X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSearchResultsI.java;h=794682412897ea634ba901595a832119749adaf8;hb=a7169b1c72607f3c9357195b4999869650a2a891;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
+ * 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