Merge branch 'spikes/mungo' into trialMerge

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

diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java
index 3d22115..aa1a98b 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;
       }
@@ -2498,10 +2500,9 @@ 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
@@ -2532,6 +2533,10 @@ public class AlignmentUtils
     {
       featureType = SequenceOntologyI.SYNONYMOUS_VARIANT;
     }
+    else if (ResidueProperties.STOP.equals(trans))
+    {
+      featureType = SequenceOntologyI.STOP_GAINED;
+    }
     else
     {
       String residue3Char = StringUtils