win_mask_gen_counts.cpp File Reference

#include <ncbi_pch.hpp>
#include <stdlib.h>
#include <vector>
#include <sstream>
#include <objects/seq/Bioseq.hpp>
#include <objects/seq/Seq_inst.hpp>
#include <objects/seq/Seq_data.hpp>
#include <objects/seq/seqport_util.hpp>
#include <objects/seq/IUPACna.hpp>
#include <objmgr/object_manager.hpp>
#include <objmgr/scope.hpp>
#include <objmgr/seq_entry_handle.hpp>
#include <objmgr/bioseq_ci.hpp>
#include <objmgr/seq_vector.hpp>
#include <algo/winmask/seq_masker_util.hpp>
#include <algo/winmask/win_mask_gen_counts.hpp>
#include <algo/winmask/win_mask_dup_table.hpp>
#include <algo/winmask/win_mask_util.hpp>
#include "algo/winmask/seq_masker_ostat_factory.hpp"

Include dependency graph for win_mask_gen_counts.cpp:

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Functions
	USING_SCOPE (objects)
static Uint4	letter (char c)
static bool	ambig (char c)
static Uint4	reverse_complement (Uint4 seq, Uint1 size)

Function Documentation

ambig()

static bool ambig ( char  c )

inlinestatic

Definition at line 75 of file win_mask_gen_counts.cpp.

Referenced by CWriteDB_Impl::AddSequence(), CWriteDB::AddSequence(), CWriteDB_SequenceFile::AddSequence(), BOOST_AUTO_TEST_CASE(), CSearch_Base< LEGACY, NHITS, derived_t >::ExtendLeft(), CSearch_Base< LEGACY, NHITS, derived_t >::ExtendRight(), CSRSearch::getNMer(), CSeqportUtil_implementation::InitAmbigNcbi4naNcbi2na(), CWinMaskCountsGenerator::process(), s_DupIdsRaw(), s_FetchRawData(), CSRSearch_Impl< index_t >::search(), CSRSearch_Impl< index_t >::searchExact(), CSRSearch_Impl< index_t >::searchOneMismatch(), CWriteDB_Volume::WriteSequence(), CWriteDB_Impl::x_ComputeHash(), CBuildDatabase::x_DupLocal(), and x_FindRSite().

letter()

static Uint4 letter ( char  c )

static

Definition at line 62 of file win_mask_gen_counts.cpp.

Referenced by _PSIComputePositionExtents(), _PSIGetLeftExtents(), _PSIGetRightExtents(), COffsetData_Factory::AddSeqSeg(), CSubjectMap_Factory::AddSequenceChunk(), CSubjectMap_Factory_TBase::AddSequenceChunk(), CTextFsm< CSeqSearch::CPatternInfo >::CState::AddTransition(), CSeqMaskerWindow::Advance(), CSeqMaskerWindowAmbig::Advance(), BlastCompressedAaLookupTableNew(), BOOST_AUTO_TEST_CASE(), CFeatGapInfo::CollectGaps(), CSeqMaskerWindow::FillWindow(), CSeqMaskerWindowAmbig::FillWindow(), CSparseKmerCounts::GetAALetter(), CBinaryKmerCounts::GetAALetter(), GetFirstInitial(), CExonSelectorApplication::GetNextExon(), CTextFsm< CSeqSearch::CPatternInfo >::CState::GetNextState(), CTextFsm< MatchType >::GetNextState(), CSRSearch::getNMer(), handle_option(), CSRSearch::SMismatchResultsEntry::init(), CSeqDBDemo_Thread::Main(), CSeqMaskerWindowPattern::MakeUnit(), CNmerIterator::Next(), CMaskWriterFasta::Print(), CWinMaskCountsGenerator::process(), CSeqMaskerUtil::reverse_complement(), s_CompOn(), s_GetCompressedProbs(), s_loadSortedMatrix(), NAdapterSearch::CSimpleUngappedAligner::s_Put(), s_StateOn(), CSequence::SetLetter(), CSRSearch::SMismatchResultsEntry::SMismatchResultsEntry(), SrchTheChar(), SPatternUnit::test(), NAdapterSearch::CUnpairedAdapterDetector::x_GetAdjacent(), CMultiAligner::x_MultiAlignClusters(), NAdapterSearch::CPairedEndAdapterDetector::CConsensusPattern::x_NextWord(), CSeqDBDemo_Thread::x_UseOID(), and x_ValidAminoAcid().

reverse_complement()

static Uint4 reverse_complement ( Uint4  seq, Uint1  size  )

static

Definition at line 120 of file win_mask_gen_counts.cpp.

References CSeqMaskerUtil::reverse_complement(), and ncbi::grid::netcache::search::fields::size.

Referenced by CWinMaskCountsGenerator::process(), s_BlastGetTranslationTable(), s_GetQuerySequence(), and s_TokenizeTRnaString().

USING_SCOPE()

USING_SCOPE

(

objects

)