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NCBI C++ ToolKit: src/gui/widgets/hit_matrix/dense_ds.cpp Source File

<

TIDRefCont>

TIDRefCont::const_iterator

(

TIDRefCont, it, cont) {

((*it)->Equals(

))

id1->

(*id2);

check_std =

;

TSegs::e_Denseg:

TSegs::e_Dendiag:

TSegs::e_Sparse:

TSegs::e_Spliced:

(

<< e.what());

(

);

(

<<

);

(based_ch || orient_ch) {

unique_ptr<IHitSeqId> s_id(

.release());

unique_ptr<IHitSeqId> q_id(

.release());

(create_hits && s_id.get() && q_id.get()) {

& score = **itSc;

(

.Which()) {

range.first =

(range.first,

);

range.second =

(range.second,

);

->GetSeqId()->Equals(*

);

TSegs::e_Denseg:

TSegs::e_Dendiag:

TSegs::e_Sparse:

TSegs::e_Spliced:

& seq_id = *

.GetSeqId();

add = (self_count == 2);

(ids.end() == std::find_if(ids.begin(), ids.end(), Eq)) {

(self_count == 0) {

TSegs::e_Denseg:

TSegs::e_Dendiag:

TSegs::e_Sparse:

TSegs::e_Spliced:

(ids.end() == std::find_if(ids.begin(), ids.end(), Eq)) {

(

= 0;

< aln_ids.size();

++ ) {

(seq_ids.end() == std::find_if(seq_ids.begin(), seq_ids.end(), Eq)) {

seq_ids.push_back(

(*seq_id));

(

= 0;

< ids.size();

++ ) {

ids[

] = ids[

]->Clone();

(! (*it)->Equals(

)) {

aligned.push_back(*it);

TIdVector::const_iterator it_id =

(ids,

);

(it_id != ids.end()) {

index_2 = min<size_t>(1,

.size() - 1);

q_index = q_id->

();

s_index = s_id->

();

vector<size_t> s_rows;

n_rows = aln_ids.size();

(

s_index = 0; s_index < n_rows; s_index++ ) {

&

= *aln_ids[s_index];

s_rows.push_back(s_index);

(

q_index = 0; q_index < n_rows; q_index++ ) {

&

= *aln_ids[q_index];

(

->GetSeqId()->Equals(

)) {

(

= 0;

< s_rows.size();

++ ) {

s_index = s_rows[

];

q_index,

s_index)

TSegs::e_Denseg:

TSegs::e_Dendiag:

TSegs::e_Sparse:

TSegs::e_Spliced:

(

<<

<<

);

q_index,

s_index)

(range.

()) {

q_index,

s_index)

list< CRef< CStd_seg > >

;

q_index,

s_index)

( ! pairwise->empty()) {

(

= 0;

<

.size();

++ ) {

(

j = 0; j < n_elem; j++ ) {

->GetBioseqHandle(*seq_id);

.push_back(it->first);

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.

TAlnSeqIdExtract::TIdVec TIdVec

Container (vector) of seq-ids.

Default IAlnSeqId implementation based on CSeq_id_Handle.

_TAlnIdVec::TIdVec TIdVec

Vector of ids used in all alignments.

@ eBothDirections

No filtering: use both direct and reverse sequences.

Wraps a CSeq_align containing CDense_seg and provides a simple API for interpreting it as a pairwise ...

static bool HasAlignment(const objects::CDense_seg &denseg, size_t q_index, size_t s_index, TDirection dir)

CDenseSegHit.

objects::CBioseq_Handle m_QueryHandle

void x_CreateHit_Denseg(const objects::CSeq_align &align, size_t q_index, size_t s_index)

creates a single hit from 2 rows of a Seq-align

void x_GetSeqAlignIds(const objects::CSeq_align &align, TSeqIdRefVector &ids, bool unique) const

bool x_GoodSeg(const TStd &std_list)

