List of usage examples for javafx.scene.control RadioButton isSelected
public final boolean isSelected()
From source file:de.pixida.logtest.designer.logreader.LogReaderEditor.java
public void runLogFileReader(final RadioButton inputTypeFile, final TextField pathInput, final TextArea logInputText) { this.parsedLogEntryItems.clear(); try {// w w w. ja v a 2 s . c o m GenericLogReader reader; if (inputTypeFile.isSelected()) { reader = new GenericLogReader(new File(pathInput.getText())); } else { reader = new GenericLogReader(new BufferedReader(new StringReader(logInputText.getText()))); } reader.overwriteCurrentSettingsWithSettingsInConfigurationFile( this.logReader.getSettingsForConfigurationFile()); this.logReader = reader; ILogEntry nextLogEntry; while ((nextLogEntry = reader.getNextEntry()) != null) { this.parsedLogEntryItems.add(new LogEntryTableRow(nextLogEntry)); } } catch (final RuntimeException re) { ExceptionDialog.showFatalException("Error reading log entries", "An error occurred while reading the log entries.", re); } }
From source file:de.pixida.logtest.designer.automaton.AutomatonEdge.java
private Node createRadioButtonInput(final ToggleGroup tg, final String propertyName, final boolean isInitiallySelected, final Consumer<Boolean> applyValue) { final RadioButton result = new RadioButton(propertyName); result.setToggleGroup(tg);//from w w w. j a v a 2s .c o m result.setSelected(isInitiallySelected); result.setOnAction(event -> { applyValue.accept(result.isSelected()); this.getGraph().handleChange(); }); return result; }
From source file:fruitproject.FruitProject.java
public void first(final Stage primaryStage) { GridPane grid = new GridPane(); grid.setAlignment(Pos.CENTER);/* w ww .j a va 2 s. c o m*/ grid.setHgap(10); grid.setVgap(10); grid.setPadding(new Insets(25, 25, 25, 25)); rows = 0; addPairs.clear(); Text lb = new Text(); lb.setText("J-Fruit"); //lb.setFont(Font.font("Tahoma", FontWeight.NORMAL, 20)); grid.add(lb, 1, 0); final ToggleGroup grp = new ToggleGroup(); RadioButton rb1 = new RadioButton(); rb1.setText("Add Fruit file"); rb1.setUserData("add"); rb1.setToggleGroup(grp); rb1.setSelected(true); grid.add(rb1, 1, 1); RadioButton rb2 = new RadioButton(); rb2.setText("Load Fruit file"); rb2.setUserData("load"); rb2.setToggleGroup(grp); grid.add(rb2, 1, 2); Label label1 = new Label("Enter File Name:"); final TextField tfFilename = new TextField(); final HBox hb = new HBox(); hb.getChildren().addAll(label1, tfFilename); hb.setSpacing(10); hb.setVisible(false); tfFilename.setText(""); grid.add(hb, 1, 3); grp.selectedToggleProperty().addListener(new ChangeListener<Toggle>() { public void changed(ObservableValue<? extends Toggle> ov, Toggle old_toggle, Toggle new_toggle) { if (grp.getSelectedToggle() != null) { // System.out.println(grp.getSelectedToggle().getUserData().toString()); if (grp.getSelectedToggle().getUserData().toString() == "load") hb.setVisible(true); else { hb.setVisible(false); tfFilename.setText(""); } } } }); if (rb2.isSelected() == true) { hb.setVisible(true); } Button btn = new Button(); btn.setText("GO"); grid.add(btn, 1, 4); btn.setOnAction(new EventHandler<ActionEvent>() { @Override public void handle(ActionEvent event) { //System.out.println("Hello World!"); if (tfFilename.getText() == "") second(""); else second(tfFilename.getText()); primaryStage.close(); } }); //StackPane root = new StackPane(); //root.getChildren().add(lb); //root.getChildren().add(rb1); //root.getChildren().add(rb2); //root.getChildren().add(btn); Scene scene = new Scene(grid, 400, 450); primaryStage.setTitle("Hello World!"); primaryStage.setScene(scene); primaryStage.show(); }
From source file:FeeBooster.java
@Override public void start(Stage primaryStage) throws Exception { // Setup the stage stage = primaryStage;/*from w ww . j ava 2s . c o m*/ primaryStage.setTitle("Bitcoin Transaction Fee Booster"); // Setup intro gridpane GridPane grid = new GridPane(); grid.setAlignment(Pos.CENTER); grid.setHgap(10); grid.setVgap(10); grid.setPadding(new Insets(25, 25, 25, 25)); // Intro Text Text scenetitle = new Text( "Welcome to the fee booster. \n\nWhat type of transaction would you like to boost the fee of?"); grid.add(scenetitle, 0, 0, 2, 3); // radio button selections VBox boostRadioVbox = new VBox(); ToggleGroup boostTypeGroup = new ToggleGroup(); RadioButton rbfRadio = new RadioButton("A transaction you sent"); rbfRadio.setToggleGroup(boostTypeGroup); boostRadioVbox.getChildren().add(rbfRadio); RadioButton cpfpRadio = new RadioButton("A transaction you received"); cpfpRadio.setToggleGroup(boostTypeGroup); rbfRadio.setSelected(true); boostRadioVbox.getChildren().add(cpfpRadio); grid.add(boostRadioVbox, 0, 3); // Instructions Text Text instruct = new Text("Please enter the raw hex or transaction id of your transaction below:"); grid.add(instruct, 0, 4); // Textbox for hex of transaction TextArea txHexTxt = new TextArea(); txHexTxt.setWrapText(true); grid.add(txHexTxt, 0, 5, 5, 1); // Next Button Button nextBtn = new Button("Next"); nextBtn.setOnAction(new EventHandler<ActionEvent>() { @Override public void handle(ActionEvent event) { // Create Transaction Transaction tx = new Transaction(); // Check if txid boolean isTxid = txHexTxt.getText().length() == 64 && txHexTxt.getText().matches("[0-9A-Fa-f]+"); if (isTxid) tx.setHash(txHexTxt.getText()); // Determine which page to go to if (Transaction.deserializeStr(txHexTxt.getText(), tx) || isTxid) { // Get the fee JSONObject apiResult = Utils .getFromAnAPI("https://api.blockcypher.com/v1/btc/main/txs/" + tx.getHash(), "GET"); // Get the fee tx.setFee(apiResult.getInt("fees")); tx.setTotalAmtPre(tx.getFee() + tx.getOutAmt()); // Get info if txid if (isTxid) { } Scene scene = null; if (rbfRadio.isSelected()) if (sceneCursor == scenes.size() - 1 || !rbf) { scene = new Scene(rbfGrid(tx), 900, 500); if (!rbf) { scenes.clear(); scenes.add(stage.getScene()); } rbf = true; } if (cpfpRadio.isSelected()) if (sceneCursor == scenes.size() - 1 || rbf) { scene = new Scene(cpfpGrid(tx), 900, 500); if (rbf) { scenes.clear(); scenes.add(stage.getScene()); } rbf = false; } if (sceneCursor != scenes.size() - 1) scene = scenes.get(sceneCursor + 1); else scenes.add(scene); sceneCursor++; stage.setScene(scene); } else { Alert alert = new Alert(Alert.AlertType.ERROR, "Please enter a valid transaction"); alert.showAndWait(); } } }); HBox btnHbox = new HBox(10); btnHbox.getChildren().add(nextBtn); // Cancel Button Button cancelBtn = new Button("Cancel"); cancelBtn.setOnAction(cancelEvent); btnHbox.getChildren().add(cancelBtn); grid.add(btnHbox, 2, 7); // Display everything Scene scene = new Scene(grid, 900, 500); scenes.add(scene); primaryStage.setScene(scene); primaryStage.show(); }
From source file:org.simmi.GeneSetHead.java
License:asdf
public void cogBlastDlg(Set<String> species) { Dialog<String> cogdlg = new Dialog(); ToggleGroup group = new ToggleGroup(); VBox vbox = new VBox(); RadioButton docker = new RadioButton("docker"); docker.setToggleGroup(group);/* www . j av a 2 s . c om*/ RadioButton local = new RadioButton("local"); local.setToggleGroup(group); docker.setSelected(true); TextField dbpath = new TextField("/cdd_delta"); TextField host = new TextField("geneset"); vbox.getChildren().add(docker); vbox.getChildren().add(local); vbox.getChildren().add(dbpath); vbox.getChildren().add(host); cogdlg.getDialogPane().setContent(vbox); /*String dbPath = "/data/Cog"; JTextField tf = new JTextField( dbPath ); JTextField host = new JTextField("localhost"); JOptionPane.showMessageDialog( null, new Object[] {tf, host} );*/ cogdlg.getDialogPane().getButtonTypes().add(ButtonType.OK); cogdlg.getDialogPane().getButtonTypes().add(ButtonType.CANCEL); cogdlg.setResultConverter(param -> { if (!param.getButtonData().isCancelButton()) { return dbpath.getText(); } return ""; }); Optional<String> ostr = cogdlg.showAndWait(); if (ostr.isPresent()) { String str = ostr.get(); if (str.length() > 0) SwingUtilities.invokeLater(() -> { geneset.cogBlast(species, dbpath.getText(), host.getText(), false, docker.isSelected()); }); } }
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;/*w w w .j av a 2s . c om*/ 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
private void showGeneTable( /*final Map<String, Gene> genemap, final List<Gene> genelist, final List<Function> funclist, final List<Set<String>> iclusterlist, final List<Set<String>> uclusterlist, final Map<Set<String>, ShareNum> specset,*/ final Map<Set<String>, ClusterInfo> clustInfoMap, final Button jb, final TableView<Gene> genetable, final TableView<Function> upper, final TableView<GeneGroup> lower, final ToolBar toolbar, final ToolBar btoolbar, final Container comp, final JApplet applet, final ComboBox<String> selcomblocal) throws IOException { //JSplitPane splitpane = new JSplitPane(); //splitpane.setOrientation(JSplitPane.VERTICAL_SPLIT); //splitpane.setDividerLocation(400); //JScrollPane scrollpane = new JScrollPane(); /*table = new JTable() { public String getToolTipText(MouseEvent me) { Point p = me.getPoint();/* w ww.ja va 2 s . c om*/ int r = rowAtPoint(p); int c = columnAtPoint(p); if (r >= 0 && r < super.getRowCount()) { Object ret = super.getValueAt(r, c); if (ret != null) { return ret.toString(); // super.getToolTipText( me ); } } return ""; } };*/ //table.setDragEnabled(true); try { final DataFlavor df = new DataFlavor("text/plain;charset=utf-8"); // System.err.println( df.getHumanPresentableName() + " " + // df.getPrimaryType() + " " + df.getSubType() + " " + // df.getMimeType() ); // DataFlavor df1 = DataFlavor.getTextPlainUnicodeFlavor(); // System.err.println( df.getHumanPresentableName() + " " + // df.getPrimaryType() + " " + df.getSubType() + " " + // df.getMimeType() ); 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 true; } protected Transferable createTransferable(JComponent c) { return new Transferable() { @Override public Object getTransferData(DataFlavor arg0) throws UnsupportedFlavorException, IOException { Map<String, List<Tegeval>> contigs = new HashMap<>(); StringBuilder ret = new StringBuilder(); for (Gene gg : gtable.getSelectionModel().getSelectedItems()) { Tegeval tv = gg.tegeval; if (!contigs.containsKey(tv.getContshort())) { List<Tegeval> ltv = new ArrayList<>(); ltv.add(tv); contigs.put(tv.getContshort().getName(), ltv); } else { List<Tegeval> ltv = contigs.get(tv.getContshort()); ltv.add(tv); } /* * ret.append( ">" + tv.cont + " " + * tv.teg + " " + tv.eval + "\n" ); * if( tv.dna != null ) { for( int i * = 0; i < tv.dna.length(); i+=70 ) * { ret.append(tv.dna.substring( i, * Math.min(i+70,tv.dna.length()) * )+"\n"); } } */ } for (String cont : contigs.keySet()) { List<Tegeval> tv = contigs.get(cont); String dna = tv.get(0).getSequence(); ret.append(">" + cont + "\n"); // + " " + tv.teg // + " " + // tv.eval + // "\n" ); if (dna != null) { for (int i = 0; i < dna.length(); i += 70) { ret.append(dna.substring(i, Math.min(i + 70, dna.length())) + "\n"); } } } for (String cont : contigs.keySet()) { List<Tegeval> ltv = contigs.get(cont); ret.append(">" + cont + "\n"); // + " " + tv.teg // + " " + // tv.eval + // "\n" ); for (Tegeval tv : ltv) { ret.append("erm\t#0000ff\t" + tv.start + "\t" + tv.stop + "\n"); } } 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; } }; } public boolean importData(TransferHandler.TransferSupport support) { Object obj = null; System.err.println(support.getDataFlavors().length); int b = Arrays.binarySearch(support.getDataFlavors(), DataFlavor.javaFileListFlavor, (o1, o2) -> o1 == o2 ? 