List of usage examples for javafx.scene.layout VBox getChildren
@Override
public ObservableList<Node> getChildren()
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);//from ww w. j a v a 2 s. c o m 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:editeurpanovisu.EditeurPanovisu.java
/** * * @param strLstPano/*w w w . j av a 2 s .c om*/ * @param iNumPano * @return */ public static Pane paneAffichageHS(String strLstPano, int iNumPano) { Pane paneHotSpots = new Pane(); paneHotSpots.setTranslateY(10); paneHotSpots.setTranslateX(10); VBox vbHotspots = new VBox(5); paneHotSpots.getChildren().add(vbHotspots); Label lblPoint; int io; for (io = 0; io < getPanoramiquesProjet()[iNumPano].getNombreHotspots(); io++) { Label lblSep = new Label(" "); Label lblSep1 = new Label(" "); VBox vbPanneauHS = new VBox(); double deplacement = 0; vbPanneauHS.setLayoutX(deplacement); Pane paneHsPanoramique = new Pane(vbPanneauHS); paneHsPanoramique.setPrefHeight(300); paneHsPanoramique.setMinHeight(300); paneHsPanoramique.setMaxHeight(300); int iNum1 = io; Timeline timBouge = new Timeline(new KeyFrame(Duration.millis(500), (ActionEvent event) -> { Circle c1 = (Circle) panePanoramique.lookup("#point" + iNum1); if (c1 != null) { if (c1.getFill() == Color.RED) { c1.setFill(Color.YELLOW); c1.setStroke(Color.RED); } else { c1.setFill(Color.RED); c1.setStroke(Color.YELLOW); } } })); timBouge.setCycleCount(Timeline.INDEFINITE); timBouge.pause(); paneHsPanoramique.setOnMouseEntered((e) -> { timBouge.play(); }); paneHsPanoramique.setOnMouseExited((e) -> { timBouge.pause(); Circle c1 = (Circle) panePanoramique.lookup("#point" + iNum1); if (c1 != null) { c1.setFill(Color.YELLOW); c1.setStroke(Color.RED); } }); paneHsPanoramique .setStyle("-fx-border-color : #777777;-fx-border-width : 1px;-fx-border-radius : 3px;"); paneHsPanoramique.setId("HS" + io); lblPoint = new Label("Point #" + (io + 1)); lblPoint.setPadding(new Insets(5, 10, 5, 5)); lblPoint.setTranslateX(-deplacement); lblPoint.getStyleClass().add("titreOutil"); Separator sepHotspots = new Separator(Orientation.HORIZONTAL); sepHotspots.setTranslateX(-deplacement); sepHotspots.setPrefWidth(321); sepHotspots.setTranslateX(2); paneHsPanoramique.setPrefWidth(325); vbPanneauHS.getChildren().addAll(lblPoint, sepHotspots); if (strLstPano != null) { Label lblLien = new Label(rbLocalisation.getString("main.panoramiqueDestination")); lblLien.setTranslateX(10); ComboBox cbDestPano = new ComboBox(); String[] strListe = strLstPano.split(";"); cbDestPano.getItems().addAll(Arrays.asList(strListe)); int iNum11 = getPanoramiquesProjet()[iNumPano].getHotspot(io).getNumeroPano(); cbDestPano.setTranslateX(10); cbDestPano.setId("cbpano" + io); cbDestPano.getSelectionModel().select(iNum11); cbDestPano.getSelectionModel().selectedIndexProperty().addListener((ov, t, t1) -> { valideHS(); if (dejaCharge) { dejaCharge = false; retireAffichageHotSpots(); Pane affHS1 = paneAffichageHS(strListePano(), iNumPano); affHS1.setId("labels"); vbVisuHotspots.getChildren().add(affHS1); } }); if (iNum11 != -1) { int iNumPan = iNum11; ImageView ivAfficheVignettePano = new ImageView( getPanoramiquesProjet()[iNum11].getImgPanoRect()); ivAfficheVignettePano.setPreserveRatio(true); ivAfficheVignettePano.setFitWidth(300); ivAfficheVignettePano.setLayoutY(10); ivAfficheVignettePano.setCursor(Cursor.HAND); ivAfficheVignettePano.setOnMouseClicked((e) -> { affichePanoChoisit(iNumPan); }); AnchorPane apVisuVignettePano = new AnchorPane(ivAfficheVignettePano); apVisuVignettePano.setPrefHeight(170); apVisuVignettePano.setTranslateX(10); vbPanneauHS.getChildren().addAll(lblLien, cbDestPano, apVisuVignettePano, lblSep); } else { vbPanneauHS.getChildren().addAll(lblLien, cbDestPano, lblSep); } } Label lblTexteHS = new Label(rbLocalisation.getString("main.texteHotspot")); lblTexteHS.setTranslateX(10); TextField tfTexteHS = new TextField(); if (getPanoramiquesProjet()[iNumPano].getHotspot(io).getStrInfo() != null) { tfTexteHS.setText(getPanoramiquesProjet()[iNumPano].getHotspot(io).getStrInfo()); } tfTexteHS.textProperty().addListener((final ObservableValue<? extends String> observable, final String oldValue, final String newValue) -> { valideHS(); }); tfTexteHS.setId("txtHS" + io); tfTexteHS.setPrefSize(200, 25); tfTexteHS.setMaxSize(200, 20); tfTexteHS.setTranslateX(60); vbPanneauHS.getChildren().addAll(lblTexteHS, tfTexteHS, lblSep1); vbHotspots.getChildren().addAll(paneHsPanoramique, lblSep); } int iNbHS = io; int iTaillePane = io * 325; for (io = 0; io < getPanoramiquesProjet()[iNumPano].getNombreHotspotImage(); io++) { Label lblSep = new Label(" "); Label lblSep1 = new Label(" "); VBox vbPanneauHsImage = new VBox(); Pane paneHsImage = new Pane(vbPanneauHsImage); int iNum = io; Timeline timBouge = new Timeline(new KeyFrame(Duration.millis(500), (ActionEvent event) -> { Circle c1 = (Circle) panePanoramique.lookup("#img" + iNum); if (c1 != null) { if (c1.getFill() == Color.BLUE) { c1.setFill(Color.YELLOW); c1.setStroke(Color.BLUE); } else { c1.setFill(Color.BLUE); c1.setStroke(Color.YELLOW); } } })); timBouge.setCycleCount(Timeline.INDEFINITE); timBouge.pause(); paneHsImage.setOnMouseEntered((e) -> { timBouge.play(); }); paneHsImage.setOnMouseExited((e) -> { Circle c1 = (Circle) panePanoramique.lookup("#img" + iNum); if (c1 != null) { c1.setFill(Color.BLUE); c1.setStroke(Color.YELLOW); } timBouge.pause(); }); paneHsImage.setStyle("-fx-border-color : #777777;-fx-border-width : 1px;-fx-border-radius : 3px;"); paneHsImage.setId("HSImg" + io); lblPoint = new Label("Image #" + (io + 1)); lblPoint.setPadding(new Insets(5, 10, 5, 5)); lblPoint.getStyleClass().add("titreOutil"); Separator sepHS = new Separator(Orientation.HORIZONTAL); sepHS.setPrefWidth(321); sepHS.setTranslateX(2); paneHsImage.setPrefWidth(325); vbPanneauHsImage.getChildren().addAll(lblPoint, sepHS); Label lblLien = new Label(rbLocalisation.getString("main.imageChoisie")); lblLien.setTranslateX(10); String strF1XML = getPanoramiquesProjet()[iNumPano].getHotspotImage(io).getStrLienImg(); Image imgChoisie = new Image( "file:" + getStrRepertTemp() + File.separator + "images" + File.separator + strF1XML); ImageView ivChoisie = new ImageView(imgChoisie); ivChoisie.setTranslateX(100); ivChoisie.setFitWidth(100); ivChoisie.setFitHeight(imgChoisie.getHeight() / imgChoisie.getWidth() * 100); vbPanneauHsImage.getChildren().addAll(lblLien, ivChoisie, lblSep); Label lblTexteHS = new Label(rbLocalisation.getString("main.texteHotspot")); lblTexteHS.setTranslateX(10); TextField tfTexteHS = new TextField(); if (getPanoramiquesProjet()[iNumPano].getHotspotImage(io).getStrInfo() != null) { tfTexteHS.setText(getPanoramiquesProjet()[iNumPano].getHotspotImage(io).getStrInfo()); } tfTexteHS.textProperty().addListener((final ObservableValue<? extends String> observable, final String oldValue, final String newValue) -> { valideHS(); }); tfTexteHS.setId("txtHSImage" + io); tfTexteHS.setPrefSize(200, 25); tfTexteHS.setMaxSize(200, 20); tfTexteHS.setTranslateX(60); vbPanneauHsImage.getChildren().addAll(lblTexteHS, tfTexteHS, lblSep1); Label lblCoulFond = new Label(rbLocalisation.getString("diapo.couleurFond")); lblCoulFond.setTranslateX(10); Label lblOpacite = new Label(rbLocalisation.getString("diapo.opacite")); lblOpacite.setTranslateX(10); if (getPanoramiquesProjet()[iNumPano].getHotspotImage(io).getStrCouleurFond().equals("")) { getPanoramiquesProjet()[iNumPano].getHotspotImage(io).setStrCouleurFond( "#" + getGestionnaireInterface().getCouleurFondTheme().toString().substring(2, 8)); } ColorPicker cpCouleurFond = new ColorPicker( Color.valueOf(getPanoramiquesProjet()[iNumPano].getHotspotImage(io).getStrCouleurFond())); if (getPanoramiquesProjet()[iNumPano].getHotspotImage(io).getOpacite() == -1) { getPanoramiquesProjet()[iNumPano].getHotspotImage(io) .setOpacite(getGestionnaireInterface().getOpaciteTheme()); } cpCouleurFond.setTranslateX(100); int i = io; cpCouleurFond.valueProperty().addListener((ov, av, nv) -> { if (getiNombrePanoramiques() != 0) { setbDejaSauve(false); getStPrincipal().setTitle(getStPrincipal().getTitle().replace(" *", "") + " *"); } getPanoramiquesProjet()[iNumPano].getHotspotImage(i) .setStrCouleurFond("#" + cpCouleurFond.getValue().toString().substring(2, 8)); }); Slider slOpacite = new Slider(0, 1, getPanoramiquesProjet()[iNumPano].getHotspotImage(io).getOpacite()); slOpacite.valueProperty().addListener((ov, av, nv) -> { if (getiNombrePanoramiques() != 0) { setbDejaSauve(false); getStPrincipal().setTitle(getStPrincipal().getTitle().replace(" *", "") + " *"); } getPanoramiquesProjet()[iNumPano].getHotspotImage(i).setOpacite(slOpacite.getValue()); }); slOpacite.setTranslateX(100); slOpacite.setPrefWidth(130); slOpacite.setMinWidth(130); slOpacite.setMaxWidth(130); vbPanneauHsImage.getChildren().addAll(lblCoulFond, cpCouleurFond, lblOpacite, slOpacite); vbHotspots.getChildren().addAll(paneHsImage, lblSep); iTaillePane += 225 + ivChoisie.getFitHeight(); paneHsImage.setPrefHeight(200 + ivChoisie.getFitHeight()); paneHsImage.setMinHeight(200 + ivChoisie.getFitHeight()); paneHsImage.setMaxHeight(200 + ivChoisie.getFitHeight()); } iNbHS += io; for (io = 0; io < getPanoramiquesProjet()[iNumPano].getNombreHotspotHTML(); io++) { Label lblSep = new Label(" "); int iNum = io; VBox vbPanneauHS = new VBox(); Pane paneHsHtml = new Pane(vbPanneauHS); Timeline timBouge = new Timeline(new KeyFrame(Duration.millis(500), (ActionEvent event) -> { Circle c1 = (Circle) panePanoramique.lookup("#html" + iNum); if (c1 != null) { if (c1.getFill() == Color.DARKGREEN) { c1.setFill(Color.YELLOWGREEN); c1.setStroke(Color.DARKGREEN); } else { c1.setFill(Color.DARKGREEN); c1.setStroke(Color.YELLOWGREEN); } } })); timBouge.setCycleCount(Timeline.INDEFINITE); timBouge.pause(); paneHsHtml.setOnMouseEntered((e) -> { timBouge.play(); }); paneHsHtml.setOnMouseExited((e) -> { timBouge.pause(); Circle c1 = (Circle) panePanoramique.lookup("#html" + iNum); if (c1 != null) { c1.setFill(Color.DARKGREEN); c1.setStroke(Color.YELLOWGREEN); } }); paneHsHtml.setStyle("-fx-border-color : #777777;-fx-border-width : 1px;-fx-border-radius : 3px;"); paneHsHtml.setId("HSHTML" + io); lblPoint = new Label("Hotspot HTML #" + (io + 1)); lblPoint.setPadding(new Insets(5, 10, 5, 5)); lblPoint.getStyleClass().add("titreOutil"); Separator sepHS = new Separator(Orientation.HORIZONTAL); sepHS.setPrefWidth(321); sepHS.setTranslateX(2); paneHsHtml.setPrefWidth(325); Label lblTexteHS = new Label(rbLocalisation.getString("main.texteHotspot")); lblTexteHS.setTranslateX(10); TextField tfTexteHS = new TextField(); if (getPanoramiquesProjet()[iNumPano].getHotspotHTML(io).getStrInfo() != null) { tfTexteHS.setText(getPanoramiquesProjet()[iNumPano].getHotspotHTML(io).getStrInfo()); } tfTexteHS.textProperty().addListener((final ObservableValue<? extends String> observable, final String oldValue, final String newValue) -> { valideHS(); }); tfTexteHS.setId("txtHSHTML" + io); tfTexteHS.setPrefSize(200, 25); tfTexteHS.setMaxSize(200, 20); tfTexteHS.setTranslateX(60); vbPanneauHS.getChildren().addAll(lblPoint, sepHS, lblTexteHS, tfTexteHS); Button btnEditeHSHTML = new Button(rbLocalisation.getString("main.editeHTML")); btnEditeHSHTML.setPrefWidth(80); btnEditeHSHTML.setTranslateX(paneHsHtml.getPrefWidth() - btnEditeHSHTML.getPrefWidth() - 10); vbPanneauHS.getChildren().addAll(btnEditeHSHTML); btnEditeHSHTML.setOnAction((e) -> { EditeurHTML editHTML = new EditeurHTML(); HotspotHTML HS = getPanoramiquesProjet()[iNumPano].getHotspotHTML(iNum); editHTML.setHsHTML(HS); Rectangle2D tailleEcran = Screen.getPrimary().getBounds(); int iHauteur = (int) tailleEcran.getHeight() - 100; int iLargeur = (int) tailleEcran.getWidth() - 100; editHTML.affiche(iLargeur, iHauteur); editHTML.addPropertyChangeListener("bValide", (ev) -> { if (ev.getNewValue().toString().equals("true")) { getPanoramiquesProjet()[iNumPano].setHotspotHTML(editHTML.getHsHTML(), iNum); dejaCharge = false; retireAffichageHotSpots(); Pane affHS1 = paneAffichageHS(strListePano(), iNumPano); affHS1.setId("labels"); vbVisuHotspots.getChildren().add(affHS1); } }); }); vbHotspots.getChildren().addAll(paneHsHtml, lblSep); paneHsHtml.setPrefHeight(120); paneHsHtml.setMinHeight(120); paneHsHtml.setMaxHeight(120); iTaillePane += 145; } iNbHS += io; for (io = 0; io < getPanoramiquesProjet()[iNumPano].getiNombreHotspotDiapo(); io++) { Label lblSep = new Label(" "); int iNum = io; VBox vbPanneauHS = new VBox(); Pane paneHsDiapo = new Pane(vbPanneauHS); Timeline timBouge = new Timeline(new KeyFrame(Duration.millis(500), (ActionEvent event) -> { Circle c1 = (Circle) panePanoramique.lookup("#dia" + iNum); if (c1 != null) { if (c1.getFill() == Color.TURQUOISE) { c1.setFill(Color.ORANGE); c1.setStroke(Color.TURQUOISE); } else { c1.setFill(Color.TURQUOISE); c1.setStroke(Color.ORANGE); } } })); timBouge.setCycleCount(Timeline.INDEFINITE); timBouge.pause(); paneHsDiapo.setOnMouseEntered((e) -> { timBouge.play(); }); paneHsDiapo.setOnMouseExited((e) -> { timBouge.pause(); Circle c1 = (Circle) panePanoramique.lookup("#html" + iNum); if (c1 != null) { c1.setFill(Color.TURQUOISE); c1.setStroke(Color.ORANGE); } }); paneHsDiapo.setStyle("-fx-border-color : #777777;-fx-border-width : 1px;-fx-border-radius : 3px;"); paneHsDiapo.setId("DIAPO" + io); lblPoint = new Label("Hotspot Diaporama #" + (io + 1)); lblPoint.setPadding(new Insets(5, 10, 5, 5)); lblPoint.getStyleClass().add("titreOutil"); Separator sepHS = new Separator(Orientation.HORIZONTAL); sepHS.setPrefWidth(321); sepHS.setTranslateX(2); paneHsDiapo.setPrefWidth(325); Label lblTexteHS = new Label(rbLocalisation.getString("main.texteHotspot")); lblTexteHS.setTranslateX(10); TextField tfTexteHS = new TextField(); if (getPanoramiquesProjet()[iNumPano].getHotspotDiapo(io).getStrInfo() != null) { tfTexteHS.setText(getPanoramiquesProjet()[iNumPano].getHotspotDiapo(io).getStrInfo()); } tfTexteHS.textProperty().addListener((final ObservableValue<? extends String> observable, final String oldValue, final String newValue) -> { valideHS(); }); tfTexteHS.setId("txtDIA" + io); tfTexteHS.setPrefSize(200, 25); tfTexteHS.setMaxSize(200, 20); tfTexteHS.setTranslateX(60); vbPanneauHS.getChildren().addAll(lblPoint, sepHS, lblTexteHS, tfTexteHS); ComboBox cbListeDiapo = new ComboBox(); for (int i = 0; i < getiNombreDiapo(); i++) { cbListeDiapo.getItems().add(diaporamas[i].getStrNomDiaporama()); } cbListeDiapo.getSelectionModel() .select(getPanoramiquesProjet()[iNumPano].getHotspotDiapo(io).getiNumDiapo()); int iii = io; cbListeDiapo.getSelectionModel().selectedIndexProperty().addListener((ov, av, nv) -> { getPanoramiquesProjet()[iNumPano].getHotspotDiapo(iii).setiNumDiapo((int) nv); }); cbListeDiapo.setTranslateX(60); vbPanneauHS.getChildren().addAll(cbListeDiapo); //Ajouter Liste Diaporamas vbHotspots.getChildren().addAll(paneHsDiapo, lblSep); paneHsDiapo.setPrefHeight(120); paneHsDiapo.setMinHeight(120); paneHsDiapo.setMaxHeight(120); iTaillePane += 145; } valideHS(); iNbHS += io; dejaCharge = true; paneHotSpots.setPrefHeight(iTaillePane); paneHotSpots.setMinHeight(iTaillePane); paneHotSpots.setMaxHeight(iTaillePane); paneHotSpots.setId("labels"); apVisuHS.setPrefHeight(paneHotSpots.getPrefHeight()); apVisuHS.setMinHeight(paneHotSpots.getPrefHeight()); apVisuHS.setMaxHeight(paneHotSpots.getPrefHeight()); vbVisuHotspots.setPrefHeight(paneHotSpots.getPrefHeight()); vbVisuHotspots.setMinHeight(paneHotSpots.getPrefHeight()); vbVisuHotspots.setMaxHeight(paneHotSpots.getPrefHeight()); return paneHotSpots; }
From source file:org.simmi.GeneSetHead.java
License:asdf
public void init(final Stage primaryStage, final Container comp, final SplitPane splitpane, final TableView<Gene> genetable, final TableView<Function> upper, final TableView<GeneGroup> lower, final MenuBar menubar, final ToolBar toolbar, final ToolBar btoolbar) { geneset.user = System.getProperty("user.name"); JavaFasta.user = geneset.user;/*from w w w. j a v a 2s . c o m*/ this.splitpane = splitpane; this.primaryStage = primaryStage; table = lower; gtable = genetable; //SerifyApplet.user = user; /*try { UIManager.setLookAndFeel("com.sun.java.swing.plaf.nimbus.NimbusLookAndFeel"); } catch (ClassNotFoundException e) { e.printStackTrace(); } catch (InstantiationException e) { e.printStackTrace(); } catch (IllegalAccessException e) { e.printStackTrace(); } catch (UnsupportedLookAndFeelException e) { e.printStackTrace(); }*/ String userhome = System.getProperty("user.home"); boolean windows = false; try { InputStream isk = GeneSet.class.getClassLoader().getResourceAsStream("org/simmi/genesetkey"); //Path gkey = Paths.get( url.toURI() ); InputStream iskp = GeneSet.class.getClassLoader().getResourceAsStream("org/simmi/genesetkey.pub"); //Path gkeypub = Paths.get( url.toURI() ); Path gkeyssh = Paths.get(userhome); //Path gkeyssh = userpath.resolve(".ssh"); if (!Files.exists(gkeyssh)) Files.createDirectory(gkeyssh); Path gkeylocal = gkeyssh.resolve("org/simmi/genesetkey"); Path gkeylocalpub = gkeyssh.resolve("org/simmi/genesetkey.pub"); if (!Files.exists(gkeylocal) && isk != null) { Files.copy(isk, gkeylocal, StandardCopyOption.REPLACE_EXISTING); } if (!Files.exists(gkeylocalpub) && iskp != null) { Files.copy(iskp, gkeylocalpub); } Set<PosixFilePermission> poset = new HashSet<PosixFilePermission>(); poset.add(PosixFilePermission.OWNER_READ); poset.add(PosixFilePermission.OWNER_WRITE); if (Files.exists(gkeylocal)) Files.setPosixFilePermissions(gkeylocal, poset); if (Files.exists(gkeylocalpub)) Files.setPosixFilePermissions(gkeylocalpub, poset); } catch (IOException e1) { e1.printStackTrace(); } catch (UnsupportedOperationException e2) { windows = true; e2.printStackTrace(); } if (windows) { File f = new File(userhome + "\\genesetkey"); f.setExecutable(false, false); f.setWritable(false, false); f.setReadable(false, false); f.setWritable(true, true); f.setReadable(true, true); } this.comp = comp; selcomb = new ComboBox<>(); searchcolcomb = new ComboBox<>(); syncolorcomb = new ComboBox<>(); searchcolcomb.getItems().add("Name"); searchcolcomb.getItems().add("Symbol"); searchcolcomb.getSelectionModel().select(0); setColors(); JMenuBar jmenubar = new JMenuBar(); Menu file = new Menu("File"); MenuItem newitem = new MenuItem("New"); newitem.setOnAction(actionEvent -> newFile()); file.getItems().add(newitem); MenuItem openitem = new MenuItem("Open"); openitem.setOnAction(actionEvent -> { try { importStuff(); } catch (IOException e3) { e3.printStackTrace(); } catch (UnavailableServiceException e3) { e3.printStackTrace(); } }); file.getItems().add(openitem); file.getItems().add(new SeparatorMenuItem()); MenuItem importitem = new MenuItem("Import genomes"); importitem.setOnAction(actionEvent -> fetchGenomes()); file.getItems().add(importitem); MenuItem exportitem = new MenuItem("Export genomes"); exportitem.setOnAction(actionEvent -> exportGenomes(geneset.speccontigMap)); file.getItems().add(exportitem); file.getItems().add(new SeparatorMenuItem()); MenuItem exportproteinitem = new MenuItem("Export protein sequences"); exportproteinitem.setOnAction(actionEvent -> exportProteinSequences(geneset.genelist)); file.getItems().add(exportproteinitem); MenuItem exportgeneitem = new MenuItem("Export gene clusters"); exportgeneitem.setOnAction(actionEvent -> exportGeneClusters(geneset.allgenegroups)); file.getItems().add(exportgeneitem); file.getItems().add(new SeparatorMenuItem()); MenuItem quititem = new MenuItem("Quit"); quititem.setOnAction(actionEvent -> System.exit(0)); file.getItems().add(quititem); Menu edit = new Menu("Edit"); MenuItem clustergenes = new MenuItem("Cluster genes"); clustergenes.setOnAction(actionEvent -> { //fxpanel.setScene( null ); /*Platform.runLater(new Runnable() { @Override public void run() { Label label1 = new Label("Id:"); tb1 = new TextField("0.5"); Label label2 = new Label("Len:"); tb2 = new TextField("0.5"); VBox vbox = new VBox(); HBox hbox1 = new HBox(); hbox1.getChildren().addAll( label1, tb1 ); HBox hbox2 = new HBox(); hbox2.getChildren().addAll( label2, tb2 ); epar = new TextField(); vbox.getChildren().add( epar ); vbox.getChildren().addAll( hbox1, hbox2 ); if( fxs == null ) fxs = new Scene( vbox ); fxs.setRoot( vbox ); fxpanel.setScene( fxs ); } });*/ JPanel panel = new JPanel(); GridBagLayout grid = new GridBagLayout(); GridBagConstraints c = new GridBagConstraints(); panel.setLayout(grid); /*JLabel label1 = new JLabel("Id:"); JTextField tb1 = new JTextField("0.5"); JLabel label2 = new JLabel("Len:"); JTextField tb2 = new JTextField("0.5"); Dimension d = new Dimension( 300, 30 ); JTextField epar = new JTextField(); epar.setSize( d ); epar.setPreferredSize( d ); c.fill = GridBagConstraints.HORIZONTAL; c.gridwidth = 1; c.gridheight = 1; c.gridx = 0; c.gridy = 0; panel.add( label1, c ); c.gridx = 1; c.gridy = 0; panel.add( tb1, c ); c.gridx = 0; c.gridy = 1; panel.add( label2, c ); c.gridx = 1; c.gridy = 1; panel.add( tb2, c ); c.gridx = 0; c.gridy = 2; c.gridwidth = 2; panel.add( epar, c ); JOptionPane.showMessageDialog(comp, new Object[] {panel}, "Clustering parameters", JOptionPane.PLAIN_MESSAGE );*/ /*if( tb1 != null ) { float id = Float.parseFloat( tb1.getText() ); float len = Float.parseFloat( tb2.getText() ); String expar = epar.getText(); tb1 = null; tb2 = null; epar = null;*/ Set<String> species = getSelspec(null, geneset.getSpecies(), null); geneset.clusterGenes(species, false); //} }); MenuItem alignclusters = new MenuItem("Align clusters"); alignclusters.setOnAction(actionEvent -> { try { String OS = System.getProperty("os.name").toLowerCase(); Map<String, String> env = new HashMap<String, String>(); env.put("create", "true"); String uristr = "jar:" + geneset.zippath.toUri(); geneset.zipuri = URI.create(uristr); geneset.zipfilesystem = FileSystems.newFileSystem(geneset.zipuri, env); //s.makeBlastCluster(zipfilesystem.getPath("/"), p, 1); Path aldir = geneset.zipfilesystem.getPath("aligned"); final Path aligneddir = Files.exists(aldir) ? aldir : Files.createDirectory(aldir); Runnable run = new Runnable() { @Override public void run() { try { geneset.zipfilesystem.close(); } catch (IOException e) { e.printStackTrace(); } } }; NativeRun nrun = new NativeRun(run); //ExecutorService es = Executors.newFixedThreadPool( Runtime.getRuntime().availableProcessors() ); Object[] cont = new Object[3]; Collection<GeneGroup> ggset; ObservableList<GeneGroup> ogg = table.getSelectionModel().getSelectedItems(); ggset = new HashSet<GeneGroup>(); if (ogg.size() == 0) { for (GeneGroup gg : geneset.allgenegroups) { //GeneGroup gg = allgenegroups.get(table.convertRowIndexToModel(r)); //gg.getCommonTag() if (gg != null && gg.getCommonTag() == null && gg.size() > 1) ggset.add(gg); } } else { for (GeneGroup gg : ogg) { //GeneGroup gg = geneset.allgenegroups.get(table.convertRowIndexToModel(r)); //gg.getCommonTag() if (gg != null && gg.getCommonTag() == null && gg.size() > 1) ggset.add(gg); } } //int i = 0; List commandsList = new ArrayList(); for (GeneGroup gg : ggset) { String fasta = gg.getFasta(true); String[] cmds = new String[] { OS.indexOf("mac") >= 0 ? "/usr/local/bin/mafft" : "/usr/bin/mafft", "-" }; Object[] paths = new Object[] { fasta.getBytes(), aligneddir.resolve(gg.getCommonId() + ".aa"), null }; commandsList.add(paths); commandsList.add(Arrays.asList(cmds)); //if( i++ > 5000 ) break; } nrun.runProcessBuilder("Running mafft", commandsList, cont, true, run, false); } catch (IOException e1) { if (geneset.zipfilesystem != null) { try { geneset.zipfilesystem.close(); } catch (IOException e2) { e2.printStackTrace(); } } e1.printStackTrace(); } }); MenuItem sharenumaction = new MenuItem("Update share numbers"); sharenumaction.setOnAction(actionEvent -> SwingUtilities.invokeLater(() -> { Set<String> specs = getSelspec(GeneSetHead.this, geneset.specList, null); geneset.updateShareNum(specs); })); MenuItem importgeneclusteringaction = new MenuItem("Import gene clustering"); importgeneclusteringaction.setOnAction(actionEvent -> SwingUtilities.invokeLater(() -> { JPanel panel = new JPanel(); GridBagLayout grid = new GridBagLayout(); GridBagConstraints c = new GridBagConstraints(); panel.setLayout(grid); JLabel label1 = new JLabel("Id:"); JTextField tb11 = new JTextField("0.5"); JLabel label2 = new JLabel("Len:"); JTextField tb21 = new JTextField("0.5"); Dimension d = new Dimension(300, 30); JTextField epar1 = new JTextField(); epar1.setSize(d); epar1.setPreferredSize(d); c.fill = GridBagConstraints.HORIZONTAL; c.gridwidth = 1; c.gridheight = 1; c.gridx = 0; c.gridy = 0; panel.add(label1, c); c.gridx = 1; c.gridy = 0; panel.add(tb11, c); c.gridx = 0; c.gridy = 1; panel.add(label2, c); c.gridx = 1; c.gridy = 1; panel.add(tb21, c); c.gridx = 0; c.gridy = 2; c.gridwidth = 2; panel.add(epar1, c); JOptionPane.showMessageDialog(comp, new Object[] { panel }, "Clustering parameters", JOptionPane.PLAIN_MESSAGE); float id = Float.parseFloat(tb11.getText()); float len = Float.parseFloat(tb21.getText()); //JFileChooser fc = new JFileChooser(); //if( fc.showOpenDialog( GeneSetHead.this ) == JFileChooser.APPROVE_OPTION ) { Serifier s = new Serifier(); //s.mseq = aas; for (String gk : geneset.refmap.keySet()) { Gene g = geneset.refmap.get(gk); if (g.tegeval.getAlignedSequence() != null) System.err.println(g.tegeval.getAlignedSequence().getName()); s.mseq.put(gk, g.tegeval.getAlignedSequence()); } Map<String, String> idspec = new HashMap<String, String>(); for (String idstr : geneset.refmap.keySet()) { if (idstr.contains(" ")) { System.err.println("coooonnnnnni " + idstr); } Gene gene = geneset.refmap.get(idstr); idspec.put(idstr, gene.getSpecies()); } //Sequences seqs = new Sequences(user, name, type, path, nseq) try { Map<String, String> env = new HashMap<String, String>(); env.put("create", "true"); String uristr = "jar:" + geneset.zippath.toUri(); geneset.zipuri = URI.create(uristr); geneset.zipfilesystem = FileSystems.newFileSystem(geneset.zipuri, env); Path root = geneset.zipfilesystem.getPath("/"); Path p = geneset.zipfilesystem.getPath("cluster.blastout"); //root.resolve("culster.blastout"); List<Set<String>> cluster = geneset.uclusterlist == null ? new ArrayList<>() : new ArrayList<>(geneset.uclusterlist); s.makeBlastCluster(root, p, 1, id, len, idspec, cluster, geneset.refmap); System.err.println(cluster.get(0)); if (geneset.uclusterlist != null) System.err.println(geneset.uclusterlist.get(0)); geneset.zipfilesystem.close(); } catch (IOException e1) { if (geneset.zipfilesystem != null) { try { geneset.zipfilesystem.close(); } catch (IOException e2) { e2.printStackTrace(); } } e1.printStackTrace(); } })); MenuItem importgenesymbolaction = new MenuItem("Import gene symbols"); importgenesymbolaction.setOnAction(actionEvent -> SwingUtilities.invokeLater(() -> { JFileChooser fc = new JFileChooser(); if (fc.showOpenDialog(GeneSetHead.this) == JFileChooser.APPROVE_OPTION) { try { Map<String, String> env = new HashMap<>(); env.put("create", "true"); //Path path = zipfile.toPath(); String uristr = "jar:" + geneset.zippath.toUri(); geneset.zipuri = URI.create(uristr /*.replace("file://", "file:")*/ ); geneset.zipfilesystem = FileSystems.newFileSystem(geneset.zipuri, env); Path nf = geneset.zipfilesystem.getPath("/smap_short.txt"); BufferedWriter bw = Files.newBufferedWriter(nf, StandardOpenOption.CREATE); File f = fc.getSelectedFile(); InputStream is = new FileInputStream(f); if (f.getName().endsWith(".gz")) is = new GZIPInputStream(is); geneset.uni2symbol(new InputStreamReader(is), bw, geneset.unimap); bw.close(); //long bl = Files.copy( new ByteArrayInputStream( baos.toByteArray() ), nf, StandardCopyOption.REPLACE_EXISTING ); geneset.zipfilesystem.close(); } catch (IOException e1) { e1.printStackTrace(); } } })); MenuItem importcazyaction = new MenuItem("Import Cazy"); importcazyaction.setOnAction(actionEvent -> SwingUtilities.invokeLater(() -> { JFileChooser fc = new JFileChooser(); if (fc.showOpenDialog(GeneSetHead.this) == JFileChooser.APPROVE_OPTION) { try { BufferedReader rd = Files.newBufferedReader(fc.getSelectedFile().toPath()); geneset.loadcazymap(geneset.cazymap, rd); } catch (IOException e1) { e1.printStackTrace(); } } })); MenuItem gene2refseqaction = new MenuItem("Gene 2 refseq"); gene2refseqaction.setOnAction(actionEvent -> { try { TextField tf = new TextField(); tf.setText("ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2refseq.gz"); Dialog<Path> dialog = new Dialog(); dialog.getDialogPane().setContent(tf); dialog.getDialogPane().getButtonTypes().add(ButtonType.OK); dialog.getDialogPane().getButtonTypes().add(ButtonType.CANCEL); dialog.setResultConverter(param -> param.getButtonData().isCancelButton() ? null : Paths.get(URI.create(tf.getText()))); Optional<Path> opath = dialog.showAndWait(); if (opath.isPresent()) { Map<String, String> env = new HashMap<>(); env.put("create", "true"); //Path path = zipfile.toPath(); String uristr = "jar:" + geneset.zippath.toUri(); geneset.zipuri = URI.create(uristr /*.replace("file://", "file:")*/); geneset.zipfilesystem = FileSystems.newFileSystem(geneset.zipuri, env); Path path = opath.get(); InputStream is = path.toUri().toURL().openStream(); if (path.getFileName().toString().endsWith(".gz")) { is = new GZIPInputStream(is); } Path nf = geneset.zipfilesystem.getPath("/org/simmi/gene2refseq_short.txt"); BufferedWriter bw = Files.newBufferedWriter(nf, StandardOpenOption.CREATE, StandardOpenOption.TRUNCATE_EXISTING, StandardOpenOption.WRITE); geneset.idMapping(new InputStreamReader(is), bw, 5, 1, geneset.refmap, null, geneset.gimap); bw.close(); } } catch (Exception e) { e.printStackTrace(); } finally { try { geneset.zipfilesystem.close(); } catch (IOException e) { e.printStackTrace(); } } }); MenuItem functionmappingaction = new MenuItem("Function mapping"); functionmappingaction.setOnAction(actionEvent -> SwingUtilities.invokeLater(() -> { final JTextField tf = new JTextField(); JButton btn = new JButton("File"); JComponent comp2 = new JComponent() { }; comp2.setLayout(new BorderLayout()); comp2.add(tf); comp2.add(btn, BorderLayout.EAST); tf.setText("http://130.208.252.239/data/sp2go.txt.gz"); final File[] file2 = new File[1]; btn.addActionListener(e -> { JFileChooser fc = new JFileChooser(); if (fc.showOpenDialog(GeneSetHead.this) == JFileChooser.APPROVE_OPTION) { file2[0] = fc.getSelectedFile(); try { tf.setText(fc.getSelectedFile().toURI().toURL().toString()); } catch (MalformedURLException e1) { e1.printStackTrace(); } } }); try { Map<String, String> env = new HashMap<>(); env.put("create", "true"); //Path path = zipfile.toPath(); String uristr = "jar:" + geneset.zippath.toUri(); geneset.zipuri = URI.create(uristr /*.replace("file://", "file:")*/ ); geneset.zipfilesystem = FileSystems.newFileSystem(geneset.zipuri, env); Path nf = geneset.zipfilesystem.getPath("/org/simmi/sp2go_short.txt"); BufferedWriter bw = Files.newBufferedWriter(nf, StandardOpenOption.CREATE, StandardOpenOption.TRUNCATE_EXISTING, StandardOpenOption.WRITE); JOptionPane.showMessageDialog(GeneSetHead.this, comp2); final JDialog dialog = new JDialog(); dialog.setTitle("Function mapping"); dialog.setDefaultCloseOperation(JDialog.DISPOSE_ON_CLOSE); dialog.setSize(400, 300); comp2 = new JComponent() { }; comp2.setLayout(new BorderLayout()); final JTextArea ta = new JTextArea(); /*final InputStream fis; if( file[0] != null ) fis = new FileInputStream( file[0] ); else { JTextField host = new JTextField("localhost"); JOptionPane.showMessageDialog(null, host); String username = System.getProperty("user.name"); String hostname = host.getText(); List<String> commandsList = Arrays.asList( new String[] {"ssh",username+"@"+hostname,"cat",tf.getText()} ); ProcessBuilder pb = new ProcessBuilder( commandsList ); Process p = pb.start(); for( Object commands : commandsList ) { if( commands instanceof List ) { for( Object cmd : (List)commands ) { ta.append(cmd+" "); } ta.append("\n"); } else { ta.append(commands+" "); } } ta.append("\n"); fis = p.getInputStream(); }*/ final JProgressBar pbar = new JProgressBar(); final Thread t = new Thread() { public void run() { try { URL url = new URL(tf.getText()); InputStream fis = url.openStream(); BufferedReader br = new BufferedReader(new InputStreamReader(new GZIPInputStream(fis))); //if( unimap != null ) unimap.clear(); //unimap = idMapping(new InputStreamReader(is), bw, 2, 0, refmap, genmap, gimap); geneset.funcMappingUni(br, geneset.unimap, bw); fis.close(); bw.close(); try { geneset.zipfilesystem.close(); } catch (Exception e2) { e2.printStackTrace(); } ; pbar.setIndeterminate(false); pbar.setEnabled(false); } catch (IOException e) { e.printStackTrace(); } } }; ta.setEditable(false); final JScrollPane sp = new JScrollPane(ta); dialog.add(comp2); comp2.add(pbar, BorderLayout.NORTH); comp2.add(sp, BorderLayout.CENTER); pbar.setIndeterminate(true); t.start(); /*okokdialog.addWindowListener( new WindowListener() { @Override public void windowOpened(WindowEvent e) {} @Override public void windowIconified(WindowEvent e) {} @Override public void windowDeiconified(WindowEvent e) {} @Override public void windowDeactivated(WindowEvent e) {} @Override public void windowClosing(WindowEvent e) {} @Override public void windowClosed(WindowEvent e) { if( pbar.isEnabled() ) { pbar.setIndeterminate( false ); pbar.setEnabled( false ); } } @Override public void windowActivated(WindowEvent e) {} });*/ dialog.setVisible(true); //long bl = Files.copy( new ByteArrayInputStream( baos.toByteArray() ), nf, StandardCopyOption.REPLACE_EXISTING ); } catch (IOException e1) { e1.printStackTrace(); } })); MenuItem importidmappingaction = new MenuItem("Import idmapping"); importidmappingaction.setOnAction(actionEvent -> SwingUtilities.invokeLater(() -> { final JTextField tf = new JTextField(); JButton btn = new JButton("File"); JComponent comp2 = new JComponent() { }; comp2.setLayout(new BorderLayout()); comp2.add(tf); comp2.add(btn, BorderLayout.EAST); tf.setText( "ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/idmapping.dat.gz"); final File[] file2 = new File[1]; btn.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { JFileChooser fc = new JFileChooser(); if (fc.showOpenDialog(GeneSetHead.this) == JFileChooser.APPROVE_OPTION) { file2[0] = fc.getSelectedFile(); try { tf.setText(fc.getSelectedFile().toURI().toURL().toString()); } catch (MalformedURLException e1) { e1.printStackTrace(); } } } }); JOptionPane.showMessageDialog(GeneSetHead.this, comp2); //Thread t = new Thread() { // public void run() { try { Map<String, String> env = new HashMap<String, String>(); env.put("create", "true"); //Path path = zipfile.toPath(); String uristr = "jar:" + geneset.zippath.toUri(); geneset.zipuri = URI.create(uristr /*.replace("file://", "file:")*/ ); geneset.zipfilesystem = FileSystems.newFileSystem(geneset.zipuri, env); Path nf = geneset.zipfilesystem.getPath("/org/simmi/idmapping_short.dat"); final BufferedWriter bw = Files.newBufferedWriter(nf, StandardOpenOption.CREATE, StandardOpenOption.WRITE, StandardOpenOption.TRUNCATE_EXISTING); final JDialog dialog = new JDialog(); dialog.setTitle("Id mapping"); dialog.setDefaultCloseOperation(JDialog.DISPOSE_ON_CLOSE); dialog.setSize(400, 300); comp2 = new JComponent() { }; comp2.setLayout(new BorderLayout()); final JTextArea ta = new JTextArea(); /*final InputStream fis; if( file[0] != null ) fis = new FileInputStream( file[0] ); else { /*Object[] cont = new Object[3]; Runnable run = new Runnable() { public void run() { try { bw.close(); geneset.zipfilesystem.close(); } catch (IOException e) { e.printStackTrace(); } } };* JTextField host = new JTextField("localhost"); JOptionPane.showMessageDialog(null, host); String username = System.getProperty("user.name"); String hostname = host.getText(); List<String> commandsList = Arrays.asList( new String[] {"ssh",username+"@"+hostname,"cat",tf.getText()} ); ProcessBuilder pb = new ProcessBuilder( commandsList ); Process p = pb.start(); for( Object commands : commandsList ) { if( commands instanceof List ) { for( Object cmd : (List)commands ) { ta.append(cmd+" "); } ta.append("\n"); } else { ta.append(commands+" "); } } ta.append("\n"); fis = p.getInputStream(); }*/ final JProgressBar pbar = new JProgressBar(); final Thread t = new Thread() { public void run() { try { URL url = new URL(tf.getText()); InputStream fis = url.openStream(); InputStream is = new GZIPInputStream(fis); if (geneset.unimap != null) geneset.unimap.clear(); geneset.unimap = geneset.idMapping(new InputStreamReader(is), bw, 2, 0, geneset.refmap, geneset.genmap, geneset.gimap); is.close(); fis.close(); bw.close(); try { geneset.zipfilesystem.close(); } catch (Exception ep) { ep.printStackTrace(); } ; pbar.setIndeterminate(false); pbar.setEnabled(false); } catch (IOException e) { e.printStackTrace(); } } }; ta.setEditable(false); final JScrollPane sp = new JScrollPane(ta); dialog.add(comp2); comp2.add(pbar, BorderLayout.NORTH); comp2.add(sp, BorderLayout.CENTER); pbar.setIndeterminate(true); t.start(); /*System.err.println( "about to run" ); for( Object commands : commandsList ) { if( commands instanceof List ) { for( Object c : (List)commands ) { System.err.print( c+" " ); } System.err.println(); } else { System.err.print( commands+" " ); } } System.err.println();*/ /*okokdialog.addWindowListener( new WindowListener() { @Override public void windowOpened(WindowEvent e) {} @Override public void windowIconified(WindowEvent e) {} @Override public void windowDeiconified(WindowEvent e) {} @Override public void windowDeactivated(WindowEvent e) {} @Override public void windowClosing(WindowEvent e) {} @Override public void windowClosed(WindowEvent e) { if( pbar.isEnabled() ) { /*String result = ta.getText().trim(); if( run != null ) { cont[0] = null; cont[1] = result; cont[2] = new Date( System.currentTimeMillis() ).toString(); run.run(); }* pbar.setIndeterminate( false ); pbar.setEnabled( false ); } } @Override public void windowActivated(WindowEvent e) {} });*/ dialog.setVisible(true); /*NativeRun nrun = new NativeRun(); nrun.runProcessBuilder("Idmapping", Arrays.asList( tf.getText().split(" ") ), run, cont, false); ProcessBuilder pb = new ProcessBuilder( tf.getText().split(" ") ); Process p = pb.start(); fis = p.getInputStream(); }*/ //long bl = Files.copy( new ByteArrayInputStream( baos.toByteArray() ), nf, StandardCopyOption.REPLACE_EXISTING ); } catch (IOException e1) { e1.printStackTrace(); try { geneset.zipfilesystem.close(); } catch (Exception e2) { e2.printStackTrace(); } ; } // } //}; //t.start(); //} })); MenuItem cogblastaction = new MenuItem("Cog blast"); cogblastaction.setOnAction(actionEvent -> SwingUtilities.invokeLater(() -> { Set<String> species = getSelspec(null, geneset.getSpecies(), null); if (species != null && species.size() > 0) Platform.runLater(() -> cogBlastDlg(species)); })); MenuItem unresolvedblastaction = new MenuItem("Unresolved blast"); unresolvedblastaction.setOnAction(actionEvent -> SwingUtilities.invokeLater(() -> { try { Set<String> species = getSelspec(null, geneset.getSpecies(), null); StringWriter sb = new StringWriter(); Path dbPath = Paths.get("/data/nr"); ObservableList<Gene> genes = gtable.getSelectionModel().getSelectedItems(); if (genes.size() > 0) { if (isGeneview()) { for (Gene g : gtable.getSelectionModel().getSelectedItems()) { //int i = table.convertRowIndexToModel(r); //Gene g = geneset.genelist.get(i); Sequence gs = g.tegeval.getProteinSequence(); gs.setName(g.id); gs.writeSequence(sb); } } else { for (GeneGroup gg : table.getSelectionModel().getSelectedItems()) { //int i = table.convertRowIndexToModel(r); //GeneGroup gg = geneset.allgenegroups.get(i); Gene g = null; for (Gene gene : gg.genes) { g = gene; break; } Sequence gs = g.tegeval.getProteinSequence(); gs.setName(g.id); gs.writeSequence(sb); } } } else { for (Gene g : geneset.genelist) { if (g.getTag() == null || g.getTag().equalsIgnoreCase("gene")) { if (species.contains(g.getSpecies())) { Sequence gs = g.tegeval.getProteinSequence(); gs.setName(g.id); gs.writeSequence(sb); /*sb.append(">" + g.id + "\n"); for (int i = 0; i < gs.length(); i += 70) { sb.append( gs.substring(i, Math.min( i + 70, gs.length() )) + "\n"); }*/ } } } } Map<String, String> env = new HashMap<>(); env.put("create", "true"); String uristr = "jar:" + geneset.zippath.toUri(); geneset.zipuri = URI.create(uristr /*.replace("file://", "file:")*/ ); geneset.zipfilesystem = FileSystems.newFileSystem(geneset.zipuri, env); Path resPath = geneset.zipfilesystem.getPath("/unresolved.blastout"); NativeRun nrun = new NativeRun(); SerifyApplet.blastpRun(nrun, sb.getBuffer(), dbPath, resPath, "-evalue 0.00001", null, true, geneset.zipfilesystem, geneset.user, primaryStage); } catch (IOException e1) { e1.printStackTrace(); } })); MenuItem importbiosystemsaction = new MenuItem("Import biosystems"); importbiosystemsaction.setOnAction(actionEvent -> { Dialog<Map<String, Set<String>>> dialog = new Dialog(); TextField gene = new TextField(); TextField biosys = new TextField(); gene.setText("ftp://ftp.ncbi.nlm.nih.gov/pub/biosystems/biosystems.20160519/biosystems_gene_all.gz"); biosys.setText("ftp://ftp.ncbi.nlm.nih.gov/pub/biosystems/biosystems.20160519/bsid2info.gz"); VBox duo = new VBox(); duo.getChildren().add(gene); duo.getChildren().add(biosys); dialog.getDialogPane().setContent(duo); dialog.getDialogPane().getButtonTypes().add(ButtonType.OK); dialog.getDialogPane().getButtonTypes().add(ButtonType.CANCEL); dialog.setResultConverter(param -> { if (!param.getButtonData().isCancelButton()) { Map<String, Set<String>> result = null; Set<String> geneidset = geneset.genelist.stream().map(g -> g.genid).collect(Collectors.toSet()); try { InputStream p = new URI(gene.getText()).toURL().openStream(); InputStream b = new URI(biosys.getText()).toURL().openStream(); if (gene.getText().endsWith(".gz")) p = new GZIPInputStream(p); if (biosys.getText().endsWith(".gz")) b = new GZIPInputStream(b); Map<String, List<String[]>> group = new BufferedReader(new