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NCBI C++ ToolKit: src/gui/widgets/aln_score/aln_scoring.cpp Source File

: m_Alignment(

),

: m_ScoreColls(

),

m_EnBgProcessing(

),

m_Listener = listener;

(grad_n > 1 && grad_n <= 0xFFFF);

(

<< job_id);

(

);

norm_done = prg->GetNormDone();

: m_ScoreColls(

),

vector<size_t> row_size(row_n);

is_mixed =

;

(!is_mixed && base_width !=

()->GetBaseWidth(

)) {

(translate && !is_mixed && base_width == 1) {

seq_len =

[

].size();

seq_len = new_seq.size();

(

= 0;

< seq_len; ++

) {

(n_i + 2 < new_seq.size());

(n_i > new_seq.size() - 2)

new_seq[n_i] = new_seq[n_i + 1] = new_seq[n_i + 2] =

[

][

];

seq_len = seq_len * 3;

(translate && base_width == 1) {

seq_len = new_seq.size();

&

,

gencode)

objects::CTrans_table& tbl =

objects::CGen_code_table::GetTransTable(gencode);

na_remainder = na.size() % 3;

na_size = na.size() - na_remainder;

aa.resize(na_size / 3 + (na_remainder ? 1 : 0));

( na.empty() )

;

(

na_i = 0; na_i < na_size; ) {

(

= 0;

< 3; ++

, ++na_i) {

= tbl.NextCodonState(

, na[na_i]);

aa[aa_i++] = tbl.GetCodonResidue(

);

(aligned_row == anchor)

(anchor_width == 3) {

}

(aligned_width == 3) {

ranges.emplace_back(curr_aln_r.

(), curr_aln_r.

());

= prot_from > prot_to;

(prot_from, prot_to);

ranges.emplace_back(curr_aln_r.

() - f_off, curr_aln_r.

() + t_off);

itC->SetFrom(aln_start);

(row_n,

);

vector<TSeqRange> ranges;

(mixed && aln_mgr->

() >= 0)

ranges.emplace_back(aln_start, aln_stop);

need_translation =

;

need_translation =

;

max_len =

((

)aln_stop - (

)aln_start) + 1;

kMaxMemoryForBuffers = 16 * 1024 * 1024;

(row_n * max_len * col_width <= kMaxMemoryForBuffers) {

= max<int>(300, kMaxMemoryForBuffers/(row_n * col_width));

(vector<TSeqRange>, r_iter, ranges) {

range = *r_iter;

start = range.GetFrom();

(pre_pos < start) {

(*m_ScoreColls)[

].push_back(0, start - pre_pos);

= float(pos - start) / (stop - start);

(p <= pos_stop) {

cons = (cons_row > -1) ?

[cons_row] : 0;

sc = ((

) (sc * grad_n)) / grad_n;

(*m_ScoreColls)[

].push_back(sc, col_width);

TScoreColl::const_pos_iterator TPosIt;

TPosIt itC_end = score_row.

();

this_score = it_sc->GetAttr();

(this_score < old_min) old_min = this_score;

(this_score > old_max) old_max = this_score;

TPosIt win_begin = itC;

TPosIt win_end = itC_end;

win_score = win_sum / (win_end - win_begin);

(win_score < new_min) {

(win_score > new_max) {

( ++itC; itC != itC_end; ++itC ) {

win_sum -= *win_begin;

(win_end < itC_end) {

win_score = win_sum/(win_end - win_begin);

(win_score < new_min) new_min = win_score;

(win_score > new_max) new_max = win_score;

norm_slope = (old_max - old_min) / (new_max - new_min);

(it_sc->GetAttr() - new_min) * norm_slope + old_min,

it_sc->GetLength() );

score_row.

(norm_score_row);

static void s_SetRangesForMixedAlignments(const IScoringAlignment *aln_mgr, vector< TSeqRange > &ranges)

ON_EVENT(CAppJobNotification, CAppJobNotification::eStateChanged, &CScoreCache::OnAJNotification) ON_EVENT(CAppJobNotification

CAppJobNotification Notification send by CAppJobEventTranslator.

CAppJobProgress Default implementation for IAppJobProgress - the class encapsulates a text message an...

CEvent - generic event implementation TODO TODO - Attachments.

class CRgbaColor provides a simple abstraction for managing colors.

virtual void OnScoringFinished()=0

virtual void OnScoringProgress(float progress, const string &msg)=0

void x_OnJobCanceled(CAppJobNotification &notn)

CScoreCache()

CScoreCache.

CRef< CScoringJob > m_Job

void x_OnJobFailed(CAppJobNotification &notn)

TScoreCollVector * m_ScoreColls

vector< TScoreColl > TScoreCollVector

void SetScoringMethod(IScoringMethod *method)

void x_OnJobCompleted(CAppJobNotification &notn)

IAlnExplorer::TNumrow TNumrow

bool x_IsJobRunning()

returns true if CScoreCache launched the job and it has not finished yet (it may have finished,...

bool x_TransferResults(CObject *result)

void OnAJNotification(CEvent *evt)

bool HasScores() const

returns "true" if CalculateScores() did produce results

void x_DeleteJob()

stop the job and destriy it

const TScoreColl & GetScores(TNumrow row) const

void CalculateScores(const TSeqRange &range=TSeqRange::GetEmpty())

Recalculate scores using current method; resets scores if no method is selected.

const CRgbaColor & GetColorForNoScore(IScoringMethod::EColorType type) const

void x_OnJobProgress(CAppJobNotification &notn)

void EnableBackgoundProcessing(bool en)

IListener * m_Listener

score storage

void SetGradNumber(int grad_n)

Sets the number of score gradations.

