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

m_TotalRange(total_range),

m_SeparateTypes(separate_types),

m_LinkGenes(link_genes),

TMap subtype_to_feats;

( ; feat_it && !

(); ++feat_it) {

( ! mapped_loc->

() && ! mapped_loc->

()) {

(subtype != prev_subtype) {

TMap::iterator it = subtype_to_feats.find(subtype);

(it == subtype_to_feats.end()) {

it = subtype_to_feats.insert(

prev_subtype = subtype;

( ! locs.empty()) {

kHistThreshold = 1000;

n_feat = feat_locs.size();

(n_feat > kHistThreshold) {

}

(n_feat > 0) {

m_RowHandle(row_handle),

m_isDataReadSync(isDataReadSync),

& descr,

include_snp =

;

found = (filter.

(subtype) != filter.

());

( ! final_set.

()) {

(sel, total_range, map_ranges, descr, separate_types, link_genes, order);

start < 0.0 || start > stop) {

gl.

(GL_SRC_ALPHA, GL_ONE_MINUS_SRC_ALPHA);

gl.

(GL_LINE_SMOOTH);

glHint(GL_LINE_SMOOTH_HINT, GL_NICEST);

gl.

(0.8, 0.8, 0.8, alpha);

gl.

(0.2, 0.2, 0.2, alpha);

( ! m_StatusText.empty()) {

rc_vp.

(vp_bottom, vp_top);

rc_vis.

(m_bottom, m_top);

TSignedRange total_r;

unique_ptr<IAlnSegmentIterator>

( ; *it; ++(*it)) {

TSignedRange range = seg.

();

ranges->

(seq_idh, range.GetFrom(), range.GetLength(),

aln_idh, aln_range.GetFrom(),

TMapRanges& map_ranges,

& descr,

descr, separate_types, link_genes, order));

errorNotification(

);

disp.

(*job,

, *

, -1,

);

(

);

job_id = it->first;

(e.GetErrCode()) {

(

<<

);

(

<< job_id);

(

= 0;

<

; ++

) {

= graphs.size();

(

<< notify.

() <<

);

(

<< notify.

() <<

);

(load_set, gene_set,

, total_range, *map_ranges,

,

,

, 10);

(load_set, sts_set,

, total_range, *map_ranges,

,

,

, 20);

(load_set, others_set,

, total_range, *map_ranges,

,

,

, 30);

m_LinkGenes(

),

m_TooltipRec(

),

&

,

m_LinkGenes(link_genes),

m_TooltipRec(

),

&

,

= feat_locs.size();

(

= 0;

<

;

++) {

SFeatRec s(feat_locs[

]);

&

,

SFeatRec s(*feat_glyph);

gl.

(GL_SRC_ALPHA, GL_ONE_MINUS_SRC_ALPHA);

gl.

(0.97, 0.97, 0.97);

(

j = 0; j < recs.size(); j++ ) {

angle = i_color * 131;

TTypeToColor s_map;

TTypeToColor::iterator it = s_map.find(subtype);

(it == s_map.end()) {

= s_map.size();

(

.GetFrom() > rc_vis.

() ||

.GetToOpen() < rc_vis.

()) {

y1 = top + ((layer == cluster.

) ? +2 : 0);

y2 = bottom + ((layer == cluster.

) ? -2 : 0);

gl.

(0.90, 0.90, 0.90);

gl.

(x1 - cl_off, y1, x2 + cl_off, y2);

gl.

(GL_LINES);

x1 =

.GetFrom() - off_x;

x2 =

.GetToOpen() - off_x;

((x2 - x1) / scale_x < 1.0) {

x1 = (x1 + x2 - scale_x) / 2;

(layer >= 0 && layer < (

)

.size()) {

(pos <

.GetFrom()) {

dist =

.GetFrom() - pos;

(pos >

.GetToOpen()) {

dist = pos -

.GetToOpen();

(min_dist < 0 || dist < min_dist) {

(

.IsSeq()) {

}

(

.IsGene() &&

.GetGene().IsSetDesc()) {

feat_title =

.GetGene().GetDesc();

