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NCBI C++ ToolKit: src/algo/sequence/demo/xcompareannotsdemo.cpp Source File

r2_len =

.m_range.GetLength();

=

.m_range.CombinationWith(

.m_range);

qry_bias = 0.5)

d_aln_len =

(aln_len);

(qry_len == 0 ? 0.0 : d_aln_len/(qry_len) * qry_bias)

+ (tgt_len == 0 ? 0.0 : d_aln_len/(tgt_len) * (1.0 - qry_bias));

best_ending_pos = ranges.size() - 1;

pos = ranges.size() - 1;

best_beginning_pos = 0;

(list<CGappedRange>, it, ranges) {

(pos >= best_beginning_pos && pos <= best_ending_pos) {

(identity_out !=

) {

aligned_len =

.m_range.GetLength() -

.m_gaps;

d = (query_len +

.m_range.GetLength() - aligned_len);

*identity_out = d == 0 ? 0 :

(aligned_len) / d;

is_spliced =

,

strip_versions =

)

(from_id && !from_id->IsLocal()) {

collapsed_len_total(0);

query_len_total += query_len;

(mapped_interval->

() || mapped_interval->

()) {

mapped_loc->

(*mapped_interval_merged);

list<CGappedRange> mapped_ranges_list;

(

it2(*mapped_interval_merged); it2; ++it2) {

mapped_ranges_list.push_back(

(it2.GetRange()));

collapsed_len =

.m_range.GetLength();

aligned_len = collapsed_len -

.m_gaps;

aligned_len_total += aligned_len;

collapsed_len_total += collapsed_len;

(aligned_len > query_len) {

<<

<<

<< aligned_len

<<

<< collapsed_len

mapped_interval_collapsed->

().SetFrom(

.m_range.GetFrom());

mapped_interval_collapsed->

().SetTo(

.m_range.GetTo());

mapped_interval_collapsed->

().SetId(*

);

mapped_loc->

(*mapped_interval_collapsed);

(mapped_identity !=

) {

*mapped_identity = 1;

d = query_len_total + collapsed_len_total - aligned_len_total;

*mapped_identity = d == 0 ? 0 :

(aligned_len_total) / d;

k = handles.size();

(

ci(scope, *loc, sa); ci; ++ci) {

long_label =

;

(use_long_label) {

long_label +

;

title =

)

annot->

().SetFtable().push_back(feat);

feat->

().SetRna(*rna_ref);

title = sequence::CDeflineGenerator().GenerateDefline(h);

add_gene =

;

add_rna =

;

is_gene =

;

(is_gene || biomol_rna) {

(

ci(scope, loc, sel); ci; ++ci) {

add_gene =

;

;

+ title);

(

ci2(scope, loc, sel); ci2; ++ci2) {

add_rna =

;

;

+ title);

unique_ptr<CObjectIStream> obj_istr;

(file_or_dir->IsDir()) {

dir(*file_or_dir);

dir_entries.push_back(file_or_dir);

path = ent->GetPath();

(!ent->IsFile())

;

(

+ path);

unique_ptr<CObjectIStream> obj_istr =

(path, serial_format);

(!obj_istr->InGoodState()) {

(

);

(!obj_istr->EndOfData()) {

*obj_istr >> *seq_entry;

(

+ path);

(

);

unique_ptr<CObjectIStream> obj_istr =

(path, serial_format);

(!obj_istr->InGoodState()) {

(

);

(!obj_istr->EndOfData()) {

*obj_istr >> *seq_annot;

(

+ path);

(

);

unique_ptr<CObjectIStream> obj_istr =

(path, serial_format);

(!obj_istr->InGoodState()) {

(

);

(

);

(

);

(

);

enclosing_alignment_length);

arg_desc->AddOptionalKey(

,

arg_desc->AddDefaultKey(

,

arg_desc->SetConstraint(

,

->Allow(

)

->Allow(

));

arg_desc->AddOptionalKey(

,

arg_desc->AddDefaultKey(

,

arg_desc->SetConstraint(

,

->Allow(

)

->Allow(

));

arg_desc->AddKey(

,

,

arg_desc->AddDefaultKey(

,

,

arg_desc->SetConstraint(

,

->Allow(

)

->Allow(

)

->Allow(

));

arg_desc->AddDefaultKey(

,

arg_desc->SetConstraint(

,

->Allow(

)

