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no more group editing mode. clustal implemented
author
amwaterhouse
<Andrew Waterhouse>
Wed, 15 Dec 2004 17:23:28 +0000
(17:23 +0000)
committer
amwaterhouse
<Andrew Waterhouse>
Wed, 15 Dec 2004 17:23:28 +0000
(17:23 +0000)
src/jalview/jbgui/GAlignFrame.java
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diff --git
a/src/jalview/jbgui/GAlignFrame.java
b/src/jalview/jbgui/GAlignFrame.java
index
be879ee
..
6c216ec
100755
(executable)
--- a/
src/jalview/jbgui/GAlignFrame.java
+++ b/
src/jalview/jbgui/GAlignFrame.java
@@
-24,7
+24,6
@@
public class GAlignFrame extends JInternalFrame
protected JMenu calculateMenu = new JMenu();
\r
protected JMenu alignMenu = new JMenu();
\r
protected JMenuItem groupsMenuItem = new JMenuItem();
\r
protected JMenu calculateMenu = new JMenu();
\r
protected JMenu alignMenu = new JMenu();
\r
protected JMenuItem groupsMenuItem = new JMenuItem();
\r
- protected JCheckBoxMenuItem groupEditingMenuItem = new JCheckBoxMenuItem();
\r
protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();
\r
protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();
\r
protected JMenuItem invertSequenceMenuItem = new JMenuItem();
\r
protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();
\r
protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();
\r
protected JMenuItem invertSequenceMenuItem = new JMenuItem();
\r
@@
-66,7
+65,6
@@
public class GAlignFrame extends JInternalFrame
protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
\r
JMenuItem njTreeBlosumMenuItem = new JMenuItem();
\r
JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
\r
protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
\r
JMenuItem njTreeBlosumMenuItem = new JMenuItem();
\r
JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
\r
- protected JMenuItem conservationColourIncMenuItem = new JMenuItem();
\r
protected JCheckBoxMenuItem consensusGraphMenuItem = new JCheckBoxMenuItem();
\r
protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
\r
JMenuItem htmlMenuItem = new JMenuItem();
\r
protected JCheckBoxMenuItem consensusGraphMenuItem = new JCheckBoxMenuItem();
\r
protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
\r
JMenuItem htmlMenuItem = new JMenuItem();
\r
@@
-82,8
+80,7
@@
public class GAlignFrame extends JInternalFrame
protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
\r
JMenuItem findMenuItem = new JMenuItem();
\r
JMenu searchMenu = new JMenu();
\r
protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
\r
JMenuItem findMenuItem = new JMenuItem();
\r
JMenu searchMenu = new JMenu();
\r
- protected JCheckBoxMenuItem modifyAlignmentMenuItem = new JCheckBoxMenuItem();
\r
- JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
\r
+ protected JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
\r
public GAlignFrame()
\r
{
\r
try
\r
public GAlignFrame()
\r
{
\r
try
\r
@@
-165,14
+162,6
@@
public class GAlignFrame extends JInternalFrame
groupsMenuItem_actionPerformed(e);
\r
}
\r
});
\r
groupsMenuItem_actionPerformed(e);
\r
}
\r
});
\r
- groupEditingMenuItem.setText("Group editing mode");
\r
- groupEditingMenuItem.addActionListener(new java.awt.event.ActionListener()
\r
- {
\r
