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NCBI C++ ToolKit: src/algo/gnomon/gnomon_engine.cpp Source File

->m_intron_params->m_intronlen.MinLen();

->m_intergenic_params->m_intergeniclen.MinLen();

->m_intron_params->m_intronlen.MaxLen();

p = exp(

->m_intron_params->m_intronlen.ClosingScore(

));

(

->m_range.Empty() )

GC_RANGE_SIZE = 200000;

gc_range(middle-GC_RANGE_SIZE/2, middle+GC_RANGE_SIZE/2);

gc_range +=

->m_range;

(c ==

|| c ==

) {

->m_gccontent =

(

->m_gccontent*100.0/length + 0.5);

->m_intron_params->SetSeqLen(

->m_range.GetLength() );

->GetHMMParameter(

->m_intergenic_params);

->m_intergenic_params->SetSeqLen(

->m_range.GetLength() );

->m_gccontent;

( cls, leftwall, rightwall,

,

,

mpp,

(), notbridgeable_gaps_len, ggapinfo, pcsf_slice

leftwall,

rightwall,

leftanchor,

rightanchor,

mpp,

consensuspenalty,

*

->m_intron_params,

cls, initial_fshifts, mpp, *

)

->m_ss->Init(

->m_seq, leftwall, rightwall, consensuspenalty, notbridgeable_gaps_len, ggapinfo, pcsf_slice);

*

->m_intron_params,

*

->m_intergenic_params,

leftanchor, rightanchor) );

->m_parse->Path()->Score();

->m_parse->GetGenes();

(!genes.empty() && !genes.back().RightComplete()) {

partial_start = genes.back().Limits().GetFrom();

(!genes.empty()) {

right = genes.back().Limits().GetTo();

right = partial_start-100;

->m_parse->PrintInfo();

TSignedSeqPos MapEditedToOrig(TSignedSeqPos edited_pos) const

int GetMinIntergenicLen() const

double GetChanceOfIntronLongerThan(int l) const

double Run(bool leftwall=true, bool rightwall=true, double mpp=10, SPhyloCSFSlice *pcsf_slice=nullptr)

list< CGeneModel > GetGenes() const

unique_ptr< SGnomonEngineImplData > m_data

CGnomonEngine(CConstRef< CHMMParameters > hmm_params, const CResidueVec &sequence, TSignedSeqRange range=TSignedSeqRange::GetWhole(), SPhyloCSFSlice *pcsf_slice=nullptr)

TSignedSeqPos PartialModelStepBack(list< CGeneModel > &genes) const

const CResidueVec & GetSeq() const

int GetMaxIntronLen() const

int GetMinIntronLen() const

void ResetRange(TSignedSeqRange range)

HMM model parameters just create it and pass to a Gnomon engine.

vector< TResidue > CResidueVec

list< CGeneModel > TGeneModelList

vector< CInDelInfo > TInDels

int TSignedSeqPos

Type for signed sequence position.

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

CRange< TSignedSeqPos > TSignedSeqRange

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

Defines classes: CDirEntry, CFile, CDir, CSymLink, CMemoryFile, CFileUtil, CFileLock,...

static SLJIT_INLINE sljit_ins l(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

SGnomonEngineImplData(CConstRef< CHMMParameters > hmm_params, CResidueVec &&sequence, TSignedSeqRange range, SPhyloCSFSlice *pcsf_slice)

const value_slice::CValueConvert< value_slice::SRunTimeCP, FROM > Convert(const FROM &value)

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