+ 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
+ Object source = evt.getSource();\r
+ if(source==clustalColour)\r
+ clustalColour_actionPerformed();\r
+ else if(source==zappoColour)\r
+ zappoColour_actionPerformed();\r
+ else if(source==taylorColour)\r
+ taylorColour_actionPerformed();\r
+ else if(source==hydrophobicityColour)\r
+ hydrophobicityColour_actionPerformed();\r
+ else if(source==helixColour)\r
+ helixColour_actionPerformed();\r
+ else if(source==strandColour)\r
+ strandColour_actionPerformed();\r
+ else if(source==clustalColour)\r
+ turnColour_actionPerformed();\r
+ else if(source==buriedColour)\r
+ buriedColour_actionPerformed();\r
+ else if(source==nucleotideMenuItem)\r
+ nucleotideMenuItem_actionPerformed();\r
+\r
+ else if(source==userDefinedColour)\r
+ userDefinedColour_actionPerformed();\r
+ else if(source==PIDColour)\r
+ PIDColour_actionPerformed();\r
+ else if(source==BLOSUM62Colour)\r
+ BLOSUM62Colour_actionPerformed();\r
+ else if(source==noColourmenuItem)\r
+ noColourmenuItem_actionPerformed();\r
+ else if(source==conservationMenuItem)\r
+ conservationMenuItem_itemStateChanged();\r
+ else if(source==unGroupMenuItem)\r
+ unGroupMenuItem_actionPerformed();\r
+\r
+ else if(source==copy)\r
+ ap.alignFrame.copy_actionPerformed();\r
+ else if(source==cut)\r
+ ap.alignFrame.cut_actionPerformed();\r
+ else if(source==toUpper || source==toLower || source==toggleCase)\r
+ {\r
+ SequenceGroup sg = ap.av.getSelectionGroup();\r
+ if (sg != null)\r
+ {\r
+ for (int g = 0; g < sg.getSize(true); g++)\r
+ {\r
+ if (source == toggleCase)\r
+ ((SequenceI) sg.getSequences(true).elementAt(g))\r
+ .toggleCase(sg.getStartRes(), sg.getEndRes() + 1);\r
+ else\r
+ ((SequenceI) sg.getSequences(true).elementAt(g))\r
+ .changeCase(source == toUpper, sg.getStartRes(),\r
+ sg.getEndRes() + 1);\r
+ }\r
+ ap.seqPanel.seqCanvas.repaint();\r
+ }\r
+ }\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