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

& title,

fixed_scale,

& y_limits)

iter = d_maps.

(g_title);

(iter == d_maps.

()) {

pair<string, SGraphObject>(

g_desc, g_name))).first;

(; graph_iter; ++graph_iter) {

<

TGraphType>

TGraphType& graph,

& g_max,

& g_min,

& vec = graph.GetValues();

(vec.empty())

;

l_max = graph.GetMax();

l_min = graph.GetMin();

(

.GetLength() == 0)

iter_gr = vec.begin();

advance(iter_gr,

(

, (

)vec.size()));

unsigned_char =

;

(

(TGraphValueType) == 1) unsigned_char =

;

(iter_gr != vec.end() && pos < map_r.

()) {

= (TDataType)(

)(*iter_gr);

= (TDataType)(*iter_gr);

(

> l_max)

g_max =

(l_max *

+

, g_max);

g_min =

(l_min *

+

, g_min);

((*iter)->IsUser() && (*iter)->GetUser().GetType().IsStr() &&

(*iter)->GetUser().GetType().GetStr() ==

) {

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

CAppJobError Default implementation for IAppJobError - encapsulates a text error message.

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

void SetAnnotName(const string &name)

void SetAxisMaxFixed(TDataType max)

void SetFixedScale(bool value)

void SetDesc(const string &desc)

void SetAxisMinFixed(TDataType min)

objects::SAnnotSelector m_Sel

our annotation selector

string x_GetGraphName(const objects::CMappedGraph &gr) const

Get a name for a graph.

void x_AddGraphToMap(CDensityMap< float > &the_map, const objects::CMappedGraph &gr, const TGraphType &graph, double &g_max, double &g_min, bool fixed_scale)

bool x_PercentileButNotMax(const objects::CMappedGraph &gr) const

Check the graph type.

CSGAnnotJob(const string &desc, objects::CBioseq_Handle handle, const objects::SAnnotSelector &sel, const TSeqRange &range)

CSGAnnotJob.

TSeqRange m_Range

target range

IAppJob::EJobState x_CreateHistFromGraph(CSeqGlyph::TObjects &glyphs, const objects::SAnnotSelector &sel, TModelUnit window, bool fixed_scale, const TAxisLimits &y_limits)

objects::CBioseq_Handle m_Handle

target sequence

void x_AddGraphObject(map< string, SGraphObject > &d_maps, const objects::CMappedGraph &gr, TModelUnit window, bool fixed_scale)

IAppJob::EJobState x_LoadCoverageGraph(CSeqGlyph::TObjects &glyphs, int level, TModelUnit window, const string &title, bool fixed_scale, const TAxisLimits &y_limits)

list< CRef< CSeqGlyph > > TObjects

CSeqGraphicJob – the base class of seqgraphic job for handling the job status such as reporting the p...

string m_Desc

Job description or name.

CFastMutex m_Mutex

mutex for guarding state access

virtual void SetTaskTotal(int total)

virtual CConstIRef< IAppJobError > GetError()

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

int m_TaskTotal

Total amount of task for a job.

CSeqGraphicJob(const string &desc=kEmptyStr)

CSeqGraphicJob.

virtual CConstIRef< IAppJobProgress > GetProgress()

return progress object, the function shall be synchronized internally.

virtual void SetTaskName(const string &name)

int m_TaskCompleted

The amount of task finished.

virtual string GetDescr() const

Returns a human readable description of the Job (optional)

virtual void SetTaskCompleted(int completed)

set total finished task number.

virtual CRef< CObject > GetResult()

Returns the Job Result.

virtual void AddTaskCompleted(int delta)

set to add newly finished task number.

CRef< CAppJobError > m_Error

virtual EJobState Run()

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

virtual EJobState x_Execute()=0

method truly doing the job.

virtual bool StopRequested() const

CConstRef< CUser_field > GetFieldRef(const string &str, const string &delim=".", NStr::ECase use_case=NStr::eCase) const

Return a field reference representing the tokenized key, or a NULL reference if the key doesn't exist...

const_iterator end() const

iterator_bool insert(const value_type &val)

const_iterator find(const key_type &key) 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.

static string GetAnnotName(const objects::CSeq_annot_Handle &annot_handle)

static const string & GetUnnamedAnnot()

Get the commonly used symbol representing a unnnamed annotation.

static string GetAnnotComment(const objects::CSeq_annot_Handle &annot_handle)

virtual bool IsCanceled() const override

virtual void AddRange(TSeqRange range, CntType score=1, bool expand=false)

EJobState

Job states (describe FSM)

TRange GetTotalRange(void) const

CConstRef< CSeq_annot > GetCompleteSeq_annot(void) const

Complete and return const reference to the current seq-annot.

const string & GetName(void) const

TSeqPos GetComp(void) const

const string & GetTitle(void) const

bool IsSetTitle(void) const

CSeq_annot_Handle GetAnnot(void) const

Get containing annot handle.

bool IsIncludedAnyNamedAnnotAccession(void) const

check if any named annot accession is included in the search

SAnnotSelector & ResetAnnotsNames(void)

Select annotations from all Seq-annots.

bool IsSetComp(void) const

string CombineWithZoomLevel(const string &acc, int zoom_level)

Combine accession string and zoom level into a string with separator.

SAnnotSelector & IncludeNamedAnnotAccession(const string &acc, int zoom_level=0)

SAnnotSelector & SetAnnotType(TAnnotType type)

Set annotation type (feat, align, graph)

SAnnotSelector & AddNamedAnnots(const CAnnotName &name)

Add named annot to set of annots names to look for.

const TNamedAnnotAccessions & GetNamedAnnotAccessions(void) const

const CSeq_loc & GetLoc(void) const

bool IsSetComment(void) const

const string & GetComment(void) const

const CSeq_graph::C_Graph & GetGraph(void) const

CRef< C > Ref(C *object)

Helper functions to get CRef<> and CConstRef<> objects.

TObjectType * GetPointer(void) THROWS_NONE

Get pointer,.

void Reset(void)

Reset reference object.

position_type GetToOpen(void) const

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.

const TStr & GetStr(void) const

Get the variant data.

const TData & GetData(void) const

Get the Data member data.

bool IsStr(void) const

Check if variant Str is selected.

const TInt & GetInt(void) const

Get the variant data.

const TByte & GetByte(void) const

Get the variant data.

const TReal & GetReal(void) const

Get the variant data.

E_Choice Which(void) const

Which variant is currently selected.

const Tdata & Get(void) const

Get the member data.

const TDesc & GetDesc(void) const

Get the Desc member data.

bool CanGetDesc(void) const

Check if it is safe to call GetDesc method.

list< CRef< CAnnotdesc > > Tdata

double value_type

The numeric datatype used by the parser.

map< string, map< string, string > > TValues

Int4 delta(size_t dimension_, const Int4 *score_)

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

static const int kInvalidJobToken

CHistogramGlyph::TMap m_Map

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