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

(

objects::CBioseq_Handle& handle,

& range, objects::SAnnotSelector& sel,

is_gaps[

/ 8] & 0x01 << (8 -

% 8);

objects::CScope& scope,

token);

, m_IsChromosome(

)

range,

, cutoff, token));

}

(level ==

) {

&

=

&

(

.object.GetObject());

sid(

);

slabel(

);

total_levels = 0;

(

level = 0; level < 2; ++level) {

isMaxSegmentsReached{

};

(start <= stop) {

(isMaxSegmentsReached) {

(isMaxSegmentsReached) {

level =

(level, max_level);

(

= start_l;

<= end_l; ++

) {

(seg)

;

over_limit =

;

(

levels = 0; levels < 4; ++levels) {

seg_count = 0;

(over_limit)

;

seg_from = seg.GetPosition();

seg_to = seg.GetEndPosition() - 1;

ref_from = seg.GetRefPosition();

ref_to = seg.GetRefEndPosition() - 1;

neg = seg.GetRefMinusStrand();

seg_r, neg, length));

seg_maps.push_back(seqmap);

<< e.

());

(seg_maps.size()) {

(

->Size() > 1 ||

(over_limit &&

->m_ObjectList.empty()) {

=

;

+=

;

->m_ObjectList.push_back(message_glyph);

}

(std::exception& ex) {

pair<const TSeqRange, CRef<CSegmentGlyph> > CSegMapPair;

CSegMapMap merge_map;

& range = segmap->GetLocation().GetTotalRange();

merge_map.insert( CSegMapPair(range, segmap) );

map_keys.

( range );

pair<CSegMapMap::iterator, CSegMapMap::iterator> the_bounds;

the_bounds = merge_map.equal_range(*iter);

(CSegMapMap::iterator it = the_bounds.first;

it != the_bounds.second; it++)

CSegMapPair pair = *it;

comp_range.

(*cr_it);

mapped_range.

(*mr_it);

ref.

(pair.second.GetPointer());

ref->SetComponentRanges(comp_range);

ref->SetMappedRanges(mapped_range);

objs.push_back(obj_ref);

objects::CBioseq_Handle handle,

& annot,

, m_SeqVector(seq_vec)

objects::SAnnotSelector& sel,

sel.SetCollectNames();

(iter->IsNamed()) {

(iter->GetName().find(

) == string::npos) {

(pre != annots.

()) {

(iter != annots.

()

&& pre->first.substr(0, 11) == iter->first.substr(0, 11)) {

<< e.

());

perfLog.

(

,

);

= is_chromosome ? 1 : 0;

unique_ptr<CSegmentSmearGlyph::CSegMap>

TSegData =

{

vector<TSegData>

;

seg_from = seg.GetPosition();

seg_to = seg.GetEndPosition() - 1;

(pre_to < seg_from) {

.push_back({

(pre_to, seg_from - 1), gap_val, 0});

ids.push_back(seg.GetRefSeqid());

(seg.GetEndPosition() > r_to) {

handles =

.GetScope().GetBioseqHandles(ids);

(

& d :

) {

(d.val != gap_val) {

the_map->AddRange(d.range, d.val,

);

->m_ObjectList.push_back(glyph);

perfLog.

(

,

);

unique_ptr<CSegmentSmearGlyph::CSegMap> the_map(

col_to.

(annot, rows - 1, to);

col_from.

(annot, 0, from);

(r_to < (

)from)

;

((*iter)->GetHeader().CanGetField_name() &&

(*iter)->GetHeader().GetField_name() ==

) {

col_gap = iter->GetPointer();

( !col_gap )

;

r_end = rows - 1;

= (r_start + r_end) / 2;

((

)from < r_from ) r_start =

;

}

((

)from != r_from && r_start < r_end - 1);

(

= (r_start + r_end) / 2; (size_t)

< rows; ++

) {

(col_from.

(annot,

, from) &&

((

)from > r_to)

;

the_map->AddRange(

(from, to), (TValType)qual,

);

->m_ObjectList.push_back(hist);

perfLog.

(

,

);

unique_ptr<CSegmentSmearGlyph::CSegMap> the_map(

the_map->Deserialize(*reader);

->m_ObjectList.push_back(hist);

<< e.

