NCBI C++ ToolKit
Classes | Typedefs | Enumerations | Enumerator | Functions | Variables
Code generated by DATATOOL from 'blastxml2.asn' (module 'NCBI-BlastOutput2')
+ Collaboration diagram for Code generated by DATATOOL from 'blastxml2.asn' (module 'NCBI-BlastOutput2'):

Classes

class  CBlastOutput2
 CBlastOutput2 –. More...
 
class  CBlastOutput2_Base
 CBlastOutput2_Base –. More...
 
class  CBlastXML2
 CBlastXML2 –. More...
 
class  CBlastXML2_Base
 CBlastXML2_Base –. More...
 
class  CErr
 CErr –. More...
 
class  CErr_Base
 CErr_Base –. More...
 
class  CHit
 A generalized representation of a pairwise alignment. More...
 
class  CHit_Base
 CHit_Base –. More...
 
class  CHitDescr
 CHitDescr –. More...
 
class  CHitDescr_Base
 Description of entries for this (possibly non-redundant) sequence. More...
 
class  CHsp
 CHsp –. More...
 
class  CHsp_Base
 CHsp_Base –. More...
 
class  CIteration
 CIteration –. More...
 
class  CIteration_Base
 CIteration_Base –. More...
 
class  CParameters
 CParameters –. More...
 
class  CParameters_Base
 CParameters_Base –. More...
 
class  CRange< Position >
 CRange –. More...
 
class  CRange_Base
 Used to specify start/stop of masking on query. More...
 
class  CReport
 CReport –. More...
 
class  CReport_Base
 CReport_Base –. More...
 
class  CResults
 CResults –. More...
 
class  CResults_Base
 CResults_Base –. More...
 
class  CSearch< LEGACY, NHITS >
 CSearch –. More...
 
class  CSearch_Base< LEGACY, NHITS, derived_t >
 CSearch_Base –. More...
 
class  CStatistics
 CStatistics –. More...
 
class  CStatistics_Base
 CStatistics_Base –. More...
 
class  CTarget
 CTarget –. More...
 
class  CTarget_Base
 CTarget_Base –. More...
 

Typedefs

typedef CBlastOutput2_Base CBlastOutput2::Tparent
 
typedef CSerialObject CBlastOutput2_Base::Tparent
 
typedef CReport CBlastOutput2_Base::TReport
 
typedef CErr CBlastOutput2_Base::TError
 
typedef Tparent::CMemberIndex< E_memberIndex, 3 > CBlastOutput2_Base::TmemberIndex
 
typedef CBlastXML2_Base CBlastXML2::Tparent
 
typedef CSerialObject CBlastXML2_Base::Tparent
 
typedef list< CRef< CBlastOutput2 > > CBlastXML2_Base::Tdata
 
typedef CErr_Base CErr::Tparent
 
typedef CSerialObject CErr_Base::Tparent
 
typedef int CErr_Base::TCode
 
typedef string CErr_Base::TMessage
 
typedef Tparent::CMemberIndex< E_memberIndex, 3 > CErr_Base::TmemberIndex
 
typedef CHit_Base CHit::Tparent
 
typedef CSerialObject CHit_Base::Tparent
 
typedef int CHit_Base::TNum
 
typedef list< CRef< CHitDescr > > CHit_Base::TDescription
 
typedef int CHit_Base::TLen
 
typedef list< CRef< CHsp > > CHit_Base::THsps
 
typedef Tparent::CMemberIndex< E_memberIndex, 5 > CHit_Base::TmemberIndex
 
typedef CHitDescr_Base CHitDescr::Tparent
 
typedef CSerialObject CHitDescr_Base::Tparent
 
typedef string CHitDescr_Base::TId
 
typedef string CHitDescr_Base::TAccession
 
typedef string CHitDescr_Base::TTitle
 
typedef NCBI_NS_NCBI::TTaxId CHitDescr_Base::TTaxid
 
typedef string CHitDescr_Base::TSciname
 
typedef Tparent::CMemberIndex< E_memberIndex, 6 > CHitDescr_Base::TmemberIndex
 
typedef CHsp_Base CHsp::Tparent
 
typedef CSerialObject CHsp_Base::Tparent
 
typedef int CHsp_Base::TNum
 
typedef double CHsp_Base::TBit_score
 
typedef double CHsp_Base::TScore
 
typedef double CHsp_Base::TEvalue
 
typedef int CHsp_Base::TIdentity
 
typedef int CHsp_Base::TPositive
 
typedef int CHsp_Base::TDensity
 
typedef int CHsp_Base::TPattern_from
 
typedef int CHsp_Base::TPattern_to
 
typedef int CHsp_Base::TQuery_from
 
typedef int CHsp_Base::TQuery_to
 
typedef string CHsp_Base::TQuery_strand
 
typedef int CHsp_Base::TQuery_frame
 
typedef int CHsp_Base::THit_from
 
typedef int CHsp_Base::THit_to
 
typedef string CHsp_Base::THit_strand
 
typedef int CHsp_Base::THit_frame
 
typedef int CHsp_Base::TAlign_len
 
typedef int CHsp_Base::TGaps
 
typedef string CHsp_Base::TQseq
 
typedef string CHsp_Base::THseq
 
typedef string CHsp_Base::TMidline
 
typedef Tparent::CMemberIndex< E_memberIndex, 23 > CHsp_Base::TmemberIndex
 
typedef CIteration_Base CIteration::Tparent
 
typedef CSerialObject CIteration_Base::Tparent
 
typedef int CIteration_Base::TIter_num
 
typedef CSearch CIteration_Base::TSearch
 
typedef Tparent::CMemberIndex< E_memberIndex, 3 > CIteration_Base::TmemberIndex
 
typedef CParameters_Base CParameters::Tparent
 
typedef CSerialObject CParameters_Base::Tparent
 
typedef string CParameters_Base::TMatrix
 
typedef double CParameters_Base::TExpect
 
typedef double CParameters_Base::TInclude
 
typedef int CParameters_Base::TSc_match
 
typedef int CParameters_Base::TSc_mismatch
 
typedef int CParameters_Base::TGap_open
 
typedef int CParameters_Base::TGap_extend
 
typedef string CParameters_Base::TFilter
 
typedef string CParameters_Base::TPattern
 
typedef string CParameters_Base::TEntrez_query
 
typedef int CParameters_Base::TCbs
 
typedef int CParameters_Base::TQuery_gencode
 
typedef int CParameters_Base::TDb_gencode
 
typedef string CParameters_Base::TBl2seq_mode
 
typedef Tparent::CMemberIndex< E_memberIndex, 15 > CParameters_Base::TmemberIndex
 
typedef CRange_Base CRange< Position >::Tparent
 
typedef CSerialObject CRange_Base::Tparent
 
typedef int CRange_Base::TFrom
 
typedef int CRange_Base::TTo
 
typedef Tparent::CMemberIndex< E_memberIndex, 3 > CRange_Base::TmemberIndex
 
typedef CReport_Base CReport::Tparent
 
typedef CSerialObject CReport_Base::Tparent
 
typedef string CReport_Base::TProgram
 
typedef string CReport_Base::TVersion
 
typedef string CReport_Base::TReference
 
typedef CTarget CReport_Base::TSearch_target
 
typedef CParameters CReport_Base::TParams
 
typedef CResults CReport_Base::TResults
 
typedef Tparent::CMemberIndex< E_memberIndex, 7 > CReport_Base::TmemberIndex
 
typedef CResults_Base CResults::Tparent
 
typedef CSerialObject CResults_Base::Tparent
 
typedef list< CRef< CIteration > > CResults_Base::TIterations
 
typedef CSearch CResults_Base::TSearch
 
typedef list< CRef< CSearch > > CResults_Base::TBl2seq
 
typedef CSearch_Base CSearch< LEGACY, NHITS >::Tparent
 
typedef CSerialObject CSearch_Base< LEGACY, NHITS, derived_t >::Tparent
 
typedef string CSearch_Base< LEGACY, NHITS, derived_t >::TQuery_id
 
typedef string CSearch_Base< LEGACY, NHITS, derived_t >::TQuery_title
 
typedef int CSearch_Base< LEGACY, NHITS, derived_t >::TQuery_len
 
typedef list< CRef< CRange > > CSearch_Base< LEGACY, NHITS, derived_t >::TQuery_masking
 
typedef list< CRef< CHit > > CSearch_Base< LEGACY, NHITS, derived_t >::THits
 
typedef CStatistics CSearch_Base< LEGACY, NHITS, derived_t >::TStat
 
typedef string CSearch_Base< LEGACY, NHITS, derived_t >::TMessage
 
typedef Tparent::CMemberIndex< E_memberIndex, 8 > CSearch_Base< LEGACY, NHITS, derived_t >::TmemberIndex
 
typedef CStatistics_Base CStatistics::Tparent
 
typedef CSerialObject CStatistics_Base::Tparent
 
typedef Int8 CStatistics_Base::TDb_num
 
typedef Int8 CStatistics_Base::TDb_len
 
typedef int CStatistics_Base::THsp_len
 
typedef Int8 CStatistics_Base::TEff_space
 
typedef double CStatistics_Base::TKappa
 
typedef double CStatistics_Base::TLambda
 
typedef double CStatistics_Base::TEntropy
 
typedef Tparent::CMemberIndex< E_memberIndex, 8 > CStatistics_Base::TmemberIndex
 
typedef CTarget_Base CTarget::Tparent
 
typedef CSerialObject CTarget_Base::Tparent
 
typedef string CTarget_Base::TDb
 
typedef list< stringCTarget_Base::TSubjects
 

Enumerations

enum class  CBlastOutput2_Base::E_memberIndex { CBlastOutput2_Base::e__allMandatory = 0 , CBlastOutput2_Base::e_report , CBlastOutput2_Base::e_error }
 
enum class  CErr_Base::E_memberIndex { CErr_Base::e__allMandatory = 0 , CErr_Base::e_code , CErr_Base::e_message }
 
enum class  CHit_Base::E_memberIndex {
  CHit_Base::e__allMandatory = 0 , CHit_Base::e_num , CHit_Base::e_id , CHit_Base::e_def ,
  CHit_Base::e_accession , CHit_Base::e_len , CHit_Base::e_hsps , CHit_Base::e__allMandatory = 0 ,
  CHit_Base::e_num , CHit_Base::e_description , CHit_Base::e_len , CHit_Base::e_hsps
}
 
enum class  CHitDescr_Base::E_memberIndex {
  CHitDescr_Base::e__allMandatory = 0 , CHitDescr_Base::e_id , CHitDescr_Base::e_accession , CHitDescr_Base::e_title ,
  CHitDescr_Base::e_taxid , CHitDescr_Base::e_sciname
}
 
enum class  CHsp_Base::E_memberIndex {
  CHsp_Base::e__allMandatory = 0 , CHsp_Base::e_num , CHsp_Base::e_bit_score , CHsp_Base::e_score ,
  CHsp_Base::e_evalue , CHsp_Base::e_query_from , CHsp_Base::e_query_to , CHsp_Base::e_hit_from ,
  CHsp_Base::e_hit_to , CHsp_Base::e_pattern_from , CHsp_Base::e_pattern_to , CHsp_Base::e_query_frame ,
  CHsp_Base::e_hit_frame , CHsp_Base::e_identity , CHsp_Base::e_positive , CHsp_Base::e_gaps ,
  CHsp_Base::e_align_len , CHsp_Base::e_density , CHsp_Base::e_qseq , CHsp_Base::e_hseq ,
  CHsp_Base::e_midline , CHsp_Base::e__allMandatory = 0 , CHsp_Base::e_num , CHsp_Base::e_bit_score ,
  CHsp_Base::e_score , CHsp_Base::e_evalue , CHsp_Base::e_identity , CHsp_Base::e_positive ,
  CHsp_Base::e_density , CHsp_Base::e_pattern_from , CHsp_Base::e_pattern_to , CHsp_Base::e_query_from ,
  CHsp_Base::e_query_to , CHsp_Base::e_query_strand , CHsp_Base::e_query_frame , CHsp_Base::e_hit_from ,
  CHsp_Base::e_hit_to , CHsp_Base::e_hit_strand , CHsp_Base::e_hit_frame , CHsp_Base::e_align_len ,
  CHsp_Base::e_gaps , CHsp_Base::e_qseq , CHsp_Base::e_hseq , CHsp_Base::e_midline
}
 
enum class  CIteration_Base::E_memberIndex {
  CIteration_Base::e__allMandatory = 0 , CIteration_Base::e_iter_num , CIteration_Base::e_query_ID , CIteration_Base::e_query_def ,
  CIteration_Base::e_query_len , CIteration_Base::e_hits , CIteration_Base::e_stat , CIteration_Base::e_message ,
  CIteration_Base::e__allMandatory = 0 , CIteration_Base::e_iter_num , CIteration_Base::e_search
}
 
enum class  CParameters_Base::E_memberIndex {
  CParameters_Base::e__allMandatory = 0 , CParameters_Base::e_matrix , CParameters_Base::e_expect , CParameters_Base::e_include ,
  CParameters_Base::e_sc_match , CParameters_Base::e_sc_mismatch , CParameters_Base::e_gap_open , CParameters_Base::e_gap_extend ,
  CParameters_Base::e_filter , CParameters_Base::e_pattern , CParameters_Base::e_entrez_query , CParameters_Base::e__allMandatory = 0 ,
  CParameters_Base::e_matrix , CParameters_Base::e_expect , CParameters_Base::e_include , CParameters_Base::e_sc_match ,
  CParameters_Base::e_sc_mismatch , CParameters_Base::e_gap_open , CParameters_Base::e_gap_extend , CParameters_Base::e_filter ,
  CParameters_Base::e_pattern , CParameters_Base::e_entrez_query , CParameters_Base::e_cbs , CParameters_Base::e_query_gencode ,
  CParameters_Base::e_db_gencode , CParameters_Base::e_bl2seq_mode
}
 
enum class  CRange_Base::E_memberIndex { CRange_Base::e__allMandatory = 0 , CRange_Base::e_from , CRange_Base::e_to }
 
enum class  CReport_Base::E_memberIndex {
  CReport_Base::e__allMandatory = 0 , CReport_Base::e_program , CReport_Base::e_version , CReport_Base::e_reference ,
  CReport_Base::e_search_target , CReport_Base::e_params , CReport_Base::e_results
}
 
enum  CResults_Base::E_Choice { CResults_Base::e_not_set = 0 , CResults_Base::e_Iterations , CResults_Base::e_Search , CResults_Base::e_Bl2seq }
 Choice variants. More...
 
enum  CResults_Base::E_ChoiceStopper { CResults_Base::e_MaxChoice = 4 }
 Maximum+1 value of the choice variant enumerator. More...
 
enum class  CSearch_Base< LEGACY, NHITS, derived_t >::E_memberIndex {
  CSearch_Base< LEGACY, NHITS, derived_t >::e__allMandatory = 0 , CSearch_Base< LEGACY, NHITS, derived_t >::e_query_id , CSearch_Base< LEGACY, NHITS, derived_t >::e_query_title , CSearch_Base< LEGACY, NHITS, derived_t >::e_query_len ,
  CSearch_Base< LEGACY, NHITS, derived_t >::e_query_masking , CSearch_Base< LEGACY, NHITS, derived_t >::e_hits , CSearch_Base< LEGACY, NHITS, derived_t >::e_stat , CSearch_Base< LEGACY, NHITS, derived_t >::e_message
}
 
enum class  CStatistics_Base::E_memberIndex {
  CStatistics_Base::e__allMandatory = 0 , CStatistics_Base::e_db_num , CStatistics_Base::e_db_len , CStatistics_Base::e_hsp_len ,
  CStatistics_Base::e_eff_space , CStatistics_Base::e_kappa , CStatistics_Base::e_lambda , CStatistics_Base::e_entropy ,
  CStatistics_Base::e__allMandatory = 0 , CStatistics_Base::e_db_num , CStatistics_Base::e_db_len , CStatistics_Base::e_hsp_len ,
  CStatistics_Base::e_eff_space , CStatistics_Base::e_kappa , CStatistics_Base::e_lambda , CStatistics_Base::e_entropy
}
 
enum  CTarget_Base::E_Choice { CTarget_Base::e_not_set = 0 , CTarget_Base::e_Db , CTarget_Base::e_Subjects }
 Choice variants. More...
 
enum  CTarget_Base::E_ChoiceStopper { CTarget_Base::e_MaxChoice = 3 }
 Maximum+1 value of the choice variant enumerator. More...
 

Functions

 CBlastOutput2::CBlastOutput2 (void)
 
 CBlastOutput2::~CBlastOutput2 (void)
 
 CBlastOutput2::CBlastOutput2 (const CBlastOutput2 &value)
 
CBlastOutput2CBlastOutput2::operator= (const CBlastOutput2 &value)
 
 CBlastOutput2_Base::CBlastOutput2_Base (void)
 
virtual CBlastOutput2_Base::~CBlastOutput2_Base (void)
 
 CBlastOutput2_Base::DECLARE_INTERNAL_TYPE_INFO ()
 
bool CBlastOutput2_Base::IsSetReport (void) const
 Check if a value has been assigned to Report data member. More...
 
bool CBlastOutput2_Base::CanGetReport (void) const
 Check if it is safe to call GetReport method. More...
 
void CBlastOutput2_Base::ResetReport (void)
 Reset Report data member. More...
 
const TReportCBlastOutput2_Base::GetReport (void) const
 Get the Report member data. More...
 
void CBlastOutput2_Base::SetReport (TReport &value)
 Assign a value to Report data member. More...
 
TReportCBlastOutput2_Base::SetReport (void)
 Assign a value to Report data member. More...
 
bool CBlastOutput2_Base::IsSetError (void) const
 Check if a value has been assigned to Error data member. More...
 
bool CBlastOutput2_Base::CanGetError (void) const
 Check if it is safe to call GetError method. More...
 
void CBlastOutput2_Base::ResetError (void)
 Reset Error data member. More...
 
const TErrorCBlastOutput2_Base::GetError (void) const
 Get the Error member data. More...
 
void CBlastOutput2_Base::SetError (TError &value)
 Assign a value to Error data member. More...
 
TErrorCBlastOutput2_Base::SetError (void)
 Assign a value to Error data member. More...
 
virtual void CBlastOutput2_Base::Reset (void)
 Reset the whole object. More...
 
 CBlastOutput2_Base::CBlastOutput2_Base (const CBlastOutput2_Base &)
 
CBlastOutput2_BaseCBlastOutput2_Base::operator= (const CBlastOutput2_Base &)
 
 CBlastXML2::CBlastXML2 (void)
 
 CBlastXML2::~CBlastXML2 (void)
 
 CBlastXML2::CBlastXML2 (const CBlastXML2 &value)
 
CBlastXML2CBlastXML2::operator= (const CBlastXML2 &value)
 
 CBlastXML2_Base::CBlastXML2_Base (void)
 
virtual CBlastXML2_Base::~CBlastXML2_Base (void)
 
 CBlastXML2_Base::DECLARE_INTERNAL_TYPE_INFO ()
 
bool CBlastXML2_Base::IsSet (void) const
 Check if a value has been assigned to data member. More...
 
bool CBlastXML2_Base::CanGet (void) const
 Check if it is safe to call Get method. More...
 
void CBlastXML2_Base::Reset (void)
 Reset data member. More...
 
const TdataCBlastXML2_Base::Get (void) const
 Get the member data. More...
 
TdataCBlastXML2_Base::Set (void)
 Assign a value to data member. More...
 
 CBlastXML2_Base::operator const Tdata & (void) const
 Conversion operator to 'const Tdata' type. More...
 
 CBlastXML2_Base::operator Tdata & (void)
 Conversion operator to 'Tdata' type. More...
 
 CBlastXML2_Base::CBlastXML2_Base (const CBlastXML2_Base &)
 
CBlastXML2_BaseCBlastXML2_Base::operator= (const CBlastXML2_Base &)
 
 CErr::CErr (void)
 
 CErr::~CErr (void)
 
 CErr::CErr (const CErr &value)
 
CErrCErr::operator= (const CErr &value)
 
 CErr_Base::CErr_Base (void)
 
virtual CErr_Base::~CErr_Base (void)
 
 CErr_Base::DECLARE_INTERNAL_TYPE_INFO ()
 
bool CErr_Base::IsSetCode (void) const
 Check if a value has been assigned to Code data member. More...
 
bool CErr_Base::CanGetCode (void) const
 Check if it is safe to call GetCode method. More...
 
void CErr_Base::ResetCode (void)
 Reset Code data member. More...
 
TCode CErr_Base::GetCode (void) const
 Get the Code member data. More...
 
void CErr_Base::SetCode (TCode value)
 Assign a value to Code data member. More...
 
TCodeCErr_Base::SetCode (void)
 Assign a value to Code data member. More...
 
bool CErr_Base::IsSetMessage (void) const
 Check if a value has been assigned to Message data member. More...
 
bool CErr_Base::CanGetMessage (void) const
 Check if it is safe to call GetMessage method. More...
 
void CErr_Base::ResetMessage (void)
 Reset Message data member. More...
 
const TMessageCErr_Base::GetMessage (void) const
 Get the Message member data. More...
 
void CErr_Base::SetMessage (const TMessage &value)
 Assign a value to Message data member. More...
 
void CErr_Base::SetMessage (TMessage &&value)
 
TMessageCErr_Base::SetMessage (void)
 Assign a value to Message data member. More...
 
virtual void CErr_Base::Reset (void)
 Reset the whole object. More...
 
