JAL-4061 JAL-4062 Find can now search features

diff --git a/src/jalview/analysis/Finder.java b/src/jalview/analysis/Finder.java
index f8cfcbf..ee296d7 100644 (file)
--- a/src/jalview/analysis/Finder.java
+++ b/src/jalview/analysis/Finder.java
@@ -20,26 +20,27 @@
  */
 package jalview.analysis;
 
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Iterator;
+import java.util.List;
 import java.util.Locale;
 
+import com.stevesoft.pat.Regex;
+
 import jalview.api.AlignViewportI;
 import jalview.api.FinderI;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SearchResultMatchI;
 import jalview.datamodel.SearchResults;
 import jalview.datamodel.SearchResultsI;
+import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
+import jalview.datamodel.features.SequenceFeaturesI;
 import jalview.util.Comparison;
 import jalview.util.MapList;
 
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Iterator;
-import java.util.List;
-
-import com.stevesoft.pat.Regex;
-
 /**
  * Implements the search algorithm for the Find dialog
  */
@@ -99,7 +100,8 @@ public class Finder implements FinderI
 
   @Override
   public void findAll(String theSearchString, boolean matchCase,
-          boolean searchDescription, boolean ignoreHidden)
+          boolean searchDescription, boolean searchFeatureDesc,
+          boolean ignoreHidden)
   {
     /*
      * search from the start
@@ -107,8 +109,8 @@ public class Finder implements FinderI
     sequenceIndex = 0;
     residueIndex = -1;
 
-    doFind(theSearchString, matchCase, searchDescription, true,
-            ignoreHidden);
+    doFind(theSearchString, matchCase, searchDescription, searchFeatureDesc,
+            true, ignoreHidden);
 
     /*
      * reset to start for next search
@@ -119,10 +121,11 @@ public class Finder implements FinderI
 
   @Override
   public void findNext(String theSearchString, boolean matchCase,
-          boolean searchDescription, boolean ignoreHidden)
+          boolean searchDescription, boolean searchFeatureDesc,
+          boolean ignoreHidden)
   {
-    doFind(theSearchString, matchCase, searchDescription, false,
-            ignoreHidden);
+    doFind(theSearchString, matchCase, searchDescription, searchFeatureDesc,
+            false, ignoreHidden);
 
     if (searchResults.isEmpty() && idMatches.isEmpty())
     {
@@ -144,7 +147,8 @@ public class Finder implements FinderI
    * @param ignoreHidden
    */
   protected void doFind(String theSearchString, boolean matchCase,
-          boolean searchDescription, boolean findAll, boolean ignoreHidden)
+          boolean searchDescription, boolean searchFeatureDesc,
+          boolean findAll, boolean ignoreHidden)
   {
     searchResults = new SearchResults();
     idMatches = new ArrayList<>();
@@ -169,7 +173,7 @@ public class Finder implements FinderI
     while ((!found || findAll) && sequenceIndex < end)
     {
       found = findNextMatch(searchString, searchPattern, searchDescription,
-              ignoreHidden);
+              searchFeatureDesc, ignoreHidden);
     }
   }
 
@@ -350,7 +354,8 @@ public class Finder implements FinderI
    * @return
    */
   protected boolean findNextMatch(String searchString, Regex searchPattern,
-          boolean matchDescription, boolean ignoreHidden)
+          boolean matchDescription, boolean matchFeatureDesc,
+          boolean ignoreHidden)
   {
     if (residueIndex < 0)
     {
@@ -380,6 +385,10 @@ public class Finder implements FinderI
       }
       else
       {
+        if (matchFeatureDesc)
+        {
+          matched = searchSequenceFeatures(residueIndex, searchPattern);
+        }
         residueIndex = Integer.MAX_VALUE;
       }
     }
@@ -543,6 +552,34 @@ public class Finder implements FinderI
   }
 
