protected JMenu viewMenu = new JMenu();
protected JMenu colourMenu = new JMenu();
protected JMenu calculateMenu = new JMenu();
- protected JMenu alignMenu = new JMenu();
- protected JMenuItem groupsMenuItem = new JMenuItem();
+ protected JMenu webService = new JMenu();
protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();
protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();
protected JMenuItem invertSequenceMenuItem = new JMenuItem();
- protected JMenuItem deselectAllColumnsMenuItem = new JMenuItem();
protected JMenuItem remove2LeftMenuItem = new JMenuItem();
protected JMenuItem remove2RightMenuItem = new JMenuItem();
protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();
protected JMenuItem removeAllGapsMenuItem = new JMenuItem();
- protected JMenuItem setGapCharMenuItem = new JMenuItem();
protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
protected JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
protected JMenuItem sortPairwiseMenuItem = new JMenuItem();
protected JMenuItem sortIDMenuItem = new JMenuItem();
protected JMenuItem sortGroupMenuItem = new JMenuItem();
- protected JMenuItem sortTreeOrderMenuItem = new JMenuItem();
protected JMenuItem removeRedundancyMenuItem = new JMenuItem();
protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();
protected JMenuItem PCAMenuItem = new JMenuItem();
JMenuItem epsFile = new JMenuItem();
JMenuItem LoadtreeMenuItem = new JMenuItem();
JMenuItem jpred = new JMenuItem();
+ protected JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
+ protected JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
+ protected JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
+ JMenuItem modifyPID = new JMenuItem();
+ JMenuItem modifyConservation = new JMenuItem();
+ protected JMenu sortByTreeMenu = new JMenu();
+ JMenu jMenu2 = new JMenu();
+ JMenu sort = new JMenu();
+ JMenu calculate = new JMenu();
+ JMenuItem preferences = new JMenuItem();
+ JMenuItem msaAlignMenuItem = new JMenuItem();
public GAlignFrame()
{
fileMenu.setMnemonic('F');
fileMenu.setText("File");
saveAlignmentMenu.setMnemonic('L');
- saveAlignmentMenu.setText("Save alignment to local file");
+ saveAlignmentMenu.setText("Save");
closeMenuItem.setMnemonic('C');
closeMenuItem.setText("Close");
closeMenuItem.addActionListener(new java.awt.event.ActionListener()
viewMenu.setText("View");
colourMenu.setText("Colour");
calculateMenu.setText("Calculate");
- alignMenu.setText("Web Service");
- groupsMenuItem.setVisible(false);
- groupsMenuItem.setText("Groups");
- groupsMenuItem.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- groupsMenuItem_actionPerformed(e);
- }
- });
+ webService.setText("Web Service");
selectAllSequenceMenuItem.setText("Select all");
+ selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+ java.awt.event.KeyEvent.VK_A, java.awt.event.KeyEvent.CTRL_MASK, false));
selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
selectAllSequenceMenuItem_actionPerformed(e);
}
});
- deselectAllSequenceMenuItem.setText("Clear selection");
+ deselectAllSequenceMenuItem.setText("Deselect All");
+ deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.
+ getKeyStroke(java.awt.event.
