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

Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/table2asn__context_8cpp_source.html below:

NCBI C++ ToolKit: src/app/table2asn/table2asn_context.cpp Source File

(create_date_desc.IsNull())

create_date_desc.Set().SetCreate_date(*date);

in_formats[2] = {

,

};

(!

.IsSetSubtype())

(

subtype :

.SetSubtype())

& col_date = subtype->SetName();

col_date =

(col_date, in_formats[p]).

(out_format);

p =

.m_cleanup.find_first_of(

);

(p == string::npos)

(

feature : annot.

().SetFtable())

(feature->IsSetData() && feature->GetData().IsBiosrc())

x_CorrectCollectionDates(

, feature->SetData().SetBiosrc());

p =

.m_cleanup.find_first_of(

);

(p == string::npos)

(seq_or_set.IsSetDescr())

(seq_or_set.IsSetAnnot())

(

annot : seq_or_set.SetAnnot())

x_CorrectCollectionDates(

, *annot);

std::runtime_error(

);

std::runtime_error(

);

& filename =

.GetFilename();

(!filename.empty())

& filename =

.GetFilename();

(!filename.empty())

constexpr std::array<string_view, 8> default_suffixes = {

string_view ext = default_suffixes[

(kind)];

(

== string_view(

) || dir ==

) {

(

& desc: descr.

())

(desc->IsUser() && desc->GetUser().IsSetType() &&

desc->GetUser().GetType().IsStr() &&

desc->GetUser().GetType().GetStr() ==

)

desc->SetUser();

descr.

().push_back(user_desc);

bioseq.

().push_back(accession);

submit->

().SetHup(

);

submit->

().SetReldate(*reldate);

submit->

().SetTool(toolname);

submit->

().SetEntrys().clear();

submit->

().SetEntrys().push_back(

);

->SetDescr().Set().push_back(pub_desc);

->Parentize();

(

src_desc: src.

())

(src_desc->Which())

(src_desc->Which())

edit::CDBLink::MergeDBLink(user_obj, src_desc->GetUser());

(new_desc.

())

dest.Set().push_back(new_desc);

new_desc->

(*src_desc);

(dest.Set().empty())

bioseq = &entry.

();

bioseq->

().clear();

bioseq->

().push_back(

);

(

bioseq_it(h_entry); bioseq_it; ++bioseq_it)

(

id_it: bioseq_it->GetBioseqCore()->GetId())

(!id_it->IsGeneral())

;

& dbtag = id_it->GetGeneral().GetDb();

(!comment.empty())

id_it->GetLabel(&comment);

std::vector<CSeq_feat*> cds;

std::vector<CSeq_feat*> rnas;

(

feat_it(h_entry); feat_it; ++feat_it)

(!feat_it->IsSetData())

(feat_it->GetData().Which())

cds.push_back((

*) &feat_it->GetOriginalFeature());

rnas.push_back((

*) &feat_it->GetOriginalFeature());

(

& seq_id: bioseq.

())

if (seq_id.Empty()) continue;

const CObject_id* obj_id;

switch (seq_id->Which())

case CSeq_id::e_Local:

obj_id = &seq_id->GetLocal();

seq_id->SetGeneral().SetTag().SetId(obj_id->GetId());

string id = obj_id->GetStr();

seq_id->SetGeneral().SetTag().SetStr(id);

seq_id->SetGeneral().SetDb(db);

(CSeq_feat::TQual::iterator it = quals.begin(); it != quals.end(); it++)

& qual_name = qual.

();

(qual_name ==

) {

qual.

(

);

(qual_name ==

) {

qual.

(

);

(CSeq_feat::TQual::iterator it = quals.begin(); it != quals.end();)

((**it).GetQual() ==

||

(**it).GetQual() ==

)

it = quals.erase(it);

need_update =

;

(entry.

())

need_update |= x_ApplyCreateDate(entry);

(

& it: descr.

())

(&it->SetOrg());

(

.IsSetTaxname())

name =

.GetTaxname();

(

.IsSetOrgname())

(

.GetOrgname().GetFlatName(name))

(

.IsSetOrg() &&

.GetOrg().IsSetOrgname())

(

.GetOrg().GetOrgname().GetFlatName(name))

(it->GetOrg().IsSetOrgname())

(it->GetOrg().GetOrgname().GetFlatName(name))

feature.