   /**
+   * Searches for a match with the sequence features, and if found, adds the
+   * sequence to the list of match ids, (but not as a duplicate). Answers true
+   * if a match was added, else false.
+   * 
+   * @param seq
+   * @param searchPattern
+   * @return
+   */
+  protected boolean searchSequenceFeatures(int from, Regex searchPattern)
+  {
+    boolean matched = false;
+    SequenceI seq = viewport.getAlignment().getSequenceAt(sequenceIndex);
+
+    SequenceFeaturesI sf = seq.getFeatures();
+    for (SequenceFeature feature : sf.getAllFeatures(null))
+    {
+      if (searchPattern.search(feature.type) || (feature.description != null
+              && searchPattern.search(feature.description)))
+      {
+        searchResults.addResult(seq, seq.findIndex(feature.getBegin()),
+                seq.findIndex(feature.getEnd()));
+        matched = true;
+      }
+    }
+    return matched;
+  }
+
+  /**
    * Searches for a match with the sequence description, and if found, adds the
    * sequence to the list of match ids (but not as a duplicate). Answers true if
    * a match was added, else false.

diff --git a/src/jalview/api/FinderI.java b/src/jalview/api/FinderI.java
index 1d57d81..967bd5c 100644 (file)
--- a/src/jalview/api/FinderI.java
+++ b/src/jalview/api/FinderI.java
@@ -20,11 +20,11 @@
  */
 package jalview.api;
 
+import java.util.List;
+
 import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.SequenceI;
 
-import java.util.List;
-
 /**
  * An interface for searching for a pattern in an aligment
  */
@@ -49,11 +49,13 @@ public interface FinderI
    * @param theSearchString
    * @param caseSensitive
    * @param searchDescription
+   * @param searchFeatureDesc
    * @param ignoreHidden
    * @return
    */
   void findAll(String theSearchString, boolean caseSensitive,
-          boolean searchDescription, boolean ignoreHidden);
+          boolean searchDescription, boolean searchFeatureDesc,
+          boolean ignoreHidden);
 
   /**
    * Finds the next match for the given search string (interpreted as a regular
@@ -71,11 +73,13 @@ public interface FinderI
    * @param theSearchString
    * @param caseSensitive
    * @param searchDescription
+   * @param searchFeatureDesc
    * @param ignoreHidden
    * @return
    */
   void findNext(String theSearchString, boolean caseSensitive,
-          boolean searchDescription, boolean ignoreHidden);
+          boolean searchDescription, boolean searchFeatureDesc,
+          boolean ignoreHidden);
 
   /**
    * 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 31c914a..43a12ae 100644 (file)
--- a/src/jalview/appletgui/Finder.java
+++ b/src/jalview/appletgui/Finder.java
@@ -172,12 +172,12 @@ public class Finder extends Panel implements ActionListener
     if (doFindAll)
     {
       finder.findAll(searchString, isCaseSensitive, doSearchDescription,
-              false);
+              false, false);
     }
     else
     {
       finder.findNext(searchString, isCaseSensitive, doSearchDescription,
-              false);
+              false, false);
     }
 
     searchResults = finder.getSearchResults();

diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java
index 358d9a4..2de06ec 100755 (executable)
--- a/src/jalview/gui/Finder.java
+++ b/src/jalview/gui/Finder.java
@@ -286,16 +286,17 @@ public class Finder extends GFinder
 
     boolean isCaseSensitive = caseSensitive.isSelected();
     boolean doSearchDescription = searchDescription.isSelected();
+    boolean doSearchfeatures = searchFeatures.isSelected();
     boolean skipHidden = ignoreHidden.isSelected();
     if (doFindAll)
     {
       finder.findAll(searchString, isCaseSensitive, doSearchDescription,
-              skipHidden);
+              doSearchfeatures, skipHidden);
     }
     else
     {
       finder.findNext(searchString, isCaseSensitive, doSearchDescription,
-              skipHidden);
+              doSearchfeatures, skipHidden);
     }
 
     searchResults = finder.getSearchResults();

diff --git a/src/jalview/jbgui/GFinder.java b/src/jalview/jbgui/GFinder.java
index c5488f0..aa79671 100755 (executable)
--- a/src/jalview/jbgui/GFinder.java
+++ b/src/jalview/jbgui/GFinder.java
@@ -65,6 +65,8 @@ public class GFinder extends JPanel
 
   protected JCheckBox searchDescription;
 
+  protected JCheckBox searchFeatures;
+
   protected JCheckBox ignoreHidden;
 
   public GFinder()
@@ -152,6 +154,10 @@ public class GFinder extends JPanel
     searchDescription
             .setText(MessageManager.getString("label.include_description"));
 
