Changeset 168

Timestamp:

08/22/09 20:23:17 (2 years ago)

Author:

martijn

Message:

Work on transitive mapping in Stack
Also added unit test and data file
Not yet implemented for mapID(Set<Xref>, ...

Location:

trunk

Files:

• bio/test/org/bridgedb/bio/TestStack.java (modified) (2 diffs)
• corelib/src/org/bridgedb/IDMapperStack.java (modified) (1 diff)
• test-data/Nugo-hs-custom.txt (added)

trunk/bio/test/org/bridgedb/bio/TestStack.java

@@ -18 +18 @@
 public class TestStack extends TestCase
 {
-
-        static final String GDB_HUMAN = 
+        private static final String GDB_HUMAN = 
                 System.getProperty ("user.home") + File.separator + 
                 "PathVisio-Data/gene databases/Hs_Derby_20081119.pgdb";
-        static final File YEAST_ID_MAPPING = new File ("../test-data/yeast_id_mapping.txt");
+        private static final File YEAST_ID_MAPPING = new File ("../test-data/yeast_id_mapping.txt");
+        private static final File NUGO_CUSTOM_MAPPINGS = new File ("/home/martijn/prg/bridgedb/test-data/Nugo-hs-custom.txt");
 
-        Set<Xref> src = new HashSet<Xref>();
-        Set<DataSource> dsset = new HashSet<DataSource>();
-        static final Xref RAD51 = new Xref ("YER095W", BioDataSource.ENSEMBL_SCEREVISIAE);
-        static final Xref INSR = new Xref ("Hs.705877", BioDataSource.UNIGENE);
-        
+        private Set<Xref> src = new HashSet<Xref>();
+        private Set<DataSource> dsset = new HashSet<DataSource>();
+        private static final Xref RAD51 = new Xref ("YER095W", BioDataSource.ENSEMBL_SCEREVISIAE);
+        private static final Xref INSR = new Xref ("Hs.705877", BioDataSource.UNIGENE);
+
+        private static final Xref NUGO = new Xref ("NuGO_eht0320285_at", BioDataSource.AFFY);
+        private static final Xref ENSEMBL = new Xref ("ENSG00000026652", BioDataSource.ENSEMBL);
+        private static final Xref ENTREZ = new Xref ("56895", BioDataSource.ENTREZ_GENE);
+
         public void setUp() throws ClassNotFoundException
         {
@@ -82 +86 @@
                 assertEquals (expected, refmap.get(RAD51));
         }
+
+        public void testTransitive() throws IDMapperException, ClassNotFoundException, MalformedURLException
+        {                
+                IDMapper textMapper = BridgeDb.connect ("idmapper-text:" + NUGO_CUSTOM_MAPPINGS.toURL());
+                IDMapper derbyMapper = BridgeDb.connect ("idmapper-pgdb:" + GDB_HUMAN);
+                IDMapperStack stack = new IDMapperStack();
+                stack.addIDMapper(derbyMapper);
+                stack.addIDMapper(textMapper);
         
+                stack.setTransitive(false);
+                
+                // test the link between NUGO and ENSEMBL that only occurs in text              
+                Set<Xref> result = stack.mapID(NUGO, null);
+                assertTrue(result.contains(ENSEMBL));
+                assertFalse(result.contains(ENTREZ));
+                                
+                // test the link between ENTREZ and ENSEMBL that only occurs in pgdb
+                result = stack.mapID(ENTREZ, null);             
+                assertFalse(result.contains(NUGO));
+                assertTrue(result.contains(ENSEMBL));
+                
+                stack.setTransitive(true);
+
+                // test transitive
+                result = stack.mapID(NUGO, null);
+                assertTrue(result.contains(ENTREZ));
+                assertTrue(result.contains(ENSEMBL));
+                
+                // and the other way around
+                result = stack.mapID(ENTREZ, null);
+                assertTrue(result.contains(NUGO));
+                assertTrue(result.contains(ENSEMBL));
+
+                // map multiple IDs
+                Set<Xref> set1 = new HashSet<Xref>();
+                set1.add (ENTREZ);
+                Map<Xref, Set<Xref>> result2 = stack.mapID(set1, null);
+                assertTrue (result2.get(ENTREZ).contains(NUGO));
+        }
 }

trunk/corelib/src/org/bridgedb/IDMapperStack.java

@@ -398 +398 @@
         private Set<Xref> mapIDtransitive(Xref ref, Set<DataSource> resultDs) throws IDMapperException 
         {
-                throw new UnsupportedOperationException();
+                // first round
+                Set<Xref> round1 = new HashSet<Xref>();
+                for (IDMapper child : gdbs)
+                {
+                        if (child != null && child.isConnected())
+                        {
+                                round1.addAll (child.mapID(ref, null));
+                        }
+                }
+                // second round
+                Set<Xref> round2 = new HashSet<Xref>();
+                for (IDMapper child : gdbs)
+                {
+                        if (child != null && child.isConnected())
+                        {
+                                for (Set<Xref> set : child.mapID(round1, resultDs).values())
+                                        round2.addAll (set);
+                        }
+                }
+                return round2;
         }