protected JMenu calculateMenu = new JMenu();\r
protected JMenu alignMenu = new JMenu();\r
protected JMenuItem groupsMenuItem = new JMenuItem();\r
- protected JCheckBoxMenuItem groupEditingMenuItem = new JCheckBoxMenuItem();\r
protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();\r
protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();\r
protected JMenuItem invertSequenceMenuItem = new JMenuItem();\r
- protected JMenuItem deleteSelectedMenuItem = new JMenuItem();\r
- protected JMenuItem moveSelectedMenuItem = new JMenuItem();\r
- protected JMenuItem copySelectedMenuItem = new JMenuItem();\r
protected JMenuItem deselectAllColumnsMenuItem = new JMenuItem();\r
protected JMenuItem remove2LeftMenuItem = new JMenuItem();\r
protected JMenuItem remove2RightMenuItem = new JMenuItem();\r
protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();\r
protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();\r
protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();\r
- protected JRadioButtonMenuItem abovePIDColour = new JRadioButtonMenuItem();\r
protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();\r
protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();\r
protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();\r
JMenuItem njTreeBlosumMenuItem = new JMenuItem();\r
JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();\r
- protected JMenuItem conservationColourIncMenuItem = new JMenuItem();\r
protected JCheckBoxMenuItem consensusGraphMenuItem = new JCheckBoxMenuItem();\r
protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();\r
JMenuItem htmlMenuItem = new JMenuItem();\r
- JMenuItem schemeKeyMenuItem = new JMenuItem();\r
JMenuItem overviewMenuItem = new JMenuItem();\r
protected JMenuItem undoMenuItem = new JMenuItem();\r
protected JMenuItem redoMenuItem = new JMenuItem();\r
protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();\r
- JMenuItem noColourmenuItem = new JMenuItem();\r
+ JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();\r
protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();\r
JMenuItem pdbTest = new JMenuItem();\r
JMenuItem printMenuItem = new JMenuItem();\r
protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();\r
JMenuItem findMenuItem = new JMenuItem();\r
JMenu searchMenu = new JMenu();\r
+ protected JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();\r
+ protected JCheckBoxMenuItem sequenceFeatures = new JCheckBoxMenuItem();\r
+ protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();\r
+ JMenuItem deleteGroups = new JMenuItem();\r
+ JMenuItem delete = new JMenuItem();\r
+ JMenuItem copy = new JMenuItem();\r
+ JMenuItem cut = new JMenuItem();\r
+ JMenu jMenu1 = new JMenu();\r
+ JMenuItem pasteNew = new JMenuItem();\r
+ JMenuItem pasteThis = new JMenuItem();\r
+ protected JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();\r
public GAlignFrame()\r
{\r
+\r
+\r
try\r
{\r
jbInit();\r
}\r
\r
ButtonGroup colours = new ButtonGroup();\r
+ colours.add(noColourmenuItem);\r
colours.add(clustalColour);\r
colours.add(zappoColour);\r
colours.add(taylorColour);\r
colours.add(strandColour);\r
colours.add(turnColour);\r
colours.add(buriedColour);\r
- colours.add(abovePIDColour);\r
colours.add(userDefinedColour);\r
colours.add(PIDColour);\r
colours.add(BLOSUM62Colour);\r
+ colours.add(nucleotideColour);\r
}\r
private void jbInit() throws Exception\r
{\r
groupsMenuItem_actionPerformed(e);\r
}\r
});\r
- groupEditingMenuItem.setText("Group editing mode");\r
- groupEditingMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- groupEditingMenuItem_actionPerformed(e);\r
- }\r
- });\r
- selectAllSequenceMenuItem.setText("Select all sequences");\r