1 : 0); try { obj = support.getTransferable().getTransferData(DataFlavor.imageFlavor); } catch (UnsupportedFlavorException e) { e.printStackTrace(); } catch (IOException e) { e.printStackTrace(); } try { if (obj != null && obj instanceof File[]) { // File[] ff = (File[])obj; // wbStuff( ff[0].getCanonicalPath() ); } else if (obj instanceof Image) { } else { obj = support.getTransferable().getTransferData(DataFlavor.stringFlavor); System.err.println(obj); URL url = null; try { url = new URL((String) obj); Image image = ImageIO.read(url); } catch (Exception e) { e.printStackTrace(); } } } catch (UnsupportedFlavorException e) { e.printStackTrace(); } catch (IOException e) { e.printStackTrace(); } return true; } }; //table.setTransferHandler(th); } catch (ClassNotFoundException e2) { e2.printStackTrace(); } final Color darkgreen = new Color(0, 128, 0); final Color darkred = new Color(128, 0, 0); final Color darkblue = new Color(0, 0, 128); final Color darkmag = new Color(128, 0, 128); /*table.setDefaultRenderer(Teg.class, new DefaultTableCellRenderer() { @Override public Component getTableCellRendererComponent(JTable table, Object value, boolean isSelected, boolean hasFocus, int row, int column) { Component label = super.getTableCellRendererComponent(table, value, isSelected, hasFocus, row, column); if( value == null ) { label.setBackground(Color.white); } else { cellRender(); } return label; } });*/ //table.setAutoResizeMode(JTable.AUTO_RESIZE_OFF); //table.setAutoCreateRowSorter(true); //scrollpane.setViewportView(table); Set<String> current = null; Set<String> currentko = null; InputStream is = GeneSet.class.getResourceAsStream("/kegg_pathways"); BufferedReader br = new BufferedReader(new InputStreamReader(is)); String line = br.readLine(); while (line != null) { if (line.startsWith(">")) { current = new HashSet<>(); currentko = new HashSet<>(); geneset.pathwaymap.put(line.substring(1), current); geneset.pathwaykomap.put(line.substring(1), currentko); } else if (!line.startsWith("K")) { if (current != null) { String str = line.split("[\t ]+")[0]; current.add(str); } } else { if (currentko != null) { String str = line.split("[\t ]+")[0]; currentko.add(str); } } line = br.readLine(); } br.close(); //FileReader fr = new FileReader("/vg454flx/ko2go.txt"); /*is = GeneSet.class.getResourceAsStream("/ko2go.txt"); InputStreamReader isr = new InputStreamReader( is ); br = new BufferedReader( isr ); line = br.readLine(); while (line != null) { String[] split = line.split(" = "); String[] subsplit = split[1].split(" "); Set<String> gos = new HashSet<String>(); for( String go : subsplit ) { gos.add( go ); } ko2go.put( split[0], gos ); line = br.readLine(); } br.close();*/ final TextField textfield = new TextField(); //JComponent topcomp = new JComponent() {}; //topcomp.setLayout(new BorderLayout()); //topcomp.add(scrollpane); textfield.setPrefSize(350, 25); final RadioButton search = new RadioButton("Search"); final RadioButton filter = new RadioButton("Filter"); ToggleGroup bgsf = new ToggleGroup(); search.setToggleGroup(bgsf); filter.setToggleGroup(bgsf); //ButtonGroup bgsf = new ButtonGroup(); //bgsf.add( search ); //bgsf.add( filter ); filter.setSelected(true); //ToolBar topcombo = new ToolBar(); // topcombo. // topcombo.setLayout( new FlowLayout() ); specombo = new ComboBox<>(); combo = new ComboBox<>(); specombo.getItems().add("Select blast species"); combo.getItems().add("Select pathway"); btoolbar.getItems().add(combo); btoolbar.getItems().add(specombo); //topcomp.add(topcombo, BorderLayout.SOUTH); //JComponent ttopcom = new JComponent() {}; //ttopcom.setLayout(new FlowLayout()); /* frame.setVisible( true ); } }; AbstractAction sharenumaction = new AbstractAction("Update share numbers") { @Override public void actionPerformed(ActionEvent e) { Set<String> specs = getSelspec(GeneSetHead.this, specList, null); updateShareNum(specs); } }; AbstractAction importgenesymbolaction = new AbstractAction("Import gene symbols") { @Override public void actionPerformed(ActionEvent e) { JFileChooser fc = new JFileChooser(); if( fc.showOpenDialog( GeneSetHead.this ) == JFileChooser.APPROVE_OPTION ) { try { Map<String,String> env = new HashMap<String,String>(); env.put("create", "true"); Path path = zipfile.toPath(); String uristr = "jar:" + path.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); InputStream is = new GZIPInputStream( new FileInputStream( fc.getSelectedFile() ) ); uni2symbol(new InputStreamReader(is), bw, unimap); bw.close(); //long bl = Files.copy( new ByteArrayInputStream( baos.toByteArray() ), nf, StandardCopyOption.REPLACE_EXISTING ); geneset.zipfilesystem.close(); } catch (IOException e1) { e1.printStackTrace(); } } } }; AbstractAction importidmappingaction = new AbstractAction("Id mapping") { @Override public void actionPerformed(ActionEvent e) { JFileChooser fc = new JFileChooser(); if( fc.showOpenDialog( GeneSetHead.this ) == JFileChooser.APPROVE_OPTION ) { try { Map<String,String> env = new HashMap<String,String>(); env.put("create", "true"); Path path = zipfile.toPath(); String uristr = "jar:" + path.toUri(); geneset.zipuri = URI.create( uristr /*.replace("file://", "file:")/ ); geneset.zipfilesystem = FileSystems.newFileSystem( geneset.zipuri, env ); Path nf = geneset.zipfilesystem.getPath("/idmapping_short.dat"); BufferedWriter bw = Files.newBufferedWriter(nf, StandardOpenOption.CREATE); InputStream is = new GZIPInputStream( new FileInputStream( fc.getSelectedFile() ) ); if( unimap != null ) unimap.clear(); unimap = idMapping(new InputStreamReader(is), bw, 2, 0, refmap, genmap, gimap); bw.close(); //long bl = Files.copy( new ByteArrayInputStream( baos.toByteArray() ), nf, StandardCopyOption.REPLACE_EXISTING ); geneset.zipfilesystem.close(); } catch (IOException e1) { e1.printStackTrace(); } } } }; final JCheckBoxMenuItem checkbox = new JCheckBoxMenuItem(); checkbox.setAction(new AbstractAction("Sort by location") { @Override public void actionPerformed(ActionEvent e) { Tegeval.locsort = checkbox.isSelected(); } }); AbstractAction saveselAction = new AbstractAction("Save selection") { @Override public void actionPerformed(ActionEvent e) { 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 { ((GeneSet)comp).saveSel( selname, val); } catch (Exception e1) { e1.printStackTrace(); } } } } }; JMenuBar menubar = new JMenuBar(); JMenu menu = new JMenu("Functions"); menu.add( importidmappingaction ); menu.add( functionmappingaction ); menu.add( importgenesymbolaction ); menu.add( fetchaction ); menu.add( blast2action ); menu.add( sharenumaction ); menu.addSeparator(); menu.add( checkbox ); menu.add( saveselAction ); menu.addSeparator(); menu.add( genomestataction ); menu.add( selectsharingaction ); menu.add( shuffletreeaction ); menu.add( presabsaction ); menu.add( freqdistaction ); menu.add( gcpaction ); menu.add( matrixaction ); menu.add( pancoreaction ); menu.add( blastaction ); menu.add( koexportaction ); menu.add( genomesizeaction ); menu.add( gcaction ); menu.add( gcskewaction ); menu.add( mltreemapaction ); menu.add( sevenaction ); menu.add( cogaction ); menu.add( genexyplotaction ); menu.add( compareplotaction ); menu.add( syntenygradientaction ); menu.add( codregaction ); menu.add( fetchcoreaction ); menu.add( loadcontiggraphaction ); menu.add( selectflankingaction ); menu.add( showflankingaction ); menu.add( showcontigsaction ); menu.add( showunresolved ); menu.add( genephyl ); menubar.add( menu ); ttopcom.add( menubar ); JMenu view = new JMenu("View"); menubar.add( view ); gb = new JRadioButtonMenuItem( new AbstractAction("Genes") { @Override public void actionPerformed(ActionEvent e) { table.setModel( defaultModel ); } }); view.add( gb ); ggb = new JRadioButtonMenuItem( new AbstractAction("Gene groups") { @Override public void actionPerformed(ActionEvent e) { table.setModel( groupModel ); } }); ButtonGroup bg = new ButtonGroup(); bg.add( gb ); bg.add( ggb ); ggb.setSelected( true ); view.add( ggb );*/ //ttopcom.add( shuffletreebutton ); //ttopcom.add( presabsbutton ); //ttopcom.add(freqdistbutton); //ttopcom.add(matrixbutton); toolbar.getItems().add(textfield); toolbar.getItems().add(search); toolbar.getItems().add(filter); toolbar.getItems().add(label); selcomblocal.getSelectionModel().selectedItemProperty().addListener((observable, oldValue, newValue) -> { String key = newValue; if (((GeneSetHead) comp).selectionMap.containsKey(key)) { Set<Integer> val = ((GeneSetHead) comp).selectionMap.get(key); if (val != null) { table.getSelectionModel().clearSelection(); for (int i : val) { //int r = table.convertRowIndexToView(i); table.getSelectionModel().select(i); } } else { System.err.println("null " + key); } } else { System.err.println("no " + key); } }); toolbar.getItems().add(selcomblocal); /*syncolorcomb.addItemListener( new ItemListener() { @Override public void itemStateChanged(ItemEvent e) { String spec = (String)syncolorcomb.getSelectedItem(); //if( spec.length() > 0 ) } });*/ toolbar.getItems().add(searchcolcomb); toolbar.getItems().add(syncolorcomb); //topcomp.add(ttopcom, BorderLayout.NORTH); table.getSelectionModel().setSelectionMode(SelectionMode.MULTIPLE); table.getSelectionModel().selectedItemProperty().addListener(e -> { label.setText(table.getItems().size() + "/" + table.getSelectionModel().getSelectedItems().size()); }); gtable.getSelectionModel().setSelectionMode(SelectionMode.MULTIPLE); gtable.getSelectionModel().selectedItemProperty().addListener(e -> { label.setText(gtable.getItems().size() + "/" + gtable.getSelectionModel().getSelectedItems().size()); }); /*JButton but = new JButton(new AbstractAction("Gene sorter") { @Override public void actionPerformed(ActionEvent e) { try { GeneSorter.mynd(genelist, table, "t.scotoductusSA01", contigs); } catch (IOException e1) { e1.printStackTrace(); } } });*/ final TextField ftextfield = new TextField(); btoolbar.getItems().add(ftextfield); ComboBox<String> scombo = new ComboBox(); scombo.getItems().add("5S/8S"); scombo.getItems().add("16S/18S"); scombo.getItems().add("23S/28S"); scombo.getSelectionModel().selectedItemProperty().addListener(e -> { String name = e.toString().split("/")[0]; InputStream iss = GeneSet.class.getResourceAsStream("/all" + name + ".fsa"); InputStreamReader isr = new InputStreamReader(iss); BufferedReader brr = new BufferedReader(isr); JTextArea textarea = new JTextArea(); JScrollPane scrollpane = new JScrollPane(textarea); try { String ln = brr.readLine(); while (ln != null) { textarea.append(ln + "\n"); ln = brr.readLine(); } } catch (IOException e1) { e1.printStackTrace(); } JFrame frame = new JFrame(); frame.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE); frame.add(scrollpane); frame.setSize(400, 300); frame.setVisible(true); }); btoolbar.getItems().add(scombo); Button swsearch = new Button("SW Search"); swsearch.setOnAction(e -> { JComponent c = new JComponent() { }; final JProgressBar pb = new JProgressBar(); final JTextArea textarea = new JTextArea(); JButton searchbut = new JButton(new AbstractAction("Blast") { @Override public void actionPerformed(ActionEvent e) { final String fasta = textarea.getText(); final SmithWater sw = new SmithWater(); final InputStream is = GeneSet.class.getResourceAsStream("/allthermus.aa"); new Thread() { public void run() { try { sw.fasta_align(new StringReader(fasta), new InputStreamReader(is), pb); List<SmithWater.ALN> alns = sw.getAlignments(); SmithWater.ALN first = null; int count = 0; String result = ""; Set<String> regnames = new HashSet<String>(); for (SmithWater.ALN aln : alns) { if (first == null) { first = aln; } else if (aln.getScore() < 3.0f * (first.getScore() / 4.0f)) break; result += aln.toString(); regnames.add(aln.getShortDestName()); if (++count == 10) break; } textarea.setText(result); for (Gene g : geneset.genelist) { boolean found = false; Tegeval tv = g.tegeval; if (regnames.contains(tv.name)) { found = true; break; } if (found) { gtable.getSelectionModel().select(g); break; } } } catch (IOException e) { e.printStackTrace(); } } }.start(); } }); c.setLayout(new BorderLayout()); JScrollPane scrollpane = new JScrollPane(textarea); c.add(scrollpane); c.add(pb, BorderLayout.NORTH); c.add(searchbut, BorderLayout.SOUTH); JFrame frame = new JFrame(); frame.