X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGAlignFrame.java;h=1b89d71c9848945444d28735db4be89efde76911;hb=d0b7395c10aec7c5da5a5662fc69783ec78fae8d;hp=4dcd0db1b641573b1a1a1580a7e4a122fae87325;hpb=18967a4d27edeae3477c9244e1706a284e99d6d7;p=jalview.git
diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 4dcd0db..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) 2006 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
@@ -24,10 +24,6 @@ import javax.swing.*;
import javax.swing.event.*;
import jalview.schemes.*;
-import java.awt.BorderLayout;
-
-
-
public class GAlignFrame
extends JInternalFrame
@@ -58,10 +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();
@@ -89,7 +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();
@@ -97,7 +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();
@@ -121,7 +115,6 @@ public class GAlignFrame
protected JMenuItem showTranslation = new JMenuItem();
public JMenuItem featureSettings = new JMenuItem();
JMenuItem fetchSequence = new JMenuItem();
- protected JCheckBoxMenuItem smoothFont = new JCheckBoxMenuItem();
JMenuItem annotationColour = new JMenuItem();
JMenuItem associatedData = new JMenuItem();
protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
@@ -142,6 +135,16 @@ public class GAlignFrame
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
@@ -152,7 +155,8 @@ public class GAlignFrame
// dynamically fill save as menu with available formats
for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
{
- JMenuItem item = new JMenuItem( jalview.io.FormatAdapter.WRITEABLE_FORMATS[i] );
+ JMenuItem item = new JMenuItem(jalview.io.FormatAdapter.
+ WRITEABLE_FORMATS[i]);
item.addActionListener(new java.awt.event.ActionListener()
{
@@ -169,45 +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)
@@ -235,7 +255,6 @@ public class GAlignFrame
setColourSelected(jalview.bin.Cache.getDefault("DEFAULT_COLOUR", "None"));
-
}
public void setColourSelected(String defaultColour)
@@ -248,8 +267,8 @@ public class GAlignFrame
switch (index)
{
case ColourSchemeProperty.NONE:
- noColourmenuItem.setSelected(true);
- break;
+ noColourmenuItem.setSelected(true);
+ break;
case ColourSchemeProperty.CLUSTAL:
clustalColour.setSelected(true);
@@ -316,26 +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");
@@ -343,7 +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));
@@ -370,7 +390,7 @@ public class GAlignFrame
invertSequenceMenuItem.setText("Invert Sequence Selection");
invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
java.awt.event.KeyEvent.VK_I,
- java.awt.event.KeyEvent.CTRL_MASK | java.awt.event.KeyEvent.SHIFT_MASK, false));
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -380,7 +400,8 @@ public class GAlignFrame
});
remove2LeftMenuItem.setText("Remove Left");
remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.
- awt.event.KeyEvent.VK_L, java.awt.event.KeyEvent.CTRL_MASK, false));
+ awt.event.KeyEvent.VK_L,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -390,7 +411,8 @@ public class GAlignFrame
});
remove2RightMenuItem.setText("Remove Right");
remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.
- awt.event.KeyEvent.VK_R, java.awt.event.KeyEvent.CTRL_MASK, false));
+ awt.event.KeyEvent.VK_R,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -401,7 +423,7 @@ public class GAlignFrame
removeGappedColumnMenuItem.setText("Remove Empty Columns");
removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke.
getKeyStroke(java.awt.event.
- KeyEvent.VK_E, java.awt.event.KeyEvent.CTRL_MASK, false));
+ KeyEvent.VK_E, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
removeGappedColumnMenuItem.addActionListener(new java.awt.event.
ActionListener()
{
@@ -412,7 +434,9 @@ public class GAlignFrame
});
removeAllGapsMenuItem.setText("Remove All Gaps");
removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
- java.awt.event.KeyEvent.VK_G, java.awt.event.KeyEvent.CTRL_MASK, false));
+ 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)
@@ -464,7 +488,8 @@ public class GAlignFrame
});
removeRedundancyMenuItem.setText("Remove Redundancy...");
removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
- java.awt.event.KeyEvent.VK_R, java.awt.event.KeyEvent.CTRL_MASK, false));
+ java.awt.event.KeyEvent.VK_D,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
removeRedundancyMenuItem.addActionListener(new java.awt.event.