+ KeyEvent.VK_ESCAPE, 0, false));
deselectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
deselectAllSequenceMenuItem_actionPerformed(e);
}
});
- invertSequenceMenuItem.setText("Invert sequence selection");
+ invertSequenceMenuItem.setText("Invert Selection");
invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
invertSequenceMenuItem_actionPerformed(e);
}
});
- deselectAllColumnsMenuItem.setText("Deselect all columns");
- deselectAllColumnsMenuItem.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- deselectAllColumnsMenuItem_actionPerformed(e);
- }
- });
- remove2LeftMenuItem.setText("Remove sequence <- left of selected column");
+ remove2LeftMenuItem.setText("Remove Left");
remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
remove2LeftMenuItem_actionPerformed(e);
}
});
- remove2RightMenuItem.setText("Remove sequence -> right of selected column");
+ remove2RightMenuItem.setText("Remove Right");
remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
remove2RightMenuItem_actionPerformed(e);
}
});
- removeGappedColumnMenuItem.setText("Remove gapped columns");
+ removeGappedColumnMenuItem.setText("Remove Empty Columns");
removeGappedColumnMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
removeGappedColumnMenuItem_actionPerformed(e);
}
});
- removeAllGapsMenuItem.setText("Remove all gaps");
+ removeAllGapsMenuItem.setText("Remove All Gaps");
removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
removeAllGapsMenuItem_actionPerformed(e);
}
});
- setGapCharMenuItem.setText("Set gap character to \".\"");
- setGapCharMenuItem.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- setGapCharMenuItem_actionPerformed(e);
- }
- });
viewBoxesMenuItem.setText("Boxes");
viewBoxesMenuItem.setState(true);
viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
viewTextMenuItem_actionPerformed(e);
}
});
- sortPairwiseMenuItem.setText("Sort by pairwise identity");
+ sortPairwiseMenuItem.setText("Pairwise Identity");
sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
sortPairwiseMenuItem_actionPerformed(e);
}
});
- sortIDMenuItem.setText("Sort by ID");
+ sortIDMenuItem.setText("ID");
sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
sortIDMenuItem_actionPerformed(e);
}
});
- sortGroupMenuItem.setText("Sort by group");
+ sortGroupMenuItem.setText("Group");
sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
sortGroupMenuItem_actionPerformed(e);
}
});
- sortTreeOrderMenuItem.setText("Sort by tree order");
- sortTreeOrderMenuItem.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- sortTreeOrderMenuItem_actionPerformed(e);
- }
- });
- removeRedundancyMenuItem.setText("Remove redundancy");
+ removeRedundancyMenuItem.setText("Remove Redundancy...");
removeRedundancyMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
removeRedundancyMenuItem_actionPerformed(e);
}
});
- pairwiseAlignmentMenuItem.setText("Pairwise alignments");
+ pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");
pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
pairwiseAlignmentMenuItem_actionPerformed(e);
}
});
- PCAMenuItem.setText("Principal component analysis");
+ PCAMenuItem.setText("Principal Component Analysis...");
PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
PCAMenuItem_actionPerformed(e);
}
});
- averageDistanceTreeMenuItem.setText("Average distance tree using PID");
+ averageDistanceTreeMenuItem.setText("Average Distance Using % Identity...");
averageDistanceTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
averageDistanceTreeMenuItem_actionPerformed(e);
}
});
- neighbourTreeMenuItem.setText("Neighbour joining tree using PID");
+ neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity...");
neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
neighbourTreeMenuItem_actionPerformed(e);
}
});
- clustalAlignMenuItem.setText("Clustal alignment");
+ clustalAlignMenuItem.setText("Clustal Alignment...");
clustalAlignMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
statusBar.setText("Status bar");
outputTextboxMenu.setMnemonic('T');
- outputTextboxMenu.setText("Output alignment via textbox");
+ outputTextboxMenu.setText("Output to Textbox");
clustalColour.setSelected(false);
- clustalColour.setText("Clustalx colours");
+ clustalColour.setText("Clustalx");
clustalColour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
clustalColour_actionPerformed(e);
}
});
- zappoColour.setText("Zappo colour scheme");
+ zappoColour.setText("Zappo");
