JAL-653 code tidy / tests for 'realise gff mappings'

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

diff --git a/test/jalview/datamodel/AlignedCodonFrameTest.java b/test/jalview/datamodel/AlignedCodonFrameTest.java
index 69e584a..4984e5e 100644 (file)
--- a/test/jalview/datamodel/AlignedCodonFrameTest.java
+++ b/test/jalview/datamodel/AlignedCodonFrameTest.java
@@ -23,6 +23,7 @@ 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.assertSame;
 import static org.testng.AssertJUnit.assertTrue;
 
 import jalview.util.MapList;
@@ -213,6 +214,10 @@ public class AlignedCodonFrameTest
             17));
   }
 
+  /**
+   * Tests for the method that tests whether any mapping to a dummy sequence can
+   * be 'realised' to a given real sequence
+   */
   @Test(groups = { "Functional" })
   public void testIsRealisableWith()
   {
@@ -238,27 +243,69 @@ public class AlignedCodonFrameTest
     seq1proxy.setName("Seq1a");
     assertFalse(acf.isRealisableWith(seq1));
     seq1proxy.setName("Seq1");
-    seq1.setName("Seq1a");
+
+    SequenceI seq1ds = seq1.getDatasetSequence();
+    seq1ds.setName("Seq1a");
     assertFalse(acf.isRealisableWith(seq1));
-    seq1.setName("Seq1");
+    seq1ds.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);
+    seq1ds.setStart(1);
+    seq1ds.setEnd(6);
     // seq1 precedes mapped region:
     assertFalse(acf.isRealisableWith(seq1));
-    seq1.setEnd(7);
+    seq1ds.setEnd(7);
     // seq1 includes first mapped base:
     assertTrue(acf.isRealisableWith(seq1));
-    seq1.setStart(13);
-    seq1.setEnd(18);
+    seq1ds.setStart(13);
+    seq1ds.setEnd(18);
     // seq1 follows mapped region:
     assertFalse(acf.isRealisableWith(seq1));
-    seq1.setStart(12);
+    seq1ds.setStart(12);
     // seq1 includes last mapped base:
     assertTrue(acf.isRealisableWith(seq1));
   }
+
+  /**
+   * Tests for the method that converts mappings to a dummy sequence to mappings
+   * to a compatible real sequence
+   */
+  @Test(groups = { "Functional" })
+  public void testRealiseWith()
+  {
+    SequenceI seq1 = new Sequence("Seq1", "tttCAACCCGGGtttaaa");
+    SequenceI seq2 = new Sequence("Seq2", "QPG");
+    SequenceI seq1proxy = new SequenceDummy("Seq1");
+    seq1.createDatasetSequence();
+    seq2.createDatasetSequence();
+
+    /*
+     * Make two mappings from Seq2 peptide to dummy sequence Seq1
+     */
+    AlignedCodonFrame acf = new AlignedCodonFrame();
+
+    // map PG to codons 7-12 (CCCGGG)
+    MapList mapping1 = new MapList(new int[] { 7, 12 }, new int[] { 2, 3 },
+            3, 1);
+    acf.addMap(seq1proxy, seq2, mapping1);
+
+    // map QP to codons 4-9 (CAACCC)
+    MapList mapping2 = new MapList(new int[] { 4, 9 }, new int[] { 1, 2 },
+            3, 1);
+    acf.addMap(seq1proxy, seq2, mapping2);
+
+    assertEquals(2, acf.getdnaSeqs().length);
+    assertSame(seq1proxy, acf.getdnaSeqs()[0]);
+    assertSame(seq1proxy, acf.getdnaSeqs()[1]);
+    assertEquals(2, acf.getProtMappings().length);
+
+    // 'realise' these mappings with the compatible sequence seq1
+    // two mappings should be updated:
+    assertEquals(2, acf.realiseWith(seq1));
+    assertSame(seq1.getDatasetSequence(), acf.getdnaSeqs()[0]);
+    assertSame(seq1.getDatasetSequence(), acf.getdnaSeqs()[1]);
+  }
 }