2004-01-05 10:43 Ilya Dondoshansky * core/blast_lookup.c (1.13): Removed unused conditional branch in BlastNaScanSubject 2004-01-05 10:44 Ilya Dondoshansky * core/blast_traceback.c (1.68): Removed unused call to GetTracebackEncoding in BLAST_TwoSequencesTraceback 2004-01-05 13:04 George Coulouris * core/blast_lookup.c (1.14): Fix fencepost error 2004-01-05 14:23 Ilya Dondoshansky * core/mb_lookup.c (1.26): Shift all query offsets by 1 for megablast lookup table, to make 0 offset impossible 2004-01-07 13:29 Ilya Dondoshansky * core/blast_lookup.c (1.15): Correction in offset range for BlastNaScanSubject 2004-01-07 16:16 Ilya Dondoshansky * core/blast_extend.c (1.46): Corrected call to left mini extension in BlastNaWordFinder 2004-01-07 16:17 Ilya Dondoshansky * core/: blast_filter.h (1.11), blast_filter.c (1.38): Added argument to CombineMaskLocations to allow linking locations with a very small gap between them 2004-01-07 16:44 Ilya Dondoshansky * core/blast_setup.c (1.65): Added a 0 argument to call to CombineMaskLocations 2004-01-13 11:20 Ilya Dondoshansky * core/blast_extend.c (1.47): Correction in left ungapped extension limit 2004-01-13 12:25 Ilya Dondoshansky * core/blast_gapalign.c (1.60): Correction in BLAST_DynProgNtGappedAlignment for extension to the right when subject offset = 0 2004-01-16 15:48 Ilya Dondoshansky * core/blast_gapalign.c (1.61): Shift starting offsets in BLAST_DynProgNtGappedAlignment to the right to the next full byte, to protect against immediate gap 2004-01-21 11:11 Ilya Dondoshansky * core/blast_hits.c (1.64): Added tie-breakers for HSP sorting 2004-01-21 13:08 Ilya Dondoshansky * core/blast_gapalign.c (1.62): Test for sentinel byte in SEMI_G_ALIGN_EX in all cases, not just position based 2004-01-22 10:30 Ilya Dondoshansky * core/blast_gapalign.c (1.63): Ending offsets in HSPs for protein alignments should be shifted by 1 2004-01-26 14:39 George Coulouris * core/: blast_lookup.c (1.16), blast_lookup.h (1.2): Use an offset rather than a pointer in LookupBackboneCell 2004-01-27 11:50 Ilya Dondoshansky * core/link_hsps.c (1.18): Set start_of_chain to FALSE for all HSPs at the beginning of link_hsps 2004-01-27 16:19 Ilya Dondoshansky * core/: blast_util.c (1.54), blast_util.h (1.35): Added GetPartialTranslation function for tblastn traceback against large subject sequences 2004-01-27 16:21 Ilya Dondoshansky * core/blast_traceback.c (1.69): Translate only parts of subject sequences if they are longer than some threshold 2004-01-27 21:57 Aaron Ucko * core/: blast_util.h (1.36), blast_util.c (1.55): Change GetPartialTranslation's return type from void to int per its body. 2004-01-28 17:07 Ilya Dondoshansky * core/blast_traceback.c (1.70): Do not allow partial translation for 2 sequences out-of-frame tblastn, since full mixed-frame sequence is already available 2004-01-30 18:50 Ilya Dondoshansky * api/seqsrc_readdb.c (1.16): If multiple volumes and range set, do not go to the next volume 2004-02-02 13:49 Ilya Dondoshansky * core/: blast_extend.c (1.48), blast_gapalign.c (1.64), blast_hits.c (1.65), blast_options.c (1.76), link_hsps.c (1.19), mb_lookup.c (1.27), phi_lookup.c (1.8): Fixes for minor compiler warnings 2004-02-02 13:53 Ilya Dondoshansky * core/blast_options.h (1.52): Removed unused argument in BLAST_FillHitSavingOptions; set PSI_SCALING_FACTOR default to 32, as it is in kappa.c 2004-02-02 14:03 Ilya Dondoshansky * core/blast_gapalign.c (1.65): Removed unused variable declarations 2004-02-03 11:17 Ilya Dondoshansky * core/blast_options.c (1.77): Require word size to be >= 12 with megablast lookup table 2004-02-03 13:33 Ilya Dondoshansky * core/blast_options.c (1.78): Correction to previous change: word size can be 11 if discontiguous words 2004-02-03 14:37 Ilya Dondoshansky * api/seqsrc_readdb.c (1.17): Removed unused variable 2004-02-03 14:54 Ilya Dondoshansky * api/seqsrc_readdb.c (1.18): Last ordinal id = number of sequences - 1 2004-02-03 15:20 Ilya Dondoshansky * core/blast_gapalign.c (1.66): If ungapped score of a new HSP is higher than gapped score of a previously extended HSP, do not discard it. 2004-02-03 16:09 Ilya Dondoshansky * core/blast_setup.c (1.66): Added message about query being completely filtered 2004-02-03 16:39 Ilya Dondoshansky * core/blast_traceback.c (1.71): Added comment and doxygen tag for cross reference about e-value calculation in BLAST_LinkHsps 2004-02-03 16:41 Ilya Dondoshansky * core/: blast_engine.c (1.98), blast_util.c (1.56): Minor correction for out-of-frame HSPs 2004-02-04 16:35 Ilya Dondoshansky * core/mb_lookup.h (1.10): Macro correction for 12/18 discontiguous template 2004-02-06 14:49 Ilya Dondoshansky * api/seqsrc_readdb.c (1.19): Fixed setting ranges in ReadDBFILE structures when first and final sequences are given 2004-02-06 17:49 Ilya Dondoshansky * core/blast_options.c (1.79): Check for NULL pointer in PSIBlastOptionsNew 2004-02-07 10:48 Aaron Ucko * core/blast_options.c (1.80): PSIBlastOptionsNew: rearrange slightly so that declarations come first. 2004-02-09 15:34 Ilya Dondoshansky * core/mb_lookup.c (1.28): Correction for ending offset in MB_LookupTableNew 2004-02-09 17:36 Ilya Dondoshansky * core/mb_lookup.c (1.29): Revert previous change, as error was in the unit tests setup 2004-02-10 09:16 Tom Madden * core/blast_dust.c (1.18): Changes from Richa Agarwala, will increase amount of sequence dusted 2004-02-10 14:54 Ilya Dondoshansky * core/blast_util.h (1.37): #define NUM_FRAMES and tweak some comments 2004-02-10 15:05 Ilya Dondoshansky * core/blast_setup.h (1.27): Made BlastScoreBlkGappedFill external again: needed in unit test 2004-02-10 16:11 George Coulouris * core/: aa_ungapped.h (1.12), blast_lookup.h (1.3), ncbi_std.h (1.24), aa_ungapped.c (1.24), blast_lookup.c (1.17): use NCBI_RESTRICT 2004-02-10 18:10 Aaron Ucko * core/ncbi_std.h (1.25): Always set NCBI_RESTRICT to __restrict on ICC, which otherwise manages to blow up. 2004-02-11 19:14 Ilya Dondoshansky * core/blast_engine.c (1.99): Added shift offset argument to TranslateHSPsToDNAPCoord 2004-02-11 19:16 Ilya Dondoshansky * core/blast_util.c (1.57): Use NUM_FRAMES macro; minor modification in BLAST_GetAllTranslations 2004-02-11 19:18 Ilya Dondoshansky * core/blast_gapalign.c (1.67): Adjust subject offsets for preliminary gapped alignment in case sequence is very long 2004-02-11 19:18 Ilya Dondoshansky * core/blast_traceback.c (1.72): Refactored the main traceback function, to make it more readable 2004-02-12 16:01 Ilya Dondoshansky * core/blast_gapalign.c (1.68): Fix type of variable in call to AdjustSubjectRange 2004-02-13 14:43 Christiam Camacho * core/: blast_def.h (1.30), blast_util.h (1.38): Consolidated preprocessor definitions to one header 2004-02-17 15:50 Ilya Dondoshansky * core/blast_options.h (1.53): Added preliminary hitlist size to BlastHitSavingOptions: it might be different from final hitlist size 2004-02-17 15:59 Ilya Dondoshansky * core/blast_engine.c (1.100): Added BlastPruneExtraHits function to delete extra hits if preliminary hit list size is larger than final hitlist size 2004-02-17 16:10 Ilya Dondoshansky * core/blast_engine.c (1.101): Reverted previous commit as it was an accident 2004-02-17 16:14 Ilya Dondoshansky * core/blast_traceback.c (1.73): Added BlastPruneExtraHits function to delete extra hits when preliminary hitlist size is larger than final hitlist size 2004-02-17 17:10 Ilya Dondoshansky * core/blast_options.c (1.81): Set preliminary hitlist size in options initialization 2004-02-17 18:47 Ilya Dondoshansky * core/blast_engine.h (1.26): Added query info argument to GetGappedScore prototype - needed to adjust coordinates if queries are concatenated 2004-02-17 18:47 Ilya Dondoshansky * core/blast_engine.c (1.102): Pass query info structure to gapped alignment, to allow for offset adjustment for concatenated queries 2004-02-17 18:48 Ilya Dondoshansky * core/blast_gapalign.h (1.29): Pass query info structure to all versions of GetGappedScore 2004-02-17 18:48 Ilya Dondoshansky * core/: blast_hits.h (1.19), blast_hits.c (1.66): Offsets in concatenated query are now adjusted inside gapped alignment functions 2004-02-17 18:49 Ilya Dondoshansky * core/blast_gapalign.c (1.69): 1. Added GetRelativeCoordinates to adjust offsets in initial HSP when queries are concatenated; 2. Corrected HSP inclusion and other comparisons in line with change that HSP coordinates are now relative; 3. No longer needed to check for sentinel bytes in SEMI_G_ALIGN_EX. 2004-02-17 18:51 Ilya Dondoshansky * core/greedy_align.c (1.14): No need to check for sentinel bytes any more 2004-02-18 10:17 Christiam Camacho * core/blast_util.h (1.39): 1. Consolidated ncbi2na mask definition, added comments. 