+ popup.add(item);\r
+\r
+ if (aa[selectedRow] == ap.av.consensus)\r
+ {\r
+ popup.addSeparator();\r
+ final CheckboxMenuItem cbmi = new CheckboxMenuItem(\r
+ "Ignore Gaps In Consensus",\r
+ ap.av.getIgnoreGapsConsensus());\r
+\r
+ cbmi.addItemListener(new ItemListener()\r
+ {\r
+ public void itemStateChanged(ItemEvent e)\r
+ {\r
+ ap.av.setIgnoreGapsConsensus(cbmi.getState());\r
+ ap.paintAlignment(true);\r
+ }\r
+ });\r
+ popup.add(cbmi);\r
+ item = new MenuItem(COPYCONS_SEQ);\r
+ item.addActionListener(this);\r
+ popup.add(item);\r
+ }\r
+\r
+ popup.show(this, evt.getX(), evt.getY());\r
+\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void copy_annotseqtoclipboard(SequenceI sq)\r
+ {\r
+ if (sq == null || sq.getLength() < 1)\r
+ {\r
+ return;\r
+ }\r
+ jalview.appletgui.AlignFrame.copiedSequences = new StringBuffer();\r
+ jalview.appletgui.AlignFrame.copiedSequences.append(sq.getName() + "\t" +\r
+ sq.getStart() + "\t" +\r
+ sq.getEnd() + "\t" +\r
+ sq.getSequenceAsString() + "\n");\r
+ if (av.hasHiddenColumns)\r
+ {\r
+ jalview.appletgui.AlignFrame.copiedHiddenColumns = new Vector();\r
+ for (int i = 0; i < av.getColumnSelection().getHiddenColumns().size(); i++)\r
+ {\r
+ int[] region = (int[])\r
+ av.getColumnSelection().getHiddenColumns().elementAt(i);\r