zappoColour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
zappoColour_actionPerformed(e);
}
});
- taylorColour.setText("Taylor colour scheme");
+ taylorColour.setText("Taylor");
taylorColour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
taylorColour_actionPerformed(e);
}
});
- hydrophobicityColour.setText("By hydrophobicity");
+ hydrophobicityColour.setText("Hydrophobicity");
hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
hydrophobicityColour_actionPerformed(e);
}
});
- helixColour.setText("Helix propensity");
+ helixColour.setText("Helix Propensity");
helixColour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
helixColour_actionPerformed(e);
}
});
- strandColour.setText("Strand propensity");
+ strandColour.setText("Strand Propensity");
strandColour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
strandColour_actionPerformed(e);
}
});
- turnColour.setText("Turn propensity");
+ turnColour.setText("Turn Propensity");
turnColour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
turnColour_actionPerformed(e);
}
});
- buriedColour.setText("Buried index");
+ buriedColour.setText("Buried Index");
buriedColour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
buriedColour_actionPerformed(e);
}
});
- userDefinedColour.setText("User defined colours");
+ userDefinedColour.setText("User Defined...");
userDefinedColour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
PIDColour_actionPerformed(e);
}
});
- BLOSUM62Colour.setText("BLOSUM62 score");
+ BLOSUM62Colour.setText("BLOSUM62 Score");
BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
BLOSUM62Colour_actionPerformed(e);
}
});
- avDistanceTreeBlosumMenuItem.setText("Average distance tree using BLOSUM62");
+ avDistanceTreeBlosumMenuItem.setText("Average Distance using BLOSUM62...");
avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
avTreeBlosumMenuItem_actionPerformed(e);
}
});
- njTreeBlosumMenuItem.setText("Neighbour joining tree using BLOSUM62");
+ njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62...");
njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
}
});
annotationPanelMenuItem.setActionCommand("");
- annotationPanelMenuItem.setText("Annotation Panel");
+ annotationPanelMenuItem.setText("Show Annotations");
annotationPanelMenuItem.setState(true);
annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener()
{
annotationPanelMenuItem_actionPerformed(e);
}
});
- colourTextMenuItem.setText("Colour text");
+ colourTextMenuItem.setText("Colour Text");
colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
colourTextMenuItem_actionPerformed(e);
}
});
- htmlMenuItem.setText("Output as HTML");
+ htmlMenuItem.setText("HTML");
htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
htmlMenuItem_actionPerformed(e);
}
});
- overviewMenuItem.setText("Overview window");
+ overviewMenuItem.setText("Overview Window...");
overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
undoMenuItem.setEnabled(false);
undoMenuItem.setMnemonic('Z');
undoMenuItem.setText("Undo");
+ undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
+ event.KeyEvent.VK_Z, java.awt.event.KeyEvent.CTRL_MASK, false));
undoMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
redoMenuItem_actionPerformed(e);
}
});
- conservationMenuItem.setText("By conservation");
+ conservationMenuItem.setText("By Conservation");
conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
noColourmenuItem_actionPerformed(e);
}
});
- wrapMenuItem.setText("Wrap alignment");
+ wrapMenuItem.setText("Wrap");
wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
printMenuItem_actionPerformed(e);
}
});
- renderGapsMenuItem.setText("Render gaps");
+ renderGapsMenuItem.setText("Show Gaps");
renderGapsMenuItem.setState(true);
renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
{
renderGapsMenuItem_actionPerformed(e);
}
});
- findMenuItem.setText("Find");
+ findMenuItem.setText("Find...");
+ findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
+ event.KeyEvent.VK_F, java.awt.event.KeyEvent.CTRL_MASK, false));
findMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
});
searchMenu.setText("Search");
- abovePIDThreshold.setText("Above PID threshold");
+ abovePIDThreshold.setText("Above Identity threshold");
abovePIDThreshold.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(ActionEvent e) {
abovePIDThreshold_actionPerformed(e);
sequenceFeatures_actionPerformed(actionEvent);
}
});
- nucleotideColour.setText("Nucleotide colours");
