Code generated by DATATOOL from 'gnomon.asn' (module 'NCBI-GNOMON')

Collaboration diagram for Code generated by DATATOOL from 'gnomon.asn' (module 'NCBI-GNOMON'):

Classes
class	CExon_params
	CExon_params –. More...
class	CExon_params_Base
	CExon_params_Base –. More...
class	CGnomon_param
	CGnomon_param –. More...
class	CGnomon_param_Base
	CGnomon_param_Base –. More...
class	CGnomon_param_Base::C_Gc_content_range
	percents More...
class	CGnomon_param_Base::C_Param
	C_Param –. More...
class	CGnomon_params
	CGnomon_params –. More...
class	CGnomon_params_Base
	CGnomon_params_Base –. More...
class	CIntergenic_params
	CIntergenic_params –. More...
class	CIntergenic_params_Base
	CIntergenic_params_Base –. More...
class	CIntron_params
	CIntron_params –. More...
class	CIntron_params_Base
	CIntron_params_Base –. More...
class	CLength_distribution_params
	CLength_distribution_params –. More...
class	CLength_distribution_params_Base
	CLength_distribution_params_Base –. More...
class	CLength_distribution_params_Base::C_Range
	C_Range –. More...
class	CMarkov_chain_array
	CMarkov_chain_array –. More...
class	CMarkov_chain_array_Base
	CMarkov_chain_array_Base –. More...
class	CMarkov_chain_params
	CMarkov_chain_params –. More...
class	CMarkov_chain_params_Base
	CMarkov_chain_params_Base –. More...
class	CMarkov_chain_params_Base::C_E_Probabilities
	C_E_Probabilities –. More...

Typedefs
typedef CExon_params_Base	CExon_params::Tparent
typedef CSerialObject	CExon_params_Base::Tparent
typedef list< double >	CExon_params_Base::TFirst_exon_phase_probabilities
typedef list< double >	CExon_params_Base::TInternal_exon_phase_probabilities
typedef CLength_distribution_params	CExon_params_Base::TFirst_exon_length
typedef CLength_distribution_params	CExon_params_Base::TInternal_exon_length
typedef CLength_distribution_params	CExon_params_Base::TLast_exon_length
typedef CLength_distribution_params	CExon_params_Base::TSingle_exon_length
typedef Tparent::CMemberIndex< E_memberIndex, 7 >	CExon_params_Base::TmemberIndex
typedef CGnomon_param_Base	CGnomon_param::Tparent
typedef CSerialObject	CGnomon_param_Base::Tparent
typedef CSerialObject	CGnomon_param_Base::C_Gc_content_range::Tparent
typedef int	CGnomon_param_Base::C_Gc_content_range::TFrom
typedef int	CGnomon_param_Base::C_Gc_content_range::TTo
typedef Tparent::CMemberIndex< E_memberIndex, 3 >	CGnomon_param_Base::C_Gc_content_range::TmemberIndex
typedef CSerialObject	CGnomon_param_Base::C_Param::Tparent
typedef CIntergenic_params	CGnomon_param_Base::C_Param::TIntergenic
typedef CIntron_params	CGnomon_param_Base::C_Param::TIntron
typedef CExon_params	CGnomon_param_Base::C_Param::TExon
typedef CMarkov_chain_array	CGnomon_param_Base::C_Param::TStart
typedef CMarkov_chain_array	CGnomon_param_Base::C_Param::TStop
typedef CMarkov_chain_array	CGnomon_param_Base::C_Param::TDonor
typedef CMarkov_chain_array	CGnomon_param_Base::C_Param::TAcceptor
typedef list< CRef< CMarkov_chain_params > >	CGnomon_param_Base::C_Param::TCoding_region
typedef CMarkov_chain_params	CGnomon_param_Base::C_Param::TNon_coding_region
typedef C_Gc_content_range	CGnomon_param_Base::TGc_content_range
typedef C_Param	CGnomon_param_Base::TParam
typedef Tparent::CMemberIndex< E_memberIndex, 3 >	CGnomon_param_Base::TmemberIndex
typedef CGnomon_params_Base	CGnomon_params::Tparent
typedef CSerialObject	CGnomon_params_Base::Tparent
typedef list< CRef< CGnomon_param > >	CGnomon_params_Base::Tdata
typedef CIntergenic_params_Base	CIntergenic_params::Tparent
typedef CSerialObject	CIntergenic_params_Base::Tparent
typedef double	CIntergenic_params_Base::TInitp
typedef double	CIntergenic_params_Base::TTo_single
typedef CLength_distribution_params	CIntergenic_params_Base::TLength
typedef Tparent::CMemberIndex< E_memberIndex, 4 >	CIntergenic_params_Base::TmemberIndex
typedef CIntron_params_Base	CIntron_params::Tparent
typedef CSerialObject	CIntron_params_Base::Tparent
typedef double	CIntron_params_Base::TInitp
typedef list< double >	CIntron_params_Base::TPhase_probabilities
typedef double	CIntron_params_Base::TTo_term
typedef CLength_distribution_params	CIntron_params_Base::TLength
typedef Tparent::CMemberIndex< E_memberIndex, 5 >	CIntron_params_Base::TmemberIndex
typedef CLength_distribution_params_Base	CLength_distribution_params::Tparent
typedef CSerialObject	CLength_distribution_params_Base::Tparent
typedef CSerialObject	CLength_distribution_params_Base::C_Range::Tparent
typedef int	CLength_distribution_params_Base::C_Range::TMin
typedef int	CLength_distribution_params_Base::C_Range::TMax
typedef Tparent::CMemberIndex< E_memberIndex, 3 >	CLength_distribution_params_Base::C_Range::TmemberIndex
typedef int	CLength_distribution_params_Base::TStep
typedef list< double >	CLength_distribution_params_Base::TP
typedef double	CLength_distribution_params_Base::TA
typedef double	CLength_distribution_params_Base::TL
typedef C_Range	CLength_distribution_params_Base::TRange
typedef Tparent::CMemberIndex< E_memberIndex, 6 >	CLength_distribution_params_Base::TmemberIndex
typedef CMarkov_chain_array_Base	CMarkov_chain_array::Tparent
typedef CSerialObject	CMarkov_chain_array_Base::Tparent
typedef int	CMarkov_chain_array_Base::TIn_exon
typedef int	CMarkov_chain_array_Base::TIn_intron
typedef list< CRef< CMarkov_chain_params > >	CMarkov_chain_array_Base::TMatrix
typedef Tparent::CMemberIndex< E_memberIndex, 4 >	CMarkov_chain_array_Base::TmemberIndex
typedef CMarkov_chain_params_Base	CMarkov_chain_params::Tparent
typedef CSerialObject	CMarkov_chain_params_Base::Tparent
typedef CSerialObject	CMarkov_chain_params_Base::C_E_Probabilities::Tparent
typedef CMarkov_chain_params	CMarkov_chain_params_Base::C_E_Probabilities::TPrev_order
typedef double	CMarkov_chain_params_Base::C_E_Probabilities::TValue
typedef int	CMarkov_chain_params_Base::TOrder
typedef C_E_Probabilities	CMarkov_chain_params_Base::C_E
typedef list< CRef< C_E_Probabilities > >	CMarkov_chain_params_Base::TProbabilities
typedef Tparent::CMemberIndex< E_memberIndex, 3 >	CMarkov_chain_params_Base::TmemberIndex

Enumerations
enum class	CExon_params_Base::E_memberIndex {   CExon_params_Base::e__allMandatory = 0 , CExon_params_Base::e_first_exon_phase_probabilities , CExon_params_Base::e_internal_exon_phase_probabilities , CExon_params_Base::e_first_exon_length ,   CExon_params_Base::e_internal_exon_length , CExon_params_Base::e_last_exon_length , CExon_params_Base::e_single_exon_length }
enum class	CGnomon_param_Base::C_Gc_content_range::E_memberIndex { CGnomon_param_Base::C_Gc_content_range::e__allMandatory = 0 , CGnomon_param_Base::C_Gc_content_range::e_from , CGnomon_param_Base::C_Gc_content_range::e_to }
enum	CGnomon_param_Base::C_Param::E_Choice {   CGnomon_param_Base::C_Param::e_not_set = 0 , CGnomon_param_Base::C_Param::e_Intergenic , CGnomon_param_Base::C_Param::e_Intron , CGnomon_param_Base::C_Param::e_Exon ,   CGnomon_param_Base::C_Param::e_Start , CGnomon_param_Base::C_Param::e_Stop , CGnomon_param_Base::C_Param::e_Donor , CGnomon_param_Base::C_Param::e_Acceptor ,   CGnomon_param_Base::C_Param::e_Coding_region , CGnomon_param_Base::C_Param::e_Non_coding_region }
	Choice variants. More...
enum	CGnomon_param_Base::C_Param::E_ChoiceStopper { CGnomon_param_Base::C_Param::e_MaxChoice = 10 }
	Maximum+1 value of the choice variant enumerator. More...
enum class	CGnomon_param_Base::E_memberIndex { CGnomon_param_Base::e__allMandatory = 0 , CGnomon_param_Base::e_gc_content_range , CGnomon_param_Base::e_param }
enum class	CIntergenic_params_Base::E_memberIndex { CIntergenic_params_Base::e__allMandatory = 0 , CIntergenic_params_Base::e_initp , CIntergenic_params_Base::e_to_single , CIntergenic_params_Base::e_length }
enum class	CIntron_params_Base::E_memberIndex {   CIntron_params_Base::e__allMandatory = 0 , CIntron_params_Base::e_initp , CIntron_params_Base::e_phase_probabilities , CIntron_params_Base::e_to_term ,   CIntron_params_Base::e_length }
enum class	CLength_distribution_params_Base::C_Range::E_memberIndex { CLength_distribution_params_Base::C_Range::e__allMandatory = 0 , CLength_distribution_params_Base::C_Range::e_min , CLength_distribution_params_Base::C_Range::e_max }
enum class	CLength_distribution_params_Base::E_memberIndex {   CLength_distribution_params_Base::e__allMandatory = 0 , CLength_distribution_params_Base::e_step , CLength_distribution_params_Base::e_p , CLength_distribution_params_Base::e_a ,   CLength_distribution_params_Base::e_l , CLength_distribution_params_Base::e_range }
enum class	CMarkov_chain_array_Base::E_memberIndex { CMarkov_chain_array_Base::e__allMandatory = 0 , CMarkov_chain_array_Base::e_in_exon , CMarkov_chain_array_Base::e_in_intron , CMarkov_chain_array_Base::e_matrix }
enum	CMarkov_chain_params_Base::C_E_Probabilities::E_Choice { CMarkov_chain_params_Base::C_E_Probabilities::e_not_set = 0 , CMarkov_chain_params_Base::C_E_Probabilities::e_Prev_order , CMarkov_chain_params_Base::C_E_Probabilities::e_Value }
	Choice variants. More...
enum	CMarkov_chain_params_Base::C_E_Probabilities::E_ChoiceStopper { CMarkov_chain_params_Base::C_E_Probabilities::e_MaxChoice = 3 }
	Maximum+1 value of the choice variant enumerator. More...
enum class	CMarkov_chain_params_Base::E_memberIndex { CMarkov_chain_params_Base::e__allMandatory = 0 , CMarkov_chain_params_Base::e_order , CMarkov_chain_params_Base::e_probabilities }

