JAL-3490 match count independent of contiguous matches count

diff --git a/src/jalview/analysis/Finder.java b/src/jalview/analysis/Finder.java
index 0d8665f..c545c7f 100644 (file)
--- a/src/jalview/analysis/Finder.java
+++ b/src/jalview/analysis/Finder.java
@@ -471,10 +471,7 @@ public class Finder implements FinderI
      */
     int[] truePositions = searchedSequenceMap
             .locateInFrom(matchStartPosition, matchEndPosition);
-    for (int i = 0; i < truePositions.length - 1; i += 2)
-    {
-      searchResults.addResult(seq, truePositions[i], truePositions[i + 1]);
-    }
+    searchResults.addResult(seq, truePositions);
   }
 
   /**

diff --git a/src/jalview/appletgui/AlignmentPanel.java b/src/jalview/appletgui/AlignmentPanel.java
index e9081b0..365f886 100644 (file)
--- a/src/jalview/appletgui/AlignmentPanel.java
+++ b/src/jalview/appletgui/AlignmentPanel.java
@@ -344,7 +344,7 @@ public class AlignmentPanel extends Panel
           int verticalOffset, boolean redrawOverview, boolean centre)
   {
     // do we need to scroll the panel?
-    if (results != null && results.getSize() > 0)
+    if (results != null && results.getCount() > 0)
     {
       AlignmentI alignment = av.getAlignment();
       int seqIndex = alignment.findIndex(results);

diff --git a/src/jalview/appletgui/Finder.java b/src/jalview/appletgui/Finder.java
index 4772580..a78e41c 100644 (file)
--- a/src/jalview/appletgui/Finder.java
+++ b/src/jalview/appletgui/Finder.java
@@ -211,13 +211,13 @@ public class Finder extends Panel implements ActionListener
         String message = (idMatches.size() > 0) ? "" + idMatches.size() + " IDs"
                 : "";
         if (idMatches.size() > 0 && searchResults != null
-                && searchResults.getSize() > 0)
+                && searchResults.getCount() > 0)
         {
           message += " and ";
         }
         if (searchResults != null)
         {
-          message += searchResults.getSize() + " subsequence matches.";
+          message += searchResults.getCount() + " subsequence matches.";
         }
         ap.alignFrame.statusBar.setText(MessageManager
                 .formatMessage("label.search_results", new String[]

diff --git a/src/jalview/datamodel/SearchResults.java b/src/jalview/datamodel/SearchResults.java
index 0074d2a..7c3bba7 100755 (executable)
--- a/src/jalview/datamodel/SearchResults.java
+++ b/src/jalview/datamodel/SearchResults.java
@@ -33,6 +33,7 @@ import java.util.List;
  */
 public class SearchResults implements SearchResultsI
 {
+  private int count;
 
   private List<SearchResultMatchI> matches = new ArrayList<>();
 
@@ -168,11 +169,30 @@ public class SearchResults implements SearchResultsI
     if (!matches.contains(m))
     {
       matches.add(m);
+      count++;
     }
     return m;
   }
 
   @Override
+  public void addResult(SequenceI seq, int[] positions)
+  {
+    /*
+     * we only increment the match count by 1 - or not at all,
+     * if the matches are all duplicates of existing
+     */
+    int beforeCount = count;
+    for (int i = 0; i < positions.length - 1; i += 2)
+    {
+      addResult(seq, positions[i], positions[i + 1]);
+    }
+    if (count > beforeCount)
+    {
+      count = beforeCount + 1;
+    }
+  }
+
+  @Override
   public boolean involvesSequence(SequenceI sequence)
   {
     final int start = sequence.getStart();
@@ -286,9 +306,9 @@ public class SearchResults implements SearchResultsI
   }
 
   @Override
-  public int getSize()
+  public int getCount()
   {
-    return matches.size();
+    return count;
   }
 
