X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FTreePanel.java;h=084f46170f73b4c25dfddc237dd420c05873563b;hb=7e82e1fed011077e5cd4cc40ac8ad3519d7c47a8;hp=74dd29a61c9792b07ebd6d39f911cbf1b9667815;hpb=b4228f9114855211ecb84c2670777e00947e8548;p=jalview.git diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java index 74dd29a..084f461 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; @@ -52,6 +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; @@ -60,6 +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; @@ -71,75 +77,102 @@ import org.jibble.epsgraphics.EpsGraphics2D; */ public class TreePanel extends GTreePanel { - String type; + String treeType; - String pwtype; + String scoreModelName; // if tree computed - TreeCanvas treeCanvas; + String treeTitle; // if tree loaded - NJTree tree; + SimilarityParamsI similarityParams; - AlignViewport av; + private TreeCanvas treeCanvas; + + TreeModel tree; + + private 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); } - 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() { - return treeCanvas.av.getAlignment(); + return getTreeCanvas().getViewport().getAlignment(); } public AlignmentViewport getViewPort() { - return treeCanvas.av; + return getTreeCanvas().getViewport(); } - 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; + 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) @@ -156,25 +189,19 @@ 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()); - 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); - if (inputData != null) - { - tl.odata = inputData; - } - tl.start(); - + }; + getViewport().addPropertyChangeListener(listener); + return listener; } @Override @@ -185,9 +212,9 @@ public class TreePanel extends GTreePanel void buildAssociatedViewMenu() { - AlignmentPanel[] aps = PaintRefresher.getAssociatedPanels(av - .getSequenceSetId()); - if (aps.length == 1 && treeCanvas.ap == aps[0]) + AlignmentPanel[] aps = PaintRefresher + .getAssociatedPanels(getViewport().getSequenceSetId()); + if (aps.length == 1 && getTreeCanvas().getAssociatedPanel() == aps[0]) { associateLeavesMenu.setVisible(false); return; @@ -195,7 +222,8 @@ 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); } @@ -209,16 +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()); } }); @@ -229,13 +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); @@ -244,19 +272,21 @@ 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()); } } @@ -266,52 +296,30 @@ 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(getViewport().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); - sm = configureScoreModel(sm); - tree = new NJTree(seqs, seqStrings, type, pwtype, sm, start, end); + ScoreModelI sm = ScoreModels.getInstance() + .getScoreModel(scoreModelName, getTreeCanvas().getAssociatedPanel()); + TreeBuilder njtree = treeType.equals(TreeBuilder.NEIGHBOUR_JOINING) + ? 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(); } @@ -320,25 +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); - } - - private void allowOriginalSeqData(boolean b) - { - originalSeqData.setVisible(b); + getTreeCanvas().setMarkPlaceholders(b); } /** @@ -346,7 +349,7 @@ public class TreePanel extends GTreePanel * * @return DOCUMENT ME! */ - public NJTree getTree() + public TreeModel getTree() { return tree; } @@ -362,7 +365,7 @@ public class TreePanel extends GTreePanel { CutAndPasteTransfer cap = new CutAndPasteTransfer(); - String newTitle = getPanelTitle(type, pwtype); + String newTitle = getPanelTitle(); NewickFile fout = new NewickFile(tree.getTopNode()); try @@ -390,8 +393,8 @@ 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); @@ -399,15 +402,15 @@ 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.hasBootstrap(), - tree.hasDistances(), tree.hasRootDistance()); + 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); @@ -429,16 +432,17 @@ public class TreePanel extends GTreePanel public void printMenu_actionPerformed(ActionEvent e) { // Putting in a thread avoids Swing painting problems - treeCanvas.startPrinting(); + getTreeCanvas().startPrinting(); } @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 @@ -452,21 +456,22 @@ 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) { } - ; - 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 = (getViewport() != null && getViewport().getAlignment() != null) + ? getViewport().getAlignment().getDataset() + : null; if (dataset != null) { al.setDataset(dataset); @@ -475,9 +480,8 @@ 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!!