X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FTreePanel.java;h=f708c482f9497054a931acc05f355196caed5226;hb=HEAD;hp=6c9c892124093b1db44a851873454f12d083b4c5;hpb=f6d3b491c392914981b65fee21df51b530ee80f7;p=jalview.git diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java index 6c9c892..f708c48 100755 --- a/src/jalview/gui/TreePanel.java +++ b/src/jalview/gui/TreePanel.java @@ -20,6 +20,28 @@ */ package jalview.gui; +import java.awt.Font; +import java.awt.Graphics; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; +import java.awt.event.KeyAdapter; +import java.awt.event.KeyEvent; +import java.beans.PropertyChangeEvent; +import java.beans.PropertyChangeListener; +import java.io.File; +import java.io.FileOutputStream; +import java.util.ArrayList; +import java.util.List; +import java.util.Locale; + +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; + import jalview.analysis.AlignmentSorter; import jalview.analysis.AverageDistanceTree; import jalview.analysis.NJTree; @@ -29,9 +51,11 @@ import jalview.analysis.scoremodels.ScoreModels; import jalview.api.analysis.ScoreModelI; import jalview.api.analysis.SimilarityParamsI; import jalview.bin.Cache; +import jalview.bin.Console; import jalview.commands.CommandI; import jalview.commands.OrderCommand; import jalview.datamodel.Alignment; +import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; import jalview.datamodel.AlignmentView; import jalview.datamodel.BinaryNode; @@ -41,34 +65,16 @@ import jalview.datamodel.NodeTransformI; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; import jalview.datamodel.SequenceNode; +import jalview.gui.ImageExporter.ImageWriterI; import jalview.io.JalviewFileChooser; import jalview.io.JalviewFileView; import jalview.io.NewickFile; +import jalview.io.exceptions.ImageOutputException; import jalview.jbgui.GTreePanel; -import jalview.util.ImageMaker; +import jalview.util.ImageMaker.TYPE; import jalview.util.MessageManager; import jalview.viewmodel.AlignmentViewport; -import java.awt.Font; -import java.awt.Graphics; -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; - -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; - /** * DOCUMENT ME! * @@ -103,6 +109,7 @@ public class TreePanel extends GTreePanel SimilarityParamsI options) { super(); + this.setFrameIcon(null); this.similarityParams = options; initTreePanel(ap, type, modelName, null, null); @@ -115,10 +122,44 @@ public class TreePanel extends GTreePanel String theTitle, AlignmentView inputData) { super(); + this.setFrameIcon(null); this.treeTitle = theTitle; initTreePanel(alignPanel, null, null, newtree, inputData); } + /** + * columnwise tree associated with positions in aa + * + * @param alignPanel + * @param fin + * @param title + * @param aa + */ + public TreePanel(AlignmentPanel alignPanel, NewickFile fin, + AlignmentAnnotation aa, String title) + { + super(); + columnWise = true; + assocAnnotation = aa; + this.setFrameIcon(null); + this.treeTitle = title; + initTreePanel(alignPanel, null, null, fin, null); + } + + boolean columnWise = false; + + AlignmentAnnotation assocAnnotation = null; + + public boolean isColumnWise() + { + return columnWise; + } + + public AlignmentAnnotation getAssocAnnotation() + { + return assocAnnotation; + } + public AlignmentI getAlignment() { return getTreeCanvas().getViewport().getAlignment(); @@ -126,6 +167,7 @@ public class TreePanel extends GTreePanel public AlignmentViewport getViewPort() { + // @Mungo - Why don't we return our own viewport ??? return getTreeCanvas().getViewport(); } @@ -133,13 +175,38 @@ public class TreePanel extends GTreePanel NewickFile newTree, AlignmentView inputData) { - setViewport(ap.av); + av = ap.av; this.treeType = type; this.scoreModelName = modelName; treeCanvas = new TreeCanvas(this, ap, scrollPane); - scrollPane.setViewportView(getTreeCanvas()); + scrollPane.setViewportView(treeCanvas); + + if (columnWise) + { + bootstrapMenu.setVisible(false); + placeholdersMenu.setState(false); + placeholdersMenu.setVisible(false); + fitToWindow.setState(false); + sortAssocViews.setVisible(false); + } + addKeyListener(new KeyAdapter() + { + @Override + public void keyPressed(KeyEvent e) + { + switch (e.getKeyCode()) + { + case 27: // escape + treeCanvas.clearSelectedLeaves(); + e.consume(); + break; + + } + + } + }); PaintRefresher.Register(this, ap.av.getSequenceSetId()); buildAssociatedViewMenu(); @@ -155,9 +222,9 @@ public class TreePanel extends GTreePanel @Override public void internalFrameClosed(InternalFrameEvent evt) { - if (getViewport() != null) + if (av != null) { - getViewport().removePropertyChangeListener(listener); + av.removePropertyChangeListener(listener); } releaseReferences(); } @@ -193,7 +260,7 @@ public class TreePanel extends GTreePanel { if (tree == null) { - System.out.println("tree is null"); + jalview.bin.Console.outPrintln("tree is null"); // TODO: deal with case when a change event is received whilst a // tree is still being calculated - should save reference for // processing message later. @@ -201,18 +268,18 @@ public class TreePanel extends GTreePanel } if (evt.getNewValue() == null) { - System.out.println( + jalview.bin.Console.outPrintln( "new alignment sequences vector value is null"); } tree.updatePlaceHolders((List) evt.getNewValue()); - getTreeCanvas().nameHash.clear(); // reset the mapping between canvas + treeCanvas.nameHash.clear(); // reset the mapping between canvas // rectangles and leafnodes repaint(); } } }; - getViewport().addPropertyChangeListener(listener); + av.addPropertyChangeListener(listener); return listener; } @@ -225,7 +292,7 @@ public class TreePanel extends GTreePanel void buildAssociatedViewMenu() { AlignmentPanel[] aps = PaintRefresher - .getAssociatedPanels(getViewport().getSequenceSetId()); + .getAssociatedPanels(av.getSequenceSetId()); if (aps.length == 1 && getTreeCanvas().getAssociatedPanel() == aps[0]) { associateLeavesMenu.setVisible(false); @@ -249,16 +316,17 @@ public class TreePanel extends GTreePanel for (i = 0; i < iSize; i++) { final AlignmentPanel ap = aps[i]; - item = new JRadioButtonMenuItem(ap.av.getViewName(), ap == getTreeCanvas().getAssociatedPanel()); + item = new JRadioButtonMenuItem(ap.av.getViewName(), + ap == treeCanvas.getAssociatedPanel()); buttonGroup.add(item); item.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent evt) { - getTreeCanvas().applyToAllViews = false; - getTreeCanvas().setAssociatedPanel(ap); - getTreeCanvas().setViewport(ap.av); + treeCanvas.applyToAllViews = false; + treeCanvas.setAssociatedPanel(ap); + treeCanvas.setViewport(ap.av); PaintRefresher.Register(thisTreePanel, ap.av.getSequenceSetId()); } }); @@ -269,13 +337,13 @@ public class TreePanel extends GTreePanel final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem( MessageManager.getString("label.all_views")); buttonGroup.add(itemf); - itemf.setSelected(getTreeCanvas().applyToAllViews); + itemf.setSelected(treeCanvas.applyToAllViews); itemf.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent evt) { - getTreeCanvas().applyToAllViews = itemf.isSelected(); + treeCanvas.applyToAllViews = itemf.isSelected(); } }); associateLeavesMenu.add(itemf); @@ -308,7 +376,7 @@ public class TreePanel extends GTreePanel if (newtree != null) { - tree = new TreeModel(getViewport().getAlignment().getSequencesArray(), odata, + tree = new TreeModel(av.getAlignment().getSequencesArray(), odata, newtree); if (tree.getOriginalData() == null) { @@ -317,21 +385,21 @@ public class TreePanel extends GTreePanel } else { - ScoreModelI sm = ScoreModels.getInstance() - .getScoreModel(scoreModelName, getTreeCanvas().getAssociatedPanel()); + ScoreModelI sm = ScoreModels.getInstance().getScoreModel( + scoreModelName, treeCanvas.getAssociatedPanel()); TreeBuilder njtree = treeType.equals(TreeBuilder.NEIGHBOUR_JOINING) - ? new