/************************************************************************** * * * National Center for Biotechnology Information * * Bldg. 38A, NIH, 8600 Rockville Pike, Bethesda, MD 20894 * * * * COPYRIGHT NOTICE * * * * This software/database is categorized as "United States Government * * Work" under the terms of the United States Copyright Act. It was * * produced as part of the author's official duties as a Government * * employee and thus can not be copyrighted. This software/database is * * freely available to the public for use without a copyright notice. * * Restrictions can not be placed on its present or future use. * * * * Although all reasonable efforts have been taken to ensure the accuracy * * and reliability of the software and data, the National Library of * * Medicine (NLM) and the U.S. Government do not and can not warrant the * * performance or results that may be obtained by using this software, * * data, or derivative works thereof. The NLM and the U.S. Government * * disclaim any and all warranties, expressed or implied, as to the * * performance, merchantability or fitness for any particular purpose or * * use. * * * * In any work or product derived from this material, proper attribution * * of the author(s) as the source of the software or data would be * * appreciated. * * * Karlin, Samuel and Stephen F. Altschul (1990). Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes. Proc. Natl. Acad. Sci. USA 87:2264-2268. Altschul, Stephen F., Warren Gish, Webb Miller, Eugene W. Myers, and David J. Lipman (1990). A basic local alignment search tool. J. Mol. Biol. 215:403-410. Gish, Warren and David J. States (1993). Identification of protein coding regions by database similarity search. Nature Genetics 3:266-72. **************************************************************************/ /* (For a better look, set tabstops every 4 columns) */ #ifndef __BLAST_H__ #define __BLAST_H__ #include #include #include #define LOCALITY "WashU" /* EXTERN should be defined in the main program module only */ #ifndef EXTERN #define EXTERN extern #ifndef INITIAL #define INITIAL(x) #endif #else #ifndef INITIAL #define INITIAL(x) = x #endif #ifndef INIT #define INIT #endif #endif /* location of substitution matrix (Dayhoff, PAM, BLOSUM, Gonnet) files */ #define BLASTMAT "/usr/ncbi/blast/matrix" /* location of database files */ #define BLASTDB "/usr/ncbi/blast/db" /* location of sequence filter programs */ #define BLASTFILTER "/usr/ncbi/blast/filter" /* location of codon frequency information files */ #define BLASTCDI "/usr/ncbi/blast/cdi" #ifdef OS_UNIX /* qsort based on the BSD UNIX version provides 2X faster sorting */ #define hsort qsort #endif enum blast_prog_id { PROG_ID_UNKNOWN = 0, PROG_ID_BLASTP, PROG_ID_BLASTN, PROG_ID_BLASTX, PROG_ID_TBLASTN, PROG_ID_TBLASTX, PROG_ID_BLAST3, PROG_ID_MAX }; #define AA_SEQTYPE BLAST_ALPHATYPE_AMINO_ACID #define NT_SEQTYPE BLAST_ALPHATYPE_NUCLEIC_ACID /* Filename extensions used by the two types of databases (a.a. and nt.) */ #define AA_HEADER_EXT ".ahd" #define