- else\r
- sequenceMenu.setVisible(false);\r
-\r
- }\r
- private void jbInit() throws Exception\r
- {\r
- groupMenu.setText("Group");\r
- copyGroup.setText("Copy region to new Alignment");\r
- copyGroup.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- copyGroup_actionPerformed(e);\r
- }\r
- });\r
- moveGroup.setText("Move sequences to new Alignment");\r
- moveGroup.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- moveGroup_actionPerformed(e);\r
- }\r
- });\r
- deleteSequences.setText("Delete sequences");\r
- deleteSequences.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- deleteSequences_actionPerformed(e);\r
- }\r
- });\r
- analyze.setText("Analyze");\r
- analyze.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- analyze_actionPerformed(e);\r
- }\r
- });\r
- defineMenu.setText("Define");\r
- groupName.setText("Name");\r
- groupName.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- groupName_actionPerformed(e);\r
- }\r
- });\r
- groupAnnotation.setText("Annotation");\r
- groupAnnotation.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- groupAnnotation_actionPerformed(e);\r
- }\r
- });\r
- sequenceMenu.setText("Sequence");\r
- sequenceName.setText("sequenceName");\r
- sequenceName.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- sequenceName_actionPerformed(e);\r
- }\r
- });\r
- residueMenu.setText("Residue");\r
- annotateResidue.setText("annotate residue???");\r
- PIDColour.setFocusPainted(false);\r
- add(groupMenu);\r
- this.add(sequenceMenu);\r
- this.add(residueMenu);\r
- groupMenu.add(defineMenu);\r
- groupMenu.addSeparator();\r
- groupMenu.add(copyGroup);\r
- groupMenu.add(moveGroup);\r
- groupMenu.add(deleteSequences);\r
- groupMenu.addSeparator();\r
- groupMenu.add(analyze);\r
- defineMenu.add(groupName);\r
- defineMenu.add(groupAnnotation);\r
- defineMenu.addSeparator();\r
- defineMenu.add(noColourmenuItem);\r
- defineMenu.add(clustalColour);\r
- defineMenu.add(zappoColour);\r
- defineMenu.add(taylorColour);\r
- defineMenu.add(hydrophobicityColour);\r
- defineMenu.add(helixColour);\r
- defineMenu.add(strandColour);\r
- defineMenu.add(turnColour);\r
- defineMenu.add(buriedColour);\r
- defineMenu.add(userDefinedColour);\r
- defineMenu.add(PIDColour);\r
- defineMenu.add(BLOSUM62Colour);\r
- defineMenu.addSeparator();\r
- defineMenu.add(abovePIDColour);\r
- defineMenu.add(conservationMenuItem);\r
-\r
- sequenceMenu.add(sequenceName);\r
- residueMenu.add(annotateResidue);\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
- {\r
- noColourmenuItem_actionPerformed(e);\r
- }\r
- });\r
-\r
- clustalColour.setSelected(false);\r
- clustalColour.setText("Clustalx colours");\r
- clustalColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- clustalColour_actionPerformed(e);\r
- }\r
- });\r
- zappoColour.setText("Zappo colour scheme");\r
- zappoColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- zappoColour_actionPerformed(e);\r
- }\r
- });\r
- taylorColour.setText("Taylor colour scheme");\r
- taylorColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- taylorColour_actionPerformed(e);\r
- }\r
- });\r
- hydrophobicityColour.setText("By hydrophobicity");\r
- hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- hydrophobicityColour_actionPerformed(e);\r
- }\r
- });\r
- helixColour.setText("Helix propensity");\r
- helixColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- helixColour_actionPerformed(e);\r
- }\r
- });\r
- strandColour.setText("Strand propensity");\r
- strandColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- strandColour_actionPerformed(e);\r
- }\r
- });\r
- turnColour.setText("Turn propensity");\r
- turnColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- turnColour_actionPerformed(e);\r
- }\r
- });\r
- buriedColour.setText("Buried index");\r
- buriedColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- buriedColour_actionPerformed(e);\r
- }\r
- });\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
- public void actionPerformed(ActionEvent e)\r
- {\r
- userDefinedColour_actionPerformed(e);\r
- }\r
- });\r
- PIDColour.setText("Percentage Identity");\r
- PIDColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- PIDColour_actionPerformed(e);\r
- }\r
- });\r
- BLOSUM62Colour.setText("BLOSUM62 score");\r
- BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- BLOSUM62Colour_actionPerformed(e);\r
- }\r
- });\r
- conservationMenuItem.setText("By conservation");\r
- conservationMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- conservationMenuItem_actionPerformed(e);\r
- }\r
- });\r
-\r
-\r
-\r
- }\r
-\r
- void refresh()\r
- {\r
- ap.seqPanel.seqCanvas.paintFlag=true;\r
- ap.seqPanel.repaint();\r
- }\r
-\r
- protected void clustalColour_actionPerformed(ActionEvent e)\r
- {\r
- getGroup().cs = new ClustalxColourScheme();\r
- refresh();\r
- }\r
-\r
- protected void zappoColour_actionPerformed(ActionEvent e)\r
- {\r
- getGroup().cs = new ZappoColourScheme();\r
- refresh();\r
- }\r
-\r
- protected void taylorColour_actionPerformed(ActionEvent e)\r
- {\r
- getGroup().cs = new TaylorColourScheme();\r
- refresh();\r
- }\r
-\r
-\r
- protected void hydrophobicityColour_actionPerformed(ActionEvent e)\r
- {\r
- getGroup().cs = new HydrophobicColourScheme();\r
- refresh();\r
- }\r
-\r
- protected void helixColour_actionPerformed(ActionEvent e)\r
- {\r
- getGroup().cs = new HelixColourScheme();\r
- refresh();\r
- }\r
-\r
- protected void strandColour_actionPerformed(ActionEvent e)\r
- {\r
- getGroup().cs = new StrandColourScheme();\r
- refresh();\r
- }\r
-\r
- protected void turnColour_actionPerformed(ActionEvent e)\r
- {\r
- getGroup().cs = new TurnColourScheme();\r
- refresh();\r
- }\r
-\r
- protected void buriedColour_actionPerformed(ActionEvent e)\r
- {\r
- getGroup().cs = new BuriedColourScheme();\r
- refresh();\r
- }\r
-\r
-\r
-/*\r
-public void conservationColourIncMenuItem_actionPerformed(ActionEvent e)\r
-{\r
-ConservationIncrementPanel cip = new ConservationIncrementPanel(viewport, alignPanel);\r
-JInternalFrame frame = new JInternalFrame();\r
-frame.setContentPane(cip);\r
-Desktop.addInternalFrame(frame, "Conservation Colour Increment", 400,90);\r
-frame.setMaximizable(false);\r