+ nucleotideColour.setText("Nucleotide");
nucleotideColour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
}
});
deleteGroups.setSelected(false);
- deleteGroups.setText("Delete all groups");
+ deleteGroups.setText("Undefine groups");
deleteGroups.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
}
});
copy.setText("Copy");
+ copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
+ KeyEvent.VK_C, java.awt.event.KeyEvent.CTRL_MASK, false));
copy.setMnemonic(KeyEvent.VK_C);
copy.addActionListener(new java.awt.event.ActionListener()
}
});
cut.setText("Cut");
+ cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
+ KeyEvent.VK_X, java.awt.event.KeyEvent.CTRL_MASK, false));
cut.setMnemonic(KeyEvent.VK_X);
cut.addActionListener(new java.awt.event.ActionListener()
{
jMenu1.setMnemonic('V');
jMenu1.setText("Paste");
pasteNew.setText("to new alignment");
+ pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
+ KeyEvent.VK_V, java.awt.event.KeyEvent.CTRL_MASK, false));
pasteNew.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
pasteThis_actionPerformed(e);
}
});
- applyToAllGroups.setText("Apply colour to all groups");
+ applyToAllGroups.setText("Apply Colour To All Groups");
applyToAllGroups.setState(true);
applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
{
}
});
createPNG.setActionCommand("Save as PNG Image");
- createPNG.setText("Save as PNG Image");
- font.setText("Change Font");
+ createPNG.setText("PNG");
+ font.setText("Font...");
font.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
font_actionPerformed(e);
}
});
- fullSeqId.setText("Show full sequence id");
+ fullSeqId.setText("Show Full Sequence ID");
fullSeqId.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
fullSeqId_actionPerformed(e);
}
});
- epsFile.setText("Save as EPS file");
+ epsFile.setText("EPS");
epsFile.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
}
});
LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");
- LoadtreeMenuItem.setText("Load assocated tree");
+ LoadtreeMenuItem.setText("Load Assocated Tree");
LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(ActionEvent e)
{
LoadtreeMenuItem_actionPerformed(e);
}
});
- jpred.setText("JPred");
+ jpred.setText("JPred...");
jpred.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()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ scaleAbove_actionPerformed(e);
+ }
+ });
+ scaleLeft.setVisible(false);
+ scaleLeft.setSelected(true);
+ scaleLeft.setText("Scale Left");
+ scaleLeft.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ scaleLeft_actionPerformed(e);
+ }
+ });
+ scaleRight.setVisible(false);
+ scaleRight.setSelected(true);
+ scaleRight.setText("Scale Right");
+ scaleRight.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ scaleRight_actionPerformed(e);
+ }
+ });
+ modifyPID.setText("Modify Identity Threshold...");
+ modifyPID.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ modifyPID_actionPerformed(e);
+ }
+ });
+ modifyConservation.setText("Modify Conservation Threshold...");
+ modifyConservation.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ modifyConservation_actionPerformed(e);
+ }
+ });
+ sortByTreeMenu.setText("Tree Order");
+ jMenu2.setText("Save as");
+ sort.setText("Sort");
+ calculate.setText("Calculate Tree");
+ preferences.setText("Preferences...");
+ preferences.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ preferences_actionPerformed(e);
+ }
+ });
+ msaAlignMenuItem.setText("Muscle Alignment...");
+ msaAlignMenuItem.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(ActionEvent e) {
+ msaAlignMenuItem_actionPerformed(e);
+ }
+ });
alignFrameMenuBar.add(fileMenu);
alignFrameMenuBar.add(editMenu);
alignFrameMenuBar.add(searchMenu);
alignFrameMenuBar.add(viewMenu);
alignFrameMenuBar.add(colourMenu);
alignFrameMenuBar.add(calculateMenu);
- alignFrameMenuBar.add(alignMenu);
fileMenu.add(saveAlignmentMenu);
+ fileMenu.add(jMenu2);
fileMenu.add(outputTextboxMenu);
- fileMenu.add(htmlMenuItem);
- fileMenu.add(epsFile);
- fileMenu.add(createPNG);
fileMenu.add(printMenuItem);
fileMenu.addSeparator();
fileMenu.add(LoadtreeMenuItem);
fileMenu.addSeparator();
fileMenu.add(closeMenuItem);
+ editMenu.add(undoMenuItem);
+ editMenu.add(redoMenuItem);
+ editMenu.add(cut);
editMenu.add(copy);
editMenu.add(jMenu1);
- editMenu.add(cut);
editMenu.add(delete);
editMenu.addSeparator();
- editMenu.add(undoMenuItem);
- editMenu.add(redoMenuItem);
- editMenu.addSeparator();
