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 5e11446..aa1a98b 100644 (file)
--- a/src/jalview/analysis/AlignmentUtils.java
+++ b/src/jalview/analysis/AlignmentUtils.java
@@ -2430,14 +2430,11 @@ public class AlignmentUtils
         {
           for (String base : alleles.split(","))
           {
-            if (!base1.equalsIgnoreCase(base))
+            if (!base1.equals(base))
             {
-              String codon = base.toUpperCase() + base2.toLowerCase()
-                      + base3.toLowerCase();
-              String canonical = base1.toUpperCase() + base2.toLowerCase()
-                      + base3.toLowerCase();
+              String codon = base + base2 + base3;
               if (addPeptideVariant(peptide, peptidePos, residue, var,
-                      codon, canonical))
+                      codon))
               {
                 count++;
               }
@@ -2459,14 +2456,11 @@ public class AlignmentUtils
         {
           for (String base : alleles.split(","))
           {
-            if (!base2.equalsIgnoreCase(base))
+            if (!base2.equals(base))
             {
-              String codon = base1.toLowerCase() + base.toUpperCase()
-                      + base3.toLowerCase();
-              String canonical = base1.toLowerCase() + base2.toUpperCase()
-                      + base3.toLowerCase();
+              String codon = base1 + base + base3;
               if (addPeptideVariant(peptide, peptidePos, residue, var,
-                      codon, canonical))
+                      codon))
               {
                 count++;
               }
@@ -2488,14 +2482,11 @@ public class AlignmentUtils
         {
           for (String base : alleles.split(","))
           {
-            if (!base3.equalsIgnoreCase(base))
+            if (!base3.equals(base))
             {
-              String codon = base1.toLowerCase() + base2.toLowerCase()
-                      + base.toUpperCase();
-              String canonical = base1.toLowerCase() + base2.toLowerCase()
-                      + base3.toUpperCase();
+              String codon = base1 + base2 + base;
               if (addPeptideVariant(peptide, peptidePos, residue, var,
-                      codon, canonical))
+                      codon))
               {
                 count++;
               }
@@ -2518,13 +2509,10 @@ public class AlignmentUtils
    * @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 canonical)
+          String residue, DnaVariant var, String codon)
   {
     /*
      * get peptide translation of codon e.g. GAT -> D
@@ -2539,7 +2527,7 @@ public class AlignmentUtils
     {
       return false;
     }
-    String desc = canonical + "/" + codon;
+    String desc = codon;
     String featureType = "";
     if (trans.equals(residue))
     {