+    searchFeatures = new JCheckBox();
+    searchFeatures
+            .setText(MessageManager.getString("label.include_features"));
+
     ignoreHidden = new JCheckBox();
     ignoreHidden.setText(MessageManager.getString("label.ignore_hidden"));
     ignoreHidden.setToolTipText(
@@ -159,6 +165,7 @@ public class GFinder extends JPanel
 
     centrePanel.add(caseSensitive);
     centrePanel.add(searchDescription);
+    centrePanel.add(searchFeatures);
     centrePanel.add(ignoreHidden);
 
     /*

diff --git a/test/jalview/analysis/FinderTest.java b/test/jalview/analysis/FinderTest.java
index 7e3bd86..42225e8 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;
@@ -40,13 +46,6 @@ 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
@@ -100,7 +99,7 @@ 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.getCount(), 1);
@@ -110,7 +109,7 @@ public class FinderTest
     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.getCount(), 2);
@@ -131,7 +130,7 @@ public class FinderTest
      * single symbol should find *all* matching symbols 
      */
     Finder f = new Finder(av);
-    f.findAll("M", false, false, false);
+    f.findAll("M", false, false, false, false);
     SearchResultsI sr = f.getSearchResults();
     assertEquals(sr.getCount(), 5);
 
@@ -148,7 +147,7 @@ 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.getCount(), 1);
     List<SearchResultMatchI> matches = sr.getResults();
@@ -163,7 +162,7 @@ public class FinderTest
     f = new Finder(av);
     String name = al.getSequenceAt(0).getName();
     al.getSequenceAt(0).setName("Q9XA0");
-    f.findAll("9", false, false, false);
+    f.findAll("9", false, false, false, false);
     sr = f.getSearchResults();
     assertEquals(sr.getCount(), 2);
     matches = sr.getResults();
@@ -179,7 +178,7 @@ public class FinderTest
      * 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());
   }
 
@@ -196,7 +195,7 @@ 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);
@@ -208,7 +207,7 @@ 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().getCount(), 1);
     List<SearchResultMatchI> matches = f.getSearchResults().getResults();
@@ -224,7 +223,7 @@ 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());
@@ -246,7 +245,7 @@ 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());
@@ -255,7 +254,7 @@ 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));
@@ -265,7 +264,7 @@ 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());
@@ -281,7 +280,7 @@ 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));
@@ -309,7 +308,7 @@ 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();
@@ -319,7 +318,7 @@ 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());
 
@@ -330,7 +329,7 @@ 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();
@@ -359,7 +358,7 @@ 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.getCount(), 1);
     SearchResultMatchI match = searchResults.getResults().get(0);
@@ -371,7 +370,7 @@ 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.getCount(), 1);
     match = searchResults.getResults().get(0);
@@ -379,7 +378,7 @@ public class FinderTest
     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.getCount(), 1);
     match = searchResults.getResults().get(0);
@@ -387,7 +386,7 @@ public class FinderTest
     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.getCount(), 1);
     match = searchResults.getResults().get(0);
@@ -395,13 +394,13 @@ public class FinderTest
     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.getCount(), 1);
     match = searchResults.getResults().get(0);
@@ -418,7 +417,7 @@ public class FinderTest
   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.getCount(), 1);
     SearchResultMatchI match = searchResults.getResults().get(0);
@@ -434,7 +433,7 @@ 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.getCount(), 2);
     SearchResultMatchI match = searchResults.getResults().get(0);
@@ -449,7 +448,7 @@ 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.getCount(), 3);
     match = searchResults.getResults().get(0);
@@ -477,7 +476,7 @@ public class FinderTest
     /*
      * 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.getCount(), 2);
     SearchResultMatchI match = searchResults.getResults().get(0);
@@ -493,7 +492,7 @@ 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.getCount(), 1);
     match = searchResults.getResults().get(0);
@@ -501,7 +500,7 @@ public class FinderTest
     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());
   }
 
@@ -524,7 +523,7 @@ 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.getCount(), 1);
@@ -536,12 +535,12 @@ 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.getCount(), 1);
@@ -549,7 +548,7 @@ public class FinderTest
     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.getCount(), 1);
@@ -581,7 +580,7 @@ public class FinderTest
      * 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));
@@ -596,7 +595,7 @@ 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));
@@ -627,7 +626,7 @@ 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.getCount(), 2);
@@ -664,7 +663,7 @@ 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.getCount(), 2);
     SearchResultMatchI match = searchResults.getResults().get(0);
@@ -686,7 +685,7 @@ 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.getCount(), 1);
     match = searchResults.getResults().get(0);
@@ -699,7 +698,7 @@ 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());
 
