X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGAlignFrame.java;h=6c1c8c6d0f96de62c00f65075c42e03818c472f1;hb=d6509fcf3a8cc90616e18cb22cec97f85c722bb8;hp=22d27e973c43b7f2dec814dc2c9b27843a174bf9;hpb=6403068c0c328cfb63af451f7fa1bd568fa0fdd3;p=jalview.git
diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 22d27e9..6c1c8c6 100755
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -1,6 +1,6 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 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
*
* This file is part of Jalview.
*
@@ -17,13 +17,35 @@
*/
package jalview.jbgui;
-import java.awt.*;
-import java.awt.event.*;
-
-import javax.swing.*;
-import javax.swing.event.*;
-
-import jalview.schemes.*;
+import jalview.schemes.ColourSchemeProperty;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.GridLayout;
+import java.awt.Toolkit;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.FocusAdapter;
+import java.awt.event.FocusEvent;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+
+import javax.swing.BorderFactory;
+import javax.swing.ButtonGroup;
+import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JInternalFrame;
+import javax.swing.JLabel;
+import javax.swing.JMenu;
+import javax.swing.JMenuBar;
+import javax.swing.JMenuItem;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JRadioButtonMenuItem;
+import javax.swing.JTabbedPane;
+import javax.swing.SwingUtilities;
+import javax.swing.event.ChangeEvent;
+import javax.swing.event.MenuEvent;
+import javax.swing.event.MenuListener;
public class GAlignFrame extends JInternalFrame
{
@@ -113,6 +135,16 @@ public class GAlignFrame extends JInternalFrame
protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
+ protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
+
+ protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
+
+ // protected JRadioButtonMenuItem covariationColour = new
+ // JRadioButtonMenuItem();
+
+ protected JRadioButtonMenuItem tcoffeeColour = new JRadioButtonMenuItem();
+
+
JMenuItem njTreeBlosumMenuItem = new JMenuItem();
JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
@@ -149,8 +181,6 @@ public class GAlignFrame extends JInternalFrame
public JCheckBoxMenuItem showSeqFeaturesHeight = new JCheckBoxMenuItem();
- protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
-
JMenuItem deleteGroups = new JMenuItem();
JMenuItem delete = new JMenuItem();
@@ -176,7 +206,7 @@ public class GAlignFrame extends JInternalFrame
JMenuItem epsFile = new JMenuItem();
JMenuItem LoadtreeMenuItem = new JMenuItem();
-
+
public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
@@ -211,18 +241,22 @@ public class GAlignFrame extends JInternalFrame
protected JMenu showProducts = new JMenu();
- public JMenuItem featureSettings = new JMenuItem();
+ public JMenuItem openFeatureSettings = new JMenuItem();
JMenuItem fetchSequence = new JMenuItem();
JMenuItem annotationColour = new JMenuItem();
+ protected JMenuItem rnahelicesColour = new JMenuItem();
+
JMenuItem associatedData = new JMenuItem();
protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
protected JCheckBoxMenuItem sortByTree = new JCheckBoxMenuItem();
+ protected JCheckBoxMenuItem listenToViewSelections = new JCheckBoxMenuItem();
+
JMenu addSequenceMenu = new JMenu();
JMenuItem addFromFile = new JMenuItem();
@@ -305,6 +339,8 @@ public class GAlignFrame extends JInternalFrame
protected JCheckBoxMenuItem showSequenceLogo = new JCheckBoxMenuItem();
+ protected JCheckBoxMenuItem normaliseSequenceLogo = new JCheckBoxMenuItem();
+
protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
private JMenuItem grpsFromSelection = new JMenuItem();
@@ -415,6 +451,9 @@ public class GAlignFrame extends JInternalFrame
colours.add(PIDColour);
colours.add(BLOSUM62Colour);
colours.add(nucleotideColour);
+ colours.add(purinePyrimidineColour);
+ // colours.add(covariationColour);
+ colours.add(tcoffeeColour);
setColourSelected(jalview.bin.Cache
.getDefault("DEFAULT_COLOUR", "None"));
@@ -484,7 +523,21 @@ public class GAlignFrame extends JInternalFrame
nucleotideColour.setSelected(true);
break;
+
+ case ColourSchemeProperty.TCOFFEE:
+ tcoffeeColour.setSelected(true);
+ break;
+
+ case ColourSchemeProperty.PURINEPYRIMIDINE:
+ purinePyrimidineColour.setSelected(true);
+ break;
+ /*
+ * case ColourSchemeProperty.COVARIATION:
+ * covariationColour.setSelected(true);
+ *
+ * break;
+ */
case ColourSchemeProperty.USER_DEFINED:
userDefinedColour.setSelected(true);
@@ -848,6 +901,31 @@ public class GAlignFrame extends JInternalFrame
BLOSUM62Colour_actionPerformed(e);
}
});
+ nucleotideColour.setText("Nucleotide");
+ nucleotideColour.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ nucleotideColour_actionPerformed(e);
+ }
+ });
+
+ purinePyrimidineColour.setText("Purine/Pyrimidine");
+ purinePyrimidineColour
+ .addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ purinePyrimidineColour_actionPerformed(e);
+ }
+ });
+ /*
+ * covariationColour.setText("Covariation");
