JAL-3017 parse multiple variant elements for uniprot 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 11fff9d..fc4f318 100644 (file)
--- a/src/jalview/ws/dbsources/Uniprot.java
+++ b/src/jalview/ws/dbsources/Uniprot.java
@@ -42,6 +42,7 @@ import java.io.Reader;
 import java.net.URL;
 import java.net.URLConnection;
 import java.util.ArrayList;
+import java.util.List;
 import java.util.Vector;
 
 import org.exolab.castor.mapping.Mapping;
@@ -302,24 +303,41 @@ public class Uniprot extends DbSourceProxyImpl
   protected static String getDescription(UniprotFeature uf)
   {
     String orig = uf.getOriginal();
-    String var = uf.getVariation();
+    List<String> variants = 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())
+    if (orig != null && !orig.isEmpty() && variants != null
+            && !variants.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(" ");
-    }
+      int p = 0;
+      for (String var : variants)
+      {
+        sb.append("p.");
+        String orig3 = ResidueProperties.aa2Triplet.get(orig);
+        sb.append(orig3 == null ? orig : StringUtils.toSentenceCase(orig3));
+        sb.append(Integer.toString(uf.getPosition()));
+        for (int c = 0, clen = var.length(); c < clen; c++)
+        {
+          char varchar = var.charAt(c);
+          String var3 = ResidueProperties.aa2Triplet.get("" + varchar);
 
+          sb.append(var3 != null ? StringUtils.toSentenceCase(var3)
+                  : "" + varchar);
+        }
+        if (++p != variants.size())
+        {
+          sb.append("<br/>");
+        }
+        else
+        {
+          sb.append(" ");
+        }
+      }
+    }
     String description = uf.getDescription();
     if (description != null)
     {