon.getName()); imageGetterList.add(imgGetter); } } } break; } } } map.put("taxonItems", taxonNames); map.put("latitude1", locality.getLatitude1()); map.put("longitude1", locality.getLongitude1()); /* Calendar cal = collectingEvent.getStartDate(); if (cal != null) { labels.add(scrDateFormat.format(cal.getTime())); } else if (collectingEvent.getVerbatimDate() != null) { labels.add(collectingEvent.getVerbatimDate()); } else { labels.add(Integer.toString(collectingEvent.getCollectingEventId())); } */ labels.add(Integer.toString(collectingEvents.size())); localities.add(locality); valueList.add(map); } // XXX Fix me shouldn't be hard coded here to make it work localityMapper.setMaxMapWidth(515); localityMapper.setMaxMapHeight(375); Color arrow = new Color(220, 220, 220); localityMapper.setArrowColor(arrow); localityMapper.setDotColor(Color.WHITE); localityMapper.setDotSize(4); localityMapper.setLabelColor(Color.RED); int inx = 0; for (Locality locality : localities) { localityMapper.addLocationAndLabel(locality, labels != null ? labels.get(inx) : null); inx++; } localityMapper.setCurrentLoc(localities.get(0)); localityMapper.setCurrentLocColor(Color.RED); // XXX DEMO (Hard Coded 'null' means everyone would have one which may not be true) // "null" ViewSet name means it should use the default ViewIFace view = AppContextMgr.getInstance().getView("LocalityMapper"); // TODO WHERE's the ERROR checking ! multiView = new MultiView(null, null, view, AltViewIFace.CreationMode.VIEW, MultiView.NO_OPTIONS); multiView.setBorder( BorderFactory.createCompoundBorder(BorderFactory.createLineBorder(new Color(138, 128, 128)), BorderFactory.createEmptyBorder(4, 4, 4, 4))); formViewObj = multiView.getCurrentViewAsFormViewObj(); formViewObj.getUIComponent().setBackground(Color.WHITE); imageJList = formViewObj.getCompById("taxonItems"); imageJList.getSelectionModel().addListSelectionListener(new ListSelectionListener() { public void valueChanged(ListSelectionEvent e) { if (!e.getValueIsAdjusting()) { String nameStr = (String) imageJList.getSelectedValue(); if (nameStr != null) { int index = nameStr.indexOf(" ("); if (index > -1) { nameStr = nameStr.substring(0, index); } } //System.out.println("Getting["+name+"]"); Image img = null; if (StringUtils.isNotEmpty(nameStr)) { img = imageMap.get(nameStr); // might return null ImageDisplay imgDisplay = formViewObj.getCompById("image"); if (img != null) { imgDisplay.setImage(new ImageIcon(img)); } else { imgDisplay.setImage((Image) null); } } } } }); // XXX TODO FIX ME! if (startCE == null || endCE == null) { return; } String startDateStr = scrDateFormat.format(startCE.getStartDate().getTime()); String endDateStr = scrDateFormat .format((endCE.getEndDate() != null ? endCE.getEndDate() : endCE.getStartDate()).getTime()); Formatter formatter = new Formatter(); titleLabel.setText(formatter .format(getResourceString("LocalityMapperTitle"), new Object[] { startDateStr, endDateStr }) .toString()); Font font = titleLabel.getFont(); titleLabel.setFont(new Font(font.getFontName(), Font.BOLD, font.getSize() + 2)); recordSetController = new ResultSetController(null, false, false, false, null, collectingEvents.size(), true); recordSetController.addListener(this); recordSetController.getPanel().setBackground(Color.WHITE); controlPanel = new ControlBarPanel(getBackground()); controlPanel.add(recordSetController.getPanel()); controlPanel.setRecordSetController(recordSetController); controlPanel.setBackground(Color.WHITE); googleBtn = new JButton(IconManager.getIcon("GoogleEarth", IconManager.STD_ICON_SIZE)); googleBtn.setMargin(new Insets(1, 1, 1, 1)); googleBtn.setBorder(BorderFactory.createEmptyBorder(1, 1, 1, 1)); googleBtn.setSize(new Dimension(18, 18)); googleBtn.setPreferredSize(new Dimension(18, 18)); googleBtn.setMaximumSize(new Dimension(18, 18)); googleBtn.setFocusable(false); googleBtn.setBackground(Color.WHITE); controlPanel.addButtons(new JButton[] { googleBtn }, false); googleBtn.