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE); frame.add(c); frame.setSize(400, 300); frame.setVisible(true); }); btoolbar.getItems().add(swsearch); btoolbar.getItems().add(jb); TableColumn<GeneGroup, String> namedesccol = new TableColumn("Desc"); namedesccol.setCellValueFactory(new PropertyValueFactory<>("name")); table.getColumns().add(namedesccol); TableColumn<GeneGroup, String> origincol = new TableColumn("Origin"); origincol.setCellValueFactory(new PropertyValueFactory<>("origin")); table.getColumns().add(origincol); TableColumn<GeneGroup, String> geneidcol = new TableColumn("Genid"); geneidcol.setCellValueFactory(new PropertyValueFactory<>("genid")); table.getColumns().add(geneidcol); TableColumn<GeneGroup, String> refidcol = new TableColumn("Refid"); refidcol.setCellValueFactory(new PropertyValueFactory<>("refid")); table.getColumns().add(refidcol); TableColumn<GeneGroup, String> unidcol = new TableColumn("Unid"); unidcol.setCellValueFactory(new PropertyValueFactory<>("unid")); table.getColumns().add(unidcol); TableColumn<GeneGroup, String> keggidcol = new TableColumn("Keggid"); keggidcol.setCellValueFactory(new PropertyValueFactory<>("keggid")); table.getColumns().add(keggidcol); TableColumn<GeneGroup, String> keggpathcol = new TableColumn("Kegg pathway"); keggpathcol.setCellValueFactory(new PropertyValueFactory<>("keggPathway")); table.getColumns().add(keggpathcol); TableColumn<GeneGroup, String> kocol = new TableColumn("KO"); kocol.setCellValueFactory(new PropertyValueFactory<>("ko")); table.getColumns().add(kocol); TableColumn<GeneGroup, String> ksymbcol = new TableColumn("Ksymbol"); ksymbcol.setCellValueFactory(new PropertyValueFactory<>("ksymbol")); table.getColumns().add(ksymbcol); TableColumn<GeneGroup, String> symbcol = new TableColumn("Symbol"); symbcol.setCellValueFactory(new PropertyValueFactory<>("symbol")); table.getColumns().add(symbcol); TableColumn<GeneGroup, String> konamecol = new TableColumn("KO name"); konamecol.setCellValueFactory(new PropertyValueFactory<>("koname")); table.getColumns().add(konamecol); TableColumn<GeneGroup, String> pbidcol = new TableColumn("Pbid"); pbidcol.setCellValueFactory(new PropertyValueFactory<>("pbid")); table.getColumns().add(pbidcol); TableColumn<GeneGroup, String> eccol = new TableColumn("Ec"); eccol.setCellValueFactory(new PropertyValueFactory<>("ec")); table.getColumns().add(eccol); TableColumn<GeneGroup, String> cognamecol = new TableColumn("Cog name"); cognamecol.setCellValueFactory(new PropertyValueFactory<>("cogname")); table.getColumns().add(cognamecol); TableColumn<GeneGroup, String> cogcol = new TableColumn("Cog"); cogcol.setCellValueFactory(new PropertyValueFactory<>("cog")); table.getColumns().add(cogcol); TableColumn<GeneGroup, String> cogannocol = new TableColumn("Cog annotation"); cogannocol.setCellValueFactory(new PropertyValueFactory<>("coganno")); table.getColumns().add(cogannocol); TableColumn<GeneGroup, String> cogsymbcol = new TableColumn("Cog symbol"); cogsymbcol.setCellValueFactory(new PropertyValueFactory<>("cogsymbol")); table.getColumns().add(cogsymbcol); TableColumn<GeneGroup, String> cazycol = new TableColumn("Cazy"); cazycol.setCellValueFactory(new PropertyValueFactory<>("cazy")); table.getColumns().add(cazycol); TableColumn<GeneGroup, String> prescol = new TableColumn("Present in"); prescol.setCellValueFactory(new PropertyValueFactory<>("presentin")); table.getColumns().add(prescol); TableColumn<GeneGroup, Integer> groupindcol = new TableColumn("Group index"); groupindcol.setCellValueFactory(new PropertyValueFactory<GeneGroup, Integer>("groupIndex")); table.getColumns().add(groupindcol); TableColumn<GeneGroup, Integer> groupcovcol = new TableColumn("Group coverage"); groupcovcol.setCellValueFactory(new PropertyValueFactory<GeneGroup, Integer>("groupCoverage")); table.getColumns().add(groupcovcol); TableColumn<GeneGroup, Integer> groupsizecol = new TableColumn("Group size"); groupsizecol.setCellValueFactory(new PropertyValueFactory<GeneGroup, Integer>("groupGeneCount")); table.getColumns().add(groupsizecol); TableColumn<GeneGroup, String> locprefcol = new TableColumn("Loc pref"); locprefcol.setCellValueFactory(new PropertyValueFactory<>("locpref")); table.getColumns().add(locprefcol); TableColumn<GeneGroup, String> avgcpcol = new TableColumn("Avg GC%"); avgcpcol.setCellValueFactory(new PropertyValueFactory<>("avggcp")); table.getColumns().add(avgcpcol); TableColumn<GeneGroup, String> numloccol = new TableColumn("#Loc"); numloccol.setCellValueFactory(new PropertyValueFactory<>("numloc")); table.getColumns().add(numloccol); TableColumn<GeneGroup, String> numlocgroupcol = new TableColumn("#Loc group"); numlocgroupcol.setCellValueFactory(new PropertyValueFactory<>("numlocgroup")); table.getColumns().add(numlocgroupcol); TableColumn<GeneGroup, ShareNum> sharenumcol = new TableColumn("Sharing number"); sharenumcol.setCellValueFactory(new PropertyValueFactory<>("sharingNumber")); table.getColumns().add(sharenumcol); TableColumn<GeneGroup, String> maxcyccol = new TableColumn("Max cyc"); maxcyccol.setCellValueFactory(new PropertyValueFactory<>("maxCyc")); table.getColumns().add(maxcyccol); TableColumn<Gene, String> gnamedesccol = new TableColumn("Desc"); gnamedesccol.setCellValueFactory(new PropertyValueFactory<>("name")); gtable.getColumns().add(gnamedesccol); TableColumn<Gene, String> gorigincol = new TableColumn("Origin"); gorigincol.setCellValueFactory(new PropertyValueFactory<>("origin")); gtable.getColumns().add(gorigincol); TableColumn<Gene, String> ggeneidcol = new TableColumn("Genid"); ggeneidcol.setCellValueFactory(new PropertyValueFactory<>("genid")); gtable.getColumns().add(ggeneidcol); TableColumn<Gene, String> grefidcol = new TableColumn("Refid"); grefidcol.setCellValueFactory(new PropertyValueFactory<>("refid")); gtable.getColumns().add(grefidcol); TableColumn<Gene, String> gunidcol = new TableColumn("Unid"); gunidcol.setCellValueFactory(new PropertyValueFactory<>("unid")); gtable.getColumns().add(gunidcol); TableColumn<Gene, String> gkeggidcol = new TableColumn("Keggid"); gkeggidcol.setCellValueFactory(new PropertyValueFactory<>("keggid")); gtable.getColumns().add(gkeggidcol); TableColumn<Gene, String> gkeggpathcol = new TableColumn("Kegg pathway"); gkeggpathcol.setCellValueFactory(new PropertyValueFactory<>("keggPathway")); gtable.getColumns().add(gkeggpathcol); TableColumn<Gene, String> gkocol = new TableColumn("KO"); gkocol.setCellValueFactory(new PropertyValueFactory<>("ko")); gtable.getColumns().add(gkocol); TableColumn<Gene, String> gksymbcol = new TableColumn("Ksymbol"); gksymbcol.setCellValueFactory(new PropertyValueFactory<>("ksymbol")); gtable.getColumns().add(gksymbcol); TableColumn<Gene, String> gsymbcol = new TableColumn("Symbol"); gsymbcol.setCellValueFactory(new PropertyValueFactory<>("symbol")); gtable.getColumns().add(gsymbcol); TableColumn<Gene, String> gkonamecol = new TableColumn("KO name"); gkonamecol.setCellValueFactory(new PropertyValueFactory<>("koname")); gtable.getColumns().add(gkonamecol); TableColumn<Gene, String> gpbidcol = new TableColumn("Pbid"); gpbidcol.setCellValueFactory(new PropertyValueFactory<>("pbid")); gtable.getColumns().add(gpbidcol); TableColumn<Gene, String> geccol = new TableColumn("Ec"); geccol.setCellValueFactory(new PropertyValueFactory<>("ec")); gtable.getColumns().add(geccol); TableColumn<Gene, String> gcognamecol = new TableColumn("Cog name"); gcognamecol.setCellValueFactory(new PropertyValueFactory<>("cogname")); gtable.getColumns().add(gcognamecol); TableColumn<Gene, String> gcogcol = new TableColumn("Cog"); gcogcol.setCellValueFactory(new PropertyValueFactory<>("cog")); gtable.getColumns().add(gcogcol); TableColumn<Gene, String> gcogannocol = new TableColumn("Cog annotation"); gcogannocol.setCellValueFactory(new PropertyValueFactory<>("coganno")); gtable.getColumns().add(gcogannocol); TableColumn<Gene, String> gcogsymbcol = new TableColumn("Cog symbol"); gcogsymbcol.setCellValueFactory(new PropertyValueFactory<>("cogsymbol")); gtable.getColumns().add(gcogsymbcol); TableColumn<Gene, String> gcazycol = new TableColumn("Cazy"); gcazycol.setCellValueFactory(new PropertyValueFactory<>("cazy")); gtable.getColumns().add(gcazycol); TableColumn<Gene, String> gprescol = new TableColumn("Present in"); gprescol.setCellValueFactory(new PropertyValueFactory<>("presentin")); gtable.getColumns().add(gprescol); TableColumn<Gene, Integer> ggroupindcol = new TableColumn("Group index"); ggroupindcol.setCellValueFactory(new PropertyValueFactory<>("groupIndex")); gtable.getColumns().add(ggroupindcol); TableColumn<Gene, Integer> ggroupcovcol = new TableColumn("Group coverage"); ggroupcovcol.setCellValueFactory(new PropertyValueFactory<>("groupCoverage")); gtable.getColumns().add(ggroupcovcol); TableColumn<Gene, Integer> ggroupsizecol = new TableColumn("Group size"); ggroupsizecol.setCellValueFactory(new PropertyValueFactory<>("groupGeneCount")); gtable.getColumns().add(ggroupsizecol); TableColumn<Gene, String> glocprefcol = new TableColumn("Loc pref"); glocprefcol.setCellValueFactory(new PropertyValueFactory<>("locpref")); gtable.getColumns().add(glocprefcol); TableColumn<Gene, String> gavgcpcol = new TableColumn("Avg GC%"); gavgcpcol.setCellValueFactory(new PropertyValueFactory<>("avggcp")); gtable.getColumns().add(gavgcpcol); TableColumn<Gene, String> gnumloccol = new TableColumn("#Loc"); gnumloccol.setCellValueFactory(new PropertyValueFactory<>("numloc")); gtable.getColumns().add(gnumloccol); TableColumn<Gene, String> gnumlocgroupcol = new TableColumn("#Loc group"); gnumlocgroupcol.setCellValueFactory(new PropertyValueFactory<>("numlocgroup")); gtable.getColumns().add(gnumlocgroupcol); TableColumn<Gene, ShareNum> gsharenumcol = new TableColumn("Sharing number"); gsharenumcol.setCellValueFactory(new PropertyValueFactory<>("sharingNumber")); gtable.getColumns().add(gsharenumcol); TableColumn<Gene, String> gmaxcyccol = new TableColumn("Max cyc"); gmaxcyccol.setCellValueFactory(new PropertyValueFactory<>("maxCyc")); gtable.getColumns().add(gmaxcyccol); /*if( upper != null ) { SwingUtilities.invokeLater( new Runnable() { public void run() { //upper.setContent( botcomp ); lower.setContent( topcomp ); } }); } else { splitpane.setBottomComponent(botcomp); splitpane.setTopComponent(topcomp); } groupModel = new TableModel() { @Override public int getRowCount() { return geneset.allgenegroups == null ? 