CPCRPrimerSeq Class Reference

Search Toolkit Book for CPCRPrimerSeq

#include <objects/seqfeat/PCRPrimerSeq.hpp>

Inheritance diagram for CPCRPrimerSeq:

Collaboration diagram for CPCRPrimerSeq:

Public Member Functions
	CPCRPrimerSeq (void)
	CPCRPrimerSeq (const std::string &data)
	Explicit constructor from the primitive type. More...
Public Member Functions inherited from CPCRPrimerSeq_Base
	CPCRPrimerSeq_Base (void)
	DECLARE_STD_ALIAS_TYPE_INFO ()
	CPCRPrimerSeq_Base (const string &data)
Public Member Functions inherited from CStringAliasBase< string >
	CStringAliasBase (void)
	CStringAliasBase (const string &value)
Public Member Functions inherited from CAliasBase< string >
	CAliasBase (void)
	CAliasBase (const string &value)
const string &	Get (void) const
string &	Set (void)
void	Set (const string &value)
	operator string (void) const
TThis &	operator* (void)
TThis *	operator-> (void)
bool	operator< (const T &value) const
bool	operator> (const T &value) const
bool	operator== (const T &value) const
bool	operator!= (const T &value) const

Static Public Member Functions
static void	Clean (string &seq)
static bool	IsValid (const string &seq, char &bad_ch)
static bool	TrimJunk (string &seq)
static bool	Fixi (string &seq)
Static Public Member Functions inherited from CAliasBase< string >
static TConstObjectPtr	GetDataPtr (const TThis *alias)

Private Types
typedef CPCRPrimerSeq_Base	Tparent

Additional Inherited Members
Public Types inherited from CAliasBase< string >
typedef CAliasBase< string >	TThis
Protected Attributes inherited from CAliasBase< string >
string	m_Data

Detailed Description

Definition at line 53 of file PCRPrimerSeq.hpp.

Member Typedef Documentation

Tparent

typedef CPCRPrimerSeq_Base CPCRPrimerSeq::Tparent

private

Definition at line 55 of file PCRPrimerSeq.hpp.

Constructor & Destructor Documentation

CPCRPrimerSeq() [1/2]

CPCRPrimerSeq::CPCRPrimerSeq ( void  )

inline

Definition at line 57 of file PCRPrimerSeq.hpp.

CPCRPrimerSeq() [2/2]

CPCRPrimerSeq::CPCRPrimerSeq ( const std::string &  data )

inlineexplicit

Explicit constructor from the primitive type.

Definition at line 60 of file PCRPrimerSeq.hpp.

Member Function Documentation

Clean()

void CPCRPrimerSeq::Clean ( string &  seq )

static

Definition at line 87 of file PCRPrimerSeq.cpp.

References NStr::ReplaceInPlace(), s_EraseSpacesOutsideBrackets(), and NStr::ToLower().

Referenced by CNewCleanup_imp::BiosourceBC(), CPCRPrimerEntry::TransferDataFromWindow(), and CNewCleanup_imp::x_PCRPrimerSetBC().

Fixi()

bool CPCRPrimerSeq::Fixi ( string &  seq )

static

Definition at line 238 of file PCRPrimerSeq.cpp.

References i, NPOS, and orig.

Referenced by BOOST_AUTO_TEST_CASE(), CMacroFunction_ModifyPrimerSeq::TheFunction(), and CPCRPrimerFixI::x_ApplyToBioSource().

IsValid()

bool CPCRPrimerSeq::IsValid ( const string &  seq, char &  bad_ch  )

static

Definition at line 153 of file PCRPrimerSeq.cpp.

References NStr::EndsWith(), NStr::Find(), isalpha(), NStr::IsBlank(), match(), NULL, sm_ValidModifiedPrimerBases, NStr::StartsWith(), str(), tolower(), and toupper().

Referenced by BOOST_AUTO_TEST_CASE(), CValidError_imp::ValidateSubSource(), and CValidError_imp::x_CheckPCRPrimer().

TrimJunk()

bool CPCRPrimerSeq::TrimJunk ( string &  seq )

static

Definition at line 215 of file PCRPrimerSeq.cpp.

References i, len, NULL, and orig.

Referenced by BOOST_AUTO_TEST_CASE(), CMacroFunction_ModifyPrimerSeq::TheFunction(), and CPCRPrimerTrimJunk::x_ApplyToBioSource().

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

• include/objects/seqfeat/PCRPrimerSeq.hpp
• src/objects/seqfeat/PCRPrimerSeq.cpp