X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FTreePanel.java;h=3b7cb1407a197080b60a794788dc2b5a93bc5add;hb=6403068c0c328cfb63af451f7fa1bd568fa0fdd3;hp=0c937dddc68958f2fd14d63dc0a9de94cbdecedd;hpb=40f08a931412edd1bc0e776033792fe3d4c0a5fa;p=jalview.git diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java index 0c937dd..3b7cb14 100755 --- a/src/jalview/gui/TreePanel.java +++ b/src/jalview/gui/TreePanel.java @@ -1,20 +1,19 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) + * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation; either version 2 - * of the License, or (at your option) any later version. + * This file is part of Jalview. * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. * - * You should have received a copy of the GNU General Public License - * along with this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * PURPOSE. See the GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License along with Jalview. If not, see . */ package jalview.gui; @@ -30,6 +29,7 @@ import javax.swing.*; import org.jibble.epsgraphics.*; import jalview.analysis.*; +import jalview.commands.CommandI; import jalview.commands.OrderCommand; import jalview.datamodel.*; import jalview.io.*; @@ -141,6 +141,10 @@ public class TreePanel extends GTreePanel if (tree == null) { System.out.println("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. + return; } if (evt.getNewValue() == null) { @@ -361,12 +365,19 @@ public class TreePanel extends GTreePanel buffer.append("PID"); } - Desktop.addInternalFrame(cap, buffer.toString(), 500, 100); + jalview.io.NewickFile fout = new jalview.io.NewickFile( + tree.getTopNode()); + try + { + cap.setText(fout.print(tree.isHasBootstrap(), tree.isHasDistances(), + tree.isHasRootDistance())); + Desktop.addInternalFrame(cap, buffer.toString(), 500, 100); + } catch (OutOfMemoryError oom) + { + new OOMWarning("generating newick tree file", oom); + cap.dispose(); + } - jalview.io.NewickFile fout = new jalview.io.NewickFile(tree - .getTopNode()); - cap.setText(fout.print(tree.isHasBootstrap(), tree.isHasDistances(), - tree.isHasRootDistance())); } /** @@ -377,8 +388,8 @@ public class TreePanel extends GTreePanel */ public void saveAsNewick_actionPerformed(ActionEvent e) { - JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache - .getProperty("LAST_DIRECTORY")); + JalviewFileChooser chooser = new JalviewFileChooser( + jalview.bin.Cache.getProperty("LAST_DIRECTORY")); chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Save tree as newick file"); chooser.setToolTipText("Save"); @@ -393,10 +404,10 @@ public class TreePanel extends GTreePanel try { - jalview.io.NewickFile fout = new jalview.io.NewickFile(tree - .getTopNode()); - String output = fout.print(tree.isHasBootstrap(), tree - .isHasDistances(), tree.isHasRootDistance()); + jalview.io.NewickFile fout = new jalview.io.NewickFile( + tree.getTopNode()); + String output = fout.print(tree.isHasBootstrap(), + tree.isHasDistances(), tree.isHasRootDistance()); java.io.PrintWriter out = new java.io.PrintWriter( new java.io.FileWriter(choice)); out.println(output); @@ -493,22 +504,77 @@ public class TreePanel extends GTreePanel /** * sort the associated alignment view by the current tree. + * * @param e */ public void sortByTree_actionPerformed(ActionEvent e) { - AlignmentPanel ap = av.getAlignPanel(); - SequenceI[] oldOrder = av.getAlignment().getSequencesArray(); - AlignmentSorter.sortByTree(av.getAlignment(), tree); - - ap.alignFrame - .addHistoryItem(new OrderCommand("Tree Sort", oldOrder, - av.alignment)); + + if (treeCanvas.applyToAllViews) + { + final ArrayList commands = new ArrayList(); + for (AlignmentPanel ap: PaintRefresher.getAssociatedPanels(av + .getSequenceSetId())) + { + commands.add(sortAlignmentIn(ap.av.getAlignPanel())); + } + av.getAlignPanel().alignFrame.addHistoryItem(new CommandI() + { + + @Override + public void undoCommand(AlignmentI[] views) + { + for (CommandI tsort:commands) + { + tsort.undoCommand(views); + } + } + + @Override + public int getSize() + { + return commands.size(); + } + + @Override + public String getDescription() + { + return "Tree Sort (many views)"; + } + + @Override + public void doCommand(AlignmentI[] views) + { - ap.paintAlignment(true); + for (CommandI tsort:commands) + { + tsort.doCommand(views); + } + } + }); + for (AlignmentPanel ap: PaintRefresher.getAssociatedPanels(av + .getSequenceSetId())) + { + // ensure all the alignFrames refresh their GI after adding an undo item + ap.alignFrame.updateEditMenuBar(); + } + } else { + treeCanvas.ap.alignFrame.addHistoryItem(sortAlignmentIn(treeCanvas.ap)); + } } + public CommandI sortAlignmentIn(AlignmentPanel ap) + { + AlignViewport av = ap.av; + SequenceI[] oldOrder = av.getAlignment().getSequencesArray(); + AlignmentSorter.sortByTree(av.getAlignment(), tree); + CommandI undo; + undo=new OrderCommand("Tree Sort", oldOrder, + av.alignment); + ap.paintAlignment(true); + return undo; + } /** * DOCUMENT ME! * @@ -690,4 +756,75 @@ public class TreePanel extends GTreePanel ex.printStackTrace(); } } + + /** + * change node labels to the annotation referred to by labelClass TODO: + * promote to a datamodel modification that can be undone TODO: make argument + * one case of a generic transformation function ie { undoStep = apply(Tree, + * TransformFunction)}; + * + * @param labelClass + */ + public void changeNames(final String labelClass) + { + tree.applyToNodes(new NodeTransformI() + { + + public void transform(BinaryNode node) + { + if (node instanceof SequenceNode + && !((SequenceNode) node).isPlaceholder() + && !((SequenceNode) node).isDummy()) + { + String newname = null; + SequenceI sq = (SequenceI) ((SequenceNode) node).element(); + if (sq != null) + { + // search dbrefs, features and annotation + DBRefEntry[] refs = jalview.util.DBRefUtils.selectRefs( + sq.getDBRef(), new String[] + { labelClass.toUpperCase() }); + if (refs != null) + { + for (int i = 0; i < refs.length; i++) + { + if (newname == null) + { + newname = new String(refs[i].getAccessionId()); + } + else + { + newname = newname + "; " + refs[i].getAccessionId(); + } + } + } + if (newname == null) + { + SequenceFeature sf[] = sq.getSequenceFeatures(); + for (int i = 0; sf != null && i < sf.length; i++) + { + if (sf[i].getType().equals(labelClass)) + { + if (newname == null) + { + newname = new String(sf[i].getDescription()); + } + else + { + newname = newname + "; " + sf[i].getDescription(); + } + } + } + } + } + if (newname != null) + { + String oldname = ((SequenceNode) node).getName(); + // TODO : save in the undo object for this modification. + ((SequenceNode) node).setName(newname); + } + } + } + }); + } }