From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Tue, 20 Jan 2015 09:46:30 +0000 (+0000)
Subject: JAL-1619 test that reordering cDNA does not change translation results
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=e06580cb9fa7255844392883e96d5f9cbc680ec1;p=jalview.git

JAL-1619 test that reordering cDNA does not change translation results
---

diff --git a/test/jalview/analysis/DnaTest.java b/test/jalview/analysis/DnaTest.java
index 43ee5f2..59938ae 100644
--- a/test/jalview/analysis/DnaTest.java
+++ b/test/jalview/analysis/DnaTest.java
@@ -5,8 +5,10 @@ import static org.junit.Assert.assertNotNull;
 import static org.junit.Assert.assertTrue;
 import jalview.api.AlignViewportI;
 import jalview.datamodel.AlignedCodon;
+import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.SequenceI;
 import jalview.gui.AlignViewport;
 import jalview.io.FormatAdapter;
 
@@ -252,6 +254,61 @@ public class DnaTest
   }
 
   /**
+   * This test generates a random cDNA alignment and its translation, then
+   * reorders the cDNA and retranslates, and verifies that the translations are
+   * the same (apart from ordering).
+   */
+  @Test
+  public void testTranslateCdna_sequenceOrderIndependent()
+  {
+    /*
+     * Generate cDNA - 8 sequences of 12 bases each.
+     */
+    AlignmentI cdna = new DnaAlignmentGenerator().generate(12, 8, 97);
+    ColumnSelection cs = new ColumnSelection();
+    AlignViewportI av = new AlignViewport(cdna, cs);
+    Dna dna = new Dna(av, new int[]
+    { 0, cdna.getWidth() - 1 });
+    AlignmentI translated = dna.translateCdna();
+
+    /*
+     * Jumble the cDNA sequences and translate.
+     */
+    SequenceI[] sorted = new SequenceI[cdna.getHeight()];
+    final int[] jumbler = new int[]
+    { 6, 7, 3, 4, 2, 0, 1, 5 };
+    int seqNo = 0;
+    for (int i : jumbler)
+    {
+      sorted[seqNo++] = cdna.getSequenceAt(i);
+    }
+    AlignmentI cdnaReordered = new Alignment(sorted);
+    av = new AlignViewport(cdnaReordered, cs);
+    dna = new Dna(av, new int[]
+    { 0, cdna.getWidth() - 1 });
+    AlignmentI translated2 = dna.translateCdna();
+
+    /*
+     * Check translated sequences are the same in both alignments.
+     */
+    System.out.println("Original");
+    System.out.println(translated.toString());
+    System.out.println("Sorted");
+    System.out.println(translated2.toString());
+
+    int sortedSequenceIndex = 0;
+    for (int originalSequenceIndex : jumbler)
+    {
+      final String translation1 = translated.getSequenceAt(
+              originalSequenceIndex).getSequenceAsString();
+      final String translation2 = translated2.getSequenceAt(sortedSequenceIndex)
+              .getSequenceAsString();
+      assertEquals(translation2, translation1);
+      sortedSequenceIndex++;
+    }
+  }
+
+  /**
    * Test that all the cases in testCompareCodonPos have a 'symmetric'
    * comparison (without checking the actual comparison result).
    */