/* =========================================================================== * * 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: blastpri.h Author: Tom Madden Contents: prototypes for "private" BLAST functions, these should not be called by outside utilities. ******************************************************************************/ /* $Revision: 6.90 $ * $Log: blastpri.h,v $ * Revision 6.90 2002/01/04 20:16:12 dondosha * Correction for single strand blastx with OOF gapping * * Revision 6.89 2001/11/13 18:17:27 dondosha * Added BlastNtWordUngappedExtend for use in Mega BLAST * * Revision 6.88 2001/10/12 15:22:49 dondosha * Added prototype for BLASTPostSearchLogic * * Revision 6.87 2001/09/07 14:46:44 dondosha * Roll back removal of threshold_first from functions and structures * * Revision 6.86 2001/09/06 20:24:34 dondosha * Removed threshold_first * * Revision 6.85 2001/08/20 21:13:41 dondosha * Added two declarations for clustering hits * * Revision 6.84 2001/07/31 16:42:40 dondosha * Added function FastaCheckDna * * Revision 6.83 2001/06/15 16:38:46 dondosha * Correction to previous changes * * Revision 6.82 2001/06/14 22:09:15 dondosha * Rearranged code for gi lists and oid masks processing to get rid of duplication * * Revision 6.81 2001/06/13 21:42:19 dondosha * Added prototypes for functions needed to deal with gi lists * * Revision 6.80 2001/06/07 19:30:03 dondosha * Pass believe query argument to BlastPrintTabulatedResults * * Revision 6.79 2001/06/06 21:22:43 dondosha * Added (query) Bioseq and SeqLoc arguments to function BlastPrintTabulatedResults * * Revision 6.78 2001/05/11 22:04:42 dondosha * Added prototype for BlastPrintTabulatedResults function * * Revision 6.77 2001/03/19 18:54:50 madden * Added BlastSeqLocFillDoubleIntEx, changed BlastSeqLocFillDoubleIntRev * * Revision 6.76 2001/02/08 20:38:30 dondosha * Added prototype for BLASTHspToStdSeg * * Revision 6.75 2001/02/07 21:08:33 dondosha * 1. Added prototypes of callback functions to handle results * 2. Two private auxiliary functions made public * * Revision 6.74 2001/01/23 20:25:43 dondosha * 1. Renamed BlastParceInputString to BlastParseInputString * 2. Recognize a double quoted string as an option value in * BlastParseInputString * * Revision 6.73 2000/12/19 18:39:50 madden * Add function BlastSetUserErrorString and BlastDeleteUserErrorString * * Revision 6.72 2000/11/17 17:51:59 dondosha * Removed is_megablast argument from BLASTSetUpSearchWithReadDbInternalEx since it is part of options * * Revision 6.71 2000/10/12 21:40:36 shavirin * Added is_oofalign to definition of the function BLASTFilterOverlapRegions(). * * Revision 6.70 2000/10/11 21:51:17 shavirin * Added definition of the function BLASTFilterOverlapRegions() * * Revision 6.69 2000/08/31 16:29:11 shavirin * Added definition of *QueryDNAP set of functions related to OOF. * * Revision 6.68 2000/08/28 21:51:53 shavirin * Added definition of the function BlastOtherReturnsFree(). * * Revision 6.67 2000/07/21 21:26:43 dondosha * Added BLASTSetUpSearchWithReadDbInternalEx with Boolean argument is_megablast * * Revision 6.66 2000/07/08 20:44:11 vakatov * Get all "#include" out of the 'extern "C" { }' scope; other cleanup... * * Revision 6.65 2000/06/13 20:54:39 shavirin * Added return of EFF_SEARCH_SPACE in the function BlastOtherReturnsPrepare * * Revision 6.64 2000/04/10 19:57:20 dondosha * Added prototype for BlastSeqLocFillDoubleIntRev * * Revision 6.63 2000/03/30 21:46:08 madden * prototypes for BLASTResultHitlistFreeEx and BlastDeleteHeap * * Revision 6.62 2000/03/29 22:16:08 dondosha * Added edit_script argument to BlastSaveCurrentHspGapped * * Revision 6.61 2000/03/08 20:51:21 madden * Add prototype for BlastGetAllowedGis * * Revision 6.60 2000/03/06 23:29:09 kans * added prototype for BlastConvertDNASeqLoc * * Revision 6.59 2000/02/17 19:00:45 shavirin * Removed theCacheSize parameter from everywhere. * * Revision 6.58 2000/02/01 18:08:59 dondosha * Added prototype for BlastSaveCurrentHspGapped * * Revision 6.57 2000/01/11 17:04:48 shavirin * Added parameter theCacheSize into BlastSearchBlkNew and BlastSearchBlkNewExtra * * Revision 6.56 1999/12/22 21:07:19 shavirin * Added definition of