 CErr_Base::CErr_Base (const CErr_Base &)
 
CErr_BaseCErr_Base::operator= (const CErr_Base &)
 
 CHit::CHit (void)
 
 CHit::~CHit (void)
 
 CHit::CHit (const CHit &value)
 
CHitCHit::operator= (const CHit &value)
 
 CHit_Base::CHit_Base (void)
 
virtual CHit_Base::~CHit_Base (void)
 
 CHit_Base::DECLARE_INTERNAL_TYPE_INFO ()
 
bool CHit_Base::IsSetNum (void) const
 hit number Check if a value has been assigned to Num data member. More...
 
bool CHit_Base::CanGetNum (void) const
 Check if it is safe to call GetNum method. More...
 
void CHit_Base::ResetNum (void)
 Reset Num data member. More...
 
TNum CHit_Base::GetNum (void) const
 Get the Num member data. More...
 
void CHit_Base::SetNum (TNum value)
 Assign a value to Num data member. More...
 
TNumCHit_Base::SetNum (void)
 Assign a value to Num data member. More...
 
bool CHit_Base::IsSetDescription (void) const
 ID, title, and taxonomy for each entry in the PIG Check if a value has been assigned to Description data member. More...
 
bool CHit_Base::CanGetDescription (void) const
 Check if it is safe to call GetDescription method. More...
 
void CHit_Base::ResetDescription (void)
 Reset Description data member. More...
 
const TDescriptionCHit_Base::GetDescription (void) const
 Get the Description member data. More...
 
TDescriptionCHit_Base::SetDescription (void)
 Assign a value to Description data member. More...
 
bool CHit_Base::IsSetLen (void) const
 length of subject Check if a value has been assigned to Len data member. More...
 
bool CHit_Base::CanGetLen (void) const
 Check if it is safe to call GetLen method. More...
 
void CHit_Base::ResetLen (void)
 Reset Len data member. More...
 
TLen CHit_Base::GetLen (void) const
 Get the Len member data. More...
 
void CHit_Base::SetLen (TLen value)
 Assign a value to Len data member. More...
 
TLenCHit_Base::SetLen (void)
 Assign a value to Len data member. More...
 
bool CHit_Base::IsSetHsps (void) const
 all HSP regions for the given subject Check if a value has been assigned to Hsps data member. More...
 
bool CHit_Base::CanGetHsps (void) const
 Check if it is safe to call GetHsps method. More...
 
void CHit_Base::ResetHsps (void)
 Reset Hsps data member. More...
 
const THspsCHit_Base::GetHsps (void) const
 Get the Hsps member data. More...
 
THspsCHit_Base::SetHsps (void)
 Assign a value to Hsps data member. More...
 
virtual void CHit_Base::Reset (void)
 Reset the whole object. More...
 
 CHit_Base::CHit_Base (const CHit_Base &)
 
CHit_BaseCHit_Base::operator= (const CHit_Base &)
 
 CHitDescr::CHitDescr (void)
 
 CHitDescr::~CHitDescr (void)
 
 CHitDescr::CHitDescr (const CHitDescr &value)
 
CHitDescrCHitDescr::operator= (const CHitDescr &value)
 
 CHitDescr_Base::CHitDescr_Base (void)
 
virtual CHitDescr_Base::~CHitDescr_Base (void)
 
 CHitDescr_Base::DECLARE_INTERNAL_TYPE_INFO ()
 
bool CHitDescr_Base::IsSetId (void) const
 SeqId of subject Check if a value has been assigned to Id data member. More...
 
bool CHitDescr_Base::CanGetId (void) const
 Check if it is safe to call GetId method. More...
 
void CHitDescr_Base::ResetId (void)
 Reset Id data member. More...
 
const TIdCHitDescr_Base::GetId (void) const
 Get the Id member data. More...
 
void CHitDescr_Base::SetId (const TId &value)
 Assign a value to Id data member. More...
 
void CHitDescr_Base::SetId (TId &&value)
 
TIdCHitDescr_Base::SetId (void)
 Assign a value to Id data member. More...
 
bool CHitDescr_Base::IsSetAccession (void) const
 accession Check if a value has been assigned to Accession data member. More...
 
bool CHitDescr_Base::CanGetAccession (void) const
 Check if it is safe to call GetAccession method. More...
 
void CHitDescr_Base::ResetAccession (void)
 Reset Accession data member. More...
 
const TAccessionCHitDescr_Base::GetAccession (void) const
 Get the Accession member data. More...
 
void CHitDescr_Base::SetAccession (const TAccession &value)
 Assign a value to Accession data member. More...
 
void CHitDescr_Base::SetAccession (TAccession &&value)
 
TAccessionCHitDescr_Base::SetAccession (void)
 Assign a value to Accession data member. More...
 
bool CHitDescr_Base::IsSetTitle (void) const
 title (definition line) of subject Check if a value has been assigned to Title data member. More...
 
bool CHitDescr_Base::CanGetTitle (void) const
 Check if it is safe to call GetTitle method. More...
 
void CHitDescr_Base::ResetTitle (void)
 Reset Title data member. More...
 
const TTitleCHitDescr_Base::GetTitle (void) const
 Get the Title member data. More...
 
void CHitDescr_Base::SetTitle (const TTitle &value)
 Assign a value to Title data member. More...
 
void CHitDescr_Base::SetTitle (TTitle &&value)
 
TTitleCHitDescr_Base::SetTitle (void)
 Assign a value to Title data member. More...
 
bool CHitDescr_Base::IsSetTaxid (void) const
 NCBI taxid (9606 for human) Check if a value has been assigned to Taxid data member. More...
 
bool CHitDescr_Base::CanGetTaxid (void) const
 Check if it is safe to call GetTaxid method. More...
 
void CHitDescr_Base::ResetTaxid (void)
 Reset Taxid data member. More...
 
TTaxid CHitDescr_Base::GetTaxid (void) const
 Get the Taxid member data. More...
 
void CHitDescr_Base::SetTaxid (TTaxid value)
 Assign a value to Taxid data member. More...
 
TTaxidCHitDescr_Base::SetTaxid (void)
 Assign a value to Taxid data member. More...
 
bool CHitDescr_Base::IsSetSciname (void) const
 binomial scientific name ("Homo sapiens" for human). More...
 
bool CHitDescr_Base::CanGetSciname (void) const
 Check if it is safe to call GetSciname method. More...
 
void CHitDescr_Base::ResetSciname (void)
 Reset Sciname data member. More...
 
const TScinameCHitDescr_Base::GetSciname (void) const
 Get the Sciname member data. More...
 
void CHitDescr_Base::SetSciname (const TSciname &value)
 Assign a value to Sciname data member. More...
 
void CHitDescr_Base::SetSciname (TSciname &&value)
 
TScinameCHitDescr_Base::SetSciname (void)
 Assign a value to Sciname data member. More...
 
virtual void CHitDescr_Base::Reset (void)
 Reset the whole object. More...
 
 CHitDescr_Base::CHitDescr_Base (const CHitDescr_Base &)
 
CHitDescr_BaseCHitDescr_Base::operator= (const CHitDescr_Base &)
 
 CHsp::CHsp (void)
 
 CHsp::~CHsp (void)
 
 CHsp::CHsp (const CHsp &value)
 
CHspCHsp::operator= (const CHsp &value)
 
 CHsp_Base::CHsp_Base (void)
 
virtual CHsp_Base::~CHsp_Base (void)
 
 CHsp_Base::DECLARE_INTERNAL_TYPE_INFO ()
 
bool CHsp_Base::IsSetNum (void) const
 HSP number Check if a value has been assigned to Num data member. More...
 
bool CHsp_Base::CanGetNum (void) const
 Check if it is safe to call GetNum method. More...
 
void CHsp_Base::ResetNum (void)
 Reset Num data member. More...
 
TNum CHsp_Base::GetNum (void) const
 Get the Num member data. More...
 
void CHsp_Base::SetNum (TNum value)
 Assign a value to Num data member. More...
 
TNumCHsp_Base::SetNum (void)
 Assign a value to Num data member. More...
 
bool CHsp_Base::IsSetBit_score (void) const
 score (in bits) of HSP Check if a value has been assigned to Bit_score data member. More...
 
bool CHsp_Base::CanGetBit_score (void) const
 Check if it is safe to call GetBit_score method. More...
 
void CHsp_Base::ResetBit_score (void)
 Reset Bit_score data member. More...
 
TBit_score CHsp_Base::GetBit_score (void) const
 Get the Bit_score member data. More...
 
void CHsp_Base::SetBit_score (TBit_score value)
 Assign a value to Bit_score data member. More...
 
TBit_scoreCHsp_Base::SetBit_score (void)
 Assign a value to Bit_score data member. More...
 
bool CHsp_Base::IsSetScore (void) const
 score of HSP Check if a value has been assigned to Score data member. More...
 
bool CHsp_Base::CanGetScore (void) const
 Check if it is safe to call GetScore method. More...
 
void CHsp_Base::ResetScore (void)
 Reset Score data member. More...
 
TScore CHsp_Base::GetScore (void) const
 Get the Score member data. More...
 
void CHsp_Base::SetScore (TScore value)
 Assign a value to Score data member. More...
 
TScoreCHsp_Base::SetScore (void)
 Assign a value to Score data member. More...
 
bool CHsp_Base::IsSetEvalue (void) const
 e-value of HSP Check if a value has been assigned to Evalue data member. More...
 
bool CHsp_Base::CanGetEvalue (void) const
 Check if it is safe to call GetEvalue method. More...
 
void CHsp_Base::ResetEvalue (void)
 Reset Evalue data member. More...
 
TEvalue CHsp_Base::GetEvalue (void) const
 Get the Evalue member data. More...
 
void CHsp_Base::SetEvalue (TEvalue value)
 Assign a value to Evalue data member. More...
 
TEvalueCHsp_Base::SetEvalue (void)
 Assign a value to Evalue data member. More...
 
bool CHsp_Base::IsSetIdentity (void) const
 number of identities in HSP Check if a value has been assigned to Identity data member. More...
 
bool CHsp_Base::CanGetIdentity (void) const
 Check if it is safe to call GetIdentity method. More...
 
void CHsp_Base::ResetIdentity (void)
 Reset Identity data member. More...
 
TIdentity CHsp_Base::GetIdentity (void) const
 Get the Identity member data. More...
 
void CHsp_Base::SetIdentity (TIdentity value)
 Assign a value to Identity data member. More...
 
TIdentityCHsp_Base::SetIdentity (void)
 Assign a value to Identity data member. More...
 
bool CHsp_Base::IsSetPositive (void) const
 number of positives in HSP Check if a value has been assigned to Positive data member. More...
 
bool CHsp_Base::CanGetPositive (void) const
 Check if it is safe to call GetPositive method. More...
 
void CHsp_Base::ResetPositive (void)
 Reset Positive data member. More...
 
TPositive CHsp_Base::GetPositive (void) const
 Get the Positive member data. More...
 
void CHsp_Base::SetPositive (TPositive value)
 Assign a value to Positive data member. More...
 
TPositiveCHsp_Base::SetPositive (void)
 Assign a value to Positive data member. More...
 
bool CHsp_Base::IsSetDensity (void) const
 score density Check if a value has been assigned to Density data member. More...
 
bool CHsp_Base::CanGetDensity (void) const
 Check if it is safe to call GetDensity method. More...
 
void CHsp_Base::ResetDensity (void)
 Reset Density data member. More...
 
TDensity CHsp_Base::GetDensity (void) const
 Get the Density member data. More...
 
void CHsp_Base::SetDensity (TDensity value)
 Assign a value to Density data member. More...
 
TDensityCHsp_Base::SetDensity (void)
 Assign a value to Density data member. More...
 
bool CHsp_Base::IsSetPattern_from (void) const
 start of PHI-BLAST pattern Check if a value has been assigned to Pattern_from data member. More...
 
bool CHsp_Base::CanGetPattern_from (void) const
 Check if it is safe to call GetPattern_from method. More...
 
void CHsp_Base::ResetPattern_from (void)
 Reset Pattern_from data member. More...
 
TPattern_from CHsp_Base::GetPattern_from (void) const
 Get the Pattern_from member data. More...
 
void CHsp_Base::SetPattern_from (TPattern_from value)
 Assign a value to Pattern_from data member. More...
 
TPattern_fromCHsp_Base::SetPattern_from (void)
 Assign a value to Pattern_from data member. More...
 
bool CHsp_Base::IsSetPattern_to (void) const
 end of PHI-BLAST pattern Check if a value has been assigned to Pattern_to data member. More...
 
bool CHsp_Base::CanGetPattern_to (void) const
 Check if it is safe to call GetPattern_to method. More...
 
void CHsp_Base::ResetPattern_to (void)
 Reset Pattern_to data member. More...
 
TPattern_to CHsp_Base::GetPattern_to (void) const
 Get the Pattern_to member data. More...
 
void CHsp_Base::SetPattern_to (TPattern_to value)
 Assign a value to Pattern_to data member. More...
 
TPattern_toCHsp_Base::SetPattern_to (void)
 Assign a value to Pattern_to data member. More...
 
bool CHsp_Base::IsSetQuery_from (void) const
 start of HSP in query Check if a value has been assigned to Query_from data member. More...
 
bool CHsp_Base::CanGetQuery_from (void) const
 Check if it is safe to call GetQuery_from method. More...
 
void CHsp_Base::ResetQuery_from (void)
 Reset Query_from data member. More...
 
TQuery_from CHsp_Base::GetQuery_from (void) const
 Get the Query_from member data. More...
 
void CHsp_Base::SetQuery_from (TQuery_from value)
 Assign a value to Query_from data member. More...
 
TQuery_fromCHsp_Base::SetQuery_from (void)
 Assign a value to Query_from data member. More...
 
bool CHsp_Base::IsSetQuery_to (void) const
 end of HSP Check if a value has been assigned to Query_to data member. More...
 
bool CHsp_Base::CanGetQuery_to (void) const
 Check if it is safe to call GetQuery_to method. More...
 
void CHsp_Base::ResetQuery_to (void)
 Reset Query_to data member. More...
 
TQuery_to CHsp_Base::GetQuery_to (void) const
 Get the Query_to member data. More...
 
void CHsp_Base::SetQuery_to (TQuery_to value)
 Assign a value to Query_to data member. More...
 
TQuery_toCHsp_Base::SetQuery_to (void)
 Assign a value to Query_to data member. More...
 
bool CHsp_Base::IsSetQuery_strand (void) const
 Strand of query (blastn) Check if a value has been assigned to Query_strand data member. More...
 
bool CHsp_Base::CanGetQuery_strand (void) const
 Check if it is safe to call GetQuery_strand method. More...
 
void CHsp_Base::ResetQuery_strand (void)
 Reset Query_strand data member. More...
 
const TQuery_strandCHsp_Base::GetQuery_strand (void) const
 Get the Query_strand member data. More...
 
void CHsp_Base::SetQuery_strand (const TQuery_strand &value)
 Assign a value to Query_strand data member. More...
 
void CHsp_Base::SetQuery_strand (TQuery_strand &&value)
 
TQuery_strandCHsp_Base::SetQuery_strand (void)
 Assign a value to Query_strand data member. More...
 
bool CHsp_Base::IsSetQuery_frame (void) const
 translation frame of query (blastx, tblastx) Check if a value has been assigned to Query_frame data member. More...
 
bool CHsp_Base::CanGetQuery_frame (void) const
 Check if it is safe to call GetQuery_frame method. More...
 
void CHsp_Base::ResetQuery_frame (void)
 Reset Query_frame data member. More...
 
TQuery_frame CHsp_Base::GetQuery_frame (void) const
 Get the Query_frame member data. More...
 
void CHsp_Base::SetQuery_frame (TQuery_frame value)
 Assign a value to Query_frame data member. More...
 
TQuery_frameCHsp_Base::SetQuery_frame (void)
 Assign a value to Query_frame data member. More...
 
bool CHsp_Base::IsSetHit_from (void) const
 start of HSP in subject Check if a value has been assigned to Hit_from data member. More...
 
bool CHsp_Base::CanGetHit_from (void) const
 Check if it is safe to call GetHit_from method. More...
 
void CHsp_Base::ResetHit_from (void)
 Reset Hit_from data member. More...
 
THit_from CHsp_Base::GetHit_from (void) const
 Get the Hit_from member data. More...
 
void CHsp_Base::SetHit_from (THit_from value)
 Assign a value to Hit_from data member. More...
 
THit_fromCHsp_Base::SetHit_from (void)
 Assign a value to Hit_from data member. More...
 
bool CHsp_Base::IsSetHit_to (void) const
 end of HSP in subject Check if a value has been assigned to Hit_to data member. More...
 
bool CHsp_Base::CanGetHit_to (void) const
 Check if it is safe to call GetHit_to method. More...
 
void CHsp_Base::ResetHit_to (void)
 Reset Hit_to data member. More...
 
THit_to CHsp_Base::GetHit_to (void) const
 Get the Hit_to member data. More...
 
void CHsp_Base::SetHit_to (THit_to value)
 Assign a value to Hit_to data member. More...
 
THit_toCHsp_Base::SetHit_to (void)
 Assign a value to Hit_to data member. More...
 
bool CHsp_Base::IsSetHit_strand (void) const
 Strand of subject (blastn) Check if a value has been assigned to Hit_strand data member. More...
 
bool CHsp_Base::CanGetHit_strand (void) const
 Check if it is safe to call GetHit_strand method. More...
 
void CHsp_Base::ResetHit_strand (void)
 Reset Hit_strand data member. More...
 
const THit_strandCHsp_Base::GetHit_strand (void) const
 Get the Hit_strand member data. More...
 
void CHsp_Base::SetHit_strand (const THit_strand &value)
 Assign a value to Hit_strand data member. More...
 
void CHsp_Base::SetHit_strand (THit_strand &&value)
 
THit_strandCHsp_Base::SetHit_strand (void)
 Assign a value to Hit_strand data member. More...
 
bool CHsp_Base::IsSetHit_frame (void) const
 translation frame of subject (tblastn, tblastx) Check if a value has been assigned to Hit_frame data member. More...
 
bool CHsp_Base::CanGetHit_frame (void) const
 Check if it is safe to call GetHit_frame method. More...
 
void CHsp_Base::ResetHit_frame (void)
 Reset Hit_frame data member. More...
 
THit_frame CHsp_Base::GetHit_frame (void) const
 Get the Hit_frame member data. More...
 
void CHsp_Base::SetHit_frame (THit_frame value)
 Assign a value to Hit_frame data member. More...
 
THit_frameCHsp_Base::SetHit_frame (void)
 Assign a value to Hit_frame data member. More...
 
bool CHsp_Base::IsSetAlign_len (void) const
 length of the alignment used Check if a value has been assigned to Align_len data member. More...
 
bool CHsp_Base::CanGetAlign_len (void) const
 Check if it is safe to call GetAlign_len method. More...
 
void CHsp_Base::ResetAlign_len (void)
 Reset Align_len data member. More...
 
TAlign_len CHsp_Base::GetAlign_len (void) const
 Get the Align_len member data. More...
 
void CHsp_Base::SetAlign_len (TAlign_len value)
 Assign a value to Align_len data member. More...
 
TAlign_lenCHsp_Base::SetAlign_len (void)
 Assign a value to Align_len data member. More...
 
bool CHsp_Base::IsSetGaps (void) const
 number of gaps in HSP Check if a value has been assigned to Gaps data member. More...
 
bool CHsp_Base::CanGetGaps (void) const
 Check if it is safe to call GetGaps method. More...
 
void CHsp_Base::ResetGaps (void)
 Reset Gaps data member. More...
 
TGaps CHsp_Base::GetGaps (void) const
 Get the Gaps member data. More...
 
void CHsp_Base::SetGaps (TGaps value)
 Assign a value to Gaps data member. More...
 
TGapsCHsp_Base::SetGaps (void)
 Assign a value to Gaps data member. More...
 
bool CHsp_Base::IsSetQseq (void) const
 alignment string for the query (with gaps) Check if a value has been assigned to Qseq data member. More...
 
bool CHsp_Base::CanGetQseq (void) const
 Check if it is safe to call GetQseq method. More...
 
void CHsp_Base::ResetQseq (void)
 Reset Qseq data member. More...
 
const TQseqCHsp_Base::GetQseq (void) const
 Get the Qseq member data. More...
 
void CHsp_Base::SetQseq (const TQseq &value)
 Assign a value to Qseq data member. More...
 
void CHsp_Base::SetQseq (TQseq &&value)
 
TQseqCHsp_Base::SetQseq (void)
 Assign a value to Qseq data member. More...
 
bool CHsp_Base::IsSetHseq (void) const
 alignment string for subject (with gaps) Check if a value has been assigned to Hseq data member. More...
 
bool CHsp_Base::CanGetHseq (void) const
 Check if it is safe to call GetHseq method. More...
 
void CHsp_Base::ResetHseq (void)
 Reset Hseq data member. More...
 
const THseqCHsp_Base::GetHseq (void) const
 Get the Hseq member data. More...
 
void CHsp_Base::SetHseq (const THseq &value)
 Assign a value to Hseq data member. More...
 
void CHsp_Base::SetHseq (THseq &&value)
 
THseqCHsp_Base::SetHseq (void)
 Assign a value to Hseq data member. More...
 
bool CHsp_Base::IsSetMidline (void) const
 formating middle line Check if a value has been assigned to Midline data member. More...
 
bool CHsp_Base::CanGetMidline (void) const
 Check if it is safe to call GetMidline method. More...
 
void CHsp_Base::ResetMidline (void)
 Reset Midline data member. More...
 
const TMidlineCHsp_Base::GetMidline (void) const
 Get the Midline member data. More...
 
void CHsp_Base::SetMidline (const TMidline &value)
 Assign a value to Midline data member. More...
 
void CHsp_Base::SetMidline (TMidline &&value)
 
TMidlineCHsp_Base::SetMidline (void)
 Assign a value to Midline data member. More...
 
virtual void CHsp_Base::Reset (void)
 Reset the whole object. More...
 
