X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FTreePanel.java;h=fafa61036f74be639d6fc533f831997cd432158a;hb=d2299844ae932a515a5007f30caf766a2c83ad97;hp=cf4960838e316f6df59d57b39a69b3bb43acdd03;hpb=7ab5d6b0ba5fec1ea4a4239e79c476d841622485;p=jalview.git diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java index cf49608..fafa610 100755 --- a/src/jalview/gui/TreePanel.java +++ b/src/jalview/gui/TreePanel.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) - * Copyright (C) 2014 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -20,26 +20,47 @@ */ package jalview.gui; -import java.beans.*; -import java.io.*; -import java.util.*; -import java.util.List; - -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! @@ -118,7 +139,7 @@ public class TreePanel extends GTreePanel return treeCanvas.av.getAlignment(); } - public AlignViewport getViewPort() + public AlignmentViewport getViewPort() { return treeCanvas.av; } @@ -140,6 +161,7 @@ public class TreePanel extends GTreePanel av.addPropertyChangeListener(new java.beans.PropertyChangeListener() { + @Override public void propertyChange(PropertyChangeEvent evt) { if (evt.getPropertyName().equals("alignment")) @@ -175,6 +197,7 @@ public class TreePanel extends GTreePanel } + @Override public void viewMenu_menuSelected() { buildAssociatedViewMenu(); @@ -210,6 +233,7 @@ public class TreePanel extends GTreePanel buttonGroup.add(item); item.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent evt) { treeCanvas.applyToAllViews = false; @@ -222,11 +246,13 @@ 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(); @@ -254,6 +280,7 @@ public class TreePanel extends GTreePanel } } + @Override public void run() { @@ -293,8 +320,26 @@ 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); } @@ -305,7 +350,7 @@ public class TreePanel extends GTreePanel av.setCurrentTree(tree); if (av.getSortByTree()) { - sortByTree_actionPerformed(null); + sortByTree_actionPerformed(); } } } @@ -349,6 +394,7 @@ public class TreePanel extends GTreePanel * @param e * DOCUMENT ME! */ + @Override public void textbox_actionPerformed(ActionEvent e) { CutAndPasteTransfer cap = new CutAndPasteTransfer(); @@ -394,12 +440,14 @@ 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")); chooser.setFileView(new JalviewFileView()); - chooser.setDialogTitle("Save tree as newick file"); + chooser.setDialogTitle(MessageManager + .getString("label.save_tree_as_newick")); chooser.setToolTipText(MessageManager.getString("action.save")); int value = chooser.showSaveDialog(null); @@ -433,12 +481,14 @@ 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()) @@ -470,8 +520,8 @@ 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) { @@ -493,8 +543,8 @@ public class TreePanel extends GTreePanel // msaorder); Desktop.addInternalFrame(af, MessageManager.formatMessage( - "label.original_data_for_params", new String[] - { this.title }), AlignFrame.DEFAULT_WIDTH, + "label.original_data_for_params", + new Object[] { this.title }), AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); } } @@ -506,6 +556,7 @@ public class TreePanel extends GTreePanel * @param e * DOCUMENT ME! */ + @Override public void fitToWindow_actionPerformed(ActionEvent e) { treeCanvas.fitToWindow = fitToWindow.isSelected(); @@ -517,7 +568,8 @@ public class TreePanel extends GTreePanel * * @param e */ - public void sortByTree_actionPerformed(ActionEvent e) + @Override + public void sortByTree_actionPerformed() { if (treeCanvas.applyToAllViews) @@ -579,7 +631,7 @@ 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; @@ -595,6 +647,7 @@ public class TreePanel extends GTreePanel * @param e * DOCUMENT ME! */ + @Override public void font_actionPerformed(ActionEvent e) { if (treeCanvas == null) @@ -624,6 +677,7 @@ public class TreePanel extends GTreePanel * @param e * DOCUMENT ME! */ + @Override public void distanceMenu_actionPerformed(ActionEvent e) { treeCanvas.setShowDistances(distanceMenu.isSelected()); @@ -635,6 +689,7 @@ public class TreePanel extends GTreePanel * @param e * DOCUMENT ME! */ + @Override public void bootstrapMenu_actionPerformed(ActionEvent e) { treeCanvas.setShowBootstrap(bootstrapMenu.isSelected()); @@ -646,6 +701,7 @@ public class TreePanel extends GTreePanel * @param e * DOCUMENT ME! */ + @Override public void placeholdersMenu_actionPerformed(ActionEvent e) { treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected()); @@ -657,6 +713,7 @@ public class TreePanel extends GTreePanel * @param e * DOCUMENT ME! */ + @Override public void epsTree_actionPerformed(ActionEvent e) { boolean accurateText = true; @@ -692,10 +749,11 @@ 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.setDialogTitle(MessageManager + .getString("label.create_eps_from_tree")); chooser.setToolTipText(MessageManager.getString("action.save")); int value = chooser.showSaveDialog(this); @@ -729,6 +787,7 @@ public class TreePanel extends GTreePanel * @param e * DOCUMENT ME! */ + @Override public void pngTree_actionPerformed(ActionEvent e) { int width = treeCanvas.getWidth(); @@ -738,11 +797,12 @@ 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.setDialogTitle(MessageManager + .getString("label.create_png_from_tree")); chooser.setToolTipText(MessageManager.getString("action.save")); int value = chooser.showSaveDialog(this); @@ -784,6 +844,7 @@ public class TreePanel extends GTreePanel tree.applyToNodes(new NodeTransformI() { + @Override public void transform(BinaryNode node) { if (node instanceof SequenceNode @@ -796,8 +857,8 @@ public class TreePanel extends GTreePanel { // search dbrefs, features and annotation DBRefEntry[] refs = jalview.util.DBRefUtils.selectRefs( - sq.getDBRef(), new String[] - { labelClass.toUpperCase() }); + sq.getDBRefs(), + new String[] { labelClass.toUpperCase() }); if (refs != null) { for (int i = 0; i < refs.length; i++)