+ }\r
+\r
+ else if (source == sequenceName)\r
+ {\r
+ editName();\r
+ }\r
+ else if (source == pdb)\r
+ {\r
+ addPDB();\r
+ }\r
+ else if (source == hideSeqs)\r
+ {\r
+ hideSequences(false);\r
+ }\r
+ else if (source == repGroup)\r
+ {\r
+ hideSequences(true);\r
+ }\r
+ else if (source == revealAll)\r
+ {\r
+ ap.av.showAllHiddenSeqs();\r
+ }\r
+\r
+ else if (source == editGroupName)\r
+ {\r
+ EditNameDialog dialog = new EditNameDialog(\r
+ getGroup().getName(),\r
+ getGroup().getDescription(),\r
+ " Group Name",\r
+ "Group Description",\r
+ ap,\r
+ "Edit Group Name / Description");\r
+\r
+ if (dialog.accept)\r
+ {\r
+\r
+ getGroup().setName(dialog.getName().replace(' ', '_'));\r
+ getGroup().setDescription(dialog.getDescription());\r
+ }\r
+\r
+ }\r
+ else if (source == copy)\r
+ {\r
+ ap.alignFrame.copy_actionPerformed();\r
+ }\r
+ else if (source == cut)\r
+ {\r
+ ap.alignFrame.cut_actionPerformed();\r
+ }\r
+ else if (source == toUpper || source == toLower || source == toggleCase)\r
+ {\r
+ SequenceGroup sg = ap.av.getSelectionGroup();\r
+ Vector regions = new Vector();\r
+ if (sg != null)\r
+ {\r
+ int start = sg.getStartRes();\r
+ int end = sg.getEndRes() + 1;\r
+\r
+ do\r
+ {\r
+ if (ap.av.hasHiddenColumns)\r
+ {\r
+ if (start == 0)\r
+ {\r
+ start = ap.av.colSel.adjustForHiddenColumns(start);\r
+ }\r
+\r
+ end = ap.av.colSel.getHiddenBoundaryRight(start);\r
+ if (start == end)\r
+ {\r
+ end = sg.getEndRes() + 1;\r
+ }\r
+ if (end > sg.getEndRes())\r
+ {\r
+ end = sg.getEndRes() + 1;\r
+ }\r
+ }\r
+\r
+ regions.addElement(new int[]\r
+ {start, end});\r
+\r
+ if (ap.av.hasHiddenColumns)\r
+ {\r
+ start = ap.av.colSel.adjustForHiddenColumns(end);\r
+ start = ap.av.colSel.getHiddenBoundaryLeft(start) + 1;\r
+ }\r
+ }\r
+ while (end < sg.getEndRes());\r
+\r
+ int[][] startEnd = new int[regions.size()][2];\r
+ for (int i = 0; i < regions.size(); i++)\r
+ {\r
+ startEnd[i] = (int[]) regions.elementAt(i);\r
+ }\r
+\r
+ String description;\r
+ int caseChange;\r
+\r
+ if (source == toggleCase)\r
+ {\r
+ description = "Toggle Case";\r
+ caseChange = ChangeCaseCommand.TOGGLE_CASE;\r
+ }\r
+ else if (source == toUpper)\r
+ {\r
+ description = "To Upper Case";\r
+ caseChange = ChangeCaseCommand.TO_UPPER;\r
+ }\r
+ else\r
+ {\r
+ description = "To Lower Case";\r
+ caseChange = ChangeCaseCommand.TO_LOWER;\r
+ }\r
+\r
+ ChangeCaseCommand caseCommand = new ChangeCaseCommand(\r
+ description, sg.getSequencesAsArray(ap.av.hiddenRepSequences),\r
+ startEnd, caseChange\r
+ );\r
+\r
+ ap.alignFrame.addHistoryItem(caseCommand);\r
+\r
+ ap.av.firePropertyChange("alignment", null,\r
+ ap.av.getAlignment().getSequences());\r
+\r
+ }\r
+ }\r
+ else\r
+ {\r
+ outputText(evt);\r
+ }\r