JAL-1636 translate stop codon as '*', mouseover * as STOP

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

diff --git a/test/jalview/analysis/AlignmentUtilsTests.java b/test/jalview/analysis/AlignmentUtilsTests.java
index d44a6bc..9c8e28c 100644 (file)
--- a/test/jalview/analysis/AlignmentUtilsTests.java
+++ b/test/jalview/analysis/AlignmentUtilsTests.java
@@ -96,7 +96,7 @@ public class AlignmentUtilsTests
   public static Sequence ts = new Sequence("short",
           "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklm");
 
-  @Test
+  @Test(groups ={ "Functional" })
   public void testExpandContext()
   {
     AlignmentI al = new Alignment(new Sequence[] {});
@@ -150,7 +150,7 @@ public class AlignmentUtilsTests
   /**
    * Test that annotations are correctly adjusted by expandContext
    */
-  @Test
+  @Test(groups ={ "Functional" })
   public void testExpandContext_annotation()
   {
     AlignmentI al = new Alignment(new Sequence[]
@@ -240,7 +240,7 @@ public class AlignmentUtilsTests
    * 
    * @throws IOException
    */
-  @Test
+  @Test(groups ={ "Functional" })
   public void testGetSequencesByName() throws IOException
   {
     final String data = ">Seq1Name\nKQYL\n" + ">Seq2Name\nRFPW\n"
@@ -278,7 +278,7 @@ public class AlignmentUtilsTests
    * 
    * @throws IOException
    */
-  @Test
+  @Test(groups ={ "Functional" })
   public void testMapProteinToCdna_noXrefs() throws IOException
   {
     List<SequenceI> protseqs = new ArrayList<SequenceI>();
@@ -341,7 +341,7 @@ public class AlignmentUtilsTests
   /**
    * Test for the alignSequenceAs method that takes two sequences and a mapping.
    */
-  @Test
+  @Test(groups ={ "Functional" })
   public void testAlignSequenceAs_withMapping_noIntrons()
   {
     MapList map = new MapList(new int[]
@@ -387,7 +387,7 @@ public class AlignmentUtilsTests
   /**
    * Test for the alignSequenceAs method that takes two sequences and a mapping.
    */
-  @Test
+  @Test(groups ={ "Functional" })
   public void testAlignSequenceAs_withMapping_withIntrons()
   {
     /*
@@ -437,7 +437,7 @@ public class AlignmentUtilsTests
   /**
    * Test for the case where not all of the protein sequence is mapped to cDNA.
    */
-  @Test
+  @Test(groups ={ "Functional" })
   public void testAlignSequenceAs_withMapping_withUnmappedProtein()
   {
     
@@ -487,7 +487,7 @@ public class AlignmentUtilsTests
   /**
    * Test for the alignSequenceAs method where we preserve gaps in introns only.
    */
-  @Test
+  @Test(groups ={ "Functional" })
   public void testAlignSequenceAs_keepIntronGapsOnly()
   {
 
@@ -506,7 +506,7 @@ public class AlignmentUtilsTests
    * Test for the method that generates an aligned translated sequence from one
    * mapping.
    */
-  @Test
+  @Test(groups ={ "Functional" })
   public void testGetAlignedTranslation_dnaLikeProtein()
   {
     // dna alignment will be replaced
@@ -530,7 +530,7 @@ public class AlignmentUtilsTests
   /**
    * Test the method that realigns protein to match mapped codon alignment.
    */
-  @Test
+  @Test(groups ={ "Functional" })
   public void testAlignProteinAsDna()
   {
     // seq1 codons are [1,2,3] [4,5,6] [7,8,9] [10,11,12]
@@ -574,32 +574,43 @@ public class AlignmentUtilsTests
    * Test the method that tests whether a CDNA sequence translates to a protein
    * sequence
    */
-  @Test
+  @Test(groups ={ "Functional" })
   public void testTranslatesAs()
   {
     assertTrue(AlignmentUtils.translatesAs("tttcccaaaggg".toCharArray(), 0,
             "FPKG".toCharArray()));
-    // with start codon
+    // with start codon (not in protein)
     assertTrue(AlignmentUtils.translatesAs("atgtttcccaaaggg".toCharArray(),
             3, "FPKG".toCharArray()));
-    // with stop codon1
+    // with stop codon1 (not in protein)
     assertTrue(AlignmentUtils.translatesAs("tttcccaaagggtaa".toCharArray(),
             0, "FPKG".toCharArray()));
-    // with stop codon2
+    // with stop codon1 (in protein as *)
+    assertTrue(AlignmentUtils.translatesAs("tttcccaaagggtaa".toCharArray(),
+            0, "FPKG*".toCharArray()));
+    // with stop codon2 (not in protein)
     assertTrue(AlignmentUtils.translatesAs("tttcccaaagggtag".toCharArray(),
             0, "FPKG".toCharArray()));
-    // with stop codon3
+    // with stop codon3 (not in protein)
     assertTrue(AlignmentUtils.translatesAs("tttcccaaagggtga".toCharArray(),
             0, "FPKG".toCharArray()));
     // with start and stop codon1
     assertTrue(AlignmentUtils.translatesAs(
-            "atgtttcccaaaggtaa".toCharArray(), 3, "FPKG".toCharArray()));
+            "atgtttcccaaagggtaa".toCharArray(), 3, "FPKG".toCharArray()));
+    // with start and stop codon1 (in protein as *)
+    assertTrue(AlignmentUtils.translatesAs(
+            "atgtttcccaaagggtaa".toCharArray(), 3, "FPKG*".toCharArray()));
     // with start and stop codon2
     assertTrue(AlignmentUtils.translatesAs(
-            "atgtttcccaaaggtag".toCharArray(), 3, "FPKG".toCharArray()));
+            "atgtttcccaaagggtag".toCharArray(), 3, "FPKG".toCharArray()));
     // with start and stop codon3
     assertTrue(AlignmentUtils.translatesAs(
-            "atgtttcccaaaggtga".toCharArray(), 3, "FPKG".toCharArray()));
+            "atgtttcccaaagggtga".toCharArray(), 3, "FPKG".toCharArray()));
+
+    // with embedded stop codon
+    assertTrue(AlignmentUtils.translatesAs(
+            "atgtttTAGcccaaaTAAgggtga".toCharArray(), 3,
+            "F*PK*G".toCharArray()));
 
