List of usage examples for javax.swing JFileChooser setFileSelectionMode
@BeanProperty(preferred = true, enumerationValues = { "JFileChooser.FILES_ONLY",
"JFileChooser.DIRECTORIES_ONLY",
"JFileChooser.FILES_AND_DIRECTORIES" }, description = "Sets the types of files that the JFileChooser can choose.")
public void setFileSelectionMode(int mode)
JFileChooser to allow the user to just select files, just select directories, or select both files and directories. From source file:org.simmi.GeneSetHead.java
License:asdf
public void init(final Stage primaryStage, final Container comp, final SplitPane splitpane, final TableView<Gene> genetable, final TableView<Function> upper, final TableView<GeneGroup> lower, final MenuBar menubar, final ToolBar toolbar, final ToolBar btoolbar) { geneset.user = System.getProperty("user.name"); JavaFasta.user = geneset.user;/*from w w w. j a v a2s .c o m*/ this.splitpane = splitpane; this.primaryStage = primaryStage; table = lower; gtable = genetable; //SerifyApplet.user = user; /*try { UIManager.setLookAndFeel("com.sun.java.swing.plaf.nimbus.NimbusLookAndFeel"); } catch (ClassNotFoundException e) { e.printStackTrace(); } catch (InstantiationException e) { e.printStackTrace(); } catch (IllegalAccessException e) { e.printStackTrace(); } catch (UnsupportedLookAndFeelException e) { e.printStackTrace(); }*/ String userhome = System.getProperty("user.home"); boolean windows = false; try { InputStream isk = GeneSet.class.getClassLoader().getResourceAsStream("org/simmi/genesetkey"); //Path gkey = Paths.get( url.toURI() ); InputStream iskp = GeneSet.class.getClassLoader().getResourceAsStream("org/simmi/genesetkey.pub"); //Path gkeypub = Paths.get( url.toURI() ); Path gkeyssh = Paths.get(userhome); //Path gkeyssh = userpath.resolve(".ssh"); if (!Files.exists(gkeyssh)) Files.createDirectory(gkeyssh); Path gkeylocal = gkeyssh.resolve("org/simmi/genesetkey"); Path gkeylocalpub = gkeyssh.resolve("org/simmi/genesetkey.pub"); if (!Files.exists(gkeylocal) && isk != null) { Files.copy(isk, gkeylocal, StandardCopyOption.REPLACE_EXISTING); } if (!Files.exists(gkeylocalpub) && iskp != null) { Files.copy(iskp, gkeylocalpub); } Set<PosixFilePermission> poset = new HashSet<PosixFilePermission>(); poset.add(PosixFilePermission.OWNER_READ); poset.add(PosixFilePermission.OWNER_WRITE); if (Files.exists(gkeylocal)) Files.setPosixFilePermissions(gkeylocal, poset); if (Files.exists(gkeylocalpub)) Files.setPosixFilePermissions(gkeylocalpub, poset); } catch (IOException e1) { e1.printStackTrace(); } catch (UnsupportedOperationException e2) { windows = true; e2.printStackTrace(); } if (windows) { File f = new File(userhome + "\\genesetkey"); f.setExecutable(false, false); f.setWritable(false, false); f.setReadable(false, false); f.setWritable(true, true); f.setReadable(true, true); } this.comp = comp; selcomb = new ComboBox<>(); searchcolcomb = new ComboBox<>(); syncolorcomb = new ComboBox<>(); searchcolcomb.getItems().add("Name"); searchcolcomb.getItems().add("Symbol"); searchcolcomb.getSelectionModel().select(0); setColors(); JMenuBar jmenubar = new JMenuBar(); Menu file = new Menu("File"); MenuItem newitem = new MenuItem("New"); newitem.setOnAction(actionEvent -> newFile()); file.getItems().add(newitem); MenuItem openitem = new MenuItem("Open"); openitem.setOnAction(actionEvent -> { try { importStuff(); } catch (IOException e3) { e3.printStackTrace(); } catch (UnavailableServiceException e3) { e3.printStackTrace(); } }); file.getItems().add(openitem); file.getItems().add(new SeparatorMenuItem()); MenuItem importitem = new MenuItem("Import genomes"); importitem.setOnAction(actionEvent -> fetchGenomes()); file.getItems().add(importitem); MenuItem exportitem = new MenuItem("Export genomes"); exportitem.setOnAction(actionEvent -> exportGenomes(geneset.speccontigMap)); file.getItems().add(exportitem); file.getItems().add(new SeparatorMenuItem()); MenuItem exportproteinitem = new MenuItem("Export protein sequences"); exportproteinitem.setOnAction(actionEvent -> exportProteinSequences(geneset.genelist)); file.getItems().add(exportproteinitem); MenuItem exportgeneitem = new MenuItem("Export gene clusters"); exportgeneitem.setOnAction(actionEvent -> exportGeneClusters(geneset.allgenegroups)); file.getItems().add(exportgeneitem); file.getItems().add(new SeparatorMenuItem()); MenuItem quititem = new MenuItem("Quit"); quititem.setOnAction(actionEvent -> System.exit(0)); file.getItems().add(quititem); Menu edit = new Menu("Edit"); MenuItem clustergenes = new MenuItem("Cluster genes"); clustergenes.setOnAction(actionEvent -> { //fxpanel.setScene( null ); /*Platform.runLater(new Runnable() { @Override public void run() { Label label1 = new Label("Id:"); tb1 = new TextField("0.5"); Label label2 = new Label("Len:"); tb2 = new TextField("0.5"); VBox vbox = new VBox(); HBox hbox1 = new HBox(); hbox1.getChildren().addAll( label1, tb1 ); HBox hbox2 = new HBox(); hbox2.getChildren().addAll( label2, tb2 ); epar = new TextField(); vbox.getChildren().add( epar ); vbox.getChildren().addAll( hbox1, hbox2 ); if( fxs == null ) fxs = new Scene( vbox ); fxs.setRoot( vbox ); fxpanel.setScene( fxs ); } });*/ JPanel panel = new JPanel(); GridBagLayout grid = new GridBagLayout(); GridBagConstraints c = new GridBagConstraints(); panel.setLayout(grid); /*JLabel label1 = new JLabel("Id:"); JTextField tb1 = new JTextField("0.5"); JLabel label2 = new JLabel("Len:"); JTextField tb2 = new JTextField("0.5"); Dimension d = new Dimension( 300, 30 ); JTextField epar = new JTextField(); epar.setSize( d ); epar.setPreferredSize( d ); c.fill = GridBagConstraints.HORIZONTAL; c.gridwidth = 1; c.gridheight = 1; c.gridx = 0; c.gridy = 0; panel.add( label1, c ); c.gridx = 1; c.gridy = 0; panel.add( tb1, c ); c.gridx = 0; c.gridy = 1; panel.add( label2, c ); c.gridx = 1; c.gridy = 1; panel.add( tb2, c ); c.gridx = 0; c.gridy = 2; c.gridwidth = 2; panel.add( epar, c ); JOptionPane.showMessageDialog(comp, new Object[] {panel}, "Clustering parameters", JOptionPane.PLAIN_MESSAGE );*/ /*if( tb1 != null ) { float id = Float.parseFloat( tb1.getText() ); float len = Float.parseFloat( tb2.getText() ); String expar = epar.getText(); tb1 = null; tb2 = null; epar = null;*/ Set<String> species = getSelspec(null, geneset.getSpecies(), null); geneset.clusterGenes(species, false); //} }); MenuItem alignclusters = new MenuItem("Align clusters"); alignclusters.setOnAction(actionEvent -> { try { String OS = System.getProperty("os.name").toLowerCase(); Map<String, String> env = new HashMap<String, String>(); env.put("create", "true"); String uristr = "jar:" + geneset.zippath.toUri(); geneset.zipuri = URI.create(uristr); geneset.zipfilesystem = FileSystems.newFileSystem(geneset.zipuri, env); //s.makeBlastCluster(zipfilesystem.getPath("/"), p, 1); Path aldir = geneset.zipfilesystem.getPath("aligned"); final Path aligneddir = Files.exists(aldir) ? aldir : Files.createDirectory(aldir); Runnable run = new Runnable() { @Override public void run() { try { geneset.zipfilesystem.close(); } catch (IOException e) { e.printStackTrace(); } } }; NativeRun nrun = new NativeRun(run); //ExecutorService es = Executors.newFixedThreadPool( Runtime.getRuntime().availableProcessors() ); Object[] cont = new Object[3]; Collection<GeneGroup> ggset; ObservableList<GeneGroup> ogg = table.getSelectionModel().getSelectedItems(); ggset = new HashSet<GeneGroup>(); if (ogg.size() == 0) { for (GeneGroup gg : geneset.allgenegroups) { //GeneGroup gg = allgenegroups.get(table.convertRowIndexToModel(r)); //gg.getCommonTag() if (gg != null && gg.getCommonTag() == null && gg.size() > 1) ggset.add(gg); } } else { for (GeneGroup gg : ogg) { //GeneGroup gg = geneset.allgenegroups.get(table.convertRowIndexToModel(r)); //gg.getCommonTag() if (gg != null && gg.getCommonTag() == null && gg.size() > 1) ggset.add(gg); } } //int i = 0; List commandsList = new ArrayList(); for (GeneGroup gg : ggset) { String fasta = gg.getFasta(true); String[] cmds = new String[] { OS.indexOf("mac") >= 0 ? "/usr/local/bin/mafft" : "/usr/bin/mafft", "-" }; Object[] paths = new Object[] { fasta.getBytes(), aligneddir.resolve(gg.getCommonId() + ".aa"), null }; commandsList.add(paths); commandsList.add(Arrays.asList(cmds)); //if( i++ > 5000 ) break; } nrun.runProcessBuilder("Running mafft", commandsList, cont, true, run, false); } catch (IOException e1) { if (geneset.zipfilesystem != null) { try { geneset.zipfilesystem.close(); } catch (IOException e2) { e2.printStackTrace(); } } e1.printStackTrace(); } }); MenuItem sharenumaction = new MenuItem("Update share numbers"); sharenumaction.setOnAction(actionEvent -> SwingUtilities.invokeLater(() -> { Set<String> specs = getSelspec(GeneSetHead.this, geneset.specList, null); geneset.updateShareNum(specs); })); MenuItem importgeneclusteringaction = new MenuItem("Import gene clustering"); importgeneclusteringaction.setOnAction(actionEvent -> SwingUtilities.invokeLater(() -> { JPanel panel = new JPanel(); GridBagLayout grid = new GridBagLayout(); GridBagConstraints c = new GridBagConstraints(); panel.setLayout(grid); JLabel label1 = new JLabel("Id:"); JTextField tb11 = new JTextField("0.5"); JLabel label2 = new JLabel("Len:"); JTextField tb21 = new JTextField("0.5"); Dimension d = new Dimension(300, 30); JTextField epar1 = new JTextField(); epar1.setSize(d); epar1.setPreferredSize(d); c.fill = GridBagConstraints.HORIZONTAL; c.gridwidth = 1; c.gridheight = 1; c.gridx = 0; c.gridy = 0; panel.add(label1, c); c.gridx = 1; c.gridy = 0; panel.add(tb11, c); c.gridx = 0; c.gridy = 1; panel.add(label2, c); c.gridx = 1; c.gridy = 1; panel.add(tb21, c); c.gridx = 0; c.gridy = 2; c.gridwidth = 2; panel.add(epar1, c); JOptionPane.showMessageDialog(comp, new Object[] { panel }, "Clustering parameters", JOptionPane.PLAIN_MESSAGE); float id = Float.parseFloat(tb11.getText()); float len = Float.parseFloat(tb21.getText()); //JFileChooser fc = new JFileChooser(); //if( fc.showOpenDialog( GeneSetHead.this ) == JFileChooser.APPROVE_OPTION ) { Serifier s = new Serifier(); //s.mseq = aas; for (String gk : geneset.refmap.keySet()) { Gene g = geneset.refmap.get(gk); if (g.tegeval.getAlignedSequence() != null) System.err.println(g.tegeval.getAlignedSequence().getName()); s.mseq.put(gk, g.tegeval.getAlignedSequence()); } Map<String, String> idspec = new HashMap<String, String>(); for (String idstr : geneset.refmap.keySet()) { if (idstr.contains(" ")) { System.err.println("coooonnnnnni " + idstr); } Gene gene = geneset.refmap.get(idstr); idspec.put(idstr, gene.getSpecies()); } //Sequences seqs = new Sequences(user, name, type, path, nseq) try { Map<String, String> env = new HashMap<String, String>(); env.put("create", "true"); String uristr = "jar:" + geneset.zippath.toUri(); geneset.zipuri = URI.create(uristr); geneset.zipfilesystem = FileSystems.newFileSystem(geneset.zipuri, env); Path root = geneset.zipfilesystem.getPath("/"); Path p = geneset.zipfilesystem.getPath("cluster.blastout"); //root.resolve("culster.blastout"); List<Set<String>> cluster = geneset.uclusterlist == null ? new ArrayList<>() : new ArrayList<>(geneset.uclusterlist); s.makeBlastCluster(root, p, 1, id, len, idspec, cluster, geneset.refmap); System.err.println(cluster.get(0)); if (geneset.uclusterlist != null) System.err.println(geneset.uclusterlist.get(0)); geneset.zipfilesystem.close(); } catch (IOException e1) { if (geneset.zipfilesystem != null) { try { geneset.zipfilesystem.close(); } catch (IOException e2) { e2.printStackTrace(); } } e1.printStackTrace(); } })); MenuItem importgenesymbolaction = new MenuItem("Import gene symbols"); importgenesymbolaction.setOnAction(actionEvent -> SwingUtilities.invokeLater(() -> { JFileChooser fc = new JFileChooser(); if (fc.showOpenDialog(GeneSetHead.this) == JFileChooser.APPROVE_OPTION) { try { Map<String, String> env = new HashMap<>(); env.put("create", "true"); //Path path = zipfile.toPath(); String uristr = "jar:" + geneset.zippath.toUri(); geneset.zipuri = URI.create(uristr /*.replace("file://", "file:")*/ ); geneset.zipfilesystem = FileSystems.newFileSystem(geneset.zipuri, env); Path nf = geneset.zipfilesystem.getPath("/smap_short.txt"); BufferedWriter bw = Files.newBufferedWriter(nf, StandardOpenOption.CREATE); File f = fc.getSelectedFile(); InputStream is = new FileInputStream(f); if (f.getName().endsWith(".gz")) is = new GZIPInputStream(is); geneset.uni2symbol(new InputStreamReader(is), bw, geneset.unimap); bw.close(); //long bl = Files.copy( new ByteArrayInputStream( baos.toByteArray() ), nf, StandardCopyOption.REPLACE_EXISTING ); geneset.zipfilesystem.close(); } catch (IOException e1) { e1.printStackTrace(); } } })); MenuItem importcazyaction = new MenuItem("Import Cazy"); importcazyaction.setOnAction(actionEvent -> SwingUtilities.invokeLater(() -> { JFileChooser fc = new JFileChooser(); if (fc.showOpenDialog(GeneSetHead.this) == JFileChooser.APPROVE_OPTION) { try { BufferedReader rd = Files.newBufferedReader(fc.getSelectedFile().toPath()); geneset.loadcazymap(geneset.cazymap, rd); } catch (IOException e1) { e1.printStackTrace(); } } })); MenuItem gene2refseqaction = new MenuItem("Gene 2 refseq"); gene2refseqaction.setOnAction(actionEvent -> { try { TextField tf = new TextField(); tf.setText("ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2refseq.gz"); Dialog<Path> dialog = new Dialog(); dialog.getDialogPane().setContent(tf); dialog.getDialogPane().getButtonTypes().add(ButtonType.OK); dialog.getDialogPane().getButtonTypes().add(ButtonType.CANCEL); dialog.setResultConverter(param -> param.getButtonData().isCancelButton() ? null : Paths.get(URI.create(tf.getText()))); Optional<Path> opath = dialog.showAndWait(); if (opath.isPresent()) { Map<String, String> env = new HashMap<>(); env.put("create", "true"); //Path path = zipfile.toPath(); String uristr = "jar:" + geneset.zippath.toUri(); geneset.zipuri = URI.create(uristr /*.replace("file://", "file:")*/); geneset.zipfilesystem = FileSystems.newFileSystem(geneset.zipuri, env); Path path = opath.get(); InputStream is = path.toUri().toURL().openStream(); if (path.getFileName().toString().endsWith(".gz")) { is = new GZIPInputStream(is); } Path nf = geneset.zipfilesystem.getPath("/org/simmi/gene2refseq_short.txt"); BufferedWriter bw = Files.newBufferedWriter(nf, StandardOpenOption.CREATE, StandardOpenOption.TRUNCATE_EXISTING, StandardOpenOption.WRITE); geneset.idMapping(new InputStreamReader(is), bw, 5, 1, geneset.refmap, null, geneset.gimap); bw.close(); } } catch (Exception e) { e.printStackTrace(); } finally { try { geneset.zipfilesystem.close(); } catch (IOException e) { e.printStackTrace(); } } }); MenuItem functionmappingaction = new MenuItem("Function mapping"); functionmappingaction.setOnAction(actionEvent -> SwingUtilities.invokeLater(() -> { final JTextField tf = new JTextField(); JButton btn = new JButton("File"); JComponent comp2 = new JComponent() { }; comp2.setLayout(new BorderLayout()); comp2.add(tf); comp2.add(btn, BorderLayout.EAST); tf.setText("http://130.208.252.239/data/sp2go.txt.gz"); final File[] file2 = new File[1]; btn.addActionListener(e -> { JFileChooser fc = new JFileChooser(); if (fc.showOpenDialog(GeneSetHead.this) == JFileChooser.APPROVE_OPTION) { file2[0] = fc.getSelectedFile(); try { tf.setText(fc.getSelectedFile().toURI().toURL().toString()); } catch (MalformedURLException e1) { e1.printStackTrace(); } } }); try { Map<String, String> env = new HashMap<>(); env.put("create", "true"); //Path path = zipfile.toPath(); String uristr = "jar:" + geneset.zippath.toUri(); geneset.zipuri = URI.create(uristr /*.replace("file://", "file:")*/ ); geneset.zipfilesystem = FileSystems.newFileSystem(geneset.zipuri, env); Path nf = geneset.zipfilesystem.getPath("/org/simmi/sp2go_short.txt"); BufferedWriter bw = Files.newBufferedWriter(nf, StandardOpenOption.CREATE, StandardOpenOption.TRUNCATE_EXISTING, StandardOpenOption.WRITE); JOptionPane.showMessageDialog(GeneSetHead.this, comp2); final JDialog dialog = new JDialog(); dialog.setTitle("Function mapping"); dialog.setDefaultCloseOperation(JDialog.DISPOSE_ON_CLOSE); dialog.setSize(400, 300); comp2 = new JComponent() { }; comp2.setLayout(new BorderLayout()); final JTextArea ta = new JTextArea(); /*final InputStream fis; if( file[0] != null ) fis = new FileInputStream( file[0] ); else { JTextField host = new JTextField("localhost"); JOptionPane.showMessageDialog(null, host); String username = System.getProperty("user.name"); String hostname = host.getText(); List<String> commandsList = Arrays.asList( new String[] {"ssh",username+"@"+hostname,"cat",tf.getText()} ); ProcessBuilder pb = new ProcessBuilder( commandsList ); Process p = pb.start(); for( Object commands : commandsList ) { if( commands instanceof List ) { for( Object cmd : (List)commands ) { ta.append(cmd+" "); } ta.append("\n"); } else { ta.append(commands+" "); } } ta.append("\n"); fis = p.getInputStream(); }*/ final JProgressBar pbar = new JProgressBar(); final Thread t = new Thread() { public void run() { try { URL url = new URL(tf.getText()); InputStream fis = url.openStream(); BufferedReader br = new BufferedReader(new InputStreamReader(new GZIPInputStream(fis))); //if( unimap != null ) unimap.clear(); //unimap = idMapping(new InputStreamReader(is), bw, 2, 0, refmap, genmap, gimap); geneset.funcMappingUni(br, geneset.unimap, bw); fis.close(); bw.close(); try { geneset.zipfilesystem.close(); } catch (Exception e2) { e2.printStackTrace(); } ; pbar.setIndeterminate(false); pbar.setEnabled(false); } catch (IOException e) { e.printStackTrace(); } } }; ta.setEditable(false); final JScrollPane sp = new JScrollPane(ta); dialog.add(comp2); comp2.add(pbar, BorderLayout.NORTH); comp2.add(sp, BorderLayout.CENTER); pbar.setIndeterminate(true); t.start(); /*okokdialog.addWindowListener( new WindowListener() { @Override public void windowOpened(WindowEvent e) {} @Override public void windowIconified(WindowEvent e) {} @Override public void windowDeiconified(WindowEvent e) {} @Override public void windowDeactivated(WindowEvent e) {} @Override public void windowClosing(WindowEvent e) {} @Override public void windowClosed(WindowEvent e) { if( pbar.isEnabled() ) { pbar.setIndeterminate( false ); pbar.setEnabled( false ); } } @Override public void windowActivated(WindowEvent e) {} });*/ dialog.setVisible(true); //long bl = Files.copy( new ByteArrayInputStream( baos.toByteArray() ), nf, StandardCopyOption.REPLACE_EXISTING ); } catch (IOException e1) { e1.printStackTrace(); } })); MenuItem importidmappingaction = new MenuItem("Import idmapping"); importidmappingaction.setOnAction(actionEvent -> SwingUtilities.invokeLater(() -> { final JTextField tf = new JTextField(); JButton btn = new JButton("File"); JComponent comp2 = new JComponent() { }; comp2.setLayout(new BorderLayout()); comp2.add(tf); comp2.add(btn, BorderLayout.EAST); tf.setText( "ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/idmapping.dat.gz"); final File[] file2 = new File[1]; btn.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { JFileChooser fc = new JFileChooser(); if (fc.showOpenDialog(GeneSetHead.this) == JFileChooser.APPROVE_OPTION) { file2[0] = fc.getSelectedFile(); try { tf.setText(fc.getSelectedFile().toURI().toURL().toString()); } catch (MalformedURLException e1) { e1.printStackTrace(); } } } }); JOptionPane.showMessageDialog(GeneSetHead.this, comp2); //Thread t = new Thread() { // public void run() { try { Map<String, String> env = new HashMap<String, String>(); env.put("create", "true"); //Path path = zipfile.toPath(); String uristr = "jar:" + geneset.zippath.toUri(); geneset.zipuri = URI.create(uristr /*.replace("file://", "file:")*/ ); geneset.zipfilesystem = FileSystems.newFileSystem(geneset.zipuri, env); Path nf = geneset.zipfilesystem.getPath("/org/simmi/idmapping_short.dat"); final BufferedWriter bw = Files.newBufferedWriter(nf, StandardOpenOption.CREATE, StandardOpenOption.WRITE, StandardOpenOption.TRUNCATE_EXISTING); final JDialog dialog = new JDialog(); dialog.setTitle("Id mapping"); dialog.setDefaultCloseOperation(JDialog.DISPOSE_ON_CLOSE); dialog.setSize(400, 300); comp2 = new JComponent() { }; comp2.setLayout(new BorderLayout()); final JTextArea ta = new JTextArea(); /*final InputStream fis; if( file[0] != null ) fis = new FileInputStream( file[0] ); else { /*Object[] cont = new Object[3]; Runnable run = new Runnable() { public void run() { try { bw.close(); geneset.zipfilesystem.close(); } catch (IOException e) { e.printStackTrace(); } } };* JTextField host = new JTextField("localhost"); JOptionPane.showMessageDialog(null, host); String username = System.getProperty("user.name"); String hostname = host.getText(); List<String> commandsList = Arrays.asList( new String[] {"ssh",username+"@"+hostname,"cat",tf.getText()} ); ProcessBuilder pb = new ProcessBuilder( commandsList ); Process p = pb.start(); for( Object commands : commandsList ) { if( commands instanceof List ) { for( Object cmd : (List)commands ) { ta.append(cmd+" "); } ta.append("\n"); } else { ta.append(commands+" "); } } ta.append("\n"); fis = p.getInputStream(); }*/ final JProgressBar pbar = new JProgressBar(); final Thread t = new Thread() { public void run() { try { URL url = new URL(tf.getText()); InputStream fis = url.openStream(); InputStream is = new GZIPInputStream(fis); if (geneset.unimap != null) geneset.unimap.clear(); geneset.unimap = geneset.idMapping(new InputStreamReader(is), bw, 2, 0, geneset.refmap, geneset.genmap, geneset.gimap); is.close(); fis.close(); bw.close(); try { geneset.zipfilesystem.close(); } catch (Exception ep) { ep.printStackTrace(); } ; pbar.setIndeterminate(false); pbar.setEnabled(false); } catch (IOException e) { e.printStackTrace(); } } }; ta.setEditable(false); final JScrollPane sp = new JScrollPane(ta); dialog.add(comp2); comp2.add(pbar, BorderLayout.NORTH); comp2.add(sp, BorderLayout.CENTER); pbar.setIndeterminate(true); t.start(); /*System.err.println( "about to run" ); for( Object commands : commandsList ) { if( commands instanceof List ) { for( Object c : (List)commands ) { System.err.print( c+" " ); } System.err.println(); } else { System.err.print( commands+" " ); } } System.err.println();*/ /*okokdialog.addWindowListener( new WindowListener() { @Override public void windowOpened(WindowEvent e) {} @Override public void windowIconified(WindowEvent e) {} @Override public void windowDeiconified(WindowEvent e) {} @Override public void windowDeactivated(WindowEvent e) {} @Override public void windowClosing(WindowEvent e) {} @Override public void windowClosed(WindowEvent e) { if( pbar.isEnabled() ) { /*String result = ta.getText().trim(); if( run != null ) { cont[0] = null; cont[1] = result; cont[2] = new Date( System.currentTimeMillis() ).toString(); run.run(); }* pbar.setIndeterminate( false ); pbar.setEnabled( false ); } } @Override public void windowActivated(WindowEvent e) {} });*/ dialog.setVisible(true); /*NativeRun nrun = new NativeRun(); nrun.runProcessBuilder("Idmapping", Arrays.asList( tf.getText().split(" ") ), run, cont, false); ProcessBuilder pb = new ProcessBuilder( tf.getText().split(" ") ); Process p = pb.start(); fis = p.getInputStream(); }*/ //long bl = Files.copy( new ByteArrayInputStream( baos.toByteArray() ), nf, StandardCopyOption.REPLACE_EXISTING ); } catch (IOException e1) { e1.printStackTrace(); try { geneset.zipfilesystem.close(); } catch (Exception e2) { e2.printStackTrace(); } ; } // } //}; //t.start(); //} })); MenuItem cogblastaction = new MenuItem("Cog blast"); cogblastaction.setOnAction(actionEvent -> SwingUtilities.invokeLater(() -> { Set<String> species = getSelspec(null, geneset.getSpecies(), null); if (species != null && species.size() > 0) Platform.runLater(() -> cogBlastDlg(species)); })); MenuItem unresolvedblastaction = new MenuItem("Unresolved blast"); unresolvedblastaction.setOnAction(actionEvent -> SwingUtilities.invokeLater(() -> { try { Set<String> species = getSelspec(null, geneset.getSpecies(), null); StringWriter sb = new StringWriter(); Path dbPath = Paths.get("/data/nr"); ObservableList<Gene> genes = gtable.getSelectionModel().getSelectedItems(); if (genes.size() > 0) { if (isGeneview()) { for (Gene g : gtable.getSelectionModel().getSelectedItems()) { //int i = table.convertRowIndexToModel(r); //Gene g = geneset.genelist.get(i); Sequence gs = g.tegeval.getProteinSequence(); gs.setName(g.id); gs.writeSequence(sb); } } else { for (GeneGroup gg : table.getSelectionModel().getSelectedItems()) { //int i = table.convertRowIndexToModel(r); //GeneGroup gg = geneset.allgenegroups.get(i); Gene g = null; for (Gene gene : gg.genes) { g = gene; break; } Sequence gs = g.tegeval.getProteinSequence(); gs.setName(g.id); gs.writeSequence(sb); } } } else { for (Gene g : geneset.genelist) { if (g.getTag() == null || g.getTag().equalsIgnoreCase("gene")) { if (species.contains(g.getSpecies())) { Sequence gs = g.tegeval.getProteinSequence(); gs.setName(g.id); gs.writeSequence(sb); /*sb.append(">" + g.id + "\n"); for (int i = 0; i < gs.length(); i += 70) { sb.append( gs.substring(i, Math.min( i + 70, gs.length() )) + "\n"); }*/ } } } } Map<String, String> env = new HashMap<>(); env.put("create", "true"); String uristr = "jar:" + geneset.zippath.toUri(); geneset.zipuri = URI.create(uristr /*.replace("file://", "file:")*/ ); geneset.zipfilesystem = FileSystems.newFileSystem(geneset.zipuri, env); Path resPath = geneset.zipfilesystem.getPath("/unresolved.blastout"); NativeRun nrun = new NativeRun(); SerifyApplet.blastpRun(nrun, sb.getBuffer(), dbPath, resPath, "-evalue 0.00001", null, true, geneset.zipfilesystem, geneset.user, primaryStage); } catch (IOException e1) { e1.printStackTrace(); } })); MenuItem importbiosystemsaction = new MenuItem("Import biosystems"); importbiosystemsaction.setOnAction(actionEvent -> { Dialog<Map<String, Set<String>>> dialog = new Dialog(); TextField gene = new TextField(); TextField biosys = new TextField(); gene.setText("ftp://ftp.ncbi.nlm.nih.gov/pub/biosystems/biosystems.20160519/biosystems_gene_all.gz"); biosys.setText("ftp://ftp.ncbi.nlm.nih.gov/pub/biosystems/biosystems.20160519/bsid2info.gz"); VBox duo = new VBox(); duo.getChildren().add(gene); duo.getChildren().add(biosys); dialog.getDialogPane().setContent(duo); dialog.getDialogPane().getButtonTypes().add(ButtonType.OK); dialog.getDialogPane().getButtonTypes().add(ButtonType.CANCEL); dialog.setResultConverter(param -> { if (!param.getButtonData().isCancelButton()) { Map<String, Set<String>> result = null; Set<String> geneidset = geneset.genelist.stream().map(g -> g.genid).collect(Collectors.toSet()); try { InputStream p = new URI(gene.getText()).toURL().openStream(); InputStream b = new URI(biosys.getText()).toURL().openStream(); if (gene.getText().endsWith(".gz")) p = new GZIPInputStream(p); if (biosys.getText().endsWith(".gz")) b = new GZIPInputStream(b); Map<String, List<String[]>> group = new BufferedReader(new InputStreamReader(p)).lines() .map(l -> l.split("\t")).filter(s -> geneidset.contains(s[1])) .collect(Collectors.groupingBy(s -> s[1])); Set<String> bsids = group.entrySet().stream().flatMap(e -> e.getValue().stream()) .map(s -> s[0]).collect(Collectors.toSet()); Map<String, String> bsid2name = new BufferedReader(new InputStreamReader(b)).lines() .map(s -> s.split("\t")).filter(s -> bsids.contains(s[0])) .collect(Collectors.toMap(s -> s[0], s -> s[2] + ":" + s[3])); result = group.entrySet().stream() .collect(Collectors.toMap(s -> s.getKey(), s -> s.getValue().stream() .map(sub -> bsid2name.get(sub[0])).collect(Collectors.toSet()))); } catch (IOException e) { e.printStackTrace(); } catch (URISyntaxException e) { e.printStackTrace(); } //Path p = Paths.get(gene.getText()); //Path b = Paths.get(biosys.getText()); return result; } return null; }); Optional<Map<String, Set<String>>> od = dialog.showAndWait(); if (od.isPresent()) { geneset.biosystemsmap = od.get(); Map<String, String> env = new HashMap<>(); env.put("create", "true"); String uristr = "jar:" + geneset.zippath.toUri(); geneset.zipuri = URI.create(uristr /*.replace("file://", "file:")*/ ); try { geneset.zipfilesystem = FileSystems.newFileSystem(geneset.zipuri, env); Path resPath = geneset.zipfilesystem.getPath("/biosystems.txt"); BufferedWriter bw = Files.newBufferedWriter(resPath, StandardOpenOption.TRUNCATE_EXISTING); geneset.biosystemsmap.entrySet().stream().forEach(e -> { try { bw.write(e.getKey() + "\t" + e.getValue().stream().collect(Collectors.joining(";")) + "\n"); } catch (IOException e1) { e1.printStackTrace(); } }); bw.close(); } catch (Exception e) { e.printStackTrace(); } finally { try { geneset.zipfilesystem.close(); } catch (IOException e) { e.printStackTrace(); } } } }); MenuItem importkeggpathwayaction = new MenuItem("Import kegg pathways"); importkeggpathwayaction.setOnAction(actionEvent -> { Set<String> keggids = new HashSet<>(); for (Gene g : geneset.genelist) { if (g.keggid != null) { int i = g.keggid.indexOf(':'); if (i > 0) { keggids.add(g.keggid.substring(0, i)); } } } System.err.println(keggids); JTextField tf = new JTextField("http://130.208.252.239/organisms/"); JOptionPane.showMessageDialog(null, tf); Map<String, String> env = new HashMap<>(); env.put("create", "true"); Path rootp = null; try { geneset.zipfilesystem = FileSystems.newFileSystem(geneset.zipuri, env); } catch (Exception ee) { ee.printStackTrace(); } for (Path root : geneset.zipfilesystem.getRootDirectories()) { rootp = root; break; } for (String kegg : keggids) { try { URL url = new URL(tf.getText() + kegg + ".tar.gz"); InputStream is = url.openStream(); GZIPInputStream gz = new GZIPInputStream(is); TarArchiveInputStream tar = new TarArchiveInputStream(gz); TarArchiveEntry tae = (TarArchiveEntry) tar.getNextEntry(); while (tae != null) { geneset.traverseTar(tar, tae, rootp); tae = (TarArchiveEntry) tar.getNextEntry(); } is.close(); } catch (IOException e1) { e1.printStackTrace(); } } try { geneset.zipfilesystem.close(); } catch (Exception ee) { ee.printStackTrace(); } ; }); edit.getItems().add(clustergenes); edit.getItems().add(alignclusters); edit.getItems().add(new