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NCBI C++ ToolKit: src/gui/widgets/seq_graphic/seqgraphic_alignment_ds.cpp Source File

, m_LinkMatePairs(

)

, m_HasCoverageGraph(

)

, m_HasQualityMap(

)

protein_method)

vector<TSeqRange> missing_ranges;

missing_ranges.emplace_back(range.

(), range.

());

missing_ranges.clear();

->GetMissingRegions(range, missing_ranges);

cost_in_sec = 0.;

(!missing_ranges.empty()) {

(

&

: missing_ranges) {

cost_in_sec =

(cost_in_sec, cost);

vector<TSeqRange> missing_ranges;

->GetMissingRegions(range, missing_ranges);

missing_ranges.emplace_back(range.

(), range.

());

(

&

: missing_ranges) {

+=

.GetLength();

cost_in_sec = 0.;

log_1024 =

(1024);

exp = (

)(

(bytes) / log_1024);

suffix =

;

suffix = suffix.substr(exp - 1, 1);

job->SetToken(token);

smear_if_overlimit,

job.

(aln_job);

job->SetToken(token);

num_reads =

->GetNumberOfReads(range);

res = num_reads < align_limit;

vector<TSeqRange> missing_ranges;

->GetMissingRegions(range, missing_ranges);

(missing_ranges.empty())

,

, aln_sel, graph_sel, range, aligns, window, cache_key));

job->SetToken(token);

vector<int>& projected_feats,

(vector<int>, iter, projected_feats) {

job->SetToken(token);

alnType = aln->GetAlignMgr().GetAlignType();

* aln = mp->GetSeqAligns().front();

(

<<

vector<string> annots;

vector<string> annots;

(tmp_meth->GetName() == name) {

(tmp_meth->GetName() == name) {

new_score =

;

(tmp_meth->GetName() == name) {

(objs.empty())

;

first_aln = first_mp->

().front().GetPointer();

(iter->second->HasScores()) {

temp_map.emplace(iter->first, iter->second);

InitAlignScore(aln.GetPointer());

(; it != it_end; ) {

(methods->empty()) {

vector<CConstIRef<IUITool> > tools;

(

= 0;

< tools.size();

++) {

(method && method->

() & aln_type) {

}

(exception& e) {

sid(

);

slabel(

);

&

=

&

(

.object.GetObject());

Checksum and hash calculation classes.

virtual bool Select(const IUITool &tool)

size_t GetSize(void) const

CSeq_annot_Handle GetAnnot(void) const

double GetCostOfLoadingInSeconds(void) const

Get collected cost of loading requested data in seconds.

void RemoveData(const string &data_key)

Removes Data from in-memory cache.

void EnableICache(bool value)

CRef< TData > GetData(const string &data_key)

Retrieves TData from in-memory cache or if not found calls TData::Init to initialize new TData instan...

static CGraphCache & GetInstance()

CRef< TData > GetCachedData(const string &data_key)

Retrieves TData from in-memory cache.

TAlignList & SetSeqAligns()

vector< CRef< CAlignGlyph > > TAlignList

static string CreateCacheKey(objects::CScope &scope, const objects::CSeq_id &seq_id, const string &remote_path)

CPileUpGraph.

virtual string GetExtensionLabel() const

returns a displayable label for this extension ( please capitalize the key words - "My Extension" )

virtual bool IsSharable() const

check if the data source can be shared.

virtual string GetExtensionIdentifier() const

CSGAlignmentDSType.

virtual ISGDataSource * CreateDS(SConstScopedObject &object) const

create an instance of the layout track type using default settings.

bool m_LinkMatePairs

link mate pair alignments

void InitAlignScoreCache(CAlignGlyph *aln, const TAlnAnchorPair &align_pair, IAlnExplorer::EAlignType sc_type)

IAlnExplorer::EAlignType GetAlignType() const

CSGAlignmentDS inline methods.