Functions
	CExon_params::CExon_params (void)
	CExon_params::~CExon_params (void)
	CExon_params::CExon_params (const CExon_params &value)
CExon_params &	CExon_params::operator= (const CExon_params &value)
	CExon_params_Base::CExon_params_Base (void)
virtual	CExon_params_Base::~CExon_params_Base (void)
	CExon_params_Base::DECLARE_INTERNAL_TYPE_INFO ()
bool	CExon_params_Base::IsSetFirst_exon_phase_probabilities (void) const
	3 elements (per end phase) Check if a value has been assigned to First_exon_phase_probabilities data member. More...
bool	CExon_params_Base::CanGetFirst_exon_phase_probabilities (void) const
	Check if it is safe to call GetFirst_exon_phase_probabilities method. More...
void	CExon_params_Base::ResetFirst_exon_phase_probabilities (void)
	Reset First_exon_phase_probabilities data member. More...
const TFirst_exon_phase_probabilities &	CExon_params_Base::GetFirst_exon_phase_probabilities (void) const
	Get the First_exon_phase_probabilities member data. More...
TFirst_exon_phase_probabilities &	CExon_params_Base::SetFirst_exon_phase_probabilities (void)
	Assign a value to First_exon_phase_probabilities data member. More...
bool	CExon_params_Base::IsSetInternal_exon_phase_probabilities (void) const
	3*3 elements (begin phase x end phase) Check if a value has been assigned to Internal_exon_phase_probabilities data member. More...
bool	CExon_params_Base::CanGetInternal_exon_phase_probabilities (void) const
	Check if it is safe to call GetInternal_exon_phase_probabilities method. More...
void	CExon_params_Base::ResetInternal_exon_phase_probabilities (void)
	Reset Internal_exon_phase_probabilities data member. More...
const TInternal_exon_phase_probabilities &	CExon_params_Base::GetInternal_exon_phase_probabilities (void) const
	Get the Internal_exon_phase_probabilities member data. More...
TInternal_exon_phase_probabilities &	CExon_params_Base::SetInternal_exon_phase_probabilities (void)
	Assign a value to Internal_exon_phase_probabilities data member. More...
bool	CExon_params_Base::IsSetFirst_exon_length (void) const
	Check if a value has been assigned to First_exon_length data member. More...
bool	CExon_params_Base::CanGetFirst_exon_length (void) const
	Check if it is safe to call GetFirst_exon_length method. More...
void	CExon_params_Base::ResetFirst_exon_length (void)
	Reset First_exon_length data member. More...
const TFirst_exon_length &	CExon_params_Base::GetFirst_exon_length (void) const
	Get the First_exon_length member data. More...
void	CExon_params_Base::SetFirst_exon_length (TFirst_exon_length &value)
	Assign a value to First_exon_length data member. More...
TFirst_exon_length &	CExon_params_Base::SetFirst_exon_length (void)
	Assign a value to First_exon_length data member. More...
bool	CExon_params_Base::IsSetInternal_exon_length (void) const
	Check if a value has been assigned to Internal_exon_length data member. More...
bool	CExon_params_Base::CanGetInternal_exon_length (void) const
	Check if it is safe to call GetInternal_exon_length method. More...
void	CExon_params_Base::ResetInternal_exon_length (void)
	Reset Internal_exon_length data member. More...
const TInternal_exon_length &	CExon_params_Base::GetInternal_exon_length (void) const
	Get the Internal_exon_length member data. More...
void	CExon_params_Base::SetInternal_exon_length (TInternal_exon_length &value)
	Assign a value to Internal_exon_length data member. More...
TInternal_exon_length &	CExon_params_Base::SetInternal_exon_length (void)
	Assign a value to Internal_exon_length data member. More...
bool	CExon_params_Base::IsSetLast_exon_length (void) const
	Check if a value has been assigned to Last_exon_length data member. More...
bool	CExon_params_Base::CanGetLast_exon_length (void) const
	Check if it is safe to call GetLast_exon_length method. More...
void	CExon_params_Base::ResetLast_exon_length (void)
	Reset Last_exon_length data member. More...
const TLast_exon_length &	CExon_params_Base::GetLast_exon_length (void) const
	Get the Last_exon_length member data. More...
void	CExon_params_Base::SetLast_exon_length (TLast_exon_length &value)
	Assign a value to Last_exon_length data member. More...
TLast_exon_length &	CExon_params_Base::SetLast_exon_length (void)
	Assign a value to Last_exon_length data member. More...
bool	CExon_params_Base::IsSetSingle_exon_length (void) const
	Check if a value has been assigned to Single_exon_length data member. More...
bool	CExon_params_Base::CanGetSingle_exon_length (void) const
	Check if it is safe to call GetSingle_exon_length method. More...
void	CExon_params_Base::ResetSingle_exon_length (void)
	Reset Single_exon_length data member. More...
const TSingle_exon_length &	CExon_params_Base::GetSingle_exon_length (void) const
	Get the Single_exon_length member data. More...
void	CExon_params_Base::SetSingle_exon_length (TSingle_exon_length &value)
	Assign a value to Single_exon_length data member. More...
TSingle_exon_length &	CExon_params_Base::SetSingle_exon_length (void)
	Assign a value to Single_exon_length data member. More...
virtual void	CExon_params_Base::Reset (void)
	Reset the whole object. More...
	CExon_params_Base::CExon_params_Base (const CExon_params_Base &)
CExon_params_Base &	CExon_params_Base::operator= (const CExon_params_Base &)
	CGnomon_param::CGnomon_param (void)
	CGnomon_param::~CGnomon_param (void)
	CGnomon_param::CGnomon_param (const CGnomon_param &value)
CGnomon_param &	CGnomon_param::operator= (const CGnomon_param &value)
	CGnomon_param_Base::CGnomon_param_Base (void)
virtual	CGnomon_param_Base::~CGnomon_param_Base (void)
	CGnomon_param_Base::DECLARE_INTERNAL_TYPE_INFO ()
	CGnomon_param_Base::C_Gc_content_range::C_Gc_content_range (void)
	CGnomon_param_Base::C_Gc_content_range::~C_Gc_content_range (void)
	CGnomon_param_Base::C_Gc_content_range::DECLARE_INTERNAL_TYPE_INFO ()
bool	CGnomon_param_Base::C_Gc_content_range::IsSetFrom (void) const
	Check if a value has been assigned to From data member. More...
bool	CGnomon_param_Base::C_Gc_content_range::CanGetFrom (void) const
	Check if it is safe to call GetFrom method. More...
void	CGnomon_param_Base::C_Gc_content_range::ResetFrom (void)
	Reset From data member. More...
TFrom	CGnomon_param_Base::C_Gc_content_range::GetFrom (void) const
	Get the From member data. More...
void	CGnomon_param_Base::C_Gc_content_range::SetFrom (TFrom value)
	Assign a value to From data member. More...
TFrom &	CGnomon_param_Base::C_Gc_content_range::SetFrom (void)
	Assign a value to From data member. More...
bool	CGnomon_param_Base::C_Gc_content_range::IsSetTo (void) const
	Check if a value has been assigned to To data member. More...
bool	CGnomon_param_Base::C_Gc_content_range::CanGetTo (void) const
	Check if it is safe to call GetTo method. More...
void	CGnomon_param_Base::C_Gc_content_range::ResetTo (void)
	Reset To data member. More...
TTo	CGnomon_param_Base::C_Gc_content_range::GetTo (void) const
	Get the To member data. More...
void	CGnomon_param_Base::C_Gc_content_range::SetTo (TTo value)
	Assign a value to To data member. More...
TTo &	CGnomon_param_Base::C_Gc_content_range::SetTo (void)
	Assign a value to To data member. More...
void	CGnomon_param_Base::C_Gc_content_range::Reset (void)
	Reset the whole object. More...
	CGnomon_param_Base::C_Gc_content_range::C_Gc_content_range (const C_Gc_content_range &)
C_Gc_content_range &	CGnomon_param_Base::C_Gc_content_range::operator= (const C_Gc_content_range &)
	CGnomon_param_Base::C_Param::C_Param (void)
	CGnomon_param_Base::C_Param::~C_Param (void)
	CGnomon_param_Base::C_Param::DECLARE_INTERNAL_TYPE_INFO ()
void	CGnomon_param_Base::C_Param::Reset (void)
	Reset the whole object. More...
void	CGnomon_param_Base::C_Param::ResetSelection (void)
	Reset the selection (set it to e_not_set). More...
E_Choice	CGnomon_param_Base::C_Param::Which (void) const
	Which variant is currently selected. More...
void	CGnomon_param_Base::C_Param::CheckSelected (E_Choice index) const
	Verify selection, throw exception if it differs from the expected. More...
void	CGnomon_param_Base::C_Param::ThrowInvalidSelection (E_Choice index) const
	Throw 'InvalidSelection' exception. More...
static string	CGnomon_param_Base::C_Param::SelectionName (E_Choice index)
	Retrieve selection name (for diagnostic purposes). More...
void	CGnomon_param_Base::C_Param::Select (E_Choice index, EResetVariant reset=eDoResetVariant)
	Select the requested variant if needed. More...
void	CGnomon_param_Base::C_Param::Select (E_Choice index, EResetVariant reset, CObjectMemoryPool *pool)
	Select the requested variant if needed, allocating CObject variants from memory pool. More...
bool	CGnomon_param_Base::C_Param::IsIntergenic (void) const
	Check if variant Intergenic is selected. More...
const TIntergenic &	CGnomon_param_Base::C_Param::GetIntergenic (void) const
	Get the variant data. More...
TIntergenic &	CGnomon_param_Base::C_Param::SetIntergenic (void)
	Select the variant. More...
void	CGnomon_param_Base::C_Param::SetIntergenic (TIntergenic &value)
	Select the variant and set its data. More...
bool	CGnomon_param_Base::C_Param::IsIntron (void) const
	Check if variant Intron is selected. More...
const TIntron &	CGnomon_param_Base::C_Param::GetIntron (void) const
	Get the variant data. More...
TIntron &	CGnomon_param_Base::C_Param::SetIntron (void)
	Select the variant. More...
void	CGnomon_param_Base::C_Param::SetIntron (TIntron &value)
	Select the variant and set its data. More...
bool	CGnomon_param_Base::C_Param::IsExon (void) const
	Check if variant Exon is selected. More...
const TExon &	CGnomon_param_Base::C_Param::GetExon (void) const
	Get the variant data. More...
TExon &	CGnomon_param_Base::C_Param::SetExon (void)
	Select the variant. More...
void	CGnomon_param_Base::C_Param::SetExon (TExon &value)
	Select the variant and set its data. More...
bool	CGnomon_param_Base::C_Param::IsStart (void) const
	Check if variant Start is selected. More...
const TStart &	CGnomon_param_Base::C_Param::GetStart (void) const
	Get the variant data. More...
TStart &	CGnomon_param_Base::C_Param::SetStart (void)
	Select the variant. More...
void	CGnomon_param_Base::C_Param::SetStart (TStart &value)
	Select the variant and set its data. More...
bool	CGnomon_param_Base::C_Param::IsStop (void) const
	Check if variant Stop is selected. More...
const TStop &	CGnomon_param_Base::C_Param::GetStop (void) const
	Get the variant data. More...
TStop &	CGnomon_param_Base::C_Param::SetStop (void)
	Select the variant. More...
void	CGnomon_param_Base::C_Param::SetStop (TStop &value)
	Select the variant and set its data. More...
bool	CGnomon_param_Base::C_Param::IsDonor (void) const
	Check if variant Donor is selected. More...
const TDonor &	CGnomon_param_Base::C_Param::GetDonor (void) const
	Get the variant data. More...
TDonor &	CGnomon_param_Base::C_Param::SetDonor (void)
	Select the variant. More...
void	CGnomon_param_Base::C_Param::SetDonor (TDonor &value)
	Select the variant and set its data. More...
bool	CGnomon_param_Base::C_Param::IsAcceptor (void) const
	Check if variant Acceptor is selected. More...
const TAcceptor &	CGnomon_param_Base::C_Param::GetAcceptor (void) const
	Get the variant data. More...
TAcceptor &	CGnomon_param_Base::C_Param::SetAcceptor (void)
	Select the variant. More...
void	CGnomon_param_Base::C_Param::SetAcceptor (TAcceptor &value)
	Select the variant and set its data. More...
bool	CGnomon_param_Base::C_Param::IsCoding_region (void) const
	Check if variant Coding_region is selected. More...
const TCoding_region &	CGnomon_param_Base::C_Param::GetCoding_region (void) const
	Get the variant data. More...
TCoding_region &	CGnomon_param_Base::C_Param::SetCoding_region (void)
	Select the variant. More...
bool	CGnomon_param_Base::C_Param::IsNon_coding_region (void) const
	Check if variant Non_coding_region is selected. More...
const TNon_coding_region &	CGnomon_param_Base::C_Param::GetNon_coding_region (void) const
	Get the variant data. More...
TNon_coding_region &	CGnomon_param_Base::C_Param::SetNon_coding_region (void)
	Select the variant. More...
void	CGnomon_param_Base::C_Param::SetNon_coding_region (TNon_coding_region &value)
	Select the variant and set its data. More...
	CGnomon_param_Base::C_Param::C_Param (const C_Param &)
C_Param &	CGnomon_param_Base::C_Param::operator= (const C_Param &)
void	CGnomon_param_Base::C_Param::DoSelect (E_Choice index, CObjectMemoryPool *pool=0)
bool	CGnomon_param_Base::IsSetGc_content_range (void) const
	Check if a value has been assigned to Gc_content_range data member. More...
bool	CGnomon_param_Base::CanGetGc_content_range (void) const
	Check if it is safe to call GetGc_content_range method. More...
void	CGnomon_param_Base::ResetGc_content_range (void)
	Reset Gc_content_range data member. More...
const TGc_content_range &	CGnomon_param_Base::GetGc_content_range (void) const
	Get the Gc_content_range member data. More...
void	CGnomon_param_Base::SetGc_content_range (TGc_content_range &value)
	Assign a value to Gc_content_range data member. More...
TGc_content_range &	CGnomon_param_Base::SetGc_content_range (void)
	Assign a value to Gc_content_range data member. More...
bool	CGnomon_param_Base::IsSetParam (void) const
	Check if a value has been assigned to Param data member. More...
bool	CGnomon_param_Base::CanGetParam (void) const
	Check if it is safe to call GetParam method. More...
void	CGnomon_param_Base::ResetParam (void)
	Reset Param data member. More...
const TParam &	CGnomon_param_Base::GetParam (void) const
	Get the Param member data. More...
void	CGnomon_param_Base::SetParam (TParam &value)
	Assign a value to Param data member. More...
TParam &	CGnomon_param_Base::SetParam (void)
	Assign a value to Param data member. More...
virtual void	CGnomon_param_Base::Reset (void)
	Reset the whole object. More...
	CGnomon_param_Base::CGnomon_param_Base (const CGnomon_param_Base &)
CGnomon_param_Base &	CGnomon_param_Base::operator= (const CGnomon_param_Base &)
	CGnomon_params::CGnomon_params (void)
	CGnomon_params::~CGnomon_params (void)
	CGnomon_params::CGnomon_params (const CGnomon_params &value)
CGnomon_params &	CGnomon_params::operator= (const CGnomon_params &value)
	CGnomon_params_Base::CGnomon_params_Base (void)
virtual	CGnomon_params_Base::~CGnomon_params_Base (void)
	CGnomon_params_Base::DECLARE_INTERNAL_TYPE_INFO ()
bool	CGnomon_params_Base::IsSet (void) const
	Check if a value has been assigned to data member. More...
bool	CGnomon_params_Base::CanGet (void) const
	Check if it is safe to call Get method. More...
void	CGnomon_params_Base::Reset (void)
	Reset data member. More...
const Tdata &	CGnomon_params_Base::Get (void) const
	Get the member data. More...
Tdata &	CGnomon_params_Base::Set (void)
	Assign a value to data member. More...
	CGnomon_params_Base::operator const Tdata & (void) const
	Conversion operator to 'const Tdata' type. More...
	CGnomon_params_Base::operator Tdata & (void)
	Conversion operator to 'Tdata' type. More...
	CGnomon_params_Base::CGnomon_params_Base (const CGnomon_params_Base &)
CGnomon_params_Base &	CGnomon_params_Base::operator= (const CGnomon_params_Base &)
	CIntergenic_params::CIntergenic_params (void)
	CIntergenic_params::~CIntergenic_params (void)
	CIntergenic_params::CIntergenic_params (const CIntergenic_params &value)
CIntergenic_params &	CIntergenic_params::operator= (const CIntergenic_params &value)
	CIntergenic_params_Base::CIntergenic_params_Base (void)
virtual	CIntergenic_params_Base::~CIntergenic_params_Base (void)
	CIntergenic_params_Base::DECLARE_INTERNAL_TYPE_INFO ()
bool	CIntergenic_params_Base::IsSetInitp (void) const
	probability of a genomic point be intergenic Check if a value has been assigned to Initp data member. More...
bool	CIntergenic_params_Base::CanGetInitp (void) const
	Check if it is safe to call GetInitp method. More...
void	CIntergenic_params_Base::ResetInitp (void)
	Reset Initp data member. More...
TInitp	CIntergenic_params_Base::GetInitp (void) const
	Get the Initp member data. More...
void	CIntergenic_params_Base::SetInitp (TInitp value)
	Assign a value to Initp data member. More...
TInitp &	CIntergenic_params_Base::SetInitp (void)
	Assign a value to Initp data member. More...
bool	CIntergenic_params_Base::IsSetTo_single (void) const
	probability of next gene to be single-exon Check if a value has been assigned to To_single data member. More...
bool	CIntergenic_params_Base::CanGetTo_single (void) const
	Check if it is safe to call GetTo_single method. More...
void	CIntergenic_params_Base::ResetTo_single (void)
	Reset To_single data member. More...
TTo_single	CIntergenic_params_Base::GetTo_single (void) const
	Get the To_single member data. More...
void	CIntergenic_params_Base::SetTo_single (TTo_single value)
	Assign a value to To_single data member. More...
TTo_single &	CIntergenic_params_Base::SetTo_single (void)
	Assign a value to To_single data member. More...
bool	CIntergenic_params_Base::IsSetLength (void) const
	Check if a value has been assigned to Length data member. More...
bool	CIntergenic_params_Base::CanGetLength (void) const
	Check if it is safe to call GetLength method. More...
void	CIntergenic_params_Base::ResetLength (void)
	Reset Length data member. More...
const TLength &	CIntergenic_params_Base::GetLength (void) const
	Get the Length member data. More...
void	CIntergenic_params_Base::SetLength (TLength &value)
	Assign a value to Length data member. More...
TLength &	CIntergenic_params_Base::SetLength (void)
	Assign a value to Length data member. More...
virtual void	CIntergenic_params_Base::Reset (void)
	Reset the whole object. More...
	CIntergenic_params_Base::CIntergenic_params_Base (const CIntergenic_params_Base &)
CIntergenic_params_Base &	CIntergenic_params_Base::operator= (const CIntergenic_params_Base &)
	CIntron_params::CIntron_params (void)
	CIntron_params::~CIntron_params (void)
	CIntron_params::CIntron_params (const CIntron_params &value)
CIntron_params &	CIntron_params::operator= (const CIntron_params &value)
	CIntron_params_Base::CIntron_params_Base (void)
virtual	CIntron_params_Base::~CIntron_params_Base (void)
	CIntron_params_Base::DECLARE_INTERNAL_TYPE_INFO ()
bool	CIntron_params_Base::IsSetInitp (void) const
	probability of a genomic point be in an intron Check if a value has been assigned to Initp data member. More...
bool	CIntron_params_Base::CanGetInitp (void) const
	Check if it is safe to call GetInitp method. More...
void	CIntron_params_Base::ResetInitp (void)
	Reset Initp data member. More...
TInitp	CIntron_params_Base::GetInitp (void) const
	Get the Initp member data. More...
void	CIntron_params_Base::SetInitp (TInitp value)
	Assign a value to Initp data member. More...
TInitp &	CIntron_params_Base::SetInitp (void)
	Assign a value to Initp data member. More...
bool	CIntron_params_Base::IsSetPhase_probabilities (void) const
	3 elements (per phase) Check if a value has been assigned to Phase_probabilities data member. More...
bool	CIntron_params_Base::CanGetPhase_probabilities (void) const
	Check if it is safe to call GetPhase_probabilities method. More...
void	CIntron_params_Base::ResetPhase_probabilities (void)
	Reset Phase_probabilities data member. More...
const TPhase_probabilities &	CIntron_params_Base::GetPhase_probabilities (void) const
	Get the Phase_probabilities member data. More...
TPhase_probabilities &	CIntron_params_Base::SetPhase_probabilities (void)
	Assign a value to Phase_probabilities data member. More...
bool	CIntron_params_Base::IsSetTo_term (void) const
	probability to be the last Check if a value has been assigned to To_term data member. More...
bool	CIntron_params_Base::CanGetTo_term (void) const
	Check if it is safe to call GetTo_term method. More...
void	CIntron_params_Base::ResetTo_term (void)
	Reset To_term data member. More...
TTo_term	CIntron_params_Base::GetTo_term (void) const
	Get the To_term member data. More...
void	CIntron_params_Base::SetTo_term (TTo_term value)
	Assign a value to To_term data member. More...
TTo_term &	CIntron_params_Base::SetTo_term (void)
	Assign a value to To_term data member. More...
bool	CIntron_params_Base::IsSetLength (void) const
	Check if a value has been assigned to Length data member. More...
bool	CIntron_params_Base::CanGetLength (void) const
	Check if it is safe to call GetLength method. More...
void	CIntron_params_Base::ResetLength (void)
	Reset Length data member. More...
const TLength &	CIntron_params_Base::GetLength (void) const
	Get the Length member data. More...
void	CIntron_params_Base::SetLength (TLength &value)
	Assign a value to Length data member. More...
TLength &	CIntron_params_Base::SetLength (void)
	Assign a value to Length data member. More...
virtual void	CIntron_params_Base::Reset (void)
	Reset the whole object. More...
	CIntron_params_Base::CIntron_params_Base (const CIntron_params_Base &)
CIntron_params_Base &	CIntron_params_Base::operator= (const CIntron_params_Base &)
	CLength_distribution_params::CLength_distribution_params (void)
	CLength_distribution_params::~CLength_distribution_params (void)
	CLength_distribution_params::CLength_distribution_params (const CLength_distribution_params &value)
CLength_distribution_params &	CLength_distribution_params::operator= (const CLength_distribution_params &value)
	CLength_distribution_params_Base::CLength_distribution_params_Base (void)
virtual	CLength_distribution_params_Base::~CLength_distribution_params_Base (void)
	CLength_distribution_params_Base::DECLARE_INTERNAL_TYPE_INFO ()
	CLength_distribution_params_Base::C_Range::C_Range (void)
	CLength_distribution_params_Base::C_Range::~C_Range (void)
	CLength_distribution_params_Base::C_Range::DECLARE_INTERNAL_TYPE_INFO ()
bool	CLength_distribution_params_Base::C_Range::IsSetMin (void) const
	Check if a value has been assigned to Min data member. More...
bool	CLength_distribution_params_Base::C_Range::CanGetMin (void) const
	Check if it is safe to call GetMin method. More...
void	CLength_distribution_params_Base::C_Range::ResetMin (void)
	Reset Min data member. More...
TMin	CLength_distribution_params_Base::C_Range::GetMin (void) const
	Get the Min member data. More...
void	CLength_distribution_params_Base::C_Range::SetMin (TMin value)
	Assign a value to Min data member. More...
TMin &	CLength_distribution_params_Base::C_Range::SetMin (void)
	Assign a value to Min data member. More...
bool	CLength_distribution_params_Base::C_Range::IsSetMax (void) const
	Check if a value has been assigned to Max data member. More...
bool	CLength_distribution_params_Base::C_Range::CanGetMax (void) const
	Check if it is safe to call GetMax method. More...
void	CLength_distribution_params_Base::C_Range::ResetMax (void)
	Reset Max data member. More...
TMax	CLength_distribution_params_Base::C_Range::GetMax (void) const
	Get the Max member data. More...
void	CLength_distribution_params_Base::C_Range::SetMax (TMax value)
	Assign a value to Max data member. More...
TMax &	CLength_distribution_params_Base::C_Range::SetMax (void)
	Assign a value to Max data member. More...
void	CLength_distribution_params_Base::C_Range::Reset (void)
	Reset the whole object. More...
	CLength_distribution_params_Base::C_Range::C_Range (const C_Range &)
C_Range &	CLength_distribution_params_Base::C_Range::operator= (const C_Range &)
bool	CLength_distribution_params_Base::IsSetStep (void) const
	Check if a value has been assigned to Step data member. More...
bool	CLength_distribution_params_Base::CanGetStep (void) const
	Check if it is safe to call GetStep method. More...
void	CLength_distribution_params_Base::ResetStep (void)
	Reset Step data member. More...
TStep	CLength_distribution_params_Base::GetStep (void) const
	Get the Step member data. More...
void	CLength_distribution_params_Base::SetStep (TStep value)
	Assign a value to Step data member. More...
TStep &	CLength_distribution_params_Base::SetStep (void)
	Assign a value to Step data member. More...
bool	CLength_distribution_params_Base::IsSetP (void) const
	P(step*(i+.5))|i=0,1,...,N-1 Check if a value has been assigned to P data member. More...
bool	CLength_distribution_params_Base::CanGetP (void) const
	Check if it is safe to call GetP method. More...
void	CLength_distribution_params_Base::ResetP (void)
	Reset P data member. More...
const TP &	CLength_distribution_params_Base::GetP (void) const
	Get the P member data. More...
TP &	CLength_distribution_params_Base::SetP (void)
	Assign a value to P data member. More...
bool	CLength_distribution_params_Base::IsSetA (void) const
	Loretz function coefficient for the tail Check if a value has been assigned to A data member. More...
bool	CLength_distribution_params_Base::CanGetA (void) const
	Check if it is safe to call GetA method. More...
void	CLength_distribution_params_Base::ResetA (void)
	Reset A data member. More...
TA	CLength_distribution_params_Base::GetA (void) const
	Get the A member data. More...
void	CLength_distribution_params_Base::SetA (TA value)
	Assign a value to A data member. More...
TA &	CLength_distribution_params_Base::SetA (void)
	Assign a value to A data member. More...
bool	CLength_distribution_params_Base::IsSetL (void) const
	Loretz function coefficient for the tail Check if a value has been assigned to L data member. More...
bool	CLength_distribution_params_Base::CanGetL (void) const
	Check if it is safe to call GetL method. More...
void	CLength_distribution_params_Base::ResetL (void)
	Reset L data member. More...
TL	CLength_distribution_params_Base::GetL (void) const
	Get the L member data. More...
void	CLength_distribution_params_Base::SetL (TL value)
	Assign a value to L data member. More...
TL &	CLength_distribution_params_Base::SetL (void)
	Assign a value to L data member. More...
bool	CLength_distribution_params_Base::IsSetRange (void) const
	Check if a value has been assigned to Range data member. More...
bool	CLength_distribution_params_Base::CanGetRange (void) const
	Check if it is safe to call GetRange method. More...
void	CLength_distribution_params_Base::ResetRange (void)
	Reset Range data member. More...
const TRange &	CLength_distribution_params_Base::GetRange (void) const
	Get the Range member data. More...
void	CLength_distribution_params_Base::SetRange (TRange &value)
	Assign a value to Range data member. More...
TRange &	CLength_distribution_params_Base::SetRange (void)
	Assign a value to Range data member. More...
virtual void	CLength_distribution_params_Base::Reset (void)
	Reset the whole object. More...
	CLength_distribution_params_Base::CLength_distribution_params_Base (const CLength_distribution_params_Base &)
CLength_distribution_params_Base &	CLength_distribution_params_Base::operator= (const CLength_distribution_params_Base &)
	CMarkov_chain_array::CMarkov_chain_array (void)
	CMarkov_chain_array::~CMarkov_chain_array (void)
	CMarkov_chain_array::CMarkov_chain_array (const CMarkov_chain_array &value)
CMarkov_chain_array &	CMarkov_chain_array::operator= (const CMarkov_chain_array &value)
	CMarkov_chain_array_Base::CMarkov_chain_array_Base (void)
virtual	CMarkov_chain_array_Base::~CMarkov_chain_array_Base (void)
	CMarkov_chain_array_Base::DECLARE_INTERNAL_TYPE_INFO ()
bool	CMarkov_chain_array_Base::IsSetIn_exon (void) const
	Check if a value has been assigned to In_exon data member. More...
bool	CMarkov_chain_array_Base::CanGetIn_exon (void) const
	Check if it is safe to call GetIn_exon method. More...
void	CMarkov_chain_array_Base::ResetIn_exon (void)
	Reset In_exon data member. More...
TIn_exon	CMarkov_chain_array_Base::GetIn_exon (void) const
	Get the In_exon member data. More...
void	CMarkov_chain_array_Base::SetIn_exon (TIn_exon value)
	Assign a value to In_exon data member. More...
TIn_exon &	CMarkov_chain_array_Base::SetIn_exon (void)
	Assign a value to In_exon data member. More...
bool	CMarkov_chain_array_Base::IsSetIn_intron (void) const
	Check if a value has been assigned to In_intron data member. More...
bool	CMarkov_chain_array_Base::CanGetIn_intron (void) const
	Check if it is safe to call GetIn_intron method. More...
void	CMarkov_chain_array_Base::ResetIn_intron (void)
	Reset In_intron data member. More...
TIn_intron	CMarkov_chain_array_Base::GetIn_intron (void) const
	Get the In_intron member data. More...
void	CMarkov_chain_array_Base::SetIn_intron (TIn_intron value)
	Assign a value to In_intron data member. More...
TIn_intron &	CMarkov_chain_array_Base::SetIn_intron (void)
	Assign a value to In_intron data member. More...
bool	CMarkov_chain_array_Base::IsSetMatrix (void) const
	in-exon+in-intron elements Check if a value has been assigned to Matrix data member. More...
bool	CMarkov_chain_array_Base::CanGetMatrix (void) const
	Check if it is safe to call GetMatrix method. More...
void	CMarkov_chain_array_Base::ResetMatrix (void)
	Reset Matrix data member. More...
const TMatrix &	CMarkov_chain_array_Base::GetMatrix (void) const
	Get the Matrix member data. More...
TMatrix &	CMarkov_chain_array_Base::SetMatrix (void)
	Assign a value to Matrix data member. More...
virtual void	CMarkov_chain_array_Base::Reset (void)
	Reset the whole object. More...
	CMarkov_chain_array_Base::CMarkov_chain_array_Base (const CMarkov_chain_array_Base &)
CMarkov_chain_array_Base &	CMarkov_chain_array_Base::operator= (const CMarkov_chain_array_Base &)
	CMarkov_chain_params::CMarkov_chain_params (void)
	CMarkov_chain_params::~CMarkov_chain_params (void)
	CMarkov_chain_params::CMarkov_chain_params (const CMarkov_chain_params &value)
CMarkov_chain_params &	CMarkov_chain_params::operator= (const CMarkov_chain_params &value)
	CMarkov_chain_params_Base::CMarkov_chain_params_Base (void)
virtual	CMarkov_chain_params_Base::~CMarkov_chain_params_Base (void)
	CMarkov_chain_params_Base::DECLARE_INTERNAL_TYPE_INFO ()
	CMarkov_chain_params_Base::C_E_Probabilities::C_E_Probabilities (void)
	CMarkov_chain_params_Base::C_E_Probabilities::~C_E_Probabilities (void)
	CMarkov_chain_params_Base::C_E_Probabilities::DECLARE_INTERNAL_TYPE_INFO ()
void	CMarkov_chain_params_Base::C_E_Probabilities::Reset (void)
	Reset the whole object. More...
void	CMarkov_chain_params_Base::C_E_Probabilities::ResetSelection (void)
	Reset the selection (set it to e_not_set). More...
E_Choice	CMarkov_chain_params_Base::C_E_Probabilities::Which (void) const
	Which variant is currently selected. More...
void	CMarkov_chain_params_Base::C_E_Probabilities::CheckSelected (E_Choice index) const
	Verify selection, throw exception if it differs from the expected. More...
void	CMarkov_chain_params_Base::C_E_Probabilities::ThrowInvalidSelection (E_Choice index) const
	Throw 'InvalidSelection' exception. More...
static string	CMarkov_chain_params_Base::C_E_Probabilities::SelectionName (E_Choice index)
	Retrieve selection name (for diagnostic purposes). More...
void	CMarkov_chain_params_Base::C_E_Probabilities::Select (E_Choice index, EResetVariant reset=eDoResetVariant)
	Select the requested variant if needed. More...
void	CMarkov_chain_params_Base::C_E_Probabilities::Select (E_Choice index, EResetVariant reset, CObjectMemoryPool *pool)
	Select the requested variant if needed, allocating CObject variants from memory pool. More...
bool	CMarkov_chain_params_Base::C_E_Probabilities::IsPrev_order (void) const
	Check if variant Prev_order is selected. More...
const TPrev_order &	CMarkov_chain_params_Base::C_E_Probabilities::GetPrev_order (void) const
	Get the variant data. More...
TPrev_order &	CMarkov_chain_params_Base::C_E_Probabilities::SetPrev_order (void)
	Select the variant. More...
void	CMarkov_chain_params_Base::C_E_Probabilities::SetPrev_order (TPrev_order &value)
	Select the variant and set its data. More...
bool	CMarkov_chain_params_Base::C_E_Probabilities::IsValue (void) const
	Check if variant Value is selected. More...
TValue	CMarkov_chain_params_Base::C_E_Probabilities::GetValue (void) const
	Get the variant data. More...
TValue &	CMarkov_chain_params_Base::C_E_Probabilities::SetValue (void)
	Select the variant. More...
void	CMarkov_chain_params_Base::C_E_Probabilities::SetValue (TValue value)
	Select the variant and set its data. More...
	CMarkov_chain_params_Base::C_E_Probabilities::C_E_Probabilities (const C_E_Probabilities &)
C_E_Probabilities &	CMarkov_chain_params_Base::C_E_Probabilities::operator= (const C_E_Probabilities &)
void	CMarkov_chain_params_Base::C_E_Probabilities::DoSelect (E_Choice index, CObjectMemoryPool *pool=0)
bool	CMarkov_chain_params_Base::IsSetOrder (void) const
	Check if a value has been assigned to Order data member. More...
bool	CMarkov_chain_params_Base::CanGetOrder (void) const
	Check if it is safe to call GetOrder method. More...
void	CMarkov_chain_params_Base::ResetOrder (void)
	Reset Order data member. More...
TOrder	CMarkov_chain_params_Base::GetOrder (void) const
	Get the Order member data. More...
void	CMarkov_chain_params_Base::SetOrder (TOrder value)
	Assign a value to Order data member. More...
TOrder &	CMarkov_chain_params_Base::SetOrder (void)
	Assign a value to Order data member. More...
bool	CMarkov_chain_params_Base::IsSetProbabilities (void) const
	Check if a value has been assigned to Probabilities data member. More...
bool	CMarkov_chain_params_Base::CanGetProbabilities (void) const
	Check if it is safe to call GetProbabilities method. More...
void	CMarkov_chain_params_Base::ResetProbabilities (void)
	Reset Probabilities data member. More...
const TProbabilities &	CMarkov_chain_params_Base::GetProbabilities (void) const
	Get the Probabilities member data. More...
TProbabilities &	CMarkov_chain_params_Base::SetProbabilities (void)
	Assign a value to Probabilities data member. More...
virtual void	CMarkov_chain_params_Base::Reset (void)
	Reset the whole object. More...
	CMarkov_chain_params_Base::CMarkov_chain_params_Base (const CMarkov_chain_params_Base &)
CMarkov_chain_params_Base &	CMarkov_chain_params_Base::operator= (const CMarkov_chain_params_Base &)

