X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FTreePanel.java;h=e8f78d83d546cd7006bc718769d901dc9aef0e1f;hb=91bea2a1185e438bfd52fc1848cf615068016192;hp=f2f0bf7362bba5b194791f62a745ab846963d615;hpb=e5c87d2dd1d3ebceea890ef92c8a6374c62d3c83;p=jalview.git diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java index f2f0bf7..e8f78d8 100755 --- a/src/jalview/gui/TreePanel.java +++ b/src/jalview/gui/TreePanel.java @@ -21,13 +21,7 @@ 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.SimilarityParamsI; import jalview.bin.Cache; import jalview.commands.CommandI; import jalview.commands.OrderCommand; @@ -35,8 +29,8 @@ 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; @@ -74,14 +68,12 @@ import org.jibble.epsgraphics.EpsGraphics2D; */ public class TreePanel extends GTreePanel { - String treeType; + String substitutionMatrix; - String scoreModelName; // if tree computed + String treeType; String treeTitle; // if tree loaded - SimilarityParamsI similarityParams; - TreeCanvas treeCanvas; TreeModel tree; @@ -92,28 +84,38 @@ public class TreePanel extends GTreePanel * Creates a new TreePanel object. * * @param ap - * @param type - * @param modelName - * @param options + * @param tree + * @param treeType + * @param substitutionMatrix */ - public TreePanel(AlignmentPanel ap, String type, String modelName, - SimilarityParamsI options) + public TreePanel(AlignmentPanel ap, TreeModel tree, String treeType, + String substitutionMatrix) { super(); - this.similarityParams = options; - initTreePanel(ap, type, modelName, null, null); + this.treeType = treeType; + this.substitutionMatrix = substitutionMatrix; + this.tree = tree; + initTreePanel(ap, tree); // We know this tree has distances. JBPNote TODO: prolly should add this as // a userdefined default // showDistances(true); } + /** + * Creates a new TreePanel object. + * + * @param alignPanel + * @param newtree + * @param theTitle + * @param inputData + */ public TreePanel(AlignmentPanel alignPanel, NewickFile newtree, String theTitle, AlignmentView inputData) { super(); this.treeTitle = theTitle; - initTreePanel(alignPanel, null, null, newtree, inputData); + initTreePanel(alignPanel, newtree, inputData); } public AlignmentI getAlignment() @@ -126,17 +128,44 @@ public class TreePanel extends GTreePanel return treeCanvas.av; } - void initTreePanel(AlignmentPanel ap, String type, String modelName, - NewickFile newTree, AlignmentView inputData) + /** + * Initialize a tree panel based on a calculated tree + * + * @param ap + * @param tree + */ + void initTreePanel(AlignmentPanel ap, TreeModel tree) + { + buildTreeCanvas(ap); + + TreeLoader tl = new TreeLoader(null, null); + tl.start(); + + } + + /** + * Initialize a tree panel based on a loaded in tree file. + * + * @param ap + * @param loadedTree + * @param inputData + */ + void initTreePanel(AlignmentPanel ap, + NewickFile loadedTree, AlignmentView inputData) { + buildTreeCanvas(ap); - av = ap.av; - this.treeType = type; - this.scoreModelName = modelName; + TreeLoader tl = new TreeLoader(loadedTree, inputData); + tl.start(); + } + +public void buildTreeCanvas(AlignmentPanel ap) { + av = ap.av; treeCanvas = new TreeCanvas(this, ap, scrollPane); scrollPane.setViewportView(treeCanvas); + PaintRefresher.Register(this, ap.av.getSequenceSetId()); buildAssociatedViewMenu(); @@ -158,8 +187,8 @@ 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()); @@ -170,8 +199,8 @@ public class TreePanel extends GTreePanel } }); - TreeLoader tl = new TreeLoader(newTree, inputData); - tl.start(); + + } @@ -183,8 +212,8 @@ 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); @@ -193,7 +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); } @@ -242,56 +272,59 @@ public class TreePanel extends GTreePanel class TreeLoader extends Thread { - private NewickFile newtree; + private NewickFile newTree; private AlignmentView odata = null; public TreeLoader(NewickFile newickFile, AlignmentView inputData) { - this.newtree = newickFile; + this.newTree = newickFile; this.odata = inputData; - if (newickFile != null) + if (newTree != null) { // Must be outside run(), as Jalview2XML tries to // update distance/bootstrap visibility at the same time - showBootstrap(newickFile.HasBootstrap()); - showDistances(newickFile.HasDistances()); + showBootstrap(newTree.hasBootstrap()); + showDistances(newTree.hasDistances()); + } + } @Override public void run() { - if (newtree != null) + if (newTree != null) { tree = new TreeModel(av.getAlignment().getSequencesArray(), odata, - newtree); + newTree); if (tree.getOriginalData() == null) { originalSeqData.setVisible(false); } + + + } - else - { - ScoreModelI sm = configureScoreModel(); - TreeBuilder njtree = treeType.equals(TreeBuilder.NEIGHBOUR_JOINING) ? new NJTree( - av, sm, similarityParams) : new AverageDistanceTree(av, sm, - similarityParams); - tree = new TreeModel(njtree); - showDistances(true); - } + showTree(tree); + } + + public void showTree(TreeModel tree) + { tree.reCount(tree.getTopNode()); tree.findHeight(tree.getTopNode()); treeCanvas.setTree(tree); treeCanvas.repaint(); + av.setCurrentTree(tree); if (av.getSortByTree()) { sortByTree_actionPerformed(); } + } } @@ -362,8 +395,8 @@ 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); @@ -371,15 +404,15 @@ 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); @@ -410,8 +443,8 @@ public class TreePanel extends GTreePanel 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 @@ -431,16 +464,16 @@ public class TreePanel extends GTreePanel { } - Object[] alAndColsel = originalData - .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); @@ -449,9 +482,8 @@ 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!!<<< @@ -461,8 +493,8 @@ 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); } } @@ -487,14 +519,14 @@ public class TreePanel extends GTreePanel * @param e */ @Override - public void sortByTree_actionPerformed() + public void sortByTree_actionPerformed()// modify for Aptx { if (treeCanvas.applyToAllViews) { - final ArrayList commands = new ArrayList(); - for (AlignmentPanel ap : PaintRefresher.getAssociatedPanels(av - .getSequenceSetId())) + final ArrayList commands = new ArrayList<>(); + for (AlignmentPanel ap : PaintRefresher + .getAssociatedPanels(av.getSequenceSetId())) { commands.add(sortAlignmentIn(ap.av.getAlignPanel())); } @@ -532,8 +564,8 @@ 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(); @@ -549,13 +581,14 @@ public class TreePanel extends GTreePanel public CommandI sortAlignmentIn(AlignmentPanel ap) { + // 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, viewport.getAlignment()); - ap.paintAlignment(true); + ap.paintAlignment(true, false); return undo; } @@ -668,8 +701,8 @@ 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); @@ -679,11 +712,13 @@ 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); @@ -715,8 +750,8 @@ 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); @@ -726,10 +761,11 @@ 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); @@ -770,9 +806,9 @@ 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++) @@ -789,19 +825,17 @@ 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(); } } } @@ -823,43 +857,34 @@ public class TreePanel extends GTreePanel * Neighbour Joining Using BLOSUM62 *

* For a tree loaded from file, just uses the file name + * * @return */ - public String getPanelTitle() + public String getPanelTitle() // to be moved/fixed { 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; - } - - /** - * Instantiate an instance of the score model, configured for the current view - * if applicable - * - * @return - */ - protected ScoreModelI configureScoreModel() - { - return ScoreModels.getInstance().getScoreModel(scoreModelName, - treeCanvas.ap); + else + { + /* + * 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 = substitutionMatrix; + + /* + * put them together as Using + */ + final String ttl = MessageManager + .formatMessage("label.treecalc_title", treecalcnm, smn); + return ttl; + } } }