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Merge branch 'develop' into feature/JAL-3551Pymol
[jalview.git] / test / jalview / ws / dbsources / EmblSourceTest.java
diff --git a/test/jalview/ws/dbsources/EmblSourceTest.java b/test/jalview/ws/dbsources/EmblSourceTest.java
index d450495..5bf215c 100644 (file)
--- a/test/jalview/ws/dbsources/EmblSourceTest.java
+++ b/test/jalview/ws/dbsources/EmblSourceTest.java
@@ -168,10 +168,10 @@ public class EmblSourceTest
     MapList cds3Map = new MapList(new int[] { 4, 6, 10, 15 }, new int[] {
         1, 3 }, 3, 1);
 
-    DBRefEntry[] dbrefs = dna.getDBRefs();
-    assertEquals(7, dbrefs.length);
+    List<DBRefEntry> dbrefs = dna.getDBRefs();
+    assertEquals(7, dbrefs.size());
 
-    DBRefEntry dbRefEntry = dbrefs[0];
+    DBRefEntry dbRefEntry = dbrefs.get(0);
     assertEquals("EMBL", dbRefEntry.getSource());
     assertEquals("X07547", dbRefEntry.getAccessionId());
     assertEquals("1", dbRefEntry.getVersion());
@@ -179,38 +179,38 @@ public class EmblSourceTest
     assertNull(dbRefEntry.getMap().getTo());
     assertEquals(mapToSelf, dbRefEntry.getMap().getMap());
 
-    dbRefEntry = dbrefs[1];
+    dbRefEntry = dbrefs.get(1);
     // DBRefEntry constructor puts dbSource in upper case
     assertEquals("EUROPEPMC", dbRefEntry.getSource());
     assertEquals("PMC107176", dbRefEntry.getAccessionId());
     assertEquals("9573186", dbRefEntry.getVersion());
     assertNull(dbRefEntry.getMap());
 
-    dbRefEntry = dbrefs[2];
+    dbRefEntry = dbrefs.get(2);
     assertEquals("MD5", dbRefEntry.getSource());
     assertEquals("ac73317", dbRefEntry.getAccessionId());
     assertEquals("0", dbRefEntry.getVersion());
     assertNull(dbRefEntry.getMap());
 
-    dbRefEntry = dbrefs[3];
+    dbRefEntry = dbrefs.get(3);
     assertEquals("UNIPROT", dbRefEntry.getSource());
     assertEquals("B0BCM4", dbRefEntry.getAccessionId());
     assertSame(peptides.get(1), dbRefEntry.getMap().getTo());
     assertEquals(cds1Map, dbRefEntry.getMap().getMap());
 
-    dbRefEntry = dbrefs[4];
+    dbRefEntry = dbrefs.get(4);
     assertEquals("UNIPROT", dbRefEntry.getSource());
     assertEquals("P0CE20", dbRefEntry.getAccessionId());
     assertSame(peptides.get(2), dbRefEntry.getMap().getTo());
     assertEquals(cds1Map, dbRefEntry.getMap().getMap());
 
-    dbRefEntry = dbrefs[5];
+    dbRefEntry = dbrefs.get(5);
     assertEquals("UNIPROT", dbRefEntry.getSource());
     assertEquals("B0BCM3", dbRefEntry.getAccessionId());
     assertSame(peptides.get(4), dbRefEntry.getMap().getTo());
     assertEquals(cds2Map, dbRefEntry.getMap().getMap());
 
-    dbRefEntry = dbrefs[6];
+    dbRefEntry = dbrefs.get(6);
     assertEquals("EMBLCDSPROTEIN", dbRefEntry.getSource());
     assertEquals("CAA12345.6", dbRefEntry.getAccessionId());
     assertSame(peptides.get(5), dbRefEntry.getMap().getTo());
@@ -229,82 +229,82 @@ public class EmblSourceTest
 