 CHsp_Base::CHsp_Base (const CHsp_Base &)
 
CHsp_BaseCHsp_Base::operator= (const CHsp_Base &)
 
 CIteration::CIteration (void)
 
 CIteration::~CIteration (void)
 
 CIteration::CIteration (const CIteration &value)
 
CIterationCIteration::operator= (const CIteration &value)
 
 CIteration_Base::CIteration_Base (void)
 
virtual CIteration_Base::~CIteration_Base (void)
 
 CIteration_Base::DECLARE_INTERNAL_TYPE_INFO ()
 
bool CIteration_Base::IsSetIter_num (void) const
 iteration number (use with psiblast) Check if a value has been assigned to Iter_num data member. More...
 
bool CIteration_Base::CanGetIter_num (void) const
 Check if it is safe to call GetIter_num method. More...
 
void CIteration_Base::ResetIter_num (void)
 Reset Iter_num data member. More...
 
TIter_num CIteration_Base::GetIter_num (void) const
 Get the Iter_num member data. More...
 
void CIteration_Base::SetIter_num (TIter_num value)
 Assign a value to Iter_num data member. More...
 
TIter_numCIteration_Base::SetIter_num (void)
 Assign a value to Iter_num data member. More...
 
bool CIteration_Base::IsSetSearch (void) const
 Check if a value has been assigned to Search data member. More...
 
bool CIteration_Base::CanGetSearch (void) const
 Check if it is safe to call GetSearch method. More...
 
void CIteration_Base::ResetSearch (void)
 Reset Search data member. More...
 
const TSearchCIteration_Base::GetSearch (void) const
 Get the Search member data. More...
 
void CIteration_Base::SetSearch (TSearch &value)
 Assign a value to Search data member. More...
 
TSearchCIteration_Base::SetSearch (void)
 Assign a value to Search data member. More...
 
virtual void CIteration_Base::Reset (void)
 Reset the whole object. More...
 
 CIteration_Base::CIteration_Base (const CIteration_Base &)
 
CIteration_BaseCIteration_Base::operator= (const CIteration_Base &)
 
 CParameters::CParameters (void)
 
 CParameters::~CParameters (void)
 
 CParameters::CParameters (const CParameters &value)
 
CParametersCParameters::operator= (const CParameters &value)
 
 CParameters_Base::CParameters_Base (void)
 
virtual CParameters_Base::~CParameters_Base (void)
 
 CParameters_Base::DECLARE_INTERNAL_TYPE_INFO ()
 
bool CParameters_Base::IsSetMatrix (void) const
 Matrix used (-M) Check if a value has been assigned to Matrix data member. More...
 
bool CParameters_Base::CanGetMatrix (void) const
 Check if it is safe to call GetMatrix method. More...
 
void CParameters_Base::ResetMatrix (void)
 Reset Matrix data member. More...
 
const TMatrixCParameters_Base::GetMatrix (void) const
 Get the Matrix member data. More...
 
void CParameters_Base::SetMatrix (const TMatrix &value)
 Assign a value to Matrix data member. More...
 
void CParameters_Base::SetMatrix (TMatrix &&value)
 
TMatrixCParameters_Base::SetMatrix (void)
 Assign a value to Matrix data member. More...
 
bool CParameters_Base::IsSetExpect (void) const
 Expectation threshold (-e) Check if a value has been assigned to Expect data member. More...
 
bool CParameters_Base::CanGetExpect (void) const
 Check if it is safe to call GetExpect method. More...
 
void CParameters_Base::ResetExpect (void)
 Reset Expect data member. More...
 
TExpect CParameters_Base::GetExpect (void) const
 Get the Expect member data. More...
 
void CParameters_Base::SetExpect (TExpect value)
 Assign a value to Expect data member. More...
 
TExpectCParameters_Base::SetExpect (void)
 Assign a value to Expect data member. More...
 
bool CParameters_Base::IsSetInclude (void) const
 Inclusion threshold (-h) Check if a value has been assigned to Include data member. More...
 
bool CParameters_Base::CanGetInclude (void) const
 Check if it is safe to call GetInclude method. More...
 
void CParameters_Base::ResetInclude (void)
 Reset Include data member. More...
 
TInclude CParameters_Base::GetInclude (void) const
 Get the Include member data. More...
 
void CParameters_Base::SetInclude (TInclude value)
 Assign a value to Include data member. More...
 
TIncludeCParameters_Base::SetInclude (void)
 Assign a value to Include data member. More...
 
bool CParameters_Base::IsSetSc_match (void) const
 match score for NT (-r) Check if a value has been assigned to Sc_match data member. More...
 
bool CParameters_Base::CanGetSc_match (void) const
 Check if it is safe to call GetSc_match method. More...
 
void CParameters_Base::ResetSc_match (void)
 Reset Sc_match data member. More...
 
TSc_match CParameters_Base::GetSc_match (void) const
 Get the Sc_match member data. More...
 
void CParameters_Base::SetSc_match (TSc_match value)
 Assign a value to Sc_match data member. More...
 
TSc_matchCParameters_Base::SetSc_match (void)
 Assign a value to Sc_match data member. More...
 
bool CParameters_Base::IsSetSc_mismatch (void) const
 mismatch score for NT (-q) Check if a value has been assigned to Sc_mismatch data member. More...
 
bool CParameters_Base::CanGetSc_mismatch (void) const
 Check if it is safe to call GetSc_mismatch method. More...
 
void CParameters_Base::ResetSc_mismatch (void)
 Reset Sc_mismatch data member. More...
 
TSc_mismatch CParameters_Base::GetSc_mismatch (void) const
 Get the Sc_mismatch member data. More...
 
void CParameters_Base::SetSc_mismatch (TSc_mismatch value)
 Assign a value to Sc_mismatch data member. More...
 
TSc_mismatchCParameters_Base::SetSc_mismatch (void)
 Assign a value to Sc_mismatch data member. More...
 
bool CParameters_Base::IsSetGap_open (void) const
 Gap opening cost (-G) Check if a value has been assigned to Gap_open data member. More...
 
bool CParameters_Base::CanGetGap_open (void) const
 Check if it is safe to call GetGap_open method. More...
 
void CParameters_Base::ResetGap_open (void)
 Reset Gap_open data member. More...
 
TGap_open CParameters_Base::GetGap_open (void) const
 Get the Gap_open member data. More...
 
void CParameters_Base::SetGap_open (TGap_open value)
 Assign a value to Gap_open data member. More...
 
TGap_openCParameters_Base::SetGap_open (void)
 Assign a value to Gap_open data member. More...
 
bool CParameters_Base::IsSetGap_extend (void) const
 Gap extension cost (-E) Check if a value has been assigned to Gap_extend data member. More...
 
bool CParameters_Base::CanGetGap_extend (void) const
 Check if it is safe to call GetGap_extend method. More...
 
void CParameters_Base::ResetGap_extend (void)
 Reset Gap_extend data member. More...
 
TGap_extend CParameters_Base::GetGap_extend (void) const
 Get the Gap_extend member data. More...
 
void CParameters_Base::SetGap_extend (TGap_extend value)
 Assign a value to Gap_extend data member. More...
 
TGap_extendCParameters_Base::SetGap_extend (void)
 Assign a value to Gap_extend data member. More...
 
bool CParameters_Base::IsSetFilter (void) const
 Filtering options (-F) Check if a value has been assigned to Filter data member. More...
 
bool CParameters_Base::CanGetFilter (void) const
 Check if it is safe to call GetFilter method. More...
 
void CParameters_Base::ResetFilter (void)
 Reset Filter data member. More...
 
const TFilterCParameters_Base::GetFilter (void) const
 Get the Filter member data. More...
 
void CParameters_Base::SetFilter (const TFilter &value)
 Assign a value to Filter data member. More...
 
void CParameters_Base::SetFilter (TFilter &&value)
 
TFilterCParameters_Base::SetFilter (void)
 Assign a value to Filter data member. More...
 
bool CParameters_Base::IsSetPattern (void) const
 PHI-BLAST pattern Check if a value has been assigned to Pattern data member. More...
 
bool CParameters_Base::CanGetPattern (void) const
 Check if it is safe to call GetPattern method. More...
 
void CParameters_Base::ResetPattern (void)
 Reset Pattern data member. More...
 
const TPatternCParameters_Base::GetPattern (void) const
 Get the Pattern member data. More...
 
void CParameters_Base::SetPattern (const TPattern &value)
 Assign a value to Pattern data member. More...
 
void CParameters_Base::SetPattern (TPattern &&value)
 
TPatternCParameters_Base::SetPattern (void)
 Assign a value to Pattern data member. More...
 
bool CParameters_Base::IsSetEntrez_query (void) const
 Limit of request to Entrez query Check if a value has been assigned to Entrez_query data member. More...
 
bool CParameters_Base::CanGetEntrez_query (void) const
 Check if it is safe to call GetEntrez_query method. More...
 
void CParameters_Base::ResetEntrez_query (void)
 Reset Entrez_query data member. More...
 
const TEntrez_queryCParameters_Base::GetEntrez_query (void) const
 Get the Entrez_query member data. More...
 
void CParameters_Base::SetEntrez_query (const TEntrez_query &value)
 Assign a value to Entrez_query data member. More...
 
void CParameters_Base::SetEntrez_query (TEntrez_query &&value)
 
TEntrez_queryCParameters_Base::SetEntrez_query (void)
 Assign a value to Entrez_query data member. More...
 
bool CParameters_Base::IsSetCbs (void) const
 composition-based stats (numbers correspond to numbering in stand-alone application parameter -comp_based_stats). More...
 
bool CParameters_Base::CanGetCbs (void) const
 Check if it is safe to call GetCbs method. More...
 
void CParameters_Base::ResetCbs (void)
 Reset Cbs data member. More...
 
TCbs CParameters_Base::GetCbs (void) const
 Get the Cbs member data. More...
 
void CParameters_Base::SetCbs (TCbs value)
 Assign a value to Cbs data member. More...
 
TCbsCParameters_Base::SetCbs (void)
 Assign a value to Cbs data member. More...
 
bool CParameters_Base::IsSetQuery_gencode (void) const
 genetic code for query (blastx or tblastx) Check if a value has been assigned to Query_gencode data member. More...
 
bool CParameters_Base::CanGetQuery_gencode (void) const
 Check if it is safe to call GetQuery_gencode method. More...
 
void CParameters_Base::ResetQuery_gencode (void)
 Reset Query_gencode data member. More...
 
TQuery_gencode CParameters_Base::GetQuery_gencode (void) const
 Get the Query_gencode member data. More...
 
void CParameters_Base::SetQuery_gencode (TQuery_gencode value)
 Assign a value to Query_gencode data member. More...
 
TQuery_gencodeCParameters_Base::SetQuery_gencode (void)
 Assign a value to Query_gencode data member. More...
 
bool CParameters_Base::IsSetDb_gencode (void) const
 genetic code for db or subjects (tblastn or tblastx) Check if a value has been assigned to Db_gencode data member. More...
 
bool CParameters_Base::CanGetDb_gencode (void) const
 Check if it is safe to call GetDb_gencode method. More...
 
void CParameters_Base::ResetDb_gencode (void)
 Reset Db_gencode data member. More...
 
TDb_gencode CParameters_Base::GetDb_gencode (void) const
 Get the Db_gencode member data. More...
 
void CParameters_Base::SetDb_gencode (TDb_gencode value)
 Assign a value to Db_gencode data member. More...
 
TDb_gencodeCParameters_Base::SetDb_gencode (void)
 Assign a value to Db_gencode data member. More...
 
bool CParameters_Base::IsSetBl2seq_mode (void) const
 bl2seq mode Check if a value has been assigned to Bl2seq_mode data member. More...
 
bool CParameters_Base::CanGetBl2seq_mode (void) const
 Check if it is safe to call GetBl2seq_mode method. More...
 
void CParameters_Base::ResetBl2seq_mode (void)
 Reset Bl2seq_mode data member. More...
 
const TBl2seq_modeCParameters_Base::GetBl2seq_mode (void) const
 Get the Bl2seq_mode member data. More...
 
void CParameters_Base::SetBl2seq_mode (const TBl2seq_mode &value)
 Assign a value to Bl2seq_mode data member. More...
 
void CParameters_Base::SetBl2seq_mode (TBl2seq_mode &&value)
 
TBl2seq_modeCParameters_Base::SetBl2seq_mode (void)
 Assign a value to Bl2seq_mode data member. More...
 
virtual void CParameters_Base::Reset (void)
 Reset the whole object. More...
 
 CParameters_Base::CParameters_Base (const CParameters_Base &)
 
CParameters_BaseCParameters_Base::operator= (const CParameters_Base &)
 
 CRange< Position >::CRange (void)
 
 CRange< Position >::~CRange (void)
 
 CRange< Position >::CRange (const CRange &value)
 
CRangeCRange< Position >::operator= (const CRange &value)
 
 CRange_Base::CRange_Base (void)
 
virtual CRange_Base::~CRange_Base (void)
 
 CRange_Base::DECLARE_INTERNAL_TYPE_INFO ()
 
bool CRange_Base::IsSetFrom (void) const
 Beginning of masked range (one-offset) Check if a value has been assigned to From data member. More...
 
bool CRange_Base::CanGetFrom (void) const
 Check if it is safe to call GetFrom method. More...
 
void CRange_Base::ResetFrom (void)
 Reset From data member. More...
 
TFrom CRange_Base::GetFrom (void) const
 Get the From member data. More...
 
void CRange_Base::SetFrom (TFrom value)
 Assign a value to From data member. More...
 
TFromCRange_Base::SetFrom (void)
 Assign a value to From data member. More...
 
bool CRange_Base::IsSetTo (void) const
 End of masked range (one-offset) Check if a value has been assigned to To data member. More...
 
bool CRange_Base::CanGetTo (void) const
 Check if it is safe to call GetTo method. More...
 
void CRange_Base::ResetTo (void)
 Reset To data member. More...
 
TTo CRange_Base::GetTo (void) const
 Get the To member data. More...
 
void CRange_Base::SetTo (TTo value)
 Assign a value to To data member. More...
 
TToCRange_Base::SetTo (void)
 Assign a value to To data member. More...
 
virtual void CRange_Base::Reset (void)
 Reset the whole object. More...
 
 CRange_Base::CRange_Base (const CRange_Base &)
 
CRange_BaseCRange_Base::operator= (const CRange_Base &)
 
 CReport::CReport (void)
 
 CReport::~CReport (void)
 
 CReport::CReport (const CReport &value)
 
CReportCReport::operator= (const CReport &value)
 
 CReport_Base::CReport_Base (void)
 
virtual CReport_Base::~CReport_Base (void)
 
 CReport_Base::DECLARE_INTERNAL_TYPE_INFO ()
 
bool CReport_Base::IsSetProgram (void) const
 BLAST program: blastp, tblastx etc. More...
 
bool CReport_Base::CanGetProgram (void) const
 Check if it is safe to call GetProgram method. More...
 
void CReport_Base::ResetProgram (void)
 Reset Program data member. More...
 
const TProgramCReport_Base::GetProgram (void) const
 Get the Program member data. More...
 
void CReport_Base::SetProgram (const TProgram &value)
 Assign a value to Program data member. More...
 
void CReport_Base::SetProgram (TProgram &&value)
 
TProgramCReport_Base::SetProgram (void)
 Assign a value to Program data member. More...
 
bool CReport_Base::IsSetVersion (void) const
 Program version Check if a value has been assigned to Version data member. More...
 
bool CReport_Base::CanGetVersion (void) const
 Check if it is safe to call GetVersion method. More...
 
void CReport_Base::ResetVersion (void)
 Reset Version data member. More...
 
const TVersionCReport_Base::GetVersion (void) const
 Get the Version member data. More...
 
void CReport_Base::SetVersion (const TVersion &value)
 Assign a value to Version data member. More...
 
void CReport_Base::SetVersion (TVersion &&value)
 
TVersionCReport_Base::SetVersion (void)
 Assign a value to Version data member. More...
 
bool CReport_Base::IsSetReference (void) const
 Steven, David, Tom and others Check if a value has been assigned to Reference data member. More...
 
bool CReport_Base::CanGetReference (void) const
 Check if it is safe to call GetReference method. More...
 
void CReport_Base::ResetReference (void)
 Reset Reference data member. More...
 
const TReferenceCReport_Base::GetReference (void) const
 Get the Reference member data. More...
 
void CReport_Base::SetReference (const TReference &value)
 Assign a value to Reference data member. More...
 
void CReport_Base::SetReference (TReference &&value)
 
TReferenceCReport_Base::SetReference (void)
 Assign a value to Reference data member. More...
 
bool CReport_Base::IsSetSearch_target (void) const
 Check if a value has been assigned to Search_target data member. More...
 
bool CReport_Base::CanGetSearch_target (void) const
 Check if it is safe to call GetSearch_target method. More...
 
void CReport_Base::ResetSearch_target (void)
 Reset Search_target data member. More...
 
const TSearch_targetCReport_Base::GetSearch_target (void) const
 Get the Search_target member data. More...
 
void CReport_Base::SetSearch_target (TSearch_target &value)
 Assign a value to Search_target data member. More...
 
TSearch_targetCReport_Base::SetSearch_target (void)
 Assign a value to Search_target data member. More...
 
bool CReport_Base::IsSetParams (void) const
 search parameters Check if a value has been assigned to Params data member. More...
 
bool CReport_Base::CanGetParams (void) const
 Check if it is safe to call GetParams method. More...
 
void CReport_Base::ResetParams (void)
 Reset Params data member. More...
 
const TParamsCReport_Base::GetParams (void) const
 Get the Params member data. More...
 
void CReport_Base::SetParams (TParams &value)
 Assign a value to Params data member. More...
 
TParamsCReport_Base::SetParams (void)
 Assign a value to Params data member. More...
 
bool CReport_Base::IsSetResults (void) const
 Check if a value has been assigned to Results data member. More...
 
bool CReport_Base::CanGetResults (void) const
 Check if it is safe to call GetResults method. More...
 
void CReport_Base::ResetResults (void)
 Reset Results data member. More...
 
const TResultsCReport_Base::GetResults (void) const
 Get the Results member data. More...
 
void CReport_Base::SetResults (TResults &value)
 Assign a value to Results data member. More...
 
TResultsCReport_Base::SetResults (void)
 Assign a value to Results data member. More...
 
virtual void CReport_Base::Reset (void)
 Reset the whole object. More...
 
 CReport_Base::CReport_Base (const CReport_Base &)
 
CReport_BaseCReport_Base::operator= (const CReport_Base &)
 
 CResults::CResults (void)
 
 CResults::~CResults (void)
 
 CResults::CResults (const CResults &value)
 
CResultsCResults::operator= (const CResults &value)
 
 CResults_Base::CResults_Base (void)
 
virtual CResults_Base::~CResults_Base (void)
 
 CResults_Base::DECLARE_INTERNAL_TYPE_INFO ()
 
virtual void CResults_Base::Reset (void)
 Reset the whole object. More...
 
virtual void CResults_Base::ResetSelection (void)
 Reset the selection (set it to e_not_set). More...
 
E_Choice CResults_Base::Which (void) const
 Which variant is currently selected. More...
 
void CResults_Base::CheckSelected (E_Choice index) const
 Verify selection, throw exception if it differs from the expected. More...
 
void CResults_Base::ThrowInvalidSelection (E_Choice index) const
 Throw 'InvalidSelection' exception. More...
 
static string CResults_Base::SelectionName (E_Choice index)
 Retrieve selection name (for diagnostic purposes). More...
 
void CResults_Base::Select (E_Choice index, EResetVariant reset=eDoResetVariant)
 Select the requested variant if needed. More...
 
void CResults_Base::Select (E_Choice index, EResetVariant reset, CObjectMemoryPool *pool)
 Select the requested variant if needed, allocating CObject variants from memory pool. More...
 
bool CResults_Base::IsIterations (void) const
 Check if variant Iterations is selected. More...
 
const TIterationsCResults_Base::GetIterations (void) const
 Get the variant data. More...
 
TIterationsCResults_Base::SetIterations (void)
 Select the variant. More...
 
bool CResults_Base::IsSearch (void) const
 Check if variant Search is selected. More...
 
const TSearchCResults_Base::GetSearch (void) const
 Get the variant data. More...
 
TSearchCResults_Base::SetSearch (void)
 Select the variant. More...
 
void CResults_Base::SetSearch (TSearch &value)
 Select the variant and set its data. More...
 
bool CResults_Base::IsBl2seq (void) const
 Check if variant Bl2seq is selected. More...
 
const TBl2seqCResults_Base::GetBl2seq (void) const
 Get the variant data. More...
 
TBl2seqCResults_Base::SetBl2seq (void)
 Select the variant. More...
 