2. Removed dead code. 2004-02-18 10:18 Christiam Camacho * core/: blast_dust.c (1.19), blast_util.c (1.58): Consolidated ncbi2na mask definition 2004-02-18 14:25 Christiam Camacho * core/: blast_util.h (1.40), blast_extend.c (1.49), blast_gapalign.c (1.70), greedy_align.c (1.15), phi_lookup.c (1.9): Rename READDB_UNPACK_BASE_N -> NCBI2NA_UNPACK_BASE 2004-02-18 14:37 Ilya Dondoshansky * api/: blast_format.c (1.37), blast_format.h (1.18): Do not use ReaddbNewArgs structure directly 2004-02-18 14:38 Ilya Dondoshansky * api/: seqsrc_readdb.c (1.20), seqsrc_readdb.h (1.9): Added function ReaddbBlastSeqSrcInit for standard initialization of the readdb-based sequence source 2004-02-18 15:36 Ilya Dondoshansky * core/: blast_gapalign.h (1.30), blast_hits.h (1.20), blast_traceback.h (1.16): BlastHSP, BlastHSPList and other related definitions moved from blast_gapalign.h to blast_hits.h 2004-02-18 15:36 Ilya Dondoshansky * core/blast_hits.c (1.67): Use a local macro instead of one from blast_gapalign.h 2004-02-19 08:35 Ilya Dondoshansky * core/blast_util.c (1.59): Integral variable size correction to eliminate Windows compiler warning 2004-02-19 08:39 Ilya Dondoshansky * core/blast_extend.c (1.50): Changed some integral variable sizes to eliminate some Windows compiler warnings 2004-02-19 16:14 Ilya Dondoshansky * core/blast_message.h (1.6): Added enum for error severities 2004-02-19 16:16 Ilya Dondoshansky * core/: blast_message.c (1.11), blast_options.c (1.82), blast_setup.c (1.67), blast_stat.c (1.46), phi_lookup.c (1.10): Use enum type for severity argument in Blast_MessageWrite 2004-02-20 11:40 Ilya Dondoshansky * api/seqsrc_readdb.c (1.21): Correction for sequence range; previous version did not work if # volumes > 2 2004-02-23 10:05 Christiam Camacho * core/blast_dust.c (1.20): Ran dos2unix on source file 2004-02-23 14:52 Tom Madden * core/mb_lookup.h (1.11): Use Int4 for pv_array_bts 2004-02-24 12:03 Jason Papadopoulos * core/: blast_gapalign.h (1.31), blast_gapalign.c (1.71): complete rewrite of low-level gapped alignment functions 2004-02-24 12:50 Ilya Dondoshansky * core/blast_def.h (1.31): Added maximal length of the queries in a set to BlastQueryInfo structure 2004-02-24 12:57 Ilya Dondoshansky * core/: blast_options.h (1.54), blast_options.c (1.83): Added function to combine all options validation functions for the C engine 2004-02-24 12:59 Ilya Dondoshansky * core/: blast_engine.h (1.27), blast_extend.h (1.16), blast_filter.h (1.12), blast_setup.h (1.28): Moved BLAST_CalcEffLengths from blast_engine.h; Added BLAST_GapAlignSetUp to set up only gapped alignment related structures 2004-02-24 13:02 Ilya Dondoshansky * core/blast_filter.h (1.13): Added argument to BlastSetUp_Filter to not do filtering for traceback search when masking is at hash only 2004-02-24 13:03 Ilya Dondoshansky * core/blast_engine.h (1.28): Moved BLAST_CalcEffLengths to blast_setup.h 2004-02-24 13:05 Ilya Dondoshansky * core/blast_extend.h (1.17): Changed first argument to BLAST_ExtendWordInit from BLAST_SequenceBlk to Uint4 query_length 2004-02-24 13:09 Ilya Dondoshansky * core/blast_engine.c (1.103): Moved effective lengths calculations to blast_setup.c; use new BLAST_GapAlignSetUp function 2004-02-24 13:10 Ilya Dondoshansky * core/blast_setup.c (1.68): Moved effective lengths calculation from blast_engine.c; added BLAST_GapAlignSetUp and BlastScoreBlkInit functions to refactor code; removed options validation from BLAST_MainSetUp - it should be done earlier 2004-02-24 13:11 Ilya Dondoshansky * core/blast_extend.c (1.51): Changed 1st argument to BLAST_ExtendWordInit from BLAST_SequenceBlk to Uint4 query_length 2004-02-24 13:12 Ilya Dondoshansky * core/blast_filter.c (1.39): Do not perform filtering if masking only at hash, and no lookup table required 2004-02-24 13:13 Ilya Dondoshansky * core/blast_gapalign.c (1.72): If output pointer is NULL on input to BLAST_GapAlignStructNew, return with normal status 2004-02-25 14:29 Ilya Dondoshansky * api/blast_seq.c (1.34): Set the maximal length of queries in BLAST_SetUpQueryInfo 2004-02-25 14:30 Ilya Dondoshansky * core/blast_gapalign.c (1.73): Return non-zero status from BLAST_GapAlignStructNew if memory allocation fails 2004-02-27 10:20 Jason Papadopoulos * core/blast_dust.c (1.21): correct rcsid 2004-02-27 10:56 Jason Papadopoulos * core/: blast_options.c (1.84), blast_traceback.c (1.74), blast_hits.c (1.68), blast_setup.c (1.69), link_hsps.c (1.20), blast_setup.h (1.29): Mike Gertz' modifications to unify handling of gapped Karlin blocks for protein and nucleotide searches. Also modified BLAST_MainSetUp to allocate gapped Karlin blocks last 2004-02-27 11:10 Jason Papadopoulos * core/: blast_gapalign.c (1.74), blast_traceback.c (1.75), blast_gapalign.h (1.32): Never preallocate memory for the low-level dynamic programming code to use 2004-02-27 17:23 Jason Papadopoulos * core/: aa_ungapped.c (1.25), aa_ungapped.h (1.13): 1. Remove unused code\n2. Add functionality to use PSSMs in ungapped extensions\n3. Modify the two-hit code to better match the original two-hit algorithm 2004-03-01 09:23 Tom Madden * core/blast_traceback.c (1.76): Moved parts of BlastHSPListGetTraceback to smaller (static) functions, made some variables in BlastHSPListGetTraceback const 2004-03-03 10:05 Jason Papadopoulos * core/blast_gapalign.c (1.75): correct several off-by-one errors 2004-03-04 16:07 Jason Papadopoulos * core/: blast_def.h (1.32), blast_engine.h (1.29), blast_gapalign.h (1.33), blast_hits.h (1.21), blast_lookup.h (1.4), blast_options.h (1.55), blast_stat.h (1.20), blast_traceback.h (1.17), aa_ungapped.c (1.26), blast_engine.c (1.104), blast_hits.c (1.69), blast_lookup.c (1.18), blast_options.c (1.85), blast_stat.c (1.47), blast_traceback.c (1.77), lookup_wrap.c (1.3), blast_gapalign.c (1.76): add RPS BLAST functionality 2004-03-04 17:38 Jason Papadopoulos * core/blast_options.h (1.56): specify a positive array size at the end of a structure to represent variable-size data 2004-03-04 18:32 Jason Papadopoulos * core/blast_engine.c (1.105): avoid directly modifying const input structures 2004-03-05 09:05 Christiam Camacho * core/blast_engine.c (1.106): Removed unused variable 2004-03-05 12:52 Jason Papadopoulos * core/: blast_engine.c (1.107), blast_hits.c (1.70), blast_setup.c (1.70), blast_stat.c (1.48), blast_traceback.c (1.78), blast_util.c (1.60), blast_def.h (1.33), blast_stat.h (1.21), blast_util.h (1.41): Allow 32-bit context numbers for queries 2004-03-08 11:39 Christiam Camacho * core/: aa_ungapped.c (1.27), blast_engine.c (1.108), blast_gapalign.c (1.77): Fix compiler warnings for MsDev 2004-03-09 13:36 Ilya Dondoshansky * core/blast_options.h (1.57): 1. Added effective lengths parameters - options will now be used only to override the real values; 2. Added calculation of cutoffs for linking of HSPs. 2004-03-09 13:37 Ilya Dondoshansky * core/blast_extend.h (1.18): Changed 2 length arguments to one in BLAST_ExtendWordInit 2004-03-09 13:38 Ilya Dondoshansky * core/blast_seqsrc.h (1.13): Added function wrapper to get average database sequence length 2004-03-09 13:39 Ilya Dondoshansky * core/blast_setup.h (1.30): Pass around effective lengths parameters instead of options; added BLAST_OneSubjectUpdateParameters to recalculate cutoffs and eff. lengths when each subject is an individual sequence 2004-03-09 13:40 Ilya Dondoshansky * core/blast_traceback.h (1.18): Added effective lengths parameters argument to BLAST_ComputeTraceback 2004-03-09 13:44 Ilya Dondoshansky * core/blast_engine.c (1.109): 1. Link HSPs and calculate e-values once per subject sequence instead of for each frame; 2. Use effective lengths parameters to calculate cutoffs; 3. Recalculate effective lengths and relevant cutoffs for each subject in a non-database search 2004-03-09 13:45 Ilya Dondoshansky * core/blast_extend.c (1.52): BLAST_ExtendWordInit now takes just one subject length argument instead of 2 to calculate average length 2004-03-09 13:46 Ilya Dondoshansky * core/blast_options.c (1.86): Corrected how cutoffs are calculated 2004-03-09 13:47 Ilya Dondoshansky * core/blast_seqsrc.c (1.16): Added function wrapper to get average subject length 2004-03-09 13:48 Ilya Dondoshansky * core/blast_setup.c (1.71): Corrected how cutoff scores are calculated 