Home - News ( United States | United Kingdom | Italy | Germany ) - Football scores

Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/gene__finder_8cpp_source.html below:

NCBI C++ ToolKit: src/objtools/format/gene_finder.cpp Source File

sequence;

m_Filtering_gene_xref(filtering_gene_xref),

*seq_id = loc_iter.GetRangeAsSeq_loc()->GetId();

unique_ptr<CFeat_CI> &feat_ci,

( m_BioseqHandle ) {

new_loc->

().SetFrom( 0 );

new_loc->

( *otherHalfOfRange );

new_loc->

( *loc.GetId() );

feat_ci.reset(

(scope, *new_loc, sel) );

loc_change_needed =

;

( CSeq_loc, loc_iter, loc ) {

( ! m_BioseqHandle.IsSynonym( loc_iter.GetSeq_id() ) ) {

loc_change_needed =

;

( loc_change_needed ) {

( CSeq_loc, loc_iter, loc ) {

( m_BioseqHandle.IsSynonym( loc_iter.GetSeq_id() ) ) {

new_loc->

( *loc_iter.GetRangeAsSeq_loc() );

feat_ci.reset(

(scope, *new_loc, sel) );

feat_ci.reset(

(scope, loc, sel) );

feat_ci.reset(

(scope, loc, sel) );

&shouldContinueToNextIteration,

&revert_locations_this_iteration,

(m_Filtering_gene_xref &&

shouldContinueToNextIteration =

;

candidate_feat_is_mixed =

( m_BioseqHandle, *candidate_feat_loc );

circular_length, norm_opt ) ;

cleaned_loc_this_iteration, circular_length, norm_opt );

( ( candidate_feat_bad_order || candidate_feat_is_mixed ) &&

revert_locations_this_iteration =

;

( (candidate_feat_bad_order || candidate_feat_is_mixed) &&

shouldContinueToNextIteration =

;

CSeq_loc_CI candidate_feat_loc_iter( feat.

() );

( ; candidate_feat_loc_iter; ++candidate_feat_loc_iter ) {

*candidate_feat_loc_iter.GetRangeAsSeq_loc(),

*cleaned_loc_this_iteration,

( x_StrandsMatch( m_Loc_original_strand, candidate_feat_loc_iter.GetStrand() ) ) {

shouldContinueToNextIteration =

;

( x_StrandsMatch( m_Loc_original_strand, candidate_feat_original_strand ) ) {

shouldContinueToNextIteration =

;

( ! x_StrandsMatch( m_Loc_original_strand, candidate_feat_original_strand ) ) {

shouldContinueToNextIteration =

;

( cur_diff < 0 ) {

( (start > stop) && (circular_length > 0) &&

cur_diff = circular_length -

( start - stop );

cur_diff =

( start - stop );

( candidate_feat_original_strand == feat_strand

out_s_feat.

();

out_g_ref =

;

( out_suppression_check_gene_ref &&

( resolved_feat ) {

out_s_feat = resolved_feat;

xref_g_ref->

(&xref_label);

( xref_label.empty() ) {

xref_g_ref =

;

also_look_at_parent_CDS =

;

also_look_at_parent_CDS =

;

( also_look_at_parent_CDS &&

pParentDecidingGeneRef &&

out_g_ref = pParentDecidingGeneRef;

(also_look_at_parent_CDS && xref_g_ref) {

out_g_ref = xref_g_ref;

( also_look_at_parent_CDS ) {

ownGeneIsOkay =

;

CSeq_loc &gene_loc = out_s_feat->

();

ownGeneIsOkay =

;

( pParentDecidingGeneRef ) {

out_s_feat.

();

out_g_ref = pParentDecidingGeneRef;

xref_g_ref =

;

}

( ownGeneIsOkay ) {

( in_parent_feat ) {

(in_feat && ! xref_g_ref) {

out_g_ref =

;

out_s_feat.