Variables
Uint4	CExon_params_Base::m_set_State [1]
list< double >	CExon_params_Base::m_First_exon_phase_probabilities
list< double >	CExon_params_Base::m_Internal_exon_phase_probabilities
CRef< TFirst_exon_length >	CExon_params_Base::m_First_exon_length
CRef< TInternal_exon_length >	CExon_params_Base::m_Internal_exon_length
CRef< TLast_exon_length >	CExon_params_Base::m_Last_exon_length
CRef< TSingle_exon_length >	CExon_params_Base::m_Single_exon_length
Uint4	CGnomon_param_Base::C_Gc_content_range::m_set_State [1]
int	CGnomon_param_Base::C_Gc_content_range::m_From
int	CGnomon_param_Base::C_Gc_content_range::m_To
E_Choice	CGnomon_param_Base::C_Param::m_choice
static const char *const	CGnomon_param_Base::C_Param::sm_SelectionNames []
NCBI_NS_NCBI::CUnionBuffer< TCoding_region >   CGnomon_param_Base::C_Param::m_Coding_region
NCBI_NS_NCBI::CSerialObject *   CGnomon_param_Base::C_Param::m_object
union {
NCBI_NS_NCBI::CUnionBuffer< TCoding_region >   CGnomon_param_Base::C_Param::m_Coding_region
NCBI_NS_NCBI::CSerialObject *   CGnomon_param_Base::C_Param::m_object
};
Uint4	CGnomon_param_Base::m_set_State [1]
CRef< TGc_content_range >	CGnomon_param_Base::m_Gc_content_range
CRef< TParam >	CGnomon_param_Base::m_Param
Uint4	CGnomon_params_Base::m_set_State [1]
list< CRef< CGnomon_param > >	CGnomon_params_Base::m_data
Uint4	CIntergenic_params_Base::m_set_State [1]
double	CIntergenic_params_Base::m_Initp
double	CIntergenic_params_Base::m_To_single
CRef< TLength >	CIntergenic_params_Base::m_Length
Uint4	CIntron_params_Base::m_set_State [1]
double	CIntron_params_Base::m_Initp
list< double >	CIntron_params_Base::m_Phase_probabilities
double	CIntron_params_Base::m_To_term
CRef< TLength >	CIntron_params_Base::m_Length
Uint4	CLength_distribution_params_Base::C_Range::m_set_State [1]
int	CLength_distribution_params_Base::C_Range::m_Min
int	CLength_distribution_params_Base::C_Range::m_Max
Uint4	CLength_distribution_params_Base::m_set_State [1]
int	CLength_distribution_params_Base::m_Step
list< double >	CLength_distribution_params_Base::m_P
double	CLength_distribution_params_Base::m_A
double	CLength_distribution_params_Base::m_L
CRef< TRange >	CLength_distribution_params_Base::m_Range
Uint4	CMarkov_chain_array_Base::m_set_State [1]
int	CMarkov_chain_array_Base::m_In_exon
int	CMarkov_chain_array_Base::m_In_intron
list< CRef< CMarkov_chain_params > >	CMarkov_chain_array_Base::m_Matrix
E_Choice	CMarkov_chain_params_Base::C_E_Probabilities::m_choice
static const char *const	CMarkov_chain_params_Base::C_E_Probabilities::sm_SelectionNames []
TValue   CMarkov_chain_params_Base::C_E_Probabilities::m_Value
NCBI_NS_NCBI::CSerialObject *   CMarkov_chain_params_Base::C_E_Probabilities::m_object
union {
TValue   CMarkov_chain_params_Base::C_E_Probabilities::m_Value
NCBI_NS_NCBI::CSerialObject *   CMarkov_chain_params_Base::C_E_Probabilities::m_object
};
Uint4	CMarkov_chain_params_Base::m_set_State [1]
int	CMarkov_chain_params_Base::m_Order
list< CRef< C_E_Probabilities > >	CMarkov_chain_params_Base::m_Probabilities

Detailed Description

Typedef Documentation

C_E

typedef C_E_Probabilities CMarkov_chain_params_Base::C_E

Definition at line 243 of file Markov_chain_params_.hpp.

TA

typedef double CLength_distribution_params_Base::TA

Definition at line 207 of file Length_distribution_params_.hpp.

TAcceptor

typedef CMarkov_chain_array CGnomon_param_Base::C_Param::TAcceptor

Definition at line 303 of file Gnomon_param_.hpp.

TCoding_region

typedef list< CRef< CMarkov_chain_params > > CGnomon_param_Base::C_Param::TCoding_region

Definition at line 304 of file Gnomon_param_.hpp.

Tdata

typedef list< CRef< CGnomon_param > > CGnomon_params_Base::Tdata

Definition at line 89 of file Gnomon_params_.hpp.

TDonor

typedef CMarkov_chain_array CGnomon_param_Base::C_Param::TDonor

Definition at line 302 of file Gnomon_param_.hpp.

TExon

typedef CExon_params CGnomon_param_Base::C_Param::TExon

Definition at line 299 of file Gnomon_param_.hpp.

TFirst_exon_length

typedef CLength_distribution_params CExon_params_Base::TFirst_exon_length

Definition at line 91 of file Exon_params_.hpp.

TFirst_exon_phase_probabilities

typedef list< double > CExon_params_Base::TFirst_exon_phase_probabilities

Definition at line 89 of file Exon_params_.hpp.

TFrom

typedef int CGnomon_param_Base::C_Gc_content_range::TFrom

Definition at line 111 of file Gnomon_param_.hpp.

TGc_content_range

typedef C_Gc_content_range CGnomon_param_Base::TGc_content_range

Definition at line 557 of file Gnomon_param_.hpp.

TIn_exon

typedef int CMarkov_chain_array_Base::TIn_exon

Definition at line 89 of file Markov_chain_array_.hpp.

TIn_intron

typedef int CMarkov_chain_array_Base::TIn_intron

Definition at line 90 of file Markov_chain_array_.hpp.

TInitp [1/2]

typedef double CIntergenic_params_Base::TInitp

Definition at line 85 of file Intergenic_params_.hpp.

TInitp [2/2]

typedef double CIntron_params_Base::TInitp

Definition at line 89 of file Intron_params_.hpp.

TIntergenic

typedef CIntergenic_params CGnomon_param_Base::C_Param::TIntergenic

Definition at line 297 of file Gnomon_param_.hpp.

TInternal_exon_length

typedef CLength_distribution_params CExon_params_Base::TInternal_exon_length

Definition at line 92 of file Exon_params_.hpp.

TInternal_exon_phase_probabilities

typedef list< double > CExon_params_Base::TInternal_exon_phase_probabilities

Definition at line 90 of file Exon_params_.hpp.

TIntron

typedef CIntron_params CGnomon_param_Base::C_Param::TIntron

Definition at line 298 of file Gnomon_param_.hpp.

TL

typedef double CLength_distribution_params_Base::TL

Definition at line 208 of file Length_distribution_params_.hpp.

TLast_exon_length

typedef CLength_distribution_params CExon_params_Base::TLast_exon_length

Definition at line 93 of file Exon_params_.hpp.

TLength [1/2]

typedef CLength_distribution_params CIntergenic_params_Base::TLength

Definition at line 87 of file Intergenic_params_.hpp.

TLength [2/2]

typedef CLength_distribution_params CIntron_params_Base::TLength

Definition at line 92 of file Intron_params_.hpp.

TMatrix

typedef list< CRef< CMarkov_chain_params > > CMarkov_chain_array_Base::TMatrix

Definition at line 91 of file Markov_chain_array_.hpp.

TMax

typedef int CLength_distribution_params_Base::C_Range::TMax

Definition at line 103 of file Length_distribution_params_.hpp.

TmemberIndex [1/9]

typedef Tparent::CMemberIndex<E_memberIndex, 7> CExon_params_Base::TmemberIndex

Definition at line 106 of file Exon_params_.hpp.

TmemberIndex [2/9]

typedef Tparent::CMemberIndex<E_memberIndex, 3> CGnomon_param_Base::C_Gc_content_range::TmemberIndex

Definition at line 120 of file Gnomon_param_.hpp.

TmemberIndex [3/9]

typedef Tparent::CMemberIndex<E_memberIndex, 3> CGnomon_param_Base::TmemberIndex

Definition at line 566 of file Gnomon_param_.hpp.

TmemberIndex [4/9]

typedef Tparent::CMemberIndex<E_memberIndex, 4> CIntergenic_params_Base::TmemberIndex

Definition at line 96 of file Intergenic_params_.hpp.

TmemberIndex [5/9]

typedef Tparent::CMemberIndex<E_memberIndex, 5> CIntron_params_Base::TmemberIndex

Definition at line 102 of file Intron_params_.hpp.

TmemberIndex [6/9]

typedef Tparent::CMemberIndex<E_memberIndex, 3> CLength_distribution_params_Base::C_Range::TmemberIndex

Definition at line 111 of file Length_distribution_params_.hpp.

TmemberIndex [7/9]

typedef Tparent::CMemberIndex<E_memberIndex, 6> CLength_distribution_params_Base::TmemberIndex

Definition at line 220 of file Length_distribution_params_.hpp.

TmemberIndex [8/9]

typedef Tparent::CMemberIndex<E_memberIndex, 4> CMarkov_chain_array_Base::TmemberIndex

Definition at line 100 of file Markov_chain_array_.hpp.

TmemberIndex [9/9]

typedef Tparent::CMemberIndex<E_memberIndex, 3> CMarkov_chain_params_Base::TmemberIndex

Definition at line 252 of file Markov_chain_params_.hpp.

TMin

typedef int CLength_distribution_params_Base::C_Range::TMin

Definition at line 102 of file Length_distribution_params_.hpp.

TNon_coding_region

typedef CMarkov_chain_params CGnomon_param_Base::C_Param::TNon_coding_region

Definition at line 305 of file Gnomon_param_.hpp.

TOrder

typedef int CMarkov_chain_params_Base::TOrder

Definition at line 242 of file Markov_chain_params_.hpp.

TP

typedef list< double > CLength_distribution_params_Base::TP

Definition at line 206 of file Length_distribution_params_.hpp.

TParam

typedef C_Param CGnomon_param_Base::TParam

Definition at line 558 of file Gnomon_param_.hpp.

Tparent [1/20]

typedef CExon_params_Base CExon_params::Tparent

private

Definition at line 67 of file Exon_params.hpp.

Tparent [2/20]

typedef CSerialObject CExon_params_Base::Tparent

private

Definition at line 78 of file Exon_params_.hpp.

Tparent [3/20]

typedef CGnomon_param_Base CGnomon_param::Tparent

private

Definition at line 67 of file Gnomon_param.hpp.

Tparent [4/20]

typedef CSerialObject CGnomon_param_Base::Tparent

private

Definition at line 82 of file Gnomon_param_.hpp.

Tparent [5/20]

typedef CSerialObject CGnomon_param_Base::C_Gc_content_range::Tparent

private

Definition at line 100 of file Gnomon_param_.hpp.

Tparent [6/20]

typedef CSerialObject CGnomon_param_Base::C_Param::Tparent

private

Definition at line 220 of file Gnomon_param_.hpp.

Tparent [7/20]

typedef CGnomon_params_Base CGnomon_params::Tparent

private

Definition at line 67 of file Gnomon_params.hpp.

Tparent [8/20]

typedef CSerialObject CGnomon_params_Base::Tparent

private

Definition at line 78 of file Gnomon_params_.hpp.

Tparent [9/20]

typedef CIntergenic_params_Base CIntergenic_params::Tparent

private

Definition at line 67 of file Intergenic_params.hpp.

Tparent [10/20]

typedef CSerialObject CIntergenic_params_Base::Tparent

private

Definition at line 74 of file Intergenic_params_.hpp.

Tparent [11/20]

typedef CIntron_params_Base CIntron_params::Tparent

private

Definition at line 67 of file Intron_params.hpp.

Tparent [12/20]

typedef CSerialObject CIntron_params_Base::Tparent

private

Definition at line 78 of file Intron_params_.hpp.

Tparent [13/20]

typedef CLength_distribution_params_Base CLength_distribution_params::Tparent

private

Definition at line 67 of file Length_distribution_params.hpp.

Tparent [14/20]

typedef CSerialObject CLength_distribution_params_Base::Tparent

private

Definition at line 74 of file Length_distribution_params_.hpp.

Tparent [15/20]

typedef CSerialObject CLength_distribution_params_Base::C_Range::Tparent

private

Definition at line 91 of file Length_distribution_params_.hpp.

Tparent [16/20]

typedef CMarkov_chain_array_Base CMarkov_chain_array::Tparent

private

Definition at line 67 of file Markov_chain_array.hpp.

Tparent [17/20]

typedef CSerialObject CMarkov_chain_array_Base::Tparent

private

Definition at line 78 of file Markov_chain_array_.hpp.

Tparent [18/20]

typedef CMarkov_chain_params_Base CMarkov_chain_params::Tparent

private

Definition at line 67 of file Markov_chain_params.hpp.

Tparent [19/20]

typedef CSerialObject CMarkov_chain_params_Base::Tparent

private

Definition at line 78 of file Markov_chain_params_.hpp.

Tparent [20/20]

typedef CSerialObject CMarkov_chain_params_Base::C_E_Probabilities::Tparent

private

Definition at line 95 of file Markov_chain_params_.hpp.

TPhase_probabilities

typedef list< double > CIntron_params_Base::TPhase_probabilities

Definition at line 90 of file Intron_params_.hpp.

TPrev_order

typedef CMarkov_chain_params CMarkov_chain_params_Base::C_E_Probabilities::TPrev_order

Definition at line 165 of file Markov_chain_params_.hpp.

TProbabilities

typedef list< CRef< C_E_Probabilities > > CMarkov_chain_params_Base::TProbabilities

Definition at line 244 of file Markov_chain_params_.hpp.

TRange

typedef C_Range CLength_distribution_params_Base::TRange

Definition at line 209 of file Length_distribution_params_.hpp.

TSingle_exon_length

typedef CLength_distribution_params CExon_params_Base::TSingle_exon_length

Definition at line 94 of file Exon_params_.hpp.

TStart

typedef CMarkov_chain_array CGnomon_param_Base::C_Param::TStart

Definition at line 300 of file Gnomon_param_.hpp.

TStep

typedef int CLength_distribution_params_Base::TStep

Definition at line 205 of file Length_distribution_params_.hpp.

TStop

typedef CMarkov_chain_array CGnomon_param_Base::C_Param::TStop

Definition at line 301 of file Gnomon_param_.hpp.

TTo

typedef int CGnomon_param_Base::C_Gc_content_range::TTo

Definition at line 112 of file Gnomon_param_.hpp.

TTo_single

typedef double CIntergenic_params_Base::TTo_single

Definition at line 86 of file Intergenic_params_.hpp.

TTo_term

typedef double CIntron_params_Base::TTo_term

Definition at line 91 of file Intron_params_.hpp.

TValue

typedef double CMarkov_chain_params_Base::C_E_Probabilities::TValue

Definition at line 166 of file Markov_chain_params_.hpp.

Enumeration Type Documentation

E_Choice [1/2]

enum CGnomon_param_Base::C_Param::E_Choice

Choice variants.

Enumerator
e_not_set	No variant selected.
e_Intergenic
e_Intron
e_Exon
e_Start
e_Stop
e_Donor
e_Acceptor
e_Coding_region	three elements (per phase)
e_Non_coding_region

Definition at line 232 of file Gnomon_param_.hpp.

E_Choice [2/2]

enum CMarkov_chain_params_Base::C_E_Probabilities::E_Choice

Choice variants.

Enumerator
e_not_set	No variant selected.
e_Prev_order
e_Value

Definition at line 107 of file Markov_chain_params_.hpp.

E_ChoiceStopper [1/2]

enum CGnomon_param_Base::C_Param::E_ChoiceStopper

Maximum+1 value of the choice variant enumerator.

Enumerator
e_MaxChoice	== e_Non_coding_region+1

Definition at line 245 of file Gnomon_param_.hpp.

E_ChoiceStopper [2/2]

enum CMarkov_chain_params_Base::C_E_Probabilities::E_ChoiceStopper

Maximum+1 value of the choice variant enumerator.

Enumerator
e_MaxChoice	== e_Value+1

Definition at line 113 of file Markov_chain_params_.hpp.

E_memberIndex [1/9]

enum CExon_params_Base::E_memberIndex

strong

Enumerator
e__allMandatory
e_first_exon_phase_probabilities
e_internal_exon_phase_probabilities
e_first_exon_length
e_internal_exon_length
e_last_exon_length
e_single_exon_length

Definition at line 97 of file Exon_params_.hpp.

E_memberIndex [2/9]

enum CGnomon_param_Base::C_Gc_content_range::E_memberIndex

strong

Enumerator
e__allMandatory
e_from
e_to

Definition at line 115 of file Gnomon_param_.hpp.

E_memberIndex [3/9]

enum CGnomon_param_Base::E_memberIndex

strong

Enumerator
e__allMandatory
e_gc_content_range
e_param

Definition at line 561 of file Gnomon_param_.hpp.

E_memberIndex [4/9]

enum CIntergenic_params_Base::E_memberIndex

strong

Enumerator
e__allMandatory
e_initp
e_to_single
e_length

Definition at line 90 of file Intergenic_params_.hpp.

E_memberIndex [5/9]

enum CIntron_params_Base::E_memberIndex

strong

Enumerator
e__allMandatory
e_initp
e_phase_probabilities
e_to_term
e_length

Definition at line 95 of file Intron_params_.hpp.

E_memberIndex [6/9]

enum CLength_distribution_params_Base::C_Range::E_memberIndex

strong

Enumerator
e__allMandatory
e_min
e_max

Definition at line 106 of file Length_distribution_params_.hpp.

E_memberIndex [7/9]

enum CLength_distribution_params_Base::E_memberIndex

strong

Enumerator
e__allMandatory
e_step
e_p
e_a
e_l
e_range

Definition at line 212 of file Length_distribution_params_.hpp.

E_memberIndex [8/9]

enum CMarkov_chain_array_Base::E_memberIndex

strong

Enumerator
e__allMandatory
e_in_exon
e_in_intron
e_matrix

Definition at line 94 of file Markov_chain_array_.hpp.

E_memberIndex [9/9]

enum CMarkov_chain_params_Base::E_memberIndex

strong

Enumerator
e__allMandatory
e_order
e_probabilities

Definition at line 247 of file Markov_chain_params_.hpp.

Function Documentation

C_E_Probabilities() [1/2]

CMarkov_chain_params_Base::C_E_Probabilities::C_E_Probabilities ( const C_E_Probabilities &  )

private

C_E_Probabilities() [2/2]

END_CHOICE_INFO CMarkov_chain_params_Base::C_E_Probabilities::C_E_Probabilities

(

void

)

Definition at line 136 of file Markov_chain_params_.cpp.

C_Gc_content_range() [1/2]

CGnomon_param_Base::C_Gc_content_range::C_Gc_content_range ( const C_Gc_content_range &  )

private

C_Gc_content_range() [2/2]

END_CLASS_INFO CGnomon_param_Base::C_Gc_content_range::C_Gc_content_range

(

void

)

Definition at line 74 of file Gnomon_param_.cpp.

References CGnomon_param_Base::C_Gc_content_range::m_set_State.

C_Param() [1/2]

CGnomon_param_Base::C_Param::C_Param ( const C_Param &  )

private

C_Param() [2/2]

END_CHOICE_INFO CGnomon_param_Base::C_Param::C_Param

(

void

)

Definition at line 371 of file Gnomon_param_.cpp.

C_Range() [1/2]

CLength_distribution_params_Base::C_Range::C_Range ( const C_Range &  )

private

C_Range() [2/2]

END_CLASS_INFO CLength_distribution_params_Base::C_Range::C_Range

(

void

)

Definition at line 69 of file Length_distribution_params_.cpp.

References CLength_distribution_params_Base::C_Range::m_set_State.

CanGet()

bool CGnomon_params_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 158 of file Gnomon_params_.hpp.

CanGetA()

bool CLength_distribution_params_Base::CanGetA ( void  ) const

inline

Check if it is safe to call GetA method.

Returns

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

Definition at line 607 of file Length_distribution_params_.hpp.

References CLength_distribution_params_Base::IsSetA().

Referenced by CLength_distribution_params_Base::GetA().

CanGetFirst_exon_length()

bool CExon_params_Base::CanGetFirst_exon_length ( void  ) const

inline

Check if it is safe to call GetFirst_exon_length method.

Returns

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

Definition at line 408 of file Exon_params_.hpp.

CanGetFirst_exon_phase_probabilities()

bool CExon_params_Base::CanGetFirst_exon_phase_probabilities ( void  ) const

inline

Check if it is safe to call GetFirst_exon_phase_probabilities method.

Returns

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

Definition at line 358 of file Exon_params_.hpp.

CanGetFrom()

bool CGnomon_param_Base::C_Gc_content_range::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 676 of file Gnomon_param_.hpp.

CanGetGc_content_range()

bool CGnomon_param_Base::CanGetGc_content_range ( void  ) const

inline

Check if it is safe to call GetGc_content_range method.

Returns

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

Definition at line 867 of file Gnomon_param_.hpp.

CanGetIn_exon()

bool CMarkov_chain_array_Base::CanGetIn_exon ( void  ) const

inline

Check if it is safe to call GetIn_exon method.

Returns

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

Definition at line 243 of file Markov_chain_array_.hpp.

References CMarkov_chain_array_Base::IsSetIn_exon().

Referenced by CMarkov_chain_array_Base::GetIn_exon().

CanGetIn_intron()

bool CMarkov_chain_array_Base::CanGetIn_intron ( void  ) const

inline

Check if it is safe to call GetIn_intron method.

Returns

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

Definition at line 290 of file Markov_chain_array_.hpp.

References CMarkov_chain_array_Base::IsSetIn_intron().

Referenced by CMarkov_chain_array_Base::GetIn_intron().

CanGetInitp() [1/2]

bool CIntergenic_params_Base::CanGetInitp ( void  ) const

inline

Check if it is safe to call GetInitp method.

Returns

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

Definition at line 246 of file Intergenic_params_.hpp.

References CIntergenic_params_Base::IsSetInitp().

Referenced by CIntergenic_params_Base::GetInitp().

