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

(

<<

<<

<< e.

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(

<< job_id);

progressSoFar->GetText(), progressSoFar->GetNormDone());

}

(

!= this_type) {

try_reverse_dir)

try_reverse_dir)

( seq_start > seq_stop ){

( seq_start, seq_stop );

from =

( seq_start, it->GetFrom() );

( aln_from > aln_to ){

( aln_from, aln_to );

aln_from =

( aln_start, it->GetFrom() );

aln_to =

( aln_stop, it->GetTo() );

= prg->GetText();

static CRef< CScope > m_Scope

Options for different alignment manager operations.

CAppJobNotification Notification send by CAppJobEventTranslator.

virtual EJobState Run()

Function that does all the useful work, called by the Engine.

virtual CRef< CObject > GetResult()

Returns the Job Result.

CRef< CSparseAln > m_SparseAln

CUpdate - notification send by CUIDataSource to the listener.

virtual void NotifyListener(CUpdate &update)

CEvent - generic event implementation TODO TODO - Attachments.

TThisType & CombineWith(const TRange &r)

bool IsSetAnchor(void) const

Check if anchor is set - always true for sparse alignments.

TSignedSeqPos GetSeqAlnStart(TNumrow row) const

TRng GetAlnRange(void) const

Get whole alignment range.

TNumrow GetNumRows(void) const

Synonym of the above.

int GetBaseWidth(TNumrow row) const

Get base width for the sequence (1 for nucleotides, 3 for proteins).

TSignedSeqPos GetSeqAlnStop(TNumrow row) const

void SetGapChar(TResidue gap_char)

Gap character modifier.

TSeqPos GetSeqStop(TNumrow row) const

virtual IAlnSegmentIterator * CreateSegmentIterator(TNumrow row, const TSignedRange &range, IAlnSegmentIterator::EFlags flags) const

Create segment iterator.

string & GetAlnSeqString(TNumrow row, string &buffer, const TSignedRange &rq_aln_rng, bool force_translation=false) const

Fetch alignment sequence data.

TSignedSeqPos GetAlnPosFromSeqPos(TNumrow row, TSeqPos seq_pos, ESearchDirection dir=eNone, bool try_reverse_dir=true) const

Map sequence position to alignment coordinates.

TSignedSeqPos GetSeqPosFromAlnPos(TNumrow for_row, TSeqPos aln_pos, ESearchDirection dir=eNone, bool try_reverse_dir=true) const

bool IsPositiveStrand(TNumrow row) const

Check direction of the row.

const objects::CBioseq_Handle & GetBioseqHandle(TNumrow row) const

Get bioseq handle for the row.

TNumrow GetAnchor(void) const

Get anchor row index.

TSeqPos GetSeqStart(TNumrow row) const

CRef< objects::CScope > GetScope(void) const

Scope accessor.

string & GetSeqString(TNumrow row, string &buffer, TSeqPos seq_from, TSeqPos seq_to, bool force_translation=false) const

Fetch sequence data for the given row and range.

bool IsNegativeStrand(TNumrow row) const

const objects::CSeq_id & GetSeqId(TNumrow row) const

Get seq-id for the row.

virtual void Init(CSparseAln &align)

CRef< CSparseAln > m_Alignment

CRef< CBuildSparseAlnJob > m_Job

virtual int GetGenCode(IAlnExplorer::TNumrow row) const

virtual bool IsSetAnchor(void) const

Anchoring methods.

virtual bool IsPositiveStrand(TNumrow row) const

virtual IAlnSegmentIterator * CreateSegmentIterator(TNumrow row, const IAlnExplorer::TSignedRange &range, IAlnSegmentIterator::EFlags flag) const

virtual void x_ClearHandles()

virtual bool IsNegativeStrand(TNumrow row) const

virtual const objects::CBioseq_Handle & GetBioseqHandle(TNumrow row) const

virtual TSeqPos GetAlnStart(void) const

virtual bool SetAnchor(TNumrow anchor)

virtual bool CanCreateConsensus()

virtual TNumrow GetNumRows(void) const

number of rows in alignment

virtual IAlnExplorer::EAlignType GetAlignType() const

virtual void SetGapChar(TResidue gap_char)

virtual bool UnsetAnchor(void)

vector< CSparseRowHandle * > THandleVector

virtual void GetSeqFromAln(TNumrow row, const TRangeColl &aln_coll, TRangeColl &seq_coll) const

virtual bool CanGetBioseqHandle(TNumrow row) const

virtual void x_OnJobProgress(CAppJobNotification &notn)

virtual TSignedSeqPos GetAlnPosFromSeqPos(TNumrow row, TSeqPos seq_pos, IAlnExplorer::ESearchDirection dir=IAlnExplorer::eNone, bool try_reverse_dir=true) const

