JAL-2897 more informative description on synonymous variants

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

diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java
index 3d22115..5e11446 100644 (file)
--- a/src/jalview/analysis/AlignmentUtils.java
+++ b/src/jalview/analysis/AlignmentUtils.java
@@ -465,7 +465,7 @@ public class AlignmentUtils
     {
       String lastCodon = String.valueOf(cdnaSeqChars,
               cdnaLength - CODON_LENGTH, CODON_LENGTH).toUpperCase();
-      for (String stop : ResidueProperties.STOP)
+      for (String stop : ResidueProperties.STOP_CODONS)
       {
         if (lastCodon.equals(stop))
         {
@@ -536,7 +536,8 @@ public class AlignmentUtils
        * allow * in protein to match untranslatable in dna
        */
       final char aaRes = aaSeqChars[aaPos];
-      if ((translated == null || "STOP".equals(translated)) && aaRes == '*')
+      if ((translated == null || ResidueProperties.STOP.equals(translated))
+              && aaRes == '*')
       {
         continue;
       }
@@ -568,7 +569,8 @@ public class AlignmentUtils
     if (dnaPos == cdnaSeqChars.length - CODON_LENGTH)
     {
       String codon = String.valueOf(cdnaSeqChars, dnaPos, CODON_LENGTH);
-      if ("STOP".equals(ResidueProperties.codonTranslate(codon)))
+      if (ResidueProperties.STOP
+              .equals(ResidueProperties.codonTranslate(codon)))
       {
         return true;
       }
@@ -2428,11 +2430,14 @@ public class AlignmentUtils
         {
           for (String base : alleles.split(","))
           {
-            if (!base1.equals(base))
+            if (!base1.equalsIgnoreCase(base))
             {
-              String codon = base + base2 + base3;
+              String codon = base.toUpperCase() + base2.toLowerCase()
+                      + base3.toLowerCase();
+              String canonical = base1.toUpperCase() + base2.toLowerCase()
+                      + base3.toLowerCase();
               if (addPeptideVariant(peptide, peptidePos, residue, var,
-                      codon))
+                      codon, canonical))
               {
                 count++;
               }
@@ -2454,11 +2459,14 @@ public class AlignmentUtils
         {
           for (String base : alleles.split(","))
           {
-            if (!base2.equals(base))
+            if (!base2.equalsIgnoreCase(base))
             {
-              String codon = base1 + base + base3;
+              String codon = base1.toLowerCase() + base.toUpperCase()
+                      + base3.toLowerCase();
+              String canonical = base1.toLowerCase() + base2.toUpperCase()
+                      + base3.toLowerCase();
               if (addPeptideVariant(peptide, peptidePos, residue, var,
-                      codon))
+                      codon, canonical))
               {
                 count++;
               }
@@ -2480,11 +2488,14 @@ public class AlignmentUtils
         {
           for (String base : alleles.split(","))
           {
-            if (!base3.equals(base))
+            if (!base3.equalsIgnoreCase(base))
             {
-              String codon = base1 + base2 + base;
+              String codon = base1.toLowerCase() + base2.toLowerCase()
+                      + base.toUpperCase();
+              String canonical = base1.toLowerCase() + base2.toLowerCase()
+                      + base3.toUpperCase();
               if (addPeptideVariant(peptide, peptidePos, residue, var,
-                      codon))
+                      codon, canonical))
               {
                 count++;
               }
@@ -2498,20 +2509,22 @@ public class AlignmentUtils
   }
 
   /**
-   * Helper method that adds a peptide variant feature, provided the given codon
-   * translates to a value different to the current residue (is a non-synonymous
-   * variant). ID and clinical_significance attributes of the dna variant (if
-   * present) are copied to the new feature.
+   * Helper method that adds a peptide variant feature. ID and
+   * clinical_significance attributes of the dna variant (if present) are copied
+   * to the new feature.
    * 
    * @param peptide
    * @param peptidePos
    * @param residue
    * @param var
    * @param codon
+   *          the variant codon e.g. aCg
+   * @param canonical
+   *          the 'normal' codon e.g. aTg
    * @return true if a feature was added, else false
    */
   static boolean addPeptideVariant(SequenceI peptide, int peptidePos,
-          String residue, DnaVariant var, String codon)
+          String residue, DnaVariant var, String codon, String canonical)
   {
     /*
      * get peptide translation of codon e.g. GAT -> D
@@ -2526,12 +2539,16 @@ public class AlignmentUtils
     {
       return false;
     }
-    String desc = codon;
+    String desc = canonical + "/" + codon;
     String featureType = "";
     if (trans.equals(residue))
     {
       featureType = SequenceOntologyI.SYNONYMOUS_VARIANT;
     }
+    else if (ResidueProperties.STOP.equals(trans))
+    {
+      featureType = SequenceOntologyI.STOP_GAINED;
+    }
     else
     {
       String residue3Char = StringUtils