X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fanalysis%2FFinderTest.java;h=0220c36effdc8f951b2c3f6e7d20368731cd3127;hb=404d5b51a7a7781ad6924df6a7ce63c754370f16;hp=43c48d062b570324b06e40d2277bf5fa0a0f4ea4;hpb=b7014049e421026d0f2d57179af9688472cd78f2;p=jalview.git diff --git a/test/jalview/analysis/FinderTest.java b/test/jalview/analysis/FinderTest.java index 43c48d0..0220c36 100644 --- a/test/jalview/analysis/FinderTest.java +++ b/test/jalview/analysis/FinderTest.java @@ -24,6 +24,12 @@ import static org.testng.Assert.assertEquals; import static org.testng.Assert.assertSame; import static org.testng.Assert.assertTrue; +import java.util.List; + +import org.testng.annotations.AfterMethod; +import org.testng.annotations.BeforeClass; +import org.testng.annotations.Test; + import jalview.api.AlignViewportI; import jalview.api.FinderI; import jalview.bin.Cache; @@ -34,19 +40,14 @@ import jalview.datamodel.HiddenColumns; import jalview.datamodel.SearchResultMatchI; import jalview.datamodel.SearchResultsI; import jalview.datamodel.Sequence; +import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceGroup; +import jalview.datamodel.SequenceI; 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 @@ -82,6 +83,12 @@ public class FinderTest DataSourceType.PASTE); av = af.getViewport(); al = av.getAlignment(); + al.getSequenceAt(0).addSequenceFeature( + new SequenceFeature("BBBB", "FeatureB", 9, 11, "")); + al.getSequenceAt(3).addSequenceFeature( + new SequenceFeature("BBAB", "FeatureA", 1, 3, "")); + al.getSequenceAt(3).addSequenceFeature( + new SequenceFeature("AAAA", "FeatureA", 9, 11, "")); } @AfterMethod(alwaysRun = true) @@ -100,20 +107,20 @@ public class FinderTest * find next match only */ Finder f = new Finder(av); - f.findNext("E.H", false, false, false); // 'E, any character, H' + f.findNext("E.H", false, 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(av); - f.findAll("E.H", false, false, false); // 'E, any character, H' + f.findAll("E.H", false, 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)); @@ -123,6 +130,20 @@ public class FinderTest assertEquals(matches.get(1).getEnd(), 6); } + @Test(groups = "Functional") + public void testFind_findAll() + { + /* + * simple JAL-3765 test + * single symbol should find *all* matching symbols + */ + Finder f = new Finder(av); + f.findAll("M", false, false, false, false); + SearchResultsI sr = f.getSearchResults(); + assertEquals(sr.getCount(), 5); + + } + /** * Test for (undocumented) find residue by position */ @@ -134,9 +155,9 @@ public class FinderTest /* * find first match should return seq1 residue 9 */ - f.findNext("9", false, false, false); + f.findNext("9", false, 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); @@ -144,11 +165,14 @@ public class FinderTest /* * find all matches should return seq1 and seq4 (others are too short) + * (and not matches in sequence ids) */ f = new Finder(av); - f.findAll("9", false, false, false); + String name = al.getSequenceAt(0).getName(); + al.getSequenceAt(0).setName("Q9XA0"); + f.findAll("9", false, 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)); @@ -156,12 +180,13 @@ 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(av); - f.findNext(" 9", false, false, false); + f.findNext(" 9", false, false, false, false); assertTrue(f.getSearchResults().isEmpty()); } @@ -178,7 +203,7 @@ public class FinderTest Finder f = new Finder(av); PA.setValue(f, "sequenceIndex", 1); PA.setValue(f, "residueIndex", -1); - f.findNext("e", false, false, false); // matches id + f.findNext("e", false, false, false, false); // matches id assertTrue(f.getSearchResults().isEmpty()); assertEquals(f.getIdMatches().size(), 1); @@ -190,9 +215,9 @@ public class FinderTest f = new Finder(av); PA.setValue(f, "sequenceIndex", 1); PA.setValue(f, "residueIndex", 0); - f.findNext("e", false, false, false); // matches in sequence + f.findNext("e", false, false, false, false); // matches in sequence assertTrue(f.getIdMatches().isEmpty()); - assertEquals(f.getSearchResults().getSize(), 1); + assertEquals(f.getSearchResults().getCount(), 1); List matches = f.getSearchResults().getResults(); assertEquals(matches.get(0).getStart(), 5); assertEquals(matches.get(0).getEnd(), 5); @@ -206,7 +231,7 @@ public class FinderTest f = new Finder(av); PA.setValue(f, "sequenceIndex", 1); PA.setValue(f, "residueIndex", 7); - f.findNext("e", false, false, false); + f.findNext("e", false, false, false, false); assertEquals(f.getIdMatches().size(), 1); assertSame(f.getIdMatches().get(0), al.getSequenceAt(2)); assertTrue(f.getSearchResults().isEmpty()); @@ -228,7 +253,7 @@ public class FinderTest * find first match only */ Finder f = new Finder(av2); - f.findNext("rAF", false, true, false); + f.findNext("rAF", false, true, false, false); assertEquals(f.getIdMatches().size(), 1); assertSame(f.getIdMatches().get(0), al2.getSequenceAt(0)); assertTrue(f.getSearchResults().isEmpty()); @@ -237,7 +262,7 @@ public class FinderTest * find all matches */ f = new Finder(av2); - f.findAll("rAF", false, true, false); + f.findAll("rAF", false, true, false, false); assertEquals(f.getIdMatches().size(), 2); assertSame(f.getIdMatches().get(0), al2.getSequenceAt(0)); assertSame(f.getIdMatches().get(1), al2.getSequenceAt(1)); @@ -247,7 +272,7 @@ public class FinderTest * case sensitive */ f = new Finder(av2); - f.findAll("RAF", true, true, false); + f.findAll("RAF", true, true, false, false); assertEquals(f.getIdMatches().size(), 1); assertSame(f.getIdMatches().get(0), al2.getSequenceAt(0)); assertTrue(f.getSearchResults().isEmpty()); @@ -263,12 +288,12 @@ public class FinderTest /* * sequence matches should have no duplicates */ - f.findAll("EFH", false, true, false); + f.findAll("EFH", false, true, false, 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); @@ -291,7 +316,7 @@ public class FinderTest * case insensitive; seq1 occurs twice in sequence id but * only one match should be returned */ - f.findAll("SEQ1", false, false, false); + f.findAll("SEQ1", false, false, false, false); assertEquals(f.getIdMatches().size(), 1); assertSame(f.getIdMatches().get(0), al.getSequenceAt(0)); SearchResultsI searchResults = f.getSearchResults(); @@ -301,7 +326,7 @@ public class FinderTest * case sensitive */ f = new Finder(av); - f.findAll("SEQ1", true, false, false); + f.findAll("SEQ1", true, false, false, false); searchResults = f.getSearchResults(); assertTrue(searchResults.isEmpty()); @@ -312,11 +337,11 @@ public class FinderTest AlignViewportI av2 = new AlignViewport(al2); al2.addSequence(new Sequence("aBz", "xyzabZpqrAbZ")); f = new Finder(av2); - f.findAll("ABZ", false, false, false); + f.findAll("ABZ", false, 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); @@ -341,9 +366,9 @@ public class FinderTest * efh should be matched in seq2 only */ FinderI f = new Finder(av); - f.findNext("EfH", false, false, false); + f.findNext("EfH", false, 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); @@ -353,39 +378,39 @@ public class FinderTest * I should be found in seq1 (twice) and seq2 (once) */ f = new Finder(av); - f.findNext("I", false, false, false); // find next: seq1/16 + f.findNext("I", false, 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.findNext("I", false, false, false); // find next: seq1/18 + f.findNext("I", false, 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.findNext("I", false, false, false); // find next: seq2/8 + f.findNext("I", false, 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.findNext("I", false, false, false); + f.findNext("I", false, 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 + f.findNext("I", false, 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); @@ -397,12 +422,12 @@ public class FinderTest * result */ @Test(groups = "Functional") - public void testFind_maximalResultOnly() + public void testFindAll_maximalResultOnly() { Finder f = new Finder(av); - f.findAll("M+", false, false, false); + f.findAll("M+", false, 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 @@ -416,9 +441,9 @@ public class FinderTest public void testFindAll() { Finder f = new Finder(av); - f.findAll("EfH", false, false, false); + f.findAll("EfH", false, 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); @@ -431,9 +456,9 @@ public class FinderTest /* * find all I should find 2 positions in seq1, 1 in seq2 */ - f.findAll("I", false, false, false); + f.findAll("I", false, 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); @@ -452,16 +477,16 @@ public class FinderTest * Test finding all matches, case-sensitive */ @Test(groups = "Functional") - public void testFind_findAllCaseSensitive() + public void testFindAll_caseSensitive() { Finder f = new Finder(av); /* * BC should match seq1/9-10 and seq2/2-3 */ - f.findAll("BC", true, false, false); + f.findAll("BC", true, 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(0)); assertEquals(match.getStart(), 9); @@ -475,15 +500,15 @@ public class FinderTest * bc should match seq3/1-2 */ f = new Finder(av); - f.findAll("bc", true, false, false); + f.findAll("bc", true, 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(), 1); assertEquals(match.getEnd(), 2); - f.findAll("bC", true, false, false); + f.findAll("bC", true, false, false, false); assertTrue(f.getSearchResults().isEmpty()); } @@ -491,7 +516,7 @@ 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 @@ -506,10 +531,10 @@ public class FinderTest av.setSelectionGroup(sg); FinderI f = new Finder(av); - f.findNext("b", false, false, false); + f.findNext("b", false, 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); @@ -518,23 +543,23 @@ public class FinderTest /* * a second Find should not return the 'b' in seq3 as outside the selection */ - f.findNext("b", false, false, false); + f.findNext("b", false, false, false, false); assertTrue(f.getSearchResults().isEmpty()); assertTrue(f.getIdMatches().isEmpty()); f = new Finder(av); - f.findNext("d", false, false, false); + f.findNext("d", false, 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.findNext("d", false, false, false); + f.findNext("d", false, 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); @@ -545,7 +570,7 @@ 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 @@ -558,17 +583,17 @@ public class FinderTest 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(av); - f.findAll("e", false, false, false); + f.findAll("e", false, 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); @@ -578,7 +603,7 @@ public class FinderTest * search for 'Q' should match two sequence ids only */ f = new Finder(av); - f.findAll("Q", false, false, false); + f.findAll("Q", false, false, false, false); assertEquals(f.getIdMatches().size(), 2); assertSame(f.getIdMatches().get(0), al.getSequenceAt(1)); assertSame(f.getIdMatches().get(1), al.getSequenceAt(2)); @@ -609,10 +634,10 @@ public class FinderTest * search for 'I' should match two sequence positions */ Finder f = new Finder(av); - f.findAll("I", false, false, false); + f.findAll("I", false, 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); @@ -624,8 +649,8 @@ public class FinderTest } /** - * Test that find does not report hidden positions, but does report matches that - * span hidden gaps + * Test that find does not report hidden positions, but does report matches + * that span hidden gaps */ @Test(groups = "Functional") public void testFind_withHiddenColumns() @@ -646,9 +671,9 @@ public class FinderTest hc.hideColumns(3, 3); al.setHiddenColumns(hc); Finder f = new Finder(av); - f.findAll("aaa", false, false, false); + f.findAll("aaa", false, 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(3)); assertEquals(match.getStart(), 1); @@ -668,9 +693,9 @@ public class FinderTest * find the visible D in seq2 */ f = new Finder(av); - f.findAll("D", false, false, false); + f.findAll("D", false, false, false, false); 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); @@ -681,7 +706,7 @@ public class FinderTest * consecutive in the visible columns */ f = new Finder(av); - f.findAll("AD", false, false, false); + f.findAll("AD", false, false, false, false); searchResults = f.getSearchResults(); assertTrue(searchResults.isEmpty()); @@ -690,9 +715,9 @@ public class FinderTest * (first run includes hidden gaps) */ f = new Finder(av); - f.findAll("aaa", false, false, false); + f.findAll("aaa", false, false, false, false); searchResults = f.getSearchResults(); - assertEquals(searchResults.getSize(), 2); + assertEquals(searchResults.getCount(), 2); match = searchResults.getResults().get(0); assertSame(match.getSequence(), al.getSequenceAt(3)); assertEquals(match.getStart(), 1); @@ -709,9 +734,9 @@ public class FinderTest */ hc.hideColumns(2, 5); f = new Finder(av); - f.findAll("aaa", false, false, false); + f.findAll("aaa", false, false, false, false); searchResults = f.getSearchResults(); - assertEquals(searchResults.getSize(), 2); + assertEquals(searchResults.getCount(), 2); match = searchResults.getResults().get(0); assertSame(match.getSequence(), al.getSequenceAt(3)); assertEquals(match.getStart(), 1); @@ -724,7 +749,7 @@ public class FinderTest /* * find all 'BE' should not match across hidden columns in seq1 */ - f.findAll("BE", false, false, false); + f.findAll("BE", false, false, false, false); assertTrue(f.getSearchResults().isEmpty()); /* @@ -734,9 +759,9 @@ public class FinderTest hc.revealAllHiddenColumns(new ColumnSelection()); hc.hideColumns(8, 13); f = new Finder(av); - f.findNext("H", false, false, false); + f.findNext("H", false, 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); @@ -753,7 +778,7 @@ public class FinderTest * --bcdEFH * aa---aMMMMMaaa */ - + /* * hide columns 2-4 and 6-7 */ @@ -761,7 +786,7 @@ public class FinderTest hc.hideColumns(2, 4); hc.hideColumns(6, 7); al.setHiddenColumns(hc); - + /* * select rows 2-3 */ @@ -777,9 +802,9 @@ public class FinderTest * should match seq2/1, seq2/7, not seq3/6 */ Finder f = new Finder(av); - f.findAll("[AH]", false, false, false); + f.findAll("[AH]", false, 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); @@ -789,4 +814,179 @@ 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, 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, 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, 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, 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, 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); + } + + @Test(groups = "Functional") + public void testFind_featuresOnly() + { + Finder f = new Finder(av); + // no match when not searching feature descriptions + f.findAll("Feature", false, false, false, true); + assertEquals(f.getSearchResults().getCount(), 0); + + // no match when case sensitive on feature descriptions + f.findAll("feature", true, false, true, true); + assertEquals(f.getSearchResults().getCount(), 0); + + // search feature descriptions - all match + f.findAll("Feature", false, false, true, true); + assertEquals(f.getSearchResults().getCount(), 3); + + List seqs = f.getSearchResults().getMatchingSubSequences(); + // assume order is preserved in results + assertEquals(al.getSequenceAt(0).getDatasetSequence(), + seqs.get(0).getDatasetSequence()); + assertEquals(seqs.get(0).getStart(), 9); + assertEquals(seqs.get(0).getEnd(), 11); + assertEquals(al.getSequenceAt(3).getDatasetSequence(), + seqs.get(1).getDatasetSequence()); + assertEquals(seqs.get(1).getStart(), 9); + assertEquals(seqs.get(1).getEnd(), 11); + assertEquals(al.getSequenceAt(3).getDatasetSequence(), + seqs.get(2).getDatasetSequence()); + assertEquals(seqs.get(2).getStart(), 1); + assertEquals(seqs.get(2).getEnd(), 3); + + SequenceI sq = null; + // search feature descriptions incrementally + // assume same order as before + f.findNext("Feature", false, false, true, true); + assertEquals(f.getSearchResults().getCount(), 1); + sq = f.getSearchResults().getMatchingSubSequences().get(0); + assertEquals(sq.getSequenceAsString(), + seqs.get(0).getSequenceAsString()); + + // .. + f.findNext("Feature", false, false, true, true); + assertEquals(f.getSearchResults().getCount(), 1); + sq = f.getSearchResults().getMatchingSubSequences().get(0); + assertEquals(sq.getSequenceAsString(), + seqs.get(1).getSequenceAsString()); + + // .. + f.findNext("Feature", false, false, true, true); + assertEquals(f.getSearchResults().getCount(), 1); + sq = f.getSearchResults().getMatchingSubSequences().get(0); + assertEquals(sq.getSequenceAsString(), + seqs.get(2).getSequenceAsString()); + + } }