InputStreamReader(p)).lines() .map(l -> l.split("\t")).filter(s -> geneidset.contains(s[1])) .collect(Collectors.groupingBy(s -> s[1])); Set<String> bsids = group.entrySet().stream().flatMap(e -> e.getValue().stream()) .map(s -> s[0]).collect(Collectors.toSet()); Map<String, String> bsid2name = new BufferedReader(new InputStreamReader(b)).lines() .map(s -> s.split("\t")).filter(s -> bsids.contains(s[0])) .collect(Collectors.toMap(s -> s[0], s -> s[2] + ":" + s[3])); result = group.entrySet().stream() .collect(Collectors.toMap(s -> s.getKey(), s -> s.getValue().stream() .map(sub -> bsid2name.get(sub[0])).collect(Collectors.toSet()))); } catch (IOException e) { e.printStackTrace(); } catch (URISyntaxException e) { e.printStackTrace(); } //Path p = Paths.get(gene.getText()); //Path b = Paths.get(biosys.getText()); return result; } return null; }); Optional<Map<String, Set<String>>> od = dialog.showAndWait(); if (od.isPresent()) { geneset.biosystemsmap = od.get(); Map<String, String> env = new HashMap<>(); env.put("create", "true"); String uristr = "jar:" + geneset.zippath.toUri(); geneset.zipuri = URI.create(uristr /*.replace("file://", "file:")*/ ); try { geneset.zipfilesystem = FileSystems.newFileSystem(geneset.zipuri, env); Path resPath = geneset.zipfilesystem.getPath("/biosystems.txt"); BufferedWriter bw = Files.newBufferedWriter(resPath, StandardOpenOption.TRUNCATE_EXISTING); geneset.biosystemsmap.entrySet().stream().forEach(e -> { try { bw.write(e.getKey() + "\t" + e.getValue().stream().collect(Collectors.joining(";")) + "\n"); } catch (IOException e1) { e1.printStackTrace(); } }); bw.close(); } catch (Exception e) { e.printStackTrace(); } finally { try { geneset.zipfilesystem.close(); } catch (IOException e) { e.printStackTrace(); } } } }); MenuItem importkeggpathwayaction = new MenuItem("Import kegg pathways"); importkeggpathwayaction.setOnAction(actionEvent -> { Set<String> keggids = new HashSet<>(); for (Gene g : geneset.genelist) { if (g.keggid != null) { int i = g.keggid.indexOf(':'); if (i > 0) { keggids.add(g.keggid.substring(0, i)); } } } System.err.println(keggids); JTextField tf = new JTextField("http://130.208.252.239/organisms/"); JOptionPane.showMessageDialog(null, tf); Map<String, String> env = new HashMap<>(); env.put("create", "true"); Path rootp = null; try { geneset.zipfilesystem = FileSystems.newFileSystem(geneset.zipuri, env); } catch (Exception ee) { ee.printStackTrace(); } for (Path root : geneset.zipfilesystem.getRootDirectories()) { rootp = root; break; } for (String kegg : keggids) { try { URL url = new URL(tf.getText() + kegg + ".tar.gz"); InputStream is = url.openStream(); GZIPInputStream gz = new GZIPInputStream(is); TarArchiveInputStream tar = new TarArchiveInputStream(gz); TarArchiveEntry tae = (TarArchiveEntry) tar.getNextEntry(); while (tae != null) { geneset.traverseTar(tar, tae, rootp); tae = (TarArchiveEntry) tar.getNextEntry(); } is.close(); } catch (IOException e1) { e1.printStackTrace(); } } try { geneset.zipfilesystem.close(); } catch (Exception ee) { ee.printStackTrace(); } ; }); edit.getItems().add(clustergenes); edit.getItems().add(alignclusters); edit.getItems().add(new SeparatorMenuItem()); edit.getItems().add(sharenumaction); edit.getItems().add(importgeneclusteringaction); edit.getItems().add(importgenesymbolaction); edit.getItems().add(importcazyaction); edit.getItems().add(functionmappingaction); edit.getItems().add(importidmappingaction); edit.getItems().add(gene2refseqaction); edit.getItems().add(importbiosystemsaction); edit.getItems().add(importkeggpathwayaction); edit.getItems().add(new SeparatorMenuItem()); edit.getItems().add(cogblastaction); edit.getItems().add(unresolvedblastaction); Menu view = new Menu("View"); gb = new RadioMenuItem("Genes"); gb.setOnAction(actionEvent -> { splitpane.getItems().remove(table); splitpane.getItems().add(0, gtable); //table.setModel( defaultModel ); }); view.getItems().add(gb); ggb = new RadioMenuItem("Gene groups"); ggb.setOnAction(actionEvent -> { splitpane.getItems().remove(gtable); splitpane.getItems().add(0, table); //table.setModel( groupModel ); }); ToggleGroup bg = new ToggleGroup(); gb.setToggleGroup(bg); ggb.setToggleGroup(bg); //ButtonGroup bg = new ButtonGroup(); //bg.add( gb ); //bg.add( ggb ); ggb.setSelected(true); view.getItems().add(ggb); ActionCollection.addAll(view, geneset.clusterMap, GeneSetHead.this, geneset.speccontigMap, table, comp, geneset.cs); Menu help = new Menu("Help"); MenuItem about = new MenuItem("About"); about.setOnAction(actionEvent -> SwingUtilities .invokeLater(() -> JOptionPane.showMessageDialog(comp, "CompGen 1.0"))); help.getItems().add(about); MenuItem test = new MenuItem("Test"); test.setOnAction(actionEvent -> { /*for( Gene g : geneset.genelist ) { Sequence seq = g.tegeval.getContig(); if( seq == null ) { System.err.println(); } }*/ for (String spec : geneset.speccontigMap.keySet()) { if (spec.contains("RAST")) { List<Sequence> lseq = geneset.speccontigMap.get(spec); for (Sequence seq : lseq) { for (Annotation a : seq.getAnnotations()) { System.err.println(a.getGene().getGeneGroup().species); /*Sequence tseq = a.getContig(); if( tseq == null ) { System.err.println(); }*/ } } } } /*for( GeneGroup gg : allgenegroups ) { if( gg.species.size() > 1 ) { System.err.println( gg.species ); } }*/ }); help.getItems().add(test); help.getItems().add(new SeparatorMenuItem()); MenuItem runserver = new MenuItem("Run server"); runserver.setOnAction(actionEvent -> { SwingUtilities.invokeLater(new Runnable() { public void run() { JSpinner spin = new JSpinner(); JOptionPane.showMessageDialog(GeneSetHead.this, spin, "Port", JOptionPane.QUESTION_MESSAGE); try { geneset.cs = WSServer.startServer(GeneSetHead.this, (Integer) spin.getValue()); } catch (UnknownHostException e1) { e1.printStackTrace(); } } }); }); help.getItems().add(runserver); help.getItems().add(new SeparatorMenuItem()); CheckMenuItem cbmi = new CheckMenuItem("Use geneset user"); help.getItems().add(cbmi); cbmi.setOnAction(actionEvent -> { if (cbmi.isSelected()) { geneset.user = "geneset"; } else geneset.user = System.getProperty("user.name"); JavaFasta.user = geneset.user; if (geneset.currentSerify != null) geneset.currentSerify.user = geneset.user; }); help.getItems().add(new SeparatorMenuItem()); MenuItem helptut = new MenuItem("Help & Tutorial"); helptut.setOnAction(actionEvent -> { try { Desktop.getDesktop().browse(new URI("http://thermusgenes.appspot.com/pancore.html")); } catch (IOException | URISyntaxException e1) { e1.printStackTrace(); } }); help.getItems().add(helptut); Menu sequencemenu = new Menu("Sequence"); MenuItem showgroupseq = new MenuItem("Show group sequences"); showgroupseq.setOnAction(actionEvent -> { //JTextArea textarea = new JTextArea(); //JScrollPane scrollpane = new JScrollPane(textarea); /*try { if (clipboardService == null) clipboardService = (ClipboardService) ServiceManager.lookup("javax.jnlp.ClipboardService"); Action action = new CopyAction("Copy", null, "Copy data", new Integer(KeyEvent.VK_CONTROL + KeyEvent.VK_C)); textarea.getActionMap().put("copy", action); grabFocus = true; } catch (Exception ee) { ee.printStackTrace(); System.err.println("Copy services not available. Copy using 'Ctrl-c'."); } textarea.setDragEnabled(true);*/ JFrame frame = null; if (geneset.currentSerify == null) { frame = new JFrame(); frame.setDefaultCloseOperation(JFrame.HIDE_ON_CLOSE); frame.setSize(400, 300); Map<String, String> env = new HashMap<String, String>(); //Path path = zipfile.toPath(); String uristr = "jar:" + geneset.zippath.toUri(); geneset.zipuri = URI.create(uristr /*.replace("file://", "file:")*/ ); try { geneset.zipfilesystem = FileSystems.newFileSystem(geneset.zipuri, env); } catch (IOException e1) { e1.printStackTrace(); } SerifyApplet sa = new SerifyApplet(geneset.zipfilesystem); sa.init(frame, null, geneset.user); //frame.add( ) geneset.currentSerify = sa; } /* else frame = (JFrame)currentSerify.cnt;*/ String[] farr = new String[] { "o.profundus", "mt.silvanus", "mt.ruber", "m.hydrothermalis", "t.thermophilus_SG0_5JP17_16", "t.thermophilusJL18", "t.thermophilusHB8", "t.thermophilusHB27", "t.scotoductusSA01", "t.scotoductus4063", "t.scotoductus1572", "t.scotoductus2101", "t.scotoductus2127", "t.scotoductus346", "t.scotoductus252", "t.antranikiani", "t.kawarayensis", "t.brockianus", "t.igniterrae", "t.eggertsoni", "t.RLM", "t.oshimai_JL2", "t.oshimai", "t.filiformis", "t.arciformis", "t.islandicus", "t.aquaticus", "t.spCCB" }; Map<Integer, String> ups = new HashMap<Integer, String>(); Set<Integer> stuck = new HashSet<Integer>(); Map<Integer, List<Tegeval>> ups2 = new HashMap<Integer, List<Tegeval>>(); //int[] rr = table.getSelectedRows(); for (Gene gg : gtable.getSelectionModel().getSelectedItems()) { //int cr = table.convertRowIndexToModel(r); //Gene gg = geneset.genelist.get(cr); if (gg.getSpecies() != null) { if (gg.genid != null && gg.genid.length() > 0) { ups.put(gg.getGroupIndex(), gg.name); stuck.add(gg.getGroupIndex()); } if (!stuck.contains(gg.getGroupIndex())) { if (!ups.containsKey(gg.getGroupIndex()) || !(gg.name.contains("unnamed") || gg.name.contains("hypot"))) ups.put(gg.getGroupIndex(), gg.name); } List<Tegeval> tlist; if (ups2.containsKey(gg.getGroupIndex())) tlist = ups2.get(gg.getGroupIndex()); else { tlist = new ArrayList<Tegeval>(); ups2.put(gg.getGroupIndex(), tlist); } //Set<String> specs = new HashSet<String>(); //textarea.append(gg.name + ":\n"); //for (String sp : gg.species.keySet()) { int count = 0; for (String sp : farr) { //Teginfo stv = gg.species.equals(sp) ? gg.teginfo : null; if (gg.getSpecies().equals(sp)) tlist.add(gg.tegeval); /*for( String key : gg.species.keySet() ) { if( key.contains("JL2") ) { System.err.println( " erm " + key ); } }*/ /*if( stv == null && gg.species.size() == 28 ) { System.err.println( gg.species ); System.err.println( sp ); }*/ //System.err.println( gg.species.keySet() ); /*if( stv == null ) { //System.err.println( sp ); } else { count++; //specs.add( sp ); for (Tegeval tv : stv.tset) { tlist.add( tv ); /*textarea.append(">" + tv.cont + " " + tv.teg + " " + tv.eval + "\n"); if (tv.dna != null) { for (int i = 0; i < tv.dna.length(); i += 70) { textarea.append(tv.dna.gg.speciessubstring(i, Math.min(i + 70, tv.dna.length())) + "\n"); } }* } }*/ } //if( count < gg.species.size() ) { // System.err.println( gg.species ); // System.err.println(); //} //if( specs.size() < 28 ) System.err.println("mu " + specs); } } try { StringWriter sb = new StringWriter(); for (int gi : ups.keySet()) { String name = ups.get(gi); List<Tegeval> tlist = ups2.get(gi); sb.append(name.replace('/', '-') + ":\n"); if (tlist.size() < 28) { for (Tegeval tv : tlist) { System.err.println(tv.name); } System.err.println(); } for (Tegeval tv : tlist) { Sequence ps = tv.getProteinSequence(); ps.setName(tv.name.substring(0, tv.name.indexOf('_'))); ps.writeSequence(sb); /*sb.append(">" + tv.name.substring(0, tv.name.indexOf('_')) + "\n"); for (int i = 0; i < ps.length(); i += 70) { sb.append( ps.substring(i, Math.min(i + 70, tv.getProteinLength() )) + "\n"); }*/ } } geneset.currentSerify.addSequences("uh", new StringReader(sb.toString()), Paths.get("/"), null); } catch (URISyntaxException | IOException e1) { e1.printStackTrace(); } frame.setVisible(true); }); sequencemenu.getItems().add(showgroupseq); MenuItem showgroupdnaseq = new MenuItem("Show group DNA sequences"); showgroupdnaseq.setOnAction(actionEvent -> { final JTextArea textarea = new JTextArea(); JScrollPane scrollpane = new JScrollPane(textarea); try { if (clipboardService == null) clipboardService = (ClipboardService) ServiceManager.lookup("javax.jnlp.ClipboardService"); Action action = new CopyAction("Copy", null, "Copy data", new Integer(KeyEvent.VK_CONTROL + KeyEvent.VK_C)); textarea.getActionMap().put("copy", action); grabFocus = true; } catch (Exception ee) { ee.printStackTrace(); System.err.println("Copy services not available. Copy using 'Ctrl-c'."); } textarea.setDragEnabled(true); try { final DataFlavor df = new DataFlavor("text/plain;charset=utf-8"); TransferHandler th = new TransferHandler() { /** * */ private static final long serialVersionUID = 1L; public int getSourceActions(JComponent c) { return TransferHandler.COPY_OR_MOVE; } public boolean canImport(TransferHandler.TransferSupport support) { return false; } protected Transferable createTransferable(JComponent c) { return new Transferable() { @Override public Object getTransferData(DataFlavor arg0) throws UnsupportedFlavorException, IOException { if (arg0.equals(df)) { return new ByteArrayInputStream(textarea.getText().getBytes()); } else { return textarea.getText(); } } @Override public DataFlavor[] getTransferDataFlavors() { return new DataFlavor[] { df, DataFlavor.stringFlavor }; } @Override public boolean isDataFlavorSupported(DataFlavor arg0) { if (arg0.equals(df) || arg0.equals(DataFlavor.stringFlavor)) { return true; } return false; } }; } public boolean importData(TransferHandler.TransferSupport support) { return false; } }; textarea.setTransferHandler(th); } catch (ClassNotFoundException e1) { e1.printStackTrace(); } Map<Integer, String> ups = new HashMap<Integer, String>(); Set<Integer> stuck = new HashSet<Integer>(); Map<Integer, List<Tegeval>> ups2 = new HashMap<Integer, List<Tegeval>>(); //int[] rr = table.getSelectedRows(); for (Gene gg : gtable.getSelectionModel().getSelectedItems()) { //int cr = table.convertRowIndexToModel(r); //Gene gg = geneset.genelist.get(cr); if (gg.getSpecies() != null) { if (gg.genid != null && gg.genid.length() > 0) { ups.put(gg.getGroupIndex(), gg.name); stuck.add(gg.getGroupIndex()); } if (!stuck.contains(gg.getGroupIndex())) { if (!ups.containsKey(gg.getGroupIndex()) || !(gg.name.contains("unnamed") || gg.name.contains("hypot"))) ups.put(gg.getGroupIndex(), gg.name); } List<Tegeval> tlist; if (ups2.containsKey(gg.getGroupIndex())) tlist = ups2.get(gg.getGroupIndex()); else { tlist = new ArrayList<Tegeval>(); ups2.put(gg.getGroupIndex(), tlist); } //textarea.append(gg.name + ":\n"); tlist.add(gg.tegeval); /*textarea.append(">" + tv.cont + " " + tv.teg + " " + tv.eval + "\n"); if (tv.dna != null) { for (int i = 0; i < tv.dna.length(); i += 70) { textarea.append(tv.dna.substring(i, Math.min(i + 70, tv.dna.length())) + "\n"); } }*/ } } for (int gi : ups.keySet()) { String name = ups.get(gi); List<Tegeval> tlist = ups2.get(gi); textarea.append(name.replace('/', '-') + ":\n"); for (Tegeval tv : tlist) { textarea.append(">" + tv.name.substring(0, tv.name.indexOf('_')) + "\n"); for (int i = 0; i < tv.getLength(); i += 70) { textarea.append(tv.getSubstring(i, Math.min(i + 70, tv.getLength())) + "\n"); } } } JFrame frame = new JFrame(); frame.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE); frame.add(scrollpane); frame.setSize(400, 300); frame.setVisible(true); }); sequencemenu.getItems().add(showgroupdnaseq); sequencemenu.getItems().add(new SeparatorMenuItem()); MenuItem showallseq = new MenuItem("Show all sequences"); showallseq.setOnAction(actionEvent -> { JFrame frame = new JFrame(); frame.setSize(800, 600); frame.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE); Serifier serifier = new Serifier(); JavaFasta jf = new JavaFasta((comp instanceof JApplet) ? (JApplet) comp : null, serifier, geneset.cs); jf.initGui(frame); Map<String, Sequence> contset = new HashMap<String, Sequence>(); //int[] rr = table.getSelectedRows(); for (Gene gg : gtable.getSelectionModel().getSelectedItems()) { //int cr = table.convertRowIndexToModel(r); //Gene gg = geneset.genelist.get(cr); Tegeval tv = gg.tegeval; String contig = tv.getContshort().getName(); Sequence seq = tv.getProteinSequence(); seq.setName(contig); serifier.mseq.put(seq.getName(), seq); //Sequence seq = new Sequence( contig, aa, serifier.mseq ); serifier.addSequence(seq); } jf.updateView(); frame.setVisible(true); }); sequencemenu.getItems().add(showallseq); MenuItem showseq = new MenuItem("Show sequences"); showseq.setOnAction(actionEvent -> { Set<GeneGroup> genegroups = new HashSet<GeneGroup>(); //int[] rr = table.getSelectedRows(); if (!isGeneview()) { for (GeneGroup gg : table.getSelectionModel().getSelectedItems()) { //int cr = table.convertRowIndexToModel(r); //GeneGroup gg = geneset.allgenegroups.get(cr); genegroups.add(gg); } } else { for (Gene gg : gtable.getSelectionModel().getSelectedItems()) { //int cr = table.convertRowIndexToModel(r); //Gene gg = geneset.genelist.get(cr); genegroups.add(gg.getGeneGroup()); } } Platform.runLater(() -> { Set<String> specs = null; if (table.getItems().size() > 1) specs = getSelspec(comp, geneset.specList, null); showSequences(comp, genegroups, false, specs); }); }); sequencemenu.getItems().add(showseq); MenuItem showseqwgenenames = new MenuItem("Show sequences w/genenames"); showseqwgenenames.setOnAction(actionEvent -> { Set<GeneGroup> genegroups = new HashSet<GeneGroup>(); //int[] rr = table.getSelectedRows(); if (!isGeneview()) { for (GeneGroup gg : table.getSelectionModel().getSelectedItems()) { //int cr = table.convertRowIndexToModel(r); //GeneGroup gg = geneset.allgenegroups.get(cr); genegroups.add(gg); } } else { for (Gene gg : gtable.getSelectionModel().getSelectedItems()) { //int cr = table.convertRowIndexToModel(r); //Gene gg = geneset.genelist.get(cr); genegroups.add(gg.getGeneGroup()); } } //Set<String> specs = null; //if( rr.length > 1 ) specs = getSelspec(comp, specList, null); showSequences(comp, genegroups, false, null, true); }); sequencemenu.getItems().add(showseqwgenenames); MenuItem showalignseq = new MenuItem("Show aligned sequences"); showalignseq.setOnAction(actionEvent -> { Set<GeneGroup> genegroups = new HashSet<GeneGroup>(); //int[] rr = table.getSelectedRows(); if (!isGeneview()) { for (GeneGroup gg : table.getSelectionModel().getSelectedItems()) { genegroups.add(gg); } } else { for (Gene gg : gtable.getSelectionModel().getSelectedItems()) { genegroups.add(gg.getGeneGroup()); } } Serifier serifier = new Serifier(); for (GeneGroup ggroup : genegroups) { for (Tegeval tv : ggroup.getTegevals()) { String selspec = tv.getContshort().getSpec();//tv.getContig(); String spec = geneset.nameFix(selspec); /*if( selspec.contains("hermus") ) spec = selspec; else { Matcher m = Pattern.compile("\\d").matcher(selspec); int firstDigitLocation = m.find() ? m.start() : 0; if( firstDigitLocation == 0 ) spec = "Thermus_" + selspec; else spec = "Thermus_" + selspec.substring(0,firstDigitLocation) + "_" + selspec.substring(firstDigitLocation); }*/ Sequence seq = tv.getAlignedSequence(); //System.err.println( "seqlen " + seq.length() ); if (seq != null) { seq.setName(spec); //Sequence seq = new Sequence( contig, seqstr, null ); serifier.addSequence(seq); } else { Sequence sb = tv.getProteinSequence(); sb.setName(spec); //Sequence sseq = new Sequence( spec, sb, serifier.mseq ); serifier.addSequence(sb); } } } showAlignedSequences(comp, serifier); }); sequencemenu.getItems().add(showalignseq); MenuItem splitseq = new MenuItem("Split/Show sequences"); splitseq.setOnAction(actionEvent -> { try { StringBuffer sb = getSelectedASeqs(table, geneset.genelist, GeneSetHead.this, geneset.specList); if (geneset.currentSerify == null) { JFrame frame = new JFrame(); frame.setDefaultCloseOperation(JFrame.HIDE_ON_CLOSE); frame.setSize(800, 600); SerifyApplet sa = new SerifyApplet(geneset.zipfilesystem); sa.init(frame, null, geneset.user); geneset.currentSerify = sa; frame.setVisible(true); } geneset.currentSerify.addSequences("uh", new StringReader(sb.toString()), Paths.get("/"), null); } catch (URISyntaxException | IOException e1) { e1.printStackTrace(); } //JTextArea textarea = new JTextArea(); //textarea.append( sb.toString() ); /*try { if (clipboardService == null) clipboardService = (ClipboardService) ServiceManager.lookup("javax.jnlp.ClipboardService"); Action action = new CopyAction("Copy", null, "Copy data", new Integer(KeyEvent.VK_CONTROL + KeyEvent.VK_C)); textarea.getActionMap().put("copy", action); grabFocus = true; } catch (Exception ee) { ee.printStackTrace(); System.err.println("Copy services not available. Copy using 'Ctrl-c'."); } * * final DataFlavor df = * DataFlavor.getTextPlainUnicodeFlavor();//new * DataFlavor("text/plain;charset=utf-8"); final String charset * = df.getParameter("charset"); final Transferable transferable * = new Transferable() { * * @Override public Object getTransferData(DataFlavor arg0) * throws UnsupportedFlavorException, IOException { String ret = * makeCopyString( detailTable ); return new * ByteArrayInputStream( ret.getBytes( charset ) ); } * * @Override public DataFlavor[] getTransferDataFlavors() { * return new DataFlavor[] { df }; } * * @Override public boolean isDataFlavorSupported(DataFlavor * arg0) { if( arg0.equals(df) ) { return true; } return false; * } }; * * TransferHandler th = new TransferHandler() { private static * final long serialVersionUID = 1L; * * public int getSourceActions(JComponent c) { return * TransferHandler.COPY_OR_MOVE; } * * public boolean canImport(TransferHandler.TransferSupport * support) { return false; } * * protected Transferable createTransferable(JComponent c) { * return transferable; } * * public boolean importData(TransferHandler.TransferSupport * support) { /*try { Object obj = * support.getTransferable().getTransferData( df ); InputStream * is = (InputStream)obj; * * byte[] bb = new byte[2048]; int r = is.read(bb); * * //importFromText( new String(bb,0,r) ); } catch * (UnsupportedFlavorException e) { e.printStackTrace(); } catch * (IOException e) { e.printStackTrace(); }* return false; } }; * textarea.setTransferHandler( th ); * textarea.setDragEnabled(true); JScrollPane scrollpane = new JScrollPane(textarea); JFrame frame = new JFrame(); frame.