X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGAlignFrame.java;h=a9cc38cf08788744e77a0cb986c3aa1929c1d43a;hb=f9252188878c02389ed1a56fe23a9cc3b06cf52f;hp=26e532694dcd370d9bc31f703482a0b3cd452ea4;hpb=ef3333028b291ce92bdae34bd2f8487d35d0a0d3;p=jalview.git
diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 26e5326..a9cc38c 100755
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -1,6 +1,6 @@
/*
* Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU General Public License
@@ -23,8 +23,11 @@ import java.awt.event.*;
import javax.swing.*;
import javax.swing.event.*;
-import jalview.gui.*;
import jalview.schemes.*;
+import java.awt.BorderLayout;
+
+
+
public class GAlignFrame
extends JInternalFrame
@@ -37,6 +40,7 @@ public class GAlignFrame
protected JMenu colourMenu = new JMenu();
protected JMenu calculateMenu = new JMenu();
protected JMenu webService = new JMenu();
+ protected JMenuItem webServiceNoServices;
protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();
protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();
protected JMenuItem invertSequenceMenuItem = new JMenuItem();
@@ -54,10 +58,9 @@ public class GAlignFrame
protected JMenuItem PCAMenuItem = new JMenuItem();
protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();
protected JMenuItem neighbourTreeMenuItem = new JMenuItem();
- protected JMenuItem clustalAlignMenuItem = new JMenuItem();
BorderLayout borderLayout1 = new BorderLayout();
public JLabel statusBar = new JLabel();
- protected JMenuItem saveAlignmentMenu = new JMenuItem();
+ protected JMenuItem saveAs = new JMenuItem();
protected JMenu outputTextboxMenu = new JMenu();
protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
@@ -85,70 +88,78 @@ public class GAlignFrame
JMenuItem printMenuItem = new JMenuItem();
public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
JMenuItem findMenuItem = new JMenuItem();
- JMenu searchMenu = new JMenu();
public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
- public JCheckBoxMenuItem sequenceFeatures = new JCheckBoxMenuItem();
+ public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
JMenuItem deleteGroups = new JMenuItem();
JMenuItem delete = new JMenuItem();
JMenuItem copy = new JMenuItem();
JMenuItem cut = new JMenuItem();
- JMenu jMenu1 = new JMenu();
+ JMenu pasteMenu = new JMenu();
JMenuItem pasteNew = new JMenuItem();
JMenuItem pasteThis = new JMenuItem();
public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
JMenuItem createPNG = new JMenuItem();
protected JMenuItem font = new JMenuItem();
- public JCheckBoxMenuItem fullSeqId = new JCheckBoxMenuItem();
+ public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
JMenuItem epsFile = new JMenuItem();
JMenuItem LoadtreeMenuItem = new JMenuItem();
- JMenuItem jnet = new JMenuItem();
public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
- JMenuItem modifyPID = new JMenuItem();
- JMenuItem modifyConservation = new JMenuItem();
+ protected JMenuItem modifyPID = new JMenuItem();
+ protected JMenuItem modifyConservation = new JMenuItem();
protected JMenu sortByTreeMenu = new JMenu();
protected JMenu sort = new JMenu();
JMenu calculate = new JMenu();
- JMenuItem msaAlignMenuItem = new JMenuItem();
JMenu jMenu2 = new JMenu();
- JMenuItem padGapsMenuitem = new JMenuItem();
