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NCBI C++ ToolKit: include/objtools/alnmgr/aln_converters.hpp Source File

objects::CSeq_align& sa,

objects::CDense_seg& ds,

objects::CPacked_seg& ps,

objects::CSeq_align::TSegs::TStd& stds,

objects::CSparse_seg& sparse_seg,

objects::CSpliced_seg& spliced_seg,

objects::CSeq_loc& loc_1,

objects::CSeq_loc& loc_2,

<

_TAlnStats>

_TAlnStats& aln_stats,

dim = aln_stats.GetDimForAln(aln_idx);

(explicit_anchor_row >= 0) {

(explicit_anchor_row >= dim) {

);

anchor_row = explicit_anchor_row;

anchor_id_idx = 0;

( aln_stats.CanBeAnchored() ) {

(it == aln_stats.GetAnchorIdMap().end()) {

);

anchor_id_idx = it->second[0];

(

= 0;

< aln_stats.GetAnchorIdVec().

(); ++

) {

& anchor_id = aln_stats.GetAnchorIdVec()[

];

(aln_stats.GetAnchorIdMap().find(anchor_id)->second.size() > 1) {

anchor_id_idx = aln_stats.GetAnchorIdxVec()[

];

anchor_id_idx = aln_stats.GetAnchorIdxVec()[

];

);

anchor_row = aln_stats.GetRowVecVec()[anchor_id_idx][aln_idx];

force_widths =

;

( aln_stats.GetIdVec()[anchor_row]->IsProtein() ) {

(

= 0;

< aln_stats.GetIdVec().

(); ++

) {

( !aln_stats.GetIdVec()[

]->IsProtein() ) {

force_widths =

;

& seq_aln = *aln_stats.GetAlnVec()[aln_idx];

_TAlnStats::TIdVec TIdVec;

TIdVec ids = aln_stats.GetSeqIdsForAln(aln_idx);

pairwises.resize(dim);

== anchor_row ? anchor_flags :

));

*pairwise_aln, seq_aln,

( force_widths ) {

pairwise_aln->ForceGenomicCoords();

( pairwise_aln->empty() ) {

pairwises[

].

(pairwise_aln);

(empty_rows == dim - 1) {

new_dim = dim - empty_rows;

target_anchor_row =

anchored_aln->

(new_dim);

( !pairwises[

]->

() ) {

(target_row == target_anchor_row) {

target_row++].Reset(pairwises[

]);

<

_TAlnStats>

out_vec.reserve(aln_stats.GetAlnCount());

(

aln_idx = 0; aln_idx < aln_stats.GetAlnCount(); ++aln_idx) {

( !anchored_aln )

;

& aln = *aln_stats.GetAlnVec()[aln_idx];

need_split =

;

(

== anchor_row)

;

(

apw_seg = apw.

(), rpw_seg = rpw.

();

rpw_seg != rpw.

(); ++apw_seg, ++rpw_seg) {

sub_anchored_aln->

(2);

sub_row->insert(sub_row->end(), *rpw_seg);

sub_anchor_row->insert(sub_anchor_row->end(), *apw_seg);

(anchor_row == 0) {

out_vec.push_back(sub_anchored_aln);

sub_anchored_aln->

(rpw_seg->GetLength());

out_vec.push_back(anchored_aln);

anchored_aln->

() += rng_it->GetLength();

CRef< CPairwiseAln > CreatePairwiseAlnFromSeqAlign(const objects::CSeq_align &seq_align)

A simple API that assumes that the seq_align has exactly two rows and you want to create a pairwise w...

void ConvertSeqAlignToPairwiseAln(CPairwiseAln &pairwise_aln, const objects::CSeq_align &sa, objects::CSeq_align::TDim row_1, objects::CSeq_align::TDim row_2, CAlnUserOptions::EDirection direction=CAlnUserOptions::eBothDirections, const TAlnSeqIdVec *ids=0)

Build pairwise alignment from the selected rows of a seq-align.

void ConvertStdsegToPairwiseAln(CPairwiseAln &pairwise_aln, const objects::CSeq_align::TSegs::TStd &stds, objects::CSeq_align::TDim row_1, objects::CSeq_align::TDim row_2, CAlnUserOptions::EDirection direction=CAlnUserOptions::eBothDirections, const TAlnSeqIdVec *ids=0)

Build pairwise alignment from the selected rows of an std-seg.

void ConvertSeqLocsToPairwiseAln(CPairwiseAln &aln, const objects::CSeq_loc &loc_1, const objects::CSeq_loc &loc_2, CAlnUserOptions::EDirection direction=CAlnUserOptions::eBothDirections)

Build pairwise alignment from a pair of seq-locs.

