+ private void jbInit()\r
+ throws Exception\r
+ {\r
+ groupMenu.setLabel("Group");\r
+ groupMenu.setLabel("Selection");\r
+ sequenceFeature.addActionListener(this);\r
+\r
+ editGroupName.addActionListener(this);\r
+ unGroupMenuItem.setLabel("Remove Group");\r
+ unGroupMenuItem.addActionListener(this);\r
+\r
+ nucleotideMenuItem.setLabel("Nucleotide");\r
+ nucleotideMenuItem.addActionListener(this);\r
+ conservationMenuItem.addItemListener(this);\r
+ abovePIDColour.addItemListener(this);\r
+ colourMenu.setLabel("Group Colour");\r
+ showBoxes.setLabel("Boxes");\r
+ showBoxes.setState(true);\r
+ showBoxes.addItemListener(this);\r
+ sequenceName.addActionListener(this);\r
+\r
+ showText.setLabel("Text");\r
+ showText.addItemListener(this);\r
+ showColourText.setLabel("Colour Text");\r
+ showColourText.addItemListener(this);\r
+ outputmenu.setLabel("Output to Textbox...");\r
+ seqMenu.setLabel("Sequence");\r
+ pdb.setLabel("View PDB Structure");\r
+ hideSeqs.setLabel("Hide Sequences");\r
+ repGroup.setLabel("Represent Group with");\r
+ revealAll.setLabel("Reveal All");\r
+ menu1.setLabel("Group");\r
+ add(groupMenu);\r
+ this.add(seqMenu);\r
+ this.add(hideSeqs);\r
+ this.add(revealAll);\r
+ groupMenu.add(editGroupName);\r
+ groupMenu.add(editMenu);\r
+ groupMenu.add(outputmenu);\r
+ groupMenu.add(sequenceFeature);\r
+ groupMenu.add(menu1);\r
+\r
+ colourMenu.add(noColourmenuItem);\r
+ colourMenu.add(clustalColour);\r
+ colourMenu.add(BLOSUM62Colour);\r
+ colourMenu.add(PIDColour);\r
+ colourMenu.add(zappoColour);\r
+ colourMenu.add(taylorColour);\r
+ colourMenu.add(hydrophobicityColour);\r
+ colourMenu.add(helixColour);\r
+ colourMenu.add(strandColour);\r
+ colourMenu.add(turnColour);\r
+ colourMenu.add(buriedColour);\r
+ colourMenu.add(nucleotideMenuItem);\r
+ colourMenu.add(userDefinedColour);\r
+ colourMenu.addSeparator();\r
+ colourMenu.add(abovePIDColour);\r
+ colourMenu.add(conservationMenuItem);\r
+\r
+ noColourmenuItem.setLabel("None");\r
+ noColourmenuItem.addActionListener(this);\r
+\r
+ clustalColour.setLabel("Clustalx colours");\r
+ clustalColour.addActionListener(this);\r
+ zappoColour.setLabel("Zappo");\r
+ zappoColour.addActionListener(this);\r
+ taylorColour.setLabel("Taylor");\r
+ taylorColour.addActionListener(this);\r
+ hydrophobicityColour.setLabel("Hydrophobicity");\r
+ hydrophobicityColour.addActionListener(this);\r
+ helixColour.setLabel("Helix propensity");\r
+ helixColour.addActionListener(this);\r
+ strandColour.setLabel("Strand propensity");\r
+ strandColour.addActionListener(this);\r
+ turnColour.setLabel("Turn propensity");\r
+ turnColour.addActionListener(this);\r
+ buriedColour.setLabel("Buried Index");\r
+ buriedColour.addActionListener(this);\r
+ abovePIDColour.setLabel("Above % Identity");\r
+\r
+ userDefinedColour.setLabel("User Defined");\r
+ userDefinedColour.addActionListener(this);\r
+ PIDColour.setLabel("Percentage Identity");\r
+ PIDColour.addActionListener(this);\r
+ BLOSUM62Colour.setLabel("BLOSUM62");\r
+ BLOSUM62Colour.addActionListener(this);\r
+ conservationMenuItem.setLabel("Conservation");\r
+\r
+ editMenu.add(copy);\r
+ copy.addActionListener(this);\r
+ editMenu.add(cut);\r
+ cut.addActionListener(this);\r
+\r
+ editMenu.add(editSequence);\r
+ editSequence.addActionListener(this);\r
+\r
+ editMenu.add(toUpper);\r
+ toUpper.addActionListener(this);\r
+ editMenu.add(toLower);\r
+ toLower.addActionListener(this);\r
+ editMenu.add(toggleCase);\r
+ seqMenu.add(sequenceName);\r
+ seqMenu.add(pdb);\r
+ seqMenu.add(repGroup);\r
+ menu1.add(unGroupMenuItem);\r
+ menu1.add(colourMenu);\r
+ menu1.add(showBoxes);\r
+ menu1.add(showText);\r
+ menu1.add(showColourText);\r
+ toggleCase.addActionListener(this);\r
+ pdb.addActionListener(this);\r
+ hideSeqs.addActionListener(this);\r
+ repGroup.addActionListener(this);\r
+ revealAll.addActionListener(this);\r
+ }\r
+\r
+ void refresh()\r
+ {\r
+ ap.paintAlignment(true);\r
+ }\r
+\r
+ protected void clustalColour_actionPerformed()\r