- JMenuItem ClustalRealign = new JMenuItem();
-
+ protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
+ protected ButtonGroup colours = new ButtonGroup();
+ JMenuItem vamsasStore = new JMenuItem();
+ protected JMenuItem showTranslation = new JMenuItem();
+ public JMenuItem featureSettings = new JMenuItem();
+ JMenuItem fetchSequence = new JMenuItem();
+ JMenuItem annotationColour = new JMenuItem();
+ JMenuItem associatedData = new JMenuItem();
+ protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
+ JMenu addSequenceMenu = new JMenu();
+ JMenuItem addFromFile = new JMenuItem();
+ JMenuItem addFromText = new JMenuItem();
+ JMenuItem addFromURL = new JMenuItem();
+ JMenuItem exportAnnotations = new JMenuItem();
+ JMenuItem exportFeatures = new JMenuItem();
+ protected JPanel statusPanel = new JPanel();
+ GridLayout gridLayout1 = new GridLayout();
+ JMenu jMenu3 = new JMenu();
+ JMenuItem showAllSeqs = new JMenuItem();
+ JMenuItem showAllColumns = new JMenuItem();
+ JMenu hideMenu = new JMenu();
+ JMenuItem hideSelSequences = new JMenuItem();
+ JMenuItem hideSelColumns = new JMenuItem();
+ protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
+ JMenuItem invertColSel = new JMenuItem();
+ protected JTabbedPane tabbedPane = new JTabbedPane();
+ JMenuItem save = new JMenuItem();
+ JMenuItem jMenuItem1 = new JMenuItem();
+ protected JMenuItem reload = new JMenuItem();
+ JMenuItem newView = new JMenuItem();
+ JMenuItem textColour = new JMenuItem();
+ JMenu jMenu1 = new JMenu();
+ JCheckBoxMenuItem jCheckBoxMenuItem1 = new JCheckBoxMenuItem();
+ JMenu jMenu4 = new JMenu();
+ protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
public GAlignFrame()
{
- ButtonGroup colours = new ButtonGroup();
- colours.add(noColourmenuItem);
- colours.add(clustalColour);
- colours.add(zappoColour);
- colours.add(taylorColour);
- colours.add(hydrophobicityColour);
- colours.add(helixColour);
- colours.add(strandColour);
- colours.add(turnColour);
- colours.add(buriedColour);
- colours.add(userDefinedColour);
- colours.add(PIDColour);
- colours.add(BLOSUM62Colour);
- colours.add(nucleotideColour);
-
- setColourSelected(jalview.bin.Cache.getDefault("DEFAULT_COLOUR", "None"));
-
-
try
{
jbInit();
setJMenuBar(alignFrameMenuBar);
- JMenuItem item;
-
// dynamically fill save as menu with available formats
- for (int i = 0; i < jalview.io.FormatAdapter.formats.size(); i++)
+ for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
{
- item = new JMenuItem( (String) jalview.io.FormatAdapter.formats.
- elementAt(
- i));
+ JMenuItem item = new JMenuItem( jalview.io.FormatAdapter.WRITEABLE_FORMATS[i] );
+
item.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -164,6 +175,85 @@ public class GAlignFrame
{
}
+ if (!System.getProperty("os.name").startsWith("Mac"))
+ {
+ closeMenuItem.setMnemonic('C');
+ outputTextboxMenu.setMnemonic('T');
+ undoMenuItem.setMnemonic('Z');
+ redoMenuItem.setMnemonic('0');
+ copy.setMnemonic('C');
+ cut.setMnemonic('U');
+ pasteMenu.setMnemonic('P');
+ reload.setMnemonic('R');
+ }
+
+
+ if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null)
+ {
+ java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
+ getUserColourSchemes().keys();
+
+ while (userColours.hasMoreElements())
+ {
+ final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.