CAlignmentConfig::EHideSraAlignments m_HideSra

Flag, indicating whether to hide duplicates and/or bad reads.

bool IsRangeCached(const TSeqRange &range) const

void InitAlignScore(CAlignGlyph *aln)

Alignment scoring.

void x_GetGraphCacheKey(string &data_key) const

TJobID m_ScoringJobID

alignment scoring job id

bool x_IsScoringJobRunning() const

void LoadAlignments(const TSeqRange &range, TModelUnit window, int align_limit, bool smear_if_overlimit, TJobToken token)

bool IsGraphCached(const TSeqRange &range) const

bool CanShowRange(const TSeqRange &range, int align_limit)

TMethods m_DNAMethods

registered DNA scoring methods

TSignedSeqPos m_MaxEndTail

Max length of unaligned tail at the end of the sequence.

TSignedSeqPos m_MaxStartTail

> Flag to show second-pass alignments (relevant to assembly to assembly alignments)

bool IsValidProteinScoringMethod(const string &name)

string m_RemotePath

url to the remote data

virtual ~CSGAlignmentDS()

void x_DeleteScoringJob()

CAlignmentConfig::EUnalignedTailsMode m_UnalignedTailsMode

Flag, indicating whether and how to display unaligned tails.

void LoadAlignFeats(const TSeqRange &range, TModelUnit window, vector< CRef< CAlignGlyph > > aligns, const vector< int > &projected_feats, TJobToken token)

bool m_HasQualityMap

Has quality map? (e.g. cSRA alignments)

void SetDefaultScoringMethods(string dna_method, string protein_method)

objects::CTSE_Handle m_DataHandle

The last loaded data.

void EnablePileUpCache(bool enable, bool enable_icache)

Uint8 m_MemoryLimit

NeedReleaseMemory's default limit 2GB.

TMethods m_ProteinMethods

registered Protein scoring methods

const TMethods & GetScoringMethods(IAlnExplorer::EAlignType aln_type)

get all the existing align scoring methods.

virtual void DeleteAllJobs()

Remove waiting jobs from queue or cancel the unfinished jobs.

CRef< CSGAlignScoringJob > m_ScoringJob

IAlnExplorer::EAlignType InitAlignType(bool isFastConfig=false)

This method might need object manager to connect to ID, and it is a block call.

set< TAlnAnchorPair > m_PartialAlnSet

bool m_CgiMode

sviewer context

list< CIRef< IScoringMethod > > TMethods

keep instances of score methods here.

double GetAlignmentCost(const TSeqRange &range) const

void CalculateAlignmentScore(CSeqGlyph::TObjects &objs, TJobToken token)

void LoadCoverageGraph(const TSeqRange &range, TModelUnit window, TJobToken token)

CAlignGlyph::TAlnAnchorPair TAlnAnchorPair

bool IsValidDNAScoringMethod(const string &name)

TAlnScoreMap m_AlnScoreMap

CIRef< ILayoutPolicy > m_LayoutPolicy

double GetGraphCost(const TSeqRange &range) const

CSGAlignmentDS(objects::CScope &scope, const objects::CSeq_id &id)

void CalcAlnStat(const TAlnMgrVec &aligns, const TSeqRange &range, TModelUnit window, TJobToken token)

bool m_HasCoverageGraph

High level coverage graph?

vector< CConstRef< IAlnGraphicDataSource > > TAlnMgrVec

string m_DNAMethod

default scoring method for DNA alignments

const string & GetDataLoader() const

virtual void ClearJobID(TJobID job_id)

IAlnExplorer::EAlignType m_AlnType

void ResetAlnScoringJob()

const string & GetDNAScoringMethod() const

bool NeedReleaseMemory() const

void InitAlignQualityScore(CAlignGlyph *aln, const TAlnAnchorPair &align_pair, IAlnExplorer::EAlignType sc_type)

void x_InitScoringMethods(IAlnExplorer::EAlignType aln_type)

string m_ProtMethod

default scoring method for protein alignments

static IAlnExplorer::EAlignType GetAlignType(const objects::CBioseq_Handle &handle, objects::SAnnotSelector &sel, bool &has_quality_map, bool isFastConfig=false)

when isFastConfig set to true, it indicates that that the call is used by seqconfig this means that s...

void SetSortBy(const string &sort_by)