the function BlastNewFindWordsEx() * * Revision 6.55 1999/12/14 15:35:13 madden * Added BlastPrintFilterWarning * * Revision 6.54 1999/11/29 12:58:59 madden * Added prototypes for BlastNTGetGappedScore, BlastNTPreliminaryGappedScore and BlastNtSaveCurrentHsp * * Revision 6.53 1999/11/02 15:24:03 madden * Add BlastParseInputString and BlastGetLetterIndex * * Revision 6.52 1999/10/05 18:16:07 shavirin * Functions tick_proc and get_db_chunk were renamed and become public. * * Revision 6.51 1999/09/22 20:59:56 egorov * Add mask DB stuff * * Revision 6.50 1999/08/20 19:48:37 madden * Changed call to BlastSearchBlkNew(Extra) * * Revision 6.49 1999/05/27 17:33:06 madden * Fixed Int2 (should have been Int4) problem * * Revision 6.48 1999/04/15 13:25:07 madden * RealBlastGetGappedAlignmentTraceback returns Int4 * * Revision 6.47 1999/04/01 21:42:47 madden * Fix memory leaks when gi list is used * * Revision 6.46 1999/03/17 16:49:10 madden * Removed comment within comment * * Revision 6.45 1999/03/04 14:18:10 egorov * Do correct filter masking when query is seqloc * The only BlastMaskTheResidues() function is changed: * * Revision 6.44 1999/02/11 13:53:31 madden * Added combine Boolean to HitRangeToSeqLoc * * Revision 6.43 1999/01/28 17:20:17 madden * Added BlastGetNonSumStatsEvalue prototype * * Revision 6.42 1999/01/28 16:05:21 madden * HspArrayPurge change * * Revision 6.41 1999/01/26 17:57:14 madden * ContextToFrame prototype added * * Revision 6.40 1999/01/19 13:26:47 madden * Change to HspArrayPurge * * Revision 6.39 1999/01/08 22:08:43 madden * BlastScaleMatrix returns factor as FloatHi * * Revision 6.38 1998/12/18 16:19:58 madden * Make BLASTSetUpSearchWithReadDbInternal public, add BlastSearchBlkNewExtra * * Revision 6.37 1998/09/17 19:53:03 madden * Added fillCandLambda * * Revision 6.36 1998/09/16 18:59:55 madden * Added subset Boolean * * Revision 6.35 1998/09/14 15:11:16 egorov * Add support for Int8 length databases; remove unused variables * * Revision 6.34 1998/09/10 22:36:10 madden * Added convertSeqAlignListToValNodeList and convertValNodeListToSeqAlignList * * Revision 6.33 1998/09/09 21:18:10 madden * Added PrintKAParametersExtra * * Revision 6.32 1998/09/04 14:45:43 madden * Moved code from blast.c blastool.c * * Revision 6.31 1998/07/21 20:58:07 madden * Changes to allow masking at hash only * * Revision 6.30 1998/06/12 16:08:50 madden * BlastHitRange stuff * * Revision 6.29 1998/06/04 16:23:04 madden * BioseqSeg to MyBioseqSeg * * Revision 6.28 1998/05/17 16:28:44 madden * Allow changes to filter options and cc filtering. * * Revision 6.27 1998/05/05 14:05:36 madden * Added functions BlastStartAwakeThread and BlastStopAwakeThread * * Revision 6.26 1998/04/24 19:28:48 madden * Added BlastScaleMatrix (and other rescaling code moved from posit.c) * * Revision 6.25 1998/04/15 20:23:49 madden * offset arg removed from BlastMaskTheResidues * * Revision 6.24 1998/03/26 14:21:35 madden * Added GetScoreSetFromBlastResultHsp prototype * * Revision 6.23 1998/03/25 22:27:27 madden * Remove GetScoreSetFromBlastResultHsp prototype * * Revision 6.22 1998/03/24 15:38:24 madden * Use BlastDoubleInt4Ptr to keep track of gis and ordinal_ids * * Revision 6.21 1998/03/18 14:14:16 madden * Support random access by gi list * * Revision 6.20 1998/03/16 14:02:13 madden * Changed call to BlastSeqIdListDestruct * * Revision 6.19 1998/02/27 16:52:07 madden * Added BlastGetSequenceFromBioseq * * Revision 6.18 1998/02/27 14:34:51 madden * Added error message prototypes * * Revision 6.17 1998/02/26 22:34:25 madden * Changes for 16 bit windows * * Revision 6.16 1998/02/26 19:11:38 madden * Added prototypes for BlastNtFindWords BlastPopulateAllWordArrays * * Revision 6.15 1998/02/19 17:17:12 madden * Use of Int4 rather than Int2 when pruning SeqAlign * * Revision 6.14 1998/02/11 17:18:17 madden * Made BlastGetGappedAlignmentTraceback functions to BlastGetGapAlgnTbck (shorter than 32 chars) * * Revision 6.13 1998/01/05 16:46:54 madden * One or both strands can be searched, as opposed to only both, changes to number of contexts * * Revision 6.12 1997/12/31 17:53:11 madden * Removed BLAST_WordFinderNew and BLAST_WordFinderDestruct prototypes * * Revision 6.11 