(feat_title !=

) {

title +=

+ feat_title;

title +=

;

title +=

;

prod_len_str;

prod_len_str +=

;

title += prod_len_str;

title +=

;

p1.second > p2.second;

vector<TIndexLenPair> feat_lens;

feat_lens.reserve(feat_n);

(

= 0;

< feat_n;

++ ) {

=

.GetLength();

std::stable_sort(feat_lens.begin(), feat_lens.end(),

);

(

= 0;

< feat_n;

++ ) {

index = feat_lens[

].first;

= feat_recs.size();

(

= 0;

<

;

++ ) {

feat_n = feat_recs.size();

(

= 0;

< feat_n;

++ ) {

[feat] = TFeatToRecFlag::mapped_type(&feat_rec,

);

(

= 0;

< feat_n;

++ ) {

(

= 0;

< feat_n;

++ ) {

(

= 0;

< feat_n;

++ ) {

(

= 0;

< feat_n;

++ ) {

cluster.push_back(&feat_rec);

vector<TFeatRecPtrLenPair> pairs;

(vector<TFeatRecPtrLenPair>, it_mrna, pairs) {

* mrna_feat_rec = it_mrna->first;

(vector<TFeatRecPtrLenPair>, it_cds, pairs) {

* cds_feat_rec = it_cds->first;

TFeatRecPtrs::const_iterator it =

std::find(cluster.begin(), cluster.end(), cds_feat_rec);

cluster.push_back(&feat_rec);

* cds_feat_rec = it->second.first;

cluster.push_back(&feat_rec);

p1.second > p2.second;

vector<TFeatRecPtrLenPair>& pairs)

=

.GetLength();

std::stable_sort(pairs.begin(), pairs.end(),

);

(found && ! it->second.second);

cl_n = cluster.size();

vector<TFeatRange> cluster_ranges(cl_n);

(

= 0;

< cluster.size();

++ ) {

cluster_ranges[

] =

;

kMinOffset = 500;

(

= 0;

< cluster.size();

++ ) {

layer_index =

.size();

(

j = 0; j < occ_n; j++ ) {

clash =

;

k_end =

(cl_n, occ_n - j);

(

k = 0; ! clash && k < k_end; k++ ) {

(layer_index + cl_n >

.size()) {

k_end = layer_index + cl_n;

(

k =

.size(); k < k_end; k++ ) {

cluster_index =

.size() - 1;

(

k = 0; k < cl_n; k++ ) {

index = size_t(layer_index + k);

[index]->m_FeatRecPtrs.push_back(rec);

it->second.second =

;

it->second.second =

;

(

.GetFrom() > 0)

.SetFrom(

.GetFrom() - 1);

.SetTo(

.GetTo() + 1);

layer_index =

.size();

(

j = 0; j <

.size(); j++ ) {

(layer_index ==

.size()) {

[layer_index]->m_FeatRecPtrs.push_back(&rec);

m_FeatLocs(feat_locs)

& loc= *it->m_MappedLoc;

->GetStart();

->GetStop();

->GetWindow();

->GetBins();

(*

)[index];

->GetMax();

(

.get() ==

|| pos_start !=

->GetStart() || pos_stop !=

->GetStop()) {

window = float(pos_stop - start) / float(

);

.reset(

(pos_start, pos_stop, window));

& loc= *it->m_MappedLoc;

->AddLocation(loc);

static CRef< CScope > m_Scope

vector< TColl * > TCollVector

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

void x_GetRecsSortedByLength(const TFeatList &input, vector< TFeatRecPtrLenPair > &pairs)

void x_GatherCluster(SFeatRec &feat_rec, TFeatRecPtrs &cluster)

virtual ~CAlignedFeatureGraph()

list< CConstRef< objects::CSeq_feat > > TFeatList

virtual bool NeedTooltip(CGlPane &pane, int vp_x, int vp_y)

virtual TVPPoint PreferredSize()

void x_RenderFeature(CGlPane &pane, const SFeatRec &rec, int layer, TModelUnit top, TModelUnit bottom)

virtual void Render(CGlPane &pane)

void x_PlaceCluster(TFeatRecPtrs &cluster)

pair< SFeatRec *, TSeqPos > TFeatRecPtrLenPair

virtual string x_GetTooltip(const SFeatRec &rec)

bool x_mRNA_CDS_ToBePlaced(const objects::CSeq_feat &feat)

CRef< objects::CScope > m_Scope

TFeatToRecFlag m_FeatToRecFlag

void x_SimpleLayout(TFeatRecPtrs &feat_recs)

void x_PlaceFeature(SFeatRec &rec)

void x_TryPlaceCDSFeature(SFeatRec &rec)

virtual string GetTooltip()

vector< SLayer * > TLayers

void x_LinkedLayout(TFeatRecPtrs &feat_recs)

vector< SFeatRec * > TFeatRecPtrs

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

IAppJobListener Interface for components that need to be notified about changes in Jobs.

