+ else if(source == pdb)\r
+ addPDB();\r
+ else if(source == hideSeqs)\r
+ hideSequences(false);\r
+ else if(source == repGroup)\r
+ hideSequences(true);\r
+ else if(source == revealAll)\r
+ {\r
+ ap.av.showAllHiddenSeqs();\r
+ ap.repaint();\r
+ }\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
+ else\r
+ outputText(evt);\r
+\r
+ }\r
+\r
+ void outputText(ActionEvent e)\r
+ {\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(false, ap.alignFrame);\r
+ Vector vseqs = new Vector();\r
+\r
+ String [] selection = ap.av.getViewAsString(true);\r
+ SequenceI [] seqs = ap.av.getSelectionAsNewSequence();\r
+ if (selection != null)\r
+ {\r
+ for (int i = 0; i < selection.length; i++)\r
+ {\r
+ Sequence seq = new Sequence(\r
+ seqs[i].getName(),\r
+ selection[i],\r
+ seqs[i].getStart(), seqs[i].getEnd());\r
+ seq.setDescription(seqs[i].getDescription());\r
+ vseqs.addElement( seq );\r
+ }\r
+ }\r
+\r
+ Frame frame = new Frame();\r
+ frame.add(cap);\r
+ jalview.bin.JalviewLite.addFrame(frame,\r
+ "Selection output - " + e.getActionCommand(),\r
+ 600, 500);\r
+\r
+ cap.setText(new jalview.io.AppletFormatAdapter().formatSequences(\r
+ e.getActionCommand(),\r
+ vseqs,\r
+ ap.av.showJVSuffix));\r
+\r