 CResults_Base::CResults_Base (const CResults_Base &)
 
CResults_BaseCResults_Base::operator= (const CResults_Base &)
 
void CResults_Base::DoSelect (E_Choice index, CObjectMemoryPool *pool=0)
 
 CSearch< LEGACY, NHITS >::CSearch (void)
 
 CSearch< LEGACY, NHITS >::~CSearch (void)
 
 CSearch< LEGACY, NHITS >::CSearch (const CSearch &value)
 
CSearchCSearch< LEGACY, NHITS >::operator= (const CSearch &value)
 
 CSearch_Base< LEGACY, NHITS, derived_t >::CSearch_Base (void)
 
virtual CSearch_Base< LEGACY, NHITS, derived_t >::~CSearch_Base (void)
 
 CSearch_Base< LEGACY, NHITS, derived_t >::DECLARE_INTERNAL_TYPE_INFO ()
 
bool CSearch_Base< LEGACY, NHITS, derived_t >::IsSetQuery_id (void) const
 SeqId of query Check if a value has been assigned to Query_id data member. More...
 
bool CSearch_Base< LEGACY, NHITS, derived_t >::CanGetQuery_id (void) const
 Check if it is safe to call GetQuery_id method. More...
 
void CSearch_Base< LEGACY, NHITS, derived_t >::ResetQuery_id (void)
 Reset Query_id data member. More...
 
const TQuery_idCSearch_Base< LEGACY, NHITS, derived_t >::GetQuery_id (void) const
 Get the Query_id member data. More...
 
void CSearch_Base< LEGACY, NHITS, derived_t >::SetQuery_id (const TQuery_id &value)
 Assign a value to Query_id data member. More...
 
void CSearch_Base< LEGACY, NHITS, derived_t >::SetQuery_id (TQuery_id &&value)
 
TQuery_idCSearch_Base< LEGACY, NHITS, derived_t >::SetQuery_id (void)
 Assign a value to Query_id data member. More...
 
bool CSearch_Base< LEGACY, NHITS, derived_t >::IsSetQuery_title (void) const
 Definition line of query Check if a value has been assigned to Query_title data member. More...
 
bool CSearch_Base< LEGACY, NHITS, derived_t >::CanGetQuery_title (void) const
 Check if it is safe to call GetQuery_title method. More...
 
void CSearch_Base< LEGACY, NHITS, derived_t >::ResetQuery_title (void)
 Reset Query_title data member. More...
 
const TQuery_titleCSearch_Base< LEGACY, NHITS, derived_t >::GetQuery_title (void) const
 Get the Query_title member data. More...
 
void CSearch_Base< LEGACY, NHITS, derived_t >::SetQuery_title (const TQuery_title &value)
 Assign a value to Query_title data member. More...
 
void CSearch_Base< LEGACY, NHITS, derived_t >::SetQuery_title (TQuery_title &&value)
 
TQuery_titleCSearch_Base< LEGACY, NHITS, derived_t >::SetQuery_title (void)
 Assign a value to Query_title data member. More...
 
bool CSearch_Base< LEGACY, NHITS, derived_t >::IsSetQuery_len (void) const
 length of query sequence Check if a value has been assigned to Query_len data member. More...
 
bool CSearch_Base< LEGACY, NHITS, derived_t >::CanGetQuery_len (void) const
 Check if it is safe to call GetQuery_len method. More...
 
void CSearch_Base< LEGACY, NHITS, derived_t >::ResetQuery_len (void)
 Reset Query_len data member. More...
 
TQuery_len CSearch_Base< LEGACY, NHITS, derived_t >::GetQuery_len (void) const
 Get the Query_len member data. More...
 
void CSearch_Base< LEGACY, NHITS, derived_t >::SetQuery_len (TQuery_len value)
 Assign a value to Query_len data member. More...
 
TQuery_lenCSearch_Base< LEGACY, NHITS, derived_t >::SetQuery_len (void)
 Assign a value to Query_len data member. More...
 
bool CSearch_Base< LEGACY, NHITS, derived_t >::IsSetQuery_masking (void) const
 Masked offsets. More...
 
bool CSearch_Base< LEGACY, NHITS, derived_t >::CanGetQuery_masking (void) const
 Check if it is safe to call GetQuery_masking method. More...
 
void CSearch_Base< LEGACY, NHITS, derived_t >::ResetQuery_masking (void)
 Reset Query_masking data member. More...
 
const TQuery_maskingCSearch_Base< LEGACY, NHITS, derived_t >::GetQuery_masking (void) const
 Get the Query_masking member data. More...
 
TQuery_maskingCSearch_Base< LEGACY, NHITS, derived_t >::SetQuery_masking (void)
 Assign a value to Query_masking data member. More...
 
bool CSearch_Base< LEGACY, NHITS, derived_t >::IsSetHits (void) const
 Hits one for every db sequence Check if a value has been assigned to Hits data member. More...
 
bool CSearch_Base< LEGACY, NHITS, derived_t >::CanGetHits (void) const
 Check if it is safe to call GetHits method. More...
 
void CSearch_Base< LEGACY, NHITS, derived_t >::ResetHits (void)
 Reset Hits data member. More...
 
const THitsCSearch_Base< LEGACY, NHITS, derived_t >::GetHits (void) const
 Get the Hits member data. More...
 
THitsCSearch_Base< LEGACY, NHITS, derived_t >::SetHits (void)
 Assign a value to Hits data member. More...
 
bool CSearch_Base< LEGACY, NHITS, derived_t >::IsSetStat (void) const
 search statistics Check if a value has been assigned to Stat data member. More...
 
bool CSearch_Base< LEGACY, NHITS, derived_t >::CanGetStat (void) const
 Check if it is safe to call GetStat method. More...
 
void CSearch_Base< LEGACY, NHITS, derived_t >::ResetStat (void)
 Reset Stat data member. More...
 
const TStatCSearch_Base< LEGACY, NHITS, derived_t >::GetStat (void) const
 Get the Stat member data. More...
 
void CSearch_Base< LEGACY, NHITS, derived_t >::SetStat (TStat &value)
 Assign a value to Stat data member. More...
 
TStatCSearch_Base< LEGACY, NHITS, derived_t >::SetStat (void)
 Assign a value to Stat data member. More...
 
bool CSearch_Base< LEGACY, NHITS, derived_t >::IsSetMessage (void) const
 Some (error?) information Check if a value has been assigned to Message data member. More...
 
bool CSearch_Base< LEGACY, NHITS, derived_t >::CanGetMessage (void) const
 Check if it is safe to call GetMessage method. More...
 
void CSearch_Base< LEGACY, NHITS, derived_t >::ResetMessage (void)
 Reset Message data member. More...
 
const TMessageCSearch_Base< LEGACY, NHITS, derived_t >::GetMessage (void) const
 Get the Message member data. More...
 
void CSearch_Base< LEGACY, NHITS, derived_t >::SetMessage (const TMessage &value)
 Assign a value to Message data member. More...
 
void CSearch_Base< LEGACY, NHITS, derived_t >::SetMessage (TMessage &&value)
 
TMessageCSearch_Base< LEGACY, NHITS, derived_t >::SetMessage (void)
 Assign a value to Message data member. More...
 
virtual void CSearch_Base< LEGACY, NHITS, derived_t >::Reset (void)
 Reset the whole object. More...
 
 CSearch_Base< LEGACY, NHITS, derived_t >::CSearch_Base (const CSearch_Base &)
 
CSearch_BaseCSearch_Base< LEGACY, NHITS, derived_t >::operator= (const CSearch_Base &)
 
 CStatistics::CStatistics (void)
 
 CStatistics::~CStatistics (void)
 
 CStatistics::CStatistics (const CStatistics &value)
 
CStatisticsCStatistics::operator= (const CStatistics &value)
 
 CStatistics_Base::CStatistics_Base (void)
 
virtual CStatistics_Base::~CStatistics_Base (void)
 
 CStatistics_Base::DECLARE_INTERNAL_TYPE_INFO ()
 
bool CStatistics_Base::IsSetDb_num (void) const
 Number of sequences in BLAST db Check if a value has been assigned to Db_num data member. More...
 
bool CStatistics_Base::CanGetDb_num (void) const
 Check if it is safe to call GetDb_num method. More...
 
void CStatistics_Base::ResetDb_num (void)
 Reset Db_num data member. More...
 
TDb_num CStatistics_Base::GetDb_num (void) const
 Get the Db_num member data. More...
 
void CStatistics_Base::SetDb_num (TDb_num value)
 Assign a value to Db_num data member. More...
 
TDb_numCStatistics_Base::SetDb_num (void)
 Assign a value to Db_num data member. More...
 
bool CStatistics_Base::IsSetDb_len (void) const
 Length of BLAST db Check if a value has been assigned to Db_len data member. More...
 
bool CStatistics_Base::CanGetDb_len (void) const
 Check if it is safe to call GetDb_len method. More...
 
void CStatistics_Base::ResetDb_len (void)
 Reset Db_len data member. More...
 
TDb_len CStatistics_Base::GetDb_len (void) const
 Get the Db_len member data. More...
 
void CStatistics_Base::SetDb_len (TDb_len value)
 Assign a value to Db_len data member. More...
 
TDb_lenCStatistics_Base::SetDb_len (void)
 Assign a value to Db_len data member. More...
 
bool CStatistics_Base::IsSetHsp_len (void) const
 Effective HSP length Check if a value has been assigned to Hsp_len data member. More...
 
bool CStatistics_Base::CanGetHsp_len (void) const
 Check if it is safe to call GetHsp_len method. More...
 
void CStatistics_Base::ResetHsp_len (void)
 Reset Hsp_len data member. More...
 
THsp_len CStatistics_Base::GetHsp_len (void) const
 Get the Hsp_len member data. More...
 
void CStatistics_Base::SetHsp_len (THsp_len value)
 Assign a value to Hsp_len data member. More...
 
THsp_lenCStatistics_Base::SetHsp_len (void)
 Assign a value to Hsp_len data member. More...
 
bool CStatistics_Base::IsSetEff_space (void) const
 Effective search space Check if a value has been assigned to Eff_space data member. More...
 
bool CStatistics_Base::CanGetEff_space (void) const
 Check if it is safe to call GetEff_space method. More...
 
void CStatistics_Base::ResetEff_space (void)
 Reset Eff_space data member. More...
 
TEff_space CStatistics_Base::GetEff_space (void) const
 Get the Eff_space member data. More...
 
void CStatistics_Base::SetEff_space (TEff_space value)
 Assign a value to Eff_space data member. More...
 
TEff_spaceCStatistics_Base::SetEff_space (void)
 Assign a value to Eff_space data member. More...
 
bool CStatistics_Base::IsSetKappa (void) const
 Karlin-Altschul parameter K Check if a value has been assigned to Kappa data member. More...
 
bool CStatistics_Base::CanGetKappa (void) const
 Check if it is safe to call GetKappa method. More...
 
void CStatistics_Base::ResetKappa (void)
 Reset Kappa data member. More...
 
TKappa CStatistics_Base::GetKappa (void) const
 Get the Kappa member data. More...
 
void CStatistics_Base::SetKappa (TKappa value)
 Assign a value to Kappa data member. More...
 
TKappaCStatistics_Base::SetKappa (void)
 Assign a value to Kappa data member. More...
 
bool CStatistics_Base::IsSetLambda (void) const
 Karlin-Altschul parameter Lambda Check if a value has been assigned to Lambda data member. More...
 
bool CStatistics_Base::CanGetLambda (void) const
 Check if it is safe to call GetLambda method. More...
 
void CStatistics_Base::ResetLambda (void)
 Reset Lambda data member. More...
 
TLambda CStatistics_Base::GetLambda (void) const
 Get the Lambda member data. More...
 
void CStatistics_Base::SetLambda (TLambda value)
 Assign a value to Lambda data member. More...
 
TLambdaCStatistics_Base::SetLambda (void)
 Assign a value to Lambda data member. More...
 
bool CStatistics_Base::IsSetEntropy (void) const
 Karlin-Altschul parameter H Check if a value has been assigned to Entropy data member. More...
 
bool CStatistics_Base::CanGetEntropy (void) const
 Check if it is safe to call GetEntropy method. More...
 
void CStatistics_Base::ResetEntropy (void)
 Reset Entropy data member. More...
 
TEntropy CStatistics_Base::GetEntropy (void) const
 Get the Entropy member data. More...
 
void CStatistics_Base::SetEntropy (TEntropy value)
 Assign a value to Entropy data member. More...
 
TEntropyCStatistics_Base::SetEntropy (void)
 Assign a value to Entropy data member. More...
 
virtual void CStatistics_Base::Reset (void)
 Reset the whole object. More...
 
 CStatistics_Base::CStatistics_Base (const CStatistics_Base &)
 
CStatistics_BaseCStatistics_Base::operator= (const CStatistics_Base &)
 
 CTarget::CTarget (void)
 
 CTarget::~CTarget (void)
 
 CTarget::CTarget (const CTarget &value)
 
CTargetCTarget::operator= (const CTarget &value)
 
 CTarget_Base::CTarget_Base (void)
 
virtual CTarget_Base::~CTarget_Base (void)
 
 CTarget_Base::DECLARE_INTERNAL_TYPE_INFO ()
 
virtual void CTarget_Base::Reset (void)
 Reset the whole object. More...
 
virtual void CTarget_Base::ResetSelection (void)
 Reset the selection (set it to e_not_set). More...
 
E_Choice CTarget_Base::Which (void) const
 Which variant is currently selected. More...
 
void CTarget_Base::CheckSelected (E_Choice index) const
 Verify selection, throw exception if it differs from the expected. More...
 
void CTarget_Base::ThrowInvalidSelection (E_Choice index) const
 Throw 'InvalidSelection' exception. More...
 
static string CTarget_Base::SelectionName (E_Choice index)
 Retrieve selection name (for diagnostic purposes). More...
 
void CTarget_Base::Select (E_Choice index, EResetVariant reset=eDoResetVariant)
 Select the requested variant if needed. More...
 
void CTarget_Base::Select (E_Choice index, EResetVariant reset, CObjectMemoryPool *pool)
 Select the requested variant if needed, allocating CObject variants from memory pool. More...
 
bool CTarget_Base::IsDb (void) const
 Check if variant Db is selected. More...
 
const TDbCTarget_Base::GetDb (void) const
 Get the variant data. More...
 
TDbCTarget_Base::SetDb (void)
 Select the variant. More...
 
void CTarget_Base::SetDb (const TDb &value)
 Select the variant and set its data. More...
 
bool CTarget_Base::IsSubjects (void) const
 Check if variant Subjects is selected. More...
 
const TSubjectsCTarget_Base::GetSubjects (void) const
 Get the variant data. More...
 
TSubjectsCTarget_Base::SetSubjects (void)
 Select the variant. More...
 
 CTarget_Base::CTarget_Base (const CTarget_Base &)
 
CTarget_BaseCTarget_Base::operator= (const CTarget_Base &)
 
void CTarget_Base::DoSelect (E_Choice index, CObjectMemoryPool *pool=0)
 

Variables

Uint4 CBlastOutput2_Base::m_set_State [1]
 
CRef< TReportCBlastOutput2_Base::m_Report
 
CRef< TErrorCBlastOutput2_Base::m_Error
 
Uint4 CBlastXML2_Base::m_set_State [1]
 
list< CRef< CBlastOutput2 > > CBlastXML2_Base::m_data
 
Uint4 CErr_Base::m_set_State [1]
 
int CErr_Base::m_Code
 
string CErr_Base::m_Message
 
list< CRef< CHitDescr > > CHit_Base::m_Description
 
Uint4 CHitDescr_Base::m_set_State [1]
 
string CHitDescr_Base::m_Id
 
string CHitDescr_Base::m_Accession
 
string CHitDescr_Base::m_Title
 
int CHitDescr_Base::m_Taxid
 
string CHitDescr_Base::m_Sciname
 
string CHsp_Base::m_Query_strand
 
string CHsp_Base::m_Hit_strand
 
CRef< TSearchCIteration_Base::m_Search
 
int CParameters_Base::m_Cbs
 
int CParameters_Base::m_Query_gencode
 
int CParameters_Base::m_Db_gencode
 
string CParameters_Base::m_Bl2seq_mode
 
Uint4 CRange_Base::m_set_State [1]
 
int CRange_Base::m_From
 
int CRange_Base::m_To
 
Uint4 CReport_Base::m_set_State [1]
 
string CReport_Base::m_Program
 
string CReport_Base::m_Version
 
string CReport_Base::m_Reference
 
CRef< TSearch_targetCReport_Base::m_Search_target
 
CRef< TParamsCReport_Base::m_Params
 
CRef< TResultsCReport_Base::m_Results
 
E_Choice CResults_Base::m_choice
 
static const char *const CResults_Base::sm_SelectionNames []
 
NCBI_NS_NCBI::CUnionBuffer< TIterations >   CResults_Base::m_Iterations
 
NCBI_NS_NCBI::CUnionBuffer< TBl2seq >   CResults_Base::m_Bl2seq
 
NCBI_NS_NCBI::CSerialObject *   CResults_Base::m_object
 
union {
   NCBI_NS_NCBI::CUnionBuffer< TIterations >   CResults_Base::m_Iterations
 
   NCBI_NS_NCBI::CUnionBuffer< TBl2seq >   CResults_Base::m_Bl2seq
 
   NCBI_NS_NCBI::CSerialObject *   CResults_Base::m_object
 
}; 
 
Uint4 CSearch_Base< LEGACY, NHITS, derived_t >::m_set_State [1]
 
string CSearch_Base< LEGACY, NHITS, derived_t >::m_Query_id
 
string CSearch_Base< LEGACY, NHITS, derived_t >::m_Query_title
 
int CSearch_Base< LEGACY, NHITS, derived_t >::m_Query_len
 
list< CRef< CRange > > CSearch_Base< LEGACY, NHITS, derived_t >::m_Query_masking
 
list< CRef< CHit > > CSearch_Base< LEGACY, NHITS, derived_t >::m_Hits
 
CRef< TStatCSearch_Base< LEGACY, NHITS, derived_t >::m_Stat
 
string CSearch_Base< LEGACY, NHITS, derived_t >::m_Message
 
Int8 CStatistics_Base::m_Db_num
 
Int8 CStatistics_Base::m_Eff_space
 
E_Choice CTarget_Base::m_choice
 
static const char *const CTarget_Base::sm_SelectionNames []
 
NCBI_NS_NCBI::CUnionBuffer< TSubjects >   CTarget_Base::m_Subjects
 
NCBI_NS_NCBI::CUnionBuffer< NCBI_NS_STD::string >   CTarget_Base::m_string
 
void *   CTarget_Base::m_dummy_pointer_for_alignment
 
union {
   NCBI_NS_NCBI::CUnionBuffer< TSubjects >   CTarget_Base::m_Subjects
 
   NCBI_NS_NCBI::CUnionBuffer< NCBI_NS_STD::string >   CTarget_Base::m_string
 
   void *   CTarget_Base::m_dummy_pointer_for_alignment
 
}; 
 

Detailed Description

Typedef Documentation

◆ TAccession

Definition at line 93 of file HitDescr_.hpp.

◆ TAlign_len

Definition at line 108 of file Hsp_.hpp.

◆ TBit_score

typedef double CHsp_Base::TBit_score

Definition at line 92 of file Hsp_.hpp.

◆ TBl2seq

typedef list< CRef< CSearch > > CResults_Base::TBl2seq

Definition at line 158 of file Results_.hpp.

◆ TBl2seq_mode

Definition at line 104 of file Parameters_.hpp.

◆ TCbs

Definition at line 101 of file Parameters_.hpp.

◆ TCode

Definition at line 91 of file Err_.hpp.

◆ Tdata

Definition at line 95 of file BlastXML2_.hpp.

◆ TDb

Definition at line 151 of file Target_.hpp.

◆ TDb_gencode

Definition at line 103 of file Parameters_.hpp.

◆ TDb_len

Definition at line 88 of file Statistics_.hpp.

◆ TDb_num

Definition at line 87 of file Statistics_.hpp.

◆ TDensity

Definition at line 97 of file Hsp_.hpp.

◆ TDescription

Definition at line 97 of file Hit_.hpp.

◆ TEff_space

Definition at line 90 of file Statistics_.hpp.

◆ TEntrez_query

Definition at line 100 of file Parameters_.hpp.

◆ TEntropy

Definition at line 93 of file Statistics_.hpp.

◆ TError

Definition at line 93 of file BlastOutput2_.hpp.

◆ TEvalue

typedef double CHsp_Base::TEvalue

Definition at line 94 of file Hsp_.hpp.

◆ TExpect

typedef double CParameters_Base::TExpect

Definition at line 92 of file Parameters_.hpp.

◆ TFilter

Definition at line 98 of file Parameters_.hpp.

◆ TFrom

Definition at line 88 of file Range_.hpp.

◆ TGap_extend

Definition at line 97 of file Parameters_.hpp.

◆ TGap_open

Definition at line 96 of file Parameters_.hpp.

◆ TGaps

Definition at line 109 of file Hsp_.hpp.

◆ THit_frame

Definition at line 107 of file Hsp_.hpp.

◆ THit_from

Definition at line 104 of file Hsp_.hpp.

◆ THit_strand

Definition at line 106 of file Hsp_.hpp.

◆ THit_to

Definition at line 105 of file Hsp_.hpp.

◆ THits

template<bool LEGACY, unsigned long NHITS, typename derived_t >
typedef list< CRef< CHit > > CSearch_Base< LEGACY, NHITS, derived_t >::THits

Definition at line 102 of file Search_.hpp.

◆ THseq

Definition at line 111 of file Hsp_.hpp.

◆ THsp_len

Definition at line 89 of file Statistics_.hpp.

◆ THsps

typedef list< CRef< CHsp > > CHit_Base::THsps

Definition at line 99 of file Hit_.hpp.

◆ TId

Definition at line 92 of file HitDescr_.hpp.

◆ TIdentity

Definition at line 95 of file Hsp_.hpp.

◆ TInclude

Definition at line 93 of file Parameters_.hpp.

◆ TIter_num

Definition at line 91 of file Iteration_.hpp.

◆ TIterations

Definition at line 156 of file Results_.hpp.

◆ TKappa

typedef double CStatistics_Base::TKappa

Definition at line 91 of file Statistics_.hpp.

◆ TLambda

typedef double CStatistics_Base::TLambda

Definition at line 92 of file Statistics_.hpp.

◆ TLen

Definition at line 98 of file Hit_.hpp.

◆ TMatrix

Definition at line 91 of file Parameters_.hpp.

◆ TmemberIndex [1/11]

Definition at line 101 of file BlastOutput2_.hpp.

◆ TmemberIndex [2/11]

Definition at line 100 of file Err_.hpp.

◆ TmemberIndex [3/11]

Definition at line 109 of file Hit_.hpp.