CAppJobNotification Notification send by CAppJobEventTranslator.

CEvent - generic event implementation TODO TODO - Attachments.

virtual void Update(double start, double stop)

vector< SMappedFeatLoc > TMappedFeatLocs

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

CFeatListItem - basic configuration data for one "feature" type.

string GetStoragekey() const

CConfigurableItems - a static list of items that can be configured.

bool GetItemBySubtype(int subtype, CFeatListItem &config_item) const

TFeatTypeItemSet m_FeatureTypes

defines what feature types / subtypes shall be shown

TGraphs m_PendingGraphs

Candidate graphs waiting for replacing the current ones.

CFeatureGraph(const IAlignRowHandle &row_handle, bool isDataReadSync)

virtual bool IsCreated() const

Graph is not considered fully functional until it has been "created" by the call to create function.

virtual const IAlnRowGraphProperties * GetProperties() const

void OnAJNotification(CEvent *evt)

void x_StartJob(const TFeatTypeItemSet &feat_set, const TSubtypeSet &filter, bool positive, CRange< TSeqPos > &total_range, TMapRanges &map_ranges, const string &descr, bool separate_types, bool link_genes, int order)

CFeatureGraphProperties m_Properties

void x_Create(double start, double stop)

CRef< TMapRanges > x_CreateMapRanges()

const IAlignRowHandle & m_RowHandle

virtual void Update(double start, double stop)

Update data according to the input range.

virtual void Render(CGlPane &pane, IAlnSegmentIterator &it)

CAppJobDispatcher::TJobID TJobID

objects::CMappingRanges TMapRanges

bool x_CancelJob(TJobID job_id)

void x_RenderStatusText(CGlPane &pane)

void x_CancelJobs()

Cancel all active jobs.

void x_OnJobFailed(CAppJobNotification &notify)

virtual void SetProperties(IAlnRowGraphProperties *props)

void x_OnJobCompleted(CAppJobNotification &notify)

CFeatureLoadingJobResult.

vector< CIRef< IRenderable > > TGraphs

virtual EJobState Run()

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

CRef< CFeatureLoadingJobResult > m_Result

CRange< TSeqPos > m_TotalRange

objects::CBioseq_Handle m_Handle

bool m_LinkGenes

links genes with CDS and mRNA

objects::CMappingRanges TMapRanges

virtual string GetDescr() const

Returns a human readable description of the Job (optional)

vector< SMappedFeatLoc > TMappedFeatLocs

CMutex m_Mutex

synchronizes access to the Job members

objects::SAnnotSelector m_Sel

CFeatureLoadingJob(const objects::CBioseq_Handle &handle, objects::SAnnotSelector &sel, const CRange< TSeqPos > &total_range, TMapRanges &ranges, const string &descr, bool separate_types, bool link_genes, int track_order)

CFeatureLoadingJob.

virtual ~CFeatureLoadingJob()

bool m_SeparateTypes

separate features by different graphs

virtual CConstIRef< IAppJobProgress > GetProgress()

return progress object, the function shall be synchronized internally.

CIRef< IAppJobError > m_Error

CRef< TMapRanges > m_MapRanges

virtual CConstIRef< IAppJobError > GetError()

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

virtual CRef< CObject > GetResult()

Returns the Job Result.

CIRef< IRenderable > x_CreateGraph(TMappedFeatLocs &feat_locs, const string &descr)

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

vector< TGraphRef > TGraphs

virtual void RemoveAllGraphs()

virtual size_t GetGraphsCount() const

virtual void Render(CGlPane &pane)

virtual bool AddGraph(TGraph *graph, bool front=false)

ELayoutPolicy m_LayoutPolicy

virtual TVPPoint PreferredSize()

void SetProperties(const SProperties &props)

virtual void SetDataSource(IHistogramGraphDS *ds)

Storage for multiple mapping ranges.

bool IntersectingWith(const TRange &r) const

class CRgbaColor provides a simple abstraction for managing colors.

