/* $Id: blastall.c,v 6.105 2001/12/17 20:23:44 madden Exp $ ************************************************************************** * * * 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. * * * ************************************************************************** * * $Log: blastall.c,v $ * Revision 6.105 2001/12/17 20:23:44 madden * comment out DO_NOT_SUPPRESS_BLAST_OP * * Revision 6.104 2001/09/06 20:24:34 dondosha * Removed threshold_first * * Revision 6.103 2001/08/28 17:34:34 madden * Add -m 9 as tabular output with comments * * Revision 6.102 2001/08/28 16:23:12 madden * Do not suppress args * * Revision 6.101 2001/07/27 21:47:35 dondosha * Fixed dummy variable declaration for call to StringToInt8 * * Revision 6.100 2001/07/26 18:21:04 dondosha * Dummy variable type correction * * Revision 6.99 2001/07/20 13:31:23 dondosha * Undeclared variable correction * * Revision 6.98 2001/07/19 22:05:47 dondosha * Made db_length option a string, to convert to Int8 value * * Revision 6.97 2001/07/05 15:40:33 madden * Comment out DO_NOT_SUPPRESS_BLAST_OP for release * * Revision 6.96 2001/07/03 20:50:33 madden * Commented out call to PrintTabularOutputHeader * * Revision 6.95 2001/06/21 21:49:55 dondosha * No need to declare extra variable vnp * * Revision 6.94 2001/06/21 21:29:08 dondosha * Fixed memory leaks: destroy all error returns, free private_slp * * Revision 6.93 2001/06/15 21:20:19 dondosha * Moved -m9 option to -m8; added header for tabular output * * Revision 6.92 2001/06/07 19:30:03 dondosha * Pass believe query argument to BlastPrintTabulatedResults * * Revision 6.91 2001/06/06 21:22:44 dondosha * Added (query) Bioseq and SeqLoc arguments to function BlastPrintTabulatedResults * * Revision 6.90 2001/05/25 19:26:36 vakatov * Nested comment typo fixed * * Revision 6.89 2001/05/23 22:38:47 dondosha * Added option -m 9 to print post-search tabulated output * * Revision 6.88 2001/04/10 19:20:52 madden * Unsuppress some options suppressed for the release * * Revision 6.87 2001/04/02 13:52:15 madden * Fix for last checkin, properly suppress some options * * Revision 6.85 2001/03/19 22:39:24 dondosha * Allow location on the first query sequence for megablast * * Revision 6.84 2001/03/13 21:58:23 madden * add support for multiple hits blastn, add option for window size * * Revision 6.83 2001/02/22 20:26:03 dondosha * If location stop is -1, make it end of sequence * * Revision 6.82 2001/02/22 20:11:58 dondosha * Previous change reversed; added option to set location on query sequence * * Revision 6.81 2001/02/22 16:16:43 shavirin * Added options for required start and required stop of the query to be * used in the Blast search. * * Revision 6.80 2001/02/22 15:38:48 dondosha * Corrected the argument number for longest intron length * * Revision 6.79 2001/02/09 22:22:36 madden * Do not use BlastPruneHitsFromSeqAlign for printing DefLines * * Revision 6.78 2001/02/08 20:41:17 dondosha * Implemented tabulated output for all translated programs * * Revision 6.77 2001/02/07 21:17:22 dondosha * Added support to produce tabulated output (-m 8 option) * * Revision 6.76 2001/01/19 20:03:47 dondosha * Uninitialized variable seqannot caused core dump with XML output * * Revision 6.75 2000/12/19 18:40:47 madden * Add calls to BlastSetUserErrorString and BlastDeleteUserErrorString * * Revision 6.74 2000/12/15 21:32:12 dondosha * Appended getargs explanation of new tblastn (-t) option * * Revision 6.73 2000/11/21 15:47:21 dondosha * Corrected default wordsize for megablast option * * Revision 6.72 2000/11/17 21:56:26 dondosha * Do not free query_lcase_mask in client-server case - already freed * * Revision 6.71 2000/11/17 20:56:50 dondosha * Returned Mega BLAST option which existed in blastcl3 and was removed * * Revision 6.70 2000/11/17 17:54:50 dondosha * Added argument to allow greedy (a la Mega BLAST) extension in blastn * * Revision 6.69 2000/11/15 15:10:27 shavirin * This revision is result of merge between blastall.c and blastcl3.c * programs. Using define BLAST_CS_API - client/server version may be * created. * * Revision 6.68 2000/11/09 15:01:00 dondosha * Set longest intron length in options in nucleotide coordinates * * Revision 6.67 2000/11/08 22:24:07 dondosha * Enabled new tblastn by adding longest intron option * * Revision 6.66 2000/11/01 16:26:50 madden * Changes from Futamura for psitblastn * * Revision 6.65 2000/10/27 19:14:40 madden * Change description of -b option * * Revision 6.64 2000/10/23 22:14:04 shavirin * Added possibility to pass valid error message into XML output in case * of failure or no hits. * * Revision 6.63 2000/10/23 19:58:22 dondosha * Open and close AsnIo outside of call(s) to BXMLPrintOutput * * Revision 6.62 2000/10/17 19:37:41 shavirin * Fixed compilation problems detected on Mac. * * Revision 6.61 2000/10/17 17:19:49 shavirin * Temporary - for toolkit release - commented OOF shift penalty parameter. * * Revision 6.60 2000/10/06 17:54:28 shavirin * Added usage of correct matrix in case of OOF alignment. * * Revision 6.59 2000/09/26 15:48:15 dondosha * Put back printing of header before results of every search when multiple queries are submitted * * Revision 6.58 2000/09/13 22:26:23 dondosha * Removed extra that is now printed in PrintDefLinesFromSeqAlign * * Revision 6.57 2000/09/13 21:39:31 dondosha * Corrected html output when input contains multiple queries * * Revision 6.56 2000/09/12 16:08:43 dondosha * Create txalign style matrix from search matrix * * Revision 6.55 2000/09/12 16:02:13 madden * do not allow -P with blastn, fix typo * * Revision 6.54 2000/09/07 20:25:59 madden * Remove L option, turn off K (culling) by default, add -P option * * Revision 6.53 2000/09/07 16:27:07 shavirin * Added option for OOF gap alignment for blastx. * * Revision 6.52 2000/08/24 14:13:23 shavirin * Added return 1 if database do not exists on any path. * * Revision 6.51 2000/08/11 18:03:58 shavirin * Added possibility to make blastx and tblastx with XML output. * * Revision 6.50 2000/08/11 17:54:08 shavirin * Added possibility to print XML output (with -m 7 option) * * Revision 6.49 2000/08/01 16:35:34 madden * Append Seq-annot, do not overwrite * * Revision 6.48 2000/06/27 15:25:18 madden * Changed master-slave to query-anchored * * Revision 6.47 2000/06/13 19:38:46 shavirin * Added ability to print XML Blast output. * * Revision 6.46 2000/06/05 19:31:31 madden * Free query->lcase_mask between searches * * Revision 6.45 2000/05/26 19:28:44 shavirin * Added adjustment of dropoff_1st_pass if dropoff_1st_pass > dropoff_2nd_pass * * Revision 6.44 2000/05/26 18:48:23 shavirin * Added two new parameters; '-y' and '-Z' * * Revision 6.43 2000/05/09 15:57:26 shavirin * Added call to the function ReadDBBioseqSetDbGeneticCode(). * * Revision 6.42 2000/04/25 20:50:45 dondosha * Removed unavailable option to use greedy algorithm * * Revision 6.41 2000/04/13 13:34:19 shavirin * Added call to ObjMgrFreeCache() back after fixes in API. * * Revision 6.40 2000/04/04 18:29:13 shavirin * Added some missing HTML tags. * * Revision 6.39 2000/03/31 19:13:33 dondosha * Changed some names related to MegaBlast * * Revision 6.38 2000/03/24 21:49:30 madden * Comment out ObjMgrFreeCache * * Revision 6.37 2000/03/02 21:06:09 shavirin * Added -U option, that allows to consider low characters in FASTA files * as filtered regions (for blastn, blastp and tblastn). * * Revision 6.36 2000/02/01 20:05:31 dondosha * Added option -B: use greedy basic alignment search if set to T * * Revision 6.35 2000/01/28 16:46:54 madden * Added function BlastGetMaskingLoc * * Revision 6.34 1999/12/17 20:48:53 egorov * Fix 'gcc -Wall' warnings and remove old stuff. * * Revision 6.33 1999/10/12 19:35:26 madden * Deallocate Mask information * * Revision 6.32 1999/08/26 14:58:06 madden * Use float for db length * * Revision 6.31 1999/05/26 13:12:56 madden * Initialized matrix to NULL * * Revision 6.30 1999/03/31 16:58:04 madden * Removed static FindProt and FindNuc * * Revision 6.29 1999/02/10 21:12:26 madden * Added HTML and GI list option, fixed filtering * * Revision 6.28 1999/01/22 17:24:51 madden * added line breaks for alignment views * * Revision 6.27 1998/12/31 18:18:27 madden * Added strand option * * Revision 6.26 1998/12/29 20:03:14 kans * calls UseLocalAsnloadDataAndErrMsg at startup * * Revision 6.25 1998/11/19 14:04:34 madden * Changed message level to SEV_WARNING * * Revision 6.24 1998/11/16 16:29:19 madden * Added ErrSetMessageLevel(SEV_INFO) * * Revision 6.23 1998/07/17 15:41:36 madden * Added effective search space flag * * Revision 6.22 1998/06/29 13:02:01 madden * Deallocate matrix * * Revision 6.21 1998/06/10 13:33:14 madden * Change -K from zero to 100 * * Revision 6.20 1998/06/05 21:48:42 madden * Added -K and -L options * * Revision 6.19 1998/05/18 18:01:04 madden * Changed args to allow filter options to be changed * * Revision 6.18 1998/05/01 18:31:02 egorov * Add new parametes to BLASTOptionSetGapParam() * * Revision 6.17 1998/04/30 14:32:32 madden * init_buff_ex arg changed to 90 for reference * * Revision 6.16 1998/04/29 14:29:30 madden * Made reference line longer * * Revision 6.15 1998/04/01 22:49:12 madden * Print No hits found message * * Revision 6.14 1998/02/25 20:50:48 madden * Added arg for db length * * Revision 6.13 1998/02/24 22:48:34 madden * Removed options for culling * * Revision 6.12 1998/01/31 21:35:17 madden * zeroed out values between searches * * Revision 6.11 1997/12/31 17:48:52 madden * Added wordsize option * * Revision 6.10 1997/12/23 21:09:47 madden * Added -K and -L for range-dependent blast * * Revision 6.9 1997/11/19 14:26:43 madden * Removed extra break statement * * Revision 6.8 1997/11/18 22:24:22 madden * Added call to BLASTOptionSetGapParams * * Revision 6.7 1997/10/27 22:26:52 madden * Added call to ObjMgrFreeCache(0) * * Revision 6.6 1997/10/23 20:26:12 madden * Use of init_buff_ex rather than init_buff * * Revision 6.5 1997/10/22 21:56:04 madden * Added matrix option * * Revision 6.3 1997/10/07 21:33:38 madden * Added BLUNT option * * Revision 6.2 1997/09/23 22:13:19 madden * enabled descriptions and alignment options * * Revision 6.1 1997/09/16 16:34:32 madden * Dbinfo printing changed for multiple db searches * * Revision 6.0 1997/08/25 18:19:14 madden * Revision changed to 6.0 * * Revision 1.16 1997/07/29 19:33:02 madden * Added TXALIGN_SHOW_QS flag * * Revision 1.15 1997/07/28 17:01:23 madden * Added include for simutil.h * * Revision 1.14 1997/07/28 14:31:09 madden * Changes for masking alignments. * * Revision 1.13 1997/07/22 19:06:35 madden * Option changes, Printing of verison info * * Revision 1.12 1997/07/18 20:09:22 madden * Conversion from blast2 output to new output * * Revision 1.3 1997/02/24 22:08:38 madden * Added reward and penalty for match and mismatch. * * Revision 1.2 1997/02/23 16:48:52 madden * Call to AcknowledgeBlastQuery added. * * Revision 1.1 1997/02/19 21:44:28 madden * Initial revision * * */ #include #include #include #include #include #include #include #include #include #include #include #include #include #include #ifdef BLAST_CS_API #include #include #endif #define DEFLINE_BUF 255 /* Used by the callback function. */ FILE *global_fp=NULL; /* Callback to print out ticks, in UNIX only due to file systems portability issues. */ #ifdef BLAST_CS_API static Boolean LIBCALLBACK tick_callback (BlastResponsePtr brp, Boolean PNTR cancel) { #if 0 fprintf(global_fp, "."); fflush(global_fp); #endif return