CanGetInitp() [2/2]

bool CIntron_params_Base::CanGetInitp ( void  ) const

inline

Check if it is safe to call GetInitp method.

Returns

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

Definition at line 285 of file Intron_params_.hpp.

References CIntron_params_Base::IsSetInitp().

Referenced by CIntron_params_Base::GetInitp().

CanGetInternal_exon_length()

bool CExon_params_Base::CanGetInternal_exon_length ( void  ) const

inline

Check if it is safe to call GetInternal_exon_length method.

Returns

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

Definition at line 438 of file Exon_params_.hpp.

CanGetInternal_exon_phase_probabilities()

bool CExon_params_Base::CanGetInternal_exon_phase_probabilities ( void  ) const

inline

Check if it is safe to call GetInternal_exon_phase_probabilities method.

Returns

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

Definition at line 383 of file Exon_params_.hpp.

CanGetL()

bool CLength_distribution_params_Base::CanGetL ( void  ) const

inline

Check if it is safe to call GetL method.

Returns

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

Definition at line 654 of file Length_distribution_params_.hpp.

References CLength_distribution_params_Base::IsSetL().

Referenced by CLength_distribution_params_Base::GetL().

CanGetLast_exon_length()

bool CExon_params_Base::CanGetLast_exon_length ( void  ) const

inline

Check if it is safe to call GetLast_exon_length method.

Returns

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

Definition at line 468 of file Exon_params_.hpp.

CanGetLength() [1/2]

bool CIntergenic_params_Base::CanGetLength ( void  ) const

inline

Check if it is safe to call GetLength method.

Returns

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

Definition at line 340 of file Intergenic_params_.hpp.

CanGetLength() [2/2]

bool CIntron_params_Base::CanGetLength ( void  ) const

inline

Check if it is safe to call GetLength method.

Returns

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

Definition at line 404 of file Intron_params_.hpp.

CanGetMatrix()

bool CMarkov_chain_array_Base::CanGetMatrix ( void  ) const

inline

Check if it is safe to call GetMatrix method.

Returns

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

Definition at line 337 of file Markov_chain_array_.hpp.

CanGetMax()

bool CLength_distribution_params_Base::C_Range::CanGetMax ( void  ) const

inline

Check if it is safe to call GetMax method.

Returns

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

Definition at line 488 of file Length_distribution_params_.hpp.

CanGetMin()

bool CLength_distribution_params_Base::C_Range::CanGetMin ( void  ) const

inline

Check if it is safe to call GetMin method.

Returns

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

Definition at line 441 of file Length_distribution_params_.hpp.

CanGetOrder()

bool CMarkov_chain_params_Base::CanGetOrder ( void  ) const

inline

Check if it is safe to call GetOrder method.

Returns

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

Definition at line 418 of file Markov_chain_params_.hpp.

References CMarkov_chain_params_Base::IsSetOrder().

Referenced by CMarkov_chain_params_Base::GetOrder().

CanGetP()

bool CLength_distribution_params_Base::CanGetP ( void  ) const

inline

Check if it is safe to call GetP method.

Returns

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

Definition at line 582 of file Length_distribution_params_.hpp.

CanGetParam()

bool CGnomon_param_Base::CanGetParam ( void  ) const

inline

Check if it is safe to call GetParam method.

Returns

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

Definition at line 897 of file Gnomon_param_.hpp.

CanGetPhase_probabilities()

bool CIntron_params_Base::CanGetPhase_probabilities ( void  ) const

inline

Check if it is safe to call GetPhase_probabilities method.

Returns

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

Definition at line 332 of file Intron_params_.hpp.

CanGetProbabilities()

bool CMarkov_chain_params_Base::CanGetProbabilities ( void  ) const

inline

Check if it is safe to call GetProbabilities method.

Returns

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

Definition at line 465 of file Markov_chain_params_.hpp.

CanGetRange()

bool CLength_distribution_params_Base::CanGetRange ( void  ) const

inline

Check if it is safe to call GetRange method.

Returns

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

Definition at line 701 of file Length_distribution_params_.hpp.

CanGetSingle_exon_length()

bool CExon_params_Base::CanGetSingle_exon_length ( void  ) const

inline

Check if it is safe to call GetSingle_exon_length method.

Returns

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

Definition at line 498 of file Exon_params_.hpp.

CanGetStep()

bool CLength_distribution_params_Base::CanGetStep ( void  ) const

inline

Check if it is safe to call GetStep method.

Returns

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

Definition at line 535 of file Length_distribution_params_.hpp.

References CLength_distribution_params_Base::IsSetStep().

Referenced by CLength_distribution_params_Base::GetStep().

CanGetTo()

bool CGnomon_param_Base::C_Gc_content_range::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 723 of file Gnomon_param_.hpp.

CanGetTo_single()

bool CIntergenic_params_Base::CanGetTo_single ( void  ) const

inline

Check if it is safe to call GetTo_single method.

Returns

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

Definition at line 293 of file Intergenic_params_.hpp.

References CIntergenic_params_Base::IsSetTo_single().

Referenced by CIntergenic_params_Base::GetTo_single().

CanGetTo_term()

bool CIntron_params_Base::CanGetTo_term ( void  ) const

inline

Check if it is safe to call GetTo_term method.

Returns

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

Definition at line 357 of file Intron_params_.hpp.

References CIntron_params_Base::IsSetTo_term().

Referenced by CIntron_params_Base::GetTo_term().

CExon_params() [1/2]

CExon_params::CExon_params ( const CExon_params &  value )

private

CExon_params() [2/2]

CExon_params::CExon_params ( void  )

inline

Definition at line 86 of file Exon_params.hpp.

CExon_params_Base() [1/2]

CExon_params_Base::CExon_params_Base ( const CExon_params_Base &  )

private

CExon_params_Base() [2/2]

END_CLASS_INFO CExon_params_Base::CExon_params_Base

(

void

)

Definition at line 145 of file Exon_params_.cpp.

References CObject::IsAllocatedInPool(), CExon_params_Base::m_set_State, CExon_params_Base::ResetFirst_exon_length(), CExon_params_Base::ResetInternal_exon_length(), CExon_params_Base::ResetLast_exon_length(), and CExon_params_Base::ResetSingle_exon_length().

CGnomon_param() [1/2]

CGnomon_param::CGnomon_param ( const CGnomon_param &  value )

private

CGnomon_param() [2/2]

CGnomon_param::CGnomon_param ( void  )

inline

Definition at line 86 of file Gnomon_param.hpp.

CGnomon_param_Base() [1/2]

CGnomon_param_Base::CGnomon_param_Base ( const CGnomon_param_Base &  )

private

CGnomon_param_Base() [2/2]

END_CLASS_INFO CGnomon_param_Base::CGnomon_param_Base

(

void

)

Definition at line 429 of file Gnomon_param_.cpp.

References CObject::IsAllocatedInPool(), CGnomon_param_Base::m_set_State, CGnomon_param_Base::ResetGc_content_range(), and CGnomon_param_Base::ResetParam().

CGnomon_params() [1/2]

CGnomon_params::CGnomon_params ( const CGnomon_params &  value )

private

CGnomon_params() [2/2]

CGnomon_params::CGnomon_params ( void  )

inline

Definition at line 86 of file Gnomon_params.hpp.

CGnomon_params_Base() [1/2]

CGnomon_params_Base::CGnomon_params_Base ( const CGnomon_params_Base &  )

private

CGnomon_params_Base() [2/2]

END_CLASS_INFO CGnomon_params_Base::CGnomon_params_Base

(

void

)

Definition at line 68 of file Gnomon_params_.cpp.

References CGnomon_params_Base::m_set_State.

CheckSelected() [1/2]

void CGnomon_param_Base::C_Param::CheckSelected ( E_Choice  index ) const

inline

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

Parameters

index

Expected selection.

Definition at line 770 of file Gnomon_param_.hpp.

CheckSelected() [2/2]

void CMarkov_chain_params_Base::C_E_Probabilities::CheckSelected ( E_Choice  index ) const

inline

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

Parameters

index

Expected selection.

Definition at line 356 of file Markov_chain_params_.hpp.

CIntergenic_params() [1/2]

CIntergenic_params::CIntergenic_params ( const CIntergenic_params &  value )

private

CIntergenic_params() [2/2]

CIntergenic_params::CIntergenic_params ( void  )

inline

Definition at line 86 of file Intergenic_params.hpp.

CIntergenic_params_Base() [1/2]

CIntergenic_params_Base::CIntergenic_params_Base ( const CIntergenic_params_Base &  )

private

CIntergenic_params_Base() [2/2]

END_CLASS_INFO CIntergenic_params_Base::CIntergenic_params_Base

(

void

)

Definition at line 85 of file Intergenic_params_.cpp.

References CObject::IsAllocatedInPool(), CIntergenic_params_Base::m_set_State, and CIntergenic_params_Base::ResetLength().

CIntron_params() [1/2]

CIntron_params::CIntron_params ( const CIntron_params &  value )

private

CIntron_params() [2/2]

CIntron_params::CIntron_params ( void  )

inline

Definition at line 86 of file Intron_params.hpp.

CIntron_params_Base() [1/2]

CIntron_params_Base::CIntron_params_Base ( const CIntron_params_Base &  )

private

CIntron_params_Base() [2/2]

END_CLASS_INFO CIntron_params_Base::CIntron_params_Base

(

void

)

Definition at line 93 of file Intron_params_.cpp.

References CObject::IsAllocatedInPool(), CIntron_params_Base::m_set_State, and CIntron_params_Base::ResetLength().

CLength_distribution_params() [1/2]

CLength_distribution_params::CLength_distribution_params ( const CLength_distribution_params &  value )

private

CLength_distribution_params() [2/2]

CLength_distribution_params::CLength_distribution_params ( void  )

inline

Definition at line 86 of file Length_distribution_params.hpp.

CLength_distribution_params_Base() [1/2]

CLength_distribution_params_Base::CLength_distribution_params_Base ( const CLength_distribution_params_Base &  )

private

CLength_distribution_params_Base() [2/2]

END_CLASS_INFO CLength_distribution_params_Base::CLength_distribution_params_Base

(

void

)

Definition at line 125 of file Length_distribution_params_.cpp.

References CObject::IsAllocatedInPool(), CLength_distribution_params_Base::m_set_State, and CLength_distribution_params_Base::ResetRange().

CMarkov_chain_array() [1/2]

CMarkov_chain_array::CMarkov_chain_array ( const CMarkov_chain_array &  value )

private

CMarkov_chain_array() [2/2]

CMarkov_chain_array::CMarkov_chain_array ( void  )

inline

Definition at line 86 of file Markov_chain_array.hpp.

CMarkov_chain_array_Base() [1/2]

CMarkov_chain_array_Base::CMarkov_chain_array_Base ( const CMarkov_chain_array_Base &  )

private

CMarkov_chain_array_Base() [2/2]

END_CLASS_INFO CMarkov_chain_array_Base::CMarkov_chain_array_Base

(

void

)

Definition at line 77 of file Markov_chain_array_.cpp.

References CMarkov_chain_array_Base::m_set_State.

CMarkov_chain_params() [1/2]

CMarkov_chain_params::CMarkov_chain_params ( const CMarkov_chain_params &  value )

private

CMarkov_chain_params() [2/2]

CMarkov_chain_params::CMarkov_chain_params ( void  )

inline

Definition at line 86 of file Markov_chain_params.hpp.

CMarkov_chain_params_Base() [1/2]

CMarkov_chain_params_Base::CMarkov_chain_params_Base ( const CMarkov_chain_params_Base &  )

private

CMarkov_chain_params_Base() [2/2]

END_CLASS_INFO CMarkov_chain_params_Base::CMarkov_chain_params_Base

(

void

)

Definition at line 172 of file Markov_chain_params_.cpp.

References CMarkov_chain_params_Base::m_set_State.

DECLARE_INTERNAL_TYPE_INFO() [1/12]

CExon_params_Base::DECLARE_INTERNAL_TYPE_INFO

(

)

DECLARE_INTERNAL_TYPE_INFO() [2/12]

CGnomon_param_Base::DECLARE_INTERNAL_TYPE_INFO

(

)

DECLARE_INTERNAL_TYPE_INFO() [3/12]

CGnomon_param_Base::C_Gc_content_range::DECLARE_INTERNAL_TYPE_INFO

(

)

DECLARE_INTERNAL_TYPE_INFO() [4/12]

CGnomon_param_Base::C_Param::DECLARE_INTERNAL_TYPE_INFO

(

)

DECLARE_INTERNAL_TYPE_INFO() [5/12]

CGnomon_params_Base::DECLARE_INTERNAL_TYPE_INFO

(

)

DECLARE_INTERNAL_TYPE_INFO() [6/12]

CIntergenic_params_Base::DECLARE_INTERNAL_TYPE_INFO

(

)

DECLARE_INTERNAL_TYPE_INFO() [7/12]

CIntron_params_Base::DECLARE_INTERNAL_TYPE_INFO

(

)

DECLARE_INTERNAL_TYPE_INFO() [8/12]

CLength_distribution_params_Base::DECLARE_INTERNAL_TYPE_INFO

(

)

DECLARE_INTERNAL_TYPE_INFO() [9/12]

CLength_distribution_params_Base::C_Range::DECLARE_INTERNAL_TYPE_INFO

(

)

DECLARE_INTERNAL_TYPE_INFO() [10/12]

CMarkov_chain_array_Base::DECLARE_INTERNAL_TYPE_INFO

(

)

DECLARE_INTERNAL_TYPE_INFO() [11/12]

CMarkov_chain_params_Base::DECLARE_INTERNAL_TYPE_INFO

(

)

DECLARE_INTERNAL_TYPE_INFO() [12/12]

CMarkov_chain_params_Base::C_E_Probabilities::DECLARE_INTERNAL_TYPE_INFO

(

)

DoSelect() [1/2]

void CGnomon_param_Base::C_Param::DoSelect ( E_Choice  index, CObjectMemoryPool *  pool = 0  )

private

Definition at line 114 of file Gnomon_param_.cpp.

References CObject::AddReference().

DoSelect() [2/2]

void CMarkov_chain_params_Base::C_E_Probabilities::DoSelect ( E_Choice  index, CObjectMemoryPool *  pool = 0  )

private

Definition at line 68 of file Markov_chain_params_.cpp.

References CObject::AddReference().

Get()

const CGnomon_params_Base::Tdata & CGnomon_params_Base::Get ( void  ) const

inline

Get the member data.

Returns

Reference to the member data.

Definition at line 164 of file Gnomon_params_.hpp.

References CGnomon_params_Base::m_data.

Referenced by CHMMParameters::SDetails::ReadParameters().

GetA()

CLength_distribution_params_Base::TA CLength_distribution_params_Base::GetA ( void  ) const

inline

Get the A member data.

Returns

Copy of the member data.

Definition at line 620 of file Length_distribution_params_.hpp.

References CLength_distribution_params_Base::CanGetA(), CLength_distribution_params_Base::m_A, and CSerialObject::ThrowUnassigned().

Referenced by CLorentz::Init().

GetAcceptor()

const CGnomon_param_Base::C_Param::TAcceptor & CGnomon_param_Base::C_Param::GetAcceptor

(

void

)

const

Get the variant data.

Returns

Reference to the data.

Definition at line 305 of file Gnomon_param_.cpp.

Referenced by CWAM_Acceptor< order >::CWAM_Acceptor().

GetCoding_region()

const CGnomon_param_Base::C_Param::TCoding_region & CGnomon_param_Base::C_Param::GetCoding_region ( void  ) const

inline

Get the variant data.

Returns

Reference to the data.

Definition at line 841 of file Gnomon_param_.hpp.

Referenced by CMC3_CodingRegion< order >::CMC3_CodingRegion().

GetDonor()

const CGnomon_param_Base::C_Param::TDonor & CGnomon_param_Base::C_Param::GetDonor

(

void

)

const

Get the variant data.

Returns

Reference to the data.

Definition at line 283 of file Gnomon_param_.cpp.

Referenced by CWAM_Donor< order >::CWAM_Donor().

GetExon()

const CGnomon_param_Base::C_Param::TExon & CGnomon_param_Base::C_Param::GetExon

(

void

)

const

Get the variant data.

Returns

Reference to the data.

Definition at line 217 of file Gnomon_param_.cpp.

Referenced by CExonParameters::CExonParameters().

GetFirst_exon_length()

const CExon_params_Base::TFirst_exon_length & CExon_params_Base::GetFirst_exon_length ( void  ) const

inline

Get the First_exon_length member data.

Returns

Reference to the member data.

Definition at line 414 of file Exon_params_.hpp.

References CExon_params_Base::m_First_exon_length, and CExon_params_Base::ResetFirst_exon_length().

Referenced by CExonParameters::CExonParameters().

GetFirst_exon_phase_probabilities()

const CExon_params_Base::TFirst_exon_phase_probabilities & CExon_params_Base::GetFirst_exon_phase_probabilities ( void  ) const

inline

Get the First_exon_phase_probabilities member data.

Returns

Reference to the member data.

Definition at line 364 of file Exon_params_.hpp.

References CExon_params_Base::m_First_exon_phase_probabilities.

Referenced by CExonParameters::CExonParameters().

GetFrom()

CGnomon_param_Base::C_Gc_content_range::TFrom CGnomon_param_Base::C_Gc_content_range::GetFrom ( void  ) const

inline

Get the From member data.

Returns

Copy of the member data.

Definition at line 689 of file Gnomon_param_.hpp.

References CSerialObject::ThrowUnassigned().

GetGc_content_range()

const CGnomon_param_Base::TGc_content_range & CGnomon_param_Base::GetGc_content_range ( void  ) const

inline

Get the Gc_content_range member data.

Returns

Reference to the member data.

Definition at line 873 of file Gnomon_param_.hpp.

References CGnomon_param_Base::m_Gc_content_range, and CGnomon_param_Base::ResetGc_content_range().

GetIn_exon()

CMarkov_chain_array_Base::TIn_exon CMarkov_chain_array_Base::GetIn_exon ( void  ) const

inline

Get the In_exon member data.

Returns

Copy of the member data.

Definition at line 256 of file Markov_chain_array_.hpp.

References CMarkov_chain_array_Base::CanGetIn_exon(), CMarkov_chain_array_Base::m_In_exon, and CSerialObject::ThrowUnassigned().

Referenced by CWAM_Acceptor< order >::CWAM_Acceptor(), CWAM_Donor< order >::CWAM_Donor(), CWAM_Stop::CWAM_Stop(), and CWMM_Start::CWMM_Start().

GetIn_intron()

CMarkov_chain_array_Base::TIn_intron CMarkov_chain_array_Base::GetIn_intron ( void  ) const

inline

Get the In_intron member data.

Returns

Copy of the member data.

Definition at line 303 of file Markov_chain_array_.hpp.

References CMarkov_chain_array_Base::CanGetIn_intron(), CMarkov_chain_array_Base::m_In_intron, and CSerialObject::ThrowUnassigned().

Referenced by CWAM_Acceptor< order >::CWAM_Acceptor(), CWAM_Donor< order >::CWAM_Donor(), CWAM_Stop::CWAM_Stop(), and CWMM_Start::CWMM_Start().

GetInitp() [1/2]

CIntergenic_params_Base::TInitp CIntergenic_params_Base::GetInitp ( void  ) const

inline

Get the Initp member data.

Returns

Copy of the member data.

Definition at line 259 of file Intergenic_params_.hpp.

References CIntergenic_params_Base::CanGetInitp(), CIntergenic_params_Base::m_Initp, and CSerialObject::ThrowUnassigned().

Referenced by CIntergenicParameters::CIntergenicParameters().

GetInitp() [2/2]

CIntron_params_Base::TInitp CIntron_params_Base::GetInitp ( void  ) const

inline

Get the Initp member data.

Returns

Copy of the member data.

Definition at line 298 of file Intron_params_.hpp.

References CIntron_params_Base::CanGetInitp(), CIntron_params_Base::m_Initp, and CSerialObject::ThrowUnassigned().

Referenced by CIntronParameters::CIntronParameters().

GetIntergenic()

const CGnomon_param_Base::C_Param::TIntergenic & CGnomon_param_Base::C_Param::GetIntergenic

(

void

)

const

Get the variant data.

Returns

Reference to the data.

Definition at line 173 of file Gnomon_param_.cpp.

Referenced by CIntergenicParameters::CIntergenicParameters().

GetInternal_exon_length()

const CExon_params_Base::TInternal_exon_length & CExon_params_Base::GetInternal_exon_length ( void  ) const

inline

Get the Internal_exon_length member data.

Returns

Reference to the member data.

Definition at line 444 of file Exon_params_.hpp.

References CExon_params_Base::m_Internal_exon_length, and CExon_params_Base::ResetInternal_exon_length().

Referenced by CExonParameters::CExonParameters().

GetInternal_exon_phase_probabilities()

const CExon_params_Base::TInternal_exon_phase_probabilities & CExon_params_Base::GetInternal_exon_phase_probabilities ( void  ) const

inline

Get the Internal_exon_phase_probabilities member data.

Returns

Reference to the member data.

Definition at line 389 of file Exon_params_.hpp.

References CExon_params_Base::m_Internal_exon_phase_probabilities.

Referenced by CExonParameters::CExonParameters().

GetIntron()

const CGnomon_param_Base::C_Param::TIntron & CGnomon_param_Base::C_Param::GetIntron

(

void

)

const

Get the variant data.

Returns

Reference to the data.

Definition at line 195 of file Gnomon_param_.cpp.

Referenced by CIntronParameters::CIntronParameters().

GetL()

CLength_distribution_params_Base::TL CLength_distribution_params_Base::GetL ( void  ) const

inline

Get the L member data.

Returns

Copy of the member data.

Definition at line 667 of file Length_distribution_params_.hpp.

References CLength_distribution_params_Base::CanGetL(), CLength_distribution_params_Base::m_L, and CSerialObject::ThrowUnassigned().

Referenced by CLorentz::Init().

GetLast_exon_length()

const CExon_params_Base::TLast_exon_length & CExon_params_Base::GetLast_exon_length ( void  ) const

inline

Get the Last_exon_length member data.

Returns

Reference to the member data.

Definition at line 474 of file Exon_params_.hpp.

References CExon_params_Base::m_Last_exon_length, and CExon_params_Base::ResetLast_exon_length().

Referenced by CExonParameters::CExonParameters().

GetLength() [1/2]

const CIntergenic_params_Base::TLength & CIntergenic_params_Base::GetLength ( void  ) const

inline

Get the Length member data.

Returns

Reference to the member data.

Definition at line 346 of file Intergenic_params_.hpp.

References CIntergenic_params_Base::m_Length, and CIntergenic_params_Base::ResetLength().

Referenced by CIntergenicParameters::CIntergenicParameters().

GetLength() [2/2]

const CIntron_params_Base::TLength & CIntron_params_Base::GetLength ( void  ) const

inline

Get the Length member data.

Returns

Reference to the member data.

Definition at line 410 of file Intron_params_.hpp.

References CIntron_params_Base::m_Length, and CIntron_params_Base::ResetLength().

Referenced by CIntronParameters::CIntronParameters().

GetMatrix()

const CMarkov_chain_array_Base::TMatrix & CMarkov_chain_array_Base::GetMatrix ( void  ) const

inline

Get the Matrix member data.