SeparatorMenuItem()); edit.getItems().add(sharenumaction); edit.getItems().add(importgeneclusteringaction); edit.getItems().add(importgenesymbolaction); edit.getItems().add(importcazyaction); edit.getItems().add(functionmappingaction); edit.getItems().add(importidmappingaction); edit.getItems().add(gene2refseqaction); edit.getItems().add(importbiosystemsaction); edit.getItems().add(importkeggpathwayaction); edit.getItems().add(new SeparatorMenuItem()); edit.getItems().add(cogblastaction); edit.getItems().add(unresolvedblastaction); Menu view = new Menu("View"); gb = new RadioMenuItem("Genes"); gb.setOnAction(actionEvent -> { splitpane.getItems().remove(table); splitpane.getItems().add(0, gtable); //table.setModel( defaultModel ); }); view.getItems().add(gb); ggb = new RadioMenuItem("Gene groups"); ggb.setOnAction(actionEvent -> { splitpane.getItems().remove(gtable); splitpane.getItems().add(0, table); //table.setModel( groupModel ); }); ToggleGroup bg = new ToggleGroup(); gb.setToggleGroup(bg); ggb.setToggleGroup(bg); //ButtonGroup bg = new ButtonGroup(); //bg.add( gb ); //bg.add( ggb ); ggb.setSelected(true); view.getItems().add(ggb); ActionCollection.addAll(view, geneset.clusterMap, GeneSetHead.this, geneset.speccontigMap, table, comp, geneset.cs); Menu help = new Menu("Help"); MenuItem about = new MenuItem("About"); about.setOnAction(actionEvent -> SwingUtilities .invokeLater(() -> JOptionPane.showMessageDialog(comp, "CompGen 1.0"))); help.getItems().add(about); MenuItem test = new MenuItem("Test"); test.setOnAction(actionEvent -> { /*for( Gene g : geneset.genelist ) { Sequence seq = g.tegeval.getContig(); if( seq == null ) { System.err.println(); } }*/ for (String spec : geneset.speccontigMap.keySet()) { if (spec.contains("RAST")) { List<Sequence> lseq = geneset.speccontigMap.get(spec); for (Sequence seq : lseq) { for (Annotation a : seq.getAnnotations()) { System.err.println(a.getGene().getGeneGroup().species); /*Sequence tseq = a.getContig(); if( tseq == null ) { System.err.println(); }*/ } } } } /*for( GeneGroup gg : allgenegroups ) { if( gg.species.size() > 1 ) { System.err.println( gg.species ); } }*/ }); help.getItems().add(test); help.getItems().add(new SeparatorMenuItem()); MenuItem runserver = new MenuItem("Run server"); runserver.setOnAction(actionEvent -> { SwingUtilities.invokeLater(new Runnable() { public void run() { JSpinner spin = new JSpinner(); JOptionPane.showMessageDialog(GeneSetHead.this, spin, "Port", JOptionPane.QUESTION_MESSAGE); try { geneset.cs = WSServer.startServer(GeneSetHead.this, (Integer) spin.getValue()); } catch (UnknownHostException e1) { e1.printStackTrace(); } } }); }); help.getItems().add(runserver); help.getItems().add(new SeparatorMenuItem()); CheckMenuItem cbmi = new CheckMenuItem("Use geneset user"); help.getItems().add(cbmi); cbmi.setOnAction(actionEvent -> { if (cbmi.isSelected()) { geneset.user = "geneset"; } else geneset.user = System.getProperty("user.name"); JavaFasta.user = geneset.user; if (geneset.currentSerify != null) geneset.currentSerify.user = geneset.user; }); help.getItems().add(new SeparatorMenuItem()); MenuItem helptut = new MenuItem("Help & Tutorial"); helptut.setOnAction(actionEvent -> { try { Desktop.getDesktop().browse(new URI("http://thermusgenes.appspot.com/pancore.html")); } catch (IOException | URISyntaxException e1) { e1.printStackTrace(); } }); help.getItems().add(helptut); Menu sequencemenu = new Menu("Sequence"); MenuItem showgroupseq = new MenuItem("Show group sequences"); showgroupseq.setOnAction(actionEvent -> { //JTextArea textarea = new JTextArea(); //JScrollPane scrollpane = new JScrollPane(textarea); /*try { if (clipboardService == null) clipboardService = (ClipboardService) ServiceManager.lookup("javax.jnlp.ClipboardService"); Action action = new CopyAction("Copy", null, "Copy data", new Integer(KeyEvent.VK_CONTROL + KeyEvent.VK_C)); textarea.getActionMap().put("copy", action); grabFocus = true; } catch (Exception ee) { ee.printStackTrace(); System.err.println("Copy services not available. Copy using 'Ctrl-c'."); } textarea.setDragEnabled(true);*/ JFrame frame = null; if (geneset.currentSerify == null) { frame = new JFrame(); frame.setDefaultCloseOperation(JFrame.HIDE_ON_CLOSE); frame.setSize(400, 300); Map<String, String> env = new HashMap<String, String>(); //Path path = zipfile.toPath(); String uristr = "jar:" + geneset.zippath.toUri(); geneset.zipuri = URI.create(uristr /*.replace("file://", "file:")*/ ); try { geneset.zipfilesystem = FileSystems.newFileSystem(geneset.zipuri, env); } catch (IOException e1) { e1.printStackTrace(); } SerifyApplet sa = new SerifyApplet(geneset.zipfilesystem); sa.init(frame, null, geneset.user); //frame.add( ) geneset.currentSerify = sa; } /* else frame = (JFrame)currentSerify.cnt;*/ String[] farr = new String[] { "o.profundus", "mt.silvanus", "mt.ruber", "m.hydrothermalis", "t.thermophilus_SG0_5JP17_16", "t.thermophilusJL18", "t.thermophilusHB8", "t.thermophilusHB27", "t.scotoductusSA01", "t.scotoductus4063", "t.scotoductus1572", "t.scotoductus2101", "t.scotoductus2127", "t.scotoductus346", "t.scotoductus252", "t.antranikiani", "t.kawarayensis", "t.brockianus", "t.igniterrae", "t.eggertsoni", "t.RLM", "t.oshimai_JL2", "t.oshimai", "t.filiformis", "t.arciformis", "t.islandicus", "t.aquaticus", "t.spCCB" }; Map<Integer, String> ups = new HashMap<Integer, String>(); Set<Integer> stuck = new HashSet<Integer>(); Map<Integer, List<Tegeval>> ups2 = new HashMap<Integer, List<Tegeval>>(); //int[] rr = table.getSelectedRows(); for (Gene gg : gtable.getSelectionModel().getSelectedItems()) { //int cr = table.convertRowIndexToModel(r); //Gene gg = geneset.genelist.get(cr); if (gg.getSpecies() != null) { if (gg.genid != null && gg.genid.length() > 0) { ups.put(gg.getGroupIndex(), gg.name); stuck.add(gg.getGroupIndex()); } if (!stuck.contains(gg.getGroupIndex())) { if (!ups.containsKey(gg.getGroupIndex()) || !(gg.name.contains("unnamed") || gg.name.contains("hypot"))) ups.put(gg.getGroupIndex(), gg.name); } List<Tegeval> tlist; if (ups2.containsKey(gg.getGroupIndex())) tlist = ups2.get(gg.getGroupIndex()); else { tlist = new ArrayList<Tegeval>(); ups2.put(gg.getGroupIndex(), tlist); } //Set<String> specs = new HashSet<String>(); //textarea.append(gg.name + ":\n"); //for (String sp : gg.species.keySet()) { int count = 0; for (String sp : farr) { //Teginfo stv = gg.species.equals(sp) ? gg.teginfo : null; if (gg.getSpecies().equals(sp)) tlist.add(gg.tegeval); /*for( String key : gg.species.keySet() ) { if( key.contains("JL2") ) { System.err.println( " erm " + key ); } }*/ /*if( stv == null && gg.species.size() == 28 ) { System.err.println( gg.species ); System.err.println( sp ); }*/ //System.err.println( gg.species.keySet() ); /*if( stv == null ) { //System.err.println( sp ); } else { count++; //specs.add( sp ); for (Tegeval tv : stv.tset) { tlist.add( tv ); /*textarea.append(">" + tv.cont + " " + tv.teg + " " + tv.eval + "\n"); if (tv.dna != null) { for (int i = 0; i < tv.dna.length(); i += 70) { textarea.append(tv.dna.gg.speciessubstring(i, Math.min(i + 70, tv.dna.length())) + "\n"); } }* } }*/ } //if( count < gg.species.size() ) { // System.err.println( gg.species ); // System.err.println(); //} //if( specs.size() < 28 ) System.err.println("mu " + specs); } } try { StringWriter sb = new StringWriter(); for (int gi : ups.keySet()) { String name = ups.get(gi); List<Tegeval> tlist = ups2.get(gi); sb.append(name.replace('/', '-') + ":\n"); if (tlist.size() < 28) { for (Tegeval tv : tlist) { System.err.println(tv.name); } System.err.println(); } for (Tegeval tv : tlist) { Sequence ps = tv.getProteinSequence(); ps.setName(tv.name.substring(0, tv.name.indexOf('_'))); ps.writeSequence(sb); /*sb.append(">" + tv.name.substring(0, tv.name.indexOf('_')) + "\n"); for (int i = 0; i < ps.length(); i += 70) { sb.append( ps.substring(i, Math.min(i + 70, tv.getProteinLength() )) + "\n"); }*/ } } geneset.currentSerify.addSequences("uh", new StringReader(sb.toString()), Paths.get("/"), null); } catch (URISyntaxException | IOException e1) { e1.printStackTrace(); } frame.setVisible(true); }); sequencemenu.getItems().add(showgroupseq); MenuItem showgroupdnaseq = new MenuItem("Show group DNA sequences"); showgroupdnaseq.setOnAction(actionEvent -> { final JTextArea textarea = new JTextArea(); JScrollPane scrollpane = new JScrollPane(textarea); try { if (clipboardService == null) clipboardService = (ClipboardService) ServiceManager.lookup("javax.jnlp.ClipboardService"); Action action = new CopyAction("Copy", null, "Copy data", new Integer(KeyEvent.VK_CONTROL + KeyEvent.VK_C)); textarea.getActionMap().put("copy", action); grabFocus = true; } catch (Exception ee) { ee.printStackTrace(); System.err.println("Copy services not available. Copy using 'Ctrl-c'."); } textarea.setDragEnabled(true); try { final DataFlavor df = new DataFlavor("text/plain;charset=utf-8"); TransferHandler th = new TransferHandler() { /** * */ private static final long serialVersionUID = 1L; public int getSourceActions(JComponent c) { return TransferHandler.COPY_OR_MOVE; } public boolean canImport(TransferHandler.TransferSupport support) { return false; } protected Transferable createTransferable(JComponent c) { return new Transferable() { @Override public Object getTransferData(DataFlavor arg0) throws UnsupportedFlavorException, IOException { if (arg0.equals(df)) { return new ByteArrayInputStream(textarea.getText().getBytes()); } else { return textarea.getText(); } } @Override public DataFlavor[] getTransferDataFlavors() { return new DataFlavor[] { df, DataFlavor.stringFlavor }; } @Override public boolean isDataFlavorSupported(DataFlavor arg0) { if (arg0.equals(df) || arg0.equals(DataFlavor.stringFlavor)) { return true; } return false; } }; } public boolean importData(TransferHandler.TransferSupport support) { return false; } }; textarea.setTransferHandler(th); } catch (ClassNotFoundException e1) { e1.printStackTrace(); } Map<Integer, String> ups = new HashMap<Integer, String>(); Set<Integer> stuck = new HashSet<Integer>(); Map<Integer, List<Tegeval>> ups2 = new HashMap<Integer, List<Tegeval>>(); //int[] rr = table.getSelectedRows(); for (Gene gg : gtable.getSelectionModel().getSelectedItems()) { //int cr = table.convertRowIndexToModel(r); //Gene gg = geneset.genelist.get(cr); if (gg.getSpecies() != null) { if (gg.genid != null && gg.genid.length() > 0) { ups.put(gg.getGroupIndex(), gg.name); stuck.add(gg.getGroupIndex()); } if (!stuck.contains(gg.getGroupIndex())) { if (!ups.containsKey(gg.getGroupIndex()) || !(gg.name.contains("unnamed") || gg.name.contains("hypot"))) ups.put(gg.getGroupIndex(), gg.name); } List<Tegeval> tlist; if (ups2.containsKey(gg.getGroupIndex())) tlist = ups2.get(gg.getGroupIndex()); else { tlist = new ArrayList<Tegeval>(); ups2.put(gg.getGroupIndex(), tlist); } //textarea.append(gg.name + ":\n"); tlist.add(gg.tegeval); /*textarea.append(">" + tv.cont + " " + tv.teg + " " + tv.eval + "\n"); if (tv.dna != null) { for (int i = 0; i < tv.dna.length(); i += 70) { textarea.append(tv.dna.substring(i, Math.min(i + 70, tv.dna.length())) + "\n"); } }*/ } } for (int gi : ups.keySet()) { String name = ups.get(gi); List<Tegeval> tlist = ups2.get(gi); textarea.append(name.replace('/', '-') + ":\n"); for (Tegeval tv : tlist) { textarea.append(">" + tv.name.substring(0, tv.name.indexOf('_')) + "\n"); for (int i = 0; i < tv.getLength(); i += 70) { textarea.append(tv.getSubstring(i, Math.min(i + 70, tv.getLength())) + "\n"); } } } JFrame frame = new JFrame(); frame.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE); frame.add(scrollpane); frame.setSize(400, 300); frame.setVisible(true); }); sequencemenu.getItems().add(showgroupdnaseq); sequencemenu.getItems().add(new SeparatorMenuItem()); MenuItem showallseq = new MenuItem("Show all sequences"); showallseq.setOnAction(actionEvent -> { JFrame frame = new JFrame(); frame.setSize(800, 600); frame.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE); Serifier serifier = new Serifier(); JavaFasta jf = new JavaFasta((comp instanceof JApplet) ? (JApplet) comp : null, serifier, geneset.cs); jf.initGui(frame); Map<String, Sequence> contset = new HashMap<String, Sequence>(); //int[] rr = table.getSelectedRows(); for (Gene gg : gtable.getSelectionModel().getSelectedItems()) { //int cr = table.convertRowIndexToModel(r); //Gene gg = geneset.genelist.get(cr); Tegeval tv = gg.tegeval; String contig = tv.getContshort().getName(); Sequence seq = tv.getProteinSequence(); seq.setName(contig); serifier.mseq.put(seq.getName(), seq); //Sequence seq = new Sequence( contig, aa, serifier.mseq ); serifier.addSequence(seq); } jf.updateView(); frame.setVisible(true); }); sequencemenu.getItems().add(showallseq); MenuItem showseq = new MenuItem("Show sequences"); showseq.setOnAction(actionEvent -> { Set<GeneGroup> genegroups = new HashSet<GeneGroup>(); //int[] rr = table.getSelectedRows(); if (!isGeneview()) { for (GeneGroup gg : table.getSelectionModel().getSelectedItems()) { //int cr = table.convertRowIndexToModel(r); //GeneGroup gg = geneset.allgenegroups.get(cr); genegroups.add(gg); } } else { for (Gene gg : gtable.getSelectionModel().getSelectedItems()) { //int cr = table.convertRowIndexToModel(r); //Gene gg = geneset.genelist.get(cr); genegroups.add(gg.getGeneGroup()); } } Platform.runLater(() -> { Set<String> specs = null; if (table.getItems().size() > 1) specs = getSelspec(comp, geneset.specList, null); showSequences(comp, genegroups, false, specs); }); }); sequencemenu.getItems().add(showseq); MenuItem showseqwgenenames = new MenuItem("Show sequences w/genenames"); showseqwgenenames.setOnAction(actionEvent -> { Set<GeneGroup> genegroups = new HashSet<GeneGroup>(); //int[] rr = table.getSelectedRows(); if (!isGeneview()) { for (GeneGroup gg : table.getSelectionModel().getSelectedItems()) { //int cr = table.convertRowIndexToModel(r); //GeneGroup gg = geneset.allgenegroups.get(cr); genegroups.add(gg); } } else { for (Gene gg : gtable.getSelectionModel().getSelectedItems()) { //int cr = table.convertRowIndexToModel(r); //Gene gg = geneset.genelist.get(cr); genegroups.add(gg.getGeneGroup()); } } //Set<String> specs = null; //if( rr.length > 1 ) specs = getSelspec(comp, specList, null); showSequences(comp, genegroups, false, null, true); }); sequencemenu.getItems().add(showseqwgenenames); MenuItem showalignseq = new MenuItem("Show aligned sequences"); showalignseq.setOnAction(actionEvent -> { Set<GeneGroup> genegroups = new HashSet<GeneGroup>(); //int[] rr = table.getSelectedRows(); if (!isGeneview()) { for (GeneGroup gg : table.getSelectionModel().getSelectedItems()) { genegroups.add(gg); } } else { for (Gene gg : gtable.getSelectionModel().getSelectedItems()) { genegroups.add(gg.getGeneGroup()); } } Serifier serifier = new Serifier(); for (GeneGroup ggroup : genegroups) { for (Tegeval tv : ggroup.getTegevals()) { String selspec = tv.getContshort().getSpec();//tv.getContig(); String spec = geneset.nameFix(selspec); /*if( selspec.contains("hermus") ) spec = selspec; else { Matcher m = Pattern.compile("\\d").matcher(selspec); int firstDigitLocation = m.find() ? m.start() : 0; if( firstDigitLocation == 0 ) spec = "Thermus_" + selspec; else spec = "Thermus_" + selspec.substring(0,firstDigitLocation) + "_" + selspec.substring(firstDigitLocation); }*/ Sequence seq = tv.getAlignedSequence(); //System.err.println( "seqlen " + seq.length() ); if (seq != null) { seq.setName(spec); //Sequence seq = new Sequence( contig, seqstr, null ); serifier.addSequence(seq); } else { Sequence sb = tv.getProteinSequence(); sb.setName(spec); //Sequence sseq = new Sequence( spec, sb, serifier.mseq ); serifier.addSequence(sb); } } } showAlignedSequences(comp, serifier); }); sequencemenu.getItems().add(showalignseq); MenuItem splitseq = new MenuItem("Split/Show sequences"); splitseq.setOnAction(actionEvent -> { try { StringBuffer sb = getSelectedASeqs(table, geneset.genelist, GeneSetHead.this, geneset.specList); if (geneset.currentSerify == null) { JFrame frame = new JFrame(); frame.setDefaultCloseOperation(JFrame.HIDE_ON_CLOSE); frame.setSize(800, 600); SerifyApplet sa = new SerifyApplet(geneset.zipfilesystem); sa.init(frame, null, geneset.user); geneset.currentSerify = sa; frame.setVisible(true); } geneset.currentSerify.addSequences("uh", new StringReader(sb.toString()), Paths.get("/"), null); } catch (URISyntaxException | IOException e1) { e1.printStackTrace(); } //JTextArea textarea = new JTextArea(); //textarea.append( sb.toString() ); /*try { if (clipboardService == null) clipboardService = (ClipboardService) ServiceManager.lookup("javax.jnlp.ClipboardService"); Action action = new CopyAction("Copy", null, "Copy data", new Integer(KeyEvent.VK_CONTROL + KeyEvent.VK_C)); textarea.getActionMap().put("copy", action); grabFocus = true; } catch (Exception ee) { ee.printStackTrace(); System.err.println("Copy services not available. Copy using 'Ctrl-c'."); } * * final DataFlavor df = * DataFlavor.getTextPlainUnicodeFlavor();//new * DataFlavor("text/plain;charset=utf-8"); final String charset * = df.getParameter("charset"); final Transferable transferable * = new Transferable() { * * @Override public Object getTransferData(DataFlavor arg0) * throws UnsupportedFlavorException, IOException { String ret = * makeCopyString( detailTable ); return new * ByteArrayInputStream( ret.getBytes( charset ) ); } * * @Override public DataFlavor[] getTransferDataFlavors() { * return new DataFlavor[] { df }; } * * @Override public boolean isDataFlavorSupported(DataFlavor * arg0) { if( arg0.equals(df) ) { return true; } return false; * } }; * * TransferHandler th = new TransferHandler() { private static * final long serialVersionUID = 1L; * * public int getSourceActions(JComponent c) { return * TransferHandler.COPY_OR_MOVE; } * * public boolean canImport(TransferHandler.TransferSupport * support) { return false; } * * protected Transferable createTransferable(JComponent c) { * return transferable; } * * public boolean importData(TransferHandler.TransferSupport * support) { /*try { Object obj = * support.getTransferable().getTransferData( df ); InputStream * is = (InputStream)obj; * * byte[] bb = new byte[2048]; int r = is.read(bb); * * //importFromText( new String(bb,0,r) ); } catch * (UnsupportedFlavorException e) { e.printStackTrace(); } catch * (IOException e) { e.printStackTrace(); }* return false; } }; * textarea.setTransferHandler( th ); * textarea.setDragEnabled(true); JScrollPane scrollpane = new JScrollPane(textarea); JFrame frame = new JFrame(); frame.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE); frame.add(scrollpane); frame.setSize(400, 300); frame.setVisible(true);*/ }); sequencemenu.getItems().add(splitseq); MenuItem showdnaseq = new MenuItem("Show DNA sequences"); showdnaseq.setOnAction(actionEvent -> { Set<GeneGroup> genegroups = new HashSet<GeneGroup>(); int rr = 0; if (!isGeneview()) { ObservableList<GeneGroup> lgg = table.getSelectionModel().getSelectedItems(); genegroups.addAll(lgg); rr = lgg.size(); } else { for (Gene gg : gtable.getSelectionModel().getSelectedItems()) { genegroups.add(gg.getGeneGroup()); rr++; } } Set<String> specs = null; if (rr > 1) specs = getSelspec(comp, geneset.specList, null); showSequences(comp, genegroups, true, specs); /*StringBuilder sb = getSelectedSeqs( table, genelist ); if( currentSerify == null ) { JFrame frame = new JFrame(); frame.setDefaultCloseOperation( JFrame.DO_NOTHING_ON_CLOSE ); frame.setSize(800, 600); SerifyApplet sa = new SerifyApplet(); sa.init( frame ); try { sa.addSequences("uh", new StringReader( sb.toString() ), "/"); } catch (URISyntaxException | IOException e1) { e1.printStackTrace(); } frame.setVisible( true ); } JTextArea textarea = new JTextArea(); JScrollPane scrollpane = new JScrollPane(textarea); try { if (clipboardService == null) clipboardService = (ClipboardService) ServiceManager.lookup("javax.jnlp.ClipboardService"); Action action = new CopyAction("Copy", null, "Copy data", new Integer(KeyEvent.VK_CONTROL + KeyEvent.VK_C)); textarea.getActionMap().put("copy", action); grabFocus = true; } catch (Exception ee) { ee.printStackTrace(); System.err.println("Copy services not available. Copy using 'Ctrl-c'."); } textarea.setDragEnabled(true); textarea.append( sb.toString() ); JFrame frame = new JFrame(); frame.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE); frame.add(scrollpane); frame.setSize(400, 300); frame.setVisible(true);*/ }); sequencemenu.getItems().add(showdnaseq); MenuItem expalldna = new MenuItem("Export all DNA sequences"); expalldna.setOnAction(actionEvent -> { JFileChooser jfc = new JFileChooser(); jfc.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY); try { Map<Integer, FileWriter> lfw = new HashMap<Integer, FileWriter>(); if (jfc.showOpenDialog(null) == JFileChooser.APPROVE_OPTION) { File f = jfc.getSelectedFile(); for (Gene gg : getGeneTable().getSelectionModel().getSelectedItems()) { FileWriter fw = null; if (lfw.containsKey(gg.getGroupIndex())) { fw = lfw.get(gg.getGroupIndex()); } else { fw = new FileWriter(new File(f, "group_" + gg.getGroupIndex() + ".fasta")); lfw.put(gg.getGroupIndex(), fw); } Tegeval tv = gg.tegeval; fw.append(">" + tv.name + " " + tv.teg + " " + tv.eval + "\n"); for (int i = 0; i < tv.getLength(); i += 70) { fw.append(tv.getSubstring(i, Math.min(i + 70, tv.getLength())) + "\n"); } } } for (int gi : lfw.keySet()) { lfw.get(gi).close(); } } catch (IOException e1) { e1.printStackTrace(); } }); sequencemenu.getItems().add(expalldna); MenuItem exprelcont = new MenuItem("Export relevant contigs"); exprelcont.setOnAction(actionEvent -> { JFileChooser jfc = new JFileChooser(); try { Map<Integer, FileWriter> lfw = new HashMap<Integer, FileWriter>(); if (jfc.showOpenDialog(null) == JFileChooser.APPROVE_OPTION) { File f = jfc.getSelectedFile(); Set<Sequence> contset = new HashSet<Sequence>(); for (Gene gg : getGeneTable().getSelectionModel().getSelectedItems()) { Tegeval tv = gg.tegeval; contset.add(tv.getContshort()); } FileWriter fw = new FileWriter(f); for (Sequence contig : contset) { fw.append(">" + contig + "\n"); if (geneset.contigmap.containsKey(contig)) { StringBuilder dna = geneset.contigmap.get(contig).getStringBuilder(); for (int i = 0; i < dna.length(); i += 70) { fw.append(dna.substring(i, Math.min(i + 70, dna.length())) + "\n"); } } } fw.close(); } for (int gi : lfw.keySet()) { lfw.get(gi).close(); } } catch (IOException e1) { e1.printStackTrace(); } }); sequencemenu.getItems().add(exprelcont); sequencemenu.getItems().add(new SeparatorMenuItem()); MenuItem viewselrange = new MenuItem("View selected range"); viewselrange.setOnAction(actionEvent -> { JFrame frame = new JFrame(); frame.setSize(800, 600); frame.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE); Serifier serifier = new Serifier(); JavaFasta jf = new JavaFasta((comp instanceof JApplet) ? (JApplet) comp : null, serifier, geneset.cs); jf.initGui(frame); Set<Sequence> contset = new HashSet<Sequence>(); Set<Tegeval> tvset = new HashSet<>(); if (isGeneview()) { for (Gene gg : getGeneTable().getSelectionModel().getSelectedItems()) { Tegeval tv = gg.tegeval; tvset.add(tv); //serifier.addAnnotation( tv ); contset.add(tv.getContshort()); } } else { for (GeneGroup gg : getGeneGroupTable().getSelectionModel().getSelectedItems()) { for (Tegeval tv : gg.getTegevals()) { tv.color = Color.red; tvset.add(tv); Sequence contig = tv.getContshort(); contset.add(contig); //serifier.addAnnotation( tv ); } } } /*Sequence seq; Sequence contig = tv.getContshort(); /*if (contset.containsKey(contig)) { seq = contset.get(contig); } else { if( contigmap.containsKey(contig) ) { StringBuilder dna = contigmap.get(contig).getStringBuilder(); seq = new Sequence(contig.getName(), dna, serifier.mseq); } else seq = new Sequence(contig.getName(), serifier.mseq); contset.put(contig, seq); } Annotation a = new Annotation(contig, contig.getName(), Color.green, serifier.mann); a.setStart(tv.start); a.setStop(tv.stop); a.setOri(tv.ori); a.setGroup(gg.name); a.setType("gene");*/ // seq.addAnnotation( new Annotation( seq, ) ); for (Sequence contig : contset) { int start = Integer.MAX_VALUE; int stop = Integer.MIN_VALUE; for (Tegeval tv : tvset) { if (contig == tv.seq) { start = Math.min(start, tv.start); stop = Math.max(stop, tv.stop); } } int rstart = 0; int rstop = contig.length(); if (contig.annset != null) for (Annotation tv : contig.annset) { if (contig == tv.seq) { if (tv.stop < start && tv.stop > rstart) { rstart = tv.stop; } if (tv.start > stop && tv.start < rstop) { rstop = tv.start; } } } start = rstart; stop = rstop; Sequence newseq = new Sequence(contig.getName(), new StringBuilder(contig.getSubstring(start, stop, 1)), serifier.mseq); /*if( contig.isReverse() ) { newseq.reverse(); newseq.complement(); }*/ serifier.addSequence(newseq); for (Tegeval tv : tvset) { Annotation newann = new Annotation(newseq, tv.start - start, tv.stop - start, tv.ori, tv.name); if (contig == tv.seq) { newseq.addAnnotation(newann); } serifier.addAnnotation(newann); } /*for( Annotation ann : contig.getAnnotations() ) { serifier.addAnnotation( ann ); }*/ /*if (seq.getAnnotations() != null) Collections.sort(seq.getAnnotations());*/ } jf.updateView(); frame.setVisible(true); }); sequencemenu.getItems().add(viewselrange); MenuItem viewwhole = new MenuItem("View whole contigs for selection"); viewwhole.setOnAction(actionEvent -> { JFrame frame = new JFrame(); frame.setSize(800, 600); frame.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE); Serifier serifier = new Serifier(); JavaFasta jf = new JavaFasta((comp instanceof JApplet) ? (JApplet) comp : null, serifier, geneset.cs); jf.initGui(frame); //Map<Sequence, Sequence> contset = new HashMap<Sequence, Sequence>(); /*int[] rr = table.getSelectedRows(); for (int r : rr) { int cr = table.convertRowIndexToModel(r); Gene gg = geneset.genelist.get(cr); if (gg.species != null) { for (String sp : gg.species.keySet()) { Teginfo stv = gg.species.get(sp); for (Tegeval tv : stv.tset) { Sequence seq; Sequence contig = tv.getContshort(); if (contset.containsKey(contig)) { seq = contset.get(contig); } else { if( GeneSet.contigmap.containsKey(contig) ) { //StringBuilder dna = GeneSet.contigmap.get(contig).seq; StringBuilder dna = contig.getSequence().getStringBuilder(); seq = new Sequence(contig.getName(), dna, serifier.mseq); } else { seq = new Sequence(contig.getName(), serifier.mseq); } contset.put(contig, seq); } /* * Annotation a = jf.new Annotation( seq, * contig, Color.red ); a.setStart( tv.start ); * a.setStop( tv.stop ); a.setOri( tv.ori ); * a.setGroup( gg.name ); a.setType( "gene" ); * jf.addAnnotation( a ); * // seq.addAnnotation( new Annotation( seq, ) ); } } } }*/ Set<Sequence> contigs = new HashSet<Sequence>(); if (isGeneview()) { for (Gene gg : getGeneTable().getSelectionModel().getSelectedItems()) { Tegeval tv = gg.tegeval; tv.color = Color.red; Sequence contig = tv.getContshort(); //contig.offset = -tv.start; contigs.add(contig); } /*Annotation a = new Annotation(contig, contig.getName(), Color.red, serifier.mann); a.setStart(tv.start); a.setStop(tv.stop); a.setOri(tv.ori); a.setGroup(g.name); a.setType("gene");*/ //serifier.addAnnotation( tv ); } else { for (GeneGroup gg : getGeneGroupTable().getSelectionModel().getSelectedItems()) { for (Tegeval tv : gg.getTegevals()) { tv.color = Color.red; Sequence contig = tv.getContshort(); //contig.offset = -tv.start; contigs.add(contig); /*Annotation a = new Annotation(contig, contig.getName(), Color.red, serifier.mann); a.setStart(tv.start); a.setStop(tv.stop); a.setOri(tv.ori); a.setGroup(gg.getCommonName()); a.setType("gene");*/ //serifier.addAnnotation( tv ); } } } //Gene gg = geneset.genelist.get(cr); //for (Gene g : geneset.genelist) { //if (g.species != null) { //for (String sp : g.species.keySet()) { for (Sequence contig : contigs) { for (Annotation ann : contig.getAnnotations()) { serifier.addAnnotation(ann); } serifier.addSequence(contig); serifier.mseq.put(contig.getName(), contig); //if(contig.getAnnotations() != null) // Collections.sort(contig.getAnnotations()); } jf.updateView(); frame.setVisible(true); }); sequencemenu.getItems().add(viewwhole); sequencemenu.getItems().add(new SeparatorMenuItem()); MenuItem viewspecseq = new MenuItem("View species sequence"); viewspecseq.setOnAction(actionEvent -> { Set<String> selspec = getSelspec(GeneSetHead.this, geneset.specList); JFrame frame = new JFrame(); frame.setSize(800, 600); frame.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE); Serifier serifier = new Serifier(); JavaFasta jf = new JavaFasta((comp instanceof JApplet) ? (JApplet) comp : null, serifier, geneset.cs); jf.initGui(frame); for (String spec : selspec) { List<Sequence> contigs = geneset.speccontigMap.get(spec); for (Sequence contig : contigs) { List<Annotation> lann = contig.getAnnotations(); if (lann != null) for (Annotation ann : lann) { serifier.addAnnotation(ann); } serifier.addSequence(contig); serifier.mseq.put(contig.getName(), contig); } } jf.updateView(); frame.setVisible(true); }); sequencemenu.getItems().add(viewspecseq); Menu windowmenu = new Menu("Tools"); MenuItem seqviewer = new MenuItem("Sequence viewer"); seqviewer.setOnAction(actionEvent -> { JFrame frame = new JFrame(); frame.setSize(800, 600); frame.