CScoreCache & GetScoreCache()

static const string & GetScoreName()

bool IsJobNeeded(TJobID job_id) const

TJobID x_LaunchJob(IAppJob &job, int report_period=1, const string &pool="ObjManagerEngine")

Launch either a background or foreground job.

bool m_Adaptive

adaptive/exact annot selector

int m_Depth

annotation resolving depth

CAppJobDispatcher::TJobID TJobID

objects::CScope & GetScope(void) const

Get the scope from the handle.

virtual void ClearJobID(TJobID job_id)

virtual void DeleteAllJobs()

Remove waiting jobs from queue or cancel the unfinished jobs.

objects::CBioseq_Handle m_Handle

void SetScoringMethod(IScoringMethod *method)

void SetAlignment(const IScoringAlignment *aln)

bool HasScores() const

returns "true" if CalculateScores() did produce results

IScoringMethod * GetScoringMethod()

void EnableBackgoundProcessing(bool en)

void SetListener(IListener *listener)

void SetGradNumber(int grad_n)

Sets the number of score gradations.

@ eSubtype_bad

These no longer need to match the FEATDEF values in the C toolkit's objfdef.h.

class CSeqGlyph defines an interface that wraps a rectilinear abstract object.

list< CRef< CSeqGlyph > > TObjects

void SetToken(TJobToken token)

CSeqGraphicJob inline methods.

CDataLoader * GetDataLoader(void) const

Alignment explorer interface.

IAlnGraphicDataSource - interface to a data source representing an abstract alignment used in graphic...

virtual bool IsCigarUnambiguous() const

Check if cigar doesn't have ambiguous M's.

virtual IAlnExplorer::EAlignType GetAlignType() const

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

virtual IAlnExplorer::TNumrow GetNumRows() const =0

virtual IAlnExplorer::TNumrow GetAnchor() const =0

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

virtual int GetType() const =0

returns combination of EAlignType flags defining types of alignments that can be colored with this me...

container_type::iterator iterator

const_iterator begin() const

const_iterator end() const

const_iterator find(const key_type &key) const

iterator_bool insert(const value_type &val)

const_iterator find(const key_type &key) const

const_iterator end() const

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

#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)

const string & GetMsg(void) const

Get message string.

void Warning(CExceptionArgs_Base &args)

void Info(CExceptionArgs_Base &args)

TAlnAnchorPair GetAlnAnchorPair(void) const

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

request an annotation selector for a given type

const IAlnGraphicDataSource & GetAlignMgr(void) const

Inline methods.

static void SetAnnot(objects::SAnnotSelector &sel, const string &annot)

help function for setting up an annotation.

void SetScore(const ISGAlnScore &score)

const objects::CSeq_align & GetAlignment(void) const

static void SetResolveDepth(objects::SAnnotSelector &sel, bool adaptive, int depth=-1)

help function for setting selector resolve depth.

static CAppJobDispatcher & GetInstance()

bool DeleteJob(TJobID job_id)

when a Job is deleted the listener is not notified

string GetName(void) const

const CTSE_Handle & GetTSE_Handle(void) const

SAnnotSelector & IncludeFeatSubtype(TFeatSubtype subtype)

Include feature subtype in the search.

SAnnotSelector & SetCollectNames(bool value=true)

Collect available annot names rather than annots.

SAnnotSelector & SetMaxSize(TMaxSize max_size)

Set maximum number of annotations to find.

SAnnotSelector & SetCollectCostOfLoading(bool value=true)

Collect cost of loading requested data.

TObjectType * GetPointer(void) THROWS_NONE

Get pointer,.

void Reset(void)

Reset reference object.

uint64_t Uint8

8-byte (64-bit) unsigned integer

position_type GetLength(void) const

static TThisType GetWhole(void)

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

static enable_if< is_arithmetic< TNumeric >::value||is_convertible< TNumeric, Int8 >::value, string >::type NumericToString(TNumeric value, TNumToStringFlags flags=0, int base=10)

Convert numeric value to string.

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.

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

string s_fromatstr(Uint8 bytes)

static const int kColorGradNumber

CSGAlignmentDS.

static const string kCSRADataLoader

static const string kBamDataLoader

static const int kInvalidJobToken

string ToStdString(const wxString &s)

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