Returns

Reference to the member data.

Definition at line 343 of file Markov_chain_array_.hpp.

References CMarkov_chain_array_Base::m_Matrix.

Referenced by CMarkovChainArray< order >::InitScore().

GetMax()

CLength_distribution_params_Base::C_Range::TMax CLength_distribution_params_Base::C_Range::GetMax ( void  ) const

inline

Get the Max member data.

Returns

Copy of the member data.

Definition at line 501 of file Length_distribution_params_.hpp.

References CSerialObject::ThrowUnassigned().

Referenced by CLorentz::Init().

GetMin()

CLength_distribution_params_Base::C_Range::TMin CLength_distribution_params_Base::C_Range::GetMin ( void  ) const

inline

Get the Min member data.

Returns

Copy of the member data.

Definition at line 454 of file Length_distribution_params_.hpp.

References CSerialObject::ThrowUnassigned().

Referenced by CLorentz::Init().

GetNon_coding_region()

const CGnomon_param_Base::C_Param::TNon_coding_region & CGnomon_param_Base::C_Param::GetNon_coding_region

(

void

)

const

Get the variant data.

Returns

Reference to the data.

Definition at line 327 of file Gnomon_param_.cpp.

Referenced by CMC_NonCodingRegion< order >::CMC_NonCodingRegion().

GetOrder()

CMarkov_chain_params_Base::TOrder CMarkov_chain_params_Base::GetOrder ( void  ) const

inline

Get the Order member data.

Returns

Copy of the member data.

Definition at line 431 of file Markov_chain_params_.hpp.

References CMarkov_chain_params_Base::CanGetOrder(), CMarkov_chain_params_Base::m_Order, and CSerialObject::ThrowUnassigned().

Referenced by CMarkovChain< 0 >::Init(), and CMarkovChain< order >::Init().

GetP()

const CLength_distribution_params_Base::TP & CLength_distribution_params_Base::GetP ( void  ) const

inline

Get the P member data.

Returns

Reference to the member data.

Definition at line 588 of file Length_distribution_params_.hpp.

References CLength_distribution_params_Base::m_P.

Referenced by CLorentz::Init().

GetParam()

const CGnomon_param_Base::TParam & CGnomon_param_Base::GetParam ( void  ) const

inline

Get the Param member data.

Returns

Reference to the member data.

Definition at line 903 of file Gnomon_param_.hpp.

References CGnomon_param_Base::m_Param, and CGnomon_param_Base::ResetParam().

GetPhase_probabilities()

const CIntron_params_Base::TPhase_probabilities & CIntron_params_Base::GetPhase_probabilities ( void  ) const

inline

Get the Phase_probabilities member data.

Returns

Reference to the member data.

Definition at line 338 of file Intron_params_.hpp.

References CIntron_params_Base::m_Phase_probabilities.

Referenced by CIntronParameters::CIntronParameters().

GetPrev_order()

const CMarkov_chain_params_Base::C_E_Probabilities::TPrev_order & CMarkov_chain_params_Base::C_E_Probabilities::GetPrev_order

(

void

)

const

Get the variant data.

Returns

Reference to the data.

Definition at line 99 of file Markov_chain_params_.cpp.

GetProbabilities()

const CMarkov_chain_params_Base::TProbabilities & CMarkov_chain_params_Base::GetProbabilities ( void  ) const

inline

Get the Probabilities member data.

Returns

Reference to the member data.

Definition at line 471 of file Markov_chain_params_.hpp.

References CMarkov_chain_params_Base::m_Probabilities.

Referenced by CMarkovChain< 0 >::Init(), and CMarkovChain< order >::Init().

GetRange()

const CLength_distribution_params_Base::TRange & CLength_distribution_params_Base::GetRange ( void  ) const

inline

Get the Range member data.

Returns

Reference to the member data.

Definition at line 707 of file Length_distribution_params_.hpp.

References CLength_distribution_params_Base::m_Range, and CLength_distribution_params_Base::ResetRange().

Referenced by CLorentz::Init().

GetSingle_exon_length()

const CExon_params_Base::TSingle_exon_length & CExon_params_Base::GetSingle_exon_length ( void  ) const

inline

Get the Single_exon_length member data.

Returns

Reference to the member data.

Definition at line 504 of file Exon_params_.hpp.

References CExon_params_Base::m_Single_exon_length, and CExon_params_Base::ResetSingle_exon_length().

Referenced by CExonParameters::CExonParameters().

GetStart()

const CGnomon_param_Base::C_Param::TStart & CGnomon_param_Base::C_Param::GetStart

(

void

)

const

Get the variant data.

Returns

Reference to the data.

Definition at line 239 of file Gnomon_param_.cpp.

Referenced by CWMM_Start::CWMM_Start().

GetStep()

CLength_distribution_params_Base::TStep CLength_distribution_params_Base::GetStep ( void  ) const

inline

Get the Step member data.

Returns

Copy of the member data.

Definition at line 548 of file Length_distribution_params_.hpp.

References CLength_distribution_params_Base::CanGetStep(), CLength_distribution_params_Base::m_Step, and CSerialObject::ThrowUnassigned().

Referenced by CLorentz::Init().

GetStop()

const CGnomon_param_Base::C_Param::TStop & CGnomon_param_Base::C_Param::GetStop

(

void

)

const

Get the variant data.

Returns

Reference to the data.

Definition at line 261 of file Gnomon_param_.cpp.

Referenced by CWAM_Stop::CWAM_Stop().

GetTo()

CGnomon_param_Base::C_Gc_content_range::TTo CGnomon_param_Base::C_Gc_content_range::GetTo ( void  ) const

inline

Get the To member data.

Returns

Copy of the member data.

Definition at line 736 of file Gnomon_param_.hpp.

References CSerialObject::ThrowUnassigned().

GetTo_single()

CIntergenic_params_Base::TTo_single CIntergenic_params_Base::GetTo_single ( void  ) const

inline

Get the To_single member data.

Returns

Copy of the member data.

Definition at line 306 of file Intergenic_params_.hpp.

References CIntergenic_params_Base::CanGetTo_single(), CIntergenic_params_Base::m_To_single, and CSerialObject::ThrowUnassigned().

Referenced by CIntergenicParameters::CIntergenicParameters().

GetTo_term()

CIntron_params_Base::TTo_term CIntron_params_Base::GetTo_term ( void  ) const

inline

Get the To_term member data.

Returns

Copy of the member data.

Definition at line 370 of file Intron_params_.hpp.

References CIntron_params_Base::CanGetTo_term(), CIntron_params_Base::m_To_term, and CSerialObject::ThrowUnassigned().

Referenced by CIntronParameters::CIntronParameters().

GetValue()

CMarkov_chain_params_Base::C_E_Probabilities::TValue CMarkov_chain_params_Base::C_E_Probabilities::GetValue ( void  ) const

inline

Get the variant data.

Returns

Copy of the variant data.

Definition at line 391 of file Markov_chain_params_.hpp.

IsAcceptor()

bool CGnomon_param_Base::C_Param::IsAcceptor ( void  ) const

inline

Check if variant Acceptor is selected.

Acceptor type is defined as 'typedef CMarkov_chain_array TAcceptor'.

Returns

• true, if the variant is selected.
• false, otherwise.

Definition at line 829 of file Gnomon_param_.hpp.

IsCoding_region()

bool CGnomon_param_Base::C_Param::IsCoding_region ( void  ) const

inline

Check if variant Coding_region is selected.

Coding_region type is defined as 'typedef list< CRef< CMarkov_chain_params > > TCoding_region'.

Returns

• true, if the variant is selected.
• false, otherwise.

Definition at line 835 of file Gnomon_param_.hpp.

IsDonor()

bool CGnomon_param_Base::C_Param::IsDonor ( void  ) const

inline

Check if variant Donor is selected.

Donor type is defined as 'typedef CMarkov_chain_array TDonor'.

Returns

• true, if the variant is selected.
• false, otherwise.

Definition at line 823 of file Gnomon_param_.hpp.

IsExon()

bool CGnomon_param_Base::C_Param::IsExon ( void  ) const

inline

Check if variant Exon is selected.

Exon type is defined as 'typedef CExon_params TExon'.

Returns

• true, if the variant is selected.
• false, otherwise.

Definition at line 805 of file Gnomon_param_.hpp.

IsIntergenic()

bool CGnomon_param_Base::C_Param::IsIntergenic ( void  ) const

inline

Check if variant Intergenic is selected.

Intergenic type is defined as 'typedef CIntergenic_params TIntergenic'.

Returns

• true, if the variant is selected.
• false, otherwise.

Definition at line 793 of file Gnomon_param_.hpp.

IsIntron()

bool CGnomon_param_Base::C_Param::IsIntron ( void  ) const

inline

Check if variant Intron is selected.

Intron type is defined as 'typedef CIntron_params TIntron'.

Returns

• true, if the variant is selected.
• false, otherwise.

Definition at line 799 of file Gnomon_param_.hpp.

IsNon_coding_region()

bool CGnomon_param_Base::C_Param::IsNon_coding_region ( void  ) const

inline

Check if variant Non_coding_region is selected.

Non_coding_region type is defined as 'typedef CMarkov_chain_params TNon_coding_region'.

Returns

• true, if the variant is selected.
• false, otherwise.

Definition at line 855 of file Gnomon_param_.hpp.

IsPrev_order()

bool CMarkov_chain_params_Base::C_E_Probabilities::IsPrev_order ( void  ) const

inline

Check if variant Prev_order is selected.

Prev_order type is defined as 'typedef CMarkov_chain_params TPrev_order'.

Returns

• true, if the variant is selected.
• false, otherwise.

Definition at line 379 of file Markov_chain_params_.hpp.

IsSet()

bool CGnomon_params_Base::IsSet ( void  ) const

inline

Check if a value has been assigned to data member.

Data member is mandatory; its type is defined as 'typedef list< CRef< CGnomon_param > > Tdata'

Returns

• true, if a value has been assigned.
• false, otherwise.

Definition at line 152 of file Gnomon_params_.hpp.

References CGnomon_params_Base::m_set_State.

IsSetA()

bool CLength_distribution_params_Base::IsSetA ( void  ) const

inline

Loretz function coefficient for the tail Check if a value has been assigned to A data member.

Data member A is mandatory; its type is defined as 'typedef double TA'

Returns

• true, if a value has been assigned.
• false, otherwise.

Definition at line 601 of file Length_distribution_params_.hpp.

References CLength_distribution_params_Base::m_set_State.

Referenced by CLength_distribution_params_Base::CanGetA(), and CLength_distribution_params_Base::SetA().

IsSetFirst_exon_length()

bool CExon_params_Base::IsSetFirst_exon_length ( void  ) const

inline

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

Data member First_exon_length is mandatory; its type is defined as 'typedef CLength_distribution_params TFirst_exon_length'

Returns

• true, if a value has been assigned.
• false, otherwise.

Definition at line 402 of file Exon_params_.hpp.

References CExon_params_Base::m_First_exon_length.

IsSetFirst_exon_phase_probabilities()

bool CExon_params_Base::IsSetFirst_exon_phase_probabilities ( void  ) const

inline

3 elements (per end phase) Check if a value has been assigned to First_exon_phase_probabilities data member.

Data member First_exon_phase_probabilities is mandatory; its type is defined as 'typedef list< double > TFirst_exon_phase_probabilities'

Returns

• true, if a value has been assigned.
• false, otherwise.

Definition at line 352 of file Exon_params_.hpp.

References CExon_params_Base::m_set_State.

IsSetFrom()

bool CGnomon_param_Base::C_Gc_content_range::IsSetFrom ( void  ) const

inline

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

Data member From is mandatory; its type is defined as 'typedef int TFrom'

Returns

• true, if a value has been assigned.
• false, otherwise.

Definition at line 670 of file Gnomon_param_.hpp.

References CGnomon_param_Base::C_Gc_content_range::m_set_State.

IsSetGc_content_range()

bool CGnomon_param_Base::IsSetGc_content_range ( void  ) const

inline

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

Data member Gc_content_range is mandatory; its type is defined as 'typedef C_Gc_content_range TGc_content_range'

Returns

• true, if a value has been assigned.
• false, otherwise.

Definition at line 861 of file Gnomon_param_.hpp.

References CGnomon_param_Base::m_Gc_content_range.

IsSetIn_exon()

bool CMarkov_chain_array_Base::IsSetIn_exon ( void  ) const

inline

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

Data member In_exon is mandatory; its type is defined as 'typedef int TIn_exon'

Returns

• true, if a value has been assigned.
• false, otherwise.

Definition at line 237 of file Markov_chain_array_.hpp.

References CMarkov_chain_array_Base::m_set_State.

Referenced by CMarkov_chain_array_Base::CanGetIn_exon(), and CMarkov_chain_array_Base::SetIn_exon().

IsSetIn_intron()

bool CMarkov_chain_array_Base::IsSetIn_intron ( void  ) const

inline

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

Data member In_intron is mandatory; its type is defined as 'typedef int TIn_intron'

Returns

• true, if a value has been assigned.
• false, otherwise.

Definition at line 284 of file Markov_chain_array_.hpp.

References CMarkov_chain_array_Base::m_set_State.

Referenced by CMarkov_chain_array_Base::CanGetIn_intron(), and CMarkov_chain_array_Base::SetIn_intron().

IsSetInitp() [1/2]

bool CIntergenic_params_Base::IsSetInitp ( void  ) const

inline

probability of a genomic point be intergenic Check if a value has been assigned to Initp data member.

Data member Initp is mandatory; its type is defined as 'typedef double TInitp'

Returns

• true, if a value has been assigned.
• false, otherwise.

Definition at line 240 of file Intergenic_params_.hpp.

References CIntergenic_params_Base::m_set_State.

Referenced by CIntergenic_params_Base::CanGetInitp(), and CIntergenic_params_Base::SetInitp().

IsSetInitp() [2/2]

bool CIntron_params_Base::IsSetInitp ( void  ) const

inline

probability of a genomic point be in an intron Check if a value has been assigned to Initp data member.

Data member Initp is mandatory; its type is defined as 'typedef double TInitp'

Returns

• true, if a value has been assigned.
• false, otherwise.

Definition at line 279 of file Intron_params_.hpp.

References CIntron_params_Base::m_set_State.

Referenced by CIntron_params_Base::CanGetInitp(), and CIntron_params_Base::SetInitp().

IsSetInternal_exon_length()

bool CExon_params_Base::IsSetInternal_exon_length ( void  ) const

inline

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

Data member Internal_exon_length is mandatory; its type is defined as 'typedef CLength_distribution_params TInternal_exon_length'

Returns

• true, if a value has been assigned.
• false, otherwise.

Definition at line 432 of file Exon_params_.hpp.

References CExon_params_Base::m_Internal_exon_length.

IsSetInternal_exon_phase_probabilities()

bool CExon_params_Base::IsSetInternal_exon_phase_probabilities ( void  ) const

inline

3*3 elements (begin phase x end phase) Check if a value has been assigned to Internal_exon_phase_probabilities data member.

Data member Internal_exon_phase_probabilities is mandatory; its type is defined as 'typedef list< double > TInternal_exon_phase_probabilities'

Returns

• true, if a value has been assigned.
• false, otherwise.

Definition at line 377 of file Exon_params_.hpp.

References CExon_params_Base::m_set_State.

IsSetL()

bool CLength_distribution_params_Base::IsSetL ( void  ) const

inline

Loretz function coefficient for the tail Check if a value has been assigned to L data member.

Data member L is mandatory; its type is defined as 'typedef double TL'

Returns

• true, if a value has been assigned.
• false, otherwise.

Definition at line 648 of file Length_distribution_params_.hpp.

References CLength_distribution_params_Base::m_set_State.

Referenced by CLength_distribution_params_Base::CanGetL(), and CLength_distribution_params_Base::SetL().

IsSetLast_exon_length()

bool CExon_params_Base::IsSetLast_exon_length ( void  ) const

inline

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

Data member Last_exon_length is mandatory; its type is defined as 'typedef CLength_distribution_params TLast_exon_length'

Returns

• true, if a value has been assigned.
• false, otherwise.

Definition at line 462 of file Exon_params_.hpp.

References CExon_params_Base::m_Last_exon_length.

IsSetLength() [1/2]

bool CIntergenic_params_Base::IsSetLength ( void  ) const

inline

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

Data member Length is mandatory; its type is defined as 'typedef CLength_distribution_params TLength'

Returns

• true, if a value has been assigned.
• false, otherwise.

Definition at line 334 of file Intergenic_params_.hpp.

References CIntergenic_params_Base::m_Length.

IsSetLength() [2/2]

bool CIntron_params_Base::IsSetLength ( void  ) const

inline

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

Data member Length is mandatory; its type is defined as 'typedef CLength_distribution_params TLength'

Returns

• true, if a value has been assigned.
• false, otherwise.

Definition at line 398 of file Intron_params_.hpp.

References CIntron_params_Base::m_Length.

IsSetMatrix()

bool CMarkov_chain_array_Base::IsSetMatrix ( void  ) const

inline

in-exon+in-intron elements Check if a value has been assigned to Matrix data member.

Data member Matrix is mandatory; its type is defined as 'typedef list< CRef< CMarkov_chain_params > > TMatrix'

Returns

• true, if a value has been assigned.
• false, otherwise.

Definition at line 331 of file Markov_chain_array_.hpp.

References CMarkov_chain_array_Base::m_set_State.

IsSetMax()

bool CLength_distribution_params_Base::C_Range::IsSetMax ( void  ) const

inline

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

Data member Max is mandatory; its type is defined as 'typedef int TMax'

Returns

• true, if a value has been assigned.
• false, otherwise.

Definition at line 482 of file Length_distribution_params_.hpp.

References CLength_distribution_params_Base::m_set_State.

IsSetMin()

bool CLength_distribution_params_Base::C_Range::IsSetMin ( void  ) const

inline

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

Data member Min is mandatory; its type is defined as 'typedef int TMin'

Returns

• true, if a value has been assigned.
• false, otherwise.

Definition at line 435 of file Length_distribution_params_.hpp.

References CLength_distribution_params_Base::C_Range::m_set_State.

IsSetOrder()

bool CMarkov_chain_params_Base::IsSetOrder ( void  ) const

inline

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

Data member Order is mandatory; its type is defined as 'typedef int TOrder'

Returns

• true, if a value has been assigned.
• false, otherwise.

Definition at line 412 of file Markov_chain_params_.hpp.

References CMarkov_chain_params_Base::m_set_State.

Referenced by CMarkov_chain_params_Base::CanGetOrder(), and CMarkov_chain_params_Base::SetOrder().

IsSetP()

bool CLength_distribution_params_Base::IsSetP ( void  ) const

inline

P(step*(i+.5))|i=0,1,...,N-1 Check if a value has been assigned to P data member.

Data member P is mandatory; its type is defined as 'typedef list< double > TP'

Returns

• true, if a value has been assigned.
• false, otherwise.

Definition at line 576 of file Length_distribution_params_.hpp.

References CLength_distribution_params_Base::m_set_State.

IsSetParam()

bool CGnomon_param_Base::IsSetParam ( void  ) const

inline

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

Data member Param is mandatory; its type is defined as 'typedef C_Param TParam'

Returns

• true, if a value has been assigned.
• false, otherwise.

Definition at line 891 of file Gnomon_param_.hpp.

References CGnomon_param_Base::m_Param.

IsSetPhase_probabilities()

bool CIntron_params_Base::IsSetPhase_probabilities ( void  ) const

inline

3 elements (per phase) Check if a value has been assigned to Phase_probabilities data member.

Data member Phase_probabilities is mandatory; its type is defined as 'typedef list< double > TPhase_probabilities'

Returns

• true, if a value has been assigned.
• false, otherwise.

Definition at line 326 of file Intron_params_.hpp.

References CIntron_params_Base::m_set_State.

IsSetProbabilities()

bool CMarkov_chain_params_Base::IsSetProbabilities ( void  ) const

inline

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

Data member Probabilities is mandatory; its type is defined as 'typedef list< CRef< C_E_Probabilities > > TProbabilities'

Returns

• true, if a value has been assigned.
• false, otherwise.

Definition at line 459 of file Markov_chain_params_.hpp.

References CMarkov_chain_params_Base::m_set_State.

IsSetRange()

bool CLength_distribution_params_Base::IsSetRange ( void  ) const

inline

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

Data member Range is mandatory; its type is defined as 'typedef C_Range TRange'

Returns

• true, if a value has been assigned.
• false, otherwise.

Definition at line 695 of file Length_distribution_params_.hpp.

References CLength_distribution_params_Base::m_Range.

IsSetSingle_exon_length()

bool CExon_params_Base::IsSetSingle_exon_length ( void  ) const

inline

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

Data member Single_exon_length is mandatory; its type is defined as 'typedef CLength_distribution_params TSingle_exon_length'

Returns

• true, if a value has been assigned.
• false, otherwise.

Definition at line 492 of file Exon_params_.hpp.

References CExon_params_Base::m_Single_exon_length.

IsSetStep()

bool CLength_distribution_params_Base::IsSetStep ( void  ) const

inline

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

Data member Step is mandatory; its type is defined as 'typedef int TStep'

Returns

• true, if a value has been assigned.
• false, otherwise.

Definition at line 529 of file Length_distribution_params_.hpp.

References CLength_distribution_params_Base::m_set_State.

Referenced by CLength_distribution_params_Base::CanGetStep(), and CLength_distribution_params_Base::SetStep().

IsSetTo()

bool CGnomon_param_Base::C_Gc_content_range::IsSetTo ( void  ) const

inline

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

Data member To is mandatory; its type is defined as 'typedef int TTo'

Returns

• true, if a value has been assigned.
• false, otherwise.

Definition at line 717 of file Gnomon_param_.hpp.

References CGnomon_param_Base::m_set_State.

IsSetTo_single()

bool CIntergenic_params_Base::IsSetTo_single ( void  ) const

inline

probability of next gene to be single-exon Check if a value has been assigned to To_single data member.

Data member To_single is mandatory; its type is defined as 'typedef double TTo_single'

Returns

• true, if a value has been assigned.
• false, otherwise.

Definition at line 287 of file Intergenic_params_.hpp.

References CIntergenic_params_Base::m_set_State.

Referenced by CIntergenic_params_Base::CanGetTo_single(), and CIntergenic_params_Base::SetTo_single().

IsSetTo_term()

bool CIntron_params_Base::IsSetTo_term ( void  ) const

inline

probability to be the last Check if a value has been assigned to To_term data member.

Data member To_term is mandatory; its type is defined as 'typedef double TTo_term'

Returns

• true, if a value has been assigned.
• false, otherwise.

Definition at line 351 of file Intron_params_.hpp.

References CIntron_params_Base::m_set_State.

Referenced by CIntron_params_Base::CanGetTo_term(), and CIntron_params_Base::SetTo_term().

IsStart()

bool CGnomon_param_Base::C_Param::IsStart ( void  ) const

inline

Check if variant Start is selected.

Start type is defined as 'typedef CMarkov_chain_array TStart'.

Returns

• true, if the variant is selected.
• false, otherwise.

Definition at line 811 of file Gnomon_param_.hpp.

