List of usage examples for javax.swing JScrollPane getViewport
public JViewport getViewport()
JViewport. From source file:edu.ku.brc.af.ui.forms.TableViewObj.java
/** * Adds a control by name so it can be looked up later. * @param formCell the FormCell def that describe the cell * @param control the control// ww w .j av a2 s . c om */ public void registerControl(final FormCellIFace formCell, final Component control) { if (skipControls > 0) { return; } if (formCell != null) { String fullCompName = appendName(formCell.getName()); JScrollPane scrollPane; Component comp; if (control instanceof JScrollPane) { scrollPane = (JScrollPane) control; comp = scrollPane.getViewport().getView(); } else { scrollPane = null; comp = control; } String fullId = appendName(formCell.getIdent()); ColumnInfo colInfo = controlsById.get(fullId); if (colInfo == null) { colInfo = new ColumnInfo(getParentClassName(), formCell, fullCompName, comp, scrollPane); controlsById.put(fullId, colInfo); } else { colInfo.setFullCompName(fullCompName); colInfo.setFormCell(formCell); } if (StringUtils.isEmpty(colInfo.getLabel())) { if (control instanceof JCheckBox) { String cbxLabel = ((JCheckBox) control).getText(); if (StringUtils.isEmpty(cbxLabel)) { cbxLabel = " "; } colInfo.setLabel(cbxLabel); } else { colInfo.setLabel(" "); } } colInfo.setComp(comp); colInfo.setScrollPane(scrollPane); columnList.add(colInfo); controlsByName.put(fullCompName, colInfo); } //log.info("RegControl["+formCell.getName()+"]"); }
From source file:base.BasePlayer.AddGenome.java
public void actionPerformed(ActionEvent event) { if (event.getSource() == download) { if (!downloading) { downloading = true;// ww w . j a va 2s . c om downloadGenome(genometable.getValueAt(genometable.getSelectedRow(), 0).toString()); downloading = false; } } else if (event.getSource() == getLinks) { URL[] urls = AddGenome.genomeHash .get(genometable.getValueAt(genometable.getSelectedRow(), 0).toString()); JPopupMenu menu = new JPopupMenu(); JTextArea area = new JTextArea(); JScrollPane menuscroll = new JScrollPane(); area.setFont(Main.menuFont); menu.add(menuscroll); menu.setPreferredSize(new Dimension( menu.getFontMetrics(Main.menuFont).stringWidth(urls[0].toString()) + Main.defaultFontSize * 10, (int) menu.getFontMetrics(Main.menuFont).getHeight() * 4)); //area.setMaximumSize(new Dimension(300, 600)); area.setLineWrap(true); area.setWrapStyleWord(true); for (int i = 0; i < urls.length; i++) { area.append(urls[i].toString() + "\n"); } area.setCaretPosition(0); area.revalidate(); menuscroll.getViewport().add(area); menu.pack(); menu.show(this, 0, 0); } else if (event.getSource() == checkEnsembl) { if (ensemblfetch) { menu.show(AddGenome.treescroll, 0, 0); } else { EnsemblFetch fetcher = new EnsemblFetch(); fetcher.execute(); } } else if (event.getSource() == checkUpdates) { URL testfile = null; try { // kattoo onko paivityksia annotaatioon String ref = selectedNode.toString(); if (AddGenome.genomeHash.get(ref) != null) { ArrayList<String> testfiles = new ArrayList<String>(); if (Main.drawCanvas != null) { for (int i = 0; i < Main.genomehash.get(ref).size(); i++) { testfiles.add(Main.genomehash.get(ref).get(i).getName().replace(".bed.gz", "")); } } testfile = AddGenome.genomeHash.get(ref)[1]; String result = Main.checkFile(testfile, testfiles); if (result.length() == 0) { Main.showError("You have newest annotation file.", "Note"); } else { int n = JOptionPane.showConfirmDialog(Main.drawCanvas, "New annotation file found: " + result + "\nDownload it now?", "Note", JOptionPane.YES_NO_OPTION); if (n == JOptionPane.YES_OPTION) { URL fileurl = new URL(testfile.getProtocol() + "://" + testfile.getHost() + testfile.getPath().substring(0, testfile.getPath().lastIndexOf("/") + 1) + result); OutputRunner runner = new OutputRunner(fileurl, ref); runner.downloadAnnotation = true; runner.execute(); } } } else { Main.showError("This genome is not from Ensembl list, could not check for updates.", "Note", AddGenome.genometable); } } catch (Exception e) { Main.showError("Cannot connect to " + testfile.getHost() + ".\nTry again later.", "Error"); e.printStackTrace(); } } else if (event.getSource() == remove) { if (!selectedNode.isLeaf()) { String removeref = selectedNode.toString(); // Boolean same = false; try { if (Main.drawCanvas != null) { if (removeref.equals(Main.refDropdown.getSelectedItem().toString())) { Main.referenceFile.close(); // same = true; if (ChromDraw.exonReader != null) { ChromDraw.exonReader.close(); } } } if (Main.genomehash.containsKey(removeref)) { for (int i = Main.genomehash.get(removeref).size() - 1; i >= 0; i--) { Main.genomehash.get(removeref).remove(i); } Main.genomehash.remove(removeref); } if (Main.drawCanvas != null) { Main.refModel.removeElement(removeref); Main.refDropdown.removeItem(removeref); Main.refDropdown.revalidate(); } for (int i = 0; i < Main.genome.getItemCount(); i++) { if (Main.genome.getItem(i).getName() != null) { if (Main.genome.getItem(i).getName().equals(removeref)) { Main.genome.remove(Main.genome.getItem(i)); break; } } } FileUtils.deleteDirectory(new File(Main.genomeDir.getCanonicalPath() + "/" + removeref)); checkGenomes(); Main.setAnnotationDrop(""); if (Main.genomehash.size() == 0) { Main.refDropdown.setSelectedIndex(0); Main.setChromDrop("-1"); } } catch (Exception e) { e.printStackTrace(); try { Main.showError("Could not delete genome folder.