X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Futil%2FComparisonTest.java;h=6f6841ddefecc1ae87fd9c816ff3f995fd6e9f6d;hb=d53885ed6e43ed0293b316fbad6865a7c2baa688;hp=9aab66c93a4550d0ced4cf72cb05e4ed5a0b2ff4;hpb=37de9310bec3501cbc6381e0c3dcb282fcaad812;p=jalview.git

diff --git a/test/jalview/util/ComparisonTest.java b/test/jalview/util/ComparisonTest.java
index 9aab66c..6f6841d 100644
--- 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()
   {
@@ -106,7 +115,7 @@ public class ComparisonTest
   @Test(groups = { "Functional" })
   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);
 
@@ -120,12 +129,14 @@ public class ComparisonTest
     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);
   }
@@ -154,7 +165,8 @@ public class ComparisonTest
   public void testPID_ungappedOnly()
   {
     // 5 identical, 2 gap-gap, 2 gap-residue, 1 mismatch
-    String seq1 = "a--b-cdefh";
+    // the extra length of seq1 is ignored
+    String seq1 = "a--b-cdefhr";
     String seq2 = "a---bcdefg";
     int length = seq1.length();
 
@@ -188,4 +200,16 @@ public class ComparisonTest
     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));
+  }
 }