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
{
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
*/
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);
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);
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
*/
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
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));
+ }
}
git://source.jalview.org / jalview.git / blobdiff