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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/AliSeqAlign_8cpp_source.html below:

NCBI C++ ToolKit: src/algo/align/prosplign/AliSeqAlign.cpp Source File

m_ali(ali), m_scope(scope), m_protein(protein), m_genomic(genomic)

exon->SetGenomic_start(

(nulpos));

exon->SetGenomic_end(

(nulpos));

exon->SetGenomic_end(

(nulpos));

exon->SetGenomic_start(

(nulpos));

nulpos = 0, nultripos = 0;

vector<CAliPiece>::const_iterator pit =

.

.begin();

vector<CAliPiece>::const_iterator pit_end =

.

.end();

(; pit != pit_end; ++pit) {

(pit->m_type ==

)

nultripos += pit->m_len;

(pit->m_type ==

|| pit->m_type ==

)

nulpos += pit->m_len;

(--pit_end != pit && pit_end->m_type !=

)

exon->SetPartial(nultripos > 0);

(; pit != pit_end; ++pit) {

(pit->m_type ==

) {

s[0] = cnseq.

(nulpos);

s[1] = cnseq.

(nulpos+1);

exon->SetDonor_after_exon().SetBases(s);

nulpos += pit->m_len;

s[0] = cnseq.

(nulpos-2);

s[1] = cnseq.

(nulpos-1);

exon->SetAcceptor_before_exon().SetBases(s);

exon->SetParts().push_back(chunk);

(pit->m_type) {

chunk->SetProduct_ins(pit->m_len);

nultripos += pit->m_len;

chunk->SetGenomic_ins(pit->m_len);

nulpos += pit->m_len;

chunk->SetDiag(pit->m_len);

nultripos += pit->m_len;

nulpos += pit->m_len;

exon->SetPartial(nultripos <

(cpseq.

.size())*3);

CRef< CProduct_pos > NultriposToProduct_pos(int nultripos)

Convert linear coordinate into (amin,frame)

bool IsForward(ENa_strand s)

@ eExtreme_Positional

numerical value

void SetExonBioStart(CRef< CSpliced_exon > exon, int nulpos, int nultripos) const

static string Seq_idToString(CRef< CSeq_id > seqid)

void SetExonBioEnd(CRef< CSpliced_exon > exon, int nulpos, int nultripos) const

static CRef< CSeq_id > StringToSeq_id(const string &id)

CRef< CSeq_align > MakeSeq_align(const CPSeq &cpseq, const CNSeq &cnseq) const

int NucPosOut(int pos) const

CAliToSeq_align(const CAli &ali, CScope &scope, const CSeq_id &protein, const CSeq_loc &genomic)

const CSeq_loc & m_genomic

const CSeq_id & m_protein

char Upper(int pos) const

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

#define NCBI_THROW(exception_class, err_code, message)

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

string GetSeqIdString(bool with_version=false) const

Return seqid string with optional version for text seqid type.

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

Optimized implementation of CSerialObject::Assign, which is not so efficient.

static SIZE_TYPE ParseFastaIds(CBioseq::TId &ids, const CTempString &s, bool allow_partial_failure=false)

Parse an entire set of |-delimited FASTA-style IDs, appending the results to IDS.

static int Score(const CRef< CSeq_id > &id)

Wrappers for use with FindBestChoice from <corelib/ncbiutil.hpp>

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

Override Assign() to incorporate cache invalidation.

bool NotNull(void) const THROWS_NONE

Check if pointer is not null – same effect as NotEmpty().

void Reset(void)

Reset reference object.

#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.

C::value_type FindBestChoice(const C &container, F score_func)

Find the best choice (lowest score) for values in a container.

void SetAmin(TAmin value)

Assign a value to Amin data member.

void SetProduct_id(TProduct_id &value)

Assign a value to Product_id data member.

void SetSegs(TSegs &value)

Assign a value to Segs data member.

TExons & SetExons(void)

Assign a value to Exons data member.

void SetProduct_length(TProduct_length value)

Assign a value to Product_length data member.

void SetDim(TDim value)

Assign a value to Dim data member.

void SetType(TType value)

Assign a value to Type data member.

void SetProduct_type(TProduct_type value)

Assign a value to Product_type data member.

TProtpos & SetProtpos(void)

Select the variant.

void SetGenomic_id(TGenomic_id &value)

Assign a value to Genomic_id data member.

void SetGenomic_strand(TGenomic_strand value)

Assign a value to Genomic_strand data member.

void SetFrame(TFrame value)

Assign a value to Frame data member.

TBounds & SetBounds(void)

Assign a value to Bounds data member.

ENa_strand

strand of nucleic acid

list< CRef< CSeq_id > > TId

Useful/utility classes and methods.

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