JAL-2898 show 'stop_gained' variants on peptide sequences

diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java
index 3d22115..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;
       }
@@ -2532,6 +2534,10 @@ public class AlignmentUtils
     {
       featureType = SequenceOntologyI.SYNONYMOUS_VARIANT;
     }
+    else if (ResidueProperties.STOP.equals(trans))
+    {
+      featureType = SequenceOntologyI.STOP_GAINED;
+    }
     else
     {
       String residue3Char = StringUtils

diff --git a/src/jalview/analysis/Dna.java b/src/jalview/analysis/Dna.java
index f3088ea..ef05a58 100644 (file)
--- a/src/jalview/analysis/Dna.java
+++ b/src/jalview/analysis/Dna.java
@@ -161,7 +161,7 @@ public class Dna
 
     int s;
     int sSize = selection.size();
-    List<SequenceI> pepseqs = new ArrayList<SequenceI>();
+    List<SequenceI> pepseqs = new ArrayList<>();
     for (s = 0; s < sSize; s++)
     {
       SequenceI newseq = translateCodingRegion(selection.get(s),
@@ -213,7 +213,7 @@ public class Dna
       if (dnarefs != null)
       {
         // intersect with pep
-        List<DBRefEntry> mappedrefs = new ArrayList<DBRefEntry>();
+        List<DBRefEntry> mappedrefs = new ArrayList<>();
         DBRefEntry[] refs = dna.getDBRefs();
         for (int d = 0; d < refs.length; d++)
         {
@@ -391,7 +391,7 @@ public class Dna
           String seqstring, AlignedCodonFrame acf,
           List<SequenceI> proteinSeqs)
   {
-    List<int[]> skip = new ArrayList<int[]>();
+    List<int[]> skip = new ArrayList<>();
     int skipint[] = null;
     ShiftList vismapping = new ShiftList(); // map from viscontigs to seqstring
     // intervals
@@ -544,7 +544,7 @@ public class Dna
             skip.add(skipint);
             skipint = null;
           }
-          if (aa.equals("STOP"))
+          if (aa.equals(ResidueProperties.STOP))
           {
             aa = STOP_ASTERIX;
           }
@@ -800,7 +800,7 @@ public class Dna
   public AlignmentI reverseCdna(boolean complement)
   {
     int sSize = selection.size();
-    List<SequenceI> reversed = new ArrayList<SequenceI>();
+    List<SequenceI> reversed = new ArrayList<>();
     for (int s = 0; s < sSize; s++)
     {
       SequenceI newseq = reverseSequence(selection.get(s).getName(),

diff --git a/src/jalview/io/gff/SequenceOntologyI.java b/src/jalview/io/gff/SequenceOntologyI.java
index 10ca7ec..307e1d1 100644 (file)
--- a/src/jalview/io/gff/SequenceOntologyI.java
+++ b/src/jalview/io/gff/SequenceOntologyI.java
@@ -48,6 +48,9 @@ public interface SequenceOntologyI
   // SO:0001992
   public static final String NONSYNONYMOUS_VARIANT = "nonsynonymous_variant";
 
+  // SO:0001587
+  public static final String STOP_GAINED = "stop_gained";
+
   // SO:0000147
   public static final String EXON = "exon";
 

diff --git a/src/jalview/schemes/ResidueProperties.java b/src/jalview/schemes/ResidueProperties.java
index 55df1d1..a4e6480 100755 (executable)
--- a/src/jalview/schemes/ResidueProperties.java
+++ b/src/jalview/schemes/ResidueProperties.java
@@ -39,14 +39,14 @@ public class ResidueProperties
 
   public static final int[] purinepyrimidineIndex;
 
-  public static final Map<String, Integer> aa3Hash = new HashMap<String, Integer>();
+  public static final Map<String, Integer> aa3Hash = new HashMap<>();
 
-  public static final Map<String, String> aa2Triplet = new HashMap<String, String>();
+  public static final Map<String, String> aa2Triplet = new HashMap<>();
 
-  public static final Map<String, String> nucleotideName = new HashMap<String, String>();
+  public static final Map<String, String> nucleotideName = new HashMap<>();
 