\nYou can do it manually by deleting folder " + Main.genomeDir.getCanonicalPath() + "/" + removeref, "Note"); } catch (IOException e1) { e1.printStackTrace(); } } } else { try { if (Main.drawCanvas != null) { if (ChromDraw.exonReader != null) { ChromDraw.exonReader.close(); } } Main.removeAnnotationFile(selectedNode.getParent().toString(), selectedNode.toString()); FileUtils.deleteDirectory(new File(Main.genomeDir.getCanonicalPath() + "/" + selectedNode.getParent().toString() + "/annotation/" + selectedNode.toString())); // root.remove(selectedNode.getParent().getIndex(selectedNode)); // root.remove // checkGenomes(); } catch (Exception e) { e.printStackTrace(); try { Main.showError("Could not delete genome folder.\nYou can do it manually by deleting folder " + Main.genomeDir.getCanonicalPath() + "/" + selectedNode.getParent().toString() + "/annotation/" + selectedNode.toString(), "Note"); } catch (IOException e1) { e1.printStackTrace(); } } treemodel.removeNodeFromParent(selectedNode); } } else if (event.getSource() == add) { if (genomeFile == null) { if (new File(genomeFileText.getText()).exists()) { genomeFile = new File(genomeFileText.getText()); } else { genomeFileText.setText("Select reference genome fasta-file."); genomeFileText.setForeground(Color.red); return; } } /*if(genomeName.getText().contains("Give name") || genomeName.getText().length() == 0) { genomeName.setText("Give name of the genome"); genomeName.setForeground(Color.red); genomeName.revalidate(); } else if(!annotation && new File(Main.userDir +"/genomes/"+genomeName.getText().trim().replace("\\s+", "_")).exists()) { genomeName.setText("This genome exists already."); genomeName.setForeground(Color.red); genomeName.revalidate(); } else */ if ((genomeFileText.getText().length() == 0 || genomeFileText.getText().startsWith("Select reference"))) { genomeFileText.setText("Select reference genome fasta-file."); genomeFileText.setForeground(Color.red); genomeFileText.revalidate(); } else { OutputRunner runner = new OutputRunner( genomeFile.getName().replace(".fasta", "").replace(".gz", ""), genomeFile, annotationFile); runner.execute(); } } else if (event.getSource() == openRef) { try { JFileChooser chooser = new JFileChooser(Main.downloadDir); chooser.setMultiSelectionEnabled(false); chooser.setFileSelectionMode(JFileChooser.FILES_ONLY); chooser.setAcceptAllFileFilterUsed(false); MyFilterFasta fastaFilter = new MyFilterFasta(); chooser.addChoosableFileFilter(fastaFilter); chooser.setDialogTitle("Select reference fasta-file"); if (Main.screenSize != null) { chooser.setPreferredSize(new Dimension((int) Main.screenSize.getWidth() / 3, (int) Main.screenSize.getHeight() / 3)); } int returnVal = chooser.showOpenDialog((Component) this.getParent()); if (returnVal == JFileChooser.APPROVE_OPTION) { genomeFile = chooser.getSelectedFile(); Main.downloadDir = genomeFile.getParent(); Main.writeToConfig("DownloadDir=" + genomeFile.getParent()); genomeFileText.setText(genomeFile.getName()); genomeFileText.revalidate(); frame.pack(); } } catch (Exception ex) { ex.printStackTrace(); } } else if (event.getSource() == openAnno) { try { JFileChooser chooser = new JFileChooser(Main.downloadDir); chooser.setMultiSelectionEnabled(false); chooser.setFileSelectionMode(JFileChooser.FILES_ONLY); chooser.setAcceptAllFileFilterUsed(false); MyFilterGFF gffFilter = new MyFilterGFF(); chooser.addChoosableFileFilter(gffFilter); chooser.setDialogTitle("Select annotation gff3-file"); if (Main.screenSize != null) { chooser.setPreferredSize(new Dimension((int) Main.screenSize.getWidth() / 3, (int) Main.screenSize.getHeight() / 3)); } int returnVal = chooser.showOpenDialog((Component) this.getParent()); if (returnVal == JFileChooser.APPROVE_OPTION) { if (genomeFile == null) { genomeFile = Main.fastahash.get(Main.hoverGenome); } annotationFile = chooser.getSelectedFile(); Main.downloadDir = annotationFile.getParent(); Main.writeToConfig("DownloadDir=" + annotationFile.getParent()); OutputRunner runner = new OutputRunner( genomeFile.getName().replace(".fasta", "").replace(".gz", ""), genomeFile, annotationFile); runner.execute(); } } catch (Exception ex) { ex.printStackTrace(); } } }
From source file:de.main.sessioncreator.DesktopApplication1View.java