());

objects::CScope& scope,

ids.reserve(

.size());

(

&& iter :

) {

(bshs.size() == ids.size());

(bshs.size() != ids.size())

(

&& iter :

) {

(bshs[

] && bshs[

].CanGetInst_Mol()) {

all_objs.push_back(sp);

->m_ObjectList.swap(all_objs);

static CRef< CScope > m_Scope

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

const TAnnotNames & GetAnnotNames(void) const

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

CJobResultBase – the basic job result class holding a token.

void AddParameter(const std::string &name, const std::string &value)

void Post(CRequestStatus::ECode status=CRequestStatus::e200_Ok)

CNcbiOstrstreamToString class helps convert CNcbiOstrstream to a string Sample usage:

class CRegistryReadView provides a nested hierarchical view at a particular key.

objects::SAnnotSelector m_Sel

our annotation selector

TSeqRange m_Range

target range

objects::CBioseq_Handle m_Handle

target sequence

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

Launch either a background or foreground job.

int m_Depth

annotation resolving depth

objects::CScope & GetScope(void) const

Get the scope from the handle.

void SetDepth(int depth)

Set the annotation selector resolving depth.

objects::CBioseq_Handle m_Handle

CSGJobResult – the data structure holding the seqgraphic job results.

virtual string GetExtensionIdentifier() const

returns the unique human-readable identifier for the extension the id should use lowercase letters se...

virtual string GetExtensionLabel() const

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

virtual ISGDataSource * CreateDS(SConstScopedObject &object) const

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

virtual bool IsSharable() const

check if the data source can be shared.

bool IsChromosome() const

bool HasComponent(const TSeqRange &range) const

void LoadSegmentMap(const TSeqRange &range, int cutoff, TJobToken token)

static void SetICacheClient(ICache *pCache)

Set cache client to use.

static bool GetEnabled()

Indicates if the segment map is enabled.

void SetSegmentLevel(ESegmentLevel level)

Set which segment level to show.

void LoadSegmentSmear(const TSeqRange &range, TModelUnit scale, const objects::CSeqVector *seq_vec=nullptr)

Used in sequence track for showing segment color.

int GetSegmentMapLevels(const TSeqRange &range) const

Get total number of segment map levels.

bool HasSegmentMap(int level, const TSeqRange &range) const

Query if there is segment maps for given level.

int x_ConceptualToRealDepth(ESegmentLevel level) const

Convert conceptual segment level to real segment depth.

static ICache * m_Cache

Cache, used to store segment smear.

bool m_IsChromosome

Flag to indicate if the sequence is a chromosome sequence.

ESegmentLevel

It is not technically correct to name a specific segment level as config/scaffold and component becau...

static bool m_Enabled

Indicates if the segment map is enabled.

void GetAnnotNames(objects::SAnnotSelector &sel, const TSeqRange &range, TAnnotNameTitleMap &names) const

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

static void SetEnabled(bool enabled=true)

Enables/disables the segment map.

string m_Annot

The named annotation storing segment map data.

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

bool HasScaffold(const TSeqRange &range) const

CSGSegmentMapJob declaration.

static bool HasSegmentMap(const objects::CBioseq_Handle &Handle, int level, const TSeqRange &range)

objects::CBioseq_Handle m_Handle

target sequence

int m_Cutoff

limit of number of segments we want to show.

TSeqRange m_Range

target range

virtual EJobState x_Execute()

method truly doing the job.

CSGSegmentMapJob(const string &desc, objects::CBioseq_Handle handle, const TSeqRange &range, int depth, int cutoff, TJobToken token)

CSGSegmentMapJob implementation.

bool x_AdaptiveDepth() const

static int GetSegmentMapLevels(const objects::CBioseq_Handle &handle, const TSeqRange &range)

IAppJob::EJobState x_MergeSeqSegments(CSegmentGlyph::TSeqMapList &seg_maps, CSeqGlyph::TObjects &objs)

merge equal segment maps into one map.

int m_Depth

Resolve depth for selector.