ESubtype GetSubtype(void) const

static const CFeatList * GetFeatList()

@ eSubtype_bad

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

list< CRef< CSeqGlyph > > TObjects

namespace ncbi::objects::

Seq-loc iterator class – iterates all intervals from a seq-loc in the correct order.

static CSeq_id_Handle GetSeq_id_Handle(const const_iterator &iter)

IAlignRowHandle provides an abstract way to access alignment row data.

virtual TSignedSeqPos GetSeqAlnStart() const =0

virtual const objects::CBioseq_Handle & GetBioseqHandle() const =0

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

virtual TSignedSeqPos GetSeqAlnStop() const =0

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

@ eRight

Towards higher aln coord (always to the right)

@ eLeft

Towards lower aln coord (always to the left)

Alignment segment iterator interface.

@ eSkipInserts

Iterate segments where at least some rows are aligned (including gap segments)

Alignment segment interface.

virtual const TSignedRange & GetRange(void) const =0

Get the selected row range.

bool IsReversed(void) const

bool IsAligned(void) const

virtual const TSignedRange & GetAlnRange(void) const =0

Get alignment range for the segment.

IRenderable class IRenderable defines an abstract interface required for rendering graphical panels i...

virtual void SetModelRect(const TModelRect &rc)=0

virtual void SetVPRect(const TVPRect &rc)=0

virtual TVPPoint PreferredSize()=0

container_type::iterator iterator

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

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

ON_EVENT(CAppJobNotification, CAppJobNotification::eStateChanged, &CFeatureGraph::OnAJNotification) TVPPoint CFeatureGraph

CRgbaColor & GetColor(CSeqFeatData::ESubtype subtype)

static const int kLayerOffY

CRgbaColor GetRandomColor(int i_color)

CRange< TSeqPos > TFeatRange

static const int kGradColors

CFeatureGraph.

pair< size_t, TSeqPos > TIndexLenPair

static bool s_ILPLonger(const TIndexLenPair &p1, const TIndexLenPair &p2)

static const int kLayerH

CAlignedFeatureGraph.

static bool s_FRPLPLonger(const CAlignedFeatureGraph::TFeatRecPtrLenPair &p1, const CAlignedFeatureGraph::TFeatRecPtrLenPair &p2)

static const int kTextOff

static const int kTootipPix

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

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...

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

request an annotation selector for a given type

virtual void Enable(GLenum glstate)=0

virtual void Begin(GLenum mode)=0

Start rendering.

CGlPoint< TVPUnit > TVPPoint

virtual void BlendFunc(GLenum sfactor, GLenum dfactor)=0

Options to be used when GL_BLEND is enabled.

void Color3d(GLdouble r, GLdouble g, GLdouble b)

IRender & GetGl()

convenience function for getting current render manager

void RectC(const TVPRect &rc)

void Vertex2d(GLdouble x, GLdouble y)

TModelUnit GetOffsetY() const

void Color4d(GLdouble r, GLdouble g, GLdouble b, GLdouble a)

TModelUnit UnProjectX(TVPUnit m_x) const

bool PtInRect(T x, T y) const

virtual void End()=0

Finish rendering (create buffer and send to renderer)

void Inflate(T d_x, T d_y)

virtual void PolygonMode(GLenum face, GLenum mode)=0

Set the polygon rasterization mode.

void SetVert(T bottom, T top)

virtual TModelUnit TextHeight(void) const

virtual void TextOut(const char *text) const

TextOut interface Write the specified text and set up state and transformation as needed.

TModelRect & GetVisibleRect(void)

TModelUnit GetScaleX(void) const

TModelUnit GetOffsetX() const

virtual void ColorC(const CRgbaColor &c)=0

Set current color (glColor{3,4}{f,d}{v,})

void Rectd(GLdouble x1, GLdouble y1, GLdouble x2, GLdouble y2)

CConstIRef< IAppJobError > GetError() const

returns non-null pointer only if job Failed

static CRgbaColor RotateColor(const CRgbaColor &c, float degrees)

Rotate the hue of the color by degrees.

static void GetLabel(const CObject &obj, string *label, ELabelType type=eDefault)

static CAppJobDispatcher & GetInstance()

CRef< CObject > GetResult() const

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

virtual bool IsCanceled() const override

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...

