From 964f27f06912574ac9d0c65c3f741852f48e558a Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Fri, 19 Feb 2016 16:42:34 +0000
Subject: [PATCH] JAL-1705 lenient DBRef matcher added (accession id only)

---
 src/jalview/util/DBRefUtils.java      |   36 +++++++++++++++++++++++++++++++++
 test/jalview/util/DBRefUtilsTest.java |   26 ++++++++++++++++++++++++
 2 files changed, 62 insertions(+)

diff --git a/src/jalview/util/DBRefUtils.java b/src/jalview/util/DBRefUtils.java
index e7053ed..424d40b 100755
--- a/src/jalview/util/DBRefUtils.java
+++ b/src/jalview/util/DBRefUtils.java
@@ -169,6 +169,25 @@ public class DBRefUtils
   }
 
   /**
+   * Returns an array of those references that match the given accession id
+   * <ul>
+   * <li>database sources are the same</li>
+   * <li>accession ids are the same</li>
+   * <li>both have no mapping, or the mappings are the same</li>
+   * </ul>
+   * 
+   * @param ref
+   *          Set of references to search
+   * @param entry
+   *          pattern to match
+   * @return
+   */
+  public static DBRefEntry[] searchRefs(DBRefEntry[] ref, String accId)
+  {
+    return searchRefs(ref, new DBRefEntry("", "", accId), matchId);
+  }
+
+  /**
    * Returns an array of those references that match the given entry, according
    * to the given comparator. Returns null if no matches.
    * 
@@ -397,6 +416,23 @@ public class DBRefUtils
   };
 
   /**
+   * accession ID only must be identical.
+   */
+  public static DbRefComp matchId = new DbRefComp()
+  {
+    @Override
+    public boolean matches(DBRefEntry refa, DBRefEntry refb)
+    {
+      if (refa.getAccessionId() != null && refb.getAccessionId() != null
+              && refb.getAccessionId().equals(refa.getAccessionId()))
+      {
+        return true;
+      }
+      return false;
+    }
+  };
+
+  /**
    * Parses a DBRefEntry and adds it to the sequence, also a PDBEntry if the
    * database is PDB.
    * <p>
diff --git a/test/jalview/util/DBRefUtilsTest.java b/test/jalview/util/DBRefUtilsTest.java
index e1eb2a6..371bb91 100644
--- a/test/jalview/util/DBRefUtilsTest.java
+++ b/test/jalview/util/DBRefUtilsTest.java
@@ -230,4 +230,30 @@ public class DBRefUtilsTest
     assertSame(ref1, matches[0]);
     assertSame(ref2, matches[1]);
   }
+
+  /**
+   * Test the method that searches for matching references based on accession id
+   * only
+   */
+  @Test(groups = { "Functional" })
+  public void testSearchRefs_accessionid()
+  {
+  
+    DBRefEntry ref1 = new DBRefEntry("Uniprot", "1", "A1234"); // matches
+    DBRefEntry ref2 = new DBRefEntry("embl", "1", "A1234"); // matches
+    // constructor does not upper-case accession id
+    DBRefEntry ref3 = new DBRefEntry("EMBL", "1", "a1234"); // no match
+    DBRefEntry ref4 = new DBRefEntry("EMBLCDS", "1", "A1235"); // no match
+    // ref5 matches although it has a mapping - ignored
+    DBRefEntry ref5 = new DBRefEntry("EMBL", "1", "A1234");
+    ref5.setMap(new Mapping(new MapList(new int[] { 1, 1 }, new int[] { 1,
+        1 }, 1, 1)));
+  
+    DBRefEntry[] matches = DBRefUtils.searchRefs(new DBRefEntry[] { ref1,
+        ref2, ref3, ref4, ref5 }, "A1234");
+    assertEquals(3, matches.length);
+    assertSame(ref1, matches[0]);
+    assertSame(ref2, matches[1]);
+    assertSame(ref5, matches[2]);
+  }
 }
-- 
1.7.10.2