().SetLocal().SetId(

++);

p =

.find_first_of(

);

(p == string::npos)

x_CorrectCollectionDates(*

, bioseq_set);

x_CorrectCollectionDates(*

, bioseq);

bioseq_set.

().Set().push_back(comment_desc);

bioseq.SetDescr().Set().push_back(comment_desc);

replace_if(begin(linkage_evidence), end(linkage_evidence),

[](

c) {

(

(c) || c ==

); },

);

unique(begin(linkage_evidence), end(linkage_evidence),

[](

,

) {

(

==

&&

==

);});

linkage_evidence.erase(it, linkage_evidence.end());

& message,

& evidenceString,

& filename,

& lineNum,

list<string> evidenceList;

(

evidence : evidenceList) {

unnormalized_evidence = evidence;

evidenceSet.

(enum_val);

stringstream msgStream;

msgStream <<

<< lineNum <<

<< filename <<

;

msgStream <<

<< unnormalized_evidence <<

;

pLEStream = make_unique<CNcbiIfstream>(linkageEvidenceFilename, ios::binary);

(!pLEStream || !pLEStream->is_open()) {

(pEC,

+ linkageEvidenceFilename);

lineNumber = 0;

(pLEStream->good() && !pLEStream->eof()) {

getline(*pLEStream, line);

countStr, evidenceStr;

stringstream msgStream;

msgStream <<

<< lineNumber <<

<< linkageEvidenceFilename <<

;

msgStream << countStr <<

;

(!evidenceSet.empty()) {

gapsizeToEvidence.emplace(

, move(evidenceSet));

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

CSeqdesc & Set(bool skip_lookup=false)

static CRef< CSeqdesc > LocateDesc(const CSeq_descr &descr, CSeqdesc::E_Choice which)

static bool EraseDesc(CSeq_descr &descr, CSeqdesc::E_Choice which)

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

static CLineErrorEx * Create(EProblem eProblem, EDiagSev eSeverity, int code, int subcode, const std::string &strSeqId, unsigned int uLine, const std::string &strErrorMessage=string(""), const std::string &strFeatureName=string(""), const std::string &strQualifierName=string(""), const std::string &strQualifierValue=string(""), const TVecOfLines &vecOfOtherLines=TVecOfLines())

Use this because the constructor is protected.

static CNcbiApplication * Instance(void)

Singleton method.

bool IsFtable(void) const

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

void SetDescr(CSeq_descr &value)

CSeq_entry * GetParentEntry(void) const

namespace ncbi::objects::

string m_genome_center_id

void ApplyUpdateDate(objects::CSeq_entry &entry) const

CDiagnosticFileSet mDiagnosticWriters

static bool GetOrgName(string &name, const objects::CSeq_entry &entry)

CDataFileSet::fileset_type mCurrentDataOutputs

void SetSeqId(objects::CSeq_entry &entry) const

void ApplyFileTracks(objects::CSeq_entry &entry) const

void SetOutputFilename(eFiles kind, const string &filename)

void ApplyAccession(objects::CSeq_entry &entry) const

CRef< objects::CSeq_id > m_accession

CDataFileSet mDataWriters

static objects::CUser_object & SetUserObject(objects::CSeq_descr &descr, const CTempString &type)

void SetOutputFile(eFiles kind, ostream &ostr)

static CRef< objects::COrg_ref > GetOrgRef(objects::CSeq_descr &descr)

CRef< CSerialObject > CreateSubmitFromTemplate(CRef< objects::CSeq_entry > &object, CRef< objects::CSeq_submit > &submit) const

