src/jalviewfx/controllers/Desktop.java

   1 package jalviewfx.controllers;
   2
   3 import jalview.bin.Cache;
   4 import jalview.datamodel.AlignmentI;
   5 import jalview.gui.AlignFrame;
   6 import jalview.gui.AlignmentPanel;
   7 import jalview.io.AppletFormatAdapter;
   8 import jalview.util.MessageManager;
   9 import jalviewfx.controllers.engine.ControlledScreen;
  10 import jalviewfx.controllers.engine.ScreensController;
  11
  12 import java.awt.print.PrinterException;
  13 import java.io.IOException;
  14 import java.net.URL;
  15 import java.util.Arrays;
  16 import java.util.List;
  17 import java.util.ResourceBundle;
  18
  19 import javafx.application.Platform;
  20 import javafx.embed.swing.SwingNode;
  21 import javafx.fxml.FXML;
  22 import javafx.fxml.Initializable;
  23 import javafx.scene.Node;
  24 import javafx.scene.control.TreeCell;
  25 import javafx.scene.control.TreeItem;
  26 import javafx.scene.control.TreeView;
  27 import javafx.scene.image.Image;
  28 import javafx.scene.image.ImageView;
  29 import javafx.util.Callback;
  30
  31 import javax.swing.JComponent;
  32
  33 import application.Project;
  34 import application.TextFieldTreeCellImpl;
  35
  36 public class Desktop implements Initializable, ControlledScreen {
  37         @FXML
  38         private MainMenuController mainMenuController;
  39         @FXML
  40         private AlignmentViewController alignmentViewController;
  41         @FXML
  42         private TreeView<String> projectExplorer;
  43         // @FXML private Canvas allignmentCanvas;
  44         @FXML
  45         private SwingNode jalviewNode;
  46
  47         private final Node rootIcon = new ImageView(new Image(getClass().getResourceAsStream("/images/Jalview_Logo_small.png")));
  48         private final Image depIcon = new Image(getClass().getResourceAsStream("/images/Jalview_Logo_small.png"));
  49         List<Project> projects = Arrays.<Project> asList(new Project("Spinach Ferodoxin", "exampleFile_2_3"), new Project("FE2S2 Representation", "exampleFile_2_3"), new Project("Mafft Alignment Ordering", "exampleFile_2_3"), new Project("Phosporylation SP", "exampleFile_2_3"), new Project("Mafft example", "exampleFile_2_3"), new Project("FS3ES", "globins"), new Project("Mafft2", "globins"), new Project("Judy", "plantfdx"), new Project("Gregory", "plantfdx"), new Project("Jacob", "plantfdx"), new Project("Isabella", "globins"));
  50
  51         ScreensController myController;
  52
  53         @Override
  54         public void setScreenParent(ScreensController screenParent) {
  55                 myController = screenParent;
  56         }
  57
  58         @Override
  59         public void initialize(URL paramURL, ResourceBundle paramResourceBundle) {
  60                 loadProjectExplorer();
  61                 try {
  62                         loadJalview();
  63                 } catch (IOException | PrinterException e) {
  64                         e.printStackTrace();
  65                 }
  66         }
  67         final static String TEST_DATA = ">FER_CAPAA/13-56 Ferredoxin\nJRFIJOIERFEOIJOIREFOIJETBGNJEWRPOKPWEOIJWEW----X-\n"
  68                         + ">FER_CAPAN/13-51 Ferredoxin, chloroplast precursor\nWFEXLFWEOPKOWEFPO--EWF-FWE-WEF-WFW-BRWGEWF---FWE-\n"
  69                         + ">FER1_SOLLC/13-56 Ferredoxin-1, chloroplast precursor\n-WEFWEFWFW3FLIKFOILKWFEIOEWFJIJWEFLIKWE-EWF--WEF-\n";
  70
  71         AlignmentI alignment;
  72         AlignmentPanel parentPanel;
  73         AlignFrame af;
  74
  75         public void loadJalview() throws IOException, PrinterException {
  76                 System.out.println("--------------> Loading jalview");
  77                 alignment = new jalview.io.FormatAdapter().readFile(TEST_DATA, AppletFormatAdapter.PASTE, "FASTA");
  78                 af = new AlignFrame(alignment, AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
  79
  80                 // parentPanel = new AlignmentPanel(af, af.getViewport());
  81                 // System.out.println("alignment Canvas : "+ allignmentCanvas);
  82                 // FXGraphics2D g = new
  83                 // FXGraphics2D(allignmentCanvas.getGraphicsContext2D());
  84                 createSwingContent(jalviewNode, af.alignPanel);
  85                 // parentPanel.paintComponent(g);
  86 //              startDesktop();
  87
  88         }
  89
  90         private void startDesktop() {
  91                 Platform.runLater(new Runnable() {
  92                         @Override
  93                         public void run() {
  94                                 try {
  95                                     Cache.initLogger();
  96                                         jalview.gui.Desktop desktop = new jalview.gui.Desktop();
  97                                         desktop.setInBatchMode(true); // indicate we are starting up
  98                                         desktop.setVisible(true);
  99                                         desktop.startServiceDiscovery();
 100
 101                                         jalview.gui.Desktop.addInternalFrame(af, MessageManager.formatMessage("label.input_cut_paste_params", new String[] { "paste" }), AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
 102                                         af.statusBar.setText(MessageManager.getString("label.successfully_pasted_alignment_file"));
 103
 104                                         //
 105 //                                      af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", true));
 106                                 } catch (Exception ex) {
 107                                         ex.printStackTrace();
 108                                 }
 109
 110                         }
 111                 });
 112         }
 113
 114         private void createSwingContent(final SwingNode swingNode, final JComponent swingComp) {
 115                 Platform.runLater(new Runnable() {
 116                         @Override
 117                         public void run() {
 118                                 swingNode.setContent(swingComp);
 119                         }
 120                 });
 121         }
 122
 123         public void loadProjectExplorer() {
 124                 rootIcon.setScaleX(.5);
 125                 rootIcon.setScaleY(.5);
 126                 TreeItem<String> rootNode = new TreeItem<String>("Project Explorer", rootIcon);
 127                 projectExplorer.setRoot(rootNode);
 128                 projectExplorer.setEditable(true);
 129                 rootNode.setExpanded(true);
 130                 for (Project project : projects) {
 131                         TreeItem<String> empLeaf = new TreeItem<String>(project.getName());
 132                         boolean found = false;
 133                         for (TreeItem<String> typeNode : rootNode.getChildren()) {
 134                                 if (typeNode.getValue().contentEquals(project.getType())) {
 135                                         typeNode.getChildren().add(empLeaf);
 136                                         found = true;
 137                                         break;
 138                                 }
 139                         }
 140                         ImageView imgView = new ImageView(depIcon);
 141                         imgView.setScaleX(.5);
 142                         imgView.setScaleY(.5);
 143                         if (!found) {
 144                                 TreeItem<String> typeNode = new TreeItem<String>(project.getType(), imgView);
 145                                 rootNode.getChildren().add(typeNode);
 146                                 typeNode.getChildren().add(empLeaf);
 147                         }
 148                 }
 149
 150                 projectExplorer.setCellFactory(new Callback<TreeView<String>, TreeCell<String>>() {
 151                         @Override
 152                         public TreeCell<String> call(TreeView<String> p) {
 153                                 return new TextFieldTreeCellImpl();
 154                         }
 155                 });
 156         }
 157
 158 }