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE); frame.add(scrollpane); frame.setSize(400, 300); frame.setVisible(true);*/ }); sequencemenu.getItems().add(splitseq); MenuItem showdnaseq = new MenuItem("Show DNA sequences"); showdnaseq.setOnAction(actionEvent -> { Set<GeneGroup> genegroups = new HashSet<GeneGroup>(); int rr = 0; if (!isGeneview()) { ObservableList<GeneGroup> lgg = table.getSelectionModel().getSelectedItems(); genegroups.addAll(lgg); rr = lgg.size(); } else { for (Gene gg : gtable.getSelectionModel().getSelectedItems()) { genegroups.add(gg.getGeneGroup()); rr++; } } Set<String> specs = null; if (rr > 1) specs = getSelspec(comp, geneset.specList, null); showSequences(comp, genegroups, true, specs); /*StringBuilder sb = getSelectedSeqs( table, genelist ); if( currentSerify == null ) { JFrame frame = new JFrame(); frame.setDefaultCloseOperation( JFrame.DO_NOTHING_ON_CLOSE ); frame.setSize(800, 600); SerifyApplet sa = new SerifyApplet(); sa.init( frame ); try { sa.addSequences("uh", new StringReader( sb.toString() ), "/"); } catch (URISyntaxException | IOException e1) { e1.printStackTrace(); } frame.setVisible( true ); } JTextArea textarea = new JTextArea(); JScrollPane scrollpane = new JScrollPane(textarea); try { if (clipboardService == null) clipboardService = (ClipboardService) ServiceManager.lookup("javax.jnlp.ClipboardService"); Action action = new CopyAction("Copy", null, "Copy data", new Integer(KeyEvent.VK_CONTROL + KeyEvent.VK_C)); textarea.getActionMap().put("copy", action); grabFocus = true; } catch (Exception ee) { ee.printStackTrace(); System.err.println("Copy services not available. Copy using 'Ctrl-c'."); } textarea.setDragEnabled(true); textarea.append( sb.toString() ); JFrame frame = new JFrame(); frame.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE); frame.add(scrollpane); frame.setSize(400, 300); frame.setVisible(true);*/ }); sequencemenu.getItems().add(showdnaseq); MenuItem expalldna = new MenuItem("Export all DNA sequences"); expalldna.setOnAction(actionEvent -> { JFileChooser jfc = new JFileChooser(); jfc.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY); try { Map<Integer, FileWriter> lfw = new HashMap<Integer, FileWriter>(); if (jfc.showOpenDialog(null) == JFileChooser.APPROVE_OPTION) { File f = jfc.getSelectedFile(); for (Gene gg : getGeneTable().getSelectionModel().getSelectedItems()) { FileWriter fw = null; if (lfw.containsKey(gg.getGroupIndex())) { fw = lfw.get(gg.getGroupIndex()); } else { fw = new FileWriter(new File(f, "group_" + gg.getGroupIndex() + ".fasta")); lfw.put(gg.getGroupIndex(), fw); } Tegeval tv = gg.tegeval; fw.append(">" + tv.name + " " + tv.teg + " " + tv.eval + "\n"); for (int i = 0; i < tv.getLength(); i += 70) { fw.append(tv.getSubstring(i, Math.min(i + 70, tv.getLength())) + "\n"); } } } for (int gi : lfw.keySet()) { lfw.get(gi).close(); } } catch (IOException e1) { e1.printStackTrace(); } }); sequencemenu.getItems().add(expalldna); MenuItem exprelcont = new MenuItem("Export relevant contigs"); exprelcont.setOnAction(actionEvent -> { JFileChooser jfc = new JFileChooser(); try { Map<Integer, FileWriter> lfw = new HashMap<Integer, FileWriter>(); if (jfc.showOpenDialog(null) == JFileChooser.APPROVE_OPTION) { File f = jfc.getSelectedFile(); Set<Sequence> contset = new HashSet<Sequence>(); for (Gene gg : getGeneTable().getSelectionModel().getSelectedItems()) { Tegeval tv = gg.tegeval; contset.add(tv.getContshort()); } FileWriter fw = new FileWriter(f); for (Sequence contig : contset) { fw.append(">" + contig + "\n"); if (geneset.contigmap.containsKey(contig)) { StringBuilder dna = geneset.contigmap.get(contig).getStringBuilder(); for (int i = 0; i < dna.length(); i += 70) { fw.append(dna.substring(i, Math.min(i + 70, dna.length())) + "\n"); } } } fw.close(); } for (int gi : lfw.keySet()) { lfw.get(gi).close(); } } catch (IOException e1) { e1.printStackTrace(); } }); sequencemenu.getItems().add(exprelcont); sequencemenu.getItems().add(new SeparatorMenuItem()); MenuItem viewselrange = new MenuItem("View selected range"); viewselrange.setOnAction(actionEvent -> { JFrame frame = new JFrame(); frame.setSize(800, 600); frame.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE); Serifier serifier = new Serifier(); JavaFasta jf = new JavaFasta((comp instanceof JApplet) ? (JApplet) comp : null, serifier, geneset.cs); jf.initGui(frame); Set<Sequence> contset = new HashSet<Sequence>(); Set<Tegeval> tvset = new HashSet<>(); if (isGeneview()) { for (Gene gg : getGeneTable().getSelectionModel().getSelectedItems()) { Tegeval tv = gg.tegeval; tvset.add(tv); //serifier.addAnnotation( tv ); contset.add(tv.getContshort()); } } else { for (GeneGroup gg : getGeneGroupTable().getSelectionModel().getSelectedItems()) { for (Tegeval tv : gg.getTegevals()) { tv.color = Color.red; tvset.add(tv); Sequence contig = tv.getContshort(); contset.add(contig); //serifier.addAnnotation( tv ); } } } /*Sequence seq; Sequence contig = tv.getContshort(); /*if (contset.containsKey(contig)) { seq = contset.get(contig); } else { if( contigmap.containsKey(contig) ) { StringBuilder dna = contigmap.get(contig).getStringBuilder(); seq = new Sequence(contig.getName(), dna, serifier.mseq); } else seq = new Sequence(contig.getName(), serifier.mseq); contset.put(contig, seq); } Annotation a = new Annotation(contig, contig.getName(), Color.green, serifier.mann); a.setStart(tv.start); a.setStop(tv.stop); a.setOri(tv.ori); a.setGroup(gg.name); a.setType("gene");*/ // seq.addAnnotation( new Annotation( seq, ) ); for (Sequence contig : contset) { int start = Integer.MAX_VALUE; int stop = Integer.MIN_VALUE; for (Tegeval tv : tvset) { if (contig == tv.seq) { start = Math.min(start, tv.start); stop = Math.max(stop, tv.stop); } } int rstart = 0; int rstop = contig.length(); if (contig.annset != null) for (Annotation tv : contig.annset) { if (contig == tv.seq) { if (tv.stop < start && tv.stop > rstart) { rstart = tv.stop; } if (tv.start > stop && tv.start < rstop) { rstop = tv.start; } } } start = rstart; stop = rstop; Sequence newseq = new Sequence(contig.getName(), new StringBuilder(contig.getSubstring(start, stop, 1)), serifier.mseq); /*if( contig.isReverse() ) { newseq.reverse(); newseq.complement(); }*/ serifier.addSequence(newseq); for (Tegeval tv : tvset) { Annotation newann = new Annotation(newseq, tv.start - start, tv.stop - start, tv.ori, tv.name); if (contig == tv.seq) { newseq.addAnnotation(newann); } serifier.addAnnotation(newann); } /*for( Annotation ann : contig.getAnnotations() ) { serifier.addAnnotation( ann ); }*/ /*if (seq.getAnnotations() != null) Collections.sort(seq.getAnnotations());*/ } jf.updateView(); frame.setVisible(true); }); sequencemenu.getItems().add(viewselrange); MenuItem viewwhole = new MenuItem("View whole contigs for selection"); viewwhole.setOnAction(actionEvent -> { JFrame frame = new JFrame(); frame.setSize(800, 600); frame.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE); Serifier serifier = new Serifier(); JavaFasta jf = new JavaFasta((comp instanceof JApplet) ? (JApplet) comp : null, serifier, geneset.cs); jf.initGui(frame); //Map<Sequence, Sequence> contset = new HashMap<Sequence, Sequence>(); /*int[] rr = table.getSelectedRows(); for (int r : rr) { int cr = table.convertRowIndexToModel(r); Gene gg = geneset.genelist.get(cr); if (gg.species != null) { for (String sp : gg.species.keySet()) { Teginfo stv = gg.species.get(sp); for (Tegeval tv : stv.tset) { Sequence seq; Sequence contig = tv.getContshort(); if (contset.containsKey(contig)) { seq = contset.get(contig); } else { if( GeneSet.contigmap.containsKey(contig) ) { //StringBuilder dna = GeneSet.contigmap.get(contig).seq; StringBuilder dna = contig.getSequence().getStringBuilder(); seq = new Sequence(contig.getName(), dna, serifier.mseq); } else { seq = new Sequence(contig.getName(), serifier.mseq); } contset.put(contig, seq); } /* * Annotation a = jf.new Annotation( seq, * contig, Color.red ); a.setStart( tv.start ); * a.setStop( tv.stop ); a.setOri( tv.ori ); * a.setGroup( gg.name ); a.setType( "gene" ); * jf.addAnnotation( a ); * // seq.addAnnotation( new Annotation( seq, ) ); } } } }*/ Set<Sequence> contigs = new HashSet<Sequence>(); if (isGeneview()) { for (Gene gg : getGeneTable().getSelectionModel().getSelectedItems()) { Tegeval tv = gg.tegeval; tv.color = Color.red; Sequence contig = tv.getContshort(); //contig.offset = -tv.start; contigs.add(contig); } /*Annotation a = new Annotation(contig, contig.getName(), Color.red, serifier.mann); a.setStart(tv.start); a.setStop(tv.stop); a.setOri(tv.ori); a.setGroup(g.name); a.setType("gene");*/ //serifier.addAnnotation( tv ); } else { for (GeneGroup gg : getGeneGroupTable().getSelectionModel().getSelectedItems()) { for (Tegeval tv : gg.getTegevals()) { tv.color = Color.red; Sequence contig = tv.getContshort(); //contig.offset = -tv.start; contigs.add(contig); /*Annotation a = new Annotation(contig, contig.getName(), Color.red, serifier.mann); a.setStart(tv.start); a.setStop(tv.stop); a.setOri(tv.ori); a.setGroup(gg.getCommonName()); a.setType("gene");*/ //serifier.addAnnotation( tv ); } } } //Gene gg = geneset.genelist.get(cr); //for (Gene g : geneset.genelist) { //if (g.species != null) { //for (String sp : g.species.keySet()) { for (Sequence contig : contigs) { for (Annotation ann : contig.getAnnotations()) { serifier.addAnnotation(ann); } serifier.addSequence(contig); serifier.mseq.put(contig.getName(), contig); //if(contig.getAnnotations() != null) // Collections.sort(contig.getAnnotations()); } jf.updateView(); frame.setVisible(true); }); sequencemenu.getItems().add(viewwhole); sequencemenu.getItems().add(new SeparatorMenuItem()); MenuItem viewspecseq = new MenuItem("View species sequence"); viewspecseq.setOnAction(actionEvent -> { Set<String> selspec = getSelspec(GeneSetHead.this, geneset.specList); JFrame frame = new JFrame(); frame.setSize(800, 600); frame.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE); Serifier serifier = new Serifier(); JavaFasta jf = new JavaFasta((comp instanceof JApplet) ? (JApplet) comp : null, serifier, geneset.cs); jf.initGui(frame); for (String spec : selspec) { List<Sequence> contigs = geneset.speccontigMap.get(spec); for (Sequence contig : contigs) { List<Annotation> lann = contig.getAnnotations(); if (lann != null) for (Annotation ann : lann) { serifier.addAnnotation(ann); } serifier.addSequence(contig); serifier.mseq.put(contig.getName(), contig); } } jf.updateView(); frame.setVisible(true); }); sequencemenu.getItems().add(viewspecseq); Menu windowmenu = new Menu("Tools"); MenuItem seqviewer = new MenuItem("Sequence viewer"); seqviewer.setOnAction(actionEvent -> { JFrame frame = new JFrame(); frame.setSize(800, 600); frame.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE); Serifier serifier = new Serifier(); JavaFasta jf = new JavaFasta((comp instanceof JApplet) ? (JApplet) comp : null, serifier, geneset.cs); jf.initGui(frame); jf.updateView(); frame.setVisible(true); }); windowmenu.getItems().add(seqviewer); windowmenu.getItems().add(new SeparatorMenuItem()); MenuItem genesorter = new MenuItem("Gene sorter"); genesorter.setOnAction(actionEvent -> { try { //if( gb.isSelected() ) new GeneSorter().mynd( GeneSetHead.this, genelist, table, null, contigmap ); //else new GeneSorter().groupMynd(GeneSetHead.this, geneset.allgenegroups, geneset.specList, geneset.genelist, table, geneset.contigmap, geneset.specset); } catch (IOException e1) { e1.printStackTrace(); } }); windowmenu.getItems().add(genesorter); MenuItem specorderaction = new MenuItem("Order species list"); specorderaction.setOnAction(actionEvent -> { TreeUtil tu = new TreeUtil(); /*corrInd.clear(); for( String spec : specList ) { corrInd.add( nameFix( spec ) ); }*/ Serifier serifier = getConcatenatedSequences(false, false); Map<String, Integer> blosumap = JavaFasta.getBlosumMap(); double[] dmat = new double[serifier.lseq.size() * serifier.lseq.size()]; Sequence.distanceMatrixNumeric(serifier.lseq, dmat, null, false, false, null, blosumap); List<String> ret = new ArrayList<String>(); for (Sequence seqname : serifier.lseq) { ret.add(seqname.getName()); //.replace(' ', '_') ); } //List<String> corrInd = currentjavafasta.getNames(); //Sequence.distanceMatrixNumeric(serifier.lseq, dmat, idxs, bootstrap, cantor, ent, blosum); Node n = tu.neighborJoin(dmat, ret, null, false, false); Comparator<Node> comp2 = (o1, o2) -> { int c1 = o1.countLeaves(); int c2 = o2.countLeaves(); if (c1 > c2) return 1; else if (c1 == c2) return 0; return -1; }; tu.arrange(n, comp2); //corrInd.clear(); List<String> ordInd = n.traverse(); for (String spec : ordInd) { System.err.println(spec); } for (String oldspec : geneset.specList) { if (!ordInd.contains(oldspec)) { ordInd.add(oldspec); } } geneset.specList = ordInd; //TableModel model = table.getModel(); //table.setModel( nullmodel ); //table.setModel( model ); //table.tableChanged( new TableModelEvent( table.getModel() ) ); //table.getColumnModel(). System.err.println(geneset.specList.size()); }); MenuItem matrixaction = new MenuItem("Relation matrix"); matrixaction.setOnAction(actionEvent -> { SwingUtilities.invokeLater(() -> { JComboBox<String> descombo = new JComboBox<String>( geneset.deset.toArray(new String[geneset.deset.size()])); JCheckBox anicheck = new JCheckBox("ANImatrix"); JCheckBox plasmidcheck = new JCheckBox("Skip plasmids"); descombo.insertItemAt("", 0); descombo.setSelectedIndex(0); JOptionPane.showMessageDialog(GeneSetHead.this, new Object[] { descombo, anicheck, plasmidcheck }); String val = descombo.getSelectedItem().toString(); Collection<GeneGroup> ss = new HashSet<>(); /*int[] rr = table.getSelectedRows(); for( int r : rr ) { ss.add( geneset.allgenegroups.get( table.convertRowIndexToModel(r) ) ); }*/ ss.addAll(table.getSelectionModel().getSelectedItems()); if (ss.isEmpty()) ss = geneset.allgenegroups; Set<String> species = getSelspec(GeneSetHead.this, geneset.specList); bimg = anicheck.isSelected() ? geneset.animatrix(species, geneset.clusterMap, val, ss, plasmidcheck.isSelected()) : geneset.bmatrix(species, geneset.clusterMap, val); JFrame f = new JFrame("Relation matrix"); f.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE); f.setSize(500, 500); /* * { public void paintComponent( Graphics g ) { * super.paintComponent(g); g.drawImage(bimg, 0, 0, this); } }; */ try { final DataFlavor df = new DataFlavor("text/plain;charset=utf-8"); final Transferable transferable = new Transferable() { @Override public Object getTransferData(DataFlavor arg0) throws UnsupportedFlavorException, IOException { StringBuilder ret = new StringBuilder(); int i = 0; for (String spc : geneset.specList) { if (++i == geneset.specList.size()) ret.append(spc + "\n"); else ret.append(spc + "\t"); } int where = 0; for (String spc1 : geneset.specList) { int wherex = 0; for (String spc2 : geneset.specList) { int spc1tot = 0; int spc2tot = 0; int totot = 0; int spc1totwocore = 0; int spc2totwocore = 0; int tototwocore = 0; for (Set<String> set : geneset.clusterMap.keySet()) { Set<Map<String, Set<String>>> erm = geneset.clusterMap.get(set); if (set.contains(spc1)) { if (set.size() < geneset.specList.size()) { spc1totwocore += erm.size(); for (Map<String, Set<String>> sm : erm) { Set<String> hset = sm.get(spc1); tototwocore += hset.size(); } if (set.contains(spc2)) { spc2totwocore += erm.size(); } if (spc2totwocore > spc1totwocore) System.err.println( "okoko " + spc1totwocore + " " + spc2totwocore); } spc1tot += erm.size(); for (Map<String, Set<String>> sm : erm) { Set<String> hset = sm.get(spc1); totot += hset.size(); } if (set.contains(spc2)) { spc2tot += erm.size(); } } } if (where == wherex) { if (where == geneset.specList.size() - 1) ret.append(0 + "\n"); else ret.append(0 + "\t"); } else { double hlut = (double) spc2totwocore / (double) spc1totwocore; double sval = hlut; // 1.0/( 1.1-hlut ); double val = Math.pow(50.0, sval - 0.3) - 1.0; double dval = Math.round(100.0 * (val)) / 100.0; if (wherex == geneset.specList.size() - 1) ret.append(dval + "\n"); else ret.append(dval + "\t"); } wherex++; } where++; } return new ByteArrayInputStream(ret.toString().getBytes()); } @Override public DataFlavor[] getTransferDataFlavors() { return new DataFlavor[] { df }; } @Override public boolean isDataFlavorSupported(DataFlavor arg0) { if (arg0.equals(df)) { return true; } return false; } }; final TransferComponent comp2 = new TransferComponent(bimg, transferable); TransferHandler th = new TransferHandler() { private static final long serialVersionUID = 1L; public int getSourceActions(JComponent c) { return TransferHandler.COPY_OR_MOVE; } public boolean canImport(TransferSupport support) { return false; } protected Transferable createTransferable(JComponent c) { return transferable; } public boolean importData(TransferSupport support) { return true; } }; comp2.setTransferHandler(th); comp2.setEnabled(true); JScrollPane fsc = new JScrollPane(comp2); comp2.setPreferredSize(new Dimension(bimg.getWidth(), bimg.getHeight())); JPopupMenu popup = new JPopupMenu(); popup.add(new AbstractAction("Save image") { @Override public void actionPerformed(ActionEvent e) { FileSaveService fss = null; FileContents fileContents = null; try { ByteArrayOutputStream baos = new ByteArrayOutputStream(); OutputStreamWriter osw = new OutputStreamWriter(baos); ImageIO.write(bimg, "png", baos); baos.close(); try { fss = (FileSaveService) ServiceManager.lookup("javax.jnlp.FileSaveService"); } catch (UnavailableServiceException e1) { fss = null; } if (fss != null) { ByteArrayInputStream bais = new ByteArrayInputStream(baos.toByteArray()); fileContents = fss.saveFileDialog(null, null, bais, "export.png"); bais.close(); OutputStream os = fileContents.getOutputStream(true); os.write(baos.toByteArray()); os.close(); } else { JFileChooser jfc = new JFileChooser(); if (jfc.showSaveDialog(GeneSetHead.this) == JFileChooser.APPROVE_OPTION) { File f = jfc.getSelectedFile(); FileOutputStream fos = new FileOutputStream(f); fos.write(baos.toByteArray()); fos.close(); Desktop.getDesktop().browse(f.toURI()); } } } catch (IOException e2) { e2.printStackTrace(); } } }); comp2.setComponentPopupMenu(popup); f.add(fsc); f.setVisible(true); } catch (ClassNotFoundException e1) { e1.printStackTrace(); } }); }); MenuItem tniaction = new MenuItem("TNI/ANI"); tniaction.setOnAction(actionEvent -> { SwingUtilities.invokeLater(() -> { Set<String> species = getSelspec(GeneSetHead.this, geneset.specList); String makeblastdb = "makeblastdb"; String OS = System.getProperty("os.name").toLowerCase(); if (OS.indexOf("mac") != -1) makeblastdb = "/usr/local/bin/makeblastdb"; for (String spec : species) { List<Sequence> lseq = geneset.speccontigMap.get(spec); ProcessBuilder pb = new ProcessBuilder(makeblastdb, "-dbtype", "nucl", "-title", spec, "-out", spec); File dir = new File(System.getProperty("user.home")); /*try { FileWriter w = new FileWriter( new File(dir, spec+".fna") ); for( Sequence seq : lseq ) { seq.writeSequence(w); } w.close(); } catch (IOException e2) { e2.printStackTrace(); }*/ pb.directory(dir); try { Process p = pb.start(); Writer fw = new OutputStreamWriter(p.getOutputStream()); for (Sequence seq : lseq) { seq.writeSequence(fw); } fw.close(); } catch (IOException e1) { e1.printStackTrace(); } } int y = 0; double[] matrix = new double[species.size() * species.size()]; for (String dbspec : species) { int x = 0; for (String spec : species) { //if( !spec.equals(dbspec) ) { final List<Sequence> lseq = geneset.speccontigMap.get(spec); String blastn = "blastn"; if (OS.indexOf("mac") != -1) blastn = "/usr/local/bin/blastn"; ProcessBuilder pb = new ProcessBuilder(blastn, "-db", dbspec, "-num_threads", Integer.toString(Runtime.getRuntime().availableProcessors()), "-num_alignments", "1", "-num_descriptions", "1"); //,"-max_hsps","1"); File dir = new File(System.getProperty("user.home")); pb.directory(dir); try { Process p = pb.start(); final BufferedWriter fw = new BufferedWriter( new OutputStreamWriter(p.getOutputStream())); Thread t = new Thread() { public void run() { try { for (Sequence seq : lseq) { seq.writeSplitSequence(fw); //seq.writeSequence(fw); } fw.close(); } catch (IOException e1) { e1.printStackTrace(); } } }; t.start(); //Path path = Paths.get("/Users/sigmar/"+spec+"_"+dbspec+".blastout"); //Files.copy(p.getInputStream(), path, StandardCopyOption.REPLACE_EXISTING); int tnum = 0; int tdenum = 0; double avg = 0.0; int count = 0; BufferedReader br = new BufferedReader(new InputStreamReader(p.getInputStream())); String line = br.readLine(); while (line != null) { if (line.startsWith(" Identities")) { int i = line.indexOf('('); String sub = line.substring(14, i - 1); String[] split = sub.split("/"); int num = Integer.parseInt(split[0]); int denum = Integer.parseInt(split[1]); avg += (double) num / (double) denum; tnum += num; tdenum += denum; count++; } line = br.readLine(); } br.close(); if (count > 0) avg /= count; double val = (double) tnum / (double) tdenum; matrix[y * species.size() + x] = avg;//val; System.err.println(spec + " on " + dbspec + " " + val); } catch (IOException e1) { e1.printStackTrace(); } //} x++; } y++; } geneset.corrInd.clear(); for (String spec : species) { geneset.corrInd.add(geneset.nameFix(spec)); } final BufferedImage bi = geneset.showRelation(geneset.corrInd, matrix, false); JFrame f = new JFrame("TNI matrix"); f.