X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGAlignFrame.java;h=bf45112c269c6f480da7d3f525b5851de958f162;hb=88bc025708f1b7881bababb92d14351760e0f9da;hp=7fb94f9afa3e7c3a74e6eb5a5b97c6943b24f48a;hpb=4a3f84f077dde7be327e3fa679cd58addc5f4ea3;p=jalview.git
diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 7fb94f9..bf45112 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
@@ -88,7 +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();
@@ -96,7 +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();
@@ -120,7 +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();
@@ -142,8 +136,16 @@ public class GAlignFrame
JMenuItem invertColSel = new JMenuItem();
protected JTabbedPane tabbedPane = new JTabbedPane();
JMenuItem save = new JMenuItem();
- JMenuItem jMenuItem1 = new JMenuItem();
- JMenuItem reload = 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();
+ JMenuItem alignmentProperties = new JMenuItem();
public GAlignFrame()
{
try
@@ -154,7 +156,8 @@ 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()
{
@@ -171,45 +174,61 @@ 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)
{
- if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
+ jalview.gui.UserDefinedColours.removeColourFromDefaults(
+ radioItem.getText());
+ colourMenu.remove(radioItem);
+ }
+ else
+ {
+ 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)
@@ -237,7 +256,6 @@ public class GAlignFrame
setColourSelected(jalview.bin.Cache.getDefault("DEFAULT_COLOUR", "None"));
-
}
public void setColourSelected(String defaultColour)
@@ -250,8 +268,8 @@ public class GAlignFrame
switch (index)
{
case ColourSchemeProperty.NONE:
- noColourmenuItem.setSelected(true);
- break;
+ noColourmenuItem.setSelected(true);
+ break;
case ColourSchemeProperty.CLUSTAL:
clustalColour.setSelected(true);
@@ -319,9 +337,11 @@ public class GAlignFrame
throws Exception
{
fileMenu.setText("File");
- saveAs.setText("Save As ...");
+ saveAs.setText("Save As...");
saveAs.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
- KeyEvent.VK_S, java.awt.event.KeyEvent.ALT_MASK, false));
+ KeyEvent.VK_S,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask() |
+ java.awt.event.KeyEvent.SHIFT_MASK, false));
saveAs.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -329,7 +349,6 @@ public class GAlignFrame
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));
@@ -337,7 +356,7 @@ public class GAlignFrame
{
public void actionPerformed(ActionEvent e)
{
- closeMenuItem_actionPerformed(e);
+ closeMenuItem_actionPerformed(false);
}
});
editMenu.setText("Edit");
@@ -345,7 +364,7 @@ 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));
@@ -372,7 +391,7 @@ public class GAlignFrame
invertSequenceMenuItem.setText("Invert Sequence Selection");
invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
java.awt.event.KeyEvent.VK_I,
- java.awt.event.KeyEvent.SHIFT_MASK, false));
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -382,7 +401,8 @@ public class GAlignFrame
});
remove2LeftMenuItem.setText("Remove Left");
remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.
- awt.event.KeyEvent.VK_L, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+ awt.event.KeyEvent.VK_L,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -392,7 +412,8 @@ public class GAlignFrame
});
remove2RightMenuItem.setText("Remove Right");
remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.
- awt.event.KeyEvent.VK_R, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+ awt.event.KeyEvent.VK_R,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -414,7 +435,9 @@ public class GAlignFrame
});
removeAllGapsMenuItem.setText("Remove All Gaps");
removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
- java.awt.event.KeyEvent.VK_G, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), 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)
@@ -466,7 +489,8 @@ public class GAlignFrame
});
removeRedundancyMenuItem.setText("Remove Redundancy...");
removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
- java.awt.event.KeyEvent.VK_D, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+ java.awt.event.KeyEvent.VK_D,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
removeRedundancyMenuItem.addActionListener(new java.awt.event.
