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Merge branch 'releases/Release_2_11_3_Branch'
[jalview.git]
/
examples
/
groovy
/
PIDmatrix.groovy
diff --git
a/examples/groovy/PIDmatrix.groovy
b/examples/groovy/PIDmatrix.groovy
index
4e2ad8d
..
76b9de7
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:
@@
-55,13
+56,13
@@
printSimilarityMatrix(false,true,SimilarityParams.Jalview)
void printSimilarityMatrix(boolean selview=false, boolean includeids=true, SimilarityParams pidMethod) {
void printSimilarityMatrix(boolean selview=false, boolean includeids=true, SimilarityParams pidMethod) {
- def currentAlignFrame = jalview.bin.Jalview.getCurrentAlignFrame()
+ def currentAlignFrame = Jalview.getCurrentAlignFrame()
jalview.gui.AlignViewport av = currentAlignFrame.getCurrentView()
jalview.datamodel.AlignmentView seqStrings = av.getAlignmentView(selview)
jalview.gui.AlignViewport av = currentAlignFrame.getCurrentView()
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()