1997/12/23 18:12:38 madden * Changes for range-dependent blast * * Revision 6.10 1997/12/12 20:38:36 madden * ContextToFrame lost last parameter * * Revision 6.9 1997/11/28 18:19:37 madden * Changes to TxDfDbInfoNew * * Revision 6.8 1997/11/07 00:48:29 madden * Added TXMATRIX defintion * * Revision 6.7 1997/10/24 20:46:55 madden * Removed BLASTResultsStructNew prototype * * Revision 6.6 1997/10/24 19:09:19 madden * Removed BlastSetReadDB and BlastGetReadDB_ID, changed to ReadDBGetDb and ReadDBGetDbId * * Revision 6.5 1997/10/03 21:27:34 madden * Added BlastGetTypes * * Revision 6.4 1997/10/02 17:29:27 madden * Added PrintDbInformationBasic * * Revision 6.3 1997/09/18 22:22:09 madden * Added prune functions * * Revision 6.2 1997/09/16 16:31:33 madden * More changes for multiple db runs * * Revision 6.1 1997/09/11 18:49:28 madden * Changes to enable searches against multiple databases. * * Revision 6.0 1997/08/25 18:52:44 madden * Revision changed to 6.0 * * Revision 1.48 1997/08/22 18:37:49 madden * Added function BlastOtherReturnsPrepare * * Revision 1.47 1997/07/24 20:34:50 madden * define change for masking * * Revision 1.46 1997/07/18 14:26:42 madden * call to AcknowledgeBlastQuery changed * * Revision 1.45 1997/07/17 20:27:11 madden * Changed defines to indicate frame * * Revision 1.44 1997/07/16 20:34:48 madden * Added function BlastConvertProteinSeqLoc * * Revision 1.43 1997/07/15 20:36:11 madden * Added BioseqSeg and SeqLocSeg * * Revision 1.42 1997/07/14 15:32:25 madden * prototype for BlastConstructErrorMessage * * Revision 1.41 1997/06/27 14:30:42 madden * prototypes for BlastAddSeqIdToList and BlastSeqIdListDestruct * * Revision 1.40 1997/06/06 21:29:36 madden * Added Boolean html to AcknowledgeBlastQuery and PrintDbInformation * * Revision 1.39 1997/06/06 19:50:58 madden * Added BlastMakeFakeBioseq and BlastDeleteFakeBioseq * * Revision 1.38 1997/05/27 20:20:08 madden * Added function BlastMaskTheResidues * * Revision 1.37 1997/04/23 21:56:07 madden * Changes in BlastGetGappedAlignmentTraceback for in-frame gapping tblastn. * * Revision 1.36 1997/04/11 21:18:45 madden * Added GetSequenceWithDenseSeg. * * Revision 1.35 1997/04/07 18:17:09 madden * Added prototype for BioseqBlastEngineCore * * Revision 1.34 1997/03/06 21:47:10 madden * Added FormatBlastParameters. * * Revision 1.33 1997/03/05 14:29:46 madden * Added prototype for BlastSaveCurrentHsp. * * Revision 1.32 1997/03/04 21:34:59 madden * Added in HspArrayPurge. * * Revision 1.31 1997/03/04 20:36:51 madden * *** empty log message *** * * Revision 1.30 1997/03/03 22:39:45 madden * Moved code from blast.c to blastutl.c. * * Revision 1.29 1997/03/03 21:48:52 madden * *** empty log message *** * * Revision 1.28 1997/03/01 18:25:33 madden * reverse flag added to BlastGetGappedAlignmentTraceback functions. * * Revision 1.27 1997/02/26 23:39:54 madden * Added Txdfline stuff. * * Revision 1.26 1997/02/12 22:19:08 madden * Added prototype for BlastNewFindWords. * * Revision 1.25 1997/02/11 19:30:54 madden * Added prototypes for BlastGetGappedScoreWithReaddb and BlastGetGapped * * Revision 1.24 1997/02/10 20:03:58 madden * Added specific to BlastAllWordNew. * * Revision 1.23 1997/02/07 22:43:03 madden * Moved BLAST_WordFinderNew and Destruct from blast.c to blastutl.c, made * non-static. * * Revision 1.22 1997/02/07 22:32:40 madden * Changed prototypes for BlastGetSubjectId and GetSeqAlignForResultHitList. * * Revision 1.21 1997/01/30 21:41:17 madden * Prototype for FormatBlastParameters added. * * Revision 1.20 1997/01/11 18:58:29 madden * Removed defunct PerformBlastSearch... functions. * * Revision 1.19 1997/01/07 20:40:29 madden * Added reverse Boolean to GetSeqAlignForResultHitList. * * Revision 1.18 1997/01/06 22:41:46 madden * Added prototype BlastGetSubjectId. * * Revision 1.17 1996/12/23 22:02:05 madden * Changes to allow two sequences to be compared. * * Revision 1.16 1996/12/20 15:31:39 madden * Removed prototype for Perform2PassBlastSearchWithReadDb. * * Revision 1.15 1996/12/20 14:22:48 madden * Added discontinuous Boolean to GetSeqAlignForResultHitList. * * Revision 1.14 1996/12/12 16:46:25 madden * Changed CONTAINED_IN_HSP. * * Revision 1.13 1996/12/08 15:19:59 madden * Added defines and prototypes for gapped alignments. * * Revision 1.12 1996/11/14 16:21:55 madden * changed CharPtr to Uint1Ptr in GetTranslation. * * Revision 1.11 1996/11/13 22:35:18 madden * Added prototype for GetTranslation. * * Revision 1.10 1996/11/05 23:19:08 madden * Changed BlastTranslateUnambiguousSequence prototype. * * Revision 1.9 1996/09/26 20:18:43 madden * Changed prototype for GetSeqAlignForResultHitList * * Revision 1.8 1996/09/12 21:12:23 madden * Removed prototypes for BLAST_WordFinderNew and BLAST_WordFinderDestruct. * * Revision 1.7 1996/09/11 22:22:12 madden * Added prototpe for BLASTPerformSearchWithReadDb. * * Revision 1.6 1996/08/26 17:24:19 shavirin * Added definition of function Win32TimeFill() * * Revision 1.5 1996/08/23 16:30:11 shavirin * Fixed NT compiler warnings type mismatch * * Revision 1.4 1996/08/15 18:58:49 madden * Changed context from Int2 to Int1 * * Revision 1.3 1996/08/14 15:20:37 madden * Added prototype for BlastTranslateUnambiguousSequence. * * Revision 1.2 1996/08/07 14:24:15 madden * Removed functions that depend on BLAST0 structures. * * Revision 1.1 1996/08/05 19:46:53 madden * Initial revision * * Revision 1.32 1996/07/31 13:10:53 madden * Added BlastSearchBlkDuplicate prototype. * * Revision 1.31 1996/07/25 20:47:49 madden * Change to arguments of Perform2PassBlastSearchWithReadDb. * * Revision 1.30 1996/07/18 22:01:35 madden * Changed call to BlastFindWords * * Revision 1.29 1996/06/21 15:15:21 madden * Removed unused prototype * * Revision 1.28 1996/06/20 16:15:57 madden * Replaced int's with Int4's. * * Revision 1.27 1996/06/17 21:07:32 madden * Added prototype for GetSeqAlignForResultHitList and some LIBCALL's. * * Revision 1.26 1996/06/17 19:02:35 madden * Removed unused prototypes. * * Revision 1.25 1996/06/13 21:16:33 madden * removed BLAST_ExtendWordNew prototype. * * Revision 1.24 1996/06/11 17:58:31 madden * removed prototype for BLAST_ExtendWordDiagResize. * * Revision 1.23 1996/06/06 14:09:22 madden * Removed blast_set_parameters prototype (it became static). * * Revision 1.22 1996/06/06 13:54:51 madden * Removed defunct function BLAST_ParameterBlkFill * * Revision 1.21 1996/06/04 15:33:55 madden * Changed BlastHitList function prototypes. * * Revision 1.20 1996/05/29 12:44:40 madden * Added prototype for BlastTimeFillStructure. * * Revision 1.19 1996/05/16 19:51:09 madden * Added documentation block. * * Revision 1.18 1996/05/14 16:15:59 madden * Added protoytpe for BLASTResultsStruc functions. * * Revision 1.17 1996/05/01 14:59:41 madden * *** empty log message *** * * Revision 1.16 1996/04/03 19:14:08 madden * added functions PerformBlastSearchWithReadDb and Perform2PassBlastSearchWithReadDb. * * Revision 1.15 1996/03/29 21:28:20 madden * *** empty log message *** * * Revision 1.14 1996/03/29 14:09:37 madden * prototype for GetSeqAlignForSparseHitList added. * * Revision 1.13 1996/02/28 21:38:36 madden * Changed prototypes for discontiguous words. * * Revision 1.12 1996/02/05 18:46:57 madden * *** empty log message *** * * Revision 1.11 1996/02/02 19:25:32 madden * Changed BlastFindWords prototype. * * Revision 1.10 1996/01/31 22:28:46 madden * Added prototype for BlastReapHitlistByEvalue. * * Revision 1.9 1996/01/17 13:47:13 madden * *** empty log message *** * * Revision 1.8 1996/01/11 15:17:58 madden * Added prototype for do_MPblast_search. * * Revision 1.7 1996/01/10 17:51:09 madden * Added SortHitListByPvalue. * * Revision 1.6 1996/01/06 18:58:45 madden * Added prototype for BlastLinkHsps. * * Revision 1.5 1995/12/30 18:39:27 madden * Added prototype for GetBLAST0KABlk. * * Revision 1.4 1995/12/28 21:26:30 madden * Added in prototype for do_blast_search. * * Revision 1.3 1995/12/26 23:05:29 madden * Added prototype for blast_set_parameters. * * Revision 1.2 1995/12/21 23:11:11 madden * BLAST_Score prototypes moved to blastkar.h. * * Revision 1.1 1995/12/19 22:31:17 madden * Initial revision * * Revision 1.1 1995/12/08 15:48:23 madden * Initial revision * * */ #ifndef __BLASTPRI__ #define __BLASTPRI__ #include #include #include #include #include #ifdef __cplusplus extern "C" { #endif typedef struct _txdbinfo { struct _txdbinfo PNTR next; Boolean is_protein; CharPtr