X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fanalysis%2FFinderTest.java;h=764c56f7ee90e6709b5ede4827cb01f8eb061281;hb=7428d315297907b3bb52ddb099a348acffb87636;hp=f05bfb329116492bc7b852c483f954cade5c2cca;hpb=1e856963b6c483b5e73c44e9b7b6d4d44b30bae8;p=jalview.git diff --git a/test/jalview/analysis/FinderTest.java b/test/jalview/analysis/FinderTest.java index f05bfb3..764c56f 100644 --- a/test/jalview/analysis/FinderTest.java +++ b/test/jalview/analysis/FinderTest.java @@ -24,6 +24,8 @@ import static org.testng.Assert.assertEquals; import static org.testng.Assert.assertSame; import static org.testng.Assert.assertTrue; +import jalview.api.AlignViewportI; +import jalview.api.FinderI; import jalview.bin.Cache; import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentI; @@ -34,15 +36,19 @@ import jalview.datamodel.SearchResultsI; import jalview.datamodel.Sequence; import jalview.datamodel.SequenceGroup; import jalview.gui.AlignFrame; +import jalview.gui.AlignViewport; import jalview.gui.JvOptionPane; import jalview.io.DataSourceType; import jalview.io.FileLoader; import java.util.List; +import org.testng.annotations.AfterMethod; import org.testng.annotations.BeforeClass; import org.testng.annotations.Test; +import junit.extensions.PA; + public class FinderTest { @BeforeClass(alwaysRun = true) @@ -56,6 +62,8 @@ public class FinderTest private AlignmentI al; + private AlignViewportI av; + @BeforeClass(groups = "Functional") public void setUp() { @@ -63,11 +71,33 @@ public class FinderTest Cache.applicationProperties.setProperty("PAD_GAPS", Boolean.FALSE.toString()); - String seqData = "seq1seq1/8-18 ABCD--EF-GHIJI\n" + "seq2 A--BCDefHI\n" - + "seq3 --bcdEFH\n" + "seq4 aa---aMMMMMaaa\n"; + //@formatter:off + String seqData = + "seq1/8-18 ABCD--EF-GHIJI\n" + + "seq2 A--BCDefHI\n" + + "seq3 --bcdEFH\n" + + "seq4 aa---aMMMMMaaa\n"; + //@formatter:on af = new FileLoader().LoadFileWaitTillLoaded(seqData, DataSourceType.PASTE); - al = af.getViewport().getAlignment(); + av = af.getViewport(); + al = av.getAlignment(); + + // JAL-3765 bug test data + String longSeqData = + ">O80429_MAIZE/2-140 Ferredoxin\n" + + "AAT---------ALSMSILR---APPPCFSSPLRLRV--AVAKPLA-APMRRQLLRAQATYNVKLITPEGEV\n" + + "ELQVPDDVYILDFAEEEGIDLPFSCRAGSCSSCAGKVVSGSVDQSDQSFLNDNQVADGWVLTCAAYPTSDVV\n" + + "IETHKEDDLL--\n" ; + af_oneseq=new FileLoader().LoadFileWaitTillLoaded(longSeqData, DataSourceType.PASTE); + av_oneseq = af_oneseq.getViewport(); + al_oneseq = av_oneseq.getAlignment(); + } + + @AfterMethod(alwaysRun = true) + public void tearDownAfterTest() + { + av.setSelectionGroup(null); } /** @@ -79,22 +109,21 @@ public class FinderTest /* * find next match only */ - Finder f = new Finder(al, null); - f.find("E.H"); // 'E, any character, H' + Finder f = new Finder(av); + f.findNext("E.H", false, false, false); // 'E, any character, H' // should match seq2 efH only SearchResultsI sr = f.getSearchResults(); - assertEquals(sr.getSize(), 1); + assertEquals(sr.getCount(), 1); List matches = sr.getResults(); assertSame(matches.get(0).getSequence(), al.getSequenceAt(1)); 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' + f = new Finder(av); + f.findAll("E.H", false, false, false); // 'E, any character, H' // should match seq2 efH and seq3 EFH sr = f.getSearchResults(); - assertEquals(sr.getSize(), 2); + assertEquals(sr.getCount(), 2); matches = sr.getResults(); assertSame(matches.get(0).getSequence(), al.getSequenceAt(1)); assertSame(matches.get(1).getSequence(), al.getSequenceAt(2)); @@ -110,14 +139,14 @@ public class FinderTest @Test(groups = "Functional") public void testFind_residueNumber() { - Finder f = new Finder(al, null); + Finder f = new Finder(av); /* * find first match should return seq1 residue 9 */ - f.find("9"); + f.findNext("9", false, false, false); SearchResultsI sr = f.getSearchResults(); - assertEquals(sr.getSize(), 