->Allow(

));

arg_desc->AddOptionalKey(

,

,

arg_desc->AddDefaultKey(

,

,

arg_desc->AddFlag(

,

);

arg_desc->AddFlag(

,

);

arg_desc->AddFlag(

,

);

arg_desc->AddFlag(

,

);

arg_desc->AddFlag(

,

);

arg_desc->AddOptionalKey(

,

,

arg_desc->AddOptionalKey(

,

,

arg_desc->AddFlag(

,

);

arg_desc->AddFlag(

,

);

arg_desc->AddFlag(

,

);

arg_desc->AddFlag(

,

);

arg_desc->SetUsageContext(

,

);

(

+ s);

(

+ s);

self_comparison =

(t_start > t_stop) {

qloc->

().SetId(*q_seq_id);

qloc->

().SetFrom(q_start);

qloc->

().SetTo(q_stop);

tloc->

().SetId(*t_seq_id);

tloc->

().SetFrom(t_start);

tloc->

().SetTo(t_stop);

tloc->

().SetStrand(t_strand);

list<CRef<CSeq_align> > TSeqAlignList;

TSeqAlignList aligns_list;

(

+ filename);

list<CRef<CSeq_align> > TSeqAlignList;

(

[

].AsString() ==

) {

*istr >> *aligns_set;

}

(

[

].AsString() ==

) {

*istr >> *aligns_annot;

}

(

[

].AsString() ==

) {

aligns_list.clear();

aligns_list.push_back(aln);

(

<<

<<

[

].AsString());

aligns_set ? aligns_set->

() :

aligns_annot ? aligns_annot->

().SetAlign() :

& seq_id = (*it)->SetSegs().SetDenseg().SetIds()[

];

(seq_id.

())

;

str_seq_id =

;

(

[

]) {

(*it)->SwapRows(0, 1);

& id_q = (*it)->GetSeq_id(0);

str_id_q =

;

str_id_t =

;

.GetLabel(&str_id_t);

str_aln =

+ str_id_q +

+ str_id_t;

(str_aln +

);

(str_aln +

);

(alnMixes[str_aln].IsNull()) alnMixes[str_aln].Reset(

(

));

(TAlnMixes, it2, alnMixes) {

str_id = it2->first;

->Assign(merged_aln->

(0));

loc->

().SetId(*

);

(

[

]) {

enclosing_alignment_length)

groupNumber = 1;

loc_label =

;

(

<< loc_label);

vector<CRef<CCompareFeats> > v;

comparisonNumber = 1;

(

);

(cf->GetMappedIdentity() <= 0) {

;}

<< groupNumber <<

<< comparisonNumber <<

;

(!cf->GetFeatQ().

()) {

<<

;

(!cf->GetFeatT().

()) {

(cf->IsMatch()) {

sResult =

;

cf->GetComparison()->GetResult(&sResult);

<< cf->GetComparison()->GetEvidenceString() <<

;

cf->GetComparison()->GetResult(&sResult);

<< cf->GetMappedIdentity() <<

;

<< cf->GetComparison()->GetRelativeOverlap() <<

;

<< cf->GetComparison()->GetSymmetricalOverlap() <<

;

shared_sites_score(0.0f);

loc1_intervals(0);

loc2_intervals(0);

cf->GetComparison()->GetSplicingSimilarity(shared_sites_score, &loc1_intervals, &loc2_intervals);

<< loc1_intervals <<

;

<< loc2_intervals <<

;

<< shared_sites_score <<

;

loc1_intervals(0);

(!cf->GetFeatQ().

()) {

(

ci(*cf->GetSelfLocQ()); ci; ++ci) {

loc2_intervals(0);

(!cf->GetFeatT().

()) {

(

ci(*cf->GetSelfLocT()); ci; ++ci) {

<< cf->GetMappedIdentity() <<

<< enclosing_alignment_length <<

ir = cf->GetIrrelevance();

<< (ir == 0 ?

: ir == 1 ?

: ir == 2 ?

:

);

(

[

]) {

<<

<< (cf->GetFeatQ().

() ?

: cf->GetFeatQ()->GetNamedQual(*it2));

<<

<< (cf->GetFeatT().

() ?

: cf->GetFeatT()->GetNamedQual(*it2));

(

[

]) {

str_tag = *it2;

(

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

tmpstr =

;

}

(str_tag ==

) {

(!db_tag.

