JAL-4062 avc operation and model method for copying SearchResultsI.getMatchingSubSequ...

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

diff --git a/test/jalview/datamodel/SearchResultsTest.java b/test/jalview/datamodel/SearchResultsTest.java
index 5d2b8a4..b1bb43c 100644 (file)
--- a/test/jalview/datamodel/SearchResultsTest.java
+++ b/test/jalview/datamodel/SearchResultsTest.java
@@ -26,6 +26,7 @@ import static org.testng.AssertJUnit.assertSame;
 import static org.testng.AssertJUnit.assertTrue;
 
 import java.util.BitSet;
+import java.util.List;
 
 import org.junit.Assert;
 import org.testng.annotations.BeforeClass;
@@ -369,4 +370,44 @@ public class SearchResultsTest
     sr.addResult(cds2, 7, 9); // start-end overlap
     assertTrue(sr.involvesSequence(cds2));
   }
+
+  /**
+   * Test extraction of Sequence objects for matched ranges on a sequence
+   */
+  @Test(groups = { "Functional" })
+  public void testGetSequences()
+  {
+    SequenceI seq1 = new Sequence("", "abcdefghijklm");
+    SequenceI seq2 = new Sequence("", "nopqrstuvwxyz");
+    seq2.setStart(23);
+    seq2.setEnd(35);
+    List<SequenceI> seqres = null;
+
+    SearchResultsI sr = new SearchResults();
+    seqres = sr.getMatchingSubSequences();
+    assertEquals(0, seqres.size());
+
+    sr.addResult(seq1, 3, 5);
+    seqres = sr.getMatchingSubSequences();
+
+    assertEquals(1, seqres.size());
+    assertEquals("cde", seqres.get(0).getSequenceAsString());
+    assertEquals(3, seqres.get(0).getStart());
+    assertEquals(seq1, seqres.get(0).getDatasetSequence());
+
+    sr.addResult(seq1, 3, 6);
+    seqres = sr.getMatchingSubSequences();
+
+    assertEquals(2, seqres.size());
+    assertEquals("cdef", seqres.get(1).getSequenceAsString());
+    assertEquals(3, seqres.get(1).getStart());
+
+    // this is a quirk - match on 26-29 yields subsequence 27-30
+    sr.addResult(seq2, 26, 29);
+    seqres = sr.getMatchingSubSequences();
+    assertEquals(3, seqres.size());
+    assertEquals("qrst", seqres.get(2).getSequenceAsString());
+    assertEquals(26, seqres.get(2).getStart());
+  }
+
 }