X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FTreePanel.java;h=ca4f84e53a4e4da494d3334a3b4d349b590cf7cc;hb=09d3b755d9b00f5c3acb44049aedd49361dc0690;hp=940305797afff589482fbbd1c2f77fd4edb8dff0;hpb=a57976ba40e1abe6d7c1940386e1a25419ef9c9d;p=jalview.git diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java index 9403057..ca4f84e 100755 --- a/src/jalview/gui/TreePanel.java +++ b/src/jalview/gui/TreePanel.java @@ -55,6 +55,7 @@ import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.awt.image.BufferedImage; import java.beans.PropertyChangeEvent; +import java.beans.PropertyChangeListener; import java.io.FileOutputStream; import java.util.ArrayList; import java.util.List; @@ -63,6 +64,8 @@ import javax.imageio.ImageIO; import javax.swing.ButtonGroup; import javax.swing.JMenuItem; import javax.swing.JRadioButtonMenuItem; +import javax.swing.event.InternalFrameAdapter; +import javax.swing.event.InternalFrameEvent; import org.jibble.epsgraphics.EpsGraphics2D; @@ -82,11 +85,11 @@ public class TreePanel extends GTreePanel SimilarityParamsI similarityParams; - TreeCanvas treeCanvas; + private TreeCanvas treeCanvas; TreeModel tree; - AlignViewport av; + private AlignViewport av; /** * Creates a new TreePanel object. @@ -118,30 +121,58 @@ public class TreePanel extends GTreePanel public AlignmentI getAlignment() { - return treeCanvas.av.getAlignment(); + return getTreeCanvas().getViewport().getAlignment(); } public AlignmentViewport getViewPort() { - return treeCanvas.av; + return getTreeCanvas().getViewport(); } void initTreePanel(AlignmentPanel ap, String type, String modelName, NewickFile newTree, AlignmentView inputData) { - av = ap.av; + setViewport(ap.av); this.treeType = type; this.scoreModelName = modelName; treeCanvas = new TreeCanvas(this, ap, scrollPane); - scrollPane.setViewportView(treeCanvas); + scrollPane.setViewportView(getTreeCanvas()); PaintRefresher.Register(this, ap.av.getSequenceSetId()); buildAssociatedViewMenu(); - av.addPropertyChangeListener(new java.beans.PropertyChangeListener() + final PropertyChangeListener listener = addAlignmentListener(); + + /* + * remove listener when window is closed, so that this + * panel can be garbage collected + */ + addInternalFrameListener(new InternalFrameAdapter() + { + @Override + public void internalFrameClosed(InternalFrameEvent evt) + { + if (getViewport() != null) + { + getViewport().removePropertyChangeListener(listener); + } + } + }); + + TreeLoader tl = new TreeLoader(newTree, inputData); + tl.start(); + + } + + /** + * @return + */ + protected PropertyChangeListener addAlignmentListener() + { + final PropertyChangeListener listener = new PropertyChangeListener() { @Override public void propertyChange(PropertyChangeEvent evt) @@ -163,16 +194,14 @@ public class TreePanel extends GTreePanel } tree.updatePlaceHolders((List) evt.getNewValue()); - treeCanvas.nameHash.clear(); // reset the mapping between canvas + getTreeCanvas().nameHash.clear(); // reset the mapping between canvas // rectangles and leafnodes repaint(); } } - }); - - TreeLoader tl = new TreeLoader(newTree, inputData); - tl.start(); - + }; + getViewport().addPropertyChangeListener(listener); + return listener; } @Override @@ -184,8 +213,8 @@ public class TreePanel extends GTreePanel void buildAssociatedViewMenu() { AlignmentPanel[] aps = PaintRefresher - .getAssociatedPanels(av.getSequenceSetId()); - if (aps.length == 1 && treeCanvas.ap == aps[0]) + .getAssociatedPanels(getViewport().getSequenceSetId()); + if (aps.length == 1 && getTreeCanvas().getAssociatedPanel() == aps[0]) { associateLeavesMenu.setVisible(false); return; @@ -208,16 +237,16 @@ public class TreePanel extends GTreePanel for (i = 0; i < iSize; i++) { final AlignmentPanel ap = aps[i]; - item = new JRadioButtonMenuItem(ap.av.viewName, ap == treeCanvas.ap); + item = new JRadioButtonMenuItem(ap.av.getViewName(), ap == getTreeCanvas().getAssociatedPanel()); buttonGroup.add(item); item.