X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FTreePanel.java;h=923d702d448f434c6b32df0d772f423236d7a0d1;hb=93d1682e83a5069aea9c1797ad8d8c2c1407b92f;hp=d8253db879df6c4548097bf52eade01af91bee94;hpb=a45774ee31d9f35d4eff46d54d7deab719afb092;p=jalview.git
diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index d8253db..923d702 100755
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.java
@@ -1,25 +1,28 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
+ * Copyright (C) 2014 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.
- *
+ *
* 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 .
+ * 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.*;
@@ -34,6 +37,7 @@ import jalview.commands.OrderCommand;
import jalview.datamodel.*;
import jalview.io.*;
import jalview.jbgui.*;
+import jalview.util.MessageManager;
/**
* DOCUMENT ME!
@@ -152,7 +156,7 @@ 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();
@@ -255,11 +259,11 @@ 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())
@@ -271,19 +275,21 @@ 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());
}
tree = new NJTree(seqs, seqStrings, type, pwtype, start, end);
@@ -392,7 +398,7 @@ public class TreePanel extends GTreePanel
jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle("Save tree as newick file");
- chooser.setToolTipText("Save");
+ chooser.setToolTipText(MessageManager.getString("action.save"));
int value = chooser.showSaveDialog(null);
@@ -484,7 +490,7 @@ public class TreePanel extends GTreePanel
// af.addSortByOrderMenuItem(ServiceName + " Ordering",
// msaorder);
- Desktop.addInternalFrame(af, "Original Data for " + this.title,
+ Desktop.addInternalFrame(af, MessageManager.formatMessage("label.original_data_for_params", new String[]{this.title}),
AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
}
}
@@ -509,72 +515,76 @@ public class TreePanel extends GTreePanel
*/
public void sortByTree_actionPerformed(ActionEvent e)
{
-
+
if (treeCanvas.applyToAllViews)
{
final ArrayList commands = new ArrayList();
- for (AlignmentPanel ap: PaintRefresher.getAssociatedPanels(av
+ 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)
+ 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)
+ for (CommandI tsort : commands)
{
tsort.doCommand(views);
- }
+ }
}
});
- for (AlignmentPanel ap: PaintRefresher.getAssociatedPanels(av
+ 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));
+ }
+ else
+ {
+ treeCanvas.ap.alignFrame
+ .addHistoryItem(sortAlignmentIn(treeCanvas.ap));
}
}
+
public CommandI sortAlignmentIn(AlignmentPanel ap)
{
AlignViewport av = ap.av;
SequenceI[] oldOrder = av.getAlignment().getSequencesArray();
AlignmentSorter.sortByTree(av.getAlignment(), tree);
CommandI undo;
- undo=new OrderCommand("Tree Sort", oldOrder,
- av.alignment);
+ undo = new OrderCommand("Tree Sort", oldOrder, av.getAlignment());
- ap.paintAlignment(true);
+ ap.paintAlignment(true);
return undo;
}
+
/**
* DOCUMENT ME!
*
@@ -682,7 +692,7 @@ public class TreePanel extends GTreePanel
{ "Encapsulated Postscript" }, "Encapsulated Postscript");
chooser.setFileView(new jalview.io.JalviewFileView());
chooser.setDialogTitle("Create EPS file from tree");
- chooser.setToolTipText("Save");
+ chooser.setToolTipText(MessageManager.getString("action.save"));
int value = chooser.showSaveDialog(this);
@@ -729,7 +739,7 @@ public class TreePanel extends GTreePanel
chooser.setFileView(new jalview.io.JalviewFileView());
chooser.setDialogTitle("Create PNG image from tree");
- chooser.setToolTipText("Save");
+ chooser.setToolTipText(MessageManager.getString("action.save"));
int value = chooser.showSaveDialog(this);