2004-05-05 11:26 dondosha * core/blast_hits.h (1.38): Renamed functions in accordance with new convention Blast_[StructName][Task] 2004-05-05 11:26 dondosha * core/blast_traceback.h (1.26): Minor change in comment 2004-05-05 11:27 dondosha * core/blast_engine.c (1.126), core/blast_hits.c (1.94), core/blast_traceback.c (1.101), core/link_hsps.c (1.31), api/twoseq_api.c (1.6): Renamed functions in blast_hits.h accordance with new convention Blast_[StructName][Task] 2004-05-05 17:16 camacho * core/: blast_stat.h (1.35), blast_stat.c (1.67): Make Blast_GetStdAlphabet and Blast_ScoreFreqNew non-static 2004-05-06 10:01 camacho * core/: blast_psi_priv.c (1.3), blast_psi_priv.h (1.3): + _PSICopyMatrix 2004-05-06 10:44 camacho * core/: blast_stat.h (1.36), blast_stat.c (1.68): Made Blast_ScoreFreqDestruct non-static 2004-05-06 11:05 camacho * core/blast_stat.c (1.69): Fix to previous commit 2004-05-06 11:26 camacho * core/matrix_freq_ratios.c (1.1): Initial revision 2004-05-06 11:28 camacho * core/matrix_freq_ratios.h (1.2): Provide an interface to retrive the matrices' frequency ratios 2004-05-06 11:59 camacho * core/: blast_stat.c (1.70), blast_stat.h (1.37): Made Blast_KarlinBlkCalc non-static 2004-05-07 11:18 papadopo * core/blast_engine.c (1.127): 1. Remove code that scaled up scores for RPS blast (along with the code that overrode const keyword to do so) 2. use BlastScoringParams in place of BlastScoringOptions 3. remove scaling of any scores passed to result structure 2004-05-07 11:19 papadopo * core/: blast_gapalign.c (1.92), blast_hits.c (1.95): use BlastScoringParameters in place of BlastScoringOptions 2004-05-07 11:22 papadopo * core/blast_options.c (1.102): 1. add functions to allocate and free BlastScoringParameters structures 2. apply a scaling factor to all cutoffs generated in HitSavingParameters or ExtentionParameters structures 2004-05-07 11:23 papadopo * core/blast_setup.c (1.84): add scale factor as an input argument to ScoreBlk creation code 2004-05-07 11:23 papadopo * core/blast_stat.c (1.71): add initialization of scale factor to ScoreBlkNew 2004-05-07 11:26 papadopo * core/blast_traceback.c (1.102): 1. Use BlastScoringParameters instead of BlastScorignOptions 2. Remove use of psi_options in all traceback functions 3. Make sure query exists before counting out-of-frame number of identities 2004-05-07 11:31 papadopo * core/blast_engine.h (1.33): change function pointer typedef of GetGappedScore to use BlastScoringParameters instead of BlastScoringOptions 2004-05-07 11:32 papadopo * core/: blast_gapalign.h (1.41), blast_hits.h (1.39): use BlastScoringParameters instead of BlastScoringOptions 2004-05-07 11:33 papadopo * core/blast_options.h (1.68): add BlastScoringParameters and functions to fill it; remove use of psi_options 2004-05-07 11:36 papadopo * core/blast_setup.h (1.37): add scale factor as input argument to BlastMainSetup and GetScoreBlk 2004-05-07 11:37 papadopo * core/blast_stat.h (1.38): add scale factor field to BALST_ScoreBlk 2004-05-07 11:37 papadopo * core/blast_traceback.h (1.27): use BlastScoringParameters instead of BlastScoringOptions, remove use of psi_options 2004-05-07 11:46 papadopo * api/twoseq_api.c (1.7): add scale factor of 1.0 to BlastMainSetUp 2004-05-10 10:27 madden * core/: blast_engine.c (1.128), blast_options.c (1.103): Correction to CalculateLinkHSPCutoffs to use gap_trigger in calculation of small cutoff 2004-05-10 10:28 madden * core/blast_options.h (1.69): Add BlastExtensionParameters as formal parameter to CalculateLinkHSPCutoffs so as to use gap_trigger in calculation of small cutoff 2004-05-11 08:25 madden * core/link_hsps.c (1.32): Adjustment for tblast[nx] 2004-05-11 08:26 madden * core/blast_engine.c (1.129): Reset subject length to original for long sequences in BLAST_SearchEngineCore, refactor function 2004-05-12 08:16 madden * core/: blast_traceback.h (1.28), blast_traceback.c (1.103): Add PSIBlastOptions to BLAST_ComputeTraceback 2004-05-12 08:18 madden * core/: blast_options.c (1.104), blast_options.h (1.70): Clean out PSIBlast options, add fields to ExtensionOptions to support smith-waterman and composition-based stats 2004-05-12 08:19 madden * core/blast_engine.c (1.130): Add psi_options to call to BLAST_ComputeTraceback 2004-05-13 10:56 camacho * core/matrix_freq_ratios.c (1.2): Fix for retrieving frequency ratios matrices 2004-05-14 09:13 camacho * core/blast_options.h (1.71): 1. Made inclusion threshold consistent with blastpgp 2. Added comments for PSIBlastOptions 2004-05-14 09:14 camacho * core/blast_options.c (1.105): Use correct definition for inclusion threshold 2004-05-14 11:05 camacho * core/greedy_align.h (1.9): Moved enums and #defines to a more private scope 2004-05-14 11:06 camacho * core/greedy_align.c (1.17): Moved enums from greedy_align.h 2004-05-14 11:06 camacho * core/blast_gapalign.c (1.93): Moved #defines from greedy_align.[hc] - Needs refactoring 2004-05-14 11:29 camacho * core/: blast_gapalign.h (1.42), greedy_align.h (1.10), blast_gapalign.c (1.94), greedy_align.c (1.18): Renamed GreedyAlignMem, ThreeVal, and MBSpace structures to avoid conflicts with C toolkit 2004-05-14 11:48 camacho * core/blast_stat.h (1.39): Removed 'tools' matrix (copied from blastkar.h) 2004-05-14 12:02 madden * core/blast_hits.c (1.96): Added typedef for BlastHSPSegment 2004-05-14 12:02 madden * core/: aa_ungapped.c (1.30), blast_extend.c (1.61), phi_extend.c (1.5), aa_ungapped.h (1.16), blast_engine.h (1.34), blast_extend.h (1.24), phi_extend.h (1.3): Rename BLAST_ExtendWord to Blast_ExtendWord in order to fix conflicts with C toolkit 2004-05-14 12:03 madden * core/blast_hits.h (1.40): Removed definition of BLASTHSPSegment 2004-05-14 12:29 dondosha * api/blast_format.c (1.49): Renamed ScoreAndEvalueToBuffers to avoid collision with new public function 2004-05-14 13:09 dondosha * core/: blast_diagnostics.c (1.1), blast_diagnostics.h (1.1): Diagnostic information returned from the BLAST engine 2004-05-14 13:09 dondosha * core/: aa_ungapped.h (1.17), blast_engine.h (1.35), blast_extend.h (1.25), blast_gapalign.h (1.43), phi_extend.h (1.4), aa_ungapped.c (1.31), blast_engine.c (1.131), blast_extend.c (1.62), blast_gapalign.c (1.95), phi_extend.c (1.6): BlastReturnStat structure changed to BlastDiagnostics and refactored 2004-05-14 13:11 dondosha * core/blast_options.c (1.106): Minor correction in setting X-dropoffs 2004-05-14 13:11 dondosha * core/blast_setup.c (1.85): Length adjustment must be calculated even when search space option is set 2004-05-14 13:11 dondosha * core/: blast_util.h (1.48), blast_util.c (1.67): Added const qualifier for query_info argument in BLAST_GetQueryLength 2004-05-14 13:12 dondosha * core/link_hsps.c (1.33): Fixed typo which lead to occasional wrong results 2004-05-14 13:14 dondosha * core/blast_hits.c (1.97): First priority in sorting HSPs in HSP lists is e-value, then score 2004-05-14 13:19 dondosha * api/: blast_returns.c (1.1), blast_returns.h (1.1): Manipulation of data returned from BLAST other than Seq-aligns 2004-05-14 13:19 dondosha * api/: blast_format.c (1.50), blast_format.h (1.21): Use BlastSeqSrc instead of readdb API; changed BlastReturnStat structure to BlastDiagnostics 2004-05-14 13:20 dondosha * api/: blast_seqalign.c (1.32), blast_seqalign.h (1.14): Subject Seq-loc not needed in BLAST_ResultsToSeqAlign: use BlastSeqSrc 2004-05-14 13:20 dondosha * api/blast_seq.c (1.40): Use NUM_FRAMES macro instead of hard-coded value 6 2004-05-14 13:24 dondosha * api/: twoseq_api.c (1.8), twoseq_api.h (1.3): Added BLAST_SummaryReturn structure; BLAST_TwoSeqLocSets function to compare sets of Seq-locs 2004-05-14 13:58 dondosha * core/: blast_gapalign.c (1.96), blast_hits.c (1.98): Moved declaration of a local variable to the top of the scope 2004-05-14 15:39 dondosha * api/seqsrc_readdb.c (1.28): Minor fix in last sequence assignment in constructor 2004-05-17 06:37 camacho * core/: blast_stat.h (1.40), blast_stat.c (1.72): Rename BLAST_ScoreFreq, BLASTMatrixStructure and BLAST_ResComp to avoid conflicts with C toolkit 2004-05-17 11:26 madden * core/blast_gapalign.h (1.44): Removed ExtensionAlgorithmType, renamed and moved to blast_options.h 2004-05-17 11:27 madden * core/blast_options.h (1.72): Added EBlastPrelimGapExt as replacement for algorithm_type in extension options 2004-05-17 11:29 madden * core/: blast_engine.c (1.132), blast_gapalign.c (1.97), blast_traceback.c (1.104): Int algorithm_type replaced with enum EBlastPrelimGapExt 2004-05-17 11:30 madden * core/blast_options.c (1.107): Int algorithm_type replaced with enum EBlastPrelimGapExt, removed include for blast_gapalign.h 2004-05-17 11:41 dondosha * core/: blast_engine.c (1.133), blast_traceback.c (1.105): Minor memory leak fix 2004-05-17 11:54 madden * core/blast_options.h (1.73): Removed unneeded enums 2004-05-17 12:26 papadopo * api/twoseq_api.c (1.9): change greedy alignment flags to enum values 2004-05-17 12:38 camacho * core/blast_setup.h (1.38): Make function declarations more readable 2004-05-17 12:43 camacho * core/blast_setup.c (1.86): Minor refactoring 2004-05-18 09:22 madden * core/: blast_kappa.c (1.1), blast_kappa.h (1.1): SmithWaterman and composition-based stats code 2004-05-18 09:23 madden * core/blast_gapalign_pri.h (1.1): Private declarations for blast_gapalign.c 2004-05-18 09:23 madden * core/blast_gapalign.c (1.98): Make ALIGN_EX non-static 2004-05-18 13:46 madden * core/blast_kappa.c (1.2): Changes for doxygen compliance 2004-05-19 10:29 dondosha * core/blast_def.h (1.41): Removed BlastReturnStat structure, as it has been refactored 2004-05-19 10:52 camacho * core/: aa_ungapped.h (1.18), blast_def.h (1.42), blast_diagnostics.h (1.2), blast_dust.h (1.10), blast_engine.h (1.36), blast_extend.h (1.26), blast_filter.h (1.18), blast_gapalign.h (1.45), blast_hits.h (1.41), blast_kappa.h (1.2), blast_lookup.h (1.8), blast_message.h (1.7), blast_options.h (1.74), blast_rps.h (1.5), blast_seg.h (1.10), blast_seqsrc.h (1.19), blast_setup.h (1.39), blast_stat.h (1.41), blast_traceback.h (1.29), blast_util.h (1.49), gapinfo.h (1.6), greedy_align.h (1.11), link_hsps.h (1.10), lookup_util.h (1.8), lookup_wrap.h (1.4), mb_lookup.h (1.12), ncbi_math.h (1.7), ncbi_std.h (1.28), pattern.h (1.3), phi_extend.h (1.5), phi_lookup.h (1.4), aa_ungapped.c (1.32), blast_diagnostics.c (1.2), blast_dust.c (1.24), blast_encoding.c (1.2), blast_engine.c (1.134), blast_extend.c (1.63), blast_filter.c (1.44), blast_gapalign.c (1.99), blast_hits.c (1.99), blast_inline.h (1.2), blast_kappa.c (1.3), blast_lookup.c (1.25), blast_message.c (1.12), blast_options.c (1.108), blast_psi_priv.c (1.4), blast_seg.c (1.22), blast_seqsrc.c (1.19), blast_setup.c (1.87), blast_stat.c (1.73), blast_traceback.c (1.106), blast_util.c (1.68), gapinfo.c (1.8), greedy_align.c (1.19), link_hsps.c (1.34), lookup_util.c (1.8), lookup_wrap.c (1.6), mb_lookup.c (1.33), ncbi_math.c (1.8), ncbi_std.c (1.13), pattern.c (1.9), phi_extend.c (1.7), phi_lookup.c (1.13): 1. Added doxygen tags to enable doxygen processing of algo/blast/core 2. Standardized copyright, CVS $Id string, $Log and rcsid formatting and i location 3. Added use of @todo doxygen keyword 2004-05-19 11:06 dondosha * core/: blast_engine.h (1.37), blast_gapalign.h (1.46), blast_stat.h (1.42), blast_traceback.h (1.30), gapinfo.h (1.7), pattern.h (1.4): Moved seedSearchItems definition to phi_lookup.c 2004-05-19 11:10 dondosha * core/: blast_engine.h (1.38), blast_gapalign.h (1.47), blast_stat.h (1.43): Previous change should not have been committed 2004-05-19 11:13 dondosha * core/: blast_traceback.h (1.31), gapinfo.h (1.8): Previous change should not have been committed 2004-05-19 11:15 dondosha * core/phi_lookup.c (1.14): Moved seedSearchItems definition from pattern.h 2004-05-19 11:19 dondosha * core/blast_gapalign.h (1.48): Moved BlastGapDP structure definition to blast_gapapign.c 2004-05-19 11:21 dondosha * core/gapinfo.h (1.9): Changed edit script operations #defines to an enum 2004-05-19 11:21 dondosha * core/blast_gapalign.c (1.100): Moved BlastGapDP definition from header file; edit script operations changed from macros to an enum 2004-05-19 11:22 dondosha * core/: blast_hits.c (1.100), blast_traceback.c (1.107): Edit script operations changed from macros to an enum 2004-05-19 11:23 dondosha * core/link_hsps.c (1.35): Use NUM_STRANDS macro instead of hard coded number 2 2004-05-19 11:23 dondosha * core/blast_util.c (1.69): Use CODON_LENGTH macro instead of hard coded number 3 2004-05-19 11:27 dondosha * api/blast_seqalign.c (1.33): Edit script operations changed from macros to an enum 2004-05-19 11:34 dondosha * core/blast_stat.h (1.44): Moved Blast_ResComp definition to source file 2004-05-19 11:34 dondosha * core/blast_stat.c (1.74): Moved Blast_ResComp definition from header file 2004-05-19 13:02 madden * core/blast_kappa.c (1.4): Move #defines for Xchar and StarChar from blast_kappa.h, make upper-case 2004-05-19 13:03 madden * core/blast_kappa.h (1.3): Remove (to blast_kappa.c) #defines for Xchar and StarChar 2004-05-19 13:05 coulouri * core/blast_lookup.h (1.9): remove dead macros 2004-05-19 15:39 madden * core/blast_kappa.c (1.5): Fix memory leak with matrix 2004-05-20 08:48 madden * core/blast_kappa.c (1.6): ANother memory leak 2004-05-20 09:08 madden * core/blast_traceback.c (1.108): Add call to Kappa_RedoAlignmentCore 2004-05-20 09:46 madden * core/blast_kappa.c (1.7): Fix problems with argument conversions identified by PC build 2004-05-20 11:20 madden * core/: blast_kappa.c (1.8), blast_kappa.h (1.4): Doxygen compliance fixes 2004-05-20 12:28 madden * core/: blast_stat.h (1.45), blast_hits.c (1.101), blast_options.c (1.109), blast_stat.c (1.75), blast_traceback.c (1.109): Make searchsp an Int8 consistent with rest of blast 2004-05-20 13:59 papadopo * core/mb_lookup.h (1.13): Remove SECOND_TEMPLATE_BIT, since megablast does not use it anymore 2004-05-24 09:26 madden * core/: blast_engine.c (1.135), blast_extend.c (1.64), blast_filter.c (1.45), blast_gapalign.c (1.101), blast_kappa.c (1.9), blast_stat.c (1.76): Fix PC compiler warnings 2004-05-24 10:09 camacho * core/: blast_hspstream.c (1.1), blast_hspstream.h (1.1): Initial revision 2004-05-24 11:09 camacho * core/blast_stat.c (1.77): Fixed conflict 2004-05-24 11:28 camacho * core/blast_hspstream.c (1.2): Fix compile error in BlastHSPStreamNew 2004-05-24 11:49 madden * core/blast_seg.h (1.11): Moved three defines and two structures to blast_seg.c 2004-05-24 11:51 madden * core/blast_seg.c (1.23): Moved three defines and two structures from blast_seg.h, prepended S to structures per C++ toolkit convention 2004-05-24 13:26 camacho * core/blast_options.c (1.110): Fix PC warning 2004-05-24 13:26 madden * core/blast_kappa.c (1.10): Doxygen fixes 2004-05-24 13:27 madden * core/blast_kappa.h (1.5): Doxygen fix 2004-05-26 11:40 dondosha * core/blast_traceback.c (1.110): Check that HSP length exceeds the min_hit_length option 2004-05-26 12:04 papadopo * core/: blast_options.h (1.75), blast_options.c (1.111): fix doxygen errors 2004-05-27 10:48 papadopo * core/: blast_options.h (1.76), blast_rps.h (1.6): fix doxygen warnings 2004-05-28 11:55 camacho * core/: blast_psi.h (1.1), blast_psi.c (1.1): Initial revision 2004-05-28 12:00 camacho * core/: blast_psi_priv.c (1.5), blast_psi_priv.h (1.4): + first port of PSSM generation engine 2004-05-28 12:20 camacho * core/blast_util.c (1.70): Fix warning detected by msvc 6 2004-05-28 13:35 camacho * core/blast_psi_priv.c (1.6): Fix msvc6 warnings 2004-06-04 11:16 papadopo * core/blast_lookup.h (1.10): fix doxygen warnings 2004-06-07 10:18 dondosha * core/blast_psi_priv.c (1.7): Added some variables initialization, to remove compiler warnings 2004-06-07 10:20 dondosha * core/blast_stat.c (1.78): Set matrix dimensions to 26 when matrix is read from a file, to make it the same as when matrix is loaded from a library 2004-06-07 10:22 dondosha * core/: blast_util.h (1.50), blast_util.c (1.71): Added Blast_GetQueryIndexFromContext and BlastQueryInfoDup functions 2004-06-07 10:24 dondosha * core/mb_lookup.h (1.14): Added doxygen comments to all macros 2004-06-07 10:32 dondosha * core/: blast_engine.c (1.136), blast_engine.h (1.39): Moved definition of the BlastCoreAuxStruct structure from blast_engine.h to blast_engine.c since it is not used elsewhere 2004-06-07 10:44 madden * core/: blast_stat.c (1.79), blast_stat.h (1.46): Doxygen fixes 2004-06-07 10:46 dondosha * core/blast_engine.c (1.137): Call CalculateLinkHSPCutoffs only for translated ungapped searches, as in old engine, instead of whenever sum statistics is used 2004-06-07 10:55 dondosha * core/blast_hits.h (1.42): Made Blast_HSPListUniqSort public 2004-06-07 10:56 dondosha * core/blast_hits.c (1.102): Changed the way HSP inclusion tests are performed after the preliminary gapped alignment: no checking for inclusion inside sorting function 2004-06-07 10:57 dondosha * core/blast_engine.c (1.138): Moved call to Blast_HSPListUniqSort outside of Blast_HSPListReevaluateWithAmbiguities 2004-06-07 11:06 dondosha * core/blast_hits.c (1.103): Removed 2 comparison functions that are no longer needed 2004-06-07 11:43 dondosha * core/blast_options.h (1.77): Made do_sum_stats option an enum, allowing to add a not-set value 2004-06-07 11:44 dondosha * core/blast_options.c (1.112): do_sum_stats option is now an enum; set do_sum_stats parameter only if option is not set; 2004-06-07 12:26 dondosha * core/blast_traceback.c (1.111): Always calculate e-values before dividing scores by the scaling factor; divide Lambda by scaling factor immediately before the e-value calculation 2004-06-07 13:06 dondosha * core/: blast_hspstream.h (1.2), blast_hspstream.c (1.3): Added optional BlastHSPStreamClose method to close stream for writing 2004-06-07 13:11 dondosha * core/blast_seqsrc.h (1.20): Added BlastSeqSrcCopy method 2004-06-07 13:12 dondosha * core/blast_seqsrc.c (1.20): Added BlastSeqSrcCopy method with a default implementation 2004-06-07 13:14 dondosha * api/seqsrc_readdb.c (1.29): Improvement in ReaddbGetSeqIdStr; added ReaddbSeqSrcCopy, using readdb_attach to allow multiple threads working with one database 2004-06-07 13:15 dondosha * api/seqsrc_readdb.h (1.10): Added ReaddbSeqSrcCopy, using readdb_attach to allow multiple threads working with one database 2004-06-07 14:22 dondosha * core/blast_hits.h (1.43): Added bit score to BlastHSP structure, and function to calculate bit scores 2004-06-07 14:23 dondosha * core/blast_engine.c (1.139): Call Blast_HSPListReevaluateWithAmbiguities only when all information is available for it 2004-06-07 14:24 dondosha * core/blast_hits.c (1.104): Added Blast_HSPListGetBitScores function to fill bit scores in an HSP list 2004-06-07 14:25 dondosha * core/blast_traceback.c (1.112): Added calculation of bit scores in HSP lists after traceback alignment is done 2004-06-07 14:40 dondosha * api/blast_format.c (1.51): Bit scores are now available in HSP structures; renamed PrintSeqDefline to Blast_SeqIdGetDefLine, made it public in preparation for tabular output 2004-06-07 14:40 dondosha * api/blast_format.h (1.22): Renamed PrintSeqDefline to Blast_SeqIdGetDefLine, made it public in preparation for tabular output 2004-06-07 14:41 dondosha * api/: blast_seqalign.c (1.34), blast_seqalign.h (1.15), twoseq_api.c (1.10): Bit scores are now available from HSP structures 2004-06-07 15:20 dondosha * core/blast_traceback.c (1.113): Do not divide Lambda by scale factor in e-value calculations for PSI-BLAST 2004-06-07 16:03 coulouri * core/blast_stat.c (1.80): use floating point constants for comparisons with floating point variables 2004-06-07 16:05 coulouri * core/blast_hits.c (1.105): remove unused variable 2004-06-08 10:58 dondosha * core/: blast_gapalign.h (1.49), blast_options.h (1.78), blast_gapalign.c (1.102): Removed is_neighboring option; let application set min_hit_length and percent_identity options instead 2004-06-08 11:01 coulouri * core/blast_psi.h (1.2): remove dead REAL_PROT_ALPHABET preprocessor symbol 2004-06-08 11:05 madden * core/blast_stat.c (1.81): Doxygen fixes 2004-06-08 11:09 dondosha * core/: blast_engine.h (1.40), blast_hits.h (1.44), blast_kappa.h (1.6), blast_traceback.h (1.32), hspstream_collector.h (1.1): Use BlastHSPStream interface in the engine instead of saving hits directly 2004-06-08 11:10 dondosha * core/blast_options.h (1.79): Removed skip_traceback option; added eSkipTbck type to traceback types enum 2004-06-08 11:12 dondosha * core/blast_gapalign.c (1.103): traceback_done field is no longer needed and removed from BlastHSPList structure 2004-06-08 11:12 dondosha * core/blast_options.c (1.113): Removed skip_traceback option; added eSkipTbck type to traceback extension types enum 2004-06-08 11:13 dondosha * core/: blast_engine.c (1.140), blast_hits.c (1.106), blast_kappa.c (1.11), blast_traceback.c (1.114), hspstream_collector.c (1.1): Use BlastHSPStream interface in the engine 2004-06-08 11:36 dondosha * api/twoseq_api.c (1.11): Use BlastHSPStream interface 2004-06-08 11:37 dondosha * api/: hspstream_queue.c (1.1), hspstream_queue.h (1.1): Queue implementation of BlastHSPStream, for on-the-fly output 2004-06-08 11:38 dondosha * api/: blast_tabular.c (1.1), blast_tabular.h (1.1): Implementation of a thread producing on-the-fly tabular output 2004-06-08 12:09 kans * api/twoseq_api.c (1.12): moved BlastHSPStream* hsp_stream definition to top of BLAST_TwoSeqLocSets function to compile in C 2004-06-08 13:29 dondosha * core/: aa_ungapped.h (1.19), blast_diagnostics.h (1.3), blast_gapalign.h (1.50), blast_hits.h (1.45), gapinfo.h (1.10), aa_ungapped.c (1.33), blast_engine.c (1.141), blast_gapalign.c (1.104), blast_hits.c (1.107), blast_kappa.c (1.12), blast_psi_priv.c (1.8), blast_setup.c (1.88), blast_traceback.c (1.115), hspstream_collector.c (1.2), link_hsps.c (1.36), ncbi_math.c (1.9), phi_lookup.c (1.15): Compiler warnings fixes 2004-06-08 13:39 dondosha * core/: blast_gapalign.h (1.51), blast_gapalign.c (1.105): Made ALIGN_EX public, as it is needed in blast_kappa.c 2004-06-08 13:46 dondosha * api/: blast_tabular.c (1.2), hspstream_queue.c (1.2), hspstream_queue.h (1.2), seqsrc_multiseq.c (1.6): Strict compiler warnings fix 2004-06-08 13:47 dondosha * api/: blast_seqalign.c (1.35), blast_seqalign.h (1.16), twoseq_api.c (1.13): Use boolean arguments for gapped calculation and out-of-frame modes instead of BlastScoringOptions 2004-06-08 13:54 dondosha * core/: blast_gapalign.h (1.52), gapinfo.h (1.11): Removed extra function declaration: it is declared in blast_gapalign_pri.h 2004-06-08 14:00 dondosha * core/blast_gapalign.c (1.106): Added #include of blast_gapalign_pri.h 2004-06-09 10:02 camacho * core/blast_engine.c (1.142): Fix compiler warning 2004-06-09 10:10 camacho * core/blast_psi.h (1.3): Removed unneeded include 2004-06-09 10:10 camacho * core/blast_options.h (1.80): Added use_best_alignment option 2004-06-09 10:11 camacho * core/blast_options.c (1.114): Set default for use_best_alignment 2004-06-09 10:20 camacho * core/blast_psi_priv.h (1.5): Updated comments 2004-06-09 10:21 camacho * core/: blast_psi.c (1.2), blast_psi_priv.c (1.9), matrix_freq_ratios.c (1.3): Removed msvc compiler warnings 2004-06-09 18:27 dondosha * core/blast_options.c (1.115): Do not reduce score cutoffs to gap_trigger value for ungapped blastn 2004-06-09 18:44 dondosha * core/blast_options.c (1.116): Set sum statistics parameter to TRUE by default for ungapped blastp 2004-06-10 09:21 madden * core/blast_stat.c (1.82): Rename RPSFillResidueProbability to Blast_FillResidueProbability, made public. Removed usage of BLAST_SCORE_1MIN/MAX, simply use BLAST_SCORE_MIN/MAX instead Removed useless defines DIMOFP0 and DIMOFP0_MAX Moved over some defines from blast_stat.h 2004-06-10 09:22 madden * core/blast_stat.h (1.47): Removed some outdated defines for OS_MAC and OS_DOS, moved some other defines to blast_stat.c Add prototype for Blast_FillResidueProbability. 2004-06-10 09:25 madden * core/blast_kappa.c (1.13): Removed function fillResidueProbability, use Blast_FillResidueProbability instead Make use of _PSIGetStandardProbabilities. Replaced defines XCHAR and STARCHAR with call to AMINOACID_TO_NCBISTDAA. 2004-06-14 11:34 dondosha * core/blast_hits.h (1.46): Added 2 small functions needed to calculate values for tabular output 2004-06-14 11:35 dondosha * core/blast_hits.c (1.108): Added 2 small functions needed to calculate values for tabular output; fix in Blast_HSPResultsSaveRPSHSPList 2004-06-14 11:37 dondosha * core/blast_engine.c (1.143): Calculate bit scores in preliminary engine for ungapped searches or when there is no traceback stage 2004-06-14 11:38 dondosha * core/blast_traceback.c (1.116): Small change in comment 2004-06-14 16:43 dondosha * api/: blast_tabular.c (1.3), blast_tabular.h (1.2): Use genetic code string directly in tabular format data structure, instead of BlastDatabaseOptions 2004-06-15 10:50 dondosha * core/blast_hits.c (1.109): Use BLASTSeqSrcRetSequence to free uncompressed sequence in Blast_HSPListReevaluateWithAmbiguities 2004-06-15 10:51 dondosha * core/blast_setup.c (1.89): Only return error if all query sequences are completely filtered, not just one of them 2004-06-15 16:01 dondosha * core/blast_gapalign.c (1.107): Correction in AdjustSubjectRange for setting subject length for very long sequences 2004-06-16 10:29 ivanov * core/blast_hits.h (1.47): Moved #include's outside extern "C" block. 