X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FTreePanel.java;h=0df1585dc6430dbdd62c7f704f3f2404dde96a1c;hb=7deae742715932ec04121b96a7cac76d0fd31bdc;hp=7f855941dcdf473e87494966fd05761506203ac3;hpb=cb5d856b1304448cae13a333cbd9017f81520d90;p=jalview.git
diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index 7f85594..0df1585 100755
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.java
@@ -1,43 +1,66 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * 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 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!
@@ -116,7 +139,7 @@ public class TreePanel extends GTreePanel
return treeCanvas.av.getAlignment();
}
- public AlignViewport getViewPort()
+ public AlignmentViewport getViewPort()
{
return treeCanvas.av;
}
@@ -138,6 +161,7 @@ public class TreePanel extends GTreePanel
av.addPropertyChangeListener(new java.beans.PropertyChangeListener()
{
+ @Override
public void propertyChange(PropertyChangeEvent evt)
{
if (evt.getPropertyName().equals("alignment"))
@@ -173,6 +197,7 @@ public class TreePanel extends GTreePanel
}
+ @Override
public void viewMenu_menuSelected()
{
buildAssociatedViewMenu();
@@ -208,6 +233,7 @@ public class TreePanel extends GTreePanel
buttonGroup.add(item);
item.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent evt)
{
treeCanvas.applyToAllViews = false;
@@ -220,11 +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();
@@ -252,6 +280,7 @@ public class TreePanel extends GTreePanel
}
}
+ @Override
public void run()
{
@@ -291,8 +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);
}
@@ -303,7 +350,7 @@ public class TreePanel extends GTreePanel
av.setCurrentTree(tree);
if (av.getSortByTree())
{
- sortByTree_actionPerformed(null);
+ sortByTree_actionPerformed();
}
}
}
@@ -347,6 +394,7 @@ public class TreePanel extends GTreePanel
* @param e
* DOCUMENT ME!
*/
+ @Override
public void textbox_actionPerformed(ActionEvent e)
{
CutAndPasteTransfer cap = new CutAndPasteTransfer();
@@ -392,12 +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);
@@ -431,12 +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())
@@ -468,8 +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)
{
@@ -490,8 +542,10 @@ public class TreePanel extends GTreePanel
// af.addSortByOrderMenuItem(ServiceName + " Ordering",
// msaorder);
- Desktop.addInternalFrame(af, MessageManager.formatMessage("label.original_data_for_params", new String[]{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);
}
}
}
@@ -502,6 +556,7 @@ public class TreePanel extends GTreePanel
* @param e
* DOCUMENT ME!
*/
+ @Override
public void fitToWindow_actionPerformed(ActionEvent e)
{
treeCanvas.fitToWindow = fitToWindow.isSelected();
@@ -513,7 +568,8 @@ public class TreePanel extends GTreePanel
*
* @param e
*/
- public void sortByTree_actionPerformed(ActionEvent e)
+ @Override
+ public void sortByTree_actionPerformed()
{
if (treeCanvas.applyToAllViews)
@@ -575,7 +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;
@@ -591,6 +647,7 @@ public class TreePanel extends GTreePanel
* @param e
* DOCUMENT ME!
*/
+ @Override
public void font_actionPerformed(ActionEvent e)
{
if (treeCanvas == null)
@@ -620,6 +677,7 @@ public class TreePanel extends GTreePanel
* @param e
* DOCUMENT ME!
*/
+ @Override
public void distanceMenu_actionPerformed(ActionEvent e)
{
treeCanvas.setShowDistances(distanceMenu.isSelected());
@@ -631,6 +689,7 @@ public class TreePanel extends GTreePanel
* @param e
* DOCUMENT ME!
*/
+ @Override
public void bootstrapMenu_actionPerformed(ActionEvent e)
{
treeCanvas.setShowBootstrap(bootstrapMenu.isSelected());
@@ -642,6 +701,7 @@ public class TreePanel extends GTreePanel
* @param e
* DOCUMENT ME!
*/
+ @Override
public void placeholdersMenu_actionPerformed(ActionEvent e)
{
treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());
@@ -653,6 +713,7 @@ public class TreePanel extends GTreePanel
* @param e
* DOCUMENT ME!
*/
+ @Override
public void epsTree_actionPerformed(ActionEvent e)
{
boolean accurateText = true;
@@ -688,10 +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);
@@ -725,6 +787,7 @@ public class TreePanel extends GTreePanel
* @param e
* DOCUMENT ME!
*/
+ @Override
public void pngTree_actionPerformed(ActionEvent e)
{
int width = treeCanvas.getWidth();
@@ -734,11 +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);
@@ -780,6 +844,7 @@ public class TreePanel extends GTreePanel
tree.applyToNodes(new NodeTransformI()
{
+ @Override
public void transform(BinaryNode node)
{
if (node instanceof SequenceNode
@@ -792,8 +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++)