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE); f.setSize(500, 500); JComponent comp2 = new JComponent() { public void paintComponent(Graphics g) { super.paintComponent(g); g.drawImage(bi, 0, 0, bi.getWidth(), bi.getHeight(), 0, 0, bi.getWidth(), bi.getHeight(), this); } }; Dimension dim = new Dimension(bi.getWidth(), bi.getHeight()); comp2.setPreferredSize(dim); comp2.setSize(dim); JScrollPane scroll = new JScrollPane(comp2); f.add(scroll); f.setVisible(true); }); }); MenuItem anitreeaction = new MenuItem("ANI tree"); anitreeaction.setOnAction(actionEvent -> { Set<String> species = getSelspec(GeneSetHead.this, geneset.specList); List<String> speclist = new ArrayList<String>(species); Collection<GeneGroup> allgg = new HashSet<GeneGroup>(); allgg.addAll(table.getSelectionModel().getSelectedItems()); if (allgg.isEmpty()) allgg = geneset.allgenegroups; Map<String, Integer> blosumap = JavaFasta.getBlosumMap(); double[] corrarr = new double[speclist.size() * speclist.size()]; int where = 0; for (String spec1 : speclist) { int wherex = 0; String spc1 = geneset.nameFix(spec1); //String spc1 = nameFix( spec1 ); for (String spec2 : speclist) { if (where != wherex) { int totalscore = 0; int totaltscore = 1; for (GeneGroup gg : allgg) { if ( /*gg.getSpecies().size() > 40 &&*/ gg.getSpecies().contains(spec1) && gg.getSpecies().contains(spec2)) { Teginfo ti1 = gg.species.get(spec1); Teginfo ti2 = gg.species.get(spec2); //if( ti1.tset.size() == 1 && ti2.tset.size() == 1 ) { //double bval = 0.0; int score = 0; int tscore = 1; for (Tegeval tv1 : ti1.tset) { for (Tegeval tv2 : ti2.tset) { Sequence seq1 = tv1.getAlignedSequence(); Sequence seq2 = tv2.getAlignedSequence(); if (seq1 != null && seq2 != null) { int mest = 0; int tmest = 0; int startcheck = 0; int start = -1; int stopcheck = 0; int stop = -1; for (int i = 0; i < seq1.length(); i++) { if (seq1.getCharAt(i) != '-') { startcheck |= 1; } if (seq2.getCharAt(i) != '-') { startcheck |= 2; } if (start == -1 && startcheck == 3) { start = i; break; } } for (int i = seq1.length() - 1; i >= 0; i--) { if (seq1.getCharAt(i) != '-') { stopcheck |= 1; } if (seq2.getCharAt(i) != '-') { stopcheck |= 2; } if (stop == -1 && stopcheck == 3) { stop = i + 1; break; } } //count += stop-start; for (int i = start; i < stop; i++) { char lc = seq1.getCharAt(i); char c = Character.toUpperCase(lc); //if( ) String comb = c + "" + c; if (blosumap.containsKey(comb)) tmest += blosumap.get(comb); } for (int i = start; i < stop; i++) { char lc = seq1.getCharAt(i); char c = Character.toUpperCase(lc); char lc2 = seq2.getCharAt(i); char c2 = Character.toUpperCase(lc2); String comb = c + "" + c2; if (blosumap.containsKey(comb)) mest += blosumap.get(comb); } double tani = (double) mest / (double) tmest; if (tani > (double) score / (double) tscore) { score = mest; tscore = tmest; } //ret = (double)score/(double)tscore; //int cval = tscore == 0 ? 0 : Math.min( 192, 512-score*512/tscore ); //return ret; } //if( where == 0 ) d1.add( gg.getCommonName() ); //else d2.add( gg.getCommonName() ); } } totalscore += score; totaltscore += tscore; /*if( bval > 0 ) { ani += bval; count++; }*/ //} } } double ani = (double) (totaltscore - totalscore) / (double) totaltscore; corrarr[where * speclist.size() + wherex] = ani; } wherex++; } where++; } TreeUtil tu = new TreeUtil(); geneset.corrInd.clear(); for (String spec : speclist) { geneset.corrInd.add(geneset.nameFix(spec)); } Node n = tu.neighborJoin(corrarr, geneset.corrInd, null, false, false); System.err.println(n); }); windowmenu.getItems().add(specorderaction); windowmenu.getItems().add(matrixaction); windowmenu.getItems().add(tniaction); windowmenu.getItems().add(anitreeaction); MenuItem neighbourhood = new MenuItem("Neighbourhood"); neighbourhood.setOnAction(actionEvent -> { try { Set<GeneGroup> genset = new HashSet<>(); if (!isGeneview()) { for (GeneGroup gg : table.getSelectionModel().getSelectedItems()) { genset.add(gg); } } else { for (Gene gene : gtable.getSelectionModel().getSelectedItems()) { genset.add(gene.getGeneGroup()); } } new Neighbour(genset).neighbourMynd(GeneSetHead.this, comp, geneset.genelist, geneset.contigmap); } catch (IOException e1) { e1.printStackTrace(); } }); windowmenu.getItems().add(neighbourhood); MenuItem synteny = new MenuItem("Synteny"); synteny.setOnAction(actionEvent -> { SwingUtilities.invokeLater(() -> { //Set<String> species = speciesFromCluster( clusterMap ); new Synteni().syntenyMynd(GeneSetHead.this, comp, geneset.genelist); }); }); windowmenu.getItems().add(synteny); MenuItem compareplotaction = new MenuItem("Gene atlas"); compareplotaction.setOnAction(actionEvent -> { SwingUtilities.invokeLater(() -> { try { new GeneCompare().comparePlot(GeneSetHead.this, comp, geneset.genelist, geneset.clusterMap, 8192, 8192); } catch (IOException e1) { e1.printStackTrace(); } }); /*gatest("MAT4726"); final JFrame frame = new JFrame(); frame.setDefaultCloseOperation( JFrame.DISPOSE_ON_CLOSE ); frame.setSize(800, 600); final JComponent c = new JComponent() { public void paintComponent( Graphics g ) { g.drawImage(bimg, 0, 0, frame); } }; c.setPreferredSize( new Dimension(bimg.getWidth(), bimg.getHeight()) ); JScrollPane scrollpane = new JScrollPane( c ); frame.add( scrollpane ); frame.setVisible( true );*/ }); windowmenu.getItems().add(compareplotaction); MenuItem syntenygradientaction = new MenuItem("Synteny gradient"); syntenygradientaction.setOnAction(actionEvent -> { SwingUtilities.invokeLater(() -> { Set<String> presel = new HashSet<>(); if (isGeneview()) { for (Gene g : gtable.getSelectionModel().getSelectedItems()) { presel.addAll(g.getGeneGroup().getSpecies()); } } else { for (GeneGroup gg : table.getSelectionModel().getSelectedItems()) { presel.addAll(gg.getSpecies()); } } new SyntGrad().syntGrad(GeneSetHead.this, 4096, 4096, presel); }); }); windowmenu.getItems().add(syntenygradientaction); MenuItem genexyplotaction = new MenuItem("Gene XY plot"); genexyplotaction.setOnAction(actionEvent -> SwingUtilities.invokeLater( () -> new XYPlot().xyPlot(GeneSetHead.this, comp, geneset.genelist, geneset.clusterMap))); windowmenu.getItems().add(genexyplotaction); MenuItem refalignaction = new MenuItem("Reference align"); refalignaction.setOnAction(actionEvent -> { SwingUtilities.invokeLater(() -> { final TableView<Gene> table12 = getGeneTable(); final Collection<String> specset = geneset.getSpecies(); //speciesFromCluster( clusterMap ); final List<String> species = new ArrayList<>(specset); TableModel model = new TableModel() { @Override public int getRowCount() { return species.size(); } @Override public int getColumnCount() { return 1; } @Override public String getColumnName(int columnIndex) { return null; } @Override public Class<?> getColumnClass(int columnIndex) { return String.class; } @Override public boolean isCellEditable(int rowIndex, int columnIndex) { return false; } @Override public Object getValueAt(int rowIndex, int columnIndex) { return geneset.nameFix(species.get(rowIndex)); } @Override public void setValueAt(Object aValue, int rowIndex, int columnIndex) { } @Override public void addTableModelListener(TableModelListener l) { } @Override public void removeTableModelListener(TableModelListener l) { } }; JTable table1 = new JTable(model); JTable table2 = new JTable(model); table1.getSelectionModel().setSelectionMode(ListSelectionModel.SINGLE_SELECTION); table2.getSelectionModel().setSelectionMode(ListSelectionModel.MULTIPLE_INTERVAL_SELECTION); JScrollPane scroll1 = new JScrollPane(table1); JScrollPane scroll2 = new JScrollPane(table2); FlowLayout flowlayout = new FlowLayout(); JComponent c = new JComponent() { }; c.setLayout(flowlayout); c.add(scroll1); c.add(scroll2); JOptionPane.showMessageDialog(comp, c); int r = table1.getSelectedRow(); int i = table1.convertRowIndexToModel(r); String spec = i == -1 ? null : species.get(i); List<Sequence> lcont = geneset.speccontigMap.get(spec); r = table2.getSelectedRow(); i = table2.convertRowIndexToModel(r); String refspec = i == -1 ? null : species.get(i); List<Sequence> lrefcont = geneset.speccontigMap.get(spec); /*ByteArrayOutputStream baos = new ByteArrayOutputStream(); Writer fw = new OutputStreamWriter( baos ); try { List<Sequence> lcont = geneset.speccontigMap.get(spec); for( Sequence seq : lcont ) { seq.writeSequence(fw); } fw.close(); } catch (IOException e1) { e1.printStackTrace(); } String comp = spec; byte[] bb = baos.toByteArray();*/ FlxReader flx = new FlxReader(); Map<String, String> env = new HashMap<String, String>(); env.put("create", "true"); //String uristr = "jar:" + geneset.zippath.toUri(); //URI geneset.zipuri = URI.create( uristr /*.replace("file://", "file:")*/ ); try { geneset.zipfilesystem = FileSystems.newFileSystem(geneset.zipuri, env); for (Path root : geneset.zipfilesystem.getRootDirectories()) { Path subf = root.resolve(spec + ".grp"); if (Files.exists(subf)) { BufferedReader br = Files.newBufferedReader(subf); Map<String, Map<String, String>> mm = flx.loadContigGraph(br); br.close(); String home = System.getProperty("user.home") + "/"; StringBuilder sb = comp != null ? flx.referenceAssembly(home, spec, refspec, lrefcont, lcont) : null; Sequence cseq = new Sequence(spec + "_chromosome", null); if (sb != null && sb.length() > 0) { br = new BufferedReader(new StringReader(sb.toString())); } else { Path sca = root.resolve(spec + ".csc"); if (!Files.exists(sca)) { sca = root.resolve(spec + ".sca"); } br = Files.newBufferedReader(sca); } //br = new BufferedReader( fr ); flx.connectContigs(br, cseq, false, new FileWriter(home + spec + "_new.fna"), spec); br.close(); } break; } } catch (Exception ex) { ex.printStackTrace(); } finally { try { geneset.zipfilesystem.close(); } catch (IOException ie) { ie.printStackTrace(); } ; } }); //flx.start( f.getParentFile().getAbsolutePath()+"/", f.getName(), false, fw, comp, bb); }); windowmenu.getItems().add(refalignaction); windowmenu.getItems().add(new SeparatorMenuItem()); MenuItem runantismash = new MenuItem("Run antismash"); runantismash.setOnAction(actionEvent -> SwingUtilities.invokeLater(new Runnable() { public void run() { try { Serifier ser = new Serifier(); Set<String> selspec = getSelspec(null, geneset.getSpecies(), null); JTextField host = new JTextField("localhost"); JOptionPane.showMessageDialog(null, host); String username = System.getProperty("user.name"); String hostname = host.getText(); /*Path[] pt = null; JFileChooser fc = new JFileChooser(); fc.setFileSelectionMode( JFileChooser.DIRECTORIES_ONLY ); if( fc.showSaveDialog(null) == JFileChooser.APPROVE_OPTION ) { pt = new Path[3]; pt[2] = fc.getSelectedFile().toPath(); }*/ List<Object> commands = new ArrayList<Object>(); //commands.add(genexyplotaction) for (String spec : selspec) { Path pp = Paths.get(userhome); Path p = pp.resolve(spec + ".gbk"); //BufferedWriter fw = Files.newBufferedWriter( p ); List<Sequence> clist = geneset.speccontigMap.get(spec); Map<String, List<Annotation>> mapan = new HashMap<String, List<Annotation>>(); Serifier serifier = new Serifier(); for (Sequence c : clist) { serifier.addSequence(c); serifier.mseq.put(c.getName(), c); List<Annotation> lann = new ArrayList<Annotation>(); if (c.getAnnotations() != null) for (Annotation ann : c.getAnnotations()) { Tegeval tv = (Tegeval) ann; Gene g = tv.getGene(); GeneGroup gg = g.getGeneGroup(); String name = g.getName(); if (gg != null && name.contains(spec)) { name = gg.getName(); } Annotation anno = new Annotation(c, tv.start, tv.stop, tv.ori, name); anno.id = tv.getGene().getId(); anno.type = "CDS"; String cazy = gg != null ? gg.getCommonCazy(geneset.cazymap) : null; if (cazy != null) anno.addDbRef("CAZY:" + cazy); lann.add(anno); } mapan.put(c.getName(), lann); } Sequences s = new Sequences(null, spec, "nucl", null, clist.size()); //serifier.addSequences(seqs); serifier.writeGenebank(p, false, true, s, mapan); //fw.close(); String apath = p.toAbsolutePath().toString(); if (hostname.equals("localhost")) { String[] cmds = { "run_antismash", apath }; //commands.add( pt ); commands.add(Arrays.asList(cmds)); } else { String aname = p.getFileName().toString(); String adir = aname.substring(0, aname.length() - 4); String cyghome = NativeRun.cygPath(userhome); String[] cmds = { "scp", apath, hostname + ":~", ";", "ssh", hostname, "run_antismash", aname, ";", "scp", "-r", hostname + ":~/" + adir, cyghome };//userhome+"~"}; //commands.add( pt ); commands.add(Arrays.asList(cmds)); } } Runnable run = new Runnable() { @Override public void run() { for (String spec : selspec) { Path p = Paths.get(userhome, spec); Map<String, String> env = new HashMap<String, String>(); env.put("create", "true"); String uristr = "jar:" + geneset.zippath.toUri(); URI zipuri = URI.create(uristr /*.replace("file://", "file:")*/ ); final List<Path> lbi = new ArrayList<Path>(); try { geneset.zipfilesystem = FileSystems.newFileSystem(geneset.zipuri, env); for (Path root : geneset.zipfilesystem.getRootDirectories()) { Path specdir = root; Files.walkFileTree(p, new SimpleFileVisitor<Path>() { @Override public FileVisitResult visitFile(Path file, BasicFileAttributes attrs) throws IOException { final Path destFile = Paths.get(specdir.toString(), file.toString()); //System.out.printf("Extracting file %s to %s\n", file, destFile); Files.copy(file, destFile, StandardCopyOption.REPLACE_EXISTING); return FileVisitResult.CONTINUE; } @Override public FileVisitResult preVisitDirectory(Path dir, BasicFileAttributes attrs) throws IOException { String specdirstr = specdir.toString(); String dirstr = dir.toString(); final Path dirToCreate = specdir .resolve(dirstr.substring(userhome.length() + 1)); if (Files.notExists(dirToCreate)) { System.out.printf("Creating directory %s\n", dirToCreate); Files.createDirectory(dirToCreate); } return FileVisitResult.CONTINUE; } }); break; } URI uri = new URI("file://" + userhome + "/" + spec + "/index.html"); Desktop.getDesktop().browse(uri); } catch (Exception ex) { ex.printStackTrace(); } finally { try { geneset.zipfilesystem.close(); } catch (Exception e) { e.printStackTrace(); } ; } } } }; NativeRun nr = new NativeRun(run); nr.runProcessBuilder("antismash", commands, new Object[3], false, run, false); } catch (IOException e1) { e1.printStackTrace(); } } })); windowmenu.getItems().add(runantismash); MenuItem runsignalp = new MenuItem("Run signalP"); runsignalp.setOnAction(actionEvent -> SwingUtilities.invokeLater(new Runnable() { public void run() { try { Serifier ser = new Serifier(); Set<String> selspec = getSelspec(null, geneset.getSpecies(), null); JTextField host = new JTextField("localhost"); JOptionPane.showMessageDialog(null, host); String username = System.getProperty("user.name"); String hostname = host.getText(); /*Path[] pt = null; JFileChooser fc = new JFileChooser(); fc.setFileSelectionMode( JFileChooser.DIRECTORIES_ONLY ); if( fc.showSaveDialog(null) == JFileChooser.APPROVE_OPTION ) { pt = new Path[3]; pt[2] = fc.getSelectedFile().toPath(); }*/ List<Object> commands = new ArrayList<Object>(); //commands.add(genexyplotaction) try { Map<String, String> env = new HashMap<String, String>(); env.put("create", "true"); String uristr = "jar:" + geneset.zippath.toUri(); URI zipuri = URI.create(uristr /*.replace("file://", "file:")*/ ); geneset.zipfilesystem = FileSystems.newFileSystem(geneset.zipuri, env); for (Path root : geneset.zipfilesystem.getRootDirectories()) { for (String spec : selspec) { /*Path specdir = root.resolve(spec+".prodigal.fsa"); if( !Files.exists(specdir) ) { if( spec.startsWith("MAT") ) { specdir = root.resolve(spec+".gbk.aa"); } else specdir = root.resolve("fn_"+spec+"_scaffolds.prodigal.fsa"); }*/ Stream<Gene> genestream = geneset.genelist.stream() .filter(gene -> spec.equals(gene.getSpecies()) && (gene.tegeval.type == null || gene.tegeval.type.length() == 0)); Path sigout = root.resolve(spec + ".signalp"); Path[] pt = new Path[] { null, sigout, null }; if (hostname.equals("localhost")) { String[] cmds = { "signalp", "-t", "gram-", "-" }; commands.add(pt); commands.add(Arrays.asList(cmds)); } else { Path p = Paths.get(spec + ".signalp"); BufferedWriter bw = Files.newBufferedWriter(p, StandardOpenOption.CREATE, StandardOpenOption.TRUNCATE_EXISTING, StandardOpenOption.WRITE); genestream.forEachOrdered(gene -> { try { gene.writeGeneIdFasta(bw); } catch (Exception e1) { e1.printStackTrace(); } }); bw.close(); //Files.copy(specdir, p, StandardCopyOption.REPLACE_EXISTING); String[] cmds = { "scp", spec + ".signalp", hostname + ":~", ";", "ssh", hostname, "signalp", "-t", "gram-", spec + ".signalp" }; //String[] cmds = {"ssh",hostname,"signalp","-t","gram-","-"}; commands.add(pt); commands.add(Arrays.asList(cmds)); } } break; } } catch (Exception ex) { ex.printStackTrace(); } Runnable run = new Runnable() { @Override public void run() { try { geneset.zipfilesystem.close(); } catch (Exception e) { e.printStackTrace(); } ; } }; NativeRun nr = new NativeRun(run); nr.runProcessBuilder("signalp", commands, new Object[3], false, run, false); } catch (IOException e1) { e1.printStackTrace(); } } })); windowmenu.getItems().add(runsignalp); MenuItem runtransm = new MenuItem("Run TransM"); runtransm.setOnAction(actionEvent -> SwingUtilities.invokeLater(new Runnable() { public void run() { try { Serifier ser = new Serifier(); Set<String> selspec = getSelspec(null, geneset.getSpecies(), null); JTextField host = new JTextField("localhost"); JOptionPane.showMessageDialog(null, host); String username = System.getProperty("user.name"); String hostname = host.getText(); /*Path[] pt = null; JFileChooser fc = new JFileChooser(); fc.setFileSelectionMode( JFileChooser.DIRECTORIES_ONLY ); if( fc.showSaveDialog(null) == JFileChooser.APPROVE_OPTION ) { pt = new Path[3]; pt[2] = fc.getSelectedFile().toPath(); }*/ List<Object> commands = new ArrayList<>(); //commands.add(genexyplotaction) try { Map<String, String> env = new HashMap<>(); env.put("create", "true"); String uristr = "jar:" + geneset.zippath.toUri(); URI zipuri = URI.create(uristr /*.replace("file://", "file:")*/ ); geneset.zipfilesystem = FileSystems.newFileSystem(geneset.zipuri, env); for (Path root : geneset.zipfilesystem.getRootDirectories()) { for (String spec : selspec) { /*Path specdir = root.resolve(spec+".prodigal.fsa"); if( !Files.exists(specdir) ) { if( spec.startsWith("MAT") ) { specdir = root.resolve(spec+".gbk.aa"); } else specdir = root.resolve("fn_"+spec+"_scaffolds.prodigal.fsa"); }*/ Stream<Gene> genestream = geneset.genelist.stream() .filter(gene -> spec.equals(gene.getSpecies()) && (gene.tegeval.type == null || gene.tegeval.type.length() == 0)); ByteArrayOutputStream baos = new ByteArrayOutputStream(); BufferedWriter bw = new BufferedWriter(new OutputStreamWriter(baos)); genestream.forEach(gene -> { try { gene.writeGeneIdFasta(bw); } catch (Exception e1) { e1.printStackTrace(); } }); bw.close(); baos.close(); String seqs = baos.toString(); seqs = seqs.replace('*', 'X'); byte[] bb = seqs.getBytes(); Path sigout = root.resolve(spec + ".tm"); Object[] pt = new Object[] { bb, sigout, null }; if (hostname.equals("localhost")) { String[] cmds = { "decodeanhmm", "-f", "/opt/tmhmm-2.0c/lib/TMHMM2.0.options", "-modelfile", "/opt/tmhmm-2.0c/lib/TMHMM2.0.model" }; commands.add(pt); commands.add(Arrays.asList(cmds)); } else { //Path p = Paths.get(spec+".tm"); //Files.copy(specdir, p, StandardCopyOption.REPLACE_EXISTING); String[] cmds = { "ssh", hostname, "decodeanhmm", "-f", "/opt/tmhmm-2.0c/lib/TMHMM2.0.options", "-modelfile", "/opt/tmhmm-2.0c/lib/TMHMM2.0.model" }; commands.add(pt); commands.add(Arrays.asList(cmds)); } } break; } } catch (Exception ex) { ex.printStackTrace(); } Runnable run = () -> { try { geneset.zipfilesystem.close(); } catch (Exception e) { e.printStackTrace(); } ; }; NativeRun nr = new NativeRun(run); nr.runProcessBuilder("transm", commands, new