JAL-2933 pass viewport in Finder constructor, find acts on viewport selection if any

diff --git a/src/jalview/analysis/Finder.java b/src/jalview/analysis/Finder.java
index 0996830..3cbef6d 100644 (file)
--- a/src/jalview/analysis/Finder.java
+++ b/src/jalview/analysis/Finder.java
@@ -20,6 +20,7 @@
  */
 package jalview.analysis;
 
+import jalview.api.AlignViewportI;
 import jalview.api.FinderI;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Range;
@@ -52,14 +53,9 @@ public class Finder implements FinderI
   private Vector<SequenceI> idMatches;
 
   /*
-   * the alignment to search over
+   * the viewport to search over
    */
-  private AlignmentI alignment;
-
-  /*
-   * (optional) selection to restrict search to
-   */
-  private SequenceGroup selection;
+  private AlignViewportI viewport;
 
   /*
    * sequence index in alignment to search from
@@ -74,20 +70,20 @@ public class Finder implements FinderI
   private int columnIndex;
 
   /**
-   * Constructor for searching an alignment
+   * Constructor for searching a viewport
    * 
-   * @param al
+   * @param av
    */
-  public Finder(AlignmentI al)
+  public Finder(AlignViewportI av)
   {
-    this.alignment = al;
+    this.viewport = av;
     this.sequenceIndex = 0;
     this.columnIndex = -1;
   }
 
   @Override
-  public void findAll(String theSearchString, SequenceGroup sg,
-          boolean matchCase, boolean searchDescription)
+  public void findAll(String theSearchString, boolean matchCase,
+          boolean searchDescription)
   {
     /*
      * search from the start
@@ -95,7 +91,7 @@ public class Finder implements FinderI
     sequenceIndex = 0;
     columnIndex = -1;
 
-    doFind(theSearchString, sg, matchCase, searchDescription, true);
+    doFind(theSearchString, matchCase, searchDescription, true);
 
     /*
      * reset to start for next search
@@ -105,10 +101,10 @@ public class Finder implements FinderI
   }
 
   @Override
-  public void findNext(String theSearchString, SequenceGroup sg,
-          boolean matchCase, boolean searchDescription)
+  public void findNext(String theSearchString, boolean matchCase,
+          boolean searchDescription)
   {
-    doFind(theSearchString, sg, matchCase, searchDescription, false);
+    doFind(theSearchString, matchCase, searchDescription, false);
     
     if (searchResults.isEmpty() && idMatches.isEmpty())
     {
@@ -121,19 +117,16 @@ public class Finder implements FinderI
   }
 
   /**
-   * Performs a 'find next' or 'find all', optionally restricted to the
-   * specified selection region
+   * Performs a 'find next' or 'find all'
    * 
    * @param theSearchString
-   * @param selectionRegion
    * @param matchCase
    * @param searchDescription
    * @param findAll
    */
-  protected void doFind(String theSearchString, SequenceGroup selectionRegion,
-          boolean matchCase, boolean searchDescription, boolean findAll)
+  protected void doFind(String theSearchString, boolean matchCase,
+          boolean searchDescription, boolean findAll)
   {
-    this.selection = selectionRegion;
     String searchString = matchCase ? theSearchString
             : theSearchString.toUpperCase();
     Regex searchPattern = new Regex(searchString);
@@ -142,11 +135,13 @@ public class Finder implements FinderI
     searchResults = new SearchResults();
     idMatches = new Vector<>();
 
+    SequenceGroup selection = viewport.getSelectionGroup();
     if (selection != null && selection.getSize() < 1)
     {
       selection = null; // ? ignore column-only selection
     }
 
+    AlignmentI alignment = viewport.getAlignment();
     int end = alignment.getHeight();
 
     while (sequenceIndex < end)
@@ -184,6 +179,7 @@ public class Finder implements FinderI
      * restrict search to (next) visible column region, 
      * in case there are hidden columns
      */
+    AlignmentI alignment = viewport.getAlignment();
     VisibleContigsIterator visibleRegions = alignment.getHiddenColumns()
             .getVisContigsIterator(column, alignment.getWidth(),
                     false);
@@ -199,6 +195,7 @@ public class Finder implements FinderI
     /*
      * restrict search to selected region if there is one
      */
+    SequenceGroup selection = viewport.getSelectionGroup();
     if (selection != null)
     {
       int selectionStart = selection.getStartRes();
@@ -233,6 +230,7 @@ public class Finder implements FinderI
   protected boolean findNextMatch(SequenceI seq, String searchString,
           Regex searchPattern, boolean matchDescription)
   {
+    SequenceGroup selection = viewport.getSelectionGroup();
     if (selection != null && !selection.contains(seq))
     {
       /*