TRUE; } #else static int LIBCALLBACK tick_callback(Int4 sequence_number, Int4 number_of_positive_hits) { #ifdef OS_UNIX /* #ifndef BLAST_CS_API */ fprintf(global_fp, "%s", "."); fflush(global_fp); /* #endif */ #endif return 0; } #endif static Int2 BlastGetMaskingLoc(FILE *infp, FILE *outfp, CharPtr instructions) { BioseqPtr bsp; Char buffer[50]; SeqEntryPtr sep; SeqLocPtr slp, slp_start, tmp_slp; if (infp == NULL || outfp == NULL || instructions == NULL) return 1; while ((sep=FastaToSeqEntryEx(infp, TRUE, NULL, TRUE)) != NULL) { bsp = NULL; SeqEntryExplore(sep, &bsp, FindNuc); if (bsp == NULL) { ErrPostEx(SEV_FATAL, 0, 0, "Unable to obtain bioseq\n"); return 2; } SeqIdWrite(bsp->id, buffer, PRINTID_FASTA_LONG, 50); fprintf(outfp, ">%s\n", buffer); slp_start = slp = BlastBioseqFilter(bsp, instructions); while (slp) { tmp_slp=NULL; while((tmp_slp = SeqLocFindNext(slp, tmp_slp))!=NULL) { fprintf(outfp, "%ld %ld\n", (long) (1+SeqLocStart(tmp_slp)), (long) (1+SeqLocStop(tmp_slp))); } slp = slp->next; } /* used for debugging. */ #if 0 {{ BioseqPtr bsp_tmp; ByteStorePtr byte_sp; Int4 index; SeqLocPtr tmp_slp_1, tmp_filter_slp; SeqPortPtr spp; Uint1Ptr tmp_query_seq, tmp_query_seq_start; Uint1 residue; FILE *tmp_fp; spp = SeqPortNew(bsp, 0, -1, 0, Seq_code_iupacna); SeqPortSet_do_virtual(spp, TRUE); tmp_query_seq_start = (Uint1Ptr) MemNew(((BioseqGetLen(bsp))+2)*sizeof(Uint1)); tmp_query_seq_start[0] = NULLB; tmp_query_seq = tmp_query_seq_start+1; index=0; while ((residue=SeqPortGetResidue(spp)) != SEQPORT_EOF) { if (IS_residue(residue)) { tmp_query_seq[index] = residue; index++; } } BlastMaskTheResidues(tmp_query_seq, BioseqGetLen(bsp), 78, slp_start, FALSE, 0); bsp_tmp = BioseqNew(); bsp_tmp->length = BioseqGetLen(bsp); byte_sp = BSNew(1); BSWrite(byte_sp, tmp_query_seq, bsp->length); bsp_tmp->seq_data = byte_sp; bsp_tmp->repr = Seq_repr_raw; bsp_tmp->seq_data_type = Seq_code_iupacna; bsp_tmp->mol = 1; bsp_tmp->id = bsp->id; bsp_tmp->descr = bsp->descr; tmp_fp = FileOpen("masked.fsa", "w"); BioseqRawToFastaExtra(bsp_tmp, tmp_fp, 50); bsp_tmp->id = NULL; bsp_tmp->descr = NULL; spp = SeqPortFree(spp); bsp_tmp = BioseqFree(bsp_tmp); tmp_query_seq_start = MemFree(tmp_query_seq_start); FileClose(tmp_fp); tmp_filter_slp = slp_start; tmp_fp = FileOpen("locations.msk", "w"); while (tmp_filter_slp) { tmp_slp_1=NULL; while((tmp_slp_1 = SeqLocFindNext(tmp_filter_slp, tmp_slp_1))!=NULL) { fprintf(tmp_fp, "%ld %ld\n", (long) (1+SeqLocStart(tmp_slp_1)), (long) (1+SeqLocStop(tmp_slp_1))); } tmp_filter_slp = tmp_filter_slp->next; } FileClose(tmp_fp); }} #endif slp_start = SeqLocSetFree(slp_start); sep = SeqEntryFree(sep); } return 0; } /* #define DO_NOT_SUPPRESS_BLAST_OP */ #define NUMARG (sizeof(myargs)/sizeof(myargs[0])) static Args myargs [] = { { "Program Name", /* 0 */ NULL, NULL, NULL, FALSE, 'p', ARG_STRING, 0.0, 0, NULL}, { "Database", /* 1 */ "nr", NULL, NULL, FALSE, 'd', ARG_STRING, 0.0, 0, NULL}, { "Query File", /* 2 */ "stdin", NULL, NULL, FALSE, 'i', ARG_FILE_IN, 0.0, 0, NULL}, { "Expectation value (E)", /* 3 */ "10.0", NULL, NULL, FALSE, 'e', ARG_FLOAT, 0.0, 0, NULL}, { "alignment view options:\n0 = pairwise,\n1 = query-anchored showing identities,\n2 = query-anchored no identities,\n3 = flat query-anchored, show identities,\n4 = flat query-anchored, no identities,\n5 = query-anchored no identities and blunt ends,\n6 = flat query-anchored, no identities and blunt ends,\n7 = XML Blast output,\n8 = tabular, \n9 tabular with comment lines", /* 4 */ "0", NULL, NULL, FALSE, 'm', ARG_INT, 0.0, 0, NULL}, { "BLAST report Output File", /* 5 */ "stdout", NULL, NULL, TRUE, 'o', ARG_FILE_OUT, 0.0, 0, NULL}, { "Filter query sequence (DUST with blastn, SEG with others)", /* 6 */ "T", NULL, NULL, FALSE, 'F', ARG_STRING, 0.0, 0, NULL}, { "Cost to open a gap (zero invokes default behavior)", /* 7 */ "0", NULL, NULL, FALSE, 'G', ARG_INT, 0.0, 0, NULL}, { "Cost to extend a gap (zero invokes default behavior)", /* 8 */ "0", NULL, NULL, FALSE, 'E', ARG_INT, 0.0, 0, NULL}, { "X dropoff value for gapped alignment (in bits) (zero invokes default behavior)", /* 9 */ "0", NULL, NULL, FALSE, 'X', ARG_INT, 0.0, 0, NULL}, { "Show GI's in deflines", /* 10 */ "F", NULL, NULL, FALSE, 'I', ARG_BOOLEAN, 0.0, 0, NULL}, { "Penalty for a nucleotide mismatch (blastn only)", /* 11 */ "-3", NULL, NULL, FALSE, 'q', ARG_INT, 0.0, 0, NULL}, { "Reward for a nucleotide match (blastn only)", /* 12 */ "1", NULL, NULL, FALSE, 'r', ARG_INT, 0.0, 0, NULL}, { "Number of database sequences to show one-line descriptions for (V)", /* 13 */ "500", NULL, NULL, FALSE, 'v', ARG_INT, 0.0, 0, NULL}, { "Number of database sequence to show alignments for (B)", /* 14 */ "250", NULL, NULL, FALSE, 'b', ARG_INT, 0.0, 0, NULL}, { "Threshold for extending hits, default if zero", /* 15 */ "0", NULL, NULL, FALSE, 'f', ARG_INT, 0.0, 0, NULL}, { "Perfom gapped alignment (not available with tblastx)", /* 16 */ "T", NULL, NULL, FALSE, 'g', ARG_BOOLEAN, 0.0, 0, NULL}, { "Query Genetic code to use", /* 17 */ "1", NULL, NULL, FALSE, 'Q', ARG_INT, 0.0, 0, NULL}, { "DB Genetic code (for tblast[nx] only)", /* 18 */ "1", NULL, NULL, FALSE, 'D', ARG_INT, 0.0, 0, NULL}, { "Number of processors to use", /* 19 */ "1", NULL, NULL, FALSE, 'a', ARG_INT, 0.0, 0, NULL}, { "SeqAlign file", /* 20 */ NULL, NULL, NULL, TRUE, 'O', ARG_FILE_OUT, 0.0, 0, NULL}, { "Believe the query defline", /* 21 */ "F", NULL, NULL, FALSE, 'J', ARG_BOOLEAN, 0.0, 0, NULL}, { "Matrix", /* 22 */ "BLOSUM62", NULL, NULL, FALSE, 'M', ARG_STRING, 0.0, 0, NULL}, { "Word size, default if zero", /* 23 */ "0", NULL, NULL, FALSE, 'W', ARG_INT, 0.0, 0, NULL}, { "Effective length of the database (use zero for the real size)", /* 24 */ "0", NULL, NULL, FALSE, 'z', ARG_STRING, 0.0, 0, NULL}, { "Number of best hits from a region to keep (off by default, if used a value of 100 is recommended)", /* 25 */ "0", NULL, NULL, FALSE, 'K', ARG_INT, 0.0, 0, NULL}, { "0 for multiple hits 1-pass, 1 for single hit 1-pass, 2 for 2-pass", /* 26 */ "0", NULL, NULL, FALSE, 'P', ARG_INT, 0.0, 0, NULL}, { "Effective length of the search space (use zero for the real size)", /* 27 */ "0", NULL, NULL, FALSE, 'Y', ARG_FLOAT, 0.0, 0, NULL}, { "Query strands to search against database (for blast[nx], and tblastx). 