+ }\r
+ else\r
+ {\r
+ outputText(evt);\r
+ }\r
+\r
+ }\r
+\r
+ void outputText(ActionEvent e)\r
+ {\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame);\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
+ new Alignment(ap.av.getSelectionAsNewSequence()),\r
+ ap.av.showJVSuffix));\r
+\r
+ }\r
+\r
+ void editName()\r
+ {\r
+ EditNameDialog dialog = new EditNameDialog(\r
+ seq.getName(),\r
+ seq.getDescription(),\r
+ " Sequence Name",\r
+ "Sequence Description",\r
+ ap.alignFrame,\r
+ "Edit Sequence Name / Description",\r
+ 500,100, true);\r
+\r
+ if (dialog.accept)\r
+ {\r
+ seq.setName(dialog.getName());\r
+ seq.setDescription(dialog.getDescription());\r
+ ap.paintAlignment(false);\r
+ }\r
+ }\r
+\r
+ void addPDB()\r
+ {\r
+ if(seq.getPDBId()!=null)\r
+ {\r
+ PDBEntry entry = (PDBEntry)seq.getPDBId().firstElement();\r
+\r
+ if ( ap.av.applet.jmolAvailable )\r
+ new jalview.appletgui.AppletJmol(entry,\r
+ new Sequence[]{seq},\r
+ null,\r
+ ap,\r
+ AppletFormatAdapter.URL);\r
+ else\r
+ new MCview.AppletPDBViewer(entry,\r
+ new Sequence[]{seq},\r
+ null,\r
+ ap,\r
+ AppletFormatAdapter.URL);\r
+\r
+ }\r
+ else\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
+\r
+ private void jbInit()\r
+ throws Exception\r
+ {\r
+ groupMenu.setLabel("Group");\r
+ groupMenu.setLabel("Selection");\r
+ sequenceFeature.addActionListener(this);\r