NCBI C++ ToolKit
Typedefs | Enumerations | Functions
utilities.hpp File Reference
#include <corelib/ncbistd.hpp>
#include <corelib/ncbistr.hpp>
#include <objects/seqfeat/Seq_feat.hpp>
#include <objects/seqfeat/SeqFeatData.hpp>
#include <objects/seqfeat/Org_ref.hpp>
#include <objects/seqset/Bioseq_set.hpp>
#include <objects/biblio/Id_pat.hpp>
#include <objects/biblio/Auth_list.hpp>
#include <objmgr/seq_vector.hpp>
#include <serial/iterator.hpp>
#include <vector>
#include <list>
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Typedefs

typedef const CSeq_feat::TDbxref TDbtags
 

Enumerations

enum  EAccessionFormatError {
  eAccessionFormat_valid = 0 , eAccessionFormat_no_start_letters , eAccessionFormat_wrong_number_of_digits , eAccessionFormat_null ,
  eAccessionFormat_too_long , eAccessionFormat_missing_version , eAccessionFormat_bad_version
}
 
enum  EDateValid {
  eDateValid_valid = 0x0 , eDateValid_bad_str = 0x01 , eDateValid_bad_year = 0x02 , eDateValid_bad_month = 0x04 ,
  eDateValid_bad_day = 0x08 , eDateValid_bad_season = 0x10 , eDateValid_bad_other = 0x20 , eDateValid_empty_date = 0x40
}
 
enum  EBioseqEndIsType { eBioseqEndIsType_None = 0 , eBioseqEndIsType_Last , eBioseqEndIsType_All }
 
enum  EDuplicateFeatureType {
  eDuplicate_Not = 0 , eDuplicate_Duplicate , eDuplicate_SameIntervalDifferentLabel , eDuplicate_DuplicateDifferentTable ,
  eDuplicate_SameIntervalDifferentLabelDifferentTable
}
 

Functions

bool IsClassInEntry (const CSeq_entry &se, CBioseq_set::EClass clss)
 
bool IsDeltaOrFarSeg (const CSeq_loc &loc, CScope *scope)
 
bool IsBlankStringList (const list< string > &str_list)
 
TGi GetGIForSeqId (const CSeq_id &id)
 
CScope::TIds GetSeqIdsForGI (TGi gi)
 
bool IsFarLocation (const CSeq_loc &loc, const CSeq_entry_Handle &seh)
 
CSeqVector GetSequenceFromLoc (const CSeq_loc &loc, CScope &scope, CBioseq_Handle::EVectorCoding coding=CBioseq_Handle::eCoding_Iupac)
 
CSeqVector GetSequenceFromFeature (const CSeq_feat &feat, CScope &scope, CBioseq_Handle::EVectorCoding coding=CBioseq_Handle::eCoding_Iupac, bool product=false)
 
string GetSequenceStringFromLoc (const CSeq_loc &loc, CScope &scope)
 
bool IsResidue (unsigned char residue)
 
CConstRef< CSeq_idGetReportableSeqIdForAlignment (const CSeq_align &align, CScope &scope)
 
string GetAccessionFromObjects (const CSerialObject *obj, const CSeq_entry *ctx, CScope &scope, int *version)
 
string GetAccessionFromBioseq (const CBioseq &bioseq, int *version)
 
string GetAccessionFromBioseqSet (const CBioseq_set &bsst, int *version)
 
CBioseq_set_Handle GetSetParent (const CBioseq_set_Handle &set, CBioseq_set::TClass set_class)
 
CBioseq_set_Handle GetSetParent (const CBioseq_Handle &bioseq, CBioseq_set::TClass set_class)
 
CBioseq_set_Handle GetGenProdSetParent (const CBioseq_set_Handle &set)
 
CBioseq_set_Handle GetGenProdSetParent (const CBioseq_Handle &set)
 
CBioseq_set_Handle GetNucProtSetParent (const CBioseq_Handle &bioseq)
 
CBioseq_Handle GetNucBioseq (const CBioseq_set_Handle &bioseq_set)
 
