X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGAlignFrame.java;h=1b89d71c9848945444d28735db4be89efde76911;hb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;hp=5a404eb255c71b6fc45d5e8a96f0eeb4768d6fd7;hpb=3e52a9c5f970c4ea43a648296893a2aa58ebd137;p=jalview.git
diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 5a404eb..1b89d71 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) 2007 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
@@ -21,6 +21,7 @@ package jalview.jbgui;
import java.awt.*;
import java.awt.event.*;
import javax.swing.*;
+import javax.swing.event.*;
import jalview.schemes.*;
@@ -53,10 +54,9 @@ 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();
@@ -84,7 +84,6 @@ 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 showSeqFeatures = new JCheckBoxMenuItem();
protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
@@ -92,7 +91,7 @@ public class GAlignFrame
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();
@@ -113,15 +112,10 @@ public class GAlignFrame
protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
protected ButtonGroup colours = new ButtonGroup();
JMenuItem vamsasStore = new JMenuItem();
- protected JCheckBoxMenuItem showTranslation = new JCheckBoxMenuItem();
+ protected JMenuItem showTranslation = new JMenuItem();
public JMenuItem featureSettings = new JMenuItem();
JMenuItem fetchSequence = new JMenuItem();
- protected JCheckBoxMenuItem smoothFont = new JCheckBoxMenuItem();
JMenuItem annotationColour = new JMenuItem();
- JMenuItem fetchSeqFeatures = new JMenuItem();
-
-
-
JMenuItem associatedData = new JMenuItem();
protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
JMenu addSequenceMenu = new JMenu();
@@ -130,21 +124,40 @@ public class GAlignFrame
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();
+ protected JMenuItem reload = new JMenuItem();
+ JMenuItem newView = new JMenuItem();
+ JMenuItem textColour = new JMenuItem();
+ JMenu formatMenu = new JMenu();
+ JMenu selectMenu = new JMenu();
+ protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
+ protected JMenuItem gatherViews = new JMenuItem();
+ protected JMenuItem expandViews = new JMenuItem();
+ JMenuItem pageSetup = new JMenuItem();
public GAlignFrame()
{
-
-
try
{
jbInit();
setJMenuBar(alignFrameMenuBar);
// 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++)
{
- JMenuItem 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)
@@ -160,45 +173,61 @@ 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)
+ if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
{
java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
getUserColourSchemes().keys();
while (userColours.hasMoreElements())
{
- final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.
+ 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))
{
- public void mousePressed(MouseEvent 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
{
- if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
+ radioItem.addActionListener(new ActionListener()
{
- 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)
+ public void actionPerformed(ActionEvent evt)
{
- jalview.gui.UserDefinedColours.removeColourFromDefaults(radioItem.getText());
- colourMenu.remove(radioItem);
+ userDefinedColour_actionPerformed(evt);
}
- else
- radioItem.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent evt)
- {
- userDefinedColour_actionPerformed(evt);
- }
- });
- }
+ });
}
- });
+ }
+ }
+ });
radioItem.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent evt)
@@ -226,7 +255,6 @@ public class GAlignFrame
setColourSelected(jalview.bin.Cache.getDefault("DEFAULT_COLOUR", "None"));
-
}
public void setColourSelected(String defaultColour)
@@ -239,8 +267,8 @@ public class GAlignFrame
switch (index)
{
case ColourSchemeProperty.NONE:
- noColourmenuItem.setSelected(true);
- break;
+ noColourmenuItem.setSelected(true);
+ break;
case ColourSchemeProperty.CLUSTAL:
clustalColour.setSelected(true);
@@ -307,26 +335,27 @@ 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");
@@ -334,7 +363,7 @@ 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));
@@ -358,7 +387,10 @@ 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)
@@ -367,6 +399,9 @@ 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)
@@ -375,6 +410,9 @@ 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)
@@ -383,6 +421,9 @@ 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()
{
@@ -392,6 +433,10 @@ 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)
@@ -442,6 +487,9 @@ 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()
{
@@ -491,7 +539,6 @@ public class GAlignFrame
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");
@@ -602,7 +649,8 @@ public class GAlignFrame
});
