X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FTreePanel.java;h=f708c482f9497054a931acc05f355196caed5226;hb=334013f9dc7b599af9062ca053d9d091a474472e;hp=30604cbfa8711fcb0bf2fe47f8aa2614d5020a2a;hpb=fab0afc9e1e7a5ca460f0cbd48545536f989a435;p=jalview.git diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java index 30604cb..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; @@ -28,9 +50,12 @@ 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.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; @@ -44,30 +69,12 @@ 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.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.beans.PropertyChangeEvent; -import java.beans.PropertyChangeListener; -import java.io.File; -import java.io.FileOutputStream; -import java.util.ArrayList; -import java.util.List; - -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! * @@ -102,6 +109,7 @@ public class TreePanel extends GTreePanel SimilarityParamsI options) { super(); + this.setFrameIcon(null); this.similarityParams = options; initTreePanel(ap, type, modelName, null, null); @@ -114,10 +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(); @@ -140,6 +182,31 @@ public class TreePanel extends GTreePanel treeCanvas = new TreeCanvas(this, ap, scrollPane); 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(); @@ -159,6 +226,7 @@ public class TreePanel extends GTreePanel { av.removePropertyChangeListener(listener); } + releaseReferences(); } }); @@ -168,6 +236,17 @@ 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() @@ -181,7 +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. @@ -189,7 +268,7 @@ public class TreePanel extends GTreePanel } if (evt.getNewValue() == null) { - System.out.println( + jalview.bin.Console.outPrintln( "new alignment sequences vector value is null"); } @@ -306,16 +385,15 @@ public class TreePanel extends GTreePanel } else { - ScoreModelI sm = ScoreModels.getInstance() - .getScoreModel(scoreModelName, - treeCanvas.getAssociatedPanel()); + ScoreModelI sm = ScoreModels.getInstance().getScoreModel( + scoreModelName, treeCanvas.getAssociatedPanel()); TreeBuilder njtree = treeType.equals(TreeBuilder.NEIGHBOUR_JOINING) ? 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()); treeCanvas.setTree(tree); @@ -394,7 +472,7 @@ public class TreePanel extends GTreePanel { // 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")); @@ -405,7 +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 +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; } @@ -574,9 +652,8 @@ public class TreePanel extends GTreePanel } else { - treeCanvas.getAssociatedPanel().alignFrame - .addHistoryItem( - sortAlignmentIn(treeCanvas.getAssociatedPanel())); + treeCanvas.getAssociatedPanel().alignFrame.addHistoryItem( + sortAlignmentIn(treeCanvas.getAssociatedPanel())); } } @@ -681,7 +758,16 @@ public class TreePanel extends GTreePanel String tree = MessageManager.getString("label.tree"); ImageExporter exporter = new ImageExporter(writer, null, imageFormat, tree); - exporter.doExport(null, this, width, height, tree.toLowerCase()); + try + { + exporter.doExport(null, this, width, height, + tree.toLowerCase(Locale.ROOT)); + } catch (ImageOutputException ioex) + { + Console.error( + "Unexpected error whilst writing " + imageFormat.toString(), + ioex); + } } /** @@ -705,24 +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(); } } } @@ -747,7 +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); } } } @@ -773,8 +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) @@ -784,7 +870,7 @@ 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; } @@ -803,8 +889,7 @@ public class TreePanel extends GTreePanel int width = treeCanvas.getWidth(); int height = treeCanvas.getHeight(); - FileOutputStream out = new FileOutputStream( - outFile); + FileOutputStream out = new FileOutputStream(outFile); EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width, height); pg.setAccurateTextMode(!textOption); @@ -814,11 +899,11 @@ public class TreePanel extends GTreePanel pg.close(); } catch (Exception ex) { - System.err.println("Error writing tree as EPS"); + jalview.bin.Console.errPrintln("Error writing tree as EPS"); ex.printStackTrace(); } } - + public AlignViewport getViewport() { return av;