();

out_g_ref = &other_ref;

out_g_ref = xref_g_ref;

ERGX_MatchQuality {

eRGX_MatchedTagForLocus,

eRGX_MatchedLocusForTag,

( top_level_seq_entry ) {

ERGX_MatchQuality match_quality = eRGX_NoMatch;

found_near_match =

;

!found_near_match && bs;

(tried.

(tse_handle) != tried.

()) {

tried.

(tse_handle);

ERGX_MatchQuality new_quality = eRGX_NoMatch;

( !new_possibilities.empty() ) {

new_quality = eRGX_MatchedAsIs;

(new_quality == eRGX_NoMatch

&& match_quality <= eRGX_MatchedLocusForTag

( !new_possibilities.empty() ) {

new_quality = eRGX_MatchedLocusForTag;

(new_quality == eRGX_NoMatch

&& match_quality <= eRGX_MatchedTagForLocus

( !new_possibilities.empty() ) {

new_quality = eRGX_MatchedTagForLocus;

(new_quality > match_quality) {

possible_feats = new_possibilities;

match_quality = new_quality;

}

(new_quality == match_quality) {

possible_feats.insert(possible_feats.end(),

new_possibilities.begin(),

new_possibilities.end());

(new_quality == eRGX_NoMatch);

(match_quality != eRGX_NoMatch

found_near_match =

;

(match_quality != eRGX_NoMatch) {

best_score = INT_MAX;

( this_feats_score < best_score ) {

feat = a_possible_feat;

best_score = this_feats_score;

(

.IsSegmented() ||

.IsEMBL() ||

.IsDDBJ() ) {

(

.CanGetMaster() ) {

isSegmented = (

.GetMaster().GetNumParts() > 1);

string::size_type length_before_decimal_point =

.GetAccession().find(

);

( length_before_decimal_point == string::npos ) {

length_before_decimal_point =

.GetAccession().length();

( length_before_decimal_point == 6 ) {

cleaned_location->

( first_strand_to_try );

needToAddGbLoaderBack =

;

( scope && (

.IsEMBL() ||

.IsDDBJ() ) &&

needToAddGbLoaderBack =

;

filtering_gene_xref );

filtering_gene_xref );

( needToAddGbLoaderBack ) {

recursion_depth )

( recursion_depth > 10 ) {

feat_ci(

.GetHandle().GetTSE_Handle(), sel, obj_id );

(! other_ref || ! xref) {

( gene_syns_list.begin(), gene_syns_list.end(),

inserter(gene_syns, gene_syns.

()) );

( gene_syns.

(*syn_iter) == gene_syns.

() ) {

CSeq_loc_CI previous_loc;

( ! previous_loc ) {

previous_loc = loc_iter;

( previous_loc.GetSeq_id().Equals( loc_iter.GetSeq_id() ) ) {

prev_to = previous_loc.GetRange().GetTo();

this_to = loc_iter.GetRange().GetTo();

( prev_to < this_to) {

(prev_to > this_to) {

previous_loc = loc_iter;

( ; loc_iter; ++loc_iter ) {

& loc_id = loc_iter.GetSeq_id();

( top_bioseq_handle.

(loc_id) ) {

new_part->

( *loc_iter.GetRangeAsSeq_loc() );

new_loc_parts.push_back( new_part );

( ; loc_iter; ++loc_iter ) {

& loc_id = loc_iter.GetSeq_id();

( top_bioseq_handle.

(loc_id) ) {

original_strand = loc_iter.GetStrand();

original_strand = loc_iter.GetStrand();

new_part->

( *loc_iter.GetRangeAsSeq_loc() );

new_loc_parts.push_back( new_part );

( ! top_bioseq_handle ) {

original_strand;

plus_seen =

;

minus_seen =

;

( CSeq_loc, loc_iter, loc ) {

( loc_iter.IsEmpty() ) {

( bioseq_handle ) {

& loc_id = loc_iter.GetSeq_id();

( ! bioseq_handle.

(loc_id) ) {

( loc_iter.GetStrand() ) {

( plus_seen && minus_seen );

static CRef< CScope > m_Scope

User-defined methods of the data storage class.