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent ae) { try { UIRegistry.displayStatusBarText("Exporting Collecting Events in KML."); // XXX I18N kmlGen.setSpeciesToImageMapper(imageURLs); kmlGen.outputToFile(System.getProperty("user.home") + File.separator + "specify.kml"); } catch (Exception ex) { edu.ku.brc.af.core.UsageTracker.incrHandledUsageCount(); edu.ku.brc.exceptions.ExceptionTracker.getInstance().capture(LocalityMapperSubPane.class, ex); ex.printStackTrace(); } } }); addMouseMotionListener(new MouseMotionListener() { public void mouseDragged(MouseEvent e) { // nothing } public void mouseMoved(MouseEvent e) { checkMouseLocation(e.getPoint(), false); } }); addMouseListener(new MouseAdapter() { @Override public void mouseClicked(MouseEvent e) { checkMouseLocation(e.getPoint(), true); } }); SwingUtilities.invokeLater(new Runnable() { public void run() { getLocalityMap(); } }); }
From source file:org.forester.archaeopteryx.ControlPanel.java
private void buildJSlider(int width, int min, int max) { _color_branches_edpl_slider = new JSlider(min, max); Dimension d = _color_branches_edpl_slider.getSize(); d.width = width;//from w w w .j a v a2s .c o m d.height = 100; _color_branches_edpl_slider.setPreferredSize(d); // _color_branches_edpl_slider.setLayout(null); // slider popup with cutoff value _slider_popup = new JPopupMenu(); JLabel text = new JLabel(); text.setText(String.valueOf(_edpl_current_cutoff)); _slider_popup.add(text); if (!_configuration.isUseNativeUI()) { _color_branches_edpl_slider.setBackground(ControlPanel.jcb_background_color); _color_branches_edpl_slider.setForeground(ControlPanel.jcb_text_color); } _color_branches_edpl_slider.setToolTipText("Set cutoff for EDPL (0.5-1.0)"); _color_branches_edpl_slider.setMinorTickSpacing(10); _color_branches_edpl_slider.setMajorTickSpacing(50); _color_branches_edpl_slider.setPaintTicks(true); _color_branches_edpl_slider.addChangeListener(new ChangeListener() { public void stateChanged(ChangeEvent e) { // get Treepanel function final TreePanel tp = getMainPanel().getCurrentTreePanel(); if (tp == null) { return; } Phylogeny phy = tp.getPhylogeny(); _edpl_next_cutoff = ((double) ((JSlider) (e.getSource())).getValue() / 100.0); tp.edplSliderMovement(_edpl_next_cutoff, _edpl_current_cutoff); _edpl_current_cutoff = _edpl_next_cutoff; // System.out.println("Neuer Wert: "+ // ((JSlider)(e.getSource())).getValue()); } }); _color_branches_edpl_slider.addMouseMotionListener(new MouseMotionListener() { @Override public void mouseMoved(MouseEvent e) { if (_color_branches_edpl_slider.isEnabled()) { _slider_popup.setVisible(false); } } @Override public void mouseDragged(MouseEvent e) { if (_color_branches_edpl_slider.isEnabled()) { // Point p = getMainPanel().getMainFrame().getLocation(); Point p = _color_branches_edpl_slider.getLocationOnScreen(); JLabel text = (JLabel) _slider_popup.getComponent(0); text.setText(String.valueOf(_edpl_current_cutoff)); int x = (int) p.getX() + 18; int y = (int) p.getY() - 25; _slider_popup.setLocation(x, y); _slider_popup.setVisible(true); } } }); }
