X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fdatamodel%2FSearchResultsTest.java;h=d8c10eeed0db090b5be80266a3f2eacf12720df5;hb=2989fded65d7eb892018bcf783425fe23bc679d9;hp=838b259ea0c93e1df519cfc9768b9d35e75428a2;hpb=6b13a606027284408286d1cd2833470d1f9b9bfe;p=jalview.git diff --git a/test/jalview/datamodel/SearchResultsTest.java b/test/jalview/datamodel/SearchResultsTest.java index 838b259..d8c10ee 100644 --- 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; @@ -205,6 +206,32 @@ public class SearchResultsTest assertFalse(m.contains(null, 3, 3)); } + @Test(groups = { "Functional" }) + public void testMatchAdjacent() + { + SequenceI seq1 = new Sequence("", "abcdefghijklm"); + SequenceI seq2 = new Sequence("", "abcdefghijklm"); + SearchResultMatchI m = new SearchResults().new Match(seq1, 2, 5); + + assertTrue(m.adjacent(seq1, 2, 5)); + assertTrue(m.adjacent(seq1, 3, 5)); + assertTrue(m.adjacent(seq1, 2, 4)); + assertTrue(m.adjacent(seq1, 3, 3)); + + assertTrue(m.adjacent(seq1, 2, 6)); + assertTrue(m.adjacent(seq1, 1, 5)); + assertTrue(m.adjacent(seq1, 1, 8)); + assertFalse(m.adjacent(seq1, 0, 0)); + assertFalse(m.adjacent(seq1, 7, 8)); + assertTrue(m.adjacent(seq1, 6, 8)); + assertTrue(m.adjacent(seq1, 5, 8)); + assertTrue(m.adjacent(seq1, 0, 1)); + + + assertFalse(m.adjacent(seq2, 3, 3)); + assertFalse(m.adjacent(null, 3, 3)); + } + /** * test markColumns for creating column selections */ @@ -214,15 +241,16 @@ 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); @@ -230,7 +258,7 @@ 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); @@ -250,11 +278,10 @@ 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 */ @@ -263,7 +290,7 @@ 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 @@ -281,8 +308,10 @@ 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()); @@ -305,6 +334,23 @@ public class SearchResultsTest } /** + * Test to verify appending creates a minimal set of results + */ + @Test(groups = { "Functional" }) + public void testAppendResult() + { + SequenceI seq1 = new Sequence("", "abcdefghijklm"); + SearchResultsI sr = new SearchResults(); + sr.appendResult(seq1, 3, 5); + assertEquals(1, sr.getCount()); + sr.appendResult(seq1, 3, 6); + assertEquals(1, sr.getCount()); + sr.appendResult(seq1, 8, 8); + assertEquals(2, sr.getCount()); + sr.appendResult(seq1, 7, 7); + assertEquals(1, sr.getCount()); + } + /** * Test for method that checks if search results matches a sequence region */ @Test(groups = { "Functional" }) @@ -367,4 +413,44 @@ 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 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()); + } + }