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NCBI C++ ToolKit: src/objtools/alnmgr/alntext.cpp Source File

phase = (prot_prev+1)%3;

aa =

[prev_not_intron_pos];

added_len =

(3-phase,

);

(prev_not_intron_pos ==

.size()-1 && phase+added_len==3 && (phase==1 ||

[prev_not_intron_pos-1]==aa)) {

prot_prev += added_len;

* p =

.c_str();

start_pos =

.size()-

;

prev_exon_pos = 0;

(phase+

>=3 &&

((prev_exon_pos=

.find_last_not_of(is_insertion?INTRON:

,start_pos-1))!=start_pos-1 ||

codon =

.substr(prev_exon_pos-phase+1,phase)+

.substr(start_pos,3-phase);

(

= prev_exon_pos-phase+1;

<=prev_exon_pos;++

) {

( ; start_pos+3 <=

.size(); start_pos += 3) {

(start_pos <

.size()) {

& triplet)

.GetCodonResidue(

.SetCodonState(triplet[0], triplet[1], triplet[2]));

prev_3_prime_splice,

cur_5_prime_splice,

& nuc_prev,

& prot_prev,

nuc_cur_start,

prot_cur_start)

prot_hole_len = prot_cur_start - prot_prev -1;

nuc_hole_len = nuc_cur_start - nuc_prev -1;

can_show_splices = prot_hole_len < nuc_hole_len -4;

(can_show_splices && prev_3_prime_splice) {

nuc_hole_len = nuc_cur_start - nuc_prev -1;

(can_show_splices && cur_5_prime_splice) {

nuc_hole_len = nuc_cur_start - nuc_prev -1;

( prot_hole_len>0 || nuc_hole_len>0 );

left_gap = (prot_hole_len-nuc_hole_len)/2;

(genomic_ci,nuc_prev,nuc_hole_len);

(prot_hole_len>nuc_hole_len)

left_gap = (nuc_hole_len-prot_hole_len)/2;

(prot_hole_len<nuc_hole_len)

(can_show_splices && cur_5_prime_splice) {

& matrix_name)

& sps = seqalign.GetSegs().GetSpliced();

(packed_mtx ==

)

prev_3_prime_splice =

;

prev_genomic_ins = 0;

nuc_cur_start -= nuc_from;

nuc_cur_end -= nuc_from;

(nuc_cur_start,nuc_cur_end);

nuc_cur_start = nuc_to - nuc_cur_start;

nuc_cur_end = nuc_to - nuc_cur_end;

prot_prev+1 != prot_cur_start || !( (prev_3_prime_splice && cur_5_prime_splice) || (prot_cur_start==0 && nuc_cur_start==0) );

(prev_3_prime_splice, cur_5_prime_splice,

genomic_ci, protein_ci,

nuc_cur_start, prot_cur_start);

prev_genomic_ins = 0;

intron_len = nuc_cur_start - nuc_prev -1;

(genomic_ci, nuc_prev, intron_len);

prev_genomic_ins = 0;

}

(chunk.

()) {

(0<=prot_prev && prot_prev<prot_len-1 && (prot_prev+1)%3==0)

prev_genomic_ins = (prev_genomic_ins+

)%3;

(prot_prev <= prot_cur_end);

(prot_prev == prot_cur_end);

(nuc_prev == nuc_cur_end);

nuc_cur_start = nuc_to - nuc_from +1;

prot_cur_start = prot_len;

(prot_prev+1 != prot_cur_start || nuc_prev+1 != nuc_cur_start) {

cur_5_prime_splice =

;

(prev_3_prime_splice, cur_5_prime_splice,

genomic_ci, protein_ci,

nuc_cur_start, prot_cur_start);

((*b)->GetId() !=

&& (*b)->GetId()->Match(nucid)) {

genomic->

().SetFrom(0);

@ eExtreme_Positional

numerical value

USING_SCOPE(ncbi::objects)

static const CTrans_table & GetTransTable(int id)

SNCBIFullScoreMatrix m_matrix

void AddProtText(objects::CSeqVector_CI &protein_ci, int &prot_prev, int len)

static const char MATCH_CHAR

static const char INTRON_CHAR

static char TranslateTriplet(const objects::CTrans_table &table, const string &triplet)

static const char INTRON_OR_GAP[]

static const char SPACE_CHAR

const objects::CTrans_table * m_trans_table

static const char BAD_OR_MISMATCH[]

static const char MISMATCH_CHAR

void AddDNAText(objects::CSeqVector_CI &genomic_ci, int &nuc_prev, int len)