name; CharPtr definition; CharPtr date; Int8 total_length; Int4 number_seqs; Boolean subset; /* Print the subset message. */ } TxDfDbInfo, *TxDfDbInfoPtr; /* Defines for the return values in "other_returns". */ #define SEQLOC_MASKING_NOTSET 0 #define SEQLOC_MASKING_PLUS1 1 #define SEQLOC_MASKING_PLUS2 2 #define SEQLOC_MASKING_PLUS3 3 #define SEQLOC_MASKING_MINUS1 4 #define SEQLOC_MASKING_MINUS2 5 #define SEQLOC_MASKING_MINUS3 6 #define TXDBINFO 10 #define TXKABLK_NOGAP 12 #define TXKABLK_GAP 13 #define TXPARAMETERS 14 #define TXMATRIX 15 #define EFF_SEARCH_SPACE 16 /* Allocates memory for TxDfDbInfoPtr. Link up new (returned) value to 'old', if non-NULL. */ TxDfDbInfoPtr LIBCALL TxDfDbInfoNew PROTO((TxDfDbInfoPtr old)); /* Deallocates memory (including strings for name, definition, and date). */ TxDfDbInfoPtr LIBCALL TxDfDbInfoDestruct PROTO((TxDfDbInfoPtr dbinfo)); /* Print a summary of the query. */ Boolean LIBCALL AcknowledgeBlastQuery PROTO((BioseqPtr bsp, Int4 line_length, FILE *outfp, Boolean believe_query, Boolean html)); /* Print a report of the database used. */ Boolean LIBCALL PrintDbReport PROTO((TxDfDbInfoPtr dbinfo, Int4 line_length, FILE *outfp)); /* Print a warning about the filtering used. */ Boolean LIBCALL BlastPrintFilterWarning PROTO((CharPtr filter_string, Int4 line_length, FILE *outfp, Boolean html)); /* print out some of the Karlin-Altschul parameters. */ Boolean LIBCALL PrintKAParameters PROTO((Nlm_FloatHi Lambda, Nlm_FloatHi K, Nlm_FloatHi H, Int4 line_length, FILE *outfp, Boolean gapped)); Boolean LIBCALL PrintKAParametersExtra PROTO((Nlm_FloatHi Lambda, Nlm_FloatHi K, Nlm_FloatHi H, Nlm_FloatHi C, Int4 line_length, FILE *outfp, Boolean gapped)); /* Print a CharPtr (VisibleString), printing a new line every time a tilde is encountered. */ Boolean LIBCALL PrintTildeSepLines PROTO((CharPtr buffer, Int4 line_length, FILE *outfp)); /* How many interations should be done in the bisection. */ #define BLAST_SAVE_ITER_MAX 20 /* TRUE if c is between a and b; f between d and f. Determines if the coordinates are already in an HSP that has been evaluated. */ #define CONTAINED_IN_HSP(a,b,c,d,e,f) (((a <= c && b >= c) && (d <= f && e >= f)) ? TRUE : FALSE) Int2 LIBCALL BlastFindWords PROTO((BlastSearchBlkPtr search, Int4 start, Int4 len, BLAST_Score threshold, Int1 context_index)); Int2 LIBCALL BlastNewFindWords PROTO((BlastSearchBlkPtr search, Int4 start, Int4 len, BLAST_Score threshold, Int1 context_index)); Int2 BlastNewFindWordsEx(LookupTablePtr lookup, BLAST_ScorePtr PNTR posMatrix, Int4 start, Int4 len, BlastAllWordPtr all_words, BLAST_Score threshold, Int4 wordsize, Int1 context_index); Int2 LIBCALL BlastLinkHsps PROTO ((BlastSearchBlkPtr search)); Int2 LIBCALL BlastReapHitlistByEvalue PROTO ((BlastSearchBlkPtr search)); Int4 LIBCALL BlastSaveCurrentHitlist PROTO((BlastSearchBlkPtr search)); BlastSearchBlkPtr LIBCALL BLASTPerformSearchWithReadDb PROTO((BlastSearchBlkPtr search, Int4 sequence_number)); BlastSearchBlkPtr LIBCALL BLASTPerformSearch PROTO((BlastSearchBlkPtr search, Int4 subject_length, Uint1Ptr subject_seq)); BLASTResultsStructPtr LIBCALL BLASTResultsStructDelete PROTO((BLASTResultsStructPtr result_struct)); SeqAlignPtr LIBCALL GetSeqAlignForResultHitList PROTO((BlastSearchBlkPtr search, Boolean getdensediag, Boolean ordinal_number, Boolean discontinuous, Boolean reverse, Boolean get_redundant_seq)); Int2 LIBCALL BlastTimeFillStructure PROTO((BlastTimeKeeperPtr btkp)); BlastSearchBlkPtr LIBCALL BlastSearchBlkDuplicate PROTO((BlastSearchBlkPtr search)); BlastSearchBlkPtr LIBCALL BlastSearchBlkNew PROTO((Int2 wordsize, Int4 qlen, CharPtr dbname, Boolean multiple_hits, BLAST_Score threshold_first, BLAST_Score threshold_second, Int4 result_size, CharPtr prog_name, BlastAllWordPtr all_words, Int2 first_context, Int2 last_context, Int4 window_size)); /* Allocates a search Block, except it only attaches to the rdfp, does not allocate it. */ BlastSearchBlkPtr LIBCALL BlastSearchBlkNewExtra PROTO((Int2 wordsize, Int4 qlen, CharPtr dbname, Boolean multiple_hits, BLAST_Score threshold_first, BLAST_Score threshold_second, Int4 result_size, CharPtr prog_name, BlastAllWordPtr all_words, Int2 first_context, Int2 