2004-03-09 13:49 Ilya Dondoshansky * core/blast_traceback.c (1.79): Use BLAST_OneSubjectUpdateParameters function to recalculate cutoffs and effective lengths for each subject in a non-database search 2004-03-09 13:51 Ilya Dondoshansky * core/link_hsps.c (1.21): Divide length adjustment for subject by 3 if it is translated 2004-03-09 15:46 Ilya Dondoshansky * core/: blast_traceback.c (1.80), blast_traceback.h (1.19): Removed const from extension parameters argument 2004-03-09 15:57 Ilya Dondoshansky * core/blast_extend.h (1.19): Removed unused macro definitions 2004-03-09 15:58 Ilya Dondoshansky * core/blast_gapalign.h (1.34): Added comments for some macros 2004-03-09 17:37 Ilya Dondoshansky * core/: aa_ungapped.h (1.14), blast_engine.h (1.30), blast_extend.h (1.20), blast_gapalign.h (1.35), blast_options.h (1.58), blast_setup.h (1.31), blast_traceback.h (1.20), link_hsps.h (1.7), phi_extend.h (1.2), aa_ungapped.c (1.28), blast_extend.c (1.53), blast_gapalign.c (1.78), blast_options.c (1.87), blast_setup.c (1.72), blast_traceback.c (1.81), link_hsps.c (1.22), phi_extend.c (1.4): Added const qualifiers to parameter arguments wherever relevant 2004-03-09 18:40 Ilya Dondoshansky * api/seqsrc_readdb.c (1.22): Added getter function for average sequence length 2004-03-09 18:43 Ilya Dondoshansky * core/blast_options.h (1.59): Removed unused single_hsp_score parameter 2004-03-10 12:31 Jason Papadopoulos * core/: blast_lookup.h (1.5), blast_options.h (1.60), blast_rps.h (1.1), lookup_wrap.h (1.2): 1. Make a separate lookup table type for RPS blast 2. Move structures describing RPS blast input information to a separate file 2004-03-10 12:33 Jason Papadopoulos * core/: aa_ungapped.c (1.29), blast_engine.c (1.110), blast_lookup.c (1.19), blast_options.c (1.88), lookup_wrap.c (1.4): Make a separate lookup table type for RPS blast 2004-03-10 13:00 Christiam Camacho * core/: blast_setup.c (1.73), blast_stat.c (1.49), blast_setup.h (1.32), blast_stat.h (1.22): Remove outdated references to blastkar 2004-03-10 13:45 Christiam Camacho * core/blast_options.h (1.61): Remove dead code 2004-03-11 10:36 Jason Papadopoulos * core/blast_rps.h (1.2): better document structures; also standardize amount of space given for score matrix string 2004-03-11 13:31 Jason Papadopoulos * core/: aa_ungapped.h (1.15), blast_engine.h (1.31), blast_gapalign.h (1.36), blast_hits.h (1.22), blast_lookup.h (1.6), blast_setup.h (1.33), blast_stat.h (1.23), blast_traceback.h (1.21), lookup_wrap.h (1.3), phi_lookup.h (1.3), blast_engine.c (1.111), blast_gapalign.c (1.79), blast_hits.c (1.71), blast_lookup.c (1.20), blast_setup.c (1.74), blast_traceback.c (1.82), blast_util.c (1.61), mb_lookup.c (1.30): fix doxygen warnings 2004-03-11 13:52 Christiam Camacho * core/: blast_def.h (1.34), blast_engine.c (1.112), blast_hits.c (1.72), blast_stat.c (1.50): Remove THREADS_IMPLEMENTED 2004-03-11 15:41 Christiam Camacho * core/: blast_def.h (1.35), blast_hits.h (1.23), blast_options.h (1.62), blast_engine.c (1.113), blast_hits.c (1.73), blast_options.c (1.89), blast_setup.c (1.75): Remove dead code 2004-03-11 16:28 Christiam Camacho * core/blast_traceback.h (1.22): Remove misleading comment 2004-03-11 18:57 Ilya Dondoshansky * core/blast_gapalign.c (1.80): Minor compiler warning fix: changed integral type of several variables 2004-03-11 18:58 Ilya Dondoshansky * core/blast_options.c (1.90): Set cutoff_score to 0 before calling BLAST_Cutoffs, so it knows what to calculate 2004-03-12 09:12 Christiam Camacho * core/lnfact.h (1.2): Move definition of lnfact to blast_seg.c 2004-03-12 09:12 Christiam Camacho * core/blast_seg.c (1.20): Move lnfact.c from header file to blast_seg.c 2004-03-12 10:18 George Coulouris * api/: blast_seq.h (1.10), blast_seqalign.h (1.13): add missing prototypes 2004-03-12 10:19 George Coulouris * core/blast_stat.h (1.24): add missing prototype 2004-03-12 10:45 Jason Papadopoulos * api/: blast_format.c (1.38), blast_seqalign.c (1.28): remove unused variables 2004-03-12 10:57 Christiam Camacho * core/: blast_extend.h (1.21), blast_engine.c (1.114), blast_extend.c (1.54): Make consistent use of New/Free functions for BLAST_ExtendWord structure 2004-03-12 11:33 Christiam Camacho * core/: blast_engine.c (1.115), blast_extend.c (1.55), blast_extend.h (1.22): Rename BLAST_ExtendWord functions to avoid collisions with C toolkit libraries 2004-03-12 11:59 Christiam Camacho * core/blast_gapalign.h (1.37): Use doxygen comments 2004-03-12 11:59 Christiam Camacho * core/blast_seqsrc.h (1.14): Minor documentation change 2004-03-12 18:08 Ilya Dondoshansky * core/: blast_extend.c (1.56), blast_gapalign.c (1.81), blast_hits.c (1.74): Minor compiler warning fix 2004-03-12 18:31 Ilya Dondoshansky * api/blast_seq.c (1.35): In BLAST_GetSequence, for subjects look only at the first SeqLoc 2004-03-12 19:18 Ilya Dondoshansky * core/blast_def.h (1.36): Added booleans for each BLAST_SequenceBlk field to keep track whether it is allocated 2004-03-12 19:19 Ilya Dondoshansky * core/: blast_util.h (1.42), blast_util.c (1.62): Added BlastSequenceBlkCopy function to copy sequence block without ownership of data 2004-03-12 19:20 Ilya Dondoshansky * core/: blast_seqsrc.h (1.15), blast_seqsrc.c (1.17): Added getters for SeqLoc, error message, returning ListNode 2004-03-12 19:21 Ilya Dondoshansky * api/seqsrc_readdb.c (1.23): Added empty getters for SeqLoc, error message, in accordance with blast_seqsrc.h prototypes 2004-03-12 19:25 Ilya Dondoshansky * api/: multiseq_src.c (1.1), multiseq_src.h (1.1): C implementation of BlastSeqSrc for a set of sequences 2004-03-15 10:03 Christiam Camacho * core/ncbi_std.h (1.26): Added #define for snprintf 2004-03-15 12:17 Ilya Dondoshansky * api/multiseq_src.c (1.2): Fixed improper C variable declaration errors 2004-03-15 14:53 Ilya Dondoshansky * core/: blast_engine.h (1.32), blast_traceback.h (1.23), blast_traceback.c (1.83): Merged TwoSequences and Database engines 2004-03-15 14:54 Ilya Dondoshansky * core/blast_engine.c (1.116): 1. Merged TwoSequences and Database engines; 2. Always use sequence source to get subject data. 2004-03-15 14:54 Ilya Dondoshansky * core/blast_setup.c (1.76): Always use sequence source to get subject data 2004-03-15 14:54 Ilya Dondoshansky * core/blast_setup.h (1.34): Removed unneeded arguments in BLAST_GapAlignSetUp 2004-03-15 19:10 Ilya Dondoshansky * core/blast_seqsrc.h (1.16): Corrected comment for GetGenDataFnPtr typedef 2004-03-16 09:43 Ilya Dondoshansky * core/blast_traceback.c (1.84): Added doxygen comments for 2 parameters in BlastHSPListGetTraceback 2004-03-16 12:18 Ilya Dondoshansky * core/blast_extend.c (1.57): Some code refactoring, eliminating duplication 2004-03-16 13:55 Christiam Camacho * core/blast_setup.h (1.35): Moved log to end of file 2004-03-16 17:18 Ilya Dondoshansky * core/blast_gapalign.c (1.82): Fixed setting of length1 and length2 fields in edit blocks after greedy alignment 2004-03-17 10:19 Christiam Camacho * core/blast_options.c (1.91): Add missing casts 2004-03-17 11:17 Ilya Dondoshansky * core/blast_extend.c (1.58): Added an explicit cast to get rid of Windows compiler warning 2004-03-17 14:00 Ilya Dondoshansky * core/blast_rps.h (1.3): Made orig_score_matrix dynamically allocated 2004-03-17 14:14 Ilya Dondoshansky * core/blast_options.h (1.63): Added macros for variable word size boolean default values 2004-03-17 16:02 Ilya Dondoshansky * core/blast_options.h (1.64): Added BLAST_WINDOW_SIZE_DISC, equal to 40, to make two-hit extension default for discontiguous megablast 2004-03-19 10:42 Jason Papadopoulos * core/lookup_wrap.c (1.5): fix incorrect cast when calculating offset array size in RPS blast 2004-03-19 11:11 Jason Papadopoulos * core/blast_traceback.c (1.85): avoid use of uninitialized variable 2004-03-22 11:16 Christiam Camacho * core/blast_util.h (1.43): Add use of \deprecated doxygen tag 2004-03-22 15:11 Ilya Dondoshansky * core/blast_options.c (1.92): Do not allow small gaps cutoff to be less than gap trigger 2004-03-22 15:11 Ilya Dondoshansky * core/: blast_hits.h (1.24), blast_hits.c (1.75), blast_engine.c (1.117): Refactored merging of HSP lists into 2 independent functions 2004-03-22 16:44 Jason Papadopoulos * core/blast_traceback.c (1.86): correction for size computation during RPS traceback stage 2004-03-23 09:15 Christiam Camacho * core/blast_hits.h (1.25): Minor doxygen fix 2004-03-23 13:55 Ilya Dondoshansky * core/: blast_hits.h (1.26), link_hsps.h (1.8): Moved everything used for linking