NJTree(getViewport(), sm, similarityParams) - : new AverageDistanceTree(getViewport(), sm, similarityParams); + ? new NJTree(av, sm, similarityParams) + : new AverageDistanceTree(av, sm, similarityParams); tree = new TreeModel(njtree); - showDistances(true); + // don't display distances for columnwise trees } - + showDistances(!columnWise); tree.reCount(tree.getTopNode()); tree.findHeight(tree.getTopNode()); - getTreeCanvas().setTree(tree); - getTreeCanvas().repaint(); - getViewport().setCurrentTree(tree); - if (getViewport().getSortByTree()) + treeCanvas.setTree(tree); + treeCanvas.repaint(); + av.setCurrentTree(tree); + if (av.getSortByTree()) { sortByTree_actionPerformed(); } @@ -340,20 +408,20 @@ public class TreePanel extends GTreePanel public void showDistances(boolean b) { - getTreeCanvas().setShowDistances(b); + treeCanvas.setShowDistances(b); distanceMenu.setSelected(b); } public void showBootstrap(boolean b) { - getTreeCanvas().setShowBootstrap(b); + treeCanvas.setShowBootstrap(b); bootstrapMenu.setSelected(b); } public void showPlaceholders(boolean b) { placeholdersMenu.setState(b); - getTreeCanvas().setMarkPlaceholders(b); + treeCanvas.setMarkPlaceholders(b); } /** @@ -402,8 +470,9 @@ public class TreePanel extends GTreePanel @Override public void saveAsNewick_actionPerformed(ActionEvent e) { + // TODO: JAL-3048 save newick file for Jalview-JS JalviewFileChooser chooser = new JalviewFileChooser( - jalview.bin.Cache.getProperty("LAST_DIRECTORY")); + Cache.getProperty("LAST_DIRECTORY")); chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle( MessageManager.getString("label.save_tree_as_newick")); @@ -414,7 +483,7 @@ public class TreePanel extends GTreePanel if (value == JalviewFileChooser.APPROVE_OPTION) { String choice = chooser.getSelectedFile().getPath(); - jalview.bin.Cache.setProperty("LAST_DIRECTORY", + Cache.setProperty("LAST_DIRECTORY", chooser.getSelectedFile().getParent()); try @@ -444,7 +513,7 @@ public class TreePanel extends GTreePanel public void printMenu_actionPerformed(ActionEvent e) { // Putting in a thread avoids Swing painting problems - getTreeCanvas().startPrinting(); + treeCanvas.startPrinting(); } @Override @@ -453,7 +522,7 @@ public class TreePanel extends GTreePanel AlignmentView originalData = tree.getOriginalData(); if (originalData == null) { - jalview.bin.Cache.log.info( + Console.info( "Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action."); return; } @@ -468,7 +537,7 @@ 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 = getViewport().getGapCharacter(); + gc = av.getGapCharacter(); } catch (Exception ex) { @@ -481,8 +550,8 @@ public class TreePanel extends GTreePanel // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]); AlignmentI al = new Alignment((SequenceI[]) alAndColsel[0]); - AlignmentI dataset = (getViewport() != null && getViewport().getAlignment() != null) - ? getViewport().getAlignment().getDataset() + AlignmentI dataset = (av != null && av.getAlignment() != null) + ? av.getAlignment().getDataset() : null; if (dataset != null) { @@ -519,7 +588,7 @@ public class TreePanel extends GTreePanel @Override public void fitToWindow_actionPerformed(ActionEvent e) { - getTreeCanvas().fitToWindow = fitToWindow.isSelected(); + treeCanvas.fitToWindow = fitToWindow.isSelected(); repaint(); } @@ -532,15 +601,15 @@ public class TreePanel extends GTreePanel public void sortByTree_actionPerformed() { - if (getTreeCanvas().applyToAllViews) + if (treeCanvas.applyToAllViews) { final ArrayList commands = new ArrayList<>(); for (AlignmentPanel ap : PaintRefresher - .getAssociatedPanels(getViewport().getSequenceSetId())) + .getAssociatedPanels(av.getSequenceSetId())) { commands.add(sortAlignmentIn(ap.av.getAlignPanel())); } - getViewport().getAlignPanel().alignFrame.addHistoryItem(new CommandI() + av.getAlignPanel().alignFrame.addHistoryItem(new CommandI() { @Override @@ -575,7 +644,7 @@ public class TreePanel extends GTreePanel } }); for (AlignmentPanel ap : PaintRefresher - .getAssociatedPanels(getViewport().getSequenceSetId())) + .getAssociatedPanels(av.getSequenceSetId())) { // ensure all the alignFrames refresh their GI after adding an undo item ap.alignFrame.updateEditMenuBar(); @@ -583,8 +652,8 @@ public class TreePanel extends GTreePanel } else { - getTreeCanvas().getAssociatedPanel().alignFrame - .addHistoryItem(sortAlignmentIn(getTreeCanvas().getAssociatedPanel())); + treeCanvas.getAssociatedPanel().alignFrame.addHistoryItem( + sortAlignmentIn(treeCanvas.getAssociatedPanel())); } } @@ -611,7 +680,7 @@ public class TreePanel extends GTreePanel @Override public void font_actionPerformed(ActionEvent e) { - if (getTreeCanvas() == null) + if (treeCanvas == null) { return; } @@ -621,14 +690,14 @@ public class TreePanel extends GTreePanel public Font getTreeFont() { - return getTreeCanvas().font; + return treeCanvas.font; } public void setTreeFont(Font f) { - if (getTreeCanvas() != null) + if (treeCanvas != null) { - getTreeCanvas().setFont(f); + treeCanvas.setFont(f); } } @@ -641,7 +710,7 @@ public class TreePanel extends GTreePanel @Override public void distanceMenu_actionPerformed(ActionEvent e) { - getTreeCanvas().setShowDistances(distanceMenu.isSelected()); + treeCanvas.setShowDistances(distanceMenu.isSelected()); } /** @@ -653,7 +722,7 @@ public class TreePanel extends GTreePanel @Override public void bootstrapMenu_actionPerformed(ActionEvent e) { - getTreeCanvas().setShowBootstrap(bootstrapMenu.isSelected()); + treeCanvas.setShowBootstrap(bootstrapMenu.isSelected()); } /** @@ -665,129 +734,39 @@ public class TreePanel extends GTreePanel @Override public void placeholdersMenu_actionPerformed(ActionEvent e) { - getTreeCanvas().setMarkPlaceholders(placeholdersMenu.isSelected()); + treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected()); } /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! + * Outputs the Tree in image format (currently EPS or PNG). The user is + * prompted for the file to save to, and for EPS (unless a preference is + * already set) for the choice of Text or Lineart for character rendering. */ @Override - public void epsTree_actionPerformed(ActionEvent e) + public void writeTreeImage(TYPE imageFormat) { - boolean accurateText = true; - - String renderStyle = jalview.bin.Cache.getDefault("EPS_RENDERING", - "Prompt each time"); - - // If we need to prompt, and if the GUI is visible then - // Prompt for EPS rendering style - if (renderStyle.equalsIgnoreCase("Prompt each time") - && !(System.getProperty("java.awt.headless") != null && System - .getProperty("java.awt.headless").equals("true"))) - { - EPSOptions eps = new EPSOptions(); - renderStyle = eps.getValue(); - - if (renderStyle == null || eps.cancelled) - { - return; - } - - } - - if (renderStyle.equalsIgnoreCase("text")) - { - accurateText = false; - } - - int width = getTreeCanvas().getWidth(); - int height = getTreeCanvas().getHeight(); - - try + int width = treeCanvas.getWidth(); + int height = treeCanvas.getHeight(); + ImageWriterI writer = new ImageWriterI() { - JalviewFileChooser chooser = new JalviewFileChooser( - ImageMaker.EPS_EXTENSION, ImageMaker.EPS_EXTENSION); - chooser.setFileView(new JalviewFileView()); - chooser.setDialogTitle( - MessageManager.getString("label.create_eps_from_tree")); - chooser.setToolTipText(MessageManager.getString("action.save")); - - int value = chooser.showSaveDialog(this); - - if (value != JalviewFileChooser.APPROVE_OPTION) + @Override + public void exportImage(Graphics g) throws Exception { - return; + treeCanvas.draw(g, width, height); } - - Cache.setProperty("LAST_DIRECTORY", - chooser.getSelectedFile().getParent()); - - FileOutputStream out = new FileOutputStream( - chooser.getSelectedFile()); - EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width, - height); - - pg.setAccurateTextMode(accurateText); - - getTreeCanvas().draw(pg, width, height); - - pg.flush(); - pg.close(); - } catch (Exception ex) - { - ex.printStackTrace(); - } - } - - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - @Override - public void pngTree_actionPerformed(ActionEvent e) - { - int width = getTreeCanvas().getWidth(); - int height = getTreeCanvas().getHeight(); - + }; + String tree = MessageManager.getString("label.tree"); + ImageExporter exporter = new ImageExporter(writer, null, imageFormat, + tree); try { - JalviewFileChooser chooser = new JalviewFileChooser( - ImageMaker.PNG_EXTENSION, ImageMaker.PNG_DESCRIPTION); - - chooser.setFileView(new jalview.io.JalviewFileView()); - chooser.setDialogTitle( - MessageManager.getString("label.create_png_from_tree")); - chooser.setToolTipText(MessageManager.getString("action.save")); - - int value = chooser.showSaveDialog(this); - - if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION) - { - return; - } - - jalview.bin.Cache.setProperty("LAST_DIRECTORY", - chooser.getSelectedFile().getParent()); - - FileOutputStream out = new FileOutputStream( - chooser.getSelectedFile()); - - BufferedImage bi = new BufferedImage(width, height, - BufferedImage.TYPE_INT_RGB); - Graphics png = bi.getGraphics(); - - getTreeCanvas().draw(png, width, height); - - ImageIO.write(bi, "png", out); - out.close(); - } catch (Exception ex) + exporter.doExport(null, this, width, height, + tree.toLowerCase(Locale.ROOT)); + } catch (ImageOutputException ioex) { - ex.printStackTrace(); + Console.error( + "Unexpected error whilst writing " + imageFormat.toString(), + ioex); } } @@ -812,24 +791,24 @@ public class TreePanel extends GTreePanel && !((SequenceNode) node).isDummy()) { String newname = null; - SequenceI sq = (SequenceI) ((SequenceNode) node).element(); + SequenceI sq = (SequenceI) ((BinaryNode) node).element(); if (sq != null) { // search dbrefs, features and annotation - DBRefEntry[] refs = jalview.util.DBRefUtils + List refs = jalview.util.DBRefUtils .selectRefs(sq.getDBRefs(), new String[] - { labelClass.toUpperCase() }); + { labelClass.toUpperCase(Locale.ROOT) }); if (refs != null) { - for (int i = 0; i < refs.length; i++) + for (int i = 0, ni = refs.size(); i < ni; i++) { if (newname == null) { - newname = new String(refs[i].getAccessionId()); + newname = new String(refs.get(i).getAccessionId()); } else { - newname = newname + "; " + refs[i].getAccessionId(); + newname += "; " + refs.get(i).getAccessionId(); } } } @@ -854,7 +833,7 @@ public class TreePanel extends GTreePanel { // String oldname = ((SequenceNode) node).getName(); // TODO : save oldname in the undo object for this modification. - ((SequenceNode) node).setName(newname); + ((BinaryNode) node).setName(newname); } } } @@ -880,8 +859,8 @@ public class TreePanel extends GTreePanel /* * i18n description of Neighbour Joining or Average Distance method */ - String treecalcnm = MessageManager - .getString("label.tree_calc_" + treeType.toLowerCase()); + String treecalcnm = MessageManager.getString( + "label.tree_calc_" + treeType.toLowerCase(Locale.ROOT)); /* * short score model name (long description can be too long) @@ -896,6 +875,35 @@ public class TreePanel extends GTreePanel return ttl; } + /** + * Builds an EPS image and writes it to the specified file. + * + * @param outFile + * @param textOption + * true for Text character rendering, false for Lineart + */ + protected void writeEpsFile(File outFile, boolean textOption) + { + try + { + int width = treeCanvas.getWidth(); + int height = treeCanvas.getHeight(); + + FileOutputStream out = new FileOutputStream(outFile); + EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width, + height); + pg.setAccurateTextMode(!textOption); + treeCanvas.draw(pg, width, height); + + pg.flush(); + pg.close(); + } catch (Exception ex) + { + jalview.bin.Console.errPrintln("Error writing tree as EPS"); + ex.printStackTrace(); + } + } + public AlignViewport getViewport() { return av;