JAL-3765 simple test that findAll finds all matches for a pattern when it is present...

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

diff --git a/test/jalview/analysis/FinderTest.java b/test/jalview/analysis/FinderTest.java
index 78a27ac..764c56f 100644 (file)
--- a/test/jalview/analysis/FinderTest.java
+++ b/test/jalview/analysis/FinderTest.java
@@ -82,6 +82,16 @@ public class FinderTest
             DataSourceType.PASTE);
     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)
@@ -103,7 +113,7 @@ 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 +123,7 @@ 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 +146,7 @@ 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 +161,7 @@ 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 +206,7 @@ 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 +282,7 @@ 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 +330,7 @@ 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 +357,7 @@ 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 +369,7 @@ 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 +377,7 @@ 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 +385,7 @@ 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 +399,7 @@ 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 +411,12 @@ 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 +432,7 @@ 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 +447,7 @@ 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 +475,7 @@ 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 +491,7 @@ 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 +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
@@ -513,7 +523,7 @@ 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 +540,7 @@ 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 +548,7 @@ 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 +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
@@ -572,7 +582,7 @@ 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 +626,7 @@ 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 +662,7 @@ 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 +684,7 @@ 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 +706,7 @@ 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 +725,7 @@ 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 +750,7 @@ 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 +793,7 @@ 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 +805,7 @@ public class FinderTest
   }
 
   @Test(groups = "Functional")
-  public void testFind_skipHiddenColumns()
+  public void testFind_ignoreHiddenColumns()
   {
     /*
      * 0    5   9
@@ -823,8 +833,10 @@ 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 +849,8 @@ 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 +862,8 @@ 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 +875,12 @@ 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 +893,33 @@ 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);
   }
 }