CSGSegmentSmearJob declaration.

void x_WriteToCache(const string &key, const CSegmentSmearGlyph::CSegMap &density_map)

string m_Annot

annotation storing the segments

static void GetAnnotNames(const objects::CBioseq_Handle &handle, const TSeqRange &range, objects::SAnnotSelector &sel, TAnnotNameTitleMap &annots)

ICache * m_Cache

cache to store segment ranges

const CSeqVector * m_SeqVector

IAppJob::EJobState x_LoadFromNetCache(const string &key)

TModelUnit m_Scale

bases per pixel

IAppJob::EJobState x_LoadFromNA()

bool x_IsGap(vector< char > is_gaps, int row) const

virtual EJobState x_Execute()

method truly doing the job.

CSGSegmentSmearJob(const string &desc, objects::CBioseq_Handle handle, const TSeqRange &range, TModelUnit scale, const string &annot, ICache *cache=0, const CSeqVector *seq_vec=nullptr)

CSGSegmentSmearJob implementation.

string x_GetCacheKey() const

IAppJob::EJobState x_LoadFromDeltaSeqs()

CSGSegmentsSeqIDJob declaration.

objects::CScope & m_Scope

scope for retrieving the CBioseq

CSGSegmentsSeqIDJob(const string &desc, CSeqGlyph::TObjects &objs, objects::CScope &scope, TJobToken token)

CSGSegmentsSeqIDJob implementation.

virtual EJobState x_Execute()

method truly doing the job.

CSeqGlyph::TObjects m_Objs

objects for post-processing

CSGSwitchPointJob declaration.

objects::CBioseq_Handle m_Handle

target sequence

virtual EJobState x_Execute()

method truly doing the job.

CSGSwitchPointJob(const string &desc, objects::CBioseq_Handle handle)

CSGSwitchPointJob implementation.

static bool IsChromosome(const objects::CBioseq_Handle &handle, objects::CScope &scope)

void SetSeqQuality(CSegmentConfig::TSegMapQuality quality)

const objects::CSeq_loc & GetLocation(void) const

access the position of this object.

vector< CRef< CSegmentGlyph > > TSeqMapList

void Serialize(IWriter &writer) const

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

list< CRef< CSeqGlyph > > TObjects

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

virtual void SetTaskTotal(int total)

virtual void SetTaskName(const string &name)

virtual void SetTaskCompleted(int completed)

set total finished task number.

void SetToken(TJobToken token)

CSeqGraphicJob inline methods.

TJobToken m_Token

Job token recognizable by job listener.

CRef< CAppJobError > m_Error

bool TryGetBool(size_t row, bool &v) const

bool TryGet(const CFeat_CI &feat_ci, Value &v) const

BLOB cache read/write/maintenance interface.

virtual IWriter * GetWriteStream(const string &key, TBlobVersion version, const string &subkey, unsigned int time_to_live=0, const string &owner=kEmptyStr)=0

Return sequential stream interface to write BLOB data.

virtual bool HasBlobs(const string &key, const string &subkey)=0

Check if any BLOB exists (any version)

virtual IReader * GetReadStream(const string &key, TBlobVersion version, const string &subkey)=0

Return sequential stream interface to read BLOB data.

container_type::iterator iterator

const_iterator begin() const

const_iterator end() const

iterator_bool insert(const value_type &val)

container_type::value_type value_type

iterator_bool insert(const value_type &val)

static unsigned char depth[2 *(256+1+29)+1]

bool Empty(const CNcbiOstrstream &src)

static const struct name_t names[]

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define LOG_POST(message)

This macro is deprecated and it's strongly recomended to move in all projects (except tests) to macro...

const string & GetMsg(void) const

Get message string.

void Warning(CExceptionArgs_Base &args)

virtual const char * what(void) const noexcept

Standard report (includes full backlog).

void Info(CExceptionArgs_Base &args)

static bool IsNAA(const string &annot, bool isStrict=false)

check if a given annotation is a named annotation accession[.version][number] when isSctrict == false...

static int GetMaxSearchSegments(const CRegistryReadView &view)

static objects::SAnnotSelector::EMaxSearchSegmentsAction GetMaxSearchSegmentsAction(const CRegistryReadView &view)

static const string & GetUnnamedAnnot()

Get the commonly used symbol representing a unnnamed annotation.

static CRegistryReadView GetSelectorRegistry()

helper functions to read selector-related tune-up info (mostly segment limits) from registry:

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

help function for setting selector resolve depth.

static bool CheckMaxSearchSegments(int actual, int max, objects::SAnnotSelector::EMaxSearchSegmentsAction action)

check actual number of segments against max and perform the action if the actual number is more than ...