diff --git a/src/jalview/api/FinderI.java b/src/jalview/api/FinderI.java
index a1a3efd..19f6136 100644 (file)
--- a/src/jalview/api/FinderI.java
+++ b/src/jalview/api/FinderI.java
@@ -1,7 +1,6 @@
 package jalview.api;
 
 import jalview.datamodel.SearchResultsI;
-import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 
 import java.util.List;
@@ -16,7 +15,7 @@ public interface FinderI
    * Performs a find for the given search string (interpreted as a regular
    * expression). Search may optionally be case-sensitive, and may optionally
    * including match in sequence description (sequence id is always searched).
-   * If <code>selection</code> is not null, then the find is restricted to the
+   * If the viewport has an active selection, then the find is restricted to the
    * selection region. Sequences matched by id or description can be retrieved
    * by getIdMatches(), and matched residue patterns by getSearchResults().
    * 
@@ -25,26 +24,25 @@ public interface FinderI
    * @param searchDescription
    * @return
    */
-  void findAll(String theSearchString, SequenceGroup selection,
-          boolean caseSensitive, boolean searchDescription);
+  void findAll(String theSearchString, boolean caseSensitive,
+          boolean searchDescription);
 
   /**
    * Finds the next match for the given search string (interpreted as a regular
    * expression), starting from the position after the last match found. Search
    * may optionally be case-sensitive, and may optionally including match in
-   * sequence description (sequence id is always searched). If
-   * <code>selection</code> is not null, then the find is restricted to the
-   * selection region. Sequences matched by id or description can be retrieved
-   * by getIdMatches(), and matched residue patterns by getSearchResults().
+   * sequence description (sequence id is always searched). If the viewport has
+   * an active selection, then the find is restricted to the selection region.
+   * Sequences matched by id or description can be retrieved by getIdMatches(),
+   * and matched residue patterns by getSearchResults().
    * 
    * @param theSearchString
-   * @param selection
    * @param caseSensitive
    * @param searchDescription
    * @return
    */
-  void findNext(String theSearchString, SequenceGroup selection,
-          boolean caseSensitive, boolean searchDescription);
+  void findNext(String theSearchString, boolean caseSensitive,
+          boolean searchDescription);
 
   /**
    * Returns the (possibly empty) list of sequences matched on sequence name or

diff --git a/src/jalview/appletgui/Finder.java b/src/jalview/appletgui/Finder.java
index 4b55574..2fc3441 100644 (file)
--- a/src/jalview/appletgui/Finder.java
+++ b/src/jalview/appletgui/Finder.java
@@ -25,7 +25,6 @@ import jalview.api.FinderI;
 import jalview.datamodel.SearchResultMatchI;
 import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.SequenceFeature;
-import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.util.MessageManager;
 
@@ -163,23 +162,20 @@ public class Finder extends Panel implements ActionListener
       /*
        * first time we searched this viewport
        */
-      finder = new jalview.analysis.Finder(av.getAlignment());
+      finder = new jalview.analysis.Finder(av);
       finders.put(av, finder);
     }
 
     String searchString = textfield.getText();
-    SequenceGroup selectionGroup = av.getSelectionGroup();
     boolean isCaseSensitive = caseSensitive.getState();
     boolean doSearchDescription = searchDescription.getState();
     if (doFindAll)
     {
-      finder.findAll(searchString, selectionGroup, isCaseSensitive,
-              doSearchDescription);
+      finder.findAll(searchString, isCaseSensitive, doSearchDescription);
     }
     else
     {
-      finder.findNext(searchString, selectionGroup, isCaseSensitive,
-              doSearchDescription);
+      finder.findNext(searchString, isCaseSensitive, doSearchDescription);
     }
 
     searchResults = finder.getSearchResults();

diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java
index dcc3518..a4d7ad0 100755 (executable)
--- a/src/jalview/gui/Finder.java
+++ b/src/jalview/gui/Finder.java
@@ -25,7 +25,6 @@ import jalview.api.FinderI;
 import jalview.datamodel.SearchResultMatchI;
 import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.SequenceFeature;
-import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.jbgui.GFinder;
 import jalview.util.MessageManager;
@@ -269,22 +268,19 @@ public class Finder extends GFinder
       /*
        * first time we've searched this viewport
        */
-      finder = new jalview.analysis.Finder(av.getAlignment());
+      finder = new jalview.analysis.Finder(av);
       finders.put(av, finder);
     }
 
