/usr/include/ncbi/rpsutil.h

/* $Id: rpsutil.h,v 6.27 2003/10/07 15:24:10 kans 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 official 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:  $RCSfile: rpsutil.h,v $
*
* Author:  Sergei Shavirin
*
* Initial Version Creation Date: 12/14/1999
*
* $Revision: 6.27 $
*
* File Description:
*         Reversed PSI BLAST utilities file
*
* $Log: rpsutil.h,v $
* Revision 6.27  2003/10/07 15:24:10  kans
* added FreeCDDAligns
*
* Revision 6.26  2003/09/23 15:59:20  dondosha
* Initialize global variable search_is_done; allow to reset it
*
* Revision 6.25  2003/09/22 16:24:17  merezhuk
* made RPSBlastSearchEx public.
*
* Revision 6.24  2003/09/15 18:34:33  merezhuk
* made RPSBlastSearchLight public  and declared in rpsutil.h
*
* Revision 6.23  2003/03/20 14:46:12  madden
* C++ comment to C comment
*
* Revision 6.22  2003/03/20 13:52:02  madden
* Changes to support SeqAnnot output with -m10/11
*
* Revision 6.21  2003/01/24 22:26:03  camacho
* RPSInit is deprecated, use RPSInitEx instead
*
* Revision 6.20  2002/12/31 22:48:54  boemker
* Added xml_mode to RPSBlastOptions to support ASN output in
* ../demo/rpsblast.c.
*
* Revision 6.19  2002/10/17 20:36:00  camacho
* Disallow -L option for tblastn
*
* Revision 6.18  2002/10/10 14:49:43  camacho
*
* 1. Removed irrelevant options: -E, -G, -S, -H
* 2. Added -L option to provide range restriction on query sequence
*
* Revision 6.17  2002/03/26 16:47:42  madden
* Add scaled Karlin-Altschul K paramter to structure
*
* Revision 6.16  2001/08/28 17:45:34  madden
* Add is_tabular_comments field to options
*
* Revision 6.15  2001/06/29 18:07:07  madden
* Add function RPSInitEx that passes in BLAST_OptionsBlkPtr
*
* Revision 6.14  2001/06/27 16:20:00  dondosha
* Enabled tabular output for RPS Blast
*
* Revision 6.13  2000/11/03 22:38:18  kans
* added RemoveDuplicateCDDs - just removes CDDs with identical locations and identical dbxrefs, keeping one with highest score - later will want to fuse overlapping CDDs with identical dbxrefs
*
* Revision 6.12  2000/10/27 15:39:33  kans
* added AnnotateRegionsFromCDD and FreeCDDRegions for common use by ripen, Sequin, and RefSeq processor
*
* Revision 6.11  2000/10/16 19:35:18  shavirin
* Function createFakeProtein() become external.
*
* Revision 6.10  2000/09/28 18:50:11  shavirin
* Added parameter BioseqPtr query_bsp to print results callback.
*
* Revision 6.9  2000/09/27 19:09:41  shavirin
* Significantly redesigned external interface to RPS Blast.
*
* Revision 6.8  2000/09/21 13:49:55  madden
* Rename CddNew and CddDestruct to CddHitNew and CddHitDestruct
*
* Revision 6.7  2000/09/20 22:13:26  madden
* Added code to get CddHit structure
*
* Revision 6.6  2000/09/13 21:26:11  lewisg
* add RPSUpdateDbSize declaration
*
* Revision 6.5  2000/05/02 17:57:19  shavirin
* Corrected path to RPS Databases changed definition of RPSInit() function.
*
* Revision 6.4  2000/03/28 20:32:27  shavirin
* Added functions RPSInfoDetach and RPSInfoAttach.
*
* Revision 6.3  2000/02/25 17:01:14  madden
* Added copyMatrix field
*
* Revision 6.2  2000/02/11 20:44:08  shavirin
* Added possibility to search PSSM database against DNA sequence.
*
* Revision 6.1  1999/12/29 19:39:47  shavirin
* Initial revision.
*
*
* ==========================================================================
*/
#ifndef _RPSUTIL_H_
#define _RPSUTIL_H_

#include <ncbi.h>
#include <blastdef.h>
#include <blastkar.h>
#include <blast.h>
#include <blastpri.h>
#include <readdb.h>
#include <profiles.h>
#include <salpacc.h>

#ifdef __cplusplus
extern "C" {
#endif

/****************************************************************************/
/* DEFINES */
/****************************************************************************/
#define RPS_ALPHABET_SIZE 26    
#define RPS_WORD_SIZE     3
#define RPS_ARRAY_SIZE 32768    /* Size of the lookup table in ModLAEntry */

