JAL-2106 removed setSourceDBRef, refactor getSourceDBRef to getPrimaryDBRefs

[jalview.git] / test / jalview / analysis / AlignmentUtilsTests.java

diff --git a/test/jalview/analysis/AlignmentUtilsTests.java b/test/jalview/analysis/AlignmentUtilsTests.java
index 727cf22..1df7fd9 100644 (file)
--- a/test/jalview/analysis/AlignmentUtilsTests.java
+++ b/test/jalview/analysis/AlignmentUtilsTests.java
@@ -997,9 +997,11 @@ public class AlignmentUtilsTests
      * sequence
      */
     DBRefEntry dbref = new DBRefEntry("ENSEMBL", "0", "dna1");
-    dna1.getDatasetSequence().setSourceDBRef(dbref);
+    dna1.getDatasetSequence().addDBRef(dbref);
+    org.testng.Assert.assertEquals(dbref, dna1.getPrimaryDBRefs().get(0));
     dbref = new DBRefEntry("ENSEMBL", "0", "dna2");
-    dna2.getDatasetSequence().setSourceDBRef(dbref);
+    dna2.getDatasetSequence().addDBRef(dbref);
+    org.testng.Assert.assertEquals(dbref, dna2.getPrimaryDBRefs().get(0));
 
     /*
      * CDS sequences are 'discovered' from dna-to-protein mappings on the alignment
@@ -2394,4 +2396,83 @@ public class AlignmentUtilsTests
     assertEquals(7, m.getStart());
     assertEquals(9, m.getEnd());
   }
+
+  /**
+   * Test the method that just copies aligned sequences, provided all sequences
+   * to be aligned share the aligned sequence's dataset
+   */
+  @Test(groups = "Functional")
+  public void testAlignAsSameSequences()
+  {
+    SequenceI dna1 = new Sequence("dna1", "cccGGGTTTaaa");
+    SequenceI dna2 = new Sequence("dna2", "CCCgggtttAAA");
+    AlignmentI al1 = new Alignment(new SequenceI[] { dna1, dna2 });
+    ((Alignment) al1).createDatasetAlignment();
+
+    SequenceI dna3 = new Sequence(dna1);
+    SequenceI dna4 = new Sequence(dna2);
+    assertSame(dna3.getDatasetSequence(), dna1.getDatasetSequence());
+    assertSame(dna4.getDatasetSequence(), dna2.getDatasetSequence());
+    String seq1 = "-cc-GG-GT-TT--aaa";
+    dna3.setSequence(seq1);
+    String seq2 = "C--C-Cgg--gtt-tAA-A-";
+    dna4.setSequence(seq2);
+    AlignmentI al2 = new Alignment(new SequenceI[] { dna3, dna4 });
+    ((Alignment) al2).createDatasetAlignment();
+    
+    assertTrue(AlignmentUtils.alignAsSameSequences(al1, al2));
+    assertEquals(seq1, al1.getSequenceAt(0).getSequenceAsString());
+    assertEquals(seq2, al1.getSequenceAt(1).getSequenceAsString());
+
+    /*
+     * add another sequence to 'aligned' - should still succeed, since
+     * unaligned sequences still share a dataset with aligned sequences
+     */
+    SequenceI dna5 = new Sequence("dna5", "CCCgggtttAAA");
+    dna5.createDatasetSequence();
+    al2.addSequence(dna5);
+    assertTrue(AlignmentUtils.alignAsSameSequences(al1, al2));
+    assertEquals(seq1, al1.getSequenceAt(0).getSequenceAsString());
+    assertEquals(seq2, al1.getSequenceAt(1).getSequenceAsString());
+
+    /*
+     * add another sequence to 'unaligned' - should fail, since now not
+     * all unaligned sequences share a dataset with aligned sequences
+     */
+    SequenceI dna6 = new Sequence("dna6", "CCCgggtttAAA");
+    dna6.createDatasetSequence();
+    al1.addSequence(dna6);
+    // JAL-2110 JBP Comment: what's the use case for this behaviour ?
+    assertFalse(AlignmentUtils.alignAsSameSequences(al1, al2));
+  }
+
+  @Test(groups = "Functional")
+  public void testAlignAsSameSequencesMultipleSubSeq()
+  {
+    SequenceI dna1 = new Sequence("dna1", "cccGGGTTTaaa");
+    SequenceI dna2 = new Sequence("dna2", "CCCgggtttAAA");
+    SequenceI as1 = dna1.deriveSequence(), as2 = dna1.deriveSequence()
+            .getSubSequence(3, 7), as3 = dna2.deriveSequence();
+    as1.insertCharAt(6, 5, '-');
+    String s_as1 = as1.getSequenceAsString();
+    as2.insertCharAt(6, 5, '-');
+    String s_as2 = as2.getSequenceAsString();
+    as3.insertCharAt(6, 5, '-');
+    String s_as3 = as3.getSequenceAsString();
+    AlignmentI aligned = new Alignment(new SequenceI[] { as1, as2, as3 });
+
+    // why do we need to cast this still ?
+    ((Alignment) aligned).createDatasetAlignment();
+    SequenceI uas1 = dna1.deriveSequence(), uas2 = dna1.deriveSequence()
+            .getSubSequence(3, 7), uas3 = dna2.deriveSequence();
+    AlignmentI tobealigned = new Alignment(new SequenceI[] { uas1, uas2,
+        uas3 });
+    ((Alignment) tobealigned).createDatasetAlignment();
+
+    assertTrue(AlignmentUtils.alignAsSameSequences(tobealigned, aligned));
+    assertEquals(s_as1, uas1.getSequenceAsString());
+    assertEquals(s_as2, uas2.getSequenceAsString());
+    assertEquals(s_as3, uas3.getSequenceAsString());
+  }
+    
 }