void ConvertDensegToPairwiseAln(CPairwiseAln &pairwise_aln, const objects::CDense_seg &ds, objects::CSeq_align::TDim row_1, objects::CSeq_align::TDim row_2, CAlnUserOptions::EDirection direction=CAlnUserOptions::eBothDirections, const TAlnSeqIdVec *ids=0)

Build pairwise alignment from the selected rows of a dense-seg.

void ConvertSparseToPairwiseAln(CPairwiseAln &pairwise_aln, const objects::CSparse_seg &sparse_seg, objects::CSeq_align::TDim row_1, objects::CSeq_align::TDim row_2, CAlnUserOptions::EDirection direction=CAlnUserOptions::eBothDirections, const TAlnSeqIdVec *ids=0)

Build pairwise alignment from the selected rows of a sparse-seg.

void ConvertSplicedToPairwiseAln(CPairwiseAln &pairwise_aln, const objects::CSpliced_seg &spliced_seg, objects::CSeq_align::TDim row_1, objects::CSeq_align::TDim row_2, CAlnUserOptions::EDirection direction=CAlnUserOptions::eBothDirections, const TAlnSeqIdVec *ids=0)

Build pairwise alignment from the selected rows of a spliced-seg.

void ConvertDendiagToPairwiseAln(CPairwiseAln &pairwise_aln, const objects::CSeq_align::TSegs::TDendiag &dendiags, objects::CSeq_align::TDim row_1, objects::CSeq_align::TDim row_2, CAlnUserOptions::EDirection direction=CAlnUserOptions::eBothDirections, const TAlnSeqIdVec *ids=0)

Build pairwise alignment from the selected rows of a dendiag.

list< CRef< CPairwiseAln > > TPairwiseAlnList

void SeqLocMapperToPairwiseAligns(const objects::CSeq_loc_Mapper_Base &mapper, TPairwiseAlnList &aligns)

Build a list of pairwise alignments from a seq-loc mapper's mappings.

void CreateAnchoredAlnVec(_TAlnStats &aln_stats, TAnchoredAlnVec &out_vec, const CAlnUserOptions &options)

Create anchored alignment from each seq-align in the stats.

void ConvertPackedsegToPairwiseAln(CPairwiseAln &pairwise_aln, const objects::CPacked_seg &ps, objects::CSeq_align::TDim row_1, objects::CSeq_align::TDim row_2, CAlnUserOptions::EDirection direction=CAlnUserOptions::eBothDirections, const TAlnSeqIdVec *ids=0)

Build pairwise alignment from the selected rows of a packed-seg.

CRef< CAnchoredAln > CreateAnchoredAlnFromAln(const _TAlnStats &aln_stats, size_t aln_idx, const CAlnUserOptions &options, objects::CSeq_align::TDim explicit_anchor_row=-1)

Create an anchored alignment from Seq-align using hints.

vector< TAlnSeqIdIRef > TAlnSeqIdVec

#define _ALNMGR_ASSERT(expr)

bool IsSet(int flags) const

int GetPolicyFlags() const

const_iterator begin() const

@ fMixedDir

contains at least one reversed range

@ fAllowOverlap

allow segments with different orientation

@ fIgnoreInsertions

allows segments not separated by gaps

@ fAllowMixedDir

enforce all policies after any modification

@ fKeepNormalized

Policies:

const_iterator end() const

Options for different alignment manager operations.

const TAlnSeqIdIRef & GetAnchorId(void) const

Get anchor id.

EDirection

Row direction flags.

@ eBothDirections

No filtering: use both direct and reverse sequences.

@ eDirect

Use only sequences whose strand is the same as that of the anchor.

@ fAnchorRowFirst

Store anchor row in the first pairwise alignment (by default it's stored in the last one).

@ fIgnoreInsertions

Do not collect and store insertions (gaps on the anchor).

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.

void SetAnchorRow(TDim anchor_row)

Modify anchor row (never do this unless you are creating a new alignment and know what you're doing).

TPairwiseAlnVector & SetPairwiseAlns(void)

Modify pairwise alns.

void SetScore(int score)

Set the total score.

TDim GetAnchorRow(void) const

Which is the anchor row?

void SetDim(TDim dim)

Modify the number of rows.

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.

container_type::const_iterator const_iterator

const_iterator find(const key_type &key) const

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

CSeq_align::C_Segs::TDendiag TDendiag

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define NCBI_THROW(exception_class, err_code, message)

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

void Reset(void)

Reset reference object.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define NCBI_XALNMGR_EXPORT

bool IsStd(void) const

Check if variant Std is selected.

const TSegs & GetSegs(void) const

Get the Segs member data.

constexpr bool empty(list< Ts... >) noexcept

const struct ncbi::grid::netcache::search::fields::SIZE size

Portable reference counted smart and weak pointers using CWeakRef, CRef, CObject and CObjectEx.

vector< CRef< CAnchoredAln > > TAnchoredAlnVec

Collection of anchored alignments.

#define row(bind, expected)

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