NCBI C++ ToolKit
Static Public Member Functions | List of all members
CWriteUtil Class Reference

Search Toolkit Book for CWriteUtil

#include <objtools/writers/write_util.hpp>

Static Public Member Functions

static CRef< CUser_objectGetDescriptor (const CSeq_annot &annot, const string &)
 
static bool GetGenomeString (const CBioSource &, string &)
 
static bool GetOrgModSubType (const COrgMod &, string &, string &)
 
static bool GetSubSourceSubType (const CSubSource &, string &, string &)
 
static bool GetBiomol (CBioseq_Handle, string &)
 
static bool GetIdType (CBioseq_Handle, string &)
 
static bool GetIdType (const CSeq_id &, string &)
 
static bool GetAaName (const CCode_break &, string &)
 
static bool GetCodeBreak (const CCode_break &, string &)
 
static bool GetTrnaProductName (const CTrna_ext &, string &)
 
static bool GetBestId (CSeq_id_Handle, CScope &, string &)
 
static bool GetBestId (const CMappedFeat &, string &)
 
static bool GetTrnaCodons (const CTrna_ext &, string &)
 
static bool GetTrnaAntiCodon (const CTrna_ext &, string &)
 
static bool GetDbTag (const CDbtag &, string &)
 
static bool IsLocationOrdered (const CSeq_loc &)
 
static bool IsSequenceCircular (CBioseq_Handle)
 
static bool NeedsQuoting (const string &)
 
static void ChangeToPackedInt (CSeq_loc &loc)
 
static CConstRef< CUser_objectGetUserObjectByType (const CUser_object &uo, const string &strType)
 
static CConstRef< CUser_objectGetUserObjectByType (const list< CRef< CUser_object > > &uos, const string &strType)
 
static CConstRef< CUser_objectGetModelEvidence (CMappedFeat)
 
static bool GetStringForModelEvidence (CMappedFeat mf, string &mestr)
 
static bool GetStringForGoMarkup (const vector< CRef< CUser_field > > &fields, string &goMarkup, bool relaxed=false)
 
static bool GetStringsForGoMarkup (const vector< CRef< CUser_field > > &fields, vector< string > &goMarkup, bool relaxed=false)
 
static bool GetListOfGoIds (const vector< CRef< CUser_field > > &fields, list< std::string > &goIds, bool relaxed=false)
 
static bool IsThreeFeatFormat (const CSeq_annot &)
 
static bool GetThreeFeatType (const CSeq_feat &, string &)
 
static bool GetThreeFeatScore (const CSeq_feat &, int &)
 
static bool GetThreeFeatRgb (const CSeq_feat &, string &)
 
static bool CompareFeatures (const CMappedFeat &lhs, const CMappedFeat &rhs)
 
static string GetStringId (const CSeq_loc &loc)
 
static bool IsNucleotideSequence (CBioseq_Handle)
 
static bool IsProteinSequence (CBioseq_Handle)
 
static bool IsTransspliced (const CSeq_feat &feature)
 
static bool IsTransspliced (const CMappedFeat &mf)
 
static bool GetTranssplicedEndpoints (const CSeq_loc &loc, unsigned int &inPoint, unsigned int &outPoint)
 
static ENa_strand GetEffectiveStrand (const CSeq_interval &)
 

Detailed Description

Definition at line 51 of file write_util.hpp.

Member Function Documentation

◆ ChangeToPackedInt()

void CWriteUtil::ChangeToPackedInt ( CSeq_loc loc)
static

◆ CompareFeatures()

bool CWriteUtil::CompareFeatures ( const CMappedFeat lhs,
const CMappedFeat rhs 
)
static

◆ GetAaName()

bool CWriteUtil::GetAaName ( const CCode_break cb,
string aaName 
)
static

◆ GetBestId() [1/2]

bool CWriteUtil::GetBestId ( const CMappedFeat mf,
string best_id 
)
static

Definition at line 685 of file write_util.cpp.

References CGenbankIdResolve::Get(), and CGenbankIdResolve::GetBestId().

◆ GetBestId() [2/2]

bool CWriteUtil::GetBestId ( CSeq_id_Handle  idh,
CScope scope,
string best_id 
)
static

◆ GetBiomol()

bool CWriteUtil::GetBiomol ( CBioseq_Handle  bsh,
string mol_str 
)
static

◆ GetCodeBreak()

bool CWriteUtil::GetCodeBreak ( const CCode_break cb,
string cbString 
)
static

◆ GetDbTag()

bool CWriteUtil::GetDbTag ( const CDbtag dbtag,
string dbTagStr 
)
static

◆ GetDescriptor()

CRef< CUser_object > CWriteUtil::GetDescriptor ( const CSeq_annot annot,
const string strType 
)
static

◆ GetEffectiveStrand()

ENa_strand CWriteUtil::GetEffectiveStrand ( const CSeq_interval interval)
static

◆ GetGenomeString()

bool CWriteUtil::GetGenomeString ( const CBioSource bs,
string genome_str 
)
static

◆ GetIdType() [1/2]

bool CWriteUtil::GetIdType ( CBioseq_Handle  bsh,
string idType 
)
static

◆ GetIdType() [2/2]

bool CWriteUtil::GetIdType ( const CSeq_id seqId,
string idType 
)
static

◆ GetListOfGoIds()

bool CWriteUtil::GetListOfGoIds ( const vector< CRef< CUser_field > > &  fields,
list< std::string > &  goIds,
bool  relaxed = false 
)
static

Definition at line 1185 of file write_util.cpp.

