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Merge branch 'features/JAL-2349_matrixvis' into features/JAL-2349_matrixvis_2112
[jalview.git]
/
examples
/
groovy
/
PIDmatrix.groovy
diff --git
a/examples/groovy/PIDmatrix.groovy
b/examples/groovy/PIDmatrix.groovy
index
4e2ad8d
..
b97abcc
100644
(file)
--- a/
examples/groovy/PIDmatrix.groovy
+++ b/
examples/groovy/PIDmatrix.groovy
@@
-22,11
+22,12
@@
import jalview.analysis.scoremodels.ScoreModels
import jalview.analysis.scoremodels.SimilarityParams
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:
* printSimilarityMatrix(selected-only, include-ids, pidMethod)
*
* Allowed values for pidMethod:
@@
-61,7
+62,7
@@
void printSimilarityMatrix(boolean selview=false, boolean includeids=true, Simil
jalview.datamodel.AlignmentView seqStrings = av.getAlignmentView(selview)
jalview.datamodel.AlignmentView seqStrings = av.getAlignmentView(selview)
- if (!selview) {
+ if (!selview || av.getSelectionGroup()==null) {
start = 0
end = av.getAlignment().getWidth()
seqs = av.getAlignment().getSequencesArray()
start = 0
end = av.getAlignment().getWidth()
seqs = av.getAlignment().getSequencesArray()
@@
-95,4
+96,4
@@
void printSimilarityMatrix(boolean selview=false, boolean includeids=true, Simil
print "\n"
}
print "\n"
}
-}
+}
\ No newline at end of file