   // lookup from modified amino acid (e.g. MSE) to canonical form (e.g. MET)
-  public static final Map<String, String> modifications = new HashMap<String, String>();
+  public static final Map<String, String> modifications = new HashMap<>();
 
   static
   {
@@ -496,25 +496,27 @@ public class ResidueProperties
    * Color.white, // R Color.white, // Y Color.white, // N Color.white, // Gap
    */
 
-  public static List<String> STOP = Arrays.asList("TGA", "TAA", "TAG");
+  public static String STOP = "STOP";
+
+  public static List<String> STOP_CODONS = Arrays.asList("TGA", "TAA", "TAG");
 
   public static String START = "ATG";
 
   /**
    * Nucleotide Ambiguity Codes
    */
-  public static final Map<String, String[]> ambiguityCodes = new Hashtable<String, String[]>();
+  public static final Map<String, String[]> ambiguityCodes = new Hashtable<>();
 
   /**
    * Codon triplets with additional symbols for unambiguous codons that include
    * ambiguity codes
    */
-  public static final Hashtable<String, String> codonHash2 = new Hashtable<String, String>();
+  public static final Hashtable<String, String> codonHash2 = new Hashtable<>();
 
   /**
    * all ambiguity codes for a given base
    */
-  public final static Hashtable<String, List<String>> _ambiguityCodes = new Hashtable<String, List<String>>();
+  public final static Hashtable<String, List<String>> _ambiguityCodes = new Hashtable<>();
 
   static
   {
@@ -638,7 +640,7 @@ public class ResidueProperties
         List<String> codesfor = _ambiguityCodes.get(r);
         if (codesfor == null)
         {
-          _ambiguityCodes.put(r, codesfor = new ArrayList<String>());
+          _ambiguityCodes.put(r, codesfor = new ArrayList<>());
         }
         if (!codesfor.contains(acode.getKey()))
         {
@@ -755,27 +757,27 @@ public class ResidueProperties
   }
 
   // Stores residue codes/names and colours and other things
-  public static Map<String, Map<String, Integer>> propHash = new Hashtable<String, Map<String, Integer>>();
+  public static Map<String, Map<String, Integer>> propHash = new Hashtable<>();
 
-  public static Map<String, Integer> hydrophobic = new Hashtable<String, Integer>();
+  public static Map<String, Integer> hydrophobic = new Hashtable<>();
 
-  public static Map<String, Integer> polar = new Hashtable<String, Integer>();
+  public static Map<String, Integer> polar = new Hashtable<>();
 
-  public static Map<String, Integer> small = new Hashtable<String, Integer>();
+  public static Map<String, Integer> small = new Hashtable<>();
 
-  public static Map<String, Integer> positive = new Hashtable<String, Integer>();
+  public static Map<String, Integer> positive = new Hashtable<>();
 
-  public static Map<String, Integer> negative = new Hashtable<String, Integer>();
+  public static Map<String, Integer> negative = new Hashtable<>();
 
-  public static Map<String, Integer> charged = new Hashtable<String, Integer>();
+  public static Map<String, Integer> charged = new Hashtable<>();
 
-  public static Map<String, Integer> aromatic = new Hashtable<String, Integer>();
+  public static Map<String, Integer> aromatic = new Hashtable<>();
 
-  public static Map<String, Integer> aliphatic = new Hashtable<String, Integer>();
+  public static Map<String, Integer> aliphatic = new Hashtable<>();
 
-  public static Map<String, Integer> tiny = new Hashtable<String, Integer>();
+  public static Map<String, Integer> tiny = new Hashtable<>();
 
-  public static Map<String, Integer> proline = new Hashtable<String, Integer>();
+  public static Map<String, Integer> proline = new Hashtable<>();
 
