- JGroup[] groups = jms.getJGroup();\r
-\r
- for (int i = 0; i < groups.length; i++)\r
- {\r
- ColourSchemeI cs = null;\r
-\r
- if (groups[i].getColour() != null)\r
- {\r
- if (groups[i].getColour().startsWith("ucs"))\r
- {\r
- cs = GetUserColourScheme(jms, groups[i].getColour());\r
- }\r
- else\r
- {\r
- cs = ColourSchemeProperty.getColour(al,\r
- groups[i].getColour());\r
- }\r
-\r
- if(cs!=null)\r
- cs.setThreshold(groups[i].getPidThreshold(), true);\r
-\r
- }\r
-\r
- Vector seqs = new Vector();\r
- int[] ids = groups[i].getSeq();\r
-\r
- for (int s = 0; s < ids.length; s++)\r
- {\r
- seqs.addElement((jalview.datamodel.SequenceI) seqids.elementAt(\r
- ids[s]));\r
- }\r
-\r
- jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(seqs,\r
- groups[i].getName(), cs, groups[i].getDisplayBoxes(),\r
- groups[i].getDisplayText(), groups[i].getColourText(),\r
- groups[i].getStart(), groups[i].getEnd());\r
-\r
- sg.setOutlineColour(new java.awt.Color(\r
- groups[i].getOutlineColour()));\r
-\r
- if (groups[i].getConsThreshold() != 0)\r
- {\r
- jalview.analysis.Conservation c = new jalview.analysis.Conservation("All",\r
- ResidueProperties.propHash, 3, sg.getSequences(false), 0,\r
- sg.getWidth() - 1);\r
- c.calculate();\r
- c.verdict(false, 25);\r
- sg.cs.setConservation(c);\r
- }\r
-\r
- al.addGroup(sg);\r
- }\r
+ jalview.analysis.Conservation c = new jalview.analysis.Conservation(\r
+ "All", ResidueProperties.propHash, 3,\r
+ sg.getSequences(null), 0, sg.getWidth() - 1);\r
+ c.calculate();\r
+ c.verdict(false, 25);\r
+ sg.cs.setConservation(c);\r