     // 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());
+    assertEquals(5, dbrefs.size());
+    assertEquals(DBRefSource.EMBL, dbrefs.get(0).getSource());
+    assertEquals("CAA30420.1", dbrefs.get(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(cds1Map.getInverse(), dbrefs.get(0).getMap().getMap());
+    assertEquals(DBRefSource.EMBLCDS, dbrefs.get(1).getSource());
+    assertEquals("CAA30420.1", dbrefs.get(1).getAccessionId());
+    assertEquals(proteinToCdsMap1, dbrefs.get(1).getMap().getMap());
+    assertEquals(DBRefSource.EMBLCDSProduct, dbrefs.get(2).getSource());
+    assertEquals("CAA30420.1", dbrefs.get(2).getAccessionId());
+    assertNull(dbrefs.get(2).getMap());
     assertEquals(new DBRefEntry(DBRefSource.UNIPROT, "2.1", "B0BCM4"),
-            dbrefs[3]);
-    assertNull(dbrefs[3].getMap());
+            dbrefs.get(3));
+    assertNull(dbrefs.get(3).getMap());
     assertEquals(new DBRefEntry(DBRefSource.UNIPROT, "0", "P0CE20"),
-            dbrefs[4]);
-    assertNull(dbrefs[4].getMap());
+            dbrefs.get(4));
+    assertNull(dbrefs.get(4).getMap());
 
     // dbrefs for first CDS first Uniprot xref
     dbrefs = peptides.get(1).getDBRefs();
-    assertEquals(2, dbrefs.length);
+    assertEquals(2, dbrefs.size());
     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.get(0));
+    assertNull(dbrefs.get(0).getMap());
+    assertEquals(DBRefSource.EMBL, dbrefs.get(1).getSource());
+    assertEquals("X07547", dbrefs.get(1).getAccessionId());
+    assertEquals(cds1Map.getInverse(), dbrefs.get(1).getMap().getMap());
 
     // dbrefs for first CDS second Uniprot xref
     dbrefs = peptides.get(2).getDBRefs();
-    assertEquals(2, dbrefs.length);
+    assertEquals(2, dbrefs.size());
     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.get(0));
+    assertNull(dbrefs.get(0).getMap());
+    assertEquals(DBRefSource.EMBL, dbrefs.get(1).getSource());
+    assertEquals("X07547", dbrefs.get(1).getAccessionId());
+    assertEquals(cds1Map.getInverse(), dbrefs.get(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(4, dbrefs.size());
+    assertEquals(DBRefSource.EMBL, dbrefs.get(0).getSource());
+    assertEquals("CAA30421.1", dbrefs.get(0).getAccessionId());
+    assertEquals(cds2Map.getInverse(), dbrefs.get(0).getMap().getMap());
+    assertEquals(DBRefSource.EMBLCDS, dbrefs.get(1).getSource());
+    assertEquals("CAA30421.1", dbrefs.get(1).getAccessionId());
+    assertEquals(proteinToCdsMap1, dbrefs.get(1).getMap().getMap());
+    assertEquals(DBRefSource.EMBLCDSProduct, dbrefs.get(2).getSource());
+    assertEquals("CAA30421.1", dbrefs.get(2).getAccessionId());
+    assertNull(dbrefs.get(2).getMap());
     assertEquals(new DBRefEntry(DBRefSource.UNIPROT, "0", "B0BCM3"),
-            dbrefs[3]);
-    assertNull(dbrefs[3].getMap());
+            dbrefs.get(3));
+    assertNull(dbrefs.get(3).getMap());
 
     // dbrefs for second CDS second Uniprot xref
     dbrefs = peptides.get(4).getDBRefs();
-    assertEquals(2, dbrefs.length);
+    assertEquals(2, dbrefs.size());
     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.get(0));
+    assertNull(dbrefs.get(0).getMap());
+    assertEquals(DBRefSource.EMBL, dbrefs.get(1).getSource());
+    assertEquals("X07547", dbrefs.get(1).getAccessionId());
+    assertEquals(cds2Map.getInverse(), dbrefs.get(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());
+    assertEquals(3, dbrefs.size());
+    assertEquals(DBRefSource.EMBL, dbrefs.get(0).getSource());
+    assertEquals("CAA12345.6", dbrefs.get(0).getAccessionId());
+    assertEquals(cds3Map.getInverse(), dbrefs.get(0).getMap().getMap());
+    assertEquals(DBRefSource.EMBLCDS, dbrefs.get(1).getSource());
+    assertEquals("CAA12345.6", dbrefs.get(1).getAccessionId());
+    assertEquals(proteinToCdsMap2, dbrefs.get(1).getMap().getMap());
+    assertEquals(DBRefSource.EMBLCDSProduct, dbrefs.get(2).getSource());
+    assertEquals("CAA12345.6", dbrefs.get(2).getAccessionId());
+    assertNull(dbrefs.get(2).getMap());
   }
 
   @Test(groups = "Functional")