AA_TABLE_EXT ".atb" #define AA_SEARCHSEQ_EXT ".bsq" #define NT_HEADER_EXT ".nhd" #define NT_TABLE_EXT ".ntb" #define NT_SEARCHSEQ_EXT ".csq" #ifdef BLASTP #undef BLASTP #define BLASTP 1 #define PROG_ID PROG_ID_BLASTP #define PROG_NAME "blastp" #define PROG_DESC "compare a protein query sequence to a protein sequence database" #define QUERY_RAW BLAST_ALPHATYPE_AMINO_ACID #define QUERY_COOKED BLAST_ALPHATYPE_AMINO_ACID #define DB_RAW BLAST_ALPHATYPE_AMINO_ACID #define DB_COOKED BLAST_ALPHATYPE_AMINO_ACID #define DEFAULT_E_MAX 10000. #define DEFAULT_E2 0.5 #define DEFAULT_M "BLOSUM62" #define DEFAULT_W 3 #define DEFAULT_T 13 /* an empirical value is computed if possible */ #define MATRIX_MAX BLAST_WORDFINDER_CONTEXT_MAX #endif #ifdef BLASTN #undef BLASTN #define BLASTN 1 #define PROG_ID PROG_ID_BLASTN #define PROG_NAME "blastn" #define PROG_DESC "compare a nucleotide query sequence to a nucleotide sequence database" #ifndef PROC_DEFAULT #define PROC_DEFAULT 4 #endif #define QUERY_RAW BLAST_ALPHATYPE_NUCLEIC_ACID #define QUERY_COOKED BLAST_ALPHATYPE_NUCLEIC_ACID #define DB_RAW BLAST_ALPHATYPE_NUCLEIC_ACID #define DB_COOKED BLAST_ALPHATYPE_NUCLEIC_ACID #define DEFAULT_E_MAX 10000. #define DEFAULT_E2 0.05 #define DEFAULT_M NULL #define DEFAULT_W 11 #define DEFAULT_T (5*DEFAULT_W) #define MATRIX_MAX 1 #endif #ifdef BLASTX #undef BLASTX #define BLASTX 1 #define PROG_ID PROG_ID_BLASTX #define PROG_NAME "blastx" #define PROG_DESC "compare a translated nucleotide query sequence to a protein sequence database" #define QUERY_RAW BLAST_ALPHATYPE_NUCLEIC_ACID #define QUERY_COOKED BLAST_ALPHATYPE_AMINO_ACID #define DB_RAW BLAST_ALPHATYPE_AMINO_ACID #define DB_COOKED BLAST_ALPHATYPE_AMINO_ACID #define DISPLAYGCODES display_gcodes #define DEFAULT_E_MAX 10000. #define DEFAULT_E2 0.25 #define DEFAULT_M "BLOSUM62" #define DEFAULT_W 3 #define DEFAULT_T 14 /* an empirical value is computed if possible */ #define MATRIX_MAX 1 #endif #ifdef TBLASTN #undef TBLASTN #define TBLASTN 1 #define PROG_ID PROG_ID_TBLASTN #define PROG_NAME "tblastn" #define PROG_DESC "compare a protein query sequence to a translated nucleotide sequence database" #define QUERY_RAW BLAST_ALPHATYPE_AMINO_ACID #define QUERY_COOKED BLAST_ALPHATYPE_AMINO_ACID #define DB_RAW BLAST_ALPHATYPE_NUCLEIC_ACID #define DB_COOKED BLAST_ALPHATYPE_AMINO_ACID #define DISPLAYGCODES display_gcodes #define DEFAULT_E_MAX 10000. #define DEFAULT_E2 0.15 #define DEFAULT_M "BLOSUM62" #define DEFAULT_W 3 #define DEFAULT_T 13 /* an empirical value is computed if possible */ #define MATRIX_MAX 1 #endif #ifdef TBLASTX #undef TBLASTX #define TBLASTX 1 #define PROG_ID PROG_ID_TBLASTX #define PROG_NAME "tblastx" #define PROG_DESC "compare a translated nucleotide query sequence to a translated nucleotide sequence database" #define QUERY_RAW BLAST_ALPHATYPE_NUCLEIC_ACID #define QUERY_COOKED BLAST_ALPHATYPE_AMINO_ACID #define DB_RAW BLAST_ALPHATYPE_NUCLEIC_ACID #define DB_COOKED BLAST_ALPHATYPE_AMINO_ACID #define DISPLAYGCODES display_gcodes #define DEFAULT_E_MAX 10000. #define DEFAULT_E2 