+ nextElement().toString());
+ radioItem.setName("USER_DEFINED");
+ radioItem.addMouseListener(new MouseAdapter()
+ {
+ public void mousePressed(MouseEvent evt)
+ {
+ if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
+ {
+ radioItem.removeActionListener(radioItem.getActionListeners()[0]);
+
+ int option = JOptionPane.showInternalConfirmDialog(jalview.gui.Desktop.desktop,
+ "Remove from default list?",
+ "Remove user defined colour",
+ JOptionPane.YES_NO_OPTION);
+ if(option == JOptionPane.YES_OPTION)
+ {
+ jalview.gui.UserDefinedColours.removeColourFromDefaults(radioItem.getText());
+ colourMenu.remove(radioItem);
+ }
+ else
+ radioItem.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent evt)
+ {
+ userDefinedColour_actionPerformed(evt);
+ }
+ });
+ }
+ }
+ });
+ radioItem.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent evt)
+ {
+ userDefinedColour_actionPerformed(evt);
+ }
+ });
+ colourMenu.insert(radioItem, 15);
+ colours.add(radioItem);
+ }
+ }
+ colours.add(noColourmenuItem);
+ colours.add(clustalColour);
+ colours.add(zappoColour);
+ colours.add(taylorColour);
+ colours.add(hydrophobicityColour);
+ colours.add(helixColour);
+ colours.add(strandColour);
+ colours.add(turnColour);
+ colours.add(buriedColour);
+ colours.add(userDefinedColour);
+ colours.add(PIDColour);
+ colours.add(BLOSUM62Colour);
+ colours.add(nucleotideColour);
+
+ setColourSelected(jalview.bin.Cache.getDefault("DEFAULT_COLOUR", "None"));
+
+
}
public void setColourSelected(String defaultColour)
@@ -244,26 +334,26 @@ public class GAlignFrame
private void jbInit()
throws Exception
{
- fileMenu.setMnemonic('F');
fileMenu.setText("File");
- saveAlignmentMenu.setMnemonic('L');
- saveAlignmentMenu.setText("Save As");
- saveAlignmentMenu.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.
- awt.event.KeyEvent.VK_S, java.awt.event.KeyEvent.CTRL_MASK, false));
- saveAlignmentMenu.addActionListener(new ActionListener()
+ saveAs.setText("Save As...");
+ saveAs.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
+ KeyEvent.VK_S,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()| java.awt.event.KeyEvent.SHIFT_MASK, false));
+ saveAs.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
- saveAlignmentMenu_actionPerformed(e);
+ saveAs_actionPerformed(e);
}
});
- closeMenuItem.setMnemonic('C');
closeMenuItem.setText("Close");
+ closeMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
+ event.KeyEvent.VK_W, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
closeMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
{
- closeMenuItem_actionPerformed(e);
+ closeMenuItem_actionPerformed(false);
}
});
editMenu.setText("Edit");
@@ -271,7 +361,7 @@ public class GAlignFrame
colourMenu.setText("Colour");
calculateMenu.setText("Calculate");
webService.setText("Web Service");
- selectAllSequenceMenuItem.setText("Select all");
+ selectAllSequenceMenuItem.setText("Select All");
selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
java.awt.event.KeyEvent.VK_A,
Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
@@ -295,7 +385,10 @@ public class GAlignFrame
deselectAllSequenceMenuItem_actionPerformed(e);
}
});
- invertSequenceMenuItem.setText("Invert Selection");
+ invertSequenceMenuItem.setText("Invert Sequence Selection");
+ invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+ java.awt.event.KeyEvent.VK_I,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -304,6 +397,8 @@ public class GAlignFrame
}
});
remove2LeftMenuItem.setText("Remove Left");
+ remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.
+ awt.event.KeyEvent.VK_L, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -312,6 +407,8 @@ public class GAlignFrame
}
});
remove2RightMenuItem.setText("Remove Right");
+ remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.
+ awt.event.KeyEvent.VK_R, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -320,6 +417,9 @@ public class GAlignFrame
}
});
removeGappedColumnMenuItem.setText("Remove Empty Columns");
+ removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke.
+ getKeyStroke(java.awt.event.
+ KeyEvent.VK_E, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
removeGappedColumnMenuItem.addActionListener(new java.awt.event.
ActionListener()
{
@@ -329,6 +429,9 @@ public class GAlignFrame
}
});
removeAllGapsMenuItem.setText("Remove All Gaps");
+ removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+ java.awt.event.KeyEvent.VK_E,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask() | java.awt.event.KeyEvent.SHIFT_MASK, false));
removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -379,6 +482,8 @@ public class GAlignFrame
}
});
removeRedundancyMenuItem.setText("Remove Redundancy...");
+ removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+ java.awt.event.KeyEvent.VK_D, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
removeRedundancyMenuItem.addActionListener(new java.awt.event.