<<< @@ -487,8 +491,8 @@ 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); } } @@ -503,7 +507,7 @@ public class TreePanel extends GTreePanel @Override public void fitToWindow_actionPerformed(ActionEvent e) { - treeCanvas.fitToWindow = fitToWindow.isSelected(); + getTreeCanvas().fitToWindow = fitToWindow.isSelected(); repaint(); } @@ -516,15 +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())) + final ArrayList commands = new ArrayList<>(); + for (AlignmentPanel ap : PaintRefresher + .getAssociatedPanels(getViewport().getSequenceSetId())) { commands.add(sortAlignmentIn(ap.av.getAlignPanel())); } - av.getAlignPanel().alignFrame.addHistoryItem(new CommandI() + getViewport().getAlignPanel().alignFrame.addHistoryItem(new CommandI() { @Override @@ -558,8 +562,8 @@ public class TreePanel extends GTreePanel } } }); - for (AlignmentPanel ap : PaintRefresher.getAssociatedPanels(av - .getSequenceSetId())) + for (AlignmentPanel ap : PaintRefresher + .getAssociatedPanels(getViewport().getSequenceSetId())) { // ensure all the alignFrames refresh their GI after adding an undo item ap.alignFrame.updateEditMenuBar(); @@ -567,21 +571,22 @@ public class TreePanel extends GTreePanel } else { - treeCanvas.ap.alignFrame - .addHistoryItem(sortAlignmentIn(treeCanvas.ap)); + getTreeCanvas().getAssociatedPanel().alignFrame + .addHistoryItem(sortAlignmentIn(getTreeCanvas().getAssociatedPanel())); } } public CommandI sortAlignmentIn(AlignmentPanel ap) { - AlignmentViewport av = ap.av; - SequenceI[] oldOrder = av.getAlignment().getSequencesArray(); - AlignmentSorter.sortByTree(av.getAlignment(), tree); + // TODO: move to alignment view controller + 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); + ap.paintAlignment(true, false); return undo; } @@ -594,7 +599,7 @@ public class TreePanel extends GTreePanel @Override public void font_actionPerformed(ActionEvent e) { - if (treeCanvas == null) + if (getTreeCanvas() == null) { return; } @@ -604,14 +609,14 @@ public class TreePanel extends GTreePanel public Font getTreeFont() { - return treeCanvas.font; + return getTreeCanvas().font; } - public void setTreeFont(Font font) + public void setTreeFont(Font f) { - if (treeCanvas != null) + if (getTreeCanvas() != null) { - treeCanvas.setFont(font); + getTreeCanvas().setFont(f); } } @@ -624,7 +629,7 @@ public class TreePanel extends GTreePanel @Override public void distanceMenu_actionPerformed(ActionEvent e) { - treeCanvas.setShowDistances(distanceMenu.isSelected()); + getTreeCanvas().setShowDistances(distanceMenu.isSelected()); } /** @@ -636,7 +641,7 @@ public class TreePanel extends GTreePanel @Override public void bootstrapMenu_actionPerformed(ActionEvent e) { - treeCanvas.setShowBootstrap(bootstrapMenu.isSelected()); + getTreeCanvas().setShowBootstrap(bootstrapMenu.isSelected()); } /** @@ -648,7 +653,7 @@ public class TreePanel extends GTreePanel @Override public void placeholdersMenu_actionPerformed(ActionEvent e) { - treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected()); + getTreeCanvas().setMarkPlaceholders(placeholdersMenu.isSelected()); } /** @@ -686,16 +691,16 @@ public class TreePanel extends GTreePanel accurateText = false; } - int width = treeCanvas.getWidth(); - int height = treeCanvas.getHeight(); + int width = getTreeCanvas().getWidth(); + int height = getTreeCanvas().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.setDialogTitle( + MessageManager.getString("label.create_eps_from_tree")); chooser.setToolTipText(MessageManager.getString("action.save")); int value = chooser.showSaveDialog(this); @@ -705,15 +710,17 @@ 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); - treeCanvas.draw(pg, width, height); + getTreeCanvas().draw(pg, width, height); pg.flush(); pg.close(); @@ -732,8 +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 { @@ -741,8 +748,8 @@ 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); @@ -752,16 +759,17 @@ 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); Graphics png = bi.getGraphics(); - treeCanvas.draw(png, width, height); + getTreeCanvas().draw(png, width, height); ImageIO.write(bi, "png", out); out.close(); @@ -796,9 +804,9 @@ 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++) @@ -815,27 +823,25 @@ 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) + { + newname = feature.getDescription(); + } + else { - if (newname == null) - { - newname = new String(sf[i].getDescription()); - } - else - { - newname = newname + "; " + sf[i].getDescription(); - } + 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); } } @@ -850,29 +856,25 @@ public class TreePanel extends GTreePanel *

* For a tree loaded from file, just uses the file name * - * @param treeType - * NJ or AV or FromFile - * @param modelOrFileName * @return */ - public static String getPanelTitle(String treeType, String modelOrFileName) + public String getPanelTitle() { - if (NJTree.FROM_FILE.equals(treeType)) + if (treeTitle != null) { - return modelOrFileName; + return treeTitle; } /* * 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()); /* - * i18n description (if any) of score model used + * short score model name (long description can be too long) */ - String smn = MessageManager.getStringOrReturn("label.score_model_", - modelOrFileName); + String smn = scoreModelName; /* * put them together as Using @@ -882,27 +884,18 @@ public class TreePanel extends GTreePanel return ttl; } - /** - * If the score model is one that requires to get state data from the current - * view, allow it to do so - * - * @param sm - * @return - */ - protected ScoreModelI configureScoreModel(ScoreModelI sm) + public AlignViewport getViewport() { - 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()); - } - } - return sm; + return av; + } + + public void setViewport(AlignViewport av) + { + this.av = av; + } + + public TreeCanvas getTreeCanvas() + { + return treeCanvas; } }