+ if ( jalview.util.Comparison.isGap( av.alignment.getSequenceAt(seq).getSequence().charAt(j)))\r
+ av.alignment.getSequenceAt(seq).deleteCharAt(j);\r
+\r
+ av.alignment.getWidth();\r
+ repaint();\r
+ seqEditOccurred=seq;\r
+ }\r
+\r
+\r
+ void updateConservation(int i)\r
+ {\r
+ /* Alignment al = (Alignment) av.getAlignment();\r
+ SequenceGroup sg = av.alignment.findGroup( al.getSequenceAt(i));\r
+ if(sg==null || !(sg.cs instanceof ConservationColourScheme))\r
+ return;\r
+\r
+ Conservation c = sg.getConservation();\r
+\r
+ c = new Conservation("All", al.cons,\r
+ ResidueProperties.propHash, 3, sg.sequences, 0,\r
+ al.getWidth());\r
+ c.calculate();\r
+ c.verdict(false, 100);\r
+ sg.setConservation(c);\r
+ ConservationColourScheme ccs = (ConservationColourScheme)sg.cs;\r
+ ccs.conserve = c;*/\r
+ }\r
+\r
+//////////////////////////////////////////\r
+/////Everything below this is for defining the boundary of the rubberband\r
+//////////////////////////////////////////\r
+ int oldSeq = -1;\r
+ public void doMousePressedDefineMode(MouseEvent evt)\r
+ {\r
+ int res = evt.getX()/av.getCharWidth() + av.getStartRes();\r
+ int seq = evt.getY()/av.getCharHeight() + av.getStartSeq();\r
+ oldSeq = seq;\r
+\r
+ stretchGroup = av.getRubberbandGroup();\r
+\r
+ if(stretchGroup == null)\r
+ stretchGroup = av.alignment.findGroup((Sequence)av.getAlignment().getSequenceAt(seq));\r
+\r
+ else if(!stretchGroup.sequences.contains((Sequence)av.getAlignment().getSequenceAt(seq))\r
+ || stretchGroup.getStartRes()>res\r
+ || stretchGroup.getEndRes()<res)\r
+ {\r
+ stretchGroup = null;\r
+\r
+ SequenceGroup[] allGroups = av.alignment.findAllGroups( (Sequence) av.\r
+ getAlignment().\r
+ getSequenceAt(seq));\r
+\r
+ if (allGroups != null)\r
+ for (int i = 0; i < allGroups.length; i++)\r
+ if (allGroups[i].getStartRes() <= res &&\r
+ allGroups[i].getEndRes() >= res)\r
+ {\r
+ stretchGroup = allGroups[i];\r
+ av.setRubberbandGroup(stretchGroup);\r
+ break;\r
+ }\r
+ }\r
+\r
+ if(stretchGroup==null)\r
+ {\r
+ // define a new group here\r
+ SequenceGroup sg = new SequenceGroup();\r
+ sg.setStartRes(res);\r
+ sg.setEndRes(res);\r
+ sg.addSequence( (Sequence)av.getAlignment().getSequenceAt(seq) );\r
+ av.setRubberbandGroup( sg );\r
+ stretchGroup = sg;\r
+ }\r
+ else if( javax.swing.SwingUtilities.isRightMouseButton(evt))\r