From source file:org.isatools.isacreator.spreadsheet.Spreadsheet.java
/** * Setup the JTable with its desired characteristics *//*from w w w . j a v a2 s. c om*/ private void setupTable() { table = new CustomTable(spreadsheetModel); table.setShowGrid(true); table.setGridColor(Color.BLACK); table.setShowVerticalLines(true); table.setShowHorizontalLines(true); table.setGridColor(UIHelper.LIGHT_GREEN_COLOR); table.setRowSelectionAllowed(true); table.setColumnSelectionAllowed(true); table.setAutoCreateColumnsFromModel(false); table.setAutoResizeMode(JTable.AUTO_RESIZE_OFF); table.getSelectionModel().addListSelectionListener(this); table.getColumnModel().getSelectionModel().addListSelectionListener(this); table.getTableHeader().setReorderingAllowed(true); table.getColumnModel().addColumnModelListener(this); try { table.setDefaultRenderer(Class.forName("java.lang.Object"), new SpreadsheetCellRenderer()); } catch (ClassNotFoundException e) { // ignore this error } table.addMouseListener(this); table.getTableHeader().addMouseMotionListener(new MouseMotionListener() { public void mouseDragged(MouseEvent event) { } public void mouseMoved(MouseEvent event) { // display a tooltip when user hovers over a column. tooltip is derived // from the description of a field from the TableReferenceObject. JTable table = ((JTableHeader) event.getSource()).getTable(); TableColumnModel colModel = table.getColumnModel(); int colIndex = colModel.getColumnIndexAtX(event.getX()); // greater than 1 to account for the row no. being the first col if (colIndex >= 1) { TableColumn tc = colModel.getColumn(colIndex); if (tc != null) { try { table.getTableHeader().setToolTipText(getFieldDescription(tc)); } catch (Exception e) { // ignore this error } } } } }); //table.getColumnModel().addColumnModelListener(this); InputMap im = table.getInputMap(JTable.WHEN_ANCESTOR_OF_FOCUSED_COMPONENT); KeyStroke tab = KeyStroke.getKeyStroke(KeyEvent.VK_TAB, 0); // Override the default tab behaviour // Tab to the next editable cell. When no editable cells goto next cell. final Action previousTabAction = table.getActionMap().get(im.get(tab)); Action newTabAction = new AbstractAction() { public void actionPerformed(ActionEvent e) { // maintain previous tab action procedure previousTabAction.actionPerformed(e); JTable table = (JTable) e.getSource(); int row = table.getSelectedRow(); int originalRow = row; int column = table.getSelectedColumn(); int originalColumn = column; while (!table.isCellEditable(row, column)) { previousTabAction.actionPerformed(e); row = table.getSelectedRow(); column = table.getSelectedColumn(); // Back to where we started, get out. if ((row == originalRow) && (column == originalColumn)) { break; } } if (table.editCellAt(row, column)) { table.getEditorComponent().requestFocusInWindow(); } } }; table.getActionMap().put(im.get(tab), newTabAction); TableColumnModel model = table.getColumnModel(); String previousColumnName = null; for (int columnIndex = 0; columnIndex < tableReferenceObject.getHeaders().size(); columnIndex++) { if (!model.getColumn(columnIndex).getHeaderValue().toString() .equals(TableReferenceObject.ROW_NO_TEXT)) { model.getColumn(columnIndex).setHeaderRenderer(columnRenderer); model.getColumn(columnIndex).setPreferredWidth(spreadsheetFunctions .calcColWidths(model.getColumn(columnIndex).getHeaderValue().toString())); // add appropriate cell editor for cell. spreadsheetFunctions.addCellEditor(model.getColumn(columnIndex), previousColumnName); previousColumnName = model.getColumn(columnIndex).getHeaderValue().toString(); } else { model.getColumn(columnIndex).setHeaderRenderer(new RowNumberCellRenderer()); } } JTableHeader header = table.getTableHeader(); header.setBackground(UIHelper.BG_COLOR); header.addMouseListener(new HeaderListener(header, columnRenderer)); table.addNotify(); }
