X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSearchResultsI.java;h=52a0467d841304c1e41b30de5f229634339101c3;hb=7c19c72efd3433b14f845c265747010d9dc596cc;hp=f7d3468392de7a4ae8b176ce6693ea639db17c22;hpb=52402128d98c6744eb6348dd788fe6e8cd34575c;p=jalview.git

diff --git a/src/jalview/datamodel/SearchResultsI.java b/src/jalview/datamodel/SearchResultsI.java
index f7d3468..52a0467 100644
--- a/src/jalview/datamodel/SearchResultsI.java
+++ b/src/jalview/datamodel/SearchResultsI.java
@@ -1,16 +1,37 @@
+/*
+ * 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
    * 
    * @param seq
    *          Sequence
@@ -18,57 +39,66 @@ public interface SearchResultsI
    *          int
    * @param end
    *          int
+   * @return
    */
-  public abstract void addResult(SequenceI seq, int start, int end);
+  SearchResultMatchI addResult(SequenceI seq, int start, int end);
 
   /**
-   * 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
-   */
-  public abstract 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
+   * @return
    */
-  public abstract int[] getResults(SequenceI sequence, int start, int end);
-
-  public abstract int getSize();
-
-  public abstract SequenceI getResultSequence(int index);
+  boolean involvesSequence(SequenceI sequence);
 
   /**
-   * Returns the start position of the i'th match in the search results.
+   * 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 i
-   * @return
+   * @param sequence
+   * @param start
+   *          first column of range (base 0, inclusive)
+   * @param end
+   *          last column of range base 0, inclusive)
+   * @return int[]
    */
-  public abstract int getResultStart(int i);
+  int[] getResults(SequenceI sequence, int start, int end);
 
   /**
-   * Returns the end position of the i'th match in the search results.
+   * Returns the number of matches found
    * 
-   * @param i
    * @return
    */
-  public abstract int getResultEnd(int i);
+  int getSize();
 
   /**
    * Returns true if no search result matches are held.
    * 
    * @return
    */
-  public abstract boolean isEmpty();
+  boolean isEmpty();
 
   /**
    * Returns the list of matches.
    * 
    * @return
    */
-  public abstract List<Match> getResults();
+  List<SearchResultMatchI> getResults();
 
+  /**
+   * Set bits in a bitfield for all columns in the given sequence collection
+   * that are highlighted
+   * 
+   * @param sqcol
+   *          the set of sequences to search for highlighted regions
+   * @param bs
+   *          bitset to set
+   * @return number of bits set
+   */
+  int markColumns(SequenceCollectionI sqcol, BitSet bs);
 }
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