JAL-1632 JAL-2416 load score matrices from file, as float[][]

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

diff --git a/test/jalview/util/ComparisonTest.java b/test/jalview/util/ComparisonTest.java
index 0c2c998..f955879 100644 (file)
--- a/test/jalview/util/ComparisonTest.java
+++ b/test/jalview/util/ComparisonTest.java
@@ -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 }));
@@ -130,6 +139,23 @@ public class ComparisonTest
             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
    */
@@ -158,4 +184,29 @@ public class ComparisonTest
     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));
+  }
 }