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

Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/validator__barcode_8cpp_source.html below:

NCBI C++ ToolKit: src/objtools/validator/validator_barcode.cpp Source File

(CBioseq_Handle::TId::const_iterator it = bsh.GetId().begin(); it != bsh.GetId().end(); ++it)

&

= *(it->GetSeqId());

(

.IsGenbank() &&

.GetGenbank().IsSetAccession())

accession =

.GetGenbank().GetAccession();

(

.IsLocal() &&

.GetLocal().IsStr())

=

.GetLocal().GetStr();

(!accession.empty())

(CBioseq_Handle::TId::const_iterator it = bsh.

().begin(); it != bsh.

().end(); ++it)

&

= *(it->GetSeqId());

(

.IsGeneral() &&

.GetGeneral().IsSetDb() &&

(

.GetGeneral().GetDb(),

))

found_rbcl(

);

found_matk(

);

& gene = feat_it->GetOriginalFeature();

}

(found_rbcl)

}

(length < 500)

forward(

);

reverse(

);

(source_ci->GetSource().IsSetPcr_primers())

((*reaction)->IsSetForward() && (*reaction)->GetForward().IsSet() && !(*reaction)->GetForward().Get().empty())

((*reaction)->IsSetReverse() && (*reaction)->GetReverse().IsSet() && !(*reaction)->GetReverse().Get().empty())

!(forward && reverse);

country(

);

((*orgmod)->IsSetSubtype() && (

((*orgmod)->IsSetSubtype() && (

&& (*orgmod)->IsSetSubname())

= (*orgmod)->GetSubname();

num_n += gap_it->length;

has_date(

);

&date = (*subsource)->GetName();

bad_format(

);

in_future(

);

(!bad_format && !in_future)

has_order(

);

has_ibol(

);

(desc_ci->GetUser().IsSetType() && desc_ci->GetUser().GetType().IsStr() &&

(desc_ci->GetUser().GetType().GetStr(),

))

is_ibol(

);

(desc_ci->GetUser().HasField(

))

(is_ibol && desc_ci->GetUser().HasField(

))

has_ibol && !has_order;

low_trace(

);

(desc_ci->GetUser().IsSetType() && desc_ci->GetUser().GetType().IsStr() &&

(desc_ci->GetUser().GetType().GetStr(),

))

(desc_ci->GetUser().HasField(

))

(

.length ||

.primers ||

.country ||

.voucher || !

.structured_voucher ||

!

.percent_n.empty() ||

.collection_date ||

.order_assignment ||

.low_trace ||

.frame_shift)

is_ibol(

);

(desc_ci->GetUser().IsSetType() && desc_ci->GetUser().GetType().IsStr() &&

(desc_ci->GetUser().GetType().GetStr(),

))

(desc_ci->GetUser().HasField(

))

frame_shift(

);

(desc_ci->GetUser().IsSetType() && desc_ci->GetUser().GetType().IsStr() &&

(desc_ci->GetUser().GetType().GetStr(),

))

(desc_ci->GetUser().HasField(

))

is_ibol && frame_shift;

has_keyword(

);

&keyword = *qual_it;

objects::CBioseq_CI b_iter(seh, objects::CSeq_inst::eMol_na);

(; b_iter; ++b_iter)

BarcodeFailures.push_back(

);

BarcodeFailures;

This iterates over the runs of Ns of each sequence.

namespace ncbi::objects::

static void IsCorrectDateFormat(const string &date_string, bool &bad_format, bool &in_future)

const CUser_field & GetField(const string &str, const string &delim=".", NStr::ECase use_case=NStr::eCase) const

Access a named field in this user field.

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

The NCBI C++ standard methods for dealing with std::string.

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

unsigned int TSeqPos

Type for sequence locations and lengths.

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

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

@ eContent

Untagged human-readable accession or the like.

TSeqPos max_gap_len_to_ignore

We completely ignore any gaps we find that have this number of bases or fewer.