#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

virtual bool Send(CEvent *evt, EDispatch disp_how=eDispatch_Default, int pool_name=ePool_Default)

Sends an event synchronously.

@ eEngine_UnknownJob

the job is not registered in the Engine

@ eUnknownJob

Job record lost.

string GetLabel(const CSeq_id &id)

TRange GetTotalRange(void) const

const CSeq_id * GetId(void) const

Get the id of the location return NULL if has multiple ids or no id at all.

void GetMrnasForGene(const CMappedFeat &gene_feat, list< CMappedFeat > &mrna_feats, CFeatTree *feat_tree=0, const SAnnotSelector *base_sel=0)

void GetCdssForGene(const CMappedFeat &gene_feat, list< CMappedFeat > &cds_feats, CFeatTree *feat_tree=0, const SAnnotSelector *base_sel=0)

CMappedFeat GetBestCdsForMrna(const CMappedFeat &mrna_feat, CFeatTree *feat_tree=0, const SAnnotSelector *base_sel=0)

@ fFGL_Content

Include its content if there is any.

const CSeq_id & GetId(const CSeq_loc &loc, CScope *scope)

If all CSeq_ids embedded in CSeq_loc refer to the same CBioseq, returns the first CSeq_id found,...

TSeqPos GetLength(const CSeq_id &id, CScope *scope)

Get sequence length if scope not null, else return max possible TSeqPos.

CRef< CSeq_loc > Map(const CSeq_loc &src_loc)

Map seq-loc.

void AddConversion(CRef< CMappingRange > cvt)

Add new mapping range to the proper place.

CConstRef< CSynonymsSet > GetSynonyms(const CSeq_id &id)

Get bioseq synonyms, resolving to the bioseq in this scope.

TSeqPos GetBioseqLength(void) const

CConstRef< CSeq_id > GetSeqId(void) const

Get id which can be used to access this bioseq handle Throws an exception if none is available.

SAnnotSelector & IncludeFeatSubtype(TFeatSubtype subtype)

Include feature subtype in the search.

const CSeq_feat & GetMappedFeature(void) const

Feature mapped to the master sequence.

SAnnotSelector & AddNamedAnnots(const CAnnotName &name)

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

SAnnotSelector & ExcludeNamedAnnots(const CAnnotName &name)

Add named annot to set of annots names to exclude.

TObjectType * GetPointer(void) const THROWS_NONE

Get pointer,.

TObjectType * GetPointer(void) THROWS_NONE

Get pointer,.

void Reset(void)

Reset reference object.

position_type GetLength(void) const

TThisType & CombineWith(const TThisType &r)

position_type GetToOpen(void) const

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

static string IntToString(int value, TNumToStringFlags flags=0, int base=10)

Convert int to string.

@ fWithCommas

Use commas as thousands separator.

static const char label[]

void SetFrom(TFrom value)

Assign a value to From data member.

TFrom GetFrom(void) const

Get the From member data.

const TLocation & GetLocation(void) const

Get the Location member data.

const TData & GetData(void) const

Get the Data member data.

const TProduct & GetProduct(void) const

Get the Product member data.

bool IsSetProduct(void) const

product of process Check if a value has been assigned to Product data member.

bool IsEmpty(void) const

Check if variant Empty is selected.

ENa_strand

strand of nucleic acid

bool IsInt(void) const

Check if variant Int is selected.

bool IsNull(void) const

Check if variant Null is selected.

bool IsPnt(void) const

Check if variant Pnt is selected.

double value_type

The numeric datatype used by the parser.

const struct ncbi::grid::netcache::search::fields::SIZE size

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

void copy(Njn::Matrix< S > *matrix_, const Njn::Matrix< T > &matrix0_)

void SetClusterIndex(int value)

const objects::CSeq_loc & GetLocation(void) const

const objects::CSeq_feat & GetFeature(void) const

int GetClusterIndex() const

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