X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Futil%2FComparisonTest.java;h=9aab66c93a4550d0ced4cf72cb05e4ed5a0b2ff4;hb=refs%2Fheads%2Freleases%2FRelease_2_10_0_Branch;hp=c52d52487c16620eec2caa3190f99209a27351a7;hpb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;p=jalview.git

diff --git a/test/jalview/util/ComparisonTest.java b/test/jalview/util/ComparisonTest.java
index c52d524..9aab66c 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 2.9.0b2)
- * 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.
  * 
@@ -49,7 +49,7 @@ 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 }));
@@ -101,10 +101,10 @@ 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 seq2 = "abcdef";
@@ -114,6 +114,78 @@ 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
+    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
+    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
+    String seq1 = "a--b-cdefh";
+    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));
   }
 }