   @Override

diff --git a/src/jalview/datamodel/SearchResultsI.java b/src/jalview/datamodel/SearchResultsI.java
index 3c3ad4e..c89f363 100644 (file)
--- a/src/jalview/datamodel/SearchResultsI.java
+++ b/src/jalview/datamodel/SearchResultsI.java
@@ -41,6 +41,17 @@ public interface SearchResultsI
   SearchResultMatchI addResult(SequenceI seq, int start, int end);
 
   /**
+   * Adds one ore more [start, end] ranges to the results (unless already added
+   * to avoid duplicates). This method only increments the match count by 1.
+   * This is for the case where a match spans ignored hidden residues - it is
+   * formally two or more contiguous matches, but only counted as one match.
+   * 
+   * @param seq
+   * @param positions
+   */
+  void addResult(SequenceI seq, int[] positions);
+
+  /**
    * adds all match results in the argument to this set
    * 
    * @param toAdd
@@ -74,11 +85,13 @@ public interface SearchResultsI
   int[] getResults(SequenceI sequence, int start, int end);
 
   /**
-   * Returns the number of matches found
+   * Returns the number of matches found. Note that if a match straddles ignored
+   * hidden residues, it is counted as one match, although formally recorded as
+   * two (or more) contiguous matched sequence regions
    * 
    * @return
    */
-  int getSize();
+  int getCount();
 
   /**
    * Returns true if no search result matches are held.

diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java
index 217a390..537c323 100755 (executable)
--- a/src/jalview/gui/Finder.java
+++ b/src/jalview/gui/Finder.java
@@ -304,11 +304,11 @@ public class Finder extends GFinder
                 : "";
         if (searchResults != null)
         {
-          if (idMatch.size() > 0 && searchResults.getSize() > 0)
+          if (idMatch.size() > 0 && searchResults.getCount() > 0)
           {
             message += " and ";
           }
-          message += searchResults.getSize()
+          message += searchResults.getCount()
                   + " subsequence matches found.";
         }
         JvOptionPane.showInternalMessageDialog(this, message, null,

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index def4be1..dc2d3e9 100644 (file)
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -893,11 +893,12 @@ public class SeqPanel extends JPanel
     AlignFrame af = Desktop.getAlignFrameFor(complement);
     FeatureRendererModel fr2 = af.getFeatureRenderer();
 
-    int j = results.getSize();
+    List<SearchResultMatchI> matches = results.getResults();
+    int j = matches.size();
     List<String> infos = new ArrayList<>();
     for (int i = 0; i < j; i++)
     {
-      SearchResultMatchI match = results.getResults().get(i);
+      SearchResultMatchI match = matches.get(i);
       int pos = match.getStart();
       if (pos == match.getEnd())
       {