last_context, ReadDBFILEPtr rdfp, Int4 window_size)); BlastSearchBlkPtr LIBCALL BlastSearchBlkDestruct PROTO((BlastSearchBlkPtr search)); BlastSearchBlkPtr BLASTSetUpSearchWithReadDbInternal PROTO((SeqLocPtr query_slp, BioseqPtr query_bsp, CharPtr prog_name, Int4 qlen, CharPtr dbname, BLAST_OptionsBlkPtr options, int (LIBCALLBACK *callback)PROTO((Int4 done, Int4 positives)), SeqIdPtr seqid_list, BlastDoubleInt4Ptr gi_list, Int4 gi_list_total, ReadDBFILEPtr rdfp)); BlastSearchBlkPtr LIBCALL BLASTSetUpSearchWithReadDbInternalEx PROTO((SeqLocPtr query_slp, BioseqPtr query_bsp, CharPtr prog_name, Int4 qlen, CharPtr dbname, BLAST_OptionsBlkPtr options, int (LIBCALLBACK *callback)PROTO((Int4 done, Int4 positives)), SeqIdPtr seqid_list, BlastDoubleInt4Ptr gi_list, Int4 gi_list_total, ReadDBFILEPtr rdfp)); Int4 LIBCALL BlastTranslateUnambiguousSequence PROTO((BlastSearchBlkPtr search, Int4 length, Uint1Ptr prot_seq, Uint1Ptr nt_seq, Int2 frame)); Uint1Ptr LIBCALL GetTranslation PROTO((Uint1Ptr query_seq, Int4 nt_length, Int2 frame, Int4Ptr length, CharPtr genetic_code)); SeqAlignPtr LIBCALL BlastGetGapAlgnTbck PROTO((BlastSearchBlkPtr search, Int4 hit_number, Boolean reverse, Boolean ordinal_number, Uint1Ptr subject, Int4 subject_length, Uint1Ptr rev_subject, Int4 rev_subject_length)); SeqAlignPtr LIBCALL BlastGetGapAlgnTbckWithReaddb PROTO((BlastSearchBlkPtr search, Int4 hit_number, Boolean ordinal_number)); Int2 LIBCALL BlastGetGappedScoreWithReaddb PROTO((BlastSearchBlkPtr search, Int4 sequence_number)); Int2 LIBCALL BlastGetGappedScore PROTO((BlastSearchBlkPtr search, Int4 subject_length, Uint1Ptr subject, Int2 frame)); Int2 LIBCALL BlastNTGetGappedScore PROTO((BlastSearchBlkPtr search, Int4 subject_length, Uint1Ptr subject)); SeqIdPtr LIBCALL BlastGetSubjectId PROTO((BlastSearchBlkPtr search, Int4 hit_number, Boolean ordinal_number, ValNodePtr *vnpp)); BlastAllWordPtr LIBCALL BlastAllWordNew PROTO((Int4 num_of_cols, Int4 wordsize, Boolean rows_allocated, Boolean specific)); BlastAllWordPtr LIBCALL BlastAllWordDestruct PROTO((BlastAllWordPtr all_words)); BLAST_HitListPtr LIBCALL BlastHitListDestruct PROTO((BLAST_HitListPtr hitlist)); BLAST_HitListPtr LIBCALL BlastHitListNew PROTO((BlastSearchBlkPtr search)); void LIBCALL BlastExtendWordExit PROTO((BlastSearchBlkPtr search)); Boolean LIBCALL FilterDNA PROTO((BioseqPtr bsp, Int4 filter)); Boolean LIBCALL FilterWithSeg PROTO((Uint1Ptr sequence, Int4 length, Uint1 alphabet)); BLASTResultHitlistPtr LIBCALL BLASTResultHitlistFree PROTO((BLASTResultHitlistPtr result)); BLASTResultHitlistPtr LIBCALL BLASTResultHitlistFreeEx PROTO((BlastSearchBlkPtr search, BLASTResultHitlistPtr result)); BLASTResultHitlistPtr LIBCALL BLASTResultHitlistNew PROTO((Int4 hspcnt)); Nlm_FloatHi LIBCALL GetDbSubjRatio PROTO((BlastSearchBlkPtr search, Int4 subject_length)); Int2 LIBCALL BlastPreliminaryGappedScore PROTO((BlastSearchBlkPtr search, Uint1Ptr subject, Int4 subject_length, Int2 frame)); Int2 LIBCALL BlastNTPreliminaryGappedScore PROTO((BlastSearchBlkPtr search, Uint1Ptr subject, Int4 subject_length)); Int2 LIBCALL BlastHitListPurge PROTO((BLAST_HitListPtr hitlist)); Int4 LIBCALL HspArrayPurge PROTO((BLAST_HSPPtr PNTR hsp_array, Int4 hspcnt, Boolean clear_num)); void BlastSaveCurrentHsp PROTO((BlastSearchBlkPtr search, BLAST_Score score, Int4 q_offset, Int4 s_offset, Int4 length, Int2 context)); void BlastSaveCurrentHspGapped PROTO((BlastSearchBlkPtr search, BLAST_Score score, Int4 q_offset, Int4 s_offset, Int4 q_length, Int4 s_length, Int2 context, GapXEditScriptPtr esp)); void BlastNtSaveCurrentHsp PROTO((BlastSearchBlkPtr search, BLAST_Score score, Int4 q_offset, Int4 s_offset, Int4 length, Int2 context, Int4 query_gap_start, Int4 subject_gap_start)); CharPtr FormatBlastParameters PROTO((BlastSearchBlkPtr search)); SeqAlignPtr LIBCALL BioseqBlastEngineCore PROTO((BlastSearchBlkPtr search, BLAST_OptionsBlkPtr options, Int4Ptr *pos_matrix)); SeqAlignPtr LIBCALL BioseqBlastEngineCoreEx PROTO((BlastSearchBlkPtr search, BLAST_OptionsBlkPtr options, Int4Ptr *pos_matrix, Boolean partial)); Uint1Ptr GetSequenceWithDenseSeg PROTO((DenseSegPtr dsp, Boolean query, Int4Ptr start, Int4Ptr length)); void BlastMaskTheResidues