TSeqPos GetBioseqLength(void) const

CSeq_entry_Handle GetSeq_entry_Handle(void) const

Get parent Seq-entry handle.

const TId & GetId(void) const

#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.

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 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 bool StartsWith(const CTempString str, const CTempString start, ECase use_case=eCase)

Check if a string starts with a specified prefix value.

static bool EqualNocase(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2)

Case-insensitive equality of a substring with another string.

static string & ReplaceInPlace(string &src, const string &search, const string &replace, SIZE_TYPE start_pos=0, SIZE_TYPE max_replace=0, SIZE_TYPE *num_replace=0)

Replace occurrences of a substring within a string.

@ fAllowTrailingSpaces

Ignore trailing whitespace characters.

@ fConvErr_NoThrow

Do not throw an exception on error.

@ fAllowLeadingSpaces

Ignore leading whitespace characters in converted string.

static const char label[]

@ eSubtype_collection_date

DD-MMM-YYYY format.

bool IsSetLocus(void) const

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

const TLocus & GetLocus(void) const

Get the Locus member data.

const TStr & GetStr(void) const

Get the variant data.

const TData & GetData(void) const

Get the Data member data.

bool IsStr(void) const

Check if variant Str is selected.

bool IsSetData(void) const

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

@ eSubtype_specimen_voucher

@ eSubtype_culture_collection

bool IsSetData(void) const

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

bool IsGene(void) const

Check if variant Gene is selected.

const TData & GetData(void) const

Get the Data member data.

const TGene & GetGene(void) const

Get the variant data.

@ eTech_barcode

barcode of life project

@ e_User

user defined object

@ e_Genbank

GenBank specific info.

@ e_Molinfo

info on the molecule and techniques

@ e_Source

source of materials, includes Org-ref

Defines a portable execute class.

#define FOR_EACH_KEYWORD_ON_GENBANKBLOCK(Itr, Var)

FOR_EACH_KEYWORD_ON_GENBANKBLOCK EDIT_EACH_KEYWORD_ON_GENBANKBLOCK.

#define FOR_EACH_PCRREACTION_IN_PCRREACTIONSET(Itr, Var)

FOR_EACH_PCRREACTION_IN_PCRREACTIONSET.

#define FOR_EACH_ORGMOD_ON_BIOSOURCE(Itr, Var)

FOR_EACH_ORGMOD_ON_BIOSOURCE EDIT_EACH_ORGMOD_ON_BIOSOURCE.

#define FOR_EACH_SUBSOURCE_ON_BIOSOURCE(Itr, Var)

FOR_EACH_SUBSOURCE_ON_BIOSOURCE EDIT_EACH_SUBSOURCE_ON_BIOSOURCE.

The params that control the behavior of CBioseqGaps_CI.

bool GetIsPrimers(CBioseq_Handle bsh)

bool BarcodeTestFails(const SBarcode &b)

bool GetLowTrace(CBioseq_Handle bsh)

string GetPercentN(CBioseq_Handle bsh)

bool GetHasCollectionDate(CBioseq_Handle bsh)

string GetSeqTitle(CBioseq_Handle bsh)

bool IsTechBarcode(CBioseq_Handle bsh)

bool GetIsVoucher(CBioseq_Handle bsh)

bool GetHasOrderAssignment(CBioseq_Handle bsh)

TBarcodeResults GetBarcodeValues(CSeq_entry_Handle seh)

bool GetHasFrameShift(CBioseq_Handle bsh)

void BarcodeTestBioseq(CBioseq_Handle bsh, SBarcode &b)

bool GetIsStructuredVoucher(CBioseq_Handle bsh)

string GetBarcodeId(CBioseq_Handle bsh)

bool GetHasKeyword(CBioseq_Handle bsh)

bool GetIsCountry(CBioseq_Handle bsh)

bool GetIsLength(CBioseq_Handle bsh)

vector< SBarcode > TBarcodeResults

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