()) {

args_str =

;

(

[

]) {

(

[

]) {

(

[

]) {

use_scopeless_mapper =

;

(

[

]) {

use_scopeless_mapper =

;

}

(

[

]) {

(

[

]) {

(

[

]) {

(

);

(getline(istr, line).good()) {

(line.size() == 0 || line.compare(0, 1,

) == 0)

;

vector<string> tokens;

(tokens.size() != 3) {

(

<<

<< line);

(use_scopeless_mapper) {

<<

<<

<<

<<

<<

<<

<<

<<

(

[

]) {

(

[

]) {

(getline(istr, line).good()) {

(line.size() == 0 || line.compare(0, 1,

) == 0)

;

vector<string> tokens;

(

[

].AsString().find(

) != string::npos && tokens[0].find(

) != string::npos)

}

(tokens.size() == 1) {

}

(tokens.size() == 6 || tokens.size() == 2) {

q_id = tokens[0];

t_id = tokens.size() == 2 ? tokens[1] : tokens[3];

(tokens.size() == 6) {

(

[

]) {

}

(tokens.size() == 3) {

(tokens[1] ==

|| tokens[2] ==

) {

loc->

().SetId(*

);

id_q->

(*ci.GetRefSeqid().GetSeqId());

loc_q->

().SetId(*id_q);

loc_q->

().SetFrom(ci.GetRefPosition());

loc_q->

().SetTo(ci.GetEndPosition());

(

<<

<< tokens.size() << line);

(

argc,

* argv[])

User-defined methods of the data storage class.

User-defined methods of the data storage class.

const TConstAlns & GetInputSeqAligns(void) const

void Merge(TMergeFlags flags=0)

const CSeq_align & GetSeqAlign(void) const

Compare multiple feature annotations on the specified seq_locs.

static int s_GetGeneId(const CSeq_feat &feat)

const CSeq_loc & GetQueryLoc() const

bool NextComparisonGroup(vector< CRef< CCompareFeats > > &v)

Return the next group of comparisons on the region (return true iff found any) A group is a set of fe...

TComparisonOptions GetOptions() const

void GetLabel(string *label) const

static string GetLoaderNameFromArgs(CReader *reader=0)

static TRegisterLoaderInfo RegisterInObjectManager(CObjectManager &om, CReader *reader=0, CObjectManager::EIsDefault is_default=CObjectManager::eDefault, CObjectManager::TPriority priority=CObjectManager::kPriority_NotSet)

Interface for handling Seq-entry objects.

CGBReleaseFile is a utility class to ease the processing of Genbank release files one Seq-entry at a ...

void RegisterHandler(ISeqEntryHandler *handler)

Register handler.

void Read(void)

Read the release file.

virtual ~CGbScopeLoader()

bool HandleSeqEntry(CRef< CSeq_entry > &entry)

user code for handling a Seq-entry goes here.

CGbScopeLoader(CScope &scope)

double GetIdentity() const

CGappedRange(const CGappedRange &r1, const CGappedRange &r2)

CGappedRange(TRange range=TRange(), unsigned gaps=0)

CRef< CSeq_loc > Map(const CSeq_loc &loc, double *mapped_identity=NULL)

CRef< CSeq_id > m_from_id

CLocMapper_Default(CSeq_loc_Mapper &mapper, CScope &scope, bool is_spliced=false, const CSeq_id *from_id=NULL, bool strip_versions=false)

string m_from_id__accession

CGappedRange CollapseRanges(list< CGappedRange > &ranges, TSeqPos query_len, double *identity_out=NULL)

CSeq_loc_Mapper & m_mapper

static double GetBiasedSymmetricIdentity(TSeqPos qry_len, TSeqPos tgt_len, TSeqPos aln_len, double qry_bias=0.5)

Storage for multiple mapping ranges.

@RNA_ref.hpp User-defined methods of the data storage class.

CRange< TSeqPos > GetSeqRange(TDim row) const

GetSeqRange NB: On a Spliced-seg, in case the product-type is protein, these only return the amin par...

TSeqPos GetSeqStop(TDim row) const

const CSeq_id & GetSeq_id(TDim row) const

Get seq-id (the first one if segments have different ids).

TSeqPos GetSeqStart(TDim row) const

namespace ncbi::objects::

CConstRef< CDbtag > GetNamedDbxref(const CTempString &db) const

Return a specified DB xref.