ActionListener()
{
@@ -422,36 +527,12 @@ public class GAlignFrame
neighbourTreeMenuItem_actionPerformed(e);
}
});
- clustalAlignMenuItem.setText("Clustal Alignment");
- clustalAlignMenuItem.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- clustalAlignMenuItem_actionPerformed(e);
- }
- });
this.getContentPane().setLayout(borderLayout1);
alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
- alignFrameMenuBar.addAncestorListener(new AncestorListener()
- {
- public void ancestorAdded(AncestorEvent event)
- {
- alignFrameMenuBar_ancestorAdded(event);
- }
-
- public void ancestorRemoved(AncestorEvent event)
- {
- }
-
- public void ancestorMoved(AncestorEvent event)
- {
- }
- });
statusBar.setBackground(Color.white);
statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
statusBar.setText("Status bar");
- outputTextboxMenu.setMnemonic('T');
outputTextboxMenu.setText("Output to Textbox");
clustalColour.setText("Clustalx");
@@ -595,7 +676,6 @@ public class GAlignFrame
}
});
undoMenuItem.setEnabled(false);
- undoMenuItem.setMnemonic('Z');
undoMenuItem.setText("Undo");
undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
java.awt.event.KeyEvent.VK_Z,
@@ -608,8 +688,9 @@ public class GAlignFrame
}
});
redoMenuItem.setEnabled(false);
- redoMenuItem.setMnemonic('0');
redoMenuItem.setText("Redo");
+ redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
+ event.KeyEvent.VK_Y, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
redoMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -642,6 +723,8 @@ public class GAlignFrame
}
});
printMenuItem.setText("Print");
+ printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
+ event.KeyEvent.VK_P, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
printMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -669,8 +752,6 @@ public class GAlignFrame
findMenuItem_actionPerformed(e);
}
});
- searchMenu.setText("Search");
-
abovePIDThreshold.setText("Above Identity Threshold");
abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
{
@@ -679,12 +760,12 @@ public class GAlignFrame
abovePIDThreshold_actionPerformed(e);
}
});
- sequenceFeatures.setText("Sequence Features");
- sequenceFeatures.addActionListener(new ActionListener()
+ showSeqFeatures.setText("Show Sequence Features");
+ showSeqFeatures.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent actionEvent)
{
- sequenceFeatures_actionPerformed(actionEvent);
+ showSeqFeatures_actionPerformed(actionEvent);
}
});
nucleotideColour.setText("Nucleotide");
@@ -696,6 +777,8 @@ public class GAlignFrame
}
});
deleteGroups.setText("Undefine groups");
+ deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
+ event.KeyEvent.VK_U, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
deleteGroups.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -707,7 +790,6 @@ public class GAlignFrame
copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
java.awt.event.KeyEvent.VK_C,
Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
- copy.setMnemonic(KeyEvent.VK_C);
copy.addActionListener(new java.awt.event.ActionListener()
{
@@ -720,7 +802,6 @@ public class GAlignFrame
cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
java.awt.event.KeyEvent.VK_X,
Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
- cut.setMnemonic(KeyEvent.VK_X);
cut.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -729,6 +810,8 @@ public class GAlignFrame
}
});
delete.setText("Delete");
+ delete.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
+ KeyEvent.VK_BACK_SPACE, 0, false));
delete.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -736,12 +819,11 @@ public class GAlignFrame
delete_actionPerformed(e);
}
});
- jMenu1.setMnemonic('V');
- jMenu1.setText("Paste");
+ pasteMenu.setText("Paste");
pasteNew.setText("To New Alignment");
pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
java.awt.event.KeyEvent.VK_V,
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()|java.awt.event.KeyEvent.SHIFT_MASK, false));
