X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fdatamodel%2FSearchResultsTest.java;h=5d2b8a4d324a2e450466f1cd08d0660b888f6684;hb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;hp=f1a6e20e740ca3d9598b858851e052060970835a;hpb=5f4e1e4c330b045e9c8bce28ee132a0fca3834d8;p=jalview.git

diff --git a/test/jalview/datamodel/SearchResultsTest.java b/test/jalview/datamodel/SearchResultsTest.java
index f1a6e20..5d2b8a4 100644
--- 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
    */
@@ -195,15 +214,16 @@ public class SearchResultsTest
     int marked = 0;
     SequenceI seq1 = new Sequence("", "abcdefghijklm");
     SequenceI seq2 = new Sequence("", "abcdefghijklm");
-    SequenceGroup s1g=new SequenceGroup(), s2g=new SequenceGroup(), sallg=new SequenceGroup();
+    SequenceGroup s1g = new SequenceGroup(), s2g = new SequenceGroup(),
+            sallg = new SequenceGroup();
     s1g.addSequence(seq1, false);
     s2g.addSequence(seq2, false);
     sallg.addSequence(seq1, false);
     sallg.addSequence(seq2, false);
-    
+
     SearchResultsI sr = new SearchResults();
     BitSet bs = new BitSet();
-    
+
     SearchResultMatchI srm = null;
     srm = sr.addResult(seq1, 1, 1);
     Assert.assertNotNull("addResult didn't return Match", srm);
@@ -211,7 +231,7 @@ public class SearchResultsTest
     assertEquals("Sequence reference not set", seq2, srm.getSequence());
     assertEquals("match start incorrect", 1, srm.getStart());
     assertEquals("match end incorrect", 2, srm.getEnd());
-    
+
     // set start/end range for groups to cover matches
 
     s1g.setStartRes(0);
@@ -231,11 +251,10 @@ public class SearchResultsTest
     assertTrue("Didn't mark expected position", bs.get(0));
     // now check return value for marking the same again
     assertEquals(
-            "Didn't count number of bits marked for existing marked set",
-            0,
+            "Didn't count number of bits marked for existing marked set", 0,
             sr.markColumns(s1g, bs));
     bs.clear();
-    
+
     /*
      * just seq2
      */
@@ -244,7 +263,7 @@ public class SearchResultsTest
     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(1));
-    
+
     /*
      * both seq1 and seq2 
      * should be same as seq2
@@ -262,10 +281,92 @@ public class SearchResultsTest
     s2g.setEndRes(1);
     sallg.setEndRes(0);
     BitSet tbs = new BitSet();
-    assertEquals("Group start/end didn't select columns to mark",1, sr.markColumns(s2g, tbs));
-    assertEquals("Group start/end didn't select columns to mark", 1, sr.markColumns(sallg, tbs));
+    assertEquals("Group start/end didn't select columns to mark", 1,
+            sr.markColumns(s2g, tbs));
+    assertEquals("Group start/end didn't select columns to mark", 1,
+            sr.markColumns(sallg, tbs));
     assertEquals(
             "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));
+  }
 }