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NCBI C++ ToolKit: include/gui/widgets/aln_multiple/feature_graph.hpp Source File

: m_Feature(feat), m_MappedLoc(&loc) {}

vector< CIRef<IRenderable> >

;

objects::SAnnotSelector& sel,

& descr,

GetDescr()

;

vector< CConstRef<objects::CSeq_feat> >

;

Layout();

IsCreated()

;

Create();

Destroy();

Update(

start,

stop);

OnAJNotification(

* evt);

x_RenderStatusText(

& pane);

& descr,

& descr,

x_CancelJob(

job_id);

x_Create(

start,

stop);

objects::CScope& scope,

&

,

Render(

& pane);

NeedTooltip(

& pane,

vp_x,

vp_y);

GetTooltip();

: m_ClusterIndex(-1) {}

: m_FeatLoc(feat_loc), m_ClusterIndex(cluster_index) {

, m_FeatGlyph(&glyph)

m_FeatLoc.m_MappedLoc.Reset(

objects::CSeq_loc);

m_FeatLoc.m_Feature.GetOriginalFeature();

*m_FeatLoc.m_MappedLoc;

m_ClusterIndex =

;

m_ClusterIndex;

m_FeatGlyph =

(m_FeatLoc.m_Feature, *m_FeatLoc.m_MappedLoc);

m_FeatGlyph->SetConfig(conf);

list< CConstRef<objects::CSeq_feat> >

;

objects::CScope& scope,

&

,

objects::CScope& scope,

&

,

x_GatherCluster(

& feat_rec,

vector<TFeatRecPtrLenPair>& pairs);

x_mRNA_CDS_ToBePlaced(

objects::CSeq_feat& feat);

x_TryPlaceCDSFeature(

& rec);

x_PlaceFeature(

& rec);

x_GetTooltip(

& rec);

()

;

()

;

(

index);

(

start,

stop);

CAlignedFeatureGraph(TMappedFeatLocs &feat_locs, objects::CScope &scope, const string &label, bool link_genes)

CRangeCollection< TSeqPos > TColl

vector< SCluster > TClusters

vector< TColl * > TCollVector

virtual void x_Init(TMappedFeatLocs &feat_locs, objects::CScope &scope, const string &label, bool link_genes)

map< const objects::CSeq_feat *, pair< SFeatRec *, bool > > TFeatToRecFlag

list< CConstRef< objects::CSeq_feat > > TFeatList

pair< SFeatRec *, TSeqPos > TFeatRecPtrLenPair

CRef< objects::CScope > m_Scope

TFeatToRecFlag m_FeatToRecFlag

void x_Init(CSeqGlyph::TObjects &glyphs, objects::CScope &scope, const string &label, bool link_genes)

vector< SMappedFeatLoc > TMappedFeatLocs

vector< SFeatRec > TFeatRecs

vector< SLayer * > TLayers

vector< SFeatRec * > TFeatRecPtrs

CAppJobNotification Notification send by CAppJobEventTranslator.

class CDensityMap generates a low-resolution view of a set of features.

CEvent - generic event implementation TODO TODO - Attachments.

const objects::CMappedFeat & GetMappedFeature(void) const

Access a new, fully remapped feature.

virtual void Update(double start, double stop)

vector< SMappedFeatLoc > TMappedFeatLocs

CRange< TSeqPos > TFeatRange

CFeatHistogramDS(TMappedFeatLocs &feat_locs, const string &label)

CFeatHistogramDS.

virtual string GetLabel() const

virtual double GetStop() const

virtual double GetValue(size_t index)

value of the sample with the given index

virtual double GetMaxValue()

virtual double GetLimit() const

returns start of the series in model space

TMappedFeatLocs m_FeatLocs

virtual double GetStart() const

virtual double GetStep() const

discrete size in model space

virtual size_t GetCount() const

number of samples in the series

objects::CFeatListItem TFeatTypeItem

set< TFeatTypeItem > TFeatTypeItemSet

TFeatTypeItemSet m_FeatureTypes

defines what feature types / subtypes shall be shown

TGraphs m_PendingGraphs

Candidate graphs waiting for replacing the current ones.

vector< SMappedFeatLoc > TMappedFeatLocs

CFeatureGraphProperties m_Properties

map< TJobID, CRef< CFeatureLoadingJob > > TJobMap

const IAlignRowHandle & m_RowHandle

CFeatureGraphProperties::TFeatTypeItemSet TFeatTypeItemSet

CAppJobDispatcher::TJobID TJobID

bool x_StartJob(objects::SAnnotSelector &sel, CRange< TSeqPos > &total_range, TMapRanges &map_ranges, const string &descr, bool separate_types, bool link_genes, int order)

objects::CMappingRanges TMapRanges

CFeatureGraphProperties::TFeatTypeItem TFeatTypeItem

virtual TVPPoint PreferredSize()

set< objects::CSeqFeatData::ESubtype > TSubtypeSet

CFeatureLoadingJobResult.

vector< CIRef< IRenderable > > TGraphs

CRef< CFeatureLoadingJobResult > m_Result

CRange< TSeqPos > m_TotalRange

vector< CConstRef< objects::CSeq_feat > > TFeatures

objects::CBioseq_Handle m_Handle

bool m_LinkGenes

links genes with CDS and mRNA

objects::CMappingRanges TMapRanges

vector< SMappedFeatLoc > TMappedFeatLocs

CMutex m_Mutex

synchronizes access to the Job members

objects::SAnnotSelector m_Sel

bool m_SeparateTypes

separate features by different graphs

CIRef< IAppJobError > m_Error

CRef< TMapRanges > m_MapRanges

CFeatureParams: the data structure holding feature rendering parameters.

TModelUnit m_LineWidth

absolute value (in pixel)

TModelUnit m_HeadHeight

ratio to bar height

TModelUnit m_TailHeight

ratio to bar height

ELabelPosition m_LabelPos

TModelUnit m_BarHeight

absolute size (in pixel)

@ ePos_Inside

inside the rendered bar

CGraphContainer CGraphContainer a composite IRenderable that manages several child IRenderable graphs...

vector< TGraphRef > TGraphs

Base class to build jobs with cancel functionality.

list< CRef< CSeqGlyph > > TObjects

IAlignRowHandle provides an abstract way to access alignment row data.

Alignment segment iterator interface.

IAlnVecRowGraph - abstract graph that can be rendered in the "expandable" space below the CAlnVecRow.

IHistogramGraphDS interface.

static DLIST_TYPE *DLIST_NAME() first(DLIST_LIST_TYPE *list)

static DLIST_TYPE *DLIST_NAME() last(DLIST_LIST_TYPE *list)

EJobState

Job states (describe FSM)

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

void Run(void)

Enter the main loop.

#define NCBI_GUIWIDGETS_ALNMULTIPLE_EXPORT

static const char label[]

const GenericPointer< typename T::ValueType > T2 value

SCluster(int first, int last, int offset)

CFeatGlyph & GetGlyph() const

CRef< CFeatGlyph > m_FeatGlyph

SFeatRec(SMappedFeatLoc &feat_loc, int cluster_index=-1)

void SetClusterIndex(int value)

SFeatRec(CFeatGlyph &glyph, int cluster_index=-1)

const objects::CSeq_loc & GetLocation(void) const

const objects::CSeq_feat & GetFeature(void) const

int GetClusterIndex() const

TFeatRecPtrs m_FeatRecPtrs

objects::CMappedFeat m_Feature

CRef< objects::CSeq_loc > m_MappedLoc

SMappedFeatLoc(const objects::CMappedFeat &feat, objects::CSeq_loc &loc)

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