1); + assertEquals(sr.getCount(), 1); List matches = sr.getResults(); assertSame(matches.get(0).getSequence(), al.getSequenceAt(0)); assertEquals(matches.get(0).getStart(), 9); @@ -125,12 +154,14 @@ public class FinderTest /* * find all matches should return seq1 and seq4 (others are too short) + * (and not matches in sequence ids) */ - f = new Finder(al, null); - f.setFindAll(true); - f.find("9"); + f = new Finder(av); + String name = al.getSequenceAt(0).getName(); + al.getSequenceAt(0).setName("Q9XA0"); + f.findAll("9", false, false, false); sr = f.getSearchResults(); - assertEquals(sr.getSize(), 2); + assertEquals(sr.getCount(), 2); matches = sr.getResults(); assertSame(matches.get(0).getSequence(), al.getSequenceAt(0)); assertSame(matches.get(1).getSequence(), al.getSequenceAt(3)); @@ -138,12 +169,13 @@ public class FinderTest assertEquals(matches.get(0).getEnd(), 9); assertEquals(matches.get(1).getStart(), 9); assertEquals(matches.get(1).getEnd(), 9); + al.getSequenceAt(0).setName(name); /* * parsing of search string as integer is strict */ - f = new Finder(al, null); - f.find(" 9"); + f = new Finder(av); + f.findNext(" 9", false, false, false); assertTrue(f.getSearchResults().isEmpty()); } @@ -154,37 +186,43 @@ public class FinderTest public void testFindNext() { /* - * start at second sequence; colIndex of -1 + * start at second sequence; residueIndex of -1 * means sequence id / description is searched */ - Finder f = new Finder(al, null, 1, -1); - f.find("e"); // matches id + Finder f = new Finder(av); + PA.setValue(f, "sequenceIndex", 1); + PA.setValue(f, "residueIndex", -1); + f.findNext("e", false, false, false); // matches id assertTrue(f.getSearchResults().isEmpty()); - assertEquals(f.getIdMatch().size(), 1); - assertSame(f.getIdMatch().get(0), al.getSequenceAt(1)); + assertEquals(f.getIdMatches().size(), 1); + assertSame(f.getIdMatches().get(0), al.getSequenceAt(1)); - // colIndex is now 0 - for use in next find next + // residueIndex is now 0 - for use in next find next // searching A--BCDefHI - assertEquals(f.getColumnIndex(), 0); - f = new Finder(al, null, 1, 0); - f.find("e"); // matches in sequence - assertTrue(f.getIdMatch().isEmpty()); - assertEquals(f.getSearchResults().getSize(), 1); + assertEquals(PA.getValue(f, "residueIndex"), 0); + f = new Finder(av); + PA.setValue(f, "sequenceIndex", 1); + PA.setValue(f, "residueIndex", 0); + f.findNext("e", false, false, false); // matches in sequence + assertTrue(f.getIdMatches().isEmpty()); + assertEquals(f.getSearchResults().getCount(), 1); List matches = f.getSearchResults().getResults(); assertEquals(matches.get(0).getStart(), 5); assertEquals(matches.get(0).getEnd(), 5); assertSame(matches.get(0).getSequence(), al.getSequenceAt(1)); // still in the second sequence - assertEquals(f.getSequenceIndex(), 1); - // next column position to search from is 7 - assertEquals(f.getColumnIndex(), 7); + assertEquals(PA.getValue(f, "sequenceIndex"), 1); + // next residue offset to search from is 5 + assertEquals(PA.getValue(f, "residueIndex"), 5); // find next from end of sequence - finds next sequence id - f = new Finder(al, null, 1, 7); - f.find("e"); - assertEquals(f.getIdMatch().size(), 1); - assertSame(f.getIdMatch().get(0), al.getSequenceAt(2)); + f = new Finder(av); + PA.setValue(f, "sequenceIndex", 1); + PA.setValue(f, "residueIndex", 7); + f.findNext("e", false, false, false); + assertEquals(f.getIdMatches().size(), 1); + assertSame(f.getIdMatches().get(0), al.getSequenceAt(2)); assertTrue(f.getSearchResults().isEmpty()); } @@ -198,39 +236,34 @@ public class FinderTest al2.getSequenceAt(0).setDescription("BRAF"); al2.getSequenceAt(1).setDescription("braf"); + AlignViewportI av2 = new AlignViewport(al2); + /* * find first match only */ - Finder f = new Finder(al2, null); - f.setIncludeDescription(true); - f.find("rAF"); - assertEquals(f.getIdMatch().size(), 1); - assertSame(f.getIdMatch().get(0), al2.getSequenceAt(0)); + Finder f = new Finder(av2); + f.findNext("rAF", false, true, false); + assertEquals(f.getIdMatches().size(), 1); + assertSame(f.getIdMatches().