JAL-3613 check sequence overlap when matching search results

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

diff --git a/src/jalview/datamodel/SearchResults.java b/src/jalview/datamodel/SearchResults.java
index cde50e5..0074d2a 100755 (executable)
--- a/src/jalview/datamodel/SearchResults.java
+++ b/src/jalview/datamodel/SearchResults.java
@@ -91,27 +91,18 @@ public class SearchResults implements SearchResultsI
       }
     }
 
-    /* (non-Javadoc)
-     * @see jalview.datamodel.SearchResultMatchI#getSequence()
-     */
     @Override
     public SequenceI getSequence()
     {
       return sequence;
     }
 
-    /* (non-Javadoc)
-     * @see jalview.datamodel.SearchResultMatchI#getStart()
-     */
     @Override
     public int getStart()
     {
       return start;
     }
 
-    /* (non-Javadoc)
-     * @see jalview.datamodel.SearchResultMatchI#getEnd()
-     */
     @Override
     public int getEnd()
     {
@@ -162,30 +153,37 @@ public class SearchResults implements SearchResultsI
       return (sequence == m.getSequence() && start == m.getStart()
               && end == m.getEnd());
     }
+
+    @Override
+    public boolean contains(SequenceI seq, int from, int to)
+    {
+      return (sequence == seq && start <= from && end >= to);
+    }
   }
 
-  /* (non-Javadoc)
-   * @see jalview.datamodel.SearchResultsI#addResult(jalview.datamodel.SequenceI, int, int)
-   */
   @Override
   public SearchResultMatchI addResult(SequenceI seq, int start, int end)
   {
     Match m = new Match(seq, start, end);
-    matches.add(m);
+    if (!matches.contains(m))
+    {
+      matches.add(m);
+    }
     return m;
   }
 
-  /* (non-Javadoc)
-   * @see jalview.datamodel.SearchResultsI#involvesSequence(jalview.datamodel.SequenceI)
-   */
   @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;
       }
@@ -193,9 +191,6 @@ public class SearchResults implements SearchResultsI
     return false;
   }
 
-  /* (non-Javadoc)
-   * @see jalview.datamodel.SearchResultsI#getResults(jalview.datamodel.SequenceI, int, int)
-   */
   @Override
   public int[] getResults(SequenceI sequence, int start, int end)
   {
@@ -267,9 +262,12 @@ public class SearchResults implements SearchResultsI
   {
     int count = 0;
     BitSet mask = new BitSet();
+    int startRes = sqcol.getStartRes();
+    int endRes = sqcol.getEndRes();
+
     for (SequenceI s : sqcol.getSequences())
     {
-      int[] cols = getResults(s, sqcol.getStartRes(), sqcol.getEndRes());
+      int[] cols = getResults(s, startRes, endRes);
       if (cols != null)
       {
         for (int pair = 0; pair < cols.length; pair += 2)
@@ -287,27 +285,18 @@ public class SearchResults implements SearchResultsI
     return count;
   }
 
-  /* (non-Javadoc)
-   * @see jalview.datamodel.SearchResultsI#getSize()
-   */
   @Override
   public int getSize()
   {
     return matches.size();
   }
 
-  /* (non-Javadoc)
-   * @see jalview.datamodel.SearchResultsI#isEmpty()
-   */
   @Override
   public boolean isEmpty()
   {
     return matches.isEmpty();
   }
 
-  /* (non-Javadoc)
-   * @see jalview.datamodel.SearchResultsI#getResults()
-   */
   @Override
   public List<SearchResultMatchI> getResults()
   {