only to a structure local to link_hsps.c 2004-03-23 13:55 Ilya Dondoshansky * core/link_hsps.c (1.23): Use local wrapper structure around BlastHSP to keep track of linking information that is not needed outside 2004-03-23 13:55 Ilya Dondoshansky * core/: blast_gapalign.c (1.83), blast_traceback.c (1.87): Use special new field to keep pattern length information in BlastHSP structure 2004-03-24 13:02 Jason Papadopoulos * api/: twoseq_api.c (1.1), twoseq_api.h (1.1): Allow C applications to use the rewritten BLAST engine for two-sequence searches 2004-03-24 13:49 Jonathan Kans * api/twoseq_api.c (1.2): needed to include blast_seq.h 2004-03-24 14:07 Ilya Dondoshansky * core/link_hsps.h (1.9): Moved ordering method types to .c file 2004-03-24 14:08 Ilya Dondoshansky * core/blast_hits.h (1.27): Moved ordering method from BlastHSP to LinkHSPStruct; added splice_junction field to BlastHSP structure instead 2004-03-24 14:09 Ilya Dondoshansky * core/: blast_extend.h (1.23), blast_extend.c (1.59): Renamed BLAST_InitHitListDestruct to BLAST_InitHitListFree; added BlastInitHitListReset to free ungapped data substructures and reset count to 0 2004-03-24 14:11 Ilya Dondoshansky * core/link_hsps.c (1.24): Ordering method moved from BlastHSP structure to LinkHSPStruct; splice_junction is now a separate field in BlastHSP structure 2004-03-24 14:11 Ilya Dondoshansky * core/: blast_engine.c (1.118), blast_gapalign.c (1.84), blast_hits.c (1.76), blast_util.c (1.63): Fixed memory leaks 2004-03-24 14:14 Jason Papadopoulos * api/: twoseq_api.c (1.3), twoseq_api.h (1.2): remove new-engine-specific headers from API header, minor cleanups 2004-03-24 17:00 Ilya Dondoshansky * api/blast_seqalign.c (1.29): ordering_method field removed from BlastHSP structure; splice_junction added 2004-03-24 17:15 Ilya Dondoshansky * api/seqsrc_readdb.c (1.24): Fixed memory leak 2004-03-25 11:21 Christiam Camacho * api/: blast_seq.c (1.36), multiseq_src.c (1.3), seqsrc_readdb.c (1.25): Fix compiler warnings 2004-03-25 18:35 Jason Papadopoulos * api/blast_format.c (1.39): add LIBCALL to extern function declaration 2004-03-26 14:13 Ilya Dondoshansky * core/: blast_hits.h (1.28), blast_engine.c (1.119), blast_hits.c (1.77): Changed BlastScoringOptions* argument to boolean gapped_calculation in BLAST_GetNonSumStatsEvalue 2004-03-26 14:16 Ilya Dondoshansky * core/blast_traceback.c (1.88): Removed unused argument new_hspcnt in HSPCheckForDegenerateAlignments; minor cleanup and fix at the end of BlastHSPListGetTraceback 2004-03-26 14:17 Ilya Dondoshansky * core/link_hsps.c (1.25): Calculate individual HSP evalues before call to new_link_hsps - they are needed for comparison with sum e-values 2004-03-26 14:19 Ilya Dondoshansky * api/: multiseq_src.c (1.4), seqsrc_readdb.c (1.26): Minor correction in assigning sequence pointer in returned sequence block 2004-03-26 15:45 Ilya Dondoshansky * core/blast_def.h (1.37), core/blast_options.h (1.65), core/blast_gapalign.c (1.85), core/blast_options.c (1.93), api/blast_format.c (1.40): Made gap_trigger parameter an integer, as in the old code 2004-03-26 17:35 Ilya Dondoshansky * core/blast_hits.c (1.78): Purge new HSP list in MergeHSPLists before adding it to combined list if some of its HSPs are deleted while merging 2004-03-29 15:57 Ilya Dondoshansky * core/greedy_align.c (1.16): In BLAST_GreedyAlign: allocate space for traceback if it has not been allocated yet 2004-03-30 10:15 Ilya Dondoshansky * core/: blast_gapalign.h (1.38), blast_gapalign.c (1.86): Made AdjustSubjectRange public as it is needed for traceback too 2004-03-30 10:15 Ilya Dondoshansky * core/blast_traceback.c (1.89): Use function AdjustSubjectRange to reduce range of subject in traceback when possible 2004-03-30 10:49 Tom Madden * core/blast_setup.h (1.36): Add prototype for BlastSetup_GetScoreBlock 2004-03-30 10:51 Tom Madden * core/blast_filter.h (1.14): Add prototype for BlastSetUp_GetFilteringLocations, BlastSetUp_MaskQuery, BlastMaskLocNew, remove no_lookup Boolean from BlastSetUp_Filter 2004-03-30 10:51 Tom Madden * core/blast_filter.c (1.40): Added BlastSetUp_GetFilteringLocations, BlastSetUp_MaskQuery, BlastMaskLocNew, remove no_lookup Boolean from BlastSetUp_Filter 2004-03-30 10:52 Tom Madden * core/blast_setup.c (1.77): Refactored BLAST_MainSetUp 2004-03-31 11:16 Ilya Dondoshansky * core/blast_hits.c (1.79): Minor: use contexts instead of frames to check if HSPs are from different queries in MergeHSPLists 2004-03-31 12:50 Jason Papadopoulos * core/: blast_setup.c (1.78), blast_stat.c (1.51), blast_stat.h (1.25): Mike Gertz' changes for length adjustment calculations 2004-04-01 09:14 Anton Lavrentiev * core/: blast_stat.c (1.52), phi_lookup.c (1.11): Spell "occurred", "occurrence", and "occurring" 2004-04-01 11:44 Ilya Dondoshansky * core/blast_hits.c (1.80): Minor fix in CombineHSPListsByScore 2004-04-01 18:10 Ilya Dondoshansky * core/blast_hits.c (1.81): Corrections in MergeHSPLists 2004-04-02 10:40 Ilya Dondoshansky * core/blast_hits.h (1.29): BlastHSPGetNumIdentical and BlastOOFGetNumIdentical become public 2004-04-02 10:41 Ilya Dondoshansky * core/: blast_hits.c (1.82), blast_traceback.c (1.90): BlastHSPGetNumIdentical and BlastOOFGetNumIdentical become public in blast_hits.[ch] 2004-04-02 11:00 Ilya Dondoshansky * core/blast_hits.h (1.30): Renamed ...GetNuIdentical to ...GetNumIdentities, to avoid collision with old C toolkit 2004-04-02 11:00 Ilya Dondoshansky * core/: blast_hits.c (1.83), blast_traceback.c (1.91): Renamed ...GetNumIdentical to ...GetNumIdentities, to avoid collision with old C toolkit 2004-04-02 13:31 Ilya Dondoshansky * core/blast_gapalign.h (1.39): Made BlastGetStartForGappedAlignment public after a minor renaming 2004-04-02 13:32 Ilya Dondoshansky * core/: blast_gapalign.c (1.87), blast_traceback.c (1.92): Removed duplicity in implementation of BlastGetStartForGappedAlignment; renamed and made public 2004-04-05 12:09 Christiam Camacho * core/blast_def.h (1.38), core/blast_dust.c (1.22), core/blast_filter.c (1.41), core/blast_filter.h (1.15), core/blast_gapalign.c (1.88), core/blast_lookup.c (1.21), core/blast_seg.c (1.21), core/mb_lookup.c (1.31), core/phi_lookup.c (1.12), api/blast_seq.c (1.37): Rename DoubleInt -> SSeqRange 2004-04-05 14:53 Tom Madden * core/blast_stat.c (1.53): Set dimensions if matrix from memory 2004-04-05 16:22 Tom Madden * core/blast_stat.h (1.26): Remove obsolete fields 2004-04-05 16:25 Ilya Dondoshansky * core/blast_hits.c (1.84): Correction in flagging HSPs for deletion during sorting for megablast; makes results independent of the order of comparison 2004-04-06 12:34 Jason Papadopoulos * core/: blast_lookup.c (1.22), blast_lookup.h (1.7): Allow for individual protein sequences to update an already-existing lookup table, by adding a bias to offsets added to that table. Only used for RPS blast DB creation at the moment 2004-04-06 16:42 Ilya Dondoshansky * core/blast_seqsrc.h (1.17): Added another type to BlastSeqSrcDataType enum 2004-04-06 23:06 Christiam Camacho * core/blast_def.h (1.39), core/blast_dust.h (1.9), core/blast_stat.h (1.27), core/blast_dust.c (1.23), core/blast_lookup.c (1.23), core/blast_options.c (1.94), core/blast_setup.c (1.79), core/blast_stat.c (1.54), core/blast_util.c (1.64), api/blast_seq.c (1.38): Added blast_encoding.[hc], refactoring blast_stat.