0 : geneset.allgenegroups.size(); } @Override public int getColumnCount() { return 32+geneset.specList.size(); } @Override public String getColumnName(int columnIndex) { if (columnIndex == 0) { return "Desc"; } else if (columnIndex == 1) { return "Origin"; } else if (columnIndex == 2) { return "Genid"; } else if (columnIndex == 3) { return "Refid"; } else if (columnIndex == 4) { return "Unid"; } else if (columnIndex == 5) { return "Keggid"; } else if (columnIndex == 6) { return "Kegg pathway"; } else if (columnIndex == 7) { return "KO"; } else if (columnIndex == 8) { return "KSymbol"; } else if (columnIndex == 9) { return "Symbol"; } else if (columnIndex == 10) { return "KO name"; } else if (columnIndex == 11) { return "Pdbid"; } else if (columnIndex == 12) { return "EC"; } else if (columnIndex == 13) { return "Cog name"; } else if (columnIndex == 14) { return "Cog"; } else if (columnIndex == 15) { return "Cog annotation"; } else if (columnIndex == 16) { return "Cog symbol"; } else if (columnIndex == 17) { return "Cazy"; } else if (columnIndex == 18) { return "Present in"; } else if (columnIndex == 19) { return "Group index"; } else if (columnIndex == 20) { return "Group coverage"; } else if (columnIndex == 21) { return "Group size"; } else if (columnIndex == 22) { return "Locprev"; } else if (columnIndex == 23) { return "Avg GC%"; } else if (columnIndex == 24) { return "# of locus"; } else if (columnIndex == 25) { return "# of loc in group"; } else if (columnIndex == 26) { return "max length"; } else if (columnIndex == 27) { return "sharing number"; } else if (columnIndex == 28) { return "# Cyc"; } else if (columnIndex == 29) { return "16S Corr"; } else if (columnIndex == 30) { return "SingalP"; } else if (columnIndex == 31) { return "TransM"; } else { String spec = geneset.specList.get( columnIndex - 32 ); if( spec != null ) { if( spec.toLowerCase().contains("thermus") ) { int i = spec.indexOf('_'); return spec.substring(i+1, spec.length()); } else return spec; } return ""; } /* else if (columnIndex == 19) { return "T.tSG0"; } else if (columnIndex == 20) { return "T.tJL18"; } else if (columnIndex == 21) { return "T.tHB8"; } else if (columnIndex == 22) { return "T.tHB27"; } else if (columnIndex == 23) { return "T.scotoSA01"; } else if (columnIndex == 24) { return "T.aqua"; } else if (columnIndex == 25) { return "T.eggert"; } else if (columnIndex == 26) { return "T.island"; } else if (columnIndex == 27) { return "T.antan"; } else if (columnIndex == 28) { return "T.scoto346"; } else if (columnIndex == 29) { return "T.scoto1572"; } else if (columnIndex == 30) { return "T.scoto252"; } else if (columnIndex == 31) { return "T.scoto2101"; } else if (columnIndex == 32) { return "T.scoto2127"; } else if (columnIndex == 33) { return "T.scoto4063"; } else if (columnIndex == 34) { return "T.oshimai"; } else if (columnIndex == 35) { return "T.brockianus"; } else if (columnIndex == 36) { return "T.filiformis"; } else if (columnIndex == 37) { return "T.igniterrae"; } else if (columnIndex == 38) { return "T.kawarayensis"; } else if (columnIndex == 39) { return "T.arciformis"; } else if (columnIndex == 40) { return "T.spCCB"; } else if (columnIndex == 41) { return "T.spRLM"; } else if (columnIndex == 42) { return "T.oshimaiJL2"; } else if (columnIndex == 43) { return "MT.silvianus"; } else if (columnIndex == 44) { return "MT.ruber"; } else if (columnIndex == 45) { return "M.hydro"; } else if (columnIndex == 46) { return "O.profu"; }* //return ""; } @Override public Class<?> getColumnClass(int columnIndex) { if( columnIndex == 19 || columnIndex == 20 || columnIndex == 28 ) return Double.class; else if(columnIndex == 10 || (columnIndex >= 17 && columnIndex <= 28) ) return Integer.class; else if (columnIndex >= 32) return Teg.class; return String.class; } @Override public boolean isCellEditable(int rowIndex, int columnIndex) { return false; } @Override public Object getValueAt(int rowIndex, int columnIndex) { GeneGroup gg = geneset.allgenegroups.get(rowIndex); if (columnIndex == 0) { return gg.getCommonName(); } else if (columnIndex == 1) { return gg.getCommonOrigin(); } else if (columnIndex == 2) { return null;//gene.genid; } else if (columnIndex == 3) { return gg.getCommonRefId(); } else if (columnIndex == 4) { return gg.getCommonUnId(); } else if (columnIndex == 5) { return gg.getKeggid(); } else if (columnIndex == 6) { return gg.getKeggPathway(); } else if (columnIndex == 7) { return gg.getCommonKO(); } else if (columnIndex == 8) { return gg.getCommonKSymbol(); } else if (columnIndex == 9) { return gg.getCommonSymbol(); //ko2name != null ? ko2name.get( gg.getCommonKO() ) : null; } else if (columnIndex == 10) { String ret = geneset.ko2name != null ? geneset.ko2name.get( gg.getCommonKO() ) : null; if( ret == null ) { String symbol = gg.getCommonSymbol(); if( symbol != null ) { if( symbol.length() <= 5 ) ret = symbol; } } return ret; } else if (columnIndex == 11) { return null;//gene.pdbid; } else if (columnIndex == 12) { return gg.getCommonEc(); } else if (columnIndex == 13) { Cog cog = gg.getCommonCog( geneset.cogmap ); if( cog != null ) { if( cog.name == null ) cog.name = geneset.cogidmap.get( cog.id ); return cog.name; } return null; } else if (columnIndex == 14) { Cog cog = gg.getCommonCog( geneset.cogmap ); return cog != null ? cog.id : null; } else if (columnIndex == 15) { Cog cog = gg.getCommonCog( geneset.cogmap ); return cog != null ? cog.annotation : null; } else if (columnIndex == 16) { Cog cog = gg.getCommonCog( geneset.cogmap ); return cog != null ? cog.genesymbol : null; } else if (columnIndex == 17) { return gg.getCommonCazy( geneset.cazymap ); } else if (columnIndex == 18) { return gg.getSpecies().size(); } else if (columnIndex == 19) { return gg.groupIndex; } else if (columnIndex == 20) { return gg.getGroupCoverage(); } else if (columnIndex == 21) { return gg.getGroupGeneCount(); } else if (columnIndex == 22) { return null;//gene.proximityGroupPreservation; } else if (columnIndex == 23) { return gg.getAvgGCPerc(); } else if (columnIndex == 24) { return gg.genes.size(); } else if (columnIndex == 25) { return gg.getGroupCount(); } else if (columnIndex == 26) { return gg.getMaxLength(); } else if (columnIndex == 27) { return geneset.specset.get( gg.getSpecies() ); } else if (columnIndex == 28) { return gg.getMaxCyc(); } else if (columnIndex == 29) { return gg.getGroupCoverage() == 39 && gg.getGroupCount() == 39 ? 0 : -1; } else if (columnIndex == 30) { return gg.getCommonSignalP(); } else if (columnIndex == 31) { return gg.getCommonTransM(); } else { String spec = geneset.specList.get( columnIndex - 32 ); Teginfo ret = geneset.getGroupTes( gg, spec ); return ret; //return null; } //return columnIndex >= 11 ? null : ""; } @Override public void setValueAt(Object aValue, int rowIndex, int columnIndex) {} @Override public void addTableModelListener(TableModelListener l) {} @Override public void removeTableModelListener(TableModelListener l) {} }; defaultModel = new TableModel() { @Override public int getRowCount() { int gs = geneset.genelist.size(); return gs; } @Override public int getColumnCount() { return 26+geneset.specList.size(); } @Override public String getColumnName(int columnIndex) { if (columnIndex == 0) { return "Desc"; } else if (columnIndex == 1) { return "Origin"; } else if (columnIndex == 2) { return "Genid"; } else if (columnIndex == 3) { return "Refid"; } else if (columnIndex == 4) { return "Unid"; } else if (columnIndex == 5) { return "Keggid"; } else if (columnIndex == 6) { return "KOid"; } else if (columnIndex == 7) { return "KSymbol"; } else if (columnIndex == 8) { return "Symbol"; } else if (columnIndex == 9) { return "KOname"; } else if (columnIndex == 10) { return "Pdbid"; } else if (columnIndex == 11) { return "ecid"; } else if (columnIndex == 12) { return "COG"; } else if (columnIndex == 13) { return "COG name"; } else if (columnIndex == 14) { return "Present in"; } else if (columnIndex == 15) { return "Group index"; } else if (columnIndex == 16) { return "Group coverage"; } else if (columnIndex == 17) { return "Group size"; } else if (columnIndex == 18) { return "Locprev"; } else if (columnIndex == 19) { return "Avg GC%"; } else if (columnIndex == 20) { return "# of locus"; } else if (columnIndex == 21) { return "# of loc in group"; } else if (columnIndex == 22) { return "max length"; } else if (columnIndex == 23) { return "sharing number"; } else if (columnIndex == 24) { return "# Cyc"; } else if (columnIndex == 25) { return "16S Corr"; } else { return geneset.specList.get( columnIndex - 26 ); } /*else if (columnIndex == 19) { return "T.tSG0"; } else if (columnIndex == 20) { return "T.tJL18"; } else if (columnIndex == 21) { return "T.tHB8"; } else if (columnIndex == 22) { return "T.tHB27"; } else if (columnIndex == 23) { return "T.scotoSA01"; } else if (columnIndex == 24) { return "T.aqua"; } else if (columnIndex == 25) { return "T.eggert"; } else if (columnIndex == 26) { return "T.island"; } else if (columnIndex == 27) { return "T.antan"; } else if (columnIndex == 28) { return "T.scoto346"; } else if (columnIndex == 29) { return "T.scoto1572"; } else if (columnIndex == 30) { return "T.scoto252"; } else if (columnIndex == 31) { return "T.scoto2101"; } else if (columnIndex == 32) { return "T.scoto2127"; } else if (columnIndex == 33) { return "T.scoto4063"; } else if (columnIndex == 34) { return "T.oshimai"; } else if (columnIndex == 35) { return "T.brockianus"; } else if (columnIndex == 36) { return "T.filiformis"; } else if (columnIndex == 37) { return "T.igniterrae"; } else if (columnIndex == 38) { return "T.kawarayensis"; } else if (columnIndex == 39) { return "T.arciformis"; } else if (columnIndex == 40) { return "T.spCCB"; } else if (columnIndex == 41) { return "T.spRLM"; } else if (columnIndex == 42) { return "T.oshimaiJL2"; } else if (columnIndex == 43) { return "MT.silvianus"; } else if (columnIndex == 44) { return "MT.ruber"; } else if (columnIndex == 45) { return "M.hydro"; } else if (columnIndex == 46) { return "O.profu"; }* } @Override public Class<?> getColumnClass(int columnIndex) { if( columnIndex == 16 || columnIndex == 19 || columnIndex == 25 ) return Double.class; else if(columnIndex >= 13 && columnIndex <= 24) return Integer.class; else if (columnIndex >= 26) return Teg.class; return String.class; } @Override public boolean isCellEditable(int rowIndex, int columnIndex) { return false; } @Override public Object getValueAt(int rowIndex, int columnIndex) { Gene gene = geneset.genelist.get(rowIndex); if (columnIndex == 0) { GeneGroup gg = gene.getGeneGroup(); return gg != null ? gene.getGeneGroup().getCommonName() : null; } else if (columnIndex == 1) { return gene.getSpecies(); } else if (columnIndex == 2) { return gene.genid; } else if (columnIndex == 3) { return gene.refid; } else if (columnIndex == 4) { return gene.uniid; } else if (columnIndex == 5) { return gene.keggid; } else if (columnIndex == 6) { GeneGroup gg = gene.getGeneGroup(); return gg != null ? gg.getCommonKO() : null; } else if (columnIndex == 7) { GeneGroup gg = gene.getGeneGroup(); return gg != null ? gg.getCommonKSymbol() : null; } else if (columnIndex == 8) { GeneGroup gg = gene.getGeneGroup(); return gg != null ? gg.getCommonSymbol() : null; //gene.symbol } else if (columnIndex == 9) { GeneGroup gg = gene.getGeneGroup(); return gg != null ? gg.getCommonKOName( geneset.ko2name ) : null; } else if (columnIndex == 10) { return gene.pdbid; } else if (columnIndex == 11) { return gene.ecid; } else if (columnIndex == 12) { Cog cog = gene.getGeneGroup() != null ? gene.getGeneGroup().getCommonCog( geneset.cogmap ) : null; if( cog != null ) return cog.id; return null; } else if (columnIndex == 13) { Cog cog = gene.getGeneGroup() != null ? gene.getGeneGroup().getCommonCog( geneset.cogmap ) : null; if( cog != null ) return cog.name; return null; } else if (columnIndex == 14) { return gene.getGeneGroup().getSpecies().size(); } else if (columnIndex == 15) { return gene.getGroupIndex(); } else if (columnIndex == 16) { return gene.getGroupCoverage(); } else if (columnIndex == 17) { return gene.getGroupGenCount(); } else if (columnIndex == 18) { return gene.proximityGroupPreservation; } else if (columnIndex == 19) { return gene.getGCPerc(); } else if (columnIndex == 20) { /*int val = 0; for (String str : gene.species.keySet()) { val += gene.species.get(str).tset.size(); }* return 1; } else if (columnIndex == 21) { return gene.getGroupCount(); } else if (columnIndex == 22) { return gene.getMaxLength(); } else if (columnIndex == 23) { GeneGroup gg = gene.getGeneGroup(); if( gg != null && gg.getSpecies() != null ) { return geneset.specset.get( gg.getSpecies() ); } return null; } else if (columnIndex == 24) { gene.getMaxCyc(); } else if (columnIndex == 25) { return gene.getGroupCoverage() == 35 && gene.getGroupCount() == 35 ? gene.corr16s : -1; } else { /*String spec = specList.get( columnIndex-26 ); /*if( spec.contains("timidus") ) { System.err.println(); }* //Teginfo set = gene.species.equals(spec) ? gene.teginfo : null; if( gene.getSpecies().equals( spec ) ) { return gene.tegeval; } else { return gene.getGeneGroup().species.get( spec ); }* return null; } return columnIndex >= 17 ? null : ""; } @Override public void setValueAt(Object aValue, int rowIndex, int columnIndex) {} @Override public void addTableModelListener(TableModelListener l) {} @Override public void removeTableModelListener(TableModelListener l) {} }; table.setModel( groupModel );*/ //table.setModel( defaultModel ); /* * Comparator<Tegeval> wrapMe = new Comparator<Tegeval>() { public int * compare(Tegeval o1, Tegeval o2) { return