CReadUtil Class Reference

Search Toolkit Book for CReadUtil

Common file reader utility functions. More...

#include <objtools/readers/read_util.hpp>

Collaboration diagram for CReadUtil:

Static Public Member Functions
static void	Tokenize (const string &instr, const string &delim, vector< string > &tokens)
	Tokenize a given string, respecting quoted substrings an atomic units. More...
static CRef< CSeq_id >	AsSeqId (const string &rawId, long flags=0, bool localInts=true)
	Convert a raw ID string to a Seq-id, based in given customization flags. More...
static bool	GetTrackName (const CSeq_annot &annot, string &value)
	Extract track information that should be present if the data originated from a UCSC data file. More...
static bool	GetTrackAssembly (const CSeq_annot &annot, string &value)
static bool	GetTrackOffset (const CSeq_annot &annot, int &value)
static bool	GetTrackValue (const CSeq_annot &annot, const string &key, string &value)
static void	AddGeneOntologyTerm (CSeq_feat &feature, const CTempString &qual, const CTempString &val)

Static Public Attributes
static const TGi	kMinNumericGi

Detailed Description

Common file reader utility functions.

Definition at line 45 of file read_util.hpp.

Member Function Documentation

AddGeneOntologyTerm()

void CReadUtil::AddGeneOntologyTerm ( CSeq_feat &  feature, const CTempString &  qual, const CTempString &  val  )

static

Definition at line 296 of file read_util.cpp.

References CUtf8::AsUTF8(), CTempString::Copy(), CLineError::Create(), eDiag_Error, eEncoding_Ascii, CTempString::empty(), ILineError::eProblem_InvalidQualifier, NStr::EqualNocase(), NStr::IsBlank(), label, CTempString::npos, CUser_field_Base::SetData(), CSeq_feat_Base::SetExt(), CUser_field_Base::SetLabel(), sParseGeneOntologyTerm(), NStr::StringToInt(), toupper(), and val.

Referenced by CFeatureTableReader_Imp::x_AddQualifierToFeature(), CNewCleanup_imp::x_ConvertGoQualifiers(), and CGff2Record::xMigrateAttributesGo().

AsSeqId()

CRef< CSeq_id > CReadUtil::AsSeqId ( const string &  rawId, long  flags = 0, bool  localInts = true  )

static

Convert a raw ID string to a Seq-id, based in given customization flags.

Recognized flags are: CReaderBase::fAllIdsAsLocal, CReaderBase::fNumericalIdsAsLocal By default, numerical IDs below 500 are recognized as local IDs, and 500 and above are considered GI numbers.

Definition at line 89 of file read_util.cpp.

References CSeq_id_Base::e_Local, NStr::eUrlDec_Percent, CReaderBase::fAllIdsAsLocal, flags, CReaderBase::fNumericIdsAsLocal, CSeq_id_Base::GetGi(), GI_CONST, CSeq_id_Base::IsGi(), CRef< C, Locker >::Reset(), CObject_id_Base::SetId(), CSeq_id_Base::SetLocal(), CObject_id_Base::SetStr(), NStr::StringToInt(), and NStr::URLDecode().

Referenced by CGffBaseColumns::GetSeqId(), CAutoSqlStandardFields::SetLocation(), CUCSCRegionReader::x_SetFeatureLocation(), CVcfReader::xAssignFeatureLocationSet(), CWiggleReader::xMakeChromId(), CWiggleReader::xMakeTable(), CMultiReaderApp::xProcessGff3(), CBedReader::xReadBedRecordRaw(), CWiggleReader::xReadFixedStepDataRaw(), CMultiReader::xReadGFF3(), CWiggleReader::xReadVariableStepDataRaw(), CBedReader::xSetFeatureLocation(), CBedReader::xSetFeatureLocationBlock(), CBedReader::xSetFeatureLocationCds(), CBedReader::xSetFeatureLocationRna(), and CBedReader::xSetFeatureLocationThick().

GetTrackAssembly()

bool CReadUtil::GetTrackAssembly ( const CSeq_annot &  annot, string &  value  )

static

Definition at line 151 of file read_util.cpp.

References GetTrackValue(), and rapidjson::value.

GetTrackName()

bool CReadUtil::GetTrackName ( const CSeq_annot &  annot, string &  value  )

static

Extract track information that should be present if the data originated from a UCSC data file.

"name" and "db" have their designated accessors to recognize their special importance. The third variant can be used to access arbitrary track values.

Parameters

annot

true if the requested information os available and the value parameter is good to use. false otherwise.

Definition at line 142 of file read_util.cpp.

References GetTrackValue(), and rapidjson::value.

GetTrackOffset()

bool CReadUtil::GetTrackOffset ( const CSeq_annot &  annot, int &  value  )

static

Definition at line 160 of file read_util.cpp.

References GetTrackValue(), offset, NStr::StringToInt(), and rapidjson::value.

GetTrackValue()

bool CReadUtil::GetTrackValue ( const CSeq_annot &  annot, const string &  key, string &  value  )

static

Definition at line 176 of file read_util.cpp.

References CAnnot_descr_Base::Get(), CUser_field_Base::GetData(), CUser_object_Base::GetData(), CSeq_annot_Base::GetDesc(), CUser_field_Base::GetLabel(), CObject_id_Base::GetStr(), CUser_field_Base::C_Data::GetStr(), CUser_object_Base::GetType(), CAnnotdesc_Base::GetUser(), CUser_field_Base::IsSetData(), CUser_object_Base::IsSetData(), CSeq_annot_Base::IsSetDesc(), CUser_field_Base::IsSetLabel(), CUser_object_Base::IsSetType(), CObject_id_Base::IsStr(), CUser_field_Base::C_Data::IsStr(), CAnnotdesc_Base::IsUser(), ncbi::grid::netcache::search::fields::key, and rapidjson::value.

Referenced by GetTrackAssembly(), GetTrackName(), and GetTrackOffset().

Tokenize()

void CReadUtil::Tokenize ( const string &  instr, const string &  delim, vector< string > &  tokens  )

static

Tokenize a given string, respecting quoted substrings an atomic units.

Definition at line 47 of file read_util.cpp.

References NStr::fSplit_MergeDelimiters, NStr::fSplit_Truncate, i, NStr::Split(), and str().

Referenced by CReaderBase::xParseTrackLine(), CBedReader::xParseTrackLine(), and CVcfReader::xProcessTrackLine().

Member Data Documentation

kMinNumericGi

const TGi CReadUtil::kMinNumericGi

static

Definition at line 67 of file read_util.hpp.

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The documentation for this class was generated from the following files:

• include/objtools/readers/read_util.hpp
• src/objtools/readers/read_util.cpp