3 is both, 1 is top, 2 is bottom", /* 28 */ "3", NULL, NULL, FALSE, 'S', ARG_INT, 0.0, 0, NULL}, { "Produce HTML output", /* 29 */ "F", NULL, NULL, FALSE, 'T', ARG_BOOLEAN, 0.0, 0, NULL}, #ifdef BLAST_CS_API { "Restrict search of database to results of Entrez2 lookup", /* 30 */ NULL, NULL, NULL, TRUE, 'u', ARG_STRING, 0.0, 0, NULL}, #else { "Restrict search of database to list of GI's", /* 30 */ NULL, NULL, NULL, TRUE, 'l', ARG_STRING, 0.0, 0, NULL}, #endif {"Use lower case filtering of FASTA sequence", /* 31 */ "F", NULL,NULL,TRUE,'U',ARG_BOOLEAN, 0.0,0,NULL}, { "Dropoff (X) for blast extensions in bits (0.0 invokes default behavior)", /* 32 */ "0.0", NULL, NULL, FALSE, 'y', ARG_FLOAT, 0.0, 0, NULL}, { "X dropoff value for final gapped alignment (in bits)", /* 33 */ "0", NULL, NULL, FALSE, 'Z', ARG_INT, 0.0, 0, NULL}, #ifdef BLAST_CS_API { "RPS Blast search", /* 34 */ "F", NULL, NULL, FALSE, 'R', ARG_BOOLEAN, 0.0, 0, NULL}, #else { "PSI-TBLASTN checkpoint file", /* 34 */ NULL, NULL, NULL, TRUE, 'R', ARG_FILE_IN, 0.0, 0, NULL}, #endif { "MegaBlast search", /* 35 */ "F", NULL, NULL, FALSE, 'n', ARG_BOOLEAN, 0.0, 0, NULL}, { "Location on query sequence",/* 36 */ NULL, NULL, NULL, TRUE, 'L', ARG_STRING, 0.0, 0, NULL}, { "Multiple Hits window size (zero for single hit algorithm)", /* 37 */ "40", NULL, NULL, FALSE, 'A', ARG_INT, 0.0, 0, NULL}, #ifdef DO_NOT_SUPPRESS_BLAST_OP { "Frame shift penalty (OOF algorithm for blastx)", /* 38 */ "0", NULL, NULL, FALSE, 'w', ARG_INT, 0.0, 0, NULL}, { "Length of the largest intron allowed in tblastn for linking HSPs (0 disables linking)", /* 39 */ "0", NULL, NULL, FALSE, 't', ARG_INT, 0.0, 0, NULL} #endif }; #ifdef BLAST_CS_API BlastNet3Hptr BNETInitializeBlast(CharPtr database, CharPtr program, FILE *outfp, Boolean db_is_na, Boolean is_rps_blast, Boolean html) { BlastNet3Hptr bl3hp; BlastResponsePtr response = NULL; BlastVersionPtr blast_version; if (! BlastInit("blastcl3", &bl3hp, &response)) { ErrPostEx(SEV_FATAL, 0, 0, "Unable to initialize BLAST service"); return NULL; } if (response && response->choice == BlastResponse_init) { blast_version = response->data.ptrvalue; } else { ErrPostEx(SEV_FATAL, 0, 0, "Unable to connect to the BLAST service"); return NULL; } BlastNetBioseqFetchEnable(bl3hp, database, db_is_na, TRUE); if(is_rps_blast == TRUE) BlastPrintVersionInfoEx("RPS-BLAST", html, blast_version->version, blast_version->date, outfp); else { init_buff_ex(90); BlastPrintVersionInfoEx(program, html, blast_version->version, blast_version->date, outfp); fprintf(outfp, "\n"); BlastPrintReference(html, 80, outfp); free_buff(); } BlastResponseFree(response); return bl3hp; } #endif /* Needed for Mega BLAST only */ #define MAX_NUM_QUERIES 16383 /* == 1/2 INT2_MAX */ Int2 Main (void) { AsnIoPtr aip, xml_aip; BioseqPtr fake_bsp = NULL, query_bsp; BioSourcePtr source; BLAST_MatrixPtr matrix; Int4Ptr PNTR txmatrix; BLAST_OptionsBlkPtr options; BLAST_KarlinBlkPtr ka_params=NULL, ka_params_gap=NULL; BlastPruneSapStructPtr prune; Boolean db_is_na, query_is_na, show_gi, believe_query=FALSE; Boolean html = FALSE; CharPtr params_buffer=NULL; Int4 number_of_descriptions, number_of_alignments; SeqAlignPtr seqalign; SeqAnnotPtr seqannot = NULL; SeqEntryPtr sep; TxDfDbInfoPtr dbinfo=NULL, dbinfo_head; Uint1 align_type, align_view, err_ticket; Uint4 align_options, print_options; ValNodePtr mask_loc, mask_loc_start, vnp, other_returns, error_returns; CharPtr blast_program, blast_database, blast_inputfile, blast_outputfile; FILE *infp, *outfp; /* Mega BLAST related variables */ SeqAlignPtr sap, next_seqalign, PNTR seqalignp; Int4 num_bsps, index; SeqLocPtr last_mask, mask_slp, slp = NULL, tmp_slp; Int2 ctr = 1; Char prefix[2]; Boolean done = TRUE; int (LIBCALLBACK *handle_results)(VoidPtr srch); Int4 from = 0, to = -1; const char *dummystr; #ifdef BLAST_CS_API BlastNet3Hptr bl3hp; Boolean status; #endif #ifdef BLAST_CS_API if (! GetArgs ("blastcl3", NUMARG, myargs)) { return (1); } #else if (! GetArgs ("blastall", NUMARG, myargs)) { return (1); } #endif UseLocalAsnloadDataAndErrMsg (); if (! SeqEntryLoad()) return 1; ErrSetMessageLevel(SEV_WARNING); blast_program = myargs [0].strvalue; #ifdef BLAST_CS_API /* For RPS Blast - anything not "blastp" - is "tblastn" */ if(myargs[34].intvalue) { if(StringICmp(blast_program, "blastp")) { StringCpy(blast_program, "blastx"); } } #endif blast_database = myargs [1].strvalue; blast_inputfile = myargs [2].strvalue; blast_outputfile = myargs [5].strvalue; if (myargs[29].intvalue) html = TRUE; if ((infp = FileOpen(blast_inputfile, "r")) == NULL) { ErrPostEx(SEV_FATAL, 0, 0, "blast: Unable to open input file %s\n", blast_inputfile); return (1); } outfp = NULL; if (blast_outputfile != NULL) { if ((outfp = FileOpen(blast_outputfile, "w")) == NULL) { ErrPostEx(SEV_FATAL, 0, 0, "blast: Unable to open output file %s\n", blast_outputfile); return (1); } } if (StringCmp("filter", blast_program) == 0) { BlastGetMaskingLoc(infp, outfp, myargs[6].strvalue); FileClose(outfp); FileClose(infp); return 0; } align_view = (Int1) myargs[4].intvalue; align_type = BlastGetTypes(blast_program, &query_is_na, &db_is_na); if(align_view < 7) { if (StringICmp("blastx", blast_program) == 