IsStop()

bool CGnomon_param_Base::C_Param::IsStop ( void  ) const

inline

Check if variant Stop is selected.

Stop type is defined as 'typedef CMarkov_chain_array TStop'.

Returns

• true, if the variant is selected.
• false, otherwise.

Definition at line 817 of file Gnomon_param_.hpp.

IsValue()

bool CMarkov_chain_params_Base::C_E_Probabilities::IsValue ( void  ) const

inline

Check if variant Value is selected.

Value type is defined as 'typedef double TValue'.

Returns

• true, if the variant is selected.
• false, otherwise.

Definition at line 385 of file Markov_chain_params_.hpp.

operator const Tdata &()

CGnomon_params_Base::operator const CGnomon_params_Base::Tdata & ( void  ) const

inline

Conversion operator to 'const Tdata' type.

Definition at line 177 of file Gnomon_params_.hpp.

operator Tdata &()

CGnomon_params_Base::operator CGnomon_params_Base::Tdata & ( void  )

inline

Conversion operator to 'Tdata' type.

Definition at line 183 of file Gnomon_params_.hpp.

operator=() [1/20]

C_E_Probabilities& CMarkov_chain_params_Base::C_E_Probabilities::operator= ( const C_E_Probabilities &  )

private

operator=() [2/20]

C_Gc_content_range& CGnomon_param_Base::C_Gc_content_range::operator= ( const C_Gc_content_range &  )

private

operator=() [3/20]

C_Param& CGnomon_param_Base::C_Param::operator= ( const C_Param &  )

private

operator=() [4/20]

C_Range& CLength_distribution_params_Base::C_Range::operator= ( const C_Range &  )

private

operator=() [5/20]

CExon_params& CExon_params::operator= ( const CExon_params &  value )

private

operator=() [6/20]

CExon_params_Base& CExon_params_Base::operator= ( const CExon_params_Base &  )

private

operator=() [7/20]

CGnomon_param& CGnomon_param::operator= ( const CGnomon_param &  value )

private

operator=() [8/20]

CGnomon_param_Base& CGnomon_param_Base::operator= ( const CGnomon_param_Base &  )

private

operator=() [9/20]

CGnomon_params& CGnomon_params::operator= ( const CGnomon_params &  value )

private

operator=() [10/20]

CGnomon_params_Base& CGnomon_params_Base::operator= ( const CGnomon_params_Base &  )

private

operator=() [11/20]

CIntergenic_params& CIntergenic_params::operator= ( const CIntergenic_params &  value )

private

operator=() [12/20]

CIntergenic_params_Base& CIntergenic_params_Base::operator= ( const CIntergenic_params_Base &  )

private

operator=() [13/20]

CIntron_params& CIntron_params::operator= ( const CIntron_params &  value )

private

operator=() [14/20]

CIntron_params_Base& CIntron_params_Base::operator= ( const CIntron_params_Base &  )

private

operator=() [15/20]

CLength_distribution_params& CLength_distribution_params::operator= ( const CLength_distribution_params &  value )

private

operator=() [16/20]

CLength_distribution_params_Base& CLength_distribution_params_Base::operator= ( const CLength_distribution_params_Base &  )

private

operator=() [17/20]

CMarkov_chain_array& CMarkov_chain_array::operator= ( const CMarkov_chain_array &  value )

private

operator=() [18/20]

CMarkov_chain_array_Base& CMarkov_chain_array_Base::operator= ( const CMarkov_chain_array_Base &  )

private

operator=() [19/20]

CMarkov_chain_params& CMarkov_chain_params::operator= ( const CMarkov_chain_params &  value )

private

operator=() [20/20]

CMarkov_chain_params_Base& CMarkov_chain_params_Base::operator= ( const CMarkov_chain_params_Base &  )

private

Reset() [1/12]

void CExon_params_Base::Reset ( void  )

virtual

Reset the whole object.

Definition at line 119 of file Exon_params_.cpp.

References CExon_params_Base::ResetFirst_exon_length(), CExon_params_Base::ResetFirst_exon_phase_probabilities(), CExon_params_Base::ResetInternal_exon_length(), CExon_params_Base::ResetInternal_exon_phase_probabilities(), CExon_params_Base::ResetLast_exon_length(), and CExon_params_Base::ResetSingle_exon_length().

Reset() [2/12]

void CGnomon_param_Base::C_Gc_content_range::Reset

(

void

)

Reset the whole object.

Definition at line 55 of file Gnomon_param_.cpp.

References CGnomon_param_Base::C_Gc_content_range::ResetFrom(), and CGnomon_param_Base::C_Gc_content_range::ResetTo().

Reset() [3/12]

void CGnomon_param_Base::C_Param::Reset

(

void

)

Reset the whole object.

Definition at line 86 of file Gnomon_param_.cpp.

References e_not_set.

Reset() [4/12]

void CGnomon_param_Base::Reset ( void  )

virtual

Reset the whole object.

Definition at line 411 of file Gnomon_param_.cpp.

References CGnomon_param_Base::ResetGc_content_range(), and CGnomon_param_Base::ResetParam().

Referenced by CGnomon_param_Base::C_Param::~C_Param().

Reset() [5/12]

void CGnomon_params_Base::Reset

(

void

)

Reset data member.

Definition at line 51 of file Gnomon_params_.cpp.

References CGnomon_params_Base::m_data, and CGnomon_params_Base::m_set_State.

Reset() [6/12]

void CIntergenic_params_Base::Reset ( void  )

virtual

Reset the whole object.

Definition at line 65 of file Intergenic_params_.cpp.

References CIntergenic_params_Base::ResetInitp(), CIntergenic_params_Base::ResetLength(), and CIntergenic_params_Base::ResetTo_single().

Reset() [7/12]

void CIntron_params_Base::Reset ( void  )

virtual

Reset the whole object.

Definition at line 71 of file Intron_params_.cpp.

References CIntron_params_Base::ResetInitp(), CIntron_params_Base::ResetLength(), CIntron_params_Base::ResetPhase_probabilities(), and CIntron_params_Base::ResetTo_term().

Reset() [8/12]

void CLength_distribution_params_Base::C_Range::Reset

(

void

)

Reset the whole object.

Definition at line 50 of file Length_distribution_params_.cpp.

References CLength_distribution_params_Base::C_Range::ResetMax(), and CLength_distribution_params_Base::C_Range::ResetMin().

Reset() [9/12]

void CLength_distribution_params_Base::Reset ( void  )

virtual

Reset the whole object.

Definition at line 101 of file Length_distribution_params_.cpp.

References CLength_distribution_params_Base::ResetA(), CLength_distribution_params_Base::ResetL(), CLength_distribution_params_Base::ResetP(), CLength_distribution_params_Base::ResetRange(), and CLength_distribution_params_Base::ResetStep().

Reset() [10/12]

void CMarkov_chain_array_Base::Reset ( void  )

virtual

Reset the whole object.

Definition at line 57 of file Markov_chain_array_.cpp.

References CMarkov_chain_array_Base::ResetIn_exon(), CMarkov_chain_array_Base::ResetIn_intron(), and CMarkov_chain_array_Base::ResetMatrix().

Reset() [11/12]

void CMarkov_chain_params_Base::C_E_Probabilities::Reset

(

void

)

Reset the whole object.

Definition at line 50 of file Markov_chain_params_.cpp.

References CMarkov_chain_params_Base::C_E_Probabilities::e_not_set, CMarkov_chain_params_Base::C_E_Probabilities::m_choice, and CMarkov_chain_params_Base::C_E_Probabilities::ResetSelection().

Reset() [12/12]

void CMarkov_chain_params_Base::Reset ( void  )

virtual

Reset the whole object.

Definition at line 154 of file Markov_chain_params_.cpp.

References CMarkov_chain_params_Base::ResetOrder(), and CMarkov_chain_params_Base::ResetProbabilities().

Referenced by CMarkov_chain_params_Base::C_E_Probabilities::~C_E_Probabilities().

ResetA()

void CLength_distribution_params_Base::ResetA ( void  )

inline

Reset A data member.

Definition at line 613 of file Length_distribution_params_.hpp.

References CLength_distribution_params_Base::m_A, and CLength_distribution_params_Base::m_set_State.

Referenced by CLength_distribution_params_Base::Reset().

ResetFirst_exon_length()

void CExon_params_Base::ResetFirst_exon_length

(

void

)

Reset First_exon_length data member.

Definition at line 63 of file Exon_params_.cpp.

References CExon_params_Base::m_First_exon_length.

Referenced by CExon_params_Base::CExon_params_Base(), CExon_params_Base::GetFirst_exon_length(), CExon_params_Base::Reset(), and CExon_params_Base::SetFirst_exon_length().

ResetFirst_exon_phase_probabilities()

void CExon_params_Base::ResetFirst_exon_phase_probabilities

(

void

)

Reset First_exon_phase_probabilities data member.

Definition at line 51 of file Exon_params_.cpp.

References CExon_params_Base::m_First_exon_phase_probabilities, and CExon_params_Base::m_set_State.

Referenced by CExon_params_Base::Reset().

ResetFrom()

void CGnomon_param_Base::C_Gc_content_range::ResetFrom ( void  )

inline

Reset From data member.

Definition at line 682 of file Gnomon_param_.hpp.

References CGnomon_param_Base::m_set_State.

Referenced by CGnomon_param_Base::C_Gc_content_range::Reset().

ResetGc_content_range()

void CGnomon_param_Base::ResetGc_content_range

(

void

)

Reset Gc_content_range data member.

Definition at line 383 of file Gnomon_param_.cpp.

References CGnomon_param_Base::m_Gc_content_range.

Referenced by CGnomon_param_Base::CGnomon_param_Base(), CGnomon_param_Base::GetGc_content_range(), CGnomon_param_Base::Reset(), and CGnomon_param_Base::SetGc_content_range().

ResetIn_exon()

void CMarkov_chain_array_Base::ResetIn_exon ( void  )

inline

Reset In_exon data member.

Definition at line 249 of file Markov_chain_array_.hpp.

References CMarkov_chain_array_Base::m_In_exon, and CMarkov_chain_array_Base::m_set_State.

Referenced by CMarkov_chain_array_Base::Reset().

ResetIn_intron()

void CMarkov_chain_array_Base::ResetIn_intron ( void  )

inline

Reset In_intron data member.

Definition at line 296 of file Markov_chain_array_.hpp.

References CMarkov_chain_array_Base::m_In_intron, and CMarkov_chain_array_Base::m_set_State.

Referenced by CMarkov_chain_array_Base::Reset().

ResetInitp() [1/2]

void CIntergenic_params_Base::ResetInitp ( void  )

inline

Reset Initp data member.

Definition at line 252 of file Intergenic_params_.hpp.

References CIntergenic_params_Base::m_Initp, and CIntergenic_params_Base::m_set_State.

Referenced by CIntergenic_params_Base::Reset().

ResetInitp() [2/2]

void CIntron_params_Base::ResetInitp ( void  )

inline

Reset Initp data member.

Definition at line 291 of file Intron_params_.hpp.

References CIntron_params_Base::m_Initp, and CIntron_params_Base::m_set_State.

Referenced by CIntron_params_Base::Reset().

ResetInternal_exon_length()

void CExon_params_Base::ResetInternal_exon_length

(

void

)

Reset Internal_exon_length data member.

Definition at line 77 of file Exon_params_.cpp.

References CExon_params_Base::m_Internal_exon_length.

Referenced by CExon_params_Base::CExon_params_Base(), CExon_params_Base::GetInternal_exon_length(), CExon_params_Base::Reset(), and CExon_params_Base::SetInternal_exon_length().

ResetInternal_exon_phase_probabilities()

void CExon_params_Base::ResetInternal_exon_phase_probabilities

(

void

)

Reset Internal_exon_phase_probabilities data member.

Definition at line 57 of file Exon_params_.cpp.

References CExon_params_Base::m_Internal_exon_phase_probabilities, and CExon_params_Base::m_set_State.

Referenced by CExon_params_Base::Reset().

ResetL()

void CLength_distribution_params_Base::ResetL ( void  )

inline

Reset L data member.

Definition at line 660 of file Length_distribution_params_.hpp.

References CLength_distribution_params_Base::m_L, and CLength_distribution_params_Base::m_set_State.

Referenced by CLength_distribution_params_Base::Reset().

ResetLast_exon_length()

void CExon_params_Base::ResetLast_exon_length

(

void

)

Reset Last_exon_length data member.

Definition at line 91 of file Exon_params_.cpp.

References CExon_params_Base::m_Last_exon_length.

Referenced by CExon_params_Base::CExon_params_Base(), CExon_params_Base::GetLast_exon_length(), CExon_params_Base::Reset(), and CExon_params_Base::SetLast_exon_length().

ResetLength() [1/2]

void CIntergenic_params_Base::ResetLength

(

void

)

Reset Length data member.

Definition at line 51 of file Intergenic_params_.cpp.

References CIntergenic_params_Base::m_Length.

Referenced by CIntergenic_params_Base::CIntergenic_params_Base(), CIntergenic_params_Base::GetLength(), CIntergenic_params_Base::Reset(), and CIntergenic_params_Base::SetLength().

ResetLength() [2/2]

void CIntron_params_Base::ResetLength

(

void

)

Reset Length data member.

Definition at line 57 of file Intron_params_.cpp.

References CIntron_params_Base::m_Length.

Referenced by CIntron_params_Base::CIntron_params_Base(), CIntron_params_Base::GetLength(), CIntron_params_Base::Reset(), and CIntron_params_Base::SetLength().

ResetMatrix()

void CMarkov_chain_array_Base::ResetMatrix

(

void

)

Reset Matrix data member.

Definition at line 51 of file Markov_chain_array_.cpp.

References CMarkov_chain_array_Base::m_Matrix, and CMarkov_chain_array_Base::m_set_State.

Referenced by CMarkov_chain_array_Base::Reset().

ResetMax()

void CLength_distribution_params_Base::C_Range::ResetMax ( void  )

inline

Reset Max data member.

Definition at line 494 of file Length_distribution_params_.hpp.

References CLength_distribution_params_Base::m_set_State.

Referenced by CLength_distribution_params_Base::C_Range::Reset().

ResetMin()

void CLength_distribution_params_Base::C_Range::ResetMin ( void  )

inline

Reset Min data member.

Definition at line 447 of file Length_distribution_params_.hpp.

References CLength_distribution_params_Base::m_set_State.

Referenced by CLength_distribution_params_Base::C_Range::Reset().

ResetOrder()

void CMarkov_chain_params_Base::ResetOrder ( void  )

inline

Reset Order data member.

Definition at line 424 of file Markov_chain_params_.hpp.

References CMarkov_chain_params_Base::m_Order, and CMarkov_chain_params_Base::m_set_State.

Referenced by CMarkov_chain_params_Base::Reset().

ResetP()

void CLength_distribution_params_Base::ResetP

(

void

)

Reset P data member.

Definition at line 81 of file Length_distribution_params_.cpp.

References CLength_distribution_params_Base::m_P, and CLength_distribution_params_Base::m_set_State.

Referenced by CLength_distribution_params_Base::Reset().

ResetParam()

void CGnomon_param_Base::ResetParam

(

void

)

Reset Param data member.

Definition at line 397 of file Gnomon_param_.cpp.

References CGnomon_param_Base::m_Param.

Referenced by CGnomon_param_Base::CGnomon_param_Base(), CGnomon_param_Base::GetParam(), CGnomon_param_Base::Reset(), and CGnomon_param_Base::SetParam().

ResetPhase_probabilities()

void CIntron_params_Base::ResetPhase_probabilities

(

void

)

Reset Phase_probabilities data member.

Definition at line 51 of file Intron_params_.cpp.

References CIntron_params_Base::m_Phase_probabilities, and CIntron_params_Base::m_set_State.

Referenced by CIntron_params_Base::Reset().

ResetProbabilities()

void CMarkov_chain_params_Base::ResetProbabilities

(

void

)

Reset Probabilities data member.

Definition at line 148 of file Markov_chain_params_.cpp.

References CMarkov_chain_params_Base::m_Probabilities, and CMarkov_chain_params_Base::m_set_State.

Referenced by CMarkov_chain_params_Base::Reset().

ResetRange()

void CLength_distribution_params_Base::ResetRange

(

void

)

Reset Range data member.

Definition at line 87 of file Length_distribution_params_.cpp.

References CLength_distribution_params_Base::m_Range.

Referenced by CLength_distribution_params_Base::CLength_distribution_params_Base(), CLength_distribution_params_Base::GetRange(), CLength_distribution_params_Base::Reset(), and CLength_distribution_params_Base::SetRange().

ResetSelection() [1/2]

void CGnomon_param_Base::C_Param::ResetSelection

(

void

)

Reset the selection (set it to e_not_set).

Definition at line 92 of file Gnomon_param_.cpp.

References e_not_set.

ResetSelection() [2/2]

void CMarkov_chain_params_Base::C_E_Probabilities::ResetSelection

(

void

)

Reset the selection (set it to e_not_set).

Definition at line 56 of file Markov_chain_params_.cpp.

References e_not_set.

Referenced by CMarkov_chain_params_Base::C_E_Probabilities::Reset().

ResetSingle_exon_length()

void CExon_params_Base::ResetSingle_exon_length

(

void

)

Reset Single_exon_length data member.

Definition at line 105 of file Exon_params_.cpp.

References CExon_params_Base::m_Single_exon_length.

Referenced by CExon_params_Base::CExon_params_Base(), CExon_params_Base::GetSingle_exon_length(), CExon_params_Base::Reset(), and CExon_params_Base::SetSingle_exon_length().

ResetStep()

void CLength_distribution_params_Base::ResetStep ( void  )

inline

Reset Step data member.

Definition at line 541 of file Length_distribution_params_.hpp.

References CLength_distribution_params_Base::m_set_State, and CLength_distribution_params_Base::m_Step.

Referenced by CLength_distribution_params_Base::Reset().

ResetTo()

void CGnomon_param_Base::C_Gc_content_range::ResetTo ( void  )

inline

Reset To data member.

Definition at line 729 of file Gnomon_param_.hpp.

References CGnomon_param_Base::m_set_State.

Referenced by CGnomon_param_Base::C_Gc_content_range::Reset().

ResetTo_single()

void CIntergenic_params_Base::ResetTo_single ( void  )

inline

Reset To_single data member.

Definition at line 299 of file Intergenic_params_.hpp.

References CIntergenic_params_Base::m_set_State, and CIntergenic_params_Base::m_To_single.

Referenced by CIntergenic_params_Base::Reset().

ResetTo_term()

void CIntron_params_Base::ResetTo_term ( void  )

inline

Reset To_term data member.

Definition at line 363 of file Intron_params_.hpp.

References CIntron_params_Base::m_set_State, and CIntron_params_Base::m_To_term.

Referenced by CIntron_params_Base::Reset().

Select() [1/4]

void CGnomon_param_Base::C_Param::Select	(	E_Choice	index,
		EResetVariant	reset,
		CObjectMemoryPool *	pool
	)

Select the requested variant if needed, allocating CObject variants from memory pool.

Select() [2/4]

void CMarkov_chain_params_Base::C_E_Probabilities::Select	(	E_Choice	index,
		EResetVariant	reset,
		CObjectMemoryPool *	pool
	)

Select the requested variant if needed, allocating CObject variants from memory pool.

Select() [3/4]

void CGnomon_param_Base::C_Param::Select	(	E_Choice	index,
		EResetVariant	reset = eDoResetVariant
	)

Select the requested variant if needed.

Parameters

index	New selection state.
reset	Flag that defines the resetting of the variant data. The data will be reset if either the current selection differs from the new one, or the flag is set to eDoResetVariant.

Select() [4/4]

void CMarkov_chain_params_Base::C_E_Probabilities::Select	(	E_Choice	index,
		EResetVariant	reset = eDoResetVariant
	)

Select the requested variant if needed.

Parameters

index	New selection state.
reset	Flag that defines the resetting of the variant data. The data will be reset if either the current selection differs from the new one, or the flag is set to eDoResetVariant.

SelectionName() [1/2]

NCBI_NS_STD::string CGnomon_param_Base::C_Param::SelectionName ( E_Choice  index )

static

Retrieve selection name (for diagnostic purposes).

Parameters

index

One of possible selection states.

Returns

Name string.

Definition at line 163 of file Gnomon_param_.cpp.

SelectionName() [2/2]

NCBI_NS_STD::string CMarkov_chain_params_Base::C_E_Probabilities::SelectionName ( E_Choice  index )

static

Retrieve selection name (for diagnostic purposes).

Parameters

index

One of possible selection states.

Returns

Name string.

Definition at line 89 of file Markov_chain_params_.cpp.

Set()

CGnomon_params_Base::Tdata & CGnomon_params_Base::Set ( void  )

inline

Assign a value to data member.

Returns

Reference to the data value.

Definition at line 170 of file Gnomon_params_.hpp.

References CGnomon_params_Base::m_data, and CGnomon_params_Base::m_set_State.

SetA() [1/2]

void CLength_distribution_params_Base::SetA ( CLength_distribution_params_Base::TA  value )

inline

Assign a value to A data member.

Parameters

value

Value to assign

Definition at line 629 of file Length_distribution_params_.hpp.

References CLength_distribution_params_Base::m_A, CLength_distribution_params_Base::m_set_State, and rapidjson::value.

SetA() [2/2]

CLength_distribution_params_Base::TA & CLength_distribution_params_Base::SetA ( void  )

inline

Assign a value to A data member.

Returns

Reference to the data value.

Definition at line 636 of file Length_distribution_params_.hpp.

References CLength_distribution_params_Base::IsSetA(), CLength_distribution_params_Base::m_A, CLength_distribution_params_Base::m_set_State, and CSerialObject::UnassignedByte().

SetAcceptor() [1/2]

void CGnomon_param_Base::C_Param::SetAcceptor

(

TAcceptor &

value

)

Select the variant and set its data.

Parameters

value

Reference to the data.

Definition at line 317 of file Gnomon_param_.cpp.

References CObject::AddReference(), and rapidjson::value.

SetAcceptor() [2/2]

CGnomon_param_Base::C_Param::TAcceptor & CGnomon_param_Base::C_Param::SetAcceptor

(

void

)

Select the variant.

Returns

Reference to the variant data.

Definition at line 311 of file Gnomon_param_.cpp.

References eDoNotResetVariant.

SetCoding_region()

CGnomon_param_Base::C_Param::TCoding_region & CGnomon_param_Base::C_Param::SetCoding_region ( void  )

inline

Select the variant.

Returns

Reference to the variant data.

Definition at line 848 of file Gnomon_param_.hpp.

References eDoNotResetVariant.

SetDonor() [1/2]

void CGnomon_param_Base::C_Param::SetDonor

(

TDonor &

value

)

Select the variant and set its data.

Parameters

value

Reference to the data.

Definition at line 295 of file Gnomon_param_.cpp.

References CObject::AddReference(), and rapidjson::value.

SetDonor() [2/2]

CGnomon_param_Base::C_Param::TDonor & CGnomon_param_Base::C_Param::SetDonor

(

void

)

Select the variant.

Returns

Reference to the variant data.

Definition at line 289 of file Gnomon_param_.cpp.