CBioseq_Handle GetNucBioseq (const CBioseq_Handle &bioseq)
 
EAccessionFormatError ValidateAccessionString (const string &accession, bool require_version)
 
bool s_IdXrefsAreReciprocal (const CSeq_feat &cds, const CSeq_feat &mrna)
 
bool s_FeatureIdsMatch (const CFeat_id &f1, const CFeat_id &f2)
 
bool s_StringHasPMID (const string &str)
 
bool HasBadCharacter (const string &str)
 
bool EndsWithBadCharacter (const string &str)
 
int CheckDate (const CDate &date, bool require_full_date=false)
 
bool IsDateInPast (const CDate &date)
 
string GetDateErrorDescription (int flags)
 
bool IsBioseqTSA (const CBioseq &seq, CScope *scope)
 
string GetValidatorLocationLabel (const CSeq_loc &loc, CScope &scope)
 
void AppendBioseqLabel (string &str, const CBioseq &sq, bool supress_context)
 
string GetBioseqIdLabel (const CBioseq &sq)
 
bool HasECnumberPattern (const string &str)
 
bool SeqIsPatent (const CBioseq &seq)
 
bool SeqIsPatent (const CBioseq_Handle &seq)
 
bool s_PartialAtGapOrNs (CScope *scope, const CSeq_loc &loc, unsigned int tag, bool only_gap=false)
 
CBioseq_Handle BioseqHandleFromLocation (CScope *m_Scope, const CSeq_loc &loc)
 
void CheckBioseqEndsForNAndGap (const CBioseq_Handle &bsh, EBioseqEndIsType &begin_n, EBioseqEndIsType &begin_gap, EBioseqEndIsType &end_n, EBioseqEndIsType &end_gap, bool &begin_ambig, bool &end_ambig)
 
bool ShouldCheckForNsAndGap (const CBioseq_Handle &bsh)
 
void CheckBioseqEndsForNAndGap (const CSeqVector &vec, EBioseqEndIsType &begin_n, EBioseqEndIsType &begin_gap, EBioseqEndIsType &end_n, EBioseqEndIsType &end_gap, bool &begin_ambig, bool &end_ambig)
 
bool IsDicistronicGene (const CSeq_feat_Handle &f)
 Indicates whether feature is a dicistronic gene. More...
 
bool IsDicistronic (const CSeq_feat_Handle &f)
 
EDuplicateFeatureType IsDuplicate (const CSeq_feat_Handle &f1, const CSeq_feat_Handle &f2, bool check_partials=false, bool case_sensitive=false)
 Reports how two features duplicate each other. More...
 
bool IsLocFullLength (const CSeq_loc &loc, const CBioseq_Handle &bsh)
 
bool PartialsSame (const CSeq_loc &loc1, const CSeq_loc &loc2)
 
bool IsSpecificHostValid (const string &host, string &error_msg)
 returns true and error_msg will be empty, if specific host is valid returns true and error_msg will be "Host is empty", if specific host is empty returns false if specific host is invalid More...
 
string FixSpecificHost (const string &host)
 returns the corrected specific host, if the specific host is invalid and can be corrected returns an empty string, if the specific host is invalid and cannot be corrected returns the original value except the preceding/trailing spaces, if the specific host is valid More...
 
bool IsCommonName (const CT3Data &data)
 
bool HasMisSpellFlag (const CT3Data &data)
 
bool FindMatchInOrgRef (const string &str, const COrg_ref &org)
 
string SpecificHostValueToCheck (const string &val)
 
bool IsLikelyTaxname (const string &val)
 
string InterpretSpecificHostResult (const string &host, const CT3Reply &reply, const string &orig_host=kEmptyStr)
 
void AdjustSpecificHostForTaxServer (string &spec_host)
 
void ConvertToEntrezTerm (string &title)
 
string TranslateCodingRegionForValidation (const CSeq_feat &feat, CScope &scope, bool &alt_start)
 
bool ReportTranslationErrors (const string &except_text)
 
bool HasBadStartCodon (const CSeq_feat &feat, CScope &scope, bool ignore_exceptions)
 
bool HasBadStartCodon (const CSeq_loc &loc, const string &transl_prot)
 
size_t CountInternalStopCodons (const string &transl_prot)
 
bool HasInternalStop (const CSeq_feat &feat, CScope &scope, bool ignore_exceptions)
 