- editMenu.add(deselectAllSequenceMenuItem);
editMenu.add(selectAllSequenceMenuItem);
+ editMenu.add(deselectAllSequenceMenuItem);
editMenu.add(invertSequenceMenuItem);
editMenu.add(deleteGroups);
- editMenu.add(groupsMenuItem);
editMenu.addSeparator();
- editMenu.add(deselectAllColumnsMenuItem);
editMenu.add(remove2LeftMenuItem);
editMenu.add(remove2RightMenuItem);
- editMenu.addSeparator();
editMenu.add(removeGappedColumnMenuItem);
editMenu.add(removeAllGapsMenuItem);
- editMenu.add(setGapCharMenuItem);
+ editMenu.add(removeRedundancyMenuItem);
+ editMenu.addSeparator();
+ editMenu.add(preferences);
+
searchMenu.add(findMenuItem);
viewMenu.add(font);
viewMenu.add(fullSeqId);
+ viewMenu.addSeparator();
viewMenu.add(wrapMenuItem);
+ viewMenu.add(scaleAbove);
+ viewMenu.add(scaleLeft);
+ viewMenu.add(scaleRight);
+ viewMenu.addSeparator();
viewMenu.add(viewBoxesMenuItem);
viewMenu.add(viewTextMenuItem);
viewMenu.add(colourTextMenuItem);
viewMenu.add(renderGapsMenuItem);
viewMenu.add(annotationPanelMenuItem);
- viewMenu.add(overviewMenuItem);
viewMenu.add(sequenceFeatures);
+ viewMenu.addSeparator();
+ viewMenu.add(overviewMenuItem);
colourMenu.add(applyToAllGroups);
colourMenu.add(noColourmenuItem);
+ colourMenu.addSeparator();
colourMenu.add(clustalColour);
+ colourMenu.add(BLOSUM62Colour);
+ colourMenu.add(PIDColour);
colourMenu.add(zappoColour);
colourMenu.add(taylorColour);
colourMenu.add(hydrophobicityColour);
colourMenu.add(buriedColour);
colourMenu.add(nucleotideColour);
colourMenu.add(userDefinedColour);
- colourMenu.add(PIDColour);
- colourMenu.add(BLOSUM62Colour);
colourMenu.addSeparator();
- colourMenu.add(abovePIDThreshold);
colourMenu.add(conservationMenuItem);
- calculateMenu.add(sortPairwiseMenuItem);
- calculateMenu.add(sortIDMenuItem);
- calculateMenu.add(sortGroupMenuItem);
- calculateMenu.add(sortTreeOrderMenuItem);
- calculateMenu.add(removeRedundancyMenuItem);
+ colourMenu.add(modifyConservation);
+ colourMenu.add(abovePIDThreshold);
+ colourMenu.add(modifyPID);
+ calculateMenu.add(sort);
+ calculateMenu.add(calculate);
calculateMenu.addSeparator();
calculateMenu.add(pairwiseAlignmentMenuItem);
calculateMenu.add(PCAMenuItem);
calculateMenu.addSeparator();
- calculateMenu.add(averageDistanceTreeMenuItem);
- calculateMenu.add(neighbourTreeMenuItem);
- calculateMenu.add(avDistanceTreeBlosumMenuItem);
- calculateMenu.add(njTreeBlosumMenuItem);
- alignMenu.add(clustalAlignMenuItem);
- alignMenu.add(jpred);
+ calculateMenu.add(webService);
+ webService.add(clustalAlignMenuItem);
+ webService.add(jpred);
+ webService.add(msaAlignMenuItem);
this.getContentPane().add(statusBar, BorderLayout.SOUTH);
jMenu1.add(pasteNew);
jMenu1.add(pasteThis);
+ jMenu2.add(htmlMenuItem);
+ jMenu2.add(epsFile);
+ jMenu2.add(createPNG);
+ sort.add(sortIDMenuItem);
+ sort.add(sortGroupMenuItem);
+ sort.add(sortByTreeMenu);
+ sort.add(sortPairwiseMenuItem);
+ calculate.add(averageDistanceTreeMenuItem);
+ calculate.add(neighbourTreeMenuItem);
+ calculate.add(avDistanceTreeBlosumMenuItem);
+ calculate.add(njTreeBlosumMenuItem);
}
protected void saveAs_actionPerformed(ActionEvent e)
}
-
-
-
protected void closeMenuItem_actionPerformed(ActionEvent e)
{
}
- protected void groupsMenuItem_actionPerformed(ActionEvent e)
- {
-
- }
-
-
protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
{
}
-
- protected void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)
- {
-
- }
-
protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
{
}
- protected void setGapCharMenuItem_actionPerformed(ActionEvent e)
- {
-
- }
-
-
-
-
protected void wrapMenuItem_actionPerformed(ActionEvent e)
{
}
-
-
protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
{
}
- protected void sortTreeOrderMenuItem_actionPerformed(ActionEvent e)
- {
-
- }
protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
{
}
+ protected void scaleAbove_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ protected void scaleLeft_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ protected void scaleRight_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ protected void modifyPID_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ protected void modifyConservation_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ protected void preferences_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ protected void msaAlignMenuItem_actionPerformed(ActionEvent e) {
+
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff