X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=test%2Fjalview%2Fanalysis%2FFinderTest.java;h=95e6c0dc52643b19ccd11da66fea2048f61d5275;hb=9e14537be510f8a57c22ea761ee7c1528d0ea486;hp=725be3352956cdca66d278c90ea6e4535ddc1dd6;hpb=bc07c82cde95d498cf6919422baf7ad3994e1bf2;p=jalview.git diff --git a/test/jalview/analysis/FinderTest.java b/test/jalview/analysis/FinderTest.java index 725be33..95e6c0d 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)); @@ -136,7 +136,7 @@ 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 +151,7 @@ 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 +196,7 @@ 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 +272,7 @@ 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 +320,7 @@ 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 +347,7 @@ 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 +359,7 @@ 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 +367,7 @@ 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 +375,7 @@ 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 +389,7 @@ 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); @@ -406,7 +406,7 @@ public class FinderTest 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 +422,7 @@ 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 +437,7 @@ 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 +465,7 @@ 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 +481,7 @@ 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); @@ -513,7 +513,7 @@ 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 +530,7 @@ 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 +538,7 @@ 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); @@ -572,7 +572,7 @@ 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 +616,7 @@ 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); @@ -652,7 +652,7 @@ 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 +674,7 @@ 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 +696,7 @@ 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 +715,7 @@ 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 +740,7 @@ 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); @@ -783,7 +783,7 @@ 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); @@ -823,8 +823,10 @@ 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 +839,8 @@ 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 +852,8 @@ 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 +865,12 @@ 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 @@ -891,7 +896,8 @@ public class FinderTest av.setSelectionGroup(selection); f.findAll("A.*H", false, false, true); searchResults = f.getSearchResults(); - assertEquals(searchResults.getSize(), 3); + 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));