diff --git a/test/jalview/analysis/FinderTest.java b/test/jalview/analysis/FinderTest.java
index 725be33..95e6c0d 100644 (file)
--- a/test/jalview/analysis/FinderTest.java
+++ b/test/jalview/analysis/FinderTest.java
@@ -103,7 +103,7 @@ public class FinderTest
     f.findNext("E.H", false, false, false); // 'E, any character, H'
     // should match seq2 efH only
     SearchResultsI sr = f.getSearchResults();
-    assertEquals(sr.getSize(), 1);
+    assertEquals(sr.getCount(), 1);
     List<SearchResultMatchI> matches = sr.getResults();
     assertSame(matches.get(0).getSequence(), al.getSequenceAt(1));
     assertEquals(matches.get(0).getStart(), 5);
@@ -113,7 +113,7 @@ public class FinderTest
     f.findAll("E.H", false, false, false); // 'E, any character, H'
     // should match seq2 efH and seq3 EFH
     sr = f.getSearchResults();
-    assertEquals(sr.getSize(), 2);
+    assertEquals(sr.getCount(), 2);
     matches = sr.getResults();
     assertSame(matches.get(0).getSequence(), al.getSequenceAt(1));
     assertSame(matches.get(1).getSequence(), al.getSequenceAt(2));
@@ -136,7 +136,7 @@ public class FinderTest
      */
     f.findNext("9", false, false, false);
     SearchResultsI sr = f.getSearchResults();
-    assertEquals(sr.getSize(), 1);
+    assertEquals(sr.getCount(), 1);
     List<SearchResultMatchI> matches = sr.getResults();
     assertSame(matches.get(0).getSequence(), al.getSequenceAt(0));
     assertEquals(matches.get(0).getStart(), 9);
@@ -151,7 +151,7 @@ public class FinderTest
     al.getSequenceAt(0).setName("Q9XA0");
     f.findAll("9", false, false, false);
     sr = f.getSearchResults();
-    assertEquals(sr.getSize(), 2);
+    assertEquals(sr.getCount(), 2);
     matches = sr.getResults();
     assertSame(matches.get(0).getSequence(), al.getSequenceAt(0));
     assertSame(matches.get(1).getSequence(), al.getSequenceAt(3));
@@ -196,7 +196,7 @@ public class FinderTest
     PA.setValue(f, "residueIndex", 0);
     f.findNext("e", false, false, false); // matches in sequence
     assertTrue(f.getIdMatches().isEmpty());
-    assertEquals(f.getSearchResults().getSize(), 1);
+    assertEquals(f.getSearchResults().getCount(), 1);
     List<SearchResultMatchI> matches = f.getSearchResults().getResults();
     assertEquals(matches.get(0).getStart(), 5);
     assertEquals(matches.get(0).getEnd(), 5);
@@ -272,7 +272,7 @@ public class FinderTest
     assertSame(f.getIdMatches().get(0), al2.getSequenceAt(0));
     assertSame(f.getIdMatches().get(1), al2.getSequenceAt(1));
 
-    assertEquals(f.getSearchResults().getSize(), 2);
+    assertEquals(f.getSearchResults().getCount(), 2);
     SearchResultMatchI match = f.getSearchResults().getResults().get(0);
     assertSame(match.getSequence(), al2.getSequenceAt(1));
     assertEquals(match.getStart(), 5);
@@ -320,7 +320,7 @@ public class FinderTest
     assertEquals(f.getIdMatches().size(), 1);
     assertSame(f.getIdMatches().get(0), al2.getSequenceAt(4));
     searchResults = f.getSearchResults();
-    assertEquals(searchResults.getSize(), 2);
+    assertEquals(searchResults.getCount(), 2);
     SearchResultMatchI match = searchResults.getResults().get(0);
     assertSame(match.getSequence(), al2.getSequenceAt(4));
     assertEquals(match.getStart(), 4);
@@ -347,7 +347,7 @@ public class FinderTest
     FinderI f = new Finder(av);
     f.findNext("EfH", false, false, false);
     SearchResultsI searchResults = f.getSearchResults();
-    assertEquals(searchResults.getSize(), 1);
+    assertEquals(searchResults.getCount(), 1);
     SearchResultMatchI match = searchResults.getResults().get(0);
     assertSame(match.getSequence(), al.getSequenceAt(1));
     assertEquals(match.getStart(), 5);
@@ -359,7 +359,7 @@ public class FinderTest
     f = new Finder(av);
     f.findNext("I", false, false, false); // find next: seq1/16
     searchResults = f.getSearchResults();
-    assertEquals(searchResults.getSize(), 1);
+    assertEquals(searchResults.getCount(), 1);
     match = searchResults.getResults().get(0);
     assertSame(match.getSequence(), al.getSequenceAt(0));
     assertEquals(match.getStart(), 16);
@@ -367,7 +367,7 @@ public class FinderTest
 
     f.findNext("I", false, false, false); // find next: seq1/18
     searchResults = f.getSearchResults();
-    assertEquals(searchResults.getSize(), 1);
+    assertEquals(searchResults.getCount(), 1);
     match = searchResults.getResults().get(0);
     assertSame(match.getSequence(), al.getSequenceAt(0));
     assertEquals(match.getStart(), 18);
@@ -375,7 +375,7 @@ public class FinderTest
 