0) { if (align_view != 0) { ErrPostEx(SEV_FATAL, 0, 0, "This option is not available with blastx"); return 1; } } else if (StringICmp("tblastx", blast_program) == 0) { if (align_view != 0) { ErrPostEx(SEV_FATAL, 0, 0, "This option is not available with tblastx"); return 1; } } } believe_query = FALSE; if (myargs[21].intvalue != 0) believe_query = TRUE; if (believe_query == FALSE && myargs[20].strvalue) { ErrPostEx(SEV_FATAL, 0, 0, "-J option must be TRUE to produce a SeqAlign file"); } options = BLASTOptionNew(blast_program, (Boolean) myargs [16].intvalue); if (options == NULL) return 3; #ifdef BLAST_CS_API if(myargs[34].intvalue) options->is_rps_blast = TRUE; #endif options->is_megablast_search = (Boolean) myargs[35].intvalue; if (options->is_megablast_search) { options->wordsize = 28; options->block_width = 0; } if (align_view == 8 && options->is_megablast_search) { options->output = (VoidPtr) outfp; handle_results = MegaBlastPrintAlignInfo; } else handle_results = NULL; BLASTOptionSetGapParams(options, myargs[22].strvalue, 0, 0); options->expect_value = (Nlm_FloatHi) myargs [3].floatvalue; number_of_descriptions = myargs[13].intvalue; number_of_alignments = myargs[14].intvalue; options->hitlist_size = MAX(number_of_descriptions, number_of_alignments); if (myargs[7].intvalue != 0) options->gap_open = myargs[7].intvalue; if (myargs[8].intvalue != 0) options->gap_extend = myargs[8].intvalue; if (myargs[9].intvalue != 0) options->gap_x_dropoff = myargs[9].intvalue; /* Multiple hits does not apply to blastn. */ if (StringICmp("blastn", blast_program)) { if (myargs[26].intvalue == 0) { options->two_pass_method = FALSE; options->multiple_hits_only = TRUE; } else if (myargs[26].intvalue == 1) { options->two_pass_method = FALSE; options->multiple_hits_only = FALSE; } else { options->two_pass_method = TRUE; options->multiple_hits_only = FALSE; } } else { /* Reverse these for blastn for now. */ if (myargs[26].intvalue == 1) { options->two_pass_method = FALSE; options->multiple_hits_only = TRUE; } else if (myargs[26].intvalue == 0) { options->two_pass_method = FALSE; options->multiple_hits_only = FALSE; } } if(myargs[33].intvalue != 0) options->gap_x_dropoff_final = myargs[33].intvalue; if (StringICmp(myargs[6].strvalue, "T") == 0) { if (StringICmp("blastn", blast_program) == 0) options->filter_string = StringSave("D"); else options->filter_string = StringSave("S"); } else { options->filter_string = StringSave(myargs[6].strvalue); } show_gi = (Boolean) myargs[10].intvalue; if (StringICmp("blastn", blast_program) == 0) { options->penalty = myargs[11].intvalue; options->reward = myargs[12].intvalue; } else { if (myargs[15].intvalue != 0) { options->threshold_second = myargs[15].intvalue; } } options->genetic_code = myargs[17].intvalue; options->db_genetic_code = myargs[18].intvalue; options->number_of_cpus = myargs[19].intvalue; if (myargs[23].intvalue != 0) { options->wordsize = myargs[23].intvalue; } if (options->is_megablast_search) { options->cutoff_s2 = options->wordsize; options->wordsize += 4; options->cutoff_s = options->wordsize; } options->db_length = StringToInt8(myargs[24].strvalue, &dummystr); options->hsp_range_max = myargs[25].intvalue; if (options->hsp_range_max != 0) options->perform_culling = TRUE; if (myargs[27].floatvalue) options->searchsp_eff = (Nlm_FloatHi) myargs[27].floatvalue; options->strand_option = myargs[28].intvalue; if(myargs [32].floatvalue != 0.0) { options->dropoff_2nd_pass = myargs [32].floatvalue; if(options->dropoff_1st_pass > options->dropoff_2nd_pass) options->dropoff_1st_pass = options->dropoff_2nd_pass; } options->window_size = myargs [37].intvalue; print_options = 0; align_options = 0; align_options += TXALIGN_COMPRESS; align_options += TXALIGN_END_NUM; if (StringICmp("blastx", blast_program) == 0) { align_options += TXALIGN_BLASTX_SPECIAL; } if (show_gi) { align_options += TXALIGN_SHOW_GI; print_options += TXALIGN_SHOW_GI; } if (myargs[16].intvalue == 0) print_options += TXALIGN_SHOW_NO_OF_SEGS; if (align_view) { align_options += TXALIGN_MASTER; if (align_view == 1 || align_view == 3) align_options += TXALIGN_MISMATCH; if (align_view == 3 || align_view == 4 || align_view == 6) align_options += TXALIGN_FLAT_INS; if (align_view == 5 || align_view == 6) align_options += TXALIGN_BLUNT_END; } else { align_options += TXALIGN_MATRIX_VAL; align_options += TXALIGN_SHOW_QS; } if (html) { align_options += TXALIGN_HTML; print_options += TXALIGN_HTML; } #ifdef BLAST_CS_API if(myargs[30].strvalue) options->entrez_query = StringSave(myargs[30].strvalue); #else if (myargs[30].strvalue) { options->gifile = StringSave(myargs[30].strvalue); } #endif /* Out-of-frame option is valid only for blastx, tblastn and psitblastnsearches */ #ifdef DO_NOT_SUPPRESS_BLAST_OP if(myargs[38].intvalue > 0) { if (!StringICmp("blastx", blast_program) || !StringICmp("tblastn", blast_program)|| !StringICmp("psitblastn", blast_program)) { if (!StringICmp("blastx", blast_program)) { options->is_ooframe = TRUE; options->shift_pen = myargs[38].intvalue; } } } #endif #ifdef DO_NOT_SUPPRESS_BLAST_OP /* Input longest intron length is in nucleotide scale; in the lower level code it will be used in protein scale */ if (myargs[39].intvalue > 0) options->longest_intron = MAX(myargs[39].intvalue, MAX_INTRON_LENGTH); #endif aip = NULL; if (myargs[20].strvalue != NULL) { if ((aip = AsnIoOpen (myargs[20].strvalue,"w")) == NULL) { ErrPostEx(SEV_FATAL, 0, 0, "blast: Unable to open output file %s\n", myargs[20].strvalue); return 1; } } if(align_view < 7) { if (html) { fprintf(outfp, "\nBLAST Search Results\n"); fprintf(outfp, "\n"); fprintf(outfp, "
\n");
       }
    } else if (align_view == 7)     
       xml_aip = AsnIoOpen(blast_outputfile, "wx");


