X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FTreePanel.java;h=7177e43bfed2c9a5ab4540478f977478dab615e3;hb=be32c14cd8e48fe0a207cd7030cb9cd46f894678;hp=161937e2c4dec85eb350b397c9be0446cdbffc13;hpb=b57a02c25e335d033c97f8a6bacd6b54f62bd2b6;p=jalview.git diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java index 161937e..7177e43 100755 --- a/src/jalview/gui/TreePanel.java +++ b/src/jalview/gui/TreePanel.java @@ -1,41 +1,66 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) - * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ 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 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.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.*; - -import java.awt.*; -import java.awt.event.*; -import java.awt.image.*; -import javax.swing.*; +import javax.imageio.ImageIO; +import javax.swing.ButtonGroup; +import javax.swing.JMenuItem; +import javax.swing.JRadioButtonMenuItem; -import org.jibble.epsgraphics.*; -import jalview.analysis.*; -import jalview.commands.CommandI; -import jalview.commands.OrderCommand; -import jalview.datamodel.*; -import jalview.io.*; -import jalview.jbgui.*; +import org.jibble.epsgraphics.EpsGraphics2D; /** * DOCUMENT ME! @@ -114,7 +139,7 @@ public class TreePanel extends GTreePanel return treeCanvas.av.getAlignment(); } - public AlignViewport getViewPort() + public AlignmentViewport getViewPort() { return treeCanvas.av; } @@ -218,7 +243,8 @@ public class TreePanel extends GTreePanel associateLeavesMenu.add(item); } - final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem("All Views"); + final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem( + "label.all_views"); buttonGroup.add(itemf); itemf.setSelected(treeCanvas.applyToAllViews); itemf.addActionListener(new ActionListener() @@ -289,8 +315,26 @@ public class TreePanel extends GTreePanel seqs = av.getSelectionGroup().getSequencesInOrder( av.getAlignment()); } - - tree = new NJTree(seqs, seqStrings, type, pwtype, start, end); + 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); + } showDistances(true); } @@ -301,7 +345,7 @@ public class TreePanel extends GTreePanel av.setCurrentTree(tree); if (av.getSortByTree()) { - sortByTree_actionPerformed(null); + sortByTree_actionPerformed(); } } } @@ -395,8 +439,8 @@ public class TreePanel extends GTreePanel 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); @@ -488,8 +532,10 @@ 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); } } } @@ -511,7 +557,8 @@ public class TreePanel extends GTreePanel * * @param e */ - public void sortByTree_actionPerformed(ActionEvent e) + @Override + public void sortByTree_actionPerformed() { if (treeCanvas.applyToAllViews) @@ -573,7 +620,7 @@ public class TreePanel extends GTreePanel public CommandI sortAlignmentIn(AlignmentPanel ap) { - AlignViewport av = ap.av; + AlignmentViewport av = ap.av; SequenceI[] oldOrder = av.getAlignment().getSequencesArray(); AlignmentSorter.sortByTree(av.getAlignment(), tree); CommandI undo; @@ -689,8 +736,8 @@ public class TreePanel extends GTreePanel { "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); @@ -736,8 +783,8 @@ public class TreePanel extends GTreePanel { "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);