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)); - assertSame(f.getIdMatch().get(1), al2.getSequenceAt(1)); + f = new Finder(av2); + f.findAll("rAF", false, true, false); + assertEquals(f.getIdMatches().size(), 2); + assertSame(f.getIdMatches().get(0), al2.getSequenceAt(0)); + assertSame(f.getIdMatches().get(1), al2.getSequenceAt(1)); assertTrue(f.getSearchResults().isEmpty()); /* * case sensitive */ - f = new Finder(al2, null); - f.setFindAll(true); - f.setCaseSensitive(true); - f.setIncludeDescription(true); - - f.find("RAF"); - assertEquals(f.getIdMatch().size(), 1); - assertSame(f.getIdMatch().get(0), al2.getSequenceAt(0)); + f = new Finder(av2); + f.findAll("RAF", true, true, false); + assertEquals(f.getIdMatches().size(), 1); + assertSame(f.getIdMatches().get(0), al2.getSequenceAt(0)); assertTrue(f.getSearchResults().isEmpty()); /* @@ -239,19 +272,17 @@ public class FinderTest al2.getSequenceAt(0).setDescription("the efh sequence"); al2.getSequenceAt(0).setName("mouseEFHkinase"); al2.getSequenceAt(1).setName("humanEFHkinase"); - f = new Finder(al2, null); - f.setFindAll(true); - f.setIncludeDescription(true); + f = new Finder(av2); /* * sequence matches should have no duplicates */ - f.find("EFH"); - assertEquals(f.getIdMatch().size(), 2); - assertSame(f.getIdMatch().get(0), al2.getSequenceAt(0)); - assertSame(f.getIdMatch().get(1), al2.getSequenceAt(1)); + f.findAll("EFH", false, true, false); + assertEquals(f.getIdMatches().size(), 2); + assertSame(f.getIdMatches().get(0), al2.getSequenceAt(0)); + assertSame(f.getIdMatches().get(1), al2.getSequenceAt(1)); - assertEquals(f.getSearchResults().getSize(), 2); + assertEquals(f.getSearchResults().getCount(), 2); SearchResultMatchI match = f.getSearchResults().getResults().get(0); assertSame(match.getSequence(), al2.getSequenceAt(1)); assertEquals(match.getStart(), 5); @@ -268,26 +299,23 @@ public class FinderTest @Test(groups = "Functional") public void testFindAll_sequenceIds() { - Finder f = new Finder(al, null); - f.setFindAll(true); + Finder f = new Finder(av); /* * case insensitive; seq1 occurs twice in sequence id but * only one match should be returned */ - f.find("SEQ1"); - assertEquals(f.getIdMatch().size(), 1); - assertSame(f.getIdMatch().get(0), al.getSequenceAt(0)); + f.findAll("SEQ1", false, false, false); + assertEquals(f.getIdMatches().size(), 1); + assertSame(f.getIdMatches().get(0), al.getSequenceAt(0)); SearchResultsI searchResults = f.getSearchResults(); assertTrue(searchResults.isEmpty()); /* * case sensitive */ - f = new Finder(al, null); - f.setFindAll(true); - f.setCaseSensitive(true); - f.find("SEQ1"); + f = new Finder(av); + f.findAll("SEQ1", true, false, false); searchResults = f.getSearchResults(); assertTrue(searchResults.isEmpty()); @@ -295,14 +323,14 @@ public class FinderTest * match both sequence id and sequence */ AlignmentI al2 = new Alignment(al); + AlignViewportI av2 = new AlignViewport(al2); al2.addSequence(new Sequence("aBz", "xyzabZpqrAbZ")); - f = new Finder(al2, null); - f.setFindAll(true); - f.find("ABZ"); - assertEquals(f.getIdMatch().size(), 1); - assertSame(f.getIdMatch().get(0), al2.getSequenceAt(4)); + f = new Finder(av2); + f.findAll("ABZ", false, false, false); + assertEquals(f.getIdMatches().size(), 1); + assertSame(f.getIdMatches().get(0), al2.getSequenceAt(4)); searchResults = f.getSearchResults(); - assertEquals(searchResults.getSize(), 2); + assertEquals(searchResults.getCount(), 2); SearchResultMatchI match = searchResults.getResults().get(0); assertSame(match.getSequence(), al2.getSequenceAt(4)); assertEquals(match.getStart(), 