[cvs] / internal / c++ / src / algo / blast / api Repository:
ViewVC logotype

Index of /internal/c++/src/algo/blast/api

Files shown:83 (Show 9 dead files)
Sticky Tag:

File Rev. Age Author Last log entry
 Parent Directory        
demo/        
Makefile.in  1.1  6 years  dicuccio  Adjusted makefiles to match C++ toolkit - removed original library makefiles, ad...
Makefile.xblast.lib  1.54  3 years  camacho  + blast_results
Makefile.xblast.lib.msvc  1.1  5 years  gorelenk  Initial revision.
bioseq_extract_data_priv.cpp  1.10  3 years  camacho  Replace ASSERT (defined in CORE) for _ASSERT (defined by C++ toolkit)
bioseq_extract_data_priv.hpp  1.8  3 years  camacho  Doxygen fixes
bl2seq.cpp  1.95  3 years  camacho  Refactor construction of CSearchResultSet so that it can be used in CBl2Seq
blast_advprot_options.cpp  1.4  3 years  camacho  Allow new varieties of composition based statistics
blast_aux.cpp  1.101  2 years  camacho  + CPSIDiagnosticsRequest
blast_aux_priv.cpp  1.12  3 years  camacho  Refactor construction of CSearchResultSet so that it can be used in CBl2Seq
blast_aux_priv.hpp  1.8  3 years  camacho  Refactor construction of CSearchResultSet so that it can be used in CBl2Seq
blast_dbindex.cpp  1.7  2 years  morgulis  Umapping unused portions of index after search is complete.
blast_memento_priv.hpp  1.6  3 years  camacho  + CFilteringMemento
blast_mtlock.cpp  1.5  4 years  dondosha  Added blast scope
blast_nucl_options.cpp  1.30  3 years  papadopo  use enum for lookup table types
blast_objmgr_priv.hpp  1.19  3 years  madden  Doxygen fixes
blast_objmgr_tools.cpp  1.77  3 years  camacho  Minor spelling correction
blast_options_cxx.cpp  1.88  2 years  papadopo  remove seed extension method
blast_options_handle.cpp  1.18  3 years  madden  Throw exception in Create if eBlastNotSet passed in
blast_options_local_priv.cpp  1.7  3 years  madden  eBlastNotSet is default in Create
blast_options_local_priv.hpp  1.18  2 years  madden  Return kInvalidFilterValue (-1) if filtering option is NULL
blast_prot_options.cpp  1.25  3 years  papadopo  use enum for lookup table types
blast_results.cpp  1.3  3 years  camacho  Refactor construction of CSearchResultSet so that it can be used in CBl2Seq
blast_rps_options.cpp  1.17  3 years  papadopo  use enum for lookup table types
blast_seqalign.cpp  1.83  2 years  camacho  Rollback change, as this was deliberate to achieve OM-independence
blast_seqalign.hpp  1.36  3 years  avagyanv  Included the blast_seqinfosrc_aux header file
blast_seqinfosrc_aux.cpp  1.2  3 years  avagyanv  fixed line endings
blast_seqsrc_adapter_priv.cpp  1.1  4 years  camacho  Initial revision of interfaces to separate preliminary and traceback stages of t...
blast_seqsrc_adapter_priv.hpp  1.2  4 years  camacho  Doxygen fixes
blast_setup.hpp  1.64  3 years  camacho  + BlastSetup_GetStrand to consolidate assignment of strand obtained from a Seq-l...
blast_setup_cxx.cpp  1.128  3 years  papadopo  correct warning message
blastx_options.cpp  1.5  4 years  camacho  CBlastOptionsHandle subclasses must call SetDefaults unconditionally. Fixes prob...
disc_nucl_options.cpp  1.14  3 years  camacho  Full byte scan defaults to false in discontig. megablast
dust_filter.cpp  1.10  3 years  madden  Add check to Blast_FindDustFilterLoc for NULL CSeq_loc
dust_filter.hpp  1.4  3 years  bealer  - Blastx filtering support, CBlastQueryVector class.
effsearchspace_calc.cpp  1.4  3 years  camacho  + GetEffSearchSpaceForContext
hspstream_queue.cpp  1.9  4 years  dondosha  Memory leak fix: if HSPList is empty on call to HSPStreamWrite, free it
local_blast.cpp  1.9  3 years  camacho  Use size_type whenever possible
local_search.cpp  1.10  2 years  camacho  Simplify CLocalSeqSearch
objmgr_query_data.cpp  1.18  3 years  camacho  Fix memory leak when exception is thrown out of CObjMgr_QueryFactory constructor...
objmgrfree_query_data.cpp  1.13  3 years  camacho  Use size_type whenever possible
phiblast_nucl_options.cpp  1.2  4 years  camacho  CBlastOptionsHandle subclasses must call SetDefaults unconditionally. Fixes prob...
