JAL-3187 initial refactoring towards peptide variant in tooltip

diff --git a/src/jalview/datamodel/MappedFeatures.java b/src/jalview/datamodel/MappedFeatures.java
index 2f90a7c..f7263d2 100644 (file)
--- a/src/jalview/datamodel/MappedFeatures.java
+++ b/src/jalview/datamodel/MappedFeatures.java
@@ -5,8 +5,9 @@ import jalview.schemes.ResidueProperties;
 import jalview.util.MappingUtils;
 import jalview.util.StringUtils;
 
-import java.util.ArrayList;
+import java.util.HashSet;
 import java.util.List;
+import java.util.Set;
 
 /**
  * A data bean to hold a list of mapped sequence features (e.g. CDS features
@@ -16,6 +17,10 @@ import java.util.List;
  */
 public class MappedFeatures
 {
+  private static final String HGV_SP = "HGVSp";
+
+  private static final String CSQ = "CSQ";
+
   /*
    * the mapping from one sequence to another
    */
@@ -41,6 +46,15 @@ public class MappedFeatures
    */
   public final List<SequenceFeature> features;
 
+  /*
+   * if the mapping is 1:3 (peptide to CDS), this holds the
+   * mapped positions i.e. codon base positions in CDS; to
+   * support calculation of peptide variants from alleles
+   */
+  public final int[] codonPos;
+
+  private final char[] baseCodon;
+
   /**
    * Constructor
    * 
@@ -58,122 +72,126 @@ public class MappedFeatures
     fromPosition = pos;
     fromResidue = res;
     features = theFeatures;
+
+    /*
+     * determine codon positions and canonical codon
+     * for a peptide-to-CDS mapping
+     */
+    codonPos = MappingUtils.flattenRanges(
+            mapping.getMap().locateInFrom(fromPosition, fromPosition));
+    if (codonPos.length == 3)
+    {
+      baseCodon = new char[3];
+      int cdsStart = fromSeq.getStart();
+      baseCodon[0] = fromSeq.getCharAt(codonPos[0] - cdsStart);
+      baseCodon[1] = fromSeq.getCharAt(codonPos[1] - cdsStart);
+      baseCodon[2] = fromSeq.getCharAt(codonPos[2] - cdsStart);
+    }
+    else
+    {
+      baseCodon = null;
+    }
   }
 
   /**
-   * Computes and returns a (possibly empty) list of HGVS notation peptide
-   * variants derived from codon allele variants
+   * Computes and returns comma-delimited HGVS notation peptide variants derived
+   * from codon allele variants. If no variants are found, answers an empty
+   * string.
    * 
    * @return
    */
-  public List<String> findProteinVariants()
+  public String findProteinVariants(SequenceFeature sf)
   {
-    List<String> vars = new ArrayList<>();
-    if (features.isEmpty())
+    if (!features.contains(sf) || baseCodon == null)
     {
-      return vars;
+      return "";
     }
 
+    StringBuilder vars = new StringBuilder();
+
     /*
-     * determine canonical codon
+     * VCF data may already contain the protein consequence
      */
-    int[] codonPos = MappingUtils.flattenRanges(
-            mapping.getMap().locateInFrom(fromPosition, fromPosition));
-    if (codonPos.length != 3)
+    String hgvsp = sf.getValueAsString(CSQ, HGV_SP);
+    if (hgvsp != null)
     {
-      // error
-      return vars;
+      int colonPos = hgvsp.indexOf(':');
+      if (colonPos >= 0)
+      {
+        String var = hgvsp.substring(colonPos + 1);
+        return var;
+      }
     }
-    final char[] baseCodon = new char[3];
-    int cdsStart = fromSeq.getStart();
-    baseCodon[0] = fromSeq.getCharAt(codonPos[0] - cdsStart);
-    baseCodon[1] = fromSeq.getCharAt(codonPos[1] - cdsStart);
-    baseCodon[2] = fromSeq.getCharAt(codonPos[2] - cdsStart);
 
-    for (SequenceFeature sf : features)
+    /*
+     * otherwise, compute codon and peptide variant
+     */
+    // todo avoid duplication of code in AlignmentUtils.buildDnaVariantsMap
+    int cdsPos = sf.getBegin();
+    if (cdsPos != sf.getEnd())
     {
-      /*
-       * VCF data may already contain the protein consequence
-       */
-      String hgvsp = sf.getValueAsString("CSQ", "HGVSp");
-      if (hgvsp != null)
-      {
-        int colonPos = hgvsp.indexOf(':');
-        if (colonPos >= 0)
-        {
-          String var = hgvsp.substring(colonPos + 1);
-          if (!vars.contains(var))
-          {
-            vars.add(var);
-          }
-          continue;
-        }
-      }
+      // not handling multi-locus variant features
+      return "";
+    }
+    if (cdsPos != codonPos[0] && cdsPos != codonPos[1]
+            && cdsPos != codonPos[2])
+    {
+      // e.g. feature on intron within spliced codon!
+      return "";
+    }
 