0.1 #define DEFAULT_M "BLOSUM62" #define DEFAULT_W 3 #define DEFAULT_T 15 /* an empirical value is computed if possible */ #define MATRIX_MAX 1 #endif #ifdef BLAST3 #undef BLAST3 #define BLAST3 1 #define PROG_ID PROG_ID_BLAST3 #define PROG_NAME "blast3" #define QUERY_RAW BLAST_ALPHATYPE_AMINO_ACID #define QUERY_COOKED BLAST_ALPHATYPE_AMINO_ACID #define DB_RAW BLAST_ALPHATYPE_AMINO_ACID #define DB_COOKED BLAST_ALPHATYPE_AMINO_ACID #define DEFAULT_E 1000. /* Need many insignificant HSPs for 3-way stuff */ #define MATRIX_MAX 1 #endif #ifndef PROG_ID #define PROG_ID PROG_ID_UNKNOWN #endif #ifndef PROG_NAME #define PROG_NAME NULL #endif #ifndef PROG_VERSION #define PROG_VERSION "not available" #endif #ifndef PROG_DATE #define PROG_DATE "not available" #endif #ifndef PROG_DESC #define PROG_DESC "not available" #endif #ifndef PROC_MAX #define PROC_MAX THREADS_MAX #endif #ifndef PROC_DEFAULT #define PROC_DEFAULT PROC_MAX #endif #if QUERY_COOKED == NT_SEQTYPE && DB_COOKED == NT_SEQTYPE #define WORDSIZE_MIN 1 /* min. length of critical word */ #define WORDSIZE_MAX 20 /* max. length of critical word */ #else #define WORDSIZE_MIN 1 /* min. length of critical word */ #define WORDSIZE_MAX 12 /* max. length of critical word */ #endif #ifndef QUERYLEN_MAX #if QUERY_COOKED == NT_SEQTYPE #define QUERYLEN_MAX 700000 #else #define QUERYLEN_MAX 50000 #endif #endif /* !QUERYLEN_MAX */ /* Define the common default parameters */ #ifndef DEFAULT_E #define DEFAULT_E 10. /* default expect for reporting HSPs */ #endif #ifndef DEFAULT_E_MAX #define DEFAULT_E_MAX 1000. #endif #ifndef DEFAULT_M #define DEFAULT_M NULL #endif #ifndef MATRIX_MAX #define MATRIX_MAX 0 #endif #ifndef QUERY_RAW #define QUERY_RAW BLAST_ALPHATYPE_UNDEFINED #endif #ifndef QUERY_COOKED #define QUERY_COOKED BLAST_ALPHATYPE_UNDEFINED #endif #ifndef DB_RAW #define DB_RAW BLAST_ALPHATYPE_UNDEFINED #endif #ifndef DB_COOKED #define DB_COOKED BLAST_ALPHATYPE_UNDEFINED #endif #ifndef DISPLAYGCODES #define DISPLAYGCODES NULL #endif #ifndef DEFAULT_E2 #define DEFAULT_E2 0.25 #endif #ifndef DEFAULT_W #define DEFAULT_W 3 #endif #ifndef DEFAULT_V #define DEFAULT_V 500 #endif #ifndef DEFAULT_C #define DEFAULT_C BLAST_GCODE_DEFAULT /* default genetic code is Standard */ #endif #ifndef REMEMBER_EXTRA /* max. no. of extra db sequences to remember above what will be reported */ #define REMEMBER_EXTRA 200 #endif #ifndef HSP_MAX /* max. no. of HSPs to save per database sequence */ #define HSP_MAX 1000 #endif #ifndef DEFAULT_showhist #define DEFAULT_showhist 0 #endif #ifndef DEFAULT_showblast #define DEFAULT_showblast 250 #endif #define NTICKS 50 /* Max. number of ticks to show in the search progress */ #define PLURAL(i) ((i) == 1 ? "" : "s") #include "error.h" #include "alphabet.h" #define _DFA_PRIVATE_ #include enum score_type { SCORET_UNDEFINED = 0, SCORET_EXPECT = 1, SCORET_PVALUE = 2 }; typedef unsigned char PACK_TYPE; /* Compressed nuc. sequence datatype */ typedef struct { Boolean valid; BLAST_StrPtr seq; int stdframe; /* standard frame number (+3, +2, +1, -1, -2, -3) */ int