import jalview.analysis.scoremodels.ScoreModels
import jalview.analysis.scoremodels.SimilarityParams
-// call the method below
-printSimilarityMatrix(false,true,SimilarityParams.Jalview)
+// generate matrix for current selection using standard Jalview PID
+
+printSimilarityMatrix(true,true,SimilarityParams.Jalview)
/**
- * prints a sequence similarity matrix in PHYLIP format.
+ * this function prints a sequence similarity matrix in PHYLIP format.
* printSimilarityMatrix(selected-only, include-ids, pidMethod)
*
* Allowed values for pidMethod:
jalview.datamodel.AlignmentView seqStrings = av.getAlignmentView(selview)
- if (!selview) {
+ if (!selview || av.getSelectionGroup()==null) {
start = 0
end = av.getAlignment().getWidth()
seqs = av.getAlignment().getSequencesArray()
print "\n"
}
-}
+}
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