CRef< CSeqVectorMakeSeqVectorForResidueCounting (const CBioseq_Handle &bsh)
 
bool HasBadProteinStart (const CSeqVector &sv)
 
bool HasBadProteinStart (const CSeq_feat &cds, CScope &scope)
 
size_t CountProteinStops (const CSeqVector &sv)
 
bool HasStopInProtein (const CSeq_feat &feat, CScope &scope)
 
void FeatureHasEnds (const CSeq_feat &feat, CScope *scope, bool &no_beg, bool &no_end)
 
CBioseq_Handle GetCDSProductSequence (const CSeq_feat &feat, CScope *scope, const CTSE_Handle &tse, bool far_fetch, bool &is_far)
 
vector< TSeqPosGetMismatches (const CSeq_feat &feat, const CBioseq_Handle &prot_handle, const string &transl_prot)
 
vector< TSeqPosGetMismatches (const CSeq_feat &feat, const CSeqVector &prot_vec, const string &transl_prot)
 
void CalculateEffectiveTranslationLengths (const string &transl_prot, const CSeqVector &prot_vec, size_t &len, size_t &prot_len)
 
bool HasNoStop (const CSeq_feat &feat, CScope *scope)
 
bool IsSequenceFetchable (const CSeq_id &id, CScope *scope=nullptr)
 
bool IsSequenceFetchable (const string &seq_id, CScope *scope=nullptr)
 
bool DoesFeatureHaveUnnecessaryException (const CSeq_feat &feat, CScope &scope)
 
bool IsNTNCNWACAccession (const string &acc)
 
bool IsNTNCNWACAccession (const CSeq_id &id)
 
bool IsNTNCNWACAccession (const CBioseq &seq)
 
bool IsNG (const CSeq_id &id)
 
bool IsNG (const CBioseq &seq)
 
bool IsTemporary (const CSeq_id &id)
 
bool IsOrganelle (int genome)
 
bool IsOrganelle (const CBioseq_Handle &seq)
 
bool IsInOrganelleSmallGenomeSet (const CSeq_id &id, CScope &scope)
 
bool BadMultipleSequenceLocation (const CSeq_loc &loc, CScope &scope)
 
bool ConsistentWithA (Char ch)
 
bool ConsistentWithC (Char ch)
 
bool ConsistentWithG (Char ch)
 
bool ConsistentWithT (Char ch)
 
bool IsBadSubmissionFirstName (const string &first)
 
bool IsBadSubmissionLastName (const string &last)
 
bool g_IsMasterAccession (const CSeq_id &id)
 

Typedef Documentation

◆ TDbtags

Definition at line 199 of file utilities.hpp.

Enumeration Type Documentation

◆ EAccessionFormatError

Enumerator
eAccessionFormat_valid 
eAccessionFormat_no_start_letters 
eAccessionFormat_wrong_number_of_digits 
eAccessionFormat_null 
eAccessionFormat_too_long 
eAccessionFormat_missing_version 
eAccessionFormat_bad_version 

Definition at line 105 of file utilities.hpp.

◆ EBioseqEndIsType

Enumerator
eBioseqEndIsType_None 
eBioseqEndIsType_Last 
eBioseqEndIsType_All 

Definition at line 156 of file utilities.hpp.

◆ EDateValid

enum EDateValid
Enumerator
eDateValid_valid 
eDateValid_bad_str 
eDateValid_bad_year 
eDateValid_bad_month 
eDateValid_bad_day 
eDateValid_bad_season 
eDateValid_bad_other 
eDateValid_empty_date 

Definition at line 122 of file utilities.hpp.