Object[3], false, run, false); } catch (IOException e1) { e1.printStackTrace(); } } })); windowmenu.getItems().add(runtransm); MenuItem runtrnascan = new MenuItem("tRNAscan"); runtrnascan.setOnAction(actionEvent -> SwingUtilities.invokeLater(() -> { try { Serifier ser = new Serifier(); Set<String> selspec = getSelspec(null, geneset.getSpecies(), null); JTextField host = new JTextField("localhost"); JOptionPane.showMessageDialog(null, host); String username = System.getProperty("user.name"); String hostname = host.getText(); /*Path[] pt = null; JFileChooser fc = new JFileChooser(); fc.setFileSelectionMode( JFileChooser.DIRECTORIES_ONLY ); if( fc.showSaveDialog(null) == JFileChooser.APPROVE_OPTION ) { pt = new Path[3]; pt[2] = fc.getSelectedFile().toPath(); }*/ List<Object> commands = new ArrayList<>(); //commands.add(genexyplotaction) try { Map<String, String> env = new HashMap<>(); env.put("create", "true"); String uristr = "jar:" + geneset.zippath.toUri(); URI zipuri = URI.create(uristr /*.replace("file://", "file:")*/ ); geneset.zipfilesystem = FileSystems.newFileSystem(geneset.zipuri, env); for (Path root : geneset.zipfilesystem.getRootDirectories()) { for (String spec : selspec) { Path specdir = root.resolve(spec + ".fna"); if (!Files.exists(specdir)) { if (spec.startsWith("MAT")) { specdir = root.resolve(spec + ".gbk.fna"); } else specdir = root.resolve("fn_" + spec + "_scaffolds.fastg"); } System.err.println(Files.exists(specdir)); Path sigout = root.resolve("trnas.txt"); if (hostname.equals("localhost1")) { Path[] pt = new Path[] { specdir, sigout, null }; String[] cmds = { "/usr/local/bin/tRNAscan-SE", "-B", "-" }; commands.add(pt); commands.add(Arrays.asList(cmds)); } else { Path[] pt = new Path[] { null, sigout, null }; Path p = Paths.get(spec + ".trnascan"); Files.copy(specdir, p, StandardCopyOption.REPLACE_EXISTING); List<String> lcmd; if (hostname.equals("localhost")) { //String[] cmds = {"/usr/local/bin/trnascan-1.4", spec + ".trnascan"}; String[] cmds = { "/usr/local/bin/tRNAscan-SE", "-B", spec + ".trnascan" }; lcmd = Arrays.asList(cmds); } else { String[] cmds = { "scp", spec + ".trnascan", hostname + ":~", ";", "ssh", hostname, "trnascan-1.4", spec + ".trnascan" }; lcmd = Arrays.asList(cmds); //String[] cmds = {"ssh",hostname,"tRNAscan-SE","-B","-"}; } commands.add(pt); commands.add(lcmd); } } break; } } catch (Exception ex) { ex.printStackTrace(); } Runnable run = () -> { try { geneset.zipfilesystem.close(); } catch (Exception e) { e.printStackTrace(); } ; }; NativeRun nr = new NativeRun(run); nr.runProcessBuilder("tRNAscan", commands, new Object[3], false, run, false); } catch (IOException e1) { e1.printStackTrace(); } })); windowmenu.getItems().add(runtrnascan); Menu select = new Menu("Select"); MenuItem breakpointselAction = new MenuItem("Select breakpoints"); breakpointselAction.setOnAction(actionEvent -> { String spec = syncolorcomb.getSelectionModel().getSelectedItem(); int rr = 0; for (Gene g : geneset.genelist) { if (!spec.equals(g.getSpecies()) && g.getSpecies().contains("eggert")) { Tegeval tv2 = g.tegeval; Annotation n2 = tv2.getNext(); Annotation p2 = tv2.getPrevious(); GeneGroup gg = g.getGeneGroup(); if (gg.getName().contains("rhodane")) { System.err.println(); } Teginfo ti = gg.getGenes(spec); int msimcount = 0; if (ti != null) { for (Tegeval tv1 : ti.tset) { int simcount = 0; Annotation n = tv1.getNext(); Annotation p = tv1.getPrevious(); GeneGroup ggg = tv1.getGene().getGeneGroup(); if (n2 != null) { if (ggg == n2.getGene().getGeneGroup()) { simcount++; } Annotation nn2 = n2.getNext(); if (nn2 != null) { if (ggg == nn2.getGene().getGeneGroup()) { simcount++; } } } if (p2 != null) { if (ggg == p2.getGene().getGeneGroup()) { simcount++; } Annotation pp2 = p2.getPrevious(); if (pp2 != null) { if (ggg == pp2.getGene().getGeneGroup()) { simcount++; } } } if (n != null) { GeneGroup ngg = n.getGene().getGeneGroup(); if (ngg == tv2.getGene().getGeneGroup()) { simcount++; } if (n2 != null) { if (ngg == n2.getGene().getGeneGroup()) { simcount++; } } if (p2 != null) { if (ngg == p2.getGene().getGeneGroup()) { simcount++; } } Annotation nn = n.getNext(); if (nn != null) { ngg = nn.getGene().getGeneGroup(); if (ngg == tv2.getGene().getGeneGroup()) { simcount++; } if (n2 != null) { if (ngg == n2.getGene().getGeneGroup()) { simcount++; } } if (p2 != null) { if (ngg == p2.getGene().getGeneGroup()) { simcount++; } } } } if (p != null) { GeneGroup pgg = p.getGene().getGeneGroup(); if (pgg == tv2.getGene().getGeneGroup()) { simcount++; } if (n2 != null) { if (pgg == n2.getGene().getGeneGroup()) { simcount++; } } if (p2 != null) { if (pgg == p2.getGene().getGeneGroup()) { simcount++; } } Annotation pp = p.getPrevious(); if (pp != null) { pgg = pp.getGene().getGeneGroup(); if (pgg == tv2.getGene().getGeneGroup()) { simcount++; } if (n2 != null) { if (pgg == n2.getGene().getGeneGroup()) { simcount++; } } if (p2 != null) { if (pgg == p2.getGene().getGeneGroup()) { simcount++; } } } } //double rat = GeneCompare.invertedGradientRatio(spec, contigs, -1.0, gg, tv); if (simcount >= msimcount) { //tv = tv1; msimcount = simcount; } //double ratio = GeneCompare.invertedGradientRatio(spec, contigs, -1.0, gg, tv); //GeneCompare.gradientColor(); } if (msimcount < 2) { gtable.getSelectionModel().select(g); } } } rr++; } /*List<Sequence> contigs = geneset.speccontigMap.get( spec ); for( Sequence c : contigs ) { for( Annotation ann : c.annset ) { Tegeval tv = (Tegeval)ann; } }*/ }); MenuItem saveselAction = new MenuItem("Save selection"); saveselAction.setOnAction(actionEvent -> { /*int[] rr = table.getSelectedRows(); if( rr.length > 0 ) { String val = Integer.toString( table.convertRowIndexToModel(rr[0]) ); for( int i = 1; i < rr.length; i++ ) { val += ","+table.convertRowIndexToModel(rr[i]); } String selname = JOptionPane.showInputDialog("Selection name"); if( comp instanceof Applet ) { try { ((GeneSetHead)comp).saveSel( selname, val); } catch (Exception e1) { e1.printStackTrace(); } } }*/ }); select.getItems().add(breakpointselAction); select.getItems().add(saveselAction); select.getItems().add(new SeparatorMenuItem()); MenuItem showall = new MenuItem("Show all"); showall.setOnAction(actionEvent -> { genefilterset.clear(); updateFilter(table, label); }); select.getItems().add(showall); MenuItem croptosel = new MenuItem("Crop to selection"); croptosel.setOnAction(actionEvent -> { Set<GeneGroup> selitems = new HashSet<>(table.getSelectionModel().getSelectedItems()); filteredData.setPredicate(p -> selitems.contains(p)); }); select.getItems().add(croptosel); MenuItem croptoinvsel = new MenuItem("Crop to inverted selection"); croptoinvsel.setOnAction(actionEvent -> { genefilterset.clear(); for (int i = 0; i < table.getItems().size(); i++) { if (!table.getSelectionModel().isSelected(i)) { genefilterset.add(i); } } updateFilter(table, label); }); select.getItems().add(croptoinvsel); MenuItem removesel = new MenuItem("Remove selection"); removesel.setOnAction(actionEvent -> { // genefilterset.clear(); //int[] rr = table.getSelectedRows(); if (genefilterset.isEmpty()) { Set<Integer> ii = new HashSet<Integer>(); for (int r : table.getSelectionModel().getSelectedIndices()) ii.add(r); for (int i = 0; i < geneset.genelist.size(); i++) { if (!ii.contains(i)) genefilterset.add(i); } } else { for (int r : table.getSelectionModel().getSelectedIndices()) { //int mr = table.convertRowIndexToModel(r); genefilterset.remove(r); } } updateFilter(table, label); }); select.getItems().add(removesel); MenuItem invsel = new MenuItem("Invert selection"); invsel.setOnAction(actionEvent -> { ObservableList<GeneGroup> selitems = table.getSelectionModel().getSelectedItems(); List<GeneGroup> newsel = new ArrayList<>(filteredData); newsel.removeAll(selitems); table.getSelectionModel().clearSelection(); newsel.stream().forEach(gg -> table.getSelectionModel().select(gg)); // genefilterset.clear(); //int[] rr = table.getSelectedRows(); /*Set<Integer> iset = new HashSet<>(); for( int r : table.getSelectionModel().getSelectedIndices() ) { iset.add( r ); } table.getSelectionModel().clearSelection(); for (int r = 0; r < table.getItems().size(); r++) { if( !iset.contains(r) ) table.getSelectionModel().select(r); /*if (table.isRowSelected(r)) table.removeRowSelectionInterval(r, r); else table.addRowSelectionInterval(r, r); }*/ }); select.getItems().add(invsel); //select.addSeparator(); select.getItems().add(new SeparatorMenuItem()); MenuItem selsinglemult = new MenuItem("Select single copy genes found in multiple strains"); selsinglemult.setOnAction(actionEvent -> { Set<String> specset = getSelspec(GeneSetHead.this, geneset.specList); for (GeneGroup gg : geneset.allgenegroups) { Set<String> checkspec = new HashSet<String>(gg.species.keySet()); checkspec.retainAll(specset); if (gg.getCommonTag() == null && checkspec.size() > 1 && gg.getTegevals().size() == gg.species.size()) {//gg.getTegevals(checkspec).size() == checkspec.size() ) { table.getSelectionModel().select(gg); //table.setro } } }); select.getItems().add(selsinglemult); MenuItem selsinglemultstrain = new MenuItem( "Select single copy genes in accessory genome of multiple strains"); selsinglemultstrain.setOnAction(actionEvent -> { Set<String> specset = getSelspec(GeneSetHead.this, geneset.specList); for (GeneGroup gg : geneset.allgenegroups) { Set<String> checkspec = new HashSet<String>(gg.species.keySet()); checkspec.retainAll(specset); if (gg.getCommonTag() == null && checkspec.size() > 1 && checkspec.size() < specset.size() && gg.getTegevals().size() == gg.species.size()) {//gg.getTegevals(checkspec).size() == checkspec.size() ) { table.getSelectionModel().select(gg); //table.setro } } }); select.getItems().add(selsinglemultstrain); MenuItem selsinglecopygenes = new MenuItem("Select single copy genes"); selsinglecopygenes.setOnAction(actionEvent -> { Set<String> specset = getSelspec(GeneSetHead.this, geneset.specList); for (GeneGroup gg : geneset.allgenegroups) { if (gg.getTegevals().size() == gg.species.size()) { table.getSelectionModel().select(gg); //table.setro } } }); select.getItems().add(selsinglecopygenes); MenuItem selduplgenes = new MenuItem("Select duplicated genes"); selduplgenes.setOnAction(actionEvent -> { for (GeneGroup gg : geneset.allgenegroups) { int cnt = 0; for (String spec : gg.species.keySet()) { Teginfo ti = gg.species.get(spec); if (ti.tset.size() == 2) { List<Tegeval> ta = new ArrayList<Tegeval>(ti.tset); if (ta.get(0).getNext() == ta.get(1) || ta.get(0).getPrevious() == ta.get(1)) cnt++; } } if ((float) cnt / (float) gg.species.size() > 0.7) { table.getSelectionModel().select(gg); } } }); select.getItems().add(selduplgenes); MenuItem seltriplgenes = new MenuItem("Select triplicated genes"); seltriplgenes.setOnAction(actionEvent -> { for (GeneGroup gg : geneset.allgenegroups) { int cnt = 0; for (String spec : gg.species.keySet()) { Teginfo ti = gg.species.get(spec); if (ti.tset.size() == 3) { List<Tegeval> ta = new ArrayList<Tegeval>(ti.tset); if ((ta.get(0).getNext() == ta.get(1) || ta.get(0).getPrevious() == ta.get(1)) && (ta.get(1).getNext() == ta.get(2) || ta.get(1).getPrevious() == ta.get(2))) cnt++; } } if ((float) cnt / (float) gg.species.size() > 0.7) { table.getSelectionModel().select(gg); } } }); select.getItems().add(seltriplgenes); MenuItem selplasmidgenes = new MenuItem("Select plasmid genes"); selplasmidgenes.setOnAction(actionEvent -> { for (GeneGroup gg : geneset.allgenegroups) { if (gg.isOnAnyPlasmid()) { table.getSelectionModel().select(gg); } /*int cnt = 0; for( String spec : gg.species.keySet() ) { Teginfo ti = gg.species.get( spec ); if( ti.tset.size() == 3 ) { List<Tegeval> ta = new ArrayList<Tegeval>( ti.tset ); if( (ta.get(0).getNext() == ta.get(1) || ta.get(0).getPrevious() == ta.get(1)) && (ta.get(1).getNext() == ta.get(2) || ta.get(1).getPrevious() == ta.get(2))) cnt++; } } if( (float)cnt / (float)gg.species.size() > 0.7 ) { int r = table.convertRowIndexToView(gg.index); table.addRowSelectionInterval(r, r); }*/ } }); select.getItems().add(selplasmidgenes); MenuItem selectphagegenes = new MenuItem("Select phage genes"); selectphagegenes.setOnAction(actionEvent -> { for (GeneGroup gg : geneset.allgenegroups) { if (gg.isInAnyPhage()) { table.getSelectionModel().select(gg); } /*int cnt = 0; for( String spec : gg.species.keySet() ) { Teginfo ti = gg.species.get( spec ); if( ti.tset.size() == 3 ) { List<Tegeval> ta = new ArrayList<Tegeval>( ti.tset ); if( (ta.get(0).getNext() == ta.get(1) || ta.get(0).getPrevious() == ta.get(1)) && (ta.get(1).getNext() == ta.get(2) || ta.get(1).getPrevious() == ta.get(2))) cnt++; } } if( (float)cnt / (float)gg.species.size() > 0.7 ) { int r = table.convertRowIndexToView(gg.index); table.addRowSelectionInterval(r, r); }*/ } }); select.getItems().add(selectphagegenes); select.getItems().add(new SeparatorMenuItem()); MenuItem selectsharingaction = new MenuItem("Select sharing"); selectsharingaction.setOnAction(actionEvent -> { RadioButton panbtn = new RadioButton("Pan"); RadioButton corebtn = new RadioButton("Core"); RadioButton blehbtn = new RadioButton("Only in"); ToggleGroup tg = new ToggleGroup(); panbtn.setToggleGroup(tg); corebtn.setToggleGroup(tg); blehbtn.setToggleGroup(tg); HBox sp = new HBox(); sp.getChildren().add(panbtn); sp.getChildren().add(corebtn); sp.getChildren().add(blehbtn); Scene scene = new Scene(sp); //FlowLayout flowlayout = new FlowLayout(); final JFXPanel c = new JFXPanel(); c.setScene(scene); /*Group root = new Group(); Scene scene = new Scene(root, javafx.scene.paint.Color.ALICEBLUE); root.getChildren().add(panbtn); root.getChildren().add(corebtn); root.getChildren().add(blehbtn); JFXPanel fxpanel = new JFXPanel(); fxpanel.setScene( scene );*/ //bg.add( panbtn ); //bg.add( corebtn ); //bg.add( blehbtn ); corebtn.setSelected(true); //Object[] objs = new Object[] { panbtn, corebtn }; //JOptionPane.showMessageDialog( geneset, objs, "Select id types", JOptionPane.PLAIN_MESSAGE ); SwingUtilities.invokeLater(new Runnable() { public void run() { final List<String> species = geneset.getSpecies(); TableModel model = new TableModel() { @Override public int getRowCount() { return species.size(); } @Override public int getColumnCount() { return 1; } @Override public String getColumnName(int columnIndex) { return null; } @Override public Class<?> getColumnClass(int columnIndex) { return String.class; } @Override public boolean isCellEditable(int rowIndex, int columnIndex) { return false; } @Override public Object getValueAt(int rowIndex, int columnIndex) { return species.get(rowIndex); } @Override public void setValueAt(Object aValue, int rowIndex, int columnIndex) { } @Override public void addTableModelListener(TableModelListener l) { } @Override public void removeTableModelListener(TableModelListener l) { } }; JTable table = new JTable(model); table.getSelectionModel().setSelectionMode(ListSelectionModel.MULTIPLE_INTERVAL_SELECTION); JScrollPane scroll = new JScrollPane(table); Object[] objs = new Object[] { scroll, c }; JOptionPane.showMessageDialog(comp, objs); final Set<String> specs = new HashSet<String>(); int[] rr = table.getSelectedRows(); for (int r : rr) { String spec = (String) table.getValueAt(r, 0); specs.add(spec); } Platform.runLater(new Runnable() { public void run() { for (GeneGroup gg : geneset.allgenegroups) { if (blehbtn.isSelected()) { Set<String> ss = new HashSet<String>(gg.species.keySet()); ss.removeAll(specs); if (ss.size() == 0) { GeneSetHead.this.table.getSelectionModel().select(gg); } } else if (gg.species.keySet().containsAll(specs) && (panbtn.isSelected() || specs.size() == gg.species.size())) { GeneSetHead.this.table.getSelectionModel().select(gg); } } } }); } }); }); select.getItems().add(selectsharingaction); MenuItem selectdirtyaction = new MenuItem("Select dirty"); selectdirtyaction.setOnAction(actionEvent -> { if (!isGeneview()) { int i = 0; for (GeneGroup gg : geneset.allgenegroups) { if (gg.containsDirty()) { table.getSelectionModel().select(gg); } i++; } } }); select.getItems().add(selectdirtyaction); MenuItem selectdesignationaction = new MenuItem("Select designation"); selectdesignationaction.setOnAction(actionEvent -> { JComboBox<String> descombo = new JComboBox<String>( geneset.deset.toArray(new String[geneset.deset.size()])); descombo.insertItemAt("", 0); descombo.setSelectedIndex(0); JOptionPane.showMessageDialog(GeneSetHead.this, descombo); String seldes = (String) descombo.getSelectedItem(); if (!isGeneview()) { int i = 0; for (GeneGroup gg : geneset.allgenegroups) { if (gg.genes != null) for (Gene g : gg.genes) { if (seldes.equals(g.tegeval.designation)) { table.getSelectionModel().select(gg); } } i++; } } }); select.getItems().add(selectdesignationaction); MenuItem blastselect = new MenuItem("Blast select"); blastselect.setOnAction(actionEvent -> SwingUtilities.invokeLater(() -> blast(false))); select.getItems().add(blastselect); MenuItem blastxselect = new MenuItem("Blastx select"); blastxselect.setOnAction(actionEvent -> SwingUtilities.invokeLater(() -> blast(true))); select.getItems().add(blastxselect); MenuItem blastnselect = new MenuItem("Blastn select"); blastnselect.setOnAction(actionEvent -> SwingUtilities.invokeLater(() -> blastn(true))); select.getItems().add(blastnselect); MenuItem blastsearch = new MenuItem("Blastn search"); blastsearch.setOnAction(actionEvent -> SwingUtilities.invokeLater(() -> blastn(false))); select.getItems().add(blastsearch); menubar.getMenus().add(file); menubar.getMenus().add(edit); menubar.getMenus().add(view); menubar.getMenus().add(sequencemenu); menubar.getMenus().add(windowmenu); menubar.getMenus().add(select); menubar.getMenus().add(help); if (comp != null) { final Window window = SwingUtilities.windowForComponent(comp); initFSKeyListener(window); if (comp instanceof JFrame || window instanceof JFrame) { JFrame frame = (JFrame) (window == null ? comp : window); if (!frame.isResizable()) frame.setResizable(true); frame.addKeyListener(keylistener); frame.setJMenuBar(jmenubar); } } final Button jb = new Button("Atlas"); jb.setOnAction(event -> { try { URL url = new URL("file:///home/sigmar/workspace/distann/bin/circle.html"); GeneSetHead.this.getAppletContext().showDocument(url, "_blank"); } catch (MalformedURLException e1) { e1.printStackTrace(); } }); try { newSoft(jb, comp, genetable, upper, lower, toolbar, btoolbar, GeneSetHead.this, selcomb); } catch (IOException e) { e.printStackTrace(); } if (comp != null) { if (comp instanceof Applet) try { ((GeneSetHead) comp).saveSel(null, null); } catch (NoSuchMethodError | Exception e1) { e1.printStackTrace(); } //comp.add( cc ); } }
From source file:editeurpanovisu.EditeurPanovisu.java