PROTO((Uint1Ptr buffer, Int4 max_length, Uint1 mask_residue, SeqLocPtr mask_slp, Boolean reverse, Int4 offset)); BioseqPtr LIBCALL BlastMakeFakeBioseq PROTO((BioseqPtr bsp, CharPtr name)); BioseqPtr LIBCALL BlastDeleteFakeBioseq PROTO((BioseqPtr fake_bsp)); Boolean BlastAddSeqIdToList PROTO((BlastSearchBlkPtr search, Int4 ordinal_id, SeqIdPtr sip)); ValNodePtr BlastConstructErrorMessage PROTO((CharPtr function, CharPtr message, Uint1 level, ValNodePtr PNTR vnpp)); BlastErrorMsgPtr BlastDestroyErrorMessage PROTO((BlastErrorMsgPtr error_msg)); ValNodePtr BlastErrorChainDestroy PROTO((ValNodePtr vnp)); ValNodePtr LIBCALL BlastOtherReturnsPrepare PROTO((BlastSearchBlkPtr search)); void LIBCALL BlastOtherReturnsFree PROTO((ValNodePtr other_returns)); SeqLocPtr BlastBioseqFilter PROTO((BioseqPtr bsp, CharPtr instructions)); SeqLocPtr BlastSeqLocFilter PROTO((SeqLocPtr slp, CharPtr instructions)); SeqLocPtr BlastBioseqFilterEx PROTO((BioseqPtr bsp, CharPtr instructions, BoolPtr mask_at_hash)); SeqLocPtr BlastSeqLocFilterEx PROTO((SeqLocPtr slp, CharPtr instructions, BoolPtr mask_at_hash)); SeqLocPtr MyBioseqSeg PROTO((BioseqPtr bsp_unfilter)); SeqLocPtr SeqLocSeg PROTO((SeqLocPtr slp)); Boolean BlastConvertProteinSeqLoc PROTO((SeqLocPtr slp, Int2 frame, Int4 full_length)); Boolean BlastConvertDNASeqLoc (SeqLocPtr slp, Int2 frame, Int4 full_length); BlastPruneSapStructPtr BlastPruneSapStructDestruct PROTO((BlastPruneSapStructPtr prune)); BlastPruneSapStructPtr BlastPruneHitsFromSeqAlign PROTO((SeqAlignPtr sap, Int4 number, BlastPruneSapStructPtr prune)); Uint1 LIBCALL BlastGetTypes PROTO((CharPtr blast_program, Boolean PNTR query_is_na, Boolean PNTR db_is_na)); BLASTResultsStructPtr BLASTResultsStructNew PROTO((Int4 results_size, Int4 max_pieces, Int4 range_max)); Int2 BlastNtFindWords PROTO((BlastSearchBlkPtr search, Int4 start, Int4 len, Int1 context_index)); BlastAllWordPtr BlastPopulateAllWordArrays PROTO((Int4 wordsize, Int4 alphabet_size)); Uint1Ptr BlastGetSequenceFromBioseq PROTO((BioseqPtr bsp, Int4Ptr length)); BlastSeqIdListPtr BlastSeqIdListNew PROTO((void)); BlastSeqIdListPtr BlastSeqIdListDestruct PROTO((BlastSeqIdListPtr seqid_list)); Boolean BlastAdjustDbNumbers PROTO((ReadDBFILEPtr rdfp_list, Int8Ptr db_length, Int4Ptr db_number, SeqIdPtr seqid_list, BlastDoubleInt4Ptr gi_list, OIDListPtr oidlist, BlastDoubleInt4Ptr PNTR gi_list_pointers, Int4 gi_list_total)); BlastGiListPtr BlastGiListDestruct PROTO((BlastGiListPtr blast_gi_list, Boolean contents)); BlastGiListPtr BlastGiListNew PROTO((BlastDoubleInt4Ptr gi_list, BlastDoubleInt4Ptr PNTR gi_list_pointers, Int4 total)); ScorePtr LIBCALL GetScoreSetFromBlastResultHsp PROTO((BLASTResultHspPtr hsp, SeqIdPtr gi_list)); Nlm_FloatHi BlastScaleMatrix PROTO((BlastMatrixRescalePtr matrix_rescale, Boolean position_dependent)); BlastMatrixRescalePtr BlastMatrixRescaleNew PROTO((Int4 alphabet_size, Int4 query_length, Uint1Ptr query, Nlm_FloatHiPtr standardProb, Int4Ptr *matrix, Int4Ptr *private_matrix, BLAST_KarlinBlkPtr *kbp_std, BLAST_KarlinBlkPtr *kbp_psi, BLAST_KarlinBlkPtr *kbp_gap_std, BLAST_KarlinBlkPtr *kbp_gap_psi, Nlm_FloatHi lambda_ideal, Nlm_FloatHi K_ideal)); BlastMatrixRescalePtr BlastMatrixRescaleDestruct PROTO((BlastMatrixRescalePtr matrix_rescale)); /* starts the awake thread using static variables in this file. */ void BlastStartAwakeThread PROTO((BlastThrInfoPtr thr_info)); /* Change the awake flag. This thread will die in one second. */ void BlastStopAwakeThread PROTO((BlastThrInfoPtr thr_info)); SeqLocPtr HitRangeToSeqLoc PROTO((BlastHitRangePtr bhrp, Int4 link_value, Boolean combine)); ValNodePtr BlastSeqLocFillDoubleInt PROTO((SeqLocPtr mask_slp, Int4 max_length, Boolean reverse)); ValNodePtr BlastSeqLocFillDoubleIntEx PROTO((SeqLocPtr mask_slp, Int4 full_query_length, Int4 max_length, Boolean reverse, Int4 offset)); ValNodePtr BlastSeqLocFillDoubleIntRev PROTO((ValNodePtr location, SeqLocPtr mask_slp, Int4 full_query_length, Int4 max_length, Int4 offset)); Int2 BlastInsertList2Heap PROTO((BlastSearchBlkPtr search, BLASTResultHitlistPtr result_hitlist)); void BlastFreeHeap PROTO((BlastSearchBlkPtr search, BLASTResultHitlistPtr result_hitlist)); ValNodePtr