References eDoNotResetVariant.

SetExon() [1/2]

void CGnomon_param_Base::C_Param::SetExon

(

TExon &

value

)

Select the variant and set its data.

Parameters

value

Reference to the data.

Definition at line 229 of file Gnomon_param_.cpp.

References CObject::AddReference(), and rapidjson::value.

SetExon() [2/2]

CGnomon_param_Base::C_Param::TExon & CGnomon_param_Base::C_Param::SetExon

(

void

)

Select the variant.

Returns

Reference to the variant data.

Definition at line 223 of file Gnomon_param_.cpp.

References eDoNotResetVariant.

SetFirst_exon_length() [1/2]

void CExon_params_Base::SetFirst_exon_length

(

CExon_params_Base::TFirst_exon_length &

value

)

Assign a value to First_exon_length data member.

Parameters

value

Reference to value.

Definition at line 72 of file Exon_params_.cpp.

References CExon_params_Base::m_First_exon_length, and rapidjson::value.

SetFirst_exon_length() [2/2]

CExon_params_Base::TFirst_exon_length & CExon_params_Base::SetFirst_exon_length ( void  )

inline

Assign a value to First_exon_length data member.

Returns

Reference to the data value.

Definition at line 423 of file Exon_params_.hpp.

References CExon_params_Base::m_First_exon_length, and CExon_params_Base::ResetFirst_exon_length().

SetFirst_exon_phase_probabilities()

CExon_params_Base::TFirst_exon_phase_probabilities & CExon_params_Base::SetFirst_exon_phase_probabilities ( void  )

inline

Assign a value to First_exon_phase_probabilities data member.

Returns

Reference to the data value.

Definition at line 370 of file Exon_params_.hpp.

References CExon_params_Base::m_First_exon_phase_probabilities, and CExon_params_Base::m_set_State.

SetFrom() [1/2]

void CGnomon_param_Base::C_Gc_content_range::SetFrom ( TFrom  value )

inline

Assign a value to From data member.

Parameters

value

Value to assign

Definition at line 698 of file Gnomon_param_.hpp.

References CGnomon_param_Base::m_set_State, and rapidjson::value.

SetFrom() [2/2]

CGnomon_param_Base::C_Gc_content_range::TFrom & CGnomon_param_Base::C_Gc_content_range::SetFrom ( void  )

inline

Assign a value to From data member.

Returns

Reference to the data value.

Definition at line 705 of file Gnomon_param_.hpp.

References CGnomon_param_Base::m_set_State, and CSerialObject::UnassignedByte().

SetGc_content_range() [1/2]

void CGnomon_param_Base::SetGc_content_range

(

CGnomon_param_Base::TGc_content_range &

value

)

Assign a value to Gc_content_range data member.

Parameters

value

Reference to value.

Definition at line 392 of file Gnomon_param_.cpp.

References CGnomon_param_Base::m_Gc_content_range, and rapidjson::value.

SetGc_content_range() [2/2]

CGnomon_param_Base::TGc_content_range & CGnomon_param_Base::SetGc_content_range ( void  )

inline

Assign a value to Gc_content_range data member.

Returns

Reference to the data value.

Definition at line 882 of file Gnomon_param_.hpp.

References CGnomon_param_Base::m_Gc_content_range, and CGnomon_param_Base::ResetGc_content_range().

SetIn_exon() [1/2]

void CMarkov_chain_array_Base::SetIn_exon ( CMarkov_chain_array_Base::TIn_exon  value )

inline

Assign a value to In_exon data member.

Parameters

value

Value to assign

Definition at line 265 of file Markov_chain_array_.hpp.

References CMarkov_chain_array_Base::m_In_exon, CMarkov_chain_array_Base::m_set_State, and rapidjson::value.

SetIn_exon() [2/2]

CMarkov_chain_array_Base::TIn_exon & CMarkov_chain_array_Base::SetIn_exon ( void  )

inline

Assign a value to In_exon data member.

Returns

Reference to the data value.

Definition at line 272 of file Markov_chain_array_.hpp.

References CMarkov_chain_array_Base::IsSetIn_exon(), CMarkov_chain_array_Base::m_In_exon, CMarkov_chain_array_Base::m_set_State, and CSerialObject::UnassignedByte().

SetIn_intron() [1/2]

void CMarkov_chain_array_Base::SetIn_intron ( CMarkov_chain_array_Base::TIn_intron  value )

inline

Assign a value to In_intron data member.

Parameters

value

Value to assign

Definition at line 312 of file Markov_chain_array_.hpp.

References CMarkov_chain_array_Base::m_In_intron, CMarkov_chain_array_Base::m_set_State, and rapidjson::value.

SetIn_intron() [2/2]

CMarkov_chain_array_Base::TIn_intron & CMarkov_chain_array_Base::SetIn_intron ( void  )

inline

Assign a value to In_intron data member.

Returns

Reference to the data value.

Definition at line 319 of file Markov_chain_array_.hpp.

References CMarkov_chain_array_Base::IsSetIn_intron(), CMarkov_chain_array_Base::m_In_intron, CMarkov_chain_array_Base::m_set_State, and CSerialObject::UnassignedByte().

SetInitp() [1/4]

void CIntergenic_params_Base::SetInitp ( CIntergenic_params_Base::TInitp  value )

inline

Assign a value to Initp data member.

Parameters

value

Value to assign

Definition at line 268 of file Intergenic_params_.hpp.

References CIntergenic_params_Base::m_Initp, CIntergenic_params_Base::m_set_State, and rapidjson::value.

SetInitp() [2/4]

void CIntron_params_Base::SetInitp ( CIntron_params_Base::TInitp  value )

inline

Assign a value to Initp data member.

Parameters

value

Value to assign

Definition at line 307 of file Intron_params_.hpp.

References CIntron_params_Base::m_Initp, CIntron_params_Base::m_set_State, and rapidjson::value.

SetInitp() [3/4]

CIntergenic_params_Base::TInitp & CIntergenic_params_Base::SetInitp ( void  )

inline

Assign a value to Initp data member.

Returns

Reference to the data value.

Definition at line 275 of file Intergenic_params_.hpp.

References CIntergenic_params_Base::IsSetInitp(), CIntergenic_params_Base::m_Initp, CIntergenic_params_Base::m_set_State, and CSerialObject::UnassignedByte().

SetInitp() [4/4]

CIntron_params_Base::TInitp & CIntron_params_Base::SetInitp ( void  )

inline

Assign a value to Initp data member.

Returns

Reference to the data value.

Definition at line 314 of file Intron_params_.hpp.

References CIntron_params_Base::IsSetInitp(), CIntron_params_Base::m_Initp, CIntron_params_Base::m_set_State, and CSerialObject::UnassignedByte().

SetIntergenic() [1/2]

void CGnomon_param_Base::C_Param::SetIntergenic

(

TIntergenic &

value

)

Select the variant and set its data.

Parameters

value

Reference to the data.

Definition at line 185 of file Gnomon_param_.cpp.

References CObject::AddReference(), and rapidjson::value.

SetIntergenic() [2/2]

CGnomon_param_Base::C_Param::TIntergenic & CGnomon_param_Base::C_Param::SetIntergenic

(

void

)

Select the variant.

Returns

Reference to the variant data.

Definition at line 179 of file Gnomon_param_.cpp.

References eDoNotResetVariant.

SetInternal_exon_length() [1/2]

void CExon_params_Base::SetInternal_exon_length

(

CExon_params_Base::TInternal_exon_length &

value

)

Assign a value to Internal_exon_length data member.

Parameters

value

Reference to value.

Definition at line 86 of file Exon_params_.cpp.

References CExon_params_Base::m_Internal_exon_length, and rapidjson::value.

SetInternal_exon_length() [2/2]

CExon_params_Base::TInternal_exon_length & CExon_params_Base::SetInternal_exon_length ( void  )

inline

Assign a value to Internal_exon_length data member.

Returns

Reference to the data value.

Definition at line 453 of file Exon_params_.hpp.

References CExon_params_Base::m_Internal_exon_length, and CExon_params_Base::ResetInternal_exon_length().

SetInternal_exon_phase_probabilities()

CExon_params_Base::TInternal_exon_phase_probabilities & CExon_params_Base::SetInternal_exon_phase_probabilities ( void  )

inline

Assign a value to Internal_exon_phase_probabilities data member.

Returns

Reference to the data value.

Definition at line 395 of file Exon_params_.hpp.

References CExon_params_Base::m_Internal_exon_phase_probabilities, and CExon_params_Base::m_set_State.

SetIntron() [1/2]

void CGnomon_param_Base::C_Param::SetIntron

(

TIntron &

value

)

Select the variant and set its data.

Parameters

value

Reference to the data.

Definition at line 207 of file Gnomon_param_.cpp.

References CObject::AddReference(), and rapidjson::value.

SetIntron() [2/2]

CGnomon_param_Base::C_Param::TIntron & CGnomon_param_Base::C_Param::SetIntron

(

void

)

Select the variant.

Returns

Reference to the variant data.

Definition at line 201 of file Gnomon_param_.cpp.

References eDoNotResetVariant.

SetL() [1/2]

void CLength_distribution_params_Base::SetL ( CLength_distribution_params_Base::TL  value )

inline

Assign a value to L data member.

Parameters

value

Value to assign

Definition at line 676 of file Length_distribution_params_.hpp.

References CLength_distribution_params_Base::m_L, CLength_distribution_params_Base::m_set_State, and rapidjson::value.

SetL() [2/2]

CLength_distribution_params_Base::TL & CLength_distribution_params_Base::SetL ( void  )

inline

Assign a value to L data member.

Returns

Reference to the data value.

Definition at line 683 of file Length_distribution_params_.hpp.

References CLength_distribution_params_Base::IsSetL(), CLength_distribution_params_Base::m_L, CLength_distribution_params_Base::m_set_State, and CSerialObject::UnassignedByte().

SetLast_exon_length() [1/2]

void CExon_params_Base::SetLast_exon_length

(

CExon_params_Base::TLast_exon_length &

value

)

Assign a value to Last_exon_length data member.

Parameters

value

Reference to value.

Definition at line 100 of file Exon_params_.cpp.

References CExon_params_Base::m_Last_exon_length, and rapidjson::value.

SetLast_exon_length() [2/2]

CExon_params_Base::TLast_exon_length & CExon_params_Base::SetLast_exon_length ( void  )

inline

Assign a value to Last_exon_length data member.

Returns

Reference to the data value.

Definition at line 483 of file Exon_params_.hpp.

References CExon_params_Base::m_Last_exon_length, and CExon_params_Base::ResetLast_exon_length().

SetLength() [1/4]

void CIntergenic_params_Base::SetLength

(

CIntergenic_params_Base::TLength &

value

)

Assign a value to Length data member.

Parameters

value

Reference to value.

Definition at line 60 of file Intergenic_params_.cpp.

References CIntergenic_params_Base::m_Length, and rapidjson::value.

SetLength() [2/4]

void CIntron_params_Base::SetLength

(

CIntron_params_Base::TLength &

value

)

Assign a value to Length data member.

Parameters

value

Reference to value.

Definition at line 66 of file Intron_params_.cpp.

References CIntron_params_Base::m_Length, and rapidjson::value.

SetLength() [3/4]

CIntergenic_params_Base::TLength & CIntergenic_params_Base::SetLength ( void  )

inline

Assign a value to Length data member.

Returns

Reference to the data value.

Definition at line 355 of file Intergenic_params_.hpp.

References CIntergenic_params_Base::m_Length, and CIntergenic_params_Base::ResetLength().

SetLength() [4/4]

CIntron_params_Base::TLength & CIntron_params_Base::SetLength ( void  )

inline

Assign a value to Length data member.

Returns

Reference to the data value.

Definition at line 419 of file Intron_params_.hpp.

References CIntron_params_Base::m_Length, and CIntron_params_Base::ResetLength().

SetMatrix()

CMarkov_chain_array_Base::TMatrix & CMarkov_chain_array_Base::SetMatrix ( void  )

inline

Assign a value to Matrix data member.

Returns

Reference to the data value.

Definition at line 349 of file Markov_chain_array_.hpp.

References CMarkov_chain_array_Base::m_Matrix, and CMarkov_chain_array_Base::m_set_State.

SetMax() [1/2]

void CLength_distribution_params_Base::C_Range::SetMax ( TMax  value )

inline

Assign a value to Max data member.

Parameters

value

Value to assign

Definition at line 510 of file Length_distribution_params_.hpp.

References CLength_distribution_params_Base::m_set_State, and rapidjson::value.

SetMax() [2/2]

CLength_distribution_params_Base::C_Range::TMax & CLength_distribution_params_Base::C_Range::SetMax ( void  )

inline

Assign a value to Max data member.

Returns

Reference to the data value.

Definition at line 517 of file Length_distribution_params_.hpp.

References CLength_distribution_params_Base::m_set_State, and CSerialObject::UnassignedByte().

SetMin() [1/2]

void CLength_distribution_params_Base::C_Range::SetMin ( TMin  value )

inline

Assign a value to Min data member.

Parameters

value

Value to assign

Definition at line 463 of file Length_distribution_params_.hpp.

References CLength_distribution_params_Base::m_set_State, and rapidjson::value.

SetMin() [2/2]

CLength_distribution_params_Base::C_Range::TMin & CLength_distribution_params_Base::C_Range::SetMin ( void  )

inline

Assign a value to Min data member.

Returns

Reference to the data value.

Definition at line 470 of file Length_distribution_params_.hpp.

References CLength_distribution_params_Base::m_set_State, and CSerialObject::UnassignedByte().

SetNon_coding_region() [1/2]

void CGnomon_param_Base::C_Param::SetNon_coding_region

(

TNon_coding_region &

value

)

Select the variant and set its data.

Parameters

value

Reference to the data.

Definition at line 339 of file Gnomon_param_.cpp.

References CObject::AddReference(), and rapidjson::value.

SetNon_coding_region() [2/2]

CGnomon_param_Base::C_Param::TNon_coding_region & CGnomon_param_Base::C_Param::SetNon_coding_region

(

void

)

Select the variant.

Returns

Reference to the variant data.

Definition at line 333 of file Gnomon_param_.cpp.

References eDoNotResetVariant.

SetOrder() [1/2]

void CMarkov_chain_params_Base::SetOrder ( CMarkov_chain_params_Base::TOrder  value )

inline

Assign a value to Order data member.

Parameters

value

Value to assign

Definition at line 440 of file Markov_chain_params_.hpp.

References CMarkov_chain_params_Base::m_Order, CMarkov_chain_params_Base::m_set_State, and rapidjson::value.

SetOrder() [2/2]

CMarkov_chain_params_Base::TOrder & CMarkov_chain_params_Base::SetOrder ( void  )

inline

Assign a value to Order data member.

Returns

Reference to the data value.

Definition at line 447 of file Markov_chain_params_.hpp.

References CMarkov_chain_params_Base::IsSetOrder(), CMarkov_chain_params_Base::m_Order, CMarkov_chain_params_Base::m_set_State, and CSerialObject::UnassignedByte().

SetP()

CLength_distribution_params_Base::TP & CLength_distribution_params_Base::SetP ( void  )

inline

Assign a value to P data member.

Returns

Reference to the data value.

Definition at line 594 of file Length_distribution_params_.hpp.

References CLength_distribution_params_Base::m_P, and CLength_distribution_params_Base::m_set_State.

SetParam() [1/2]

void CGnomon_param_Base::SetParam

(

CGnomon_param_Base::TParam &

value

)

Assign a value to Param data member.

Parameters

value

Reference to value.

Definition at line 406 of file Gnomon_param_.cpp.

References CGnomon_param_Base::m_Param, and rapidjson::value.

SetParam() [2/2]

CGnomon_param_Base::TParam & CGnomon_param_Base::SetParam ( void  )

inline

Assign a value to Param data member.

Returns

Reference to the data value.

Definition at line 912 of file Gnomon_param_.hpp.

References CGnomon_param_Base::m_Param, and CGnomon_param_Base::ResetParam().

SetPhase_probabilities()

CIntron_params_Base::TPhase_probabilities & CIntron_params_Base::SetPhase_probabilities ( void  )

inline

Assign a value to Phase_probabilities data member.

Returns

Reference to the data value.

Definition at line 344 of file Intron_params_.hpp.

References CIntron_params_Base::m_Phase_probabilities, and CIntron_params_Base::m_set_State.

SetPrev_order() [1/2]

void CMarkov_chain_params_Base::C_E_Probabilities::SetPrev_order

(

TPrev_order &

value

)

Select the variant and set its data.

Parameters

value

Reference to the data.

Definition at line 111 of file Markov_chain_params_.cpp.

References CObject::AddReference(), and rapidjson::value.

SetPrev_order() [2/2]

CMarkov_chain_params_Base::C_E_Probabilities::TPrev_order & CMarkov_chain_params_Base::C_E_Probabilities::SetPrev_order

(

void

)

Select the variant.

Returns

Reference to the variant data.

Definition at line 105 of file Markov_chain_params_.cpp.

References eDoNotResetVariant.

SetProbabilities()

CMarkov_chain_params_Base::TProbabilities & CMarkov_chain_params_Base::SetProbabilities ( void  )

inline

Assign a value to Probabilities data member.

Returns

Reference to the data value.

Definition at line 477 of file Markov_chain_params_.hpp.

References CMarkov_chain_params_Base::m_Probabilities, and CMarkov_chain_params_Base::m_set_State.

SetRange() [1/2]

void CLength_distribution_params_Base::SetRange

(

CLength_distribution_params_Base::TRange &

value

)

Assign a value to Range data member.

Parameters

value

Reference to value.

Definition at line 96 of file Length_distribution_params_.cpp.

References CLength_distribution_params_Base::m_Range, and rapidjson::value.

SetRange() [2/2]

CLength_distribution_params_Base::TRange & CLength_distribution_params_Base::SetRange ( void  )

inline

Assign a value to Range data member.

Returns

Reference to the data value.

Definition at line 716 of file Length_distribution_params_.hpp.

References CLength_distribution_params_Base::m_Range, and CLength_distribution_params_Base::ResetRange().

SetSingle_exon_length() [1/2]

void CExon_params_Base::SetSingle_exon_length

(

CExon_params_Base::TSingle_exon_length &

value

)

Assign a value to Single_exon_length data member.

Parameters

value

Reference to value.

Definition at line 114 of file Exon_params_.cpp.

References CExon_params_Base::m_Single_exon_length, and rapidjson::value.

SetSingle_exon_length() [2/2]

CExon_params_Base::TSingle_exon_length & CExon_params_Base::SetSingle_exon_length ( void  )

inline

Assign a value to Single_exon_length data member.

Returns

Reference to the data value.

Definition at line 513 of file Exon_params_.hpp.

References CExon_params_Base::m_Single_exon_length, and CExon_params_Base::ResetSingle_exon_length().

SetStart() [1/2]

void CGnomon_param_Base::C_Param::SetStart

(

TStart &

value

)

Select the variant and set its data.

Parameters

value

Reference to the data.

Definition at line 251 of file Gnomon_param_.cpp.

References CObject::AddReference(), and rapidjson::value.

SetStart() [2/2]

CGnomon_param_Base::C_Param::TStart & CGnomon_param_Base::C_Param::SetStart

(

void

)

Select the variant.

Returns

Reference to the variant data.

Definition at line 245 of file Gnomon_param_.cpp.

References eDoNotResetVariant.

SetStep() [1/2]

void CLength_distribution_params_Base::SetStep ( CLength_distribution_params_Base::TStep  value )

inline

Assign a value to Step data member.

Parameters

value

Value to assign

Definition at line 557 of file Length_distribution_params_.hpp.

References CLength_distribution_params_Base::m_set_State, CLength_distribution_params_Base::m_Step, and rapidjson::value.

SetStep() [2/2]

CLength_distribution_params_Base::TStep & CLength_distribution_params_Base::SetStep ( void  )

inline

Assign a value to Step data member.

Returns

Reference to the data value.

Definition at line 564 of file Length_distribution_params_.hpp.

References CLength_distribution_params_Base::IsSetStep(), CLength_distribution_params_Base::m_set_State, CLength_distribution_params_Base::m_Step, and CSerialObject::UnassignedByte().

SetStop() [1/2]

void CGnomon_param_Base::C_Param::SetStop

(

TStop &

value

)

Select the variant and set its data.

Parameters

value

Reference to the data.

Definition at line 273 of file Gnomon_param_.cpp.

References CObject::AddReference(), and rapidjson::value.

SetStop() [2/2]

CGnomon_param_Base::C_Param::TStop & CGnomon_param_Base::C_Param::SetStop

(

void

)

Select the variant.

Returns

Reference to the variant data.

Definition at line 267 of file Gnomon_param_.cpp.

References eDoNotResetVariant.

SetTo() [1/2]

void CGnomon_param_Base::C_Gc_content_range::SetTo ( TTo  value )

inline

Assign a value to To data member.

Parameters

value

Value to assign

Definition at line 745 of file Gnomon_param_.hpp.

References CGnomon_param_Base::m_set_State, and rapidjson::value.

SetTo() [2/2]

CGnomon_param_Base::C_Gc_content_range::TTo & CGnomon_param_Base::C_Gc_content_range::SetTo ( void  )

inline

Assign a value to To data member.

Returns

Reference to the data value.

Definition at line 752 of file Gnomon_param_.hpp.

References CGnomon_param_Base::m_set_State, and CSerialObject::UnassignedByte().

SetTo_single() [1/2]

void CIntergenic_params_Base::SetTo_single ( CIntergenic_params_Base::TTo_single  value )

inline

Assign a value to To_single data member.

Parameters

value

Value to assign

Definition at line 315 of file Intergenic_params_.hpp.

References CIntergenic_params_Base::m_set_State, CIntergenic_params_Base::m_To_single, and rapidjson::value.

SetTo_single() [2/2]

CIntergenic_params_Base::TTo_single & CIntergenic_params_Base::SetTo_single ( void  )

inline

Assign a value to To_single data member.

Returns

Reference to the data value.

Definition at line 322 of file Intergenic_params_.hpp.

References CIntergenic_params_Base::IsSetTo_single(), CIntergenic_params_Base::m_set_State, CIntergenic_params_Base::m_To_single, and CSerialObject::UnassignedByte().

SetTo_term() [1/2]

void CIntron_params_Base::SetTo_term ( CIntron_params_Base::TTo_term  value )

inline

Assign a value to To_term data member.

Parameters

value

Value to assign

Definition at line 379 of file Intron_params_.hpp.

References CIntron_params_Base::m_set_State, CIntron_params_Base::m_To_term, and rapidjson::value.

SetTo_term() [2/2]

CIntron_params_Base::TTo_term & CIntron_params_Base::SetTo_term ( void  )

inline

Assign a value to To_term data member.

Returns

Reference to the data value.

Definition at line 386 of file Intron_params_.hpp.

References CIntron_params_Base::IsSetTo_term(), CIntron_params_Base::m_set_State, CIntron_params_Base::m_To_term, and CSerialObject::UnassignedByte().

SetValue() [1/2]

void CMarkov_chain_params_Base::C_E_Probabilities::SetValue ( TValue  value )

inline

Select the variant and set its data.

Parameters

value

Variant data.