-    SequenceGroup selectionGroup = av.getSelectionGroup();
     boolean isCaseSensitive = caseSensitive.isSelected();
     boolean doSearchDescription = searchDescription.isSelected();
     if (doFindAll)
     {
-      finder.findAll(searchString, selectionGroup, isCaseSensitive,
-              doSearchDescription);
+      finder.findAll(searchString, isCaseSensitive, doSearchDescription);
     }
     else
     {
-      finder.findNext(searchString, selectionGroup, isCaseSensitive,
-              doSearchDescription);
+      finder.findNext(searchString, isCaseSensitive, doSearchDescription);
     }
 
     searchResults = finder.getSearchResults();

diff --git a/test/jalview/analysis/FinderTest.java b/test/jalview/analysis/FinderTest.java
index e453dd3..e2a94ef 100644 (file)
--- a/test/jalview/analysis/FinderTest.java
+++ b/test/jalview/analysis/FinderTest.java
@@ -24,6 +24,7 @@ import static org.testng.Assert.assertEquals;
 import static org.testng.Assert.assertSame;
 import static org.testng.Assert.assertTrue;
 
+import jalview.api.AlignViewportI;
 import jalview.api.FinderI;
 import jalview.bin.Cache;
 import jalview.datamodel.Alignment;
@@ -35,12 +36,14 @@ import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceGroup;
 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;
 
@@ -59,6 +62,8 @@ public class FinderTest
 
   private AlignmentI al;
 
+  private AlignViewportI av;
+
   @BeforeClass(groups = "Functional")
   public void setUp()
   {
@@ -70,7 +75,14 @@ public class FinderTest
             + "seq3 --bcdEFH\n" + "seq4 aa---aMMMMMaaa\n";
     af = new FileLoader().LoadFileWaitTillLoaded(seqData,
             DataSourceType.PASTE);
-    al = af.getViewport().getAlignment();
+    av = af.getViewport();
+    al = av.getAlignment();
+  }
+
+  @AfterMethod
+  public void tearDownAfterTest()
+  {
+    av.setSelectionGroup(null);
   }
 
   /**
@@ -82,8 +94,8 @@ public class FinderTest
     /*
      * find next match only
      */
-    Finder f = new Finder(al);
-    f.findNext("E.H", null, false, false); // 'E, any character, H'
+    Finder f = new Finder(av);
+    f.findNext("E.H", false, false); // 'E, any character, H'
     // should match seq2 efH only
     SearchResultsI sr = f.getSearchResults();
     assertEquals(sr.getSize(), 1);
@@ -92,8 +104,8 @@ public class FinderTest
     assertEquals(matches.get(0).getStart(), 5);
     assertEquals(matches.get(0).getEnd(), 7);
 
-    f = new Finder(al);
-    f.findAll("E.H", null, false, false); // 'E, any character, H'
+    f = new Finder(av);
+    f.findAll("E.H", false, false); // 'E, any character, H'
     // should match seq2 efH and seq3 EFH
     sr = f.getSearchResults();
     assertEquals(sr.getSize(), 2);
@@ -112,12 +124,12 @@ public class FinderTest
   @Test(groups = "Functional")
   public void testFind_residueNumber()
   {
-    Finder f = new Finder(al);
+    Finder f = new Finder(av);
 
     /*
      * find first match should return seq1 residue 9
      */
-    f.findNext("9", null, false, false);
+    f.findNext("9", false, false);
     SearchResultsI sr = f.getSearchResults();
     assertEquals(sr.getSize(), 1);
     List<SearchResultMatchI> matches = sr.getResults();
@@ -128,8 +140,8 @@ public class FinderTest
     /*
      * find all matches should return seq1 and seq4 (others are too short)
      */
-    f = new Finder(al);
-    f.findAll("9", null, false, false);
+    f = new Finder(av);
+    f.findAll("9", false, false);
     sr = f.getSearchResults();
     assertEquals(sr.getSize(), 2);
     matches = sr.getResults();
@@ -143,8 +155,8 @@ public class FinderTest
     /*
      * parsing of search string as integer is strict
      */
-    f = new Finder(al);
-    f.findNext(" 9", null, false, false);
+    f = new Finder(av);
+    f.findNext(" 9", false, false);
     assertTrue(f.getSearchResults().isEmpty());
   }
 