ActionListener()
{
@@ -514,7 +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");
@@ -625,7 +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)
@@ -650,8 +675,6 @@ public class GAlignFrame
}
});
overviewMenuItem.setText("Overview Window");
- overviewMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
- event.KeyEvent.VK_O, java.awt.event.KeyEvent.CTRL_MASK, false));
overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -660,7 +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,
@@ -673,10 +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, java.awt.event.KeyEvent.CTRL_MASK, false));
+ event.KeyEvent.VK_Y, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
redoMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -708,7 +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)
@@ -736,8 +759,6 @@ public class GAlignFrame
findMenuItem_actionPerformed(e);
}
});
- searchMenu.setText("Search");
-
abovePIDThreshold.setText("Above Identity Threshold");
abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
{
@@ -764,7 +785,7 @@ public class GAlignFrame
});
deleteGroups.setText("Undefine groups");
deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
- event.KeyEvent.VK_U, java.awt.event.KeyEvent.CTRL_MASK, false));
+ event.KeyEvent.VK_U, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
deleteGroups.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -776,7 +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()
{
@@ -789,7 +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)
@@ -798,6 +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)
@@ -805,12 +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)
@@ -819,6 +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)
@@ -827,7 +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)
@@ -854,7 +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)
@@ -926,13 +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.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
- event.KeyEvent.VK_P, java.awt.event.KeyEvent.CTRL_MASK, false));
- 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)
@@ -958,14 +994,6 @@ public class GAlignFrame
}
});
- /* tabbedPane.addChangeListener(new ChangeListener()
- {
- public void stateChanged(ChangeEvent ece)
- {
-
- tabSelected();
- }
- });*/
featureSettings.setText("Feature Settings...");
featureSettings.addActionListener(new ActionListener()
{
@@ -982,15 +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()
{
@@ -1008,7 +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)
@@ -1092,8 +1112,7 @@ public class GAlignFrame
hideSelColumns_actionPerformed(e);
}
});
- hiddenMarkers.setText("Hidden Markers");
- hiddenMarkers.setState(true);
+ hiddenMarkers.setText("Show Hidden Markers");
hiddenMarkers.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -1103,7 +1122,10 @@ public class GAlignFrame
});
invertColSel.setText("Invert Column Selection");
invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
- event.KeyEvent.VK_I, java.awt.event.KeyEvent.CTRL_MASK, false));
+ event.KeyEvent.VK_I,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
+ | java.awt.event.KeyEvent.ALT_MASK,
+ false));
invertColSel.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -1113,12 +1135,12 @@ public class GAlignFrame
});
tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
{
- public void stateChanged(ChangeEvent evt)
- {
- JTabbedPane pane = (JTabbedPane)evt.getSource();
- int sel = pane.getSelectedIndex();
- tabSelectionChanged(sel);
- }
+ public void stateChanged(ChangeEvent evt)
+ {
+ JTabbedPane pane = (JTabbedPane) evt.getSource();
+ int sel = pane.getSelectedIndex();
+ tabSelectionChanged(sel);
+ }
});
tabbedPane.addMouseListener(new MouseAdapter()
{
@@ -1134,23 +1156,107 @@ public class GAlignFrame
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);
@@ -1161,15 +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(invertColSel);
- editMenu.add(deleteGroups);
- editMenu.addSeparator();
editMenu.add(remove2LeftMenuItem);
editMenu.add(remove2RightMenuItem);
editMenu.add(removeGappedColumnMenuItem);
@@ -1177,23 +1277,13 @@ 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.add(hiddenMarkers);
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(showSeqFeatures);
@@ -1201,6 +1291,7 @@ public class GAlignFrame
viewMenu.addSeparator();
viewMenu.add(overviewMenuItem);
colourMenu.add(applyToAllGroups);
+ colourMenu.add(textColour);
colourMenu.addSeparator();
colourMenu.add(noColourmenuItem);
colourMenu.add(clustalColour);
@@ -1229,12 +1320,14 @@ public class GAlignFrame
calculateMenu.addSeparator();
calculateMenu.add(showTranslation);
calculateMenu.add(autoCalculate);
- webServiceNoServices=new JMenuItem("");
- webService.add(webServiceNoServices);jMenu1.add(pasteNew);
- jMenu1.add(pasteThis);
+ webServiceNoServices = new JMenuItem("");
+ webService.add(webServiceNoServices);
+ 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);
@@ -1252,6 +1345,26 @@ public class GAlignFrame
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)
@@ -1287,7 +1400,7 @@ public class GAlignFrame
{
}
- protected void closeMenuItem_actionPerformed(ActionEvent e)
+ protected void closeMenuItem_actionPerformed(boolean b)
{
}
@@ -1512,7 +1625,6 @@ public class GAlignFrame
}
-
public void createEPS(java.io.File f)
{
}
@@ -1545,9 +1657,7 @@ public class GAlignFrame
{
}
-
-
- protected void saveAlignmentMenu_actionPerformed(ActionEvent e)
+ protected void saveAs_actionPerformed(ActionEvent e)
{
}
@@ -1555,7 +1665,6 @@ public class GAlignFrame
{
}
-
public void vamsasStore_actionPerformed(ActionEvent e)
{
@@ -1591,7 +1700,6 @@ public class GAlignFrame
}
-
public void associatedData_actionPerformed(ActionEvent e)
{
@@ -1661,4 +1769,49 @@ public class GAlignFrame
{
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)
+ {
+
+ }
}