public void getAreasBacgroundW(File f) { fileHelper.getAreas(f);/*from w w w . j a v a 2 s .c o m*/ Iterator<Map.Entry<String, List>> it = fileHelper.areaMap.entrySet().iterator(); while (it.hasNext()) { DefaultListModel dlm = new DefaultListModel(); JList list = new JList(dlm); list.setSelectionMode(ListSelectionModel.MULTIPLE_INTERVAL_SELECTION); JScrollPane scrollPane = new JScrollPane(list); scrollPane.getViewport().setView(list); Map.Entry en = it.next(); wizardtabpAreas.addTab(en.getKey().toString().substring(3), scrollPane); for (Object o : fileHelper.areaMap.get(en.getKey().toString())) { dlm.addElement(o); } MouseListener mouseListener = new MouseAdapter() { @Override public void mouseClicked(MouseEvent mouseEvent) { JList tabList = (JList) mouseEvent.getSource(); if (mouseEvent.getClickCount() == 2) { int index = tabList.locationToIndex(mouseEvent.getPoint()); if (index >= 0) { Object o = tabList.getModel().getElementAt(index); wizardtaChoosenAreas.append(o.toString() + "\n"); } } } }; list.addMouseListener(mouseListener); ListSelectionListener listListener = new ListSelectionListener() { public void valueChanged(ListSelectionEvent e) { JList list = (JList) e.getSource(); if (e.getValueIsAdjusting() == false) { if (list.getSelectedIndex() == -1) { //No selection, disable add button. wizardbtnAddAreas.setEnabled(false); } else { //Selection, enable the add button. wizardbtnAddAreas.setEnabled(true); } } } }; list.addListSelectionListener(listListener); } }
From source file:edu.ku.brc.af.ui.forms.FormViewObj.java
@Override public void registerControl(final FormCellIFace formCell, final Component control) { if (formCell != null) { boolean isThis = formCell.getName().equals("this"); if (controlsById.get(formCell.getIdent()) != null) { throw new RuntimeException( "Two controls have the same id [" + formCell.getIdent() + "] " + formViewDef.getName()); }/*from w w w .ja va 2s.c om*/ if (!isThis && controlsByName.get(formCell.getName()) != null) { throw new RuntimeException( "Two controls have the same name [" + formCell.getName() + "] " + formViewDef.getName()); } if (!hasRequiredFields && formCell instanceof FormCellFieldIFace && ((FormCellFieldIFace) formCell).isRequired()) { hasRequiredFields = true; } JScrollPane scrPane; Component comp; if (control instanceof JScrollPane) { scrPane = (JScrollPane) control; comp = scrPane.getViewport().getView(); } else { scrPane = null; comp = control; } FVOFieldInfo fieldInfo = new FVOFieldInfo(formCell, comp, scrPane, controlsById.size()); controlsById.put(formCell.getIdent(), fieldInfo); if (!isThis) { controlsByName.put(formCell.getName(), fieldInfo); } compsList.add(fieldInfo); if (comp instanceof FormControlSaveable) { saveableList.add((FormControlSaveable) comp); } } }
From source file:edu.ku.brc.af.ui.forms.FormViewObj.java
/** * Sets the component into the object/* w w w.j a v a 2s .co m*/ * @param formComp the UI component that represents this viewable */ public void setFormComp(final JComponent formComp) { // Remove existing component if (this.formComp != null) { mainComp.remove(this.formComp); } // add new component if (MultiView.isOptionOn(options, MultiView.NO_SCROLLBARS)) { if (ViewFactory.isFormTransparent()) { formComp.setOpaque(false); } this.mainComp.add(formComp, BorderLayout.CENTER); this.formComp = formComp; } else { JScrollPane scrollPane = new JScrollPane(formComp, ScrollPaneConstants.VERTICAL_SCROLLBAR_AS_NEEDED, ScrollPaneConstants.HORIZONTAL_SCROLLBAR_AS_NEEDED); scrollPane.getVerticalScrollBar().setUnitIncrement(10); scrollPane.setBorder(null); this.mainComp.add(scrollPane, BorderLayout.CENTER); this.formComp = scrollPane; if (ViewFactory.isFormTransparent()) { scrollPane.setOpaque(false); scrollPane.getViewport().setOpaque(false); } } if (businessRules != null && !hasInitBR) { businessRules.initialize(this); hasInitBR = true; } // This is needed to make the form layout correctly //XXX I hate that I have to do this SwingUtilities.invokeLater(new Runnable() { public void run() { //mainComp.invalidate(); //mainComp.validate(); //mainComp.doLayout(); UIRegistry.forceTopFrameRepaint(); } }); }
From source file:base.BasePlayer.FileRead.java
static void setTable(BedTrack track) { JScrollPane addpane = new JScrollPane(); addpane.setPreferredSize(new Dimension(500, 400)); BedTable add = new BedTable((int) Main.screenSize.width, (int) Main.screenSize.height, addpane, track); addpane.getViewport().add(add); addpane.getVerticalScrollBar().addAdjustmentListener(new AdjustmentListener() { public void adjustmentValueChanged(AdjustmentEvent event) { if (VariantHandler.tabs.getSelectedIndex() > 2) { VariantHandler.tables.get(VariantHandler.tabs.getSelectedIndex() - 3).repaint(); }// w ww.j a va 2s . com } }); VariantHandler.tables.add(add); VariantHandler.tablescrolls.add(addpane); track.setTable(add); add.resizeTable(VariantHandler.tableScroll.getViewport().getWidth()); if (track.file != null) { /*if(track.file.getName().length() > 10) { VariantHandler.tabs.add(track.file.getName().substring(0, 10) +"...", addpane); add.setName(track.file.getName().substring(0, 10) +"..."); } else {*/ VariantHandler.tabs.add(track.file.getName().replace(".pfm", ""), addpane); add.setName(track.file.getName()); // } } else { /*if(FilenameUtils.getName(track.url.getFile()).length() > 10) { VariantHandler.tabs.add(FilenameUtils.getName(track.url.getFile()).substring(0, 10) +"...", addpane); add.setName(FilenameUtils.getName(track.url.getFile()).substring(0, 10) +"..."); } else {*/ VariantHandler.tabs.add(FilenameUtils.getName(track.url.getFile()), addpane); add.setName(FilenameUtils.getName(track.url.getFile())); // } } //VariantHandler.clusterTable.addHeaderColumn(track); MethodLibrary.addHeaderColumns(track); VariantHandler.tabs.revalidate(); }
