JAL-3490 match count independent of contiguous matches count

[jalview.git] / test / jalview / datamodel / SearchResultsTest.java

diff --git a/test/jalview/datamodel/SearchResultsTest.java b/test/jalview/datamodel/SearchResultsTest.java
index f1a6e20..838b259 100644 (file)
--- a/test/jalview/datamodel/SearchResultsTest.java
+++ b/test/jalview/datamodel/SearchResultsTest.java
@@ -25,14 +25,14 @@ import static org.testng.AssertJUnit.assertFalse;
 import static org.testng.AssertJUnit.assertSame;
 import static org.testng.AssertJUnit.assertTrue;
 
-import jalview.gui.JvOptionPane;
-
 import java.util.BitSet;
 
 import org.junit.Assert;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
+import jalview.gui.JvOptionPane;
+
 public class SearchResultsTest
 {
 
@@ -186,6 +186,25 @@ public class SearchResultsTest
     assertEquals(5, m.getEnd());
   }
 
+  @Test(groups = { "Functional" })
+  public void testMatchContains()
+  {
+    SequenceI seq1 = new Sequence("", "abcdefghijklm");
+    SequenceI seq2 = new Sequence("", "abcdefghijklm");
+    SearchResultMatchI m = new SearchResults().new Match(seq1, 2, 5);
+
+    assertTrue(m.contains(seq1, 2, 5));
+    assertTrue(m.contains(seq1, 3, 5));
+    assertTrue(m.contains(seq1, 2, 4));
+    assertTrue(m.contains(seq1, 3, 3));
+
+    assertFalse(m.contains(seq1, 2, 6));
+    assertFalse(m.contains(seq1, 1, 5));
+    assertFalse(m.contains(seq1, 1, 8));
+    assertFalse(m.contains(seq2, 3, 3));
+    assertFalse(m.contains(null, 3, 3));
+  }
+
   /**
    * test markColumns for creating column selections
    */
@@ -268,4 +287,84 @@ public class SearchResultsTest
             "Didn't set expected number of columns in total for two successive marks",
             2, tbs.cardinality());
   }
+
+  /**
+   * Test to verify adding doesn't create duplicate results
+   */
+  @Test(groups = { "Functional" })
+  public void testAddResult()
+  {
+    SequenceI seq1 = new Sequence("", "abcdefghijklm");
+    SearchResultsI sr = new SearchResults();
+    sr.addResult(seq1, 3, 5);
+    assertEquals(1, sr.getCount());
+    sr.addResult(seq1, 3, 5);
+    assertEquals(1, sr.getCount());
+    sr.addResult(seq1, 3, 6);
+    assertEquals(2, sr.getCount());
+  }
+
+  /**
+   * Test for method that checks if search results matches a sequence region
+   */
+  @Test(groups = { "Functional" })
+  public void testInvolvesSequence()
+  {
+    SequenceI dataset = new Sequence("genome", "ATGGCCCTTTAAGCAACATTT");
+    // first 'exon':
+    SequenceI cds1 = new Sequence("cds1/1-12", "ATGGCCCTTTAA");
+    cds1.setDatasetSequence(dataset);
+    // overlapping second 'exon':
+    SequenceI cds2 = new Sequence("cds2/7-18", "CTTTAAGCAACA");
+    cds2.setDatasetSequence(dataset);
+    // unrelated sequence
+    SequenceI cds3 = new Sequence("cds3", "ATGGCCCTTTAAGCAACA");
+
+    SearchResults sr = new SearchResults();
+    assertFalse(sr.involvesSequence(cds1));
+
+    /*
+     * cds1 and cds2 share the same dataset sequence, but
+     * only cds1 overlaps match 4:6 (fixes bug JAL-3613)
+     */
+    sr.addResult(dataset, 4, 6);
+    assertTrue(sr.involvesSequence(cds1));
+    assertFalse(sr.involvesSequence(cds2));
+    assertFalse(sr.involvesSequence(cds3));
+
+    /*
+     * search results overlap cds2 only
+     */
+    sr = new SearchResults();
+    sr.addResult(dataset, 18, 18);
+    assertFalse(sr.involvesSequence(cds1));
+    assertTrue(sr.involvesSequence(cds2));
+
+    /*
+     * add a search result overlapping cds1
+     */
+    sr.addResult(dataset, 1, 1);
+    assertTrue(sr.involvesSequence(cds1));
+    assertTrue(sr.involvesSequence(cds2));
+
+    /*
+     * single search result overlapping both
+     */
+    sr = new SearchResults();
+    sr.addResult(dataset, 10, 12);
+    assertTrue(sr.involvesSequence(cds1));
+    assertTrue(sr.involvesSequence(cds2));
+
+    /*
+     * search results matching aligned sequence
+     */
+    sr = new SearchResults();
+    sr.addResult(cds1, 10, 12);
+    assertTrue(sr.involvesSequence(cds1));
+    assertFalse(sr.involvesSequence(cds2));
+    sr.addResult(cds2, 1, 3); // no start-end overlap
+    assertFalse(sr.involvesSequence(cds2));
+    sr.addResult(cds2, 7, 9); // start-end overlap
+    assertTrue(sr.involvesSequence(cds2));
+  }
 }