- 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
- SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);\r
-\r
- if(sequence==null || res>sequence.getLength())\r
- return;\r
-\r
- stretchGroup = av.getSelectionGroup();\r
-\r
- if(stretchGroup == null)\r
- {\r
- stretchGroup = av.alignment.findGroup( sequence );\r
- av.setSelectionGroup( stretchGroup );\r
- }\r
-\r
- else if(!stretchGroup.sequences.contains(sequence)\r
- || stretchGroup.getStartRes()>res\r
- || stretchGroup.getEndRes()<res)\r
- {\r
- stretchGroup = null;\r
-\r
- SequenceGroup[] allGroups = av.alignment.findAllGroups( sequence );\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.setSelectionGroup(stretchGroup);\r
- break;\r
- }\r
- }\r