JAL-2898 show 'stop_gained' variants on peptide sequences

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

diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java
index 9278361..bdc5fc1 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;
       }
@@ -2428,10 +2430,14 @@ public class AlignmentUtils
         {
           for (String base : alleles.split(","))
           {
-            String codon = base + base2 + base3;
-            if (addPeptideVariant(peptide, peptidePos, residue, var, codon))
+            if (!base1.equals(base))
             {
-              count++;
+              String codon = base + base2 + base3;
+              if (addPeptideVariant(peptide, peptidePos, residue, var,
+                      codon))
+              {
+                count++;
+              }
             }
           }
         }
@@ -2450,10 +2456,14 @@ public class AlignmentUtils
         {
           for (String base : alleles.split(","))
           {
-            String codon = base1 + base + base3;
-            if (addPeptideVariant(peptide, peptidePos, residue, var, codon))
+            if (!base2.equals(base))
             {
-              count++;
+              String codon = base1 + base + base3;
+              if (addPeptideVariant(peptide, peptidePos, residue, var,
+                      codon))
+              {
+                count++;
+              }
             }
           }
         }
@@ -2472,10 +2482,14 @@ public class AlignmentUtils
         {
           for (String base : alleles.split(","))
           {
-            String codon = base1 + base2 + base;
-            if (addPeptideVariant(peptide, peptidePos, residue, var, codon))
+            if (!base3.equals(base))
             {
-              count++;
+              String codon = base1 + base2 + base;
+              if (addPeptideVariant(peptide, peptidePos, residue, var,
+                      codon))
+              {
+                count++;
+              }
             }
           }
         }
@@ -2507,57 +2521,71 @@ public class AlignmentUtils
      * e.g. multibase variants or HGMD_MUTATION etc
      * are currently ignored here
      */
-    String trans = codon.contains("-") ? "-"
+    String trans = codon.contains("-") ? null
             : (codon.length() > CODON_LENGTH ? null
                     : ResidueProperties.codonTranslate(codon));
-    if (trans != null && !trans.equals(residue))
+    if (trans == null)
+    {
+      return false;
+    }
+    String desc = 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
               .toSentenceCase(ResidueProperties.aa2Triplet.get(residue));
       String trans3Char = StringUtils
               .toSentenceCase(ResidueProperties.aa2Triplet.get(trans));
-      String desc = "p." + residue3Char + peptidePos + trans3Char;
-      SequenceFeature sf = new SequenceFeature(
-              SequenceOntologyI.SEQUENCE_VARIANT, desc, peptidePos,
-              peptidePos, var.getSource());
-      StringBuilder attributes = new StringBuilder(32);
-      String id = (String) var.variant.getValue(ID);
-      if (id != null)
-      {
-        if (id.startsWith(SEQUENCE_VARIANT))
-        {
-          id = id.substring(SEQUENCE_VARIANT.length());
-        }
-        sf.setValue(ID, id);
-        attributes.append(ID).append("=").append(id);
-        // TODO handle other species variants JAL-2064
-        StringBuilder link = new StringBuilder(32);
-        try
-        {
-          link.append(desc).append(" ").append(id).append(
-                  "|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=")
-                  .append(URLEncoder.encode(id, "UTF-8"));
-          sf.addLink(link.toString());
-        } catch (UnsupportedEncodingException e)
-        {
-          // as if
-        }
-      }
-      String clinSig = (String) var.variant.getValue(CLINICAL_SIGNIFICANCE);
-      if (clinSig != null)
+      desc = "p." + residue3Char + peptidePos + trans3Char;
+      featureType = SequenceOntologyI.NONSYNONYMOUS_VARIANT;
+    }
+    SequenceFeature sf = new SequenceFeature(featureType, desc, peptidePos,
+            peptidePos, var.getSource());
+
+    StringBuilder attributes = new StringBuilder(32);
+    String id = (String) var.variant.getValue(ID);
+    if (id != null)
+    {
+      if (id.startsWith(SEQUENCE_VARIANT))
       {
-        sf.setValue(CLINICAL_SIGNIFICANCE, clinSig);
-        attributes.append(";").append(CLINICAL_SIGNIFICANCE).append("=")
-                .append(clinSig);
+        id = id.substring(SEQUENCE_VARIANT.length());
       }
-      peptide.addSequenceFeature(sf);
-      if (attributes.length() > 0)
+      sf.setValue(ID, id);
+      attributes.append(ID).append("=").append(id);
+      // TODO handle other species variants JAL-2064
+      StringBuilder link = new StringBuilder(32);
+      try
       {
-        sf.setAttributes(attributes.toString());
+        link.append(desc).append(" ").append(id).append(
+                "|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=")
+                .append(URLEncoder.encode(id, "UTF-8"));
+        sf.addLink(link.toString());
+      } catch (UnsupportedEncodingException e)
+      {
+        // as if
       }
-      return true;
     }
-    return false;
+    String clinSig = (String) var.variant.getValue(CLINICAL_SIGNIFICANCE);
+    if (clinSig != null)
+    {
+      sf.setValue(CLINICAL_SIGNIFICANCE, clinSig);
+      attributes.append(";").append(CLINICAL_SIGNIFICANCE).append("=")
+              .append(clinSig);
+    }
+    peptide.addSequenceFeature(sf);
+    if (attributes.length() > 0)
+    {
+      sf.setAttributes(attributes.toString());
+    }
+    return true;
   }
 
   /**