◆ TmemberIndex [4/11]

Definition at line 107 of file HitDescr_.hpp.

◆ TmemberIndex [5/11]

Definition at line 140 of file Hsp_.hpp.

◆ TmemberIndex [6/11]

Definition at line 100 of file Iteration_.hpp.

◆ TmemberIndex [7/11]

Definition at line 124 of file Parameters_.hpp.

◆ TmemberIndex [8/11]

Definition at line 97 of file Range_.hpp.

◆ TmemberIndex [9/11]

Definition at line 114 of file Report_.hpp.

◆ TmemberIndex [10/11]

template<bool LEGACY, unsigned long NHITS, typename derived_t >
typedef Tparent::CMemberIndex<E_memberIndex, 8> CSearch_Base< LEGACY, NHITS, derived_t >::TmemberIndex

Definition at line 117 of file Search_.hpp.

◆ TmemberIndex [11/11]

Definition at line 106 of file Statistics_.hpp.

◆ TMessage [1/2]

Definition at line 92 of file Err_.hpp.

◆ TMessage [2/2]

template<bool LEGACY, unsigned long NHITS, typename derived_t >
typedef string CSearch_Base< LEGACY, NHITS, derived_t >::TMessage

Definition at line 104 of file Search_.hpp.

◆ TMidline

Definition at line 112 of file Hsp_.hpp.

◆ TNum [1/2]

Definition at line 96 of file Hit_.hpp.

◆ TNum [2/2]

Definition at line 91 of file Hsp_.hpp.

◆ TParams

Definition at line 101 of file Report_.hpp.

◆ Tparent [1/28]

Definition at line 69 of file BlastOutput2.hpp.

◆ Tparent [2/28]

Definition at line 81 of file BlastOutput2_.hpp.

◆ Tparent [3/28]

Definition at line 69 of file BlastXML2.hpp.

◆ Tparent [4/28]

Definition at line 84 of file BlastXML2_.hpp.

◆ Tparent [5/28]

typedef CErr_Base CErr::Tparent
private

Definition at line 69 of file Err.hpp.

◆ Tparent [6/28]

Definition at line 80 of file Err_.hpp.

◆ Tparent [7/28]

typedef CHit_Base CHit::Tparent
private

Definition at line 69 of file Hit.hpp.

◆ Tparent [8/28]

Definition at line 85 of file Hit_.hpp.

◆ Tparent [9/28]

Definition at line 69 of file HitDescr.hpp.

◆ Tparent [10/28]

Definition at line 81 of file HitDescr_.hpp.

◆ Tparent [11/28]

typedef CHsp_Base CHsp::Tparent
private

Definition at line 69 of file Hsp.hpp.

◆ Tparent [12/28]

Definition at line 80 of file Hsp_.hpp.

◆ Tparent [13/28]

Definition at line 69 of file Iteration.hpp.

◆ Tparent [14/28]

Definition at line 80 of file Iteration_.hpp.

◆ Tparent [15/28]

Definition at line 69 of file Parameters.hpp.

◆ Tparent [16/28]

Definition at line 80 of file Parameters_.hpp.

◆ Tparent [17/28]

template<class Position >
typedef CRange_Base CRange< Position >::Tparent
private

Definition at line 69 of file Range.hpp.

◆ Tparent [18/28]

Definition at line 77 of file Range_.hpp.

◆ Tparent [19/28]

typedef CReport_Base CReport::Tparent
private

Definition at line 69 of file Report.hpp.

◆ Tparent [20/28]

Definition at line 86 of file Report_.hpp.

◆ Tparent [21/28]

Definition at line 69 of file Results.hpp.

◆ Tparent [22/28]

Definition at line 85 of file Results_.hpp.

◆ Tparent [23/28]

template<bool LEGACY, unsigned long NHITS>
typedef CSearch_Base CSearch< LEGACY, NHITS >::Tparent
private

Definition at line 69 of file Search.hpp.

◆ Tparent [24/28]

template<bool LEGACY, unsigned long NHITS, typename derived_t >
typedef CSerialObject CSearch_Base< LEGACY, NHITS, derived_t >::Tparent
private

Definition at line 87 of file Search_.hpp.

◆ Tparent [25/28]

Definition at line 69 of file Statistics.hpp.

◆ Tparent [26/28]

Definition at line 76 of file Statistics_.hpp.

◆ Tparent [27/28]

typedef CTarget_Base CTarget::Tparent
private

Definition at line 69 of file Target.hpp.

◆ Tparent [28/28]

Definition at line 81 of file Target_.hpp.

◆ TPattern

Definition at line 99 of file Parameters_.hpp.

◆ TPattern_from

Definition at line 98 of file Hsp_.hpp.

◆ TPattern_to

Definition at line 99 of file Hsp_.hpp.

◆ TPositive

Definition at line 96 of file Hsp_.hpp.

◆ TProgram

Definition at line 97 of file Report_.hpp.

◆ TQseq

Definition at line 110 of file Hsp_.hpp.

◆ TQuery_frame

Definition at line 103 of file Hsp_.hpp.

◆ TQuery_from

Definition at line 100 of file Hsp_.hpp.

◆ TQuery_gencode

Definition at line 102 of file Parameters_.hpp.

◆ TQuery_id

template<bool LEGACY, unsigned long NHITS, typename derived_t >
typedef string CSearch_Base< LEGACY, NHITS, derived_t >::TQuery_id

Definition at line 98 of file Search_.hpp.

◆ TQuery_len

template<bool LEGACY, unsigned long NHITS, typename derived_t >
typedef int CSearch_Base< LEGACY, NHITS, derived_t >::TQuery_len

Definition at line 100 of file Search_.hpp.

◆ TQuery_masking

template<bool LEGACY, unsigned long NHITS, typename derived_t >
typedef list< CRef< CRange > > CSearch_Base< LEGACY, NHITS, derived_t >::TQuery_masking

Definition at line 101 of file Search_.hpp.

◆ TQuery_strand

Definition at line 102 of file Hsp_.hpp.

◆ TQuery_title

template<bool LEGACY, unsigned long NHITS, typename derived_t >
typedef string CSearch_Base< LEGACY, NHITS, derived_t >::TQuery_title

Definition at line 99 of file Search_.hpp.

◆ TQuery_to

Definition at line 101 of file Hsp_.hpp.

◆ TReference

Definition at line 99 of file Report_.hpp.

◆ TReport

Definition at line 92 of file BlastOutput2_.hpp.

◆ TResults

Definition at line 102 of file Report_.hpp.

◆ TSc_match

Definition at line 94 of file Parameters_.hpp.

◆ TSc_mismatch

Definition at line 95 of file Parameters_.hpp.

◆ TSciname

Definition at line 96 of file HitDescr_.hpp.

◆ TScore

typedef double CHsp_Base::TScore

Definition at line 93 of file Hsp_.hpp.

◆ TSearch [1/2]

Definition at line 92 of file Iteration_.hpp.

◆ TSearch [2/2]

Definition at line 157 of file Results_.hpp.

◆ TSearch_target

Definition at line 100 of file Report_.hpp.

◆ TStat

template<bool LEGACY, unsigned long NHITS, typename derived_t >
typedef CStatistics CSearch_Base< LEGACY, NHITS, derived_t >::TStat

Definition at line 103 of file Search_.hpp.

◆ TSubjects

Definition at line 152 of file Target_.hpp.

◆ TTaxid

Definition at line 95 of file HitDescr_.hpp.

◆ TTitle

Definition at line 94 of file HitDescr_.hpp.

◆ TTo

Definition at line 89 of file Range_.hpp.

◆ TVersion

Definition at line 98 of file Report_.hpp.

Enumeration Type Documentation

◆ E_Choice [1/2]

Choice variants.

Enumerator
e_not_set 

No variant selected.

e_Iterations 
e_Search 

iterative search (psi and delta blast) db search

e_Bl2seq 

bl2seq

Definition at line 97 of file Results_.hpp.

◆ E_Choice [2/2]

Choice variants.

Enumerator
e_not_set 

No variant selected.

e_Db 

BLAST Database name.

e_Subjects 

Subject IDs.

Definition at line 93 of file Target_.hpp.

◆ E_ChoiceStopper [1/2]

Maximum+1 value of the choice variant enumerator.

Enumerator
e_MaxChoice 

== e_Bl2seq+1

Definition at line 104 of file Results_.hpp.

◆ E_ChoiceStopper [2/2]

Maximum+1 value of the choice variant enumerator.

Enumerator
e_MaxChoice 

== e_Subjects+1

Definition at line 99 of file Target_.hpp.

◆ E_memberIndex [1/11]

Enumerator
e__allMandatory 
e_report 
e_error 

Definition at line 96 of file BlastOutput2_.hpp.

◆ E_memberIndex [2/11]

Enumerator
e__allMandatory 
e_code 
e_message 

Definition at line 95 of file Err_.hpp.

◆ E_memberIndex [3/11]

Enumerator
e__allMandatory 
e_num 
e_id 
e_def 
e_accession 
e_len 
e_hsps 
e__allMandatory 
e_num 
e_description 
e_len 
e_hsps 

Definition at line 102 of file Hit_.hpp.

◆ E_memberIndex [4/11]

Enumerator
e__allMandatory 
e_id 
e_accession 
e_title 
e_taxid 
e_sciname 

Definition at line 99 of file HitDescr_.hpp.

◆ E_memberIndex [5/11]

Enumerator
e__allMandatory 
e_num 
e_bit_score 
e_score 
e_evalue 
e_query_from 
e_query_to 
e_hit_from 
e_hit_to 
e_pattern_from 
e_pattern_to 
e_query_frame 
e_hit_frame 
e_identity 
e_positive 
e_gaps 
e_align_len 
e_density 
e_qseq 
e_hseq 
e_midline 
e__allMandatory 
e_num 
e_bit_score 
e_score 
e_evalue 
e_identity 
e_positive 
e_density 
e_pattern_from 
e_pattern_to 
e_query_from 
e_query_to 
e_query_strand 
e_query_frame 
e_hit_from 
e_hit_to 
e_hit_strand 
e_hit_frame 
e_align_len 
e_gaps 
e_qseq 
e_hseq 
e_midline 

Definition at line 115 of file Hsp_.hpp.

◆ E_memberIndex [6/11]

Enumerator
e__allMandatory 
e_iter_num 
e_query_ID 
e_query_def 
e_query_len 
e_hits 
e_stat 
e_message 
e__allMandatory 
e_iter_num 
e_search 

Definition at line 95 of file Iteration_.hpp.

◆ E_memberIndex [7/11]

Enumerator
e__allMandatory 
e_matrix 
e_expect 
e_include 
e_sc_match 
e_sc_mismatch 
e_gap_open 
e_gap_extend 
e_filter 
e_pattern 
e_entrez_query 
e__allMandatory 
e_matrix 
e_expect 
e_include 
e_sc_match 
e_sc_mismatch 
e_gap_open 
e_gap_extend 
e_filter 
e_pattern 
e_entrez_query 
e_cbs 
e_query_gencode 
e_db_gencode 
e_bl2seq_mode 

Definition at line 107 of file Parameters_.hpp.

◆ E_memberIndex [8/11]

Enumerator
e__allMandatory 
e_from 
e_to 

Definition at line 92 of file Range_.hpp.

◆ E_memberIndex [9/11]

Enumerator
e__allMandatory 
e_program 
e_version 
e_reference 
e_search_target 
e_params 
e_results 

Definition at line 105 of file Report_.hpp.

◆ E_memberIndex [10/11]

template<bool LEGACY, unsigned long NHITS, typename derived_t >
enum CSearch_Base::E_memberIndex
strong
Enumerator
e__allMandatory 
e_query_id 
e_query_title 
e_query_len 
e_query_masking 
e_hits 
e_stat 
e_message 

Definition at line 107 of file Search_.hpp.

◆ E_memberIndex [11/11]

Enumerator
e__allMandatory 
e_db_num 
e_db_len 
e_hsp_len 
e_eff_space 
e_kappa 
e_lambda 
e_entropy 
e__allMandatory 
e_db_num 
e_db_len 
e_hsp_len 
e_eff_space 
e_kappa 
e_lambda 
e_entropy 

Definition at line 96 of file Statistics_.hpp.

Function Documentation

◆ CanGet()

bool CBlastXML2_Base::CanGet ( void  ) const
inline

Check if it is safe to call Get method.

Returns
  • true, if the data member is getatable.
  • false, otherwise.

Definition at line 164 of file BlastXML2_.hpp.

◆ CanGetAccession()

bool CHitDescr_Base::CanGetAccession ( void  ) const
inline

Check if it is safe to call GetAccession method.

Returns
  • true, if the data member is getatable.
  • false, otherwise.

Definition at line 387 of file HitDescr_.hpp.

References CHitDescr_Base::IsSetAccession().

Referenced by CHitDescr_Base::GetAccession().

◆ CanGetAlign_len()

bool CHsp_Base::CanGetAlign_len ( void  ) const

Check if it is safe to call GetAlign_len method.

Returns
  • true, if the data member is getatable.
  • false, otherwise.

◆ CanGetBit_score()

bool CHsp_Base::CanGetBit_score ( void  ) const

Check if it is safe to call GetBit_score method.

Returns
  • true, if the data member is getatable.
  • false, otherwise.

◆ CanGetBl2seq_mode()

bool CParameters_Base::CanGetBl2seq_mode ( void  ) const
inline

Check if it is safe to call GetBl2seq_mode method.

Returns
  • true, if the data member is getatable.
  • false, otherwise.

Definition at line 1321 of file Parameters_.hpp.

References CParameters_Base::IsSetBl2seq_mode().

Referenced by CParameters_Base::GetBl2seq_mode().

◆ CanGetCbs()

bool CParameters_Base::CanGetCbs ( void  ) const
inline

Check if it is safe to call GetCbs method.

Returns
  • true, if the data member is getatable.
  • false, otherwise.

Definition at line 1180 of file Parameters_.hpp.

References CParameters_Base::IsSetCbs().

Referenced by CParameters_Base::GetCbs().

◆ CanGetCode()

bool CErr_Base::CanGetCode ( void  ) const
inline

Check if it is safe to call GetCode method.

Returns
  • true, if the data member is getatable.
  • false, otherwise.

Definition at line 211 of file Err_.hpp.

References CErr_Base::IsSetCode().

Referenced by CErr_Base::GetCode().

◆ CanGetDb_gencode()

bool CParameters_Base::CanGetDb_gencode ( void  ) const
inline

Check if it is safe to call GetDb_gencode method.

Returns
  • true, if the data member is getatable.
  • false, otherwise.

Definition at line 1274 of file Parameters_.hpp.

References CParameters_Base::IsSetDb_gencode().

Referenced by CParameters_Base::GetDb_gencode().

◆ CanGetDb_len()

bool CStatistics_Base::CanGetDb_len ( void  ) const

Check if it is safe to call GetDb_len method.

Returns
  • true, if the data member is getatable.
  • false, otherwise.

◆ CanGetDb_num()

bool CStatistics_Base::CanGetDb_num ( void  ) const

Check if it is safe to call GetDb_num method.

Returns
  • true, if the data member is getatable.
  • false, otherwise.

◆ CanGetDensity()

bool CHsp_Base::CanGetDensity ( void  ) const

Check if it is safe to call GetDensity method.

Returns
  • true, if the data member is getatable.
  • false, otherwise.

◆ CanGetDescription()

bool CHit_Base::CanGetDescription ( void  ) const
inline

Check if it is safe to call GetDescription method.

Returns
  • true, if the data member is getatable.
  • false, otherwise.

Definition at line 334 of file Hit_.hpp.

◆ CanGetEff_space()

bool CStatistics_Base::CanGetEff_space ( void  ) const

Check if it is safe to call GetEff_space method.

Returns
  • true, if the data member is getatable.
  • false, otherwise.

◆ CanGetEntrez_query()

bool CParameters_Base::CanGetEntrez_query ( void  ) const

Check if it is safe to call GetEntrez_query method.

Returns
  • true, if the data member is getatable.
  • false, otherwise.

◆ CanGetEntropy()

bool CStatistics_Base::CanGetEntropy ( void  ) const

Check if it is safe to call GetEntropy method.

Returns
  • true, if the data member is getatable.
  • false, otherwise.

◆ CanGetError()

bool CBlastOutput2_Base::CanGetError ( void  ) const
inline

Check if it is safe to call GetError method.

Returns
  • true, if the data member is getatable.
  • false, otherwise.

Definition at line 232 of file BlastOutput2_.hpp.

References CBlastOutput2_Base::IsSetError().

Referenced by CBlastOutput2_Base::GetError().

◆ CanGetEvalue()

bool CHsp_Base::CanGetEvalue ( void  ) const

Check if it is safe to call GetEvalue method.

Returns
  • true, if the data member is getatable.
  • false, otherwise.

◆ CanGetExpect()

bool CParameters_Base::CanGetExpect ( void  ) const

Check if it is safe to call GetExpect method.

Returns
  • true, if the data member is getatable.
  • false, otherwise.

◆ CanGetFilter()

bool CParameters_Base::CanGetFilter ( void  ) const

Check if it is safe to call GetFilter method.

Returns
  • true, if the data member is getatable.
  • false, otherwise.

◆ CanGetFrom()

bool CRange_Base::CanGetFrom ( void  ) const
inline

Check if it is safe to call GetFrom method.

Returns
  • true, if the data member is getatable.
  • false, otherwise.

Definition at line 209 of file Range_.hpp.

References CRange_Base::IsSetFrom().

Referenced by CRange_Base::GetFrom().

◆ CanGetGap_extend()

bool CParameters_Base::CanGetGap_extend ( void  ) const

Check if it is safe to call GetGap_extend method.

Returns
  • true, if the data member is getatable.
  • false, otherwise.

◆ CanGetGap_open()

bool CParameters_Base::CanGetGap_open ( void  ) const

Check if it is safe to call GetGap_open method.

Returns
  • true, if the data member is getatable.
  • false, otherwise.

◆ CanGetGaps()

bool CHsp_Base::CanGetGaps ( void  ) const

Check if it is safe to call GetGaps method.

Returns
  • true, if the data member is getatable.
  • false, otherwise.

◆ CanGetHit_frame()

bool CHsp_Base::CanGetHit_frame ( void  ) const

Check if it is safe to call GetHit_frame method.

Returns
  • true, if the data member is getatable.
  • false, otherwise.

◆ CanGetHit_from()

bool CHsp_Base::CanGetHit_from ( void  ) const

Check if it is safe to call GetHit_from method.

Returns
  • true, if the data member is getatable.
  • false, otherwise.

◆ CanGetHit_strand()

bool CHsp_Base::CanGetHit_strand ( void  ) const
inline

Check if it is safe to call GetHit_strand method.

Returns
  • true, if the data member is getatable.
  • false, otherwise.

Definition at line 1742 of file Hsp_.hpp.

References CHsp_Base::IsSetHit_strand().

Referenced by CHsp_Base::GetHit_strand().

◆ CanGetHit_to()

bool CHsp_Base::CanGetHit_to ( void  ) const

Check if it is safe to call GetHit_to method.

Returns
  • true, if the data member is getatable.
  • false, otherwise.

◆ CanGetHits()

template<bool LEGACY, unsigned long NHITS, typename derived_t >
bool CSearch_Base< LEGACY, NHITS, derived_t >::CanGetHits ( void  ) const
inline

Check if it is safe to call GetHits method.

Returns
  • true, if the data member is getatable.
  • false, otherwise.

Definition at line 581 of file Search_.hpp.

◆ CanGetHseq()

bool CHsp_Base::CanGetHseq ( void  ) const

Check if it is safe to call GetHseq method.

Returns
  • true, if the data member is getatable.
  • false, otherwise.

◆ CanGetHsp_len()

bool CStatistics_Base::CanGetHsp_len ( void  ) const

Check if it is safe to call GetHsp_len method.

Returns
  • true, if the data member is getatable.
  • false, otherwise.

◆ CanGetHsps()

bool CHit_Base::CanGetHsps ( void  ) const

Check if it is safe to call GetHsps method.

Returns
  • true, if the data member is getatable.
  • false, otherwise.

◆ CanGetId()

bool CHitDescr_Base::CanGetId ( void  ) const
inline

Check if it is safe to call GetId method.

Returns
  • true, if the data member is getatable.
  • false, otherwise.

Definition at line 340 of file HitDescr_.hpp.

References CHitDescr_Base::IsSetId().

Referenced by CHitDescr_Base::GetId().

◆ CanGetIdentity()

bool CHsp_Base::CanGetIdentity ( void  ) const

Check if it is safe to call GetIdentity method.

Returns
  • true, if the data member is getatable.
  • false, otherwise.

◆ CanGetInclude()

bool CParameters_Base::CanGetInclude ( void  ) const

Check if it is safe to call GetInclude method.

Returns
  • true, if the data member is getatable.
  • false, otherwise.

◆ CanGetIter_num()

bool CIteration_Base::CanGetIter_num ( void  ) const

Check if it is safe to call GetIter_num method.

Returns
  • true, if the data member is getatable.
  • false, otherwise.

◆ CanGetKappa()

bool CStatistics_Base::CanGetKappa ( void  ) const

Check if it is safe to call GetKappa method.

Returns
  • true, if the data member is getatable.
  • false, otherwise.

◆ CanGetLambda()

bool CStatistics_Base::CanGetLambda ( void  ) const

Check if it is safe to call GetLambda method.

Returns
  • true, if the data member is getatable.
  • false, otherwise.

◆ CanGetLen()

bool CHit_Base::CanGetLen ( void  ) const

Check if it is safe to call GetLen method.

Returns
  • true, if the data member is getatable.
  • false, otherwise.

◆ CanGetMatrix()

bool CParameters_Base::CanGetMatrix ( void  ) const

Check if it is safe to call GetMatrix method.