pasteNew.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -750,6 +832,9 @@ public class GAlignFrame
}
});
pasteThis.setText("Add To This Alignment");
+ pasteThis.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+ java.awt.event.KeyEvent.VK_V,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
pasteThis.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -758,7 +843,6 @@ public class GAlignFrame
}
});
applyToAllGroups.setText("Apply Colour To All Groups");
- applyToAllGroups.setState(true);
applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -783,13 +867,14 @@ public class GAlignFrame
font_actionPerformed(e);
}
});
- fullSeqId.setText("Show Full Sequence ID");
- fullSeqId.setState(true);
- fullSeqId.addActionListener(new java.awt.event.ActionListener()
+
+ seqLimits.setText("Show Sequence Limits");
+ seqLimits.setState( jalview.bin.Cache.getDefault("SHOW_JVSUFFIX",true));
+ seqLimits.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
{
- fullSeqId_actionPerformed(e);
+ seqLimit_actionPerformed(e);
}
});
epsFile.setText("EPS");
@@ -801,7 +886,7 @@ public class GAlignFrame
}
});
LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");
- LoadtreeMenuItem.setText("Load Assocated Tree");
+ LoadtreeMenuItem.setText("Load Associated Tree");
LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -809,14 +894,6 @@ public class GAlignFrame
LoadtreeMenuItem_actionPerformed(e);
}
});
- jnet.setText("JNet");
- jnet.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- jpred_actionPerformed(e);
- }
- });
scaleAbove.setVisible(false);
scaleAbove.setText("Scale Above");
scaleAbove.addActionListener(new java.awt.event.ActionListener()
@@ -865,57 +942,281 @@ public class GAlignFrame
sortByTreeMenu.setText("By Tree Order");
sort.setText("Sort");
calculate.setText("Calculate Tree");
- msaAlignMenuItem.setText("Muscle Alignment");
- msaAlignMenuItem.addActionListener(new java.awt.event.ActionListener()
+
+ jMenu2.setText("Export Image");
+ padGapsMenuitem.setText("Pad Gaps");
+ padGapsMenuitem.setState( jalview.bin.Cache.getDefault("PAD_GAPS", false));
+ padGapsMenuitem.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
- msaAlignMenuItem_actionPerformed(e);
+ padGapsMenuitem_actionPerformed(e);
}
});
- jMenu2.setText("Export");
- padGapsMenuitem.setText("Pad Gaps");
- padGapsMenuitem.addActionListener(new ActionListener()
+ vamsasStore.setVisible(false);
+ vamsasStore.setText("VAMSAS store");
+ vamsasStore.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
- padGapsMenuitem_actionPerformed(e);
+ vamsasStore_actionPerformed(e);
+ }
+ });
+ showTranslation.setText("Translate cDNA");
+ showTranslation.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ showTranslation_actionPerformed(e);
+ }
+ });
+
+
+ featureSettings.setText("Feature Settings...");
+ featureSettings.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ featureSettings_actionPerformed(e);
+ }
+ });
+ fetchSequence.setText("Fetch Sequence(s)...");
+ fetchSequence.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ fetchSequence_actionPerformed(e);
+ }
+ });
+
+ annotationColour.setText("By Annotation...");
+ annotationColour.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ annotationColour_actionPerformed(e);
+ }
+ });
+ associatedData.setText("Load Features / Annotations");
+ associatedData.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ associatedData_actionPerformed(e);
+ }
+ });
+ autoCalculate.setText("Autocalculate Consensus");
+ autoCalculate.setState( jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true));
+ autoCalculate.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ autoCalculate_actionPerformed(e);
+ }
+ });
+ addSequenceMenu.setText("Add Sequences");
+ addFromFile.setText("From File");
+ addFromFile.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ addFromFile_actionPerformed(e);
+ }
+ });
+ addFromText.setText("From Textbox");
