+ assertEquals(cds3Map, dbRefEntry.getMap().getMap());
+
+ /*
+ * verify peptides have dbrefs
+ * - to EMBL sequence (with inverse 1:3 cds mapping)
+ * - to EMBLCDS (with 1:3 mapping)
+ * - direct (no mapping) to other protein accessions
+ */
+ MapList proteinToCdsMap1 = new MapList(new int[] { 1, 4 }, new int[] {
+ 1, 12 }, 1, 3);
+ MapList proteinToCdsMap2 = new MapList(new int[] { 1, 3 }, new int[] {
+ 1, 9 }, 1, 3);
+
+ // dbrefs for first CDS EMBL product CAA30420.1
+ dbrefs = peptides.get(0).getDBRefs();
+ assertEquals(5, dbrefs.length);
+ assertEquals(DBRefSource.EMBL, dbrefs[0].getSource());
+ assertEquals("CAA30420.1", dbrefs[0].getAccessionId());
+ // TODO: verify getPrimaryDBRefs() for peptide products
+ assertEquals(cds1Map.getInverse(), dbrefs[0].getMap().getMap());
+ assertEquals(DBRefSource.EMBLCDS, dbrefs[1].getSource());
+ assertEquals("CAA30420.1", dbrefs[1].getAccessionId());
+ assertEquals(proteinToCdsMap1, dbrefs[1].getMap().getMap());
+ assertEquals(DBRefSource.EMBLCDSProduct, dbrefs[2].getSource());
+ assertEquals("CAA30420.1", dbrefs[2].getAccessionId());
+ assertNull(dbrefs[2].getMap());
+ assertEquals(new DBRefEntry(DBRefSource.UNIPROT, "2.1", "B0BCM4"),
+ dbrefs[3]);
+ assertNull(dbrefs[3].getMap());
+ assertEquals(new DBRefEntry(DBRefSource.UNIPROT, "0", "P0CE20"),
+ dbrefs[4]);
+ assertNull(dbrefs[4].getMap());
+
+ // dbrefs for first CDS first Uniprot xref
+ dbrefs = peptides.get(1).getDBRefs();
+ assertEquals(2, dbrefs.length);
+ assertEquals(new DBRefEntry(DBRefSource.UNIPROT, "2.1", "B0BCM4"),
+ dbrefs[0]);
+ assertNull(dbrefs[0].getMap());
+ assertEquals(DBRefSource.EMBL, dbrefs[1].getSource());
+ assertEquals("X07547", dbrefs[1].getAccessionId());
+ assertEquals(cds1Map.getInverse(), dbrefs[1].getMap().getMap());
+
+ // dbrefs for first CDS second Uniprot xref
+ dbrefs = peptides.get(2).getDBRefs();
+ assertEquals(2, dbrefs.length);
+ assertEquals(new DBRefEntry(DBRefSource.UNIPROT, "0", "P0CE20"),
+ dbrefs[0]);
+ assertNull(dbrefs[0].getMap());
+ assertEquals(DBRefSource.EMBL, dbrefs[1].getSource());
+ assertEquals("X07547", dbrefs[1].getAccessionId());
+ assertEquals(cds1Map.getInverse(), dbrefs[1].getMap().getMap());
+
+ // dbrefs for second CDS EMBL product CAA30421.1
+ dbrefs = peptides.get(3).getDBRefs();
+ assertEquals(4, dbrefs.length);
+ assertEquals(DBRefSource.EMBL, dbrefs[0].getSource());
+ assertEquals("CAA30421.1", dbrefs[0].getAccessionId());
+ assertEquals(cds2Map.getInverse(), dbrefs[0].getMap().getMap());
+ assertEquals(DBRefSource.EMBLCDS, dbrefs[1].getSource());
+ assertEquals("CAA30421.1", dbrefs[1].getAccessionId());
+ assertEquals(proteinToCdsMap1, dbrefs[1].getMap().getMap());
+ assertEquals(DBRefSource.EMBLCDSProduct, dbrefs[2].getSource());
+ assertEquals("CAA30421.1", dbrefs[2].getAccessionId());
+ assertNull(dbrefs[2].getMap());
+ assertEquals(new DBRefEntry(DBRefSource.UNIPROT, "0", "B0BCM3"),
+ dbrefs[3]);
+ assertNull(dbrefs[3].getMap());
+
+ // dbrefs for second CDS second Uniprot xref
+ dbrefs = peptides.get(4).getDBRefs();
+ assertEquals(2, dbrefs.length);
+ assertEquals(new DBRefEntry(DBRefSource.UNIPROT, "0", "B0BCM3"),
+ dbrefs[0]);
+ assertNull(dbrefs[0].getMap());
+ assertEquals(DBRefSource.EMBL, dbrefs[1].getSource());
+ assertEquals("X07547", dbrefs[1].getAccessionId());
+ assertEquals(cds2Map.getInverse(), dbrefs[1].getMap().getMap());
+
+ // dbrefs for third CDS inferred EMBL product CAA12345.6
+ dbrefs = peptides.get(5).getDBRefs();
+ assertEquals(3, dbrefs.length);
+ assertEquals(DBRefSource.EMBL, dbrefs[0].getSource());
+ assertEquals("CAA12345.6", dbrefs[0].getAccessionId());
+ assertEquals(cds3Map.getInverse(), dbrefs[0].getMap().getMap());
+ assertEquals(DBRefSource.EMBLCDS, dbrefs[1].getSource());
+ assertEquals("CAA12345.6", dbrefs[1].getAccessionId());
+ assertEquals(proteinToCdsMap2, dbrefs[1].getMap().getMap());
+ assertEquals(DBRefSource.EMBLCDSProduct, dbrefs[2].getSource());
+ assertEquals("CAA12345.6", dbrefs[2].getAccessionId());
+ assertNull(dbrefs[2].getMap());