TScoreCollVector * m_ScoreColls

IScoringMethod::TScore TScore

IAlnExplorer::TNumrow TNumrow

void x_UpdateBuffer(TSeqPos start, TSeqPos stop, int &state, bool translate=false)

Fetches sequence from CAlnVec.

char x_BufferGetSeq(TSeqPos pos, TNumrow row) const

Sequence buffer management routins.

virtual EJobState Run()

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

virtual CRef< CObject > GetResult()

Returns the Job Result.

string m_Descr

buffer row length

const IScoringAlignment * GetAlignment() const

void x_WindowAvgScores(size_t window_size)

void x_AllocBuffer(TSeqPos row_len)

CRef< CAppJobError > m_Error

virtual string GetDescr() const

Returns a human readable description of the Job (optional)

CRef< CScoringJobResult > m_Result

normalized [0, 1.0] progress

vector< string > m_vRows

Sequence buffer data members.

virtual CConstIRef< IAppJobProgress > GetProgress()

return progress object, the function shall be synchronized internally.

TScoreCollVector * m_ScoreColls

void x_CalculateSequenceScores(IRowScoringMethod &method)

void TranslateNAToAA(const string &na, string &aa, int &state, int gencode=1) const

IScoringMethod::TScoreVector TScoreVector

void x_CalculateAlignmentScores(IColumnScoringMethod &method)

vector< TScoreColl > TScoreCollVector

TScoreCollVector * GetResults()

transfers ownership

virtual CConstIRef< IAppJobError > GetError()

Returns IAppJobError object describing internal error that caused the Job to fail.

TSeqPos m_RowLength

Aln position corresponding to the first column of the buffer.

CScoringJob(CScoringParams &params)

CScoringJob.

CScoringParams m_Params

score storage

void x_BufferGetColumn(TSeqPos pos, string &column) const

Alignment segment iterator interface.

@ eSkipGaps

Skip gap segments (show only aligned ranges)

Alignment segment interface.

virtual const TSignedRange & GetAlnRange(void) const =0

Get alignment range for the segment.

IColumnScoringMethod - column-based method.

virtual void UpdateSettings(const IScoringAlignment &aln)

Set alignment specifi settings.

virtual void CalculateScores(char cons, const string &column, IScoringMethod::TScore &col_score, IScoringMethod::TScoreVector &scores)=0

virtual bool CanCalculateScores(const IScoringAlignment &aln)=0

Do we have what it takes to calculate scores? e.g. a master row selected?

virtual bool NeedsTranslation() const

IRowScoringMethod - row-based method.

virtual void CalculateScores(IAlnExplorer::TNumrow row, const IScoringAlignment &aln, IScoringMethod::TScoreColl &scores)=0

virtual TSeqPos GetAlnStart() const =0

virtual bool IsMixedAlign() const

New interfaces to handle alignemnt with mixed type (protein-to-genomic) To make them backward compati...

virtual TSeqPos GetBaseWidth(IAlnExplorer::TNumrow) const =0

virtual TSeqPos GetAlnStop() const =0

virtual string & GetAlnSeqString(IAlnExplorer::TNumrow row, string &buffer, const IAlnExplorer::TSignedRange &aln_range) const =0

virtual IAlnExplorer::TNumrow GetNumRows() const =0

virtual IAlnExplorer::TNumrow GetAnchor() const =0

virtual IAlnSegmentIterator * CreateSegmentIterator(IAlnExplorer::TNumrow, const IAlnExplorer::TSignedRange &, IAlnSegmentIterator::EFlags) const =0

virtual TSignedSeqPos GetSeqPosFromAlnPos(IAlnExplorer::TNumrow for_row, TSeqPos aln_pos, IAlnExplorer::ESearchDirection dir=IAlnExplorer::eNone, bool try_reverse_dir=true) const =0

IScoringMethod represents an abstract algorithm for calculating alignment scores and assigning colors...

IWindowScoringMethod - Method that can be windowed, i.e.

virtual size_t GetWindowSize() const =0

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

static const char * column

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.

CConstIRef< IAppJobError > GetError() const

returns non-null pointer only if job Failed

const_pos_iterator begin_pos() const

static CAppJobDispatcher & GetInstance()

CRef< CObject > GetResult() const

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

const_pos_iterator end_pos() const

virtual bool IsCanceled() const override

position_type GetLength(void) const

void swap(CAttrRangeCollection &c)

bool DeleteJob(TJobID job_id)

when a Job is deleted the listener is not notified

EJobState

Job states (describe FSM)

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

void push_back(const attr_type &attr)

#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

TObjectType * GetPointer(void) THROWS_NONE

Get pointer,.

void Reset(void)

Reset reference object.

position_type GetLength(void) const

#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.

unsigned int

A callback function used to compare two keys in a database.

Defines classes: CDirEntry, CFile, CDir, CSymLink, CMemoryFile, CFileUtil, CFileLock,...

Process information in the NCBI Registry, including working with configuration files.

The NCBI C++/STL use hints.

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

static const TSeqPos kPageSize

#define row(bind, expected)

CConstIRef< IScoringAlignment > m_Alignment

CIRef< IScoringMethod > m_Method

TSeqRange m_VisibleRange

Visible range in the alignment coordinates if range is not empty scoring is applied to this range onl...

CScoringParams()

CScoringParams.

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