JAL-2738 compute VCF on peptide, extract AF (allele frequency) score

[jalview.git] / src / jalview / analysis / AlignmentUtils.java

diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java
index 2b9b9f9..41fe77e 100644 (file)
--- a/src/jalview/analysis/AlignmentUtils.java
+++ b/src/jalview/analysis/AlignmentUtils.java
@@ -105,6 +105,15 @@ public class AlignmentUtils
     {
       return variant == null ? null : variant.getFeatureGroup();
     }
+
+    /**
+     * toString for aid in the debugger only
+     */
+    @Override
+    public String toString()
+    {
+      return base + ":" + (variant == null ? "" : variant.getDescription());
+    }
   }
 
   /**
@@ -2542,6 +2551,22 @@ public class AlignmentUtils
         // not handling multi-locus variant features
         continue;
       }
+
+      /*
+       * extract dna variants to a string array
+       */
+      String alls = (String) sf.getValue("alleles");
+      if (alls == null)
+      {
+        continue; // non-SNP VCF variant perhaps - can't process this
+      }
+      String[] alleles = alls.toUpperCase().split(",");
+      int i = 0;
+      for (String allele : alleles)
+      {
+        alleles[i++] = allele.trim(); // lose any space characters "A, G"
+      }
+
       int[] mapsTo = dnaToProtein.locateInTo(dnaCol, dnaCol);
       if (mapsTo == null)
       {
@@ -2560,21 +2585,6 @@ public class AlignmentUtils
       }
 
       /*
-       * extract dna variants to a string array
-       */
-      String alls = (String) sf.getValue("alleles");
-      if (alls == null)
-      {
-        continue;
-      }
-      String[] alleles = alls.toUpperCase().split(",");
-      int i = 0;
-      for (String allele : alleles)
-      {
-        alleles[i++] = allele.trim(); // lose any space characters "A, G"
-      }
-
-      /*
        * get this peptide's codon positions e.g. [3, 4, 5] or [4, 7, 10]
        */
       int[] codon = peptidePosition == lastPeptidePostion ? lastCodon