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

CRef< CScope > m_scope_for_mapper

map< int, map< string, string > > m_id_map

void x_ProcessMappingRanges()

CRef< CScope > m_scope_id

CSeq_id_Handle m_q_id_prev

virtual void Init(void)

Initialize the application.

void x_ProcessSeqAlignSetFromFile(string filename)

CRef< CMappingRanges > m_mapping_ranges

void x_ProcessMappingRange(string q_id, TSeqPos q_start, TSeqPos q_stop, string t_id, TSeqPos t_start, TSeqPos t_stop)

void x_ProcessComparison(CCompareSeqRegions &comparator, TSeqPos enclosing_alignment_length)

virtual int Run(void)

Run the application.

CSeq_id_Handle m_t_id_prev

CZipStreamDecompressor – zlib based decompression stream processor.

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

API (CDeflineGenerator) for computing sequences' titles ("definitions").

std::ofstream out("events_result.xml")

main entry point for tests

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

static const char * str(char *buf, int n)

void reset(element_type *p=0, EOwnership ownership=eTakeOwnership)

Reset will delete the old pointer (if owned), set content to the new value, and assume the ownership ...

unsigned int TSeqPos

Type for sequence locations and lengths.

virtual const CArgs & GetArgs(void) const

Get parsed command line arguments.

int AppMain(int argc, const char *const *argv, const char *const *envp=0, EAppDiagStream diag=eDS_Default, const char *conf=NcbiEmptyCStr, const string &name=NcbiEmptyString)

Main function (entry point) for the NCBI application.

virtual void SetupArgDescriptions(CArgDescriptions *arg_desc)

Setup the command line argument descriptions.

#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 CNcbiArguments & GetArguments(void) const

Get the application's cached unprocessed command-line arguments.

void swap(NCBI_NS_NCBI::pair_base_member< T1, T2 > &pair1, NCBI_NS_NCBI::pair_base_member< T1, T2 > &pair2)

@ eTakeOwnership

An object can take ownership of another.

string & Print(string &str) const

Print (append) all arguments to the string "str" and return "str".

CArgs & Assign(const CArgs &other)

Copy contents of another object into this one.

vector< string > TStringArray

Some values types can contain several value lists.

@ fAllowMultiple

Repeated key arguments are legal (use with AddKey)

@ eInputFile

Name of file (must exist and be readable)

@ eString

An arbitrary string.

@ eInteger

Convertible into an integer number (int or Int8)

@ fCheckFileHeader

Check (and skip) gzip file header on decompression stage.

void SetDiagPostFlag(EDiagPostFlag flag)

Set the specified flag (globally).

EDiagSev SetDiagPostLevel(EDiagSev post_sev=eDiag_Error)

Set the threshold severity for posting the messages.

#define ERR_POST(message)

Error posting with file, line number information but without error codes.

void SetDiagTrace(EDiagTrace how, EDiagTrace dflt=eDT_Default)

Set the diagnostic trace settings.

#define LOG_POST(message)

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

@ eDPF_All

All flags (except for the "unusual" ones!)

@ eDS_Default

Try standard log file (app.name + ".log") in /log/, use stderr on failure.

@ eDT_Enable

Enable messages of severity "eDiag_Trace".

@ eDiag_Info

Informational message.

@ eDiag_Warning

Warning message.

void Error(CExceptionArgs_Base &args)

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

void Warning(CExceptionArgs_Base &args)

void Fatal(CExceptionArgs_Base &args)

#define NCBI_REPORT_EXCEPTION(title, ex)

Generate a report on the exception.

void Info(CExceptionArgs_Base &args)

TEntries GetEntries(const string &mask=kEmptyStr, TGetEntriesFlags flags=0) const

Get directory entries based on the specified "mask".

ESerialDataFormat

Data file format.

@ eSerial_AsnText

ASN.1 text.

@ eSerial_AsnBinary

ASN.1 binary.

const string AsFastaString(void) const

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

Optimized implementation of CSerialObject::Assign, which is not so efficient.

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

CSeq_id & Set(const CTempString &the_id, TParseFlags flags=fParse_AnyRaw)

Reassign based on flat specifications; arguments interpreted as with constructors.

string GetLabel(const CSeq_id &id)

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

int Compare(const CSeq_loc &loc) const

void Add(const CSeq_loc &other)

Simple adding of seq-locs.

void GetLabel(string *label) const

Appends a label suitable for display (e.g., error messages) label must point to an existing string ob...

void SetNull(void)

Override all setters to incorporate cache invalidation.

virtual bool EndOfData(void)

Check if there is still some meaningful data that can be read; in text streams this function will ski...

static CObjectIStream * Open(ESerialDataFormat format, CNcbiIstream &inStream, bool deleteInStream)

Create serial object reader and attach it to an input stream.