phiblast_prot_options.cpp  1.3  4 years  camacho  CBlastOptionsHandle subclasses must call SetDefaults unconditionally. Fixes prob...
prelim_search_runner.hpp  1.5  2 years  camacho  Fix compiler warning
prelim_stage.cpp  1.19  2 years  camacho  + interface to reset iteration bookmark
psi_pssm_input.cpp  1.18  3 years  ucko  CPsiBlastInputData::x_GetSubjectSequence(): use string::erase() rather than stri...
psibl2seq.cpp  1.11  4 years  camacho  Refactorings to allow CPsiBl2Seq to produce Seq-aligns in the same format as CBl...
psiblast.cpp  1.3  4 years  camacho  Doxygen fixes
psiblast_aux_priv.cpp  1.22  2 years  camacho  Minor fix
psiblast_aux_priv.hpp  1.8  3 years  camacho  Data type change in CPsiBlastAlignmentProcessor::THitIdentifiers
psiblast_impl.cpp  1.8  3 years  camacho  Replace ASSERT (defined in CORE) for _ASSERT (defined by C++ toolkit)
psiblast_impl.hpp  1.3  3 years  camacho  Doxygen fixes
psiblast_iteration.cpp  1.6  3 years  camacho  Data type change in CPsiBlastAlignmentProcessor::THitIdentifiers
psiblast_options.cpp  1.9  4 years  camacho  explicitely set filtering to false
psiblast_subject.cpp  1.2  3 years  camacho  Replace ASSERT (defined in CORE) for _ASSERT (defined by C++ toolkit)
psiblast_subject.hpp  1.2  4 years  camacho  + IPsiBlastSubject::ResetBlastSeqSrcIteration
pssm_engine.cpp  1.48  3 years  camacho  Replace ASSERT (defined in CORE) for _ASSERT (defined by C++ toolkit)
query_data.cpp  1.3  3 years  camacho  Use size_type whenever possible
remote_blast.cpp  1.50  3 years  bealer  - Allow X-dropoff in eBoth version of BlastOptions. - Check and handle Cutoff ty...
remote_search.cpp  1.5  3 years  bealer  - Prioritize sequence data over seq-locs.
remote_services.cpp  1.5  3 years  camacho  + GetOrganismSpecificRepeatsDatabases
repeats_filter.hpp  1.11  3 years  bealer  - Blastx filtering support, CBlastQueryVector class.
repeats_filter_cxx.cpp  1.37  3 years  camacho  Fix compiler warning
rps_aux.cpp  1.8  3 years  papadopo  rearrange headers
rpstblastn_options.cpp  1.5  4 years  camacho  CBlastOptionsHandle subclasses must call SetDefaults unconditionally. Fixes prob...
seqinfosrc_bioseq.cpp  1.5  3 years  camacho  Replace ASSERT (defined in CORE) for _ASSERT (defined by C++ toolkit)
seqinfosrc_bioseq.hpp  1.4  3 years  camacho  Added missing closing doxygen brackets
seqinfosrc_seqdb.cpp  1.6  3 years  bealer  - Add HasGiList() to IBlastSeqInfoSrc and classes derived thereof.
seqinfosrc_seqvec.cpp  1.6  3 years  bealer  - Add HasGiList() to IBlastSeqInfoSrc and classes derived thereof.
seqsrc_adapter_seqdb_priv.cpp  1.1  4 years  camacho  Initial revision of interfaces to separate preliminary and traceback stages of t...
seqsrc_adapter_seqdb_priv.hpp  1.1  4 years  camacho  Initial revision of interfaces to separate preliminary and traceback stages of t...
seqsrc_multiseq.cpp  1.39  2 years  camacho  + interface to reset iteration bookmark
seqsrc_query_factory.cpp  1.6  2 years  camacho  + interface to reset iteration bookmark
seqsrc_seqdb.cpp  1.42  2 years  camacho  + interface to reset iteration bookmark
setup_factory.cpp  1.17  3 years  madden  Change to LookupTableWrapInit prototype
subject_psi_database.cpp  1.3  4 years  camacho  + IPsiBlastSubject::ResetBlastSeqSrcIteration
subject_psi_database.hpp  1.2  4 years  camacho  + IPsiBlastSubject::ResetBlastSeqSrcIteration
subject_psi_sequences.cpp  1.1  4 years  camacho  Initial revision
subject_psi_sequences.hpp  1.1  4 years  camacho  Initial revision
tblastn_options.cpp  1.7  3 years  camacho  + Change base class to CBlastAdvancedProteinOptionsHandle to support composition...
tblastx_options.cpp  1.6  4 years  camacho  CBlastOptionsHandle subclasses must call SetDefaults unconditionally. Fixes prob...
traceback_stage.cpp  1.25  2 years  camacho  Fix to use the proper messages structure
uniform_search.cpp  1.14  3 years  camacho  Moved classes defined in blast_results.hpp to blast_results.cpp
version.cpp  1.9  3 years  camacho  Doxygen fixes
NCBI Systems Team
 ViewVC Help
Powered by ViewVC 1.0.8