◆ EDuplicateFeatureType

Enumerator
eDuplicate_Not 
eDuplicate_Duplicate 
eDuplicate_SameIntervalDifferentLabel 
eDuplicate_DuplicateDifferentTable 
eDuplicate_SameIntervalDifferentLabelDifferentTable 

Definition at line 191 of file utilities.hpp.

Function Documentation

◆ AdjustSpecificHostForTaxServer()

void AdjustSpecificHostForTaxServer ( string spec_host)

◆ AppendBioseqLabel()

void AppendBioseqLabel ( string str,
const CBioseq sq,
bool  supress_context 
)

◆ BadMultipleSequenceLocation()

bool BadMultipleSequenceLocation ( const CSeq_loc loc,
CScope scope 
)

◆ BioseqHandleFromLocation()

CBioseq_Handle BioseqHandleFromLocation ( CScope m_Scope,
const CSeq_loc loc 
)

◆ CalculateEffectiveTranslationLengths()

void CalculateEffectiveTranslationLengths ( const string transl_prot,
const CSeqVector prot_vec,
size_t &  len,
size_t &  prot_len 
)

◆ CheckBioseqEndsForNAndGap() [1/2]

void CheckBioseqEndsForNAndGap ( const CBioseq_Handle bsh,
EBioseqEndIsType begin_n,
EBioseqEndIsType begin_gap,
EBioseqEndIsType end_n,
EBioseqEndIsType end_gap,
bool begin_ambig,
bool end_ambig 
)

◆ CheckBioseqEndsForNAndGap() [2/2]

void CheckBioseqEndsForNAndGap ( const CSeqVector vec,
EBioseqEndIsType begin_n,
EBioseqEndIsType begin_gap,
EBioseqEndIsType end_n,
EBioseqEndIsType end_gap,
bool begin_ambig,
bool end_ambig 
)

◆ CheckDate()

int CheckDate ( const CDate date,
bool  require_full_date = false 
)

◆ ConsistentWithA()

bool ConsistentWithA ( Char  ch)

◆ ConsistentWithC()

bool ConsistentWithC ( Char  ch)

◆ ConsistentWithG()

bool ConsistentWithG ( Char  ch)

◆ ConsistentWithT()

bool ConsistentWithT ( Char  ch)

◆ ConvertToEntrezTerm()

void ConvertToEntrezTerm ( string title)

◆ CountInternalStopCodons()

size_t CountInternalStopCodons ( const string transl_prot)

◆ CountProteinStops()

size_t CountProteinStops ( const CSeqVector sv)

Definition at line 2504 of file utilities.cpp.

Referenced by HasStopInProtein(), and CValidError_bioseq::ValidateRawConst().

◆ DoesFeatureHaveUnnecessaryException()

bool DoesFeatureHaveUnnecessaryException ( const CSeq_feat feat,
CScope scope 
)

◆ EndsWithBadCharacter()

bool EndsWithBadCharacter ( const string str)

Definition at line 768 of file utilities.cpp.

References NStr::EndsWith(), and str().

Referenced by CSingleFeatValidator::ValidateCharactersInField().

◆ FeatureHasEnds()

void FeatureHasEnds ( const CSeq_feat feat,
CScope scope,
bool no_beg,
bool no_end 
)

◆ FindMatchInOrgRef()

bool FindMatchInOrgRef ( const string str,
const COrg_ref org 
)

◆ FixSpecificHost()

string FixSpecificHost ( const string host)

returns the corrected specific host, if the specific host is invalid and can be corrected returns an empty string, if the specific host is invalid and cannot be corrected returns the original value except the preceding/trailing spaces, if the specific host is valid

Definition at line 2189 of file utilities.cpp.

References val.

Referenced by BOOST_AUTO_TEST_CASE().

◆ g_IsMasterAccession()

bool g_IsMasterAccession ( const CSeq_id id)

◆ GetAccessionFromBioseq()

string GetAccessionFromBioseq ( const CBioseq bioseq,
int version 
)

Definition at line 427 of file utilities.cpp.

References s_GetBioseqAcc(), and version.