@ eExtreme_Positional

numerical value

User-defined methods of the data storage class.

bool x_StrandsMatch(ENa_strand feat_strand, ENa_strand candidate_feat_original_strand)

void processSAnnotSelector(SAnnotSelector &sel)

CGeneSearchPlugin(const CSeq_loc &location, CScope &scope, const CGene_ref *filtering_gene_xref)

void setUpFeatureIterator(CBioseq_Handle &ignored_bioseq_handle, unique_ptr< CFeat_CI > &feat_ci, TSeqPos circular_length, CRange< TSeqPos > &range, const CSeq_loc &loc, SAnnotSelector &sel, CScope &scope, ENa_strand &strand)

void processMainLoop(bool &shouldContinueToNextIteration, CRef< CSeq_loc > &cleaned_loc_this_iteration, CRef< CSeq_loc > &candidate_feat_loc, sequence::EOverlapType &overlap_type_this_iteration, bool &revert_locations_this_iteration, CBioseq_Handle &ignored_bioseq_handle, const CMappedFeat &feat, TSeqPos circular_length, SAnnotSelector::EOverlapType annot_overlap_type)

CBioseq_Handle m_BioseqHandle

void postProcessDiffAmount(Int8 &cur_diff, CRef< CSeq_loc > &cleaned_loc, CRef< CSeq_loc > &candidate_feat_loc, CScope &scope, SAnnotSelector &sel, TSeqPos circular_length)

void processLoc(CBioseq_Handle &ignored_bioseq_handle, CRef< CSeq_loc > &loc, TSeqPos circular_length)

static ENa_strand GeneSearchNormalizeLoc(CBioseq_Handle top_bioseq_handle, CRef< CSeq_loc > &loc, const TSeqPos circular_length, TGeneSearchLocOpt opt=0)

static CConstRef< CSeq_feat > GetFeatViaSubsetThenExtremesIfPossible_Helper_subset(CBioseqContext &ctx, CScope *scope, const CSeq_loc &location, CSeqFeatData::E_Choice sought_type, const CGene_ref *filtering_gene_xref)

static CConstRef< CGene_ref > GetSuppressionCheckGeneRef(const CSeq_feat_Handle &feat)

static CSeq_feat_Handle ResolveGeneXref(const CGene_ref *xref_g_ref, const CSeq_entry_Handle &top_level_seq_entry)

This does plain, simple resolution of a CGene_ref to its gene.

static CConstRef< CSeq_feat > ResolveGeneObjectId(CBioseqContext &ctx, const CSeq_feat_Handle &feat, int recursion_depth=0)

static CConstRef< CSeq_feat > GetFeatViaSubsetThenExtremesIfPossible_Helper(CBioseqContext &ctx, CScope *scope, const CSeq_loc &location, CSeqFeatData::E_Choice sought_type, const CGene_ref *filtering_gene_xref)

static bool GeneMatchesXref(const CGene_ref *other_ref, const CGene_ref *xref)

static CConstRef< CSeq_feat > GetFeatViaSubsetThenExtremesIfPossible_Helper_extremes(CBioseqContext &ctx, CScope *scope, const CSeq_loc &location, CSeqFeatData::E_Choice sought_type, const CGene_ref *filtering_gene_xref)

static CConstRef< CSeq_feat > GetFeatViaSubsetThenExtremesIfPossible(CBioseqContext &ctx, CSeqFeatData::E_Choice feat_type, CSeqFeatData::ESubtype feat_subtype, const CSeq_loc &location, CSeqFeatData::E_Choice sought_type, const CGene_ref *filtering_gene_xref)

static void GetAssociatedGeneInfo(const CSeq_feat_Handle &in_feat, CBioseqContext &ctx, const CConstRef< CSeq_loc > &feat_loc, CConstRef< CGene_ref > &out_suppression_check_gene_ref, const CGene_ref *&out_g_ref, CConstRef< CSeq_feat > &out_s_feat, const CSeq_feat_Handle &in_parent_feat)