annotationPanelMenuItem.setActionCommand("");
annotationPanelMenuItem.setText("Show Annotations");
- annotationPanelMenuItem.setState( jalview.bin.Cache.getDefault("SHOW_ANNOTATIONS",true));
+ annotationPanelMenuItem.setState(jalview.bin.Cache.getDefault(
+ "SHOW_ANNOTATIONS", true));
annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -635,7 +683,6 @@ public class GAlignFrame
}
});
undoMenuItem.setEnabled(false);
- undoMenuItem.setMnemonic('Z');
undoMenuItem.setText("Undo");
undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
java.awt.event.KeyEvent.VK_Z,
@@ -648,8 +695,9 @@ 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)
@@ -681,7 +729,9 @@ public class GAlignFrame
wrapMenuItem_actionPerformed(e);
}
});
- printMenuItem.setText("Print");
+ 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)
@@ -709,8 +759,6 @@ public class GAlignFrame
findMenuItem_actionPerformed(e);
}
});
- searchMenu.setText("Search");
-
abovePIDThreshold.setText("Above Identity Threshold");
abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
{
@@ -736,6 +784,8 @@ 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)
@@ -747,7 +797,6 @@ 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()
{
@@ -760,7 +809,6 @@ 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)
@@ -769,6 +817,8 @@ 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)
@@ -776,12 +826,12 @@ 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)
@@ -790,6 +840,9 @@ 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)
@@ -798,7 +851,6 @@ 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)
@@ -825,7 +877,7 @@ public class GAlignFrame
});
seqLimits.setText("Show Sequence Limits");
- seqLimits.setState( jalview.bin.Cache.getDefault("SHOW_JVSUFFIX",true));
+ seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
seqLimits.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -897,11 +949,26 @@ public class GAlignFrame
});
sortByTreeMenu.setText("By Tree Order");
sort.setText("Sort");
+ sort.addMenuListener(new MenuListener()
+ {
+ public void menuSelected(MenuEvent e)
+ {
+ buildTreeMenu();
+ }
+
+ public void menuDeselected(MenuEvent e)
+ {
+ }
+
+ public void menuCanceled(MenuEvent e)
+ {
+ }
+ });
calculate.setText("Calculate Tree");
- jMenu2.setText("Export");
+ jMenu2.setText("Export Image");
padGapsMenuitem.setText("Pad Gaps");
- padGapsMenuitem.setState( jalview.bin.Cache.getDefault("PAD_GAPS", false));
+ padGapsMenuitem.setState(jalview.bin.Cache.getDefault("PAD_GAPS", false));
padGapsMenuitem.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -927,14 +994,6 @@ public class GAlignFrame
}
});
- /* tabbedPane.addChangeListener(new ChangeListener()
- {
- public void stateChanged(ChangeEvent ece)
- {
-
- tabSelected();
- }
- });*/
featureSettings.setText("Feature Settings...");
featureSettings.addActionListener(new ActionListener()
{
@@ -951,15 +1010,7 @@ public class GAlignFrame
fetchSequence_actionPerformed(e);
}
});
- smoothFont.setText("Smooth Fonts");
- smoothFont.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- smoothFont_actionPerformed(e);
- }
- });
- smoothFont.setState( jalview.bin.Cache.getDefault("ANTI_ALIAS",false));
+
annotationColour.setText("By Annotation...");
annotationColour.addActionListener(new ActionListener()
{
@@ -968,14 +1019,6 @@ public class GAlignFrame
annotationColour_actionPerformed(e);
}
});
- fetchSeqFeatures.setText("Fetch Sequence Features");
- fetchSeqFeatures.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- fetchSeqFeatures_actionPerformed(e);
- }
- });
associatedData.setText("Load Features / Annotations");
associatedData.addActionListener(new ActionListener()
{
@@ -985,7 +1028,7 @@ public class GAlignFrame
}
});
autoCalculate.setText("Autocalculate Consensus");
- autoCalculate.setState( jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true));
+ autoCalculate.setState(jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true));
autoCalculate.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -1034,22 +1077,186 @@ public class GAlignFrame
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);
+ }
+ });
+ 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)
+ {
+ 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);
+ }
+ });
+ formatMenu.setText("Format");
+ selectMenu.setText("Select");
+ idRightAlign.setText("Right Align Sequence Id");
+ idRightAlign.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ idRightAlign_actionPerformed(e);
+ }
+ });
+ gatherViews.setEnabled(false);
+ gatherViews.setText("Gather Views");
+ gatherViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
+ event.KeyEvent.VK_G, 0, false));
+ gatherViews.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ gatherViews_actionPerformed(e);
+ }
+ });