2004-06-16 10:53 dondosha * core/: blast_dust.h (1.11), blast_engine.h (1.41), blast_filter.h (1.19), blast_kappa.h (1.7), blast_seg.h (1.12), blast_setup.h (1.40), blast_traceback.h (1.33), blast_util.h (1.51), gapinfo.h (1.12), hspstream_collector.h (1.2), link_hsps.h (1.11), lookup_wrap.h (1.5), mb_lookup.h (1.15): Moved extern "C" after the #includes 2004-06-16 11:18 camacho * core/blast_psi.c (1.3): Add missing casts 2004-06-16 11:22 camacho * core/blast_psi_priv.c (1.10): Fixes to add new unit tests 2004-06-16 15:34 madden * core/: blast_stat.c (1.83), blast_stat.h (1.48): Doxygen fixes, made some params const 2004-06-16 17:23 dondosha * api/: blast_returns.c (1.2), blast_seqalign.c (1.36): Minor memory leak fix 2004-06-17 16:46 camacho * core/blast_options.c (1.117): Use consistent return values for errors 2004-06-17 16:46 camacho * core/blast_psi_priv.h (1.6): doxygen fixes 2004-06-17 16:47 camacho * core/blast_psi_priv.c (1.11): Minor fix to extent sizes 2004-06-17 16:47 camacho * core/blast_psi.h (1.4): doxygen fix 2004-06-18 10:01 madden * core/blast_stat.c (1.84): Doxygen fixes, made some input params const, do not set deprecated sbp->maxscore 2004-06-18 10:02 madden * core/blast_stat.h (1.49): Doxygen fixes, remove deprecated karlinK and maxscore from BlastScoreBlk 2004-06-21 08:52 camacho * core/: blast_lookup.c (1.26), blast_stat.c (1.85), blast_psi.c (1.4), blast_psi_priv.c (1.12), blast_psi_priv.h (1.7), blast_rps.h (1.7), blast_psi.h (1.5): Replace PSI_ALPHABET_SIZE for BLASTAA_SIZE 2004-06-21 08:53 camacho * core/blast_encoding.h (1.4): Remove PSI_ALPHABET_SIZE as it is identical to BLASTAA_SIZE 2004-06-21 10:22 madden * core/blast_kappa.c (1.14): Makes new code consistent with changes by Mike Gertz to kappa.c (submitted by A. Schaffer). For secondary alignments with Smith-Waterman on, use the E-value from the X-drop alignment computed by ALIGN that has more flexibility in which positions are allowed in the dynamic program. Add a sort of alignments for the same query-subject pair because the use of X-drop alignments occasionally reorders such alignments. 2004-06-21 10:52 madden * core/: blast_kappa.c (1.15), blast_kappa.h (1.8), blast_stat.h (1.50): Doxygen fixes 2004-06-22 12:22 dondosha * api/: hspstream_queue.c (1.3), hspstream_queue.h (1.3): Added doxygen comments 2004-06-22 12:45 camacho * core/blast_def.h (1.43), core/blast_engine.c (1.144), core/blast_filter.c (1.46), core/blast_gapalign.c (1.108), core/blast_hits.c (1.110), core/blast_kappa.c (1.16), core/blast_options.c (1.118), core/blast_setup.c (1.90), core/blast_traceback.c (1.117), core/blast_util.c (1.72), core/hspstream_collector.c (1.3), core/link_hsps.c (1.37), api/blast_format.c (1.52), api/blast_returns.c (1.3), api/blast_seq.c (1.41), api/blast_seqalign.c (1.37), api/seqsrc_multiseq.c (1.7), api/twoseq_api.c (1.14): Changed the blast_type_* definitions for the EBlastProgramType enumeration. 2004-06-22 13:49 dondosha * core/hspstream_collector.h (1.3): 1. Added doxygen comments; 2. Added locking mechanism for writing results from multiple threads. 2004-06-22 13:51 dondosha * core/hspstream_collector.c (1.4): 1. Added locking mechanism for writing results from multiple threads; 2. Added more doxygen comments; 2004-06-22 13:52 dondosha * core/: blast_options.h (1.81), link_hsps.h (1.12), blast_engine.c (1.145), blast_options.c (1.119), blast_setup.c (1.91), blast_traceback.c (1.118), link_hsps.c (1.38): Moved parameters specific to HSP linking into a independent structure 2004-06-23 10:03 dondosha * core/blast_engine.c (1.146): Call BLASTSeqSrcRetSequence instead of BlastSequenceBlkClean 2004-06-23 10:04 dondosha * core/blast_util.c (1.73): Set allocated booleans to FALSE in BlastSequenceBlkClean after freeing respective buffers 2004-06-23 10:20 dondosha * api/seqsrc_readdb.c (1.30): RetSequence for readdb is equivalent to BlastSequenceBlkClean, so just call it instead of duplicating code 2004-06-23 10:21 dondosha * api/: blast_mtlock.c (1.1), blast_mtlock.h (1.1): Callbacks for BLAST locking mechanism using connect library 2004-06-23 10:43 dondosha * core/blast_options.c (1.120): Return 0 from PSIBlastOptionsNew if NULL pointer argument is provided 2004-06-23 10:52 kans * api/blast_mtlock.c (1.2): fixed Blast_MT_LOCKInit to compile in C 2004-06-23 14:02 dondosha * api/blast_returns.c (1.4): Return NULL from Blast_GetDbSummary if this is not a database search 2004-06-24 11:41 papadopo * core/blast_gapalign.c (1.109): Traceback computations must compensate for rows of the traceback array not beginning at offset 0 of the subject sequence 2004-06-24 17:10 dondosha * api/: blast_format.c (1.53), blast_format.h (1.23): Removed dead code: function BLAST_PrintIntermediateResults 2004-06-24 17:17 dondosha * api/blast_tabular.c (1.4): Boolean argument in ScoreAndEvalueToBuffers changed to Uint1 2004-06-25 13:36 camacho * core/blast_psi.c (1.5): Added assertions 2004-06-25 16:16 camacho * core/blast_psi_priv.c (1.13): 1. Minor fixes to sequence weights calculation 2. Add comments 2004-06-25 16:31 camacho * core/blast_psi_priv.c (1.14): Remove C++ comments 2004-06-28 09:37 madden * core/blast_def.h (1.44): Add typedef for BlastMaskInformation 2004-06-28 09:38 madden * core/: blast_setup.h (1.41), blast_setup.c (1.92): Change BLAST_MainSetUp to use BlastMaskInformation rather than BlastMaskLoc 2004-06-28 11:02 papadopo * core/blast_hits.h (1.48): correct convention for hsp_num_max arg of HSPListAppend and HSPListsMerge 2004-06-28 11:58 madden * api/twoseq_api.c (1.15): Use BlastMaskInformation for BLAST_MainSetUp 2004-06-28 17:06 dondosha * core/: blast_hits.c (1.111), blast_kappa.c (1.17), blast_traceback.c (1.119): Memory leak fix 2004-06-28 17:27 dondosha * api/blast_format.c (1.54): Do not close AsnIoPtr twice in case of XML output 2004-06-28 17:41 dondosha * core/blast_options.c (1.121): Test for NULL input in BlastHitSavingParametersFree 2004-06-28 22:45 dondosha * api/blast_format.c (1.55): Title of HTML output should say BLAST instead of MEGABLAST 2004-06-29 13:26 dondosha * core/blast_engine.c (1.147): Call ParametersFree type functions to free parameter structures instead of sfree 2004-06-29 13:27 dondosha * core/blast_kappa.c (1.18): Minor memory leak fix 2004-06-30 08:53 madden * api/: blast_format.c (1.56), blast_format.h (1.24): Remove redundant (copied) typedefs for BlastPruneSapStruct and MBXml 2004-06-30 10:22 kans * api/blast_format.c (1.57): undef BUFFER_LENGTH (previously defined in blastpri.h) 2004-06-30 11:20 dondosha * core/: greedy_align.h (1.12), greedy_align.c (1.20): Renamed typedef edit_op_t to MBEditOpType 2004-07-01 10:23 madden * api/blast_format.c (1.58): Properly set align_options if align_view is non-zero 2004-07-01 12:56 madden * api/blast_format.c (1.59): Make formatting consistent with current megablast 2004-07-01 15:36 dondosha * api/: blast_format.c (1.60), blast_returns.c (1.5), blast_returns.h (1.2): Use functions and definitions from newly created blfmtutl.[ch] instead of static ones 2004-07-02 10:01 dondosha * api/blast_tabular.c (1.5): Fix in query info initialization for tabular thread 2004-07-02 12:28 dondosha * api/blast_seqalign.c (1.38): Removed a wrong SeqIdSetFree call 2004-07-02 12:44 dondosha * api/seqsrc_multiseq.c (1.8): Fixed minor memory leak 2004-07-02 13:57 camacho * core/blast_psi_priv.h (1.8): Made _PSIUpdatePositionCounts non-static 2004-07-02 14:00 camacho * core/blast_psi_priv.c (1.15): 1. Document rationale for order in which sequences are compared in _PSIPurgeNearIdenticalAlignments. 2. Fix in _PSIPurgeSimilarAlignments to take into account the X residues 3. Refactorings in sequence weight calculation functions: - Simplification of _PSICheckSequenceWeights - Addition of _PSISpreadGapWeights - Reorganization of _PSICalculateNormalizedSequenceWeights 2004-07-02 15:23 dondosha * core/: gapinfo.h (1.13), greedy_align.h (1.13): Added doxygen comments 2004-07-02 15:27 dondosha * core/phi_lookup.c (1.16): Added doxygen comments 2004-07-02 15:35 dondosha * core/blast_extend.h (1.27): Added doxygen comments 2004-07-02 15:40 camacho * core/: blast_psi.c (1.6), blast_psi_priv.c (1.16): Fixes for handling out-of-memory conditions 2004-07-06 09:32 madden * api/blast_input.c (1.11): make sure old (possibly freed) locations are not accesses for masking 2004-07-06 11:23 camacho * core/blast_psi_priv.c (1.17): Fix memory acccess error 2004-07-06 11:26 dondosha * core/blast_def.h (1.45): Minor change in comment 2004-07-06 11:28 dondosha * core/blast_dust.h (1.12): Added doxygen comment; removed unused argument in static function 2004-07-06 11:29 dondosha * core/phi_extend.h (1.6): Added one doxygen comment 2004-07-06 11:29 dondosha * core/phi_lookup.h (1.5): Added more doxygen comments 2004-07-06 11:30 dondosha * core/: pattern.h (1.5), ncbi_std.h (1.29): Added some doxygen comments 2004-07-06 11:30 dondosha * core/lookup_wrap.h (1.6): Added a doxygen comment 2004-07-06 11:32 dondosha * core/blast_diagnostics.h (1.4): Added mutex locking mechanism from connect library; added doxygen comments 2004-07-06 11:33 dondosha * core/blast_engine.h (1.42): Added BLAST_PreliminarySearchEngine function, allowing to separate preliminary search stage from traceback 2004-07-06 11:35 dondosha * core/: blast_filter.h (1.20), blast_gapalign.h (1.53), blast_hits.h (1.49), blast_options.h (1.82), blast_setup.h (1.42), blast_util.h (1.52), hspstream_collector.h (1.4), link_hsps.h (1.13), blast_traceback.h (1.34): Use EBlastProgramType enumeration type instead of Uint1 for program argument in all functions 2004-07-06 11:36 dondosha * core/blast_seqsrc.h (1.21): Removed next_oid field from iterator structure: its function belongs elsewhere 2004-07-06 11:38 dondosha * core/blast_diagnostics.c (1.3): Added mutex locking mechanism from connect library; added doxygen comments 2004-07-06 11:39 dondosha * core/blast_engine.c (1.148): Refactored code, allowing separation of preliminary search stage from traceback; use EBlastProgramType for program argument in all functions 2004-07-06 11:40 dondosha * core/blast_dust.c (1.25): Removed unused argument from a static function; added doxygen comments 2004-07-06 11:42 dondosha * core/: blast_filter.c (1.47), blast_gapalign.c (1.110), blast_hits.c (1.112), blast_options.c (1.122), blast_setup.c (1.93), blast_util.c (1.74), hspstream_collector.c (1.5), link_hsps.c (1.39): Use EBlastProgramType enumeration type instead of Uint1 for program argument in all functions 2004-07-06 11:43 dondosha * core/blast_traceback.c (1.120): Use EBlastProgramType enumeration type instead of Uint1 for program argument in all functions; Added Blast_RunTracebackSearch to run traceback stage of BLAST only 2004-07-06 12:02 dondosha * api/seqsrc_readdb.c (1.31): Iterator structure does not have next_oid field any more, but it is not needed anyway 2004-07-06 12:03 dondosha * api/: blast_format.c (1.61), blast_format.h (1.25): Do not free Seq-aligns inside BLAST_FormatResults 2004-07-06 15:56 dondosha * api/: blast_prelim.c (1.1), blast_prelim.h (1.1): Driver for a thread performing preliminary stage of BLAST in a multi-threaded run 2004-07-06 18:11 dondosha * api/blast_seqalign.c (1.39): Minor memory leak fix 2004-07-06 18:25 dondosha * core/blast_engine.c (1.149): Large memory leak fix 2004-07-06 18:37 kans * api/blast_format.c (1.62): in BLAST_FormatResults, second parameter to BlastProgram2Number call needs EBlastProgramType* cast 2004-07-06 18:46 dondosha * api/: blast_format.c (1.63), blast_format.h (1.26): Use EBlastProgramType instead of Uint1 for program arguments 2004-07-07 11:05 camacho * core/blast_options.c (1.123): Handle eBlastTypeUndefined in switch stmt 2004-07-07 13:44 dondosha * api/blast_tabular.h (1.3): Added options to show only gi or only accession 2004-07-07 13:44 dondosha * api/blast_tabular.c (1.6): Added options to show only gi or only accession; fixed memory leaks 2004-07-07 16:02 dondosha * core/blast_hits.c (1.113): Return -1 from Blast_HSPInit if return pointer argument is null 2004-07-07 17:08 camacho * core/blast_hits.c (1.114): Fix to previous commit 2004-07-08 08:29 madden * api/blast_input.h (1.11): total length of query to be returned is an input value, ctr is now an Int2Ptr following convention of FastaToSeqEntryForDb 2004-07-08 08:30 madden * api/blast_input.c (1.12): total length of query to be returned is an input value, ctr is now an Int2Ptr following convention of FastaToSeqEntryForDb, fix some return values 2004-07-09 12:14 dondosha * api/seqsrc_readdb.c (1.32): Use last_oid_assigned field only from the head link in rdfp chain 2004-07-12 08:56 madden * api/blast_input.c (1.13): Clean up BLAST_GetQuerySeqLoc, add error messages for bad returns 2004-07-12 09:29 madden * api/blast_seq.c (1.42): Add check to BLAST_SetUpQuery for NULL input 2004-07-12 12:01 madden * api/: blast_input.c (1.14), blast_input.h (1.12): BLAST_GetQuerySeqLoc now returns total number of letters read, -1 on error 2004-07-12 12:03 madden * api/: blast_format.c (1.64), blast_format.h (1.27): Addition of BlastPrintLogReport 2004-07-12 12:26 papadopo * core/: aa_ungapped.c (1.34), blast_engine.c (1.150), blast_extend.c (1.65), blast_inline.h (1.3), blast_lookup.c (1.27), lookup_wrap.c (1.7), mb_lookup.c (1.34), phi_extend.c (1.8), phi_lookup.c (1.17), blast_lookup.h (1.11), mb_lookup.h (1.16), phi_lookup.h (1.6): Prepend 'Blast' to {MB|PHI|RPS}LookupTable 2004-07-13 13:29 dondosha * core/blast_hits.c (1.115): Free packed sequence before retrieving unpacked sequence in Blast_HSPListReevaluateWithAmbiguities 2004-07-13 13:33 dondosha * api/seqsrc_readdb.c (1.33): Implemented OID list iteration 2004-07-14 09:15 madden * api/: blast_format.c (1.65), blast_format.h (1.28): Clean up of Blast_SeqIdGetDefLine 2004-07-14 09:15 madden * api/blast_tabular.c (1.7): Call to Blast_SeqIdGetDefLine changed 2004-07-14 09:16 madden * api/blast_returns.c (1.6): Print out reward/penalty for blastn 2004-07-14 09:17 madden * api/: blast_input.c (1.15), blast_input.h (1.13): Add believe_query Boolean to BLAST_GetQuerySeqLoc 2004-07-14 14:04 camacho * core/blast_stat.c (1.86): Add const type qualifier to BlastScoreBlk in BlastScoreFreqCalc & Blast_KarlinBlkIdealCalc 