@ fFGL_Content

Include its content if there is any.

@ fFGL_Type

Always include the feature's type.

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.

ENa_strand GetStrand(const CSeq_loc &loc, CScope *scope=0)

Returns eNa_strand_unknown if multiple Bioseqs in loc Returns eNa_strand_other if multiple strands in...

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.

CRef< CSeq_loc > Seq_loc_Merge(const CSeq_loc &loc, CSeq_loc::TOpFlags flags, CScope *scope)

Merge ranges in the seq-loc.

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.

string GetAccessionForId(const objects::CSeq_id &id, CScope &scope, EAccessionVersion use_version=eWithAccessionVersion, EGetIdType flags=0)

Retrieve the accession string for a Seq-id.

const CMolInfo * GetMolInfo(const CBioseq &bioseq)

Retrieve the MolInfo object for a given bioseq handle.

@ eWithoutAccessionVersion

accession only, even if version is available

@ eGetId_ForceAcc

return only an accession based seq-id

CRef< CSeq_loc > Map(const CSeq_loc &src_loc)

Map seq-loc.

void ResetHistory(EActionIfLocked action=eKeepIfLocked)

Clean all unused TSEs from the scope's cache and release the memory.

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.

CSeq_entry_Handle AddTopLevelSeqEntry(CSeq_entry &top_entry, TPriority pri=kPriority_Default, EExist action=eExist_Default)

Add seq_entry, default priority is higher than for defaults or loaders Add object to the score with p...

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

void GetAllTSEs(TTSE_Handles &tses, enum ETSEKind kind=eManualTSEs)

CSeq_annot_Handle AddSeq_annot(CSeq_annot &annot, TPriority pri=kPriority_Default, EExist action=eExist_Throw)

Add Seq-annot, return its CSeq_annot_Handle.

void UpdateAnnotIndex(void)

void AddScope(CScope &scope, TPriority pri=kPriority_Default)

Add the scope's datasources as a single group with the given priority All data sources (data loaders ...

vector< CSeq_entry_Handle > TTSE_Handles

@ eSeqMap_Up

map from segments to the top level bioseq

SAnnotSelector & IncludeFeatSubtype(TFeatSubtype subtype)

Include feature subtype in the search.

SAnnotSelector & SetFeatType(TFeatType type)

Set feature type (also set annotation type to feat)

SAnnotSelector & SetExactDepth(bool value=true)

SetExactDepth() specifies that annotations will be searched on the segment level specified by SetReso...

SAnnotSelector & SetResolveAll(void)

SetResolveAll() is equivalent to SetResolveMethod(eResolve_All).

SAnnotSelector & SetOverlapTotalRange(void)

Check overlapping only of total ranges.

SAnnotSelector & SetAdaptiveDepth(bool value=true)

SetAdaptiveDepth() requests to restrict subsegment resolution depending on annotations found on lower...

SAnnotSelector & SetResolveDepth(int depth)

SetResolveDepth sets the limit of subsegment resolution in searching annotations.

SAnnotSelector & SetSearchUnresolved(void)

SAnnotSelector & IncludeFeatType(TFeatType type)

Include feature type in the search.

SAnnotSelector & SetMaxSize(TMaxSize max_size)

Set maximum number of annotations to find.

SAnnotSelector & SetOverlapIntervals(void)

Check overlapping of individual intervals.

SAnnotSelector & SetSortOrder(ESortOrder sort_order)

Set sort order of annotations.

@ eSortOrder_None

do not sort annotations for faster retrieval

@ eSeqRef

reference to Bioseq

bool IsNull(void) const THROWS_NONE

Check if pointer is null – same effect as Empty().

TObjectType * GetPointer(void) THROWS_NONE

Get pointer,.

void Reset(void)

Reset reference object.

void Reset(void)

Reset reference object.

bool IsNull(void) const THROWS_NONE

Check if pointer is null – same effect as Empty().

static void EnableGlobally(bool enable=true)

Enable (or disable, if called with enable = false) loading plugins from DLLs in general.

position_type GetLength(void) const

IO_PREFIX::istream CNcbiIstream

Portable alias for istream.

