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use static_cast to address implicit conversion warnings JIRA SB-3592
Replaced auto_ptr with unique_ptr. JIRA CXX-11620
Take out err msg ref to gi list, JIRA
JIRA SB-2391 Apply patches to fix multiple memory leaks in BLAST libraries and unit tests
JIRA SB-2403 Remove warning pending more focused implementation
Exclude magicblast from "No seeds found" warning message JIRA SB-2403
JIRA SB-2403 Issue warning if no seeds produced for query
Fix split query MT core dump, JIRA:SB-1958
Multithread database word counting for magicblast JIRA SB-1720
Remove rcsid JIRA SB-1682
Fix thread return type, JIRA:SB-1530
Add unit tests to ensure that if all queries are fully masked, the BLAST search throws an exception, but if at least 1 sequence is valid (i.e.: not fully masked), then no exception is thrown and warnings are properly recorded. Consolidate the definition of the error message associated with not being able to calculate ungapped Karlin-Altschul parameters. JIRA SB-1242
JIRA SB-984 svn merge -r 363868:369339 $NCBISVN/toolkit/branches/morgulis/mbidx2/private_api/src svn merge -r 363748:368082 $NCBISVN/toolkit/branches/morgulis/mbidx2/private_api/include 1. Removed -old_style_index option from blastn. 2. Index version is now automatically detected. 3. Only the seed sets that are accessed by currently running search threads are retained in memory.
Remove num_ident for gapped search in stdseg, JIRA:SB-952
Added bit score to Stdseg, JIRA:SB-952
removed unused 'any_query_removed_hsps'
report which query exceeded hsp limit in ComputeBlastHSPResults
Convert results from prelmin search to seq-locs, JIRA:SB-952
Pacify compiler warnings
Indexed MegaBLAST interface changes. 1. Removed concurrent search of multiple volumes. 2. Removed BlastSeqSrc interface to indexed search.
Address MT issues with genetic code singleton JIRA SB-853
Pacify MSVC compiler JIRA SB-831
Throw exception with more specific message. Fix JIRA SB-800
Fix an bug in representing the cache size. Fix JIRA SB-768
Remove spurious printf; JIRA SB-620
Integrate rmblastn code from Robert Hubley; JIRA SB-620
Finalize hspwriter before merging split queries. JIRA SB-610
Change so that CLocalBlast does not throw on completely masked sequence, JIRA SB-393
Merged changes from 'branches/blast/staging' (Revisions 160959:161393) into 'trunk/c++'. Pre-BLAST 2.2.21 release merge JIRA SB-166
Rename relocated header.
Fix blast_unit_test DLL build.
Merged changes from 'branches/blast/staging' (Revisions 151140:151309) into 'trunk/c++'. Pre-release BLAST 2.2.20 merge. JIRA SB-166
Merged changes from 'branches/blast/staging' (Revisions 141064:141255) into 'trunk/c++'. Merge in preparation for in-house update of BLAST command line binaries
Merged changes from 'branches/blast/staging' (Revisions 133277:134300) into 'trunk/c++'. Added mask_subjects, updates to BLAST binaries
Merged changes from 'branches/blast/staging' (Revisions 121879:122238) into 'trunk/c++'. Bi-weekly merge
Merged changes from 'branches/blast/staging' (Revisions 115659:115843) into 'trunk/c++'. Bi-weekly merge
Merged changes from 'branches/blast/staging' (Revisions 114987:115213) into 'trunk/c++'. Bi-weekly merge
Merged changes up to r113774 from 'branches/blast/staging' into 'trunk/c++'. Biweekly merge: fix missing headers from gene_info
From Aleksandr Morgulis: Use the value of -num_threads option to set the number of threads in indexed search.
1. Add optional batch read method to HSPStream
2. Implement batch read for HSPListCollector, configured to
return batches of HSPLists in order of increasing subject OID
3. Remove sort_on_read boolean from HSPListCollector
4. Modify blast traceback to fetch subject sequences only once, and use
the batch read HSPStream method to process all HSPLists that
hit to that subject sequence
5. Make CBlastPrelimSearch explicitly sort HSPLists by best e-value
Implement multi-threading for query splitting
Fixed svn properties in trunk/c++.
From Aleksandr Morgulis: Move initialization of the megablast database index from the application to the API layer.
Remove dead code
Introduced query splitting
remove deleted header
MT fixes
1) Revamping of CArgs to CBlastOptions functionality in libblastinput 2) Removal of blastall/megablast, first check in of psiblast, blastp (still under development)
+ interface to reset iteration bookmark
Remove PssmWithParameters header
add initialization for indexed databases
Add a (trivial) non-inline destructor to avoid compilation errors under GCC 2.95, and perhaps some other compilers.
store options memento in auto_ptr
retrieve warning messages so that they can be combined with other setup errors/warnings
Move CPrelimSearchThread to prelim_search_runner.hpp
Replace ASSERT (defined in CORE) for _ASSERT (defined by C++ toolkit)
+ interruptible api support
Doxygen fixes
Changes to conform to PsiBlastSetupScoreBlock signature change
+ pssm input
Change data type passed to CThread::Join to long
+ CBlastPrelimSearch::ComputeBlastHSPResults, proper retrieval of TSearchMessages
+ output parameter to CSetupFactory::CreateScoreBlk for the masked query regions
Doxygen fixes
CPrelimSearchRunner moved to a separate header
Add assertions to CPrelimSearchRunner
Initial revision of interfaces to separate preliminary and traceback stages of the BLAST search
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