JAL-653 (experimental) methods to resolve dummy to real sequence

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

diff --git a/test/jalview/datamodel/AlignedCodonFrameTest.java b/test/jalview/datamodel/AlignedCodonFrameTest.java
index a0757cc..69e584a 100644 (file)
--- a/test/jalview/datamodel/AlignedCodonFrameTest.java
+++ b/test/jalview/datamodel/AlignedCodonFrameTest.java
@@ -21,7 +21,9 @@
 package jalview.datamodel;
 
 import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertFalse;
 import static org.testng.AssertJUnit.assertNull;
+import static org.testng.AssertJUnit.assertTrue;
 
 import jalview.util.MapList;
 
@@ -176,4 +178,87 @@ public class AlignedCodonFrameTest
     assertEquals("[C, T, T]", Arrays.toString(acf.getMappedCodon(
             aseq1.getDatasetSequence(), 13)));
   }
+
+  @Test(groups = { "Functional" })
+  public void testCouldReplaceSequence()
+  {
+    SequenceI seq1 = new Sequence("Seq1/10-21", "aaacccgggttt");
+    SequenceI seq2 = new Sequence("Seq2", "PG");
+    SequenceI seq1proxy = new SequenceDummy("Seq1");
+
+    // map to region within sequence is ok
+    assertTrue(AlignedCodonFrame.couldReplaceSequence(seq1proxy, seq1, 12,
+            17));
+    // map to region overlapping sequence is ok
+    assertTrue(AlignedCodonFrame.couldReplaceSequence(seq1proxy, seq1, 5,
+            10));
+    assertTrue(AlignedCodonFrame.couldReplaceSequence(seq1proxy, seq1, 21,
+            26));
+    // map to region before sequence is not ok
+    assertFalse(AlignedCodonFrame.couldReplaceSequence(seq1proxy, seq1, 4,
+            9));
+    // map to region after sequence is not ok
+    assertFalse(AlignedCodonFrame.couldReplaceSequence(seq1proxy, seq1, 22,
+            27));
+
+    /*
+     * test should fail if name doesn't match
+     */
+    seq1proxy.setName("Seq1a");
+    assertFalse(AlignedCodonFrame.couldReplaceSequence(seq1proxy, seq1, 12,
+            17));
+    seq1proxy.setName("Seq1");
+    seq1.setName("Seq1a");
+    assertFalse(AlignedCodonFrame.couldReplaceSequence(seq1proxy, seq1, 12,
+            17));
+  }
+
+  @Test(groups = { "Functional" })
+  public void testIsRealisableWith()
+  {
+    SequenceI seq1 = new Sequence("Seq1", "tttaaaCCCGGGtttaaa");
+    SequenceI seq2 = new Sequence("Seq2", "PG");
+    SequenceI seq1proxy = new SequenceDummy("Seq1");
+    seq1.createDatasetSequence();
+    seq2.createDatasetSequence();
+    MapList mapList = new MapList(new int[] { 7, 12 }, new int[] { 2, 3 },
+            3, 1);
+    AlignedCodonFrame acf = new AlignedCodonFrame();
+    acf.addMap(seq1proxy, seq2, mapList);
+
+    /*
+     * Seq2 is mapped to SequenceDummy seq1proxy bases 4-9
+     * This is 'realisable' from real sequence Seq1
+     */
+    assertTrue(acf.isRealisableWith(seq1));
+
+    /*
+     * test should fail if name doesn't match
+     */
+    seq1proxy.setName("Seq1a");
+    assertFalse(acf.isRealisableWith(seq1));
+    seq1proxy.setName("Seq1");
+    seq1.setName("Seq1a");
+    assertFalse(acf.isRealisableWith(seq1));
+    seq1.setName("Seq1");
+
+    /*
+     * test should fail if no sequence overlap with mapping of bases 7-12
+     * use artificial start/end values to test this
+     */
+    seq1.setStart(1);
+    seq1.setEnd(6);
+    // seq1 precedes mapped region:
+    assertFalse(acf.isRealisableWith(seq1));
+    seq1.setEnd(7);
+    // seq1 includes first mapped base:
+    assertTrue(acf.isRealisableWith(seq1));
+    seq1.setStart(13);
+    seq1.setEnd(18);
+    // seq1 follows mapped region:
+    assertFalse(acf.isRealisableWith(seq1));
+    seq1.setStart(12);
+    // seq1 includes last mapped base:
+    assertTrue(acf.isRealisableWith(seq1));
+  }
 }