@@ -708,7 +707,7 @@ 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.getCount(), 2);
     match = searchResults.getResults().get(0);
@@ -727,7 +726,7 @@ 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.getCount(), 2);
     match = searchResults.getResults().get(0);
@@ -742,7 +741,7 @@ 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());
 
     /*
@@ -752,7 +751,7 @@ 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.getCount(), 1);
     match = searchResults.getResults().get(0);
@@ -795,7 +794,7 @@ 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.getCount(), 2);
     SearchResultMatchI match = searchResults.getResults().get(0);
@@ -832,7 +831,7 @@ public class FinderTest
      * aaaMMMMaaa
      */
     Finder f = new Finder(av);
-    f.findAll("abe", false, false, true); // true = ignore hidden
+    f.findAll("abe", false, false, false, true); // true = ignore hidden
     SearchResultsI searchResults = f.getSearchResults();
 
     /*
@@ -851,7 +850,7 @@ public class FinderTest
     assertEquals(match.getEnd(), 12);
 
     f = new Finder(av);
-    f.findNext("a.E", false, false, true);
+    f.findNext("a.E", false, false, false, true);
     searchResults = f.getSearchResults();
     assertEquals(searchResults.getCount(), 1);
     assertEquals(searchResults.getResults().size(), 2);
@@ -864,7 +863,7 @@ public class FinderTest
     assertEquals(match.getStart(), 12); // E
     assertEquals(match.getEnd(), 12);
 
-    f.findNext("a.E", false, false, true);
+    f.findNext("a.E", false, false, false, true);
     searchResults = f.getSearchResults();
     assertEquals(searchResults.getCount(), 1);
     assertEquals(searchResults.getResults().size(), 2);
@@ -881,7 +880,7 @@ public class FinderTest
      * find all matching across two hidden column regions
      * note one 'match' is returned as three contiguous matches
      */
-    f.findAll("BEG", false, false, true);
+    f.findAll("BEG", false, false, false, true);
     searchResults = f.getSearchResults();
     assertEquals(searchResults.getCount(), 1);
     assertEquals(searchResults.getResults().size(), 3);
@@ -908,7 +907,7 @@ public class FinderTest
     selection.setEndRes(9);
     al.getSequences().forEach(seq -> selection.addSequence(seq, false));
     av.setSelectionGroup(selection);
-    f.findAll("A.*H", false, false, true);
+    f.findAll("A.*H", false, false, false, true);
     searchResults = f.getSearchResults();
     assertEquals(searchResults.getCount(), 1);
     assertEquals(searchResults.getResults().size(), 3);

diff --git a/test/jalview/controller/AlignViewControllerTest.java b/test/jalview/controller/AlignViewControllerTest.java
index ca3b55c..e8e0bb1 100644 (file)
--- a/test/jalview/controller/AlignViewControllerTest.java
+++ b/test/jalview/controller/AlignViewControllerTest.java
@@ -23,6 +23,13 @@ package jalview.controller;
 import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertTrue;
 
+import java.awt.Color;
+import java.util.Arrays;
+import java.util.BitSet;
+
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
 import jalview.analysis.Finder;
 import jalview.api.AlignViewControllerI;
 import jalview.api.FeatureColourI;
@@ -40,13 +47,6 @@ import jalview.io.DataSourceType;
 import jalview.io.FileLoader;
 import jalview.schemes.FeatureColour;
 
-import java.awt.Color;
-import java.util.Arrays;
-import java.util.BitSet;
-
-import org.testng.annotations.BeforeClass;
-import org.testng.annotations.Test;
-
 public class AlignViewControllerTest
 {
 
@@ -226,7 +226,7 @@ public class AlignViewControllerTest
      *  test Match/Find works first
      */
     FinderI f = new Finder(af.getViewport());
-    f.findAll("M+", true, false, false);
+    f.findAll("M+", true, false, false, false);
     assertEquals(
             "Finder found different set of results to manually created SearchResults",
             sr, f.getSearchResults());