+ }\r
+\r
+ void addPDB()\r
+ {\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame);\r
+ cap.setText("Paste your PDB file here.");\r
+ cap.setPDBImport(seq);\r
+ Frame frame = new Frame();\r
+ frame.add(cap);\r
+ jalview.bin.JalviewLite.addFrame(frame, "Paste PDB file ", 400, 300);\r
+ }\r
+\r
+ private void jbInit()\r
+ throws Exception\r
+ {\r
+ groupMenu.setLabel("Group");\r
+ groupMenu.setLabel("Selection");\r
+\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
+\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
+\r
+ add(groupMenu);\r
+ this.add(seqMenu);\r
+ this.add(hideSeqs);\r
+ this.add(revealAll);\r
+ groupMenu.add(editMenu);\r
+ groupMenu.add(outputmenu);\r
+ groupMenu.addSeparator();\r
+ groupMenu.add(unGroupMenuItem);\r
+ groupMenu.add(colourMenu);\r
+ groupMenu.add(showBoxes);\r
+ groupMenu.add(showText);\r
+ groupMenu.add(showColourText);\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