X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FTreePanel.java;h=5e14fce7d3fa1410e1ed54ae8b041c08e26941e0;hb=f4766a7bbcfae845fc95923b01fa14ff83d589ff;hp=477c28d393d3598421347095845bfcdfab36c4be;hpb=d87d21c30c8d1f6a70f7d04f3f33e5210d0f367a;p=jalview.git diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java index 477c28d..5e14fce 100755 --- a/src/jalview/gui/TreePanel.java +++ b/src/jalview/gui/TreePanel.java @@ -21,10 +21,13 @@ package jalview.gui; import jalview.analysis.AlignmentSorter; +import jalview.analysis.AverageDistanceTree; import jalview.analysis.NJTree; +import jalview.analysis.TreeBuilder; +import jalview.analysis.TreeModel; import jalview.analysis.scoremodels.ScoreModels; import jalview.api.analysis.ScoreModelI; -import jalview.api.analysis.ViewBasedAnalysisI; +import jalview.api.analysis.SimilarityParamsI; import jalview.bin.Cache; import jalview.commands.CommandI; import jalview.commands.OrderCommand; @@ -32,8 +35,8 @@ import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentI; import jalview.datamodel.AlignmentView; import jalview.datamodel.BinaryNode; -import jalview.datamodel.ColumnSelection; import jalview.datamodel.DBRefEntry; +import jalview.datamodel.HiddenColumns; import jalview.datamodel.NodeTransformI; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; @@ -71,68 +74,46 @@ import org.jibble.epsgraphics.EpsGraphics2D; */ public class TreePanel extends GTreePanel { - String type; + String treeType; - String pwtype; + String scoreModelName; // if tree computed + + String treeTitle; // if tree loaded + + SimilarityParamsI similarityParams; TreeCanvas treeCanvas; - NJTree tree; + TreeModel tree; AlignViewport av; /** * Creates a new TreePanel object. * - * @param av - * DOCUMENT ME! - * @param seqVector - * DOCUMENT ME! + * @param ap * @param type - * DOCUMENT ME! - * @param pwtype - * DOCUMENT ME! - * @param s - * DOCUMENT ME! - * @param e - * DOCUMENT ME! + * @param modelName + * @param options */ - public TreePanel(AlignmentPanel ap, String type, String pwtype) + public TreePanel(AlignmentPanel ap, String type, String modelName, + SimilarityParamsI options) { super(); - initTreePanel(ap, type, pwtype, null, null); + this.similarityParams = options; + initTreePanel(ap, type, modelName, null, null); // We know this tree has distances. JBPNote TODO: prolly should add this as // a userdefined default // showDistances(true); } - /** - * Creates a new TreePanel object. - * - * @param av - * DOCUMENT ME! - * @param seqVector - * DOCUMENT ME! - * @param newtree - * DOCUMENT ME! - * @param type - * DOCUMENT ME! - * @param pwtype - * DOCUMENT ME! - */ - public TreePanel(AlignmentPanel ap, String type, String pwtype, - NewickFile newtree) - { - super(); - initTreePanel(ap, type, pwtype, newtree, null); - } - - public TreePanel(AlignmentPanel av, String type, String pwtype, - NewickFile newtree, AlignmentView inputData) + public TreePanel(AlignmentPanel alignPanel, NewickFile newtree, + String theTitle, AlignmentView inputData) { super(); - initTreePanel(av, type, pwtype, newtree, inputData); + this.treeTitle = theTitle; + initTreePanel(alignPanel, null, null, newtree, inputData); } public AlignmentI getAlignment() @@ -145,13 +126,13 @@ public class TreePanel extends GTreePanel return treeCanvas.av; } - void initTreePanel(AlignmentPanel ap, String type, String pwtype, + void initTreePanel(AlignmentPanel ap, String type, String modelName, NewickFile newTree, AlignmentView inputData) { av = ap.av; - this.type = type; - this.pwtype = pwtype; + this.treeType = type; + this.scoreModelName = modelName; treeCanvas = new TreeCanvas(this, ap, scrollPane); scrollPane.setViewportView(treeCanvas); @@ -177,11 +158,11 @@ public class TreePanel extends GTreePanel } if (evt.getNewValue() == null) { - System.out - .println("new alignment sequences vector value is null"); + System.out.println( + "new alignment sequences vector value is null"); } - tree.UpdatePlaceHolders((List) evt.getNewValue()); + tree.updatePlaceHolders((List) evt.getNewValue()); treeCanvas.nameHash.clear(); // reset the mapping between canvas // rectangles and leafnodes repaint(); @@ -189,11 +170,7 @@ public class TreePanel extends GTreePanel } }); - TreeLoader tl = new TreeLoader(newTree); - if (inputData != null) - { - tl.odata = inputData; - } + TreeLoader tl = new TreeLoader(newTree, inputData); tl.start(); } @@ -206,8 +183,8 @@ public class TreePanel extends GTreePanel void buildAssociatedViewMenu() { - AlignmentPanel[] aps = PaintRefresher.getAssociatedPanels(av - .getSequenceSetId()); + AlignmentPanel[] aps = PaintRefresher + .getAssociatedPanels(av.getSequenceSetId()); if (aps.length == 1 && treeCanvas.ap == aps[0]) { associateLeavesMenu.setVisible(false); @@ -216,7 +193,8 @@ public class TreePanel extends GTreePanel associateLeavesMenu.setVisible(true); - if ((viewMenu.getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem)) + if ((viewMenu + .getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem)) { viewMenu.insertSeparator(viewMenu.getItemCount() - 1); } @@ -265,19 +243,21 @@ public class TreePanel extends GTreePanel class TreeLoader extends Thread { - NewickFile newtree; + private NewickFile newtree; - jalview.datamodel.AlignmentView odata = null; + private AlignmentView odata = null; - public TreeLoader(NewickFile newtree) + public TreeLoader(NewickFile newickFile, AlignmentView inputData) { - this.newtree = newtree; - if (newtree != null) + this.newtree = newickFile; + this.odata = inputData; + + if (newickFile != null) { // Must be outside run(), as Jalview2XML tries to // update distance/bootstrap visibility at the same time - showBootstrap(newtree.HasBootstrap()); - showDistances(newtree.HasDistances()); + showBootstrap(newickFile.HasBootstrap()); + showDistances(newickFile.HasDistances()); } } @@ -287,60 +267,21 @@ public class TreePanel extends GTreePanel if (newtree != null) { - if (odata == null) - { - tree = new NJTree(av.getAlignment().getSequencesArray(), newtree); - } - else - { - tree = new NJTree(av.getAlignment().getSequencesArray(), odata, - newtree); - } - if (!tree.hasOriginalSequenceData()) + tree = new TreeModel(av.getAlignment().getSequencesArray(), odata, + newtree); + if (tree.getOriginalData() == null) { - allowOriginalSeqData(false); + originalSeqData.setVisible(false); } } else { - int start, end; - SequenceI[] seqs; - boolean selview = av.getSelectionGroup() != null - && av.getSelectionGroup().getSize() > 1; - AlignmentView seqStrings = av.getAlignmentView(selview); - if (!selview) - { - start = 0; - end = av.getAlignment().getWidth(); - seqs = av.getAlignment().getSequencesArray(); - } - else - { - start = av.getSelectionGroup().getStartRes(); - end = av.getSelectionGroup().getEndRes() + 1; - seqs = av.getSelectionGroup().getSequencesInOrder( - av.getAlignment()); - } - ScoreModelI sm = ScoreModels.getInstance().forName(pwtype); - if (sm instanceof ViewBasedAnalysisI) - { - try - { - sm = sm.getClass().newInstance(); - ((ViewBasedAnalysisI) sm) - .configureFromAlignmentView(treeCanvas.ap); - } catch (Exception q) - { - Cache.log.error("Couldn't create