     // wrong protein
     assertFalse(AlignmentUtils.translatesAs("tttcccaaaggg".toCharArray(),
@@ -613,7 +624,7 @@ public class AlignmentUtilsTests
    * 
    * @throws IOException
    */
-  @Test
+  @Test(groups ={ "Functional" })
   public void testMapProteinToCdna_withStartAndStopCodons()
           throws IOException
   {
@@ -706,7 +717,7 @@ public class AlignmentUtilsTests
    * 
    * @throws IOException
    */
-  @Test
+  @Test(groups ={ "Functional" })
   public void testMapProteinToCdna_withXrefs() throws IOException
   {
     List<SequenceI> protseqs = new ArrayList<SequenceI>();
@@ -782,7 +793,7 @@ public class AlignmentUtilsTests
    * 
    * @throws IOException
    */
-  @Test
+  @Test(groups ={ "Functional" })
   public void testMapProteinToCdna_prioritiseXrefs() throws IOException
   {
     List<SequenceI> protseqs = new ArrayList<SequenceI>();
@@ -832,7 +843,7 @@ public class AlignmentUtilsTests
    * Test the method that shows or hides sequence annotations by type(s) and
    * selection group.
    */
-  @Test
+  @Test(groups ={ "Functional" })
   public void testShowOrHideSequenceAnnotations()
   {
     SequenceI seq1 = new Sequence("Seq1", "AAA");
@@ -940,7 +951,7 @@ public class AlignmentUtilsTests
   /**
    * Tests for the method that checks if one sequence cross-references another
    */
-  @Test
+  @Test(groups ={ "Functional" })
   public void testHasCrossRef()
   {
     assertFalse(AlignmentUtils.hasCrossRef(null, null));
@@ -969,7 +980,7 @@ public class AlignmentUtilsTests
    * Tests for the method that checks if either sequence cross-references the
    * other
    */
-  @Test
+  @Test(groups ={ "Functional" })
   public void testHaveCrossRef()
   {
     assertFalse(AlignmentUtils.hasCrossRef(null, null));
@@ -999,7 +1010,7 @@ public class AlignmentUtilsTests
   /**
    * Test the method that extracts the exon-only part of a dna alignment.
    */
-  @Test
+  @Test(groups ={ "Functional" })
   public void testMakeExonAlignment()
   {
     SequenceI dna1 = new Sequence("dna1", "aaaGGGcccTTTaaa");
@@ -1094,7 +1105,7 @@ public class AlignmentUtilsTests
    * already has a protein product (Uniprot translation) which in turn has an
    * x-ref to the EMBLCDS record.
    */
-  @Test
+  @Test(groups ={ "Functional" })
   public void testMakeExonSequences()
   {
     SequenceI dna1 = new Sequence("dna1", "aaaGGGcccTTTaaa");
@@ -1136,7 +1147,7 @@ public class AlignmentUtilsTests
    * its product mappings, for the case where there are multiple exon mappings
    * to different protein products.
    */
-  @Test
+  @Test(groups ={ "Functional" })
   public void testMakeExonAlignment_multipleProteins()
   {
     SequenceI dna1 = new Sequence("dna1", "aaaGGGcccTTTaaa");
@@ -1267,4 +1278,22 @@ public class AlignmentUtilsTests
     assertEquals(1, peptideMappings.size());
     assertSame(pep3.getDatasetSequence(), peptideMappings.get(0).getTo());
   }
+
+  @Test(groups = { "Functional" })
+  public void testIsMappable()
+  {
+    SequenceI dna1 = new Sequence("dna1", "cgCAGtgGT");
+    SequenceI aa1 = new Sequence("aa1", "RSG");
+    AlignmentI al1 = new Alignment(new SequenceI[] { dna1 });
+    AlignmentI al2 = new Alignment(new SequenceI[] { aa1 });
+
+    assertFalse(AlignmentUtils.isMappable(null, null));
+    assertFalse(AlignmentUtils.isMappable(al1, null));
+    assertFalse(AlignmentUtils.isMappable(null, al1));
+    assertFalse(AlignmentUtils.isMappable(al1, al1));
+    assertFalse(AlignmentUtils.isMappable(al2, al2));
+
+    assertTrue(AlignmentUtils.isMappable(al1, al2));
+    assertTrue(AlignmentUtils.isMappable(al2, al1));
+  }
 }