[hc] 2004-04-06 23:10 Christiam Camacho * core/: blast_encoding.h (1.1), blast_encoding.c (1.1): Initial revision 2004-04-07 15:05 Christiam Camacho * core/blast_encoding.h (1.2): Minor fix in #ifdef guards 2004-04-07 15:11 Christiam Camacho * core/: blast_psi_priv.c (1.1), blast_psi_priv.h (1.1): Initial revision 2004-04-07 17:43 Christiam Camacho * core/blast_psi_priv.h (1.2): Removed unneeded #include directive 2004-04-07 18:08 Jonathan Kans * core/blast_psi_priv.c (1.2): needed to include blast_def.h for sfree prototype 2004-04-08 09:53 Jason Papadopoulos * core/blast_stat.c (1.55): fix doxygen warning 2004-04-09 09:41 George Coulouris * core/ncbi_std.h (1.27): correctly define NCBI_INLINE on hpux 2004-04-09 10:11 Jason Papadopoulos * core/blast_hits.h (1.31): add doxygen comment for RPSUpdateResults 2004-04-09 10:23 Jason Papadopoulos * core/blast_rps.h (1.4): add doxygen comments 2004-04-09 10:48 Christiam Camacho * core/blast_encoding.h (1.3): Added doxygen comments 2004-04-09 10:49 Jason Papadopoulos * core/blast_traceback.h (1.24): add doxygen comments for BLAST_RPSTraceback 2004-04-09 18:17 Jason Papadopoulos * core/blast_hits.h (1.32): corrected comment block 2004-04-12 14:56 Tom Madden * core/blast_stat.h (1.28): Rename BLAST_ResFreq to Blast_ResFreq, add prototypes for Blast_ResFreqNew, Blast_ResFreqDestruct, and Blast_ResFreqStdComp 2004-04-12 14:57 Tom Madden * core/blast_stat.c (1.56): Rename BLAST_ResFreq to Blast_ResFreq, make Blast_ResFreqNew, Blast_ResFreqDestruct, and Blast_ResFreqStdComp non-static 2004-04-16 10:12 Jason Papadopoulos * core/blast_def.h (1.40): remove psitblastn, add rpsblast and rpstblastn defines 2004-04-16 10:13 Jason Papadopoulos * core/blast_engine.c (1.120): remove psitblastn, add rpsblast and rpstblastn defines, add translated RPS code 2004-04-16 10:15 Jason Papadopoulos * core/blast_gapalign.c (1.89): restore PSSM pointer for all code paths GetGappedScore, add use of RPS-specific defines instead of booleans 2004-04-16 10:15 Jason Papadopoulos * core/blast_hits.c (1.85): add use of RPS-specific defines instead of booleans 2004-04-16 10:17 Jason Papadopoulos * core/blast_options.c (1.95): add use of RPS-specific defines, remove RPS argument to FillLookupTableOptions 2004-04-16 10:17 Jason Papadopoulos * core/blast_options.h (1.66): remove RPS argument to FillLookupTableOptions 2004-04-16 10:18 Jason Papadopoulos * core/blast_setup.c (1.80): add statistical corrections for translated RPS blast 2004-04-16 10:20 Jason Papadopoulos * core/blast_traceback.c (1.93): make RPS PSSM correction specific to non-translated RPS blast, add use of RPS program defines 2004-04-16 10:21 Jason Papadopoulos * core/blast_util.c (1.65): add RPS program defines, remove psitblastn program 2004-04-16 10:22 Jason Papadopoulos * core/link_hsps.c (1.26): remove use of psitblastn define 2004-04-16 10:42 Jason Papadopoulos * api/blast_format.c (1.41): 1. Make query_is_na and db_is_na into input arguments, rather than computing them from scratch 2. remove check for type blastn when deciding on Karlin block to use (Mike Gertz' changes make this unnecessary) 2004-04-16 10:43 Jason Papadopoulos * api/blast_format.h (1.19): Make query_is_na and db_is_na into input arguments 2004-04-16 10:44 Jason Papadopoulos * api/blast_seq.c (1.39): add use of RPS-specific program defines 2004-04-16 10:44 Jason Papadopoulos * api/blast_seqalign.c (1.30): add use of RPS-specific program defines, remove check for blastn when pointing to Karlin blocks 2004-04-16 10:45 Jason Papadopoulos * api/twoseq_api.c (1.4): remove unneeded RPS argument to FillLookupTableOptions 2004-04-16 10:56 Jason Papadopoulos * core/blast_gapalign.h (1.40): remove unneeded RPS blast Boolean 2004-04-19 08:58 Tom Madden * core/: blast_stat.c (1.57), blast_hits.c (1.86), blast_options.c (1.96), blast_setup.c (1.81), blast_traceback.c (1.94), link_hsps.c (1.27), blast_stat.h (1.29): Changed BLAST_KarlinBlk to Blast_KarlinBlk to avoid conflict with blastkar.h structure, renamed some functions to start with Blast_Karlin, made Blast_KarlinBlkDestruct public 2004-04-19 11:03 Jason Papadopoulos * api/: blast_format.c (1.42), blast_seqalign.c (1.31): rename BLAST_KarlinBlk to Blast_KarlinBlk 2004-04-19 11:07 Christiam Camacho * core/matrix_freq_ratios.h (1.1): Moved from old posit.h 2004-04-19 14:34 Tom Madden * core/blast_util.c (1.66): Make genetic_code arg to BLAST_GetAllTranslations and BLAST_GetTranslationTable const 2004-04-19 14:36 Tom Madden * core/blast_util.h (1.44): Make genetic_code a const on a few functions 2004-04-21 10:32 Christiam Camacho * core/blast_engine.c (1.121): Removed dead code 2004-04-21 11:31 Aaron Ucko * core/blast_engine.c (1.122): Don't try to include blast_psi.h, since it doesn't exist and the code compiles properly without it. 2004-04-21 13:00 Tom Madden * core/blast_options.c (1.97): Removed set but not read variable 2004-04-21 13:19 Viatcheslav Gorelenkov * core/blast_util.h (1.45): Added export prefix to declaration of BlastProgram2Number , Added include of . 2004-04-21 13:29 Tom Madden * core/: blast_hits.h (1.33), blast_hits.c (1.87): Cleaned up API for saving HSPs, HSPLists and HitLists 2004-04-21 13:30 Tom Madden * core/: blast_engine.c (1.123), blast_gapalign.c (1.90): Use cleaned up API for saving HSPs, HSPLists, HitLists 2004-04-21 13:32 Tom Madden * core/blast_traceback.c (1.95): Use cleaned up API for saving HSPs, HSPLists, HitLists, use a const Uint1* instead of dboptions in BlastHSPListGetTraceback 2004-04-21 13:42 Tom Madden * core/blast_setup.c (1.82): Removed redundant line 2004-04-21 14:00 Viatcheslav Gorelenkov * core/blast_util.h (1.46): Removed include of 'mswin_export.h'. Added include of ''blast_export.h . 2004-04-21 14:03 Tom Madden * core/blast_hits.c (1.88): Put declaration first in function 2004-04-21 14:04 Tom Madden * core/blast_hits.c (1.89): Last fix did not handle case of allocation failure 2004-04-21 14:34 Viatcheslav Gorelenkov * core/blast_util.h (1.47): Added conditionally include of 'blast_export.h' and define NCBI_XBLAST_EXPORT. 2004-04-21 15:37 Tom Madden * core/blast_hits.c (1.90): Implementation for Blast_HSPNew 2004-04-22 11:29 Christiam Camacho * core/blast_hits.h (1.34): Expanded comment for RPSUpdateResults 2004-04-22 18:15 Ilya Dondoshansky * api/: blast_format.c (1.43), blast_format.h (1.20): Use old C toolkit function to determine alignment type for call to txalign; removed unneeded arguments to BLAST_FormatResults 2004-04-22 18:18 Ilya Dondoshansky * core/blast_options.c (1.98): Set lookup table type correctly in BLAST_FillLookupTableOptions - needed for C driver only 2004-04-22 18:37 Ilya Dondoshansky * api/blast_format.c (1.44): Use LIBCALL in forward extern declaration 2004-04-22 18:40 Ilya Dondoshansky * core/link_hsps.c (1.28): 1. Split away code finding splice junctions from the new_link_hsps function; 2. Skip finding splice junctions if uncompressed sequence is not available. 2004-04-23 09:20 Tom Madden * core/blast_stat.h (1.30): Change: BLAST_KARLIN_K_SUMLIMIT_DEFAULT from 0.01 to 0.00001 2004-04-23 09:21 Tom Madden * core/blast_stat.c (1.58): Rewrote BlastKarlinLHtoK to do the following and more: 1. fix a bug whereby the wrong formula was used when high score == 1 and low score == -1; 2. fix a methodological error of truncating the first sum and trying to make it converge quickly by adding terms of a geometric progression, even though the geometric progression estimate is not correct in all cases; the old adjustment code is left in for historical purposes but #ifdef'd out 3. Eliminate the Boolean bi_modal_score variable. The old test that set the value of bi_modal_score would frequently fail to choose the correct value due to rounding error. 4. changed numerous local variable names to make them more meaningful; 5. added substantial comments to explain what the procedure is doing and what each variable represents 2004-04-23 09:49 Tom Madden * core/blast_stat.c (1.59): Cleaned up ifndef in BlastKarlinLHtoK 2004-04-23 10:02 Jason Papadopoulos * core/blast_options.c (1.99): ignore validation of LookupTableOptions if performing an RPS search 2004-04-23 15:06 Christiam Camacho * core/blast_stat.c (1.60): Do NOT use lowercase names for #defines 2004-04-23 16:55 Ilya Dondoshansky * core/blast_gapalign.c (1.91): Added tie-breaking conditions in score_compare_match 2004-04-27 11:56 George Coulouris * core/: blast_extend.c (1.60), blast_inline.h (1.1), blast_lookup.c (1.24), mb_lookup.c (1.32): refactor inlines 2004-04-28 10:38 Tom Madden * core/blast_stat.h (1.31): Changes from Mike Gertz: - Added a function prototype for BLAST_GapDecayDivisor - Removed the function prototypes for BLAST_GapDecay and BLAST_GapDecayInverse - Modified function prototypes for BLAST_SmallGapSumE, BLAST_LargeGapSumE and BLAST_UnevenGapSumE 2004-04-28 10:38 Tom Madden * core/blast_filter.h (1.16): Added prototype for Blast_MaskTheResidues 2004-04-28 10:39 Tom Madden * core/blast_filter.c (1.42): Renamed MaskTheResidues to Blast_MaskTheResidues, made it non-static and cleaned up parameter names 2004-04-28 10:40 Tom Madden * core/blast_stat.c (1.61): Changes from Mike Gertz: - I created the new routine BLAST_GapDecayDivisor that computes a divisor used to weight the evalue of a collection of distinct alignments. - I removed BLAST_GapDecay and BLAST_GapDecayInverse which had become redundant. - I modified the BLAST_Cutoffs routine so that it uses the value returned by BLAST_GapDecayDivisor to weight evalues. - I modified BLAST_SmallGapSumE, BLAST_LargeGapSumE and BLAST_UnevenGapSumE no longer refer to the gap_prob parameter. Replaced the gap_decay_rate parameter of each of these routines with a weight_divisor parameter. Added documentation. 