+ selectAllSequenceMenuItem.setText("Select all");\r
selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
selectAllSequenceMenuItem_actionPerformed(e);\r
}\r
});\r
- deselectAllSequenceMenuItem.setText("Clear sequence selection");\r
+ deselectAllSequenceMenuItem.setText("Clear selection");\r
deselectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
invertSequenceMenuItem_actionPerformed(e);\r
}\r
});\r
- deleteSelectedMenuItem.setText("Delete selected sequences");\r
- deleteSelectedMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- deleteSelectedMenuItem_actionPerformed(e);\r
- }\r
- });\r
- moveSelectedMenuItem.setText("Move selected sequences to new alignment");\r
- moveSelectedMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- moveSelectedMenuItem_actionPerformed(e);\r
- }\r
- });\r
- copySelectedMenuItem.setText("Copy selected sequences to new alignment");\r
- copySelectedMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- copySelectedMenuItem_actionPerformed(e);\r
- }\r
- });\r
deselectAllColumnsMenuItem.setText("Deselect all columns");\r
deselectAllColumnsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
{\r
removeAllGapsMenuItem_actionPerformed(e);\r
}\r
});\r
- setGapCharMenuItem.setText("Set gap character to \"-\"");\r
+ setGapCharMenuItem.setText("Set gap character to \".\"");\r
setGapCharMenuItem.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
statusBar.setText("Status bar");\r
outputTextboxMenu.setMnemonic('T');\r
outputTextboxMenu.setText("Output alignment via textbox");\r
- clustalColour.setEnabled(false);\r
clustalColour.setSelected(false);\r
clustalColour.setText("Clustalx colours");\r
clustalColour.addActionListener(new java.awt.event.ActionListener()\r
clustalColour_actionPerformed(e);\r
}\r
});\r
- zappoColour.setSelected(true);\r
zappoColour.setText("Zappo colour scheme");\r
zappoColour.addActionListener(new java.awt.event.ActionListener()\r
{\r
buriedColour_actionPerformed(e);\r
}\r
});\r
- abovePIDColour.setEnabled(false);\r
- abovePIDColour.setText("Above PID threshold only");\r
- abovePIDColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- abovePIDColour_actionPerformed(e);\r
- }\r
- });\r
userDefinedColour.setText("User defined colours");\r
userDefinedColour.addActionListener(new java.awt.event.ActionListener()\r
{\r
userDefinedColour_actionPerformed(e);\r
}\r
});\r
- PIDColour.setEnabled(false);\r
- PIDColour.setText("By PID");\r
+ PIDColour.setText("Percentage Identity");\r
PIDColour.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
PIDColour_actionPerformed(e);\r
}\r
});\r
- BLOSUM62Colour.setText("By BLOSUM62 score");\r
+ BLOSUM62Colour.setText("BLOSUM62 score");\r
BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
njTreeBlosumMenuItem_actionPerformed(e);\r
}\r
});\r
- conservationColourIncMenuItem.setEnabled(false);\r
- conservationColourIncMenuItem.setText("Conservation Colour Increment");\r
- conservationColourIncMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- conservationColourIncMenuItem_actionPerformed(e);\r
- }\r
- });\r
consensusGraphMenuItem.setActionCommand("");\r
consensusGraphMenuItem.setText("Consensus graph");\r
consensusGraphMenuItem.setState(true);\r
htmlMenuItem_actionPerformed(e);\r
}\r
});\r
- schemeKeyMenuItem.setText("Colour Scheme Key");\r
- schemeKeyMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- schemeKeyMenuItem_actionPerformed(e);\r
- }\r
- });\r
overviewMenuItem.setText("Overview window");\r
overviewMenuItem.addActionListener(new java.awt.event.ActionListener()\r
{\r
}\r
});\r
noColourmenuItem.setText("None");\r
+ noColourmenuItem.setSelected(true);\r
noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
noColourmenuItem_actionPerformed(e);\r
