Load ncbi (6.1.20031028) into ncbi-tools6/branches/upstream/current.

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diff --git a/algo/blast/core/link_hsps.h b/algo/blast/core/link_hsps.h
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+/* $Id: link_hsps.h,v 1.6 2003/08/11 14:57:16 dondosha Exp $
+* ===========================================================================
+*
+*                            PUBLIC DOMAIN NOTICE
+*               National Center for Biotechnology Information
+*
+*  This software/database is a "United States Government Work" under the
+*  terms of the United States Copyright Act.  It was written as part of
+*  the author's offical duties as a United States Government employee and
+*  thus cannot be copyrighted.  This software/database is freely available
+*  to the public for use. The National Library of Medicine and the U.S.
+*  Government have not placed any restriction on its use or reproduction.
+*
+*  Although all reasonable efforts have been taken to ensure the accuracy
+*  and reliability of the software and data, the NLM and the U.S.
+*  Government do not and cannot warrant the performance or results that
+*  may be obtained by using this software or data. The NLM and the U.S.
+*  Government disclaim all warranties, express or implied, including
+*  warranties of performance, merchantability or fitness for any particular
+*  purpose.
+*
+*  Please cite the author in any work or product based on this material.
+*
+* ===========================================================================*/
+
+/*****************************************************************************
+
+File name: link_hsps.h
+
+Author: Ilya Dondoshansky
+
+Contents: Functions to link HSPs using sum statistics
+
+******************************************************************************
+ * $Revision: 1.6 $
+ * */
+#ifndef __LINK_HSPS__
+#define __LINK_HSPS__
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+#include <algo/blast/core/blast_hits.h>
+
+#define BLAST_SMALL_GAPS 0
+#define BLAST_LARGE_GAPS 1
+
+/* The helper arrays contains the info used frequently in the inner 
+ * for loops. -cfj
+ * One array of helpers will be allocated for each thread. See comments 
+ * preceding link_hsps in link_hsps.c for more info.
+ */
+typedef struct LinkHelpStruct {
+  BlastHSP* ptr;
+  Int4 q_off_trim;
+  Int4 s_off_trim;
+  Int4 sum[BLAST_NUMBER_OF_ORDERING_METHODS];
+  Int4 maxsum1;
+  Int4 next_larger;
+} LinkHelpStruct;
+
+/** Link HSPs using sum statistics.
+ * @param program_number BLAST program [in]
+ * @param hsp_list List of HSPs [in]
+ * @param query_info Query information block [in]
+ * @param subject Subject sequence block [in]
+ * @param sbp Scoring and statistical data [in]
+ * @param hit_params Hit saving parameters [in]
+ * @param gapped_calculation Is this a gapped search? [in]
+ */
+Int2 
+BLAST_LinkHsps(Uint1 program_number, BlastHSPList* hsp_list, 
+   BlastQueryInfo* query_info, BLAST_SequenceBlk* subject, 
+   BlastScoreBlk* sbp, BlastHitSavingParameters* hit_params,
+   Boolean gapped_calculation);
+
+#ifdef __cplusplus
+}
+#endif
+#endif /* !__LINK_HSPS__ */
+