From source file:base.BasePlayer.Main.java
void setMenuBar() { //filemenu.addMouseListener(this); //toolmenu.addMouseListener(this); filemenu = new JMenu("File"); toolmenu = new JMenu("Tools"); help = new JMenu("Help"); about = new JMenu("About"); menubar = new JMenuBar(); //help.addMouseListener(this); exit = new JMenuItem("Exit"); manual = new JButton("Online manual"); manual.addActionListener(new ActionListener() { @Override//from w w w .j av a 2s .c o m public void actionPerformed(ActionEvent arg0) { Main.gotoURL("https://baseplayer.fi/BPmanual"); } }); // opensamples = new JMenuItem("Add samples"); zoomout = new JButton("Zoom out"); back = new JButton("<<"); forward = new JButton(">>"); manage = new JButton("Variant Manager"); openvcfs = new JMenuItem("Add VCFs", open); openbams = new JMenuItem("Add BAMs", open); average = new JMenuItem("Coverage calculator"); update = new JMenuItem("Update"); update.setVisible(false); errorlog = new JMenuItem("View log"); //helpLabel = new JLabel("This is pre-release version of BasePlayer\nContact: help@baseplayer.fi\n\nUniversity of Helsinki"); addURL = new JMenu("Add from URL"); urlField = new JTextField("Enter URL"); addtracks = new JMenuItem("Add tracks"); fromURL = new JMenuItem("Add track from URL"); addcontrols = new JMenuItem("Add controls"); pleiadesButton = new JMenuItem("PLEIADES"); saveProject = new JMenuItem("Save project"); saveProjectAs = new JMenuItem("Save project as..."); openProject = new JMenuItem("Open project"); clear = new JMenuItem("Clear data"); clearMemory = new JMenuItem("Clean memory"); // welcome = new JMenuItem("Welcome screen"); filemenu.add(openvcfs); filemenu.add(openbams); variantCaller = new JMenuItem("Variant Caller"); tbrowser = new JMenuItem("Table Browser"); bconvert = new JMenuItem("BED converter"); peakCaller = new JMenuItem("Peak Caller"); addtracks = new JMenuItem("Add tracks", open); filemenu.add(addtracks); addcontrols = new JMenuItem("Add controls", open); filemenu.add(addcontrols); filemenu.add(fromURL); if (pleiades) { pleiadesButton.setPreferredSize(buttonDimension); pleiadesButton.addActionListener(this); filemenu.add(pleiadesButton); } filemenu.add(new JSeparator()); openProject = new JMenuItem("Open project", open); filemenu.add(openProject); saveProject = new JMenuItem("Save project", save); filemenu.add(saveProject); saveProjectAs = new JMenuItem("Save project as...", save); filemenu.add(saveProjectAs); filemenu.add(new JSeparator()); filemenu.add(genome); filemenu.add(update); filemenu.add(clear); filemenu.add(new JSeparator()); filemenu.add(exit); exit.addActionListener(this); menubar.add(filemenu); manage.addActionListener(this); manage.addMouseListener(this); update.addActionListener(this); average.addActionListener(this); average.setEnabled(false); average.setToolTipText("No bam/cram files opened"); tbrowser.addActionListener(this); bconvert.addActionListener(this); toolmenu.add(tbrowser); toolmenu.add(average); toolmenu.add(variantCaller); toolmenu.add(bconvert); fromURL.addMouseListener(this); fromURL.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent arg0) { final JPopupMenu menu = new JPopupMenu(); final JTextField area = new JTextField(); JButton add = new JButton("Fetch"); JLabel label = new JLabel("Paste track URL below"); JScrollPane menuscroll = new JScrollPane(); add.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { try { String urltext = area.getText().trim(); Boolean size = true; if (urltext.contains("pleiades")) { openPleiades(urltext); return; } if (!FileRead.isTrackFile(urltext)) { showError("The file format is not supported.\n" + "Supported formats: bed, bigwig, bigbed, gff, bedgraph", "Error"); return; } if (!urltext.toLowerCase().endsWith(".bw") && !urltext.toLowerCase().endsWith(".bigwig") && !urltext.toLowerCase().endsWith(".bb") && !urltext.toLowerCase().endsWith(".bigbed")) { URL url = null; try { url = new URL(urltext); } catch (Exception ex) { menu.setVisible(false); Main.showError("Please paste whole url (protocol included)", "Error"); return; } URL testurl = url; HttpURLConnection huc = (HttpURLConnection) testurl.openConnection(); huc.setRequestMethod("HEAD"); int responseCode = huc.getResponseCode(); if (responseCode != 404) { SeekableStream stream = SeekableStreamFactory.getInstance().getStreamFor(url); TabixReader tabixReader = null; String index = null; try { if (stream.length() / (double) 1048576 >= Settings.settings .get("bigFile")) { size = false; } tabixReader = new TabixReader(urltext, urltext + ".tbi", stream); index = urltext + ".tbi"; testurl = new URL(index); huc = (HttpURLConnection) testurl.openConnection(); huc.setRequestMethod("HEAD"); responseCode = huc.getResponseCode(); if (responseCode == 404) { menu.setVisible(false); Main.showError("Index file (.tbi) not found in the URL.", "Error"); return; } } catch (Exception ex) { try { tabixReader = new TabixReader(urltext, urltext.substring(0, urltext.indexOf(".gz")) + ".tbi", stream); index = urltext.substring(0, urltext.indexOf(".gz")) + ".tbi"; } catch (Exception exc) { menu.setVisible(false); Main.showError("Could