a scoremodel instance for " - + sm.getName()); - } - tree = new NJTree(seqs, seqStrings, type, pwtype, sm, start, end); - } - else - { - tree = new NJTree(seqs, seqStrings, type, pwtype, null, start, - end); - } + ScoreModelI sm = ScoreModels.getInstance() + .getScoreModel(scoreModelName, treeCanvas.ap); + TreeBuilder njtree = treeType.equals(TreeBuilder.NEIGHBOUR_JOINING) + ? new NJTree(av, sm, similarityParams) + : new AverageDistanceTree(av, sm, similarityParams); + tree = new TreeModel(njtree); showDistances(true); } @@ -374,17 +315,12 @@ public class TreePanel extends GTreePanel treeCanvas.setMarkPlaceholders(b); } - private void allowOriginalSeqData(boolean b) - { - originalSeqData.setVisible(b); - } - /** * DOCUMENT ME! * * @return DOCUMENT ME! */ - public NJTree getTree() + public TreeModel getTree() { return tree; } @@ -400,26 +336,14 @@ public class TreePanel extends GTreePanel { CutAndPasteTransfer cap = new CutAndPasteTransfer(); - StringBuffer buffer = new StringBuffer(); - - if (type.equals(NJTree.AVERAGE_DISTANCE)) - { - buffer.append("Average distance tree using "); - } - else - { - buffer.append("Neighbour joining tree using "); - } - - ScoreModelI sm = ScoreModels.getInstance().forName(pwtype); - buffer.append(sm.getName()); + String newTitle = getPanelTitle(); NewickFile fout = new NewickFile(tree.getTopNode()); try { - cap.setText(fout.print(tree.isHasBootstrap(), tree.isHasDistances(), - tree.isHasRootDistance())); - Desktop.addInternalFrame(cap, buffer.toString(), 500, 100); + cap.setText(fout.print(tree.hasBootstrap(), tree.hasDistances(), + tree.hasRootDistance())); + Desktop.addInternalFrame(cap, newTitle, 500, 100); } catch (OutOfMemoryError oom) { new OOMWarning("generating newick tree file", oom); @@ -440,8 +364,8 @@ public class TreePanel extends GTreePanel JalviewFileChooser chooser = new JalviewFileChooser( jalview.bin.Cache.getProperty("LAST_DIRECTORY")); chooser.setFileView(new JalviewFileView()); - chooser.setDialogTitle(MessageManager - .getString("label.save_tree_as_newick")); + chooser.setDialogTitle( + MessageManager.getString("label.save_tree_as_newick")); chooser.setToolTipText(MessageManager.getString("action.save")); int value = chooser.showSaveDialog(null); @@ -449,15 +373,15 @@ public class TreePanel extends GTreePanel if (value == JalviewFileChooser.APPROVE_OPTION) { String choice = chooser.getSelectedFile().getPath(); - jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser - .getSelectedFile().getParent()); + jalview.bin.Cache.setProperty("LAST_DIRECTORY", + chooser.getSelectedFile().getParent()); try { jalview.io.NewickFile fout = new jalview.io.NewickFile( tree.getTopNode()); - String output = fout.print(tree.isHasBootstrap(), - tree.isHasDistances(), tree.isHasRootDistance()); + String output = fout.print(tree.hasBootstrap(), tree.hasDistances(), + tree.hasRootDistance()); java.io.PrintWriter out = new java.io.PrintWriter( new java.io.FileWriter(choice)); out.println(output); @@ -485,10 +409,11 @@ public class TreePanel extends GTreePanel @Override public void originalSeqData_actionPerformed(ActionEvent e) { - if (!tree.hasOriginalSequenceData()) + AlignmentView originalData = tree.getOriginalData(); + if (originalData == null) { - jalview.bin.Cache.log - .info("Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action."); + jalview.bin.Cache.log.info( + "Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action."); return; } // decide if av alignment is sufficiently different to original data to @@ -507,16 +432,17 @@ public class TreePanel