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent evt) { - treeCanvas.applyToAllViews = false; - treeCanvas.ap = ap; - treeCanvas.av = ap.av; + getTreeCanvas().applyToAllViews = false; + getTreeCanvas().setAssociatedPanel(ap); + getTreeCanvas().setViewport(ap.av); PaintRefresher.Register(thisTreePanel, ap.av.getSequenceSetId()); } }); @@ -228,13 +257,13 @@ public class TreePanel extends GTreePanel final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem( MessageManager.getString("label.all_views")); buttonGroup.add(itemf); - itemf.setSelected(treeCanvas.applyToAllViews); + itemf.setSelected(getTreeCanvas().applyToAllViews); itemf.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent evt) { - treeCanvas.applyToAllViews = itemf.isSelected(); + getTreeCanvas().applyToAllViews = itemf.isSelected(); } }); associateLeavesMenu.add(itemf); @@ -267,7 +296,7 @@ public class TreePanel extends GTreePanel if (newtree != null) { - tree = new TreeModel(av.getAlignment().getSequencesArray(), odata, + tree = new TreeModel(getViewport().getAlignment().getSequencesArray(), odata, newtree); if (tree.getOriginalData() == null) { @@ -277,20 +306,20 @@ public class TreePanel extends GTreePanel else { ScoreModelI sm = ScoreModels.getInstance() - .getScoreModel(scoreModelName, treeCanvas.ap); + .getScoreModel(scoreModelName, getTreeCanvas().getAssociatedPanel()); TreeBuilder njtree = treeType.equals(TreeBuilder.NEIGHBOUR_JOINING) - ? new NJTree(av, sm, similarityParams) - : new AverageDistanceTree(av, sm, similarityParams); + ? new NJTree(getViewport(), sm, similarityParams) + : new AverageDistanceTree(getViewport(), sm, similarityParams); tree = new TreeModel(njtree); showDistances(true); } tree.reCount(tree.getTopNode()); tree.findHeight(tree.getTopNode()); - treeCanvas.setTree(tree); - treeCanvas.repaint(); - av.setCurrentTree(tree); - if (av.getSortByTree()) + getTreeCanvas().setTree(tree); + getTreeCanvas().repaint(); + getViewport().setCurrentTree(tree); + if (getViewport().getSortByTree()) { sortByTree_actionPerformed(); } @@ -299,20 +328,20 @@ public class TreePanel extends GTreePanel public void showDistances(boolean b) { - treeCanvas.setShowDistances(b); + getTreeCanvas().setShowDistances(b); distanceMenu.setSelected(b); } public void showBootstrap(boolean b) { - treeCanvas.setShowBootstrap(b); + getTreeCanvas().setShowBootstrap(b); bootstrapMenu.setSelected(b); } public void showPlaceholders(boolean b) { placeholdersMenu.setState(b); - treeCanvas.setMarkPlaceholders(b); + getTreeCanvas().setMarkPlaceholders(b); } /** @@ -403,7 +432,7 @@ public class TreePanel extends GTreePanel public void printMenu_actionPerformed(ActionEvent e) { // Putting in a thread avoids Swing painting problems - treeCanvas.startPrinting(); + getTreeCanvas().startPrinting(); } @Override @@ -427,7 +456,7 @@ public class TreePanel extends GTreePanel { // we try to get the associated view's gap character // but this may fail if the view was closed... - gc = av.getGapCharacter(); + gc = getViewport().getGapCharacter(); } catch (Exception ex) { @@ -440,8 +469,8 @@ public class TreePanel extends GTreePanel // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]); AlignmentI al = new Alignment((SequenceI[]) alAndColsel[0]); - AlignmentI dataset = (av != null && av.getAlignment() != null) - ? av.getAlignment().getDataset() + AlignmentI dataset = (getViewport() != null && getViewport().getAlignment() != null) + ? getViewport().getAlignment().getDataset() : null; if (dataset != null) { @@ -478,7 +507,7 @@ public class TreePanel extends GTreePanel @Override public void fitToWindow_actionPerformed(ActionEvent e) { - treeCanvas.fitToWindow = fitToWindow.isSelected(); + getTreeCanvas().fitToWindow = fitToWindow.isSelected(); repaint(); } @@ -491,15 +520,15 @@ public class TreePanel extends