X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSearchResultsI.java;h=794682412897ea634ba901595a832119749adaf8;hb=a7169b1c72607f3c9357195b4999869650a2a891;hp=93183f222325cc92f544239717a2af24b4a3e5b4;hpb=1145ab823ba8ffd317754588efeb259d70c1f4a1;p=jalview.git
diff --git a/src/jalview/datamodel/SearchResultsI.java b/src/jalview/datamodel/SearchResultsI.java
index 93183f2..7946824 100644
--- a/src/jalview/datamodel/SearchResultsI.java
+++ b/src/jalview/datamodel/SearchResultsI.java
@@ -1,3 +1,23 @@
+/*
+ * 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.datamodel;
import java.util.BitSet;
@@ -11,19 +31,34 @@ public interface SearchResultsI
{
/**
- * Adds one region to the results
+ * 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
+ */
+ void addSearchResults(SearchResultsI toAdd);
+
+ /**
* Answers true if the search results include the given sequence (or its
* dataset sequence), else false
*
@@ -50,11 +85,13 @@ public interface SearchResultsI
int[] getResults(SequenceI sequence, int start, int end);
/**
- * Returns the number of matches found
+ * 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
*
* @return
*/
- int getSize();
+ int getCount();
/**
* Returns true if no search result matches are held.
@@ -81,4 +118,12 @@ public interface SearchResultsI
* @return number of bits set
*/
int markColumns(SequenceCollectionI sqcol, BitSet bs);
+
+ /**
+ * Return sub-sequences corresponding to distinct contiguous ranges in the
+ * matching set
+ *
+ * @return list of sequence objects
+ */
+ List getMatchingSubSequences();
}
\ No newline at end of file