+\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
+\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(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