+ addFromText.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ addFromText_actionPerformed(e);
+ }
+ });
+ addFromURL.setText("From URL");
+ addFromURL.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ addFromURL_actionPerformed(e);
+ }
+ });
+ exportFeatures.setText("Export Features...");
+ exportFeatures.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ exportFeatures_actionPerformed(e);
+ }
+ });
+ exportAnnotations.setText("Export Annotations...");
+ exportAnnotations.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ exportAnnotations_actionPerformed(e);
+ }
+ });
+ statusPanel.setLayout(gridLayout1);
+ jMenu3.setText("Show");
+ showAllSeqs.setText("All Sequences");
+ showAllSeqs.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ showAllSeqs_actionPerformed(e);
+ }
+ });
+ showAllColumns.setText("All Columns");
+ showAllColumns.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ showAllColumns_actionPerformed(e);
+ }
+ });
+ hideMenu.setText("Hide");
+ hideSelSequences.setText("Selected Sequences");
+ hideSelSequences.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ hideSelSequences_actionPerformed(e);
+ }
+ });
+ hideSelColumns.setText("Selected Columns");
+ hideSelColumns.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ hideSelColumns_actionPerformed(e);
+ }
+ });
+ hiddenMarkers.setText("Show Hidden Markers");
+ hiddenMarkers.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ hiddenMarkers_actionPerformed(e);
}
});
- ClustalRealign.setText("Clustal Realign");
- ClustalRealign.addActionListener(new ActionListener()
+ invertColSel.setText("Invert Column Selection");
+ invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
+ event.KeyEvent.VK_I,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
+ |java.awt.event.KeyEvent.ALT_MASK,
+ false));
+ invertColSel.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
- ClustalRealign_actionPerformed(e);
+ invertColSel_actionPerformed(e);
}
});
+ tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
+ {
+ public void stateChanged(ChangeEvent evt)
+ {
+ JTabbedPane pane = (JTabbedPane)evt.getSource();
+ int sel = pane.getSelectedIndex();
+ tabSelectionChanged(sel);
+ }
+ });
+ tabbedPane.addMouseListener(new MouseAdapter()
+ {
+ public void mousePressed(MouseEvent e)
+ {
+ tabbedPane_mousePressed(e);
+ }
+ });
+ tabbedPane.addFocusListener(new FocusAdapter()
+ {
+ public void focusGained(FocusEvent e)
+ {
+ tabbedPane_focusGained(e);
+ }
+ });
+ save.setText("Save");
+ save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
+ KeyEvent.VK_S, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+ save.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ save_actionPerformed(e);
+ }
+ });
+ reload.setEnabled(false);
+ reload.setText("Reload");
+ reload.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ reload_actionPerformed(e);
+ }
+ });
+ newView.setText("New View");
+ newView.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
+ KeyEvent.VK_T, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+ newView.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ newView_actionPerformed(e);
+ }
+ });
+ tabbedPane.setToolTipText(" Right-click to rename tab"
+ +"
Press X to eXpand tabs, G to reGroup.");
+ textColour.setText("Text Colour");
+ textColour.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ textColour_actionPerformed(e);
+ }
+ });
+ jMenu1.setText("Format");
+ jCheckBoxMenuItem1.setText("Right Align Ids");
+ jMenu4.setText("Select");
+ idRightAlign.setText("Right Align Sequence Id");
+ idRightAlign.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ idRightAlign_actionPerformed(e);
+ }
+ });
+
alignFrameMenuBar.add(fileMenu);
alignFrameMenuBar.add(editMenu);
- alignFrameMenuBar.add(searchMenu);
+ alignFrameMenuBar.add(jMenu4);
alignFrameMenuBar.add(viewMenu);
+ alignFrameMenuBar.add(jMenu1);
alignFrameMenuBar.add(colourMenu);
alignFrameMenuBar.add(calculateMenu);
- fileMenu.add(saveAlignmentMenu);