Returns
  • true, if the data member is getatable.
  • false, otherwise.

◆ CanGetMessage() [1/2]

bool CErr_Base::CanGetMessage ( void  ) const
inline

Check if it is safe to call GetMessage method.

Returns
  • true, if the data member is getatable.
  • false, otherwise.

Definition at line 258 of file Err_.hpp.

References CErr_Base::IsSetMessage().

Referenced by CErr_Base::GetMessage().

◆ CanGetMessage() [2/2]

template<bool LEGACY, unsigned long NHITS, typename derived_t >
bool CSearch_Base< LEGACY, NHITS, derived_t >::CanGetMessage ( void  ) const
inline

Check if it is safe to call GetMessage method.

Returns
  • true, if the data member is getatable.
  • false, otherwise.

Definition at line 627 of file Search_.hpp.

References CSearch_Base< LEGACY, NHITS, derived_t >::IsSetMessage().

Referenced by CSearch_Base< LEGACY, NHITS, derived_t >::GetMessage().

◆ CanGetMidline()

bool CHsp_Base::CanGetMidline ( void  ) const

Check if it is safe to call GetMidline method.

Returns
  • true, if the data member is getatable.
  • false, otherwise.

◆ CanGetNum() [1/2]

bool CHit_Base::CanGetNum ( void  ) const

Check if it is safe to call GetNum method.

Returns
  • true, if the data member is getatable.
  • false, otherwise.

◆ CanGetNum() [2/2]

bool CHsp_Base::CanGetNum ( void  ) const

Check if it is safe to call GetNum method.

Returns
  • true, if the data member is getatable.
  • false, otherwise.

◆ CanGetParams()

bool CReport_Base::CanGetParams ( void  ) const
inline

Check if it is safe to call GetParams method.

Returns
  • true, if the data member is getatable.
  • false, otherwise.

Definition at line 554 of file Report_.hpp.

◆ CanGetPattern()

bool CParameters_Base::CanGetPattern ( void  ) const

Check if it is safe to call GetPattern method.

Returns
  • true, if the data member is getatable.
  • false, otherwise.

◆ CanGetPattern_from()

bool CHsp_Base::CanGetPattern_from ( void  ) const

Check if it is safe to call GetPattern_from method.

Returns
  • true, if the data member is getatable.
  • false, otherwise.

◆ CanGetPattern_to()

bool CHsp_Base::CanGetPattern_to ( void  ) const

Check if it is safe to call GetPattern_to method.

Returns
  • true, if the data member is getatable.
  • false, otherwise.

◆ CanGetPositive()

bool CHsp_Base::CanGetPositive ( void  ) const

Check if it is safe to call GetPositive method.

Returns
  • true, if the data member is getatable.
  • false, otherwise.

◆ CanGetProgram()

bool CReport_Base::CanGetProgram ( void  ) const
inline

Check if it is safe to call GetProgram method.

Returns
  • true, if the data member is getatable.
  • false, otherwise.

Definition at line 383 of file Report_.hpp.

References CReport_Base::IsSetProgram().

Referenced by CReport_Base::GetProgram().

◆ CanGetQseq()

bool CHsp_Base::CanGetQseq ( void  ) const

Check if it is safe to call GetQseq method.

Returns
  • true, if the data member is getatable.
  • false, otherwise.

◆ CanGetQuery_frame()

bool CHsp_Base::CanGetQuery_frame ( void  ) const

Check if it is safe to call GetQuery_frame method.

Returns
  • true, if the data member is getatable.
  • false, otherwise.

◆ CanGetQuery_from()

bool CHsp_Base::CanGetQuery_from ( void  ) const

Check if it is safe to call GetQuery_from method.

Returns
  • true, if the data member is getatable.
  • false, otherwise.

◆ CanGetQuery_gencode()

bool CParameters_Base::CanGetQuery_gencode ( void  ) const
inline

Check if it is safe to call GetQuery_gencode method.

Returns
  • true, if the data member is getatable.
  • false, otherwise.

Definition at line 1227 of file Parameters_.hpp.

References CParameters_Base::IsSetQuery_gencode().

Referenced by CParameters_Base::GetQuery_gencode().

◆ CanGetQuery_id()

template<bool LEGACY, unsigned long NHITS, typename derived_t >
bool CSearch_Base< LEGACY, NHITS, derived_t >::CanGetQuery_id ( void  ) const
inline

Check if it is safe to call GetQuery_id method.

Returns
  • true, if the data member is getatable.
  • false, otherwise.

Definition at line 415 of file Search_.hpp.

References CSearch_Base< LEGACY, NHITS, derived_t >::IsSetQuery_id().

Referenced by CSearch_Base< LEGACY, NHITS, derived_t >::GetQuery_id().

◆ CanGetQuery_len()

template<bool LEGACY, unsigned long NHITS, typename derived_t >
bool CSearch_Base< LEGACY, NHITS, derived_t >::CanGetQuery_len ( void  ) const
inline

Check if it is safe to call GetQuery_len method.

Returns
  • true, if the data member is getatable.
  • false, otherwise.

Definition at line 509 of file Search_.hpp.

References CSearch_Base< LEGACY, NHITS, derived_t >::IsSetQuery_len().

Referenced by CSearch_Base< LEGACY, NHITS, derived_t >::GetQuery_len().

◆ CanGetQuery_masking()

template<bool LEGACY, unsigned long NHITS, typename derived_t >
bool CSearch_Base< LEGACY, NHITS, derived_t >::CanGetQuery_masking ( void  ) const
inline

Check if it is safe to call GetQuery_masking method.

Returns
  • true, if the data member is getatable.
  • false, otherwise.

Definition at line 556 of file Search_.hpp.

◆ CanGetQuery_strand()

bool CHsp_Base::CanGetQuery_strand ( void  ) const
inline

Check if it is safe to call GetQuery_strand method.

Returns
  • true, if the data member is getatable.
  • false, otherwise.

Definition at line 1554 of file Hsp_.hpp.

References CHsp_Base::IsSetQuery_strand().

Referenced by CHsp_Base::GetQuery_strand().

◆ CanGetQuery_title()

template<bool LEGACY, unsigned long NHITS, typename derived_t >
bool CSearch_Base< LEGACY, NHITS, derived_t >::CanGetQuery_title ( void  ) const
inline

Check if it is safe to call GetQuery_title method.

Returns
  • true, if the data member is getatable.
  • false, otherwise.

Definition at line 462 of file Search_.hpp.

References CSearch_Base< LEGACY, NHITS, derived_t >::IsSetQuery_title().

Referenced by CSearch_Base< LEGACY, NHITS, derived_t >::GetQuery_title().

◆ CanGetQuery_to()

bool CHsp_Base::CanGetQuery_to ( void  ) const

Check if it is safe to call GetQuery_to method.

Returns
  • true, if the data member is getatable.
  • false, otherwise.

◆ CanGetReference()

bool CReport_Base::CanGetReference ( void  ) const
inline

Check if it is safe to call GetReference method.

Returns
  • true, if the data member is getatable.
  • false, otherwise.

Definition at line 477 of file Report_.hpp.

References CReport_Base::IsSetReference().

Referenced by CReport_Base::GetReference().

◆ CanGetReport()

bool CBlastOutput2_Base::CanGetReport ( void  ) const
inline

Check if it is safe to call GetReport method.

Returns
  • true, if the data member is getatable.
  • false, otherwise.

Definition at line 211 of file BlastOutput2_.hpp.

References CBlastOutput2_Base::IsSetReport().

Referenced by CBlastOutput2_Base::GetReport().

◆ CanGetResults()

bool CReport_Base::CanGetResults ( void  ) const
inline

Check if it is safe to call GetResults method.

Returns
  • true, if the data member is getatable.
  • false, otherwise.

Definition at line 584 of file Report_.hpp.

◆ CanGetSc_match()

bool CParameters_Base::CanGetSc_match ( void  ) const

Check if it is safe to call GetSc_match method.

Returns
  • true, if the data member is getatable.
  • false, otherwise.

◆ CanGetSc_mismatch()

bool CParameters_Base::CanGetSc_mismatch ( void  ) const

Check if it is safe to call GetSc_mismatch method.

Returns
  • true, if the data member is getatable.
  • false, otherwise.

◆ CanGetSciname()

bool CHitDescr_Base::CanGetSciname ( void  ) const
inline

Check if it is safe to call GetSciname method.

Returns
  • true, if the data member is getatable.
  • false, otherwise.

Definition at line 528 of file HitDescr_.hpp.

References CHitDescr_Base::IsSetSciname().

Referenced by CHitDescr_Base::GetSciname().

◆ CanGetScore()

bool CHsp_Base::CanGetScore ( void  ) const

Check if it is safe to call GetScore method.

Returns
  • true, if the data member is getatable.
  • false, otherwise.

◆ CanGetSearch()

bool CIteration_Base::CanGetSearch ( void  ) const
inline

Check if it is safe to call GetSearch method.

Returns
  • true, if the data member is getatable.
  • false, otherwise.

Definition at line 258 of file Iteration_.hpp.

◆ CanGetSearch_target()

bool CReport_Base::CanGetSearch_target ( void  ) const
inline

Check if it is safe to call GetSearch_target method.

Returns
  • true, if the data member is getatable.
  • false, otherwise.

Definition at line 524 of file Report_.hpp.

◆ CanGetStat()

template<bool LEGACY, unsigned long NHITS, typename derived_t >
bool CSearch_Base< LEGACY, NHITS, derived_t >::CanGetStat ( void  ) const
inline

Check if it is safe to call GetStat method.

Returns
  • true, if the data member is getatable.
  • false, otherwise.

Definition at line 606 of file Search_.hpp.

References CSearch_Base< LEGACY, NHITS, derived_t >::IsSetStat().

Referenced by CSearch_Base< LEGACY, NHITS, derived_t >::GetStat().

◆ CanGetTaxid()

bool CHitDescr_Base::CanGetTaxid ( void  ) const
inline

Check if it is safe to call GetTaxid method.

Returns
  • true, if the data member is getatable.
  • false, otherwise.

Definition at line 481 of file HitDescr_.hpp.

References CHitDescr_Base::IsSetTaxid().

Referenced by CHitDescr_Base::GetTaxid().

◆ CanGetTitle()

bool CHitDescr_Base::CanGetTitle ( void  ) const
inline

Check if it is safe to call GetTitle method.

Returns
  • true, if the data member is getatable.
  • false, otherwise.

Definition at line 434 of file HitDescr_.hpp.

References CHitDescr_Base::IsSetTitle().

Referenced by CHitDescr_Base::GetTitle().

◆ CanGetTo()

bool CRange_Base::CanGetTo ( void  ) const
inline

Check if it is safe to call GetTo method.

Returns
  • true, if the data member is getatable.
  • false, otherwise.

Definition at line 256 of file Range_.hpp.

References CRange_Base::IsSetTo().

Referenced by CRange_Base::GetTo().

◆ CanGetVersion()

bool CReport_Base::CanGetVersion ( void  ) const
inline

Check if it is safe to call GetVersion method.

Returns
  • true, if the data member is getatable.
  • false, otherwise.

Definition at line 430 of file Report_.hpp.

References CReport_Base::IsSetVersion().

Referenced by CReport_Base::GetVersion().

◆ CBlastOutput2() [1/2]

CBlastOutput2::CBlastOutput2 ( const CBlastOutput2 value)
private

◆ CBlastOutput2() [2/2]

CBlastOutput2::CBlastOutput2 ( void  )
inline

Definition at line 88 of file BlastOutput2.hpp.

◆ CBlastOutput2_Base() [1/2]

CBlastOutput2_Base::CBlastOutput2_Base ( const CBlastOutput2_Base )
private

◆ CBlastOutput2_Base() [2/2]

END_CLASS_INFO CBlastOutput2_Base::CBlastOutput2_Base ( void  )

Definition at line 106 of file BlastOutput2_.cpp.

References CBlastOutput2_Base::m_set_State.

◆ CBlastXML2() [1/2]

CBlastXML2::CBlastXML2 ( const CBlastXML2 value)
private

◆ CBlastXML2() [2/2]

CBlastXML2::CBlastXML2 ( void  )
inline

Definition at line 88 of file BlastXML2.hpp.

◆ CBlastXML2_Base() [1/2]

CBlastXML2_Base::CBlastXML2_Base ( const CBlastXML2_Base )
private

◆ CBlastXML2_Base() [2/2]

END_CLASS_INFO CBlastXML2_Base::CBlastXML2_Base ( void  )

Definition at line 70 of file BlastXML2_.cpp.

References CBlastXML2_Base::m_set_State.

◆ CErr() [1/2]

CErr::CErr ( const CErr value)
private

◆ CErr() [2/2]

CErr::CErr ( void  )
inline

Definition at line 88 of file Err.hpp.

◆ CErr_Base() [1/2]

CErr_Base::CErr_Base ( const CErr_Base )
private

◆ CErr_Base() [2/2]

END_CLASS_INFO CErr_Base::CErr_Base ( void  )

Definition at line 76 of file Err_.cpp.

References CErr_Base::m_set_State.

◆ CheckSelected() [1/2]

void CResults_Base::CheckSelected ( E_Choice  index) const
inline

Verify selection, throw exception if it differs from the expected.

Parameters
indexExpected selection.

Definition at line 266 of file Results_.hpp.

References CResults_Base::m_choice, and CResults_Base::ThrowInvalidSelection().

Referenced by CResults_Base::GetBl2seq(), CResults_Base::GetIterations(), and CResults_Base::GetSearch().

◆ CheckSelected() [2/2]

void CTarget_Base::CheckSelected ( E_Choice  index) const
inline

Verify selection, throw exception if it differs from the expected.

Parameters
indexExpected selection.

Definition at line 240 of file Target_.hpp.

References CTarget_Base::m_choice, and CTarget_Base::ThrowInvalidSelection().

Referenced by CTarget_Base::GetDb(), and CTarget_Base::GetSubjects().

◆ CHit() [1/2]

CHit::CHit ( const CHit value)
private

◆ CHit() [2/2]

CHit::CHit ( void  )

◆ CHit_Base() [1/2]

CHit_Base::CHit_Base ( const CHit_Base )
private

◆ CHit_Base() [2/2]

CHit_Base::CHit_Base ( void  )

◆ CHitDescr() [1/2]

CHitDescr::CHitDescr ( const CHitDescr value)
private

◆ CHitDescr() [2/2]

CHitDescr::CHitDescr ( void  )
inline

Definition at line 88 of file HitDescr.hpp.

◆ CHitDescr_Base() [1/2]

CHitDescr_Base::CHitDescr_Base ( const CHitDescr_Base )
private

◆ CHitDescr_Base() [2/2]

END_CLASS_INFO CHitDescr_Base::CHitDescr_Base ( void  )

Definition at line 100 of file HitDescr_.cpp.

References CHitDescr_Base::m_set_State.

◆ CHsp() [1/2]

CHsp::CHsp ( const CHsp value)
private

◆ CHsp() [2/2]

CHsp::CHsp ( void  )

◆ CHsp_Base() [1/2]

CHsp_Base::CHsp_Base ( const CHsp_Base )
private

◆ CHsp_Base() [2/2]

CHsp_Base::CHsp_Base ( void  )

◆ CIteration() [1/2]

CIteration::CIteration ( const CIteration value)
private

◆ CIteration() [2/2]

CIteration::CIteration ( void  )

◆ CIteration_Base() [1/2]

CIteration_Base::CIteration_Base ( const CIteration_Base )
private

◆ CIteration_Base() [2/2]

CIteration_Base::CIteration_Base ( void  )

◆ CParameters() [1/2]

CParameters::CParameters ( const CParameters value)
private

◆ CParameters() [2/2]

CParameters::CParameters ( void  )

◆ CParameters_Base() [1/2]

CParameters_Base::CParameters_Base ( const CParameters_Base )
private

◆ CParameters_Base() [2/2]

CParameters_Base::CParameters_Base ( void  )

◆ CRange() [1/2]

template<class Position >
CRange< Position >::CRange ( const CRange< Position > &  value)
private

◆ CRange() [2/2]

template<class Position >
CRange< Position >::CRange ( void  )
inline

Definition at line 88 of file Range.hpp.

◆ CRange_Base() [1/2]

CRange_Base::CRange_Base ( const CRange_Base )
private

◆ CRange_Base() [2/2]

END_CLASS_INFO CRange_Base::CRange_Base ( void  )

Definition at line 70 of file Range_.cpp.

References CRange_Base::m_set_State.

◆ CReport() [1/2]

CReport::CReport ( const CReport value)
private

◆ CReport() [2/2]

CReport::CReport ( void  )
inline

Definition at line 88 of file Report.hpp.

◆ CReport_Base() [1/2]

CReport_Base::CReport_Base ( const CReport_Base )
private

◆ CReport_Base() [2/2]

END_CLASS_INFO CReport_Base::CReport_Base ( void  )

◆ CResults() [1/2]

CResults::CResults ( const CResults value)
private

◆ CResults() [2/2]

CResults::CResults ( void  )
inline

Definition at line 88 of file Results.hpp.

◆ CResults_Base() [1/2]

CResults_Base::CResults_Base ( const CResults_Base )
private

◆ CResults_Base() [2/2]

END_CHOICE_INFO CResults_Base::CResults_Base ( void  )

Definition at line 150 of file Results_.cpp.

◆ CSearch() [1/2]

template<bool LEGACY, unsigned long NHITS>
CSearch< LEGACY, NHITS >::CSearch ( const CSearch< LEGACY, NHITS > &  value)
private

◆ CSearch() [2/2]

template<bool LEGACY, unsigned long NHITS>
CSearch< LEGACY, NHITS >::CSearch ( void  )
inline

Definition at line 88 of file Search.hpp.

◆ CSearch_Base() [1/2]

template<bool LEGACY, unsigned long NHITS, typename derived_t >
CSearch_Base< LEGACY, NHITS, derived_t >::CSearch_Base ( const CSearch_Base< LEGACY, NHITS, derived_t > &  )
private

◆ CSearch_Base() [2/2]

template<bool LEGACY, unsigned long NHITS, typename derived_t >
END_CLASS_INFO CSearch_Base< LEGACY, NHITS, derived_t >::CSearch_Base ( void  )

◆ CStatistics() [1/2]

CStatistics::CStatistics ( const CStatistics value)
private

◆ CStatistics() [2/2]

CStatistics::CStatistics ( void  )

◆ CStatistics_Base() [1/2]

CStatistics_Base::CStatistics_Base ( const CStatistics_Base )
private

◆ CStatistics_Base() [2/2]

CStatistics_Base::CStatistics_Base ( void  )

◆ CTarget() [1/2]

CTarget::CTarget ( const CTarget value)
private

◆ CTarget() [2/2]

CTarget::CTarget ( void  )

◆ CTarget_Base() [1/2]

CTarget_Base::CTarget_Base ( const CTarget_Base )
private

◆ CTarget_Base() [2/2]

CTarget_Base::CTarget_Base ( void  )

◆ DECLARE_INTERNAL_TYPE_INFO() [1/14]

CBlastOutput2_Base::DECLARE_INTERNAL_TYPE_INFO ( )

◆ DECLARE_INTERNAL_TYPE_INFO() [2/14]

CBlastXML2_Base::DECLARE_INTERNAL_TYPE_INFO ( )

◆ DECLARE_INTERNAL_TYPE_INFO() [3/14]

CErr_Base::DECLARE_INTERNAL_TYPE_INFO ( )

◆ DECLARE_INTERNAL_TYPE_INFO() [4/14]

CHit_Base::DECLARE_INTERNAL_TYPE_INFO ( )

◆ DECLARE_INTERNAL_TYPE_INFO() [5/14]

CHitDescr_Base::DECLARE_INTERNAL_TYPE_INFO ( )

◆ DECLARE_INTERNAL_TYPE_INFO() [6/14]

CHsp_Base::DECLARE_INTERNAL_TYPE_INFO ( )

◆ DECLARE_INTERNAL_TYPE_INFO() [7/14]

CIteration_Base::DECLARE_INTERNAL_TYPE_INFO ( )

◆ DECLARE_INTERNAL_TYPE_INFO() [8/14]

CParameters_Base::DECLARE_INTERNAL_TYPE_INFO ( )

◆ DECLARE_INTERNAL_TYPE_INFO() [9/14]

CRange_Base::DECLARE_INTERNAL_TYPE_INFO ( )

◆ DECLARE_INTERNAL_TYPE_INFO() [10/14]

CReport_Base::DECLARE_INTERNAL_TYPE_INFO ( )

◆ DECLARE_INTERNAL_TYPE_INFO() [11/14]

CResults_Base::DECLARE_INTERNAL_TYPE_INFO ( )

◆ DECLARE_INTERNAL_TYPE_INFO() [12/14]

template<bool LEGACY, unsigned long NHITS, typename derived_t >
CSearch_Base< LEGACY, NHITS, derived_t >::DECLARE_INTERNAL_TYPE_INFO ( )

◆ DECLARE_INTERNAL_TYPE_INFO() [13/14]

CStatistics_Base::DECLARE_INTERNAL_TYPE_INFO ( )

◆ DECLARE_INTERNAL_TYPE_INFO() [14/14]

CTarget_Base::DECLARE_INTERNAL_TYPE_INFO ( )

◆ DoSelect() [1/2]

void CResults_Base::DoSelect ( E_Choice  index,
CObjectMemoryPool pool = 0 
)
private

◆ DoSelect() [2/2]

void CTarget_Base::DoSelect ( E_Choice  index,
CObjectMemoryPool pool = 0 
)
private

◆ Get()

const CBlastXML2_Base::Tdata & CBlastXML2_Base::Get ( void  ) const
inline

Get the member data.

Returns
Reference to the member data.

Definition at line 170 of file BlastXML2_.hpp.

References CBlastXML2_Base::m_data.

