X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fanalysis%2FFinderTest.java;h=771712d691ac421c5476d1482d4beda1e8246839;hb=745806901cdcda04d9b5c496cb5249a03af19971;hp=4fdafde4307672222798c785283e6221ffc29e42;hpb=7d67fb613ec026dc9a265e351e7fab542e3f1d61;p=jalview.git diff --git a/test/jalview/analysis/FinderTest.java b/test/jalview/analysis/FinderTest.java index 4fdafde..771712d 100644 --- a/test/jalview/analysis/FinderTest.java +++ b/test/jalview/analysis/FinderTest.java @@ -24,12 +24,15 @@ import static org.testng.Assert.assertEquals; import static org.testng.Assert.assertSame; import static org.testng.Assert.assertTrue; +import jalview.bin.Cache; import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentI; import jalview.datamodel.SearchResultMatchI; import jalview.datamodel.SearchResultsI; import jalview.datamodel.Sequence; +import jalview.datamodel.SequenceGroup; import jalview.gui.AlignFrame; +import jalview.gui.JvOptionPane; import jalview.io.DataSourceType; import jalview.io.FileLoader; @@ -40,6 +43,13 @@ import org.testng.annotations.Test; public class FinderTest { + @BeforeClass(alwaysRun = true) + public void setUpJvOptionPane() + { + JvOptionPane.setInteractiveMode(false); + JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); + } + private AlignFrame af; private AlignmentI al; @@ -47,7 +57,11 @@ public class FinderTest @BeforeClass(groups = "Functional") public void setUp() { - String seqData = "seq1 ABCD--EF-GHI\n" + "seq2 A--BCDefHI\n" + Cache.loadProperties("test/jalview/io/testProps.jvprops"); + Cache.applicationProperties.setProperty("PAD_GAPS", + Boolean.FALSE.toString()); + + String seqData = "seq1seq1/8-16 ABCD--EF-GHI\n" + "seq2 A--BCDefHI\n" + "seq3 --bcdEFH\n" + "seq4 aa---aMMMMMaaa\n"; af = new FileLoader().LoadFileWaitTillLoaded(seqData, DataSourceType.PASTE); @@ -55,19 +69,31 @@ public class FinderTest } /** - * Test for find all matches of a regular expression + * Test for find matches of a regular expression */ @Test(groups = "Functional") - public void testFindAll_regex() + public void testFind_regex() { + /* + * find next match only + */ Finder f = new Finder(al, null); - f.setFindAll(true); f.find("E.H"); // 'E, any character, H' + // should match seq2 efH only + SearchResultsI sr = f.getSearchResults(); + assertEquals(sr.getSize(), 1); + List matches = sr.getResults(); + assertSame(al.getSequenceAt(1), matches.get(0).getSequence()); + assertEquals(matches.get(0).getStart(), 5); + assertEquals(matches.get(0).getEnd(), 7); + f = new Finder(al, null); + f.setFindAll(true); + f.find("E.H"); // 'E, any character, H' // should match seq2 efH and seq3 EFH - SearchResultsI sr = f.getSearchResults(); + sr = f.getSearchResults(); assertEquals(sr.getSize(), 2); - List matches = sr.getResults(); + matches = sr.getResults(); assertSame(al.getSequenceAt(1), matches.get(0).getSequence()); assertSame(al.getSequenceAt(2), matches.get(1).getSequence()); assertEquals(matches.get(0).getStart(), 5); @@ -83,19 +109,40 @@ public class FinderTest public void testFind_residueNumber() { Finder f = new Finder(al, null); - f.setFindAll(true); - f.find("9"); - // seq1 and seq4 have 9 residues; no match in other sequences + /* + * find first match should return seq1 residue 9 + */ + f.find("9"); SearchResultsI sr = f.getSearchResults(); - assertEquals(sr.getSize(), 2); + assertEquals(sr.getSize(), 1); List matches = sr.getResults(); assertSame(al.getSequenceAt(0), matches.get(0).getSequence()); + assertEquals(matches.get(0).getStart(), 9); + assertEquals(matches.get(0).getEnd(), 9); + + /* + * find all matches should return seq1 and seq4 (others are too short) + */ + f = new Finder(al, null); + f.setFindAll(true); + f.find("9"); + sr = f.getSearchResults(); + assertEquals(sr.getSize(), 2); + matches = sr.getResults(); + assertSame(al.getSequenceAt(0), matches.get(0).getSequence()); assertSame(al.getSequenceAt(3), matches.get(1).getSequence()); assertEquals(matches.get(0).getStart(), 9); assertEquals(matches.get(0).getEnd(), 9); assertEquals(matches.get(1).getStart(), 9); assertEquals(matches.get(1).getEnd(), 9); + + /* + * parsing of search string as integer is strict + */ + f = new Finder(al, null); + f.find(" 9"); + assertTrue(f.getSearchResults().isEmpty()); } /** @@ -142,15 +189,28 @@ public class FinderTest * Test for matching within sequence descriptions */ @Test(groups = "Functional") - public void testFindAll_inDescription() + public void testFind_inDescription() { AlignmentI al2 = new Alignment(al); al2.getSequenceAt(0).setDescription("BRAF"); al2.getSequenceAt(1).setDescription("braf"); + + /* + * find first match only + */ Finder f = new Finder(al2, null); - f.setFindAll(true); f.setIncludeDescription(true); + f.find("rAF"); + assertEquals(f.getIdMatch().size(), 1); + assertSame(f.getIdMatch().get(0), al2.getSequenceAt(0)); + assertTrue(f.getSearchResults().isEmpty()); + /* + * find all matches + */ + f = new Finder(al2, null); + f.setFindAll(true); + f.setIncludeDescription(true); f.find("rAF"); assertEquals(f.getIdMatch().size(), 2); assertSame(f.getIdMatch().get(0), al2.getSequenceAt(0)); @@ -209,7 +269,8 @@ public class FinderTest f.setFindAll(true); /* - * case insensitive + * case insensitive; seq1 occurs twice in sequence id but + * only one match should be returned */ f.find("SEQ1"); assertEquals(f.getIdMatch().size(), 1); @@ -247,17 +308,47 @@ public class FinderTest } /** - * Test finding all matches of a sequence pattern in an alignment + * Test finding next match of a sequence pattern in an alignment + */ + @Test(groups = "Functional") + public void testFind() + { + Finder f = new Finder(al, null); + f.find("EfH"); + SearchResultsI searchResults = f.getSearchResults(); + assertEquals(searchResults.getSize(), 1); + SearchResultMatchI match = searchResults.getResults().get(0); + assertSame(al.getSequenceAt(1), match.getSequence()); + assertEquals(5, match.getStart()); + assertEquals(7, match.getEnd()); + } + + /** + * Test for JAL-2302 to verify that sub-matches are not included in a find all + * result */ @Test(groups = "Functional") - public void testFindAll_simpleMatch() + public void testFind_maximalResultOnly() { Finder f = new Finder(al, null); f.setFindAll(true); + f.find("M+"); + SearchResultsI searchResults = f.getSearchResults(); + assertEquals(searchResults.getSize(), 1); + SearchResultMatchI match = searchResults.getResults().get(0); + assertSame(al.getSequenceAt(3), match.getSequence()); + assertEquals(4, match.getStart()); // dataset sequence positions + assertEquals(8, match.getEnd()); // base 1 + } - /* - * case insensitive first - */ + /** + * Test finding all matches of a sequence pattern in an alignment + */ + @Test(groups = "Functional") + public void testFind_findAll() + { + Finder f = new Finder(al, null); + f.setFindAll(true); f.find("EfH"); SearchResultsI searchResults = f.getSearchResults(); assertEquals(searchResults.getSize(), 2); @@ -269,41 +360,163 @@ public class FinderTest assertSame(al.getSequenceAt(2), match.getSequence()); assertEquals(4, match.getStart()); assertEquals(6, match.getEnd()); + } - /* - * case sensitive - */ - f = new Finder(al, null); - f.setFindAll(true); + /** + * Test finding all matches, case-sensitive + */ + @Test(groups = "Functional") + public void testFind_findAllCaseSensitive() + { + Finder f = new Finder(al, null); f.setCaseSensitive(true); + f.setFindAll(true); f.find("BC"); - searchResults = f.getSearchResults(); + SearchResultsI searchResults = f.getSearchResults(); assertEquals(searchResults.getSize(), 2); - match = searchResults.getResults().get(0); + SearchResultMatchI match = searchResults.getResults().get(0); assertSame(al.getSequenceAt(0), match.getSequence()); - assertEquals(2, match.getStart()); - assertEquals(3, match.getEnd()); + assertEquals(match.getStart(), 9); + assertEquals(match.getEnd(), 10); match = searchResults.getResults().get(1); assertSame(al.getSequenceAt(1), match.getSequence()); + assertEquals(match.getStart(), 2); + assertEquals(match.getEnd(), 3); + } + + /** + * Test finding next match of a sequence pattern in a selection group + */ + @Test(groups = "Functional") + public void testFind_inSelection() + { + /* + * select sequences 2 and 3, columns 4-6 which contains + * BCD + * cdE + */ + SequenceGroup sg = new