X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Futil%2FComparisonTest.java;h=2e646f585165679be37e1d7d74e9ebcbed6e07f3;hb=2669c44fcae1f976692d840b61bc37c80d9a4322;hp=05522dd3505f77a2785739623e727c1ddcbd0855;hpb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;p=jalview.git

diff --git a/test/jalview/util/ComparisonTest.java b/test/jalview/util/ComparisonTest.java
index 05522dd..2e646f5 100644
--- a/test/jalview/util/ComparisonTest.java
+++ b/test/jalview/util/ComparisonTest.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -26,12 +26,21 @@ import static org.testng.AssertJUnit.assertTrue;
 
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
+import jalview.gui.JvOptionPane;
 
+import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
 public class ComparisonTest
 {
 
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
   @Test(groups = { "Functional" })
   public void testIsGap()
   {
@@ -49,7 +58,7 @@ public class ComparisonTest
    * AGCTU. Test is not case-sensitive and ignores gaps.
    */
   @Test(groups = { "Functional" })
-  public void testIsNucleotide()
+  public void testIsNucleotide_sequences()
   {
     SequenceI seq = new Sequence("eightypercent", "agctuAGCPV");
     assertFalse(Comparison.isNucleotide(new SequenceI[] { seq }));
@@ -76,15 +85,15 @@ public class ComparisonTest
     seq = new Sequence("DNA", "ACTugGCCAG");
     SequenceI seq2 = new Sequence("Protein", "FLIMVSPTYW");
     /*
-     * 90% DNA:
+     * 90% DNA but one protein sequence - expect false
      */
-    assertTrue(Comparison.isNucleotide(new SequenceI[] { seq, seq, seq,
+    assertFalse(Comparison.isNucleotide(new SequenceI[] { seq, seq, seq,
         seq, seq, seq, seq, seq, seq, seq2 }));
-    assertTrue(Comparison.isNucleotide(new SequenceI[][] {
+    assertFalse(Comparison.isNucleotide(new SequenceI[][] {
         new SequenceI[] { seq }, new SequenceI[] { seq, seq, seq },
         new SequenceI[] { seq, seq, seq, seq, seq, seq2 } }));
     /*
-     * 80% DNA:
+     * 80% DNA but one protein sequence - Expect false
      */
     assertFalse(Comparison.isNucleotide(new SequenceI[] { seq, seq, seq,
         seq, seq, seq, seq, seq, seq2, seq2 }));
@@ -101,12 +110,12 @@ public class ComparisonTest
   }
 
   /**
-   * Test percentage identity calculation for two sequences.
+   * Test the percentage identity calculation for two sequences
    */
   @Test(groups = { "Functional" })
-  public void testPID_matchGaps()
+  public void testPID_includingGaps()
   {
-    String seq1 = "ABCDEF";
+    String seq1 = "ABCDEFG"; // extra length here is ignored
     String seq2 = "abcdef";
     assertEquals("identical", 100f, Comparison.PID(seq1, seq2), 0.001f);
 
@@ -114,6 +123,93 @@ public class ComparisonTest
     seq2 = "abcdefghijklmnopqrstuvwxyz";
     assertEquals("identical", 100f, Comparison.PID(seq1, seq2), 0.001f);
 
-    seq2 = "a---bcdef";
+    // 5 identical, 2 gap-gap, 2 gap-residue, 1 mismatch
+    seq1 = "a--b-cdefh";
+    seq2 = "a---bcdefg";
+    int length = seq1.length();
+
+    // match gap-residue, match gap-gap: 9/10 identical
+    // TODO should gap-gap be included in a PID score? JAL-791
+    assertEquals(90f, Comparison.PID(seq1, seq2, 0, length, true, false),
+            0.001f);
+    // overloaded version of the method signature above:
+    assertEquals(90f, Comparison.PID(seq1, seq2), 0.001f);
+
+    // don't match gap-residue, match gap-gap: 7/10 identical
+    // TODO should gap-gap be included in a PID score?
+    assertEquals(70f, Comparison.PID(seq1, seq2, 0, length, false, false),
+            0.001f);
+  }
+
+  @Test(groups = { "Functional" })
+  public void testIsNucleotide()
+  {
+    assertTrue(Comparison.isNucleotide('a'));
+    assertTrue(Comparison.isNucleotide('A'));
+    assertTrue(Comparison.isNucleotide('c'));
+    assertTrue(Comparison.isNucleotide('C'));
+    assertTrue(Comparison.isNucleotide('g'));
+    assertTrue(Comparison.isNucleotide('G'));
+    assertTrue(Comparison.isNucleotide('t'));
+    assertTrue(Comparison.isNucleotide('T'));
+    assertTrue(Comparison.isNucleotide('u'));
+    assertTrue(Comparison.isNucleotide('U'));
+    assertFalse(Comparison.isNucleotide('-'));
+    assertFalse(Comparison.isNucleotide('P'));
+  }
+
+  /**
+   * Test the percentage identity calculation for two sequences
+   */
+  @Test(groups = { "Functional" })
+  public void testPID_ungappedOnly()
+  {
+    // 5 identical, 2 gap-gap, 2 gap-residue, 1 mismatch
+    // the extra length of seq1 is ignored
+    String seq1 = "a--b-cdefhr";
+    String seq2 = "a---bcdefg";
+    int length = seq1.length();
+
+    /*
+     * As currently coded, 'ungappedOnly' ignores gap-residue but counts
+     * gap-gap. Is this a bug - should gap-gap also be ignored, giving a PID of
+     * 5/6?
+     * 
+     * Note also there is no variant of the calculation that penalises
+     * gap-residue i.e. counts it as a mismatch. This would give a score of 5/8
+     * (if we ignore gap-gap) or 5/10 (if we count gap-gap as a match).
+     */
+    // match gap-residue, match gap-gap: 7/8 identical
+    assertEquals(87.5f, Comparison.PID(seq1, seq2, 0, length, true, true),
+            0.001f);
+
+    // don't match gap-residue with 'ungapped only' - same as above
+    assertEquals(87.5f, Comparison.PID(seq1, seq2, 0, length, false, true),
+            0.001f);
+  }
+
+  @Test(groups = { "Functional" })
+  public void testIsNucleotideSequence()
+  {
+    assertFalse(Comparison.isNucleotideSequence(null, true));
+    assertTrue(Comparison.isNucleotideSequence("", true));
+    assertTrue(Comparison.isNucleotideSequence("aAgGcCtTuU", true));
+    assertTrue(Comparison.isNucleotideSequence("aAgGcCtTuU", false));
+    assertFalse(Comparison.isNucleotideSequence("xAgGcCtTuU", false));
+    assertFalse(Comparison.isNucleotideSequence("aAgGcCtTuUx", false));
+    assertTrue(Comparison.isNucleotideSequence("a A-g.GcCtTuU", true));
+    assertFalse(Comparison.isNucleotideSequence("a A-g.GcCtTuU", false));
+  }
+
+  @Test(groups = { "Functional" })
+  public void testIsSameResidue()
+  {
+    assertTrue(Comparison.isSameResidue('a', 'a', false));
+    assertTrue(Comparison.isSameResidue('a', 'a', true));
+    assertTrue(Comparison.isSameResidue('A', 'a', false));
+    assertTrue(Comparison.isSameResidue('a', 'A', false));
+
+    assertFalse(Comparison.isSameResidue('a', 'A', true));
+    assertFalse(Comparison.isSameResidue('A', 'a', true));
   }
 }