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 <blfmtutl.h> 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 <blfmtutl.h>
2004-06-30 15:52 camacho
* demo/: formatdb.c (6.93), formatrpsdb.c (1.3), fastacmd.c (6.31):
Added #include <blfmtutl.h>
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