W; BLAST_Score S2, /* cutoff score for this context */ S, /* equiv. HSP cutoff for this reading context */ X, /* drop-off score for this reading frame */ T, maxscore, /* maximum achievable score */ highs_exp; /* expected high score */ double E, E2; BLAST_ScoreBlkPtr sbp; BLAST_KarlinBlkPtr kbp; BLAST_WFSearchStats wfstats; } Contxt, PNTR ContxtPtr; #ifdef MPROC_AVAIL /* Multiprocessing context, one for each processor */ typedef struct mpcontext { long realHSP, hasHSP, hsp_max_exceeded; BLAST_HitListPtr firsthl; } MPContext, *MPContextPtr; #define MP mp #define MPC mp, #define MPPROTO MPContextPtr #define MPPROTOC MPContextPtr, #define MPDEF MPContextPtr mp; #define MPPTR mp-> #define MPINIT(n) {mp = &mpc[(n)];} #else /* !MPROC_AVAIL */ /* Dummy definitions when multiprocessing is not used */ #define MP #define MPC #define MPPROTO #define MPPROTOC #define MPDEF #define MPPTR #define MPINIT(n) #endif /* !MPROC_AVAIL */ #ifdef BLAST3 struct record { BLAST_Score score; BLAST_Score scor3; unsigned long seq2; unsigned long seq3; long start1; long dg2; long dg3; long length; }; #define RECORD_MAX 40000 #endif typedef struct { int id;/* genetic code identifiers selected from NCBI Toolbox domain */ CharPtr name; /* visible name for this code */ CharPtr code; /* the genetic code itself */ CharPtr inits; /* potential initiator methionines */ } GenCode, PNTR GenCodePtr; typedef struct score_hist { unsigned long PNTR hist; unsigned long below, above; int dim; /* dimension of *hist (0...dim-1) */ double minval, maxval, base, incr; } ScoreHist, PNTR ScoreHistPtr; typedef enum { ALTSCORE_SPECIFIC = 0, /* specific value provided in "altscore" element */ ALTSCORE_MIN = 1, /* minium of any value observed in the matrix */ ALTSCORE_MAX, /* maximum of any value observed in the matrix */ ALTSCORE_NA /* juxtaposition of residue(s) not allowed */ } AltScoreClass, PNTR AltScoreClassPtr; typedef struct altscores { Boolean c1any, c2any; BLAST_Letter c1, c2; AltScoreClass class; BLAST_Score altscore; } AltScore, PNTR AltScorePtr; #define TOP_STRAND 1 #define BOTTOM_STRAND 2 #include "blastasn.h" #include "dbase.h" void LIBCALL usage PROTO((void)); void LIBCALL busage VPROTO((enum blast_error err, char *format, ...)); int LIBCALL parse_args PROTO((int argc, CharPtr PNTR argv)); void banner PROTO((BlastIoPtr boutp, CharPtr progname, CharPtr desc, CharPtr version, CharPtr rel_date, Link1BlkPtr citation, Link1BlkPtr notice, BLAST_AlphaType PNTR susage, BLAST_AlphaType PNTR qusage)); int LIBCALL std_defaults PROTO((void)); int LIBCALL parm_ensure_flag PROTO((CharPtr opt, int minlen)); int LIBCALL parm_ensure_int PROTO((CharPtr opt, int minlen, int value)); int LIBCALL parm_ensure_long PROTO((CharPtr opt, int minlen, long value)); int LIBCALL parm_ensure_double PROTO((CharPtr opt, int minlen, CharPtr format, double value)); BLAST_StrPtr get_query PROTO((CharPtr filename, BLAST_AlphabetPtr ap, BLAST_AlphaType sequsage[2], unsigned W, int strands)); void query_ack PROTO((BLAST_StrPtr sp, int strands)); BLAST_ScoreBlkPtr get_weights PROTO((int