+\r
+ ChangeCaseCommand caseCommand = new ChangeCaseCommand(\r
+ description, sg.getSequencesAsArray(true), startEnd, caseChange\r
+ );\r
+\r
+ ap.alignFrame.addHistoryItem(caseCommand);\r
+\r
+\r
+ ap.av.firePropertyChange("alignment", null,\r
+ ap.av.getAlignment().getSequences());\r
+\r
+ }\r
+ }\r
+ else\r
+ outputText(evt);\r
+\r
+ }\r
+\r
+ void outputText(ActionEvent e)\r
+ {\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(true, 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
+ }\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