- public void actionPerformed(ActionEvent e)
\r
- {
\r
- groupEditingMenuItem_actionPerformed(e);
\r
- }
\r
- });
\r
selectAllSequenceMenuItem.setText("Select all sequences");
\r
selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
\r
{
\r
selectAllSequenceMenuItem.setText("Select all sequences");
\r
selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
\r
{
\r
@@
-374,7
+363,6
@@
public class GAlignFrame extends JInternalFrame
statusBar.setText("Status bar");
\r
outputTextboxMenu.setMnemonic('T');
\r
outputTextboxMenu.setText("Output alignment via textbox");
\r
statusBar.setText("Status bar");
\r
outputTextboxMenu.setMnemonic('T');
\r
outputTextboxMenu.setText("Output alignment via textbox");
\r
- clustalColour.setEnabled(false);
\r
clustalColour.setSelected(false);
\r
clustalColour.setText("Clustalx colours");
\r
clustalColour.addActionListener(new java.awt.event.ActionListener()
\r
clustalColour.setSelected(false);
\r
clustalColour.setText("Clustalx colours");
\r
clustalColour.addActionListener(new java.awt.event.ActionListener()
\r
@@
-448,7
+436,7
@@
public class GAlignFrame extends JInternalFrame
userDefinedColour_actionPerformed(e);
\r
}
\r
});
\r
userDefinedColour_actionPerformed(e);
\r
}
\r
});
\r
- PIDColour.setText("By PID");
\r
+ PIDColour.setText("Percentage Identity");
\r
PIDColour.addActionListener(new java.awt.event.ActionListener()
\r
{
\r
public void actionPerformed(ActionEvent e)
\r
PIDColour.addActionListener(new java.awt.event.ActionListener()
\r
{
\r
public void actionPerformed(ActionEvent e)
\r
@@
-456,7
+444,7
@@
public class GAlignFrame extends JInternalFrame
PIDColour_actionPerformed(e);
\r
}
\r
});
\r
PIDColour_actionPerformed(e);
\r
}
\r
});
\r
- BLOSUM62Colour.setText("By BLOSUM62 score");
\r
+ BLOSUM62Colour.setText("BLOSUM62 score");
\r
BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
\r
{
\r
public void actionPerformed(ActionEvent e)
\r
BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
\r
{
\r
public void actionPerformed(ActionEvent e)
\r
@@
-480,15
+468,6
@@
public class GAlignFrame extends JInternalFrame
njTreeBlosumMenuItem_actionPerformed(e);
\r
}
\r
});
\r
njTreeBlosumMenuItem_actionPerformed(e);
\r
}
\r
});
\r
- conservationColourIncMenuItem.setEnabled(false);
\r
- conservationColourIncMenuItem.setText("Conservation Colour Increment");
\r
- conservationColourIncMenuItem.addActionListener(new java.awt.event.ActionListener()
\r
- {
\r
- public void actionPerformed(ActionEvent e)
\r
- {
\r
- conservationColourIncMenuItem_actionPerformed(e);
\r
- }
\r
- });
\r
consensusGraphMenuItem.setActionCommand("");
\r
consensusGraphMenuItem.setText("Consensus graph");
\r
consensusGraphMenuItem.setState(true);
\r
consensusGraphMenuItem.setActionCommand("");
\r
consensusGraphMenuItem.setText("Consensus graph");
\r
consensusGraphMenuItem.setState(true);
\r
@@
-611,16
+590,13
@@
public class GAlignFrame extends JInternalFrame
}
\r
});
\r
searchMenu.setText("Search");
\r
}
\r
});
\r
searchMenu.setText("Search");
\r
- modifyAlignmentMenuItem.setText("Modify alignment");
\r
- modifyAlignmentMenuItem.addActionListener(new java.awt.event.ActionListener()
\r
- {
\r
- public void actionPerformed(ActionEvent e)
\r
- {
\r
