/* $Id: wwwblast.h,v 6.8 2000/10/31 20:17:13 shavirin 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: wwwblast.h,v $ * * Author: Sergei Shavirin * * Initial Creation Date: 03/15/2000 * * $Revision: 6.8 $ * * File Description: * Definitions for standalone WWW Blast CGI program. * * $Log: wwwblast.h,v $ * Revision 6.8 2000/10/31 20:17:13 shavirin * Added definition of the function TestSTDOut(void); * * Revision 6.7 2000/09/27 22:18:04 shavirin * Added possibility to limit search to results of entrez query. * * Revision 6.6 2000/09/12 22:00:24 dondosha * Added matrix to BLASTPrintData structure * * Revision 6.5 2000/09/08 20:15:12 dondosha * Added WWWBlastErrMessageEx, taking a CharPtr seq_info argument * * Revision 6.4 2000/09/05 15:25:20 shavirin * Added #include to remove warning. * * Revision 6.3 2000/08/28 20:20:21 dondosha * Added a SeqLoc linked list argument to WWWBlastInfo structure for multiple query search * * Revision 6.2 2000/08/09 20:29:16 shavirin * Added new parameters to the info structure xml_output and CHARPosFreqs * * Revision 6.1 2000/05/17 15:52:42 shavirin * Initial revision in new location. * * * ========================================================================== */ #include #include #include #include #include #include #include #include #include #include #ifdef NCBI_CLIENT_SERVER #include #endif typedef enum { BLASTNoError = 0, /* no error */ BLASTNetwork = -1, BLASTNoSpace = -2, BLASTBadFileName = -3, BLASTNotImplemented = -4, BLASTErrProgram = -5, /* program missing from posting data */ BLASTErrDatalib = -6, /* datalib missing from posting data */ BLASTErrProgName = -7, /* program name is not supported */ BLASTErrNoSequence = -8, /* NULL sequence passed to the engine */ BLASTErrCombination = -9, /* Invalid program/database combination */ BLASTNoMemory = -10, /* too bad ... */ BLASTNCBI_DATA = -11, /* DATA files missing on any path */ BLASTFastaToSE = -12, /* FastaToSeqEntry() returned NULL */ BLASTErrOptions = -13, /* Badly formatted options */ BLASTErrNoQueue = -14, /* Queue overloaded */ BLASTConfigFile = -15, /* Error reading config file */ BLASTEntrez = -16, /* Cannot connect to Entrez */ BLASTAccesssion = -17, /* Invalid of unavailable accession */ BLASTSendmail = -18, /* Cannot start sendmail process */ BLASTAddress = -19, /* Invalid return address */ BLASTOptionStr = -20, /* Invalidly formatted advanced string */ BLASTErrAccType = -21, /* wrong type of sequence identifier */ BLASTErrClient = -22, /* cannot connect to the Blast service */ BLASTErrServer = -23, /* Error from the server side */ BLASTMiscError = -99 /* undefined internal error */ } BLASTErrCode; #define MAX_DB_NUM 256 /* Max. total number of concurrent running requests */ #define DEFAULT_RUN_MAX 2 /* Max. total number of waiting requests */ #define DEFAULT_QUEUE_MAX 100 #define NUM_CPU_TO_USE 4 #define DEFAULT_DESCRIPTIONS 100 #define DEFAULT_ALIGNMENTS 50 #define DEFAULT_EXPECT 10 /* CPU time limit. */ #define DEFAULT_CPU_LIMIT 3600 typedef struct BLASTConfig { Int4 run_max; Int4 queue_max; Int4 num_cpu; Int4 niceval; CharPtr allow_db[MAX_DB_NUM]; } BLASTConfig, PNTR BLASTConfigPtr; typedef struct _www_blast_info { BLAST_OptionsBlkPtr options; WWWInfoPtr info; BLASTErrCode error_code; CharPtr ConfigFile; CharPtr program, database, blast_type; BioseqPtr query_bsp; BioseqPtr fake_bsp; Int4 number_of_descriptions, number_of_alignments; Boolean query_is_na, db_is_na, align_type, show_gi, show_overview; Boolean believe_query; Uint4 align_options, print_options; Int4 align_view, input_type, color_schema; Boolean is_phi_blast; Boolean show_tax_blast; Boolean xml_output; BLASTConfigPtr blast_config; CharPtr www_root_path; SeqLocPtr query_slp; /* For multiple query search */ /* Limitation to list of gis - due to may be entrez query */ BlastDoubleInt4Ptr gi_list; Int4 gi_list_total; } WWWBlastInfo, PNTR WWWBlastInfoPtr; /* Structures used in PHI/PSI Blast searches */ typedef struct GIList { Int4 gi; struct GIList *next; } GIList, PNTR GIListPtr; typedef struct PSIData { CharPtr matrix62; CharPtr CHARPosFreqs; GIListPtr PrevCheckedGIs; GIListPtr PrevGoodGIs; Int4 StepNumber; Nlm_FloatHi karlinK; } PSIData, PNTR PSIDataPtr; typedef struct BLASTPrintData { SeqAlignPtr seqalign; BLAST_KarlinBlkPtr ka_params, ka_params_gap; TxDfDbInfoPtr dbinfo; CharPtr buffer; ValNodePtr mask_loc; PSIDataPtr psidata; SeqLocPtr seqloc; ValNodePtr vnp; /* PHI-BLAST output. */ ValNodePtr info_vnp; /* PHI-Blast info strings */ BLAST_MatrixPtr matrix; /* Needed for the positives computation */ } BLASTPrintData, PNTR BLASTPrintDataPtr; /* ------------------------------------------- */ void WWWBlastInfoFree(WWWBlastInfoPtr theInfo); void WWWBlastErrMessageEx(BLASTErrCode error_code, CharPtr error_msg, CharPtr seq_info); void WWWBlastErrMessage(BLASTErrCode error_code, CharPtr error_msg); WWWBlastInfoPtr WWWBlastReadArgs(CharPtr type); Boolean BLAST_Time(CharPtr string, Int4 len, time_t seconds); Boolean WWWValidateOptions(WWWBlastInfoPtr theInfo); Boolean WWWCreateSearchOptions(WWWBlastInfoPtr theInfo); Boolean TestSTDOut(void); /* PSI/PHI Blast-related function */ void BLASTPrintDataFree(BLASTPrintDataPtr data); Boolean SplitSeqAlign(SeqAlignPtr seqalign, SeqAlignPtr *GoodSeqAlignment_ptr, SeqAlignPtr *BadSeqAlignment_ptr, SeqAlignPtr *lastGood_ptr, Int2Ptr *marks_ptr, Int2Ptr countBad_ptr, Int2Ptr countGood_ptr, Nlm_FloatHi ethresh_old); BLASTPrintDataPtr PSIBlastSearch(WWWBlastInfoPtr theInfo); BLASTPrintDataPtr PHIBlastSearch(WWWBlastInfoPtr theInfo);