4); @@ -319,13 +347,17 @@ public class FinderTest @Test(groups = "Functional") public void testFind_findNext() { + // "seq1/8-18 ABCD--EF-GHIJI\n" + + // "seq2 A--BCDefHI\n" + + // "seq3 --bcdEFH\n" + + // "seq4 aa---aMMMMMaaa\n"; /* * efh should be matched in seq2 only */ - Finder f = new Finder(al, null); - f.find("EfH"); + FinderI f = new Finder(av); + f.findNext("EfH", false, false, false); SearchResultsI searchResults = f.getSearchResults(); - assertEquals(searchResults.getSize(), 1); + assertEquals(searchResults.getCount(), 1); SearchResultMatchI match = searchResults.getResults().get(0); assertSame(match.getSequence(), al.getSequenceAt(1)); assertEquals(match.getStart(), 5); @@ -334,33 +366,44 @@ public class FinderTest /* * I should be found in seq1 (twice) and seq2 (once) */ - f = new Finder(al, null); - f.find("I"); // find next: seq1/16 + f = new Finder(av); + f.findNext("I", false, false, false); // find next: seq1/16 searchResults = f.getSearchResults(); - assertEquals(searchResults.getSize(), 1); + assertEquals(searchResults.getCount(), 1); match = searchResults.getResults().get(0); assertSame(match.getSequence(), al.getSequenceAt(0)); assertEquals(match.getStart(), 16); assertEquals(match.getEnd(), 16); - f.find("I"); // find next: seq1/18 + f.findNext("I", false, false, false); // find next: seq1/18 searchResults = f.getSearchResults(); - assertEquals(searchResults.getSize(), 1); + assertEquals(searchResults.getCount(), 1); match = searchResults.getResults().get(0); assertSame(match.getSequence(), al.getSequenceAt(0)); assertEquals(match.getStart(), 18); assertEquals(match.getEnd(), 18); - f.find("I"); // find next: seq2/8 + f.findNext("I", false, false, false); // find next: seq2/8 searchResults = f.getSearchResults(); - assertEquals(searchResults.getSize(), 1); + assertEquals(searchResults.getCount(), 1); match = searchResults.getResults().get(0); assertSame(match.getSequence(), al.getSequenceAt(1)); assertEquals(match.getStart(), 8); assertEquals(match.getEnd(), 8); - f.find("I"); + f.findNext("I", false, false, false); assertTrue(f.getSearchResults().isEmpty()); + + /* + * find should reset to start of alignment after a failed search + */ + f.findNext("I", false, false, false); // find next: seq1/16 + searchResults = f.getSearchResults(); + assertEquals(searchResults.getCount(), 1); + match = searchResults.getResults().get(0); + assertSame(match.getSequence(), al.getSequenceAt(0)); + assertEquals(match.getStart(), 16); + assertEquals(match.getEnd(), 16); } /** @@ -368,13 +411,12 @@ public class FinderTest * result */ @Test(groups = "Functional") - public void testFind_maximalResultOnly() + public void testFindAll_maximalResultOnly() { - Finder f = new Finder(al, null); - f.setFindAll(true); - f.find("M+"); + Finder f = new Finder(av); + f.findAll("M+", false, false, false); SearchResultsI searchResults = f.getSearchResults(); - assertEquals(searchResults.getSize(), 1); + assertEquals(searchResults.getCount(), 1); SearchResultMatchI match = searchResults.getResults().get(0); assertSame(match.getSequence(), al.getSequenceAt(3)); assertEquals(match.getStart(), 4); // dataset sequence positions @@ -385,13 +427,12 @@ public class FinderTest * Test finding all matches of a sequence pattern in an alignment */ @Test(groups = "Functional") - public void testFind_findAll() + public void testFindAll() { - Finder f = new Finder(al, null); - f.setFindAll(true); - f.find("EfH"); + Finder f = new Finder(av); + f.findAll("EfH", false, false, false); SearchResultsI searchResults = f.getSearchResults(); - assertEquals(searchResults.getSize(), 2); + assertEquals(searchResults.getCount(), 2); SearchResultMatchI match = searchResults.getResults().get(0); assertSame(match.getSequence(), al.getSequenceAt(1)); assertEquals(match.getStart(), 5); @@ -404,9 +445,9 @@ public class