◆ GetAccession()

const CHitDescr_Base::TAccession & CHitDescr_Base::GetAccession ( void  ) const
inline

Get the Accession member data.

Returns
Reference to the member data.

Definition at line 393 of file HitDescr_.hpp.

References CHitDescr_Base::CanGetAccession(), CHitDescr_Base::m_Accession, and CSerialObject::ThrowUnassigned().

◆ GetAlign_len()

TAlign_len CHsp_Base::GetAlign_len ( void  ) const

Get the Align_len member data.

Returns
Copy of the member data.

◆ GetBit_score()

TBit_score CHsp_Base::GetBit_score ( void  ) const

Get the Bit_score member data.

Returns
Copy of the member data.

◆ GetBl2seq()

const CResults_Base::TBl2seq & CResults_Base::GetBl2seq ( void  ) const
inline

Get the variant data.

Returns
Reference to the data.

Definition at line 321 of file Results_.hpp.

References CResults_Base::CheckSelected(), CResults_Base::e_Bl2seq, and CResults_Base::m_Bl2seq.

◆ GetBl2seq_mode()

const CParameters_Base::TBl2seq_mode & CParameters_Base::GetBl2seq_mode ( void  ) const
inline

Get the Bl2seq_mode member data.

Returns
Reference to the member data.

Definition at line 1327 of file Parameters_.hpp.

References CParameters_Base::CanGetBl2seq_mode(), CParameters_Base::m_Bl2seq_mode, and CSerialObject::ThrowUnassigned().

◆ GetCbs()

CParameters_Base::TCbs CParameters_Base::GetCbs ( void  ) const
inline

Get the Cbs member data.

Returns
Copy of the member data.

Definition at line 1193 of file Parameters_.hpp.

References CParameters_Base::CanGetCbs(), CParameters_Base::m_Cbs, and CSerialObject::ThrowUnassigned().

◆ GetCode()

CErr_Base::TCode CErr_Base::GetCode ( void  ) const
inline

Get the Code member data.

Returns
Copy of the member data.

Definition at line 224 of file Err_.hpp.

References CErr_Base::CanGetCode(), CErr_Base::m_Code, and CSerialObject::ThrowUnassigned().

◆ GetDb()

const CTarget_Base::TDb & CTarget_Base::GetDb ( void  ) const
inline

Get the variant data.

Returns
Reference to the data.

Definition at line 269 of file Target_.hpp.

References CTarget_Base::CheckSelected(), CTarget_Base::e_Db, and CTarget_Base::m_string.

◆ GetDb_gencode()

CParameters_Base::TDb_gencode CParameters_Base::GetDb_gencode ( void  ) const
inline

Get the Db_gencode member data.

Returns
Copy of the member data.

Definition at line 1287 of file Parameters_.hpp.

References CParameters_Base::CanGetDb_gencode(), CParameters_Base::m_Db_gencode, and CSerialObject::ThrowUnassigned().

◆ GetDb_len()

TDb_len CStatistics_Base::GetDb_len ( void  ) const

Get the Db_len member data.

Returns
Copy of the member data.

◆ GetDb_num()

TDb_num CStatistics_Base::GetDb_num ( void  ) const

Get the Db_num member data.

Returns
Copy of the member data.

◆ GetDensity()

TDensity CHsp_Base::GetDensity ( void  ) const

Get the Density member data.

Returns
Copy of the member data.

◆ GetDescription()

const CHit_Base::TDescription & CHit_Base::GetDescription ( void  ) const
inline

Get the Description member data.

Returns
Reference to the member data.

Definition at line 340 of file Hit_.hpp.

References CHit_Base::m_Description.

◆ GetEff_space()

TEff_space CStatistics_Base::GetEff_space ( void  ) const

Get the Eff_space member data.

Returns
Copy of the member data.

◆ GetEntrez_query()

const TEntrez_query& CParameters_Base::GetEntrez_query ( void  ) const

Get the Entrez_query member data.

Returns
Reference to the member data.

◆ GetEntropy()

TEntropy CStatistics_Base::GetEntropy ( void  ) const

Get the Entropy member data.

Returns
Copy of the member data.

◆ GetError()

const CBlastOutput2_Base::TError & CBlastOutput2_Base::GetError ( void  ) const
inline

Get the Error member data.

Returns
Reference to the member data.

Definition at line 238 of file BlastOutput2_.hpp.

References CBlastOutput2_Base::CanGetError(), CBlastOutput2_Base::m_Error, and CSerialObject::ThrowUnassigned().

◆ GetEvalue()

TEvalue CHsp_Base::GetEvalue ( void  ) const

Get the Evalue member data.

Returns
Copy of the member data.

◆ GetExpect()

TExpect CParameters_Base::GetExpect ( void  ) const

Get the Expect member data.

Returns
Copy of the member data.

◆ GetFilter()

const TFilter& CParameters_Base::GetFilter ( void  ) const

Get the Filter member data.

Returns
Reference to the member data.

◆ GetFrom()

CRange_Base::TFrom CRange_Base::GetFrom ( void  ) const
inline

Get the From member data.

Returns
Copy of the member data.

Definition at line 222 of file Range_.hpp.

References CRange_Base::CanGetFrom(), CRange_Base::m_From, and CSerialObject::ThrowUnassigned().

Referenced by SGraphMaker::AddActualGap(), CAlignCollapser::AddAlignment(), CMultAlign::AddAlignment(), CAlignmentSmear::AddAlignment(), CChain::AddAllMembersAndCoverage(), CGeneModel::AddExon(), CModelExon::AddFrom(), CGeneModel::AddGgapExon(), CGeneModel::AddNormalExon(), CGBProjectHelper::AddProjectItemsFromRID(), CGraphRanges::AddRange(), CDepthCollection::AddRange(), CDensityMap< CntType >::AddRange(), CSAM_CIGAR_Formatter::AddRow(), CFeatureGenerator::SImplementation::AdjustAlignment(), AdjustCdregionFrame(), CAdjustForConsensusSpliceSite::AdjustCDS(), CEditSequence::AdjustFeatureLocations(), CEditSeqEndsWithAlign::AdjustLoc(), CAlignmentAssistant::AdjustLoc(), CEditSequence::AdjustProtFeatureLocations(), AlignModelToSeqalign(), AlnFromRangeAscendingSort(), CAlnGraphic::AlnGraphicDisplay(), CFeatTrim::Apply(), CFuseJoinsInLocs::apply(), CGroupExplode::apply(), CExplodeRNAFeats::apply(), CModelCompare::AreSimilar(), CDiscrepancyVisitorImpl< _Name >::Autofix(), BadSeqLocSortOrder(), SAnnotObject_Key::begin(), BOOST_AUTO_TEST_CASE(), CRawSeqToDeltaSeqByLoc::ByAssemblyGapFeatures_impl(), CEquivRangeBuilder::CalcMatches(), CEquivRange::CalcRelative(), CEquivRange::CalcRelativeDuo(), CChain::CalculateDropLimits(), CChainer::CChainerImpl::CalculateSpliceWeights(), CChain::CalculateSupportAndWeightFromMembers(), CAlignMap::CAlignMap(), CAlnGraphic::CAlnGraphic(), CChainer::CChainerImpl::CanIncludeJinI(), CAnnotObject_Ref::CAnnotObject_Ref(), CChain::CChain(), CGeneModel::CdsInvariant(), CdsTrnaOverlapStr(), CFeatHistogramDS::CFeatHistogramDS(), CSeqMapSwitchPoint::ChangeSwitchPoint(), CheckAdjustStartAndStop(), CChainer::CChainerImpl::CheckCompatibility(), CChain::CheckSecondaryCapPolyAEnds(), CheckSparseAln(), CMultAlign::CheckWord(), CIdRangeMap::CIdRangeMap(), CAlignCollapser::CleanSelfTranscript(), CCDSInfo::Clip(), CGeneModel::Clip(), CChain::ClipChain(), CAlignCollapser::ClipESTorSR(), CChain::ClipLowCoverageUTR(), CAlignCollapser::ClipNotSupportedFlanks(), CChain::ClipToCap(), CChain::ClipToPolyA(), IAlnMultiDataSource::CollectAlignStats(), CollectAttributes(), CChainer::CChainerImpl::CombineCompatibleChains(), CombineCorrectionsAndIndels(), CCDSInfo::CombineWith(), CSeq_loc_Conversion::CombineWith(), SPhyloCSFSlice::CompactRange(), CDiscrepancyContext::Compare(), CMultiAlignerTest::CompareDomainHits(), CAnnotCompare::CompareFeats(), Convert_Seq_feat_Seq_loc_Gen_Loc_TotalRange(), ConvertSeqLocsToPairwiseAln(), CSeq_loc_Conversion::ConvertSimpleLoc(), ConvertStdsegToPairwiseAln(), CProteinAlignText::CProteinAlignText(), CAnnotationASN1::CImplementationData::create_cdregion_feature(), CAnnotationASN1::CImplementationData::create_internal_feature(), CAnnotationASN1::CImplementationData::create_packed_int_seqloc(), CChainer::CChainerImpl::CreateChainsForPartialProteins(), CSegmentGlyph::CSegmentGlyph(), CSeq_loc_Conversion::CSeq_loc_Conversion(), CShowBlastDefline::CShowBlastDefline(), CCDSInfo::Cut(), CGeneModel::CutExons(), CAlignModel::CutExons(), CEquivRange::Distance(), CIntervalTree::DoDelete(), Does5primerAbutGap(), CIntervalTree::DoInsert(), CAlignGlyph::DrawPWAlignElem(), CRenderingContext::DrawStrandIndicators(), DumpSparseAln(), CChainer::CChainerImpl::Duplicate5pendsAndShortCDSes(), CMultAlign::EmitSequenceFromBase(), CMultAlign::EmitSequenceFromRead(), NSnpAnnot::EstimateSNPCount(), CMacroEngineParallel::Exec(), CPrefetchSeqData::Execute(), ExonNumsForInterval(), CLocationEditPolicy::Extend5(), CGnomonAnnotator::ExtendJustThisChain(), CBlastDBExtractor::ExtractFasta(), CEquivRangeBuilder::ExtractRangesFromSeqAlign(), CAlignCollapser::FillGapsInAlignmentAndAddToGenomicGaps(), CAlignCollapser::FilterAlignments(), FindAllCodonInstances(), CChainer::CChainerImpl::FindContainedAlignments(), CProSplign::FindGlobalAlignment(), FindNewLocations(), CSplitCDSwithTooManyXs::FindNewLocations(), CChainer::CChainerImpl::FindOptimalChainForProtein(), FindPolyA(), FindPolyTail(), CChainer::FindSelenoproteinsClipProteinsToStartStop(), FindStartsStops(), CVecscreen::FromRangeAscendingSort(), FromRangeAscendingSort(), CAlnGraphic::FromRangeAscendingSort(), CChainer::CChainerImpl::FsTouch(), CScore_StartStopCodon::Get(), CAlignCommon::GetAlignment(), CDensegGraphicDataSource::GetAlnPosFromSeqPos(), SChunkTranslator::GetAlnPosFromSeqPos(), CSparseAlignment::GetAlnSeqString(), CDensegGraphicDataSource::GetAlnSeqString(), CSparseAln::GetAlnSeqString(), CSparseMultiDataSource::GetAlnStart(), CSparseAlnGraphicDataSource::GetAlnStart(), CGnomonEngine::GetAnnot(), CScoreBuilder::GetBlastScoreProtToNucl(), CFeatureGenerator::SImplementation::GetCds(), CGeneModel::GetCdsDnaSequence(), CSeqUtils::GetCdsMappingInfoFromRna(), CConvertBadCdsAndRnaToMiscFeat::getCdsOverlap(), IAlnGraphicDataSource::GetCigarAtAlnPos(), CAlignCollapser::GetCollapsedAlgnments(), CExonFromCds::GetCommand(), CMultAlign::GetCounts(), CSeq_loc_Conversion::GetDstInterval(), CSeq_loc_Conversion::GetDstPoint(), CAlignmentAssistant::GetFeatures(), CEditSequence::GetFeatures(), CSeqTextDataSourceInterval::GetFeaturesAtPosition(), CModelExon::GetFrom(), CAnnotMapping_Info::GetFrom(), CParse::GetGenes(), CAlignFormatUtil::GetGraphiscLink(), CSeqMapSwitchPoint::GetInsert(), CGuiObjectInfoSeq_align::GetInsertionRanges(), CSeqTextDataSource::GetIntervalBreaks(), CHandleRange::GetLeft(), CSeqUtils::GetLocPlacements(), CAlignFormatUtil::GetMasterCoverage(), CGeneModel::GetProtein(), CEditSequence::GetProteinFeatures(), GetProteinWeight(), CDenseSegHitElement::GetQueryStart(), CStdSegHitElement::GetQueryStart(), CHit::GetRangeFromSeq1(), CHit::GetRangeFromSeq2(), CMaskedRangeSet::GetRanges(), CAlnMap::GetResidueIndexMap(), CConvertBadCdsAndRnaToMiscFeat::getRnaOverlap(), CCodingPropensity::GetScore(), CGnomonEngine::GetScore(), CEditScript::GetScore(), CMatchesListCtrl::GetSelectedLocations(), CSeqTextDataSourceInterval::GetSeqData(), CDensegGraphicDataSource::GetSeqPosFromAlnPos(), SChunkTranslator::GetSeqPosFromAlnPos(), CSeq_align::GetSeqStart(), CSpliced_seg::GetSeqStart(), CGuiObjectInfoSeq_align::GetSeqString(), CAlnVec::GetSeqString(), IAlnGraphicDataSource::GetSeqString(), CDensegGraphicDataSource::GetSeqString(), CSparseAlignment::GetSeqString(), CSparseAln::GetSeqString(), CSegmentGlyph::GetSignature(), CSNPDbSeqIterator::GetSNPCount(), GetSortedCuts(), CDensityMap< score_type >::GetStart(), CDenseSegHitElement::GetSubjectStart(), CStdSegHitElement::GetSubjectStart(), CAlignFormatUtil::GetUniqSeqCoverage(), CRenderingContext::GetVisibleFrom(), CRenderingContext::GetVisSeqFrom(), CGeneModel::HasCompatibleOverlap(), CCrossPanelIR::HitTest(), Include(), CChainer::CChainerImpl::IncludeInContained(), CSparseAlignment::Init(), CSeqScores::Init(), CAlnGraphic::Init(), CAlignCollapser::InitContig(), CIntervalTree::Insert(), CSegmentedRangeCollection::insert(), CCddInputData::CHit::IntersectWith(), CIntervalTree::IntervalsOverlapping(), CLocationEditPolicy::Is3AtEndOfSeq(), CLocationEditPolicy::Is5AtEndOfSeq(), CGeneModel::isCompatible(), IsExtendable(), CAlnMap::CAlnChunk::IsGap(), CRenderingContext::IsInVisibleRange(), CGeneModel::isNMD(), C2DLayoutEngine::Layout(), CChainer::CChainerImpl::LeftRight(), CSeqGlyph::LessBySeqPos(), CSeqTextDataSourceInterval::LookForSpliceJunctions(), CChainer::CChainerImpl::LRCanChainItoJ(), CChainer::CChainerImpl::LRIinit(), CChain::MainPeaks(), CChainer::CChainerImpl::MakeChains(), CEditScript::MakeEditScript(), CScoreUniqSeqCoverage::MakeScore(), Map(), CGnomonAnnotator_Base::MapOneModelToEditedContig(), CGnomonAnnotator_Base::MapOneModelToOrigContig(), CAlignMap::MapRangeEditedToOrig(), CAlignMap::MapRangeOrigToEdited(), SChainMember::MarkIncluded(), SChainMember::MarkPostponed(), SChainMember::MarkUnwantedCopiesForChain(), CHitList::MatchOverlappingSubHits(), CGeneModel::MutualExtension(), CSeqGraphicPane::NextPrevSplice(), CSeqGraphicPane::OnSearchTip(), CGeneModel::OpenLeftEnd(), CPairwise_CI::operator bool(), AlignSeqOrder::operator()(), AlignsLeftEndFirst::operator()(), SRangeSorter< T >::operator()(), SGlyphRangeSorter::operator()(), SSortSourceByLoc::operator()(), GenomeOrderD::operator()(), LeftOrder::operator()(), LeftOrderD::operator()(), RightOrder::operator()(), RightOrderD::operator()(), CRangeCmp::operator()(), SRangeStartSort::operator()(), CRangeWithFuzz::operator+=(), operator<(), SFShiftsCluster::operator<(), operator<<(), ParseAttributes(), PatchTargetSequence(), CChain::PeaksAndLimits(), CAlignModel::PolyALen(), CAlnVecPrinter::PopsetStyle(), CGnomonAnnotator::Predict(), CRenderingContext::PrepareContext(), CMultAlign::PrepareReads(), CTabularFormatter_MismatchPositions::Print(), CTabularFormatter_ExonIntrons::Print(), CTabularFormatter_NearestGap::Print(), CTabularFormatter_StartCodonChanges::Print(), CAlnBuildApp::PrintAnchoredAln(), printGFF3(), PrintSAM(), CResolveRequest::Process(), readGFF3(), CDense_seg::RemapToLoc(), CAlignCollapser::RemoveNotSupportedIntronsFromProt(), CAlignCollapser::RemoveNotSupportedIntronsFromTranscript(), CAlignMarkHandler::Render(), CRuler::Render(), CLinearSelHandler::Render(), CChainer::CChainerImpl::ReplicatePStops(), CGnomonEngine::ResetRange(), CHit::ResolveSubHitConflicts(), RestoreModelReadingFrame(), CChain::RestoreReasonableConfirmedStart(), RetrievePartsOfLargeChromosome(), CChainer::CChainerImpl::RightLeft(), CAgpExportJob::Run(), CTestCompartApplication::Run(), CTestBMApp::Run(), CAlnTestApp::Run(), CDensityMap< score_type >::RunLenIterator(), CAdvancedAlignCleanup::RunSplignOnCompartment(), s_AdjustInternalCutLocations(), s_AlignDist(), s_BasicValidation(), s_CheckAbutting(), s_CheckMixLoc(), s_CollectBestOverlaps(), s_Contains(), s_CreateMappingInfo(), s_DoNWalign(), s_FixMinusStrandRange(), s_GetCigarString(), s_GetCountIdentityMismatch(), s_GetLinkoutUrl(), s_GetSplicedSegIdentityMismatch(), s_GetTrimCoordinates(), s_GetUncoveredLength(), variation::CVariationUtil::CVariantPropertiesIndex::s_GetUTRLocs(), s_IntervalsMatchGaps(), s_IsLocationEndAtOtherLocationInternalEndpoint(), s_IsNotSubrange(), s_LocationsTouch(), s_MapSlaveFeatureToMaster(), s_MergeCuts(), CSequenceUpdater::s_OffsetLocation(), s_PartialAtGapOrNs(), s_PrintLocAsJavascriptArray(), s_ProcessAlignSet(), s_Seq_align_Seq_loc(), s_SeqLocToRangeInfoMap(), s_SeqLocToRangeInfoMapByStrand(), s_SeqLocToTotalRangeInfoMap(), s_SeqLocToTotalRangesInfoMapByStrand(), s_SetRangesForMixedAlignments(), s_SortEquivBySubjt(), s_SortMergeNodeByQuery(), s_SortMergeNodeByQuery_Minus(), s_SortMergeNodeBySubjt(), s_Test_CheckIntervals(), s_TestForOverlapEx(), s_UpdateSeqGraphLoc(), SAlignExtended::SAlignExtended(), CViewGraphic::SaveSettingsAtProject(), CHangScorer::ScoreAlignments(), CClippedScorer::ScoreAlignments(), CGnomonEngine::SelectBestReadingFrame(), CMultAlign::SeqCountsBetweenTwoStrongWords(), CAutoDefExonListClause::SeqLocIntersect(), CFeatureSearchJob::SeqLocToString(), CCDSInfo::Set5PrimeCdsLimit(), CHistogramGlyph::SetAxisRange(), CReportEntry::SetCds(), CChain::SetConfirmedEnds(), CChain::SetConfirmedStartStopForCompleteProteins(), CChainer::CChainerImpl::SetConfirmedStartStopForProteinAlignments(), CChain::SetConsistentCoverage(), CChainer::CChainerImpl::SetFlagsForChains(), CBlastDBExtractor::SetSeqId(), CCDSInfo::SetStop(), CAlignMap::ShrinkToRealPoints(), CAlignMap::ShrinkToRealPointsOnEdited(), CAlignCompare::SAlignment::Slice(), CEquivRangeBuilder::SliceOnQuery(), CEquivRangeBuilder::SliceOnSubjt(), SortHspByMasterStartAscending(), spliced_exon(), CEquivRangeBuilder::SplitIntersections(), CBlobSplitterImpl::SplitPieces(), CSeqTextPane::STG_SetSubtypesForFeature(), CCDSInfo::Strand(), StrictlyContainedInDels(), CCddInputData::CHit::Subtract(), CLocMapper_Default::CGappedRange::ToString(), CGeneModel::TranscriptLimits(), CLiteAlign::TranscriptSeq(), MarkupCappedEst::transform_align(), CutShortPartialExons::transform_align(), ProjectCDS::transform_align(), TrimAlignment::transform_align(), RemoveTrailingNs::transform_model(), CChainer::CChainerImpl::TrimAlignmentsIncludedInDifferentGenes(), CGeneModel::TrimEdgesToFrameInOtherAlignGaps(), CFeatureGenerator::SImplementation::TrimHolesToCodons(), CSplignTrim::TrimHolesToCodons(), TrimAlignment::TrimProtein(), CAlignmentAssistant::TrimQualityScores(), TrimSeqAlign(), TrimSeqFeat(), TrimAlignment::TrimTranscript(), CLocationsListCtrl::UpdateData(), CAnnotMapping_Info::UpdateMappedSeq_loc(), CSpliced_seg::Validate(), CValidError_graph::ValidateGraphsOnBioseq(), CSpliceProblems::ValidateSpliceCdregion(), CSpliceProblems::ValidateSpliceMrna(), CMultAlign::Variations(), VariBandAlign(), CAlnVwrApp::View9(), x_AddConstraint(), CSGAnnotJob::x_AddGraphObject(), CSGAnnotJob::x_AddGraphToMap(), CGuiObjectInfoSeq_feat::x_AddGroupLocationRows(), CGuiObjectInfoSeq_feat::x_AddLocationRows(), CPhrap_Read::x_AddQualityFeat(), CFeatureItem::x_AddQualsProt(), CSequenceSearchJob::x_AddToResults(), CVectorTrimPanel::x_AdjustDensegAlignment(), CFeatGlyph::x_AdjustFrame(), CVectorTrimPanel::x_AdjustInternalCutLocations(), CAlignMarkHandler::x_AlnRangeFromSeqRange(), CAdjustForConsensusSpliceSite::x_AlsoAdjustmRNA(), COligoSpecificityCheck::x_AnalyzeLeftAndRightPrimer(), COligoSpecificityCheck::x_AnalyzeOnePrimer(), COligoSpecificityCheck::x_AnalyzePrimerSpecificity(), CMultiAligner::x_AssignRPSResFreqs(), CDensityMap< score_type >::x_BinN(), CVecscreen::x_BuildNonOverlappingRange(), CAlignGlyph::x_CalcIntervals(), CDensityMap< score_type >::x_CalcNbins(), CVisibleRange::x_Clamp(), CAdvancedAlignCleanup::x_CleanupProsplignAsGenomic(), CSGAlignStatJob::x_CollectAlignStats(), x_CollectCoverageGraph(), CFeatureGenerator::SImplementation::x_CollectMrnaSequence(), CRangeSet< CPairwiseAln::TPos >::x_CombineWithAndKeepAbutting(), CMultiAligner::x_ComputeProfileRangeAlignment(), CAlignGlyph::x_ConvertAlnTaillRngToSeqRng(), CAlnSpanVertModel::x_ConvertRowsToSpans(), CSeq_align_Mapper_Base::x_ConvertSegment(), CSeq_align_Mapper::x_ConvertSegmentCvt(), CFeatureGenerator::SImplementation::x_CreateCdsFeature(), CSGAlignmentJob::x_CreateFeatGlyph(), CSGFeatureJob::x_CreateFeatHist(), CMacroBioData::x_CreateFeatIterator(), CSGFeatureJob::x_CreateFeatSmear(), CSGAnnotJob::x_CreateHistFromGraph(), CSGAlignStatJob::x_CreatePileUpGraphs(), CAlnGraphic::x_DisplayMaster(), CCpgSearchJob::x_DoSearch(), CMergeTree::x_Dot_Nodes(), CAlignSmearGlyph::x_Draw(), CClonePlacementGlyph::x_Draw(), CCommentGlyph::x_Draw(), CGeneGroup::x_Draw(), CLinkedFeatsGroup::x_Draw(), CMatePairGlyph::x_Draw(), CSegmentGlyph::x_Draw(), CFeatGlyph::x_DrawAdditionalInfo(), CVcfGlyph::x_DrawAdditionalInfo(), CAlignGlyph::x_DrawAlignRowSequence(), CLayoutGroup::x_DrawBoundary(), CLinkedFeatsGroup::x_DrawChildrenOnParent(), CCrossPanelIR::x_DrawCrossAlignment(), CSeqGlyph::x_DrawException(), CFeatGlyph::x_DrawFeatureBar(), CLinkedFeatsGroup::x_DrawFeatureBar(), CFeatGlyph::x_DrawFeatureBar_sv(), CAlignGlyph::x_DrawGaps(), CSeqGlyph::x_DrawInnerLabelColumns(), CSeqGlyph::x_DrawInnerLabels(), CFeatGlyph::x_DrawInnerLabels(), CVcfGlyph::x_DrawInnerLabels(), CAlignGlyph::x_DrawInserts(), CAlignGlyph::x_DrawInternalUnalignedRegions(), CLDBlockLine::x_DrawLabel(), CLinkedFeatsGroup::x_DrawLabels(), CFeatGlyph::x_DrawLabelWithXPinned(), CVcfGlyph::x_DrawLabelWithXPinned(), CFeatGlyph::x_DrawLabelWithYPinned(), CVcfGlyph::x_DrawLabelWithYPinned(), CAlignGlyph::x_DrawMultiAlign(), CAlignGlyph::x_DrawMultiAlignLabel(), CCdsGlyph::x_DrawProtSeqWithMapping(), CAlignGlyph::x_DrawPWAlign(), CFeatGlyph::x_DrawRNAProductSequence(), CFeatGlyph::x_DrawRuler(), CCrossPanelIR::x_DrawSequence(), CAlignGlyph::x_DrawTailGlyphs(), CAlignGlyph::x_DrawUnalignedBar(), CAlignGlyph::x_DrawUnalignedRowSequence(), CVcfGlyph::x_DrawVariationBar(), SGraphMaker::x_EndGraph(), CMergeTree::x_EvalGap(), CSnpJob::x_Execute(), CSGAlignStatJob::x_Execute(), CSGSeqGraphJob::x_Execute(), CBinsJob::x_Execute(), CEpigenomicsJob::x_Execute(), CSGFeatureJob::x_Execute(), CGeneModelFeatJob::x_Execute(), CSGCalcFeatHistJob::x_Execute(), CSGSegmentMapJob::x_Execute(), CSFTranslationJob::x_Execute(), CVcfFeatureJob::x_Execute(), CBlastFastaInputSource::x_FastaToSeqLoc(), CBinsJob::x_FetchGraphs(), CSnpJob::x_FetchGraphs(), COligoSpecificityCheck::x_FillGlobalAlignInfo(), CMultiAligner::x_FindConservedColumns(), CMultiAligner::x_FindConsistentHitSubset(), CMultiAligner::x_FindConstraints(), CMultiAligner::x_FindDomainHits(), CMultiAligner::x_FindInClusterConstraints(), CMultiAligner::x_FindLocalHits(), CMultiAligner::x_FindLocalInClusterHits(), COligoSpecificityCheck::x_FindOverlappingHSP(), CMultiAligner::x_FindPatternHits(), CMultiAligner::x_FindRPSHits(), CAlnVecRow::x_ForEachAlnSeg(), CCIGAR_Formatter::x_FormatLine(), CAlnGraphic::x_FormatScale(), CAlnVecRow::x_GetAlignmentTooltip_Helper(), CAlnVecRow::x_GetAlignmentTooltip_Insert(), CGuiObjectInfoSeq_align::x_GetAlignmentTooltip_Insert(), CSGAlignmentJob::x_GetAlignSmear(), CDensegGraphicDataSource::x_GetAlnStringFromCigar(), CSixFramesTransTrack::x_GetCurrentTransRange(), CAnnotObject_Less::x_GetExtremes(), CObjectIndex::x_GetFeatureCode(), CDisplaySeqalign::x_GetFeatureInfo(), CVecscreen::x_GetMatchType(), CGuiObjectInfoSeq_feat::x_GetProductSequence(), x_GetProfileMatchRanges(), CMultiAlignView::x_GetRowSeqLoc(), COligoSpecificityCheck::x_GetSlaveRangeGivenMasterRange(), CGuiObjectInfoSeq_feat::x_GetSplicedSeqTitle(), CFeatTrim::x_GetStartOffset(), CMacroEngineParallel::x_GetThreadCount(), CAlnVecRow::x_GetTooltipSequence(), CVectorTrimPanel::x_GetTrimCoordinates(), CCreateGeneModelTask::x_Group_By_GeneID(), CCleanup::x_HasShortIntron(), CAlignMarkHandler::x_HitTest(), CPairwise_CI::x_Init(), CSeq_align_Mapper_Base::x_Init(), CSeq_loc_Mapper_Base::x_InitAlign(), CAlignMarkHandler::x_InitDeltaMap(), CSeq_loc_Mapper::x_InitGCSequence(), CSeq_loc_Mapper_Base::x_InitializeLocs(), CDenseg_CI::x_InitIterator(), CBlastHitMatrix::x_InitPort(), CDenseg_CI::x_InitSegment(), CPairwise_CI::x_InitSegment(), CSparse_CI::x_InitSegment(), CSeqGlyph::x_IntersectVisible(), CAdjustForConsensusSpliceSite::x_IntronLength(), CVectorTrimPanel::x_IsCompleteCut(), CValidError_bioseq::x_IsPartialAtSpliceSiteOrGap(), CHapmapJob::x_Load(), CLDBlockJob::x_Load(), CSGAlignmentJob::x_LoadAlignmentFeats(), CSGAlignmentJob::x_LoadAlignments(), CBatchFeatJob::x_LoadFeatProducts(), CSGSegmentSmearJob::x_LoadFromDeltaSeqs(), CSGSegmentSmearJob::x_LoadFromNA(), CSGSegmentSmearJob::x_LoadFromNetCache(), CLDBlockJob::x_LoadFtable(), CSGSegmentSmearJob::x_LoadGaps(), CSGSeqGraphJob::x_LoadSeqTable(), CGraphOverlay::x_LoadSettings(), CGraphTrack::x_LoadSettings(), CSnpJob::x_MakeHistogramFromFtable(), CMappingRange::x_Map_Fuzz(), CSeq_loc_Mapper_Base::x_MapInterval(), CSeq_loc_Mapper_Base::x_MapNextRange(), CVectorTrimPanel::x_MergeCuts(), CAlnGraphic::x_MergeDifferentSeq(), CVecscreen::x_MergeInclusiveSeqalign(), COligoSpecificityCheck::x_NW_alignment(), CLinearSelHandler::x_OnChangeSelRange(), CTextSelHandler::x_OnChangeSelRange(), CGraphOverlay::x_OnLayoutChanged(), CDisplaySeqalign::x_OutputSeq(), CAlnSpanVertModel::x_PopulateRows(), CBinsJob::x_PreFetchFtable(), CAnnotObject_Info::x_ProcessAlign(), CSGFeatureJob::x_ProcessCachedBigBed(), CSGFeatureJob::x_ProcessCachedVcfTabix(), CGeneModelFeatJob::x_ProcessLandMarkFeatures(), CSeq_loc_Mapper_Base::x_PushMappedRange(), CMultiAligner::x_RealignBlocks(), CAlnVecRow::x_RenderAlignSegments(), CRuler::x_RenderAllPosLabels(), CAlnVecRow::x_RenderAveragableScores(), CAlignGlyph::x_RenderAveragableScores(), CRuler::x_RenderBackground(), CSeqTextPane::x_RenderCodons(), CTraceGraph::x_RenderConfGraph(), CSequenceTrack::x_RenderContent(), CTraceGraph::x_RenderContour(), CTraceGraph::x_RenderCurveSegment(), CFeaturePanel::x_RenderFeatureGrid(), CFeaturePanel::x_RenderHairLineSelections(), CTraceGraph::x_RenderIntensityGraphs(), CAlignGlyph::x_RenderNonAveragableScores(), CRuler::x_RenderOriginAndMetric(), CRuler::x_RenderScale(), CAlnVecRow::x_RenderSequence(), CSeqGraphicPane::x_RenderTooltipConnector(), CAlnVecRow::x_RenderUnaligned(), CInversionMergeAligner::x_RunMerger(), COligoSpecificityCheck::x_SavePrimerInfo(), COligoSpecificityCheck::x_SequencesMappedToSameTarget(), CMultiAligner::x_SetDomainHits(), CHitMatrixWidget::x_SetPortLimits(), CReportEntry::x_SetRnaCds(), CCrossAlnRenderer::x_SetupModelLimits(), CSeqGraphicRenderer::x_SetupModelLimits(), CAdjustForConsensusSpliceSite::x_ShiftExonPairBackward(), CAdjustForConsensusSpliceSite::x_ShiftExonPairForward(), CUnorderedSplitter::x_SplitDeltaExt(), CUnorderedSplitter::x_SplitSeqData(), CUnorderedSplitter::x_StripDistantAlignments(), x_TestGetSeqLocInfoVector(), CVectorTrimPanel::x_TrimFeatureLocations(), CUnorderedSplitter::x_TrimRows(), CFeatTrim::x_TrimTrnaExt(), CClonePlacementGlyph::x_UpdateBoundingBox(), CFeatGlyph::x_UpdateBoundingBox(), CLayoutTrack::x_UpdateBoundingBox(), CNamedGroup::x_UpdateBoundingBox(), CTraceGlyph::x_UpdateBoundingBox(), CVcfGlyph::x_UpdateBoundingBox(), CAdjustForConsensusSpliceSite::x_UpdateExonFeatures(), CGraphOverlay::x_UpdateLegend(), CHistogramGlyph::x_UpdateLegend(), CAlignMarkHandler::x_UpdateMarks(), x_UpdateRanges(), CVectorTrimPanel::x_UpdateSeqGraphLoc(), CSeq_annot_SortedIter::x_Valid(), CRNAValidator::x_ValidateAnticodon(), CValidError_graph::x_ValidateGraphOnDeltaBioseq(), CPsiBl2SeqTestFixture::x_ValidatePssmVsGi129295(), CPsiBl2SeqTestFixture::x_ValidatePssmVsGi7450545(), CSplitQueryTestFixture::x_ValidateQuerySeqLocsPerChunk(), CValidError_align::x_ValidateSeqLength(), CMultiAligner::x_ValidateUserHits(), CHitMatrixWidget::x_ZoomToHits(), CGff2Writer::xAssignFeatureAttributePartial(), CGff3Writer::xAssignSourceEndpoints(), CGffIdGenerator::xExtractFeatureLocation(), CGff3Writer::xWriteSequenceHeader(), and CAlnMultiWidget::ZoomToSelection().