- fileMenu.add(jMenu2);
+ alignFrameMenuBar.add(webService);
+ fileMenu.add(fetchSequence);
+ fileMenu.add(addSequenceMenu);
+ fileMenu.add(reload);
+ fileMenu.addSeparator();
+ fileMenu.add(vamsasStore);
+ fileMenu.add(save);
+ fileMenu.add(saveAs);
fileMenu.add(outputTextboxMenu);
fileMenu.add(printMenuItem);
fileMenu.addSeparator();
+ fileMenu.add(jMenu2);
+ fileMenu.add(exportFeatures);
+ fileMenu.add(exportAnnotations);
fileMenu.add(LoadtreeMenuItem);
+ fileMenu.add(associatedData);
fileMenu.addSeparator();
fileMenu.add(closeMenuItem);
editMenu.add(undoMenuItem);
editMenu.add(redoMenuItem);
editMenu.add(cut);
editMenu.add(copy);
- editMenu.add(jMenu1);
+ editMenu.add(pasteMenu);
editMenu.add(delete);
editMenu.addSeparator();
- editMenu.add(selectAllSequenceMenuItem);
- editMenu.add(deselectAllSequenceMenuItem);
- editMenu.add(invertSequenceMenuItem);
- editMenu.add(deleteGroups);
- editMenu.addSeparator();
editMenu.add(remove2LeftMenuItem);
editMenu.add(remove2RightMenuItem);
editMenu.add(removeGappedColumnMenuItem);
@@ -923,23 +1224,19 @@ public class GAlignFrame
editMenu.add(removeRedundancyMenuItem);
editMenu.addSeparator();
editMenu.add(padGapsMenuitem);
- searchMenu.add(findMenuItem);
- viewMenu.add(font);
+ viewMenu.add(newView);
+ viewMenu.addSeparator();
+ viewMenu.add(jMenu3);
+ viewMenu.add(hideMenu);
viewMenu.addSeparator();
- viewMenu.add(wrapMenuItem);
- viewMenu.add(fullSeqId);
- viewMenu.add(scaleAbove);
- viewMenu.add(scaleLeft);
- viewMenu.add(scaleRight);
- viewMenu.add(viewBoxesMenuItem);
- viewMenu.add(viewTextMenuItem);
- viewMenu.add(colourTextMenuItem);
- viewMenu.add(renderGapsMenuItem);
viewMenu.add(annotationPanelMenuItem);
- viewMenu.add(sequenceFeatures);
+ viewMenu.addSeparator();
+ viewMenu.add(showSeqFeatures);
+ viewMenu.add(featureSettings);
viewMenu.addSeparator();
viewMenu.add(overviewMenuItem);
colourMenu.add(applyToAllGroups);
+ colourMenu.add(textColour);
colourMenu.addSeparator();
colourMenu.add(noColourmenuItem);
colourMenu.add(clustalColour);
@@ -959,20 +1256,18 @@ public class GAlignFrame
colourMenu.add(modifyConservation);
colourMenu.add(abovePIDThreshold);
colourMenu.add(modifyPID);
+ colourMenu.add(annotationColour);
calculateMenu.add(sort);
calculateMenu.add(calculate);
calculateMenu.addSeparator();
calculateMenu.add(pairwiseAlignmentMenuItem);
calculateMenu.add(PCAMenuItem);
calculateMenu.addSeparator();
- calculateMenu.add(webService);
- webService.add(clustalAlignMenuItem);
- webService.add(msaAlignMenuItem);
- webService.add(jnet);
- webService.add(ClustalRealign);
- this.getContentPane().add(statusBar, BorderLayout.SOUTH);
- jMenu1.add(pasteNew);
- jMenu1.add(pasteThis);
+ calculateMenu.add(showTranslation);
+ calculateMenu.add(autoCalculate);
+ webServiceNoServices=new JMenuItem("");
+ webService.add(webServiceNoServices);pasteMenu.add(pasteNew);
+ pasteMenu.add(pasteThis);
sort.add(sortIDMenuItem);
sort.add(sortGroupMenuItem);
sort.add(sortPairwiseMenuItem);
@@ -983,17 +1278,72 @@ public class GAlignFrame
jMenu2.add(htmlMenuItem);
jMenu2.add(epsFile);
jMenu2.add(createPNG);
+ addSequenceMenu.add(addFromFile);
+ addSequenceMenu.add(addFromText);
+ addSequenceMenu.add(addFromURL);
+ this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
+ statusPanel.add(statusBar, null);
+ this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
+ jMenu3.add(showAllColumns);
+ jMenu3.add(showAllSeqs);
+ hideMenu.add(hideSelColumns);
+ hideMenu.add(hideSelSequences);
+ jMenu1.add(font);
+ jMenu1.addSeparator();
+ jMenu1.add(wrapMenuItem);
+ jMenu1.add(scaleAbove);
+ jMenu1.add(scaleLeft);
+ jMenu1.add(scaleRight);
+ jMenu1.add(seqLimits);
+ jMenu1.add(idRightAlign);
+ jMenu1.add(hiddenMarkers);
+ jMenu1.add(viewBoxesMenuItem);
+ jMenu1.add(viewTextMenuItem);
+ jMenu1.add(colourTextMenuItem);
+ jMenu1.add(renderGapsMenuItem);
+ jMenu4.add(findMenuItem);
+ jMenu4.addSeparator();
+ jMenu4.add(selectAllSequenceMenuItem);