o1.compareTo(o2); } }; * DefaultRowSorter<TableModel, Integer> rowsorter = * (DefaultRowSorter<TableModel,Integer>)table.getRowSorter(); for( int * i = 10; i < 23; i++ ) { rowsorter.setComparator(i, * NullComparators.atEnd(wrapMe)); } */ /*table.getRowSorter().addRowSorterListener( new RowSorterListener() { @Override public void sorterChanged(RowSorterEvent e) { for (String cstr : geneset.contigmap.keySet()) { Sequence c = geneset.contigmap.get(cstr); //c.count = 0; c.loc = 0.0; } if( table.getModel() == defaultModel ) { for (Gene g : geneset.genelist) { Tegeval tv = g.tegeval; // int first = tv.cont.indexOf('_'); // int sec = tv.cont.indexOf('_',first+1); Sequence cont = tv.getContshort(); // tv.cont.substring(0,sec); if( cont != null && geneset.contigmap.containsKey(cont.getName()) ) { Sequence c = geneset.contigmap.get(cont.getName()); //c.count++; int val = table.convertRowIndexToView(g.index); c.loc += (double) val; } } } for( JSplitPane gsplitpane : splitpaneList ) { gsplitpane.repaint(); } } });*/ ftable = upper; ftable.getSelectionModel().setSelectionMode(SelectionMode.MULTIPLE); /*ftable = new JTable() { public String getToolTipText(MouseEvent me) { Point p = me.getPoint(); int r = rowAtPoint(p); int c = columnAtPoint(p); if (r >= 0 && r < super.getRowCount()) { Object ret = super.getValueAt(r, c); if (ret != null) { return ret.toString(); // super.getToolTipText( me ); } } return ""; } };*/ ContextMenu fpopup = new ContextMenu(); MenuItem amigo = new MenuItem("Amigo lookup"); amigo.setOnAction(e -> { String go = ftable.getSelectionModel().getSelectedItem().getGo(); try { // GeneSetHead.this.getAppletContext(). Desktop.getDesktop() .browse(new URI("http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=" + go)); } catch (IOException e1) { e1.printStackTrace(); } catch (URISyntaxException e1) { e1.printStackTrace(); } }); fpopup.getItems().add(amigo); MenuItem keggl = new MenuItem("KEGG lookup"); keggl.setOnAction(e -> { String kegg = ftable.getSelectionModel().getSelectedItem().getKegg(); try { Desktop.getDesktop().browse(new URI("http://www.genome.jp/dbget-bin/www_bget?rn:" + kegg)); } catch (IOException e1) { e1.printStackTrace(); } catch (URISyntaxException e1) { e1.printStackTrace(); } }); fpopup.getItems().add(keggl); MenuItem ecl = new MenuItem("EC lookup"); ecl.setOnAction(e -> { String ec = ftable.getSelectionModel().getSelectedItem().getEc(); try { Desktop.getDesktop().browse(new URI("http://enzyme.expasy.org/EC/" + ec)); } catch (IOException e1) { e1.printStackTrace(); } catch (URISyntaxException e1) { e1.printStackTrace(); } }); fpopup.getItems().add(ecl); fpopup.getItems().add(new SeparatorMenuItem()); MenuItem excelreport = new MenuItem("Excel report"); excelreport.setOnAction(e -> { Workbook workbook = new XSSFWorkbook(); Sheet sheet = workbook.createSheet("enzyme"); int k = 0; for (Function f : ftable.getSelectionModel().getSelectedItems()) { //String ec = (String)ftable.getValueAt(r, 1); //String go = (String)ftable.getValueAt(r, 0); //int i = ftable.getSelectionModel().convertRowIndexToModel(r); //Function f = geneset.funclist.get(i); for (GeneGroup gg : f.getGeneGroups()) { for (String spec : gg.getSpecies()) { Teginfo ti = gg.getGenes(spec); Row row = sheet.createRow(k++); Cell ecell = row.createCell(0); ecell.setCellValue("EC:" + f.getEc()); Cell ncell = row.createCell(1); ncell.setCellValue(f.getName()); Cell spell = row.createCell(2); spell.setCellValue(spec); Cell seqcell = row.createCell(3); seqcell.setCellValue(ti.tset.size()); } /*for( Gene g :gg.genes ) { Row row = sheet.createRow(k++); Cell ecell = row.createCell(0); ecell.setCellValue( "EC:"+f.ec ); Cell ncell = row.createCell(1); ncell.setCellValue( f.name ); Cell spell = row.createCell(2); spell.setCellValue( g.getSpecies() ); Cell seqcell = row.createCell(3); seqcell.setCellValue( g.tegeval.getAlignedSequence().toString() ); }*/ } sheet.createRow(k++); } try { Path tempfile = Files.createTempFile("enzyme", ".xlsx"); OutputStream os = Files.newOutputStream(tempfile); workbook.write(os); os.close(); Desktop.getDesktop().open(tempfile.toFile()); } catch (FileNotFoundException e1) { e1.printStackTrace(); } catch (IOException e1) { e1.printStackTrace(); } }); fpopup.getItems().add(excelreport); ftable.setContextMenu(fpopup); ContextMenu popup = new ContextMenu(); MenuItem splitaction = new MenuItem("Split"); splitaction.setOnAction(e -> { Dialog<Set<GeneGroup>> dialog = new Dialog<>(); dialog.setResizable(true); GridPane grid = new GridPane(); grid.setHgap(10); grid.setVgap(10); grid.setPadding(new Insets(20, 20, 10, 10)); TextField len = new TextField(); len.setPromptText("0.5"); TextField id = new TextField(); id.setPromptText("0.5"); grid.add(new Label("%Length:"), 0, 0); grid.add(len, 1, 0); grid.add(new Label("%Identity:"), 0, 1); grid.add(id, 1, 1); final ListView<GeneGroup> list = new ListView<>(); list.setPrefWidth(400); grid.add(list, 0, 2, 2, 1); final GeneGroup gg = table.getSelectionModel().getSelectedItem(); list.setItems(FXCollections.singletonObservableList(gg)); Label groupsize = new Label("" + gg.genes.size()); grid.add(groupsize, 0, 3, 2, 1); len.textProperty().addListener((observable, oldValue, newValue) -> { if (!newValue.equals(oldValue)) { double d = 0; try { d = Double.parseDouble(newValue); } catch (Exception ex) { } if (d > 0) { Set<GeneGroup> ggmap = new HashSet<>(); Map<String, Integer> blosumMap = JavaFasta.getBlosumMap(false); for (Gene gene : gg.genes) { if (ggmap.stream().flatMap(f -> f.genes.stream()).noneMatch(p -> gene == p)) { Set<Gene> ggset = new HashSet<>(); Sequence seq1 = gene.tegeval.getAlignedSequence(); for (Gene cgene : gg.genes) { Sequence seq2 = cgene.tegeval.getAlignedSequence(); int[] tscore = GeneCompare.blosumValue(seq1, seq1, seq2, blosumMap); int sscore = GeneCompare.blosumValue(seq1, seq2, blosumMap); double dval = (double) (sscore - tscore[1]) / (double) (tscore[0] - tscore[1]); if (dval > d) { ggset.add(cgene); } } System.err.println(ggset.size()); Set<GeneGroup> osubgg = ggmap.stream().filter(f -> { Set<Gene> gs = new HashSet<>(ggset); gs.retainAll(f.genes); return gs.size() > 0; }).collect(Collectors.toSet()); GeneGroup subgg; if (osubgg.size() > 0) { Iterator<GeneGroup> git = osubgg.iterator(); subgg = git.next(); while (git.hasNext()) { GeneGroup remgg = git.next(); subgg.addGenes(remgg.genes); ggmap.remove(remgg); } } else { subgg = new GeneGroup(); subgg.setCogMap(gg.getCogMap()); subgg.setKonameMap(gg.getKonameMap()); subgg.setSpecSet(gg.getSpecSet()); ggmap.add(subgg); } subgg.addGenes(ggset); } } Set<GeneGroup> sgg = ggmap.stream().collect(Collectors.toSet()); List<GeneGroup> lgg = new ArrayList(sgg); list.setItems(FXCollections.observableList(lgg)); dialog.setResultConverter(param -> sgg); } } }); dialog.getDialogPane().setContent(grid); dialog.getDialogPane().getButtonTypes().add(ButtonType.OK); dialog.getDialogPane().getButtonTypes().add(ButtonType.CANCEL); Optional<Set<GeneGroup>> ogg = dialog.showAndWait(); ogg.ifPresent(c -> { geneset.allgenegroups.remove(gg); geneset.allgenegroups.addAll(c); Map<String, String> env = new HashMap<>(); env.put("create", "true"); try { geneset.zipfilesystem = FileSystems.newFileSystem(geneset.zipuri, env); for (Path root : geneset.zipfilesystem.getRootDirectories()) { Files.walk(root).filter(f -> f.toString().startsWith("/aligned")) .filter(f -> f.toString().endsWith(".aa")).filter(f -> { String filename = f.getFileName().toString(); return gg.genes.stream().anyMatch(g -> { String fnid = filename.substring(0, filename.length() - 3); return g.name.equals(fnid); }); }).forEach(p -> { try { Files.deleteIfExists(p); } catch (IOException e1) { e1.printStackTrace(); } }); /*for( Gene g : gg.genes ) { if( g.keggpathway != null ) { String sub = g.keggpathway.substring(0,3); Path subf = root.resolve(sub); if( Files.exists(subf) ) { String[] split = g.keggpathway.split(" "); for( String s : split ) { Path pimg = subf.resolve(s+".png"); if( Files.exists(pimg) ) { showKeggPathway( sub, pimg ); } } } } }*/ final Path p = root.resolve("/aligned"); c.stream().forEach(fgg -> { Path np = p.resolve(fgg.genes.iterator().next().getName()); try { Writer w = Files.newBufferedWriter(np); fgg.getFasta(w, false); w.close(); } catch (IOException e1) { e1.printStackTrace(); } }); break; } geneset.zipfilesystem.close(); } catch (Exception ex) { ex.printStackTrace(); } }); }); popup.getItems().add(splitaction); MenuItem joinaction = new MenuItem("Join"); popup.getItems().add(joinaction); popup.getItems().add(new SeparatorMenuItem()); MenuItem showkegg = new MenuItem("Show KEGG pathway"); showkegg.setOnAction(e -> { GeneGroup gg = table.getSelectionModel().getSelectedItem(); Map<String, String> env = new HashMap<>(); env.put("create", "true"); /*String uristr = "jar:" + geneset.zippath.toUri(); URI zipuri = URI.create( uristr /*.replace("file://", "file:")* ); final List<Path> lbi = new ArrayList<>();*/ boolean shown = false; try { geneset.zipfilesystem = FileSystems.newFileSystem(geneset.zipuri, env); for (Path root : geneset.zipfilesystem.getRootDirectories()) { for (Gene g : gg.genes) { if (g.keggpathway != null) { String sub = g.keggpathway.substring(0, 3); Path subf = root.resolve(sub); if (Files.exists(subf)) { String[] split = g.keggpathway.split(" "); for (String s : split) { Path pimg = subf.resolve(s + ".png"); if (Files.exists(pimg)) { showKeggPathway(sub, pimg); shown = true; break; } } } } } break; } geneset.zipfilesystem.close(); } catch (Exception ex) { ex.printStackTrace(); } if (!shown) { for (Gene g : gg.genes) { if (g.keggpathway != null) { String[] keggsplit = g.keggpathway.split(";"); Arrays.stream(keggsplit).map(s -> s.split(":")[0]).findFirst().ifPresent(c -> { try { Desktop.getDesktop().browse( URI.create("http://www.genome.jp/dbget-bin/www_bget?map" + c.substring(2))); } catch (IOException e1) { e1.printStackTrace(); } }); } } } }); popup.getItems().add(showkegg); MenuItem plasmid = new MenuItem("Plasmid"); plasmid.setOnAction(e -> { Gene g = gtable.getSelectionModel().getSelectedItem(); Sequence contig = g.tegeval.getContshort(); String contigstr = contig.toString(); contig.plasmid = !geneset.plasmids.contains(contigstr); if (contig.plasmid) geneset.plasmids.add(contigstr); else geneset.plasmids.remove(contigstr); 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); //fs = FileSystems.newFileSystem( uri, env ); //FileSystem fs = FileSystems.newFileSystem(uri, env); ByteArrayOutputStream baos = new ByteArrayOutputStream(); for (String contigname : geneset.plasmids) { baos.write((contigname + "\n").getBytes()); } Path nf = geneset.zipfilesystem.getPath("/plasmids.txt"); long bl = Files.copy(new ByteArrayInputStream(baos.toByteArray()), nf, StandardCopyOption.REPLACE_EXISTING); //System.err.println( "eeerm " + bl ); geneset.zipfilesystem.close(); /*Writer writer = Files.newBufferedWriter(nf, StandardCharsets.UTF_8, StandardOpenOption.CREATE); for( String phage : phageset ) { writer.write( phage + "\n" ); } writer.close();*/ //writer.write("hello"); } catch (IOException e1) { e1.printStackTrace(); } }); popup.getItems().add(plasmid); MenuItem designate = new MenuItem("Designate"); designate.setOnAction(e -> { SwingUtilities.invokeLater(() -> { JComboBox<String> descombo = new JComboBox<>( geneset.deset.toArray(new String[geneset.deset.size()])); descombo.setEditable(true); JOptionPane.showMessageDialog(GeneSetHead.this, descombo); String val = descombo.getSelectedItem().toString(); geneset.deset.add(val); for (Gene g : gtable.getSelectionModel().getSelectedItems()) { g.tegeval.designation = val; if (g.id != null) { geneset.designations.put(g.id, val); } else { System.err.println(g.refid); } //ta.append( g.tegeval.id + "\n" ); } 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); //fs = FileSystems.newFileSystem( uri, env ); //FileSystem fs = FileSystems.newFileSystem(uri, env); ByteArrayOutputStream baos = new ByteArrayOutputStream(); for (String geneid : geneset.designations.keySet()) { String design = geneset.designations.get(geneid); baos.write((geneid + "\t" + design + "\n").getBytes()); } Path nf = geneset.zipfilesystem.getPath("/designations.txt"); long bl = Files.copy(new ByteArrayInputStream(baos.toByteArray()), nf, StandardCopyOption.REPLACE_EXISTING); //System.err.println( "eeerm " + bl ); geneset.zipfilesystem.close(); /*Writer writer = Files.newBufferedWriter(nf, StandardCharsets.UTF_8, StandardOpenOption.CREATE); for( String phage : phageset ) { writer.write( phage + "\n" ); } writer.close();*/ //writer.write("hello"); } catch (IOException e1) { e1.printStackTrace(); } /*JFrame frame = new JFrame("Ids"); frame.setDefaultCloseOperation( JFrame.DISPOSE_ON_CLOSE ); frame.setSize(800, 600); JTextArea ta = new JTextArea(); JScrollPane sp = new JScrollPane( ta ); frame.add( sp ); frame.setVisible( true );*/ }); }); popup.getItems().add(designate); MenuItem koname = new MenuItem("KO to name"); koname.setOnAction(e -> { Set<String> koids = new HashSet<>(); for (Gene g : geneset.genelist) { if (g.koid != null && g.koid.length() > 0 && !