CGlPoint< TModelUnit > TModelPoint

virtual bool IsCanceled() const override

EJobState

Job states (describe FSM)

void GetLabel(string *label, ELabelType type=eDefault, TLabelFlags flags=fLabel_Default) const

Append a label for this Seq-id to the supplied string.

CConstRef< CSeq_id > GetSeqId(void) const

static CSeq_id_Handle GetHandle(const CSeq_id &id)

Normal way of getting a handle, works for any seq-id.

@ eContent

Untagged human-readable accession or the like.

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,...

@ eGetId_Best

return the "best" gi (uses FindBestScore(), with CSeq_id::CalculateScore() as the score function

vector< CBioseq_Handle > TBioseqHandles

vector< CSeq_id_Handle > TIds

@ eGetBioseq_Loaded

Search in all loaded TSEs in the scope.

@ eGetBioseq_All

Search bioseq, load if not loaded yet.

TSeqPos GetBioseqLength(void) const

CConstRef< CSeq_annot > GetCompleteSeq_annot(void) const

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

size_t GetSeq_tableNumRows(void) const

bool CanGetInst_Mol(void) const

SSeqMapSelector & SetResolveCount(size_t res_cnt)

Set max depth of resolving seq-map.

CSeqMap::ESegmentType GetType(void) const

TSeqPos GetPosition(void) const

return position of current segment in sequence

const CSeqMap_CI & GetCurrentSeqMap_CI() const

vector< CRef< CSeqMapSwitchPoint > > TSeqMapSwitchPoints

TSeqMapSwitchPoints GetAllSwitchPoints(const CBioseq_Handle &seq, const TSeqMapSwitchAligns &aligns)

@ eSeqRef

reference to Bioseq

TObjectType * GetPointer(void) THROWS_NONE

Get pointer,.

void Reset(void)

Reset reference object.

bool Empty(void) const THROWS_NONE

Check if CRef is empty – not pointing to any object, which means having a null value.

position_type GetLength(void) const

CRange< TSeqPos > TSeqRange

typedefs for sequence ranges

static TThisType GetWhole(void)

#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.

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

const TColumns & GetColumns(void) const

Get the Columns member data.

vector< CRef< CSeqTable_column > > TColumns

@ eField_id_location_to

interval to

@ eField_id_location_from

interval from

bool IsLocal(void) const

Check if variant Local is selected.

list< CRef< CSeq_align > > TAssembly

const TInst & GetInst(void) const

Get the Inst member data.

bool IsSetAssembly(void) const

how was this assembled? Check if a value has been assigned to Assembly data member.

bool IsSetHist(void) const

sequence history Check if a value has been assigned to Hist data member.

TTech GetTech(void) const

Get the Tech member data.

bool IsSetInst(void) const

the sequence data Check if a value has been assigned to Inst data member.

const TAssembly & GetAssembly(void) const

Get the Assembly member data.

const THist & GetHist(void) const

Get the Hist member data.

const TSeq_table & GetSeq_table(void) const

Get the variant data.

bool IsSetTech(void) const

Check if a value has been assigned to Tech data member.

const TData & GetData(void) const

Get the Data member data.

const TMolinfo & GetMolinfo(void) const

Get the variant data.

@ eTech_htgs_2

ordered High Throughput sequence contig

@ eTech_htgs_3

finished High Throughput sequence

@ eTech_htgs_1

unordered High Throughput sequence contig

@ eTech_wgs

whole genome shotgun sequencing

@ e_Molinfo

info on the molecule and techniques

Interfaces for a local cache of versioned binary large objects (BLOBS).

const struct ncbi::grid::netcache::search::fields::KEY key

const GenericPointer< typename T::ValueType > T2 value

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

Defines NCBI C++ API for timing-and-logging, classes, and macros.

CSegmentConfig::ESequenceQuality SGetSeqQuality(CMolInfo_Base::TTech tech)

utility function

const int kSegmentLoadLimit

static SLJIT_INLINE sljit_ins l(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

static SLJIT_INLINE sljit_ins msg(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

#define row(bind, expected)

Selector used in CSeqMap methods returning iterators.

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