2004-04-28 10:41 Tom Madden * core/link_hsps.c (1.29): Changes from Mike Gertz - modified the link_hsps routine to apply the gap_prob parameter to the result of BLAST_SmallGapSumE and BLAST_LargeGapSumE. - further modified link_hsps to use BLAST_GapDecayDivisor to weight tests based on multiple collections of HSPs. - removed all reference to gap_prob from the new_link_hsps. - further modified new_link_hsps to use BLAST_GapDecayDivisor to weight tests based on multiple collections of HSPs. 2004-04-28 12:06 Jason Papadopoulos * api/blast_format.c (1.45): revert RPS program names to their conventional counterparts before formatting 2004-04-28 15:29 Jonathan Kans * api/blast_format.c (1.46): in MBXmlInit, moved all variables to top of function before first statement - works in C++ but not in C 2004-04-28 15:36 Ilya Dondoshansky * core/: blast_seqsrc.h (1.18), blast_seqsrc.c (1.18), blast_traceback.c (1.96): Added BLASTSeqSrcRetSequence function, needed for work with CSeqDB 2004-04-28 15:39 Ilya Dondoshansky * api/seqsrc_readdb.c (1.27): Added implementation of BLASTSeqSrcRetSequence function 2004-04-28 15:50 Ilya Dondoshansky * api/multiseq_src.c (1.5): Added implementation of BLASTSeqSrcRetSequence 2004-04-29 11:08 Tom Madden * core/blast_options.c (1.100): Add BlastScoringOptionsDup 2004-04-29 11:09 Tom Madden * core/: blast_filter.c (1.43), blast_filter.h (1.17): Made (input) filter_string const for a few functions 2004-04-29 11:09 Tom Madden * core/blast_options.h (1.67): Add BlastScoringOptionsDup prototype 2004-04-29 11:15 Ilya Dondoshansky * core/: blast_hits.h (1.35), blast_engine.c (1.124), blast_hits.c (1.91): Moved reevaluation with ambiguities out of the BLAST_SaveHitlist 2004-04-29 12:07 Ilya Dondoshansky * core/: blast_hits.h (1.36), blast_hits.c (1.92): Made ReevaluateHSPListWithAmbiguities public 2004-04-29 13:41 Jason Papadopoulos * core/blast_options.c (1.101), api/blast_format.c (1.47): Scale down the search space when calculating the S2 cutoff score for a translated RPS search 2004-04-29 15:53 Jason Papadopoulos * core/blast_setup.c (1.83): use ideal ungapped Karlin parameters for translated RPS blast, instead of trying to use the query 2004-04-29 15:58 Christiam Camacho * core/: blast_stat.c (1.62), blast_traceback.c (1.97): Use generic matrix allocator/deallocator from blast_psi_priv.h 2004-04-29 16:32 Jason Papadopoulos * core/blast_stat.c (1.63): remove RPS_SCORE_MIN, since it turned out to be a workaround for a bug that has since been fixed 2004-04-30 08:58 Christiam Camacho * core/: blast_stat.c (1.64), blast_stat.h (1.32): Replace RPSKarlinLambdaNR by Blast_KarlinLambdaNR 2004-04-30 10:37 Jason Papadopoulos * core/blast_traceback.c (1.98): Add test for NULL PSSM 2004-04-30 10:39 Jason Papadopoulos * core/blast_stat.c (1.65): 1. Remove unneeded #defines 2. use BLAST_SCORE_RANGE_MAX during RPS PSSM creation instead of (possibly incompatible) RPS_SCORE_MAX 3. return NULL instead of FALSE on an error 2004-04-30 10:40 Jason Papadopoulos * core/blast_stat.h (1.33): change BLAST_SCORE_1MAX to 10000 2004-04-30 12:51 Ilya Dondoshansky * core/: blast_hits.h (1.37), blast_engine.c (1.125), blast_hits.c (1.93), blast_traceback.c (1.99), link_hsps.c (1.30): Changed a number of function names to have the same conventional Blast_ prefix 2004-04-30 14:09 Ilya Dondoshansky * api/twoseq_api.c (1.5): Changed prefix in some function calls from BLAST_ to Blast_ 2004-01-05 15:44 George Coulouris * debruijn.c (1.3): Fix fencepost error, improve argument handling 2004-01-07 09:40 Jason Papadopoulos * blast_driver.c (1.16): initialize all fields of readdb struct 2004-01-12 14:47 Jonathan Kans * tbl2asn.c (6.77): decline to instantiate protein titles if feature indexes were dropped, raised version number 2004-01-26 14:40 George Coulouris * copymat.c (6.29): * Correct buffer overrun * Use offset rather than pointer in LookupBackboneCell 2004-01-27 15:47 Ilya Dondoshansky * megablast.c (6.111): Set no_traceback option to 2 for -D4, 1 for -D0, 0 for others 2004-01-28 12:40 Jonathan Kans * tbl2asn.c (6.78): added ReplaceOneRNA - processing of .rna file somehow disappeared from source code in cvs 2004-01-28 13:22 Jonathan Kans * tbl2asn.c (6.79): do not set RNA editing exception if different, require entry in feature table 2004-01-29 09:56 Christiam Camacho * formatdb.c (6.92): Removed -A option, FORMATDB_VER_TEXT no longer supported 2004-01-30 15:34 George Coulouris * copymat.c (6.30): fix minor nit to FileWrite call 2004-02-02 13:54 Ilya Dondoshansky * blast_driver.c (1.17): Removed unused argument in BLAST_FillHitSavingOptions 2004-02-06 00:32 Christiam Camacho * rpsblast.c (6.53): Properly close ASN.1 stream 2004-02-06 17:50 Ilya Dondoshansky * blast_driver.c (1.18): Do not initialize PSI BLAST options if it is not PSI BLAST 2004-02-09 16:24 Aaron Ucko * debruijn.c (1.4): Fix another fencepost error -- the previous revision seems to have overshot. 2004-02-09 18:14 Christiam Camacho * rpsblast.c (6.54): Fix to prevent printing multiple Seq-annots in ASN.1 output 2004-02-10 13:49 George Coulouris * blastall.c (6.137): do not allow 1-hit blastn searches 2004-02-12 16:34 Jason Papadopoulos * blast_driver.c (1.19): (Re) initialize all fields of readdb struct 2004-02-18 10:18 Ilya Dondoshansky * blastclust.c (6.40): Minor fix when freeing title strings 2004-02-18 14:40 Ilya Dondoshansky * blast_driver.c (1.20): Use ReaddbBlastSeqSrcInit function 2004-02-18 15:42 Ilya Dondoshansky * blastclust.c (6.41): Cleaned up how id strings are retrieved for output 2004-02-20 11:40 Ilya Dondoshansky * blast_driver.c (1.21): Added oid range argument 2004-02-24 10:18 Ilya Dondoshansky * blastclust.c (6.42): Fixed several memory leaks for nucleotide clustering 2004-02-24 13:26 Ilya Dondoshansky * blast_driver.c (1.22): Call BLAST_ValidateOptions before doing the set up 2004-02-24 13:40 Ilya Dondoshansky * blast_driver.c (1.23): Removed unneeded lookup options argument from call to BLAST_MainSetUp 2004-02-26 11:25 Christiam Camacho * bl2seq.c (6.60): Fix uninitialized variable errors that caused core dumps on empty input files 2004-02-26 13:27 Jonathan Kans * testcgi.c (6.31): add comment for how to build on Linus 2004-02-27 09:22 George Coulouris * blastall.c (6.138): Correct typo 2004-02-27 16:48 Jonathan Kans * testcgi.c (6.32): paths to tRNAscan-SE and seg are in current directory (same as CGI) 2004-03-04 16:16 Jason Papadopoulos * copymat.c (6.31): add (unused) RPS blast parameter to FillLookupTable call 2004-03-04 16:16 Jason Papadopoulos * blast_driver.c (1.24): add RPS BLAST functionality 2004-03-04 18:03 Jason Papadopoulos * blast_driver.c (1.25): add some casts to avoid Sun cc compile errors 2004-03-05 14:57 Jason Papadopoulos * blast_driver.c (1.26): Do not attempt to print database information if there is no database (i.e. for a two-sequences search) 2004-03-08 10:37 Jason Papadopoulos * blast_driver.c (1.27): remove use of global variables 2004-03-08 11:18 Jonathan Kans * tbl2asn.c (6.80): added -u GenProdSet to NucProtSet post-submission conversion, taken from Sequin 2004-03-10 12:48 Jason Papadopoulos * blast_driver.c (1.28): change handling of RPS arguments in FillLookupTableOptions and LookupTableWrapInit 2004-03-10 15:21 Jason Papadopoulos * copymat.c (6.32): add (unused) RPS blast parameters to FillLookupTableOptions 2004-03-10 17:22 Jonathan Kans * tbl2asn.c (6.81): if Seq-submit was read, get Submit-block, add back on top of Seq-entry 2004-03-15 15:03 Ilya Dondoshansky * blast_driver.c (1.29): Use sequence source for non-database subjects 2004-03-17 11:00 Jason Papadopoulos * blast_driver.c (1.30): look through the standard search path for RPS data files 2004-03-17 11:17 Jason Papadopoulos * blast_driver.c (1.31): correction to previous checkin 2004-03-17 14:03 Ilya Dondoshansky * blast_driver.c (1.32): orig_score_matrix in RPSInfo is now dynamically allocated 2004-03-18 10:14 George Coulouris * blastall.c (6.139): do not dereference null seqalignptr 2004-03-18 12:56 Jonathan Kans * asn2fsa.c (1.1): initial checkin, chimp2fa -> genome2fa -> asn2fsa, replacement for asn2fast uses SeqPortStream 2004-03-22 10:56 Jonathan Kans * tbl2asn.c (6.82): CopyGene checks for gene xref first, -w flag along with -s allows type of bioseq set to be specified 2004-03-24 17:55 Ilya Dondoshansky * megablast.c (6.112): Ignore -m option when on-the-fly tabular output is returned 2004-03-25 16:17 Jonathan Kans * asn2fsa.c (1.2): added -l lock in advance parameter 2004-03-25 16:20 Ken Katz * spideymain.c (6.10): All SPI_is_acceptor_* functions have been corrected: 'N' no longer contributes to nor subtracts from the score, log odds are calculated and the scores added; they are however all antilogged because there are too many places in the code where the score is expected to be between 0 and 1. Also, corrected sequence frequency determination in SPI_is_acceptor_user and SPI_is_donor_user, as well as correcting for 'N'. Finally, and this all began with, I added matrices for Dictyostelium - command line -r -m 2004-03-25 17:12 Ilya Dondoshansky * blast_driver.c (1.33): 1. Added blast_seq.h include; 2. Changed strtok_r to strtok, to allow compilation on Windows; 3. Added longest intron argument. 