@@ -158,10 +170,10 @@ public class FinderTest
      * start at second sequence; colIndex of -1
      * means sequence id / description is searched
      */
-    Finder f = new Finder(al);
+    Finder f = new Finder(av);
     PA.setValue(f, "sequenceIndex", 1);
     PA.setValue(f, "columnIndex", -1);
-    f.findNext("e", null, false, false); // matches id
+    f.findNext("e", false, false); // matches id
 
     assertTrue(f.getSearchResults().isEmpty());
     assertEquals(f.getIdMatches().size(), 1);
@@ -170,10 +182,10 @@ public class FinderTest
     // colIndex is now 0 - for use in next find next
     // searching A--BCDefHI
     assertEquals(PA.getValue(f, "columnIndex"), 0);
-    f = new Finder(al);
+    f = new Finder(av);
     PA.setValue(f, "sequenceIndex", 1);
     PA.setValue(f, "columnIndex", 0);
-    f.findNext("e", null, false, false); // matches in sequence
+    f.findNext("e", false, false); // matches in sequence
     assertTrue(f.getIdMatches().isEmpty());
     assertEquals(f.getSearchResults().getSize(), 1);
     List<SearchResultMatchI> matches = f.getSearchResults().getResults();
@@ -186,10 +198,10 @@ public class FinderTest
     assertEquals(PA.getValue(f, "columnIndex"), 7);
 
     // find next from end of sequence - finds next sequence id
-    f = new Finder(al);
+    f = new Finder(av);
     PA.setValue(f, "sequenceIndex", 1);
     PA.setValue(f, "columnIndex", 7);
-    f.findNext("e", null, false, false);
+    f.findNext("e", false, false);
     assertEquals(f.getIdMatches().size(), 1);
     assertSame(f.getIdMatches().get(0), al.getSequenceAt(2));
     assertTrue(f.getSearchResults().isEmpty());
@@ -205,11 +217,13 @@ public class FinderTest
     al2.getSequenceAt(0).setDescription("BRAF");
     al2.getSequenceAt(1).setDescription("braf");
 
+    AlignViewportI av2 = new AlignViewport(al2);
+
     /*
      * find first match only
      */
-    Finder f = new Finder(al2);
-    f.findNext("rAF", null, false, true);
+    Finder f = new Finder(av2);
+    f.findNext("rAF", false, true);
     assertEquals(f.getIdMatches().size(), 1);
     assertSame(f.getIdMatches().get(0), al2.getSequenceAt(0));
     assertTrue(f.getSearchResults().isEmpty());
@@ -217,8 +231,8 @@ public class FinderTest
     /*
      * find all matches
      */
-    f = new Finder(al2);
-    f.findAll("rAF", null, false, true);
+    f = new Finder(av2);
+    f.findAll("rAF", false, true);
     assertEquals(f.getIdMatches().size(), 2);
     assertSame(f.getIdMatches().get(0), al2.getSequenceAt(0));
     assertSame(f.getIdMatches().get(1), al2.getSequenceAt(1));
@@ -227,8 +241,8 @@ public class FinderTest
     /*
      * case sensitive
      */
-    f = new Finder(al2);
-    f.findAll("RAF", null, true, true);
+    f = new Finder(av2);
+    f.findAll("RAF", true, true);
     assertEquals(f.getIdMatches().size(), 1);
     assertSame(f.getIdMatches().get(0), al2.getSequenceAt(0));
     assertTrue(f.getSearchResults().isEmpty());
@@ -239,12 +253,12 @@ public class FinderTest
     al2.getSequenceAt(0).setDescription("the efh sequence");
     al2.getSequenceAt(0).setName("mouseEFHkinase");
     al2.getSequenceAt(1).setName("humanEFHkinase");
-    f = new Finder(al2);
+    f = new Finder(av2);
 
