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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/alnmulti__ds__builder_8cpp_source.html below:

NCBI C++ ToolKit: src/gui/widgets/aln_multiple/alnmulti_ds_builder.cpp Source File

: m_CreateSparse(

)

, m_SyncCreate(

)

& sid = (*it)->GetSeqId();

handles.push_back(h);

(

);

TIDToAligns align_map;

TIDToAligns::const_iterator it = align_map.find(idh);

(it == align_map.end()) {

(TIDToAligns, it_map, align_map) {

& aln_set = it_map->second;

(aln_set.

() > max_al) {

max_al = aln_set.

();

max_h = it_map->first;

(

<< s_id);

TSegs& segs = align.

();

(segs.Which()) {

TSegs::e_Denseg:

TSegs::e_Dendiag:

(TSegs::TStd, it_s, segs.GetStd()) {

TSegs::e_Sparse:

TSegs::e_Spliced:

aligns.push_back(*it);

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

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

USING_SCOPE(ncbi::objects)

Container mapping seq-aligns to vectors of participating seq-ids.

void push_back(const CSeq_align &aln)

Adding an alignment.

CConstRef< objects::CSeq_id > m_MasterId

CDataChangeNotifier::IListener * m_Listener

Try to set anchor automatically.

void GetBioseqHandles(vector< CBioseq_Handle > &handles)

bool m_CreateSparse

control alignment building

TAnchoredAlnVector m_AnchoredAlns

bool x_IsLinear(const objects::CStd_seg &seg)

returns true if CStd_seg is linear

void x_GetLinearAlignments(TAlignVector &aligns)

vector< CConstRef< objects::CSeq_align > > TAlignVector

void Init(objects::CScope &scope, const objects::CSeq_align &align)

initial data set from which an alignment will be build

virtual ~CAlnMultiDSBuilder()

TAlignVector m_OrigAligns

CAlnStats< TAlnIdMap > TAlnStats

CRef< objects::CScope > m_Scope

CRef< IAlnMultiDataSource > x_CreateSparseDataSource()

void x_PreCreateSparseDataSource()

vector< CConstRef< objects::CSeq_annot > > TAnnotVector

CRef< IAlnMultiDataSource > CreateDataSource()

CRef< IAlnMultiDataSource > x_CreateAlnVecDataSource()

CRef< TAlnStats > m_AlnStats

void x_TestAlignments()

Analyzes m_OrigAligns and decides how to build an alignment from it.

void PreCreateDataSource(bool sparse)

_TAlnIdVec::TIdVec TIdVec

Vector of ids used in all alignments.

CAlnVecMultiDataSource - implementation of IAlnMultiDataSource for CAlnVec-based alignments.

virtual void SetListener(IListener *pListener)

Subscribe a new listener.

virtual void Init(CSparseAln &align)

Template class for iteration on objects of class C (non-medifiable version)

iterator_bool insert(const value_type &val)

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

static objects::SAnnotSelector GetAnnotSelector(TAnnotFlags flags=0)

request an annotation selector for a given type

CConstRef< CSeq_id > GetSeqId(void) const

static CSeq_id_Handle GetHandle(const CSeq_id &id)

Normal way of getting a handle, works for any seq-id.

TObjectType * GetPointer(void) const THROWS_NONE

Get pointer,.

TObjectType * GetPointer(void) THROWS_NONE

Get pointer,.

void Reset(void)

Reset reference object.

void Reset(void)

Reset reference object.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

double Elapsed(void) const

Return time elapsed since first Start() or last Restart() call (in seconds).

void Start(void)

Start the timer.

const TSegs & GetSegs(void) const

Get the Segs member data.

bool IsAlign(void) const

Check if variant Align is selected.

const TData & GetData(void) const

Get the Data member data.

double value_type

The numeric datatype used by the parser.

Defines: CTimeFormat - storage class for time format.

set< CGeneModel, SAlignOrder > TAlignSet

void ExtractSeqAligns(const T &obj, vector< CConstRef< objects::CSeq_align > > &aligns)

This is the place where elements of the new Alignment Library will be collected.

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