- void updateConservation(int i)\r
- {\r
- if(av.getGlobalColourScheme() instanceof jalview.schemes.ClustalxColourScheme)\r
- {\r
- av.setGlobalColourScheme(\r
- new jalview.schemes.ClustalxColourScheme(av.alignment.getSequences(),av.alignment.getWidth() ));\r
- }\r
- av.updateConservation();\r
- av.updateConsensus();\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
- if(stretchGroup!=null && res>stretchGroup.getStartRes() && res<stretchGroup.getEndRes())\r
- av.setSelectionGroup(stretchGroup);\r
- else\r
- stretchGroup = null;\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
-\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 );\r
- av.setSelectionGroup( sg );\r
- stretchGroup = sg;\r
-\r
- if(av.getConservationSelected())\r
- SliderPanel.setConservationSlider(ap, av.getGlobalColourScheme(), "Background");\r
- if(av.getAbovePIDThreshold())\r
- SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(), "Background");\r
+ if (cs instanceof ConservationColourScheme)\r
+ {\r
+ ConservationColourScheme ccs = (ConservationColourScheme) cs;\r
+ Conservation c = new Conservation("All",\r
+ ResidueProperties.propHash, 3, av.alignment.getSequences(),\r
+ 0, av.alignment.getWidth() - 1);\r
+ c.calculate();\r
+ c.verdict(false, av.ConsPercGaps);\r
+\r
+ if (ccs.cs instanceof ClustalxColourScheme)\r
+ {\r
+ ClustalxColourScheme cxs = (ClustalxColourScheme) ccs.cs;\r
+ cxs.resetClustalX(av.alignment.getSequences(),\r
+ av.alignment.getWidth());\r
+ ccs = new ConservationColourScheme(c, cxs);\r
+ av.setGlobalColourScheme(ccs);\r
+ }\r
+ else\r
+ {\r
+ ccs = new ConservationColourScheme(c, ccs.cs);\r
+ av.setGlobalColourScheme(ccs);\r
+ }\r
+ }\r