X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fdatamodel%2FAlignedCodonFrameTest.java;h=f2dd968d95dba8e29b0fbbba0c10ba94d15921c9;hb=ce36ce68c3ec8d050f70163833e28f58e26bde89;hp=989ed7c3d8ff660f99d538ccdc9e4ec0ff1681e3;hpb=da768251d307c7ce11283d72e0e522b2c5fac526;p=jalview.git

diff --git a/test/jalview/datamodel/AlignedCodonFrameTest.java b/test/jalview/datamodel/AlignedCodonFrameTest.java
index 989ed7c..f2dd968 100644
--- a/test/jalview/datamodel/AlignedCodonFrameTest.java
+++ b/test/jalview/datamodel/AlignedCodonFrameTest.java
@@ -74,6 +74,9 @@ public class AlignedCodonFrameTest
      */
     assertEquals(aa.getSequenceAt(1), acf.findAlignedSequence(cdna
             .getSequenceAt(0).getDatasetSequence(), aa));
+    // can also find this from the dna aligned sequence
+    assertEquals(aa.getSequenceAt(1),
+            acf.findAlignedSequence(cdna.getSequenceAt(0), aa));
 
     assertEquals(cdna.getSequenceAt(0), acf.findAlignedSequence(aa
             .getSequenceAt(1).getDatasetSequence(), cdna));
@@ -448,4 +451,30 @@ public class AlignedCodonFrameTest
     assertArrayEquals(new int[] { 2, 2 },
             acf.getMappedRegion(seq2, seq1, 6));
   }
+
+  /**
+   * Tests for addMap. See also tests for MapList.addMapList
+   */
+  @Test(groups = { "Functional" })
+  public void testAddMap()
+  {
+    final Sequence seq1 = new Sequence("Seq1", "c-G-TA-gC-gT-T");
+    seq1.createDatasetSequence();
+    final Sequence aseq1 = new Sequence("Seq1", "-V-L");
+    aseq1.createDatasetSequence();
+  
+    AlignedCodonFrame acf = new AlignedCodonFrame();
+    MapList map = new MapList(new int[] { 2, 4, 6, 6, 8, 9 }, new int[] {
+        1, 2 }, 3, 1);
+    acf.addMap(seq1.getDatasetSequence(), aseq1.getDatasetSequence(), map);
+    assertEquals(1, acf.getMappingsFromSequence(seq1).size());
+    Mapping before = acf.getMappingsFromSequence(seq1).get(0);
+
+    /*
+     * add the same map again, verify it doesn't get duplicated
+     */
+    acf.addMap(seq1.getDatasetSequence(), aseq1.getDatasetSequence(), map);
+    assertEquals(1, acf.getMappingsFromSequence(seq1).size());
+    assertSame(before, acf.getMappingsFromSequence(seq1).get(0));
+  }
 }