CRef< objects::CSeq_entry > m_entry_template

static void AddUserTrack(objects::CSeq_descr &SD, const string &type, const string &label, const string &data)

void CorrectCollectionDates(objects::CSeq_entry &entry) const

CDiagnosticFileSet::fileset_type mCurrentDiagnosticOutputs

void SmartFeatureAnnotation(objects::CSeq_entry &entry) const

CRef< objects::CSeq_submit > m_submit_template

string GenerateOutputFilename(eFiles kind, string_view basename=kEmptyStr) const

void MergeWithTemplate(objects::CSeq_entry &entry) const

void OpenDiagnosticOutputs()

void RenameProteinIdsQuals(objects::CSeq_feat &feature) const

void CloseDiagnosticOutputs()

void ApplyComments(objects::CSeq_entry &entry) const

void UpdateSubmitObject(CRef< objects::CSeq_submit > &submit) const

CRef< CSerialObject > CreateSeqEntryFromTemplate(CRef< objects::CSeq_entry > object) const

std::ostream & GetOstream(eFiles suffix)

bool ApplyCreateUpdateDates(objects::CSeq_entry &entry) const

string m_ResultsDirectory

void RemoveProteinIdsQuals(objects::CSeq_feat &feature) const

static void MergeSeqDescr(objects::CSeq_entry &dest, const objects::CSeq_descr &src, bool only_set)

static bool IsDBLink(const objects::CSeqdesc &desc)

static void UpdateTaxonFromTable(objects::CBioseq &bioseq)

void CopyFeatureIdsToComments(objects::CSeq_entry &entry) const

void MakeGenomeCenterId(objects::CSeq_entry &entry) const

CTempString implements a light-weight string on top of a storage buffer whose lifetime management is ...

virtual bool PutError(const ILineError &)=0

Store error in the container, and return true if error was stored fine, and return false if the calle...

@ eProblem_GeneralParsingError

void SetFilename(enum_type _enum, const std::string &filename)

void SetUseMT(bool use_mt)

fileset_type MakeNewFileset()

void Open(enum_type _enum, const std::string &filename)

iterator_bool insert(const value_type &val)

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

unsigned int TSeqPos

Type for sequence locations and lengths.

CVersionInfo GetVersion(void) const

Get the program version information.

@ eDiag_Error

Error message.

virtual bool Remove(TRemoveFlags flags=eRecursive) const

Remove a directory entry.

static void SplitPath(const string &path, string *dir=0, string *base=0, string *ext=0)

Split a path string into its basic components.

@ fIgnoreMissing

Ignore missed entries.

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

Set object to copy of another one.

#define ENUM_METHOD_NAME(EnumName)

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

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

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...

CRef< C > Ref(C *object)

Helper functions to get CRef<> and CConstRef<> objects.

void Reset(void)

Reset reference object.

bool NotEmpty(void) const THROWS_NONE

Check if CRef is not empty – pointing to an object and has a non-null value.

bool IsNull(void) const THROWS_NONE

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

bool Empty(void) const THROWS_NONE

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

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

static int CompareNocase(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2)

Case-insensitive compare of a substring with another string.

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 TNumeric StringToNumeric(const CTempString str, TStringToNumFlags flags=0, int base=10)

Convert string to a numeric value.

static void TruncateSpacesInPlace(string &str, ETrunc where=eTrunc_Both)

Truncate whitespace in a string (in-place)

static int Compare(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2, ECase use_case=eCase)

Compare of a substring with another string.

static bool SplitInTwo(const CTempString str, const CTempString delim, string &str1, string &str2, TSplitFlags flags=0)

Split a string into two pieces using the specified delimiters.

size_type find_first_of(const CTempString match, size_type pos=0) const

Find the first occurrence of any character in the matching string within the current string,...

static string & ToLower(string &str)

Convert string to lower case – string& version.

@ fConvErr_NoThrow

Do not throw an exception on error.

@ fSplit_Tokenize

All delimiters are merged and trimmed, to get non-empty tokens only.

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

Transform time to string.

bool IsEmpty(void) const

Is time object empty (date and time)?

static bool ValidateString(const string &str, const CTimeFormat &fmt=kEmptyStr)

Validate if string match time format.

@ eCurrent

Use current time. See also CCurrentTime.

virtual string Print(void) const

Print version information.

@ eSubtype_collection_date

DD-MMM-YYYY format.

bool IsStr(void) const

Check if variant Str is selected.

bool IsSetType(void) const

type of object within class Check if a value has been assigned to Type data member.

void SetNum(TNum value)

Assign a value to Num data member.

const TStr & GetStr(void) const

Get the variant data.

void SetLabel(TLabel &value)

Assign a value to Label data member.

