Merge branch 'documentation/JAL-3407_2.11.1_release' into develop

[jalview.git] / examples / groovy / ComputePeptideVariants.groovy

diff --git a/examples/groovy/ComputePeptideVariants.groovy b/examples/groovy/ComputePeptideVariants.groovy
new file mode 100644 (file)
index 0000000..6caa69c
--- /dev/null
+++ b/examples/groovy/ComputePeptideVariants.groovy
@@ -0,0 +1,32 @@
+import jalview.datamodel.SequenceFeature
+import jalview.gui.Desktop
+def af = jalview.bin.Jalview.currentAlignFrame
+def av = af.viewport
+def fr = Desktop.getAlignFrameFor(av.codingComplement).getFeatureRenderer()
+def counts = 0
+def countm = 0
+for (seq in av.alignment.sequences) 
+{
+   ds = seq.datasetSequence
+   for (res = ds.start ; res <= ds.end; res++) 
+   {
+     mf = fr.findComplementFeaturesAtResidue(seq, res)
+     if (mf != null)
+     {
+         for (feature in mf.features)
+         {
+           variant = mf.findProteinVariants(feature)
+           if (!"".equals(variant))
+           {
+               type = variant.contains("=") ? "synonymous_variant" : "missense_variant"
+               if (type.equals("synonymous_variant")) counts++ else countm++;
+               sf = new SequenceFeature(type, variant, res, res, null)
+               seq.addSequenceFeature(sf)
+           }
+         }
+     }
+   }
+}
+af.getFeatureRenderer().featuresAdded()
+af.alignPanel.paintAlignment(true, true)
+println "Added " + countm + " missense and " + counts + " synonymous variants"
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