                  /* Futamura: Setting up the psitblastn options */
#ifndef BLAST_CS_API
    if (NULL != myargs[34].strvalue) {
          options->recoverCheckpoint = TRUE;
          options->freqCheckpoint = TRUE;
    }
    options->CheckpointFileName=myargs[34].strvalue;
#endif

#ifdef BLAST_CS_API
    bl3hp = BNETInitializeBlast(blast_database, blast_program, outfp, 
                                db_is_na, options->is_rps_blast, html);
#else
    ReadDBBioseqFetchEnable ("blastall", blast_database, db_is_na, TRUE);
#endif
    
    /* --- Main loop over all FASTA entries in the input file ---- */

    if (myargs[36].strvalue) {       
        CharPtr delimiters = " ,;";
        CharPtr location;
        location = myargs[36].strvalue;
        from = atoi(StringTokMT(location, delimiters, &location)) - 1;
        to = atoi(location) - 1;
        from = MAX(from, 0);
    }

    while (TRUE) {
       if (options->is_megablast_search) {
          StrCpy(prefix, "");
          slp = NULL;
	  num_bsps = 0;
          done = TRUE;
	  SeqMgrHoldIndexing(TRUE);
	  mask_slp = last_mask = NULL;
	  while ((sep=FastaToSeqEntryForDb(infp, query_is_na, NULL,
					   believe_query, prefix, &ctr, 
					   &mask_slp)) != NULL) {
	     
	     if (mask_slp) {
		if (!last_mask)
		   options->query_lcase_mask = last_mask = mask_slp;
		else {
		   last_mask->next = mask_slp;
		   last_mask = last_mask->next;
		}
		mask_slp = NULL;
	     }
	     query_bsp = NULL;
	     if (query_is_na) 
		SeqEntryExplore(sep, &query_bsp, FindNuc);
	     else
		SeqEntryExplore(sep, &query_bsp, FindProt);
	     
	     if (query_bsp == NULL) {
		ErrPostEx(SEV_FATAL, 0, 0, "Unable to obtain bioseq\n");
		return 2;
	     }
	     
             /* Only for the first query */
             if (num_bsps == 0) {
                 to = MIN(to, query_bsp->length - 1);
                 
                 /* -1 means end of sequence */
                 if (to < 0)
                     to = query_bsp->length - 1;
                 if (from >= query_bsp->length || to < 0) {
                     ErrPostEx(SEV_FATAL, 0, 0, 
                               "Location outside of the query sequence range\n");
                     return 3;
                 }
                 slp = SeqLocIntNew(from, to, options->strand_option, 
                                    SeqIdFindBest(query_bsp->id, SEQID_GI));
             } else 
                 ValNodeAddPointer(&slp, SEQLOC_WHOLE,
                                   SeqIdDup(SeqIdFindBest(query_bsp->id,
                                                          SEQID_GI)));
	     num_bsps++;
	     if (num_bsps >= MAX_NUM_QUERIES) {
                done = FALSE;
		break;
	     }
	     /*sep = MemFree(sep);*/ /* Do not free the underlying Bioseq */
	  }
	  SeqMgrHoldIndexing(FALSE);
          if (num_bsps == 0) 
             break;
       } else {
          if(myargs[31].intvalue) {
             sep = FastaToSeqEntryForDb (infp, query_is_na, NULL, believe_query, NULL, NULL, &options->query_lcase_mask);
             
          } else {
             sep = FastaToSeqEntryEx(infp, query_is_na, NULL, believe_query);
          }
          
          if(sep == NULL)
             break;
          
          query_bsp = NULL;
          if (query_is_na) {
             SeqEntryExplore(sep, &query_bsp, FindNuc);
          } else {
             SeqEntryExplore(sep, &query_bsp, FindProt);
          }
          
          if (query_bsp == NULL) {
             ErrPostEx(SEV_FATAL, 0, 0, "Unable to obtain bioseq\n");
             return 2;
          }
        
          if(believe_query)
             fake_bsp = query_bsp;
          else 
             fake_bsp = BlastMakeFakeBioseq(query_bsp, NULL);

	  err_ticket = BlastSetUserErrorString(NULL, query_bsp->id, believe_query);
        
          /* If fake_bsp created mask should be updated to use it's id */
          BLASTUpdateSeqIdInSeqInt(options->query_lcase_mask, fake_bsp->id);
        
          source = BioSourceNew();
          source->org = OrgRefNew();
          source->org->orgname = OrgNameNew();
          source->org->orgname->gcode = options->genetic_code;
          ValNodeAddPointer(&(query_bsp->descr), Seq_descr_source, source);
       }

       global_fp = outfp;
          
       if(align_view < 7) {
#ifndef BLAST_CS_API
           init_buff_ex(90);
           BlastPrintVersionInfo(blast_program, html, outfp);
           fprintf(outfp, "\n");
           BlastPrintReference(html, 90, outfp);
           fprintf(outfp, "\n");
#else
           fprintf(outfp, "\n");
#endif            
           if (!options->is_megablast_search)
              AcknowledgeBlastQuery(query_bsp, 70, outfp, believe_query, html);