     /*
      * sequence matches should have no duplicates
      */
-    f.findAll("EFH", null, false, true);
+    f.findAll("EFH", false, true);
     assertEquals(f.getIdMatches().size(), 2);
     assertSame(f.getIdMatches().get(0), al2.getSequenceAt(0));
     assertSame(f.getIdMatches().get(1), al2.getSequenceAt(1));
@@ -266,13 +280,13 @@ public class FinderTest
   @Test(groups = "Functional")
   public void testFindAll_sequenceIds()
   {
-    Finder f = new Finder(al);
+    Finder f = new Finder(av);
 
     /*
      * case insensitive; seq1 occurs twice in sequence id but
      * only one match should be returned
      */
-    f.findAll("SEQ1", null, false, false);
+    f.findAll("SEQ1", false, false);
     assertEquals(f.getIdMatches().size(), 1);
     assertSame(f.getIdMatches().get(0), al.getSequenceAt(0));
     SearchResultsI searchResults = f.getSearchResults();
@@ -281,8 +295,8 @@ public class FinderTest
     /*
      * case sensitive
      */
-    f = new Finder(al);
-    f.findAll("SEQ1", null, true, false);
+    f = new Finder(av);
+    f.findAll("SEQ1", true, false);
     searchResults = f.getSearchResults();
     assertTrue(searchResults.isEmpty());
 
@@ -290,9 +304,10 @@ public class FinderTest
      * match both sequence id and sequence
      */
     AlignmentI al2 = new Alignment(al);
+    AlignViewportI av2 = new AlignViewport(al2);
     al2.addSequence(new Sequence("aBz", "xyzabZpqrAbZ"));
-    f = new Finder(al2);
-    f.findAll("ABZ", null, false, false);
+    f = new Finder(av2);
+    f.findAll("ABZ", false, false);
     assertEquals(f.getIdMatches().size(), 1);
     assertSame(f.getIdMatches().get(0), al2.getSequenceAt(4));
     searchResults = f.getSearchResults();
@@ -316,8 +331,8 @@ public class FinderTest
     /*
      * efh should be matched in seq2 only
      */
-    FinderI f = new Finder(al);
-    f.findNext("EfH", null, false, false);
+    FinderI f = new Finder(av);
+    f.findNext("EfH", false, false);
     SearchResultsI searchResults = f.getSearchResults();
     assertEquals(searchResults.getSize(), 1);
     SearchResultMatchI match = searchResults.getResults().get(0);
@@ -328,8 +343,8 @@ public class FinderTest
     /*
      * I should be found in seq1 (twice) and seq2 (once)
      */
-    f = new Finder(al);
-    f.findNext("I", null, false, false); // find next: seq1/16
+    f = new Finder(av);
+    f.findNext("I", false, false); // find next: seq1/16
     searchResults = f.getSearchResults();
     assertEquals(searchResults.getSize(), 1);
     match = searchResults.getResults().get(0);
@@ -337,7 +352,7 @@ public class FinderTest
     assertEquals(match.getStart(), 16);
     assertEquals(match.getEnd(), 16);
 
-    f.findNext("I", null, false, false); // find next: seq1/18
+    f.findNext("I", false, false); // find next: seq1/18
     searchResults = f.getSearchResults();
     assertEquals(searchResults.getSize(), 1);
     match = searchResults.getResults().get(0);
@@ -345,7 +360,7 @@ public class FinderTest
     assertEquals(match.getStart(), 18);
     assertEquals(match.getEnd(), 18);
 
-    f.findNext("I", null, false, false); // find next: seq2/8
+    f.findNext("I", false, false); // find next: seq2/8
     searchResults = f.getSearchResults();
     assertEquals(searchResults.getSize(), 1);
     match = searchResults.getResults().get(0);
@@ -353,13 +368,13 @@ public class FinderTest
     assertEquals(match.getStart(), 8);
     assertEquals(match.getEnd(), 8);
 
-    f.findNext("I", null, false, false);
+    f.findNext("I", false, false);
     assertTrue(f.getSearchResults().isEmpty());
 