extends GTreePanel } catch (Exception ex) { } - ; - Object[] alAndColsel = tree.seqData.getAlignmentAndColumnSelection(gc); + + Object[] alAndColsel = originalData.getAlignmentAndHiddenColumns(gc); if (alAndColsel != null && alAndColsel[0] != null) { // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]); AlignmentI al = new Alignment((SequenceI[]) alAndColsel[0]); - AlignmentI dataset = (av != null && av.getAlignment() != null) ? av - .getAlignment().getDataset() : null; + AlignmentI dataset = (av != null && av.getAlignment() != null) + ? av.getAlignment().getDataset() + : null; if (dataset != null) { al.setDataset(dataset); @@ -525,9 +451,8 @@ public class TreePanel extends GTreePanel if (true) { // make a new frame! - AlignFrame af = new AlignFrame(al, - (ColumnSelection) alAndColsel[1], AlignFrame.DEFAULT_WIDTH, - AlignFrame.DEFAULT_HEIGHT); + AlignFrame af = new AlignFrame(al, (HiddenColumns) alAndColsel[1], + AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); // >>>This is a fix for the moment, until a better solution is // found!!<<< @@ -537,8 +462,8 @@ public class TreePanel extends GTreePanel // msaorder); Desktop.addInternalFrame(af, MessageManager.formatMessage( - "label.original_data_for_params", - new Object[] { this.title }), AlignFrame.DEFAULT_WIDTH, + "label.original_data_for_params", new Object[] + { this.title }), AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); } } @@ -569,8 +494,8 @@ public class TreePanel extends GTreePanel if (treeCanvas.applyToAllViews) { final ArrayList commands = new ArrayList(); - for (AlignmentPanel ap : PaintRefresher.getAssociatedPanels(av - .getSequenceSetId())) + for (AlignmentPanel ap : PaintRefresher + .getAssociatedPanels(av.getSequenceSetId())) { commands.add(sortAlignmentIn(ap.av.getAlignPanel())); } @@ -608,8 +533,8 @@ public class TreePanel extends GTreePanel } } }); - for (AlignmentPanel ap : PaintRefresher.getAssociatedPanels(av - .getSequenceSetId())) + for (AlignmentPanel ap : PaintRefresher + .getAssociatedPanels(av.getSequenceSetId())) { // ensure all the alignFrames refresh their GI after adding an undo item ap.alignFrame.updateEditMenuBar(); @@ -625,11 +550,11 @@ public class TreePanel extends GTreePanel public CommandI sortAlignmentIn(AlignmentPanel ap) { - AlignmentViewport av = ap.av; - SequenceI[] oldOrder = av.getAlignment().getSequencesArray(); - AlignmentSorter.sortByTree(av.getAlignment(), tree); + AlignmentViewport viewport = ap.av; + SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); + AlignmentSorter.sortByTree(viewport.getAlignment(), tree); CommandI undo; - undo = new OrderCommand("Tree Sort", oldOrder, av.getAlignment()); + undo = new OrderCommand("Tree Sort", oldOrder, viewport.getAlignment()); ap.paintAlignment(true); return undo; @@ -657,11 +582,11 @@ public class TreePanel extends GTreePanel return treeCanvas.font; } - public void setTreeFont(Font font) + public void setTreeFont(Font f) { if (treeCanvas != null) { - treeCanvas.setFont(font); + treeCanvas.setFont(f); } } @@ -744,8 +669,8 @@ public class TreePanel extends GTreePanel JalviewFileChooser chooser = new JalviewFileChooser( ImageMaker.EPS_EXTENSION, ImageMaker.EPS_EXTENSION); chooser.setFileView(new JalviewFileView()); - chooser.setDialogTitle(MessageManager - .getString("label.create_eps_from_tree")); + chooser.setDialogTitle( + MessageManager.getString("label.create_eps_from_tree")); chooser.setToolTipText(MessageManager.getString("action.save")); int value = chooser.showSaveDialog(this); @@ -755,11 +680,13 @@ public class