Search Toolkit Book for BlastInitialWordParameters
Parameter block that contains a pointer to BlastInitialWordOptions and the values derived from it. More...
#include <algo/blast/core/blast_parameters.h>
Collaboration diagram for BlastInitialWordParameters:
Public Attributes | |
| BlastInitialWordOptions * | options |
| The original (unparsed) options. More... | |
| Int4 | x_dropoff_max |
| largest X-drop cutoff across all contexts More... | |
| Int4 | cutoff_score_min |
| smallest cutoff score across all contexts More... | |
| BlastUngappedCutoffs * | cutoffs |
| cutoff values (one per context) More... | |
| ESeedContainerType | container_type |
| How to store offset pairs for initial seeds? More... | |
| Int4 | nucl_score_table [256] |
| the combined score of all match/mismatch combinations for aligning four bases More... | |
| Boolean | matrix_only_scoring |
| Use the scoring matrix ( not table ) to score ungapped and gapped alignments -RMH-. More... | |
| Boolean | ungapped_extension |
| Should an ungapped extension be performed? More... | |
Detailed Description
Parameter block that contains a pointer to BlastInitialWordOptions and the values derived from it.
Definition at line 108 of file blast_parameters.h.
Member Data Documentation
◆ container_type
| ESeedContainerType BlastInitialWordParameters::container_type |
How to store offset pairs for initial seeds?
Definition at line 114 of file blast_parameters.h.
Referenced by BlastExtendWordNew(), BlastInitialWordParametersNew(), BOOST_AUTO_TEST_CASE(), s_BlastNaExtend(), s_BlastNaExtendAligned(), s_BlastNaExtendDirect(), s_BlastSmallNaExtend(), s_BlastSmallNaExtendAlignedOneByte(), and NuclWordFinderTextFixture::setupExtendWord().
◆ cutoff_score_min
| Int4 BlastInitialWordParameters::cutoff_score_min |
smallest cutoff score across all contexts
Definition at line 112 of file blast_parameters.h.
Referenced by BlastInitialWordParametersUpdate(), BlastLinkHSPParametersUpdate(), BOOST_AUTO_TEST_CASE(), CalculateLinkHSPCutoffs(), printBlastInitialWordParamters(), s_FillReturnCutoffsInfo(), LinkHspTestFixture::setupCutoffScores(), and NuclWordFinderTextFixture::setupExtendWord().
◆ cutoffs
| BlastUngappedCutoffs* BlastInitialWordParameters::cutoffs |
cutoff values (one per context)
Definition at line 113 of file blast_parameters.h.
Referenced by Blast_HSPReevaluateWithAmbiguitiesUngapped(), BlastInitialWordParametersFree(), BlastInitialWordParametersNew(), BlastInitialWordParametersUpdate(), BlastRPSWordFinder(), MB_IndexedWordFinder(), printBlastInitialWordParamters(), s_BlastAaWordFinder_OneHit(), s_BlastAaWordFinder_TwoHit(), s_BlastnDiagHashExtendInitialHit(), s_BlastnDiagTableExtendInitialHit(), and NuclWordFinderTextFixture::setupExtendWord().
◆ matrix_only_scoring
| Boolean BlastInitialWordParameters::matrix_only_scoring |
Use the scoring matrix ( not table ) to score ungapped and gapped alignments -RMH-.
Definition at line 118 of file blast_parameters.h.
Referenced by BlastInitialWordParametersNew(), s_BlastnDiagHashExtendInitialHit(), and s_BlastnDiagTableExtendInitialHit().
◆ nucl_score_table
| Int4 BlastInitialWordParameters::nucl_score_table[256] |
the combined score of all match/mismatch combinations for aligning four bases
Definition at line 116 of file blast_parameters.h.
Referenced by BlastInitialWordParametersNew(), MB_IndexedWordFinder(), s_BlastnDiagHashExtendInitialHit(), s_BlastnDiagTableExtendInitialHit(), and NuclWordFinderTextFixture::setupExtendWord().
◆ options
| BlastInitialWordOptions* BlastInitialWordParameters::options |
The original (unparsed) options.
Definition at line 109 of file blast_parameters.h.
Referenced by BlastExtendWordNew(), BlastInitialWordParametersNew(), BlastInitialWordParametersUpdate(), BOOST_AUTO_TEST_CASE(), s_BlastnDiagHashExtendInitialHit(), s_BlastnDiagTableExtendInitialHit(), NuclWordFinderTextFixture::setupExtendWord(), and NuclWordFinderTextFixture::~NuclWordFinderTextFixture().
◆ ungapped_extension
| Boolean BlastInitialWordParameters::ungapped_extension |
Should an ungapped extension be performed?
Definition at line 121 of file blast_parameters.h.
Referenced by BlastInitialWordParametersNew(), BlastNaWordFinder(), MB_IndexedWordFinder(), s_BlastnDiagHashExtendInitialHit(), s_BlastnDiagTableExtendInitialHit(), and NuclWordFinderTextFixture::setupExtendWord().
◆ x_dropoff_max
| Int4 BlastInitialWordParameters::x_dropoff_max |
largest X-drop cutoff across all contexts
Definition at line 111 of file blast_parameters.h.
Referenced by BlastInitialWordParametersUpdate(), BOOST_AUTO_TEST_CASE(), printBlastInitialWordParamters(), s_FillReturnCutoffsInfo(), LinkHspTestFixture::setupCutoffScores(), and NuclWordFinderTextFixture::setupExtendWord().
The documentation for this struct was generated from the following file:
- include/algo/blast/core/blast_parameters.h