From source file:base.BasePlayer.Main.java
public Main() { super(new GridBagLayout()); try {//from w w w .j av a2s .c o m //UIManager.put("PopupMenu.border", BorderFactory.createMatteBorder(0, 20, 0, 0, new Color(230,230,230))); //URL fontUrl = new URL("http://www.webpagepublicity.com/" + // "free-fonts/a/Airacobra%20Condensed.ttf"); // URL fontUrl = new URL("C:/HY-Data/RKATAINE/WinPython-64bit-3.5.3.1Qt5/python-3.5.3.amd64/share/numdifftools/docs/_build/html/_static/fonts/Inconsolata-Regular.ttf"); // URL fonturl = this.getClass().getResource("OpenSans-Regular.ttf"); // menuFont = Font.createFont(Font.TRUETYPE_FONT, new File(fonturl.getFile())); // C:\HY-Data\RKATAINE\WinPython-64bit-3.5.3.1Qt5\python-3.5.3.amd64\Lib\site-packages\reportlab\fonts Launcher.fromMain = true; Launcher.main(args); VariantHandler.main(argsit); glass = Toolkit.getDefaultToolkit().getImage(getClass().getResource("icons/glass.jpg")); ToolTipManager.sharedInstance().setInitialDelay(100); // ToolTipManager.sharedInstance().setDismissDelay(2000); UIManager.put("ToolTip.background", new Color(255, 255, 214)); UIManager.put("ToolTip.border", BorderFactory.createCompoundBorder( UIManager.getBorder("ToolTip.border"), BorderFactory.createEmptyBorder(4, 4, 4, 4))); lineseparator = System.getProperty("line.separator"); proxysettings = new ProxySettings(); panel = new JPanel(new GridBagLayout()); //menuFont = menuFont.deriveFont(Font.PLAIN,12); Draw.defaultFont = menuFont; gd = GraphicsEnvironment.getLocalGraphicsEnvironment().getDefaultScreenDevice(); width = gd.getDisplayMode().getWidth(); height = gd.getDisplayMode().getHeight(); if (Launcher.fontSize.equals("")) { if (width < 1500) { defaultFontSize = 11; buttonHeight = Main.defaultFontSize * 2; buttonWidth = Main.defaultFontSize * 6; } else if (width < 2000) { defaultFontSize = 12; buttonHeight = Main.defaultFontSize * 2 + 4; buttonWidth = Main.defaultFontSize * 6 + 4; } else if (width < 3000) { defaultFontSize = 15; buttonHeight = Main.defaultFontSize * 2 + 4; buttonWidth = Main.defaultFontSize * 6 + 4; } else { defaultFontSize = 19; buttonHeight = Main.defaultFontSize * 2 + 4; buttonWidth = Main.defaultFontSize * 6 + 4; } } else { try { defaultFontSize = Integer.parseInt(Launcher.fontSize); } catch (Exception e) { defaultFontSize = 12; } } menuFont = new Font("SansSerif", Font.PLAIN, Main.defaultFontSize); menuFontBold = new Font("SansSerif", Font.BOLD, Main.defaultFontSize); // menuFont = new Font("SansSerif", Font.BOLD, Main.defaultFontSize); } catch (Exception e) { e.printStackTrace(); } FileSystemView fsv = FileSystemView.getFileSystemView(); File[] paths = File.listRoots(); for (File path : paths) { if (fsv.getSystemDisplayName(path).contains("merit")) { pleiades = true; } } screenSize = new Dimension(width, height); drawHeight = (int) (screenSize.getHeight() * 0.6); sidebarWidth = (int) (screenSize.getWidth() * 0.1); drawWidth = (int) (screenSize.getWidth() - sidebarWidth); thisMainListener = this; try { htsjdk.samtools.util.Log.setGlobalLogLevel(htsjdk.samtools.util.Log.LogLevel.ERROR); /* for(int