IO_PREFIX::ifstream CNcbiIfstream

Portable alias for ifstream.

static string DoubleToString(double value, int precision=-1, TNumToStringFlags flags=0)

Convert double to string.

static int StringToInt(const CTempString str, TStringToNumFlags flags=0, int base=10)

Convert string to int.

static list< string > & Split(const CTempString str, const CTempString delim, list< string > &arr, TSplitFlags flags=0, vector< SIZE_TYPE > *token_pos=NULL)

Split a string using specified delimiters.

static bool EndsWith(const CTempString str, const CTempString end, ECase use_case=eCase)

Check if a string ends with a specified suffix value.

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

Convert int to string.

static SIZE_TYPE Find(const CTempString str, const CTempString pattern, ECase use_case=eCase, EDirection direction=eForwardSearch, SIZE_TYPE occurrence=0)

Find the pattern in the string.

static unsigned int StringToUInt(const CTempString str, TStringToNumFlags flags=0, int base=10)

Convert string to unsigned int.

static string UInt8ToString(Uint8 value, TNumToStringFlags flags=0, int base=10)

Convert UInt8 to string.

@ eNocase

Case insensitive compare.

string AsString(const CTimeFormat &format=kEmptyStr, TSeconds out_tz=eCurrentTimeZone) const

Transform time to string.

CTime & SetCurrent(void)

Make the time current in the presently active time zone.

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

TId GetId(void) const

Get the variant data.

void SetType(TType value)

Assign a value to Type data member.

Tdata & Set(void)

Assign a value to data member.

TDim GetDim(void) const

Get the Dim member data.

const TData & GetData(void) const

Get the Data member data.

void SetLocation(TLocation &value)

Assign a value to Location data member.

const TId & GetId(void) const

Get the Id member data.

const TLocal & GetLocal(void) const

Get the variant 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.

void SetTitle(const TTitle &value)

Assign a value to Title data member.

bool IsGene(void) const

Check if variant Gene is selected.

bool CanGetId(void) const

Check if it is safe to call GetId method.

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 CanGetId(void) const

Check if it is safe to call GetId method.

void SetData(TData &value)

Assign a value to Data data member.

const TProduct & GetProduct(void) const

Get the Product member data.

const TXref & GetXref(void) const

Get the Xref member data.

vector< CRef< CSeqFeatXref > > TXref

bool CanGetProduct(void) const

Check if it is safe to call GetProduct method.

bool IsEmpty(void) const

Check if variant Empty is selected.

ENa_strand

strand of nucleic acid

bool IsGi(void) const

Check if variant Gi is selected.

bool IsWhole(void) const

Check if variant Whole is selected.

bool IsNull(void) const

Check if variant Null is selected.

@ eNa_strand_both

in forward orientation

TSeq & SetSeq(void)

Select the variant.

void SetData(TData &value)

Assign a value to Data data member.

TId & SetId(void)

Assign a value to Id data member.

void SetInst(TInst &value)

Assign a value to Inst data member.

TBiomol GetBiomol(void) const

Get the Biomol member data.

@ eRepr_virtual

no seq data

@ eBiomol_other_genetic

other genetic material

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

Defines command line argument related classes.

Defines unified interface to application:

Defines NCBI C++ exception handling.

Portable reference counted smart and weak pointers using CWeakRef, CRef, CObject and CObjectEx.

std::istream & in(std::istream &in_, double &x_)

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

Plugin manager (using class factory paradigm).

static bool GetSeqId(const T &d, set< string > &labels, const string name="", bool detect=false, bool found=false)

static const sljit_gpr r1

static const sljit_gpr r2

#define row(bind, expected)

Selector used in CSeqMap methods returning iterators.

bool IsInScope(CScope &scope, const CSeq_id &id)

string GetIdStartStopStrandStr(const CSeq_loc &loc, CScope &scope, bool use_long_label)

bool IsManualScope(CScope &scope)

TLoadScopeMethod LoadScope(string arg_path, CScope &scope, ESerialDataFormat serial_format)

void AddSpanningSentinelFeat(CScope &scope, const CSeq_id &id, CSeqFeatData::E_Choice type, string title="Sentinel")

void AddDefaultSentinelFeats(CScope &scope, const CSeq_loc &loc)

ESerialDataFormat StringToSerialFormat(string str)

int main(int argc, const char *argv[])

void AddSentinelRNASeq(CScope &scope, const CSeq_id &id)

unique_ptr< CObjectIStream > GetIStream(string path, ESerialDataFormat serial_format)

string GetProductLabel(const CSeq_feat &feat, CScope &scope)

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