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE); Serifier serifier = new Serifier(); JavaFasta jf = new JavaFasta((comp instanceof JApplet) ? (JApplet) comp : null, serifier, geneset.cs); jf.initGui(frame); jf.updateView(); frame.setVisible(true); }); windowmenu.getItems().add(seqviewer); windowmenu.getItems().add(new SeparatorMenuItem()); MenuItem genesorter = new MenuItem("Gene sorter"); genesorter.setOnAction(actionEvent -> { try { //if( gb.isSelected() ) new GeneSorter().mynd( GeneSetHead.this, genelist, table, null, contigmap ); //else new GeneSorter().groupMynd(GeneSetHead.this, geneset.allgenegroups, geneset.specList, geneset.genelist, table, geneset.contigmap, geneset.specset); } catch (IOException e1) { e1.printStackTrace(); } }); windowmenu.getItems().add(genesorter); MenuItem specorderaction = new MenuItem("Order species list"); specorderaction.setOnAction(actionEvent -> { TreeUtil tu = new TreeUtil(); /*corrInd.clear(); for( String spec : specList ) { corrInd.add( nameFix( spec ) ); }*/ Serifier serifier = getConcatenatedSequences(false, false); Map<String, Integer> blosumap = JavaFasta.getBlosumMap(); double[] dmat = new double[serifier.lseq.size() * serifier.lseq.size()]; Sequence.distanceMatrixNumeric(serifier.lseq, dmat, null, false, false, null, blosumap); List<String> ret = new ArrayList<String>(); for (Sequence seqname : serifier.lseq) { ret.add(seqname.getName()); //.replace(' ', '_') ); } //List<String> corrInd = currentjavafasta.getNames(); //Sequence.distanceMatrixNumeric(serifier.lseq, dmat, idxs, bootstrap, cantor, ent, blosum); Node n = tu.neighborJoin(dmat, ret, null, false, false); Comparator<Node> comp2 = (o1, o2) -> { int c1 = o1.countLeaves(); int c2 = o2.countLeaves(); if (c1 > c2) return 1; else if (c1 == c2) return 0; return -1; }; tu.arrange(n, comp2); //corrInd.clear(); List<String> ordInd = n.traverse(); for (String spec : ordInd) { System.err.println(spec); } for (String oldspec : geneset.specList) { if (!ordInd.contains(oldspec)) { ordInd.add(oldspec); } } geneset.specList = ordInd; //TableModel model = table.getModel(); //table.setModel( nullmodel ); //table.setModel( model ); //table.tableChanged( new TableModelEvent( table.getModel() ) ); //table.getColumnModel(). System.err.println(geneset.specList.size()); }); MenuItem matrixaction = new MenuItem("Relation matrix"); matrixaction.setOnAction(actionEvent -> { SwingUtilities.invokeLater(() -> { JComboBox<String> descombo = new JComboBox<String>( geneset.deset.toArray(new String[geneset.deset.size()])); JCheckBox anicheck = new JCheckBox("ANImatrix"); JCheckBox plasmidcheck = new JCheckBox("Skip plasmids"); descombo.insertItemAt("", 0); descombo.setSelectedIndex(0); JOptionPane.showMessageDialog(GeneSetHead.this, new Object[] { descombo, anicheck, plasmidcheck }); String val = descombo.getSelectedItem().toString(); Collection<GeneGroup> ss = new HashSet<>(); /*int[] rr = table.getSelectedRows(); for( int r : rr ) { ss.add( geneset.allgenegroups.get( table.convertRowIndexToModel(r) ) ); }*/ ss.addAll(table.getSelectionModel().getSelectedItems()); if (ss.isEmpty()) ss = geneset.allgenegroups; Set<String> species = getSelspec(GeneSetHead.this, geneset.specList); bimg = anicheck.isSelected() ? geneset.animatrix(species, geneset.clusterMap, val, ss, plasmidcheck.isSelected()) : geneset.bmatrix(species, geneset.clusterMap, val); JFrame f = new JFrame("Relation matrix"); f.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE); f.setSize(500, 500); /* * { public void paintComponent( Graphics g ) { * super.paintComponent(g); g.drawImage(bimg, 0, 0, this); } }; */ try { final DataFlavor df = new DataFlavor("text/plain;charset=utf-8"); final Transferable transferable = new Transferable() { @Override public Object getTransferData(DataFlavor arg0) throws UnsupportedFlavorException, IOException { StringBuilder ret = new StringBuilder(); int i = 0; for (String spc : geneset.specList) { if (++i == geneset.specList.size()) ret.append(spc + "\n"); else ret.append(spc + "\t"); } int where = 0; for (String spc1 : geneset.specList) { int wherex = 0; for (String spc2 : geneset.specList) { int spc1tot = 0; int spc2tot = 0; int totot = 0; int spc1totwocore = 0; int spc2totwocore = 0; int tototwocore = 0; for (Set<String> set : geneset.clusterMap.keySet()) { Set<Map<String, Set<String>>> erm = geneset.clusterMap.get(set); if (set.contains(spc1)) { if (set.size() < geneset.specList.size()) { spc1totwocore += erm.size(); for (Map<String, Set<String>> sm : erm) { Set<String> hset = sm.get(spc1); tototwocore += hset.size(); } if (set.contains(spc2)) { spc2totwocore += erm.size(); } if (spc2totwocore > spc1totwocore) System.err.println( "okoko " + spc1totwocore + " " + spc2totwocore); } spc1tot += erm.size(); for (Map<String, Set<String>> sm : erm) { Set<String> hset = sm.get(spc1); totot += hset.size(); } if (set.contains(spc2)) { spc2tot += erm.size(); } } } if (where == wherex) { if (where == geneset.specList.size() - 1) ret.append(0 + "\n"); else ret.append(0 + "\t"); } else { double hlut = (double) spc2totwocore / (double) spc1totwocore; double sval = hlut; // 1.0/( 1.1-hlut ); double val = Math.pow(50.0, sval - 0.3) - 1.0; double dval = Math.round(100.0 * (val)) / 100.0; if (wherex == geneset.specList.size() - 1) ret.append(dval + "\n"); else ret.append(dval + "\t"); } wherex++; } where++; } return new ByteArrayInputStream(ret.toString().getBytes()); } @Override public DataFlavor[] getTransferDataFlavors() { return new DataFlavor[] { df }; } @Override public boolean isDataFlavorSupported(DataFlavor arg0) { if (arg0.equals(df)) { return true; } return false; } }; final TransferComponent comp2 = new TransferComponent(bimg, transferable); TransferHandler th = new TransferHandler() { private static final long serialVersionUID = 1L; public int getSourceActions(JComponent c) { return TransferHandler.COPY_OR_MOVE; } public boolean canImport(TransferSupport support) { return false; } protected Transferable createTransferable(JComponent c) { return transferable; } public boolean importData(TransferSupport support) { return true; } }; comp2.setTransferHandler(th); comp2.setEnabled(true); JScrollPane fsc = new JScrollPane(comp2); comp2.setPreferredSize(new Dimension(bimg.getWidth(), bimg.getHeight())); JPopupMenu popup = new JPopupMenu(); popup.add(new AbstractAction("Save image") { @Override public void actionPerformed(ActionEvent e) { FileSaveService fss = null; FileContents fileContents = null; try { ByteArrayOutputStream baos = new ByteArrayOutputStream(); OutputStreamWriter osw = new OutputStreamWriter(baos); ImageIO.write(bimg, "png", baos); baos.close(); try { fss = (FileSaveService) ServiceManager.lookup("javax.jnlp.FileSaveService"); } catch (UnavailableServiceException e1) { fss = null; } if (fss != null) { ByteArrayInputStream bais = new ByteArrayInputStream(baos.toByteArray()); fileContents = fss.saveFileDialog(null, null, bais, "export.png"); bais.close(); OutputStream os = fileContents.getOutputStream(true); os.write(baos.toByteArray()); os.close(); } else { JFileChooser jfc = new JFileChooser(); if (jfc.showSaveDialog(GeneSetHead.this) == JFileChooser.APPROVE_OPTION) { File f = jfc.getSelectedFile(); FileOutputStream fos = new FileOutputStream(f); fos.write(baos.toByteArray()); fos.close(); Desktop.getDesktop().browse(f.toURI()); } } } catch (IOException e2) { e2.printStackTrace(); } } }); comp2.setComponentPopupMenu(popup); f.add(fsc); f.setVisible(true); } catch (ClassNotFoundException e1) { e1.printStackTrace(); } }); }); MenuItem tniaction = new MenuItem("TNI/ANI"); tniaction.setOnAction(actionEvent -> { SwingUtilities.invokeLater(() -> { Set<String> species = getSelspec(GeneSetHead.this, geneset.specList); String makeblastdb = "makeblastdb"; String OS = System.getProperty("os.name").toLowerCase(); if (OS.indexOf("mac") != -1) makeblastdb = "/usr/local/bin/makeblastdb"; for (String spec : species) { List<Sequence> lseq = geneset.speccontigMap.get(spec); ProcessBuilder pb = new ProcessBuilder(makeblastdb, "-dbtype", "nucl", "-title", spec, "-out", spec); File dir = new File(System.getProperty("user.home")); /*try { FileWriter w = new FileWriter( new File(dir, spec+".fna") ); for( Sequence seq : lseq ) { seq.writeSequence(w); } w.close(); } catch (IOException e2) { e2.printStackTrace(); }*/ pb.directory(dir); try { Process p = pb.start(); Writer fw = new OutputStreamWriter(p.getOutputStream()); for (Sequence seq : lseq) { seq.writeSequence(fw); } fw.close(); } catch (IOException e1) { e1.printStackTrace(); } } int y = 0; double[] matrix = new double[species.size() * species.size()]; for (String dbspec : species) { int x = 0; for (String spec : species) { //if( !spec.equals(dbspec) ) { final List<Sequence> lseq = geneset.speccontigMap.get(spec); String blastn = "blastn"; if (OS.indexOf("mac") != -1) blastn = "/usr/local/bin/blastn"; ProcessBuilder pb = new ProcessBuilder(blastn, "-db", dbspec, "-num_threads", Integer.toString(Runtime.getRuntime().availableProcessors()), "-num_alignments", "1", "-num_descriptions", "1"); //,"-max_hsps","1"); File dir = new File(System.getProperty("user.home")); pb.directory(dir); try { Process p = pb.start(); final BufferedWriter fw = new BufferedWriter( new OutputStreamWriter(p.getOutputStream())); Thread t = new Thread() { public void run() { try { for (Sequence seq : lseq) { seq.writeSplitSequence(fw); //seq.writeSequence(fw); } fw.close(); } catch (IOException e1) { e1.printStackTrace(); } } }; t.start(); //Path path = Paths.get("/Users/sigmar/"+spec+"_"+dbspec+".blastout"); //Files.copy(p.getInputStream(), path, StandardCopyOption.REPLACE_EXISTING); int tnum = 0; int tdenum = 0; double avg = 0.0; int count = 0; BufferedReader br = new BufferedReader(new InputStreamReader(p.getInputStream())); String line = br.readLine(); while (line != null) { if (line.startsWith(" Identities")) { int i = line.indexOf('('); String sub = line.substring(14, i - 1); String[] split = sub.split("/"); int num = Integer.parseInt(split[0]); int denum = Integer.parseInt(split[1]); avg += (double) num / (double) denum; tnum += num; tdenum += denum; count++; } line = br.readLine(); } br.close(); if (count > 0) avg /= count; double val = (double) tnum / (double) tdenum; matrix[y * species.size() + x] = avg;//val; System.err.println(spec + " on " + dbspec + " " + val); } catch (IOException e1) { e1.printStackTrace(); } //} x++; } y++; } geneset.corrInd.clear(); for (String spec : species) { geneset.corrInd.add(geneset.nameFix(spec)); } final BufferedImage bi = geneset.showRelation(geneset.corrInd, matrix, false); JFrame f = new JFrame("TNI matrix"); f.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE); f.setSize(500, 500); JComponent comp2 = new JComponent() { public void paintComponent(Graphics g) { super.paintComponent(g); g.drawImage(bi, 0, 0, bi.getWidth(), bi.getHeight(), 0, 0, bi.getWidth(), bi.getHeight(), this); } }; Dimension dim = new Dimension(bi.getWidth(), bi.getHeight()); comp2.setPreferredSize(dim); comp2.setSize(dim); JScrollPane scroll = new JScrollPane(comp2); f.add(scroll); f.setVisible(true); }); }); MenuItem anitreeaction = new MenuItem("ANI tree"); anitreeaction.setOnAction(actionEvent -> { Set<String> species = getSelspec(GeneSetHead.this, geneset.specList); List<String> speclist = new ArrayList<String>(species); Collection<GeneGroup> allgg = new HashSet<GeneGroup>(); allgg.addAll(table.getSelectionModel().getSelectedItems()); if (allgg.isEmpty()) allgg = geneset.allgenegroups; Map<String, Integer> blosumap = JavaFasta.getBlosumMap(); double[] corrarr = new double[speclist.size() * speclist.size()]; int where = 0; for (String spec1 : speclist) { int wherex = 0; String spc1 = geneset.nameFix(spec1); //String spc1 = nameFix( spec1 ); for (String spec2 : speclist) { if (where != wherex) { int totalscore = 0; int totaltscore = 1; for (GeneGroup gg : allgg) { if ( /*gg.getSpecies().size() > 40 &&*/ gg.getSpecies().contains(spec1) && gg.getSpecies().contains(spec2)) { Teginfo ti1 = gg.species.get(spec1); Teginfo ti2 = gg.species.get(spec2); //if( ti1.tset.size() == 1 && ti2.tset.size() == 1 ) { //double bval = 0.0; int score = 0; int tscore = 1; for (Tegeval tv1 : ti1.tset) { for (Tegeval tv2 : ti2.tset) { Sequence seq1 = tv1.getAlignedSequence(); Sequence seq2 = tv2.getAlignedSequence(); if (seq1 != null && seq2 != null) { int mest = 0; int tmest = 0; int startcheck = 0; int start = -1; int stopcheck = 0; int stop = -1; for (int i = 0; i < seq1.length(); i++) { if (seq1.getCharAt(i) != '-') { startcheck |= 1; } if (seq2.getCharAt(i) != '-') { startcheck |= 2; } if (start == -1 && startcheck == 3) { start = i; break; } } for (int i = seq1.length() - 1; i >= 0; i--) { if (seq1.getCharAt(i) != '-') { stopcheck |= 1; } if (seq2.getCharAt(i) != '-') { stopcheck |= 2; } if (stop == -1 && stopcheck == 3) { stop = i + 1; break; } } //count += stop-start; for (int i = start; i < stop; i++) { char lc = seq1.getCharAt(i); char c = Character.toUpperCase(lc); //if( ) String comb = c + "" + c; if (blosumap.containsKey(comb)) tmest += blosumap.get(comb); } for (int i = start; i < stop; i++) { char lc = seq1.getCharAt(i); char c = Character.toUpperCase(lc); char lc2 = seq2.getCharAt(i); char c2 = Character.toUpperCase(lc2); String comb = c + "" + c2; if (blosumap.containsKey(comb)) mest += blosumap.get(comb); } double tani = (double) mest / (double) tmest; if (tani > (double) score / (double) tscore) { score = mest; tscore = tmest; } //ret = (double)score/(double)tscore; //int cval = tscore == 0 ? 0 : Math.min( 192, 512-score*512/tscore ); //return ret; } //if( where == 0 ) d1.add( gg.getCommonName() ); //else d2.add( gg.getCommonName() ); } } totalscore += score; totaltscore += tscore; /*if( bval > 0 ) { ani += bval; count++; }*/ //} } } double ani = (double) (totaltscore - totalscore) / (double) totaltscore; corrarr[where * speclist.size() + wherex] = ani; } wherex++; } where++; } TreeUtil tu = new TreeUtil(); geneset.corrInd.clear(); for (String spec : speclist) { geneset.corrInd.add(geneset.nameFix(spec)); } Node n = tu.neighborJoin(corrarr, geneset.corrInd, null, false, false); System.err.println(n); }); windowmenu.getItems().add(specorderaction); windowmenu.getItems().add(matrixaction); windowmenu.getItems().add(tniaction); windowmenu.getItems().add(anitreeaction); MenuItem neighbourhood = new MenuItem("Neighbourhood"); neighbourhood.setOnAction(actionEvent -> { try { Set<GeneGroup> genset = new HashSet<>(); if (!isGeneview()) { for (GeneGroup gg : table.getSelectionModel().getSelectedItems()) { genset.add(gg); } } else { for (Gene gene : gtable.getSelectionModel().getSelectedItems()) { genset.add(gene.getGeneGroup()); } } new Neighbour(genset).neighbourMynd(GeneSetHead.this, comp, geneset.genelist, geneset.contigmap); } catch (IOException e1) { e1.printStackTrace(); } }); windowmenu.getItems().add(neighbourhood); MenuItem synteny = new MenuItem("Synteny"); synteny.setOnAction(actionEvent -> { SwingUtilities.invokeLater(() -> { //Set<String> species = speciesFromCluster( clusterMap ); new Synteni().syntenyMynd(GeneSetHead.this, comp, geneset.genelist); }); }); windowmenu.getItems().add(synteny); MenuItem compareplotaction = new MenuItem("Gene atlas"); compareplotaction.setOnAction(actionEvent -> { SwingUtilities.invokeLater(() -> { try { new GeneCompare().comparePlot(GeneSetHead.this, comp, geneset.genelist, geneset.clusterMap, 8192, 8192); } catch (IOException e1) { e1.printStackTrace(); } }); /*gatest("MAT4726"); final JFrame frame = new JFrame(); frame.setDefaultCloseOperation( JFrame.DISPOSE_ON_CLOSE ); frame.setSize(800, 600); final JComponent c = new JComponent() { public void paintComponent( Graphics g ) { g.drawImage(bimg, 0, 0, frame); } }; c.setPreferredSize( new Dimension(bimg.getWidth(), bimg.getHeight()) ); JScrollPane scrollpane = new JScrollPane( c ); frame.add( scrollpane ); frame.setVisible( true );*/ }); windowmenu.getItems().add(compareplotaction); MenuItem syntenygradientaction = new MenuItem("Synteny gradient"); syntenygradientaction.setOnAction(actionEvent -> { SwingUtilities.invokeLater(() -> { Set<String> presel = new HashSet<>(); if (isGeneview()) { for (Gene g : gtable.getSelectionModel().getSelectedItems()) { presel.addAll(g.getGeneGroup().getSpecies()); } } else { for (GeneGroup gg : table.getSelectionModel().getSelectedItems()) { presel.addAll(gg.getSpecies()); } } new SyntGrad().syntGrad(GeneSetHead.this, 4096, 4096, presel); }); }); windowmenu.getItems().add(syntenygradientaction); MenuItem genexyplotaction = new MenuItem("Gene XY plot"); genexyplotaction.setOnAction(actionEvent -> SwingUtilities.invokeLater( () -> new XYPlot().xyPlot(GeneSetHead.this, comp, geneset.genelist, geneset.clusterMap))); windowmenu.getItems().add(genexyplotaction); MenuItem refalignaction = new MenuItem("Reference align"); refalignaction.setOnAction(actionEvent -> { SwingUtilities.invokeLater(() -> { final TableView<Gene> table12 = getGeneTable(); final Collection<String> specset = geneset.getSpecies(); //speciesFromCluster( clusterMap ); final List<String> species = new ArrayList<>(specset); TableModel model = new TableModel() { @Override public int getRowCount() { return species.size(); } @Override public int getColumnCount() { return 1; } @Override public String getColumnName(int columnIndex) { return null; } @Override public Class<?