TSeqRange GetStdSegRange(const TStd &std_list, size_t row)

vector< CConstRef< objects::CSeq_id > > TSeqIdRefVector

virtual bool SelectDefaultIds()

selects default query and subject

TSeqRange m_SubjectHitsRange

objects::CBioseq_Handle m_SubjectHandle

virtual void GetAlignedIdsForParams(const IHitSeqId &id, const TIdVector &ids, TIdVector &aligned, const SParams &params)

returns a list of ids that will be aligned with the specified id if the given params are applied.

void x_CreateHits_Diagonal(const objects::CSeq_align &align, size_t q_index, size_t s_index)

virtual objects::CBioseq_Handle GetSubjectHandle()

virtual void SetParams(const SParams &params, bool create_hits)

virtual void GetParams(SParams &params) const

TValueRange GetScoreRange(const string &name) const

const THitAdapterCont & GetHits() const

virtual objects::CScope & GetScope()

bool x_CanCreateRowBased()

THIdToHandleMap m_HIdToHandleMap

list of Ids for all sequences

unique_ptr< IHitSeqId > m_QueryID

void x_CalculateHitsRange()

void Init(objects::CScope &scope, TAlignVector &aligns)

void x_CreateHit_Std(const objects::CSeq_align &align, size_t q_index, size_t s_index)

virtual string GetLabel(const IHitSeqId &id)

CAlnIdMap< TAlnPtrVector, TIdExtract > TAlnIdMap

TSeqRange GetQueryHitsRange()

void x_CreateIds(TIdVector &seq_ids, const SParams &params) const

void x_GetAlignedSeqIds(const CSeq_align &align, const IHitSeqId &id, TSeqIdRefVector &ids) const

virtual IHitSeqId & GetSubjectId() const

void x_CreateHits(const objects::CSeq_align &align)

virtual IHitSeqId & GetQueryId() const

objects::CSeq_align::TSegs::TStd TStd

virtual void GetAlignedIds(const IHitSeqId &id, TIdVector &aligned)

unique_ptr< IHitSeqId > m_SubjectID

CAlnStats< TAlnIdMap > TAlnStats

virtual objects::CBioseq_Handle GetBioseqHandle(const IHitSeqId &id)

void x_TestAndSelectAligns(TAlignVector &aligns)

TSeqRange GetSubjectHitsRange()

unique_ptr< TAlnIdMap > m_AlnIdMap

CAlnSeqIdsExtract< CAlnSeqId > TIdExtract

virtual objects::CBioseq_Handle GetQueryHandle()

virtual void GetHitSeqIdsForParams(TIdVector &ids, const SParams &params) const

returns a list of ids that Data Source will create if the given params are applied.

void x_TestAndSelectAlign(const objects::CSeq_align &align)

virtual bool SelectIds(const IHitSeqId &q_id, const IHitSeqId &s_id)

Creates Hits for all pairwise alignments between selected by Query and Subject IDs.

void x_UpdateScoreMap()

builds a map of all scores found in the alignments

virtual ~CHitMatrixDataSource()

CRef< objects::CScope > m_Scope

CHitMatrixDataSource()

CHitMatrixDataSource.

TSeqRange m_QueryHitsRange

void x_CreateHit(const objects::CSeq_align &align, size_t q_index, size_t s_index)

virtual bool CanCreateRowBased() const

CRef< TAlnStats > m_AlnStats

virtual void GetScoreNames(vector< string > &names) const

virtual const TIdVector & GetHitSeqIds()

returns list of all seq ids in the Data Source

CConstRef< objects::CSeq_id > m_SeqId

virtual bool Equals(const IHitSeqId &id) const

CHitSeqId.

CHitSeqId(const objects::CSeq_id &id)

virtual IHitSeqId * Clone() const

virtual bool Equals(const IHitSeqId &id) const

virtual CConstRef< objects::CSeq_id > GetSeqId() const

returns CSeq_id associated with IHitSeqId

CHitSeqRowId(int row, const objects::CSeq_id &id)

CHitSeqRowId.

virtual IHitSeqId * Clone() const

CConstRef< objects::CSeq_id > m_SeqId

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

bool operator()(IHitSeqId *id) const

CSeqIdEquals(const CRef< CSeq_id > &id)