FinderTest /* * find all I should find 2 positions in seq1, 1 in seq2 */ - f.find("I"); + f.findAll("I", false, false, false); searchResults = f.getSearchResults(); - assertEquals(searchResults.getSize(), 3); + assertEquals(searchResults.getCount(), 3); match = searchResults.getResults().get(0); assertSame(match.getSequence(), al.getSequenceAt(0)); assertEquals(match.getStart(), 16); @@ -425,18 +466,16 @@ public class FinderTest * Test finding all matches, case-sensitive */ @Test(groups = "Functional") - public void testFind_findAllCaseSensitive() + public void testFindAll_caseSensitive() { - Finder f = new Finder(al, null); - f.setCaseSensitive(true); - f.setFindAll(true); + Finder f = new Finder(av); /* * BC should match seq1/9-10 and seq2/2-3 */ - f.find("BC"); + f.findAll("BC", true, false, false); SearchResultsI searchResults = f.getSearchResults(); - assertEquals(searchResults.getSize(), 2); + assertEquals(searchResults.getCount(), 2); SearchResultMatchI match = searchResults.getResults().get(0); assertSame(match.getSequence(), al.getSequenceAt(0)); assertEquals(match.getStart(), 9); @@ -449,18 +488,16 @@ public class FinderTest /* * bc should match seq3/1-2 */ - f = new Finder(al, null); - f.setCaseSensitive(true); - f.setFindAll(true); - f.find("bc"); + f = new Finder(av); + f.findAll("bc", true, false, false); searchResults = f.getSearchResults(); - assertEquals(searchResults.getSize(), 1); + assertEquals(searchResults.getCount(), 1); match = searchResults.getResults().get(0); assertSame(match.getSequence(), al.getSequenceAt(2)); assertEquals(match.getStart(), 1); assertEquals(match.getEnd(), 2); - f.find("bC"); + f.findAll("bC", true, false, false); assertTrue(f.getSearchResults().isEmpty()); } @@ -468,7 +505,7 @@ public class FinderTest * Test finding next match of a sequence pattern in a selection group */ @Test(groups = "Functional") - public void testFind_inSelection() + public void testFindNext_inSelection() { /* * select sequences 2 and 3, columns 4-6 which contains @@ -480,12 +517,13 @@ public class FinderTest sg.setEndRes(5); sg.addSequence(al.getSequenceAt(1), false); sg.addSequence(al.getSequenceAt(2), false); + av.setSelectionGroup(sg); - Finder f = new Finder(al, sg); - f.find("b"); - assertTrue(f.getIdMatch().isEmpty()); + FinderI f = new Finder(av); + f.findNext("b", false, false, false); + assertTrue(f.getIdMatches().isEmpty()); SearchResultsI searchResults = f.getSearchResults(); - assertEquals(searchResults.getSize(), 1); + assertEquals(searchResults.getCount(), 1); SearchResultMatchI match = searchResults.getResults().get(0); assertSame(match.getSequence(), al.getSequenceAt(1)); assertEquals(match.getStart(), 2); @@ -494,23 +532,23 @@ public class FinderTest /* * a second Find should not return the 'b' in seq3 as outside the selection */ - f.find("b"); + f.findNext("b", false, false, false); assertTrue(f.getSearchResults().isEmpty()); - assertTrue(f.getIdMatch().isEmpty()); + assertTrue(f.getIdMatches().isEmpty()); - f = new Finder(al, sg); - f.find("d"); - assertTrue(f.getIdMatch().isEmpty()); + f = new Finder(av); + f.findNext("d", false, false, false); + assertTrue(f.getIdMatches().isEmpty()); searchResults = f.getSearchResults(); - assertEquals(searchResults.getSize(), 1); + assertEquals(searchResults.getCount(), 1); match = searchResults.getResults().get(0); assertSame(match.getSequence(), al.getSequenceAt(1)); assertEquals(match.getStart(), 4); assertEquals(match.getEnd(), 4); - f.find("d"); - assertTrue(f.getIdMatch().isEmpty()); + f.findNext("d", false, false, false); + assertTrue(f.getIdMatches().isEmpty()); searchResults = f.getSearchResults(); - assertEquals(searchResults.getSize(), 1); + assertEquals(searchResults.getCount(), 1); match = searchResults.getResults().get(0); assertSame(match.getSequence(), al.getSequenceAt(2)); assertEquals(match.getStart(), 