Merge branch 'bug/JAL-2920_uniprotvariantfeature' into releases/Release_2_10_4_Branch

diff --git a/resources/uniprot_mapping.xml b/resources/uniprot_mapping.xml
index 6344d1e..832d3e5 100755 (executable)
--- a/resources/uniprot_mapping.xml
+++ b/resources/uniprot_mapping.xml
@@ -62,13 +62,19 @@
                </field>
                <field name="position">
                 <bind-xml name="position" node="attribute" location="location/position"/>
-                </field>
+               </field>
                <field name="begin">
                 <bind-xml name="position" node="attribute" location="location/begin"/>
-                </field>
-               <field name="end">
-                <bind-xml name="position" node="attribute" location="location/end"/>
-                </field>
+               </field>
+    <field name="end">
+      <bind-xml name="position" node="attribute" location="location/end"/>
+    </field>
+    <field name="variation">
+     <bind-xml name="variation"/>
+    </field>
+    <field name="original">
+     <bind-xml name="original"/>
+    </field>
         </class>
        
           <class name="jalview.datamodel.xdb.uniprot.UniprotSequence">

diff --git a/src/jalview/datamodel/xdb/uniprot/UniprotFeature.java b/src/jalview/datamodel/xdb/uniprot/UniprotFeature.java
index b1ed275..4c2ae24 100644 (file)
--- a/src/jalview/datamodel/xdb/uniprot/UniprotFeature.java
+++ b/src/jalview/datamodel/xdb/uniprot/UniprotFeature.java
@@ -27,7 +27,11 @@ public class UniprotFeature
 {
   private String type;
 
-  private String description;
+  private String description = null;
+
+  private String original = null;
+
+  private String variation = null;
 
   private String status;
 
@@ -47,7 +51,19 @@ public class UniprotFeature
 
   public String getDescription()
   {
-    return description;
+    if (description == null && variation == null && original == null)
+    {
+      return null;
+    }
+    return (description == null ? "" : description)
+            + (variation != null
+                    ? (description != null ? " " : "") + "Variation: '"
+                            + variation + "'"
+                    : "")
+            + (original != null
+                    ? ((description != null || variation != null) ? " "
+                            : "") + "Original: '" + original + "'"
+                    : "");
   }
 
   public void setDescription(String d)
@@ -95,4 +111,24 @@ public class UniprotFeature
     this.begin = p;
     this.end = p;
   }
+
+  public String getOriginal()
+  {
+    return original;
+  }
+
+  public void setOriginal(String original)
+  {
+    this.original = original;
+  }
+
+  public String getVariation()
+  {
+    return variation;
+  }
+
+  public void setVariation(String variant)
+  {
+    this.variation = variant;
+  }
 }

diff --git a/test/jalview/ws/dbsources/UniprotTest.java b/test/jalview/ws/dbsources/UniprotTest.java
index f98ef85..c603a11 100644 (file)
--- a/test/jalview/ws/dbsources/UniprotTest.java
+++ b/test/jalview/ws/dbsources/UniprotTest.java
@@ -63,6 +63,9 @@ public class UniprotTest
           + "<feature type=\"signal peptide\" evidence=\"7\"><location><begin position=\"1\"/><end position=\"18\"/></location></feature>"
           + "<feature type=\"propeptide\" description=\"Activation peptide\" id=\"PRO_0000027399\" evidence=\"9 16 17 18\"><location><begin position=\"19\"/><end position=\"20\"/></location></feature>"
           + "<feature type=\"chain\" description=\"Granzyme B\" id=\"PRO_0000027400\"><location><begin position=\"21\"/><end position=\"247\"/></location></feature>"
+          + "<feature type=\"sequence variant\"><original>M</original><variation>L</variation><location><position position=\"41\"/></location></feature>"
+          + "<feature type=\"sequence variant\" description=\"Pathogenic\"><original>M</original><variation>L</variation><location><position position=\"41\"/></location></feature>"
+          + "<feature type=\"sequence variant\" description=\"Pathogenic\"><original>M</original><location><position position=\"41\"/></location></feature>"
           + "<sequence length=\"10\" mass=\"27410\" checksum=\"8CB760AACF88FE6C\" modified=\"2008-01-15\" version=\"1\">MHAPL VSKDL</sequence></entry>"
           + "</uniprot>";
 
@@ -98,7 +101,7 @@ public class UniprotTest
      * Check sequence features
      */
     Vector<UniprotFeature> features = entry.getFeature();
-    assertEquals(3, features.size());
+    assertEquals(6, features.size());
     UniprotFeature sf = features.get(0);
     assertEquals("signal peptide", sf.getType());
     assertNull(sf.getDescription());
@@ -118,6 +121,27 @@ public class UniprotTest
     assertEquals(21, sf.getBegin());
     assertEquals(247, sf.getEnd());
 
+    sf = features.get(3);
+    assertEquals("sequence variant", sf.getType());
+    assertEquals("Variation: 'L' Original: 'M'", sf.getDescription());
+    assertEquals(41, sf.getPosition());
+    assertEquals(41, sf.getBegin());
+    assertEquals(41, sf.getEnd());
+
+    sf = features.get(4);
+    assertEquals("sequence variant", sf.getType());
+    assertEquals("Pathogenic Variation: 'L' Original: 'M'",
+            sf.getDescription());
+    assertEquals(41, sf.getPosition());
+    assertEquals(41, sf.getBegin());
+    assertEquals(41, sf.getEnd());
+
+    sf = features.get(5);
+    assertEquals("sequence variant", sf.getType());
+    assertEquals("Pathogenic Original: 'M'", sf.getDescription());
+    assertEquals(41, sf.getPosition());
+    assertEquals(41, sf.getBegin());
+    assertEquals(41, sf.getEnd());
     /*
      * Check cross-references
      */