2004-07-14 14:05 camacho * core/blast_stat.h (1.51): Add const type qualifier to BlastScoreBlk in Blast_KarlinBlkIdealCalc 2004-07-15 10:50 madden * core/blast_stat.c (1.87): Doxygen fix 2004-07-15 10:51 madden * core/blast_engine.c (1.151): Check some return values in BLAST_SearchEngine 2004-07-15 13:01 madden * core/blast_engine.c (1.152): BlastSeqSrcIteratorNew now called with zero instead of BLAST_DB_CHUNK_SIZE 2004-07-15 13:02 madden * core/blast_seqsrc.c (1.21): BlastSeqSrcIteratorNew now sets chunk_sz to default if it is zero 2004-07-15 13:02 madden * core/blast_engine.h (1.43): Remove #define for BLAST_DB_CHUNK_SIZE 2004-07-15 13:03 madden * core/blast_seqsrc.h (1.22): Add extern declaration for kBlastSeqSrcDefaultChunkSize, change comment 2004-07-16 09:57 camacho * core/: blast_stat.h (1.52), blast_stat.c (1.88): documentation fixes 2004-07-16 13:31 dondosha * core/blast_options.c (1.124): When one-hit word finder is used for protein searches, reduce cutoff score, like it is done in old engine 2004-07-16 13:32 dondosha * core/blast_engine.c (1.153): Get out of BlastSeqSrc iteration if error status is returned; check return status from Blast_HSPListAppend and BLAST_SearchEngineCore functions 2004-07-16 14:48 dondosha * api/: blast_returns.h (1.3), twoseq_api.h (1.4): Moved BLAST_KAParameters and BLAST_SummaryReturn from twoseq_api.h to blast_returns.h 2004-07-16 14:48 dondosha * api/twoseq_api.c (1.16): Minor memory leak fix 2004-07-16 14:49 dondosha * api/blast_returns.c (1.7): Added Blast_SummaryReturnFree function 2004-07-16 15:24 dondosha * api/seqsrc_multiseq.c (1.9): Copy SeqId in MultiSeqGetSeqId 2004-07-19 09:53 dondosha * core/: blast_seqsrc.h (1.23), blast_seqsrc.c (1.22): Removed GetSeqLoc method 2004-07-19 09:56 dondosha * api/: seqsrc_multiseq.c (1.10), seqsrc_readdb.c (1.34): Removed GetSeqLoc method 2004-07-19 10:59 dondosha * api/: seqsrc_multiseq.c (1.11), twoseq_api.c (1.17): Renamed multiseq_src to seqsrc_multiseq 2004-07-20 15:33 madden * core/mb_lookup.c (1.35): Break up MB_LookupTableNew and remove unused #defines, add static functions MB_FillDiscTable and MB_FillContigTable 2004-07-21 13:01 papadopo * api/: blast_format.c (1.66), blast_returns.c (1.8), blast_returns.h (1.4), blast_seq.c (1.43), blast_seq.h (1.11), twoseq_api.c (1.18): Fix MSVC6 compile warnings 2004-07-21 14:40 papadopo * api/: blast_returns.c (1.9), blast_returns.h (1.5), blast_seq.c (1.44), blast_seq.h (1.12), blast_seqalign.c (1.40), blast_seqalign.h (1.17), blast_tabular.c (1.8), blast_tabular.h (1.4), seqsrc_multiseq.c (1.12), seqsrc_multiseq.h (1.2), twoseq_api.c (1.19): 1. fix more MSVC warnings 2. convert 'Uint1 program' to 'EBlastProgramType program' 2004-07-22 13:45 camacho * core/blast_psi.c (1.7): 1. Reduced size of returned PSSM to query size (from query size + 1) by number of residues in alphabet. 2. Changed diagnostics structure allocation routine. 2004-07-22 13:46 camacho * core/blast_psi.h (1.6): 1. Changed diagnostics structure contents. 2. Documentation changes. 2004-07-22 15:05 camacho * core/blast_psi_priv.h (1.9): 1. Removed information content from PsiSequenceWeights structure. 2. Added functions to calculate information content. 2004-07-22 15:06 camacho * core/blast_psi_priv.c (1.18): 1. Fix in _PSICheckSequenceWeights. 2. Added functions to calculate information content. 3. Cleaned up PSIComputeResidueFrequencies. 4. Removed unneeded code to set populate extra column in PSSMs. 5. Added collection of information content and gapless column weights to diagnostics structure 2004-07-23 14:13 camacho * core/blast_setup.c (1.94): Added initialization of kbp_gap_psi field of BlastScoreBlk 2004-07-29 10:10 papadopo * core/blast_lookup.c (1.28): 1. Remove neighbor array from BlastLookupTable 2. Remove MakeAllWordSequence() 3. Modify lookup table construction: - For non-PSSM searches, batch neighboring for exact matches - For all protein searches, build a lexicographic list of all words recursively, and prune batches of low-scoring words 2004-07-29 10:11 papadopo * core/blast_lookup.h (1.12): remove neighbor array from BlastLookupTable 2004-07-29 15:16 camacho * core/: blast_psi.c (1.8), blast_psi_priv.c (1.19), blast_psi_priv.h (1.10): Moved PSIExtractQuerySequenceInfo 2004-07-29 15:53 papadopo * api/twoseq_api.c (1.20): use local enum, rather than blast-engine-wide standard enum, for user-specified blast program 2004-07-30 10:27 camacho * core/: blast_hits.h (1.50), blast_util.h (1.53): Removed function prototypes with no implementation 2004-07-30 16:18 papadopo * api/twoseq_api.h (1.5): Force two-sequence program codes to be deliberately different from the internal program codes used in the engine 2004-07-30 16:19 papadopo * api/twoseq_api.c (1.21): 1. Fix enum type warning in solaris 2. use calloc to initialize default fields of SummaryOptions structure 2004-08-02 09:23 camacho * core/blast_psi.h (1.7): Various renaming of structures, in progress 2004-08-02 09:25 camacho * core/: blast_psi.c (1.9), blast_psi_priv.c (1.20), blast_psi_priv.h (1.11): 1. Various renaming of structures, in progress 2. Addition of PsiDiagnostics structures, in progress 2004-08-03 12:13 madden * core/mb_lookup.c (1.36): Use helper array to estimate longest chain size 2004-08-03 13:41 dondosha * core/blast_seqsrc.h (1.24): Removed deprecated enum values 2004-08-03 13:42 dondosha * core/blast_hits.c (1.116): Minor fix in reallocation condition in Blast_HSPListSaveHSP 2004-08-03 13:44 dondosha * core/blast_extend_pri.h (1.1): Declarations of some functions previously static in blast_extend.c 2004-08-03 16:12 dondosha * core/: blast_stat.h (1.53), blast_stat.c (1.89): Renamed BlastScoreBlkMatCreate to BlastScoreBlkNuclMatrixCreate and made it public 2004-08-03 16:13 dondosha * core/blast_extend.h (1.28): Added diagonal array structure type for blastn using one integer instead of 2 2004-08-03 16:16 dondosha * core/blast_options.h (1.83): Added initial word options validation; use diagonal array structure with one integer for blastn 2004-08-03 16:17 dondosha * core/: aa_ungapped.c (1.35), blast_extend.c (1.66): Diagonal structure changed so it can use array of integers for blastn or array of 2-integer structures for other programs 2004-08-03 16:19 dondosha * core/blast_options.c (1.125): Added initial word options validation; set seed container type and extension method appropriately 2004-08-03 17:06 dondosha * core/blast_stat.c (1.90): Removed unused variable 2004-08-03 17:51 papadopo * api/twoseq_api.c (1.22): add extra parameter to BLAST_ValidateOptions 2004-08-03 17:59 dondosha * api/twoseq_api.c (1.23): Convert return filtering locations back to nucleotide coordinates for translated programs 2004-08-04 16:08 camacho * core/blast_psi.h (1.8): 1. Completed implementation of diagnostics request/response structures. 2. Removed unneeded fields from multiple sequence alignment data structures. 3. Added documentation 2004-08-04 16:13 camacho * core/blast_psi.c (1.10): 1. Reorganized file, limited contents to high level interface only. 2. Use of new diagnostics request/response structures as well as new structures from blast_psi_priv.h 2004-08-04 16:18 camacho * core/: blast_psi_priv.c (1.21), blast_psi_priv.h (1.12): 1. Renaming of structures and functions that pertain to the internals of PSSM engine. 2. Updated documentation (in progress) 2004-08-05 13:19 madden * api/blast_seq.c (1.45): BlastMaskLocFromSeqLoc now handles NULL input gracefully 2004-08-05 13:20 madden * api/blast_format.c (1.67): Balance call to BioseqLock with call to BioseqUnlock 2004-08-05 15:54 dondosha * core/blast_options.c (1.126): Allow stride 1 for discontiguous megablast in options validation 2004-08-05 16:39 dondosha * core/: blast_extend.h (1.29), blast_options.h (1.84), aa_ungapped.c (1.36), blast_engine.c (1.154), blast_extend.c (1.67), blast_options.c (1.127): Implemented stacks initial word container for all blastn extension methods 2004-08-06 12:22 dondosha * core/blast_options.c (1.128): In initial word options validation, return after first encountered error 2004-08-06 13:31 madden * api/blast_seq.c (1.46): Add more protection to BlastMaskLocFromSeqLoc against invalid input, fix leak in BLAST_GetSequence 2004-08-06 13:32 madden * api/: blast_format.c (1.68), blast_format.h (1.29): Add BLAST_PrintSummaryReturns to format contents of BLAST_PrintSummaryReturns 2004-08-09 09:05 madden * api/: twoseq_api.h (1.6), twoseq_api.c (1.24): 1.) added parameters to BLAST_TwoSeqLocSets to allow input of masking sequence and return Boolean for masking at hash. 2.) changed Options so that no guessing should take place, megablast and longest_intron can be set directly. 2004-08-09 10:20 dondosha * core/mb_lookup.c (1.37): Minor compiler warning fix 2004-08-10 10:48 papadopo * api/twoseq_api.c (1.25): 1. Only turn on megablast if the first input sequence is large 2. If eSensitive is specified for a blastn search and megablast is turned on, always turn on discontiguous megablast, ignoring any user specified word size 3. For blastn searches, always turn AG striding on if a non-default word size is specified 2004-08-10 10:49 papadopo * api/twoseq_api.h (1.7): Update doxygen comments to reflect slight changes in the way searches are set up 2004-08-10 10:52 ivanov * core/: blast_def.h (1.46), blast_dust.h (1.13), blast_filter.h (1.21), blast_gapalign.h (1.54), blast_hits.h (1.51), blast_hspstream.h (1.3), blast_options.h (1.85), blast_seqsrc.h (1.25), blast_setup.h (1.43), blast_traceback.h (1.35), blast_util.h (1.54): Added export specifier NCBI_XBLAST_EXPORT 2004-08-10 12:40 vakatov * core/blast_export.h (1.1): Initial revision 2004-08-11 07:58 ivanov * core/blast_def.h (1.47): Added export specifier NCBI_XBLAST_EXPORT for sfree() 2004-08-11 07:58 ivanov * core/blast_setup.h (1.44): Added more export specifiers NCBI_XBLAST_EXPORT 2004-08-11 07:59 ivanov * core/blast_seqsrc.h (1.26): Added export specifier NCBI_XBLAST_EXPORT 2004-08-12 09:01 madden * core/blast_options.c (1.129): Add static function BlastFindValidKarlinBlk to look for valid Karlin blocks in an array of them, prevents use of bogus (-1) Karlin-Altschul parameters 2004-08-13 13:44 dondosha * core/blast_stat.c (1.91): Doxygenized comments for BLAST_UnevenGapSumE 2004-08-13 13:45 dondosha * core/hspstream_collector.c (1.6): Minor memory leak fix 2004-08-13 13:46 dondosha * core/blast_util.c (1.75): Use #defined macros instead of hard coded constants for number of frames and strands; check for NULL input in BlastQueryInfoFree 2004-08-13 18:32 camacho * core/blast_psi_priv.c (1.22): Refactoring of _PSIPurgeSimilarAlignments to use finite state machine 2004-08-16 10:57 camacho * core/blast_kappa.c (1.19): Renamed, changed type of scoreRange 2004-08-16 13:18 dondosha * api/blast_format.c (1.69): Acknowledge all queries, and print "No hits found" message for those that do not have hits 2004-08-16 15:43 dondosha * core/blast_hits.h (1.52): Removed splice_junction field from HSP structure 2004-08-16 15:44 dondosha * core/blast_options.h (1.86): Added overlap_size field to LinkHSPParameters and its default value 2004-08-16 15:45 dondosha * core/: blast_options.c (1.130), blast_traceback.c (1.121), link_hsps.c (1.40): Implemented uneven gap linking of HSPs for blastx 2004-08-16 15:47 dondosha * api/blast_seqalign.c (1.41): Removed setting of splice_junction score type 2004-08-17 09:38 madden * core/blast_options.h (1.87): Add min_diag_separation to BlastHitSavingOptions 2004-08-17 09:38 madden * core/blast_gapalign.c (1.111): Allow choice of different culling based upon value of min_diag_separation 2004-08-17 16:42 dondosha * core/mb_lookup.c (1.38): Corrected the extent of scanning of database sequence for discontiguous words with stride 1 2004-08-17 17:32 dondosha * api/blast_format.c (1.70): If no results found for any of the queries, still acknowledge all of them and print "no hits found" message 2004-08-17 18:18 dondosha * api/: seqsrc_multiseq.c (1.13), seqsrc_multiseq.h (1.3): Added copy function, needed for BLAST run with tabular thread 2004-08-18 14:13 camacho * core/blast_util.h (1.55): Remove unneeded windows dll export directive 2004-08-30 12:28 dondosha * core/: blast_hits.h (1.53), blast_engine.c (1.155), blast_hits.c (1.117), link_hsps.c (1.41): Use gap decay rate in e-value calculation for singleton HSPs when doing linking 2004-08-30 12:41 dondosha * core/blast_filter.h (1.22): Changed comment for BLAST_ComplementMaskLocations to indicate clearly that resulting locations are relative to the concatenated sequence and not individual queries 2004-08-30 12:52 dondosha * core/blast_options.h (1.88): Added E in front of enum names ESeedExtensionMethod and ESeedContainerType 2004-08-31 12:13 camacho * core/: blast_psi_priv.c (1.23), blast_psi_priv.h (1.13): Documentation changes 2004-08-31 12:58 dondosha * api/: blast_format.c (1.71), blast_format.h (1.30), blast_returns.c (1.10), blast_returns.h (1.6), blast_seqalign.c (1.42), blast_seqalign.h (1.18), twoseq_api.c (1.26): Eliminated use of BlastSeqSrc on the API level for regular search 2004-08-31 12:59 dondosha * api/: blast_tabular.c (1.9), blast_tabular.h (1.5): Added option to print sequences in tabular output for