(geneset.ko2name != null && geneset.ko2name.containsKey(g.koid))) koids.add(g.koid); } try { Map<String, String> ko2name = new HashMap<>(); int cnt = 0; for (String koid : koids) { URL url = new URL("http://www.kegg.jp/dbget-bin/www_bget?ko:" + koid); InputStream is0 = url.openStream(); StringBuilder sb = new StringBuilder(); BufferedReader br0 = new BufferedReader(new InputStreamReader(is0)); String line0 = br0.readLine(); while (line0 != null) { sb.append(line0); line0 = br0.readLine(); } br0.close(); int i = sb.indexOf("<nobr>Name</nobr>"); if (i != -1) { int k = sb.indexOf(":hidden\">"); if (k != -1) { k = sb.indexOf(":hidden\">", k + 9); if (k != -1) { String koname0 = sb.substring(k + 9, sb.indexOf("<br>", k)); ko2name.put(koid, koname0); System.err.println(koid + "\t" + koname0); } } } System.err.println(ko2name.size() + " " + koids.size()); //if( cnt++ > 20 ) break; } FileWriter fw = new FileWriter("~ko2name.txt"); for (String koid : ko2name.keySet()) { fw.write(koid + "\t" + ko2name.get(koid) + "\n"); } fw.close(); } catch (IOException e1) { e1.printStackTrace(); } }); popup.getItems().add(koname); popup.getItems().add(new SeparatorMenuItem()); MenuItem genegainloss = new MenuItem("Gene gain/loss"); genegainloss.setOnAction(e -> { Map<Node, List<GeneGroup>> nodeGainMap = new HashMap<>(); Map<Node, List<GeneGroup>> nodeLossMap = new HashMap<>(); /*String treestr = ""; JFileChooser fc = new JFileChooser(); if( fc.showOpenDialog( applet ) == JFileChooser.APPROVE_OPTION ) { File file = fc.getSelectedFile(); try { byte[] bb = Files.readAllBytes( Paths.get(file.toURI()) ); treestr = new String( bb ); } catch (IOException e1) { e1.printStackTrace(); } }*/ Serifier serifier = getConcatenatedSequences(false, true); String tree = serifier.getFastTree(serifier.lseq, geneset.user, false); TreeUtil tu = new TreeUtil(); Node n = tu.parseTreeRecursive(tree, false); TableModel model = new TableModel() { @Override public int getRowCount() { return geneset.getSpecies().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.getSpecies().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); FlowLayout flowlayout = new FlowLayout(); JComponent c = new JComponent() { }; c.setLayout(flowlayout); c.add(scroll); JOptionPane.showMessageDialog(comp, c); List<String> rootgroup = new ArrayList<>(); int[] rr = table.getSelectedRows(); for (int r : rr) { rootgroup.add((String) table.getValueAt(r, 0)); } //String[] sobj = {"mt.ruber", "mt.silvanus", "o.profundus", "m.hydrothermalis"}; Node newnode = tu.getParent(n, new HashSet<>(rootgroup)); tu.rerootRecur(n, newnode); File f = new File("/home/sigmar/gain_list.txt"); try { PrintStream ps = new PrintStream(f); geneset.assignGain(newnode, nodeGainMap, ps); ps.close(); } catch (FileNotFoundException e1) { e1.printStackTrace(); } f = new File("/home/sigmar/loss_list.txt"); try { PrintStream ps = new PrintStream(f); geneset.assignLoss(newnode, nodeLossMap, ps); ps.close(); } catch (FileNotFoundException e1) { e1.printStackTrace(); } }); popup.getItems().add(genegainloss); MenuItem concattree = new MenuItem("Concatenate tree"); concattree.setOnAction(e -> { Serifier serifier = getConcatenatedSequences(false, true); boolean succ = true; if (comp instanceof Applet) { try { JSObject win = JSObject.getWindow((Applet) comp); StringWriter sw = new StringWriter(); serifier.writeFasta(serifier.lseq, sw, null); sw.close(); win.call("fasttree", new Object[] { sw.toString() }); } catch (NoSuchMethodError | Exception e1) { e1.printStackTrace(); succ = false; } } /*if( !succ ) { String tree = serifier.getFastTree(); if( cs.connections().size() > 0 ) { cs.sendToAll( tree ); } else if( Desktop.isDesktopSupported() ) { cs.message = tree; //String uristr = "http://webconnectron.appspot.com/Treedraw.html?tree="+URLEncoder.encode( tree, "UTF-8" ); String uristr = "http://webconnectron.appspot.com/Treedraw.html?ws=127.0.0.1:8887"; try { Desktop.getDesktop().browse( new URI(uristr) ); } catch (IOException | URISyntaxException e1) { e1.printStackTrace(); } } System.err.println( tree ); }*/ showAlignedSequences(comp, serifier); }); popup.getItems().add(concattree); MenuItem majocons = new MenuItem("Majority rule consensus"); majocons.setOnAction(e -> { Serifier serifier = new Serifier(); Set<GeneGroup> genegroups = new HashSet<GeneGroup>(); if (!isGeneview()) { genegroups.addAll(table.getSelectionModel().getSelectedItems()); } else { for (Gene gg : gtable.getSelectionModel().getSelectedItems()) { genegroups.add(gg.getGeneGroup()); } } TreeUtil treeutil = new TreeUtil(); Map<Set<String>, NodeSet> nmap = new HashMap<Set<String>, NodeSet>(); for (GeneGroup ggroup : genegroups) { //List<Sequence> seqlist = new ArrayList<Sequence>(); for (Tegeval tv : ggroup.getTegevals()) { String spec = tv.getContshort().getSpec(); Sequence seq = tv.getAlignedSequence(); //Sequence seq = new Sequence( spec, null ); //if( seqstr != null && seqstr.length() > 0 ) seq.append( seqstr ); serifier.addSequence(seq); } String tree = serifier.getFastTree(serifier.lseq, geneset.user, false); Node n = treeutil.parseTreeRecursive(tree, false); treeutil.setLoc(0); n.nodeCalcMap(nmap); } Node guidetree = null; /*********************************** Serifier serifier = getConcatenatedSequences(); String tree = serifier.getFastTree(); guidetree = treeutil.parseTreeRecursive( tree, false );*/ Node root = DataTable.majoRuleConsensus(treeutil, nmap, guidetree, false); String tree = root.toString(); if (geneset.cs.connections().size() > 0) { geneset.cs.sendToAll(tree); } else if (Desktop.isDesktopSupported()) { geneset.cs.message = tree; //String uristr = "http://webconnectron.appspot.com/Treedraw.html?tree="+URLEncoder.encode( tree, "UTF-8" ); String uristr = "http://webconnectron.appspot.com/Treedraw.html?ws=127.0.0.1:8887"; try { Desktop.getDesktop().browse(new URI(uristr)); } catch (IOException | URISyntaxException e1) { e1.printStackTrace(); } } }); popup.getItems().add(majocons); MenuItem addsim = new MenuItem("Add similar"); addsim.setOnAction(e -> { /*int r = table.getSelectedRow(); int c = table.getSelectedColumn(); Object o = table.getValueAt(r, c); if (c >= 18) { for (int i = 0; i < table.getRowCount(); i++) { Object no = table.getValueAt(i, c); if (no != null && !table.isRowSelected(i)) table.addRowSelectionInterval(i, i); } } else { for (int i = 0; i < table.getRowCount(); i++) { Object no = table.getValueAt(i, c); if (o.equals(no) && !table.isRowSelected(i)) table.addRowSelectionInterval(i, i); } }*/ }); popup.getItems().add(addsim); MenuItem selsim = new MenuItem("Select similar"); selsim.setOnAction(e -> { /*int r = table.getSelectedRow(); int c = table.getSelectedColumn(); Object o = table.getValueAt(r, c); table.removeRowSelectionInterval(0, table.getRowCount() - 1); if (c >= 18) { for (int i = 0; i < table.getRowCount(); i++) { Object no = table.getValueAt(i, c); if (no != null) table.addRowSelectionInterval(i, i); } } else { for (int i = 0; i < table.getRowCount(); i++) { Object no = table.getValueAt(i, c); if (o.equals(no)) table.addRowSelectionInterval(i, i); } }*/ }); popup.getItems().add(selsim); MenuItem tabtxt = new MenuItem("Table text"); tabtxt.setOnAction(e -> { /*JTextArea ta = new JTextArea(); ta.setDragEnabled(true); JScrollPane scrollpane = new JScrollPane(ta); StringBuilder sb = new StringBuilder(); int[] rr = table.getSelectedRows(); for (int r : rr) { for (int c = 0; c < table.getColumnCount() - 1; c++) { Object o = table.getValueAt(r, c); if (c > 18) { if (o != null) { String val = o.toString(); int k = val.indexOf(' '); sb.append(val.substring(0, k)); sb.append("\t" + val.substring(k + 1)); } else sb.append("\t"); } else { if (o != null) { sb.append(o.toString()); } } sb.append("\t"); } Object o = table.getValueAt(r, table.getColumnCount() - 1); if (o != null) { String val = o.toString(); int k = val.indexOf(' '); sb.append(val.substring(0, k)); sb.append("\t" + val.substring(k + 1)); } else sb.append("\t"); sb.append("\n"); } ta.setText(sb.toString()); JFrame frame = new JFrame(); frame.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE); frame.add(scrollpane); frame.setSize(400, 300); frame.setVisible(true);*/ }); popup.getItems().add(tabtxt); popup.getItems().add(new SeparatorMenuItem()); MenuItem ncbil = new MenuItem("NCBI lookup"); ncbil.setOnAction(e -> { /*int r = table.getSelectedRow(); if (r >= 0) { String ref = (String) table.getValueAt(r, 2); try { Desktop.getDesktop().browse(new URI("http://www.ncbi.nlm.nih.gov/gene?term=" + ref)); } catch (IOException e1) { e1.printStackTrace(); } catch (URISyntaxException e1) { e1.printStackTrace(); } }*/ }); popup.getItems().add(ncbil); table.setContextMenu(popup); gtable.setContextMenu(popup); TableColumn<Function, String> gocol = new TableColumn("GO"); gocol.setCellValueFactory(new PropertyValueFactory<>("go")); ftable.getColumns().add(gocol); TableColumn<Function, String> ecfcol = new TableColumn("EC"); ecfcol.setCellValueFactory(new PropertyValueFactory<>("ec")); ftable.getColumns().add(ecfcol); TableColumn<Function, String> metacyccol = new TableColumn("MetaCyc"); metacyccol.setCellValueFactory(new PropertyValueFactory<>("metacyc")); ftable.getColumns().add(metacyccol); TableColumn<Function, String> keggcol = new TableColumn("KEGG"); keggcol.setCellValueFactory(new PropertyValueFactory<>("kegg")); ftable.getColumns().add(keggcol); TableColumn<Function, String> funcovcol = new TableColumn("Funciton coverage"); funcovcol.setCellValueFactory(new PropertyValueFactory<>("speciesCount")); ftable.getColumns().add(funcovcol); TableColumn<Function, String> numprotcol = new TableColumn("Number of proteins"); numprotcol.setCellValueFactory(new PropertyValueFactory<>("groupCount")); ftable.getColumns().add(numprotcol); TableColumn<Function, String> namecol = new TableColumn("Name"); namecol.setCellValueFactory(new PropertyValueFactory<>("name")); ftable.getColumns().add(namecol); TableColumn<Function, String> namespacecol = new TableColumn("Namespace"); namespacecol.setCellValueFactory(new PropertyValueFactory<>("namespace")); ftable.getColumns().add(namespacecol); TableColumn<Function, String> desccol = new TableColumn("Desc"); desccol.setCellValueFactory(new PropertyValueFactory<>("desc")); ftable.getColumns().add(desccol); ftable.setColumnResizePolicy(TableView.CONSTRAINED_RESIZE_POLICY); //ftable.setAutoCreateRowSorter(true); /*ftablemodel = new TableModel() { @Override public int getRowCount() { return geneset.funclist.size(); } @Override public int getColumnCount() { return 9; } @Override public String getColumnName(int columnIndex) { if (columnIndex == 0) return "GO"; else if (columnIndex == 1) return "EC"; else if (columnIndex == 2) return "MetaCyc"; else if (columnIndex == 3) return "KEGG"; else if (columnIndex == 4) return "Function coverage"; else if (columnIndex == 5) return "Number of proteins"; else if (columnIndex == 6) return "Name"; else if (columnIndex == 7) return "Namespace"; else if (columnIndex == 8) return "Def"; return ""; } @Override public Class<?