+ expandViews.setEnabled(false);
+ expandViews.setText("Expand Views");
+ expandViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
+ event.KeyEvent.VK_X, 0, false));
+ expandViews.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ expandViews_actionPerformed(e);
+ }
+ });
+ pageSetup.setText("Page Setup ...");
+ pageSetup.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ pageSetup_actionPerformed(e);
+ }
+ });
+
alignFrameMenuBar.add(fileMenu);
alignFrameMenuBar.add(editMenu);
- alignFrameMenuBar.add(searchMenu);
+ alignFrameMenuBar.add(selectMenu);
alignFrameMenuBar.add(viewMenu);
+ alignFrameMenuBar.add(formatMenu);
alignFrameMenuBar.add(colourMenu);
alignFrameMenuBar.add(calculateMenu);
alignFrameMenuBar.add(webService);
- fileMenu.add(addSequenceMenu);
fileMenu.add(fetchSequence);
+ fileMenu.add(addSequenceMenu);
+ fileMenu.add(reload);
fileMenu.addSeparator();
fileMenu.add(vamsasStore);
- fileMenu.add(saveAlignmentMenu);
- fileMenu.add(jMenu2);
+ fileMenu.add(save);
+ fileMenu.add(saveAs);
fileMenu.add(outputTextboxMenu);
+ fileMenu.add(pageSetup);
fileMenu.add(printMenuItem);
fileMenu.addSeparator();
+ fileMenu.add(jMenu2);
fileMenu.add(exportFeatures);
fileMenu.add(exportAnnotations);
fileMenu.add(LoadtreeMenuItem);
@@ -1060,14 +1267,9 @@ public class GAlignFrame
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);
@@ -1075,27 +1277,21 @@ public class GAlignFrame
editMenu.add(removeRedundancyMenuItem);
editMenu.addSeparator();
editMenu.add(padGapsMenuitem);
- searchMenu.add(findMenuItem);
- viewMenu.add(font);
- viewMenu.add(smoothFont);
+ viewMenu.add(newView);
+ viewMenu.add(expandViews);
+ viewMenu.add(gatherViews);
+ viewMenu.addSeparator();
+ viewMenu.add(jMenu3);
+ viewMenu.add(hideMenu);
viewMenu.addSeparator();
- viewMenu.add(wrapMenuItem);
- viewMenu.add(seqLimits);
- 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.addSeparator();
- viewMenu.add(fetchSeqFeatures);
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);
@@ -1124,14 +1320,14 @@ public class GAlignFrame
calculateMenu.addSeparator();
calculateMenu.add(showTranslation);
calculateMenu.add(autoCalculate);
- webServiceNoServices=new JMenuItem("");
+ webServiceNoServices = new JMenuItem("");
webService.add(webServiceNoServices);
- this.getContentPane().add(statusBar, BorderLayout.SOUTH);
- jMenu1.add(pasteNew);
- jMenu1.add(pasteThis);
+ pasteMenu.add(pasteNew);
+ pasteMenu.add(pasteThis);
sort.add(sortIDMenuItem);
sort.add(sortGroupMenuItem);
sort.add(sortPairwiseMenuItem);
+ sort.add(sortByTreeMenu);
calculate.add(averageDistanceTreeMenuItem);
calculate.add(neighbourTreeMenuItem);
calculate.add(avDistanceTreeBlosumMenuItem);
@@ -1142,6 +1338,33 @@ public class GAlignFrame
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);
+ formatMenu.add(font);
+ formatMenu.addSeparator();
+ formatMenu.add(wrapMenuItem);
+ formatMenu.add(scaleAbove);
+ formatMenu.add(scaleLeft);
+ formatMenu.add(scaleRight);
+ formatMenu.add(seqLimits);
+ formatMenu.add(idRightAlign);
+ formatMenu.add(hiddenMarkers);
+ formatMenu.add(viewBoxesMenuItem);
+ formatMenu.add(viewTextMenuItem);
+ formatMenu.add(colourTextMenuItem);
+ formatMenu.add(renderGapsMenuItem);
+ selectMenu.add(findMenuItem);
+ selectMenu.addSeparator();
+ selectMenu.add(selectAllSequenceMenuItem);
+ selectMenu.add(deselectAllSequenceMenuItem);
+ selectMenu.add(invertSequenceMenuItem);
+ selectMenu.add(invertColSel);
+ selectMenu.add(deleteGroups);
}
protected void outputText_actionPerformed(ActionEvent e)
@@ -1177,7 +1400,7 @@ public class GAlignFrame
{
}
- protected void closeMenuItem_actionPerformed(ActionEvent e)
+ protected void closeMenuItem_actionPerformed(boolean b)
{
}
@@ -1402,7 +1625,6 @@ public class GAlignFrame
}
-
public void createEPS(java.io.File f)
{
}
@@ -1435,9 +1657,7 @@ public class GAlignFrame
{
}
-
-
- protected void saveAlignmentMenu_actionPerformed(ActionEvent e)
+ protected void saveAs_actionPerformed(ActionEvent e)
{
}
@@ -1445,7 +1665,6 @@ public class GAlignFrame
{
}
-
public void vamsasStore_actionPerformed(ActionEvent e)
{
@@ -1481,17 +1700,117 @@ public class GAlignFrame
}
- public void fetchSeqFeatures_actionPerformed(ActionEvent e)
+ public void associatedData_actionPerformed(ActionEvent e)
{
}
- public void associatedData_actionPerformed(ActionEvent e)
+ public void autoCalculate_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();
+ }
+
+ 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)
+ {
+
+ }
+
+ public void expandViews_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ public void gatherViews_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ public void buildTreeMenu()
+ {
+
+ }
+
+ public void pageSetup_actionPerformed(ActionEvent e)
{
}