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

<< (aln_rng.

() ?

:

)

<< aln_seq_id_iref->AsString()

<<

<< aln_seq_id_iref->GetBaseWidth()

<<

;

cout <<

<< pairwise_aln.

() <<

<< endl;

<<

<< anchored_aln.

() <<

<< anchored_aln.

() <<

<< endl;

<< **pairwise_aln_i;

ostream & operator<<(ostream &out, const CPairwiseAln::TRng &rng)

@ fMixedDir

contains at least one reversed range

@ fNotValidated

State flags:

@ fAllowOverlap

allow segments with different orientation

@ fAllowAbutting

allow segments overlapping on the first sequence

@ fInvalid

collection was modified and not validated

@ fAllowMixedDir

enforce all policies after any modification

@ fKeepNormalized

Policies:

@ fReversed

contains at least one direct range

@ fUnsorted

one or more policies violated

CAlignRange Represents an element of pairwise alignment of two sequences.

Query-anchored alignment can be 2 or multi-dimentional.

const TPairwiseAlnVector & GetPairwiseAlns(void) const

The vector of pairwise alns.

vector< CRef< CPairwiseAln > > TPairwiseAlnVector

TDim GetDim(void) const

How many rows.

int GetScore(void) const

What is the total score?

A pairwise aln is a collection of ranges for a pair of rows.

const TAlnSeqIdIRef & GetFirstId(void) const

Get first sequence id.

const TAlnSeqIdIRef & GetSecondId(void) const

Get second sequence id.

Alignment segment interface.

virtual const TSignedRange & GetRange(void) const =0

Get the selected row range.

ESegTypeFlags

binary OR of ESegTypeFlags

@ fAligned

Aligned segment.

@ fInvalid

The iterator is in bad state.

@ fIndel

Either anchor or the selected row is not present in the segment.

@ fUnaligned

The range on the selected sequence does not participate in the alignment (the alignment range of the ...

@ fReversed

The selected row is reversed (relative to the anchor).

@ fGap

Both anchor row and the selected row are not included in the segment (some other row is present and t...

virtual TSegTypeFlags GetType(void) const =0

Get current segment type.

virtual const TSignedRange & GetAlnRange(void) const =0

Get alignment range for the segment.

std::ofstream out("events_result.xml")

main entry point for tests

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

position_type GetLength(void) const

position_type GetToOpen(void) const

position_type GetSecondFrom(void) const

position_type GetFirstFrom(void) const

position_type GetLength(void) const

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

static string UIntToString(unsigned int value, TNumToStringFlags flags=0, int base=10)

Convert UInt to string.

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

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