JAL-4062 avc operation and model method for copying SearchResultsI.getMatchingSubSequ...

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

diff --git a/src/jalview/datamodel/SearchResults.java b/src/jalview/datamodel/SearchResults.java
index d1e3fcc..909a0fe 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<>();
 
@@ -91,27 +92,18 @@ 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 +154,56 @@ 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);
+      count++;
+    }
     return m;
   }
 
-  /* (non-Javadoc)
-   * @see jalview.datamodel.SearchResultsI#involvesSequence(jalview.datamodel.SequenceI)
-   */
+  @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;
       }
@@ -193,9 +211,6 @@ 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)
   {
@@ -219,8 +234,8 @@ public class SearchResults implements SearchResultsI
       {
         mfound = true;
         matchStart = sequence.findIndex(m.start) - 1;
-        matchEnd = m.start == m.end ? matchStart : sequence
-                .findIndex(m.end) - 1;
+        matchEnd = m.start == m.end ? matchStart
+                : sequence.findIndex(m.end) - 1;
       }
 
       if (mfound)
@@ -290,27 +305,18 @@ public class SearchResults implements SearchResultsI
     return count;
   }
 
-  /* (non-Javadoc)
-   * @see jalview.datamodel.SearchResultsI#getSize()
-   */
   @Override
-  public int getSize()
+  public int getCount()
   {
-    return matches.size();
+    return count;
   }
 
-  /* (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()
   {
@@ -343,8 +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)
@@ -362,4 +370,27 @@ public class SearchResults implements SearchResultsI
   {
     matches.addAll(toAdd.getResults());
   }
+
+  @Override
+  public List<SequenceI> getMatchingSubSequences()
+  {
+    List<SequenceI> seqs = new ArrayList<>();
+
+    /*
+     * assemble dataset sequences, and template new sequence features,
+     * for the amend features dialog
+     */
+    for (SearchResultMatchI match : matches)
+    {
+      SequenceI seq = match.getSequence();
+      while (seq.getDatasetSequence() != null)
+      {
+        seq = seq.getDatasetSequence();
+      }
+      // getSubSequence is index-base0, findIndex returns index-base1
+      seqs.add(seq.getSubSequence(seq.findIndex(match.getStart()) - 1,
+              seq.findIndex(match.getEnd())));
+    }
+    return seqs;
+  }
 }