i=0;i<snow.length; i++) { snow[i][0] = (height*Math.random()); snow[i][1] = (4*Math.random() +1); snow[i][2] = (12*Math.random() -6); snow[i][3] = (2*Math.random() +1); }*/ frame.addWindowListener(new java.awt.event.WindowAdapter() { @Override public void windowClosing(java.awt.event.WindowEvent windowEvent) { /*if (JOptionPane.showConfirmDialog(frame, "Are you sure to close this window?", "Really Closing?", JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE) == JOptionPane.YES_OPTION){ System.exit(0); }*/ if (configChanged) { try { BufferedWriter fileWriter = new BufferedWriter(new FileWriter(Launcher.configfile)); for (int i = 0; i < Launcher.config.size(); i++) { fileWriter.write(Launcher.config.get(i) + lineseparator); } fileWriter.close(); } catch (Exception e) { e.printStackTrace(); } } } }); baseMap.put((byte) 'A', 1); baseMap.put((byte) 'C', 2); baseMap.put((byte) 'G', 3); baseMap.put((byte) 'T', 4); baseMap.put((byte) 'N', 5); baseMap.put((byte) 'I', 6); baseMap.put((byte) 'D', 7); mutTypes.put("TA", 0); mutTypes.put("AT", 0); mutTypes.put("TC", 1); mutTypes.put("AG", 1); mutTypes.put("TG", 2); mutTypes.put("AC", 2); mutTypes.put("CA", 3); mutTypes.put("GT", 3); mutTypes.put("CG", 4); mutTypes.put("GC", 4); mutTypes.put("CT", 5); mutTypes.put("GA", 5); getBase.put((byte) 'A', "A"); getBase.put((byte) 'C', "C"); getBase.put((byte) 'G', "G"); getBase.put((byte) 'T', "T"); getBase.put((byte) 'N', "N"); getBase.put((byte) 'a', "A"); getBase.put((byte) 'c', "C"); getBase.put((byte) 'g', "G"); getBase.put((byte) 't', "T"); getBase.put((byte) 'n', "N"); java.net.URL imgUrl = getClass().getResource("icons/save.gif"); save = new ImageIcon(imgUrl); imgUrl = getClass().getResource("icons/open.gif"); open = new ImageIcon(imgUrl); imgUrl = getClass().getResource("icons/settings.png"); settingsIcon = new ImageIcon(imgUrl); userDir = new File(Main.class.getProtectionDomain().getCodeSource().getLocation().getPath()).getParent() .replace("%20", " "); settings = new JMenuItem("Settings", settingsIcon); // Average.frame.setVisible(false); try { savedir = Launcher.defaultSaveDir; path = Launcher.defaultDir; gerp = Launcher.gerpfile; defaultGenome = Launcher.defaultGenome; defaultAnnotation = Launcher.defaultAnnotation; isProxy = Launcher.isProxy; proxyHost = Launcher.proxyHost; proxyPort = Launcher.proxyPort; proxyType = Launcher.proxyType; if (isProxy) { ProxySettings.useProxy.setSelected(true); } if (!proxyHost.equals("")) { ProxySettings.hostField.setText(proxyHost); } if (!proxyPort.equals("")) { ProxySettings.portField.setText(proxyPort); } if (!Launcher.proxyType.equals("")) { ProxySettings.proxytypes.setSelectedItem(proxyType); } if (Launcher.backColor.equals("")) { Draw.backColor = new Color(90, 90, 90); } else { Draw.backColor = new Color(Integer.parseInt(Launcher.backColor), Integer.parseInt(Launcher.backColor), Integer.parseInt(Launcher.backColor)); Settings.graySlider.setValue(Integer.parseInt(Launcher.backColor)); } if (Launcher.genomeDir.equals("")) { genomeDir = new File(userDir + "/genomes/"); } else { if (new File(Launcher.genomeDir).exists()) { genomeDir = new File(Launcher.genomeDir); } else { genomeDir = new File(userDir + "/genomes/"); } } annotationfile = defaultAnnotation; controlDir = Launcher.ctrldir; trackDir = Launcher.trackDir; projectDir = Launcher.projectDir; downloadDir = Launcher.downloadDir; } catch (Exception e) { e.printStackTrace(); } File[] genomes = genomeDir.listFiles(new FilenameFilter() { public boolean accept(File dir, String name) { return !name.contains(".txt") && !name.startsWith("."); } }); chromHeight = (int) (drawHeight * 0.1); drawDimensions = new Dimension(drawWidth, drawHeight - chromHeight); bedDimensions = new Dimension(drawWidth, bedHeight); chromDimensions = new Dimension(drawWidth - Main.sidebarWidth - 1, drawHeight); drawCanvas = new Draw((int) drawDimensions.getWidth(), (int) drawDimensions.getHeight()); controlDraw = new ControlCanvas((int) bedDimensions.getWidth(), (int) bedDimensions.getHeight()); iconImage = Toolkit.getDefaultToolkit().getImage(getClass().getResource("icons/icon.png")); frame.setIconImage(iconImage); /* if(args.length > 0) { for(int i = 0; i<args.length; i++) { if(args[i].startsWith("-opendir")) { path = args[i].substring(9).replace(" ", ""); } else if(args[i].startsWith("-ctrldir")) { Control.path = args[i].substring(9).replace(" ", ""); } } }*/ // BGZIPInputStream in = this.getClass().getResourceAsStream("SELEX_1505_representative_matrices.bedhead.gz"); searchField.getDocument().addDocumentListener(new DocumentListener() { private String searchstring; public void changedUpdate(DocumentEvent e) { if (searchField.getText().contains(";")) { searchList = searchField.getText().split(";"); for (int i = 0; i < searchList.length; i++) { warn(searchList[i].replace(" ", "")); } } else { warn(searchField.getText().replace(" ", "")); } } public void removeUpdate(DocumentEvent e) { if (searchField.getText().contains(";")) { searchList = searchField.getText().split(";"); for (int i = 0; i < searchList.length; i++) { warn(searchList[i].replace(" ", "")); } } else { warn(searchField.getText().replace(" ", "")); } } public void insertUpdate(DocumentEvent e) { if (searchField.getText().contains(";")) { searchList = searchField.getText().split(";"); for (int i = 0; i < searchList.length; i++) { warn(searchList[i].replace(" ", "")); } } else { warn(searchField.getText().replace(" ", "")); } } public void warn(String searchtext) { if (searchTable.containsKey(searchtext.toUpperCase())) { if (searchTable.get(searchtext.toUpperCase())[0] .equals(Main.chromosomeDropdown.getSelectedItem())) { searchChrom = searchTable.get(searchtext.toUpperCase())[0]; searchStart = Integer.parseInt(searchTable.get(searchtext.toUpperCase())[1]); searchEnd = Integer.parseInt(searchTable.get(searchtext.toUpperCase())[2]); } else { chromDraw.repaint(); searchStart = -1; searchEnd = -1; } chromDraw.repaint(); searchField.setForeground(Color.black); } else if (searchField.getText().toUpperCase().matches("CHR.{1,2}(?!:)")) { if (Main.chromnamevector.contains(searchtext.toUpperCase().substring(3))) { searchField.setForeground(Color.black); } else { chromDraw.repaint(); searchField.setForeground(Color.red); } } else if (searchtext.toUpperCase().replace(",", "").matches("(CHR)?(.+:)?\\d+(-\\d+)?")) { searchField.setForeground(Color.black); if (searchtext.contains(":")) { searchstring = searchtext.substring(searchtext.indexOf(":") + 1).replace(",", ""); } else { chromDraw.repaint(); searchstring = searchtext.replace(",", ""); } if (!searchstring.contains("-")) { try { searchStart = Integer.parseInt(searchstring); } catch (Exception ex) { } searchEnd = -1; } else { try { searchStart = Integer .parseInt(searchstring.substring(0, searchstring.indexOf("-"))); searchEnd = Integer.parseInt(searchstring.substring(searchstring.indexOf("-") + 1)); } catch (Exception ex) { } } chromDraw.repaint(); } else { chromDraw.repaint(); searchField.setForeground(Color.red); searchStart = -1; searchEnd = -1; } } }); try { A = Toolkit.getDefaultToolkit().getImage(getClass().getResource("SELEX/A.png")); C = Toolkit.getDefaultToolkit().getImage(getClass().getResource("SELEX/C.png")); G = Toolkit.getDefaultToolkit().getImage(getClass().getResource("SELEX/G.png")); T = Toolkit.getDefaultToolkit().getImage(getClass().getResource("SELEX/T.png")); } catch (Exception e) { e.printStackTrace(); } ErrorLog.main(args); this.setBackground(Color.black); UIManager.put("FileChooser.readOnly", Boolean.TRUE); panel.setBackground(Draw.sidecolor); panel.setBorder(BorderFactory.createLineBorder(Color.white)); searchField.addKeyListener(this); frame.addKeyListener(this); frame.getContentPane().setBackground(Color.black); glassPane.addMouseListener(this); glassPane.addMouseMotionListener(new MouseMotionListener() { @Override public void mouseDragged(MouseEvent arg0) { } @Override public void mouseMoved(MouseEvent event) { // g.drawRect(drawScroll.getWidth()/2-Main.canceltextwidth/2-Main.defaultFontSize/2, Main.drawScroll.getViewport().getHeight()*2/3+Draw.loadingFont.getSize()*3-Main.defaultFontSize/4, Main.canceltextwidth+Main.defaultFontSize, Draw.loadingFont.getSize()+Main.defaultFontSize/2); if (drawCanvas.loading && event.getX() > drawScroll.getWidth() / 2 - Main.canceltextwidth / 2 - Main.defaultFontSize / 2 && event.getX() < drawScroll.getWidth() / 2 + Main.canceltextwidth / 2 + Main.defaultFontSize / 2 && event.getY() > frame.getHeight() * 1 / 3 + Draw.loadingFont.getSize() * 3 - Main.defaultFontSize / 4 && event.getY() < frame.getHeight() * 1 / 3 + Draw.loadingFont.getSize() * 4 + Main.defaultFontSize / 2) { if (!Main.cancelhover) { Main.cancelhover = true; Main.glassPane.requestFocus(); } } else { if (Main.cancelhover) { Main.cancelhover = false; Main.glassPane.requestFocus(false); } } } }); background.put((byte) 'A', 0.3); background.put((byte) 'C', 0.2); background.put((byte) 'G', 0.2); background.put((byte) 'T', 0.3); bases = new Hashtable<String, String>(); bases.put("A", "A"); bases.put("C", "C"); bases.put("G", "G"); bases.put("T", "T"); bases.put("N", "N"); bases.put("delA", "delA"); bases.put("delC", "delC"); bases.put("delG", "delG"); bases.put("delT", "delT"); bases.put("insA", "insA"); bases.put("insC", "insC"); bases.put("insG", "insG"); bases.put("insT", "insT"); chromDraw = new ChromDraw(drawWidth, chromHeight); VariantCaller.main(argsit); PeakCaller.main(argsit); tablebrowser = new TableBrowser(); bedconverter = new BEDconvert(); try { File annodir; File[] annotations; addGenome.addMouseListener(this); genome = new JMenu("Genomes"); genome.setName("genomeMenu"); genome.add(addGenome); genome.addComponentListener(this); File[] fastadir; String[] empty = {}; refModel = new DefaultComboBoxModel<String>(empty); refDropdown = new SteppedComboBox(refModel); refDropdown.addMouseListener(this); String[] emptygenes = {}; refDropdown.addActionListener(refDropActionListener); geneModel = new DefaultComboBoxModel<String>(emptygenes); geneDropdown = new SteppedComboBox(geneModel); geneDropdown.addMouseListener(this); if (genomes != null) { for (int i = 0; i < genomes.length; i++) { if (!genomes[i].isDirectory()) { continue; } annodir = new File(genomes[i].getAbsolutePath() + "/annotation/"); if (genomes[i].isDirectory()) { fastadir = genomes[i].listFiles(); for (int f = 0; f < fastadir.length; f++) { if (fastadir[f].isDirectory()) { continue; } if (fastadir[f].getName().contains(".fai")) { continue; } else if (fastadir[f].getName().contains(".fa")) { fastahash.put(genomes[i].getName(), fastadir[f]); } } } annotations = annodir.listFiles(); genomehash.put(genomes[i].getName(), new ArrayList<File>()); refModel.addElement(genomes[i].getName()); if (genomes[i].getName().length() > reflength) { reflength = genomes[i].getName().length(); } JMenu addMenu = new JMenu(genomes[i].getName()); addMenu.addMouseListener(this); addMenu.setName(genomes[i].getName()); JMenuItem addAnnotation = new JMenuItem("Add new annotation file..."); addAnnotation.addMouseListener(this); addAnnotation.setName("add_annotation"); addMenu.add(addAnnotation); JLabel addLabel = new JLabel(" Select annotation: "); labels.add(addLabel); addMenu.add(addLabel); addMenu.add(new JSeparator()); genome.add(addMenu); addMenu.addComponentListener(this); if (annotations != null) { for (int j = 0; j < annotations.length; j++) { annofiles = annotations[j].listFiles(); for (int f = 0; f < annofiles.length; f++) { if (annofiles[f].getName().endsWith(".bed.gz")) { if (annofiles[f].getName() .substring(0, annofiles[f].getName().indexOf(".bed.gz")) .length() > annolength) { annolength = annofiles[f].getName().length(); } genomehash.get(genomes[i].getName()).add(annofiles[f].getAbsoluteFile()); JMenuItem additem = new JMenuItem(annofiles[f].getName().substring(0, annofiles[f].getName().indexOf(".bed.gz"))); additem.setName(annofiles[f].getName().substring(0, annofiles[f].getName().indexOf(".bed.gz"))); additem.addMouseListener(this); addMenu.add(additem); additem.addComponentListener(this); break; } } } } } refModel.addElement("Add new reference..."); } if (genomes.length == 0) { /*if(Launcher.firstStart) { Main.writeToConfig("FirstStart=false"); }*/ AddGenome.createAndShowGUI(); AddGenome.frame.setTitle("Add new genome"); AddGenome.remove.setEnabled(false); AddGenome.download.setEnabled(false); AddGenome.frame.setLocation((int) (screenSize.getWidth() / 2 - AddGenome.frame.getWidth() / 2), (int) (screenSize.getHeight() / 6)); AddGenome.frame.setState(JFrame.NORMAL); AddGenome.frame.setVisible(true); AddGenome.frame.setAlwaysOnTop(true); /* WelcomeScreen.main(args); WelcomeScreen.frame.setVisible(true); WelcomeScreen.frame.setLocation(frame.getLocationOnScreen().x+frame.getWidth()/2 - WelcomeScreen.frame.getWidth()/2, frame.getLocationOnScreen().y+frame.getHeight()/6); */ if (genomes.length != 0) { if (!genomehash.containsKey(defaultGenome)) { setChromDrop(genomes[0].getName()); defaultGenome = genomes[0].getName(); } else { setChromDrop(defaultGenome); } getBands(); getExons(); } else { setChromDrop(null); } } else { if (!genomehash.containsKey(defaultGenome)) { setChromDrop(genomes[0].getName()); defaultGenome = genomes[0].getName(); } else { setChromDrop(defaultGenome); } getBands(); getExons(); } if (Launcher.firstStart) { WelcomeScreen.createAndShowGUI(); WelcomeScreen.frame.setLocation( (int) (screenSize.getWidth() / 2 - WelcomeScreen.frame.getWidth() / 2), (int) (screenSize.getHeight() / 6)); WelcomeScreen.frame.setVisible(true); } setMenuBar(); setButtons(); Settings.main(args); // Settings.main(args); frame.requestFocus(); drawCanvas.addKeyListener(this); bedCanvas.addKeyListener(this); setFonts(); chromLabel.setText("Chromosome " + chromosomeDropdown.getSelectedItem().toString()); CheckUpdates check = new CheckUpdates(); check.execute(); // Main.drawCanvas.loading("test"); Main.drawCanvas.splits.get(0) .setCytoImage(Main.chromDraw.createBands(Main.drawCanvas.splits.get(0))); } catch (Exception e) { e.printStackTrace(); } } catch (Exception ex) { ex.printStackTrace(); Main.showError(ex.getMessage(), "Error"); } }