JAL-3863 passing test to verify a uniprot accession with canonical flag set is transf...

[jalview.git] / test / jalview / datamodel / SequenceTest.java

diff --git a/test/jalview/datamodel/SequenceTest.java b/test/jalview/datamodel/SequenceTest.java
index 4ac8c5b..5ae7dd9 100644 (file)
--- a/test/jalview/datamodel/SequenceTest.java
+++ b/test/jalview/datamodel/SequenceTest.java
@@ -34,6 +34,7 @@ import jalview.commands.EditCommand.Action;
 import jalview.datamodel.PDBEntry.Type;
 import jalview.gui.JvOptionPane;
 import jalview.util.MapList;
+import jalview.ws.params.InvalidArgumentException;
 
 import java.io.File;
 import java.util.ArrayList;
@@ -615,9 +616,9 @@ public class SequenceTest
     assertNotNull(newDs);
     assertNotSame(ds, newDs);
     assertNotNull(sq.getDBRefs());
-    assertEquals(1, sq.getDBRefs().length);
-    assertNotSame(dbr1, sq.getDBRefs()[0]);
-    assertEquals(dbr1, sq.getDBRefs()[0]);
+    assertEquals(1, sq.getDBRefs().size());
+    assertNotSame(dbr1, sq.getDBRefs().get(0));
+    assertEquals(dbr1, sq.getDBRefs().get(0));
 
     /*
      * internal delete with sequence features
@@ -678,8 +679,8 @@ public class SequenceTest
     assertEquals(4, sq.getEnd());
     assertSame(ds, PA.getValue(sq, "datasetSequence"));
     assertNotNull(sq.getDBRefs());
-    assertEquals(1, sq.getDBRefs().length);
-    assertSame(dbr1, sq.getDBRefs()[0]);
+    assertEquals(1, sq.getDBRefs().size());
+    assertSame(dbr1, sq.getDBRefs().get(0));
   }
 
   @Test(groups = { "Functional" })
@@ -913,12 +914,12 @@ public class SequenceTest
             new AlignmentAnnotation("Test annot", "Test annot description",
                     annots));
     Assert.assertEquals(sq.getDescription(), "Test sequence description..");
-    Assert.assertEquals(sq.getDBRefs().length, 5); // DBRefs are on dataset
+    Assert.assertEquals(sq.getDBRefs().size(), 5); // DBRefs are on dataset
                                                    // sequence
     Assert.assertEquals(sq.getAllPDBEntries().size(), 4);
     Assert.assertNotNull(sq.getAnnotation());
     Assert.assertEquals(sq.getAnnotation()[0].annotations.length, 2);
-    Assert.assertEquals(sq.getDatasetSequence().getDBRefs().length, 5); // same
+    Assert.assertEquals(sq.getDatasetSequence().getDBRefs().size(), 5); // same
                                                                         // as
                                                                         // sq.getDBRefs()
     Assert.assertEquals(sq.getDatasetSequence().getAllPDBEntries().size(),
@@ -929,11 +930,11 @@ public class SequenceTest
 
     Assert.assertEquals(derived.getDescription(),
             "Test sequence description..");
-    Assert.assertEquals(derived.getDBRefs().length, 5); // come from dataset
+    Assert.assertEquals(derived.getDBRefs().size(), 5); // come from dataset
     Assert.assertEquals(derived.getAllPDBEntries().size(), 4);
     Assert.assertNotNull(derived.getAnnotation());
     Assert.assertEquals(derived.getAnnotation()[0].annotations.length, 2);
-    Assert.assertEquals(derived.getDatasetSequence().getDBRefs().length, 5);
+    Assert.assertEquals(derived.getDatasetSequence().getDBRefs().size(), 5);
     Assert.assertEquals(derived.getDatasetSequence().getAllPDBEntries()
             .size(), 4);
     Assert.assertNotNull(derived.getDatasetSequence().getAnnotation());
@@ -1012,10 +1013,10 @@ public class SequenceTest
     // but that doesn't distinguish it from an aligned sequence
     // which has not yet generated a dataset sequence
     // NB getDBRef looks inside dataset sequence if not null
-    DBRefEntry[] dbrefs = copy.getDBRefs();
-    assertEquals(1, dbrefs.length);
-    assertFalse(dbrefs[0] == seq1.getDBRefs()[0]);
-    assertTrue(dbrefs[0].equals(seq1.getDBRefs()[0]));
+    List<DBRefEntry> dbrefs = copy.getDBRefs();
+    assertEquals(1, dbrefs.size());
+    assertFalse(dbrefs.get(0) == seq1.getDBRefs().get(0));
+    assertTrue(dbrefs.get(0).equals(seq1.getDBRefs().get(0)));
   }
 
   @Test(groups = { "Functional" })
@@ -1044,9 +1045,9 @@ public class SequenceTest
 
     // getDBRef looks inside dataset sequence and this is shared,
     // so holds the same dbref objects
-    DBRefEntry[] dbrefs = copy.getDBRefs();
-    assertEquals(1, dbrefs.length);
-    assertSame(dbrefs[0], seq1.getDBRefs()[0]);
+    List<DBRefEntry> dbrefs = copy.getDBRefs();
+    assertEquals(1, dbrefs.size());
+    assertSame(dbrefs.get(0), seq1.getDBRefs().get(0));
   }
 