/****************************************************************************/
/* TYPEDEFS */
/****************************************************************************/

typedef BLAST_Score RPScoreRow[RPS_ALPHABET_SIZE];

typedef struct _RPSLookupHeader {
    Int4 info[8];               /* Information to be determined */
} RPSLookupHeader, PNTR RPSLookupHeaderPtr;

typedef struct _RPSLookup {
    Nlm_MemMapPtr mmLookup;     /* Memory map pointer for the lookup file */
    Int4Ptr  looktbl;           /* Main pointer to the set of lookups */
    Int4Ptr offsets;            /* Offsets to specific lookup tables */
    Int4Ptr header;             /* Lookup header information */
    Int4    entries;            /* Number of entries in the table */
} RPSLookup, PNTR RPSLookupPtr;

typedef struct _RPSequence {   
    UcharPtr sequence;          /* Pointer to the mem-mapped file */
    Int4 number;                /* Number in the database */
    Int4 seqlen;                /* Length of the sequence */
    CharPtr description;        /* Actually this is defline */
    Int4Ptr PNTR posMatrix;     /* PSI Matrix of the sequence */
    Int4Ptr PNTR copyMatrix;     /* copy of Matrix for rescaling. */
    ModLAEntry  *mod_lt;        /* Lookup table for the sequence */
    ModLookupPositionPtr mod_lookup_table_memory; /* Memory tail */
    Int4 num_pos_added;         /* Elements of lookup structure */
    Int4 num_unique_pos_added;  /* Elements of lookup structure */
    Int4 mod_lookup_table_size; /* Elements of lookup structure */
    SeqIdPtr  seqid;            /* Sequence ID in BLAST Database */
} RPSequence, PNTR RPSequencePtr;    

typedef struct _RPSInfo {
    ReadDBFILEPtr rdfp;         /* Handle of the sequence database */
    Nlm_MemMapPtr mmMatrix;     /* Memory map pointer for the matrix file */
    Int4 matrixCount;           /* Total number of PSSM matrixes */
    Int4Ptr offsets;            /* Offsets of matrixes in the file */
    Nlm_FloatHiPtr karlinK;      /* Karlin-Altschul K paramter from the aux file. */
    RPScoreRow PNTR bigMatrix;  /* PSI Matrixes for all sequences */
    RPSLookupPtr lookup;        /* Precalculated lookup tables */
    Boolean query_is_prot;      /* Do we need translate query sequence ? */
    Int4 start, stop;           /* Range restriction for the query */
    SeqLocPtr query_slp;        /* Created from the above 2 fields, for
                                   individual thread use only, supported for
                                   blastp only */
} RPSInfo, PNTR RPSInfoPtr;
    
/* Aron Bauer's structure used to save CDD hits. */
typedef struct _cdd_hit {
  CharPtr             CDDid;
  CharPtr             ShortName;
  CharPtr             Definition;
  Int4                start;
  Int4                stop;
  Int4                score;
  Nlm_FloatHi         evalue;
  Nlm_FloatHi         bit_score;
  struct _cdd_hit PNTR next;
} CddHit, PNTR CddHitPtr;

typedef struct _rps_blast_options {
    Boolean query_is_protein;
    CharPtr rps_database;
    BLAST_OptionsBlkPtr options;
    Int4 number_of_descriptions, number_of_alignments;
    Boolean html;
    Boolean believe_query;
    Uint4 align_options, print_options;
    Boolean is_xml_output;
    Boolean is_asn1_output;
    char* asn1_mode;  /* "w" or "wb" */
    AsnIoPtr aip;
    Int4 num_threads;

    /* These parameters are for foprmating convinience only */

    ReadDBFILEPtr rdfp;         /* Handle of the sequence database */
    FILE *outfp;                /* Output file opened descriptor */
    CharPtr out_filename;       /* Output filename */
   Boolean is_tabular;
   Boolean is_tabular_comments;
} RPSBlastOptions, PNTR RPSBlastOptionsPtr;

/* Definitions of multi-threaded batch RPS Blast search */    
typedef SeqEntryPtr (LIBCALLBACK *RPSReadBSPCallback)(SeqLocPtr PNTR slp, 
                                                      VoidPtr user_data);
typedef Boolean   (LIBCALLBACK *RPSHandleResultsCallback)(BioseqPtr bsp, RPSBlastOptionsPtr rpsbop, SeqAlignPtr sap, ValNodePtr other_returns, ValNodePtr error_returns, VoidPtr user_data);
Boolean RPSBlastSearchMT(RPSBlastOptionsPtr rpsbop, 
                         RPSReadBSPCallback bsp_callback, 
                         VoidPtr bsp_user_data,
                         RPSHandleResultsCallback print_callback, 
                         VoidPtr print_user_data);

/****************************************************************************/
/* FINCTION DEFINITIONS */
/****************************************************************************/

/* ----------------------  RPSInitEx --------------------------
   Purpose:     Initialize main structures of the RPS Search
                
