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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/cigar_8cpp_source.html below:

NCBI C++ ToolKit: src/objtools/readers/cigar.cpp Source File

:

(GuessFormat(s, fmt))

(

pos = 0; pos < s.size(); ++pos) {

(

((

) s[pos])) {

(

== eLengthFirst) {

}

(

((

) s[pos])) {

pos2 = s.find_first_not_of(

, pos + 1);

*

kAlnum

=

;

first_alnum = s.find_first_of(kAlnum);

last_alnum = s.find_last_of(kAlnum);

(first_alnum == last_alnum) {

(first_alnum !=

&&

((

) s[first_alnum])) {

, first_alnum);

(first_alnum < last_alnum);

(

((

) s[first_alnum])) {

,

}

(

((

) s[last_alnum])) {

,

}

(

((

) s[last_alnum])) {

,

}

(s.find_first_of(

) ==

) {

, first_alnum);

loc->

().SetId().Assign(

);

loc->

().SetFrom(pos);

loc->

().SetTo(pos);

refsign = 1, refscale = 1, tgtsign = 1, tgtscale = 1;

shifty =

;

refid->Assign(ref.

());

it->len * refscale * refsign);

it->len * tgtscale * tgtsign);

refpos += it->len * refscale * refsign;

tgtpos += it->len * tgtscale * tgtsign;

tgtpos += it->len * tgtscale * tgtsign;

refpos += it->len * refscale * refsign;

seg->SetLoc().push_back(refseg);

seg->SetLoc().push_back(tgtseg);

align->

().SetStd().push_back(seg);

(refscale == tgtscale) {

bool IsReverse(ENa_strand s)

Code to handle Concise Idiosyncratic Gapped Alignment Report notation.

CRef< CSeq_align > CreateDensegFromStdseg(SSeqIdChooser *SeqIdChooser=0) const

---------------------------------------------------------------------------- PRE : the Seq-align has ...

TSeqPos GetLength(void) const

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

int TSignedSeqPos

Type for signed sequence position.

#define NCBI_THROW2(exception_class, err_code, message, extra)

Throw exception with extra parameter.

CRef< CSeq_loc > x_NextChunk(const CSeq_id &id, TSeqPos pos, TSignedSeqPos len) const

static EFormat GuessFormat(const string &s, EFormat fmt)

SCigarAlignment::EOperation op

EFormat

Length-first (ENSEMBL) and operation-first (original) variants both exist; allowing for the possibili...

CRef< CSeq_align > operator()(const CSeq_interval &ref, const CSeq_interval &tgt) const

vector< SSegment > TSegments

@ eLengthFirstIfAmbiguous

@ eForwardShift

only documented by GFF3 (same for R)

@ eIntron

not documented by GFF3

@ eNotSet

for internal use only

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

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

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.

NCBI_NS_STD::string::size_type SIZE_TYPE

static int StringToInt(const CTempString str, TStringToNumFlags flags=0, int base=10)

Convert string to int.

void SetSegs(TSegs &value)

Assign a value to Segs data member.

void SetDim(TDim value)

Assign a value to Dim data member.

void SetType(TType value)

Assign a value to Type data member.

@ eType_partial

mapping pieces together

const TId & GetId(void) const

Get the Id member data.

TFrom GetFrom(void) const

Get the From member data.

bool IsSetStrand(void) const

Check if a value has been assigned to Strand data member.

TStrand GetStrand(void) const

Get the Strand member data.

TTo GetTo(void) const

Get the To member data.

The blob sat and sat key Both must be positive integers</td > n< td > Non empty string The interpretation of the blob id depends on a processor Cassandra n processor expects the following format

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