Referenced by CValidError_imp::PostErr().

◆ GetAccessionFromBioseqSet()

string GetAccessionFromBioseqSet ( const CBioseq_set bsst,
int version 
)

◆ GetAccessionFromObjects()

string GetAccessionFromObjects ( const CSerialObject obj,
const CSeq_entry ctx,
CScope scope,
int version 
)

◆ GetBioseqIdLabel()

string GetBioseqIdLabel ( const CBioseq sq)

◆ GetCDSProductSequence()

CBioseq_Handle GetCDSProductSequence ( const CSeq_feat feat,
CScope scope,
const CTSE_Handle tse,
bool  far_fetch,
bool is_far 
)

◆ GetDateErrorDescription()

string GetDateErrorDescription ( int  flags)

◆ GetGenProdSetParent() [1/2]

CBioseq_set_Handle GetGenProdSetParent ( const CBioseq_Handle set)

Definition at line 575 of file utilities.cpp.

References CBioseq_set_Base::eClass_gen_prod_set, and GetSetParent().

◆ GetGenProdSetParent() [2/2]

CBioseq_set_Handle GetGenProdSetParent ( const CBioseq_set_Handle set)

◆ GetGIForSeqId()

TGi GetGIForSeqId ( const CSeq_id id)

◆ GetMismatches() [1/2]

vector<TSeqPos> GetMismatches ( const CSeq_feat feat,
const CBioseq_Handle prot_handle,
const string transl_prot 
)

◆ GetMismatches() [2/2]

vector<TSeqPos> GetMismatches ( const CSeq_feat feat,
const CSeqVector prot_vec,
const string transl_prot 
)

◆ GetNucBioseq() [1/2]

CBioseq_Handle GetNucBioseq ( const CBioseq_Handle bioseq)

◆ GetNucBioseq() [2/2]

CBioseq_Handle GetNucBioseq ( const CBioseq_set_Handle bioseq_set)

◆ GetNucProtSetParent()

CBioseq_set_Handle GetNucProtSetParent ( const CBioseq_Handle bioseq)

◆ GetReportableSeqIdForAlignment()

CConstRef<CSeq_id> GetReportableSeqIdForAlignment ( const CSeq_align align,
CScope scope 
)

◆ GetSeqIdsForGI()

CScope::TIds GetSeqIdsForGI ( TGi  gi)

◆ GetSequenceFromFeature()

CSeqVector GetSequenceFromFeature ( const CSeq_feat feat,
CScope scope,
CBioseq_Handle::EVectorCoding  coding = CBioseq_Handle::eCoding_Iupac,
bool  product = false 
)

◆ GetSequenceFromLoc()

CSeqVector GetSequenceFromLoc ( const CSeq_loc loc,
CScope scope,
CBioseq_Handle::EVectorCoding  coding = CBioseq_Handle::eCoding_Iupac 
)

◆ GetSequenceStringFromLoc()

string GetSequenceStringFromLoc ( const CSeq_loc loc,
CScope scope 
)

◆ GetSetParent() [1/2]

CBioseq_set_Handle GetSetParent ( const CBioseq_Handle bioseq,
CBioseq_set::TClass  set_class 
)

◆ GetSetParent() [2/2]

CBioseq_set_Handle GetSetParent ( const CBioseq_set_Handle set,
CBioseq_set::TClass  set_class 
)

◆ GetValidatorLocationLabel()

string GetValidatorLocationLabel ( const CSeq_loc loc,
CScope scope 
)

◆ HasBadCharacter()

bool HasBadCharacter ( const string str)

Definition at line 755 of file utilities.cpp.

References NStr::Find(), and str().

Referenced by CSingleFeatValidator::ValidateCharactersInField().

◆ HasBadProteinStart() [1/2]

bool HasBadProteinStart ( const CSeq_feat cds,
CScope scope 
)

◆ HasBadProteinStart() [2/2]

bool HasBadProteinStart ( const CSeqVector sv)

◆ HasBadStartCodon() [1/2]

bool HasBadStartCodon ( const CSeq_feat feat,
CScope scope,
bool  ignore_exceptions 
)

◆ HasBadStartCodon() [2/2]

bool HasBadStartCodon ( const CSeq_loc loc,
const string transl_prot 
)

Definition at line 2307 of file utilities.cpp.