> getColumnClass(int columnIndex) { if( columnIndex == 4 || columnIndex == 5 ) return Integer.class; return String.class; } @Override public boolean isCellEditable(int rowIndex, int columnIndex) { return false; } @Override public Object getValueAt(int rowIndex, int columnIndex) { Function func = geneset.funclist.get(rowIndex); if( columnIndex == 0 ) return func.go; else if( columnIndex == 1 ) return func.ec; else if( columnIndex == 2 ) return func.metacyc; else if( columnIndex == 3 ) return func.kegg; else if( columnIndex == 4 ) return func.getSpeciesCount(); else if( columnIndex == 5 ) return table.getModel() == groupModel ? func.getGroupSize() : func.getGeneCount(); else if( columnIndex == 6 ) return func.name; else if( columnIndex == 7 ) return func.namespace; else if( columnIndex == 8 ) return func.desc; return null; } @Override public void setValueAt(Object aValue, int rowIndex, int columnIndex) { } @Override public void addTableModelListener(TableModelListener l) { } @Override public void removeTableModelListener(TableModelListener l) { } }; ftable.setModel( ftablemodel ); fscrollpane.setViewportView(ftable);*/ updateFilter(ftable, null); updateFilter(table, label); combo.getSelectionModel().selectedItemProperty().addListener((observable, oldValue, newValue) -> { String sel = newValue; filterset.clear(); if (geneset.pathwaymap.containsKey(sel)) { Set<String> enz = geneset.pathwaymap.get(sel); for (Function f : geneset.funclist) { if (f.getEc() != null && enz.contains(f.getEc())) { filterset.add(f.index); } } } updateFilter(ftable, null); }); specombo.getSelectionModel().selectedItemProperty().addListener((observable, oldValue, newValue) -> { String sel = newValue; genefilterset.clear(); for (Gene g : geneset.genelist) { Tegeval tv = g.tegeval; if (sel.equals(tv.teg)) { //System.out.println(g.name + " " + sp + " " + sel + " " + tv.eval); genefilterset.add(g.index); } } updateFilter(table, label); }); MenuItem findcon = new MenuItem("Find conserved terms"); findcon.setOnAction(e -> { Set<Integer> res = new HashSet<>(); for (Function f : geneset.funclist) { if (f.getGeneGroups() != null) { Set<String> check = new HashSet<>(); for (GeneGroup g : f.getGeneGroups()) { //Gene g = genemap.get(str); if (g.species != null) { if (check.isEmpty()) check.addAll(g.species.keySet()); else if (!(check.size() == g.species.size() && check.containsAll(g.species.keySet()))) { check.clear(); break; } } } if (!check.isEmpty()) res.add(f.index); } } filterset.clear(); for (int i : res) { filterset.add(i); } updateFilter(ftable, null); }); fpopup.getItems().add(findcon); fpopup.getItems().add(new SeparatorMenuItem()); MenuItem showgen = new MenuItem("Show genes"); showgen.setOnAction(e -> { genefilterset.clear(); Set<GeneGroup> sset = new HashSet<>(); for (Function f : (ObservableList<Function>) ftable.getSelectionModel().getSelectedItems()) { if (!isGeneview()) { sset.addAll(f.getGeneGroups()); /*if( sset != null ) for (GeneGroup gg : sset) { //Gene g = genemap.get(s); genefilterset.add(gg.index); }*/ } else { /*Set<Gene> sset = f.getGeneentries(); for (Gene g : sset) { //Gene g = genemap.get(s); genefilterset.add(g.index); }*/ } } //int[] rows = sset.stream().mapToInt( gg -> sortedData.indexOf(gg) ).toArray(); //table.getSelectionModel().selectIndices(rows[0], rows); filteredData.setPredicate(genegroup -> { return sset.contains(genegroup); }); if (label != null) label.setText( table.getItems().size() + "/" + table.getSelectionModel().getSelectedIndices().size()); }); fpopup.getItems().add(showgen); table.getSelectionModel().selectedItemProperty().addListener(e -> { // table.clearSelection(); tableisselecting = true; if (!ftableisselecting && filterset.isEmpty()) { //ftable.removeRowSelectionInterval(0, ftable.getRowCount() - 1); if (!isGeneview()) { for (GeneGroup gg : table.getSelectionModel().getSelectedItems()) { for (Function f : gg.getFunctions()) { try { ftable.getSelectionModel().select(f); //int rf = ftable.convertRowIndexToView(f.index); //if( rf >= 0 && rf < ftable.getRowCount() ) ftable.addRowSelectionInterval(rf, rf); } catch (Exception ex) { ex.printStackTrace(); } } } } else { for (Gene g : gtable.getSelectionModel().getSelectedItems()) { if (g.funcentries != null) { for (Function f : g.funcentries) { //Function f = funcmap.get(go); try { ftable.getSelectionModel().select(f); //int rf = ftable.convertRowIndexToView(f.index); //if( rf >= 0 && rf < ftable.getRowCount() ) ftable.addRowSelectionInterval(rf, rf); } catch (Exception ex) { ex.printStackTrace(); } } } } } } tableisselecting = false; }); ftable.setOnKeyPressed(ke -> { if (ke.getCode() == KeyCode.ESCAPE) { ffilteredData.setPredicate(null); } }); table.setOnKeyPressed(ke -> { if (ke.getCode() == KeyCode.ESCAPE) { GeneGroup selgg = table.getSelectionModel().getSelectedItem(); List<GeneGroup> sel = new ArrayList<>(filteredData); filteredData.setPredicate(null); int[] rows = sel.stream().mapToInt(gg -> sortedData.indexOf(gg)).toArray(); if (rows.length > 0) table.getSelectionModel().selectIndices(rows[0], rows); if (label != null) label.setText( table.getItems().size() + "/" + table.getSelectionModel().getSelectedIndices().size()); table.scrollTo(selgg); //genefilterset.clear(); //updateFilter(table, genefilter, label); //geneset.scrollToSelection( table ); } }); table.setOnMousePressed(e -> { tableisselecting = true; if (!ftableisselecting && e.getClickCount() == 2) { /* * int[] rr = ftable.getSelectedRows(); int minr = * ftable.getRowCount(); int maxr = 0; for( int r : rr ) { * if( r < minr ) minr = r; if( r > maxr ) maxr = r; } * ftable.removeRowSelectionInterval(minr, maxr); */ // ftable.removeRowSelectionInterval(0, filterset.isEmpty() // ? ftable.getRowCount()-1 : filterset.size()-1 ); Set<Function> fset = new HashSet<>(); filterset.clear(); if (!isGeneview()) { for (GeneGroup gg : table.getSelectionModel().getSelectedItems()) { fset.addAll(gg.getFunctions()); } } else { for (Gene g : gtable.getSelectionModel().getSelectedItems()) { if (g.funcentries != null) { for (Function f : g.funcentries) { //Function f = funcmap.get(go); // ftable.getRowSorter().convertRowIndexToView(index) // int rf = ftable.convertRowIndexToView( // f.index ); filterset.add(f.index); // ftable.addRowSelectionInterval(rf, rf); } } } } ffilteredData.setPredicate(p -> fset.contains(p)); } tableisselecting = false; }); ftable.setOnMousePressed(e -> { ftableisselecting = true; Set<GeneGroup> ggset = new HashSet<>(); if (!tableisselecting && e.getClickCount() == 2) { genefilterset.clear(); for (Function f : (ObservableList<Function>) ftable.getSelectionModel().getSelectedItems()) { if (f.getGeneentries() != null) { if (!isGeneview()) { ggset.addAll(f.getGeneGroups()); } else { for (Gene g : f.getGeneentries()) { //Gene g = genemap.get(ref); // int rf = table.convertRowIndexToView( g.index // ); // table.addRowSelectionInterval(rf, rf); genefilterset.add(g.index); } } } } filteredData.setPredicate(p -> ggset.contains(p)); } ftableisselecting = false; }); ftable.getSelectionModel().selectedItemProperty().addListener(e -> { ftableisselecting = true; if (!tableisselecting && genefilterset.isEmpty()) { table.getSelectionModel().clearSelection(); //table.removeRowSelectionInterval(0, table.getRowCount() - 1); for (Function f : ftable.getSelectionModel().getSelectedItems()) { if (f.getGeneentries() != null) { for (Gene g : f.getGeneentries()) { table.getSelectionModel().select(g.getGeneGroup()); //Gene g = genemap.get(ref); /*int i = g.getGroupIndex(); if( i >= 0 && i <= table.getItems().size() ) { int rf = table.convertRowIndexToView(i); table.addRowSelectionInterval(rf, rf); }*/ } } } } ftableisselecting = false; }); textfield.setOnKeyPressed(e -> { String text = textfield.getText().toLowerCase(); if (e.getCode() == KeyCode.ENTER) { searchi = searchcolcomb.getSelectionModel().getSelectedItem().equals("Symbol") ? searchTable(table, text, searchi, e.isAltDown(), 8, 9, 10, 16) : searchTable(table, text, searchi, e.isAltDown(), 0); } }); textfield.textProperty().addListener((observable, oldValue, newValue) -> { //String text = textfield.getText().toLowerCase(); String lowerCaseFilter = newValue.toLowerCase(); Predicate<GeneGroup> p = genegroup -> { if (newValue == null || newValue.isEmpty()) { return true; } if (searchcolcomb.getSelectionModel().getSelectedItem().equals("Symbol")) { if ((genegroup.getCogsymbol() != null && genegroup.getCogsymbol().toLowerCase().contains(lowerCaseFilter)) || (genegroup.getSymbol() != null && genegroup.getSymbol().toLowerCase().contains(lowerCaseFilter)) || (genegroup.getKoname() != null && genegroup.getKoname().toLowerCase().contains(lowerCaseFilter))) { return true; // Filter matches first name. } } else { if (genegroup.getName().toLowerCase().contains(lowerCaseFilter) || genegroup.genes.stream() .anyMatch(gg -> gg.getName().toLowerCase().contains(lowerCaseFilter))) { return true; // Filter matches first name. } /* else if (genegroup.getLastName().toLowerCase().contains(lowerCaseFilter)) { return true; // Filter matches last name. }*/ } return false; // Does not match. }; if (filter.isSelected()) { filteredData.setPredicate(p); if (label != null) label.setText( table.getItems().size() + "/" + table.getSelectionModel().getSelectedIndices().size()); //if( searchcolcomb.getSelectionModel().getSelectedItem().equals("Symbol") ) updateFilter(0, text, table, genefilter, genefilterset, label, 8, 9, 10, 16 ); //else updateFilter(0, text, table, genefilter, genefilterset, label, 0 ); } else { Optional<GeneGroup> ogg = filteredData.stream().filter(p).findFirst(); if (ogg.isPresent()) { GeneGroup gg = ogg.get(); table.getSelectionModel().select(gg); table.scrollTo(gg); } //searchi = searchcolcomb.getSelectionModel().getSelectedItem().equals("Symbol") ? searchTable( table, text, 0, false, 8, 9, 10, 16 ) : searchTable( table, text, 0, false, 0 ); } }); /*textfield.getDocument().addDocumentListener(new DocumentListener() { public void changedUpdate(DocumentEvent e) { String text = textfield.getText().toLowerCase(); if( filter.isSelected() ) { if( searchcolcomb.getSelectionModel().getSelectedItem().equals("Symbol") ) updateFilter(0, text, table, genefilter, genefilterset, label, 8, 9, 10, 16 ); else updateFilter(0, text, table, genefilter, genefilterset, label, 0 ); } else { searchi = searchcolcomb.getSelectionModel().getSelectedItem().equals("Symbol") ? searchTable( table, text, 0, false, 8, 9, 10, 16 ) : searchTable( table, text, 0, false, 0 ); } } public void insertUpdate(DocumentEvent e) { String text = textfield.getText().toLowerCase(); if( filter.isSelected() ) { if( searchcolcomb.getSelectionModel().getSelectedItem().equals("Symbol") ) updateFilter(1, text, table, genefilter, genefilterset, label, 8, 9, 10, 16); else updateFilter(1, text, table, genefilter, genefilterset, label, 0); } else { searchi = searchcolcomb.getSelectionModel().getSelectedItem().equals("Symbol") ? searchTable( table, text, 0, false, 8, 9, 10, 16 ) : searchTable( table, text, 0, false, 0 ); } } public void removeUpdate(DocumentEvent e) { String text = textfield.getText().toLowerCase(); if( filter.isSelected() ) { if( searchcolcomb.getSelectionModel().getSelectedItem().equals("Symbol") ) updateFilter(2, text, table, genefilter, genefilterset, label, 8, 9, 10, 16 ); else updateFilter(2, text, table, genefilter, genefilterset, label, 0); } else { searchi = searchTable( table, text, 0, false, searchcolcomb.getSelectionModel().getSelectedItem().equals("Symbol") ? 