matid, CharPtr mname, BLAST_AlphabetPtr ap1, BLAST_AlphabetPtr ap2, ValNodePtr altscores)); int LIBCALL apply_altscores PROTO((BLAST_ScoreBlkPtr sbp, ValNodePtr altscores)); double LIBCALL context_count PROTO((ContxtPtr ctxp, int nctx)); int LIBCALL set_context PROTO((ContxtPtr ctxp, int W, enum blast_sensitivity sensitivity, double Xbits, double avglen, double dblen)); int LIBCALL context_expect_set PROTO((ContxtPtr ctxp, int nctx)); BLAST_KarlinBlkPtr LIBCALL lambdak PROTO((BLAST_StrPtr, BLAST_ScoreBlkPtr)); int LIBCALL adjust_kablks PROTO((ContxtPtr ctx0, int nctx, ContxtPtr stdctx)); int LIBCALL stk_context_parms PROTO((ValNodePtr PNTR stp, ContxtPtr ctxp0, int nctx, ContxtPtr stdctxp)); int LIBCALL stk_context_stats PROTO((ValNodePtr PNTR stp, ContxtPtr ctxp0, int nctx)); GenCodePtr find_gcode PROTO((int id)); int LIBCALL display_gcodes PROTO((FILE *fp)); void init_gcode PROTO((BLAST_AlphabetPtr, GenCodePtr, unsigned char [64], unsigned char [64])); BLAST_Letter codon2aa PROTO((BLAST_AlphabetPtr, UcharPtr, BLAST_Letter, BLAST_Letter, BLAST_Letter)); void sort_HSPs PROTO((BLAST_HitListPtr)); void sort_hitlists_by_seqid PROTO((void)); DBFilePtr LIBCALL initdb PROTO((BlastIoPtr biop, CharPtr dbname, BLAST_AlphaType restype, BSRV_DbDescPtr ddp)); BLAST_StrPtr LIBCALL revcomp PROTO((BLAST_StrPtr)); int LIBCALL get_seq_from_fasta PROTO((CharPtr buf, BLAST_Coord start, unsigned long len, MFILE *mfp, off_t offset, int line_len)); int LIBCALL get_seq_from_fasta_xl PROTO((BLAST_LetterPtr buf, BLAST_Coord start, size_t len, MFILE *mfp, off_t offset, int line_len, BLAST_AlphabetPtr ap)); int LIBCALL get_seq_from_cseq PROTO((BLAST_LetterPtr buf, BLAST_Coord start, unsigned long len, MFILE *mfp, unsigned char *c_seq0, off_t offset)); int LIBCALL get_seq_from_cseq_xl PROTO((CharPtr buf, BLAST_Coord start, unsigned long len, MFILE *mfp, unsigned char *c_seq0, off_t offset, CharPtr xltab)); void get_headers PROTO((DBFilePtr dbfp, BLAST_HitListPtr hlp)); int print_headers PROTO((FILE *fp, BLAST_HitListPtr hlp, double maxpval, int hasframe)); int LIBCALL dbtag_id PROTO((CharPtr fastaId)); int wrap PROTO((FILE *fp, char *pref, char *s, int slen, int linelen, int margin)); int print_HSPs PROTO((BlastIoPtr biop, BLAST_HitListPtr hlp, double maxpval, int (*)())); int LIBCALL print_p PROTO((BlastIoPtr biop, BLAST_HitListPtr hlp)); int LIBCALL print_n PROTO((BlastIoPtr biop, BLAST_HitListPtr hlp)); int LIBCALL print_x PROTO((BlastIoPtr biop, BLAST_HitListPtr hlp)); int LIBCALL print_t PROTO((BlastIoPtr biop, BLAST_HitListPtr hlp)); int LIBCALL print_tx PROTO((BlastIoPtr biop, BLAST_HitListPtr hlp)); BLAST_HSPPtr LIBCALL eval_hits PROTO((BLAST_HSPPtr, double)); BLAST_HSPPtr LIBCALL sump PROTO((BLAST_ConfigPtr, BLAST_HSPPtr, double)); void process_hits PROTO((TaskBlkPtr, BLAST_HitListPtr, double)); BLAST_Score fmaxscore PROTO((BLAST_StrPtr sp, BLAST_Coord start, BLAST_Coord len, BLAST_ScoreBlkPtr sbp)); void pvals PROTO((BLAST_HitListPtr hlp, unsigned long qlen, unsigned long tlen, unsigned long dblen)); int get_fasta