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NCBI C++ ToolKit: src/objmgr/util/bioseqgaps_ci.cpp Source File

: m_bioseq_CI(entry_h, params.mol_filter, params.level_filter),

( m_Params.max_num_gaps_per_seq < 1 ||

m_Params.max_num_seqs < 1)

( m_Params.mol_filter ) {

<<

(m_Params.mol_filter) );

pos_to_try = out_pos + out_len;

pos_to_start_looking,

& out_len_of_gap )

curr_pos = pos_to_start_looking;

( ; curr_pos < bioseq_len; ++curr_pos ) {

( residue == gap_residue ) {

out_pos_of_gap = curr_pos;

( curr_pos < bioseq_len && ! bDone ) {

curr_pos = pos_after_end_of_segment;

( ; curr_pos < pos_after_end_of_segment; ++curr_pos) {

( seqvec[curr_pos] != gap_residue ) {

out_len_of_gap = (curr_pos - out_pos_of_gap);

<<

(eSegmentType) );

out_len_of_gap = (curr_pos - out_pos_of_gap);

This iterates over the runs of Ns of each sequence.

Include a standard set of the NCBI C++ Toolkit most basic headers.

unsigned int TSeqPos

Type for sequence locations and lengths.

const TSeqPos kInvalidSeqPos

Define special value for invalid sequence position.

#define NCBI_USER_THROW(message)

Throw a quick-and-dirty runtime exception of type 'CException' with the given error message and error...

#define NCBI_USER_THROW_FMT(message)

Throw a "user exception" with message processed as output to ostream.

TSeqPos length

the length of the current gap

size_t num_seqs_seen_so_far

This indicates how many sequences we've seen so far, including the one we're currently on.

CBioseq_CI m_bioseq_CI

This points to the bioseq we're currently on.

SCurrentGapInfo m_infoOnCurrentGap

This indicates information about the gap we're currently on.

TSeqPos max_num_seqs

We only return gaps on up to this many sequences.

EFindNext

This indicates what happened when we tried to run x_FindNextGapOnBioseq.

Params m_Params

This holds the params the caller gave when this object was initially created.

virtual const SCurrentGapInfo & x_GetCurrent(void) const

This gives info on the gap we're currently on.

TSeqPos max_num_gaps_per_seq

We only return up to this many gaps for each sequence.

virtual void x_NextBioseq(void)

This advances m_bioseq_CI although it has extra logic to terminate m_bioseq_CI if we've exceeded the ...

TSeqPos start_pos

the 0-based position at which the current gap starts on the current sequence.

virtual void x_Next(void)

This moves this iterator to the next relevant gap.

virtual EFindNext x_FindNextGapOnBioseq(const CBioseq_Handle &bioseq_h, const TSeqPos pos_to_start_looking, TSeqPos &out_pos_of_gap, TSeqPos &out_len_of_gap) const

This finds the next gap on the bioseq, starting at given pos.

CSeq_id_Handle seq_id

The seq-id that this gap is on.

size_t num_gaps_seen_so_far_on_this_seq

how many gaps we've seen so far on this sequence.

TSeqPos max_gap_len_to_ignore

We completely ignore any gaps we find that have this number of bases or fewer.

@ eFindNext_Found

Another relevant gap was found, and the output parameters are filled in to represent information abou...

@ eFindNext_NotFound

No more relevant gaps were found on this bioseq.

CSeq_id_Handle GetAccessSeq_id_Handle(void) const

Get any CSeq_id_Handle handle that can be used to access this bioseq Use GetSeq_id_Handle() if it's n...

CScope & GetScope(void) const

Get scope this handle belongs to.

@ eCoding_Iupac

Set coding to printable coding (Iupacna or Iupacaa)

TSeqPos GetEndPosition(void) const

return end position of current segment in sequence (exclusive)

CSeqMap::ESegmentType GetType(void) const

const CSeqMap & GetSeqMap(void) const

CSeqMap_CI FindSegment(TSeqPos pos, CScope *scope) const

Find segment containing the position.

TResidue GetGapChar(ECaseConversion case_cvt=eCaseConversion_none) const

Return gap symbol corresponding to the selected coding.

@ eSeqData

real sequence data

#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.

@ eMol_not_set

> cdna = rna

@ eMol_na

just a nucleic acid

The params that control the behavior of CBioseqGaps_CI.

This indicates the state of the iterator right now.

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