JAL-3613 check sequence overlap when matching search results

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

diff --git a/test/jalview/datamodel/SearchResultsTest.java b/test/jalview/datamodel/SearchResultsTest.java
index addf68e..a302d6e 100644 (file)
--- a/test/jalview/datamodel/SearchResultsTest.java
+++ b/test/jalview/datamodel/SearchResultsTest.java
@@ -28,39 +28,34 @@ import static org.testng.AssertJUnit.assertTrue;
 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
 {
 
-  @Test(groups = { "Functional" })
-  public void testToString()
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
   {
-    SequenceI seq = new Sequence("", "abcdefghijklm");
-    SearchResultsI sr = new SearchResults();
-    sr.addResult(seq, 1, 1);
-    assertEquals("0a", sr.toString());
-    sr.addResult(seq, 3, 5);
-    assertEquals("0a2cde", sr.toString());
-
-    seq = new Sequence("", "pqrstuvwxy");
-    sr.addResult(seq, 6, 7);
-    assertEquals("0a2cde5uv", sr.toString());
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
   }
 
   @Test(groups = { "Functional" })
-  public void testGetCharacters()
+  public void testToString()
   {
-    SequenceI seq = new Sequence("", "abcdefghijklm");
-    SearchResults sr = new SearchResults();
+    SequenceI seq = new Sequence("Seq1", "abcdefghijklm");
+    SearchResultsI sr = new SearchResults();
     sr.addResult(seq, 1, 1);
-    assertEquals("a", sr.getCharacters());
+    assertEquals("[Seq1/1-1]", sr.toString());
     sr.addResult(seq, 3, 5);
-    assertEquals("acde", sr.getCharacters());
+    assertEquals("[Seq1/1-1, Seq1/3-5]", sr.toString());
 
-    seq = new Sequence("", "pqrstuvwxy");
+    seq = new Sequence("Seq2", "pqrstuvwxy");
     sr.addResult(seq, 6, 7);
-    assertEquals("acdeuv", sr.getCharacters());
+    assertEquals("[Seq1/1-1, Seq1/3-5, Seq2/6-7]", sr.toString());
   }
 
   @Test(groups = { "Functional" })
@@ -77,7 +72,7 @@ public class SearchResultsTest
     assertTrue(sr2.equals(sr1)); // reflexive
 
     /*
-     * only one result is not empty
+     * if only one result is not empty
      */
     sr1.addResult(seq1, 1, 1);
     assertTrue(sr1.equals(sr1));
@@ -191,6 +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
    */
@@ -248,7 +262,7 @@ public class SearchResultsTest
     assertEquals("Didn't mark expected number", 2, bs.cardinality());
     assertEquals("Didn't return count of number of bits marked", 2, marked);
     assertTrue("Didn't mark expected position (1)", bs.get(0));
-    assertTrue("Didn't mark expected position (2)", bs.get(0));
+    assertTrue("Didn't mark expected position (2)", bs.get(1));
     
     /*
      * both seq1 and seq2 
@@ -273,4 +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.getSize());
+    sr.addResult(seq1, 3, 5);
+    assertEquals(1, sr.getSize());
+    sr.addResult(seq1, 3, 6);
+    assertEquals(2, sr.getSize());
+  }
+
+  /**
+   * 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));
+  }
 }