7 : 0 ); } } });*/ ftextfield.textProperty().addListener(new javafx.beans.value.ChangeListener<String>() { public void changed(ObservableValue<? extends String> observable, String oldValue, String newValue) { //String text = textfield.getText().toLowerCase(); if (filter.isSelected()) { ffilteredData.setPredicate(function -> { // If filter text is empty, display all persons. if (newValue == null || newValue.isEmpty()) { return true; } // Compare first name and last name of every person with filter text. String lowerCaseFilter = newValue.toLowerCase(); boolean desc = function.getDesc() != null && function.getDesc().toLowerCase().contains(lowerCaseFilter); boolean name = function.getName() != null && function.getName().toLowerCase().contains(lowerCaseFilter); boolean go = function.getGo() != null && function.getGo().toLowerCase().contains(lowerCaseFilter); boolean ec = function.getEc() != null && function.getEc().toLowerCase().contains(lowerCaseFilter); if (desc || name || go || ec) { return true; // Filter matches first name. } /* else if (genegroup.getLastName().toLowerCase().contains(lowerCaseFilter)) { return true; // Filter matches last name. }*/ return false; // Does not match. }); } else { //searchi = searchcolcomb.getSelectionModel().getSelectedItem().equals("Symbol") ? searchTable( table, text, 0, false, 8, 9, 10, 16 ) : searchTable( table, text, 0, false, 0 ); } } }); /*ftextfield.getDocument().addDocumentListener(new DocumentListener() { public void changedUpdate(DocumentEvent e) { updateFilter(0, ftextfield.getText(), ftable, rowfilter, filterset, null, 6); } public void insertUpdate(DocumentEvent e) { updateFilter(1, ftextfield.getText(), ftable, rowfilter, filterset, null, 6); } public void removeUpdate(DocumentEvent e) { updateFilter(2, ftextfield.getText(), ftable, rowfilter, filterset, null, 6); } });*/ MenuItem kegggl = new MenuItem("KEGG gene lookup"); kegggl.setOnAction(e -> { Gene g = gtable.getSelectionModel().getSelectedItem(); try { Desktop.getDesktop().browse(new URI("http://www.genome.jp/dbget-bin/www_bget?" + g.keggid)); } catch (IOException e1) { e1.printStackTrace(); } catch (URISyntaxException e1) { e1.printStackTrace(); } }); popup.getItems().add(kegggl); MenuItem showgenes = new MenuItem("Show genes with same sharing"); showgenes.setOnAction(e -> { genefilterset.clear(); GeneGroup gg = table.getSelectionModel().getSelectedItem(); for (GeneGroup g : geneset.allgenegroups) { if (gg.species != null && g.species != null) { Set<String> ggset = gg.species.keySet(); Set<String> gset = g.species.keySet(); if (gset.size() == ggset.size() && gset.containsAll(ggset)) { genefilterset.add(g.index); } } } updateFilter(table, label); }); popup.getItems().add(showgenes); MenuItem showshared = new MenuItem("Show shared function"); showshared.setOnAction(e -> { filterset.clear(); Set<Function> startfunc = new HashSet<Function>(); if (isGeneview()) { for (Gene gg : gtable.getSelectionModel().getSelectedItems()) { if (gg.funcentries != null) { if (startfunc.isEmpty()) { startfunc.addAll(gg.funcentries); } else { startfunc.retainAll(gg.funcentries); } } /*if (startfunc == null) startfunc = new HashSet<Function>(gg.funcentries); else { startfunc.retainAll(gg.funcentries); }*/ } } else { for (GeneGroup gg : table.getSelectionModel().getSelectedItems()) { Set<Function> fset = gg.getFunctions(); if (startfunc.isEmpty()) { startfunc.addAll(fset); } else { startfunc.retainAll(fset); } } } for (Function f : geneset.funclist) { filterset.add(f.index); } updateFilter(ftable, null); }); popup.getItems().add(showshared); MenuItem showall = new MenuItem("Show all functions"); showall.setOnAction(e -> { filterset.clear(); Set<Function> startfunc = null; if (isGeneview()) { for (Gene gg : gtable.getSelectionModel().getSelectedItems()) { if (gg.funcentries != null) { for (Function f : gg.funcentries) { filterset.add(f.index); } } } } else { for (GeneGroup gg : table.getSelectionModel().getSelectedItems()) { Set<Function> fset = gg.getFunctions(); for (Function f : fset) { filterset.add(f.index); } } } updateFilter(ftable, null); }); popup.getItems().add(showall); popup.getItems().add(new SeparatorMenuItem()); MenuItem showgenegroups = new MenuItem("Show gene groups in proximity"); showgenegroups.setOnAction(e -> { proxi(filteredData, false); updateFilter(table, label); }); popup.getItems().add(showgenegroups); MenuItem selgenegroups = new MenuItem("Select gene groups in proximity"); selgenegroups.setOnAction(e -> { genefilterset.clear(); proxi(filteredData, false); for (int i : genefilterset) { table.getSelectionModel().select(i); } //table.tableChanged( new TableModelEvent( table.getModel() ) ); if (label != null) label.setText(table.getItems().size() + "/" + table.getSelectionModel().getSelectedItems().size()); //updateFilter(table, genefilter, label); }); popup.getItems().add(selgenegroups); MenuItem selgenes = new MenuItem("Select genes in proximity"); selgenes.setOnAction(e -> { genefilterset.clear(); proxi(filteredData, true); for (int i : genefilterset) { table.getSelectionModel().select(i); } //table.tableChanged( new TableModelEvent( table.getModel() ) ); if (label != null) label.setText(table.getItems().size() + "/" + table.getSelectionModel().getSelectedItems().size()); //updateFilter(table, genefilter, label); }); popup.getItems().add(selgenes); MenuItem addgene = new MenuItem("Add gene groups in proximity"); addgene.setOnAction(e -> { proxi(filteredData, false); updateFilter(table, label); }); popup.getItems().add(addgene); MenuItem remgene = new MenuItem("Remove gene groups in proximity"); remgene.setOnAction(e -> { ObservableList<Integer> rr = table.getSelectionModel().getSelectedIndices(); if (genefilterset.isEmpty()) { Set<Integer> ii = new HashSet<>(); for (int r : rr) ii.add(r); for (int i = 0; i < geneset.genelist.size(); i++) { if (!ii.contains(i)) genefilterset.add(i); } } proxi(filteredData, false); updateFilter(table, label); }); popup.getItems().add(remgene); popup.getItems().add(new SeparatorMenuItem()); MenuItem showrel = new MenuItem("Show related genes"); showrel.setOnAction(e -> { genefilterset.clear(); relati(gtable, geneset.genelist, genefilterset, geneset.uclusterlist, false); updateFilter(gtable, label); }); popup.getItems().add(showrel); MenuItem addrel = new MenuItem("Add related genes"); addrel.setOnAction(e -> { relati(gtable, geneset.genelist, genefilterset, geneset.uclusterlist, false); updateFilter(gtable, label); }); popup.getItems().add(addrel); MenuItem remrel = new MenuItem("Remove related genes"); remrel.setOnAction(e -> { ObservableList<Integer> rr = gtable.getSelectionModel().getSelectedIndices(); if (genefilterset.isEmpty()) { Set<Integer> ii = new HashSet<>(); for (int r : rr) ii.add(r); for (int i = 0; i < geneset.genelist.size(); i++) { if (!ii.contains(i)) genefilterset.add(i); } } relati(gtable, geneset.genelist, genefilterset, geneset.uclusterlist, true); updateFilter(table, label); }); popup.getItems().add(remrel); popup.getItems().add(new SeparatorMenuItem()); MenuItem showcloserel = new MenuItem("Show closely related genes"); showcloserel.setOnAction(e -> { genefilterset.clear(); Set<String> ct = new HashSet<>(); for (Gene gg : gtable.getSelectionModel().getSelectedItems()) { // genefilterset.add( gg.index ); Tegeval tv = gg.tegeval; for (Set<String> uset : geneset.iclusterlist) { if (uset.contains(tv.name)) { ct.addAll(uset); break; } } } for (Gene g : geneset.genelist) { Tegeval tv = g.tegeval; if (ct.contains(tv.name)) { genefilterset.add(g.index); break; } } updateFilter(table, label); }); popup.getItems().add(showcloserel); MenuItem showdist = new MenuItem("Show distance matrix"); showdist.setOnAction(e -> { JTextArea textarea = new JTextArea(); 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); JScrollPane scrollpane = new JScrollPane(textarea); Gene gg = gtable.getSelectionModel().getSelectedItem(); if (gg.getSpecies() != null) { for (String s : geneset.corrInd) { if (s.equals(geneset.corrInd.get(0))) textarea.append(s); else textarea.append("\t" + s); } int i = 0; int j = 0; int len = 16; double[] min = new double[len]; double[] max = new double[len]; for (i = 0; i < len; i++) { min[i] = Double.MAX_VALUE; max[i] = 0.0; } double[] corrarr = gg.corrarr; boolean symmetrize = true; if (symmetrize) { for (i = 0; i < len; i++) { for (int k = i + 1; k < len; k++) { corrarr[i * len + k] = (corrarr[k * len + i] + corrarr[i * len + k]) / 2.0; corrarr[k * len + i] = corrarr[i * len + k]; } } } for (i = 0; i < len; i++) { for (int k = 0; k < len; k++) { if (corrarr[i * len + k] < min[i]) min[i] = corrarr[i * len + k]; if (corrarr[i * len + k] > max[i]) max[i] = corrarr[i * len + k]; } /*for (int k = 0; k < len; k++) { corrarr[i * 16 + k] = corrarr[i * 16 + k] - min; }*/ } i = 0; for (double d : corrarr) { double dval = d; if (i % len == 0) textarea.append("\n" + dval); else textarea.append("\t" + dval); i++; } textarea.append("\n"); i = 0; for (double d : corrarr) { double dval = Math.exp((d - min[i / len]) / 20.0 + 1.0) / 100.0; // 0.0 ? // 0.0 : // 100.0/d; if (i % len == 0) textarea.append("\n" + dval); else textarea.append("\t" + dval); i++; } double[] newcorr = Arrays.copyOf(corrarr, corrarr.length); textarea.append("\nD matrix\n"); i = 0; for (double d : corrarr) { double dval = max[i / len] - d; newcorr[i] = dval; if (i % len == 0) textarea.append("\n" + dval); else textarea.append("\t" + dval); i++; } TreeUtil treeutil = new TreeUtil(); treeutil.neighborJoin(newcorr, geneset.corrInd, null, true, true); } /* * int[] rr = table.getSelectedRows(); for( int r : rr ) { int * cr = table.convertRowIndexToModel(r); Gene gg = * genelist.get(cr); if( gg.species != null ) { textarea.append( * gg.name + ":\n" ); for( String sp : gg.species.keySet() ) { * Teginfo stv = gg.species.get( sp ); for( Tegeval tv : * stv.tset ) { textarea.append( ">" + tv.cont + " " + tv.teg + * " " + tv.eval + "\n" ); for( int i = 0; i < tv.seq.length(); * i+=70 ) { int end = Math.min(i+70,tv.seq.length()); * textarea.append( tv.seq.substring(i, end)+"\n" ); //new * String( tv.seq, i, Math.min(i+70,tv.seq.length()) )+"\n"); } * //textarea.append( ">" + tv.cont + " " + tv.teg + " " + * tv.eval + "\n" + tv.seq + "\n" ); } } } } */ JFrame frame = new JFrame(); frame.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE); frame.add(scrollpane); frame.setSize(400, 300); frame.setVisible(true); }); /* * final List<String> reglist = new ArrayList<String>(); final * Map<String,Gene> regidx = new TreeMap<String,Gene>(); * * for( Gene g : geneset.genelist ) { if( g.species != null ) { for( String key * : g.species.keySet() ) { Set<Tegeval> stv = g.species.get(key); for( * Tegeval tv : stv ) { regidx.put(tv.cont, g); } } } } * * for( String key : regidx.keySet() ) { reglist.add(key); } * * final JTable contigtable = new JTable(); * contigtable.setAutoCreateRowSorter( true ); contigtable.setModel( new * TableModel() { * * @Override public int getRowCount() { return reglist.size(); } * * @Override public int getColumnCount() { return 1; } * * @Override public String getColumnName(int columnIndex) { return * "Region"; } * * @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 reglist.get(rowIndex); } * * @Override public void setValueAt(Object aValue, int rowIndex, int * columnIndex) { // TODO Auto-generated method stub * * } * * @Override public void addTableModelListener(TableModelListener l) { * // TODO Auto-generated method stub * * } * * @Override public void removeTableModelListener(TableModelListener l) * { // TODO Auto-generated method stub * * } }); * * contigtable.getSelectionModel().addListSelectionListener( new * ListSelectionListener() { * * @Override public void valueChanged(ListSelectionEvent e) { * genefilterset.clear(); int[] rr = contigtable.getSelectedRows(); for( * int r : rr ) { String s = (String)contigtable.getValueAt(r, 0); Gene * g = regidx.get( s ); * * genefilterset.add( g.index ); updateFilter(table, genefilter, label); * //int k = table.convertRowIndexToView(g.index); //if( k != -1 * )table.addRowSelectionInterval(k, k); } } }); JScrollPane * contigscroll = new JScrollPane( contigtable ); * * JSplitPane mainsplit = new JSplitPane( JSplitPane.HORIZONTAL_SPLIT ); * mainsplit.setLeftComponent( contigscroll ); * mainsplit.setRightComponent( splitpane ); */ }