blastn 2004-09-01 09:19 madden * core/blast_inline.h (1.4): Add BlastGetMaskLocIndexFromContext and BlastIsReverseStrand for use in blast_mask 2004-09-01 09:20 madden * core/blast_filter.c (1.48): Fix for filtering on minus strand, use BlastGetMaskLocIndexFromContext and BlastIsReverseStrand 2004-09-02 15:19 madden * core/ncbi_std.h (1.30): Add ECC to #define for restrict 2004-09-07 09:32 coulouri * core/: blast_lookup.c (1.29), lookup_wrap.c (1.8), blast_lookup.h (1.13): remove dead code, rename misleading function 2004-09-07 13:20 dondosha * core/: blast_engine.h (1.44), blast_util.h (1.56): Minor fix in doxygen comment 2004-09-07 16:23 dondosha * core/blast_seg.c (1.24): Added some doxygen comments 2004-09-08 12:02 dondosha * core/: blast_hits.h (1.54), blast_hits.c (1.118): Added function to reverse the order of HSP lists in BlastHSPResults 2004-09-08 12:03 dondosha * core/hspstream_collector.c (1.7): Reverse order of HSP lists in arrays in the Close method for non-database searches, to make sure they are returned in correct order 2004-09-08 12:07 dondosha * api/: blast_seqalign.c (1.43), blast_seqalign.h (1.19): Added function Blast_AdjustOffsetsInSeqAlign to adjust offsets independently for all query-subject pairs in multi-sequence BLAST results 2004-09-08 13:33 dondosha * core/blast_hits.c (1.119): Added missing return in Blast_HSPResultsReverseOrder; removed unused function Blast_HSPResultsRPSUpdate 2004-09-13 08:39 madden * core/blast_def.h (1.48): Change of BlastSeqLoc and BlastMaskLoc definitions 2004-09-13 08:39 madden * core/: blast_lookup.h (1.14), lookup_wrap.h (1.7), mb_lookup.h (1.17), phi_lookup.h (1.7), lookup_wrap.c (1.9), mb_lookup.c (1.39), phi_lookup.c (1.18), blast_lookup.c (1.30), blast_dust.c (1.26), blast_seg.c (1.25): Use BlastSeqLoc rather than ListNode 2004-09-13 08:40 madden * core/: blast_filter.h (1.23), blast_filter.c (1.49): Changes for redefinition of BlastSeqLoc and BlastMaskLoc 2004-09-13 11:14 madden * api/blast_seq.h (1.13): Add prototypes for BlastSeqLocFromSeqLoc and BlastMaskLocDNAToProtein 2004-09-13 11:15 madden * api/: blast_input.c (1.16), blast_seq.c (1.47), twoseq_api.c (1.27): Changes for BlastSeqLoc and BlastMaskLoc 2004-09-13 12:35 madden * api/blast_seq.h (1.14): uncomment prototype for BlastMaskLocToSeqLoc 2004-09-13 12:36 madden * api/blast_format.c (1.72): Add include for blast_seq.h 2004-09-13 12:36 madden * api/blast_input.c (1.17): Add include for blast_filter.h 2004-09-13 12:39 dondosha * core/blast_gapalign.c (1.112): 1. Removed unused argument in static function CheckGappedAlignmentsForOverlap; 2. Do not compare HSPs from different contexts in CheckGappedAlignmentsForOverlap; 3. Removed unused fields in local GapData structure. 2004-09-13 15:33 camacho * core/blast_options.c (1.131): Add comments 2004-09-13 15:47 dondosha * api/blast_seqalign.c (1.44): Removed a debugging ASSERT statement that is not needed 2004-09-14 10:31 madden * api/: blast_seq.c (1.48), blast_seq.h (1.15): Make mask_loc param in BlastMaskLocToSeqLoc const 2004-09-14 17:16 camacho * core/: blast_options.h (1.89), blast_options.c (1.132), blast_psi.c (1.11), blast_psi_priv.c (1.24): Add structure group customization to ignore query 2004-09-14 17:43 camacho * core/blast_stat.h (1.54): Minor correction in comment 2004-09-16 08:41 madden * api/: blast_seq.c (1.49), blast_seq.h (1.16): Remove commented out BlastMaskLocFromSeqLoc 2004-09-16 10:19 dondosha * core/blast_traceback.h (1.36): Added missing prototype for Blast_RunTracebackSearch, used in blast_driver.c 2004-09-16 11:45 coulouri * core/blast_filter.c (1.50): don't dereference null pointer 2004-09-16 22:04 camacho * core/blast_psi.h (1.9): 1. Renaming of diagnostics structure fields. 2. Documentation update. 2004-09-16 22:05 camacho * core/blast_psi.c (1.12): Renaming of diagnostics structure fields. 2004-09-16 22:06 camacho * core/blast_psi_priv.c (1.25): Renaming of diagnostics structure fields 2004-09-17 09:08 camacho * core/blast_psi.h (1.10): Added doxygen comments 2004-09-21 09:43 dondosha * core/blast_hits.h (1.55): Made comparison function for sorting HSPs by evalue public 2004-09-21 09:43 dondosha * core/blast_lookup.h (1.15): Save number of database sequences in RPS lookup table 2004-09-21 09:45 dondosha * core/blast_engine.c (1.156): 1. Initialize auxiliary BlastQueryInfo for concatenated database inside BLAST_SearchEngineCore and pass real query_info in its input argument. 2. Relink HSPs after reevaluation with ambiguities if sum statistics is used. 3. Sort HSPs in HSP lists by e-value/score before passing them to BlastHSPStream. 2004-09-21 09:45 dondosha * core/blast_filter.c (1.51): Memory leak fixes in BlastMaskLocFree and CombineMaskLocations 2004-09-21 09:46 dondosha * core/blast_gapalign.c (1.113): Do not compare scores when sorting HSPs in CheckGappedAlignmentsForOverlap, as it is not needed there 2004-09-21 09:47 dondosha * core/blast_hits.c (1.120): 1. Made comparison function for sorting HSPs by evalue public, since it is needed; 2. Sort HSPs in each HSP list by score when saving HSPLists for RPS BLAST. 2004-09-21 09:47 dondosha * core/blast_kappa.c (1.20): Check if HSP lists are sorted coming into the traceback 2004-09-21 09:47 dondosha * core/blast_lookup.c (1.31): Save number of database sequences in RPS lookup table 2004-09-21 09:48 dondosha * core/blast_setup.c (1.95): Modification of search space for RPS tblastn no longer needed 2004-09-21 09:48 dondosha * core/blast_traceback.c (1.122): 1. Create auxiliary BlastQueryInfo for database sequence inside Blast_TracebackFromHSPList and pass real query_info in its input argument. 2. Choose correct Karlin block in HSPSetScores for RPS tblastn; 3. Sort HSPs by e-value before call to BLASTCheckHSPInclusion, and again after relinking HSPs with sum statistics. 4. Assign query contexts in HSPs in Blast_HSPListRPSUpdate for RPS tblastn - needed for correct calculation of bit scores. 5. Check if HSP lists are sorted coming into the traceback 2004-09-21 09:49 dondosha * core/link_hsps.c (1.42): Reset numbers of HSPs in linked sets before relinking them 2004-09-21 09:52 dondosha * api/blast_seq.c (1.50): 1. Translate query into 6 frames for RPS tblastn, same as for blastx; 2. Do not make last_context field in BlastQueryInfo smaller for plus-strand-only search 2004-09-21 10:01 dondosha * api/blast_tabular.c (1.10): Check if HSPs in HSP lists are sorted coming out of BlastHSPStream 2004-09-21 10:47 dondosha * core/blast_traceback.c (1.123): Substitute query info by subject sequence info for protein RPS blast 2004-09-21 16:42 coulouri * core/blast_dust.c (1.27): treat left and right ends of sequence symmetrically 2004-09-22 18:00 camacho * core/blast_options.h (1.90): Remove obsolete comment 2004-09-23 10:57 dondosha * core/: link_hsps.h (1.14), blast_engine.c (1.157), blast_traceback.c (1.124): Changed BLAST_SequenceBlk subject argument to subject length in BLAST_LinkHsps, because only length is needed 2004-09-23 10:59 dondosha * core/link_hsps.c (1.43): Changed BLAST_SequenceBlk subject argument to subject length in BLAST_LinkHsps; separate HSPs from different strands for ungapped blastn 2004-09-23 11:00 dondosha * core/blast_options.c (1.133): Reset gap_prob in CalculateLinkHSPCutoffs when necessary; fixed a doxygen comment 2004-09-23 13:03 dondosha * api/blast_format.c (1.73): Fix in traversing the list of mask locations when the first query in a set does not have a mask 2004-09-23 15:51 camacho * core/blast_psi_priv.c (1.26): Added sanity checks 2004-09-24 10:19 camacho * core/hspstream_collector.h (1.5): Removed obsolete comment 2004-09-28 12:20 papadopo * core/blast_options.c (1.134): From Michael Gertz: 1. Disallow setting longest intron for programs other than tblastn and blastx; previously it was possible to set it to a negative value. 2. For ungapped blastx and tblastn, if longest_intron is not set (i.e. = 0) or (longest_intron - 2)/3 is nonpositive, call link_hsps. Otherwise call new_link_hsps. 3. For gapped blastx or tblastn, if longest_intron is not set (i.e. = 0), set it to 122. Then call new_link_hsps if (longest_intron - 2)/3 is positive. Otherwise turn off sum statistics. 2004-09-28 12:23 papadopo * core/blast_stat.c (1.92): From Michael Gertz: 1. Pass the effective size of the search space into BLAST_SmallGapSumE, BLAST_LargeGapSumE and BLAST_UnevenGapSumE. The routines use this value in a simplified formula to compute the e-value of singleton sets. 2. Caused all routines for calculating the significance of multiple distinct alignments (BLAST_SmallGapSumE, BLAST_LargeGapSumE and BLAST_UnevenGapSumE) to use sum_{i in linked_set} (\lambda_i s_i - \ln K_i) as the weighted sum score, where (\lambda_i, K_i) are taken from the appropriate query context. 2004-09-28 12:24 papadopo * core/blast_def.h (1.49): From Michael Gertz: Introduced DEFAULT_LONGEST_INTRON to represent the default value of the longest intron parameter. 2004-09-28 12:26 papadopo * core/blast_stat.h (1.55): From Michael Gertz: Pass the effective size of the search space into BLAST_SmallGapSumE, BLAST_LargeGapSumE and BLAST_UnevenGapSumE. 2004-09-28 12:30 papadopo * core/link_hsps.c (1.44): From Michael Gertz: 1. Caused all routines for calculating the significance of multiple distinct alignments (BLAST_SmallGapSumE, BLAST_LargeGapSumE and BLAST_UnevenGapSumE) to use sum_{i in linked_set} (\lambda_i s_i - \ln K_i) as the weighted sum score, where (\lambda_i, K_i) are taken from the appropriate query context. This change affects e-values for blastx and tblastx. 2. When computing normalized sum scores, use the ungapped values of (lambda, K) for ungapped alignments. 3. In SumHSPEvalue, for blastx, the subject_length must be divided by 3. 4. Pass the effective search space size into BLAST_SmallGapSumE, BLAST_LargeGapSumE and BLAST_UnevenGapSumE. The routines use this value in a simplified formula to compute the e-value of singleton sets. 5. Sort HSPs in Blast_UnevenGapLinkHSPs by normalized score, rather than score; for blastx, this places HSPs in the correct order of significance. 6. In Blast_UnevenGapLinkHSPs, set xsum field of every HSP to the appropriate value for a singleton set before doing any linking. 7. In both Blast_EvenGapLinkHSPs and Blast_UnevenGapLinkHSPs use normalized sum score, rather than raw sum score, everywhere when choosing linked sets 2004-09-29 10:53 coulouri * core/blast_seqsrc.h (1.27): doxygen fixes 2004-09-29 16:39 papadopo * core/blast_stat.c (1.93): Retrieve the ungapped lambda from the actual score matrix underlying an RPS search, not just that of BLOSUM62 2004-09-29 16:41 papadopo * core/blast_traceback.c (1.125): pass the name of the underlying score matrix to RPSCalculatePSSM 2004-09-29 16:45 papadopo * core/blast_stat.h (1.56): pass the name of the underlying score matrix to RPSCalculatePSSM 2004-09-29 18:44 camacho * core/blast_gapalign.c (1.114): Use more meaningful identifier names 2004-09-30 09:43 madden * core/blast_seg.c (1.26): Moved structure Alpha from blast_seg.h, changed some defines to consts added doxygen comments, Cleaned up naming conventions, removed dead code 2004-09-30 09:43 madden * core/blast_seg.h (1.13): Moved structure Alpha to blast_seg.c 2004-10-01 09:58 camacho * core/: blast_stat.c (1.94), blast_traceback.c (1.126): Remove extra PSSM column for RPS-BLAST 2004-10-01 09:59 camacho * core/blast_psi_priv.c (1.27): Use calloc where needed 2004-10-01 10:52 camacho * core/blast_stat.c (1.95): Add PAM250 to list of matrices to load from tables library 2004-10-04 08:41 madden * core/blast_seg.h (1.14): Doxygen comments 2004-10-04 08:42 madden * core/blast_seg.c (1.27): Add doxygen comments, improve variable names 2004-10-04 09:38 camacho * core/blast_stat.c (1.96): Do not use hard coded constants in RPSfindUngappedLambda 2004-10-04 09:41 madden * core/blast_diagnostics.h (1.5): Add cutoff_score to BlastRawCutoffs 2004-10-04 09:42 madden * core/blast_engine.c (1.158): Set cutoff_score in call to FillReturnCutoffsInfo 2004-10-04 10:00 madden * api/: blast_format.c (1.74), blast_format.h (1.31): Fixes for XML and std. BLAST report, remove BLAST_PrintSummaryReturns (use Blast_PrintOutputFooter) 2004-10-04 10:02 madden * api/blast_returns.h (1.7): Add structs Blast_DatabaseStats and Blast_SearchParams, simplify Blast_GetParametersBuffer buffer 2004-10-04 10:03 madden * api/blast_returns.c (1.11): Add functions to fill Blast_DatabaseStats and Blast_SearchParams, simplify Blast_GetParametersBuffer buffer, print all relevant lines for footer 2004-10-04 10:04 madden * api/: twoseq_api.c (1.28), twoseq_api.h (1.8): Rename of BLAST_SummaryReturn to Blast_SummaryReturn, change in Blast_Diagnostics ownership 2004-10-04 12:32 kans * api/blast_format.c (1.75): CodeWarrior did not like BlastPrintVersionInfo being called with const char* program_name argument, so cast to (CharPtr) within BLAST_PrintOutputHeader 2004-10-04 13:07 dondosha * core/greedy_align.h (1.14): Moved ICEIL definition from source file; added GREEDY_MAX_COST_FRACTION instead of ERROR_FRACTION 2004-10-04 13:08 dondosha * core/greedy_align.c (1.21): Moved ICEIL definition to header file; use GREEDY_MAX_COST_FRACTION instead of ERROR_FRACTION 2004-10-04 