endRes = end;\r
}\r
\r
+ public SequenceI [] getSelectionAsNewSequences(AlignmentI align)\r
+ {\r
+ int iSize = sequences.size();\r
+ SequenceI [] seqs = new SequenceI[iSize];\r
+ SequenceI [] inorder = getSequencesInOrder(align);\r
+\r
+ char ch;\r
+ int sres, eres;\r
+\r
+ for (int i = 0; i < iSize; i++)\r
+ {\r
+ SequenceI seq = inorder[i];\r
+\r
+ //FIND START RES\r
+ //Returns residue following index if gap\r
+ sres = seq.findPosition(startRes);\r
+\r
+ //FIND END RES\r
+ //Need to find the residue preceeding index if gap\r
+ eres = 0;\r
+\r
+ for (int j = 0; j < endRes + 1 && j < seq.getLength(); j++)\r
+ {\r
+ ch = seq.getCharAt(j);\r
+ if (!jalview.util.Comparison.isGap( (ch)))\r
+ {\r
+ eres++;\r
+ }\r
+ }\r
+\r
+ if (eres > 0)\r
+ {\r
+ eres += seq.getStart() - 1;\r
+ }\r
+\r
+ seqs[i] = new Sequence(seq.getName(),\r
+ seq.getSequence(startRes, endRes + 1),\r
+ sres,\r
+ eres);\r
+ seqs[i].setDescription(seq.getDescription());\r
+ seqs[i].setDBRef(seq.getDBRef());\r
+ seqs[i].setSequenceFeatures(seq.getSequenceFeatures());\r
+ if (seq.getDatasetSequence() != null)\r
+ seqs[i].setDatasetSequence(seq.getDatasetSequence());\r
+\r
+ if(seq.getAnnotation()!=null)\r
+ {\r
+ for(int a=0; a<seq.getAnnotation().length; a++)\r
+ seqs[i].addAlignmentAnnotation(seq.getAnnotation()[a]);\r
+ }\r
+ }\r
+\r
+ return seqs;\r
+\r
+ }\r
+\r
public Vector getSequences(boolean includeHidden)\r
{\r
if(!includeHidden)\r
if(cs == null)\r
return;\r
\r
- cs.setConsensus(AAFrequency.calculate(sequences, 0, getWidth()));\r
-\r
-\r
- if (cs instanceof ClustalxColourScheme)\r
+ try\r
{\r
- ((ClustalxColourScheme) cs).resetClustalX(sequences, getWidth());\r
- }\r
+ cs.setConsensus(AAFrequency.calculate(sequences, 0, getWidth()));\r
\r
+ if (cs instanceof ClustalxColourScheme)\r
+ {\r
+ ( (ClustalxColourScheme) cs).resetClustalX(sequences, getWidth());\r
+ }\r
\r
- if (cs.conservationApplied())\r
- {\r
+ if (cs.conservationApplied())\r
+ {\r
Conservation c = new Conservation(groupName,\r
- ResidueProperties.propHash, 3, sequences, 0, getWidth());\r
+ ResidueProperties.propHash, 3, sequences,\r
+ 0, getWidth());\r
c.calculate();\r
c.verdict(false, 25);\r
\r
-\r
cs.setConservation(c);\r
\r
if (cs instanceof ClustalxColourScheme)\r
{\r
- ((ClustalxColourScheme) cs).resetClustalX(sequences,\r
- getWidth());\r
+ ( (ClustalxColourScheme) cs).resetClustalX(sequences,\r
+ getWidth());\r
}\r
+ }\r
+ }\r
+ catch (java.lang.OutOfMemoryError err)\r
+ {\r
+ System.out.println("Out of memory loading groups: " + err);\r
}\r
+\r
}\r
\r
/**\r