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 2004-05-05 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