◆ GetGap_extend()

TGap_extend CParameters_Base::GetGap_extend ( void  ) const

Get the Gap_extend member data.

Returns
Copy of the member data.

◆ GetGap_open()

TGap_open CParameters_Base::GetGap_open ( void  ) const

Get the Gap_open member data.

Returns
Copy of the member data.

◆ GetGaps()

TGaps CHsp_Base::GetGaps ( void  ) const

Get the Gaps member data.

Returns
Copy of the member data.

◆ GetHit_frame()

THit_frame CHsp_Base::GetHit_frame ( void  ) const

Get the Hit_frame member data.

Returns
Copy of the member data.

◆ GetHit_from()

THit_from CHsp_Base::GetHit_from ( void  ) const

Get the Hit_from member data.

Returns
Copy of the member data.

◆ GetHit_strand()

const CHsp_Base::THit_strand & CHsp_Base::GetHit_strand ( void  ) const
inline

Get the Hit_strand member data.

Returns
Reference to the member data.

Definition at line 1748 of file Hsp_.hpp.

References CHsp_Base::CanGetHit_strand(), CHsp_Base::m_Hit_strand, and CSerialObject::ThrowUnassigned().

◆ GetHit_to()

THit_to CHsp_Base::GetHit_to ( void  ) const

Get the Hit_to member data.

Returns
Copy of the member data.

◆ GetHits()

template<bool LEGACY, unsigned long NHITS, typename derived_t >
const CSearch_Base::THits & CSearch_Base< LEGACY, NHITS, derived_t >::GetHits ( void  ) const
inline

Get the Hits member data.

Returns
Reference to the member data.

Definition at line 587 of file Search_.hpp.

References CSearch_Base< LEGACY, NHITS, derived_t >::m_Hits.

Referenced by CSearch< LEGACY, NHITS >::CalcNSort().

◆ GetHseq()

const THseq& CHsp_Base::GetHseq ( void  ) const

Get the Hseq member data.

Returns
Reference to the member data.

◆ GetHsp_len()

THsp_len CStatistics_Base::GetHsp_len ( void  ) const

Get the Hsp_len member data.

Returns
Copy of the member data.

◆ GetHsps()

const THsps& CHit_Base::GetHsps ( void  ) const

Get the Hsps member data.

Returns
Reference to the member data.

◆ GetId()

const CHitDescr_Base::TId & CHitDescr_Base::GetId ( void  ) const
inline

Get the Id member data.

Returns
Reference to the member data.

Definition at line 346 of file HitDescr_.hpp.

References CHitDescr_Base::CanGetId(), CHitDescr_Base::m_Id, and CSerialObject::ThrowUnassigned().

◆ GetIdentity()

TIdentity CHsp_Base::GetIdentity ( void  ) const

Get the Identity member data.

Returns
Copy of the member data.

◆ GetInclude()

TInclude CParameters_Base::GetInclude ( void  ) const

Get the Include member data.

Returns
Copy of the member data.

◆ GetIter_num()

TIter_num CIteration_Base::GetIter_num ( void  ) const

Get the Iter_num member data.

Returns
Copy of the member data.

◆ GetIterations()

const CResults_Base::TIterations & CResults_Base::GetIterations ( void  ) const
inline

Get the variant data.

Returns
Reference to the data.

Definition at line 295 of file Results_.hpp.

References CResults_Base::CheckSelected(), CResults_Base::e_Iterations, and CResults_Base::m_Iterations.

◆ GetKappa()

TKappa CStatistics_Base::GetKappa ( void  ) const

Get the Kappa member data.

Returns
Copy of the member data.

◆ GetLambda()

TLambda CStatistics_Base::GetLambda ( void  ) const

Get the Lambda member data.

Returns
Copy of the member data.

◆ GetLen()

TLen CHit_Base::GetLen ( void  ) const

Get the Len member data.

Returns
Copy of the member data.

◆ GetMatrix()

const TMatrix& CParameters_Base::GetMatrix ( void  ) const

Get the Matrix member data.

Returns
Reference to the member data.

◆ GetMessage() [1/2]

const CErr_Base::TMessage & CErr_Base::GetMessage ( void  ) const
inline

Get the Message member data.

Returns
Reference to the member data.

Definition at line 264 of file Err_.hpp.

References CErr_Base::CanGetMessage(), CErr_Base::m_Message, and CSerialObject::ThrowUnassigned().

◆ GetMessage() [2/2]

template<bool LEGACY, unsigned long NHITS, typename derived_t >
const CSearch_Base::TMessage & CSearch_Base< LEGACY, NHITS, derived_t >::GetMessage ( void  ) const
inline

Get the Message member data.

Returns
Reference to the member data.

Definition at line 633 of file Search_.hpp.

References CSearch_Base< LEGACY, NHITS, derived_t >::CanGetMessage(), CSearch_Base< LEGACY, NHITS, derived_t >::m_Message, and CSerialObject::ThrowUnassigned().

◆ GetMidline()

const TMidline& CHsp_Base::GetMidline ( void  ) const

Get the Midline member data.

Returns
Reference to the member data.

◆ GetNum() [1/2]

TNum CHit_Base::GetNum ( void  ) const

Get the Num member data.

Returns
Copy of the member data.

◆ GetNum() [2/2]

TNum CHsp_Base::GetNum ( void  ) const

Get the Num member data.

Returns
Copy of the member data.

◆ GetParams()

const CReport_Base::TParams & CReport_Base::GetParams ( void  ) const
inline

Get the Params member data.

Returns
Reference to the member data.

Definition at line 560 of file Report_.hpp.

References CReport_Base::m_Params, and CReport_Base::ResetParams().

◆ GetPattern()

const TPattern& CParameters_Base::GetPattern ( void  ) const

Get the Pattern member data.

Returns
Reference to the member data.

◆ GetPattern_from()

TPattern_from CHsp_Base::GetPattern_from ( void  ) const

Get the Pattern_from member data.

Returns
Copy of the member data.

◆ GetPattern_to()

TPattern_to CHsp_Base::GetPattern_to ( void  ) const

Get the Pattern_to member data.

Returns
Copy of the member data.

◆ GetPositive()

TPositive CHsp_Base::GetPositive ( void  ) const

Get the Positive member data.

Returns
Copy of the member data.

◆ GetProgram()

const CReport_Base::TProgram & CReport_Base::GetProgram ( void  ) const
inline

Get the Program member data.

Returns
Reference to the member data.

Definition at line 389 of file Report_.hpp.

References CReport_Base::CanGetProgram(), CReport_Base::m_Program, and CSerialObject::ThrowUnassigned().

◆ GetQseq()

const TQseq& CHsp_Base::GetQseq ( void  ) const

Get the Qseq member data.

Returns
Reference to the member data.

◆ GetQuery_frame()

TQuery_frame CHsp_Base::GetQuery_frame ( void  ) const

Get the Query_frame member data.

Returns
Copy of the member data.

◆ GetQuery_from()

TQuery_from CHsp_Base::GetQuery_from ( void  ) const

Get the Query_from member data.

Returns
Copy of the member data.

◆ GetQuery_gencode()

CParameters_Base::TQuery_gencode CParameters_Base::GetQuery_gencode ( void  ) const
inline

Get the Query_gencode member data.

Returns
Copy of the member data.

Definition at line 1240 of file Parameters_.hpp.

References CParameters_Base::CanGetQuery_gencode(), CParameters_Base::m_Query_gencode, and CSerialObject::ThrowUnassigned().

◆ GetQuery_id()

template<bool LEGACY, unsigned long NHITS, typename derived_t >
const CSearch_Base::TQuery_id & CSearch_Base< LEGACY, NHITS, derived_t >::GetQuery_id ( void  ) const
inline

Get the Query_id member data.

Returns
Reference to the member data.

Definition at line 421 of file Search_.hpp.

References CSearch_Base< LEGACY, NHITS, derived_t >::CanGetQuery_id(), CSearch_Base< LEGACY, NHITS, derived_t >::m_Query_id, and CSerialObject::ThrowUnassigned().