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

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

diff --git a/test/jalview/analysis/AlignmentUtilsTests.java b/test/jalview/analysis/AlignmentUtilsTests.java
index 3ada6fa..c436818 100644 (file)
--- a/test/jalview/analysis/AlignmentUtilsTests.java
+++ b/test/jalview/analysis/AlignmentUtilsTests.java
@@ -317,4 +317,162 @@ public class AlignmentUtilsTests
     assertTrue(Arrays.equals(new int[]
     { 1, 3 }, mapList.getToRanges()));
   }
+
+  /**
+   * Test for the alignSequenceAs method that takes two sequences and a mapping.
+   */
+  @Test
+  public void testAlignSequenceAs_withMapping_noIntrons()
+  {
+    /*
+     * Simple case: no gaps in dna
+     */
+    SequenceI dna = new Sequence("Seq1", "GGGAAA");
+    dna.createDatasetSequence();
+    SequenceI protein = new Sequence("Seq1", "-A-L-");
+    protein.createDatasetSequence();
+    AlignedCodonFrame acf = new AlignedCodonFrame();
+    MapList map = new MapList(new int[]
+    { 1, 6 }, new int[]
+    { 1, 2 }, 3, 1);
+    acf.addMap(dna.getDatasetSequence(), protein.getDatasetSequence(), map);
+
+    /*
+     * No existing gaps in dna:
+     */
+    AlignmentUtils.alignSequenceAs(dna, protein, acf, "---", '-', false,
+            false);
+    assertEquals("---GGG---AAA", dna.getSequenceAsString());
+
+    /*
+     * Now introduce gaps in dna but ignore them when realigning.
+     */
+    dna.setSequence("-G-G-G-A-A-A-");
+    AlignmentUtils.alignSequenceAs(dna, protein, acf, "---", '-', false,
+            false);
+    assertEquals("---GGG---AAA", dna.getSequenceAsString());
+
+    /*
+     * Now include gaps in dna when realigning. First retaining 'mapped' gaps
+     * only, i.e. those within the exon region.
+     */
+    dna.setSequence("-G-G--G-A--A-A-");
+    AlignmentUtils.alignSequenceAs(dna, protein, acf, "---", '-', true,
+            false);
+    assertEquals("---G-G--G---A--A-A", dna.getSequenceAsString());
+
+    /*
+     * Include all gaps in dna when realigning (within and without the exon
+     * region). The leading gap, and the gaps between codons, are subsumed by
+     * the protein alignment gap.
+     */
+    dna.setSequence("-G-GG--AA-A-");
+    AlignmentUtils.alignSequenceAs(dna, protein, acf, "---", '-', true,
+            true);
+    assertEquals("---G-GG---AA-A-", dna.getSequenceAsString());
+
+    /*
+     * Include only unmapped gaps in dna when realigning (outside the exon
+     * region). The leading gap, and the gaps between codons, are subsumed by
+     * the protein alignment gap.
+     */
+    dna.setSequence("-G-GG--AA-A-");
+    AlignmentUtils.alignSequenceAs(dna, protein, acf, "---", '-', false,
+            true);
+    assertEquals("---GGG---AAA-", dna.getSequenceAsString());
+  }
+
+  /**
+   * Test for the alignSequenceAs method that takes two sequences and a mapping.
+   */
+  @Test
+  public void testAlignSequenceAs_withMapping_withIntrons()
+  {
+    /*
+     * Simple case: no gaps in dna
+     */
+    SequenceI dna = new Sequence("Seq1", "GGGAAACCCTTTGGG");
+    dna.createDatasetSequence();
+    SequenceI protein = new Sequence("Seq1", "-A-L-");
+    protein.createDatasetSequence();
+    AlignedCodonFrame acf = new AlignedCodonFrame();
+
+    /*
+     * Exons at codon 2 (AAA) and 4 (TTT)
+     */
+    MapList map = new MapList(new int[]
+    { 4, 6, 10, 12 }, new int[]
+    { 1, 2 }, 3, 1);
+    acf.addMap(dna.getDatasetSequence(), protein.getDatasetSequence(), map);
+
+    /*
+     * Align dna as "-A-L-". The protein 'gaps' follow the introns, i.e are
+     * placed immediately before the mapped codons.
+     */
+    AlignmentUtils.alignSequenceAs(dna, protein, acf, "---", '-', false,
+            false);
+    assertEquals("GGG---AAACCC---TTTGGG", dna.getSequenceAsString());
+
+    /*
+     * Add gaps to dna - but ignore when realigning.
+     */
+    dna.setSequence("-G-G-G--A--A---AC-CC-T-TT-GG-G-");
+    AlignmentUtils.alignSequenceAs(dna, protein, acf, "---", '-', false,
+            false);
+    assertEquals("GGG---AAACCC---TTTGGG", dna.getSequenceAsString());
+
+    /*
+     * Add gaps to dna - include within exons only when realigning.
+     */
+    dna.setSequence("-G-G-G--A--A---A-C-CC-T-TT-GG-G-");
+    AlignmentUtils.alignSequenceAs(dna, protein, acf, "---", '-', true,
+            false);
+    assertEquals("GGG---A--A---ACCC---T-TTGGG", dna.getSequenceAsString());
+
+    /*
+     * Include gaps outside exons only when realigning.
+     */
+    dna.setSequence("-G-G-G--A--A---A-C-CC-T-TT-GG-G-");
+    AlignmentUtils.alignSequenceAs(dna, protein, acf, "---", '-', false,
+            true);
+    assertEquals("-G-G-G---AAA-C-CC---TTT-GG-G-", dna.getSequenceAsString());
+
+    /*
+     * Include all gaps in dna when realigning.
+     */
+    dna.setSequence("-G-G-G--A--A---A-C-CC-T-TT-GG-G-");
+    AlignmentUtils.alignSequenceAs(dna, protein, acf, "---", '-', true,
+            true);
+    assertEquals("-G-G-G---A--A---A-C-CC---T-TT-GG-G-",
+            dna.getSequenceAsString());
+  }
+
+  /**
+   * Test for the case where not all of the protein sequence is mapped to cDNA.
+   */
+  @Test
+  public void testAlignSequenceAs_withMapping_withUnmappedProtein()
+  {
+    SequenceI dna = new Sequence("Seq1", "GGGAAACCCTTTGGG");
+    dna.createDatasetSequence();
+    SequenceI protein = new Sequence("Seq1", "-A-L-P-");
+    protein.createDatasetSequence();
+    AlignedCodonFrame acf = new AlignedCodonFrame();
+
+    /*
+     * Exons at codon 2 (AAA) and 4 (TTT) mapped to A and P
+     */
+    MapList map = new MapList(new int[]
+    { 4, 6, 10, 12 }, new int[]
+    { 1, 1, 3, 3 }, 3, 1);
+    acf.addMap(dna.getDatasetSequence(), protein.getDatasetSequence(), map);
+
+    /*
+     * Align dna as "-A-L-P-". Currently, does nothing (aborts realignment).
+     * Change this test first if different behaviour wanted.
+     */
+    AlignmentUtils.alignSequenceAs(dna, protein, acf, "---", '-', false,
+            false);
+    assertEquals("GGGAAACCCTTTGGG", dna.getSequenceAsString());
+  }
 }