   static
   {
@@ -1149,7 +1151,7 @@ public class ResidueProperties
     String cdn = codonHash2.get(lccodon.toUpperCase());
     if ("*".equals(cdn))
     {
-      return "STOP";
+      return STOP;
     }
     return cdn;
   }
@@ -1157,7 +1159,7 @@ public class ResidueProperties
   public static Hashtable<String, String> toDssp3State;
   static
   {
-    toDssp3State = new Hashtable<String, String>();
+    toDssp3State = new Hashtable<>();
     toDssp3State.put("H", "H");
     toDssp3State.put("E", "E");
     toDssp3State.put("C", " ");
@@ -2525,7 +2527,7 @@ public class ResidueProperties
   // / cut here
   public static void main(String[] args)
   {
-    Hashtable<String, Vector<String>> aaProps = new Hashtable<String, Vector<String>>();
+    Hashtable<String, Vector<String>> aaProps = new Hashtable<>();
     System.out.println("my %aa = {");
     // invert property hashes
     for (String pname : propHash.keySet())
@@ -2536,7 +2538,7 @@ public class ResidueProperties
         Vector<String> aprops = aaProps.get(rname);
         if (aprops == null)
         {
-          aprops = new Vector<String>();
+          aprops = new Vector<>();
           aaProps.put(rname, aprops);
         }
         Integer hasprop = phash.get(rname);
@@ -2578,7 +2580,7 @@ public class ResidueProperties
   public static List<String> getResidues(boolean forNucleotide,
           boolean includeAmbiguous)
   {
-    List<String> result = new ArrayList<String>();
+    List<String> result = new ArrayList<>();
     if (forNucleotide)
     {
       for (String nuc : nucleotideName.keySet())

diff --git a/test/jalview/analysis/AlignmentUtilsTests.java b/test/jalview/analysis/AlignmentUtilsTests.java
index 3e8390f..be6ba60 100644 (file)
--- a/test/jalview/analysis/AlignmentUtilsTests.java
+++ b/test/jalview/analysis/AlignmentUtilsTests.java
@@ -2157,23 +2157,8 @@ public class AlignmentUtilsTests
             sf.links.get(0));
     assertEquals(ensembl, sf.getFeatureGroup());
 
-    // AAA -> TAA -> stop codon
-    sf = sfs.get(1);
-    assertEquals(1, sf.getBegin());
-    assertEquals(1, sf.getEnd());
-    assertEquals("nonsynonymous_variant", sf.getType());
-    assertEquals("p.Lys1null", sf.getDescription()); // stop codon badly handled
-    assertEquals("var3", sf.getValue("ID"));
-    assertEquals("Bad", sf.getValue("clinical_significance"));
-    assertEquals("ID=var3;clinical_significance=Bad", sf.getAttributes());
-    assertEquals(1, sf.links.size());
-    assertEquals(
-            "p.Lys1null var3|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var3",
-            sf.links.get(0));
-    assertEquals(dbSnp, sf.getFeatureGroup());
-
     // AAA -> CAA -> K/Q
-    sf = sfs.get(2);
+    sf = sfs.get(1);
     assertEquals(1, sf.getBegin());
     assertEquals(1, sf.getEnd());
     assertEquals("nonsynonymous_variant", sf.getType());
@@ -2188,7 +2173,7 @@ public class AlignmentUtilsTests
     assertEquals(dbSnp, sf.getFeatureGroup());
 
     // AAA -> GAA -> K/E
-    sf = sfs.get(3);
+    sf = sfs.get(2);
     assertEquals(1, sf.getBegin());
     assertEquals(1, sf.getEnd());
     assertEquals("nonsynonymous_variant", sf.getType());
@@ -2203,6 +2188,21 @@ public class AlignmentUtilsTests
             sf.links.get(0));
     assertEquals(ensembl, sf.getFeatureGroup());
 
+    // AAA -> TAA -> stop codon
+    sf = sfs.get(3);
+    assertEquals(1, sf.getBegin());
+    assertEquals(1, sf.getEnd());
+    assertEquals("stop_gained", sf.getType());
+    assertEquals("TAA", sf.getDescription());
+    assertEquals("var3", sf.getValue("ID"));
+    assertEquals("Bad", sf.getValue("clinical_significance"));
+    assertEquals("ID=var3;clinical_significance=Bad", sf.getAttributes());
+    assertEquals(1, sf.links.size());
+    assertEquals(
+            "TAA var3|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var3",
+            sf.links.get(0));
+    assertEquals(dbSnp, sf.getFeatureGroup());
+
     // AAA -> AAG synonymous
     sf = sfs.get(4);
     assertEquals(1, sf.getBegin());