JAL-1619 refactoring / tests to support 'align linked dna as protein'

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

diff --git a/test/jalview/datamodel/AlignmentTest.java b/test/jalview/datamodel/AlignmentTest.java
index 8912155..dbd063c 100644 (file)
--- a/test/jalview/datamodel/AlignmentTest.java
+++ b/test/jalview/datamodel/AlignmentTest.java
@@ -60,11 +60,13 @@ public class AlignmentTest
    * Helper method to load an alignment and ensure dataset sequences are set up.
    * 
    * @param data
-   * @param format TODO
+   * @param format
+   *          TODO
    * @return
    * @throws IOException
    */
-  protected AlignmentI loadAlignment(final String data, String format) throws IOException
+  protected AlignmentI loadAlignment(final String data, String format)
+          throws IOException
   {
     Alignment a = new FormatAdapter().readFile(data,
             AppletFormatAdapter.PASTE, format);
@@ -83,8 +85,7 @@ public class AlignmentTest
     int i = 0;
     for (AlignmentAnnotation ann : al.getAlignmentAnnotation())
     {
-      ann.setCalcId("CalcIdFor"
-              + al.getSequenceAt(i).getName());
+      ann.setCalcId("CalcIdFor" + al.getSequenceAt(i).getName());
       i++;
     }
   }
@@ -180,9 +181,92 @@ public class AlignmentTest
     al2.addCodonFrame(acf);
 
     al1.alignAs(al2);
-    assertEquals("ACG---GCUCCA------ACT", al1.getSequenceAt(0)
+    assertEquals("AC-G---G--CUC-CA------A-CT", al1.getSequenceAt(0)
             .getSequenceAsString());
-    assertEquals("---CGT---TAACGA---AGT---", al1.getSequenceAt(1)
+    assertEquals("---CG-T---TA--ACG---A---AGT", al1.getSequenceAt(1)
+            .getSequenceAsString());
+  }
+
+  /**
+   * Test aligning cdna (with introns) as per protein alignment.
+   * 
+   * @throws IOException
+   */
+  @Test
+  public void testAlignAs_cdnaAsProteinWithIntrons() throws IOException
+  {
+    /*
+     * Load alignments and add mappings for cDNA to protein
+     */
+    AlignmentI al1 = loadAlignment(CDNA_SEQS_1, "FASTA");
+    AlignmentI al2 = loadAlignment(AA_SEQS_1, "FASTA");
+    AlignedCodonFrame acf = new AlignedCodonFrame();
+    MapList ml = new MapList(new int[]
+    { 1, 12 }, new int[]
+    { 1, 4 }, 3, 1);
+    acf.addMap(al1.getSequenceAt(0), al2.getSequenceAt(0), ml);
+    acf.addMap(al1.getSequenceAt(1), al2.getSequenceAt(1), ml);
+    al2.addCodonFrame(acf);
+
+    al1.alignAs(al2);
+    assertEquals("AC-G---G--CUC-CA------A-CT", al1.getSequenceAt(0)
+            .getSequenceAsString());
+    assertEquals("---CG-T---TA--ACG---A---AGT", al1.getSequenceAt(1)
+            .getSequenceAsString());
+  }
+
+  /**
+   * Test aligning dna as per protein alignment, for the case where there are
+   * introns (i.e. some dna sites have no mapping from a peptide).
+   * 
+   * @throws IOException
+   */
+  @Test
+  public void testAlignAs_dnaAsProtein_withIntrons() throws IOException
+  {
+    /*
+     * Load alignments and add mappings for cDNA to protein
+     */
+    String dna1 = "A-Aa-gG-GCC-cT-TT";
+    String dna2 = "c--CCGgg-TT--T-AA-A";
+    AlignmentI al1 = loadAlignment(">Seq1\n" + dna1 + "\n>Seq2\n" + dna2
+            + "\n", "FASTA");
+    AlignmentI al2 = loadAlignment(">Seq1\n-P--YK\n>Seq2\nG-T--F\n",
+            "FASTA");
+    AlignedCodonFrame acf = new AlignedCodonFrame();
+    // Seq1 has intron at dna positions 3,4,9 so splice is AAG GCC TTT
+    // Seq2 has intron at dna positions 1,5,6 so splice is CCG TTT AAA
+    MapList ml1 = new MapList(new int[]
+    { 1, 2, 5, 8, 10, 12 }, new int[]
+    { 1, 3 }, 3, 1);
+    acf.addMap(al1.getSequenceAt(0), al2.getSequenceAt(0), ml1);
+    MapList ml2 = new MapList(new int[]
+    { 2, 4, 7, 12 }, new int[]
+    { 1, 3 }, 3, 1);
+    acf.addMap(al1.getSequenceAt(1), al2.getSequenceAt(1), ml2);
+    al2.addCodonFrame(acf);
+
+    /*
+     * Align ignoring gaps in dna introns and exons
+     */
+    ((Alignment) al1).alignAs(al2, false, false);
+    assertEquals("---AAagG------GCCcTTT", al1.getSequenceAt(0)
+            .getSequenceAsString());
+    assertEquals("cCCGgg---TTT------AAA", al1.getSequenceAt(1)
+            .getSequenceAsString());
+
+    /*
+     * Reset and realign, preserving gaps in dna introns and exons
+     */
+    al1.getSequenceAt(0).setSequence(dna1);
+    al1.getSequenceAt(1).setSequence(dna2);
+    ((Alignment) al1).alignAs(al2, true, true);
+    // String dna1 = "A-Aa-gG-GCC-cT-TT";
+    // String dna2 = "c--CCGgg-TT--T-AA-A";
+    // assumption: we include 'the greater of' protein/dna gap lengths, not both
+    assertEquals("---A-Aa-gG------GCC-cT-TT", al1.getSequenceAt(0)
+            .getSequenceAsString());
+    assertEquals("c--CCGgg---TT--T------AA-A", al1.getSequenceAt(1)
             .getSequenceAsString());
   }
 }