3); @@ -521,7 +559,7 @@ public class FinderTest * Test finding all matches of a search pattern in a selection group */ @Test(groups = "Functional") - public void testFind_findAllInSelection() + public void testFindAll_inSelection() { /* * select sequences 2 and 3, columns 4-6 which contains @@ -533,18 +571,18 @@ public class FinderTest sg.setEndRes(5); sg.addSequence(al.getSequenceAt(1), false); sg.addSequence(al.getSequenceAt(2), false); + av.setSelectionGroup(sg); /* * search for 'e' should match two sequence ids and one residue */ - Finder f = new Finder(al, sg); - f.setFindAll(true); - f.find("e"); - assertEquals(f.getIdMatch().size(), 2); - assertSame(f.getIdMatch().get(0), al.getSequenceAt(1)); - assertSame(f.getIdMatch().get(1), al.getSequenceAt(2)); + Finder f = new Finder(av); + f.findAll("e", false, false, false); + assertEquals(f.getIdMatches().size(), 2); + assertSame(f.getIdMatches().get(0), al.getSequenceAt(1)); + assertSame(f.getIdMatches().get(1), al.getSequenceAt(2)); SearchResultsI searchResults = f.getSearchResults(); - assertEquals(searchResults.getSize(), 1); + assertEquals(searchResults.getCount(), 1); SearchResultMatchI match = searchResults.getResults().get(0); assertSame(match.getSequence(), al.getSequenceAt(2)); assertEquals(match.getStart(), 4); @@ -553,12 +591,11 @@ public class FinderTest /* * 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)); + f = new Finder(av); + f.findAll("Q", false, false, false); + assertEquals(f.getIdMatches().size(), 2); + assertSame(f.getIdMatches().get(0), al.getSequenceAt(1)); + assertSame(f.getIdMatches().get(1), al.getSequenceAt(2)); assertTrue(f.getSearchResults().isEmpty()); } @@ -580,16 +617,16 @@ public class FinderTest sg.addSequence(al.getSequenceAt(1), false); sg.addSequence(al.getSequenceAt(2), false); sg.addSequence(al.getSequenceAt(3), false); - + av.setSelectionGroup(sg); + /* * search for 'I' should match two sequence positions */ - Finder f = new Finder(al, sg); - f.setFindAll(true); - f.find("I"); - assertTrue(f.getIdMatch().isEmpty()); + Finder f = new Finder(av); + f.findAll("I", false, false, false); + assertTrue(f.getIdMatches().isEmpty()); SearchResultsI searchResults = f.getSearchResults(); - assertEquals(searchResults.getSize(), 2); + assertEquals(searchResults.getCount(), 2); SearchResultMatchI match = searchResults.getResults().get(0); assertSame(match.getSequence(), al.getSequenceAt(0)); assertEquals(match.getStart(), 16); @@ -601,7 +638,8 @@ public class FinderTest } /** - * Test that find does not report hidden positions + * Test that find does not report hidden positions, but does report matches that + * span hidden gaps */ @Test(groups = "Functional") public void testFind_withHiddenColumns() @@ -615,44 +653,92 @@ public class FinderTest */ /* - * hide 2-4 (CD- -BC bcd ---) + * hide column 3 only, search for aaa + * should find two matches: aa-[-]-aa and trailing aaa */ HiddenColumns hc = new HiddenColumns(); - hc.hideColumns(2, 4); + hc.hideColumns(3, 3); al.setHiddenColumns(hc); + Finder f = new Finder(av); + f.findAll("aaa", false, false, false); + SearchResultsI searchResults = f.getSearchResults(); + assertEquals(searchResults.getCount(), 2); + SearchResultMatchI match = searchResults.getResults().get(0); + assertSame(match.getSequence(), al.getSequenceAt(3)); + assertEquals(match.getStart(), 1); + assertEquals(match.getEnd(), 3); + match = searchResults.getResults().get(1); + assertSame(match.getSequence(), al.getSequenceAt(3)); + assertEquals(match.getStart(), 9); + assertEquals(match.getEnd(), 11); + + /* + * hide 2-4 (CD- -BC bcd ---) + */ + hc.hideColumns(2, 4); /* * find all search for D should ignore hidden positions in seq1 and seq3, * find the visible D in seq2 */ - Finder f = new Finder(al, null); - f.setFindAll(true); - f.find("D"); - SearchResultsI searchResults = f.getSearchResults(); - assertEquals(searchResults.getSize(), 1); - SearchResultMatchI match = searchResults.getResults().get(0); + f = new Finder(av); + f.findAll("D", false, false, false); + searchResults = f.getSearchResults(); + assertEquals(searchResults.getCount(), 1); + match = searchResults.getResults().get(0); assertSame(match.getSequence(), al.getSequenceAt(1)); assertEquals(match.getStart(), 4); assertEquals(match.getEnd(), 4); /* + * search for AD should fail although these are now + * consecutive in the visible columns + */ + f = new Finder(av); + f.findAll("AD", false, false, false); + searchResults = f.getSearchResults(); + assertTrue(searchResults.isEmpty()); + + /* + * find all 'aaa' should find both start and end of seq4 + * (first run includes hidden gaps) + */ + f = new Finder(av); + f.findAll("aaa", false, false, false); + searchResults = f.getSearchResults(); + assertEquals(searchResults.getCount(), 2); + match = searchResults.getResults().get(0); + assertSame(match.getSequence(), al.getSequenceAt(3)); + assertEquals(match.getStart(), 1); + assertEquals(match.getEnd(), 3); + match = searchResults.getResults().get(1); + assertSame(match.getSequence(), al.getSequenceAt(3)); + assertEquals(match.getStart(), 9); + assertEquals(match.getEnd(), 11); + + /* * hide columns 2-5: - * find all 'aaa' should find end of seq4 only + * find all 'aaa' should match twice in seq4 + * (first match partly hidden, second all visible) */ hc.hideColumns(2, 5); - f = new Finder(al, null); - f.find("aaa"); + f = new Finder(av); + f.findAll("aaa", false, false, false); searchResults = f.getSearchResults(); - assertEquals(searchResults.getSize(), 1); + assertEquals(searchResults.getCount(), 2); match = searchResults.getResults().get(0); assertSame(match.getSequence(), al.getSequenceAt(3)); + assertEquals(match.getStart(), 1); + assertEquals(match.getEnd(), 3); + match = searchResults.getResults().get(1); + assertSame(match.getSequence(), al.getSequenceAt(3)); assertEquals(match.getStart(), 9); assertEquals(match.getEnd(), 11); /* * find all 'BE' should not match across hidden columns in seq1 */ - f.find("BE"); + f.findAll("BE", false, false, false); assertTrue(f.getSearchResults().isEmpty()); /* @@ -661,10 +747,10 @@ public class FinderTest */ hc.revealAllHiddenColumns(new ColumnSelection()); hc.hideColumns(8, 13); - f = new Finder(al, null); - f.find("H"); + f = new Finder(av); + f.findNext("H", false, false, false); searchResults = f.getSearchResults(); - assertEquals(searchResults.getSize(), 1); + assertEquals(searchResults.getCount(), 1); match = searchResults.getResults().get(0); assertSame(match.getSequence(), al.getSequenceAt(2)); assertEquals(match.getStart(), 6); @@ -698,16 +784,16 @@ public class FinderTest sg.addSequence(al.getSequenceAt(2), false); sg.setStartRes(0); sg.setEndRes(13); + av.setSelectionGroup(sg); /* * find all search for A or H * should match seq2/1, seq2/7, not seq3/6 */ - Finder f = new Finder(al, sg); - f.setFindAll(true); - f.find("[AH]"); + Finder f = new Finder(av); + f.findAll("[AH]", false, false, false); SearchResultsI searchResults = f.getSearchResults(); - assertEquals(searchResults.getSize(), 2); + assertEquals(searchResults.getCount(), 2); SearchResultMatchI match = searchResults.getResults().get(0); assertSame(match.getSequence(), al.getSequenceAt(1)); assertEquals(match.getStart(), 1); @@ -717,4 +803,123 @@ public class FinderTest assertEquals(match.getStart(), 7); assertEquals(match.getEnd(), 7); } + + @Test(groups = "Functional") + public void testFind_ignoreHiddenColumns() + { + /* + * 0 5 9 + * ABCD--EF-GHI + * A--BCDefHI + * --bcdEFH + * aa---aMMMMMaaa + */ + HiddenColumns hc = new HiddenColumns(); + hc.hideColumns(2, 4); + hc.hideColumns(7, 7); + al.setHiddenColumns(hc); + + /* + * now have + * 015689 + * AB-E-GHI + * A-DeHI + * --EF + * aaaMMMMaaa + */ + Finder f = new Finder(av); + f.findAll("abe", false, false, true); // true = ignore hidden + SearchResultsI searchResults = f.getSearchResults(); + + /* + * match of seq1 ABE made up of AB and E + * note only one match is counted + */ + assertEquals(searchResults.getCount(), 1); + assertEquals(searchResults.getResults().size(), 2); + SearchResultMatchI match = searchResults.getResults().get(0); + assertSame(match.getSequence(), al.getSequenceAt(0)); + assertEquals(match.getStart(), 8); // A + assertEquals(match.getEnd(), 9); // B + match = searchResults.getResults().get(1); + assertSame(match.getSequence(), al.getSequenceAt(0)); + assertEquals(match.getStart(), 12); // E + assertEquals(match.getEnd(), 12); + + f = new Finder(av); + f.findNext("a.E", false, false, true); + searchResults = f.getSearchResults(); + assertEquals(searchResults.getCount(), 1); + assertEquals(searchResults.getResults().size(), 2); + match = searchResults.getResults().get(0); + assertSame(match.getSequence(), al.getSequenceAt(0)); + assertEquals(match.getStart(), 8); // A + assertEquals(match.getEnd(), 9); // B + match = searchResults.getResults().get(1); + assertSame(match.getSequence(), al.getSequenceAt(0)); + assertEquals(match.getStart(), 12); // E + assertEquals(match.getEnd(), 12); + + f.findNext("a.E", false, false, true); + searchResults = f.getSearchResults(); + assertEquals(searchResults.getCount(), 1); + assertEquals(searchResults.getResults().size(), 2); + match = searchResults.getResults().get(0); + assertSame(match.getSequence(), al.getSequenceAt(1)); + assertEquals(match.getStart(), 1); // a + assertEquals(match.getEnd(), 1); + match = searchResults.getResults().get(1); + assertSame(match.getSequence(), al.getSequenceAt(1)); + assertEquals(match.getStart(), 4); // D + assertEquals(match.getEnd(), 5); // e + + /* + * find all matching across two hidden column regions + * note one 'match' is returned as three contiguous matches + */ + f.findAll("BEG", false, false, true); + searchResults = f.getSearchResults(); + assertEquals(searchResults.getCount(), 1); + assertEquals(searchResults.getResults().size(), 3); + match = searchResults.getResults().get(0); + assertSame(match.getSequence(), al.getSequenceAt(0)); + assertEquals(match.getStart(), 9); // B + assertEquals(match.getEnd(), 9); + match = searchResults.getResults().get(1); + assertSame(match.getSequence(), al.getSequenceAt(0)); + assertEquals(match.getStart(), 12); // E + assertEquals(match.getEnd(), 12); + match = searchResults.getResults().get(2); + assertSame(match.getSequence(), al.getSequenceAt(0)); + assertEquals(match.getStart(), 14); // G + assertEquals(match.getEnd(), 14); + + /* + * now select columns 0-9 and search for A.*H + * this should match in the second sequence (split as 3 matches) + * but not the first (as H is outside the selection) + */ + SequenceGroup selection = new SequenceGroup(); + selection.setStartRes(0); + selection.setEndRes(9); + al.getSequences().forEach(seq -> selection.addSequence(seq, false)); + av.setSelectionGroup(selection); + f.findAll("A.*H", false, false, true); + searchResults = f.getSearchResults(); + assertEquals(searchResults.getCount(), 1); + assertEquals(searchResults.getResults().size(), 3); + // match made of contiguous matches A, DE, H + match = searchResults.getResults().get(0); + assertSame(match.getSequence(), al.getSequenceAt(1)); + assertEquals(match.getStart(), 1); // A + assertEquals(match.getEnd(), 1); + match = searchResults.getResults().get(1); + assertSame(match.getSequence(), al.getSequenceAt(1)); + assertEquals(match.getStart(), 4); // D + assertEquals(match.getEnd(), 5); // E + match = searchResults.getResults().get(2); + assertSame(match.getSequence(), al.getSequenceAt(1)); + assertEquals(match.getStart(), 7); // H (there is no G) + assertEquals(match.getEnd(), 7); + } }