/** * * @param primaryStage//from w w w .j a v a 2 s . c o m * @param width * @param height * @throws Exception */ private void creeEnvironnement(Stage primaryStage, int width, int height) throws Exception { popUp = new PopUpDialogController(); primaryStage.setMaximized(true); double largeurOutils = 380; hauteurInterface = height; largeurInterface = width; /** * Cration des lments constitutifs de l'cran */ VBox root = new VBox(); creeMenu(root, width); tabPaneEnvironnement = new TabPane(); // tabPaneEnvironnement.setTranslateZ(5); tabPaneEnvironnement.setMinHeight(height - 60); tabPaneEnvironnement.setMaxHeight(height - 60); Pane barreStatus = new Pane(); barreStatus.setPrefSize(width + 20, 30); barreStatus.setTranslateY(25); barreStatus.setStyle("-fx-background-color:#c00;-fx-border-color:#aaa"); tabVisite = new Tab(); Pane visualiseur; Pane panneauPlan; tabInterface = new Tab(); tabPlan = new Tab(); gestionnaireInterface.creeInterface(width, height - 60); visualiseur = gestionnaireInterface.tabInterface; gestionnairePlan.creeInterface(width, height - 60); panneauPlan = gestionnairePlan.tabInterface; tabInterface.setContent(visualiseur); tabPlan.setContent(panneauPlan); HBox hbEnvironnement = new HBox(); TextArea txtTitrePano; TextArea tfTitreVisite; RadioButton radSphere; RadioButton radCube; CheckBox chkAfficheTitre; CheckBox chkAfficheInfo; tabPaneEnvironnement.getTabs().addAll(tabVisite, tabInterface, tabPlan); //tabPaneEnvironnement.setTranslateY(80); tabPaneEnvironnement.setSide(Side.TOP); tabPaneEnvironnement.getSelectionModel().selectedItemProperty() .addListener((ObservableValue<? extends Tab> ov, Tab t, Tab t1) -> { gestionnaireInterface.rafraichit(); }); tabVisite.setText(rb.getString("main.creationVisite")); tabVisite.setClosable(false); tabInterface.setText(rb.getString("main.creationInterface")); tabInterface.setClosable(false); tabPlan.setText(rb.getString("main.tabPlan")); tabPlan.setClosable(false); tabPlan.setDisable(true); tabVisite.setContent(hbEnvironnement); double largeur; String labelStyle = "-fx-color : white;-fx-background-color : #fff;-fx-padding : 5px; -fx-border : 1px solid #777;-fx-width : 100px;-fx-margin : 5px; "; scene = new Scene(root, width, height, Color.rgb(221, 221, 221)); // if (systemeExploitation.indexOf("inux") != -1) { // root.setStyle("-fx-font-size : 7pt;-fx-font-family: sans-serif;"); // } else { root.setStyle("-fx-font-size : 9pt;-fx-font-family: Arial;"); // } panneauOutils = new ScrollPane(); panneauOutils.setId("panOutils"); // panneauOutils.setStyle("-fx-background-color : #ccc;"); outils = new VBox(); paneChoixPanoramique = new VBox(); paneChoixPanoramique.setTranslateX(10); paneChoixPanoramique.setId("choixPanoramique"); Label lblTitreVisite = new Label(rb.getString("main.titreVisite")); lblTitreVisite.setStyle("-fx-font-size : 10pt;-fx-font-weight : bold;"); lblTitreVisite.setPadding(new Insets(15, 5, 5, 0)); lblTitreVisite.setMinWidth(largeurOutils - 20); lblTitreVisite.setAlignment(Pos.CENTER); tfTitreVisite = new TextArea(); tfTitreVisite.setId("titreVisite"); tfTitreVisite.setPrefSize(200, 25); tfTitreVisite.setMaxSize(340, 25); Separator sepTitre = new Separator(Orientation.HORIZONTAL); sepTitre.setMinHeight(10); Label lblChoixPanoramiqueEntree = new Label(rb.getString("main.panoEntree")); lblChoixPanoramiqueEntree.setStyle("-fx-font-size : 10pt;-fx-font-weight : bold;"); lblChoixPanoramiqueEntree.setPadding(new Insets(15, 5, 5, 0)); lblChoixPanoramiqueEntree.setMinWidth(largeurOutils - 20); lblChoixPanoramiqueEntree.setAlignment(Pos.CENTER); lblChoixPanoramique = new Label(rb.getString("main.panoAffiche")); lblChoixPanoramique.setStyle("-fx-font-size : 10pt;-fx-font-weight : bold;"); lblChoixPanoramique.setPadding(new Insets(10, 5, 5, 0)); lblChoixPanoramique.setMinWidth(largeurOutils - 20); lblChoixPanoramique.setAlignment(Pos.CENTER); Separator sepPano = new Separator(Orientation.HORIZONTAL); sepPano.setMinHeight(10); listeChoixPanoramique.setVisibleRowCount(10); listeChoixPanoramique.setTranslateX(60); Pane fond = new Pane(); fond.setCursor(Cursor.HAND); ImageView ivSupprPanoramique = new ImageView( new Image("file:" + repertAppli + File.separator + "images/suppr.png", 30, 30, true, true)); fond.setTranslateX(260); fond.setTranslateY(-40); Tooltip t = new Tooltip(rb.getString("main.supprimePano")); t.setStyle(tooltipStyle); Tooltip.install(fond, t); fond.getChildren().add(ivSupprPanoramique); fond.setOnMouseClicked((MouseEvent me) -> { retirePanoCourant(); }); listeChoixPanoramiqueEntree.setTranslateX(60); Separator sepInfo = new Separator(Orientation.HORIZONTAL); Label lblTitrePano = new Label(rb.getString("main.titrePano")); lblTitrePano.setStyle("-fx-font-size : 10pt;-fx-font-weight : bold;"); lblTitrePano.setPadding(new Insets(5, 5, 5, 0)); lblTitrePano.setMinWidth(largeurOutils - 20); lblTitrePano.setAlignment(Pos.CENTER); txtTitrePano = new TextArea(); txtTitrePano.setId("txttitrepano"); txtTitrePano.setPrefSize(200, 25); txtTitrePano.setMaxSize(340, 25); txtTitrePano.textProperty().addListener((final ObservableValue<? extends String> observable, final String oldValue, final String newValue) -> { clickBtnValidePano(); }); paneChoixPanoramique.getChildren().addAll(lblTitreVisite, tfTitreVisite, lblChoixPanoramiqueEntree, listeChoixPanoramiqueEntree, sepPano, lblChoixPanoramique, listeChoixPanoramique, fond, lblTitrePano, txtTitrePano, sepInfo); paneChoixPanoramique.setSpacing(10); /* modifier pour afficher le panneau des derniers fichiers; */ //outils.getChildren().addAll(lastFiles, paneChoixPanoramique); outils.getChildren().addAll(paneChoixPanoramique); paneChoixPanoramique.setVisible(false); /* Cration du panneau d'info du panoramique */ vuePanoramique = new ScrollPane(); coordonnees = new HBox(); pano = new Pane(); panneau2 = new AnchorPane(); lblLong = new Label(""); lblLat = new Label(""); imagePanoramique = new ImageView(); primaryStage.setScene(scene); //scene.getStylesheets().add("file:css/test.css"); /** * */ vuePanoramique.setPrefSize(width - largeurOutils - 20, height - 130); vuePanoramique.setMaxSize(width - largeurOutils - 20, height - 130); vuePanoramique.setVbarPolicy(ScrollPane.ScrollBarPolicy.NEVER); vuePanoramique.setHbarPolicy(ScrollPane.ScrollBarPolicy.NEVER); vuePanoramique.setTranslateY(5); //vuePanoramique.setStyle("-fx-background-color : #c00;"); /** * */ panneauOutils.setContent(outils); panneauOutils.setVbarPolicy(ScrollPane.ScrollBarPolicy.AS_NEEDED); panneauOutils.setHbarPolicy(ScrollPane.ScrollBarPolicy.NEVER); panneauOutils.setPrefSize(largeurOutils, height - 240); panneauOutils.setMaxWidth(largeurOutils); panneauOutils.setMaxHeight(height - 240); panneauOutils.setTranslateY(15); panneauOutils.setTranslateX(20); // panneauOutils.setStyle("-fx-background-color : #ccc;"); /** * */ pano.setCursor(Cursor.CROSSHAIR); outils.setPrefWidth(largeurOutils - 20); // outils.setStyle("-fx-background-color : #ccc;"); outils.minHeight(height - 130); outils.setLayoutX(10); // lblLong.setStyle(labelStyle); // lblLat.setStyle(labelStyle); lblLong.setPrefSize(100, 15); lblLat.setPrefSize(100, 15); lblLat.setTranslateX(50); // panneau2.setStyle("-fx-background-color : #ddd;"); panneau2.setPrefSize(width - largeurOutils - 20, height - 140); imagePanoramique.setCache(true); largeur = largeurMax - 60; imagePanoramique.setFitWidth(largeur); imagePanoramique.setFitHeight(largeur / 2.0d); imagePanoramique.setLayoutX((largeurMax - largeur) / 2.d); pano.getChildren().add(imagePanoramique); pano.setPrefSize(imagePanoramique.getFitWidth(), imagePanoramique.getFitHeight()); pano.setMaxSize(imagePanoramique.getFitWidth(), imagePanoramique.getFitHeight()); pano.setLayoutY(20); lblLong.setTranslateX(50); lblLat.setTranslateX(80); coordonnees.getChildren().setAll(lblLong, lblLat); vuePanoramique.setContent(panneau2); hbEnvironnement.getChildren().setAll(vuePanoramique, panneauOutils); AnchorPane paneEnv = new AnchorPane(); paneAttends = new AnchorPane(); paneAttends.setPrefHeight(250); paneAttends.setPrefWidth(400); paneAttends.setStyle("-fx-background-color : #ccc;" + "-fx-border-color: #666;" + "-fx-border-radius: 5px;" + "-fx-border-width: 1px;"); paneAttends.setLayoutX((width - 400) / 2.d); paneAttends.setLayoutY((height - 250) / 2.d - 55); ProgressIndicator p1 = new ProgressIndicator(); p1.setPrefSize(100, 100); p1.setLayoutX(150); p1.setLayoutY(50); Label lblAttends = new Label(rb.getString("main.attendsChargement")); lblAttends.setMinWidth(400); lblAttends.setAlignment(Pos.CENTER); lblAttends.setLayoutY(20); lblCharge = new Label(); lblCharge.setMinWidth(400); lblCharge.setLayoutY(200); paneAttends.getChildren().addAll(lblAttends, p1, lblCharge); paneAttends.setVisible(false); paneEnv.getChildren().addAll(tabPaneEnvironnement, paneAttends); // paneEnv.getChildren().addAll(tabPaneEnvironnement); root.getChildren().addAll(paneEnv); panneau2.getChildren().setAll(coordonnees, pano); primaryStage.show(); popUp.affichePopup(); lblDragDrop = new Label(rb.getString("main.dragDrop")); lblDragDrop.setMinHeight(vuePanoramique.getPrefHeight()); lblDragDrop.setMaxHeight(vuePanoramique.getPrefHeight()); lblDragDrop.setMinWidth(vuePanoramique.getPrefWidth()); lblDragDrop.setMaxWidth(vuePanoramique.getPrefWidth()); lblDragDrop.setAlignment(Pos.CENTER); lblDragDrop.setTextFill(Color.web("#c9c7c7")); lblDragDrop.setTextAlignment(TextAlignment.CENTER); lblDragDrop.setWrapText(true); lblDragDrop.setStyle("-fx-font-size:72px"); lblDragDrop.setTranslateY(-100); panneau2.getChildren().addAll(lblDragDrop, afficheLegende()); }
From source file:editeurpanovisu.EditeurPanovisu.java
/** * * @param primaryStage//w w w . jav a 2 s .c om * @param racine * @param taille * @throws Exception */ private void creeMenu(VBox racine, int taille) throws Exception { //Pane myPane = (Pane) FXMLLoader.load(getClass().getResource("menuPrincipal.fxml")); VBox myPane = new VBox(); myPane.setPrefHeight(80); myPane.setPrefWidth(3000); MenuBar menuPrincipal = new MenuBar(); menuPrincipal.setMinHeight(25); menuPrincipal.setPrefHeight(29); menuPrincipal.setPrefWidth(3000); /* Menu projets */ Menu menuProjet = new Menu(rb.getString("projets")); menuPrincipal.getMenus().add(menuProjet); nouveauProjet = new MenuItem(rb.getString("nouveauProjet")); nouveauProjet.setAccelerator(KeyCombination.keyCombination("Ctrl+N")); menuProjet.getItems().add(nouveauProjet); chargeProjet = new MenuItem(rb.getString("ouvrirProjet")); chargeProjet.setAccelerator(KeyCombination.keyCombination("Ctrl+O")); menuProjet.getItems().add(chargeProjet); sauveProjet = new MenuItem(rb.getString("sauverProjet")); sauveProjet.setDisable(true); sauveProjet.setAccelerator(KeyCombination.keyCombination("Ctrl+S")); menuProjet.getItems().add(sauveProjet); sauveSousProjet = new MenuItem(rb.getString("sauverProjetSous")); sauveSousProjet.setDisable(true); sauveSousProjet.setAccelerator(KeyCombination.keyCombination("Shift+Ctrl+S")); menuProjet.getItems().add(sauveSousProjet); derniersProjets = new Menu(rb.getString("derniersProjets")); // derniersProjets.setDisable(true); menuProjet.getItems().add(derniersProjets); fichHistoFichiers = new File(repertConfig.getAbsolutePath() + File.separator + "derniersprojets.cfg"); nombreHistoFichiers = 0; if (fichHistoFichiers.exists()) { FileReader fr; fr = new FileReader(fichHistoFichiers); try (BufferedReader br = new BufferedReader(fr)) { while ((texteHisto = br.readLine()) != null) { MenuItem menuDerniersFichiers = new MenuItem(texteHisto); derniersProjets.getItems().add(menuDerniersFichiers); histoFichiers[nombreHistoFichiers] = texteHisto; nombreHistoFichiers++; menuDerniersFichiers.setOnAction((ActionEvent e) -> { MenuItem mnu = (MenuItem) e.getSource(); try { try { projetChargeNom(mnu.getText()); } catch (InterruptedException ex) { Logger.getLogger(EditeurPanovisu.class.getName()).log(Level.SEVERE, null, ex); } } catch (IOException ex) { Logger.getLogger(EditeurPanovisu.class.getName()).log(Level.SEVERE, null, ex); } }); } } } SeparatorMenuItem sep1 = new SeparatorMenuItem(); menuProjet.getItems().add(sep1); fermerProjet = new MenuItem(rb.getString("quitterApplication")); fermerProjet.setAccelerator(KeyCombination.keyCombination("Ctrl+Q")); menuProjet.getItems().add(fermerProjet); /* Menu affichage */ Menu menuAffichage = new Menu(rb.getString("affichage")); menuPrincipal.getMenus().add(menuAffichage); affichageVisite = new MenuItem(rb.getString("main.creationVisite")); affichageVisite.setAccelerator(KeyCombination.keyCombination("Ctrl+1")); menuAffichage.getItems().add(affichageVisite); affichageInterface = new MenuItem(rb.getString("main.creationInterface")); affichageInterface.setAccelerator(KeyCombination.keyCombination("Ctrl+2")); menuAffichage.getItems().add(affichageInterface); affichagePlan = new MenuItem(rb.getString("main.tabPlan")); affichagePlan.setAccelerator(KeyCombination.keyCombination("Ctrl+3")); affichagePlan.setDisable(true); menuAffichage.getItems().add(affichagePlan); SeparatorMenuItem sep3 = new SeparatorMenuItem(); menuAffichage.getItems().add(sep3); configTransformation = new MenuItem(rb.getString("affichageConfiguration")); menuAffichage.getItems().add(configTransformation); /* Menu panoramiques */ menuPanoramique = new Menu(rb.getString("panoramiques")); menuPanoramique.setDisable(true); menuPrincipal.getMenus().add(menuPanoramique); ajouterPano = new MenuItem(rb.getString("ajouterPanoramiques")); ajouterPano.setAccelerator(KeyCombination.keyCombination("Ctrl+A")); menuPanoramique.getItems().add(ajouterPano); ajouterPlan = new MenuItem(rb.getString("ajouterPlan")); ajouterPlan.setAccelerator(KeyCombination.keyCombination("Ctrl+P")); menuPanoramique.getItems().add(ajouterPlan); ajouterPlan.setDisable(true); SeparatorMenuItem sep2 = new SeparatorMenuItem(); menuPanoramique.getItems().add(sep2); visiteGenere = new MenuItem(rb.getString("genererVisite")); visiteGenere.setDisable(true); visiteGenere.setAccelerator(KeyCombination.keyCombination("Ctrl+V")); menuPanoramique.getItems().add(visiteGenere); /* Menu Modles */ menuModeles = new Menu(rb.getString("menuModele")); menuPrincipal.getMenus().add(menuModeles); chargerModele = new MenuItem(rb.getString("modeleCharger")); menuModeles.getItems().add(chargerModele); sauverModele = new MenuItem(rb.getString("modeleSauver")); menuModeles.getItems().add(sauverModele); /* Menu transformations */ menuTransformation = new Menu(rb.getString("outils")); menuPrincipal.getMenus().add(menuTransformation); equi2CubeTransformation = new MenuItem(rb.getString("outilsEqui2Cube")); menuTransformation.getItems().add(equi2CubeTransformation); cube2EquiTransformation = new MenuItem(rb.getString("outilsCube2Equi")); menuTransformation.getItems().add(cube2EquiTransformation); /* Menu Aide */ Menu menuAide = new Menu(rb.getString("aide")); menuPrincipal.getMenus().add(menuAide); aide = new MenuItem(rb.getString("aideAide")); aide.setAccelerator(KeyCombination.keyCombination("Ctrl+H")); menuAide.getItems().add(aide); SeparatorMenuItem sep4 = new SeparatorMenuItem(); menuAide.getItems().add(sep4); aPropos = new MenuItem(rb.getString("aideAPropos")); menuAide.getItems().add(aPropos); /* barre de boutons */ HBox barreBouton = new HBox(); barreBouton.getStyleClass().add("menuBarreOutils1"); barreBouton.setPrefHeight(50); barreBouton.setMinHeight(50); barreBouton.setPrefWidth(3000); /* Bouton nouveau Projet */ ScrollPane spBtnNouvprojet = new ScrollPane(); spBtnNouvprojet.getStyleClass().add("menuBarreOutils"); spBtnNouvprojet.setHbarPolicy(ScrollPane.ScrollBarPolicy.NEVER); spBtnNouvprojet.setPrefHeight(35); spBtnNouvprojet.setMaxHeight(35); spBtnNouvprojet.setPadding(new Insets(2)); spBtnNouvprojet.setPrefWidth(35); HBox.setMargin(spBtnNouvprojet, new Insets(5, 15, 0, 15)); imgNouveauProjet = new ImageView( new Image("file:" + repertAppli + File.separator + "images/nouveauProjet.png")); spBtnNouvprojet.setContent(imgNouveauProjet); Tooltip t0 = new Tooltip(rb.getString("nouveauProjet")); t0.setStyle(tooltipStyle); spBtnNouvprojet.setTooltip(t0); barreBouton.getChildren().add(spBtnNouvprojet); /* Bouton ouvrir Projet */ ScrollPane spBtnOuvrirProjet = new ScrollPane(); spBtnOuvrirProjet.getStyleClass().add("menuBarreOutils"); spBtnOuvrirProjet.setHbarPolicy(ScrollPane.ScrollBarPolicy.NEVER); spBtnOuvrirProjet.setPrefHeight(35); spBtnOuvrirProjet.setMaxHeight(35); spBtnOuvrirProjet.setPadding(new Insets(2)); spBtnOuvrirProjet.setPrefWidth(35); HBox.setMargin(spBtnOuvrirProjet, new Insets(5, 15, 0, 0)); imgChargeProjet = new ImageView( new Image("file:" + repertAppli + File.separator + "images/ouvrirProjet.png")); spBtnOuvrirProjet.setContent(imgChargeProjet); Tooltip t1 = new Tooltip(rb.getString("ouvrirProjet")); t1.setStyle(tooltipStyle); spBtnOuvrirProjet.setTooltip(t1); barreBouton.getChildren().add(spBtnOuvrirProjet); /* Bouton sauve Projet */ ScrollPane spBtnSauveProjet = new ScrollPane(); spBtnSauveProjet.getStyleClass().add("menuBarreOutils"); spBtnSauveProjet.setHbarPolicy(ScrollPane.ScrollBarPolicy.NEVER); spBtnSauveProjet.setPrefHeight(35); spBtnSauveProjet.setMaxHeight(35); spBtnSauveProjet.setPadding(new Insets(2)); spBtnSauveProjet.setPrefWidth(35); HBox.setMargin(spBtnSauveProjet, new Insets(5, 15, 0, 0)); imgSauveProjet = new ImageView( new Image("file:" + repertAppli + File.separator + "images/sauveProjet.png")); spBtnSauveProjet.setContent(imgSauveProjet); Tooltip t2 = new Tooltip(rb.getString("sauverProjet")); t2.setStyle(tooltipStyle); spBtnSauveProjet.setTooltip(t2); barreBouton.getChildren().add(spBtnSauveProjet); Separator sepImages = new Separator(Orientation.VERTICAL); sepImages.prefHeight(200); barreBouton.getChildren().add(sepImages); imgSauveProjet.setDisable(true); imgSauveProjet.setOpacity(0.3); /* Bouton Ajoute Panoramique */ ScrollPane spBtnAjoutePano = new ScrollPane(); spBtnAjoutePano.getStyleClass().add("menuBarreOutils"); spBtnAjoutePano.setHbarPolicy(ScrollPane.ScrollBarPolicy.NEVER); spBtnAjoutePano.setPrefHeight(35); spBtnAjoutePano.setMaxHeight(35); spBtnAjoutePano.setPadding(new Insets(2)); spBtnAjoutePano.setPrefWidth(35); HBox.setMargin(spBtnAjoutePano, new Insets(5, 15, 0, 15)); imgAjouterPano = new ImageView( new Image("file:" + repertAppli + File.separator + "images/ajoutePanoramique.png")); spBtnAjoutePano.setContent(imgAjouterPano); Tooltip t3 = new Tooltip(rb.getString("ajouterPanoramiques")); t3.setStyle(tooltipStyle); spBtnAjoutePano.setTooltip(t3); barreBouton.getChildren().add(spBtnAjoutePano); imgAjouterPano.setDisable(true); imgAjouterPano.setOpacity(0.3); /* Bouton Ajoute Panoramique */ ScrollPane spBtnAjoutePlan = new ScrollPane(); spBtnAjoutePlan.getStyleClass().add("menuBarreOutils"); spBtnAjoutePlan.setHbarPolicy(ScrollPane.ScrollBarPolicy.NEVER); spBtnAjoutePlan.setPrefHeight(35); spBtnAjoutePlan.setMaxHeight(35); spBtnAjoutePlan.setPadding(new Insets(2)); spBtnAjoutePlan.setPrefWidth(35); HBox.setMargin(spBtnAjoutePlan, new Insets(5, 15, 0, 15)); imgAjouterPlan = new ImageView(new Image("file:" + repertAppli + File.separator + "images/ajoutePlan.png")); spBtnAjoutePlan.setContent(imgAjouterPlan); Tooltip t31 = new Tooltip(rb.getString("ajouterPlan")); t31.setStyle(tooltipStyle); spBtnAjoutePlan.setTooltip(t31); barreBouton.getChildren().add(spBtnAjoutePlan); imgAjouterPlan.setDisable(true); imgAjouterPlan.setOpacity(0.3); /* Bouton Gnre */ ScrollPane spBtnGenereVisite = new ScrollPane(); spBtnGenereVisite.getStyleClass().add("menuBarreOutils"); spBtnGenereVisite.setHbarPolicy(ScrollPane.ScrollBarPolicy.NEVER); spBtnGenereVisite.setPrefHeight(35); spBtnGenereVisite.setMaxHeight(35); spBtnGenereVisite.setPadding(new Insets(2)); spBtnGenereVisite.setPrefWidth(70); HBox.setMargin(spBtnGenereVisite, new Insets(5, 15, 0, 0)); imgVisiteGenere = new ImageView( new Image("file:" + repertAppli + File.separator + "images/genereVisite.png")); spBtnGenereVisite.setContent(imgVisiteGenere); Tooltip t4 = new Tooltip(rb.getString("genererVisite")); t4.setStyle(tooltipStyle); spBtnGenereVisite.setTooltip(t4); barreBouton.getChildren().add(spBtnGenereVisite); imgVisiteGenere.setDisable(true); imgVisiteGenere.setOpacity(0.3); Separator sepImages1 = new Separator(Orientation.VERTICAL); sepImages1.prefHeight(200); barreBouton.getChildren().add(sepImages1); /* Bouton equi -> faces de Cube */ ScrollPane spBtnEqui2Cube = new ScrollPane(); spBtnEqui2Cube.getStyleClass().add("menuBarreOutils"); spBtnEqui2Cube.setHbarPolicy(ScrollPane.ScrollBarPolicy.NEVER); spBtnEqui2Cube.setPrefHeight(35); spBtnEqui2Cube.setMaxHeight(35); spBtnEqui2Cube.setPadding(new Insets(2)); spBtnEqui2Cube.setPrefWidth(109); HBox.setMargin(spBtnEqui2Cube, new Insets(5, 15, 0, 250)); imgEqui2Cube = new ImageView(new Image("file:" + repertAppli + File.separator + "images/equi2cube.png")); spBtnEqui2Cube.setContent(imgEqui2Cube); Tooltip t6 = new Tooltip(rb.getString("outilsEqui2Cube")); t6.setStyle(tooltipStyle); spBtnEqui2Cube.setTooltip(t6); barreBouton.getChildren().add(spBtnEqui2Cube); /* Bouton faces de cube -> equi */ ScrollPane spBtnCube2Equi = new ScrollPane(); spBtnCube2Equi.getStyleClass().add("menuBarreOutils"); spBtnCube2Equi.setHbarPolicy(ScrollPane.ScrollBarPolicy.NEVER); spBtnCube2Equi.setPrefHeight(35); spBtnCube2Equi.setMaxHeight(35); spBtnCube2Equi.setPadding(new Insets(2)); spBtnCube2Equi.setPrefWidth(109); HBox.setMargin(spBtnCube2Equi, new Insets(5, 25, 0, 0)); imgCube2Equi = new ImageView(new Image("file:" + repertAppli + File.separator + "images/cube2equi.png")); spBtnCube2Equi.setContent(imgCube2Equi); Tooltip t5 = new Tooltip(rb.getString("outilsCube2Equi")); t5.setStyle(tooltipStyle); spBtnCube2Equi.setTooltip(t5); barreBouton.getChildren().add(spBtnCube2Equi); myPane.getChildren().addAll(menuPrincipal, barreBouton); racine.getChildren().add(myPane); nouveauProjet.setOnAction((ActionEvent e) -> { projetsNouveau(); }); chargeProjet.setOnAction((ActionEvent e) -> { try { try { projetCharge(); } catch (InterruptedException ex) { Logger.getLogger(EditeurPanovisu.class.getName()).log(Level.SEVERE, null, ex); } } catch (IOException ex) { Logger.getLogger(EditeurPanovisu.class.getName()).log(Level.SEVERE, null, ex); } }); sauveProjet.setOnAction((ActionEvent e) -> { try { projetSauve(); } catch (IOException ex) { Logger.getLogger(EditeurPanovisu.class.getName()).log(Level.SEVERE, null, ex); } }); sauveSousProjet.setOnAction((ActionEvent e) -> { try { projetSauveSous(); } catch (IOException ex) { Logger.getLogger(EditeurPanovisu.class.getName()).log(Level.SEVERE, null, ex); } }); visiteGenere.setOnAction((ActionEvent e) -> { try { genereVisite(); } catch (IOException ex) { Logger.getLogger(EditeurPanovisu.class.getName()).log(Level.SEVERE, null, ex); } }); fermerProjet.setOnAction((ActionEvent e) -> { try { projetsFermer(); } catch (IOException ex) { Logger.getLogger(EditeurPanovisu.class.getName()).log(Level.SEVERE, null, ex); } }); ajouterPano.setOnAction((ActionEvent e) -> { try { panoramiquesAjouter(); } catch (InterruptedException ex) { Logger.getLogger(EditeurPanovisu.class.getName()).log(Level.SEVERE, null, ex); } }); ajouterPlan.setOnAction((ActionEvent e) -> { planAjouter(); }); aPropos.setOnAction((ActionEvent e) -> { aideapropos(); }); aide.setOnAction((ActionEvent e) -> { AideDialogController.affiche(); }); chargerModele.setOnAction((ActionEvent e) -> { try { modeleCharger(); } catch (IOException ex) { Logger.getLogger(EditeurPanovisu.class.getName()).log(Level.SEVERE, null, ex); } }); sauverModele.setOnAction((ActionEvent e) -> { try { modeleSauver(); } catch (IOException ex) { Logger.getLogger(EditeurPanovisu.class.getName()).log(Level.SEVERE, null, ex); } }); cube2EquiTransformation.setOnAction((ActionEvent e) -> { transformationCube2Equi(); }); equi2CubeTransformation.setOnAction((ActionEvent e) -> { transformationEqui2Cube(); }); affichageVisite.setOnAction((ActionEvent e) -> { tabPaneEnvironnement.getSelectionModel().select(0); }); affichageInterface.setOnAction((ActionEvent e) -> { tabPaneEnvironnement.getSelectionModel().select(1); }); affichagePlan.setOnAction((ActionEvent e) -> { if (!tabPlan.isDisabled()) { tabPaneEnvironnement.getSelectionModel().select(2); } }); configTransformation.setOnAction((ActionEvent e) -> { try { ConfigDialogController cfg = new ConfigDialogController(); cfg.afficheFenetre(); } catch (IOException ex) { Logger.getLogger(EditeurPanovisu.class.getName()).log(Level.SEVERE, null, ex); } }); spBtnNouvprojet.setOnMouseClicked((MouseEvent t) -> { projetsNouveau(); }); spBtnOuvrirProjet.setOnMouseClicked((MouseEvent t) -> { try { try { projetCharge(); } catch (InterruptedException ex) { Logger.getLogger(EditeurPanovisu.class.getName()).log(Level.SEVERE, null, ex); } } catch (IOException ex) { Logger.getLogger(EditeurPanovisu.class.getName()).log(Level.SEVERE, null, ex); } }); spBtnSauveProjet.setOnMouseClicked((MouseEvent t) -> { try { projetSauve(); } catch (IOException ex) { Logger.getLogger(EditeurPanovisu.class.getName()).log(Level.SEVERE, null, ex); } }); spBtnAjoutePano.setOnMouseClicked((MouseEvent t) -> { try { panoramiquesAjouter(); } catch (InterruptedException ex) { Logger.getLogger(EditeurPanovisu.class.getName()).log(Level.SEVERE, null, ex); } }); spBtnAjoutePlan.setOnMouseClicked((MouseEvent t) -> { planAjouter(); }); spBtnGenereVisite.setOnMouseClicked((MouseEvent t) -> { try { genereVisite(); } catch (IOException ex) { Logger.getLogger(EditeurPanovisu.class.getName()).log(Level.SEVERE, null, ex); } }); spBtnEqui2Cube.setOnMouseClicked((MouseEvent t) -> { transformationEqui2Cube(); }); spBtnCube2Equi.setOnMouseClicked((MouseEvent t) -> { transformationCube2Equi(); }); }