SequenceGroup(); + sg.setStartRes(3); + sg.setEndRes(5); + sg.addSequence(al.getSequenceAt(1), false); + sg.addSequence(al.getSequenceAt(2), false); + + Finder f = new Finder(al, sg); + f.find("b"); + assertTrue(f.getIdMatch().isEmpty()); + SearchResultsI searchResults = f.getSearchResults(); + assertEquals(searchResults.getSize(), 1); + SearchResultMatchI match = searchResults.getResults().get(0); + assertSame(al.getSequenceAt(1), match.getSequence()); assertEquals(2, match.getStart()); + assertEquals(2, match.getEnd()); + + /* + * a second Find should not return the 'b' in seq3 as outside the selection + */ + f.find("b"); + assertTrue(f.getSearchResults().isEmpty()); + assertTrue(f.getIdMatch().isEmpty()); + + f = new Finder(al, sg); + f.find("d"); + assertTrue(f.getIdMatch().isEmpty()); + searchResults = f.getSearchResults(); + assertEquals(searchResults.getSize(), 1); + match = searchResults.getResults().get(0); + assertSame(al.getSequenceAt(1), match.getSequence()); + assertEquals(4, match.getStart()); + assertEquals(4, match.getEnd()); + f.find("d"); + assertTrue(f.getIdMatch().isEmpty()); + searchResults = f.getSearchResults(); + assertEquals(searchResults.getSize(), 1); + match = searchResults.getResults().get(0); + assertSame(al.getSequenceAt(2), match.getSequence()); + assertEquals(3, match.getStart()); assertEquals(3, match.getEnd()); } /** - * Test for JAL-2302 to verify that sub-matches are not included in a find all - * result + * Test finding all matches of a search pattern in a selection group */ @Test(groups = "Functional") - public void testFind_maximalResultOnly() + public void testFind_findAllInSelection() { - Finder f = new Finder(al, null); + /* + * select sequences 2 and 3, columns 4-6 which contains + * BCD + * cdE + */ + SequenceGroup sg = new SequenceGroup(); + sg.setStartRes(3); + sg.setEndRes(5); + sg.addSequence(al.getSequenceAt(1), false); + sg.addSequence(al.getSequenceAt(2), false); + + /* + * search for 'e' should match two sequence ids and one residue + */ + Finder f = new Finder(al, sg); f.setFindAll(true); - f.find("M+"); + f.find("e"); + assertEquals(f.getIdMatch().size(), 2); + assertSame(f.getIdMatch().get(0), al.getSequenceAt(1)); + assertSame(f.getIdMatch().get(1), al.getSequenceAt(2)); SearchResultsI searchResults = f.getSearchResults(); assertEquals(searchResults.getSize(), 1); SearchResultMatchI match = searchResults.getResults().get(0); - assertSame(al.getSequenceAt(3), match.getSequence()); - assertEquals(4, match.getStart()); // dataset sequence positions - assertEquals(8, match.getEnd()); // base 1 + assertSame(al.getSequenceAt(2), match.getSequence()); + assertEquals(4, match.getStart()); + assertEquals(4, match.getEnd()); + + /* + * search for 'Q' should match two sequence ids only + */ + f = new Finder(al, sg); + f.setFindAll(true); + f.find("Q"); + assertEquals(f.getIdMatch().size(), 2); + assertSame(f.getIdMatch().get(0), al.getSequenceAt(1)); + assertSame(f.getIdMatch().get(1), al.getSequenceAt(2)); + assertTrue(f.getSearchResults().isEmpty()); + } + + /** + * Test finding in selection with a sequence too short to reach it + */ + @Test(groups = "Functional") + public void testFind_findAllInSelectionWithShortSequence() + { + /* + * select all sequences, columns 10-12 + * BCD + * cdE + */ + SequenceGroup sg = new SequenceGroup(); + sg.setStartRes(9); + sg.setEndRes(11); + sg.addSequence(al.getSequenceAt(0), false); + sg.addSequence(al.getSequenceAt(1), false); + sg.addSequence(al.getSequenceAt(2), false); + sg.addSequence(al.getSequenceAt(3), false); + + /* + * search for 'I' should match two sequence positions + */ + Finder f = new Finder(al, sg); + f.setFindAll(true); + f.find("I"); + assertTrue(f.getIdMatch().isEmpty()); + SearchResultsI searchResults = f.getSearchResults(); + assertEquals(searchResults.getSize(), 2); + SearchResultMatchI match = searchResults.getResults().get(0); + assertSame(al.getSequenceAt(0), match.getSequence()); + assertEquals(16, match.getStart()); + assertEquals(16, match.getEnd()); + match = searchResults.getResults().get(1); + assertSame(al.getSequenceAt(1), match.getSequence()); + assertEquals(8, match.getStart()); + assertEquals(8, match.getEnd()); } }