X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FTreePanel.java;h=b730df46207d5c38c689c0fd379283f3b9190d83;hb=9d2408483e451285fd555c3cd6e0273977acbaa7;hp=82f356588c0f982f5e92bb0d9fde96ddeffe6a48;hpb=90c2f45e60ed604705e81dd8af31bf0bfd3dbdef;p=jalview.git diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java index 82f3565..b730df4 100755 --- a/src/jalview/gui/TreePanel.java +++ b/src/jalview/gui/TreePanel.java @@ -20,6 +20,8 @@ */ package jalview.gui; +import java.util.Locale; + import jalview.analysis.AlignmentSorter; import jalview.analysis.AverageDistanceTree; import jalview.analysis.NJTree; @@ -28,7 +30,6 @@ import jalview.analysis.TreeModel; import jalview.analysis.scoremodels.ScoreModels; import jalview.api.analysis.ScoreModelI; import jalview.api.analysis.SimilarityParamsI; -import jalview.bin.Cache; import jalview.commands.CommandI; import jalview.commands.OrderCommand; import jalview.datamodel.Alignment; @@ -41,11 +42,12 @@ 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.jbgui.GTreePanel; -import jalview.util.ImageMaker; +import jalview.util.ImageMaker.TYPE; import jalview.util.MessageManager; import jalview.viewmodel.AlignmentViewport; @@ -53,14 +55,13 @@ 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.File; 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; @@ -85,11 +86,11 @@ public class TreePanel extends GTreePanel SimilarityParamsI similarityParams; - TreeCanvas treeCanvas; + private TreeCanvas treeCanvas; TreeModel tree; - AlignViewport av; + private AlignViewport av; /** * Creates a new TreePanel object. @@ -121,12 +122,13 @@ public class TreePanel extends GTreePanel public AlignmentI getAlignment() { - return treeCanvas.av.getAlignment(); + return getTreeCanvas().getViewport().getAlignment(); } public AlignmentViewport getViewPort() { - return treeCanvas.av; + // @Mungo - Why don't we return our own viewport ??? + return getTreeCanvas().getViewport(); } void initTreePanel(AlignmentPanel ap, String type, String modelName, @@ -155,7 +157,11 @@ public class TreePanel extends GTreePanel @Override public void internalFrameClosed(InternalFrameEvent evt) { - av.removePropertyChangeListener(listener); + if (av != null) + { + av.removePropertyChangeListener(listener); + } + releaseReferences(); } }); @@ -165,6 +171,17 @@ public class TreePanel extends GTreePanel } /** + * Ensure any potentially large object references are nulled + */ + public void releaseReferences() + { + this.tree = null; + this.treeCanvas.tree = null; + this.treeCanvas.nodeHash = null; + this.treeCanvas.nameHash = null; + } + + /** * @return */ protected PropertyChangeListener addAlignmentListener() @@ -211,7 +228,7 @@ public class TreePanel extends GTreePanel { AlignmentPanel[] aps = PaintRefresher .getAssociatedPanels(av.getSequenceSetId()); - if (aps.length == 1 && treeCanvas.ap == aps[0]) + if (aps.length == 1 && getTreeCanvas().getAssociatedPanel() == aps[0]) { associateLeavesMenu.setVisible(false); return; @@ -234,7 +251,8 @@ 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 == treeCanvas.getAssociatedPanel()); buttonGroup.add(item); item.addActionListener(new ActionListener() { @@ -242,8 +260,8 @@ public class TreePanel extends GTreePanel public void actionPerformed(ActionEvent evt) { treeCanvas.applyToAllViews = false; - treeCanvas.ap = ap; - treeCanvas.av = ap.av; + treeCanvas.setAssociatedPanel(ap); + treeCanvas.setViewport(ap.av); PaintRefresher.Register(thisTreePanel, ap.av.getSequenceSetId()); } }); @@ -303,7 +321,8 @@ public class TreePanel extends GTreePanel else { ScoreModelI sm = ScoreModels.getInstance() - .getScoreModel(scoreModelName, treeCanvas.ap); + .getScoreModel(scoreModelName, + treeCanvas.getAssociatedPanel()); TreeBuilder njtree = treeType.equals(TreeBuilder.NEIGHBOUR_JOINING) ? new NJTree(av, sm, similarityParams) : new AverageDistanceTree(av, sm, similarityParams); @@ -387,6 +406,7 @@ 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")); chooser.setFileView(new JalviewFileView()); @@ -568,8 +588,9 @@ public class TreePanel extends GTreePanel } else { - treeCanvas.ap.alignFrame - .addHistoryItem(sortAlignmentIn(treeCanvas.ap)); + treeCanvas.getAssociatedPanel().alignFrame + .addHistoryItem( + sortAlignmentIn(treeCanvas.getAssociatedPanel())); } } @@ -654,126 +675,27 @@ public class TreePanel extends GTreePanel } /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - @Override - public void epsTree_actionPerformed(ActionEvent e) - { - 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 = treeCanvas.getWidth(); - int height = treeCanvas.getHeight(); - - try - { - 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) - { - return; - } - - 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); - - treeCanvas.draw(pg, width, height); - - pg.flush(); - pg.close(); - } catch (Exception ex) - { - ex.printStackTrace(); - } - } - - /** - * 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 pngTree_actionPerformed(ActionEvent e) + public void writeTreeImage(TYPE imageFormat) { int width = treeCanvas.getWidth(); int height = treeCanvas.getHeight(); - - try + ImageWriterI writer = new ImageWriterI() { - 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) + @Override + public void exportImage(Graphics g) throws Exception { - return; + treeCanvas.draw(g, width, height); } - - 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(); - - treeCanvas.draw(png, width, height); - - ImageIO.write(bi, "png", out); - out.close(); - } catch (Exception ex) - { - ex.printStackTrace(); - } + }; + String tree = MessageManager.getString("label.tree"); + ImageExporter exporter = new ImageExporter(writer, null, imageFormat, + tree); + exporter.doExport(null, this, width, height, tree.toLowerCase(Locale.ROOT)); } /** @@ -801,20 +723,20 @@ public class TreePanel extends GTreePanel 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(); } } } @@ -866,7 +788,7 @@ public class TreePanel extends GTreePanel * i18n description of Neighbour Joining or Average Distance method */ String treecalcnm = MessageManager - .getString("label.tree_calc_" + treeType.toLowerCase()); + .getString("label.tree_calc_" + treeType.toLowerCase(Locale.ROOT)); /* * short score model name (long description can be too long) @@ -876,8 +798,53 @@ 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; } + + /** + * 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) + { + System.err.println("Error writing tree as EPS"); + ex.printStackTrace(); + } + } + + public AlignViewport getViewport() + { + return av; + } + + public void setViewport(AlignViewport av) + { + this.av = av; + } + + public TreeCanvas getTreeCanvas() + { + return treeCanvas; + } }