X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FTreePanel.java;h=44f9feffa638f11dc82a40649526cd6a144e0f76;hb=838e4f91d4a53dd315640dbc9ff6ef7a815ee576;hp=cc63ee43334916f5a806c0b19b03e9b3e358afc5;hpb=1b85d0acd9a09b646ac2dd6f1ea6db5db6f3731d;p=jalview.git diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java index cc63ee4..44f9fef 100755 --- a/src/jalview/gui/TreePanel.java +++ b/src/jalview/gui/TreePanel.java @@ -1,38 +1,66 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1) + * Copyright (C) 2015 The Jalview Authors * * This file is part of Jalview. * * 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. - * + * 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 Jalview. If not, see . + * You should have received a copy of the GNU General Public License + * 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.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.schemes.ResidueProperties; +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! @@ -111,7 +139,7 @@ public class TreePanel extends GTreePanel return treeCanvas.av.getAlignment(); } - public AlignViewport getViewPort() + public AlignmentViewport getViewPort() { return treeCanvas.av; } @@ -151,7 +179,7 @@ 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(); @@ -215,7 +243,8 @@ 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() @@ -254,11 +283,11 @@ 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()) @@ -270,22 +299,42 @@ 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 = ResidueProperties.getScoreModel(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); } @@ -296,7 +345,7 @@ public class TreePanel extends GTreePanel av.setCurrentTree(tree); if (av.getSortByTree()) { - sortByTree_actionPerformed(null); + sortByTree_actionPerformed(); } } } @@ -364,16 +413,16 @@ public class TreePanel extends GTreePanel buffer.append("PID"); } - - jalview.io.NewickFile fout = new jalview.io.NewickFile(tree - .getTopNode()); - try { + jalview.io.NewickFile fout = new jalview.io.NewickFile( + tree.getTopNode()); + try + { cap.setText(fout.print(tree.isHasBootstrap(), tree.isHasDistances(), - tree.isHasRootDistance())); + tree.isHasRootDistance())); Desktop.addInternalFrame(cap, buffer.toString(), 500, 100); } catch (OutOfMemoryError oom) { - new OOMWarning("generating newick tree file",oom); + new OOMWarning("generating newick tree file", oom); cap.dispose(); } @@ -387,11 +436,12 @@ 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"); + chooser.setDialogTitle(MessageManager + .getString("label.save_tree_as_newick")); + chooser.setToolTipText(MessageManager.getString("action.save")); int value = chooser.showSaveDialog(null); @@ -403,10 +453,10 @@ 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); @@ -483,8 +533,10 @@ 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); } } } @@ -506,17 +558,77 @@ public class TreePanel extends GTreePanel * * @param e */ - public void sortByTree_actionPerformed(ActionEvent e) + @Override + public void sortByTree_actionPerformed() { - AlignmentPanel ap = av.getAlignPanel(); + + 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) + { + 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; } /** @@ -622,11 +734,12 @@ public class TreePanel extends GTreePanel { jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser( jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[] - { "eps" }, new String[] - { "Encapsulated Postscript" }, "Encapsulated Postscript"); + { "eps" }, new String[] { "Encapsulated Postscript" }, + "Encapsulated Postscript"); chooser.setFileView(new jalview.io.JalviewFileView()); - chooser.setDialogTitle("Create EPS file from tree"); - chooser.setToolTipText("Save"); + chooser.setDialogTitle(MessageManager + .getString("label.create_eps_from_tree")); + chooser.setToolTipText(MessageManager.getString("action.save")); int value = chooser.showSaveDialog(this); @@ -668,12 +781,13 @@ public class TreePanel extends GTreePanel { 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"); + { "png" }, new String[] { "Portable network graphics" }, + "Portable network graphics"); 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); @@ -725,9 +839,9 @@ public class TreePanel extends GTreePanel if (sq != null) { // search dbrefs, features and annotation - DBRefEntry[] refs = jalview.util.DBRefUtils.selectRefs(sq - .getDBRef(), new String[] - { labelClass.toUpperCase() }); + DBRefEntry[] refs = jalview.util.DBRefUtils.selectRefs( + sq.getDBRef(), + new String[] { labelClass.toUpperCase() }); if (refs != null) { for (int i = 0; i < refs.length; i++)