13:08 dondosha * core/blast_gapalign.c (1.115): Added all missing doxygen comments 2004-10-04 13:10 dondosha * core/: blast_hits.h (1.56), blast_hits.c (1.121): Added functions for sorting HSP list by score and by e-value; same functions check if list is already sorted before proceeding with sort 2004-10-04 13:11 dondosha * core/blast_engine.c (1.159): Use new Blast_HSPListSortByEvalue function for sorting HSPs in HSP lists 2004-10-04 13:11 dondosha * core/blast_kappa.c (1.21): Use new Blast_HSPListSortByScore function for checking if HSPs in HSP lists are sorted before proceeding with traceback 2004-10-04 13:13 dondosha * core/blast_traceback.c (1.127): Use Blast_HSPListSortByScore and Blast_HSPListSortByEvalue functions to sort HSPs in HSP lists by score before proceeding with traceback and by e-value after traceback is done 2004-10-04 14:12 dondosha * api/blast_tabular.c (1.11): Removed call to deleted Blast_HSPListCheckIfSorted function 2004-10-04 14:19 madden * api/blast_format.c (1.76): Revert casting away const in call to BlastPrintVersionInfo, that function has been fixed 2004-10-05 10:23 papadopo * core/blast_gapalign.c (1.116): use new greedy alignment enums when constructing greedy traceback 2004-10-05 10:24 papadopo * core/greedy_align.h (1.15): 1. Add doxygen comments 2. Change traceback structures to include the traceback operation as a C bitfield, rather than being defined explicitly 2004-10-05 10:28 papadopo * core/greedy_align.c (1.22): 1. Bail out of non-affine greedy alignment if either the entire first sequence or the entire second sequence matches 2. Removed redundant code, removed functions that are defined once and then used once, removed functions that are only wrappers for other functions (i.e. whose body is a single function call) 3. Reformatted code, added doxygen comments, changed variable names 2004-10-05 17:32 camacho * core/blast_stat.c (1.97): Return 1 to indicate error in BlastScoreBlkMatrixLoad 2004-10-05 17:33 camacho * core/blast_stat.h (1.57): Update documentation about BlastScoreBlkMatrixLoad 2004-10-06 10:06 papadopo * core/: greedy_align.c (1.23), greedy_align.h (1.16): more doxygen fixes 2004-10-06 10:47 dondosha * core/: blast_seqsrc.h (1.28), blast_seqsrc.c (1.23): Removed functions that are no longer needed 2004-10-06 10:48 dondosha * core/blast_setup.c (1.96): Call BLAST_ComplementMaskLocations only if lookup table segments are requested in BLAST_MainSetUp 2004-10-06 10:59 dondosha * api/: seqsrc_multiseq.c (1.14), seqsrc_multiseq.h (1.4), seqsrc_readdb.c (1.35): Remove functions that are no longer supported by interface 2004-10-06 11:00 dondosha * api/blast_tabular.c (1.12): Use readdb structure directly to retrieve subject Seq-id 2004-10-06 11:00 dondosha * api/: blast_seq.c (1.51), blast_seq.h (1.17): Made query Seq-loc argument for BlastMaskLocToSeqLoc const 2004-10-06 11:00 dondosha * api/: blast_prelim.c (1.2), blast_seqalign.c (1.45): Minor memory leak fix 2004-10-06 11:01 dondosha * api/blast_returns.c (1.12): Removed unused arguments from Blast_SummarySearchParamsFill; minor syntax fix 2004-10-06 11:01 dondosha * api/blast_format.c (1.77): Removed unused variables 2004-10-06 14:16 dondosha * api/blast_seq.c (1.52): Cast const SeqLoc* to SeqLoc* when assigning to an iterating pointer 2004-10-06 15:03 dondosha * api/: blast_tback.c (1.1), blast_tback.h (1.1): API level function(s) for performing traceback stage of BLAST 2004-10-06 15:03 dondosha * core/blast_traceback.h (1.37): Moved Blast_RunTracebackSearch to distrib/algo/blast/api/blast_tback.h 2004-10-06 15:03 dondosha * core/blast_traceback.c (1.128): Moved Blast_RunTracebackSearch to distrib/algo/blast/api/blast_tback.c 2004-10-06 16:03 papadopo * core/greedy_align.h (1.17): ANSI C does not allow enums to be bitfields 2004-10-07 10:05 papadopo * core/greedy_align.c (1.24): minor doxygen fix 2004-10-08 08:52 madden * core/blast_seg.c (1.28): Fix return type for shiftwin1 2004-10-08 11:31 dondosha * core/blast_gapalign.c (1.117): Corrected error return value in BLAST_ProtGappedAlignment 2004-10-13 12:03 camacho * core/blast_psi_priv.c (1.28): Add assertions as sanity checks 2004-10-13 13:44 dondosha * core/blast_options.c (1.135): Added comment for setting of ungapped X-dropoff in BlastInitialWordParametersUpdate 2004-10-14 10:18 papadopo * core/blast_traceback.c (1.129): for RPS traceback, skip over PSSMs that generate bad statistics 2004-10-14 10:42 papadopo * core/blast_traceback.c (1.130): add doxygen comment that a warning will eventually be needed when the condition fixed in the previous checkin is encountered 2004-10-14 13:08 madden * core/blast_options.h (1.91): Add avg_subject_length parameter to BlastHitSavingParametersNew and BlastHitSavingParametersUpdate 2004-10-14 13:10 madden * core/blast_setup.c (1.97): BlastHitSavingParametersNew and BlastHitSavingParametersUpdate changes, set total_length for all searches 2004-10-14 13:10 madden * core/blast_options.c (1.136): BlastHitSavingParametersNew and BlastHitSavingParametersUpdate changes for gapped sum statistics 2004-10-14 13:11 madden * core/blast_gapalign.c (1.118): Only send gapped HSPs on for linking if above proper threshold 2004-10-14 13:40 madden * core/blast_seg.c (1.29): Replace LN2 by NCBIMATH_LN2, LN2 is deprecated 2004-10-15 13:49 camacho * core/blast_psi.c (1.13): Avoid double freeing return value of PSICreatePssmWithDiagnostics in case of errors 2004-10-18 10:33 camacho * core/: blast_psi.c (1.14), blast_psi_priv.c (1.29), blast_psi_priv.h (1.14): 1. Added validation routines 2. Fixed bug in calculating sequence weights 3. Expanded error codes 2004-10-18 11:14 bealer * core/blast_gapalign.c (1.119): - Add tiebreaking tests to Blast_GappedScorePrelimTest 2004-10-18 12:37 dondosha * api/blast_tabular.c (1.13): Fixed determination of subject id buffer when database is formatted without indices and accession-only ids are requested 2004-10-19 10:28 camacho * core/blast_psi_priv.c (1.30): Fix memory access error 2004-10-19 12:03 dondosha * core/blast_hits.h (1.57): Added best_evalue field to BlastHSPList structure, necessary because HSPs are sorted by score only, so 1st HSP may not have the best e-value; Added function Blast_HSPListIsSortedByScore with boolean return value. 2004-10-19 12:03 dondosha * core/blast_extend.h (1.30): Added functions to sort initial HSP list by score and to check if it is sorted 2004-10-19 12:04 dondosha * core/blast_traceback.h (1.38): Pass BlastSeqSrc to BLAST_RPSTraceback, to allow sequence retrieval for calculation of identities 2004-10-19 12:05 dondosha * core/: aa_ungapped.c (1.37), blast_extend.c (1.68): Sort initial hit lists by score at the end of the WordFinder routines 2004-10-19 12:06 dondosha * core/blast_engine.c (1.160): Pass BlastSeqSrc to BLAST_RPSTraceback, to allow sequence retrieval for calculation of identities; do not sort HSP lists by e-value - they are always sorted by score now. 2004-10-19 12:06 dondosha * core/blast_gapalign.c (1.120): Sort HSP arrays by score at the end of all GetGappedScore routines. Sorting of initial hit lists by score moved to the WordFinder routines. Do not create unnecessary array of pointers to initial HSP structures. 2004-10-19 12:07 dondosha * core/blast_hits.c (1.122): 1. Added Blast_HSPListIsSortedByScore function to allow quick checks of whether HSP array is sorted; 2. Check HSPs for NULL in Blast_HSPListSortByScore; 3. Make sure HSPs are sorted by score on entrance and exit of all public functions after the preliminary gapped alignment; 4. Store HSPs in a heap if HSP limit is reached; 5. Fill and use the best_evalue field in BlastHSPList structure. 2004-10-19 12:08 dondosha * core/blast_traceback.c (1.131): 1. Sort HSPs by score only, not by e-value after traceback; 2. Pass BlastSeqSrc to BLAST_RPSTraceback, to allow sequence retrieval for calculation of identities. 2004-10-19 12:09 dondosha * core/link_hsps.c (1.45): Sort HSPs by score before BLAST_LinkHsps exits; find best evalue and save it in a corresponding structure field. 2004-10-19 12:10 dondosha * api/blast_seqalign.c (1.46): Sort HSPs by e-value before converting results to Seq-align, since they are sorted by score coming in. 2004-10-19 16:14 camacho * core/blast_psi.c (1.15): added more assertions for sanity checking 2004-05-05 11:30 dondosha * demo/blast_driver.c (1.40): Renamed functions in blast_hits.h accordance with new convention Blast_[StructName][Task] 2004-05-07 11:47 papadopo * demo/blast_driver.c (1.41): add scale factor to BlastMainSetUp 2004-05-13 12:58 kans * tools/rpsutil.c (6.70): in AnnotateRegionsFromCDD, do not put cdd->ShortName into comment if same as cdd->Definition 2004-05-13 14:24 coulouri * demo/fmerge.c (6.6): obsolete 2004-05-13 14:42 coulouri * demo/blastall.c (6.143): disable -B for blastcl3 2004-05-13 16:54 coulouri * demo/fastacmd.c (6.30): spell 'loci' correctly 2004-05-14 08:10 camacho * demo/makemat.c (6.14): Added comments to special cases 2004-05-14 08:13 camacho * tools/: posit.h (6.24), posit.c (6.62): Made posDemographics non-static for testing purposes. 2004-05-14 10:39 bealer * tools/blastool.c (6.265): - Adjust ethresh to .001 for PSI blast. 2004-05-14 10:41 bealer * tools/blastool.c (6.266): - Er. I mean .002, as per blastpgp. 2004-05-14 11:38 dondosha * tools/blastool.c (6.267): Use newly public function ScoreAndEvalueToBuffers from txalign.h instead of a static function 2004-05-14 13:24 dondosha * demo/blast_driver.c (1.42): Changed BlastReturnStat to BlastDiagnostics 2004-05-17 12:26 papadopo * demo/blast_driver.c (1.43): change greedy alignment flags to enum values 2004-05-21 09:53 dondosha * tools/: blastool.c (6.268), blastutl.c (6.435), mblast.c (6.203): Use BLAST_HSPFree to free BLAST_HSP structures, hence no need to call GapXEditBlockDelete in multiple places 2004-05-21 09:53 dondosha * tools/blast.c (6.406): Fix in BLASTMergeHitLists 2004-05-25 17:42 dondosha * tools/blastutl.c (6.436): Fix in previous change: in some cases edit block should not be freed when BLAST_HSP is freed 2004-05-27 13:35 dondosha * tools/mblast.c (6.204): Do not flag HSPs for deletion in sorting before doing inclusion tests 2004-05-27 13:36 dondosha * tools/blastutl.c (6.437): Minor fix for previous 2 changes 2004-05-27 13:37 dondosha * demo/megablast.c (6.114): Do not call GapXEditBlockDelete in formatting callback - this is now done when HSPs are freed 2004-06-01 16:34 dondosha * tools/blastutl.c (6.438): Fix in previous change; memory leak fix 2004-06-03 12:10 dondosha * tools/kappa.c (6.40): Fix in Kappa_SearchParametersNew: allocate correct number of rows for matrices 2004-06-07 16:03 coulouri * tools/blastkar.c (6.101): use floating point constants for comparisons with floating point variables 2004-06-08 10:03 camacho * tools/posit.c (6.63): Alejandro Schaffer's fix to spread out gap costs in posDemographics. 2004-06-08 10:07 kans * demo/blast_driver.c (1.44): removed extraneous BlastScoreBlk* sbp parameter from BLAST_ResultsToSeqAlign 2004-06-08 11:41 dondosha * demo/blast_driver.c (1.45): 1. Use BlastHSPStream interface; 2. Added possibility to produce on-the-fly tabular output; 3. Set traceback extension option properly depending on command line options 2004-06-08 13:47 dondosha * demo/blast_driver.c (1.46): Use boolean arguments for gapped calculation and out-of-frame modes instead of BlastScoringOptions 2004-06-14 17:11 papadopo * tools/kappa.c (6.41): From Michael Gertz: - Added several casts where casts occur in blast_kappa.c. These casts should have no real effect; the log of blast_kappa.c indicates that they suppress compiler warnings. - Changed the type of one variable that holds a score from Nlm_FloatHi to Int4. - moved the definition Kappa_ForbiddenRanges and relevant routines earlier in the file. - fixed some comments. - made a few (~5) changes in whitespace. 2004-06-18 11:50 madden * tools/kappa.c (6.42): For secondary alignments with Smith-Waterman on, use the E-value from the X-drop alignment computed by ALIGN that has more flexibility in which positions are allowed in the dynamic program. Add a sort of alignments for the same query-subject pair because the use of X-drop alignments occasionally reorders such alignments. Changes from Mike Gertz, submitted by Alejandro Schaffer. 2004-06-22 10:16 camacho * tools/: posit.h (6.25), posit.c (6.64): Changed signature of posFreqsToMatrix, added use of SFreqRatios structure from algo/blast/core/ to obtain underlying matrices' frequency ratios. This change results in using the frequency ratios to provide the scores for the PSSM in columns where all residue frequencies are 0. Previously the standard scoring matrix were used. 2004-06-22 10:16 camacho * tools/: blastutl.c (6.439), posit2.c (6.10): Changed invocation of posFreqsToMatrix to conform with new signature 2004-06-22 10:16 camacho * tools/kappa.c (6.43): Use SFreqRatios structure from algo/blast/core to obtain underlying matrices' frequency ratios. 2004-06-22 12:45 camacho * demo/: blast_driver.c (1.47), copymat.c (6.37): Changed the blast_type_* definitions for the EBlastProgramType enumeration from algo/blast. 