X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fanalysis%2FFinderTest.java;h=7e3bd86f2e341cc9ffd2e50396d3d5b2631defa1;hb=5faac1104c41690e38e259fae5bb700236021360;hp=78a27acfbc1ff08d08f4305dd818b058fa91b761;hpb=4016a0a5baf92cea3f1303fdaae3804244857427;p=jalview.git diff --git a/test/jalview/analysis/FinderTest.java b/test/jalview/analysis/FinderTest.java index 78a27ac..7e3bd86 100644 --- a/test/jalview/analysis/FinderTest.java +++ b/test/jalview/analysis/FinderTest.java @@ -103,7 +103,7 @@ public class FinderTest 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); @@ -113,7 +113,7 @@ public class FinderTest 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)); @@ -123,6 +123,20 @@ 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); + SearchResultsI sr = f.getSearchResults(); + assertEquals(sr.getCount(), 5); + + } + /** * Test for (undocumented) find residue by position */ @@ -136,7 +150,7 @@ public class FinderTest */ 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); @@ -151,7 +165,7 @@ public class FinderTest 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)); @@ -196,7 +210,7 @@ public class FinderTest PA.setValue(f, "residueIndex", 0); f.findNext("e", 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); @@ -272,7 +286,7 @@ public class FinderTest 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); @@ -320,7 +334,7 @@ public class FinderTest 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); @@ -347,7 +361,7 @@ public class FinderTest 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); @@ -359,7 +373,7 @@ public class FinderTest 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); @@ -367,7 +381,7 @@ public class FinderTest 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); @@ -375,7 +389,7 @@ public class FinderTest 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); @@ -389,7 +403,7 @@ public class FinderTest */ 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); @@ -401,12 +415,12 @@ 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); 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 @@ -422,7 +436,7 @@ public class FinderTest 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); @@ -437,7 +451,7 @@ public class FinderTest */ 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); @@ -465,7 +479,7 @@ public class FinderTest */ 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); @@ -481,7 +495,7 @@ public class FinderTest 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); @@ -495,7 +509,7 @@ 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 @@ -513,7 +527,7 @@ public class FinderTest 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); @@ -530,7 +544,7 @@ public class FinderTest 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); @@ -538,7 +552,7 @@ public class FinderTest 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); @@ -549,7 +563,7 @@ 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 @@ -562,7 +576,7 @@ 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 */ @@ -572,7 +586,7 @@ public class FinderTest 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); @@ -616,7 +630,7 @@ public class FinderTest 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); @@ -628,8 +642,8 @@ 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() @@ -652,7 +666,7 @@ public class FinderTest Finder f = new Finder(av); f.findAll("aaa", 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); @@ -674,7 +688,7 @@ public class FinderTest f = new Finder(av); f.findAll("D", 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); @@ -696,7 +710,7 @@ public class FinderTest f = new Finder(av); f.findAll("aaa", 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); @@ -715,7 +729,7 @@ public class FinderTest f = new Finder(av); f.findAll("aaa", 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); @@ -740,7 +754,7 @@ public class FinderTest 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); @@ -757,7 +771,7 @@ public class FinderTest * --bcdEFH * aa---aMMMMMaaa */ - + /* * hide columns 2-4 and 6-7 */ @@ -765,7 +779,7 @@ public class FinderTest hc.hideColumns(2, 4); hc.hideColumns(6, 7); al.setHiddenColumns(hc); - + /* * select rows 2-3 */ @@ -783,7 +797,7 @@ public class FinderTest 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); @@ -795,7 +809,7 @@ public class FinderTest } @Test(groups = "Functional") - public void testFind_skipHiddenColumns() + public void testFind_ignoreHiddenColumns() { /* * 0 5 9 @@ -823,8 +837,10 @@ public class FinderTest /* * match of seq1 ABE made up of AB and E + * note only one match is counted */ - assertEquals(searchResults.getSize(), 2); + 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 @@ -837,7 +853,8 @@ public class FinderTest f = new Finder(av); f.findNext("a.E", false, false, true); searchResults = f.getSearchResults(); - assertEquals(searchResults.getSize(), 2); + 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 @@ -849,7 +866,8 @@ public class FinderTest f.findNext("a.E", false, false, true); searchResults = f.getSearchResults(); - assertEquals(searchResults.getSize(), 2); + 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 @@ -861,11 +879,12 @@ public class FinderTest /* * find all matching across two hidden column regions - * note one 'match' is reported as three contiguous matches + * note one 'match' is returned as three contiguous matches */ f.findAll("BEG", false, false, true); searchResults = f.getSearchResults(); - assertEquals(searchResults.getSize(), 3); + 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 @@ -878,5 +897,33 @@ public class FinderTest 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); } }