CRef< objects::CScope > m_Scope

virtual TNumrow GetAnchor(void) const

virtual bool IsEmpty() const

virtual TSeqPos GetSeqStop(TNumrow row) const

virtual bool x_IsJobRunning()

virtual ~CSparseMultiDataSource()

virtual TSeqPos GetBaseWidth(TNumrow row) const

virtual bool CanChangeAnchor(void) const

virtual void x_CreateHandles()

void OnAppJobNotification(CEvent *evt)

virtual void GetAlnFromSeq(TNumrow row, const TRangeColl &seq_coll, TRangeColl &aln_coll) const

virtual TSignedSeqPos GetSeqPosFromAlnPos(TNumrow for_row, TSeqPos aln_pos, IAlnExplorer::ESearchDirection dir=IAlnExplorer::eNone, bool try_reverse_dir=true) const

virtual bool CanGetId(TNumrow row) const

CSparseAlignment::TNumrow TNumrow

virtual int GetConsensusRow() const

returns index of the Consensus row or -1 if it doesn't exist

virtual void CreateConsensus()

virtual TSeqPos GetSeqStart(TNumrow row) const

virtual string & GetSeqString(TNumrow row, string &buffer, const IAlnExplorer::TRange &seq_rng) const

virtual const objects::CSeq_id & GetSeqId(TNumrow row) const

virtual string & GetAlnSeqString(TNumrow row, string &buffer, const IAlnExplorer::TSignedRange &aln_rng) const

virtual bool CanGetSeqString(TNumrow row) const

virtual void x_DeleteJob()

virtual const IAlignRowHandle * GetRowHandle(TNumrow row) const

virtual TSeqPos GetAlnStop(void) const

IAlignRowHandle provides an abstract way to access alignment row data.

virtual int GetGenCode() const =0

ESearchDirection

Position search options.

@ eRight

Towards higher aln coord (always to the right)

@ eLeft

Towards lower aln coord (always to the left)

IAlnExplorer::TResidue TResidue

IAlnExplorer::TNumrow TNumrow

Alignment segment iterator interface.

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

int TSignedSeqPos

Type for signed sequence position.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

void swap(NCBI_NS_NCBI::pair_base_member< T1, T2 > &pair1, NCBI_NS_NCBI::pair_base_member< T1, T2 > &pair2)

#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 Error(CExceptionArgs_Base &args)

#define NCBI_THROW(exception_class, err_code, message)

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

const string & GetMsg(void) const

Get message string.

CConstIRef< IAppJobError > GetError() const

returns non-null pointer only if job Failed

static CAppJobDispatcher & GetInstance()

CRef< CObject > GetResult() const

returns non-null pointer only if Completed or Running and has temporary results available

bool DeleteJob(TJobID job_id)

when a Job is deleted the listener is not notified

TJobID StartJob(IAppJob &job, const string &engine_name, IEngineParams *params=NULL)

Starts a Job on the specified engine in "passive mode" - no notifications or progress reports will be...

CConstIRef< IAppJobProgress > GetProgress() const

returns non-null pointer only if notification type is eProgress

#define END_EVENT_MAP()

Ends definition of Command Map.

#define BEGIN_EVENT_MAP(thisClass, baseClass)

Begins definition of Command Map for CEventHandler-derived class.

TJobState GetState() const

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

bool IsNucleotide(void) const

TObjectType * GetPointer(void) THROWS_NONE

Get pointer,.

void Reset(void)

Reset reference object.

CRange< TSeqPos > TSeqRange

typedefs for sequence ranges

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

static void text(MDB_val *v)

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

ON_EVENT(CAppJobNotification, CAppJobNotification::eStateChanged, &CSparseMultiDataSource::OnAppJobNotification) ON_EVENT(CAppJobNotification

CSparseMultiDataSource.

USING_SCOPE(ncbi::objects)

#define row(bind, expected)

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