X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSearchResultsI.java;h=794682412897ea634ba901595a832119749adaf8;hb=f3d6a13271e3f34dfb4e40d6a2a7df1d392f8014;hp=dc18bb88a0c9f6f7e68492ef03017921ec02d21c;hpb=ac7571ed0fd171c2a68c3db71f2635bd6cb8777e;p=jalview.git

diff --git a/src/jalview/datamodel/SearchResultsI.java b/src/jalview/datamodel/SearchResultsI.java
index dc18bb8..7946824 100644
--- a/src/jalview/datamodel/SearchResultsI.java
+++ b/src/jalview/datamodel/SearchResultsI.java
@@ -1,82 +1,129 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.datamodel;
 
-import jalview.datamodel.SearchResults.Match;
-
+import java.util.BitSet;
 import java.util.List;
 
+/**
+ * An interface describing the result of a search or other operation which
+ * highlights matched regions of an alignment
+ */
 public interface SearchResultsI
 {
 
   /**
-   * This method replaces the old search results which merely held an alignment
-   * index of search matches. This broke when sequences were moved around the
-   * alignment
+   * Adds one region to the results (unless already added, to avoid duplicates)
    * 
    * @param seq
-   *          Sequence
    * @param start
-   *          int
    * @param end
-   *          int
+   * @return
+   */
+  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
    */
-  public abstract void addResult(SequenceI seq, int start, int end);
+  void addSearchResults(SearchResultsI toAdd);
 
   /**
-   * Quickly check if the given sequence is referred to in the search results
+   * Answers true if the search results include the given sequence (or its
+   * dataset sequence), else false
    * 
    * @param sequence
-   *          (specific alignment sequence or a dataset sequence)
-   * @return true if the results involve sequence
+   * @return
    */
-  public abstract boolean involvesSequence(SequenceI sequence);
+  boolean involvesSequence(SequenceI sequence);
 
   /**
-   * This Method returns the search matches which lie between the start and end
-   * points of the sequence in question . It is optimised for returning objects
-   * for drawing on SequenceCanvas
+   * Returns an array of [from, to, from, to..] matched columns (base 0) between
+   * the given start and end columns of the given sequence. Returns null if no
+   * matches overlap the specified region.
+   * <p>
+   * Implementations should provide an optimised method to return locations to
+   * highlight on a visible portion of an alignment.
    * 
    * @param sequence
-   *          sequence to highlight columns according to matches
    * @param start
-   *          - first column of visible region
+   *          first column of range (base 0, inclusive)
    * @param end
-   *          - last column of visible region
-   * @return int[] ranges within start/end index on sequence
+   *          last column of range base 0, inclusive)
+   * @return int[]
    */
-  public abstract int[] getResults(SequenceI sequence, int start, int end);
-
-  public abstract int getSize();
-
-  public abstract SequenceI getResultSequence(int index);
+  int[] getResults(SequenceI sequence, int start, int end);
 
   /**
-   * Returns the start position of the i'th match in the search results.
+   * 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
    * 
-   * @param i
    * @return
    */
-  public abstract int getResultStart(int i);
+  int getCount();
 
   /**
-   * Returns the end position of the i'th match in the search results.
+   * Returns true if no search result matches are held.
    * 
-   * @param i
    * @return
    */
-  public abstract int getResultEnd(int i);
+  boolean isEmpty();
 
   /**
-   * Returns true if no search result matches are held.
+   * Returns the list of matches.
    * 
    * @return
    */
-  public abstract boolean isEmpty();
+  List<SearchResultMatchI> getResults();
 
   /**
-   * Returns the list of matches.
+   * Set bits in a bitfield for all columns in the given sequence collection
+   * that are highlighted
    * 
-   * @return
+   * @param sqcol
+   *          the set of sequences to search for highlighted regions
+   * @param bs
+   *          bitset to set
+   * @return number of bits set
    */
-  public abstract List<Match> getResults();
+  int markColumns(SequenceCollectionI sqcol, BitSet bs);
 
+  /**
+   * Return sub-sequences corresponding to distinct contiguous ranges in the
+   * matching set
+   * 
+   * @return list of sequence objects
+   */
+  List<SequenceI> getMatchingSubSequences();
 }
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