     /*
      * find should reset to start of alignment after a failed search
      */
-    f.findNext("I", null, false, false); // find next: seq1/16
+    f.findNext("I", false, false); // find next: seq1/16
     searchResults = f.getSearchResults();
     assertEquals(searchResults.getSize(), 1);
     match = searchResults.getResults().get(0);
@@ -375,8 +390,8 @@ public class FinderTest
   @Test(groups = "Functional")
   public void testFind_maximalResultOnly()
   {
-    Finder f = new Finder(al);
-    f.findAll("M+", null, false, false);
+    Finder f = new Finder(av);
+    f.findAll("M+", false, false);
     SearchResultsI searchResults = f.getSearchResults();
     assertEquals(searchResults.getSize(), 1);
     SearchResultMatchI match = searchResults.getResults().get(0);
@@ -391,8 +406,8 @@ public class FinderTest
   @Test(groups = "Functional")
   public void testFind_findAll()
   {
-    Finder f = new Finder(al);
-    f.findAll("EfH", null, false, false);
+    Finder f = new Finder(av);
+    f.findAll("EfH", false, false);
     SearchResultsI searchResults = f.getSearchResults();
     assertEquals(searchResults.getSize(), 2);
     SearchResultMatchI match = searchResults.getResults().get(0);
@@ -407,7 +422,7 @@ public class FinderTest
     /*
      * find all I should find 2 positions in seq1, 1 in seq2
      */
-    f.findAll("I", null, false, false);
+    f.findAll("I", false, false);
     searchResults = f.getSearchResults();
     assertEquals(searchResults.getSize(), 3);
     match = searchResults.getResults().get(0);
@@ -430,12 +445,12 @@ public class FinderTest
   @Test(groups = "Functional")
   public void testFind_findAllCaseSensitive()
   {
-    Finder f = new Finder(al);
+    Finder f = new Finder(av);
 
     /*
      * BC should match seq1/9-10 and seq2/2-3
      */
-    f.findAll("BC", null, true, false);
+    f.findAll("BC", true, false);
     SearchResultsI searchResults = f.getSearchResults();
     assertEquals(searchResults.getSize(), 2);
     SearchResultMatchI match = searchResults.getResults().get(0);
@@ -450,8 +465,8 @@ public class FinderTest
     /*
      * bc should match seq3/1-2
      */
-    f = new Finder(al);
-    f.findAll("bc", null, true, false);
+    f = new Finder(av);
+    f.findAll("bc", true, false);
     searchResults = f.getSearchResults();
     assertEquals(searchResults.getSize(), 1);
     match = searchResults.getResults().get(0);
@@ -459,7 +474,7 @@ public class FinderTest
     assertEquals(match.getStart(), 1);
     assertEquals(match.getEnd(), 2);
 
-    f.findAll("bC", null, true, false);
+    f.findAll("bC", true, false);
     assertTrue(f.getSearchResults().isEmpty());
   }
 
@@ -479,9 +494,10 @@ public class FinderTest
     sg.setEndRes(5);
     sg.addSequence(al.getSequenceAt(1), false);
     sg.addSequence(al.getSequenceAt(2), false);
+    av.setSelectionGroup(sg);
 
-    FinderI f = new Finder(al);
-    f.findNext("b", sg, false, false);
+    FinderI f = new Finder(av);
+    f.findNext("b", false, false);
     assertTrue(f.getIdMatches().isEmpty());
     SearchResultsI searchResults = f.getSearchResults();
     assertEquals(searchResults.getSize(), 1);
@@ -493,12 +509,12 @@ public class FinderTest
     /*
      * a second Find should not return the 'b' in seq3 as outside the selection
      */
-    f.findNext("b", sg, false, false);
+    f.findNext("b", false, false);
     assertTrue(f.getSearchResults().isEmpty());
     assertTrue(f.getIdMatches().isEmpty());
 
