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JAL-1645 source formatting and organise imports
[jalview.git]
/
src
/
jalview
/
gui
/
TreePanel.java
diff --git
a/src/jalview/gui/TreePanel.java
b/src/jalview/gui/TreePanel.java
index
6ce68b3
..
d2c86c8
100755
(executable)
--- 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.
*
*
* This file is part of Jalview.
*
@@
-43,6
+43,7
@@
import jalview.io.NewickFile;
import jalview.jbgui.GTreePanel;
import jalview.schemes.ResidueProperties;
import jalview.util.MessageManager;
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.Font;
import java.awt.Graphics;
@@
-138,7
+139,7
@@
public class TreePanel extends GTreePanel
return treeCanvas.av.getAlignment();
}
return treeCanvas.av.getAlignment();
}
- public AlignViewport getViewPort()
+ public AlignmentViewport getViewPort()
{
return treeCanvas.av;
}
{
return treeCanvas.av;
}
@@
-242,7
+243,8
@@
public class TreePanel extends GTreePanel
associateLeavesMenu.add(item);
}
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()
buttonGroup.add(itemf);
itemf.setSelected(treeCanvas.applyToAllViews);
itemf.addActionListener(new ActionListener()
@@
-343,7
+345,7
@@
public class TreePanel extends GTreePanel
av.setCurrentTree(tree);
if (av.getSortByTree())
{
av.setCurrentTree(tree);
if (av.getSortByTree())
{
- sortByTree_actionPerformed(null);
+ sortByTree_actionPerformed();
}
}
}
}
}
}
@@
-437,7
+439,8
@@
public class TreePanel extends GTreePanel
JalviewFileChooser chooser = new JalviewFileChooser(
jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new JalviewFileView());
JalviewFileChooser chooser = new JalviewFileChooser(
jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle(MessageManager.getString("label.save_tree_as_newick"));
+ chooser.setDialogTitle(MessageManager
+ .getString("label.save_tree_as_newick"));
chooser.setToolTipText(MessageManager.getString("action.save"));
int value = chooser.showSaveDialog(null);
chooser.setToolTipText(MessageManager.getString("action.save"));
int value = chooser.showSaveDialog(null);
@@
-531,8
+534,8
@@
public class TreePanel extends GTreePanel
// msaorder);
Desktop.addInternalFrame(af, MessageManager.formatMessage(
// 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);
}
}
AlignFrame.DEFAULT_HEIGHT);
}
}
@@
-555,7
+558,8
@@
public class TreePanel extends GTreePanel
*
* @param e
*/
*
* @param e
*/
- public void sortByTree_actionPerformed(ActionEvent e)
+ @Override
+ public void sortByTree_actionPerformed()
{
if (treeCanvas.applyToAllViews)
{
if (treeCanvas.applyToAllViews)
@@
-617,7
+621,7
@@
public class TreePanel extends GTreePanel
public CommandI sortAlignmentIn(AlignmentPanel ap)
{
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;
SequenceI[] oldOrder = av.getAlignment().getSequencesArray();
AlignmentSorter.sortByTree(av.getAlignment(), tree);
CommandI undo;
@@
-730,10
+734,11
@@
public class TreePanel extends GTreePanel
{
jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
{
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.setFileView(new jalview.io.JalviewFileView());
- chooser.setDialogTitle(MessageManager.getString("label.create_eps_from_tree"));
+ chooser.setDialogTitle(MessageManager
+ .getString("label.create_eps_from_tree"));
chooser.setToolTipText(MessageManager.getString("action.save"));
int value = chooser.showSaveDialog(this);
chooser.setToolTipText(MessageManager.getString("action.save"));
int value = chooser.showSaveDialog(this);
@@
-776,11
+781,12
@@
public class TreePanel extends GTreePanel
{
jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
{
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.setFileView(new jalview.io.JalviewFileView());
- chooser.setDialogTitle(MessageManager.getString("label.create_png_from_tree"));
+ chooser.setDialogTitle(MessageManager
+ .getString("label.create_png_from_tree"));
chooser.setToolTipText(MessageManager.getString("action.save"));
int value = chooser.showSaveDialog(this);
chooser.setToolTipText(MessageManager.getString("action.save"));
int value = chooser.showSaveDialog(this);
@@
-834,8
+840,8
@@
public class TreePanel extends GTreePanel
{
// search dbrefs, features and annotation
DBRefEntry[] refs = jalview.util.DBRefUtils.selectRefs(
{
// search dbrefs, features and annotation
DBRefEntry[] refs = jalview.util.DBRefUtils.selectRefs(
- sq.getDBRef(), new String[]
- { labelClass.toUpperCase() });
+ sq.getDBRef(),
+ new String[] { labelClass.toUpperCase() });
if (refs != null)
{
for (int i = 0; i < refs.length; i++)
if (refs != null)
{
for (int i = 0; i < refs.length; i++)