+ * covariationColour.addActionListener(new java.awt.event.ActionListener() {
+ * public void actionPerformed(ActionEvent e) {
+ * covariationColour_actionPerformed(e); } });
+ */
+
avDistanceTreeBlosumMenuItem.setText("Average Distance Using BLOSUM62");
avDistanceTreeBlosumMenuItem
.addActionListener(new java.awt.event.ActionListener()
@@ -1067,6 +1145,16 @@ public class GAlignFrame extends JInternalFrame
}
});
+ normaliseSequenceLogo.setText("Normalise Consensus Logo");
+ normaliseSequenceLogo.addActionListener(new ActionListener()
+ {
+
+ public void actionPerformed(ActionEvent e)
+ {
+ normaliseSequenceLogo_actionPerformed(e);
+ }
+
+ });
applyAutoAnnotationSettings.setText("Apply to all groups");
applyAutoAnnotationSettings.setState(false);
applyAutoAnnotationSettings.setVisible(true);
@@ -1088,6 +1176,18 @@ 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);
+ }
+ } );
+
+
deleteGroups.setText("Undefine groups");
deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
java.awt.event.KeyEvent.VK_U, Toolkit.getDefaultToolkit()
@@ -1200,7 +1300,7 @@ 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)
@@ -1208,6 +1308,7 @@ public class GAlignFrame extends JInternalFrame
LoadtreeMenuItem_actionPerformed(e);
}
});
+
scaleAbove.setVisible(false);
scaleAbove.setText("Scale Above");
scaleAbove.addActionListener(new java.awt.event.ActionListener()
@@ -1362,8 +1463,8 @@ public class GAlignFrame extends JInternalFrame
* public void actionPerformed(ActionEvent e) {
* showProducts_actionPerformed(e); } });
*/
- featureSettings.setText("Feature Settings...");
- featureSettings.addActionListener(new ActionListener()
+ openFeatureSettings.setText("Feature Settings...");
+ openFeatureSettings.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
@@ -1387,6 +1488,16 @@ public class GAlignFrame extends JInternalFrame
annotationColour_actionPerformed(e);
}
});
+
+ rnahelicesColour.setText("By RNA helices");
+ rnahelicesColour.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ rnahelicesColour_actionPerformed(e);
+ }
+ });
+
associatedData.setText("Load Features / Annotations");
associatedData.addActionListener(new ActionListener()
{
@@ -1416,7 +1527,18 @@ public class GAlignFrame extends JInternalFrame
sortByTreeOption_actionPerformed(e);
}
});
-
+
+ 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.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ listenToViewSelections_actionPerformed(e);
+ }
+ });
+
addSequenceMenu.setText("Add Sequences");
addFromFile.setText("From File");
addFromFile.addActionListener(new ActionListener()
@@ -1716,6 +1838,7 @@ public class GAlignFrame extends JInternalFrame
autoAnnMenu.add(applyAutoAnnotationSettings);
autoAnnMenu.add(showConsensusHistogram);
autoAnnMenu.add(showSequenceLogo);
+ autoAnnMenu.add(normaliseSequenceLogo);
autoAnnMenu.addSeparator();
autoAnnMenu.add(showGroupConservation);
autoAnnMenu.add(showGroupConsensus);
@@ -1724,7 +1847,7 @@ public class GAlignFrame extends JInternalFrame
viewMenu.add(showSeqFeatures);
// viewMenu.add(showSeqFeaturesHeight);
- viewMenu.add(featureSettings);
+ viewMenu.add(openFeatureSettings);
tooltipSettingsMenu.add(showDbRefsMenuitem);
tooltipSettingsMenu.add(showNpFeatsMenuitem);
viewMenu.add(tooltipSettingsMenu);
@@ -1747,6 +1870,9 @@ public class GAlignFrame extends JInternalFrame
colourMenu.add(turnColour);
colourMenu.add(buriedColour);
colourMenu.add(nucleotideColour);
+ colourMenu.add(purinePyrimidineColour);
+ // colourMenu.add(covariationColour);
+ colourMenu.add(tcoffeeColour);
colourMenu.add(userDefinedColour);
colourMenu.addSeparator();
colourMenu.add(conservationMenuItem);
@@ -1754,6 +1880,7 @@ public class GAlignFrame extends JInternalFrame
colourMenu.add(abovePIDThreshold);
colourMenu.add(modifyPID);
colourMenu.add(annotationColour);
+ colourMenu.add(rnahelicesColour);
calculateMenu.add(sort);
calculateMenu.add(calculateTree);
calculateMenu.addSeparator();
@@ -1819,6 +1946,21 @@ 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);
+ }
+
+ 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)
@@ -2119,6 +2261,14 @@ public class GAlignFrame extends JInternalFrame
{
}
+ protected void purinePyrimidineColour_actionPerformed(ActionEvent e)
+ {
+ }
+
+ /*
+ * protected void covariationColour_actionPerformed(ActionEvent e) { }
+ */
+
protected void noColourmenuItem_actionPerformed(ActionEvent e)
{
}
@@ -2202,7 +2352,32 @@ public class GAlignFrame extends JInternalFrame
protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
{
+
+ }
+
+ /**
+ * 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 + */ + protected void loadScores_actionPerformed(ActionEvent 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 + */ + protected void tcoffeeColorScheme_actionPerformed(ActionEvent event) { + } + protected void jpred_actionPerformed(ActionEvent e) { @@ -2271,6 +2446,11 @@ public class GAlignFrame extends JInternalFrame } + public void rnahelicesColour_actionPerformed(ActionEvent e) + { + + } + public void associatedData_actionPerformed(ActionEvent e) {