not read tabix file.", "Error"); } } if (tabixReader != null && index != null) { stream.close(); tabixReader.close(); menu.setVisible(false); FileRead filereader = new FileRead(); filereader.readBED(urltext, index, size); } } else { menu.setVisible(false); Main.showError("Not a valid URL", "Error"); } } else { URL url = null; try { url = new URL(urltext); } catch (Exception ex) { Main.showError("Please paste whole url (protocol included)", "Error"); return; } final URL testurl = url; HttpURLConnection huc = (HttpURLConnection) testurl.openConnection(); huc.setRequestMethod("HEAD"); int responseCode = huc.getResponseCode(); if (responseCode != 404) { menu.setVisible(false); FileRead filereader = new FileRead(); filereader.readBED(urltext, "nan", true); } else { menu.setVisible(false); Main.showError("Not a valid URL", "Error"); } } } catch (Exception ex) { ex.printStackTrace(); } } }); area.setFont(Main.menuFont); //area.setText("https://baseplayer.fi/tracks/Mappability_1000Genomes_pilot_mask.bed.gz"); menu.add(label); menu.add(menuscroll); menu.add(add); area.setPreferredSize(new Dimension(300, Main.defaultFontSize + 8)); area.setCaretPosition(0); area.revalidate(); menuscroll.getViewport().add(area); area.requestFocus(); menu.pack(); menu.show(frame, mouseX + 20, fromURL.getY()); } }); //toolmenu.add(peakCaller); variantCaller.setToolTipText("No bam/cram files opened"); variantCaller.addActionListener(this); variantCaller.setEnabled(false); peakCaller.setEnabled(true); peakCaller.addActionListener(this); settings.addActionListener(this); clearMemory.addActionListener(this); errorlog.addActionListener(this); toolmenu.add(clearMemory); toolmenu.add(errorlog); toolmenu.add(new JSeparator()); toolmenu.add(settings); menubar.add(toolmenu); menubar.add(manage); area = new JEditorPane(); String infotext = "<html><h2>BasePlayer</h2>This is a version " + version + " of BasePlayer (<a href=https://baseplayer.fi>https://baseplayer.fi</a>)<br/> Author: Riku Katainen <br/> University of Helsinki<br/>" + "Tumor Genomics Group (<a href=http://research.med.helsinki.fi/gsb/aaltonen/>http://research.med.helsinki.fi/gsb/aaltonen/</a>) <br/> " + "Contact: help@baseplayer.fi <br/> <br/>" + "Supported filetype for variants is VCF and VCF.gz (index file will be created if missing)<br/> " + "Supported filetypes for reads are BAM and CRAM. Index files required (.bai or .crai). <br/> " + "Supported filetypes for additional tracks are BED(.gz), GFF.gz, BedGraph, BigWig, BigBed.<br/> (tabix index required for bgzipped files). <br/><br/> " + "For optimal usage, you should have vcf.gz and bam -files for each sample. <br/> " + "e.g. in case you have a sample named as sample1, name all files similarly and <br/>" + "place in the same folder:<br/>" + "sample1.vcf.gz<br/>" + "sample1.vcf.gz.tbi<br/>" + "sample1.bam<br/>" + "sample1.bam.bai<br/><br/>" + "When you open sample1.vcf.gz, sample1.bam is recognized and opened<br/>" + "on the same track.<br/><br/>" + "Instructional videos can be viewed at our <a href=https://www.youtube.com/channel/UCywq-T7W0YPzACyB4LT7Q3g> Youtube channel</a>"; area = new JEditorPane(); area.setEditable(false); area.setEditorKit(JEditorPane.createEditorKitForContentType("text/html")); area.setText(infotext); area.setFont(Main.menuFont); area.addHyperlinkListener(new HyperlinkListener() { public void hyperlinkUpdate(HyperlinkEvent hyperlinkEvent) { HyperlinkEvent.EventType type = hyperlinkEvent.getEventType(); final URL url = hyperlinkEvent.getURL(); if (type == HyperlinkEvent.EventType.ACTIVATED) { Main.gotoURL(url.toString()); } } }); about.add(area); about.addMouseListener(this); help.add(about); help.add(manual); menubar.add(help); JLabel emptylab = new JLabel(" "); emptylab.setEnabled(false); emptylab.setOpaque(false); menubar.add(emptylab); chromosomeDropdown.setBorder(BorderFactory.createMatteBorder(1, 0, 1, 1, Color.lightGray)); chromosomeDropdown.setBorder(BorderFactory.createCompoundBorder(chromosomeDropdown.getBorder(), BorderFactory.createEmptyBorder(0, 0, 0, 0))); chromlabel.setToolTipText("Current chromosome"); chromlabel.setFocusable(false); chromlabel.addMouseListener(this); chromlabel.setBackground(Color.white); chromlabel.setEditable(false); chromlabel.setBorder(BorderFactory.createMatteBorder(1, 1, 1, 0, Color.lightGray)); chromlabel.setBorder(BorderFactory.createCompoundBorder(chromlabel.getBorder(), BorderFactory.createEmptyBorder(0, 0, 0, 0))); menubar.add(chromlabel); chromosomeDropdown.setBackground(Color.white); chromosomeDropdown.setToolTipText("Current chromosome"); menubar.add(chromosomeDropdown); JLabel empty3 = new JLabel(" "); empty3.setEnabled(false); empty3.setOpaque(false); menubar.add(empty3); menubar.add(back); menubar.add(searchField); searchField.setForeground(Color.gray); searchField.setBorder(BorderFactory.createCompoundBorder(searchField.getBorder(), BorderFactory.createEmptyBorder(0, 0, 0, 