GTreePanel public void sortByTree_actionPerformed() { - if (treeCanvas.applyToAllViews) + if (getTreeCanvas().applyToAllViews) { final ArrayList commands = new ArrayList<>(); for (AlignmentPanel ap : PaintRefresher - .getAssociatedPanels(av.getSequenceSetId())) + .getAssociatedPanels(getViewport().getSequenceSetId())) { commands.add(sortAlignmentIn(ap.av.getAlignPanel())); } - av.getAlignPanel().alignFrame.addHistoryItem(new CommandI() + getViewport().getAlignPanel().alignFrame.addHistoryItem(new CommandI() { @Override @@ -534,7 +563,7 @@ public class TreePanel extends GTreePanel } }); for (AlignmentPanel ap : PaintRefresher - .getAssociatedPanels(av.getSequenceSetId())) + .getAssociatedPanels(getViewport().getSequenceSetId())) { // ensure all the alignFrames refresh their GI after adding an undo item ap.alignFrame.updateEditMenuBar(); @@ -542,8 +571,8 @@ public class TreePanel extends GTreePanel } else { - treeCanvas.ap.alignFrame - .addHistoryItem(sortAlignmentIn(treeCanvas.ap)); + getTreeCanvas().getAssociatedPanel().alignFrame + .addHistoryItem(sortAlignmentIn(getTreeCanvas().getAssociatedPanel())); } } @@ -570,7 +599,7 @@ public class TreePanel extends GTreePanel @Override public void font_actionPerformed(ActionEvent e) { - if (treeCanvas == null) + if (getTreeCanvas() == null) { return; } @@ -580,14 +609,14 @@ public class TreePanel extends GTreePanel public Font getTreeFont() { - return treeCanvas.font; + return getTreeCanvas().font; } public void setTreeFont(Font f) { - if (treeCanvas != null) + if (getTreeCanvas() != null) { - treeCanvas.setFont(f); + getTreeCanvas().setFont(f); } } @@ -600,7 +629,7 @@ public class TreePanel extends GTreePanel @Override public void distanceMenu_actionPerformed(ActionEvent e) { - treeCanvas.setShowDistances(distanceMenu.isSelected()); + getTreeCanvas().setShowDistances(distanceMenu.isSelected()); } /** @@ -612,7 +641,7 @@ public class TreePanel extends GTreePanel @Override public void bootstrapMenu_actionPerformed(ActionEvent e) { - treeCanvas.setShowBootstrap(bootstrapMenu.isSelected()); + getTreeCanvas().setShowBootstrap(bootstrapMenu.isSelected()); } /** @@ -624,7 +653,7 @@ public class TreePanel extends GTreePanel @Override public void placeholdersMenu_actionPerformed(ActionEvent e) { - treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected()); + getTreeCanvas().setMarkPlaceholders(placeholdersMenu.isSelected()); } /** @@ -662,8 +691,8 @@ public class TreePanel extends GTreePanel accurateText = false; } - int width = treeCanvas.getWidth(); - int height = treeCanvas.getHeight(); + int width = getTreeCanvas().getWidth(); + int height = getTreeCanvas().getHeight(); try { @@ -691,7 +720,7 @@ public class TreePanel extends GTreePanel pg.setAccurateTextMode(accurateText); - treeCanvas.draw(pg, width, height); + getTreeCanvas().draw(pg, width, height); pg.flush(); pg.close(); @@ -710,8 +739,8 @@ public class TreePanel extends GTreePanel @Override public void pngTree_actionPerformed(ActionEvent e) { - int width = treeCanvas.getWidth(); - int height = treeCanvas.getHeight(); + int width = getTreeCanvas().getWidth(); + int height = getTreeCanvas().getHeight(); try { @@ -740,7 +769,7 @@ public class TreePanel extends GTreePanel BufferedImage.TYPE_INT_RGB); Graphics png = bi.getGraphics(); - treeCanvas.draw(png, width, height); + getTreeCanvas().draw(png, width, height); ImageIO.write(bi, "png", out); out.close(); @@ -850,8 +879,23 @@ public class TreePanel extends GTreePanel /* * put them together as Using */ - final String ttl = MessageManager.formatMessage("label.treecalc_title", + final String ttl = MessageManager.formatMessage("label.calc_title", treecalcnm, smn); return ttl; } + + public AlignViewport getViewport() + { + return av; + } + + public void setViewport(AlignViewport av) + { + this.av = av; + } + + public TreeCanvas getTreeCanvas() + { + return treeCanvas; + } }