/* $Id: rpsutil.h,v 6.16 2001/08/28 17:45:34 madden 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: 6.16 $ * * File Description: * Reversed PSI BLAST utilities file * * $Log: rpsutil.h,v $ * 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 #include #include #include #include #include #include #include #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 */ RPScoreRow PNTR bigMatrix; /* PSI Matrixes for all sequences */ RPSLookupPtr lookup; /* Precalculated lookup tables */ Boolean query_is_prot; /* Do we need translate query sequence ? */ } 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; 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 */ /****************************************************************************/ /* ---------------------- RPSInit -------------------------- Purpose: Initialize main structures of the RPS Search Parameters: database - BLAST database of the sequence set corresponding to PSI matrix set Returns: Poiner to created RPSInfoPtr ------------------------------------------------------------------*/ RPSInfoPtr RPSInitEx(CharPtr database, Int4 query_is_prot, BLAST_OptionsBlkPtr blast_options); 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); 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); #ifdef __cplusplus } #endif #endif /* _RPSUTIL_H_ */