PROTO((BLAST_StrPtr, BLAST_AlphabetPtr, FILE *, int noisy, int qres_option)); int put_fasta PROTO((BLAST_StrPtr, FILE *)); int seqfilter PROTO((CharPtr cmd, CharPtr name, size_t namelen, BLAST_StrPtr sp)); CharPtr _cdecl pick_filter PROTO((CharPtr cmdstring, BLAST_AlphaType restype)); int LIBCALL format_parms PROTO((ValNodePtr PNTR)); int LIBCALL format_stats PROTO((ValNodePtr PNTR)); int LIBCALL print_stack PROTO((BlastIoPtr, CharPtr cp, ValNodePtr stk)); void LIBCALL stkprint VPROTO((ValNodePtr PNTR stk, char *format, ...)); void LIBCALL stkprintnl VPROTO((ValNodePtr PNTR stk)); int hsp_asnout PROTO((AsnIoPtr aip, BLAST_HSPPtr hp, BLAST_ScoreBlkPtr)); int hsp_print PROTO((FILE *fp, BLAST_HSPPtr hp, int compat)); long nox_coord PROTO((unsigned long seqlen, int frame, unsigned long off)); long nt_coord PROTO((unsigned long seqlen, int frame, unsigned long off)); long apo_to_nt1 PROTO((unsigned long ntlen, int frame, unsigned long aaoff)); long apo_to_nt3 PROTO((unsigned long ntlen, int frame, unsigned long aaoff)); CharPtr str_frame PROTO((int frame)); CharPtr str_strand PROTO((int frame)); void sort_hitlists PROTO((BLAST_HitListPtr PNTR first, int (*)())); void print_hist PROTO((BLAST_Score score_hist_dim, unsigned long *score_hist, BLAST_Score S, BLAST_Score T, BLAST_KarlinBlkPtr kbp, double qlen, double dblen, unsigned long nbr_seqs)); size_t hsp_count PROTO((BLAST_HitListPtr hlp)); size_t hitlist_count PROTO((BLAST_HitListPtr hlp)); void hitlist_truncate PROTO((BLAST_HitListPtr PNTR hlpp, unsigned cnt)); void hitlist_save PROTO((BLAST_HLPoolPtr pbp, BLAST_HitListPtr PNTR head, BLAST_HitListPtr hlp)); EXTERN int (*spanfunc) PROTO((BLAST_HSPPtr hp1, BLAST_HSPPtr hp2)) INITIAL(span2); EXTERN CharPtr overlap_option; EXTERN Boolean gi_option; EXTERN Boolean qtype_option; EXTERN Boolean qres_option; #ifndef IDLEN_MAX #define IDLEN_MAX 25 #endif EXTERN int idlen_max INITIAL(IDLEN_MAX); EXTERN Contxt ctx[BLAST_WORDFINDER_CONTEXT_MAX]; EXTERN int nctx; EXTERN double ctxfactor; EXTERN Boolean ctxfactor_set; int LIBCALL get_dbdesc_bld_date PROTO((BSRV_DbDescPtr ddp, CharPtr fname)); int LIBCALL get_dbdesc_rel_date PROTO((BSRV_DbDescPtr ddp)); int cmp_hitlists_by_seqid PROTO((BLAST_HitListPtr *, BLAST_HitListPtr *)); int ckseqtype PROTO((BLAST_StrPtr str)); int translate PROTO((BLAST_StrPtr nsp, BLAST_StrPtr t1, BLAST_StrPtr t2, BLAST_StrPtr t3, BLAST_AlphabetPtr ntap, BLAST_AlphabetPtr aaap, unsigned char gcode[64])); int btranslate PROTO((BLAST_StrPtr nsp, BLAST_StrPtr t1, BLAST_StrPtr t2, BLAST_StrPtr t3, BLAST_AlphabetPtr ntap, BLAST_AlphabetPtr aaap, unsigned char revgcode[64])); void trans2 PROTO((BLAST_LetterPtr nt, BLAST_LetterPtr aa, int len, BLAST_AlphabetPtr ap, unsigned char gcode[64])); void rtrans2 PROTO((BLAST_LetterPtr nt, BLAST_LetterPtr aa, int len, BLAST_AlphabetPtr ap, unsigned char revgcode[64])); void trans2b PROTO((BLAST_LetterPtr nt, BLAST_LetterPtr aa, int len, BLAST_AlphabetPtr ap, unsigned char gcode[64])); void rtrans2b PROTO((BLAST_LetterPtr nt, BLAST_LetterPtr aa, int len, BLAST_AlphabetPtr