-      /*
-       * otherwise, compute codon and peptide variant
-       */
-      // todo avoid duplication of code in AlignmentUtils.buildDnaVariantsMap
-      int cdsPos = sf.getBegin();
-      if (cdsPos != sf.getEnd())
-      {
-        // not handling multi-locus variant features
-        continue;
-      }
-      if (cdsPos != codonPos[0] && cdsPos != codonPos[1]
-              && cdsPos != codonPos[2])
-      {
-        // e.g. feature on intron within spliced codon!
-        continue;
-      }
+    String alls = (String) sf.getValue(Gff3Helper.ALLELES);
+    if (alls == null)
+    {
+      return "";
+    }
+
+    String from3 = StringUtils.toSentenceCase(
+            ResidueProperties.aa2Triplet.get(String.valueOf(fromResidue)));
 
-      String alls = (String) sf.getValue(Gff3Helper.ALLELES);
-      if (alls == null)
+    /*
+     * make a peptide variant for each SNP allele 
+     * e.g. C,G,T gives variants G and T for base C
+     */
+    Set<String> variantPeptides = new HashSet<>();
+    String[] alleles = alls.toUpperCase().split(",");
+    for (String allele : alleles)
+    {
+      allele = allele.trim().toUpperCase();
+      if (allele.length() > 1 || "-".equals(allele))
       {
-        continue;
+        continue; // multi-locus variant
       }
-      String from3 = StringUtils.toSentenceCase(
-              ResidueProperties.aa2Triplet
-                      .get(String.valueOf(fromResidue)));
+      char[] variantCodon = new char[3];
+      variantCodon[0] = baseCodon[0];
+      variantCodon[1] = baseCodon[1];
+      variantCodon[2] = baseCodon[2];
 
       /*
-       * make a peptide variant for each SNP allele 
-       * e.g. C,G,T gives variants G and T for base C
+       * poke variant base into canonical codon
        */
-      String[] alleles = alls.toUpperCase().split(",");
-      for (String allele : alleles)
+      int i = cdsPos == codonPos[0] ? 0 : (cdsPos == codonPos[1] ? 1 : 2);
+      variantCodon[i] = allele.toUpperCase().charAt(0);
+      String codon = new String(variantCodon);
+      String peptide = ResidueProperties.codonTranslate(codon);
+      if (fromResidue != peptide.charAt(0))
       {
-        allele = allele.trim().toUpperCase();
-        if (allele.length() > 1 || "-".equals(allele))
-        {
-          continue; // multi-locus variant
-        }
-        char[] variantCodon = new char[3];
-        variantCodon[0] = baseCodon[0];
-        variantCodon[1] = baseCodon[1];
-        variantCodon[2] = baseCodon[2];
-
-        /*
-         * poke variant base into canonical codon
-         */
-        int i = cdsPos == codonPos[0] ? 0 : (cdsPos == codonPos[1] ? 1 : 2);
-        variantCodon[i] = allele.toUpperCase().charAt(0);
-        String codon = new String(variantCodon);
-        String peptide = ResidueProperties.codonTranslate(codon);
-        if (fromResidue != peptide.charAt(0))
+        String to3 = ResidueProperties.STOP.equals(peptide) ? "STOP"
+                : StringUtils.toSentenceCase(
+                        ResidueProperties.aa2Triplet.get(peptide));
+        String var = "p." + from3 + fromPosition + to3;
+        if (!variantPeptides.contains(peptide)) // duplicate consequence
         {
-          String to3 = ResidueProperties.STOP.equals(peptide) ? "STOP"
-                  : StringUtils.toSentenceCase(
-                  ResidueProperties.aa2Triplet.get(peptide));
-          String var = "p." + from3 + fromPosition + to3;
-          if (!vars.contains(var))
+          variantPeptides.add(peptide);
+          if (vars.length() > 0)
           {
-            vars.add(var);
+            vars.append(",");
           }
+          vars.append(var);
         }
       }
     }
 
-    return vars;
+    return vars.toString();
   }
 }

diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java
index 8accd0d..1ceabd1 100644 (file)
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -845,6 +845,8 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
             pdbfilename);
     if (label != null)
     {
+      // change comma to pipe separator (newline token for Jmol)
+      label = label.replace(',', '|');
       StringTokenizer toks = new StringTokenizer(strInfo, " ");
       StringBuilder sb = new StringBuilder();
       sb.append("select ").append(String.valueOf(pdbResNum)).append(":")

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 14c3818..c648e53 100644 (file)
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -910,12 +910,12 @@ public class SeqPanel extends JPanel
                 .findComplementFeaturesAtResidue(ds, pos);
         if (mf != null)
         {
-          List<String> pv = mf.findProteinVariants();
-          for (String s : pv)
+          for (SequenceFeature sf : mf.features)
           {
-            if (!infos.contains(s))
+            String pv = mf.findProteinVariants(sf);
+            if (!infos.contains(pv))
             {
-              infos.addAll(pv);
+              infos.add(pv);
             }
           }
         }