JAL-3017 parse multiple variant elements for uniprot feature

[jalview.git] / src / jalview / datamodel / xdb / uniprot / UniprotFeature.java

diff --git a/src/jalview/datamodel/xdb/uniprot/UniprotFeature.java b/src/jalview/datamodel/xdb/uniprot/UniprotFeature.java
index 4c2ae24..3bae87e 100644 (file)
--- a/src/jalview/datamodel/xdb/uniprot/UniprotFeature.java
+++ b/src/jalview/datamodel/xdb/uniprot/UniprotFeature.java
@@ -20,6 +20,8 @@
  */
 package jalview.datamodel.xdb.uniprot;
 
+import java.util.Vector;
+
 /**
  * A data model class for binding from Uniprot XML via uniprot_mapping.xml
  */
@@ -31,7 +33,7 @@ public class UniprotFeature
 
   private String original = null;
 
-  private String variation = null;
+  private Vector<String> variation = null;
 
   private String status;
 
@@ -55,15 +57,36 @@ public class UniprotFeature
     {
       return null;
     }
-    return (description == null ? "" : description)
-            + (variation != null
-                    ? (description != null ? " " : "") + "Variation: '"
-                            + variation + "'"
-                    : "")
-            + (original != null
-                    ? ((description != null || variation != null) ? " "
-                            : "") + "Original: '" + original + "'"
-                    : "");
+    StringBuilder sb = new StringBuilder();
+    if (description != null)
+    {
+      sb.append(description);
+    }
+    if (variation != null && variation.size() > 0)
+    {
+      int i = 0;
+      for (String var : variation)
+      {
+        if (i++ > 0)
+        {
+          sb.append(",");
+        }
+        if (sb.length() > 0)
+        {
+          sb.append(" ");
+        }
+        sb.append("Variation: '" + var + "'");
+      }
+    }
+    if (original != null)
+    {
+      if (sb.length() > 0)
+      {
+        sb.append(" ");
+      }
+      sb.append("Original: '" + original + "'");
+    }
+    return sb.toString();
   }
 
   public void setDescription(String d)
@@ -122,12 +145,12 @@ public class UniprotFeature
     this.original = original;
   }
 
-  public String getVariation()
+  public Vector<String> getVariation()
   {
     return variation;
   }
 
-  public void setVariation(String variant)
+  public void setVariation(Vector<String> variant)
   {
     this.variation = variant;
   }