            /* Here we first check, that database do no exists */

#ifndef BLAST_CS_API
           if(!PrintDbInformation(blast_database, !db_is_na, 70, outfp, html))
                return 1;
#else

            {{
                BlastDbinfoPtr dbinfo;
                static Boolean not_first_time;

                /* For CS version we will print database info ones to 
                   decrease network traffic */                

                if(!not_first_time) {
                    dbinfo = BlastRequestDbInfo(bl3hp, blast_database, !db_is_na);
                    if (dbinfo)
                        PrintDbInformationBasic(blast_database, !db_is_na, 70, dbinfo->definition, dbinfo->number_seqs, dbinfo->total_length, outfp, html);
                    dbinfo = BlastDbinfoFree(dbinfo);
                    not_first_time = TRUE;
                }
            }}
#endif    /* BLAST_CS_API */        
            free_buff();
        }
#ifdef OS_UNIX
        if(align_view < 7) {
#ifdef BLAST_CS_API
            fprintf(global_fp, "%s", "Searching... please wait.. ");
#else
            fprintf(global_fp, "%s", "Searching");
#endif
        }
#endif
        other_returns = NULL;
        error_returns = NULL;

        if (options->is_megablast_search) {
#ifdef BLAST_CS_API
           seqalign = MegaBlastSeqLocNetCore(bl3hp, slp, blast_program, 
                                   blast_database, options, 
                                   &other_returns, &error_returns,
                                   align_view < 7 ? tick_callback : NULL,
                                   &status);
#else
           seqalignp = BioseqMegaBlastEngineByLoc(slp, blast_program,
			           blast_database, options, &other_returns, 
                                   &error_returns, 
                                   align_view < 7 ? tick_callback : NULL,
                                   NULL, NULL, 0, handle_results);
           seqalign = NULL;
	   for (index=0; indexnext = seqalignp[index];
                 while (sap->next != NULL)
                    sap = sap->next;
              }
           }
           seqalignp = MemFree(seqalignp);
#endif
        } else if (!myargs[36].strvalue) {       
#ifdef BLAST_CS_API
           seqalign = BlastBioseqNetCore(bl3hp, fake_bsp, blast_program, 
                                      blast_database, options,
				      &other_returns, &error_returns,
                                      align_view < 7 ? tick_callback : NULL,
				      NULL, &status);
#else
           seqalign = BioseqBlastEngineWithCallback(fake_bsp, blast_program, blast_database, options, &other_returns, &error_returns, align_view < 7 ? tick_callback : NULL, handle_results);
#endif
        } else { /* Location on query provided */
           to = MIN(to, fake_bsp->length - 1);
           
           /* -1 means end of sequence */
           if (to < 0)
              to = fake_bsp->length - 1;
           if (from >= fake_bsp->length || to < 0) {
              ErrPostEx(SEV_FATAL, 0, 0, 
                        "Location outside of the query sequence range\n");
              return 3;
           }
           slp = SeqLocIntNew(from, to, options->strand_option, 
                              fake_bsp->id);
#ifdef BLAST_CS_API
           seqalign = BlastSeqLocNetCore(bl3hp, slp, blast_program, 
                                         blast_database, options,
                                         &other_returns, &error_returns,
                                         align_view < 7 ? tick_callback : NULL,
                                         NULL, &status);
#else
           seqalign = BioseqBlastEngineByLocWithCallback(slp, blast_program, blast_database, options, &other_returns, &error_returns, align_view < 7 ? tick_callback : NULL, NULL, NULL, 0, handle_results);
#endif
           
        }
#if 0
        seqalign = BLASTFilterOverlapRegions(seqalign, 0, !db_is_na, 
                                             options->is_ooframe, FALSE);
#endif
        
        BlastErrorPrint(error_returns);

        dbinfo = NULL;
        ka_params = NULL;
        ka_params_gap = NULL;
        params_buffer = NULL;
        mask_loc = NULL;
        matrix = NULL;
        txmatrix = NULL;
        for (vnp=other_returns; vnp; vnp = vnp->next) {
            switch (vnp->choice) {
            case TXDBINFO:
                dbinfo = vnp->data.ptrvalue;
                break;
            case TXKABLK_NOGAP:
                ka_params = vnp->data.ptrvalue;
                break;
            case TXKABLK_GAP:
                ka_params_gap = vnp->data.ptrvalue;
                break;
            case TXPARAMETERS:
                params_buffer = vnp->data.ptrvalue;
                break;
            case TXMATRIX:
                matrix = vnp->data.ptrvalue;
                if (matrix)
                   txmatrix = BlastMatrixToTxMatrix(matrix);
                break;
            case SEQLOC_MASKING_NOTSET:
            case SEQLOC_MASKING_PLUS1:
            case SEQLOC_MASKING_PLUS2:
            case SEQLOC_MASKING_PLUS3:
            case SEQLOC_MASKING_MINUS1:
            case SEQLOC_MASKING_MINUS2:
            case SEQLOC_MASKING_MINUS3:
                ValNodeAddPointer(&mask_loc, vnp->choice, vnp->data.ptrvalue);
                break;
            default:
                break;
            }
        }	
        
        
#ifdef OS_UNIX
        fflush(global_fp);
#endif
        
#ifdef OS_UNIX
        if(align_view < 7) {
            fprintf(global_fp, "%s", "done");
        }
#endif
        
        ReadDBBioseqSetDbGeneticCode(options->db_genetic_code);

        tmp_slp = slp;
        if (slp)
           query_bsp = NULL;

        if (getenv("POST_BLAST_CLUSTER_HITS") != NULL)
           BlastClusterHitsFromSeqAlign(seqalign, blast_program, blast_database, 
                                        options, 0.9, 1.6, 0.5, TRUE);

        if (seqalign) {
           if (align_view == 8 || align_view == 9) {
	      if (align_view == 9)
              	PrintTabularOutputHeader(blast_database, query_bsp, slp, 
                                       blast_program, 0, believe_query,
                                       global_fp);

