X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FTreePanel.java;h=7df1f71d678e42d7c6e65ed389ad3d0aa69daf46;hb=18fb9dd58b1f0c4277b269c5e8bc2d3ed98394a5;hp=646cbb4bd8c0865e4de845e5d90b758a2da82c85;hpb=eb53458ceff17b79d613ec208b5185f541eb6320;p=jalview.git diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java index 646cbb4..7df1f71 100755 --- a/src/jalview/gui/TreePanel.java +++ b/src/jalview/gui/TreePanel.java @@ -1,39 +1,67 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) - * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * - * 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. + * + * 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 this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.gui; -import java.beans.*; -import java.io.*; -import java.util.*; -import javax.imageio.*; - -import java.awt.*; -import java.awt.event.*; -import java.awt.image.*; -import javax.swing.*; - -import org.jibble.epsgraphics.*; -import jalview.analysis.*; +import jalview.analysis.AlignmentSorter; +import jalview.analysis.NJTree; +import jalview.analysis.scoremodels.ScoreModels; +import jalview.api.analysis.ScoreModelI; +import jalview.api.analysis.ViewBasedAnalysisI; +import jalview.bin.Cache; +import jalview.commands.CommandI; import jalview.commands.OrderCommand; -import jalview.datamodel.*; -import jalview.io.*; -import jalview.jbgui.*; +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.NodeTransformI; +import jalview.datamodel.SequenceFeature; +import jalview.datamodel.SequenceI; +import jalview.datamodel.SequenceNode; +import jalview.io.JalviewFileChooser; +import jalview.io.JalviewFileView; +import jalview.io.NewickFile; +import jalview.jbgui.GTreePanel; +import jalview.util.ImageMaker; +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.awt.image.BufferedImage; +import java.beans.PropertyChangeEvent; +import java.io.FileOutputStream; +import java.util.ArrayList; +import java.util.List; + +import javax.imageio.ImageIO; +import javax.swing.ButtonGroup; +import javax.swing.JMenuItem; +import javax.swing.JRadioButtonMenuItem; + +import org.jibble.epsgraphics.EpsGraphics2D; /** * DOCUMENT ME! @@ -79,27 +107,6 @@ public class TreePanel extends GTreePanel // 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) { @@ -112,7 +119,7 @@ public class TreePanel extends GTreePanel return treeCanvas.av.getAlignment(); } - public AlignViewport getViewPort() + public AlignmentViewport getViewPort() { return treeCanvas.av; } @@ -134,6 +141,7 @@ public class TreePanel extends GTreePanel av.addPropertyChangeListener(new java.beans.PropertyChangeListener() { + @Override public void propertyChange(PropertyChangeEvent evt) { if (evt.getPropertyName().equals("alignment")) @@ -141,7 +149,9 @@ 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. + // 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) @@ -150,7 +160,7 @@ public class TreePanel extends GTreePanel .println("new alignment sequences vector value is null"); } - tree.UpdatePlaceHolders((Vector) evt.getNewValue()); + tree.UpdatePlaceHolders((List) evt.getNewValue()); treeCanvas.nameHash.clear(); // reset the mapping between canvas // rectangles and leafnodes repaint(); @@ -167,6 +177,7 @@ public class TreePanel extends GTreePanel } + @Override public void viewMenu_menuSelected() { buildAssociatedViewMenu(); @@ -202,6 +213,7 @@ public class TreePanel extends GTreePanel buttonGroup.add(item); item.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent evt) { treeCanvas.applyToAllViews = false; @@ -214,11 +226,13 @@ public class TreePanel extends GTreePanel associateLeavesMenu.add(item); } - final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem("All Views"); + final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem( + MessageManager.getString("label.all_views")); buttonGroup.add(itemf); itemf.setSelected(treeCanvas.applyToAllViews); itemf.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent evt) { treeCanvas.applyToAllViews = itemf.isSelected(); @@ -246,6 +260,7 @@ public class TreePanel extends GTreePanel } } + @Override public void run() { @@ -253,11 +268,11 @@ public class TreePanel extends GTreePanel { if (odata == null) { - tree = new NJTree(av.alignment.getSequencesArray(), newtree); + tree = new NJTree(av.getAlignment().getSequencesArray(), newtree); } else { - tree = new NJTree(av.alignment.getSequencesArray(), odata, + tree = new NJTree(av.getAlignment().getSequencesArray(), odata, newtree); } if (!tree.hasOriginalSequenceData()) @@ -269,22 +284,42 @@ public class TreePanel extends GTreePanel { int start, end; SequenceI[] seqs; - AlignmentView seqStrings = av.getAlignmentView(av - .getSelectionGroup() != null); - if (av.getSelectionGroup() == null) + boolean selview = av.getSelectionGroup() != null + && av.getSelectionGroup().getSize() > 1; + AlignmentView seqStrings = av.getAlignmentView(selview); + if (!selview) { start = 0; - end = av.alignment.getWidth(); - seqs = av.alignment.getSequencesArray(); + end = av.getAlignment().getWidth(); + seqs = av.getAlignment().getSequencesArray(); } else { start = av.getSelectionGroup().getStartRes(); end = av.getSelectionGroup().getEndRes() + 1; - seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment); + 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); } - - tree = new NJTree(seqs, seqStrings, type, pwtype, start, end); showDistances(true); } @@ -295,7 +330,7 @@ public class TreePanel extends GTreePanel av.setCurrentTree(tree); if (av.getSortByTree()) { - sortByTree_actionPerformed(null); + sortByTree_actionPerformed(); } } } @@ -339,36 +374,25 @@ public class TreePanel extends GTreePanel * @param e * DOCUMENT ME! */ + @Override public void textbox_actionPerformed(ActionEvent e) { CutAndPasteTransfer cap = new CutAndPasteTransfer(); - StringBuffer buffer = new StringBuffer(); + String newTitle = getPanelTitle(type, pwtype); - if (type.equals("AV")) + NewickFile fout = new NewickFile(tree.getTopNode()); + try { - buffer.append("Average distance tree using "); - } - else + cap.setText(fout.print(tree.isHasBootstrap(), tree.isHasDistances(), + tree.isHasRootDistance())); + Desktop.addInternalFrame(cap, newTitle, 500, 100); + } catch (OutOfMemoryError oom) { - buffer.append("Neighbour joining tree using "); + new OOMWarning("generating newick tree file", oom); + cap.dispose(); } - if (pwtype.equals("BL")) - { - buffer.append("BLOSUM62"); - } - else - { - buffer.append("PID"); - } - - Desktop.addInternalFrame(cap, buffer.toString(), 500, 100); - - jalview.io.NewickFile fout = new jalview.io.NewickFile(tree - .getTopNode()); - cap.setText(fout.print(tree.isHasBootstrap(), tree.isHasDistances(), - tree.isHasRootDistance())); } /** @@ -377,13 +401,15 @@ public class TreePanel extends GTreePanel * @param e * DOCUMENT ME! */ + @Override 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"); + chooser.setDialogTitle(MessageManager + .getString("label.save_tree_as_newick")); + chooser.setToolTipText(MessageManager.getString("action.save")); int value = chooser.showSaveDialog(null); @@ -395,10 +421,10 @@ 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); @@ -416,12 +442,14 @@ public class TreePanel extends GTreePanel * @param e * DOCUMENT ME! */ + @Override public void printMenu_actionPerformed(ActionEvent e) { // Putting in a thread avoids Swing painting problems treeCanvas.startPrinting(); } + @Override public void originalSeqData_actionPerformed(ActionEvent e) { if (!tree.hasOriginalSequenceData()) @@ -453,8 +481,8 @@ public class TreePanel extends GTreePanel { // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]); - Alignment al = new Alignment((SequenceI[]) alAndColsel[0]); - Alignment dataset = (av != null && av.getAlignment() != null) ? av + AlignmentI al = new Alignment((SequenceI[]) alAndColsel[0]); + AlignmentI dataset = (av != null && av.getAlignment() != null) ? av .getAlignment().getDataset() : null; if (dataset != null) { @@ -475,8 +503,10 @@ public class TreePanel extends GTreePanel // af.addSortByOrderMenuItem(ServiceName + " Ordering", // msaorder); - Desktop.addInternalFrame(af, "Original Data for " + this.title, - AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); + Desktop.addInternalFrame(af, MessageManager.formatMessage( + "label.original_data_for_params", + new Object[] { this.title }), AlignFrame.DEFAULT_WIDTH, + AlignFrame.DEFAULT_HEIGHT); } } } @@ -487,6 +517,7 @@ public class TreePanel extends GTreePanel * @param e * DOCUMENT ME! */ + @Override public void fitToWindow_actionPerformed(ActionEvent e) { treeCanvas.fitToWindow = fitToWindow.isSelected(); @@ -495,20 +526,80 @@ public class TreePanel extends GTreePanel /** * sort the associated alignment view by the current tree. + * * @param e */ - public void sortByTree_actionPerformed(ActionEvent e) + @Override + public void sortByTree_actionPerformed() + { + + 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) + { + + 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) { - AlignmentPanel ap = av.getAlignPanel(); + AlignmentViewport av = ap.av; SequenceI[] oldOrder = av.getAlignment().getSequencesArray(); AlignmentSorter.sortByTree(av.getAlignment(), tree); - - ap.alignFrame - .addHistoryItem(new OrderCommand("Tree Sort", oldOrder, - av.alignment)); + CommandI undo; + undo = new OrderCommand("Tree Sort", oldOrder, av.getAlignment()); ap.paintAlignment(true); - + return undo; } /** @@ -517,6 +608,7 @@ public class TreePanel extends GTreePanel * @param e * DOCUMENT ME! */ + @Override public void font_actionPerformed(ActionEvent e) { if (treeCanvas == null) @@ -546,6 +638,7 @@ public class TreePanel extends GTreePanel * @param e * DOCUMENT ME! */ + @Override public void distanceMenu_actionPerformed(ActionEvent e) { treeCanvas.setShowDistances(distanceMenu.isSelected()); @@ -557,6 +650,7 @@ public class TreePanel extends GTreePanel * @param e * DOCUMENT ME! */ + @Override public void bootstrapMenu_actionPerformed(ActionEvent e) { treeCanvas.setShowBootstrap(bootstrapMenu.isSelected()); @@ -568,6 +662,7 @@ public class TreePanel extends GTreePanel * @param e * DOCUMENT ME! */ + @Override public void placeholdersMenu_actionPerformed(ActionEvent e) { treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected()); @@ -579,6 +674,7 @@ public class TreePanel extends GTreePanel * @param e * DOCUMENT ME! */ + @Override public void epsTree_actionPerformed(ActionEvent e) { boolean accurateText = true; @@ -612,23 +708,22 @@ public class TreePanel extends GTreePanel try { - jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser( - jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[] - { "eps" }, new String[] - { "Encapsulated Postscript" }, "Encapsulated Postscript"); - chooser.setFileView(new jalview.io.JalviewFileView()); - chooser.setDialogTitle("Create EPS file from tree"); - chooser.setToolTipText("Save"); + JalviewFileChooser chooser = new JalviewFileChooser( + ImageMaker.EPS_EXTENSION, ImageMaker.EPS_EXTENSION); + chooser.setFileView(new JalviewFileView()); + chooser.setDialogTitle(MessageManager + .getString("label.create_eps_from_tree")); + chooser.setToolTipText(MessageManager.getString("action.save")); int value = chooser.showSaveDialog(this); - if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION) + if (value != JalviewFileChooser.APPROVE_OPTION) { return; } - jalview.bin.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); @@ -651,6 +746,7 @@ public class TreePanel extends GTreePanel * @param e * DOCUMENT ME! */ + @Override public void pngTree_actionPerformed(ActionEvent e) { int width = treeCanvas.getWidth(); @@ -658,14 +754,13 @@ public class TreePanel extends GTreePanel try { - jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser( - jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[] - { "png" }, new String[] - { "Portable network graphics" }, "Portable network graphics"); + JalviewFileChooser chooser = new JalviewFileChooser( + ImageMaker.PNG_EXTENSION, ImageMaker.PNG_DESCRIPTION); chooser.setFileView(new jalview.io.JalviewFileView()); - chooser.setDialogTitle("Create PNG image from tree"); - chooser.setToolTipText("Save"); + chooser.setDialogTitle(MessageManager + .getString("label.create_png_from_tree")); + chooser.setToolTipText(MessageManager.getString("action.save")); int value = chooser.showSaveDialog(this); @@ -692,55 +787,69 @@ 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)}; + * 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() { + tree.applyToNodes(new NodeTransformI() + { + @Override public void transform(BinaryNode node) { - if (node instanceof SequenceNode && !((SequenceNode) node).isPlaceholder() && !((SequenceNode) node).isDummy()) + if (node instanceof SequenceNode + && !((SequenceNode) node).isPlaceholder() + && !((SequenceNode) node).isDummy()) { - String newname=null; + String newname = null; SequenceI sq = (SequenceI) ((SequenceNode) node).element(); - if (sq!=null) + if (sq != null) { // search dbrefs, features and annotation - DBRefEntry[] refs = jalview.util.DBRefUtils.selectRefs(sq.getDBRef(), new String[] {labelClass.toUpperCase()}); - if (refs!=null) + DBRefEntry[] refs = jalview.util.DBRefUtils.selectRefs( + sq.getDBRefs(), + new String[] { labelClass.toUpperCase() }); + if (refs != null) { - for (int i=0; i + * Neighbour Joining Using BLOSUM62 + *

+ * 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) + { + if (NJTree.FROM_FILE.equals(treeType)) + { + return modelOrFileName; + } + + /* + * i18n description of Neighbour Joining or Average Distance method + */ + String treecalcnm = MessageManager.getString("label.tree_calc_" + + treeType.toLowerCase()); + + /* + * i18n description (if any) of score model used + */ + String smn = MessageManager.getStringOrReturn("label.score_model_", + modelOrFileName); + + /* + * put them together as Using + */ + final String ttl = MessageManager.formatMessage("label.treecalc_title", + treecalcnm, smn); + return ttl; + } }