JAL-2920 use HGVS notation for protein variant feature

[jalview.git] / src / jalview / ws / dbsources / Uniprot.java

diff --git a/src/jalview/ws/dbsources/Uniprot.java b/src/jalview/ws/dbsources/Uniprot.java
index 6b09eb6..11fff9d 100644 (file)
--- a/src/jalview/ws/dbsources/Uniprot.java
+++ b/src/jalview/ws/dbsources/Uniprot.java
@@ -32,6 +32,8 @@ import jalview.datamodel.SequenceI;
 import jalview.datamodel.xdb.uniprot.UniprotEntry;
 import jalview.datamodel.xdb.uniprot.UniprotFeature;
 import jalview.datamodel.xdb.uniprot.UniprotFile;
+import jalview.schemes.ResidueProperties;
+import jalview.util.StringUtils;
 import jalview.ws.seqfetcher.DbSourceProxyImpl;
 
 import java.io.InputStream;
@@ -278,7 +280,7 @@ public class Uniprot extends DbSourceProxyImpl
       for (UniprotFeature uf : entry.getFeature())
       {
         SequenceFeature copy = new SequenceFeature(uf.getType(),
-                uf.getDescription(), uf.getBegin(), uf.getEnd(), "Uniprot");
+                getDescription(uf), uf.getBegin(), uf.getEnd(), "Uniprot");
         copy.setStatus(uf.getStatus());
         sequence.addSequenceFeature(copy);
       }
@@ -291,6 +293,43 @@ public class Uniprot extends DbSourceProxyImpl
   }
 
   /**
+   * Constructs a feature description from the description and (optionally)
+   * original and variant fields of the Uniprot XML feature
+   * 
+   * @param uf
+   * @return
+   */
+  protected static String getDescription(UniprotFeature uf)
+  {
+    String orig = uf.getOriginal();
+    String var = uf.getVariation();
+    StringBuilder sb = new StringBuilder();
+
+    /*
+     * append variant in standard format if present
+     * e.g. p.Arg59Lys
+     */
+    if (orig != null && !orig.isEmpty() && var != null && !var.isEmpty())
+    {
+      sb.append("p.");
+      String orig3 = ResidueProperties.aa2Triplet.get(orig);
+      sb.append(orig3 == null ? orig : StringUtils.toSentenceCase(orig3));
+      sb.append(Integer.toString(uf.getPosition()));
+      String var3 = ResidueProperties.aa2Triplet.get(var);
+      sb.append(var3 == null ? var : StringUtils.toSentenceCase(var3));
+      sb.append(" ");
+    }
+
+    String description = uf.getDescription();
+    if (description != null)
+    {
+      sb.append(description);
+    }
+
+    return sb.toString();
+  }
+
+  /**
    * 
    * @param entry
    *          UniportEntry