2004-03-25 18:52 Jason Papadopoulos * blast_driver.c (1.34): add missing header files 2004-03-26 16:42 George Coulouris * blastall.c (6.140): remove unused variables 2004-03-31 12:59 Ilya Dondoshansky * blastpgp.c (6.119): Fix for XML output for multiple queries: append full XML outputs in one file 2004-04-01 08:43 Anton Lavrentiev * entrezcf.c (6.3), seedtop.c (6.9): Spell "occurred", "occurrence", and "occurring" 2004-04-02 12:28 Jonathan Kans * asn2fsa.c (1.3): added -e line length argument 2004-04-02 12:35 Jonathan Kans * asn2fsa.c (1.4): locking also done if single record read 2004-04-05 11:35 Jonathan Kans * tbl2asn.c (6.83): -h copies SEQID_GENERAL on mrna->product to mrna->comment 2004-04-06 08:15 Christiam Camacho * copymat.c (6.33): Rename DoubleInt -> SSeqRange 2004-04-07 17:48 Christiam Camacho * copymat.c (6.34): Add missing header file 2004-04-08 18:13 Jonathan Kans * asn2fsa.c (1.5): added -h argument to CacheFarComponents 2004-04-12 18:01 Jonathan Kans * asn2fsa.c (1.6): CacheFarComponents only saves FASTA for Bioseqs that are raw or constructed 2004-04-13 13:27 Jonathan Kans * asn2fsa.c (1.7): cache raw and constructed, near segmented, and delta literal 2004-04-16 10:48 Jason Papadopoulos * copymat.c (6.35): remove unneeded argument to FillLookupTableOptions 2004-04-16 10:50 Jason Papadopoulos * blast_driver.c (1.35): add use of RPS-specific programs, remove -B option 2004-04-19 08:28 Jonathan Kans * asn2fsa.c (1.8), asn2gb.c (6.57): if gzcat cannot be found, look for zcat 2004-04-19 11:09 Jonathan Kans * flint.c (1.1): initial checkin of program that reads catenated FASTA and reformats with desired number of bases per line 2004-04-19 13:58 Jonathan Kans * flint.c (1.2): rewritten to allow piping 2004-04-20 10:55 Alexander Morgulis * blastall.c (6.141): 1. Fixed query offsets in results when -B option is used. 2. Fixes for lower case masking handling with -B option. 2004-04-20 14:38 Jonathan Kans * flint.c (1.3): only copy sequence if IS_ALPHA, added -b block length argument to use spaces to separate blocks within lines 2004-04-20 17:04 Jonathan Kans * flint.c (1.4): added -g group length argument 2004-04-21 10:43 Jonathan Kans * asn2fsa.c (1.9): pass defaults to new blocklen, grouplen, and do_defline parameters in BioseqFastaStream and SeqEntryFastaStream 2004-04-22 18:16 Ilya Dondoshansky * blast_driver.c (1.36): Removed unneeded arguments to BLAST_FormatResults 2004-04-23 10:00 Jason Papadopoulos * blast_driver.c (1.37): fill in gap init and extend penalties from RPS data if performing a RPS search 2004-04-23 10:26 Jonathan Kans * asn2gb.c (6.58): post runtime to terminal at end 2004-04-23 15:34 Jonathan Kans * tbl2asn.c (6.84): CopyGene needed to SeqLocFree temp->location 2004-04-23 17:11 Jason Papadopoulos * copymat.c (6.36): force the thick backbone (dumped to the RPS .loo file) to contain the number of cells assumed by RPS blast 2004-04-26 10:44 Jonathan Kans * asn2gb.c (6.59): -f q makes INSDSet nucleotide alternative to -f x GBSet 2004-04-26 12:49 Jonathan Kans * asn2gb.c (6.60): PRODUCE_OLD_GBSEQ replaces PRODUCE_INSDSEQ, so default is now INSD 2004-04-26 12:50 Jonathan Kans * gbseqget.c (6.12): need to pass PRODUCE_OLD_GBSEQ because INSDSeq replacement for GBSeq is now default 2004-04-26 12:51 Jonathan Kans * gbseqget.c (6.13): corrected name passed to getargs 2004-04-26 12:53 Jonathan Kans * insdseqget.c (1.1): initial checkin - uses new collaboration-approved specification 2004-04-28 12:05 Jason Papadopoulos * blast_driver.c (1.38): do not revert RPS program names before formatting (leave that to the formatting code) 2004-04-28 16:54 Colleen Bollin * tbl2asn.c (6.85): Replaced old alignment reader with new alignment reader, added optional arguments to specify beginning, middle, end, missing, and match characters and protein alignments. 2004-04-29 15:56 Ilya Dondoshansky * blastall.c (6.142), blastpgp.c (6.120), megablast.c (6.113): Mask filtered locations in query sequence lines in XML output 2004-04-30 08:53 George Coulouris * .BLAST_VERSION (1.2): bump version to 2.2.9 2004-04-30 11:33 Ilya Dondoshansky * rpsblast.c (6.55): Added argument in call to BXMLPrintOutput 2004-04-30 13:03 Ilya Dondoshansky * blast_driver.c (1.39): Changed prefix of some functions from BLAST_ to conventional Blast_ 2004-04-30 15:21 Jonathan Kans * asn2fsa.c (1.10): threaded prefetching - initial checkin 2004-04-30 15:41 Jonathan Kans * asn2fsa.c (1.11), asn2gb.c (6.61): call ErrSetLogfile to prevent error.log from being created by default if multi-threaded prefetching used 2004-01-05 17:09 Tom Madden * blastdef.h (6.153): Put back dashes in date 2004-01-06 12:48 Ilya Dondoshansky * kappa.c (6.36): Do not free Karlin block in RedoAlignmentCore, because its pointer is passed outside 2004-01-06 17:36 Ilya Dondoshansky * blastpri.h (6.110): Added BLAST_HSPFree function that frees the edit block and the HSP 2004-01-06 17:37 Ilya Dondoshansky * blast.c (6.397), mblast.c (6.195): Use BLAST_HSPfree function 2004-01-06 17:37 Ilya Dondoshansky * blastutl.c (6.423): Use BLAST_HSPfree function; in particular fixes a bug with wrong memory being freed 2004-01-09 13:13 Ilya Dondoshansky * blastutl.c (6.424): In [Get,Check]StartForGappedAlignment: if posMatrix not available, use square matrix for calculations 2004-01-12 18:06 Christiam Camacho * readdb.c (6.425): Sort link bit gi lists 2004-01-13 10:46 Ilya Dondoshansky * mblast.c (6.196): Changed cast to nearest integer in length adjustment calculation 2004-01-14 12:01 Ilya Dondoshansky * blastutl.c (6.425): Gapped alignment is position based only if posMatrix exists 2004-01-16 18:43 Ilya Dondoshansky * blastpri.h (6.111), blastutl.c (6.426), mblast.h (6.49), mblast.c (6.197): No more need for special argument for partial search: it is set in options 2004-01-23 16:13 Christiam Camacho * readdb.c (6.426): 1. Refactored code to create multiple volumes. 2. Set the maximum sequence file size to 1GB. 2004-01-23 17:29 Ilya Dondoshansky * mblast.c (6.198): Increase hitlist size for preliminary alignment if traceback is delayed 2004-01-25 00:06 Ilya Dondoshansky * blastutl.c (6.427): Translate only relevant parts of long subject sequences for tblastn traceback 2004-01-26 08:52 Christiam Camacho * readdb.c (6.427): Do not use snprintf 2004-01-27 15:31 Tom Madden * kappa.c (6.37): remove extra setting of kbp_gap 2004-01-27 15:46 Ilya Dondoshansky * blastdef.h (6.154), mblast.c (6.199): Allow values 0, 1, 2 for no_traceback megablast option 2004-01-28 11:54 Ilya Dondoshansky * blastutl.c (6.428): Restored the code that shifts subject coordinates for blastn traceback with long subject sequences 2004-01-28 14:34 Christiam Camacho * readdb.c (6.428): Added sanity check for alias files 2004-01-29 15:48 George Coulouris * readdb.c (6.429): Only limit volume sizes on 32-bit platforms 2004-01-30 11:54 Ilya Dondoshansky * blastutl.c (6.429): Check if HSP needs to be deleted after reevaluation with ambiguities, after greedy traceback 2004-02-02 17:53 Christiam Camacho * readdb.c (6.430): Use new database format as default in API 2004-02-03 12:54 Ilya Dondoshansky * blast.c (6.398): Correction to revision 6.391 in function BlastGetDbChunk 2004-02-03 18:45 Ilya Dondoshansky * readdb.c (6.431), blastutl.c (6.430), readdb.h (6.144): Added readdb_get_sequence_length_ex with extra argument to calculate length exactly; readdb_get_sequence_length now calculates approximate length 2004-02-04 10:35 Christiam Camacho * blastdef.h (6.155), blastutl.c (6.431), readdb.c (6.432), readdb.h (6.145): Rollback to fix problems in release 2.2.7 2004-02-04 16:54 Ilya Dondoshansky * lookup.h (6.34): Macro correction for 12/18 discontiguous template 2004-02-06 14:25 Christiam Camacho * kappa.c (6.38): Alejandro Schaffer's corrections to RedoAlignmentCore pointed out by Mike Gertz: 1. Corrected the rule for assigning newSW->isfirstAlignment 2. Changed upper bound on assignment to forbiddenRanges 3. Assigned a value to newScore earlier 4. Eliminated use of skipThis 5. Restored value of search->gapAlign at the end 2004-02-09 15:53 Christiam Camacho * readdb.c (6.433): Add FDBAddPig call from FDBAddSequence2 2004-02-11 15:51 Colleen Bollin * actutils.c (6.36): use error log instead of popup message to indicate that BLAST found no sequence similarity 2004-02-23 10:42 Christiam Camacho * scoremat.asn (1.7): 1. Gave default value to Score-matrix::byrow field 2. Updated documentation 2004-02-24 09:06 Christiam Camacho * readdb.c (6.434), readdb.h (6.146): Added support for approximate sequence length calculation for nucleotide sequences. 