References eExtreme_Biological, and CSeq_loc::IsPartialStart().

Referenced by HasBadStartCodon().

◆ HasECnumberPattern()

bool HasECnumberPattern ( const string str)

◆ HasInternalStop()

bool HasInternalStop ( const CSeq_feat feat,
CScope scope,
bool  ignore_exceptions 
)

◆ HasMisSpellFlag()

bool HasMisSpellFlag ( const CT3Data data)

Definition at line 1966 of file utilities.cpp.

References data, NStr::EqualNocase(), and ITERATE.

Referenced by CSpecificHostRequest::AddReply(), and InterpretSpecificHostResult().

◆ HasNoStop()

bool HasNoStop ( const CSeq_feat feat,
CScope scope 
)

◆ HasStopInProtein()

bool HasStopInProtein ( const CSeq_feat feat,
CScope scope 
)

◆ InterpretSpecificHostResult()

string InterpretSpecificHostResult ( const string host,
const CT3Reply reply,
const string orig_host = kEmptyStr 
)

◆ IsBadSubmissionFirstName()

bool IsBadSubmissionFirstName ( const string first)

◆ IsBadSubmissionLastName()

bool IsBadSubmissionLastName ( const string last)

◆ IsBioseqTSA()

bool IsBioseqTSA ( const CBioseq seq,
CScope scope 
)

◆ IsBlankStringList()

bool IsBlankStringList ( const list< string > &  str_list)

Definition at line 114 of file utilities.cpp.

References NStr::IsBlank(), ITERATE, and str().

Referenced by CValidError_imp::HasName().

◆ IsClassInEntry()

bool IsClassInEntry ( const CSeq_entry se,
CBioseq_set::EClass  clss 
)

Definition at line 79 of file utilities.cpp.

References si.

Referenced by IsDeltaOrFarSeg().

◆ IsCommonName()

bool IsCommonName ( const CT3Data data)

◆ IsDateInPast()

bool IsDateInPast ( const CDate date)

◆ IsDeltaOrFarSeg()

bool IsDeltaOrFarSeg ( const CSeq_loc loc,
CScope scope 
)

◆ IsDicistronic()

bool IsDicistronic ( const CSeq_feat_Handle f)

Definition at line 1825 of file utilities.cpp.

References f(), NStr::FindNoCase(), and NPOS.

Referenced by IsDicistronicGene().

◆ IsDicistronicGene()

bool IsDicistronicGene ( const CSeq_feat_Handle f)

Indicates whether feature is a dicistronic gene.

Parameters
fSeq-feat-Handle [in]
Returns
Boolean

Definition at line 1818 of file utilities.cpp.

References CSeqFeatData::eSubtype_gene, f(), and IsDicistronic().

Referenced by CValidError_bioseq::x_SuppressDicistronic().

◆ IsDuplicate()

EDuplicateFeatureType IsDuplicate ( const CSeq_feat_Handle f1,
const CSeq_feat_Handle f2,
bool  check_partials = false,
bool  case_sensitive = false 
)

◆ IsFarLocation()

bool IsFarLocation ( const CSeq_loc loc,
const CSeq_entry_Handle seh 
)

◆ IsInOrganelleSmallGenomeSet()

bool IsInOrganelleSmallGenomeSet ( const CSeq_id id,
CScope scope 
)

◆ IsLikelyTaxname()

bool IsLikelyTaxname ( const string val)

◆ IsLocFullLength()

bool IsLocFullLength ( const CSeq_loc loc,
const CBioseq_Handle bsh 
)

◆ IsNG() [1/2]

bool IsNG ( const CBioseq seq)

Definition at line 2801 of file utilities.cpp.

References FOR_EACH_SEQID_ON_BIOSEQ, and IsNG().