CConstRef< CSeq_id > m_Id

CSeqIdEquals(const CConstRef< CSeq_id > &id)

CSeqIdEquals(const CSeq_id &id)

bool operator()(const CSeq_id &id) const

bool operator()(CConstRef< CSeq_id > &id) const

Wraps a CSeq_align containing CStd_seg and provides a simple API for interpreting it as a pairwise al...

static bool HasAlignment(const TStd &std_list, size_t q_index, size_t s_index, TDirection dir)

TSignedSeqPos GetSeqStop(TDim row) const

TSignedSeqPos GetSeqStart(TDim row) const

Wrapper interface for seq-ids used in alignments.

virtual const CSeq_id & GetSeqId(void) const =0

Get CSeq_id.

virtual TSeqPos GetQueryLength() const =0

virtual TSignedSeqPos GetQueryStart() const =0

virtual TSeqPos GetSubjectLength() const =0

virtual TSignedSeqPos GetSubjectStart() const =0

vector< CConstRef< objects::CSeq_align > > TAlignVector

vector< IHitSeqId * > TIdVector

vector< IHit * > THitAdapterCont

pair< double, double > TValueRange

IHitSeqId - abstract identifier of a sequence in an alignment.

virtual IHitSeqId * Clone() const =0

virtual TDim GetElemsCount() const =0

virtual const IHitElement & GetElem(TDim elem_index) const =0

container_type::const_iterator const_iterator

container_type::iterator iterator

const_iterator end() const

const_iterator find(const key_type &key) const

iterator_bool insert(const value_type &val)

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

bool FIdEqual(const CConstRef< CSeq_id > &id1, const CConstRef< CSeq_id > &id2)

USING_SCOPE(ncbi::objects)

TIDRefCont::const_iterator find_id(const TIDRefCont &cont, const IHitSeqId &id)

static const struct name_t names[]

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define ERR_POST(message)

Error posting with file, line number information but without error codes.

#define LOG_POST(message)

This macro is deprecated and it's strongly recomended to move in all projects (except tests) to macro...

void Info(CExceptionArgs_Base &args)

static void GetLabel(const CObject &obj, string *label, ELabelType type=eDefault)

virtual bool Equals(const CSerialObject &object, ESerialRecursionMode how=eRecursive) const

Check if both objects contain the same values.

ENa_strand GetStrand(void) const

Get the location's strand.

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

TObjectType * GetPointer(void) THROWS_NONE

Get pointer,.

void Reset(void)

Reset reference object.

TObjectType & GetObject(void)

Get object.

TThisType & CombineWith(const TThisType &r)

static TThisType GetEmpty(void)

TThisType & Set(position_type from, position_type to)

CRange< TSeqPos > TSeqRange

typedefs for sequence ranges

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

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

Convert int to string.

const TDenseg & GetDenseg(void) const

Get the variant data.

vector< CRef< CSeq_loc > > TLoc

E_Choice Which(void) const

Which variant is currently selected.

vector< CRef< CScore > > TScore

const TLoc & GetLoc(void) const

Get the Loc member data.

bool IsSetSegs(void) const

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

bool CanGetSegs(void) const

Check if it is safe to call GetSegs method.

const TStd & GetStd(void) const

Get the variant data.

const TValue & GetValue(void) const

Get the Value member data.

bool CanGetId(void) const

Check if it is safe to call GetId method.

bool IsStd(void) const

Check if variant Std is selected.

list< CRef< CSeq_align > > Tdata

const TScore & GetScore(void) const

Get the Score member data.

const TDisc & GetDisc(void) const

Get the variant data.

const TId & GetId(void) const

Get the Id member data.

const Tdata & Get(void) const

Get the member data.

const TSegs & GetSegs(void) const

Get the Segs member data.

bool IsDenseg(void) const

Check if variant Denseg is selected.

ENa_strand

strand of nucleic acid

const GenericPointer< typename T::ValueType > T2 value

double r(size_t dimension_, const Int4 *score_, const double *prob_, double theta_)

static bool GetSeqId(const T &d, set< string > &labels, const string name="", bool detect=false, bool found=false)

#define row(bind, expected)

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