   /**
@@ -1145,39 +1146,39 @@ public class SequenceTest
     assertNull(sq.getDBRefs());
     DBRefEntry dbref = new DBRefEntry("Uniprot", "1", "P00340");
     sq.addDBRef(dbref);
-    assertEquals(1, sq.getDBRefs().length);
-    assertSame(dbref, sq.getDBRefs()[0]);
+    assertEquals(1, sq.getDBRefs().size());
+    assertSame(dbref, sq.getDBRefs().get(0));
 
     /*
      * change of version - new entry
      */
     DBRefEntry dbref2 = new DBRefEntry("Uniprot", "2", "P00340");
     sq.addDBRef(dbref2);
-    assertEquals(2, sq.getDBRefs().length);
-    assertSame(dbref, sq.getDBRefs()[0]);
-    assertSame(dbref2, sq.getDBRefs()[1]);
+    assertEquals(2, sq.getDBRefs().size());
+    assertSame(dbref, sq.getDBRefs().get(0));
+    assertSame(dbref2, sq.getDBRefs().get(1));
 
     /*
      * matches existing entry - not added
      */
     sq.addDBRef(new DBRefEntry("UNIPROT", "1", "p00340"));
-    assertEquals(2, sq.getDBRefs().length);
+    assertEquals(2, sq.getDBRefs().size());
 
     /*
      * different source = new entry
      */
     DBRefEntry dbref3 = new DBRefEntry("UniRef", "1", "p00340");
     sq.addDBRef(dbref3);
-    assertEquals(3, sq.getDBRefs().length);
-    assertSame(dbref3, sq.getDBRefs()[2]);
+    assertEquals(3, sq.getDBRefs().size());
+    assertSame(dbref3, sq.getDBRefs().get(2));
 
     /*
      * different ref = new entry
      */
     DBRefEntry dbref4 = new DBRefEntry("UniRef", "1", "p00341");
     sq.addDBRef(dbref4);
-    assertEquals(4, sq.getDBRefs().length);
-    assertSame(dbref4, sq.getDBRefs()[3]);
+    assertEquals(4, sq.getDBRefs().size());
+    assertSame(dbref4, sq.getDBRefs().get(3));
 
     /*
      * matching ref with a mapping - map updated
@@ -1187,8 +1188,8 @@ public class SequenceTest
         1, 1 }, 3, 1));
     dbref5.setMap(map);
     sq.addDBRef(dbref5);
-    assertEquals(4, sq.getDBRefs().length);
-    assertSame(dbref4, sq.getDBRefs()[3]);
+    assertEquals(4, sq.getDBRefs().size());
+    assertSame(dbref4, sq.getDBRefs().get(3));
     assertSame(map, dbref4.getMap());
 
     /*
@@ -1198,8 +1199,8 @@ public class SequenceTest
     DBRefEntry dbref6 = new DBRefEntry(dbref2.getSource(), "3",
             dbref2.getAccessionId());
     sq.addDBRef(dbref6);
-    assertEquals(4, sq.getDBRefs().length);
-    assertSame(dbref2, sq.getDBRefs()[1]);
+    assertEquals(4, sq.getDBRefs().size());
+    assertSame(dbref2, sq.getDBRefs().get(1));
     assertEquals("3", dbref2.getVersion());
 
     /*
@@ -1209,8 +1210,8 @@ public class SequenceTest
     DBRefEntry dbref7 = new DBRefEntry(dbref3.getSource(), "3",
             dbref3.getAccessionId());
     sq.addDBRef(dbref7);
-    assertEquals(4, sq.getDBRefs().length);
-    assertSame(dbref3, sq.getDBRefs()[2]);
+    assertEquals(4, sq.getDBRefs().size());
+    assertSame(dbref3, sq.getDBRefs().get(2));
     assertEquals("3", dbref2.getVersion());
   }
 
@@ -1224,7 +1225,7 @@ public class SequenceTest
     assertTrue(primaryDBRefs.isEmpty());
 
     // empty dbrefs
-    sq.setDBRefs(new DBRefEntry[] {});
+       sq.setDBRefs(null);
     primaryDBRefs = sq.getPrimaryDBRefs();
     assertTrue(primaryDBRefs.isEmpty());
 
@@ -2174,4 +2175,15 @@ public class SequenceTest
     assertEquals(0, seq.firstResidueOutsideIterator(cs.iterator()));
 
   }
+  @Test(groups= {"Functional"})
+  public void testTransferAnnotation() {
+    Sequence origSeq = new Sequence("MYSEQ","THISISASEQ");
+    Sequence toSeq = new Sequence("MYSEQ","THISISASEQ");
+    origSeq.addDBRef(new DBRefEntry("UNIPROT", "0", "Q12345", null, true));
+    toSeq.transferAnnotation(origSeq, null);
+    assertTrue(toSeq.getDBRefs().size()>0);
+    
+    assertTrue(toSeq.getDBRefs().get(0).isCanonical());
+    
+  }
 }