-    f = new Finder(al);
-    f.findNext("d", sg, false, false);
+    f = new Finder(av);
+    f.findNext("d", false, false);
     assertTrue(f.getIdMatches().isEmpty());
     searchResults = f.getSearchResults();
     assertEquals(searchResults.getSize(), 1);
@@ -506,7 +522,7 @@ public class FinderTest
     assertSame(match.getSequence(), al.getSequenceAt(1));
     assertEquals(match.getStart(), 4);
     assertEquals(match.getEnd(), 4);
-    f.findNext("d", sg, false, false);
+    f.findNext("d", false, false);
     assertTrue(f.getIdMatches().isEmpty());
     searchResults = f.getSearchResults();
     assertEquals(searchResults.getSize(), 1);
@@ -532,12 +548,13 @@ public class FinderTest
     sg.setEndRes(5);
     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(al);
-    f.findAll("e", sg, false, false);
+    Finder f = new Finder(av);
+    f.findAll("e", false, false);
     assertEquals(f.getIdMatches().size(), 2);
     assertSame(f.getIdMatches().get(0), al.getSequenceAt(1));
     assertSame(f.getIdMatches().get(1), al.getSequenceAt(2));
@@ -551,8 +568,8 @@ public class FinderTest
     /*
      * search for 'Q' should match two sequence ids only
      */
-    f = new Finder(al);
-    f.findAll("Q", sg, false, false);
+    f = new Finder(av);
+    f.findAll("Q", false, false);
     assertEquals(f.getIdMatches().size(), 2);
     assertSame(f.getIdMatches().get(0), al.getSequenceAt(1));
     assertSame(f.getIdMatches().get(1), al.getSequenceAt(2));
@@ -577,12 +594,13 @@ public class FinderTest
     sg.addSequence(al.getSequenceAt(1), false);
     sg.addSequence(al.getSequenceAt(2), false);
     sg.addSequence(al.getSequenceAt(3), false);
-  
+    av.setSelectionGroup(sg);
+
     /*
      * search for 'I' should match two sequence positions
      */
-    Finder f = new Finder(al);
-    f.findAll("I", sg, false, false);
+    Finder f = new Finder(av);
+    f.findAll("I", false, false);
     assertTrue(f.getIdMatches().isEmpty());
     SearchResultsI searchResults = f.getSearchResults();
     assertEquals(searchResults.getSize(), 2);
@@ -621,8 +639,8 @@ public class FinderTest
      * find all search for D should ignore hidden positions in seq1 and seq3,
      * find the visible D in seq2
      */
-    Finder f = new Finder(al);
-    f.findAll("D", null, false, false);
+    Finder f = new Finder(av);
+    f.findAll("D", false, false);
     SearchResultsI searchResults = f.getSearchResults();
     assertEquals(searchResults.getSize(), 1);
     SearchResultMatchI match = searchResults.getResults().get(0);
@@ -635,8 +653,8 @@ public class FinderTest
      * find all 'aaa' should find end of seq4 only
      */
     hc.hideColumns(2, 5);
-    f = new Finder(al);
-    f.findAll("aaa", null, false, false);
+    f = new Finder(av);
+    f.findAll("aaa", false, false);
     searchResults = f.getSearchResults();
     assertEquals(searchResults.getSize(), 1);
     match = searchResults.getResults().get(0);
@@ -647,7 +665,7 @@ public class FinderTest
     /*
      * find all 'BE' should not match across hidden columns in seq1
      */
-    f.findAll("BE", null, false, false);
+    f.findAll("BE", false, false);
     assertTrue(f.getSearchResults().isEmpty());
 
     /*
@@ -656,8 +674,8 @@ public class FinderTest
      */
     hc.revealAllHiddenColumns(new ColumnSelection());
     hc.hideColumns(8, 13);
-    f = new Finder(al);
-    f.findNext("H", null, false, false);
+    f = new Finder(av);
+    f.findNext("H", false, false);
     searchResults = f.getSearchResults();
     assertEquals(searchResults.getSize(), 1);
     match = searchResults.getResults().get(0);
@@ -693,13 +711,14 @@ public class FinderTest
     sg.addSequence(al.getSequenceAt(2), false);
     sg.setStartRes(0);
     sg.setEndRes(13);
+    av.setSelectionGroup(sg);
 
     /*
      * find all search for A or H
      * should match seq2/1, seq2/7, not seq3/6
      */
-    Finder f = new Finder(al);
-    f.findAll("[AH]", sg, false, false);
+    Finder f = new Finder(av);
+    f.findAll("[AH]", false, false);
     SearchResultsI searchResults = f.getSearchResults();
     assertEquals(searchResults.getSize(), 2);
     SearchResultMatchI match = searchResults.getResults().get(0);

diff --git a/test/jalview/controller/AlignViewControllerTest.java b/test/jalview/controller/AlignViewControllerTest.java
index ad86f32..2669c99 100644 (file)
--- a/test/jalview/controller/AlignViewControllerTest.java
+++ b/test/jalview/controller/AlignViewControllerTest.java
@@ -223,8 +223,8 @@ public class AlignViewControllerTest
     /*
      *  test Match/Find works first
      */
-    FinderI f = new Finder(af.getViewport().getAlignment());
-    f.findAll("M+", null, true, false);
+    FinderI f = new Finder(af.getViewport());
+    f.findAll("M+", true, false);
     assertEquals(
             "Finder found different set of results to manually created SearchResults",
             sr, f.getSearchResults());