     f.findNext("I", false, false, false); // find next: seq2/8
     searchResults = f.getSearchResults();
-    assertEquals(searchResults.getSize(), 1);
+    assertEquals(searchResults.getCount(), 1);
     match = searchResults.getResults().get(0);
     assertSame(match.getSequence(), al.getSequenceAt(1));
     assertEquals(match.getStart(), 8);
@@ -389,7 +389,7 @@ public class FinderTest
      */
     f.findNext("I", false, false, false); // find next: seq1/16
     searchResults = f.getSearchResults();
-    assertEquals(searchResults.getSize(), 1);
+    assertEquals(searchResults.getCount(), 1);
     match = searchResults.getResults().get(0);
     assertSame(match.getSequence(), al.getSequenceAt(0));
     assertEquals(match.getStart(), 16);
@@ -406,7 +406,7 @@ public class FinderTest
     Finder f = new Finder(av);
     f.findAll("M+", false, false, false);
     SearchResultsI searchResults = f.getSearchResults();
-    assertEquals(searchResults.getSize(), 1);
+    assertEquals(searchResults.getCount(), 1);
     SearchResultMatchI match = searchResults.getResults().get(0);
     assertSame(match.getSequence(), al.getSequenceAt(3));
     assertEquals(match.getStart(), 4); // dataset sequence positions
@@ -422,7 +422,7 @@ public class FinderTest
     Finder f = new Finder(av);
     f.findAll("EfH", false, false, false);
     SearchResultsI searchResults = f.getSearchResults();
-    assertEquals(searchResults.getSize(), 2);
+    assertEquals(searchResults.getCount(), 2);
     SearchResultMatchI match = searchResults.getResults().get(0);
     assertSame(match.getSequence(), al.getSequenceAt(1));
     assertEquals(match.getStart(), 5);
@@ -437,7 +437,7 @@ public class FinderTest
      */
     f.findAll("I", false, false, false);
     searchResults = f.getSearchResults();
-    assertEquals(searchResults.getSize(), 3);
+    assertEquals(searchResults.getCount(), 3);
     match = searchResults.getResults().get(0);
     assertSame(match.getSequence(), al.getSequenceAt(0));
     assertEquals(match.getStart(), 16);
@@ -465,7 +465,7 @@ public class FinderTest
      */
     f.findAll("BC", true, false, false);
     SearchResultsI searchResults = f.getSearchResults();
-    assertEquals(searchResults.getSize(), 2);
+    assertEquals(searchResults.getCount(), 2);
     SearchResultMatchI match = searchResults.getResults().get(0);
     assertSame(match.getSequence(), al.getSequenceAt(0));
     assertEquals(match.getStart(), 9);
@@ -481,7 +481,7 @@ public class FinderTest
     f = new Finder(av);
     f.findAll("bc", true, false, false);
     searchResults = f.getSearchResults();
-    assertEquals(searchResults.getSize(), 1);
+    assertEquals(searchResults.getCount(), 1);
     match = searchResults.getResults().get(0);
     assertSame(match.getSequence(), al.getSequenceAt(2));
     assertEquals(match.getStart(), 1);
@@ -513,7 +513,7 @@ public class FinderTest
     f.findNext("b", false, false, false);
     assertTrue(f.getIdMatches().isEmpty());
     SearchResultsI searchResults = f.getSearchResults();
-    assertEquals(searchResults.getSize(), 1);
+    assertEquals(searchResults.getCount(), 1);
     SearchResultMatchI match = searchResults.getResults().get(0);
     assertSame(match.getSequence(), al.getSequenceAt(1));
     assertEquals(match.getStart(), 2);
@@ -530,7 +530,7 @@ public class FinderTest
     f.findNext("d", false, false, false);
     assertTrue(f.getIdMatches().isEmpty());
     searchResults = f.getSearchResults();
-    assertEquals(searchResults.getSize(), 1);
+    assertEquals(searchResults.getCount(), 1);
     match = searchResults.getResults().get(0);
     assertSame(match.getSequence(), al.getSequenceAt(1));
     assertEquals(match.getStart(), 4);
@@ -538,7 +538,7 @@ public class FinderTest
     f.findNext("d", false, false, false);