TreePanel extends GTreePanel return; } - Cache.setProperty("LAST_DIRECTORY", chooser.getSelectedFile() - .getParent()); + Cache.setProperty("LAST_DIRECTORY", + chooser.getSelectedFile().getParent()); - FileOutputStream out = new FileOutputStream(chooser.getSelectedFile()); - EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width, height); + FileOutputStream out = new FileOutputStream( + chooser.getSelectedFile()); + EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width, + height); pg.setAccurateTextMode(accurateText); @@ -791,8 +718,8 @@ public class TreePanel extends GTreePanel ImageMaker.PNG_EXTENSION, ImageMaker.PNG_DESCRIPTION); chooser.setFileView(new jalview.io.JalviewFileView()); - chooser.setDialogTitle(MessageManager - .getString("label.create_png_from_tree")); + chooser.setDialogTitle( + MessageManager.getString("label.create_png_from_tree")); chooser.setToolTipText(MessageManager.getString("action.save")); int value = chooser.showSaveDialog(this); @@ -802,10 +729,11 @@ public class TreePanel extends GTreePanel return; } - jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser - .getSelectedFile().getParent()); + jalview.bin.Cache.setProperty("LAST_DIRECTORY", + chooser.getSelectedFile().getParent()); - FileOutputStream out = new FileOutputStream(chooser.getSelectedFile()); + FileOutputStream out = new FileOutputStream( + chooser.getSelectedFile()); BufferedImage bi = new BufferedImage(width, height, BufferedImage.TYPE_INT_RGB); @@ -846,9 +774,9 @@ public class TreePanel extends GTreePanel if (sq != null) { // search dbrefs, features and annotation - DBRefEntry[] refs = jalview.util.DBRefUtils.selectRefs( - sq.getDBRefs(), - new String[] { labelClass.toUpperCase() }); + DBRefEntry[] refs = jalview.util.DBRefUtils + .selectRefs(sq.getDBRefs(), new String[] + { labelClass.toUpperCase() }); if (refs != null) { for (int i = 0; i < refs.length; i++) @@ -865,31 +793,64 @@ public class TreePanel extends GTreePanel } if (newname == null) { - SequenceFeature sf[] = sq.getSequenceFeatures(); - for (int i = 0; sf != null && i < sf.length; i++) + List features = sq.getFeatures() + .getPositionalFeatures(labelClass); + for (SequenceFeature feature : features) { - if (sf[i].getType().equals(labelClass)) + if (newname == null) { - if (newname == null) - { - newname = new String(sf[i].getDescription()); - } - else - { - newname = newname + "; " + sf[i].getDescription(); - } + newname = feature.getDescription(); + } + else + { + newname = newname + "; " + feature.getDescription(); } } } } if (newname != null) { - String oldname = ((SequenceNode) node).getName(); - // TODO : save in the undo object for this modification. + // String oldname = ((SequenceNode) node).getName(); + // TODO : save oldname in the undo object for this modification. ((SequenceNode) node).setName(newname); } } } }); } + + /** + * Formats a localised title for the tree panel, like + *

+ * Neighbour Joining Using BLOSUM62 + *

+ * For a tree loaded from file, just uses the file name + * + * @return + */ + public String getPanelTitle() + { + if (treeTitle != null) + { + return treeTitle; + } + + /* + * i18n description of Neighbour Joining or Average Distance method + */ + String treecalcnm = MessageManager + .getString("label.tree_calc_" + treeType.toLowerCase()); + + /* + * short score model name (long description can be too long) + */ + String smn = scoreModelName; + + /* + * put them together as Using + */ + final String ttl = MessageManager.formatMessage("label.treecalc_title", + treecalcnm, smn); + return ttl; + } }