+ jMenu4.add(deselectAllSequenceMenuItem);
+ jMenu4.add(invertSequenceMenuItem);
+ jMenu4.add(invertColSel);
+ jMenu4.add(deleteGroups);
}
protected void outputText_actionPerformed(ActionEvent e)
{
}
+ public void addFromFile_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ public void addFromText_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ public void addFromURL_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ public void exportFeatures_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ public void exportAnnotations_actionPerformed(ActionEvent e)
+ {
+
+ }
+
protected void htmlMenuItem_actionPerformed(ActionEvent e)
{
}
- protected void closeMenuItem_actionPerformed(ActionEvent e)
+ protected void closeMenuItem_actionPerformed(boolean b)
{
}
@@ -1097,10 +1447,6 @@ public class GAlignFrame
{
}
- protected void clustalAlignMenuItem_actionPerformed(ActionEvent e)
- {
- }
-
protected void clustalColour_actionPerformed(ActionEvent e)
{
}
@@ -1169,7 +1515,7 @@ public class GAlignFrame
{
}
- public void sequenceFeatures_actionPerformed(ActionEvent actionEvent)
+ public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
{
}
@@ -1213,10 +1559,16 @@ public class GAlignFrame
{
}
- protected void fullSeqId_actionPerformed(ActionEvent e)
+ protected void seqLimit_actionPerformed(ActionEvent e)
{
}
+ public void seqDBRef_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+
public void createEPS(java.io.File f)
{
}
@@ -1249,27 +1601,145 @@ public class GAlignFrame
{
}
- protected void preferences_actionPerformed(ActionEvent e)
+
+
+ protected void saveAs_actionPerformed(ActionEvent e)
{
}
- protected void msaAlignMenuItem_actionPerformed(ActionEvent e)
+ protected void padGapsMenuitem_actionPerformed(ActionEvent e)
{
}
- protected void alignFrameMenuBar_ancestorAdded(AncestorEvent event)
+
+ public void vamsasStore_actionPerformed(ActionEvent e)
{
+
}
- protected void saveAlignmentMenu_actionPerformed(ActionEvent e)
+ public void vamsasLoad_actionPerformed(ActionEvent e)
{
+
}
- protected void padGapsMenuitem_actionPerformed(ActionEvent e)
+ public void showTranslation_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ public void featureSettings_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ public void fetchSequence_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ public void smoothFont_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ public void annotationColour_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+
+ public void associatedData_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ public void autoCalculate_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ public void showAllSeqs_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ public void showAllColumns_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ public void hideSelSequences_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ public void hideSelColumns_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ public void hiddenMarkers_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ public void findPdbId_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ public void enterPdbId_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ public void pdbFile_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ public void invertColSel_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ public void tabSelectionChanged(int sel)
+ {
+
+ }
+
+ public void tabbedPane_mousePressed(MouseEvent e)
{
+
+ }
+
+ public void tabbedPane_focusGained(FocusEvent e)
+ {
+ requestFocus();
}
- protected void ClustalRealign_actionPerformed(ActionEvent e)
+ public void save_actionPerformed(ActionEvent e)
{
+
+ }
+
+ public void reload_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ public void newView_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ public void textColour_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ public void idRightAlign_actionPerformed(ActionEvent e)
+ {
+
}
}