X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGAlignFrame.java;h=533a698749c7de93ea7707de3c1477c6fec0c59c;hb=28787d9646cca5dd77190930f59b7ff32cf995b4;hp=b53bcc30b250e720bac9d483ebcbde84d08df3f9;hpb=cc407171f5746de69ca1d4af653984d778affeb9;p=jalview.git
diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index b53bcc3..533a698 100755
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -1,13 +1,13 @@
/*
- * 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 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
*
* 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
@@ -145,8 +145,7 @@ public class GAlignFrame extends JInternalFrame
// JRadioButtonMenuItem();
protected JRadioButtonMenuItem tcoffeeColour = new JRadioButtonMenuItem();
-
-
+
JMenuItem njTreeBlosumMenuItem = new JMenuItem();
JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
@@ -208,7 +207,7 @@ public class GAlignFrame extends JInternalFrame
JMenuItem epsFile = new JMenuItem();
JMenuItem LoadtreeMenuItem = new JMenuItem();
-
+
public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
@@ -525,10 +524,10 @@ public class GAlignFrame extends JInternalFrame
nucleotideColour.setSelected(true);
break;
-
+
case ColourSchemeProperty.TCOFFEE:
- tcoffeeColour.setSelected(true);
- break;
+ tcoffeeColour.setSelected(true);
+ break;
case ColourSchemeProperty.PURINEPYRIMIDINE:
purinePyrimidineColour.setSelected(true);
@@ -1192,18 +1191,19 @@ public class GAlignFrame extends JInternalFrame
nucleotideColour_actionPerformed(e);
}
});
-
+
tcoffeeColour.setText("T-Coffee scores");
tcoffeeColour.setEnabled(false);
- tcoffeeColour.addActionListener( new ActionListener() {
-
- @Override
- public void actionPerformed(ActionEvent e) {
- tcoffeeColorScheme_actionPerformed(e);
- }
- } );
-
-
+ tcoffeeColour.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ tcoffeeColorScheme_actionPerformed(e);
+ }
+ });
+
deleteGroups.setText("Undefine groups");
deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
java.awt.event.KeyEvent.VK_U, Toolkit.getDefaultToolkit()
@@ -1316,7 +1316,7 @@ public class GAlignFrame extends JInternalFrame
}
});
LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");
- LoadtreeMenuItem.setText("Load Associated Tree");
+ LoadtreeMenuItem.setText("Load Associated Tree");
LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -1324,7 +1324,7 @@ public class GAlignFrame extends JInternalFrame
LoadtreeMenuItem_actionPerformed(e);
}
});
-
+
scaleAbove.setVisible(false);
scaleAbove.setText("Scale Above");
scaleAbove.addActionListener(new java.awt.event.ActionListener()
@@ -1533,9 +1533,10 @@ public class GAlignFrame extends JInternalFrame
}
});
sortByTree.setText("Sort Alignment With New Tree");
- sortByTree.setToolTipText("Enable this to automatically sort
the alignment when you open
a new tree.");
- sortByTree.setState(jalview.bin.Cache.getDefault(
- "SORT_BY_TREE", false));
+ sortByTree
+ .setToolTipText("Enable this to automatically sort
the alignment when you open
a new tree.");
+ sortByTree
+ .setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false));
sortByTree.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -1545,8 +1546,9 @@ public class GAlignFrame extends JInternalFrame
});
listenToViewSelections.setText("Listen for selections");
- listenToViewSelections.setToolTipText("When selected, selections in this view will mirror
selections made on the same sequences in other views.");
- listenToViewSelections.setState(false);
+ listenToViewSelections
+ .setToolTipText("When selected, selections in this view will mirror
selections made on the same sequences in other views.");
+ listenToViewSelections.setState(false);
listenToViewSelections.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -1963,21 +1965,22 @@ public class GAlignFrame extends JInternalFrame
selectMenu.add(invertColSel);
selectMenu.add(deleteGroups);
selectMenu.add(grpsFromSelection);
- // TODO - determine if the listenToViewSelections button is needed : see bug JAL-574
- //selectMenu.addSeparator();
- //selectMenu.add(listenToViewSelections);
+ // TODO - determine if the listenToViewSelections button is needed : see bug
+ // JAL-574
+ // selectMenu.addSeparator();
+ // selectMenu.add(listenToViewSelections);
}
protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
{
// TODO Auto-generated method stub
-
+
}
protected void listenToViewSelections_actionPerformed(ActionEvent e)
{
// TODO Auto-generated method stub
-
+
}
protected void showAllhidden_actionPerformed(ActionEvent e)
@@ -2376,30 +2379,32 @@ public class GAlignFrame extends JInternalFrame
{
}
-
+
/**
- * Template method to handle the 'load T-Coffee scores' menu event.
+ * Template method to handle the 'load T-Coffee scores' menu event.
*
* Subclasses override this method to provide a custom action.
- *
- * @param event The raised event
+ *
+ * @param event
+ * The raised event
*/
- protected void loadScores_actionPerformed(ActionEvent event) {
-
+ protected void loadScores_actionPerformed(ActionEvent event)
+ {
+
}
-
/**
- * Template method to handle the 'Color T-Coffee scores' menu event.
+ * Template method to handle the 'Color T-Coffee scores' menu event.
*
* Subclasses override this method to provide a custom action.
- *
- * @param event The raised event
+ *
+ * @param event
+ * The raised event
*/
- protected void tcoffeeColorScheme_actionPerformed(ActionEvent event) {
-
+ protected void tcoffeeColorScheme_actionPerformed(ActionEvent event)
+ {
+
}
-
protected void jpred_actionPerformed(ActionEvent e)
{