From source file:editeurpanovisu.EditeurPanovisu.java
/** * * @param vbRacine panel d'installation du menu * @throws Exception Exceptions/* w ww .ja v a 2 s. c o m*/ */ private static void creeMenu(VBox vbRacine) throws Exception { VBox vbMonPanneau = new VBox(); vbMonPanneau.setPrefHeight(80); vbMonPanneau.setPrefWidth(3000); mbarPrincipal.setMinHeight(29); mbarPrincipal.setPrefHeight(29); mbarPrincipal.setMaxHeight(29); mbarPrincipal.setPrefWidth(3000); if (isMac()) { mbarPrincipal.setUseSystemMenuBar(true); } /* Menu projets */ Menu mnuProjet = new Menu(rbLocalisation.getString("projets")); mbarPrincipal.getMenus().add(mnuProjet); mniNouveauProjet = new MenuItem(rbLocalisation.getString("nouveauProjet")); mniNouveauProjet.setAccelerator(new KeyCodeCombination(KeyCode.N, KeyCombination.SHORTCUT_DOWN)); mnuProjet.getItems().add(mniNouveauProjet); mniChargeProjet = new MenuItem(rbLocalisation.getString("ouvrirProjet")); mniChargeProjet.setAccelerator(new KeyCodeCombination(KeyCode.O, KeyCombination.SHORTCUT_DOWN)); mnuProjet.getItems().add(mniChargeProjet); mniSauveProjet = new MenuItem(rbLocalisation.getString("sauverProjet")); mniSauveProjet.setDisable(true); mniSauveProjet.setAccelerator(new KeyCodeCombination(KeyCode.S, KeyCombination.SHORTCUT_DOWN)); mnuProjet.getItems().add(mniSauveProjet); mniSauveSousProjet = new MenuItem(rbLocalisation.getString("sauverProjetSous")); mniSauveSousProjet.setDisable(true); mniSauveSousProjet.setAccelerator( new KeyCodeCombination(KeyCode.S, KeyCombination.SHORTCUT_DOWN, KeyCodeCombination.SHIFT_DOWN)); mnuProjet.getItems().add(mniSauveSousProjet); mnuDerniersProjets = new Menu(rbLocalisation.getString("derniersProjets")); mnuProjet.getItems().add(mnuDerniersProjets); fileHistoFichiers = new File(fileRepertConfig.getAbsolutePath() + File.separator + "derniersprojets.cfg"); nombreHistoFichiers = 0; if (fileHistoFichiers.exists()) { try (BufferedReader brHistoFichiers = new BufferedReader( new InputStreamReader(new FileInputStream(fileHistoFichiers), "UTF-8"))) { while ((strTexteHisto = brHistoFichiers.readLine()) != null) { MenuItem menuDerniersFichiers = new MenuItem(strTexteHisto); mnuDerniersProjets.getItems().add(menuDerniersFichiers); strHistoFichiers[nombreHistoFichiers] = strTexteHisto; nombreHistoFichiers++; menuDerniersFichiers.setOnAction((e) -> { MenuItem mniSousMenu = (MenuItem) e.getSource(); try { try { projetChargeNom(mniSousMenu.getText()); } catch (InterruptedException ex) { Logger.getLogger(EditeurPanovisu.class.getName()).log(Level.SEVERE, null, ex); } } catch (IOException ex) { Logger.getLogger(EditeurPanovisu.class.getName()).log(Level.SEVERE, null, ex); } }); } } } SeparatorMenuItem sepMenu1 = new SeparatorMenuItem(); mnuProjet.getItems().add(sepMenu1); mniFermerProjet = new MenuItem(rbLocalisation.getString("quitterApplication")); mniFermerProjet.setAccelerator(new KeyCodeCombination(KeyCode.A, KeyCombination.SHORTCUT_DOWN)); mnuProjet.getItems().add(mniFermerProjet); /* Menu affichage */ Menu mnuAffichage = new Menu(rbLocalisation.getString("affichage")); mbarPrincipal.getMenus().add(mnuAffichage); mniAffichageVisite = new MenuItem(rbLocalisation.getString("main.creationVisite")); mniAffichageVisite.setAccelerator(new KeyCodeCombination(KeyCode.DIGIT1, KeyCombination.SHORTCUT_DOWN)); mnuAffichage.getItems().add(mniAffichageVisite); mniAffichageInterface = new MenuItem(rbLocalisation.getString("main.creationInterface")); mniAffichageInterface.setAccelerator(new KeyCodeCombination(KeyCode.DIGIT2, KeyCombination.SHORTCUT_DOWN)); mnuAffichage.getItems().add(mniAffichageInterface); setMniAffichagePlan(new MenuItem(rbLocalisation.getString("main.tabPlan"))); getMniAffichagePlan().setAccelerator(new KeyCodeCombination(KeyCode.DIGIT3, KeyCombination.SHORTCUT_DOWN)); getMniAffichagePlan().setDisable(true); mnuAffichage.getItems().add(getMniAffichagePlan()); mniOutilsLoupe = new MenuItem(rbLocalisation.getString("main.loupe")); mniOutilsLoupe.setAccelerator(new KeyCodeCombination(KeyCode.L, KeyCombination.SHORTCUT_DOWN)); mnuAffichage.getItems().add(mniOutilsLoupe); SeparatorMenuItem sep3 = new SeparatorMenuItem(); mnuAffichage.getItems().add(sep3); mniConfigTransformation = new MenuItem(rbLocalisation.getString("affichageConfiguration")); mnuAffichage.getItems().add(mniConfigTransformation); /* Menu panoramiques */ mnuPanoramique = new Menu(rbLocalisation.getString("panoramiques")); mnuPanoramique.setDisable(true); mbarPrincipal.getMenus().add(mnuPanoramique); mniAjouterPano = new MenuItem(rbLocalisation.getString("ajouterPanoramiques")); mniAjouterPano.setAccelerator(new KeyCodeCombination(KeyCode.A, KeyCombination.SHORTCUT_DOWN)); mnuPanoramique.getItems().add(mniAjouterPano); setMniAjouterPlan(new MenuItem(rbLocalisation.getString("ajouterPlan"))); getMniAjouterPlan().setAccelerator(new KeyCodeCombination(KeyCode.P, KeyCombination.SHORTCUT_DOWN)); mnuPanoramique.getItems().add(getMniAjouterPlan()); getMniAjouterPlan().setDisable(true); SeparatorMenuItem sep2 = new SeparatorMenuItem(); mnuPanoramique.getItems().add(sep2); mniVisiteGenere = new MenuItem(rbLocalisation.getString("genererVisite")); mniVisiteGenere.setDisable(true); mniVisiteGenere.setAccelerator(new KeyCodeCombination(KeyCode.V, KeyCombination.SHORTCUT_DOWN)); mnuPanoramique.getItems().add(mniVisiteGenere); /* Menu Modles */ mnuModeles = new Menu(rbLocalisation.getString("menuModele")); mbarPrincipal.getMenus().add(mnuModeles); mniChargerModele = new MenuItem(rbLocalisation.getString("modeleCharger")); mnuModeles.getItems().add(mniChargerModele); mniSauverModele = new MenuItem(rbLocalisation.getString("modeleSauver")); mnuModeles.getItems().add(mniSauverModele); /* Menu transformations */ mnuTransformation = new Menu(rbLocalisation.getString("outils")); mbarPrincipal.getMenus().add(mnuTransformation); mniEqui2CubeTransformation = new MenuItem(rbLocalisation.getString("outilsEqui2Cube")); mnuTransformation.getItems().add(mniEqui2CubeTransformation); mniCube2EquiTransformation = new MenuItem(rbLocalisation.getString("outilsCube2Equi")); mnuTransformation.getItems().add(mniCube2EquiTransformation); SeparatorMenuItem sep6 = new SeparatorMenuItem(); mnuTransformation.getItems().add(sep6); mniOutilsBarre = new MenuItem(rbLocalisation.getString("outilsBarre")); mniOutilsBarre.setAccelerator(new KeyCodeCombination(KeyCode.B, KeyCombination.SHORTCUT_DOWN)); mnuTransformation.getItems().add(mniOutilsBarre); mniOutilsDiaporama = new MenuItem(rbLocalisation.getString("outilsDiaporama")); mniOutilsDiaporama.setAccelerator(new KeyCodeCombination(KeyCode.D, KeyCombination.SHORTCUT_DOWN)); mnuTransformation.getItems().add(mniOutilsDiaporama); /* Menu Aide */ Menu mnuAide = new Menu(rbLocalisation.getString("aide")); mbarPrincipal.getMenus().add(mnuAide); mniAide = new MenuItem(rbLocalisation.getString("aideAide")); mniAide.setAccelerator(new KeyCodeCombination(KeyCode.H, KeyCombination.SHORTCUT_DOWN)); mnuAide.getItems().add(mniAide); SeparatorMenuItem sep4 = new SeparatorMenuItem(); mnuAide.getItems().add(sep4); mniAPropos = new MenuItem(rbLocalisation.getString("aideAPropos")); mnuAide.getItems().add(mniAPropos); // // } // /* barre de boutons */ hbBarreBouton = new HBox(); hbBarreBouton.getStyleClass().add("menuBarreOutils1"); hbBarreBouton.setPrefHeight(50); hbBarreBouton.setMinHeight(50); hbBarreBouton.setPrefWidth(3000); /* Bouton nouveau Projet */ ScrollPane spBtnNouvprojet = new ScrollPane(); spBtnNouvprojet.getStyleClass().add("menuBarreOutils"); spBtnNouvprojet.setHbarPolicy(ScrollPane.ScrollBarPolicy.NEVER); spBtnNouvprojet.setPrefHeight(35); spBtnNouvprojet.setMaxHeight(35); spBtnNouvprojet.setPadding(new Insets(2)); spBtnNouvprojet.setPrefWidth(35); HBox.setMargin(spBtnNouvprojet, new Insets(5, 15, 0, 15)); ivNouveauProjet = new ImageView( new Image("file:" + getStrRepertAppli() + File.separator + "images/nouveauProjet.png")); spBtnNouvprojet.setContent(ivNouveauProjet); Tooltip tltpNouveauProjet = new Tooltip(rbLocalisation.getString("nouveauProjet")); tltpNouveauProjet.setStyle(getStrTooltipStyle()); spBtnNouvprojet.setTooltip(tltpNouveauProjet); hbBarreBouton.getChildren().add(spBtnNouvprojet); /* Bouton ouvrir Projet */ ScrollPane spBtnOuvrirProjet = new ScrollPane(); spBtnOuvrirProjet.getStyleClass().add("menuBarreOutils"); spBtnOuvrirProjet.setHbarPolicy(ScrollPane.ScrollBarPolicy.NEVER); spBtnOuvrirProjet.setPrefHeight(35); spBtnOuvrirProjet.setMaxHeight(35); spBtnOuvrirProjet.setPadding(new Insets(2)); spBtnOuvrirProjet.setPrefWidth(35); HBox.setMargin(spBtnOuvrirProjet, new Insets(5, 15, 0, 0)); ivChargeProjet = new ImageView( new Image("file:" + getStrRepertAppli() + File.separator + "images/ouvrirProjet.png")); spBtnOuvrirProjet.setContent(ivChargeProjet); Tooltip tltpOuvrirProjet = new Tooltip(rbLocalisation.getString("ouvrirProjet")); tltpOuvrirProjet.setStyle(getStrTooltipStyle()); spBtnOuvrirProjet.setTooltip(tltpOuvrirProjet); hbBarreBouton.getChildren().add(spBtnOuvrirProjet); /* Bouton sauve Projet */ ScrollPane spBtnSauveProjet = new ScrollPane(); spBtnSauveProjet.getStyleClass().add("menuBarreOutils"); spBtnSauveProjet.setHbarPolicy(ScrollPane.ScrollBarPolicy.NEVER); spBtnSauveProjet.setPrefHeight(35); spBtnSauveProjet.setMaxHeight(35); spBtnSauveProjet.setPadding(new Insets(2)); spBtnSauveProjet.setPrefWidth(35); HBox.setMargin(spBtnSauveProjet, new Insets(5, 15, 0, 0)); ivSauveProjet = new ImageView( new Image("file:" + getStrRepertAppli() + File.separator + "images/sauveProjet.png")); spBtnSauveProjet.setContent(ivSauveProjet); Tooltip tltpSauverProjet = new Tooltip(rbLocalisation.getString("sauverProjet")); tltpSauverProjet.setStyle(getStrTooltipStyle()); spBtnSauveProjet.setTooltip(tltpSauverProjet); hbBarreBouton.getChildren().add(spBtnSauveProjet); Separator sepImages = new Separator(Orientation.VERTICAL); sepImages.prefHeight(200); hbBarreBouton.getChildren().add(sepImages); ivSauveProjet.setDisable(true); ivSauveProjet.setOpacity(0.3); /* Bouton Ajoute Panoramique */ ScrollPane spBtnAjoutePano = new ScrollPane(); spBtnAjoutePano.getStyleClass().add("menuBarreOutils"); spBtnAjoutePano.setHbarPolicy(ScrollPane.ScrollBarPolicy.NEVER); spBtnAjoutePano.setPrefHeight(35); spBtnAjoutePano.setMaxHeight(35); spBtnAjoutePano.setPadding(new Insets(2)); spBtnAjoutePano.setPrefWidth(35); HBox.setMargin(spBtnAjoutePano, new Insets(5, 15, 0, 15)); ivAjouterPano = new ImageView( new Image("file:" + getStrRepertAppli() + File.separator + "images/ajoutePanoramique.png")); spBtnAjoutePano.setContent(ivAjouterPano); Tooltip tltpAjouterPano = new Tooltip(rbLocalisation.getString("ajouterPanoramiques")); tltpAjouterPano.setStyle(getStrTooltipStyle()); spBtnAjoutePano.setTooltip(tltpAjouterPano); hbBarreBouton.getChildren().add(spBtnAjoutePano); ivAjouterPano.setDisable(true); ivAjouterPano.setOpacity(0.3); /* Bouton Ajoute Panoramique */ ScrollPane spBtnAjoutePlan = new ScrollPane(); spBtnAjoutePlan.getStyleClass().add("menuBarreOutils"); spBtnAjoutePlan.setHbarPolicy(ScrollPane.ScrollBarPolicy.NEVER); spBtnAjoutePlan.setPrefHeight(35); spBtnAjoutePlan.setMaxHeight(35); spBtnAjoutePlan.setPadding(new Insets(2)); spBtnAjoutePlan.setPrefWidth(35); HBox.setMargin(spBtnAjoutePlan, new Insets(5, 15, 0, 15)); setIvAjouterPlan( new ImageView(new Image("file:" + getStrRepertAppli() + File.separator + "images/ajoutePlan.png"))); spBtnAjoutePlan.setContent(getIvAjouterPlan()); Tooltip tltpAjouterPlan = new Tooltip(rbLocalisation.getString("ajouterPlan")); tltpAjouterPlan.setStyle(getStrTooltipStyle()); spBtnAjoutePlan.setTooltip(tltpAjouterPlan); hbBarreBouton.getChildren().add(spBtnAjoutePlan); getIvAjouterPlan().setDisable(true); getIvAjouterPlan().setOpacity(0.3); /* Bouton Gnre */ ScrollPane spBtnGenereVisite = new ScrollPane(); spBtnGenereVisite.getStyleClass().add("menuBarreOutils"); spBtnGenereVisite.setHbarPolicy(ScrollPane.ScrollBarPolicy.NEVER); spBtnGenereVisite.setPrefHeight(35); spBtnGenereVisite.setMaxHeight(35); spBtnGenereVisite.setPadding(new Insets(2)); spBtnGenereVisite.setPrefWidth(70); HBox.setMargin(spBtnGenereVisite, new Insets(5, 15, 0, 0)); ivVisiteGenere = new ImageView( new Image("file:" + getStrRepertAppli() + File.separator + "images/genereVisite.png")); spBtnGenereVisite.setContent(ivVisiteGenere); Tooltip tltpGenererVisite = new Tooltip(rbLocalisation.getString("genererVisite")); tltpGenererVisite.setStyle(getStrTooltipStyle()); spBtnGenereVisite.setTooltip(tltpGenererVisite); hbBarreBouton.getChildren().add(spBtnGenereVisite); ivVisiteGenere.setDisable(true); ivVisiteGenere.setOpacity(0.3); Separator sepImages1 = new Separator(Orientation.VERTICAL); sepImages1.prefHeight(200); hbBarreBouton.getChildren().add(sepImages1); /* Bouton equi -> faces de Cube */ ScrollPane spBtnEqui2Cube = new ScrollPane(); spBtnEqui2Cube.getStyleClass().add("menuBarreOutils"); spBtnEqui2Cube.setHbarPolicy(ScrollPane.ScrollBarPolicy.NEVER); spBtnEqui2Cube.setPrefHeight(35); spBtnEqui2Cube.setMaxHeight(35); spBtnEqui2Cube.setPadding(new Insets(2)); spBtnEqui2Cube.setPrefWidth(109); HBox.setMargin(spBtnEqui2Cube, new Insets(5, 15, 0, 250)); ivEqui2Cube = new ImageView( new Image("file:" + getStrRepertAppli() + File.separator + "images/equi2cube.png")); spBtnEqui2Cube.setContent(ivEqui2Cube); Tooltip tltpEqui2Cube = new Tooltip(rbLocalisation.getString("outilsEqui2Cube")); tltpEqui2Cube.setStyle(getStrTooltipStyle()); spBtnEqui2Cube.setTooltip(tltpEqui2Cube); hbBarreBouton.getChildren().add(spBtnEqui2Cube); /* Bouton faces de cube -> equi */ ScrollPane spBtnCube2Equi = new ScrollPane(); spBtnCube2Equi.getStyleClass().add("menuBarreOutils"); spBtnCube2Equi.setHbarPolicy(ScrollPane.ScrollBarPolicy.NEVER); spBtnCube2Equi.setPrefHeight(35); spBtnCube2Equi.setMaxHeight(35); spBtnCube2Equi.setPadding(new Insets(2)); spBtnCube2Equi.setPrefWidth(109); HBox.setMargin(spBtnCube2Equi, new Insets(5, 25, 0, 0)); ivCube2Equi = new ImageView( new Image("file:" + getStrRepertAppli() + File.separator + "images/cube2equi.png")); spBtnCube2Equi.setContent(ivCube2Equi); Tooltip tltpCube2Equi = new Tooltip(rbLocalisation.getString("outilsCube2Equi")); tltpCube2Equi.setStyle(getStrTooltipStyle()); spBtnCube2Equi.setTooltip(tltpCube2Equi); hbBarreBouton.getChildren().add(spBtnCube2Equi); if (isMac()) { mbarPrincipal.setMaxHeight(0); hbBarreBouton.setTranslateY(-30); } vbMonPanneau.getChildren().addAll(mbarPrincipal, hbBarreBouton); vbRacine.getChildren().add(vbMonPanneau); mniNouveauProjet.setOnAction((e) -> { projetsNouveau(); }); mniChargeProjet.setOnAction((e) -> { try { try { projetCharge(); } catch (InterruptedException ex) { Logger.getLogger(EditeurPanovisu.class.getName()).log(Level.SEVERE, null, ex); } } catch (IOException ex) { Logger.getLogger(EditeurPanovisu.class.getName()).log(Level.SEVERE, null, ex); } }); mniSauveProjet.setOnAction((e) -> { try { projetSauve(); } catch (IOException ex) { Logger.getLogger(EditeurPanovisu.class.getName()).log(Level.SEVERE, null, ex); } }); mniSauveSousProjet.setOnAction((e) -> { try { projetSauveSous(); } catch (IOException ex) { Logger.getLogger(EditeurPanovisu.class.getName()).log(Level.SEVERE, null, ex); } }); mniVisiteGenere.setOnAction((e) -> { try { genereVisite(); } catch (IOException ex) { Logger.getLogger(EditeurPanovisu.class.getName()).log(Level.SEVERE, null, ex); } }); mniFermerProjet.setOnAction((e) -> { try { projetsFermer(); } catch (IOException ex) { Logger.getLogger(EditeurPanovisu.class.getName()).log(Level.SEVERE, null, ex); } }); mniAjouterPano.setOnAction((e) -> { try { panoramiquesAjouter(); } catch (InterruptedException ex) { Logger.getLogger(EditeurPanovisu.class.getName()).log(Level.SEVERE, null, ex); } }); getMniAjouterPlan().setOnAction((e) -> { planAjouter(); }); mniAPropos.setOnAction((e) -> { aideapropos(); }); mniAide.setOnAction((e) -> { AideDialogController.affiche(); }); mniChargerModele.setOnAction((e) -> { try { modeleCharger(); } catch (IOException ex) { Logger.getLogger(EditeurPanovisu.class.getName()).log(Level.SEVERE, null, ex); } }); mniSauverModele.setOnAction((e) -> { try { modeleSauver(); } catch (IOException ex) { Logger.getLogger(EditeurPanovisu.class.getName()).log(Level.SEVERE, null, ex); } }); mniCube2EquiTransformation.setOnAction((e) -> { transformationCube2Equi(); }); mniEqui2CubeTransformation.setOnAction((e) -> { transformationEqui2Cube(); }); mniOutilsBarre.setOnAction((e) -> { creerEditerBarre(""); }); mniOutilsDiaporama.setOnAction((e) -> { creerEditerDiaporama(""); }); mniOutilsLoupe.setOnAction((e) -> { e.consume(); setAfficheLoupe(!isAfficheLoupe()); apLoupe.setVisible(isAfficheLoupe()); Point p = MouseInfo.getPointerInfo().getLocation(); if (p.x < getiTailleLoupe() + 80 && p.y < getiTailleLoupe() + 160) { apLoupe.setLayoutX(ivImagePanoramique.getFitWidth() - getiTailleLoupe() + 5); apLoupe.setLayoutY(35); strPositLoupe = "droite"; } else { apLoupe.setLayoutX(35); apLoupe.setLayoutY(35); strPositLoupe = "gauche"; } }); mniAffichageVisite.setOnAction((e) -> { tpEnvironnement.getSelectionModel().select(0); }); mniAffichageInterface.setOnAction((e) -> { tpEnvironnement.getSelectionModel().select(1); }); getMniAffichagePlan().setOnAction((e) -> { if (!tabPlan.isDisabled()) { tpEnvironnement.getSelectionModel().select(2); } }); mniConfigTransformation.setOnAction((e) -> { try { ConfigDialogController cfg = new ConfigDialogController(); cfg.afficheFenetre(); } catch (IOException ex) { Logger.getLogger(EditeurPanovisu.class.getName()).log(Level.SEVERE, null, ex); } }); spBtnNouvprojet.setOnMouseClicked((t) -> { projetsNouveau(); }); spBtnOuvrirProjet.setOnMouseClicked((t) -> { try { try { projetCharge(); } catch (InterruptedException ex) { Logger.getLogger(EditeurPanovisu.class.getName()).log(Level.SEVERE, null, ex); } } catch (IOException ex) { Logger.getLogger(EditeurPanovisu.class.getName()).log(Level.SEVERE, null, ex); } }); spBtnSauveProjet.setOnMouseClicked((t) -> { try { projetSauve(); } catch (IOException ex) { Logger.getLogger(EditeurPanovisu.class.getName()).log(Level.SEVERE, null, ex); } }); spBtnAjoutePano.setOnMouseClicked((t) -> { try { panoramiquesAjouter(); } catch (InterruptedException ex) { Logger.getLogger(EditeurPanovisu.class.getName()).log(Level.SEVERE, null, ex); } }); spBtnAjoutePlan.setOnMouseClicked((t) -> { planAjouter(); }); spBtnGenereVisite.setOnMouseClicked((t) -> { try { genereVisite(); } catch (IOException ex) { Logger.getLogger(EditeurPanovisu.class.getName()).log(Level.SEVERE, null, ex); } }); spBtnEqui2Cube.setOnMouseClicked((t) -> { transformationEqui2Cube(); }); spBtnCube2Equi.setOnMouseClicked((t) -> { transformationCube2Equi(); }); }