JAL-3763 test coverage for AlignedCodonFrame.markMappedRegion

[jalview.git] / src / jalview / datamodel / SearchResults.java

diff --git a/src/jalview/datamodel/SearchResults.java b/src/jalview/datamodel/SearchResults.java
index 31736e5..5c929fc 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<>();
 
@@ -168,18 +169,41 @@ 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();
+    final int end = sequence.getEnd();
+
     SequenceI ds = sequence.getDatasetSequence();
-    for (SearchResultMatchI _m : matches)
+    for (SearchResultMatchI m : matches)
     {
-      SequenceI matched = _m.getSequence();
-      if (matched != null && (matched == sequence || matched == ds))
+      SequenceI matched = m.getSequence();
+      if (matched != null && (matched == sequence || matched == ds)
+              && (m.getEnd() >= start) && (m.getStart() <= end))
       {
         return true;
       }
@@ -282,9 +306,9 @@ public class SearchResults implements SearchResultsI
   }
 
   @Override
-  public int getSize()
+  public int getCount()
   {
-    return matches.size();
+    return count;
   }
 
   @Override
@@ -325,8 +349,10 @@ public class SearchResults implements SearchResultsI
   }
 
   /**
-   * Two SearchResults are considered equal if they contain the same matches in
-   * the same order.
+   * Two SearchResults are considered equal if they contain the same matches
+   * (Sequence, start position, end position) in the same order
+   * 
+   * @see Match#equals(Object)
    */
   @Override
   public boolean equals(Object obj)