Find the gene associated with the given feature.

static bool CanUseExtremesToFindGene(CBioseqContext &ctx, const CSeq_loc &location)

static bool BadSeqLocSortOrderCStyle(CBioseq_Handle &bioseq_handle, const CSeq_loc &location)

static bool IsMixedStrand(CBioseq_Handle bioseq_handle, const CSeq_loc &loc)

@ fGeneSearchLocOpt_RemoveFar

void GetLabel(string *label) const

bool IsSuppressed(void) const

ESubtype GetSubtype(void) const

@ eSubtype_transit_peptide_aa

@ eSubtype_sig_peptide_aa

@ eSubtype_mat_peptide_aa

namespace ncbi::objects::

TSeq_feat_Handles GetGenesWithLocus(const string &locus, bool tag) const

vector< CSeq_feat_Handle > TSeq_feat_Handles

TSeq_feat_Handles GetGenesByRef(const CGene_ref &ref) const

iterator_bool insert(const value_type &val)

const_iterator begin() const

const_iterator find(const key_type &key) const

const_iterator end() const

static const char location[]

SAFE_CONST_STATIC_STRING(kGbLoader, "GBLOADER")

Public API for finding the gene(s) on a given feature using the same criteria as the flatfile generat...

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.

const TSeqPos kInvalidSeqPos

Define special value for invalid sequence position.

virtual void Assign(const CSerialObject &source, ESerialRecursionMode how=eRecursive)

Override Assign() to incorporate cache invalidation.

void SetId(CSeq_id &id)

set the 'id' field in all parts of this location

void Add(const CSeq_loc &other)

Simple adding of seq-locs.

void SetStrand(ENa_strand strand)

Set the strand for all of the location's ranges.

@ eOrder_Biological

Iterate sub-locations in positional order.

CMappedFeat GetBestOverlappingFeat(const CMappedFeat &feat, CSeqFeatData::ESubtype need_subtype, sequence::EOverlapType overlap_type, CFeatTree *feat_tree=0, const SAnnotSelector *base_sel=0)

TSeqPos GetStop(const CSeq_loc &loc, CScope *scope, ESeqLocExtremes ext=eExtreme_Positional)

If only one CBioseq is represented by CSeq_loc, returns the position at the stop of the location.

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.

TSeqPos GetStart(const CSeq_loc &loc, CScope *scope, ESeqLocExtremes ext=eExtreme_Positional)

If only one CBioseq is represented by CSeq_loc, returns the position at the start of the location.

sequence::ECompare Compare(const CSeq_loc &loc1, const CSeq_loc &loc2, CScope *scope)

Returns the sequence::ECompare containment relationship between CSeq_locs.

CSeq_id_Handle GetIdHandle(const CSeq_loc &loc, CScope *scope)

bool IsSameBioseq(const CSeq_id &id1, const CSeq_id &id2, CScope *scope, CScope::EGetBioseqFlag get_flag=CScope::eGetBioseq_All)

Determines if two CSeq_ids represent the same CBioseq.

@ fCompareOverlapping

Check if seq-locs are overlapping.

@ eOverlap_SubsetRev

1st is a subset of 2nd ranges

@ eOverlap_Contained

2nd contained within 1st extremes

@ eSame

CSeq_locs contain each other.

@ eNoOverlap

CSeq_locs do not overlap or abut.

CMappedFeat GetMappedCDSForProduct(const CBioseq_Handle &product)

void AddDataLoader(const string &loader_name, TPriority pri=kPriority_Default)

Add data loader by name.

static CRef< CObjectManager > GetInstance(void)

Return the existing object manager or create one.

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

void AddDefaults(TPriority pri=kPriority_Default)

Add default data loaders from object manager.

CDataLoader * FindDataLoader(const string &loader_name) const

Try to find a registered data loader by name.

