Search Toolkit Book for BlastScoringParameters
Scoring parameters block Contains scoring-related information that is actually used for the blast search. More...
#include <algo/blast/core/blast_parameters.h>
Collaboration diagram for BlastScoringParameters:
Public Attributes | |
| BlastScoringOptions * | options |
| User-provided values for these params. More... | |
| Int2 | reward |
| Reward for a match. More... | |
| Int2 | penalty |
| Penalty for a mismatch. More... | |
| Int4 | gap_open |
| Extra penalty for starting a gap (scaled version) More... | |
| Int4 | gap_extend |
| Penalty for each gap residue (scaled version) More... | |
| Int4 | shift_pen |
| Penalty for shifting a frame in out-of-frame gapping (scaled version) More... | |
| double | scale_factor |
| multiplier for all cutoff scores More... | |
Detailed Description
Scoring parameters block Contains scoring-related information that is actually used for the blast search.
Definition at line 199 of file blast_parameters.h.
Member Data Documentation
◆ gap_extend
| Int4 BlastScoringParameters::gap_extend |
Penalty for each gap residue (scaled version)
Definition at line 204 of file blast_parameters.h.
Referenced by ALIGN_EX(), BLAST_GapAlignStructNew(), BLAST_GappedAlignmentWithTraceback(), BLAST_GreedyGappedAlignment(), Blast_HSPReevaluateWithAmbiguitiesGapped(), Blast_SemiGappedAlign(), BLAST_SmithWatermanGetGappedScore(), BlastScoringParametersNew(), CBlastScoringParameters::DebugDump(), JumperGappedAlignmentCompressedWithTraceback(), printBlastScoringParameters(), s_BlastAlignPackedNucl(), s_BlastGreedyAlignMemAlloc(), s_GappingParamsNew(), s_OutOfFrameAlignWithTraceback(), s_OutOfFrameGappedAlign(), s_RecordInitialSearch(), s_RescaleSearch(), s_RestoreSearch(), s_RestrictedGappedAlign(), s_RPSComputeTraceback(), and SmithWatermanScoreWithTraceback().
◆ gap_open
| Int4 BlastScoringParameters::gap_open |
Extra penalty for starting a gap (scaled version)
Definition at line 203 of file blast_parameters.h.
Referenced by ALIGN_EX(), BLAST_GapAlignStructNew(), BLAST_GappedAlignmentWithTraceback(), BLAST_GreedyGappedAlignment(), Blast_HSPReevaluateWithAmbiguitiesGapped(), Blast_SemiGappedAlign(), BLAST_SmithWatermanGetGappedScore(), BlastScoringParametersNew(), CBlastScoringParameters::DebugDump(), JumperGappedAlignmentCompressedWithTraceback(), printBlastScoringParameters(), s_BlastAlignPackedNucl(), s_BlastGreedyAlignMemAlloc(), s_GappingParamsNew(), s_OutOfFrameAlignWithTraceback(), s_OutOfFrameGappedAlign(), s_RecordInitialSearch(), s_RescaleSearch(), s_RestoreSearch(), s_RestrictedGappedAlign(), s_RPSComputeTraceback(), and SmithWatermanScoreWithTraceback().
◆ options
| BlastScoringOptions* BlastScoringParameters::options |
User-provided values for these params.
Definition at line 200 of file blast_parameters.h.
Referenced by BLAST_ComputeTraceback(), BLAST_ComputeTraceback_MT(), BLAST_GappedAlignmentWithTraceback(), BLAST_GetGappedScore(), Blast_HSPListReevaluateUngapped(), BLAST_PreliminarySearchEngine(), Blast_RedoAlignmentCore_MT(), Blast_TracebackFromHSPList(), BlastScoringParametersNew(), BOOST_AUTO_TEST_CASE(), PHIGappedAlignmentWithTraceback(), PHIGetGappedScore(), printBlastScoringParameters(), s_BlastProtGappedAlignment(), s_BlastSearchEngineCore(), s_BlastSearchEngineOneContext(), s_HSPListPostTracebackUpdate(), and SmithWatermanScoreWithTraceback().
◆ penalty
| Int2 BlastScoringParameters::penalty |
Penalty for a mismatch.
Definition at line 202 of file blast_parameters.h.
Referenced by BLAST_GapAlignStructNew(), BLAST_GreedyGappedAlignment(), Blast_HSPReevaluateWithAmbiguitiesGapped(), BlastNaExtendJumper(), BlastScoringParametersNew(), CBlastScoringParameters::DebugDump(), JumperGappedAlignmentCompressedWithTraceback(), printBlastScoringParameters(), s_BlastGreedyAlignMemAlloc(), and s_CreateHSP().
◆ reward
| Int2 BlastScoringParameters::reward |
Reward for a match.
Definition at line 201 of file blast_parameters.h.
Referenced by BLAST_GreedyGappedAlignment(), Blast_HSPReevaluateWithAmbiguitiesGapped(), BlastScoringParametersNew(), CBlastScoringParameters::DebugDump(), JumperGappedAlignmentCompressedWithTraceback(), printBlastScoringParameters(), and s_BlastGreedyAlignMemAlloc().
◆ scale_factor
| double BlastScoringParameters::scale_factor |
multiplier for all cutoff scores
Definition at line 207 of file blast_parameters.h.
Referenced by BlastScoringParametersNew(), CBlastScoringParameters::DebugDump(), printBlastScoringParameters(), s_BlastSearchEngineCore(), s_FillReturnCutoffsInfo(), s_HSPListPostTracebackUpdate(), s_RecordInitialSearch(), s_RescaleSearch(), s_RestoreSearch(), and s_RPSComputeTraceback().
◆ shift_pen
| Int4 BlastScoringParameters::shift_pen |
Penalty for shifting a frame in out-of-frame gapping (scaled version)
Definition at line 205 of file blast_parameters.h.
Referenced by BlastScoringParametersNew(), CBlastScoringParameters::DebugDump(), printBlastScoringParameters(), s_OutOfFrameAlignWithTraceback(), s_OutOfFrameGappedAlign(), and s_RPSComputeTraceback().
The documentation for this struct was generated from the following file:
- include/algo/blast/core/blast_parameters.h
