NCBI C++ ToolKit
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Search Toolkit Book for BlastInitialWordOptions
Options needed for initial word finding and processing. More...
#include <algo/blast/core/blast_options.h>
Public Attributes | |
double | gap_trigger |
Score in bits for starting gapped extension. More... | |
Int4 | window_size |
Maximal allowed distance between 2 hits in case 2 hits are required to trigger the extension. More... | |
Int4 | scan_range |
Maximal number of gaps allowed between 2 hits. More... | |
double | x_dropoff |
X-dropoff value (in bits) for the ungapped extension. More... | |
EBlastProgramType | program_number |
indicates blastn, blastp, etc. More... | |
Options needed for initial word finding and processing.
Definition at line 297 of file blast_options.h.
double BlastInitialWordOptions::gap_trigger |
Score in bits for starting gapped extension.
Definition at line 298 of file blast_options.h.
Referenced by BlastInitialWordParametersUpdate(), CBlastOptionsLocal::GetGapTrigger(), and CBlastOptionsLocal::SetGapTrigger().
EBlastProgramType BlastInitialWordOptions::program_number |
indicates blastn, blastp, etc.
Definition at line 304 of file blast_options.h.
Referenced by s_BlastnDiagHashExtendInitialHit(), s_BlastnDiagTableExtendInitialHit(), and CBlastOptionsLocal::SetProgram().
Int4 BlastInitialWordOptions::scan_range |
Maximal number of gaps allowed between 2 hits.
Definition at line 301 of file blast_options.h.
Referenced by BlastInitialWordOptionsValidate(), CBlastOptionsLocal::GetOffDiagonalRange(), s_BlastnDiagHashExtendInitialHit(), s_BlastnDiagTableExtendInitialHit(), and CBlastOptionsLocal::SetOffDiagonalRange().
Int4 BlastInitialWordOptions::window_size |
Maximal allowed distance between 2 hits in case 2 hits are required to trigger the extension.
Definition at line 299 of file blast_options.h.
Referenced by BLAST_FillInitialWordOptions(), BlastExtendWordNew(), BlastInitialWordOptionsValidate(), BOOST_AUTO_TEST_CASE(), CBlastInitialWordOptions::DebugDump(), CIndexedDb_New::DoPreSearch(), CBlastOptionsLocal::GetWindowSize(), CIndexedDb_Old::PreSearch(), s_BlastnDiagHashExtendInitialHit(), s_BlastnDiagTableExtendInitialHit(), NuclWordFinderTextFixture::setupExtendWord(), and CBlastOptionsLocal::SetWindowSize().
double BlastInitialWordOptions::x_dropoff |
X-dropoff value (in bits) for the ungapped extension.
Definition at line 302 of file blast_options.h.
Referenced by BLAST_FillInitialWordOptions(), BlastInitialWordOptionsValidate(), BlastInitialWordParametersNew(), BOOST_AUTO_TEST_CASE(), CBlastInitialWordOptions::DebugDump(), CBlastOptionsLocal::GetXDropoff(), LinkHspTestFixture::setupCutoffScores(), and CBlastOptionsLocal::SetXDropoff().