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

(

& align, deque<char>& target_id_pool) : m_range(align.Limits()), m_align_id(align.ID()), m_weight(align.Weight()) {

(acc.begin(),acc.end(),back_inserter(target_id_pool));

target_id_pool.push_back(0);

m_align_id = -m_align_id;

.GetSource().m_acc <

.GetSource().m_acc;

char & operator[](TSignedSeqPos p)

TSignedSeqPos FullLength() const

const char & operator[](TSignedSeqPos p) const

void Init(const CSeqVector &sv, TSignedSeqPos from, TSignedSeqPos to)

string substr(TSignedSeqPos p, TSignedSeqPos l) const

SCorrectionData GetGenomicCorrections() const

CAlignModel FillGapsInAlignmentAndAddToGenomicGaps(const CAlignModel &align, int fill)

void ClipProteinToStartStop(CAlignModel &align)

void CleanExonEdge(int ie, CAlignModel &align, const string &transcript, bool right_edge) const

bool RemoveNotSupportedIntronsFromProt(CAlignModel &align)

CAlignCollapser(string contig="", CScope *scope=0, bool nofilteringcollapsing=false)

void AddAlignment(CAlignModel &align)

bool m_no_lr_only_introns

void InitContig(string contig, CScope *scope)

TInDels GetGenomicGaps() const

vector< double > m_coverage

map< CAlignCommon, deque< SAlignIndividual > > Tdata

map< tuple< int, TSignedSeqPos, EStrand >, CAlignModel > m_special_aligns

void ClipNotSupportedFlanks(CAlignModel &align, double clip_threshold, double min_lim=0)

bool RemoveNotSupportedIntronsFromTranscript(CAlignModel &align, bool check_introns_on_both_strands) const

map< CAlignCommon, deque< char > > Tidpool

void GetOnlyOtherAlignments(TAlignModelClusterSet &clsset)

bool CheckAndInsert(const CAlignModel &align, TAlignModelClusterSet &clsset) const

void SetGenomicCorrections(const SCorrectionData &correction_data)

TAlignIntrons m_align_introns

SCorrectionData m_correction_data

void ClipESTorSR(CAlignModel &align, double clip_threshold, double min_lim)

TIntMap m_genomic_gaps_len

void GetCollapsedAlgnments(TAlignModelClusterSet &clsset)

TAlignModelList m_aligns_for_filtering_only

bool m_use_long_reads_tss

map< SIntron, SIntronData > TAlignIntrons

TIntMap GetContigGaps() const

void CleanSelfTranscript(CAlignModel &align, const string &trans) const

void AddFlexible(int status, TSignedSeqPos pos, EStrand strand, Int8 id, double weight)

static void SetupArgDescriptions(CArgDescriptions *arg_desc)

bool operator<(const CAlignCommon &cas) const

CAlignModel GetAlignment(const SAlignIndividual &ali, const deque< char > &target_id_pool) const

vector< SIntron > Tintrons

const Tintrons & GetIntrons() const

string TargetAccession() const

list< CAlignModel > TAlignModelList

vector< CInDelInfo > TInDels

int TSignedSeqPos

Type for signed sequence position.

void GetSeqData(TSeqPos start, TSeqPos stop, string &buffer) const

Fill the buffer string with the sequence data for the interval [start, stop).

int64_t Int8

8-byte (64-bit) signed integer

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_SCOPE(ns)

Define a new scope.

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

Defines command line argument related classes.

void copy(Njn::Matrix< S > *matrix_, const Njn::Matrix< T > &matrix0_)

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

bool operator()(const CInDelInfo &a, const CInDelInfo &b) const

SAlignIndividual(const CAlignModel &align, deque< char > &target_id_pool)

TSignedSeqPos m_target_id

list< TSignedSeqRange > m_confirmed_intervals

map< int, char > m_replacements

TInDels m_correction_indels

bool operator<(const SIntron &i) const

SIntron(int a, int b, int strand, bool oriented, const string &sig)

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