TStr & SetStr(void)

Select the variant.

void SetType(TType &value)

Assign a value to Type data member.

void SetData(TData &value)

Assign a value to Data data member.

const TType & GetType(void) const

Get the Type member data.

TSub & SetSub(void)

Select the variant.

void SetQual(const TQual &value)

Assign a value to Qual data member.

bool IsSetComment(void) const

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

bool IsSetQual(void) const

qualifiers Check if a value has been assigned to Qual data member.

void SetComment(const TComment &value)

Assign a value to Comment data member.

void SetId(TId &value)

Assign a value to Id data member.

bool CanGetVal(void) const

Check if it is safe to call GetVal method.

bool IsSetId(void) const

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

vector< CRef< CGb_qual > > TQual

const TQual & GetQual(void) const

Get the Qual member data.

TQual & SetQual(void)

Assign a value to Qual data member.

void ResetQual(void)

Reset Qual data member.

bool IsSetClass(void) const

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

const TDescr & GetDescr(void) const

Get the Descr member data.

TSet & SetSet(void)

Select the variant.

TClass GetClass(void) const

Get the Class member data.

const TSet & GetSet(void) const

Get the variant data.

bool IsSeq(void) const

Check if variant Seq is selected.

bool IsSetDescr(void) const

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

E_Choice Which(void) const

Which variant is currently selected.

bool IsSet(void) const

Check if variant Set is selected.

void ResetDescr(void)

Reset Descr data member.

void SetDescr(TDescr &value)

Assign a value to Descr data member.

TSeq & SetSeq(void)

Select the variant.

TSeq_set & SetSeq_set(void)

Assign a value to Seq_set data member.

@ eClass_nuc_prot

nuc acid and coded proteins

@ eClass_genbank

converted genbank

void SetData(TData &value)

Assign a value to Data data member.

TId & SetId(void)

Assign a value to Id data member.

const TUser & GetUser(void) const

Get the variant data.

void ResetDescr(void)

Reset Descr data member.

void SetPub(TPub &value)

Assign a value to Pub data member.

TPub & SetPub(void)

Select the variant.

const Tdata & Get(void) const

Get the member data.

TComment & SetComment(void)

Select the variant.

void Select(E_Choice index, EResetVariant reset=eDoResetVariant)

Select the requested variant if needed.

TSource & SetSource(void)

Select the variant.

bool IsSetDescr(void) const

descriptors Check if a value has been assigned to Descr data member.

bool IsSet(void) const

Check if a value has been assigned to data member.

void SetDescr(TDescr &value)

Assign a value to Descr data member.

TUser & SetUser(void)

Select the variant.

Tdata & Set(void)

Assign a value to data member.

const TDescr & GetDescr(void) const

Get the Descr member data.

TUpdate_date & SetUpdate_date(void)

Select the variant.

bool IsUser(void) const

Check if variant User is selected.

@ e_User

user defined object

@ e_Update_date

date of last update

@ e_Pub

a reference to the publication

@ e_Molinfo

info on the molecule and techniques

@ e_Create_date

date entry first created/released

@ e_Source

source of materials, includes Org-ref

void SetSub(TSub &value)

Assign a value to Sub data member.

void SetData(TData &value)

Assign a value to Data data member.

for(len=0;yy_str[len];++len)

if(yy_accept[yy_current_state])

void VisitAllSetandSeq(objects::CSeq_entry &entry, _Mset mset, _Mseq mseq)

void VisitAllBioseqs(objects::CSeq_entry &entry, _M &&m)

const CharType(& source)[N]

bool AssignLocalIdIfEmpty(CSeq_feat &feature, int &id)

static void s_NormalizeLinkageEvidenceString(string &linkage_evidence)

static CGapsEditor::TEvidenceSet s_ProcessEvidenceString(const string &evidenceString, const string &filename, const size_t &lineNum, ILineErrorListener *pEC)

static void s_PostError(ILineErrorListener *pEC, const string &message, size_t lineNum=0)

void g_LoadLinkageEvidence(const string &linkageEvidenceFilename, CGapsEditor::TCountToEvidenceMap &gapsizeToEvidence, ILineErrorListener *pEC)

static CS_CONTEXT * context

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