ap, unsigned char gcode[64])); ScoreHistPtr LIBCALL ScoreHistNew PROTO((double minval, double maxval, unsigned ncols)); ScoreHistPtr LIBCALL ScoreHistDup PROTO((ScoreHistPtr)); void LIBCALL ScoreHistAddPoint PROTO((ScoreHistPtr shp, double value)); int LIBCALL ScoreHistPrint PROTO((ScoreHistPtr shp, FILE *fp, double real_expect, unsigned long real_observed)); void LIBCALL ScoreHistAdd PROTO((ScoreHistPtr sum, ScoreHistPtr shp)); void RunWild PROTO((int jobid, char *desc, unsigned long n, void (*func)())); void collate_hits PROTO((BLAST_WordFinderPtr)); long tot_real PROTO((void)); int merge_purge PROTO((TaskBlkPtr tp)); FILE *ckopen PROTO((char *fname, char *mode, int die)); VoidPtr ckalloc PROTO((size_t amt)), /* storage allocator */ ckrealloc PROTO((VoidPtr ptr,size_t amt)), /* realloc() */ ckalloc0 PROTO((size_t amt)); /* with zero initialization */ void bfatal VPROTO((enum blast_error blastapp_errno, char *format, ...)); int LIBCALL fatal_msg PROTO((FILE *fp, char *msg)); void exit_code PROTO((enum blast_error, CharPtr reason)); void warning VPROTO((char *format, ...)); void ckwarnings PROTO((void)); void SigTerm PROTO((int sig)); enum Dbtag_ids { Dbtag_unk = -1, Dbtag_notset = 0, Dbtag_lcl = 1, Dbtag_bbs, Dbtag_bbm, Dbtag_gim, Dbtag_gb, Dbtag_emb, Dbtag_pir, Dbtag_sp, Dbtag_pat, Dbtag_oth, Dbtag_gnl, Dbtag_gi, Dbtag_dbj, Dbtag_prf, Dbtag_pdb, Dbtag_gp }; EXTERN CharPtr filtercmd INITIAL(""); EXTERN double gapdecayrate INITIAL(0.5); EXTERN DBFilePtr dbfp; EXTERN BSRV_DbDesc dbdesc; /* Non-zero ==> show the hit-extension histogram */ EXTERN int showhist INITIAL(DEFAULT_showhist); /* Non-zero ==> show full pairwise alignments */ EXTERN int showblast INITIAL(DEFAULT_showblast); EXTERN Nlm_Boolean echofilter_flag; EXTERN double Meff, /* Effective length of the query sequence */ Neff; /* Effective length of the database */ /* First, Last, and Current HitLists */ EXTERN BLAST_HitListPtr firsthl; EXTERN BLAST_HitListPtr cmphl; EXTERN ScoreHistPtr shp; /* histogram of log(expectations) */ EXTERN Boolean C_set, E_set, E2_set, S_set, S2_set, M_set, N_set, T_set, X_set, V_set, Y_set, Z_set, W_set ; EXTERN int W INITIAL(DEFAULT_W), /* word length used in blast algorithm */ W_max INITIAL(WORDSIZE_MAX), C INITIAL(DEFAULT_C), /* genetic code */ dbgcode INITIAL(DEFAULT_C) /* genetic code for TBLASTX database xlation */ ; EXTERN BLAST_Score S, /* equivalent cutoff score for reporting HSP(s) */ S2, /* primary cutoff score for saving HSPs */ X, T ; EXTERN double E INITIAL(DEFAULT_E), /* Expected number of database sequences reported */ E_max INITIAL(DEFAULT_E_MAX), E2 INITIAL(DEFAULT_E2) /* Expected no. of HSPs per avg. sequence comparison */ ; EXTERN CharPtr M_default INITIAL(DEFAULT_M); EXTERN ValNodePtr M; EXTERN int nmats; EXTERN int matrix_max INITIAL(MATRIX_MAX); EXTERN BLAST_Score s_reward INITIAL(5), s_penalty INITIAL(-4); EXTERN ValNodePtr altscore; /* adjustments to be made to scoring matrix */ EXTERN ValNodePtr hsp_si; /* score information for HSPs */ EXTERN int hsp_max INITIAL(HSP_MAX); /* max. no. of