   Parameters:  database - BLAST database of the sequence set corresponding 
                           to PSI matrix set
                query_is_prot - Whether query sequence is protein or nucleotide
                blast_options - BLAST options block
   Returns:     Poiner to created RPSInfoPtr
  ------------------------------------------------------------------*/
RPSInfoPtr RPSInitEx(CharPtr database, Int4 query_is_prot, BLAST_OptionsBlkPtr blast_options);
/*** This function is DEPRECATED. Please use RPSInitEx instead (01/24/03) ***/
RPSInfoPtr RPSInit(CharPtr database, Int4 query_is_prot);

/* ----------------------  RPSClose --------------------------
   Purpose:     De-initialize main structures of the RPS Search
                
   Parameters:  rpsinfo -  Poiner to created RPSInfoPtr

   Returns:     none
  ------------------------------------------------------------------*/
void RPSClose(RPSInfoPtr rpsinfo);

/* ----------------------  RPSGetSequence --------------------------
   Purpose:     To get sequence information by sequence number
                
   Parameters:  rpsinfo -  Poiner to created RPSInfoPtr
                seqnum - Number of the sequence to be retrieved
   Returns:     Poiner to created RPSequencePtr
  ------------------------------------------------------------------*/
RPSequencePtr RPSGetSequence(RPSInfoPtr rpsinfo, Int4 seqnum);

/* ----------------------  RPSequenceFree --------------------------
   Purpose:     De-initialize RPSequencePtr structure
                
   Parameters:  rpseqp -  Poiner to RPSequencePtr structure

   Returns:     none
  ------------------------------------------------------------------*/
void RPSequenceFree(RPSequencePtr rpseqp);

/* ----------------------  RPSequenceFree --------------------------
   Purpose:     Basic function to do search of the query sequence
                against RPS Blast database

   Parameters:  search - main Blast search structure
                query_bsp - input query sequence Bioseq
                rpsinfo - main object of RPS database

   Returns:     SeqAlign pointer.
  ------------------------------------------------------------------*/
SeqAlignPtr RPSBlastSearch (BlastSearchBlkPtr search,
                            BioseqPtr query_bsp, RPSInfoPtr rpsinfo);
/* ---------------------- RPSBlastSearchLight ----------------------
   Purpose:     create an alignment based on the passed result structure,
                will not make rps search at this point. used in SPLITD.

   Parameters:  search - main Blast search structure
                query_bsp - input query sequence Bioseq
                rpsinfo - main object of RPS database
                ready_result_struct - BLAST results structure
   -----------------------------------------------------------------*/ 
SeqAlignPtr RPSBlastSearchLight (BlastSearchBlkPtr search,
                                 BioseqPtr query_bsp, RPSInfoPtr rpsinfo,
                                 BLASTResultsStructPtr   ready_result_struct);
/* -----------------------------------------------------------------
   Purpose:     support RPS searches with Net-result-struct type of results 
   Parameters:  search    - main Blast search structure
                query_bsp - input query sequence Bioseq
                rpsinfo   - main object of RPS database
                partial   - weather search is partial or not
   -----------------------------------------------------------------*/
SeqAlignPtr RPSBlastSearchEx (BlastSearchBlkPtr search,
                              BioseqPtr query_bsp, RPSInfoPtr rpsinfo, Boolean partial);

RPSInfoPtr RPSInfoAttach(RPSInfoPtr rpsinfo);
void RPSInfoDetach(RPSInfoPtr rpsinfo);
void RPSUpdateDbSize(BLAST_OptionsBlkPtr options, RPSInfoPtr rpsinfo, Int4 query_length);

BioseqPtr createFakeProtein(void);

/*
	Functions to retrieve CDD hit information.
*/

CddHitPtr CddHitDestruct(CddHitPtr cdd); /* frees memory for every CddHitPtr in linked list. */
CddHitPtr CddHitNew(void); /* produces only one CddHitPtr. */
CddHitPtr RPSBgetCddHits(SeqAlignPtr sap);

/* functions to take BlastBioseqNet result and annotate region features on proteins */

NLM_EXTERN void AnnotateRegionsFromCDD (BioseqPtr bsp, SeqAlignPtr salp, FloatHi expectValue);
NLM_EXTERN void RemoveDuplicateCDDs (SeqEntryPtr topsep);
NLM_EXTERN void FreeCDDRegions (SeqEntryPtr topsep);
NLM_EXTERN void FreeCDDAligns (SeqEntryPtr topsep);

/* Reset the global variable responsible for testing whether search is done */
NLM_EXTERN void ResetRPS(void);

#ifdef __cplusplus
}
#endif

#endif /* _RPSUTIL_H_ */
libncbi6-dev 6.1.20120620-7 / usr / include / ncbi / rpsutil.h