}\r
});\r
- wrapMenuItem.setEnabled(false);\r
wrapMenuItem.setText("Wrap alignment");\r
wrapMenuItem.addActionListener(new java.awt.event.ActionListener()\r
{\r
}\r
});\r
searchMenu.setText("Search");\r
+\r
+ abovePIDThreshold.setText("Above PID threshold");\r
+ abovePIDThreshold.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ abovePIDThreshold_actionPerformed(e);\r
+ }\r
+ });\r
+ sequenceFeatures.setSelected(true);\r
+ sequenceFeatures.setText("Sequence Features");\r
+ sequenceFeatures.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent actionEvent)\r
+ {\r
+ sequenceFeatures_actionPerformed(actionEvent);\r
+ }\r
+ });\r
+ nucleotideColour.setText("Nucleotide colours");\r
+ nucleotideColour.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ nucleotideColour_actionPerformed(e);\r
+ }\r
+ });\r
+ deleteGroups.setSelected(false);\r
+ deleteGroups.setText("Delete all groups");\r
+ deleteGroups.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ deleteGroups_actionPerformed(e);\r
+ }\r
+ });\r
+ copy.setText("Copy");\r
+ copy.setMnemonic(KeyEvent.VK_C);\r
+\r
+ copy.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ copy_actionPerformed(e);\r
+ }\r
+ });\r
+ cut.setText("Cut");\r
+ cut.setMnemonic(KeyEvent.VK_X);\r
+ cut.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ cut_actionPerformed(e);\r
+ }\r
+ });\r
+ delete.setText("Delete");\r
+ delete.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ delete_actionPerformed(e);\r
+ }\r
+ });\r
+ jMenu1.setMnemonic('V');\r
+ jMenu1.setText("Paste");\r
+ pasteNew.setText("to new alignment");\r
+ pasteNew.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ pasteNew_actionPerformed(e);\r
+ }\r
+ });\r
+ pasteThis.setText("add to this alignment");\r
+ pasteThis.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ pasteThis_actionPerformed(e);\r
+ }\r
+ });\r
+ applyToAllGroups.setText("Apply colour to all groups");\r
+ applyToAllGroups.setState(true);\r
+ applyToAllGroups.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ applyToAllGroups_actionPerformed(e);\r
+ }\r
+ });\r
alignFrameMenuBar.add(fileMenu);\r
alignFrameMenuBar.add(editMenu);\r
alignFrameMenuBar.add(searchMenu);\r
fileMenu.add(printMenuItem);\r
fileMenu.addSeparator();\r
fileMenu.add(closeMenuItem);\r
+ editMenu.add(copy);\r
+ editMenu.add(jMenu1);\r
+ editMenu.add(cut);\r
+ editMenu.add(delete);\r
+ editMenu.addSeparator();\r
editMenu.add(undoMenuItem);\r
editMenu.add(redoMenuItem);\r
editMenu.addSeparator();\r
- editMenu.add(groupsMenuItem);\r
- editMenu.add(groupEditingMenuItem);\r
- editMenu.addSeparator();\r
- editMenu.add(selectAllSequenceMenuItem);\r
editMenu.add(deselectAllSequenceMenuItem);\r
+ editMenu.add(selectAllSequenceMenuItem);\r
editMenu.add(invertSequenceMenuItem);\r
- editMenu.addSeparator();\r
- editMenu.add(copySelectedMenuItem);\r
- editMenu.add(moveSelectedMenuItem);\r
- editMenu.add(deleteSelectedMenuItem);\r
+ editMenu.add(deleteGroups);\r
+ editMenu.add(groupsMenuItem);\r
editMenu.addSeparator();\r
editMenu.add(deselectAllColumnsMenuItem);\r
editMenu.add(remove2LeftMenuItem);\r
editMenu.add(removeGappedColumnMenuItem);\r
editMenu.add(removeAllGapsMenuItem);\r
editMenu.add(setGapCharMenuItem);\r
- editMenu.addSeparator();\r
searchMenu.add(findMenuItem);\r
fontMenu.add(fontNameMenuItem);\r
fontMenu.add(fontSizeMenuItem);\r
viewMenu.add(renderGapsMenuItem);\r
viewMenu.add(consensusGraphMenuItem);\r
viewMenu.add(overviewMenuItem);\r
+ viewMenu.add(sequenceFeatures);\r
+ colourMenu.add(applyToAllGroups);\r
colourMenu.add(noColourmenuItem);\r
colourMenu.add(clustalColour);\r
colourMenu.add(zappoColour);\r
colourMenu.add(strandColour);\r
colourMenu.add(turnColour);\r
