+ public void itemStateChanged(ItemEvent evt)\r
+ {\r
+ if(evt.getSource()==abovePIDColour)\r
+ abovePIDColour_itemStateChanged();\r
+ else if(evt.getSource()==showColourText)\r
+ showColourText_itemStateChanged();\r
+ else if(evt.getSource()==showText)\r
+ showText_itemStateChanged();\r
+ else if(evt.getSource()==showBoxes)\r
+ showBoxes_itemStateChanged() ;\r
+ }\r
+\r
+ public void actionPerformed(ActionEvent evt)\r
+ {\r
+ if(evt.getSource()==clustalColour)\r
+ clustalColour_actionPerformed();\r
+ else if(evt.getSource()==zappoColour)\r
+ zappoColour_actionPerformed();\r
+ else if(evt.getSource()==taylorColour)\r
+ taylorColour_actionPerformed();\r
+ else if(evt.getSource()==hydrophobicityColour)\r
+ hydrophobicityColour_actionPerformed();\r
+ else if(evt.getSource()==helixColour)\r
+ helixColour_actionPerformed();\r
+ else if(evt.getSource()==strandColour)\r
+ strandColour_actionPerformed();\r
+ else if(evt.getSource()==clustalColour)\r
+ turnColour_actionPerformed();\r
+ else if(evt.getSource()==buriedColour)\r
+ buriedColour_actionPerformed();\r
+ else if(evt.getSource()==nucleotideMenuItem)\r
+ nucleotideMenuItem_actionPerformed();\r
+\r
+ else if(evt.getSource()==userDefinedColour)\r
+ userDefinedColour_actionPerformed();\r
+ else if(evt.getSource()==PIDColour)\r
+ PIDColour_actionPerformed();\r
+ else if(evt.getSource()==BLOSUM62Colour)\r
+ BLOSUM62Colour_actionPerformed();\r
+ else if(evt.getSource()==noColourmenuItem)\r
+ noColourmenuItem_actionPerformed();\r
+ else if(evt.getSource()==conservationMenuItem)\r
+ conservationMenuItem_itemStateChanged();\r
+ else if(evt.getSource()==unGroupMenuItem)\r
+ unGroupMenuItem_actionPerformed();\r
+\r
+ }\r
+\r
+ void addPDB(Sequence seq)\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