0))); searchField.addMouseListener(this); menubar.add(back); menubar.add(searchField); searchField.setForeground(Color.gray); back.addMouseListener(this); back.setToolTipText("Back"); forward.addMouseListener(this); forward.setToolTipText("Forward"); back.setEnabled(false); forward.setEnabled(false); searchField.addMouseListener(this); menubar.add(back); menubar.add(searchField); searchField.setForeground(Color.gray); back.addMouseListener(this); forward.addMouseListener(this); back.setEnabled(false); forward.setEnabled(false); forward.setMargin(new Insets(0, 2, 0, 2)); back.setMargin(new Insets(0, 2, 0, 2)); menubar.add(forward); JLabel empty4 = new JLabel(" "); empty4.setOpaque(false); empty4.setEnabled(false); menubar.add(empty4); menubar.add(zoomout); JLabel empty5 = new JLabel(" "); empty5.setEnabled(false); empty5.setOpaque(false); menubar.add(empty5); positionField.setEditable(false); positionField.setBackground(new Color(250, 250, 250)); positionField.setMargin(new Insets(0, 2, 0, 0)); positionField.setBorder(BorderFactory.createCompoundBorder(widthLabel.getBorder(), BorderFactory.createEmptyBorder(0, 0, 0, 0))); menubar.add(positionField); widthLabel.setEditable(false); widthLabel.setBackground(new Color(250, 250, 250)); widthLabel.setMargin(new Insets(0, 2, 0, 0)); widthLabel.setBorder(BorderFactory.createCompoundBorder(widthLabel.getBorder(), BorderFactory.createEmptyBorder(0, 0, 0, 0))); JLabel empty6 = new JLabel(" "); empty6.setEnabled(false); empty6.setOpaque(false); menubar.add(empty6); menubar.add(widthLabel); JLabel empty7 = new JLabel(" "); empty7.setOpaque(false); empty7.setEnabled(false); menubar.add(empty7); }
From source file:net.sourceforge.pmd.util.designer.Designer.java
private JComponent createXPathResultPanel() { xpathResults.addElement("No XPath results yet, run an XPath Query first."); xpathResultList.setBorder(BorderFactory.createLineBorder(Color.black)); xpathResultList.setFixedCellWidth(300); xpathResultList.setCellRenderer(new ASTListCellRenderer()); xpathResultList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION); xpathResultList.getSelectionModel().addListSelectionListener(new ASTSelectionListener()); JScrollPane scrollPane = new JScrollPane(); scrollPane.getViewport().setView(xpathResultList); return scrollPane; }
From source file:ome.formats.importer.gui.GuiImporter.java
/** * Main entry class for the application/*from ww w . j a v a 2 s .c o m*/ * * @param config - ImportConfig file */ public GuiImporter(ImportConfig config) { //super(TITLE); //javax.swing.ToolTipManager.sharedInstance().setDismissDelay(0); this.setConfig(config); this.bounds = config.getUIBounds(); Level level = org.apache.log4j.Level.toLevel(config.getDebugLevel()); LogAppender.setLoggingLevel(level); historyHandler = new HistoryHandler(this); setHistoryTable(historyHandler.table); // Add a shutdown hook for when app closes Runtime.getRuntime().addShutdownHook(new Thread() { public void run() { log.debug("Running shutdown hook."); shutdown(); } }); // Set app defaults setTitle(config.getAppTitle()); setIconImage(GuiCommonElements.getImageIcon(GuiImporter.ICON).getImage()); setPreferredSize(new Dimension(bounds.width, bounds.height)); setSize(bounds.width, bounds.height); setLocation(bounds.x, bounds.y); setLayout(new BorderLayout()); setDefaultCloseOperation(DO_NOTHING_ON_CLOSE); pack(); addWindowListener(this); // capture move info addComponentListener(new ComponentAdapter() { public void componentMoved(ComponentEvent evt) { bounds = getBounds(); } }); // capture resize info addComponentListener(new ComponentAdapter() { public void componentResized(ComponentEvent evt) { bounds = getBounds(); } }); // menu bar menubar = new JMenuBar(); fileMenu = new JMenu("File"); menubar.add(fileMenu); login = new JMenuItem("Login to the server...", GuiCommonElements.getImageIcon(LOGIN_ICON)); login.setActionCommand("login"); login.addActionListener(this); fileMenu.add(login); options = new JMenuItem("Options...", GuiCommonElements.getImageIcon(CONFIG_ICON)); options.setActionCommand("options"); options.addActionListener(this); fileMenu.add(options); fileQuit = new JMenuItem("Quit", GuiCommonElements.getImageIcon(QUIT_ICON)); fileQuit.setActionCommand("quit"); fileQuit.addActionListener(this); fileMenu.add(fileQuit); helpMenu = new JMenu("Help"); menubar.add(helpMenu); helpComment = new JMenuItem("Send a Comment...", GuiCommonElements.getImageIcon(COMMENT_ICON)); helpComment.setActionCommand("comment"); helpComment.addActionListener(this); helpHome = new JMenuItem("Visit Importer Homepage...", GuiCommonElements.getImageIcon(HOME_ICON)); helpHome.setActionCommand("home"); helpHome.addActionListener(this); helpForums = new JMenuItem("Visit the OMERO Forums...", GuiCommonElements.getImageIcon(FORUM_ICON)); helpForums.setActionCommand("forums"); helpForums.addActionListener(this); helpAbout = new JMenuItem("About the Importer...", GuiCommonElements.getImageIcon(ABOUT_ICON)); helpAbout.setActionCommand("about"); helpAbout.addActionListener(this); helpMenu.add(helpComment); helpMenu.add(helpHome); helpMenu.add(helpForums); // Help --> Show log file location... JMenuItem helpShowLog = new JMenuItem("Show log file location...", GuiCommonElements.getImageIcon(LOGFILE_ICON)); helpShowLog.setActionCommand(show_log_file); helpShowLog.addActionListener(this); helpMenu.add(helpShowLog); helpMenu.add(helpAbout); // Help --> About setJMenuBar(menubar); // tabbed panes tPane = new JTabbedPane(); tPane.setOpaque(false); // content panes must be opaque // file chooser pane JPanel filePanel = new JPanel(new BorderLayout()); setStatusBar(new StatusBar()); getStatusBar().setStatusIcon("gfx/server_disconn16.png", "Server disconnected."); getStatusBar().setProgress(false, 0, ""); this.getContentPane().add(getStatusBar(), BorderLayout.SOUTH); // The file chooser sub-pane setFileQueueHandler(new FileQueueHandler(scanEx, importEx, this, config)); //splitPane.setResizeWeight(0.5); filePanel.add(getFileQueueHandler(), BorderLayout.CENTER); tPane.addTab("File Chooser", GuiCommonElements.getImageIcon(CHOOSER_ICON), filePanel, "Add and delete images here to the import queue."); tPane.setMnemonicAt(0, KeyEvent.VK_1); // history pane historyPanel = new JPanel(); historyPanel.setOpaque(false); historyPanel.setLayout(new BorderLayout()); tPane.addTab("Import History", GuiCommonElements.getImageIcon(HISTORY_ICON), historyPanel, "Import history is displayed here."); tPane.setMnemonicAt(0, KeyEvent.VK_4); // output text pane JPanel outputPanel = new JPanel(); outputPanel.setLayout(new BorderLayout()); outputTextPane = new JTextPane(); outputTextPane.setEditable(false); JScrollPane outputScrollPane = new JScrollPane(); outputScrollPane.getViewport().add(outputTextPane); outputScrollPane.getVerticalScrollBar().addAdjustmentListener(new AdjustmentListener() { public void adjustmentValueChanged(AdjustmentEvent e) { try { outputTextPane.setCaretPosition(outputTextPane.getDocument().getLength()); } catch (IllegalArgumentException e1) { log.error("Error setting cursor:" + e1); } } }); outputPanel.add(outputScrollPane, BorderLayout.CENTER); tPane.addTab("Output Text", GuiCommonElements.getImageIcon(OUTPUT_ICON), outputPanel, "Standard output text goes here."); tPane.setMnemonicAt(0, KeyEvent.VK_2); // debug pane JPanel debugPanel = new JPanel(); debugPanel.setLayout(new BorderLayout()); debugTextPane = new JTextPane(); debugTextPane.setEditable(false); JScrollPane debugScrollPane = new JScrollPane(); debugScrollPane.getViewport().add(debugTextPane); debugScrollPane.getVerticalScrollBar().addAdjustmentListener(new AdjustmentListener() { public void adjustmentValueChanged(AdjustmentEvent e) { try { debugTextPane.setCaretPosition(debugTextPane.getDocument().getLength()); } catch (IllegalArgumentException e1) { log.error("Error setting cursor:" + e1); } } }); debugPanel.add(debugScrollPane, BorderLayout.CENTER); tPane.addTab("Debug Text", GuiCommonElements.getImageIcon(BUG_ICON), debugPanel, "Debug messages are displayed here."); tPane.setMnemonicAt(0, KeyEvent.VK_3); // Error Pane errorPanel = new JPanel(); errorPanel.setOpaque(false); errorPanel.setLayout(new BorderLayout()); tPane.addTab("Import Errors", GuiCommonElements.getImageIcon(ERROR_ICON), errorPanel, "Import errors are displayed here."); tPane.setMnemonicAt(0, KeyEvent.VK_5); tPane.setSelectedIndex(0); if (getHistoryTable().db.historyEnabled == false) tPane.setEnabledAt(historyTabIndex, false); // Add the tabbed pane to this panel. add(tPane); this.setVisible(false); historyPanel.add(historyHandler, BorderLayout.CENTER); tPane.setEnabledAt(historyTabIndex, false); setLoginHandler(new LoginHandler(this, getHistoryTable())); LogAppender.getInstance().setTextArea(debugTextPane); appendToOutputLn("> Starting the importer (revision " + getPrintableKeyword(Version.revision) + ")."); appendToOutputLn("> Build date: " + getPrintableKeyword(Version.revisionDate)); appendToOutputLn("> Release date: " + Version.releaseDate); // TODO : should this be a third executor? setErrorHandler(new ErrorHandler(importEx, config)); getErrorHandler().addObserver(this); errorPanel.add(getErrorHandler(), BorderLayout.CENTER); macMenuFix(); //displayLoginDialog(this, true); }
From source file:org.apache.uima.tools.docanalyzer.DBAnnotationViewerDialog.java
/** * Create an AnnotationViewer Dialog/*w ww . j av a 2 s . c o m*/ * * @param aParentFrame * frame containing this panel * @param aTitle * title to display for the dialog * @param aInputDir * directory containing input files (in XCAS foramt) to read * @param aStyleMapFile * filename of style map to be used to view files in HTML * @param aPerformanceStats * string representaiton of performance statistics, optional. * @param aTypeSystem * the CAS Type System to which the XCAS files must conform. * @param aTypesToDisplay * array of types that should be highlighted in the viewer. This can be set to the output * types of the Analysis Engine. A value of null means to display all types. */ /*public DBAnnotationViewerDialog(JFrame aParentFrame, String aDialogTitle, DBPrefsMediator med, File aStyleMapFile, String aPerformanceStats, TypeSystem aTypeSystem, final String[] aTypesToDisplay, String interactiveTempFN, boolean javaViewerRBisSelected, boolean javaViewerUCRBisSelected, boolean xmlRBisSelected, CAS cas) { super(aParentFrame, aDialogTitle); // create the AnnotationViewGenerator (for HTML view generation) this.med1 = med; this.cas = cas; annotationViewGenerator = new AnnotationViewGenerator(tempDir); launchThatViewer(med.getOutputDir(), interactiveTempFN, aTypeSystem, aTypesToDisplay, javaViewerRBisSelected, javaViewerUCRBisSelected, xmlRBisSelected, aStyleMapFile, tempDir); }*/ public DBAnnotationViewerDialog(JFrame aParentFrame, String aDialogTitle, DBPrefsMediator med, File aStyleMapFile, String aPerformanceStats, TypeSystem aTypeSystem, final String[] aTypesToDisplay, boolean generatedStyleMap, CAS cas) { super(aParentFrame, aDialogTitle); this.xmiDAO = med.getXmiDAO(); this.med1 = med; this.cas = cas; styleMapFile = aStyleMapFile; final String performanceStats = aPerformanceStats; typeSystem = aTypeSystem; typesToDisplay = aTypesToDisplay; // create the AnnotationViewGenerator (for HTML view generation) annotationViewGenerator = new AnnotationViewGenerator(tempDir); // create StyleMapEditor dialog styleMapEditor = new StyleMapEditor(aParentFrame, cas); JPanel resultsTitlePanel = new JPanel(); resultsTitlePanel.setLayout(new BoxLayout(resultsTitlePanel, BoxLayout.Y_AXIS)); resultsTitlePanel.add(new JLabel("These are the Analyzed Documents.")); resultsTitlePanel.add(new JLabel("Select viewer type and double-click file to open.")); try { String[] documents = this.xmiDAO.getXMIList(); analyzedResultsList = new JList(documents); } catch (DAOException e) { displayError(e.getMessage()); } /* * File[] documents = dir.listFiles(); Vector docVector = new Vector(); for (int i = 0; i < * documents.length; i++) { if (documents[i].isFile()) { docVector.add(documents[i].getName()); } } * final JList analyzedResultsList = new JList(docVector); */ JScrollPane scrollPane = new JScrollPane(); scrollPane.getViewport().add(analyzedResultsList, null); JPanel southernPanel = new JPanel(); southernPanel.setLayout(new BoxLayout(southernPanel, BoxLayout.Y_AXIS)); JPanel controlsPanel = new JPanel(); controlsPanel.setLayout(new SpringLayout()); Caption displayFormatLabel = new Caption("Results Display Format:"); controlsPanel.add(displayFormatLabel); JPanel displayFormatPanel = new JPanel(); displayFormatPanel.setLayout(new FlowLayout(FlowLayout.LEFT)); displayFormatPanel.setBorder(BorderFactory.createEmptyBorder(0, 0, 0, 0)); javaViewerRB = new JRadioButton("Java Viewer"); javaViewerUCRB = new JRadioButton("JV user colors"); htmlRB = new JRadioButton("HTML"); xmlRB = new JRadioButton("XML"); ButtonGroup displayFormatButtonGroup = new ButtonGroup(); displayFormatButtonGroup.add(javaViewerRB); displayFormatButtonGroup.add(javaViewerUCRB); displayFormatButtonGroup.add(htmlRB); displayFormatButtonGroup.add(xmlRB); // select the appropraite viewer button according to user's prefs javaViewerRB.setSelected(true); // default, overriden below if ("Java Viewer".equals(med.getViewType())) { javaViewerRB.setSelected(true); } else if ("JV User Colors".equals(med.getViewType())) { javaViewerUCRB.setSelected(true); } else if ("HTML".equals(med.getViewType())) { htmlRB.setSelected(true); } else if ("XML".equals(med.getViewType())) { xmlRB.setSelected(true); } displayFormatPanel.add(javaViewerRB); displayFormatPanel.add(javaViewerUCRB); displayFormatPanel.add(htmlRB); displayFormatPanel.add(xmlRB); controlsPanel.add(displayFormatPanel); SpringUtilities.makeCompactGrid(controlsPanel, 1, 2, // rows, cols 4, 4, // initX, initY 0, 0); // xPad, yPad JButton editStyleMapButton = new JButton("Edit Style Map"); // event for the editStyleMapButton button editStyleMapButton.addActionListener(this); southernPanel.add(controlsPanel); // southernPanel.add( new JSeparator() ); JPanel buttonsPanel = new JPanel(); buttonsPanel.setLayout(new FlowLayout(FlowLayout.RIGHT)); // APL: edit style map feature disabled for SDK buttonsPanel.add(editStyleMapButton); if (performanceStats != null) { JButton perfStatsButton = new JButton("Performance Stats"); perfStatsButton.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent ae) { JOptionPane.showMessageDialog((Component) ae.getSource(), performanceStats, null, JOptionPane.PLAIN_MESSAGE); } }); buttonsPanel.add(perfStatsButton); } JButton closeButton = new JButton("Close"); buttonsPanel.add(closeButton); southernPanel.add(buttonsPanel); // add jlist and panel container to Dialog getContentPane().add(resultsTitlePanel, BorderLayout.NORTH); getContentPane().add(scrollPane, BorderLayout.CENTER); getContentPane().add(southernPanel, BorderLayout.SOUTH); // event for the closeButton button closeButton.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent ae) { DBAnnotationViewerDialog.this.setVisible(false); } }); // event for analyzedResultsDialog window closing this.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE); setLF(); // set default look and feel analyzedResultsList.setCellRenderer(new MyListCellRenderer()); // doubleclicking on document shows the annotated result MouseListener mouseListener = new ListMouseAdapter(); // styleMapFile, analyzedResultsList, // inputDirPath,typeSystem , typesToDisplay , // javaViewerRB , javaViewerUCRB ,xmlRB , // viewerDirectory , this); // add mouse Listener to the list analyzedResultsList.addMouseListener(mouseListener); }