> getColumnClass(int columnIndex) { return String.class; } @Override public boolean isCellEditable(int rowIndex, int columnIndex) { return false; } @Override public Object getValueAt(int rowIndex, int columnIndex) { return geneset.nameFix(species.get(rowIndex)); } @Override public void setValueAt(Object aValue, int rowIndex, int columnIndex) { } @Override public void addTableModelListener(TableModelListener l) { } @Override public void removeTableModelListener(TableModelListener l) { } }; JTable table1 = new JTable(model); JTable table2 = new JTable(model); table1.getSelectionModel().setSelectionMode(ListSelectionModel.SINGLE_SELECTION); table2.getSelectionModel().setSelectionMode(ListSelectionModel.MULTIPLE_INTERVAL_SELECTION); JScrollPane scroll1 = new JScrollPane(table1); JScrollPane scroll2 = new JScrollPane(table2); FlowLayout flowlayout = new FlowLayout(); JComponent c = new JComponent() { }; c.setLayout(flowlayout); c.add(scroll1); c.add(scroll2); JOptionPane.showMessageDialog(comp, c); int r = table1.getSelectedRow(); int i = table1.convertRowIndexToModel(r); String spec = i == -1 ? null : species.get(i); List<Sequence> lcont = geneset.speccontigMap.get(spec); r = table2.getSelectedRow(); i = table2.convertRowIndexToModel(r); String refspec = i == -1 ? null : species.get(i); List<Sequence> lrefcont = geneset.speccontigMap.get(spec); /*ByteArrayOutputStream baos = new ByteArrayOutputStream(); Writer fw = new OutputStreamWriter( baos ); try { List<Sequence> lcont = geneset.speccontigMap.get(spec); for( Sequence seq : lcont ) { seq.writeSequence(fw); } fw.close(); } catch (IOException e1) { e1.printStackTrace(); } String comp = spec; byte[] bb = baos.toByteArray();*/ FlxReader flx = new FlxReader(); Map<String, String> env = new HashMap<String, String>(); env.put("create", "true"); //String uristr = "jar:" + geneset.zippath.toUri(); //URI geneset.zipuri = URI.create( uristr /*.replace("file://", "file:")*/ ); try { geneset.zipfilesystem = FileSystems.newFileSystem(geneset.zipuri, env); for (Path root : geneset.zipfilesystem.getRootDirectories()) { Path subf = root.resolve(spec + ".grp"); if (Files.exists(subf)) { BufferedReader br = Files.newBufferedReader(subf); Map<String, Map<String, String>> mm = flx.loadContigGraph(br); br.close(); String home = System.getProperty("user.home") + "/"; StringBuilder sb = comp != null ? flx.referenceAssembly(home, spec, refspec, lrefcont, lcont) : null; Sequence cseq = new Sequence(spec + "_chromosome", null); if (sb != null && sb.length() > 0) { br = new BufferedReader(new StringReader(sb.toString())); } else { Path sca = root.resolve(spec + ".csc"); if (!Files.exists(sca)) { sca = root.resolve(spec + ".sca"); } br = Files.newBufferedReader(sca); } //br = new BufferedReader( fr ); flx.connectContigs(br, cseq, false, new FileWriter(home + spec + "_new.fna"), spec); br.close(); } break; } } catch (Exception ex) { ex.printStackTrace(); } finally { try { geneset.zipfilesystem.close(); } catch (IOException ie) { ie.printStackTrace(); } ; } }); //flx.start( f.getParentFile().getAbsolutePath()+"/", f.getName(), false, fw, comp, bb); }); windowmenu.getItems().add(refalignaction); windowmenu.getItems().add(new SeparatorMenuItem()); MenuItem runantismash = new MenuItem("Run antismash"); runantismash.setOnAction(actionEvent -> SwingUtilities.invokeLater(new Runnable() { public void run() { try { Serifier ser = new Serifier(); Set<String> selspec = getSelspec(null, geneset.getSpecies(), null); JTextField host = new JTextField("localhost"); JOptionPane.showMessageDialog(null, host); String username = System.getProperty("user.name"); String hostname = host.getText(); /*Path[] pt = null; JFileChooser fc = new JFileChooser(); fc.setFileSelectionMode( JFileChooser.DIRECTORIES_ONLY ); if( fc.showSaveDialog(null) == JFileChooser.APPROVE_OPTION ) { pt = new Path[3]; pt[2] = fc.getSelectedFile().toPath(); }*/ List<Object> commands = new ArrayList<Object>(); //commands.add(genexyplotaction) for (String spec : selspec) { Path pp = Paths.get(userhome); Path p = pp.resolve(spec + ".gbk"); //BufferedWriter fw = Files.newBufferedWriter( p ); List<Sequence> clist = geneset.speccontigMap.get(spec); Map<String, List<Annotation>> mapan = new HashMap<String, List<Annotation>>(); Serifier serifier = new Serifier(); for (Sequence c : clist) { serifier.addSequence(c); serifier.mseq.put(c.getName(), c); List<Annotation> lann = new ArrayList<Annotation>(); if (c.getAnnotations() != null) for (Annotation ann : c.getAnnotations()) { Tegeval tv = (Tegeval) ann; Gene g = tv.getGene(); GeneGroup gg = g.getGeneGroup(); String name = g.getName(); if (gg != null && name.contains(spec)) { name = gg.getName(); } Annotation anno = new Annotation(c, tv.start, tv.stop, tv.ori, name); anno.id = tv.getGene().getId(); anno.type = "CDS"; String cazy = gg != null ? gg.getCommonCazy(geneset.cazymap) : null; if (cazy != null) anno.addDbRef("CAZY:" + cazy); lann.add(anno); } mapan.put(c.getName(), lann); } Sequences s = new Sequences(null, spec, "nucl", null, clist.size()); //serifier.addSequences(seqs); serifier.writeGenebank(p, false, true, s, mapan); //fw.close(); String apath = p.toAbsolutePath().toString(); if (hostname.equals("localhost")) { String[] cmds = { "run_antismash", apath }; //commands.add( pt ); commands.add(Arrays.asList(cmds)); } else { String aname = p.getFileName().toString(); String adir = aname.substring(0, aname.length() - 4); String cyghome = NativeRun.cygPath(userhome); String[] cmds = { "scp", apath, hostname + ":~", ";", "ssh", hostname, "run_antismash", aname, ";", "scp", "-r", hostname + ":~/" + adir, cyghome };//userhome+"~"}; //commands.add( pt ); commands.add(Arrays.asList(cmds)); } } Runnable run = new Runnable() { @Override public void run() { for (String spec : selspec) { Path p = Paths.get(userhome, spec); Map<String, String> env = new HashMap<String, String>(); env.put("create", "true"); String uristr = "jar:" + geneset.zippath.toUri(); URI zipuri = URI.create(uristr /*.replace("file://", "file:")*/ ); final List<Path> lbi = new ArrayList<Path>(); try { geneset.zipfilesystem = FileSystems.newFileSystem(geneset.zipuri, env); for (Path root : geneset.zipfilesystem.getRootDirectories()) { Path specdir = root; Files.walkFileTree(p, new SimpleFileVisitor<Path>() { @Override public FileVisitResult visitFile(Path file, BasicFileAttributes attrs) throws IOException { final Path destFile = Paths.get(specdir.toString(), file.toString()); //System.out.printf("Extracting file %s to %s\n", file, destFile); Files.copy(file, destFile, StandardCopyOption.REPLACE_EXISTING); return FileVisitResult.CONTINUE; } @Override public FileVisitResult preVisitDirectory(Path dir, BasicFileAttributes attrs) throws IOException { String specdirstr = specdir.toString(); String dirstr = dir.toString(); final Path dirToCreate = specdir .resolve(dirstr.substring(userhome.length() + 1)); if (Files.notExists(dirToCreate)) { System.out.printf("Creating directory %s\n", dirToCreate); Files.createDirectory(dirToCreate); } return FileVisitResult.CONTINUE; } }); break; } URI uri = new URI("file://" + userhome + "/" + spec + "/index.html"); Desktop.getDesktop().browse(uri); } catch (Exception ex) { ex.printStackTrace(); } finally { try { geneset.zipfilesystem.close(); } catch (Exception e) { e.printStackTrace(); } ; } } } }; NativeRun nr = new NativeRun(run); nr.runProcessBuilder("antismash", commands, new Object[3], false, run, false); } catch (IOException e1) { e1.printStackTrace(); } } })); windowmenu.getItems().add(runantismash); MenuItem runsignalp = new MenuItem("Run signalP"); runsignalp.setOnAction(actionEvent -> SwingUtilities.invokeLater(new Runnable() { public void run() { try { Serifier ser = new Serifier(); Set<String> selspec = getSelspec(null, geneset.getSpecies(), null); JTextField host = new JTextField("localhost"); JOptionPane.showMessageDialog(null, host); String username = System.getProperty("user.name"); String hostname = host.getText(); /*Path[] pt = null; JFileChooser fc = new JFileChooser(); fc.setFileSelectionMode( JFileChooser.DIRECTORIES_ONLY ); if( fc.showSaveDialog(null) == JFileChooser.APPROVE_OPTION ) { pt = new Path[3]; pt[2] = fc.getSelectedFile().toPath(); }*/ List<Object> commands = new ArrayList<Object>(); //commands.add(genexyplotaction) try { Map<String, String> env = new HashMap<String, String>(); env.put("create", "true"); String uristr = "jar:" + geneset.zippath.toUri(); URI zipuri = URI.create(uristr /*.replace("file://", "file:")*/ ); geneset.zipfilesystem = FileSystems.newFileSystem(geneset.zipuri, env); for (Path root : geneset.zipfilesystem.getRootDirectories()) { for (String spec : selspec) { /*Path specdir = root.resolve(spec+".prodigal.fsa"); if( !Files.exists(specdir) ) { if( spec.startsWith("MAT") ) { specdir = root.resolve(spec+".gbk.aa"); } else specdir = root.resolve("fn_"+spec+"_scaffolds.prodigal.fsa"); }*/ Stream<Gene> genestream = geneset.genelist.stream() .filter(gene -> spec.equals(gene.getSpecies()) && (gene.tegeval.type == null || gene.tegeval.type.length() == 0)); Path sigout = root.resolve(spec + ".signalp"); Path[] pt = new Path[] { null, sigout, null }; if (hostname.equals("localhost")) { String[] cmds = { "signalp", "-t", "gram-", "-" }; commands.add(pt); commands.add(Arrays.asList(cmds)); } else { Path p = Paths.get(spec + ".signalp"); BufferedWriter bw = Files.newBufferedWriter(p, StandardOpenOption.CREATE, StandardOpenOption.TRUNCATE_EXISTING, StandardOpenOption.WRITE); genestream.forEachOrdered(gene -> { try { gene.writeGeneIdFasta(bw); } catch (Exception e1) { e1.printStackTrace(); } }); bw.close(); //Files.copy(specdir, p, StandardCopyOption.REPLACE_EXISTING); String[] cmds = { "scp", spec + ".signalp", hostname + ":~", ";", "ssh", hostname, "signalp", "-t", "gram-", spec + ".signalp" }; //String[] cmds = {"ssh",hostname,"signalp","-t","gram-","-"}; commands.add(pt); commands.add(Arrays.asList(cmds)); } } break; } } catch (Exception ex) { ex.printStackTrace(); } Runnable run = new Runnable() { @Override public void run() { try { geneset.zipfilesystem.close(); } catch (Exception e) { e.printStackTrace(); } ; } }; NativeRun nr = new NativeRun(run); nr.runProcessBuilder("signalp", commands, new Object[3], false, run, false); } catch (IOException e1) { e1.printStackTrace(); } } })); windowmenu.getItems().add(runsignalp); MenuItem runtransm = new MenuItem("Run TransM"); runtransm.setOnAction(actionEvent -> SwingUtilities.invokeLater(new Runnable() { public void run() { try { Serifier ser = new Serifier(); Set<String> selspec = getSelspec(null, geneset.getSpecies(), null); JTextField host = new JTextField("localhost"); JOptionPane.showMessageDialog(null, host); String username = System.getProperty("user.name"); String hostname = host.getText(); /*Path[] pt = null; JFileChooser fc = new JFileChooser(); fc.setFileSelectionMode( JFileChooser.DIRECTORIES_ONLY ); if( fc.showSaveDialog(null) == JFileChooser.APPROVE_OPTION ) { pt = new Path[3]; pt[2] = fc.getSelectedFile().toPath(); }*/ List<Object> commands = new ArrayList<>(); //commands.add(genexyplotaction) try { Map<String, String> env = new HashMap<>(); env.put("create", "true"); String uristr = "jar:" + geneset.zippath.toUri(); URI zipuri = URI.create(uristr /*.replace("file://", "file:")*/ ); geneset.zipfilesystem = FileSystems.newFileSystem(geneset.zipuri, env); for (Path root : geneset.zipfilesystem.getRootDirectories()) { for (String spec : selspec) { /*Path specdir = root.resolve(spec+".prodigal.fsa"); if( !Files.exists(specdir) ) { if( spec.startsWith("MAT") ) { specdir = root.resolve(spec+".gbk.aa"); } else specdir = root.resolve("fn_"+spec+"_scaffolds.prodigal.fsa"); }*/ Stream<Gene> genestream = geneset.genelist.stream() .filter(gene -> spec.equals(gene.getSpecies()) && (gene.tegeval.type == null || gene.tegeval.type.length() == 0)); ByteArrayOutputStream baos = new ByteArrayOutputStream(); BufferedWriter bw = new BufferedWriter(new OutputStreamWriter(baos)); genestream.forEach(gene -> { try { gene.writeGeneIdFasta(bw); } catch (Exception e1) { e1.printStackTrace(); } }); bw.close(); baos.close(); String seqs = baos.toString(); seqs = seqs.replace('*', 'X'); byte[] bb = seqs.getBytes(); Path sigout = root.resolve(spec + ".tm"); Object[] pt = new Object[] { bb, sigout, null }; if (hostname.equals("localhost")) { String[] cmds = { "decodeanhmm", "-f", "/opt/tmhmm-2.0c/lib/TMHMM2.0.options", "-modelfile", "/opt/tmhmm-2.0c/lib/TMHMM2.0.model" }; commands.add(pt); commands.add(Arrays.asList(cmds)); } else { //Path p = Paths.get(spec+".tm"); //Files.copy(specdir, p, StandardCopyOption.REPLACE_EXISTING); String[] cmds = { "ssh", hostname, "decodeanhmm", "-f", "/opt/tmhmm-2.0c/lib/TMHMM2.0.options", "-modelfile", "/opt/tmhmm-2.0c/lib/TMHMM2.0.model" }; commands.add(pt); commands.add(Arrays.asList(cmds)); } } break; } } catch (Exception ex) { ex.printStackTrace(); } Runnable run = () -> { try { geneset.zipfilesystem.close(); } catch (Exception e) { e.printStackTrace(); } ; }; NativeRun nr = new NativeRun(run); nr.runProcessBuilder("transm", commands, new Object[3], false, run, false); } catch (IOException e1) { e1.printStackTrace(); } } })); windowmenu.getItems().add(runtransm); MenuItem runtrnascan = new MenuItem("tRNAscan"); runtrnascan.setOnAction(actionEvent -> SwingUtilities.invokeLater(() -> { try { Serifier ser = new Serifier(); Set<String> selspec = getSelspec(null, geneset.getSpecies(), null); JTextField host = new JTextField("localhost"); JOptionPane.showMessageDialog(null, host); String username = System.getProperty("user.name"); String hostname = host.getText(); /*Path[] pt = null; JFileChooser fc = new JFileChooser(); fc.setFileSelectionMode( JFileChooser.DIRECTORIES_ONLY ); if( fc.showSaveDialog(null) == JFileChooser.APPROVE_OPTION ) { pt = new Path[3]; pt[2] = fc.getSelectedFile().toPath(); }*/ List<Object> commands = new ArrayList<>(); //commands.add(genexyplotaction) try { Map<String, String> env = new HashMap<>(); env.put("create", "true"); String uristr = "jar:" + geneset.zippath.toUri(); URI zipuri = URI.create(uristr /*.replace("file://", "file:")*/ ); geneset.zipfilesystem = FileSystems.newFileSystem(geneset.zipuri, env); for (Path root : geneset.zipfilesystem.getRootDirectories()) { for (String spec : selspec) { Path specdir = root.resolve(spec + ".fna"); if (!Files.exists(specdir)) { if (spec.startsWith("MAT")) { specdir = root.resolve(spec + ".gbk.fna"); } else specdir = root.resolve("fn_" + spec + "_scaffolds.fastg"); } System.err.println(Files.exists(specdir)); Path sigout = root.resolve("trnas.txt"); if (hostname.equals("localhost1")) { Path[] pt = new Path[] { specdir, sigout, null }; String[] cmds = { "/usr/local/bin/tRNAscan-SE", "-B", "-" }; commands.add(pt); commands.add(Arrays.asList(cmds)); } else { Path[] pt = new Path[] { null, sigout, null }; Path p = Paths.get(spec + ".trnascan"); Files.copy(specdir, p, StandardCopyOption.REPLACE_EXISTING); List<String> lcmd; if (hostname.equals("localhost")) { //String[] cmds = {"/usr/local/bin/trnascan-1.4", spec + ".trnascan"}; String[] cmds = { "/usr/local/bin/tRNAscan-SE", "-B", spec + ".trnascan" }; lcmd = Arrays.asList(cmds); } else { String[] cmds = { "scp", spec + ".trnascan", hostname + ":~", ";", "ssh", hostname, "trnascan-1.4", spec + ".trnascan" }; lcmd = Arrays.asList(cmds); //String[] cmds = {"ssh",hostname,"tRNAscan-SE","-B","-"}; } commands.add(pt); commands.add(lcmd); } } break; } } catch (Exception ex) { ex.printStackTrace(); } Runnable run = () -> { try { geneset.zipfilesystem.close(); } catch (Exception e) { e.printStackTrace(); } ; }; NativeRun nr = new NativeRun(run); nr.runProcessBuilder("tRNAscan", commands, new Object[3], false, run, false); } catch (IOException e1) { e1.printStackTrace(); } })); windowmenu.getItems().add(runtrnascan); Menu select = new Menu("Select"); MenuItem breakpointselAction = new MenuItem("Select breakpoints"); breakpointselAction.setOnAction(actionEvent -> { String spec = syncolorcomb.getSelectionModel().getSelectedItem(); int rr = 0; for (Gene g : geneset.genelist) { if (!spec.equals(g.getSpecies()) && g.getSpecies().contains("eggert")) { Tegeval tv2 = g.tegeval; Annotation n2 = tv2.getNext(); Annotation p2 = tv2.getPrevious(); GeneGroup gg = g.getGeneGroup(); if (gg.getName().contains("rhodane")) { System.err.println(); } Teginfo ti = gg.getGenes(spec); int msimcount = 0; if (ti != null) { for (Tegeval tv1 : ti.tset) { int simcount = 0; Annotation n = tv1.getNext(); Annotation p = tv1.getPrevious(); GeneGroup ggg = tv1.getGene().getGeneGroup(); if (n2 != null) { if (ggg == n2.getGene().getGeneGroup()) { simcount++; } Annotation nn2 = n2.getNext(); if (nn2 != null) { if (ggg == nn2.getGene().getGeneGroup()) { simcount++; } } } if (p2 != null) { if (ggg == p2.getGene().getGeneGroup()) { simcount++; } Annotation pp2 = p2.getPrevious(); if (pp2 != null) { if (ggg == pp2.getGene().getGeneGroup()) { simcount++; } } } if (n != null) { GeneGroup ngg = n.getGene().getGeneGroup(); if (ngg == tv2.getGene().getGeneGroup()) { simcount++; } if (n2 != null) { if (ngg == n2.getGene().getGeneGroup()) { simcount++; } } if (p2 != null) { if (ngg == p2.getGene().getGeneGroup()) { simcount++; } } Annotation nn = n.getNext(); if (nn != null) { ngg = nn.getGene().getGeneGroup(); if (ngg == tv2.getGene().getGeneGroup()) { simcount++; } if (n2 != null) { if (ngg == n2.getGene().getGeneGroup()) { simcount++; } } if (p2 != null) { if (ngg == p2.getGene().getGeneGroup()) { simcount++; } } } } if (p != null) { GeneGroup pgg = p.getGene().getGeneGroup(); if (pgg == tv2.getGene().getGeneGroup()) { simcount++; } if (n2 != null) { if (pgg == n2.getGene().getGeneGroup()) { simcount++; } } if (p2 != null) { if (pgg == p2.getGene().getGeneGroup()) { simcount++; } } Annotation pp = p.getPrevious(); if (pp != null) { pgg = pp.getGene().getGeneGroup(); if (pgg == tv2.getGene().getGeneGroup()) { simcount++; } if (n2 != null) { if (pgg == n2.getGene().getGeneGroup()) { simcount++; } } if (p2 != null) { if (pgg == p2.getGene().getGeneGroup()) { simcount++; } } } } //double rat = GeneCompare.invertedGradientRatio(spec, contigs, -1.0, gg, tv); if (simcount >= msimcount) { //tv = tv1; msimcount = simcount; } //double ratio = GeneCompare.invertedGradientRatio(spec, contigs, -1.0, gg, tv); //GeneCompare.gradientColor(); } if (msimcount < 2) { gtable.getSelectionModel().select(g); } } } rr++; } /*List<Sequence> contigs = geneset.speccontigMap.get( spec ); for( Sequence c : contigs ) { for( Annotation ann : c.annset ) { Tegeval tv = (Tegeval)ann; } }*/ }); MenuItem saveselAction = new MenuItem("Save selection"); saveselAction.setOnAction(actionEvent -> { /*int[] rr = table.getSelectedRows(); if( rr.length > 0 ) { String val = Integer.toString( table.convertRowIndexToModel(rr[0]) ); for( int i = 1; i < rr.length; i++ ) { val += ","+table.convertRowIndexToModel(rr[i]); } String selname = JOptionPane.showInputDialog("Selection name"); if( comp instanceof Applet ) { try { ((GeneSetHead)comp).saveSel( selname, val); } catch (Exception e1) { e1.printStackTrace(); } } }*/ }); select.getItems().add(breakpointselAction); select.getItems().add(saveselAction); select.getItems().add(new SeparatorMenuItem()); MenuItem showall = new MenuItem("Show all"); showall.setOnAction(actionEvent -> { genefilterset.clear(); updateFilter(table, label); }); select.getItems().add(showall); MenuItem croptosel = new MenuItem("Crop to selection"); croptosel.setOnAction(actionEvent -> { Set<GeneGroup> selitems = new HashSet<>(table.getSelectionModel().getSelectedItems()); filteredData.setPredicate(p -> selitems.contains(p)); }); select.getItems().add(croptosel); MenuItem croptoinvsel = new MenuItem("Crop to inverted selection"); croptoinvsel.setOnAction(actionEvent -> { genefilterset.clear(); for (int i = 0; i < table.getItems().size(); i++) { if (!table.getSelectionModel().isSelected(i)) { genefilterset.add(i); } } updateFilter(table, label); }); select.getItems().add(croptoinvsel); MenuItem removesel = new MenuItem("Remove selection"); removesel.setOnAction(actionEvent -> { // genefilterset.clear(); //int[] rr = table.getSelectedRows(); if (genefilterset.isEmpty()) { Set<Integer> ii = new HashSet<Integer>(); for (int r : table.getSelectionModel().getSelectedIndices()) ii.add(r); for (int i = 0; i < geneset.genelist.size(); i++) { if (!ii.contains(i)) genefilterset.add(i); } } else { for (int r : table.getSelectionModel().getSelectedIndices()) { //int mr = table.convertRowIndexToModel(r); genefilterset.remove(r); } } updateFilter(table, label); }); select.getItems().add(removesel); MenuItem invsel = new MenuItem("Invert selection"); invsel.setOnAction(actionEvent -> { ObservableList<GeneGroup> selitems = table.getSelectionModel().getSelectedItems(); List<GeneGroup> newsel = new ArrayList<>(filteredData); newsel.removeAll(selitems); table.getSelectionModel().clearSelection(); newsel.stream().forEach(gg -> table.getSelectionModel().select(gg)); // genefilterset.clear(); //int[] rr = table.getSelectedRows(); /*Set<Integer> iset = new HashSet<>(); for( int r : table.getSelectionModel().getSelectedIndices() ) { iset.add( r ); } table.getSelectionModel().clearSelection(); for (int r = 0; r < table.getItems().size(); r++) { if( !iset.contains(r) ) table.getSelectionModel().select(r); /*if (table.isRowSelected(r)) table.removeRowSelectionInterval(r, r); else table.addRowSelectionInterval(r, r); }*/ }); select.getItems().add(invsel); //select.addSeparator(); select.getItems().add(new SeparatorMenuItem()); MenuItem selsinglemult = new MenuItem("Select single copy genes found in multiple strains"); selsinglemult.setOnAction(actionEvent -> { Set<String> specset = getSelspec(GeneSetHead.this, geneset.specList); for (GeneGroup gg : geneset.allgenegroups) { Set<String> checkspec = new HashSet<String>(gg.species.keySet()); checkspec.retainAll(specset); if (gg.getCommonTag() == null && checkspec.size() > 1 && gg.getTegevals().size() == gg.species.size()) {//gg.getTegevals(checkspec).size() == checkspec.size() ) { table.getSelectionModel().select(gg); //table.setro } } }); select.getItems().add(selsinglemult); MenuItem selsinglemultstrain = new MenuItem( "Select single copy genes in accessory genome of multiple strains"); selsinglemultstrain.setOnAction(actionEvent -> { Set<String> specset = getSelspec(GeneSetHead.this, geneset.specList); for (GeneGroup gg : geneset.allgenegroups) { Set<String> checkspec = new HashSet<String>(gg.species.keySet()); checkspec.retainAll(specset); if (gg.getCommonTag() == null && checkspec.size() > 1 && checkspec.size() < specset.size() && gg.getTegevals().size() == gg.species.size()) {//gg.getTegevals(checkspec).size() == checkspec.size() ) { table.getSelectionModel().select(gg); //table.setro } } }); select.getItems().add(selsinglemultstrain); MenuItem selsinglecopygenes = new MenuItem("Select single copy genes"); selsinglecopygenes.setOnAction(actionEvent -> { Set<String> specset = getSelspec(GeneSetHead.this, geneset.specList); for (GeneGroup gg : geneset.allgenegroups) { if (gg.getTegevals().size() == gg.species.size()) { table.getSelectionModel().select(gg); //table.setro } } }); select.getItems().add(selsinglecopygenes); MenuItem selduplgenes = new MenuItem("Select duplicated genes"); selduplgenes.setOnAction(actionEvent -> { for (GeneGroup gg : geneset.allgenegroups) { int cnt = 0; for (String spec : gg.species.keySet()) { Teginfo ti = gg.species.get(spec); if (ti.tset.size() == 2) { List<Tegeval> ta = new ArrayList<Tegeval>(ti.tset); if (ta.get(0).getNext() == ta.get(1) || ta.get(0).getPrevious() == ta.get(1)) cnt++; } } if ((float) cnt / (float) gg.species.size() > 0.7) { table.getSelectionModel().select(gg); } } }); select.getItems().add(selduplgenes); MenuItem seltriplgenes = new MenuItem("Select triplicated genes"); seltriplgenes.setOnAction(actionEvent -> { for (GeneGroup gg : geneset.allgenegroups) { int cnt = 0; for (String spec : gg.species.keySet()) { Teginfo ti = gg.species.get(spec); if (ti.tset.size() == 3) { List<Tegeval> ta = new ArrayList<Tegeval>(ti.tset); if ((ta.get(0).getNext() == ta.get(1) || ta.get(0).getPrevious() == ta.get(1)) && (ta.get(1).getNext() == ta.get(2) || ta.get(1).getPrevious() == ta.get(2))) cnt++; } } if ((float) cnt / (float) gg.species.size() > 0.7) { table.getSelectionModel().select(gg); } } }); select.getItems().add(seltriplgenes); MenuItem selplasmidgenes = new MenuItem("Select plasmid genes"); selplasmidgenes.setOnAction(actionEvent -> { for (GeneGroup gg : geneset.allgenegroups) { if (gg.isOnAnyPlasmid()) { table.getSelectionModel().select(gg); } /*int cnt = 0; for( String spec : gg.species.keySet() ) { Teginfo ti = gg.species.get( spec ); if( ti.tset.size() == 3 ) { List<Tegeval> ta = new ArrayList<Tegeval>( ti.tset ); if( (ta.get(0).getNext() == ta.get(1) || ta.get(0).getPrevious() == ta.get(1)) && (ta.get(1).getNext() == ta.get(2) || ta.get(1).getPrevious() == ta.get(2))) cnt++; } } if( (float)cnt / (float)gg.species.size() > 0.7 ) { int r = table.convertRowIndexToView(gg.index); table.addRowSelectionInterval(r, r); }*/ } }); select.getItems().add(selplasmidgenes); MenuItem selectphagegenes = new MenuItem("Select phage genes"); selectphagegenes.setOnAction(actionEvent -> { for (GeneGroup gg : geneset.allgenegroups) { if (gg.isInAnyPhage()) { table.getSelectionModel().select(gg); } /*int cnt = 0; for( String spec : gg.species.keySet() ) { Teginfo ti = gg.species.get( spec ); if( ti.tset.size() == 3 ) { List<Tegeval> ta = new ArrayList<Tegeval>( ti.tset ); if( (ta.get(0).getNext() == ta.get(1) || ta.get(0).getPrevious() == ta.get(1)) && (ta.get(1).getNext() == ta.get(2) || ta.get(1).getPrevious() == ta.get(2))) cnt++; } } if( (float)cnt / (float)gg.species.size() > 0.7 ) { int r = table.convertRowIndexToView(gg.index); table.addRowSelectionInterval(r, r); }*/ } }); select.getItems().add(selectphagegenes); select.getItems().add(new SeparatorMenuItem()); MenuItem selectsharingaction = new MenuItem("Select sharing"); selectsharingaction.setOnAction(actionEvent -> { RadioButton panbtn = new RadioButton("Pan"); RadioButton corebtn = new RadioButton("Core"); RadioButton blehbtn = new RadioButton("Only in"); ToggleGroup tg = new ToggleGroup(); panbtn.setToggleGroup(tg); corebtn.setToggleGroup(tg); blehbtn.setToggleGroup(tg); HBox sp = new HBox(); sp.getChildren().add(panbtn); sp.getChildren().add(corebtn); sp.getChildren().add(blehbtn); Scene scene = new Scene(sp); //FlowLayout flowlayout = new FlowLayout(); final JFXPanel c = new JFXPanel(); c.setScene(scene); /*Group root = new Group(); Scene scene = new Scene(root, javafx.scene.paint.Color.ALICEBLUE); root.getChildren().add(panbtn); root.getChildren().add(corebtn); root.getChildren().add(blehbtn); JFXPanel fxpanel = new JFXPanel(); fxpanel.setScene( scene );*/ //bg.add( panbtn ); //bg.add( corebtn ); //bg.add( blehbtn ); corebtn.setSelected(true); //Object[] objs = new Object[] { panbtn, corebtn }; //JOptionPane.showMessageDialog( geneset, objs, "Select id types", JOptionPane.PLAIN_MESSAGE ); SwingUtilities.invokeLater(new Runnable() { public void run() { final List<String> species = geneset.getSpecies(); TableModel model = new TableModel() { @Override public int getRowCount() { return species.size(); } @Override public int getColumnCount() { return 1; } @Override public String getColumnName(int columnIndex) { return null; } @Override public Class<?