ActionListener()
{
@@ -516,7 +540,6 @@ 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");
@@ -627,7 +650,8 @@ 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)
@@ -660,7 +684,6 @@ public class GAlignFrame
}
});
undoMenuItem.setEnabled(false);
- undoMenuItem.setMnemonic('Z');
undoMenuItem.setText("Undo");
undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
java.awt.event.KeyEvent.VK_Z,
@@ -673,7 +696,6 @@ 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));
@@ -708,7 +730,7 @@ 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()
@@ -738,8 +760,6 @@ public class GAlignFrame
findMenuItem_actionPerformed(e);
}
});
- searchMenu.setText("Search");
-
abovePIDThreshold.setText("Above Identity Threshold");
abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
{
@@ -778,7 +798,6 @@ 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()
{
@@ -791,7 +810,6 @@ 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)
@@ -809,12 +827,12 @@ 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)
@@ -823,6 +841,9 @@ 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)
@@ -857,7 +878,7 @@ 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)
@@ -929,11 +950,26 @@ 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 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)
@@ -959,7 +995,6 @@ public class GAlignFrame
}
});
-
featureSettings.setText("Feature Settings...");
featureSettings.addActionListener(new ActionListener()
{
@@ -976,14 +1011,6 @@ public class GAlignFrame
fetchSequence_actionPerformed(e);
}
});
- smoothFont.setText("Smooth Fonts");
- smoothFont.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- smoothFont_actionPerformed(e);
- }
- });
annotationColour.setText("By Annotation...");
annotationColour.addActionListener(new ActionListener()
@@ -1002,7 +1029,7 @@ 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)
@@ -1086,7 +1113,7 @@ public class GAlignFrame
hideSelColumns_actionPerformed(e);
}
});
- hiddenMarkers.setText("Hidden Markers");
+ hiddenMarkers.setText("Show Hidden Markers");
hiddenMarkers.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -1096,7 +1123,10 @@ public class GAlignFrame
});
invertColSel.setText("Invert Column Selection");
invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
- event.KeyEvent.VK_I, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+ event.KeyEvent.VK_I,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
+ | java.awt.event.KeyEvent.ALT_MASK,
+ false));
invertColSel.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -1106,12 +1136,12 @@ 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()
{
@@ -1137,10 +1167,8 @@ public class GAlignFrame
save_actionPerformed(e);
}
});
- reload.setMnemonic('R');
+ reload.setEnabled(false);
reload.setText("Reload");
- // reload.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
- // KeyEvent.VK_R, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
reload.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -1148,11 +1176,81 @@ public class GAlignFrame
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);
+ }
+ });
+ alignmentProperties.setText("Alignment Properties...");
+ alignmentProperties.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent actionEvent)
+ {
+ alignmentProperties();
+ }
+ });
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);
@@ -1164,6 +1262,7 @@ public class GAlignFrame
fileMenu.add(save);
fileMenu.add(saveAs);
fileMenu.add(outputTextboxMenu);
+ fileMenu.add(pageSetup);
fileMenu.add(printMenuItem);
fileMenu.addSeparator();
fileMenu.add(jMenu2);
@@ -1177,15 +1276,9 @@ 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);
@@ -1193,30 +1286,23 @@ 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);
viewMenu.add(featureSettings);
viewMenu.addSeparator();
+ viewMenu.add(alignmentProperties);
+ viewMenu.addSeparator();
viewMenu.add(overviewMenuItem);
colourMenu.add(applyToAllGroups);
+ colourMenu.add(textColour);
colourMenu.addSeparator();
colourMenu.add(noColourmenuItem);
colourMenu.add(clustalColour);
@@ -1245,12 +1331,14 @@ 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);
@@ -1268,6 +1356,26 @@ 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)
@@ -1303,7 +1411,7 @@ public class GAlignFrame
{
}
- protected void closeMenuItem_actionPerformed(ActionEvent e)
+ protected void closeMenuItem_actionPerformed(boolean b)
{
}
@@ -1528,7 +1636,6 @@ public class GAlignFrame
}
-
public void createEPS(java.io.File f)
{
}
@@ -1561,8 +1668,6 @@ public class GAlignFrame
{
}
-
-
protected void saveAs_actionPerformed(ActionEvent e)
{
}
@@ -1571,7 +1676,6 @@ public class GAlignFrame
{
}
-
public void vamsasStore_actionPerformed(ActionEvent e)
{
@@ -1607,7 +1711,6 @@ public class GAlignFrame
}
-
public void associatedData_actionPerformed(ActionEvent e)
{
@@ -1687,4 +1790,44 @@ public class GAlignFrame
{
}
+
+ 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)
+ {
+
+ }
+
+ public void alignmentProperties()
+ {
+
+ }
}