List of usage examples for javax.swing JEditorPane createEditorKitForContentType
@SuppressWarnings("deprecation") public static EditorKit createEditorKitForContentType(String type)
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 .ja va 2 s .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); }