     assertTrue(f.getIdMatches().isEmpty());
     searchResults = f.getSearchResults();
-    assertEquals(searchResults.getSize(), 1);
+    assertEquals(searchResults.getCount(), 1);
     match = searchResults.getResults().get(0);
     assertSame(match.getSequence(), al.getSequenceAt(2));
     assertEquals(match.getStart(), 3);
@@ -572,7 +572,7 @@ public class FinderTest
     assertSame(f.getIdMatches().get(0), al.getSequenceAt(1));
     assertSame(f.getIdMatches().get(1), al.getSequenceAt(2));
     SearchResultsI searchResults = f.getSearchResults();
-    assertEquals(searchResults.getSize(), 1);
+    assertEquals(searchResults.getCount(), 1);
     SearchResultMatchI match = searchResults.getResults().get(0);
     assertSame(match.getSequence(), al.getSequenceAt(2));
     assertEquals(match.getStart(), 4);
@@ -616,7 +616,7 @@ public class FinderTest
     f.findAll("I", false, false, false);
     assertTrue(f.getIdMatches().isEmpty());
     SearchResultsI searchResults = f.getSearchResults();
-    assertEquals(searchResults.getSize(), 2);
+    assertEquals(searchResults.getCount(), 2);
     SearchResultMatchI match = searchResults.getResults().get(0);
     assertSame(match.getSequence(), al.getSequenceAt(0));
     assertEquals(match.getStart(), 16);
@@ -652,7 +652,7 @@ public class FinderTest
     Finder f = new Finder(av);
     f.findAll("aaa", false, false, false);
     SearchResultsI searchResults = f.getSearchResults();
-    assertEquals(searchResults.getSize(), 2);
+    assertEquals(searchResults.getCount(), 2);
     SearchResultMatchI match = searchResults.getResults().get(0);
     assertSame(match.getSequence(), al.getSequenceAt(3));
     assertEquals(match.getStart(), 1);
@@ -674,7 +674,7 @@ public class FinderTest
     f = new Finder(av);
     f.findAll("D", false, false, false);
     searchResults = f.getSearchResults();
-    assertEquals(searchResults.getSize(), 1);
+    assertEquals(searchResults.getCount(), 1);
     match = searchResults.getResults().get(0);
     assertSame(match.getSequence(), al.getSequenceAt(1));
     assertEquals(match.getStart(), 4);
@@ -696,7 +696,7 @@ public class FinderTest
     f = new Finder(av);
     f.findAll("aaa", false, false, false);
     searchResults = f.getSearchResults();
-    assertEquals(searchResults.getSize(), 2);
+    assertEquals(searchResults.getCount(), 2);
     match = searchResults.getResults().get(0);
     assertSame(match.getSequence(), al.getSequenceAt(3));
     assertEquals(match.getStart(), 1);
@@ -715,7 +715,7 @@ public class FinderTest
     f = new Finder(av);
     f.findAll("aaa", false, false, false);
     searchResults = f.getSearchResults();
-    assertEquals(searchResults.getSize(), 2);
+    assertEquals(searchResults.getCount(), 2);
     match = searchResults.getResults().get(0);
     assertSame(match.getSequence(), al.getSequenceAt(3));
     assertEquals(match.getStart(), 1);
@@ -740,7 +740,7 @@ public class FinderTest
     f = new Finder(av);
     f.findNext("H", false, false, false);
     searchResults = f.getSearchResults();
-    assertEquals(searchResults.getSize(), 1);
+    assertEquals(searchResults.getCount(), 1);
     match = searchResults.getResults().get(0);
     assertSame(match.getSequence(), al.getSequenceAt(2));
     assertEquals(match.getStart(), 6);
@@ -783,7 +783,7 @@ public class FinderTest
     Finder f = new Finder(av);
     f.findAll("[AH]", false, false, false);
     SearchResultsI searchResults = f.getSearchResults();
-    assertEquals(searchResults.getSize(), 2);
+    assertEquals(searchResults.getCount(), 2);
     SearchResultMatchI match = searchResults.getResults().get(0);
     assertSame(match.getSequence(), al.getSequenceAt(1));
     assertEquals(match.getStart(), 1);
@@ -823,8 +823,10 @@ public class FinderTest
 