              BlastPrintTabulatedResults(seqalign, query_bsp, slp, 
                                         number_of_alignments,
                                         blast_program, 
                                         !options->gapped_calculation,
                                         believe_query, from, 0, global_fp);
              SeqAlignSetFree(seqalign);
           } else {
           while (seqalign) {
              if (!options->is_megablast_search)
                 next_seqalign = NULL;
              else {
                 DenseSegPtr dsp, next_dsp;
                 BioseqPtr bsp;
                 
                 sap = seqalign;
                 while (sap != NULL) { 
                    if (sap->next != NULL) {
                       dsp = (DenseSegPtr) (sap->segs);
                       next_dsp = (DenseSegPtr) (sap->next->segs);
                       
                       if (SeqIdComp(dsp->ids, next_dsp->ids) != SIC_YES) {
                          next_seqalign = sap->next;
                          sap->next = NULL;
                       }
                    } else
                       next_seqalign = NULL;
                    sap = sap->next;
                 }
                 
                 dsp = (DenseSegPtr) (seqalign->segs);
                 while (tmp_slp && SeqIdComp(dsp->ids, SeqLocId(tmp_slp)) != SIC_YES)
                    tmp_slp = tmp_slp->next;
                 if (tmp_slp == NULL) /* Should never happen */
                    break;
                 bsp = BioseqLockById(SeqLocId(tmp_slp));
                 init_buff_ex(85);
                 fprintf(outfp, "\n");
                 AcknowledgeBlastQuery(bsp, 70, outfp, believe_query, html);
                 free_buff();
                 BioseqUnlock(bsp);
              }
              if(align_view == 7 && !options->is_ooframe) {
                 BXMLPrintOutput(xml_aip, seqalign, 
                                 options, blast_program, blast_database, 
                                 fake_bsp, other_returns, 0, NULL);
                 AsnIoReset(xml_aip);
                 SeqAlignSetFree(seqalign);
              } else {
                 seqannot = SeqAnnotNew();
                 seqannot->type = 2;
                 AddAlignInfoToSeqAnnot(seqannot, align_type);
                 seqannot->data = seqalign;
                 if (aip) {
                    SeqAnnotAsnWrite((SeqAnnotPtr) seqannot, aip, NULL);
                    AsnIoReset(aip);
                 }
                 if (outfp) { /* Uncacheing causes problems with ordinal nos. vs. gi's. */
                    ObjMgrSetHold();
                    init_buff_ex(85);
                    PrintDefLinesFromSeqAlignEx2(seqalign, 80, outfp, print_options, FIRST_PASS, 
			NULL, number_of_descriptions, NULL, NULL);
                    free_buff();
                    
                    prune = BlastPruneHitsFromSeqAlign(seqalign, number_of_alignments, NULL);
                    seqannot->data = prune->sap;

                    if(options->is_ooframe) {
                        OOFShowBlastAlignment(seqalign, /*mask*/ NULL,
                                              outfp, align_options, txmatrix);
                    } else {
                        if (align_view != 0)
                            ShowTextAlignFromAnnot(seqannot, 60, outfp, NULL, NULL, align_options, txmatrix, mask_loc, NULL);
                        else
                            ShowTextAlignFromAnnot(seqannot, 60, outfp, NULL, NULL, align_options, txmatrix, mask_loc, FormatScoreFunc);
                    }
                    
                    seqannot->data = seqalign;
                    prune = BlastPruneSapStructDestruct(prune);
                    ObjMgrClearHold();
                    
                    ObjMgrFreeCache(0);
                    
                 }
                 seqannot = SeqAnnotFree(seqannot);
              } /* if XML Printing */
              if (options->is_megablast_search)
                 tmp_slp = tmp_slp->next;
              if (seqannot)
                 seqannot = SeqAnnotFree(seqannot);
              seqalign = next_seqalign;
           }
           }
        } else {         /* seqalign is NULL */
           if(align_view == 7 && !options->is_ooframe) {
              BlastErrorMsgPtr error_msg;
              CharPtr message;
              
              if (error_returns == NULL) {
                 message = "No hits found";
              } else {
                 error_msg = error_returns->data.ptrvalue;
                 message = error_msg->msg;
              }
           
              BXMLPrintOutput(xml_aip, NULL, 
                              options, blast_program, blast_database, 
                              fake_bsp, other_returns, 0, message);
              
              AsnIoReset(xml_aip);
           } else if (align_view < 8) {
              fprintf(outfp, "\n\n ***** No hits found ******\n\n");
           }
           if (error_returns != NULL) {
              for (vnp = error_returns; vnp; vnp = vnp->next) {
                 BlastDestroyErrorMessage((BlastErrorMsgPtr)vnp->data.ptrvalue);
              }
              ValNodeFree(error_returns);
           }
        }
        
        slp = SeqLocSetFree(slp);
        matrix = BLAST_MatrixDestruct(matrix);
        if (txmatrix)
           txmatrix = TxMatrixDestruct(txmatrix);
        
        if(html) {
           fprintf(outfp, "
\n");
        }
        
        init_buff_ex(85);
        dbinfo_head = dbinfo;
        
        if(align_view < 7 && done) {
           while (dbinfo) {
              PrintDbReport(dbinfo, 70, outfp);
              dbinfo = dbinfo->next;
           }
        }
        dbinfo_head = TxDfDbInfoDestruct(dbinfo_head);
        
        if (ka_params) {
           if(align_view < 7 && done) {
              PrintKAParameters(ka_params->Lambda, ka_params->K, ka_params->H, 70, outfp, FALSE);
           }
           MemFree(ka_params);
        }
        
        if (ka_params_gap) {
           if(align_view < 7 && done) {
              PrintKAParameters(ka_params_gap->Lambda, ka_params_gap->K, ka_params_gap->H, 70, outfp, TRUE);
           }
           MemFree(ka_params_gap);
        }
        
        if(align_view < 7 && done) {
           PrintTildeSepLines(params_buffer, 70, outfp);
        }
        
        MemFree(params_buffer);
        free_buff();
        mask_loc_start = mask_loc;
        while (mask_loc) {
           SeqLocSetFree(mask_loc->data.ptrvalue);
           mask_loc = mask_loc->next;
        }
        ValNodeFree(mask_loc_start);
        
        if(!believe_query)
           fake_bsp = BlastDeleteFakeBioseq(fake_bsp);
        
        other_returns = ValNodeFree(other_returns);
        if (done) 
           sep = SeqEntryFree(sep);
#ifndef BLAST_CS_API
        /* This is freed earlier in client-server case */
        options->query_lcase_mask = SeqLocSetFree(options->query_lcase_mask);
#endif
        if (html)
           fprintf(outfp, "
\n

\n
");
        
        if (!options->is_megablast_search) 
           BlastDeleteUserErrorString(err_ticket);
    } /* while(TRUE)  - main loop of the program over all FASTA entries */
    
#ifdef BLAST_CS_API
    BlastNetBioseqFetchDisable(bl3hp, blast_database, db_is_na);
    BlastFini(bl3hp);
#else
    ReadDBBioseqFetchDisable();
#endif
    
    aip = AsnIoClose(aip);
    
    if(align_view < 7) {
        if (html) {
            fprintf(outfp, "
\n\n\n");
        }
    } else if (align_view == 7)
        xml_aip = AsnIoClose(xml_aip);
    
    options = BLASTOptionDelete(options);
    FileClose(infp);
    
    return 0;
}