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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/fasta__aln__builder_8cpp_source.html below:

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

: m_DS(new

), m_LastAlignmentPos(0), m_LastReferencePos(kNoPos),

m_LastOtherPos(kNoPos), m_LastState(eDoubleGap),

m_LastNonDGState(eDoubleGap)

m_DS->SetIds().push_back(reference_id);

m_DS->SetIds().push_back(other_id);

(reference_pos !=

) {

(other_pos !=

) {

Helper class to build pairwise alignments, with double gaps automatically spliced out.

Helper class to build pairwise alignments, with double gaps automatically spliced out.

unsigned int TSeqPos

Type for sequence locations and lengths.

int TSignedSeqPos

Type for signed sequence position.

void x_EnsurePos(TSignedSeqPos &pos, TSignedSeqPos last_pos, TSeqPos alignment_pos)

TSignedSeqPos m_LastReferencePos

void AddData(TSeqPos alignment_pos, TSignedSeqPos reference_pos, TSignedSeqPos other_pos)

TSeqPos m_LastAlignmentPos

CRef< CSeq_align > GetCompletedAlignment(void)

EState x_State(TSignedSeqPos reference_pos, TSignedSeqPos other_pos)

TSignedSeqPos m_LastOtherPos

#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.

TLens & SetLens(void)

Assign a value to Lens data member.

void SetSegs(TSegs &value)

Assign a value to Segs data member.

const TLens & GetLens(void) const

Get the Lens member data.

void SetDim(TDim value)

Assign a value to Dim data member.

void SetType(TType value)

Assign a value to Type data member.

TStarts & SetStarts(void)

Assign a value to Starts data member.

void SetNumseg(TNumseg value)

Assign a value to Numseg data member.

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