JAL-2996 JAL-3053 ~ | : [] {} () treated as gap characters.

[jalview.git] / test / jalview / util / ComparisonTest.java

diff --git a/test/jalview/util/ComparisonTest.java b/test/jalview/util/ComparisonTest.java
index 2426a72..bd3b52e 100644 (file)
--- a/test/jalview/util/ComparisonTest.java
+++ b/test/jalview/util/ComparisonTest.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
- * 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 +26,22 @@ import static org.testng.AssertJUnit.assertTrue;
 
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
+import jalview.gui.JvOptionPane;
 
+import org.testng.Assert;
+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()
   {
@@ -42,6 +52,23 @@ public class ComparisonTest
     assertFalse(Comparison.isGap('x'));
     assertFalse(Comparison.isGap('*'));
     assertFalse(Comparison.isGap('G'));
+
+    // consistency - test Comparison.isGap covers all gapChars
+    StringBuilder missing = new StringBuilder();
+    for (int i = 0, iSize = Comparison.GapChars.length(); i < iSize; i++)
+    {
+      char gc = Comparison.GapChars.charAt(i);
+      if (!Comparison.isGap(gc))
+      {
+        missing.append(gc);
+      }
+    }
+    if (missing.length() > 0)
+    {
+      Assert.fail(
+              "Comparison.GapChars contains symbols not covered by Comparison.isGap: '"
+              + missing.toString() + "'");
+    }
   }
 
   /**
@@ -49,7 +76,7 @@ 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 }));
@@ -101,12 +128,12 @@ 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 +141,93 @@ 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));
   }
 }