2004-02-24 09:07 Christiam Camacho * blast.c (6.399), mblast.c (6.200): Use approximate sequence length calculation for entrez-limited nucleotide blast databases. 2004-02-24 09:07 Christiam Camacho * blastool.c (6.259): BlastAdjustDbNumbers is DEPRECATED 2004-02-24 11:32 Christiam Camacho * readdb.c (6.435): Use correct calling convention for win32 2004-02-26 10:52 Jason Papadopoulos * blast.c (6.400), blastconcat.c (1.6), blastool.c (6.260), blastutl.c (6.432), mblast.c (6.201): Mike Gertz' modifications to unify handling of gapped Karlin blocks between protein and nucleotide searches 2004-03-03 08:39 Jonathan Kans * salptool.c (6.32): changed defaulf to default 2004-03-11 09:11 Colleen Bollin * salptool.c (6.33): in CCNormalizeSeqAlignId, unlock bioseqs that have been locked to avoid the ObjMgrDelete: deleting locked object error message on closing the record. 2004-03-11 10:01 Colleen Bollin * salptool.c (6.34): Make sure unneeded bioseqs from farpointer alignments are deleted 2004-03-15 13:45 George Coulouris * readdb.c (6.436): Throw fatal error if BSRebuildDNA_4na() fails 2004-03-17 15:33 Colleen Bollin * dotseq.c (6.13): In DOT_InitMainInfobyLoc, exit function and return NULL if unable to determine ID or Bioseq from SeqLoc provided. This change averts a core dump. 2004-03-18 10:09 Jason Papadopoulos * rpsutil.c (6.69): use the score as a tiebreaker during final sort of seqaligns in RPS blast 2004-03-22 10:24 Ilya Dondoshansky * blastool.c (6.261): Do not set gapped-search-specific options for tblastx 2004-03-22 10:35 Ilya Dondoshansky * blast.c (6.401): 1. Do not allow cutoff score for saving HSPs to be smaller than gap trigger; 2. When merging hitlists with a restriction on number of HSPs, keep best scoring ones. 2004-03-22 17:04 Ilya Dondoshansky * blastool.c (6.262): Do not reassign kbp_gap pointers for megablast traceback, as they are already set due to recent changes 2004-03-22 17:10 Ilya Dondoshansky * blastutl.c (6.433): Use kbp_gap instead of kbp pointers in megablast traceback 2004-03-25 16:20 Ken Katz * spidey.c (6.68), spidey.h (6.19): All SPI_is_acceptor_* functions have been corrected: 'N' no longer contributes to nor subtracts from the score, log odds are calculated and the scores added; they are however all antilogged because there are too many places in the code where the score is expected to be between 0 and 1. Also, corrected sequence frequency determination in SPI_is_acceptor_user and SPI_is_donor_user, as well as correcting for 'N'. Finally, and this all began with, I added matrices for Dictyostelium - command line -r -m 2004-03-29 00:17 Christiam Camacho * readdb.c (6.437): Fix to Int4ListConcat 2004-03-31 12:58 Ilya Dondoshansky * xmlblast.c (6.32), xmlblast.h (6.13): Added PSIXmlReset function to allow keeping the AsnIoPtr between outputs for multiple queries in blastpgp 2004-03-31 12:58 Jason Papadopoulos * blast.c (6.402), blastkar.c (6.96), blastkar.h (6.35), blastpri.h (6.112), mblast.c (6.202): Mike Gertz' changes for length adjustment calculations 2004-03-31 13:12 Jason Papadopoulos * kappa.c (6.39): Mike Gertz' refactoring of RedoAlignmentCore 2004-03-31 13:39 Jonathan Kans * blastkar.h (6.36): fixed typo in BlastBlastComputeLengthAdjustment 2004-04-01 08:43 Anton Lavrentiev * blastkar.c (6.97), pattern1.c (6.18), pseed3.c (6.42), readdb.c (6.438), seed.h (6.19), tfuns.c (6.12): Spell "occurred", "occurrence", and "occurring" 2004-04-09 12:05 Ken Katz * spidey.c (6.69): Added sanity check (must be 3 intervals to go through the loop) to SPI_CheckMrnaOrder() 2004-04-13 13:22 Christiam Camacho * readdb.c (6.439): Optimization to Int4ListReadFromFile 2004-04-13 17:02 Tom Madden * blastdef.h (6.156): Add ignore_gilist Boolean to Options for use in formatting 2004-04-13 17:03 Tom Madden * blast.c (6.403): Use ignore_gilist Boolean to determine whether gilist lookup should occur 2004-04-16 14:14 Christiam Camacho * readdb.h (6.147): Made division field in DI_Record larger 2004-04-20 10:55 Alexander Morgulis * blast.c (6.404), blastconcat.c (1.7), blastconcat.h (1.2), blastconcatdef.h (1.3): 1. Fixed query offsets in results when -B option is used. 2. Fixes for lower case masking handling with -B option. 2004-04-21 09:54 Christiam Camacho * blastconcat.c (1.8): Remove unused variable 2004-04-21 12:54 Christiam Camacho * readdb.c (6.440): Added removal for PIG files 2004-04-21 15:25 George Coulouris * blastconcat.c (1.9): do not cast lvalues 2004-04-22 12:40 Ilya Dondoshansky * blastutl.c (6.434): Set search->subject_id to correct ordinal id, needed for finding splice junctions in HSP links at traceback stage 2004-04-23 09:19 Tom Madden * blastkar.c (6.98): Rewrote BlastKarlinLHtoK to do the following and more: 1. fix a bug whereby the wrong formula was used when high score == 1 and low score == -1; 2. fix a methodological error of truncating the first sum and trying to make it converge quickly by adding terms of a geometric progression, even though the geometric progression estimate is not correct in all cases; the old adjustment code is left in for historical purposes but #ifdef'd out 3. Eliminate the Boolean bi_modal_score variable. The old test that set the value of bi_modal_score would frequently fail to choose the correct value due to rounding error. 4. changed numerous local variable names to make them more meaningful; 5. added substantial comments to explain what the procedure is doing and what each variable represents 2004-04-23 09:20 Tom Madden * blastkar.h (6.37): Change: BLAST_KARLIN_K_SUMLIMIT_DEFAULT from 0.01 to 0.00001 2004-04-23 09:49 Tom Madden * blastkar.c (6.99): Cleaned up ifndef in BlastKarlinLHtoK 2004-04-28 10:36 Tom Madden * blastkar.c (6.100): Changes from Mike Gertz: - I created the new routine BlastGapDecayDivisor that computes a divisor used to weight the evalue of a collection of distinct alignments. - I removed BlastGapDecay and BlastGapDecayInverse which had become redundant. - I modified the BlastCutoffs routine so that it uses the value returned by BlastGapDecayDivisor to weight evalues. - I modified BlastSmallGapSumE, BlastLargeGapSumE and BlastUnevenGapSumE no longer refer to the gap_prob parameter. Replaced the gap_decay_rate parameter of each of these routines with a weight_divisor parameter. Added documentation. 2004-04-28 10:36 Tom Madden * blastkar.h (6.38): Changes from Mike Gertz: - Added a function prototype for BlastGapDecayDivisor - Removed the function prototypes for BlastGapDecay and BlastGapDecayInverse - Modified function prototypes for BlastSmallGapSumE, BlastLargeGapSumE and BlastUnevenGapSumE 2004-04-28 10:37 Tom Madden * blast.c (6.405): Changes from Mike Gertz - modified the link_hsps routine to apply the gap_prob parameter to the result of BlastSmallGapSumE and BlastLargeGapSumE. - further modified link_hsps to use BlastGapDecayDivisor to weight tests based on multiple collections of HSPs. - removed all reference to gap_prob from the new_link_hsps. - further modified new_link_hsps to use BlastGapDecayDivisor to weight tests based on multiple collections of HSPs. 2004-04-28 16:32 Colleen Bollin * salptool.c (6.35): initialized some variables 2004-04-28 16:32 Kevin Bealer * blastool.c (6.263): - Fix BLAST_Wizard defaults for PSI-Blast: comp-based-stats=TRUE, E=0.005. 2004-04-29 15:55 Ilya Dondoshansky * xmlblast.c (6.33), xmlblast.h (6.14): Mask filtered locations in query sequence lines 2004-04-30 08:45 George Coulouris * blastdef.h (6.157): bump version to 2.2.9 2004-04-30 11:25 Ilya Dondoshansky * blastool.c (6.264): Added argument in call to BXMLGetHspFromSeqAlign