> getColumnClass(int columnIndex) { return String.class; } @Override public boolean isCellEditable(int rowIndex, int columnIndex) { return false; } @Override public Object getValueAt(int rowIndex, int columnIndex) { return species.get(rowIndex); } @Override public void setValueAt(Object aValue, int rowIndex, int columnIndex) { } @Override public void addTableModelListener(TableModelListener l) { } @Override public void removeTableModelListener(TableModelListener l) { } }; JTable table = new JTable(model); table.getSelectionModel().setSelectionMode(ListSelectionModel.MULTIPLE_INTERVAL_SELECTION); JScrollPane scroll = new JScrollPane(table); Object[] objs = new Object[] { scroll, c }; JOptionPane.showMessageDialog(comp, objs); final Set<String> specs = new HashSet<String>(); int[] rr = table.getSelectedRows(); for (int r : rr) { String spec = (String) table.getValueAt(r, 0); specs.add(spec); } Platform.runLater(new Runnable() { public void run() { for (GeneGroup gg : geneset.allgenegroups) { if (blehbtn.isSelected()) { Set<String> ss = new HashSet<String>(gg.species.keySet()); ss.removeAll(specs); if (ss.size() == 0) { GeneSetHead.this.table.getSelectionModel().select(gg); } } else if (gg.species.keySet().containsAll(specs) && (panbtn.isSelected() || specs.size() == gg.species.size())) { GeneSetHead.this.table.getSelectionModel().select(gg); } } } }); } }); }); select.getItems().add(selectsharingaction); MenuItem selectdirtyaction = new MenuItem("Select dirty"); selectdirtyaction.setOnAction(actionEvent -> { if (!isGeneview()) { int i = 0; for (GeneGroup gg : geneset.allgenegroups) { if (gg.containsDirty()) { table.getSelectionModel().select(gg); } i++; } } }); select.getItems().add(selectdirtyaction); MenuItem selectdesignationaction = new MenuItem("Select designation"); selectdesignationaction.setOnAction(actionEvent -> { JComboBox<String> descombo = new JComboBox<String>( geneset.deset.toArray(new String[geneset.deset.size()])); descombo.insertItemAt("", 0); descombo.setSelectedIndex(0); JOptionPane.showMessageDialog(GeneSetHead.this, descombo); String seldes = (String) descombo.getSelectedItem(); if (!isGeneview()) { int i = 0; for (GeneGroup gg : geneset.allgenegroups) { if (gg.genes != null) for (Gene g : gg.genes) { if (seldes.equals(g.tegeval.designation)) { table.getSelectionModel().select(gg); } } i++; } } }); select.getItems().add(selectdesignationaction); MenuItem blastselect = new MenuItem("Blast select"); blastselect.setOnAction(actionEvent -> SwingUtilities.invokeLater(() -> blast(false))); select.getItems().add(blastselect); MenuItem blastxselect = new MenuItem("Blastx select"); blastxselect.setOnAction(actionEvent -> SwingUtilities.invokeLater(() -> blast(true))); select.getItems().add(blastxselect); MenuItem blastnselect = new MenuItem("Blastn select"); blastnselect.setOnAction(actionEvent -> SwingUtilities.invokeLater(() -> blastn(true))); select.getItems().add(blastnselect); MenuItem blastsearch = new MenuItem("Blastn search"); blastsearch.setOnAction(actionEvent -> SwingUtilities.invokeLater(() -> blastn(false))); select.getItems().add(blastsearch); menubar.getMenus().add(file); menubar.getMenus().add(edit); menubar.getMenus().add(view); menubar.getMenus().add(sequencemenu); menubar.getMenus().add(windowmenu); menubar.getMenus().add(select); menubar.getMenus().add(help); if (comp != null) { final Window window = SwingUtilities.windowForComponent(comp); initFSKeyListener(window); if (comp instanceof JFrame || window instanceof JFrame) { JFrame frame = (JFrame) (window == null ? comp : window); if (!frame.isResizable()) frame.setResizable(true); frame.addKeyListener(keylistener); frame.setJMenuBar(jmenubar); } } final Button jb = new Button("Atlas"); jb.setOnAction(event -> { try { URL url = new URL("file:///home/sigmar/workspace/distann/bin/circle.html"); GeneSetHead.this.getAppletContext().showDocument(url, "_blank"); } catch (MalformedURLException e1) { e1.printStackTrace(); } }); try { newSoft(jb, comp, genetable, upper, lower, toolbar, btoolbar, GeneSetHead.this, selcomb); } catch (IOException e) { e.printStackTrace(); } if (comp != null) { if (comp instanceof Applet) try { ((GeneSetHead) comp).saveSel(null, null); } catch (NoSuchMethodError | Exception e1) { e1.printStackTrace(); } //comp.add( cc ); } }
From source file:org.simmi.GeneSetHead.java
License:asdf
public void exportGenomes(Map<String, List<Sequence>> speccontigMap) { JCheckBox joincontigs = new JCheckBox("Join contigs"); JCheckBox translations = new JCheckBox("Include translations"); JComponent[] comps = new JComponent[] { joincontigs, translations }; List scl = getSelspecContigs(Arrays.asList(comps), speccontigMap); if (scl.get(0) instanceof String) { List<String> lspec = (List<String>) scl; JFileChooser filechooser = new JFileChooser(); filechooser.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY); if (filechooser.showSaveDialog(this) == JFileChooser.APPROVE_OPTION) { for (String spec : lspec) { Map<String, List<Annotation>> mapan = new HashMap<String, List<Annotation>>(); List<Sequence> contigs = geneset.speccontigMap.get(spec); Serifier serifier = new Serifier(); for (Sequence c : contigs) { serifier.addSequence(c); serifier.mseq.put(c.getName(), c); List<Annotation> lann = new ArrayList(); if (c.getAnnotations() != null) for (Annotation ann : c.getAnnotations()) { Tegeval tv = (Tegeval) ann; GeneGroup gg = tv.getGene().getGeneGroup(); Annotation anno = new Annotation(c, tv.start, tv.stop, tv.ori, gg != null ? gg.getName() : tv.getGene().getName()); anno.type = "CDS"; anno.id = tv.getGene().id; String cazy = gg != null ? gg.getCommonCazy(geneset.cazymap) : null; if (cazy != null) anno.addDbRef("CAZY:" + cazy); Cog cog = gg != null ? gg.getCog(geneset.cogmap) : null; if (cog != null) anno.addDbRef("COG:" + cog.id); String ec = gg != null ? gg.getEc() : null; if (ec != null) anno.addDbRef("EC:" + ec); lann.add(anno); }/*from w w w.j ava2s . c om*/ mapan.put(c.getName(), lann); } Sequences s = new Sequences(null, spec, "nucl", null, contigs.size()); try { serifier.writeGenebank(filechooser.getSelectedFile().toPath().resolve(spec + ".gbk"), !joincontigs.isSelected(), translations.isSelected(), s, mapan); } catch (IOException e) { e.printStackTrace(); } } } } else { Map<String, List<Annotation>> mapan = new HashMap<>(); List<Sequence> contigs = (List<Sequence>) scl; Serifier serifier = new Serifier(); for (Sequence c : contigs) { serifier.addSequence(c); serifier.mseq.put(c.getName(), c); List<Annotation> lann = new ArrayList<>(); if (c.getAnnotations() != null) for (Annotation ann : c.getAnnotations()) { Tegeval tv = (Tegeval) ann; GeneGroup gg = tv.getGene().getGeneGroup(); Annotation anno = new Annotation(c, tv.start, tv.stop, tv.ori, gg != null ? gg.getName() : tv.getGene().getName()); anno.type = "CDS"; anno.id = tv.getGene().id; String cazy = gg != null ? gg.getCommonCazy(geneset.cazymap) : null; if (cazy != null) anno.addDbRef("CAZY:" + cazy); lann.add(anno); } mapan.put(c.getName(), lann); } Sequences s = new Sequences(null, contigs.get(0).getSpec(), "nucl", null, contigs.size()); JFileChooser filechooser = new JFileChooser(); if (filechooser.showSaveDialog(this) == JFileChooser.APPROVE_OPTION) { try { serifier.writeGenebank(filechooser.getSelectedFile().toPath(), !joincontigs.isSelected(), translations.isSelected(), s, mapan); } catch (IOException e) { e.printStackTrace(); } } //serifier.addSequences(seqs); } }
From source file:org.simmi.GeneSetHead.java
License:asdf
public void exportGeneClusters(List<GeneGroup> allgenegroups) { JFileChooser filechooser = new JFileChooser(); filechooser.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY); if (filechooser.showSaveDialog(this) == JFileChooser.APPROVE_OPTION) { try {/*from ww w . j a va 2 s .c om*/ Path dbPath = filechooser.getSelectedFile().toPath(); for (GeneGroup gg : allgenegroups) { if (gg != null && gg.getCommonTag() == null) { Path file = dbPath.resolve(gg.getCommonId() + ".aa"); BufferedWriter bw = Files.newBufferedWriter(file); gg.getFasta(bw, true); bw.close(); /*StringBuilder sb = g.tegeval.getProteinSequence(); if( sb.toString().contains("0") ) { System.err.println( g.id ); } bw.append(">" + g.id + "\n"); for (int i = 0; i < sb.length(); i += 70) { bw.append( sb.substring(i, Math.min(i + 70, sb.length())) + "\n"); }*/ } } //serifier.writeGenebank( filechooser.getSelectedFile(), !joincontigs.isSelected(), translations.isSelected(), s, mapan); } catch (IOException e) { e.printStackTrace(); } } }
From source file:org.sintef.thingml.FilePanel.java
public FilePanel(final ThingMLPanel editor, final ThingMLFrame frame, File rootF) { this.setLayout(new BorderLayout()); add(new JScrollPane(tree), BorderLayout.CENTER); File root = rootF;/*from w w w. j a v a 2 s. c o m*/ if (root == null) { JFileChooser filechooser = new JFileChooser(); filechooser.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY); filechooser.setDialogTitle("Select base directory for ThingML files"); File dir = ThingMLSettings.getInstance().get_default_work_dir(); if (dir != null) { filechooser.setSelectedFile(dir); } int returnVal = filechooser.showOpenDialog(null); if (filechooser.getSelectedFile() != null && returnVal == JFileChooser.APPROVE_OPTION) { ThingMLSettings.getInstance().store_default_work_dir(filechooser.getSelectedFile()); root = filechooser.getSelectedFile(); } else { System.exit(0); } } FileFilter fileFilter = new FileFilter() { @Override public boolean accept(File f) { return f.getName().endsWith(".thingml"); } }; final File root2 = root; try { simpleFileManager = new SimpleFileManager(root, fileFilter); } catch (IOException e) { e.printStackTrace(); } tree.setModel(new DefaultTreeModel(simpleFileManager.getDirectoryTree())); simpleFileManager.startMonitoring(); FileMonitor fileMonitor = simpleFileManager.getFileMonitor(); fileMonitor.addClient(this); tree.addTreeSelectionListener(new TreeSelectionListener() { @Override public void valueChanged(TreeSelectionEvent e) { TreePath path = e.getNewLeadSelectionPath(); String file = path.getLastPathComponent().toString(); while (path.getParentPath() != null) { path = path.getParentPath(); file = path.getLastPathComponent() + "/" + file; } if (file.indexOf("/") > -1) { File fileF = new File(root2 + "/" + file.substring(file.indexOf("/"))); if (fileF.isFile()) { try { final InputStream input = new FileInputStream(fileF.getAbsolutePath()); final java.util.List<String> packLines = IOUtils.readLines(input); String content = ""; for (String line : packLines) { content += line + "\n"; } input.close(); editor.loadText(content, fileF); frame.setTitle("ThingML Editor : " + e.getNewLeadSelectionPath().getLastPathComponent().toString()); } catch (Exception ex) { ex.printStackTrace(); } } } } }); }
From source file:org.sleeksnap.ScreenSnapper.java
/** * Upload a file to the file service by selecting in another window */// w w w. j a v a2 s . c om public void selectFile() { final JFileChooser chooser = new JFileChooser(); chooser.setFileSelectionMode(JFileChooser.FILES_ONLY); final int returnVal = chooser.showOpenDialog(null); if (returnVal == JFileChooser.APPROVE_OPTION) { final File file = chooser.getSelectedFile(); final int confirm = JOptionPane.showConfirmDialog(null, Language.getString("uploadConfirm", file.getName()), Language.getString("uploadConfirmTitle"), JOptionPane.YES_NO_OPTION, JOptionPane.WARNING_MESSAGE); if (confirm == JOptionPane.YES_OPTION) { JOptionPane.showMessageDialog(null, Language.getString("fileUploading"), Language.getString("fileUploadTitle"), JOptionPane.INFORMATION_MESSAGE); upload(new FileUpload(file.getAbsoluteFile())); } else { JOptionPane.showMessageDialog(null, Language.getString("fileUploadCanceled"), Language.getString("fileUploadTitle"), JOptionPane.INFORMATION_MESSAGE); } } }
From source file:org.sleuthkit.autopsy.modules.hashdatabase.HashDbManager.java
private String searchForFile() { String filePath = null;/*ww w . ja v a 2s. c o m*/ JFileChooser fc = new JFileChooser(); fc.setDragEnabled(false); fc.setFileSelectionMode(JFileChooser.FILES_ONLY); String[] EXTENSION = new String[] { "txt", "idx", "hash", "Hash", "kdb" }; //NON-NLS FileNameExtensionFilter filter = new FileNameExtensionFilter( NbBundle.getMessage(this.getClass(), "HashDbManager.fileNameExtensionFilter.title"), EXTENSION); fc.setFileFilter(filter); fc.setMultiSelectionEnabled(false); if (fc.showOpenDialog(null) == JFileChooser.APPROVE_OPTION) { File f = fc.getSelectedFile(); try { filePath = f.getCanonicalPath(); } catch (IOException ex) { Logger.getLogger(HashDbManager.class.getName()).log(Level.WARNING, "Couldn't get selected file path", ex); //NON-NLS } } return filePath; }
From source file:org.sonar.scanner.protocol.viewer.ScannerReportViewerApp.java
private void loadReport() { final JFileChooser fc = new JFileChooser(); fc.setDialogTitle("Choose scanner report directory"); File lastReport = getLastUsedReport(); if (lastReport != null) { fc.setCurrentDirectory(lastReport); }/*from ww w. ja va 2 s .c om*/ fc.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY); fc.setFileHidingEnabled(false); fc.setApproveButtonText("Open scanner report"); int returnVal = fc.showOpenDialog(frame); if (returnVal == JFileChooser.APPROVE_OPTION) { File file = fc.getSelectedFile(); try { setLastUsedReport(file); loadReport(file); } catch (Exception e) { JOptionPane.showMessageDialog(frame, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE); exit(); } } else { exit(); } }
From source file:org.spoutcraft.launcher.settings.LauncherDirectories.java
public File selectInstallDir(File workDir) { int result = JOptionPane.showConfirmDialog(splash, "No installation of technic found. \n\nTechnic Launcher will install at: \n" + workDir.getAbsolutePath() + " \n\nWould you like to change the install directory?", "Install Technic Launcher", JOptionPane.YES_NO_OPTION, JOptionPane.INFORMATION_MESSAGE); if (result == JOptionPane.YES_OPTION) { JFileChooser fileChooser = new JFileChooser(workDir); fileChooser.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY); int changeInst = fileChooser.showOpenDialog(splash); if (changeInst == JFileChooser.APPROVE_OPTION) { workDir = fileChooser.getSelectedFile(); if (!ZipUtils.checkLaunchDirectory(workDir)) { JOptionPane.showMessageDialog(splash, "Please select an empty directory, or your default install folder with settings.yml in it.", "Invalid Location", JOptionPane.WARNING_MESSAGE); return selectInstallDir(workDir); }/*from www .j a v a2 s . c o m*/ } workDir.mkdirs(); } return workDir; }
From source file:org.spoutcraft.launcher.util.Utils.java
public static File selectInstallDir(File workDir) { int result = JOptionPane.showConfirmDialog(splash, "No installation of technic found. \n\nTechnic Launcher will install at: \n" + workDir.getAbsolutePath() + " \n\nWould you like to change the install directory?", "Install Technic Launcher", JOptionPane.YES_NO_OPTION, JOptionPane.INFORMATION_MESSAGE); if (result == JOptionPane.YES_OPTION) { JFileChooser fileChooser = new JFileChooser(workDir); fileChooser.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY); int changeInst = fileChooser.showOpenDialog(splash); if (changeInst == JFileChooser.APPROVE_OPTION) { workDir = fileChooser.getSelectedFile(); if (!FileUtils.checkLaunchDirectory(workDir)) { JOptionPane.showMessageDialog(splash, "Please select an empty directory, or your default install folder with settings.yml in it.", "Invalid Location", JOptionPane.WARNING_MESSAGE); return selectInstallDir(workDir); }/*from ww w . ja v a 2 s. c om*/ } workDir.mkdirs(); } return workDir; }
From source file:org.stanwood.nwn2.gui.MainWindow.java
private void addNewGUIFile() { File dir = settings.getGUIXMLBrowseDirLastDir( new File(settings.getNWN2Dir(NWN2GuiSettings.DEFAULT_NWN2_DIR), "UI" + File.separator + "default")); JFileChooser fc = new JFileChooser(dir); fc.setFileSelectionMode(JFileChooser.FILES_ONLY); fc.setFileFilter(new FileFilter() { @Override/*w w w .j a v a 2 s . com*/ public String getDescription() { return "NWN2 GUI (*.xml)"; } @Override public boolean accept(File f) { return f.isDirectory() || f.getName().toLowerCase().endsWith(".xml"); } }); fc.showOpenDialog(MainWindow.this); File selFile = fc.getSelectedFile(); if (selFile != null) { guiFileListModel.addElement(selFile); guiFileList.setSelectedIndex(guiFileListModel.getSize() - 1); settings.setGUIXMLBrowseDirLastDir(selFile.getParentFile()); updateEnabledState(); saveChanges(); } }