convertSeqAlignListToValNodeList(SeqAlignPtr seqAlignList, SeqAlignPtr * lastSeqAligns, Int4 numLastSeqAligns); SeqAlignPtr convertValNodeListToSeqAlignList(ValNodePtr seqAlignDoubleList, SeqAlignPtr ** lastSeqAligns, Int4 * numLastSeqAligns); void LIBCALL fillCandLambda(seedSearchItems * seedSearch, Char *matrixName, BLAST_OptionsBlkPtr options); Int4 RealBlastGetGappedAlignmentTraceback(BlastSearchBlkPtr search, Uint1Ptr subject, Int4 subject_length, Uint1Ptr rev_subject, Int4 rev_subject_length, SeqIdPtr subject_id, BLAST_HSPPtr *hsp_array, Int4 hspcnt, SeqAlignPtr *head, BlastHitRangePtr bhrp, Int4 min_score_to_keep, Boolean reverse, Int4 ordinal_id, Boolean do_traceback); Int2 ContextToFrame PROTO((BlastSearchBlkPtr search, Int2 context_number)); int LIBCALLBACK score_compare_hsps PROTO((VoidPtr v1, VoidPtr v2)); Int2 LIBCALL BlastGetNonSumStatsEvalue PROTO((BlastSearchBlkPtr search)); Boolean BlastGetDbChunk(ReadDBFILEPtr rdfp, Int4Ptr start, Int4Ptr stop, Int4Ptr id_list, Int4Ptr id_list_number, BlastThrInfoPtr thr_info); void BlastTickProc(Int4 sequence_number, BlastThrInfoPtr thr_info); Boolean BlastParseInputString(CharPtr string, CharPtr letters, CharPtr PNTR *values_in, CharPtr PNTR ErrorMessage); Int4 BlastGetLetterIndex(CharPtr letters, Char ch); SeqIdPtr BlastGetAllowedGis PROTO((BlastSearchBlkPtr search, Int4 ordinal_id, SeqIdPtr PNTR seqid)); Int4 BlastDeleteHeap PROTO((BLASTHeapPtr which_heap, Int4 position)); /* Functions used for printing error messages. */ Uint1 BlastSetUserErrorString(CharPtr string, SeqIdPtr sip, Boolean use_id); void BlastDeleteUserErrorString(Uint1 err_id); /* Functions used in OOF calculations */ BlastSequenceBlkPtr PNTR LIBCALL BlastMakeCopyQueryDNAP PROTO((BlastSequenceBlkPtr PNTR bsbpp_in)); void LIBCALL BlastFreeQueryDNAP PROTO((BlastSequenceBlkPtr PNTR bsbpp)); BlastSequenceBlkPtr PNTR LIBCALL BlastCreateQueryDNAP PROTO((BlastSearchBlkPtr search, Int4 length)); /* ----------------------------------------------------------------- This function will filter given SeqAlignPtr for overlaping regions for the same query/subject pair. Another input parameter is percentage of overlapping required for the alignment to be removed from SeqAlignPtr ---------------------------------------------------------------- */ SeqAlignPtr BLASTFilterOverlapRegions(SeqAlignPtr sap, Int4 pct, Boolean subject_is_aa, Boolean is_ooframe, Boolean sort_array); /* End of functions used in OOF calculations */ Int4 BlastGetNumIdentical PROTO((Uint1Ptr query, Uint1Ptr subject, Int4 q_start, Int4 s_start, Int4 length, Boolean reverse)); SeqIdPtr GetTheSeqAlignID PROTO((SeqIdPtr seq_id)); StdSegPtr BLASTHspToStdSeg PROTO((BlastSearchBlkPtr search, Int4 subject_length, BLAST_HSPPtr hsp, SeqIdPtr sip, Boolean reverse, SeqIdPtr gi_list)); /* Callbacks to handle results instead of saving hit lists */ #define BUFFER_LENGTH 255 #define LARGE_BUFFER_LENGTH 1024 int LIBCALLBACK BlastPrintAlignInfo PROTO((VoidPtr srch)); int LIBCALLBACK MegaBlastPrintAlignInfo PROTO((VoidPtr srch)); void BlastPrintTabulatedResults PROTO((SeqAlignPtr seqalign, BioseqPtr query_bsp, SeqLocPtr query_slp, Int4 num_alignments, CharPtr blast_program, Boolean is_ungapped, Boolean believe_query, Int4 q_shift, Int4 s_shift, FILE *fp)); void BlastProcessGiLists PROTO((BlastSearchBlkPtr search, BLAST_OptionsBlkPtr options, BlastDoubleInt4Ptr gi_list, Int4Ptr gi_list_size)); Boolean FastaCheckDna PROTO((CharPtr seq)); BLASTHSPSegmentPtr BLASTHSPSegmentFromSeqAlign PROTO((SeqAlignPtr sap)); SeqAlignPtr BlastClusterHitsFromSeqAlign PROTO((SeqAlignPtr seqalign, CharPtr prog_name, CharPtr database, BLAST_OptionsBlkPtr options, FloatHi length_thresh, FloatHi score_thresh, FloatHi overlap_thresh, Boolean two_sided)); SeqAlignPtr RedoAlignmentCore PROTO((BlastSearchBlkPtr search, BLAST_OptionsBlkPtr options, Int4 hitlist_count, Boolean adjustParameters, Boolean SmithWaterman)); void BLASTResultFreeHsp PROTO((BLASTResultHitlistPtr result)); SeqAlignPtr BLASTPostSearchLogic PROTO((BlastSearchBlkPtr search,BLAST_OptionsBlkPtr options)); Boolean BlastNtWordUngappedExtend PROTO((BlastSearchBlkPtr search, Int4 q_off, Int4 s_off, Int4 cutoff)); #ifdef __cplusplus } #endif #endif /* !__BLASTPRI__ */