     /*
      * match of seq1 ABE made up of AB and E
+     * note only one match is counted
      */
-    assertEquals(searchResults.getSize(), 2);
+    assertEquals(searchResults.getCount(), 1);
+    assertEquals(searchResults.getResults().size(), 2);
     SearchResultMatchI match = searchResults.getResults().get(0);
     assertSame(match.getSequence(), al.getSequenceAt(0));
     assertEquals(match.getStart(), 8); // A
@@ -837,7 +839,8 @@ public class FinderTest
     f = new Finder(av);
     f.findNext("a.E", false, false, true);
     searchResults = f.getSearchResults();
-    assertEquals(searchResults.getSize(), 2);
+    assertEquals(searchResults.getCount(), 1);
+    assertEquals(searchResults.getResults().size(), 2);
     match = searchResults.getResults().get(0);
     assertSame(match.getSequence(), al.getSequenceAt(0));
     assertEquals(match.getStart(), 8); // A
@@ -849,7 +852,8 @@ public class FinderTest
 
     f.findNext("a.E", false, false, true);
     searchResults = f.getSearchResults();
-    assertEquals(searchResults.getSize(), 2);
+    assertEquals(searchResults.getCount(), 1);
+    assertEquals(searchResults.getResults().size(), 2);
     match = searchResults.getResults().get(0);
     assertSame(match.getSequence(), al.getSequenceAt(1));
     assertEquals(match.getStart(), 1); // a
@@ -861,11 +865,12 @@ public class FinderTest
 
     /*
      * find all matching across two hidden column regions
-     * note one 'match' is reported as three contiguous matches
+     * note one 'match' is returned as three contiguous matches
      */
     f.findAll("BEG", false, false, true);
     searchResults = f.getSearchResults();
-    assertEquals(searchResults.getSize(), 3);
+    assertEquals(searchResults.getCount(), 1);
+    assertEquals(searchResults.getResults().size(), 3);
     match = searchResults.getResults().get(0);
     assertSame(match.getSequence(), al.getSequenceAt(0));
     assertEquals(match.getStart(), 9); // B
@@ -891,7 +896,8 @@ public class FinderTest
     av.setSelectionGroup(selection);
     f.findAll("A.*H", false, false, true);
     searchResults = f.getSearchResults();
-    assertEquals(searchResults.getSize(), 3);
+    assertEquals(searchResults.getCount(), 1);
+    assertEquals(searchResults.getResults().size(), 3);
     // match made of contiguous matches A, DE, H
     match = searchResults.getResults().get(0);
     assertSame(match.getSequence(), al.getSequenceAt(1));

diff --git a/test/jalview/datamodel/SearchResultsTest.java b/test/jalview/datamodel/SearchResultsTest.java
index a302d6e..838b259 100644 (file)
--- a/test/jalview/datamodel/SearchResultsTest.java
+++ b/test/jalview/datamodel/SearchResultsTest.java
@@ -297,11 +297,11 @@ public class SearchResultsTest
     SequenceI seq1 = new Sequence("", "abcdefghijklm");
     SearchResultsI sr = new SearchResults();
     sr.addResult(seq1, 3, 5);
-    assertEquals(1, sr.getSize());
+    assertEquals(1, sr.getCount());
     sr.addResult(seq1, 3, 5);
-    assertEquals(1, sr.getSize());
+    assertEquals(1, sr.getCount());
     sr.addResult(seq1, 3, 6);
-    assertEquals(2, sr.getSize());
+    assertEquals(2, sr.getCount());
   }
 
   /**