- modifyAlignmentMenuItem_actionPerformed(e);
\r
+
\r
+ abovePIDThreshold.setText("Above PID threshold");
\r
+ abovePIDThreshold.addActionListener(new java.awt.event.ActionListener() {
\r
+ public void actionPerformed(ActionEvent e) {
\r
+ abovePIDThreshold_actionPerformed(e);
\r
}
\r
});
\r
}
\r
});
\r
- abovePIDThreshold.setEnabled(false);
\r
- abovePIDThreshold.setText("Above PID threshold");
\r
alignFrameMenuBar.add(fileMenu);
\r
alignFrameMenuBar.add(editMenu);
\r
alignFrameMenuBar.add(searchMenu);
\r
alignFrameMenuBar.add(fileMenu);
\r
alignFrameMenuBar.add(editMenu);
\r
alignFrameMenuBar.add(searchMenu);
\r
@@
-638,9
+614,7
@@
public class GAlignFrame extends JInternalFrame
editMenu.add(undoMenuItem);
\r
editMenu.add(redoMenuItem);
\r
editMenu.addSeparator();
\r
editMenu.add(undoMenuItem);
\r
editMenu.add(redoMenuItem);
\r
editMenu.addSeparator();
\r
- editMenu.add(modifyAlignmentMenuItem);
\r
editMenu.add(groupsMenuItem);
\r
editMenu.add(groupsMenuItem);
\r
- editMenu.add(groupEditingMenuItem);
\r
editMenu.addSeparator();
\r
editMenu.add(selectAllSequenceMenuItem);
\r
editMenu.add(deselectAllSequenceMenuItem);
\r
editMenu.addSeparator();
\r
editMenu.add(selectAllSequenceMenuItem);
\r
editMenu.add(deselectAllSequenceMenuItem);
\r
@@
-674,15
+648,12
@@
public class GAlignFrame extends JInternalFrame
colourMenu.add(turnColour);
\r
colourMenu.add(buriedColour);
\r
colourMenu.add(userDefinedColour);
\r
colourMenu.add(turnColour);
\r
colourMenu.add(buriedColour);
\r
colourMenu.add(userDefinedColour);
\r
- colourMenu.add(abovePIDThreshold);
\r
- colourMenu.addSeparator();
\r
- colourMenu.add(conservationMenuItem);
\r
- colourMenu.add(conservationColourIncMenuItem);
\r
- colourMenu.addSeparator();
\r
-
\r
colourMenu.add(PIDColour);
\r
colourMenu.add(BLOSUM62Colour);
\r
colourMenu.addSeparator();
\r
colourMenu.add(PIDColour);
\r
colourMenu.add(BLOSUM62Colour);
\r
colourMenu.addSeparator();
\r
+ colourMenu.add(abovePIDThreshold);
\r
+ colourMenu.add(conservationMenuItem);
\r
+ colourMenu.addSeparator();
\r
colourMenu.add(schemeKeyMenuItem);
\r
calculateMenu.add(sortPairwiseMenuItem);
\r
calculateMenu.add(sortIDMenuItem);
\r
colourMenu.add(schemeKeyMenuItem);
\r
calculateMenu.add(sortPairwiseMenuItem);
\r
calculateMenu.add(sortIDMenuItem);
\r
@@
-742,10
+713,6
@@
public class GAlignFrame extends JInternalFrame
\r
}
\r
\r
\r
}
\r
\r
- protected void groupEditingMenuItem_actionPerformed(ActionEvent e)
\r
- {
\r
-
\r
- }
\r
\r
protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
\r
{
\r
\r
protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
\r
{
\r
@@
-951,13
+918,6
@@
public class GAlignFrame extends JInternalFrame
}
\r
\r
\r
}
\r
\r
\r
- protected void conservationColourIncMenuItem_actionPerformed(ActionEvent e)
\r
- {
\r
-
\r
- }
\r
-
\r
-
\r
-
\r
\r
protected void userDefinedColour_actionPerformed(ActionEvent e)
\r
{
\r
\r
protected void userDefinedColour_actionPerformed(ActionEvent e)
\r
{
\r
@@
-1009,8
+969,8
@@
public class GAlignFrame extends JInternalFrame
\r
}
\r
\r
\r
}
\r
\r
- protected void modifyAlignmentMenuItem_actionPerformed(ActionEvent e)
\r
- {
\r
+
\r
+ protected void abovePIDThreshold_actionPerformed(ActionEvent e) {
\r
\r
}
\r
\r
\r
}
\r
\r