CObjectManager & GetObjectManager(void)

Get object manager controlling this scope.

void RemoveDataLoader(const string &loader_name, EActionIfLocked action=eThrowIfLocked)

Revoke data loader from the scope.

const CSeq_feat::TXref & GetXref(void) const

virtual CConstRef< CSeq_feat > GetSeq_feat(void) const

const CSeqFeatData & GetData(void) const

bool IsSetXref(void) const

const CTSE_Handle & GetTSE_Handle(void) const

bool IsSetExcept_text(void) const

virtual const CSeq_loc & GetLocation(void) const

const string & GetExcept_text(void) const

CScope & GetScope(void) const

Get scope this handle belongs to.

CSeqFeatData::ESubtype GetFeatSubtype(void) const

CSeqFeatData::E_Choice GetFeatType(void) const

const CGene_ref * GetGeneXref(void) const

get gene (if present) from Seq-feat.xref list

bool IsSynonym(const CSeq_id &id) const

Check if this id can be used to obtain this bioseq handle.

const CSeq_loc & GetLocation(void) const

const CSeq_feat & GetOriginalFeature(void) const

Get original feature with unmapped location/product.

SAnnotSelector & SetIgnoreFarLocationsForSorting(const CBioseq_Handle &handle)

Set handle used for determining what locations are "near".

EOverlapType GetOverlapType(void) const

Get the selected overlap type.

EOverlapType

Flag to indicate location overlapping method.

SAnnotSelector & SetLimitTSE(const CTSE_Handle &limit)

Limit annotations to those from the TSE only.

SAnnotSelector & SetIgnoreStrand(bool value=true)

Ignore strand when testing for range overlap.

@ eOverlap_Intervals

default - overlapping of individual intervals

@ eOverlap_TotalRange

overlapping of total ranges only

TObjectType * ReleaseOrNull(void)

Release a reference to the object and return a pointer to the object.

TObjectType * GetPointer(void) THROWS_NONE

Get pointer,.

void Reset(void)

Reset reference object.

void Reset(void)

Reset reference object.

static const SAutoMax kMax_Auto

Generic stand-in for type-specific kMax_* constants from ncbi_limits.h, useful in any context with ex...

int64_t Int8

8-byte (64-bit) signed integer

#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.

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

bool IsSetSyn(void) const

synonyms for locus Check if a value has been assigned to Syn data member.

const TSyn & GetSyn(void) const

Get the Syn member data.

bool IsSetLocus_tag(void) const

systematic gene name (e.g., MI0001, ORF0069) Check if a value has been assigned to Locus_tag data mem...

bool IsSetLocus(void) const

Official gene symbol Check if a value has been assigned to Locus data member.

const TLocus_tag & GetLocus_tag(void) const

Get the Locus_tag member data.

const TLocus & GetLocus(void) const

Get the Locus member data.

const TData & GetData(void) const

Get the Data member data.

bool IsSetData(void) const

the specific data Check if a value has been assigned to Data data member.

bool IsCdregion(void) const

Check if variant Cdregion is selected.

const TLocal & GetLocal(void) const

Get the variant data.

const TLocation & GetLocation(void) const

Get the Location member data.

E_Choice

Choice variants.

bool IsLocal(void) const

Check if variant Local is selected.

const TId & GetId(void) const

Get the Id member data.

bool IsGene(void) const

Check if variant Gene is selected.

const TData & GetData(void) const

Get the Data member data.

bool IsSetData(void) const

the specific data Check if a value has been assigned to Data data member.

const TGene & GetGene(void) const

Get the variant data.

bool IsSetId(void) const

the feature copied Check if a value has been assigned to Id data member.

vector< CRef< CSeqFeatXref > > TXref

ENa_strand

strand of nucleic acid

list< CRef< CSeq_loc > > Tdata

@ eNa_strand_both

in forward orientation

unsigned int

A callback function used to compare two keys in a database.

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

Selector used in CSeqMap methods returning iterators.

RetroSearch is an open source project built by @garambo | Open a GitHub Issue

Search and Browse the WWW like it's 1997 | Search results from DuckDuckGo

HTML: 3.2 | Encoding: UTF-8 | Version: 0.7.4