2004-06-23 10:46 dondosha * demo/blast_driver.c (1.48): Added number of threads option; at this time it only triggers locking mechanism for writing results 2004-06-23 10:53 camacho * tools/: posit.h (6.26), posit.c (6.65): Copy renamed versions of SFreqRatios and its *{New,Free} functions to avoid dependency ncbitool -> blast 2004-06-23 10:53 camacho * tools/kappa.c (6.44): Use renamed FreqRatios structure from posit.h 2004-06-23 17:08 dondosha * tools/xmlblast.c (6.34): Fixed masking of filtered locations for translated queries 2004-06-24 15:02 dondosha * demo/blastpgp.c (6.121): Exit with error status if PGPReadBlastOptions returns NULL 2004-06-24 17:16 dondosha * tools/blastool.c (6.269): Boolean argument in ScoreAndEvalueToBuffers changed to Uint1, so pass 0 instead of FALSE 2004-06-24 17:48 dondosha * demo/blastpgp.c (6.122): Made ungapped search option deprecated 2004-06-25 16:58 dondosha * demo/blastpgp.c (6.123): Ungapped option not supported for multi-iterational search, but OK otherwise 2004-06-25 17:54 dondosha * tools/posit.c (6.66): Choose ideal values for lambda and K correctly for ungapped search 2004-06-28 09:45 madden * demo/blast_driver.c (1.49): Use BlastMaskInformation for BLAST_MainSetUp, set TXALIGN_SHOW_NO_OF_SEGS if ungapped 2004-06-28 10:02 papadopo * demo/formatrpsdb.c (1.1): Initial revision 2004-06-28 22:46 dondosha * demo/blast_driver.c (1.50): Set parameters properly for HTML option 2004-06-29 12:00 papadopo * demo/formatrpsdb.c (1.2): add explicit prototype for BlastGetVersionNumber(), use enum value instead of explicit 0 2004-06-29 16:59 camacho * tools/readdb.h (6.148): Added last_oid_assigned to ReadDBSharedInfo structure 2004-06-30 08:28 madden * tools/: blast.h (6.68), blastpri.h (6.113): Removed some function prototypes and moved to blfmtutl.h 2004-06-30 08:29 madden * tools/blastdef.h (6.158): Removed typedef for BlastPruneSapStruct and some defines, moved to blfmtutl.h 2004-06-30 08:29 madden * tools/: blastool.c (6.270), blastutl.c (6.440): Moved some functions to blfmtutl.c 2004-06-30 08:31 madden * tools/: blfmtutl.c (1.1), blfmtutl.h (1.1): Structures and prototypes for blast formatting utilities 2004-06-30 08:32 madden * tools/xmlblast.c (6.35): Added include for blfmtutl.h, removed unused variable 2004-06-30 08:33 madden * demo/: blastall.c (6.144), megablast.c (6.115), blastpgp.c (6.124): Add include for blfmtutl.h 2004-06-30 08:51 madden * demo/megablast.c (6.116): Use enums (BlastArguments) for arguments, these are consistent with the ones used in blast_driver.c 2004-06-30 09:38 madden * tools/blfmtutl.h (1.2): Add prototypes for add_string_to_buffer and add_string_to_bufferEx 2004-06-30 09:42 kans * tools/: blastool.c (6.271), impatool.c (6.12), readdb.c (6.442): include to clear up Mac compiler missing prototype errors 2004-06-30 09:57 kans * tools/impatool.c (6.13): add_string_to_bufferEx had to be LIBCALL because of blfmtutl.h prototype 2004-06-30 10:14 madden * tools/impatool.c (6.14): Remove add_string_to_bufferEx, already defined in blfmtutl.c 2004-06-30 12:03 kans * demo/bl2seq.c (6.61): include 2004-06-30 15:52 camacho * demo/: formatdb.c (6.93), formatrpsdb.c (1.3), fastacmd.c (6.31): Added #include 2004-06-30 17:03 madden * demo/blastclust.c (6.44): Add include for blfmtutl.h 2004-07-06 09:40 madden * demo/blast_driver.c (1.51): Properly filter_slp for maskInfo in mask-at-hash case 2004-07-06 12:04 dondosha * demo/blast_driver.c (1.52): Multi-threaded search implemented and option added to use it 2004-07-06 12:40 dondosha * demo/blast_driver.c (1.53): Use EBlastProgramType for program 2004-07-06 18:29 dondosha * demo/blast_driver.c (1.54): Free seqalign in the end, since it is no longer done in BLAST_FormatResults 2004-07-07 11:41 dondosha * demo/blast_driver.c (1.55): Added printing of tabular output header for on-the-fly case 2004-07-07 13:45 dondosha * demo/blast_driver.c (1.56): Added options to show only gi or only accession in tabular output 2004-07-08 08:30 madden * demo/blast_driver.c (1.57): Parameters of BLAST_GetQuerySeqLoc changed 2004-07-08 11:50 dondosha * demo/megablast.c (6.117): Added comment that -Q option must be used together with -D2 2004-07-08 12:48 dondosha * demo/megablast.c (6.118): Emit a warning if unable to open file for masked query, and do not attempt to write to it then 2004-07-08 12:50 dondosha * demo/megablast.c (6.119): Tiny addition to previous check-in: added file name in warning message 2004-07-08 15:49 camacho * tools/: readdb.c (6.443), readdb.h (6.149): Contributions from ID1 Group: 1) SI_Record structure. 2) Refactoring of FDBAddSequence2 to allow addition of non-redundant sequences when creating BLAST databases. 2004-07-08 17:25 kans * tools/readdb.c (6.444): fixed Mac compiler error in FDBExtend4Sequence 2004-07-09 11:40 dondosha * tools/readdb.c (6.445): Fix in ReadDBOpenMHdrAndSeqFiles: increment nthreads if at least one of header or sequence files is already mapped 2004-07-09 13:09 camacho * tools/readdb.h (6.150): Updated documentation for last_oid_assigned 2004-07-09 16:18 madden * demo/megablast.c (6.120): Init mqfp to NULL to prevent crash if unused 2004-07-12 12:02 madden * demo/blast_driver.c (1.58): Change for BLAST_GetQuerySeqLoc, which now returns total number of letters read, -1 on error 2004-07-12 12:30 papadopo * demo/: formatrpsdb.c (1.4), copymat.c (6.38): LookupTable->BlastLookupTable 2004-07-13 09:54 camacho * tools/posit.c (6.67): Fix memory leak 2004-07-13 13:31 camacho * tools/readdb.c (6.446): Fix for genmask to count only non-redundant sequences added to the masked databases instead of all sequences. 2004-07-13 15:57 dondosha * tools/readdb.c (6.447): Tiny memory leak fix 2004-07-14 09:18 madden * demo/blast_driver.c (1.59): Change to BLAST_GetQuerySeqLoc call 2004-07-14 09:54 madden * demo/megablast.c (6.121): Optionally use new engine for searches 2004-07-14 14:35 camacho * tools/readdb.h (6.151): Added comments for readdb_get_header_ex 2004-07-14 14:35 camacho * tools/readdb.c (6.448): Remove unneeded error message in readdb_get_header_ex 2004-07-15 08:20 madden * demo/megablast.c (6.122): Remove or replace (with ErrPostEx) fprintf to stderr 2004-07-15 16:23 madden * demo/: blast_driver.c (1.60), megablast.c (6.123): Check status of BLAST_SearchEngine, ErrPostEx if status non-zero 2004-07-15 17:00 dondosha * tools/blastool.c (6.272): Print Accession.Version in megablast tabular output subject ids; print number of sequences in # Query comment if multiple queries 2004-07-19 11:01 dondosha * demo/blast_driver.c (1.61): Renamed multiseq_src to seqsrc_multiseq 2004-07-19 12:43 dondosha * demo/megablast.c (6.124): Renamed multiseq_src to seqsrc_multiseq 2004-07-19 13:05 papadopo * tools/blastutl.c (6.441): specify (unused) 'output-to-scoremat' parameter 2004-07-19 13:13 papadopo * tools/: posit.h (6.27), posit.c (6.68): add capability to perform input and output of residue frequencies in scoremat form; also call PSIMatrixFrequencyRatiosNew before restarting from checkpoint 2004-07-19 13:16 papadopo * demo/blastpgp.c (6.125): add capability to perform input and output of residue frequencies in scoremat form 2004-07-19 13:17 papadopo * demo/formatrpsdb.c (1.5): if an input scoremat only contains residue frequencies, perform impala-specific scaling and create a PSSM 2004-07-19 13:19 papadopo * demo/makemat.c (6.15): explicitly call PSIMatrixFrequencyRatiosNew before reading in any checkpoint files 2004-07-19 13:34 papadopo * tools/scoremat.asn (1.8): change weights and position frequencies to type REAL, remove their associated scaling factors 2004-07-19 14:16 madden * demo/megablast.c (6.125): Remove include for seqsrc_multiseq.h, not needed 2004-07-19 18:37 dondosha * tools/readdb.c (6.449): Added mutex lock/unlock around shared info manipulation in readdb_destruct_element 2004-07-21 14:45 papadopo * demo/blast_driver.c (1.62): 1. initialize num_threads before use 2. fix MSVC warnings 2004-07-22 11:18 jianye * tools/blfmtutl.c (1.2): correct blast paper url 2004-07-22 12:16 camacho * tools/readdb.c (6.450): Guard against arguments longer than PATH_MAX to FindBlastDBFile 2004-07-24 14:55 camacho * tools/blastutl.c (6.442): Fix to GetSequenceWithDenseSeg when sequence cannot be found 2004-07-24 14:56 camacho * tools/posit.c (6.69): Fix in posDemographics when GetSequenceWithDenseSeg cannot find sequence data 2004-07-26 14:32 madden * demo/megablast.c (6.126): Moved call to BLAST_FillScoringOptions before call to GetLambdaFast 2004-07-26 16:51 camacho * tools/readdb.c (6.451): Fix mismatched data type 2004-07-27 15:18 madden * demo/megablast.c (6.127): Allow use of BLAST DB with oidlist with new engine 2004-07-27 15:59 papadopo * tools/kappa.c (6.45): Changes by Michael Gertz to allow RedoAlignmentCore to be used for tblastn searches. The current version of the code uses two heuristics: 1) a heuristic that skips doing re-alignment for an HSP if the old alignment of the HSP is contained in a higher-scoring HSP that has already been re-aligned. 2) a heuristic that attempts to ensure that all alignments in the list of redone alignments has distinct ends. The original code also used these heuristics, but the code that implements the heuristics has been rewritten. As a result, RedoAlignmentCore will occasionally report better-scoring alignments. This is still a heuristic; which HSPs are reported still depends on the order in which they are re-aligned. 2004-07-27 16:20 madden * demo/megablast.c (6.128): Use -V to force use of old engine 2004-07-28 13:19 kans * tools/kappa.c (6.46): HeapSort callbacks are int LIBCALLBACK for compilation on the PC 2004-07-28 14:49 coulouri * demo/blastall.c (6.145): fix printf specifier 2004-07-28 20:05 coulouri * demo/blastall.c (6.146): fix blastcl3 umr 2004-07-29 10:15 papadopo * demo/formatrpsdb.c (1.6): remove (obsolete) call to MakeAllWordSequence 2004-07-30 10:46 madden * demo/megablast.c (6.129): Set greedy Boolean before calling BLAST_FillScoringOptions 2004-08-02 16:08 dondosha * demo/blastclust.c (6.45): Write and read header integers separately instead of as a structure; changed first number from 1 byte to 4, to prevent padding with garbage 2004-08-03 10:02 madden * demo/bl2seq.c (6.62): Introduce enum to make myargs more readable 2004-08-03 12:45 madden * demo/megablast.c (6.130): Remove redundant include 2004-08-03 17:51 papadopo * demo/blast_driver.c (1.63): add extra parameter to BLAST_ValidateOptions 2004-08-03 18:05 dondosha * demo/blast_driver.c (1.64): Added arguments to restrict query/subject to intervals; call AdjustOffSetsInSeqAlign to remap coordinates for subsequences 2004-08-04 10:32 dondosha * demo/megablast.c (6.131): Added new argument to BLAST_ValidateOptions call for new engine 2004-08-05 10:08 dondosha * demo/blast_driver.c (1.65): Set ag_blast argument to FALSE for protein search options initialization 2004-08-05 10:18 dondosha * demo/megablast.c (6.132): Set ag_blast argument for options initialization to FALSE for non-blastn searches 2004-08-05 13:29 camacho * tools/scoremat.asn (1.9): Changes to Score-matrix specification: 1. is_protein has a default value of TRUE 2. identifier becomes optional 3. unassigned and other members of freq-Ratios are removed. 2004-08-05 13:30 camacho * tools/posit.c (6.70): Remove initialization of identifier as it is no longer required 2004-08-05 15:33 madden * tools/readdb.c (6.452): Add ownership 38 and 52 to Refseq for proteins 2004-08-05 17:52 camacho * tools/blastutl.c (6.443): Gracefully handle inability to calculate ungapped lambda for PSSM in psiblast2sequences 2004-08-06 09:56 madden * tools/readdb.c (6.453): Add owner 45 to is_REFSEQ_PROTEIN 2004-08-06 13:55 madden * tools/readdb.c (6.454): Add new owners to is_REFSEQ_RNA 2004-08-09 09:08 madden * demo/bl2seq.c (6.63): Bl2seq now can run queries with new blast engine 2004-08-12 09:41 madden * demo/megablast.c (6.133): Enable use of mulitple threads for new engine 2004-08-12 11:59 madden * demo/megablast.c (6.134): Fix problem with relative database path for new engine, eliminate use of SeqSrc to get database name 2004-08-16 10:26 madden * demo/bl2seq.c (6.64): Fix bad frees for blastx filtering locations 2004-08-16 15:37 dondosha * tools/: blast.c (6.407), blastool.c (6.273), blastutl.c (6.444): Enabled uneven gap HSP linking for blastx 2004-08-17 09:40 madden * demo/megablast.c (6.135): Changes to support discontiguous megablast and perform ungapped search before a greedy gapped alignment 2004-08-17 13:22 madden * demo/blastall.c (6.147): Add BlastArguments enum for command-line arguments 2004-08-17 16:32 madden * demo/megablast.c (6.136): Enable ARG_QUERYLOC for new engine, add function Megablast_GetLoc to parse location 2004-08-23 13:03 papadopo * tools/: blastpri.h (6.114), blastutl.c (6.445): From Michael Gertz: make CopyResultHspToHSP public 2004-08-23 13:09 papadopo * tools/: posit.h (6.28), posit.c (6.71): From Michael Gertz: move static arrays out of header and into the one file that needs them 2004-08-23 13:12 papadopo * tools/kappa.c (6.47): From Michael Gertz: Backported some changes to getStartFreqRatios and computeScaledStandardMatrix from algo/blast/core/blast_kappa.c code. Also a few straightforward changes to getStartFreqRatios, because the code has diverged slightly 2004-08-23 15:37 papadopo * tools/kappa.c (6.48): From Michael Gertz: fix memory leak in getStartFreqRatios 2004-08-25 10:45 camacho * tools/readdb.h (6.152), tools/readdb.c (6.455), demo/formatdb.c (6.94): Refactorings to allow formatdb process multiple deflines 2004-08-25 10:47 camacho * demo/formatrpsdb.c (1.7): Removed duplicate code 2004-08-26 15:01 dondosha * tools/blastool.c (6.274): Retrieve Bioseq before attempting to calculate number of identities in alignment segments 2004-08-27 12:11 dondosha * tools/blast.c (6.408): Changes in new_link_hsps from Mike Gertz: adjust singleton sets e-values by gap decay divisor; use effective db length for sum e-value calculations 2004-08-31 13:04 dondosha * demo/blast_driver.c (1.66): Print sequences in tabular output with -B 2 option; believe query deflines if tabular output requested 2004-08-31 13:05 dondosha * demo/megablast.c (6.137): BlastSeqSrc is no longer used on seqalign creation and formatting stages 2004-08-31 13:07 dondosha * tools/blastool.c (6.275): For PRINT_SEQUENCES option in tabular output, always show query on forward strand; reverse complement subject is necessary 2004-09-08 12:08 dondosha * demo/blast_driver.c (1.67): Call new Blast_AdjustOffsetsInSeqAlign function to adjust offsets for subsequences results, instead of AdjustOffSetsInSeqAlign which deals with one sequence pair at a time 2004-09-09 09:47 papadopo * tools/kappa.c (6.49): from Michael Gertz: remove unnecessary check for the presence of Selenocysteine in translated sequences 2004-09-09 16:58 camacho * tools/readdb.c (6.456): Add sanity checks in readdb_read_alias_file 2004-09-13 11:15 madden * demo/: bl2seq.c (6.65), blast_driver.c (1.68): Changes for BlastSeqLoc and BlastMaskLoc 2004-09-13 11:16 madden * demo/megablast.c (6.138): Use BlastSeqLoc rather than ListNode 2004-09-13 14:33 dondosha * tools/mblast.c (6.205): Advance mask pointer in the list when one of the queries in a set is discarded due to being too short, and also has a lower case mask 2004-09-14 11:53 dondosha * demo/blast_driver.c (1.69): Check if lower case mask exists before translating its coordinates to protein scale 2004-09-15 13:40 papadopo * demo/copymat.c (6.39): change use of ListNode to use of BlastSeqLoc for lookup table creation 2004-09-15 14:06 papadopo * demo/formatrpsdb.c (1.8): 1. Verify that the scale factor is the same for all input scoremats 2. Do not use the scoremat 'identifier' field to determine the underlying score matrix; hardwire to BLOSUM62 temporarily 3. Use BlastSeqLoc's instead of ListNodes 2004-09-15 14:33 papadopo * tools/blast.c (6.409): From Michael Gertz: modify two-hit ungapped code to compute the correct end offset even if an extension to the right does not happen 2004-09-21 09:53 dondosha * demo/blast_driver.c (1.70): For RPS tblastn query is now translated at the API level 2004-09-21 09:58 dondosha * tools/blast.c (6.410): 1. Assign HSP contexts and subject frames before linking HSPs after reevaluation with ambiguities for ungapped blastn - necessary to distinguish HSPs from different strands; 2. Use ideal Karlin-Altschul parameters for RPS tblastn instead of those for a fake protein. 2004-09-21 09:59 dondosha * tools/rpsutil.c (6.71): Use query length in protein scale for search space calculation for RPS tblastn; do not multiply search space by extra 6 2004-09-21 10:45 camacho * tools/profiles.h (6.15): Add header inclusion guards and extern "C" {} 2004-09-21 12:28 dondosha * tools/blast.c (6.411): Make sure first change in previous revision is applied only to blastn 2004-09-21 17:42 dondosha * tools/readdb.c (6.457): Initialize BlastDefLine before call to FDBAddBioseq in FastaToBlastDB 2004-09-22 12:44 dondosha * tools/blast.c (6.412): Assign frames in ungapped blastn before any attempt to link HSPs, not only before second linking 2004-09-27 12:29 madden * tools/: readdb.h (6.153), readdb.c (6.458): Make title on SI_Record dynamically allocated 2004-09-28 11:28 papadopo * tools/blast.c (6.413): From Michael Gertz: 1. Undo previous fix to ungapped PSSM wordfinder (not necessary) 2. Modify square-matrix ungapped wordfinder to avoid occaisional incorrect choice of start offset for right extensions 3. Call BlastLinkHsps if and only if search->pbp->do_sum_stats is true; previously used the program number to decide 4. For ungapped blastx and tblastn, if longest_intron is not set (i.e. = 0) or (longest_intron - 2)/3 is nonpositive, call link_hsps. Otherwise call new_link_hsps. 5. For gapped blastx, tblastn or psitblastn, if longest_intron is not set (i.e. = 0), set it to 122. Then call new_link_hsps if (longest_intron - 2)/3 is positive. Otherwise turn off sum statistics. 6. In BlastLinkHsps, enabled the use of new_link_hsps for psitblastn. 7. Caused all routines for calculating the significance of multiple distinct alignments (BlastSmallGapSumE, BlastLargeGapSumE and BlastUnevenGapSumE) to use sum_{i in linked_set} (\lambda_i s_i - \ln K_i) as the weighted sum score. This change affects e-values in blastx and tblastx. 8. When computing normalized sum scores, use the ungapped values of (lambda, K) for ungapped alignments. 9. In SumHSPEvalue, for blastx, the subject_length must be divided by 3. 10. Pass the effective database size into BlastSmallGapSumE, BlastLargeGapSumE and BlastUnevenGapSumE. The routines use this value in a simplified formula to compute the e-value of singleton sets. 11. Sort HSPs in new_link_hsps by normalized score, rather than score; for blastx, this places HSPs in the correct order of significance. 2004-09-28 11:41 papadopo * tools/blast.c (6.414): Documentation of additional changes in 6.413: - In new_link_hsps, set xsum field of every HSP to the appropriate value for a singleton set before doing any linking. - In both link_hsps and new_link_hsps use normalized sum score, rather than raw sum score, everywhere when choosing linked sets - Delete code in new_link_hsps for finding splice junctions. - Delete some unused variables in link_hsps. 2004-09-28 11:52 papadopo * tools/blast.c (6.415): From Michael Gertz: 1. Undo previous fix to ungapped PSSM wordfinder (not necessary) 2. Modify square-matrix ungapped wordfinder to avoid occaisional incorrect choice of start offset for right extensions 3. Call BlastLinkHsps if and only if search->pbp->do_sum_stats is true; previously used the program number to decide 4. For ungapped blastx and tblastn, if longest_intron is not set (i.e. = 0) or (longest_intron - 2)/3 is nonpositive, call link_hsps. Otherwise call new_link_hsps. 5. For gapped blastx, tblastn or psitblastn, if longest_intron is not set (i.e. = 0), set it to 122. Then call new_link_hsps if (longest_intron - 2)/3 is positive. Otherwise turn off sum statistics. 6. In BlastLinkHsps, enabled the use of new_link_hsps for psitblastn. 7. Caused all routines for calculating the significance of multiple distinct alignments (BlastSmallGapSumE, BlastLargeGapSumE and BlastUnevenGapSumE) to use sum_{i in linked_set} (\lambda_i s_i - \ln K_i) as the weighted sum score. This change affects e-values in blastx and tblastx. 8. When computing normalized sum scores, use the ungapped values of (lambda, K) for ungapped alignments. 9. In SumHSPEvalue, for blastx, the subject_length must be divided by 3. 10. Pass the effective database size into BlastSmallGapSumE, BlastLargeGapSumE and BlastUnevenGapSumE. The routines use this value in a simplified formula to compute the e-value of singleton sets. 11. Sort HSPs in new_link_hsps by normalized score, rather than score; for blastx, this places HSPs in the correct order of significance. 12. In new_link_hsps, set xsum field of every HSP to the appropriate value for a singleton set before doing any linking. 13. In both link_hsps and new_link_hsps use normalized sum score, rather than raw sum score, everywhere when choosing linked sets 14. Delete code in new_link_hsps for finding splice junctions. 15. Delete some unused variables in link_hsps. 2004-09-28 11:59 papadopo * tools/blast.c (6.416): Items 1 and 2 of version 6.414 were mistakenly left out 2004-09-28 12:02 papadopo * tools/blastdef.h (6.159): From Michael Gertz: Changed the "sumscore" field of an HSP to "xsum" to represent a normalized sum score of linked HSPs; the normalized score is more appropriate/useful in doing linking. 2004-09-28 12:04 papadopo * tools/: blastkar.h (6.39), blastkar.c (6.102): From Michael Gertz: 1. Pass the effective database size into BlastSmallGapSumE, BlastLargeGapSumE and BlastUnevenGapSumE. The routines use this value in a simplified formula to compute the e-value of singleton sets. 2. Caused all routines for calculating the significance of multiple distinct alignments (BlastSmallGapSumE, BlastLargeGapSumE and BlastUnevenGapSumE) to use sum_{i in linked_set} (\lambda_i s_i - \ln K_i) as the weighted sum score, where (\lambda_i, K_i) are taken from the appropriate query context. 2004-09-28 12:05 papadopo * tools/blastutl.c (6.446): From Michael Gertz: In BlastGappedScoreInternal, changed a reference to the sumscore field of an HSP to a reference to the xsum field of an HSP. 2004-09-28 12:06 papadopo * demo/blastall.c (6.148): From Michael Gertz: 1. Disabled ungapped psitblastn. 2. The longest_intron parameter no longer has a minimum value of 4000. 3. Changed the command line help for the longest_intron parameter. 2004-09-29 16:12 papadopo * demo/blast_driver.c (1.71): Do not hardwire use of BLOSUM62 for RPS searches 2004-09-30 08:10 madden * tools/blast.c (6.417): Add function BlastReapHitlistByScore, use on gapped tblastn and blastx HSPs that do not acheive a high enough score for continued processing 2004-10-04 09:35 camacho * tools/impatool.c (6.15): Do not use hard coded constants in IMPALAfindUngappedLambda 2004-10-04 10:05 madden * demo/: bl2seq.c (6.66), megablast.c (6.139), blast_driver.c (1.72): Use Blast_PrintOutputFooter rather than BLAST_PrintSummaryReturns 2004-10-04 13:54 madden * tools/: blfmtutl.h (1.3), blfmtutl.c (1.3): BlastPrintVersionInfo[Ex] now takes const char* as arg for program 2004-10-04 14:00 madden * tools/readdb.c (6.459): Further fixes for SI_Record.title 2004-10-06 11:02 dondosha * demo/blast_driver.c (1.73): Get database name directly instead of using BlastSeqSrc; small memory leak fix; Pass subject Seq-loc to Blast_SummaryReturnFill for 2-sequences case 2004-10-06 11:02 dondosha * demo/megablast.c (6.140): Free BlastSeqSrc before creating Seq-align 2004-10-06 15:12 dondosha * demo/: blast_driver.c (1.74), megablast.c (6.141): Added #include for blast_tback.h 2004-10-07 09:07 madden * tools/blast.c (6.418): Cast int to FloatHi to prevent wrap-around 2004-10-12 10:05 camacho * tools/scoremat.asn (1.10): Reorganization and documentation of score matrix specification. 2004-10-12 11:06 papadopo * tools/: posit.h (6.29), posit.c (6.72): 1. Modify residue frequency IO to comply with new scoremat spec 2. Remove check that residue frequencies read from scoremat are <= 1.0 3. Pass gap open and gap extend penalties into BposComputation and CposComputation, so that scoremats can contain them 2004-10-12 11:12 papadopo * demo/formatrpsdb.c (1.9): 1. Modify scoremat IO to comply with new scoremat spec 2. Remove check that residue frequencies read from scoremat are <= 1.0 3. Add input argument to specify the underlying score matrix, or to use the score matrix specified in the scoremat if present 2004-10-12 11:14 papadopo * demo/blastpgp.c (6.126): add gap open and extend penalties to [BC]posComputation calls 2004-10-18 09:01 madden * tools/blast.c (6.419): Changes from Mike Gertz: - In xsum_compare_hsps change the comparison tests so that nil HSPs are less than any non-nil HSP. Previously, this function would return 0 if either HSP was nil, which would result in sort routines terminating before the non-nil HSPs in the list were fully sorted. - In rev_compare_hsps_cfj, reversed the order of the comparsion on query.frame to make the sort order consistent with the sort used in algo/blast/core/link_hsps.c. 2004-10-18 09:02 madden * tools/blastutl.c (6.447): Changes from Mike Gertz: - In score_compare_hsps, query_offset_compare_hsp and query_end_compare_hsp, change the comparison tests so that nil HSPs are less than any non-nil HSP. Previously, these comparison functions would return 0 if either HSP was nil, which would result in sort routines terminating before the non-nil HSPs in the list were fully sorted. - In score_compare_hsps, copied the set of tie-breakers from the corresponding routine in algo/blast/core/blast_hits.c. - In RealBlastGetGappedAlignmentTraceback, the HSP list must be sorted before BLASTCheckHSPInclusion is invoked. 2004-10-19 11:28 coulouri * tools/blfmtutl.c (1.4): bump version and date 2004-10-19 15:41 dondosha * tools/blast.h (6.69): Added hitlist_size argument to BlastPruneSeqAlignByGiList; Added new function BlastPruneSeqAlignBySortedGiList 2004-10-19 15:42 dondosha * tools/blastutl.c (6.448): Optimized algorithm in BlastPruneSeqAlignByGiList to make it up to 25 times faster; Added new function BlastPruneSeqAlignBySortedGiList 2004-10-20 15:58 dondosha * tools/xmlblast.c (6.36): Replace sequence data in Bioseq, as done in txalign.c, to assure proper masking and identities/positives calculation for all programs