JAL-3490 match count independent of contiguous matches count

[jalview.git] / test / jalview / analysis / FinderTest.java

diff --git a/test/jalview/analysis/FinderTest.java b/test/jalview/analysis/FinderTest.java
index 725be33..95e6c0d 100644 (file)
--- 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<SearchResultMatchI> 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<SearchResultMatchI> 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<SearchResultMatchI> 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));