CProteinAlignText(objects::CScope &scope, const objects::CSeq_align &seqalign, const string &matrix_name="BLOSUM62")

void AddSpliceText(objects::CSeqVector_CI &genomic_ci, int &nuc_prev, char match)

void TranslateDNA(int phase, size_t len, bool is_insertion)

void AddHoleText(bool prev_3_prime_splice, bool cur_5_prime_splice, objects::CSeqVector_CI &genomic_ci, objects::CSeqVector_CI &protein_ci, int &nuc_prev, int &prot_prev, int nuc_cur_start, int prot_cur_start)

static CRef< objects::CSeq_loc > GetGenomicBounds(objects::CScope &scope, const objects::CSeq_align &seqalign)

void MatchText(size_t len, bool is_match=false)

static const char BAD_PIECE_CHAR

static const char POSIT_CHAR

static const char GAP_CHAR

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

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

void swap(NCBI_NS_NCBI::pair_base_member< T1, T2 > &pair1, NCBI_NS_NCBI::pair_base_member< T1, T2 > &pair2)

#define NCBI_THROW(exception_class, err_code, message)

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

void SetPacked_int(TPacked_int &v)

virtual void Assign(const CSerialObject &source, ESerialRecursionMode how=eRecursive)

Override Assign() to incorporate cache invalidation.

TRange GetTotalRange(void) const

TSeqPos GetStart(ESeqLocExtremes ext) const

Return start and stop positions of the seq-loc.

const CSeq_id * GetId(void) const

Get the id of the location return NULL if has multiple ids or no id at all.

void SetStrand(ENa_strand strand)

Set the strand for all of the location's ranges.

void SetNull(void)

Override all setters to incorporate cache invalidation.

TSeqPos GetStop(ESeqLocExtremes ext) const

TSeqPos GetLength(const CSeq_id &id, CScope *scope)

Get sequence length if scope not null, else return max possible TSeqPos.

CRef< CSeq_loc > Seq_loc_Merge(const CSeq_loc &loc, CSeq_loc::TOpFlags flags, CScope *scope)

Merge ranges in the seq-loc.

const COrg_ref & GetOrg_ref(const CBioseq_Handle &handle)

Return the org-ref associated with a given sequence.

@ eCoding_Iupac

Set coding to printable coding (Iupacna or Iupacaa)

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

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

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

NCBI_NS_STD::string::size_type SIZE_TYPE

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

const TDonor_after_exon & GetDonor_after_exon(void) const

Get the Donor_after_exon member data.

const TGenomic_id & GetGenomic_id(void) const

Get the Genomic_id member data.

bool CanGetAcceptor_before_exon(void) const

Check if it is safe to call GetAcceptor_before_exon method.

bool CanGetBases(void) const

Check if it is safe to call GetBases method.

bool CanGetBounds(void) const

Check if it is safe to call GetBounds method.

TMatch GetMatch(void) const

Get the variant data.

const TProduct_id & GetProduct_id(void) const

Get the Product_id member data.

TGenomic_start GetGenomic_start(void) const

Get the Genomic_start member data.

const TAcceptor_before_exon & GetAcceptor_before_exon(void) const

Get the Acceptor_before_exon member data.

bool IsMismatch(void) const

Check if variant Mismatch is selected.

TProduct_length GetProduct_length(void) const

Get the Product_length member data.

TDiag GetDiag(void) const

Get the variant data.

TMismatch GetMismatch(void) const

Get the variant data.

TGenomic_strand GetGenomic_strand(void) const

Get the Genomic_strand member data.

const TParts & GetParts(void) const

Get the Parts member data.

const TProduct_start & GetProduct_start(void) const

Get the Product_start member data.

const TProduct_end & GetProduct_end(void) const

Get the Product_end member data.

const TSpliced & GetSpliced(void) const

Get the variant data.

list< CRef< CSeq_loc > > TBounds

bool IsGenomic_ins(void) const

Check if variant Genomic_ins is selected.

bool IsMatch(void) const

Check if variant Match is selected.

TGenomic_ins GetGenomic_ins(void) const

Get the variant data.

list< CRef< CSpliced_exon > > TExons

const TExons & GetExons(void) const

Get the Exons member data.

bool IsDiag(void) const

Check if variant Diag is selected.

const TBases & GetBases(void) const

Get the Bases member data.

list< CRef< CSpliced_exon_chunk > > TParts

bool CanGetDonor_after_exon(void) const

Check if it is safe to call GetDonor_after_exon method.

TGenomic_end GetGenomic_end(void) const

Get the Genomic_end member data.

bool IsProduct_ins(void) const

Check if variant Product_ins is selected.

TProduct_ins GetProduct_ins(void) const

Get the variant data.

const TSegs & GetSegs(void) const

Get the Segs member data.

const TBounds & GetBounds(void) const

Get the Bounds member data.

ENa_strand

strand of nucleic acid

bool IsWhole(void) const

Check if variant Whole is selected.

<!DOCTYPE HTML >< html > n< header > n< title > PubSeq Gateway Help Page</title > n< style > n table

static int match(PCRE2_SPTR start_eptr, PCRE2_SPTR start_ecode, uint16_t top_bracket, PCRE2_SIZE frame_size, pcre2_match_data *match_data, match_block *mb)

const SNCBIPackedScoreMatrix * NCBISM_GetStandardMatrix(const char *name)

void NCBISM_Unpack(const SNCBIPackedScoreMatrix *psm, SNCBIFullScoreMatrix *fsm)

Expand a packed score matrix into an unpacked one, which callers can proceed to index directly by sta...

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