colourMenu.add(buriedColour);\r
+ colourMenu.add(nucleotideColour);\r
colourMenu.add(userDefinedColour);\r
- colourMenu.addSeparator();\r
- colourMenu.add(conservationMenuItem);\r
- colourMenu.add(conservationColourIncMenuItem);\r
- colourMenu.addSeparator();\r
- colourMenu.add(abovePIDColour);\r
colourMenu.add(PIDColour);\r
colourMenu.add(BLOSUM62Colour);\r
colourMenu.addSeparator();\r
- colourMenu.add(schemeKeyMenuItem);\r
+ colourMenu.add(abovePIDThreshold);\r
+ colourMenu.add(conservationMenuItem);\r
calculateMenu.add(sortPairwiseMenuItem);\r
calculateMenu.add(sortIDMenuItem);\r
calculateMenu.add(sortGroupMenuItem);\r
alignMenu.add(clustalAlignMenuItem);\r
alignMenu.add(pdbTest);\r
this.getContentPane().add(statusBar, BorderLayout.SOUTH);\r
+ jMenu1.add(pasteNew);\r
+ jMenu1.add(pasteThis);\r
}\r
\r
protected void saveAs_actionPerformed(ActionEvent e)\r
\r
}\r
\r
- protected void groupEditingMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
\r
protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
{\r
\r
}\r
\r
- protected void deleteSelectedMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void moveSelectedMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void copySelectedMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
\r
protected void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)\r
{\r
}\r
\r
\r
- protected void conservationColourIncMenuItem_actionPerformed(ActionEvent e)\r
- {\r
\r
- }\r
+ protected void userDefinedColour_actionPerformed(ActionEvent e)\r
+ {\r
+\r
+ }\r
+\r
+ protected void PIDColour_actionPerformed(ActionEvent e)\r
+ {\r
\r
+ }\r
\r
- protected void abovePIDColour_actionPerformed(ActionEvent e)\r
+ protected void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
{\r
\r
}\r
\r
\r
- protected void userDefinedColour_actionPerformed(ActionEvent e)\r
+ protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
{\r
\r
}\r
\r
- protected void PIDColour_actionPerformed(ActionEvent e)\r
+ protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
{\r
\r
}\r
\r
- protected void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
+ protected void pdbTest_actionPerformed(ActionEvent e)\r
{\r
\r
}\r
\r
- protected void schemeKeyMenuItem_actionPerformed(ActionEvent e)\r
+ protected void printMenuItem_actionPerformed(ActionEvent e)\r
{\r
\r
}\r
\r
- protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
+ protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
{\r
\r
}\r
\r
- protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
+ protected void findMenuItem_actionPerformed(ActionEvent e)\r
{\r
\r
}\r
\r
- protected void pdbTest_actionPerformed(ActionEvent e)\r
+\r
+ protected void abovePIDThreshold_actionPerformed(ActionEvent e) {\r
+\r
+ }\r
+\r
+ public void sequenceFeatures_actionPerformed(ActionEvent actionEvent)\r
{\r
\r
}\r
\r
- protected void printMenuItem_actionPerformed(ActionEvent e)\r
+ protected void nucleotideColour_actionPerformed(ActionEvent e)\r
{\r
\r
}\r
\r
- protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
+ protected void deleteGroups_actionPerformed(ActionEvent e)\r
{\r
\r
}\r
\r
- protected void findMenuItem_actionPerformed(ActionEvent e)\r
+ protected void copy_actionPerformed(ActionEvent e)\r
+ {\r
+\r
+ }\r
+\r
+\r
+ protected void cut_actionPerformed(ActionEvent e)\r
+ {\r
+\r
+ }\r
+\r
+ protected void delete_actionPerformed(ActionEvent e)\r
+ {\r
+\r
+ }\r
+\r
+ protected void pasteNew_actionPerformed(ActionEvent e)\r
{\r
\r
}\r
\r
+ protected void pasteThis_actionPerformed(ActionEvent e)\r
+ {\r
+\r
+ }\r
+\r
+ protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
+ {\r
+\r
+ }\r
+\r
+\r
+\r
}\r
git://source.jalview.org / jalview.git / blobdiff