JAL-4061 tests, bugfixes and TODOs for matching feature(s) and descriptions incrementally

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

diff --git a/test/jalview/analysis/FinderTest.java b/test/jalview/analysis/FinderTest.java
index 43c48d0..62e219d 100644 (file)
--- 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<SearchResultMatchI> 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<SearchResultMatchI> 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<SearchResultMatchI> 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 +814,155 @@ 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<SequenceI> 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);
+  }
 }