Definition at line 405 of file Markov_chain_params_.hpp.

References eDoNotResetVariant, and rapidjson::value.

SetValue() [2/2]

CMarkov_chain_params_Base::C_E_Probabilities::TValue & CMarkov_chain_params_Base::C_E_Probabilities::SetValue ( void  )

inline

Select the variant.

Returns

Reference to the variant data.

Definition at line 398 of file Markov_chain_params_.hpp.

References eDoNotResetVariant.

ThrowInvalidSelection() [1/2]

void CGnomon_param_Base::C_Param::ThrowInvalidSelection

(

E_Choice

index

)

const

Throw 'InvalidSelection' exception.

Parameters

index

Expected selection.

Definition at line 168 of file Gnomon_param_.cpp.

References DIAG_COMPILE_INFO.

ThrowInvalidSelection() [2/2]

void CMarkov_chain_params_Base::C_E_Probabilities::ThrowInvalidSelection

(

E_Choice

index

)

const

Throw 'InvalidSelection' exception.

Parameters

index

Expected selection.

Definition at line 94 of file Markov_chain_params_.cpp.

References DIAG_COMPILE_INFO.

Which() [1/2]

CGnomon_param_Base::C_Param::E_Choice CGnomon_param_Base::C_Param::Which ( void  ) const

inline

Which variant is currently selected.

Returns

Choice state enumerator.

Definition at line 764 of file Gnomon_param_.hpp.

Which() [2/2]

CMarkov_chain_params_Base::C_E_Probabilities::E_Choice CMarkov_chain_params_Base::C_E_Probabilities::Which ( void  ) const

inline

Which variant is currently selected.

Returns

Choice state enumerator.

Definition at line 350 of file Markov_chain_params_.hpp.

References CMarkov_chain_params_Base::C_E_Probabilities::m_choice.

~C_E_Probabilities()

CMarkov_chain_params_Base::C_E_Probabilities::~C_E_Probabilities

(

void

)

Definition at line 142 of file Markov_chain_params_.cpp.

References CMarkov_chain_params_Base::Reset().

~C_Gc_content_range()

CGnomon_param_Base::C_Gc_content_range::~C_Gc_content_range

(

void

)

Definition at line 81 of file Gnomon_param_.cpp.

~C_Param()

CGnomon_param_Base::C_Param::~C_Param

(

void

)

Definition at line 377 of file Gnomon_param_.cpp.

References CGnomon_param_Base::Reset().

~C_Range()

CLength_distribution_params_Base::C_Range::~C_Range

(

void

)

Definition at line 76 of file Length_distribution_params_.cpp.

~CExon_params()

CExon_params::~CExon_params

(

void

)

Definition at line 50 of file Exon_params.cpp.

~CExon_params_Base()

CExon_params_Base::~CExon_params_Base ( void  )

virtual

Definition at line 157 of file Exon_params_.cpp.

~CGnomon_param()

CGnomon_param::~CGnomon_param

(

void

)

Definition at line 50 of file Gnomon_param.cpp.

~CGnomon_param_Base()

CGnomon_param_Base::~CGnomon_param_Base ( void  )

virtual

Definition at line 439 of file Gnomon_param_.cpp.

~CGnomon_params()

CGnomon_params::~CGnomon_params

(

void

)

Definition at line 50 of file Gnomon_params.cpp.

~CGnomon_params_Base()

CGnomon_params_Base::~CGnomon_params_Base ( void  )

virtual

Definition at line 74 of file Gnomon_params_.cpp.

~CIntergenic_params()

CIntergenic_params::~CIntergenic_params

(

void

)

Definition at line 50 of file Intergenic_params.cpp.

~CIntergenic_params_Base()

CIntergenic_params_Base::~CIntergenic_params_Base ( void  )

virtual

Definition at line 95 of file Intergenic_params_.cpp.

~CIntron_params()

CIntron_params::~CIntron_params

(

void

)

Definition at line 50 of file Intron_params.cpp.

~CIntron_params_Base()

CIntron_params_Base::~CIntron_params_Base ( void  )

virtual

Definition at line 103 of file Intron_params_.cpp.

~CLength_distribution_params()

CLength_distribution_params::~CLength_distribution_params

(

void

)

Definition at line 50 of file Length_distribution_params.cpp.

~CLength_distribution_params_Base()

CLength_distribution_params_Base::~CLength_distribution_params_Base ( void  )

virtual

Definition at line 135 of file Length_distribution_params_.cpp.

~CMarkov_chain_array()

CMarkov_chain_array::~CMarkov_chain_array

(

void

)

Definition at line 50 of file Markov_chain_array.cpp.

~CMarkov_chain_array_Base()

CMarkov_chain_array_Base::~CMarkov_chain_array_Base ( void  )

virtual

Definition at line 84 of file Markov_chain_array_.cpp.

~CMarkov_chain_params()

CMarkov_chain_params::~CMarkov_chain_params

(

void

)

Definition at line 50 of file Markov_chain_params.cpp.

~CMarkov_chain_params_Base()

CMarkov_chain_params_Base::~CMarkov_chain_params_Base ( void  )

virtual

Definition at line 179 of file Markov_chain_params_.cpp.

Variable Documentation

union { ... }

union { ... }

m_A

double CLength_distribution_params_Base::m_A

private

Definition at line 420 of file Length_distribution_params_.hpp.

Referenced by BEGIN_NAMED_BASE_CLASS_INFO(), CLength_distribution_params_Base::GetA(), CLength_distribution_params_Base::ResetA(), and CLength_distribution_params_Base::SetA().

m_choice [1/2]

E_Choice CGnomon_param_Base::C_Param::m_choice

private

Definition at line 545 of file Gnomon_param_.hpp.

m_choice [2/2]

E_Choice CMarkov_chain_params_Base::C_E_Probabilities::m_choice

private

Definition at line 230 of file Markov_chain_params_.hpp.

Referenced by CMarkov_chain_params_Base::C_E_Probabilities::Reset(), and CMarkov_chain_params_Base::C_E_Probabilities::Which().

m_Coding_region [1/2]

NCBI_NS_NCBI::CUnionBuffer<TCoding_region> CGnomon_param_Base::C_Param::m_Coding_region

Definition at line 552 of file Gnomon_param_.hpp.

[2/2]

NCBI_NS_NCBI::CUnionBuffer<TCoding_region> { ... } ::m_Coding_region

Definition at line 552 of file Gnomon_param_.hpp.

m_data

list< CRef< CGnomon_param > > CGnomon_params_Base::m_data

private

Definition at line 139 of file Gnomon_params_.hpp.

Referenced by CGnomon_params_Base::Get(), CGnomon_params_Base::Reset(), and CGnomon_params_Base::Set().

m_First_exon_length

CRef< TFirst_exon_length > CExon_params_Base::m_First_exon_length

private

Definition at line 336 of file Exon_params_.hpp.

Referenced by CExon_params_Base::GetFirst_exon_length(), CExon_params_Base::IsSetFirst_exon_length(), CExon_params_Base::ResetFirst_exon_length(), and CExon_params_Base::SetFirst_exon_length().

m_First_exon_phase_probabilities

list< double > CExon_params_Base::m_First_exon_phase_probabilities

private

Definition at line 334 of file Exon_params_.hpp.

Referenced by CExon_params_Base::GetFirst_exon_phase_probabilities(), CExon_params_Base::ResetFirst_exon_phase_probabilities(), and CExon_params_Base::SetFirst_exon_phase_probabilities().

m_From

int CGnomon_param_Base::C_Gc_content_range::m_From

private

Definition at line 210 of file Gnomon_param_.hpp.

m_Gc_content_range

CRef< TGc_content_range > CGnomon_param_Base::m_Gc_content_range

private

Definition at line 656 of file Gnomon_param_.hpp.

Referenced by BEGIN_NAMED_BASE_CLASS_INFO(), CGnomon_param_Base::GetGc_content_range(), CGnomon_param_Base::IsSetGc_content_range(), CGnomon_param_Base::ResetGc_content_range(), and CGnomon_param_Base::SetGc_content_range().

m_In_exon

int CMarkov_chain_array_Base::m_In_exon

private

Definition at line 222 of file Markov_chain_array_.hpp.

Referenced by CMarkov_chain_array_Base::GetIn_exon(), CMarkov_chain_array_Base::ResetIn_exon(), and CMarkov_chain_array_Base::SetIn_exon().

m_In_intron

int CMarkov_chain_array_Base::m_In_intron

private

Definition at line 223 of file Markov_chain_array_.hpp.

Referenced by CMarkov_chain_array_Base::GetIn_intron(), CMarkov_chain_array_Base::ResetIn_intron(), and CMarkov_chain_array_Base::SetIn_intron().

m_Initp [1/2]

double CIntergenic_params_Base::m_Initp

private

Definition at line 225 of file Intergenic_params_.hpp.

Referenced by CIntergenic_params_Base::GetInitp(), CIntergenic_params_Base::ResetInitp(), and CIntergenic_params_Base::SetInitp().

m_Initp [2/2]

double CIntron_params_Base::m_Initp

private

Definition at line 263 of file Intron_params_.hpp.

Referenced by CIntron_params_Base::GetInitp(), CIntron_params_Base::ResetInitp(), and CIntron_params_Base::SetInitp().

m_Internal_exon_length

CRef< TInternal_exon_length > CExon_params_Base::m_Internal_exon_length

private

Definition at line 337 of file Exon_params_.hpp.

Referenced by CExon_params_Base::GetInternal_exon_length(), CExon_params_Base::IsSetInternal_exon_length(), CExon_params_Base::ResetInternal_exon_length(), and CExon_params_Base::SetInternal_exon_length().

m_Internal_exon_phase_probabilities

list< double > CExon_params_Base::m_Internal_exon_phase_probabilities

private

Definition at line 335 of file Exon_params_.hpp.

Referenced by CExon_params_Base::GetInternal_exon_phase_probabilities(), CExon_params_Base::ResetInternal_exon_phase_probabilities(), and CExon_params_Base::SetInternal_exon_phase_probabilities().

m_L

double CLength_distribution_params_Base::m_L

private

Definition at line 421 of file Length_distribution_params_.hpp.

Referenced by BEGIN_NAMED_BASE_CLASS_INFO(), CLength_distribution_params_Base::GetL(), CLength_distribution_params_Base::ResetL(), and CLength_distribution_params_Base::SetL().

m_Last_exon_length

CRef< TLast_exon_length > CExon_params_Base::m_Last_exon_length

private

Definition at line 338 of file Exon_params_.hpp.

Referenced by CExon_params_Base::GetLast_exon_length(), CExon_params_Base::IsSetLast_exon_length(), CExon_params_Base::ResetLast_exon_length(), and CExon_params_Base::SetLast_exon_length().

m_Length [1/2]

CRef< TLength > CIntergenic_params_Base::m_Length

private

Definition at line 227 of file Intergenic_params_.hpp.

Referenced by CIntergenic_params_Base::GetLength(), CIntergenic_params_Base::IsSetLength(), CIntergenic_params_Base::ResetLength(), and CIntergenic_params_Base::SetLength().

m_Length [2/2]

CRef< TLength > CIntron_params_Base::m_Length

private

Definition at line 266 of file Intron_params_.hpp.

Referenced by CIntron_params_Base::GetLength(), CIntron_params_Base::IsSetLength(), CIntron_params_Base::ResetLength(), and CIntron_params_Base::SetLength().

m_Matrix

list< CRef< CMarkov_chain_params > > CMarkov_chain_array_Base::m_Matrix

private

Definition at line 224 of file Markov_chain_array_.hpp.

Referenced by CMarkov_chain_array_Base::GetMatrix(), CMarkov_chain_array_Base::ResetMatrix(), and CMarkov_chain_array_Base::SetMatrix().

m_Max

int CLength_distribution_params_Base::C_Range::m_Max

private

Definition at line 202 of file Length_distribution_params_.hpp.

m_Min

int CLength_distribution_params_Base::C_Range::m_Min

private

Definition at line 201 of file Length_distribution_params_.hpp.

[1/4]

NCBI_NS_NCBI::CSerialObject* { ... } ::m_object

Definition at line 553 of file Gnomon_param_.hpp.

m_object [2/4]

NCBI_NS_NCBI::CSerialObject* CGnomon_param_Base::C_Param::m_object

Definition at line 553 of file Gnomon_param_.hpp.

m_object [3/4]

NCBI_NS_NCBI::CSerialObject* CMarkov_chain_params_Base::C_E_Probabilities::m_object

Definition at line 238 of file Markov_chain_params_.hpp.

[4/4]

NCBI_NS_NCBI::CSerialObject* { ... } ::m_object

Definition at line 238 of file Markov_chain_params_.hpp.

m_Order

int CMarkov_chain_params_Base::m_Order

private

Definition at line 336 of file Markov_chain_params_.hpp.

Referenced by BEGIN_NAMED_BASE_CLASS_INFO(), CMarkov_chain_params_Base::GetOrder(), CMarkov_chain_params_Base::ResetOrder(), and CMarkov_chain_params_Base::SetOrder().

m_P

list< double > CLength_distribution_params_Base::m_P

private

Definition at line 419 of file Length_distribution_params_.hpp.

Referenced by BEGIN_NAMED_BASE_CLASS_INFO(), CLength_distribution_params_Base::GetP(), CLength_distribution_params_Base::ResetP(), and CLength_distribution_params_Base::SetP().

m_Param

CRef< TParam > CGnomon_param_Base::m_Param

private

Definition at line 657 of file Gnomon_param_.hpp.

Referenced by BEGIN_NAMED_BASE_CLASS_INFO(), CGnomon_param_Base::GetParam(), CGnomon_param_Base::IsSetParam(), CGnomon_param_Base::ResetParam(), and CGnomon_param_Base::SetParam().

m_Phase_probabilities

list< double > CIntron_params_Base::m_Phase_probabilities

private

Definition at line 264 of file Intron_params_.hpp.

Referenced by CIntron_params_Base::GetPhase_probabilities(), CIntron_params_Base::ResetPhase_probabilities(), and CIntron_params_Base::SetPhase_probabilities().

m_Probabilities

list< CRef< C_E_Probabilities > > CMarkov_chain_params_Base::m_Probabilities

private

Definition at line 337 of file Markov_chain_params_.hpp.

Referenced by BEGIN_NAMED_BASE_CLASS_INFO(), CMarkov_chain_params_Base::GetProbabilities(), CMarkov_chain_params_Base::ResetProbabilities(), and CMarkov_chain_params_Base::SetProbabilities().

m_Range

CRef< TRange > CLength_distribution_params_Base::m_Range

private

Definition at line 422 of file Length_distribution_params_.hpp.

Referenced by BEGIN_NAMED_BASE_CLASS_INFO(), CLength_distribution_params_Base::GetRange(), CLength_distribution_params_Base::IsSetRange(), CLength_distribution_params_Base::ResetRange(), and CLength_distribution_params_Base::SetRange().

m_set_State [1/10]

Uint4 CExon_params_Base::m_set_State[1]

private

Definition at line 333 of file Exon_params_.hpp.

Referenced by CExon_params_Base::CExon_params_Base(), CExon_params_Base::IsSetFirst_exon_phase_probabilities(), CExon_params_Base::IsSetInternal_exon_phase_probabilities(), CExon_params_Base::ResetFirst_exon_phase_probabilities(), CExon_params_Base::ResetInternal_exon_phase_probabilities(), CExon_params_Base::SetFirst_exon_phase_probabilities(), and CExon_params_Base::SetInternal_exon_phase_probabilities().

m_set_State [2/10]

Uint4 CGnomon_param_Base::C_Gc_content_range::m_set_State[1]

private

Definition at line 209 of file Gnomon_param_.hpp.

Referenced by CGnomon_param_Base::C_Gc_content_range::C_Gc_content_range(), and CGnomon_param_Base::C_Gc_content_range::IsSetFrom().

m_set_State [3/10]

Uint4 CGnomon_param_Base::m_set_State[1]

private

Definition at line 655 of file Gnomon_param_.hpp.

Referenced by BEGIN_NAMED_CLASS_INFO(), CGnomon_param_Base::CGnomon_param_Base(), CGnomon_param_Base::C_Gc_content_range::IsSetTo(), CGnomon_param_Base::C_Gc_content_range::ResetFrom(), CGnomon_param_Base::C_Gc_content_range::ResetTo(), CGnomon_param_Base::C_Gc_content_range::SetFrom(), and CGnomon_param_Base::C_Gc_content_range::SetTo().

m_set_State [4/10]

Uint4 CGnomon_params_Base::m_set_State[1]

private

Definition at line 138 of file Gnomon_params_.hpp.

Referenced by CGnomon_params_Base::CGnomon_params_Base(), CGnomon_params_Base::IsSet(), CGnomon_params_Base::Reset(), and CGnomon_params_Base::Set().

m_set_State [5/10]

Uint4 CIntergenic_params_Base::m_set_State[1]

private

Definition at line 224 of file Intergenic_params_.hpp.

Referenced by CIntergenic_params_Base::CIntergenic_params_Base(), CIntergenic_params_Base::IsSetInitp(), CIntergenic_params_Base::IsSetTo_single(), CIntergenic_params_Base::ResetInitp(), CIntergenic_params_Base::ResetTo_single(), CIntergenic_params_Base::SetInitp(), and CIntergenic_params_Base::SetTo_single().

m_set_State [6/10]

Uint4 CIntron_params_Base::m_set_State[1]

private

Definition at line 262 of file Intron_params_.hpp.

Referenced by CIntron_params_Base::CIntron_params_Base(), CIntron_params_Base::IsSetInitp(), CIntron_params_Base::IsSetPhase_probabilities(), CIntron_params_Base::IsSetTo_term(), CIntron_params_Base::ResetInitp(), CIntron_params_Base::ResetPhase_probabilities(), CIntron_params_Base::ResetTo_term(), CIntron_params_Base::SetInitp(), CIntron_params_Base::SetPhase_probabilities(), and CIntron_params_Base::SetTo_term().

m_set_State [7/10]

Uint4 CLength_distribution_params_Base::C_Range::m_set_State[1]

private

Definition at line 200 of file Length_distribution_params_.hpp.

Referenced by CLength_distribution_params_Base::C_Range::C_Range(), and CLength_distribution_params_Base::C_Range::IsSetMin().

m_set_State [8/10]

Uint4 CLength_distribution_params_Base::m_set_State[1]

private

Definition at line 417 of file Length_distribution_params_.hpp.

Referenced by BEGIN_NAMED_BASE_CLASS_INFO(), BEGIN_NAMED_CLASS_INFO(), CLength_distribution_params_Base::CLength_distribution_params_Base(), CLength_distribution_params_Base::IsSetA(), CLength_distribution_params_Base::IsSetL(), CLength_distribution_params_Base::C_Range::IsSetMax(), CLength_distribution_params_Base::IsSetP(), CLength_distribution_params_Base::IsSetStep(), CLength_distribution_params_Base::ResetA(), CLength_distribution_params_Base::ResetL(), CLength_distribution_params_Base::C_Range::ResetMax(), CLength_distribution_params_Base::C_Range::ResetMin(), CLength_distribution_params_Base::ResetP(), CLength_distribution_params_Base::ResetStep(), CLength_distribution_params_Base::SetA(), CLength_distribution_params_Base::SetL(), CLength_distribution_params_Base::C_Range::SetMax(), CLength_distribution_params_Base::C_Range::SetMin(), CLength_distribution_params_Base::SetP(), and CLength_distribution_params_Base::SetStep().

m_set_State [9/10]

Uint4 CMarkov_chain_array_Base::m_set_State[1]

private

Definition at line 221 of file Markov_chain_array_.hpp.

Referenced by CMarkov_chain_array_Base::CMarkov_chain_array_Base(), CMarkov_chain_array_Base::IsSetIn_exon(), CMarkov_chain_array_Base::IsSetIn_intron(), CMarkov_chain_array_Base::IsSetMatrix(), CMarkov_chain_array_Base::ResetIn_exon(), CMarkov_chain_array_Base::ResetIn_intron(), CMarkov_chain_array_Base::ResetMatrix(), CMarkov_chain_array_Base::SetIn_exon(), CMarkov_chain_array_Base::SetIn_intron(), and CMarkov_chain_array_Base::SetMatrix().

m_set_State [10/10]

Uint4 CMarkov_chain_params_Base::m_set_State[1]

private

Definition at line 335 of file Markov_chain_params_.hpp.

Referenced by BEGIN_NAMED_BASE_CLASS_INFO(), CMarkov_chain_params_Base::CMarkov_chain_params_Base(), CMarkov_chain_params_Base::IsSetOrder(), CMarkov_chain_params_Base::IsSetProbabilities(), CMarkov_chain_params_Base::ResetOrder(), CMarkov_chain_params_Base::ResetProbabilities(), CMarkov_chain_params_Base::SetOrder(), and CMarkov_chain_params_Base::SetProbabilities().

m_Single_exon_length

CRef< TSingle_exon_length > CExon_params_Base::m_Single_exon_length

private

Definition at line 339 of file Exon_params_.hpp.

Referenced by CExon_params_Base::GetSingle_exon_length(), CExon_params_Base::IsSetSingle_exon_length(), CExon_params_Base::ResetSingle_exon_length(), and CExon_params_Base::SetSingle_exon_length().

m_Step

int CLength_distribution_params_Base::m_Step

private

Definition at line 418 of file Length_distribution_params_.hpp.

Referenced by BEGIN_NAMED_BASE_CLASS_INFO(), CLength_distribution_params_Base::GetStep(), CLength_distribution_params_Base::ResetStep(), and CLength_distribution_params_Base::SetStep().

m_To

int CGnomon_param_Base::C_Gc_content_range::m_To

private

Definition at line 211 of file Gnomon_param_.hpp.

m_To_single

double CIntergenic_params_Base::m_To_single

private

Definition at line 226 of file Intergenic_params_.hpp.

Referenced by CIntergenic_params_Base::GetTo_single(), CIntergenic_params_Base::ResetTo_single(), and CIntergenic_params_Base::SetTo_single().

m_To_term

double CIntron_params_Base::m_To_term

private

Definition at line 265 of file Intron_params_.hpp.

Referenced by CIntron_params_Base::GetTo_term(), CIntron_params_Base::ResetTo_term(), and CIntron_params_Base::SetTo_term().

m_Value [1/2]

TValue CMarkov_chain_params_Base::C_E_Probabilities::m_Value

Definition at line 237 of file Markov_chain_params_.hpp.

[2/2]

TValue { ... } ::m_Value

Definition at line 237 of file Markov_chain_params_.hpp.

sm_SelectionNames [1/2]

const char *const CGnomon_param_Base::C_Param::sm_SelectionNames

staticprivate

Initial value:

= {
    "not set",
    "intergenic",
    "intron",
    "exon",
    "start",
    "stop",
    "donor",
    "acceptor",
    "coding-region",
    "non-coding-region"
}

Definition at line 549 of file Gnomon_param_.hpp.

sm_SelectionNames [2/2]

const char *const CMarkov_chain_params_Base::C_E_Probabilities::sm_SelectionNames

staticprivate

Initial value:

= {
    "not set",
    "prev-order",
    "value"
}

Definition at line 234 of file Markov_chain_params_.hpp.