/* $Id: stsutil.h,v 6.0 1997/08/25 18:54:52 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: stsutil.h,v $ * * Author: Sergei Shavirin * * Version Creation Date: 12/18/1996 * * $Revision: 6.0 $ * * File Description: Header file for NCBI STS Search Tool utilities * * $Log: stsutil.h,v $ * Revision 6.0 1997/08/25 18:54:52 madden * Revision changed to 6.0 * * Revision 1.2 1997/05/23 15:23:22 shavirin * STS library on this step was made independent from little/big * endian and memory mapping * * Revision 1.1 1996/12/18 20:53:38 shavirin * Initial revision * * * ========================================================================== */ #ifndef _STSUTILH_ #define _STSUTILH_ stsutil /****************************************************************************/ /* DEFINES & TYPEDEFS */ /****************************************************************************/ typedef struct StsResult { Int4 id_sts; /* STS database reference ID number */ Int4 gi; /* GI currently is not available */ CharPtr acc; /* GenBank Accession number */ Int4 pos; /* Start position of STS in query sequence */ CharPtr sts_name; /* STS name from STS database */ Int4 real_len; /* Amplicon length detected in search */ Int4 exp_len; /* Amplicon length, that was expected */ CharPtr org; /* Organism STS belong to */ CharPtr chrom; /* Chromosom ( may be few ) */ CharPtr pr1; /* First STS primer */ CharPtr pr2; /* Second STS primer */ CharPtr sequence; /* Piece of query sequence containing STS */ Int4 start; /* Start of STS in returned piece */ struct StsResult *next; /* Pointer to the next Result structure */ } StsResult, PNTR StsResultPtr; typedef struct STSOrg { Int4 id; /* Organism id number (used only in this search) */ Int4 num; /* Number of entries in STS dump file */ CharPtr string; /* Organism name as a string */ } STSOrg, PNTR STSOrgPtr; typedef struct STSDbNames { CharPtr sts_db_name; /* Override default STS database name */ CharPtr sts_map_name; /* Override default STS map file name */ CharPtr sts_org_name; /* Override default STS organism list name */ } STSDbNames, PNTR STSDbNamesPtr; typedef struct STSData { CharPtr sts_db_name; /* STS database filename */ CharPtr sts_org_name; /* Organism index name */ CharPtr sts_map_name; /* Formatted STS search file */ Int4 margin; CharPtr MMAddress; /* address of MM hash file */ Nlm_MemMapPtr mmp; /* Memory mapping pointer */ STSOrgPtr PNTR OrgTable; /* Pointer to organism table */ FILE *fd_stsdb; /* File with STS db information */ } STSData, PNTR STSDataPtr; #define MAXORGNUM 50 /* Maximum number of organisms to be initialized */ /****************************************************************************/ /* FINCTION DEFINITIONS */ /****************************************************************************/ #ifdef __cplusplus extern "C" { #endif /* ------------------------- STSSearch --------------------------- Purpose: To search given string in IUPACna encoding for STS primer pairs. Parameters: query - Input IUPACna string organism - index of organism in STS search database 0 will search all organisms result - returned STSResult structure of found STS if result == NULL no hits found Returns: FALSE returned in case of fatal error NOTE: First check for returned TRUE if search was correct then check if result not == NULL. Result is linked list, so few entries may be returned at once. ------------------------------------------------------------------*/ Boolean STSSearch(CharPtr query, Int4 organism, StsResultPtr PNTR result ); Boolean STSSearch_r(STSDataPtr sts_data, CharPtr query, Int4 organism, StsResultPtr PNTR result_out); /* ----------------------- InitSTSSearch -------------------------- Purpose: All main structures, tables and memory mappings will be initiated. To override default filenames of main STS Search files use non-NULL parameter Parameters: Structure, that contains filenames of 3 main files used in search - override default names. Returns: Number of STS in initialised database of -1 if error. NOTE: Default filenames will be set to centralized place accessible via NFS. To speed up initialization reccommended to copy these files on local computer and initialise "db_name" structure. ------------------------------------------------------------------*/ Int4 InitSTSSearch(STSDbNamesPtr db_names); Int4 InitSTSSearch_r(STSDbNamesPtr db_name, STSDataPtr PNTR data_out); /* ----------------------- FiniSTSSearch ------------------------- Purpose: Terminate memory mapping, deallocate structures and close opened files. Parameters: None Returns: FALSE if error, TRUE mean success NOTE: ------------------------------------------------------------------*/ Boolean FiniSTSSearch(void); /* ----------------------- STSGetOrgTable ------------------------- Purpose: To return pointer to OrgTable used in STS Search if It was not yet initialised filename will be used to initialize it NULL initialize default filename Parameters: none Returns: Pointer to global Orgtable (non-reentrant) ------------------------------------------------------------------*/ STSOrgPtr PNTR STSGetOrgTable(void); /* ---------------------- STSGetOrganismIndex --------------------- Purpose: To return organism index by organism name Parameters: Organism name Returns: Index in OrgTable NOTE: OrgTable will be initialized with default filename if it was not done before ------------------------------------------------------------------*/ Int4 STSGetOrganismIndex(STSDataPtr sts_data, CharPtr name); /* ---------------------- STSGetOrganismName ---------------------- Purpose: To return Organism name by index Parameters: Inderx in STS Search OrgTable Returns: Pointer to organism name NOTE: OrgTable will be initialized with default filename if it was not done before ------------------------------------------------------------------*/ CharPtr STSGetOrganismName(STSDataPtr sts_data, Int4 id); /* ------------------------- STSResultNew ------------------------- Purpose: To allocate space for Result structure Parameters: None Returns: Pointer to allocated STSResult structure NOTE: ------------------------------------------------------------------*/ StsResultPtr StsResultNew(void); /* ------------------------- STSResultFree ------------------------ Purpose: To deallocate result structure Parameters: STSResult structure Returns: None NOTE: ------------------------------------------------------------------*/ void StsResultFree(StsResultPtr result); void STSDataFree(STSDataPtr sts_data); #ifdef __cplusplus } #endif #endif