◆ IsNG() [2/2]

bool IsNG ( const CSeq_id id)

Definition at line 2790 of file utilities.cpp.

References GetAccession(), and NStr::StartsWith().

Referenced by IsNG(), and CValidError_bioseq::ValidateSeqIds().

◆ IsNTNCNWACAccession() [1/3]

bool IsNTNCNWACAccession ( const CBioseq seq)

Definition at line 2777 of file utilities.cpp.

References FOR_EACH_SEQID_ON_BIOSEQ, and IsNTNCNWACAccession().

◆ IsNTNCNWACAccession() [2/3]

bool IsNTNCNWACAccession ( const CSeq_id id)

Definition at line 2766 of file utilities.cpp.

References GetAccession(), and IsNTNCNWACAccession().

◆ IsNTNCNWACAccession() [3/3]

bool IsNTNCNWACAccession ( const string acc)

◆ IsOrganelle() [1/2]

bool IsOrganelle ( const CBioseq_Handle seq)

◆ IsOrganelle() [2/2]

bool IsOrganelle ( int  genome)

◆ IsResidue()

bool IsResidue ( unsigned char  residue)
inline

◆ IsSequenceFetchable() [1/2]

bool IsSequenceFetchable ( const CSeq_id id,
CScope scope = nullptr 
)

◆ IsSequenceFetchable() [2/2]

bool IsSequenceFetchable ( const string seq_id,
CScope scope = nullptr 
)

Definition at line 2740 of file utilities.cpp.

References IsSequenceFetchable().

◆ IsSpecificHostValid()

bool IsSpecificHostValid ( const string host,
string error_msg 
)

returns true and error_msg will be empty, if specific host is valid returns true and error_msg will be "Host is empty", if specific host is empty returns false if specific host is invalid

Definition at line 2182 of file utilities.cpp.

References CTaxValidationAndCleanup::IsOneSpecificHostValid(), and val.

Referenced by BOOST_AUTO_TEST_CASE(), and CMakeBadSpecificHostTable::x_CheckSpecificHosts().

◆ IsTemporary()

bool IsTemporary ( const CSeq_id id)

◆ MakeSeqVectorForResidueCounting()

CRef<CSeqVector> MakeSeqVectorForResidueCounting ( const CBioseq_Handle bsh)

◆ PartialsSame()

bool PartialsSame ( const CSeq_loc loc1,
const CSeq_loc loc2 
)

◆ ReportTranslationErrors()

bool ReportTranslationErrors ( const string except_text)

◆ s_FeatureIdsMatch()

bool s_FeatureIdsMatch ( const CFeat_id f1,
const CFeat_id f2 
)

◆ s_IdXrefsAreReciprocal()

bool s_IdXrefsAreReciprocal ( const CSeq_feat cds,
const CSeq_feat mrna 
)

◆ s_PartialAtGapOrNs()

bool s_PartialAtGapOrNs ( CScope scope,
const CSeq_loc loc,
unsigned int  tag,
bool  only_gap = false 
)

◆ s_StringHasPMID()

bool s_StringHasPMID ( const string str)

◆ SeqIsPatent() [1/2]

bool SeqIsPatent ( const CBioseq seq)

◆ SeqIsPatent() [2/2]

bool SeqIsPatent ( const CBioseq_Handle seq)

Definition at line 1170 of file utilities.cpp.

References CBioseq_Handle::GetCompleteBioseq(), and SeqIsPatent().

◆ ShouldCheckForNsAndGap()

bool ShouldCheckForNsAndGap ( const CBioseq_Handle bsh)

◆ SpecificHostValueToCheck()

string SpecificHostValueToCheck ( const string val)

◆ TranslateCodingRegionForValidation()

string TranslateCodingRegionForValidation ( const CSeq_feat feat,
CScope scope,
bool alt_start 
)

◆ ValidateAccessionString()

EAccessionFormatError ValidateAccessionString ( const string accession,
bool  require_version 
)
Modified on Sat Apr 20 12:20:21 2024 by modify_doxy.py rev. 669887