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NCBI C++ ToolKit: include/algo/gnomon/chainer.hpp Source File

1 #ifndef ALGO_GNOMON___CHAINER__HPP 2 #define ALGO_GNOMON___CHAINER__HPP 68 template

class

Container,

class

Predicate>

71 typedef typename

Container::iterator Iterator;

72

Iterator __first = c.begin();

73

Iterator __last = c.end();

74 while

(__first != __last) {

75 if

((*__pred)(*__first)) {

78

__first = c.erase(__first);

85 template

class

Container,

class

UnaryFunction>

88 typedef typename

Container::iterator Iterator;

89

Iterator __first = c.begin();

90

Iterator __last = c.end();

91 for

(;__first != __last;++__first)

120 void

EnableSeqMasking();

127 void

MapAlignmentsToEditedContig(

TAlignModelList

& alignments)

const

;

154 double

m_pcsf_factor = 0.;

165 void

SetIntersectLimit(

int value

);

166 void

SetTrim(

int

trim);

167 void

SetMinPolyA(

int

minpolya);

169 void

SetMinInframeFrac(

double

mininframefrac);

173 void

SetNumbering(

int

idnext,

int

idinc);

182 void

SetConfirmedStartStopForProteinAlignments(

TAlignModelList

& alignments);

186 void

FindSelenoproteinsClipProteinsToStartStop(

TGeneModelList

& clust);

269 static void

ArgsToChainer(

CChainer

* chainer,

const CArgs

& args, objects::CScope& scope);

void remove_if(Container &c, Predicate *__pred)

void transform(Container &c, UnaryFunction *op)

CChainer(const CChainer &value)

void SetOnlyBestFs(bool onlybestfs)

unique_ptr< CChainerImpl > m_data

unique_ptr< CGnomonEngine > m_gnomon

map< int, char > m_replaced_bases

map< int, TInDels::const_iterator > TGgapInfo

void SetPCSF(const CPhyloCSFData *pcsf_datap)

TGgapInfo m_inserted_seqs

TInDels m_reversed_corrections

map< int, char > m_replacements

unique_ptr< SPhyloCSFSlice > m_pcsf_slice

void SetGenomic(const CSeq_id &seqid, objects::CScope &scope, const SCorrectionData &correction_data, TSignedSeqRange range=TSignedSeqRange::GetWhole(), const string &mask_annots=kEmptyStr)

TIntMap m_confirmed_bases_len

TIntMap m_confirmed_bases_orig_len

CAlignMap m_edited_contig_map

CRef< CHMMParameters > m_hmm_params

void SetGenomic(const CSeq_id &seqid, objects::CScope &scope, const string &mask_annots=kEmptyStr, const TGeneModelList *models=0)

TIntMap m_notbridgeable_gaps_len

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

vector< TResidue > CResidueVec

list< CAlignModel > TAlignModelList

list< CGeneModel > TGeneModelList

vector< CInDelInfo > TInDels

static TThisType GetWhole(void)

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_SCOPE(ns)

Define a new scope.

#define NCBI_XALGOGNOMON_EXPORT

void AddComment(CSeq_feat &feat, const string &comment)

Magic spell ;-) needed for some weird compilers... very empiric.

const GenericPointer< typename T::ValueType > T2 value

virtual bool model_predicate(CGeneModel &align)

CutShortPartialExons(int minex)

virtual void transform_align(CAlignModel &align)

virtual bool model_predicate(CGeneModel &align)

HasLongIntron(CGnomonEngine &gnomon)

virtual bool model_predicate(CGeneModel &align)

HasShortIntron(CGnomonEngine &gnomon)

virtual bool model_predicate(CGeneModel &align)

LowSupport_Noncoding(int _minsupport)

MarkupCappedEst(const set< string > &_caps, int _capgap)

virtual void transform_align(CAlignModel &align)

const set< string > & caps

MarkupTrustedGenes(const set< string > &_trusted_genes)

virtual void transform_align(CAlignModel &align)

const set< string > & trusted_genes

bool operator()(CGeneModel &a)

bool operator()(CAlignModel &a)

virtual bool align_predicate(CAlignModel &a)

virtual bool model_predicate(CGeneModel &)

virtual string GetComment()

ProteinWithBigHole(double hthresh, double hmaxlen, CGnomonEngine &gnomon)

virtual bool model_predicate(CGeneModel &align)

double m_utr_clip_threshold

virtual bool model_predicate(CGeneModel &align)

void operator()(CGeneModel &a)

virtual void transform_model(CGeneModel &)

void operator()(CAlignModel &a)

virtual ~TransformFunction()

virtual void transform_align(CAlignModel &a)

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