Referenced by CGff2Writer::xAssignFeatureAttributesGoMarkup().

◆ GetModelEvidence()

CConstRef< CUser_object > CWriteUtil::GetModelEvidence ( CMappedFeat  mf)
static

◆ GetOrgModSubType()

bool CWriteUtil::GetOrgModSubType ( const COrgMod mod,
string subtype,
string subname 
)
static

Definition at line 188 of file write_util.cpp.

References COrgMod::GetSubtypeName(), mod(), and subname.

Referenced by CGff3Writer::xAssignSourceAttributesOrgMod().

◆ GetStringForGoMarkup()

bool CWriteUtil::GetStringForGoMarkup ( const vector< CRef< CUser_field > > &  fields,
string goMarkup,
bool  relaxed = false 
)
static

Definition at line 1125 of file write_util.cpp.

References GetStringsForGoMarkup(), NStr::Join(), and strings.

◆ GetStringForModelEvidence()

bool CWriteUtil::GetStringForModelEvidence ( CMappedFeat  mf,
string mestr 
)
static

◆ GetStringId()

string CWriteUtil::GetStringId ( const CSeq_loc loc)
static

Definition at line 1274 of file write_util.cpp.

References CSeq_id::AsFastaString(), and CSeq_loc::GetId().

Referenced by CompareFeatures().

◆ GetStringsForGoMarkup()

bool CWriteUtil::GetStringsForGoMarkup ( const vector< CRef< CUser_field > > &  fields,
vector< string > &  goMarkup,
bool  relaxed = false 
)
static

◆ GetSubSourceSubType()

bool CWriteUtil::GetSubSourceSubType ( const CSubSource sub,
string subtype,
string subname 
)
static

◆ GetThreeFeatRgb()

bool CWriteUtil::GetThreeFeatRgb ( const CSeq_feat feat,
string color 
)
static

◆ GetThreeFeatScore()

bool CWriteUtil::GetThreeFeatScore ( const CSeq_feat feat,
int score 
)
static

◆ GetThreeFeatType()

bool CWriteUtil::GetThreeFeatType ( const CSeq_feat feat,
string threeFeatType 
)
static

◆ GetTranssplicedEndpoints()

bool CWriteUtil::GetTranssplicedEndpoints ( const CSeq_loc loc,
unsigned int inPoint,
unsigned int outPoint 
)
static

◆ GetTrnaAntiCodon()

bool CWriteUtil::GetTrnaAntiCodon ( const CTrna_ext trna,
string acStr 
)
static

◆ GetTrnaCodons()

bool CWriteUtil::GetTrnaCodons ( const CTrna_ext trna,
string codonStr 
)
static

◆ GetTrnaProductName()

bool CWriteUtil::GetTrnaProductName ( const CTrna_ext trna,
string name 
)
static

◆ GetUserObjectByType() [1/2]

CConstRef< CUser_object > CWriteUtil::GetUserObjectByType ( const CUser_object uo,
const string strType 
)
static

◆ GetUserObjectByType() [2/2]

CConstRef< CUser_object > CWriteUtil::GetUserObjectByType ( const list< CRef< CUser_object > > &  uos,
const string strType 
)
static

Definition at line 823 of file write_util.cpp.

References GetUserObjectByType().

◆ IsLocationOrdered()

bool CWriteUtil::IsLocationOrdered ( const CSeq_loc loc)
static

◆ IsNucleotideSequence()

bool CWriteUtil::IsNucleotideSequence ( CBioseq_Handle  bsh)
static

◆ IsProteinSequence()

bool CWriteUtil::IsProteinSequence ( CBioseq_Handle  bsh)
static

◆ IsSequenceCircular()

bool CWriteUtil::IsSequenceCircular ( CBioseq_Handle  bsh)
static

◆ IsThreeFeatFormat()

bool CWriteUtil::IsThreeFeatFormat ( const CSeq_annot annot)
static

◆ IsTransspliced() [1/2]

bool CWriteUtil::IsTransspliced ( const CMappedFeat mf)
static

Definition at line 1366 of file write_util.cpp.

References CMappedFeat::GetMappedFeature(), and IsTransspliced().

◆ IsTransspliced() [2/2]

bool CWriteUtil::IsTransspliced ( const CSeq_feat feature)
static

◆ NeedsQuoting()

bool CWriteUtil::NeedsQuoting ( const string str)
static

Definition at line 604 of file write_util.cpp.

References str().


The documentation for this class was generated from the following files:
Modified on Wed Jun 19 17:02:38 2024 by modify_doxy.py rev. 669887