HSPs to save per db seq */ EXTERN int hsp_max_exceeded; /* no. of times hsp_max was exceeded */ EXTERN int hsp_max_max; /* max. number of HSPs to report */ EXTERN long V INITIAL(DEFAULT_V); EXTERN Boolean top INITIAL(TRUE), bottom INITIAL(TRUE), dbtop INITIAL(TRUE), dbbottom INITIAL(TRUE) ; EXTERN int query_strands INITIAL(TOP_STRAND | BOTTOM_STRAND), db_strands INITIAL(TOP_STRAND | BOTTOM_STRAND); EXTERN int minframe INITIAL(0), maxframe INITIAL(6); EXTERN PACK_TYPE *c_seq; /* Pointer to compressed database sequence */ EXTERN long numhits; /* No. of word hits against database */ EXTERN long totHSP; /* Total no. of HSPs found against the database */ EXTERN long hasHSP; /* No. of db sequences with at least one HSP */ EXTERN long realHSP; /* No. of db sequences actually saved */ EXTERN int VBlim; EXTERN int remember_max; EXTERN int remember_cut; EXTERN Boolean consistency_flag INITIAL(TRUE); EXTERN Boolean cdi_flag INITIAL(FALSE); EXTERN CharPtr cdi_file; /* codon frequencies filename */ EXTERN Boolean sump_option INITIAL(TRUE); EXTERN Boolean prune_option; EXTERN volatile sig_atomic_t purge_flag; EXTERN Boolean stats_flag; EXTERN Boolean warning_option; EXTERN int nprocs; /* Count of the current number of processes */ EXTERN int numprocs INITIAL(PROC_DEFAULT); EXTERN const int proc_max INITIAL(PROC_MAX); #ifdef MPROC_AVAIL EXTERN MPContext mpc[THREADS_MAX]; #endif /* MPROC_AVAIL */ EXTERN BLAST_WFSearchStats totstats; EXTERN ScoreHistPtr score_hist[THREADS_MAX]; EXTERN ValNodePtr hitlist_cmp_criteria; EXTERN ValNodePtr hsp_cmp_criteria; EXTERN int (LIBCALLBACK *displaygcodes)() INITIAL(DISPLAYGCODES); EXTERN double overlap_fraction INITIAL(0.125); EXTERN Boolean overlap_fraction_set INITIAL(FALSE); EXTERN long Qlen, Qoffset, Slen, Soffset; EXTERN long NWstart, NWlen; EXTERN Boolean NWstart_set, NWlen_set; EXTERN int prog_id INITIAL(PROG_ID); EXTERN CharPtr prog_name INITIAL(PROG_NAME); EXTERN CharPtr prog_version INITIAL(PROG_VERSION); EXTERN CharPtr prog_desc INITIAL(PROG_DESC); EXTERN CharPtr prog_rel_date INITIAL(PROG_DATE); EXTERN BLAST_AlphaType qusage[2] #ifdef INIT = { QUERY_RAW, QUERY_COOKED } #endif ; EXTERN BLAST_AlphaType susage[2] #ifdef INIT = { DB_RAW, DB_COOKED } #endif ; EXTERN ValNodePtr parmstk, statstk; EXTERN BLAST_AlphabetPtr ncbiaa, blastaa; EXTERN BLAST_AlphabetPtr nt2ap, nt4ap; EXTERN unsigned char gcode[64], revgcode[64]; /* genetic codes for query */ EXTERN unsigned char db_gcode[64], db_revgcode[64]; /* genetic codes for db */ EXTERN unsigned long seqbogus; /* # of db sequences with non-ACGT codes */ EXTERN unsigned long dfanstates, dfastatesize, dfasize, dfaextent; EXTERN Cputime_t t0, t1, t2, t3, t4; EXTERN long dbrecmin INITIAL(-1); EXTERN long dbrecmax; EXTERN long dbreccnt; EXTERN BlastIo b_out; EXTERN int progress_period INITIAL(60); /* period (in seconds) for progress messages */ #if defined(__DATE__) && defined(__TIME__) EXTERN CharPtr cc_date INITIAL(__DATE__), cc_time INITIAL(__TIME__); #endif /* defined(__DATE__) && defined(__TIME__) */ #endif /* __BLAST_H__ */