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CStrainSerotypeInfluenza Class Reference

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#include <gui/packages/pkg_sequence_edit/strain_serotype_influenza.hpp>

+ Inheritance diagram for CStrainSerotypeInfluenza:
+ Collaboration diagram for CStrainSerotypeInfluenza:

Public Types

enum  ECommandInfluenza {
  eCommandInfluenza_parse , eCommandInfluenza_add , eCommandInfluenza_fixup , eCommandSplitQualsAtCommas ,
  eCommandSplitStructuredCollections , eCommandTrimOrganismNames
}
 

Public Member Functions

 CStrainSerotypeInfluenza (ECommandInfluenza type)
 
CRef< CCmdCompositeGetCommand (objects::CSeq_entry_Handle tse, const string &title)
 
- Public Member Functions inherited from IModifyBiosourceQuals
virtual ~IModifyBiosourceQuals ()
 

Private Member Functions

virtual bool x_ApplyToBioSource (objects::CBioSource &biosource)
 
bool x_AddToInfluenzaNames (objects::CBioSource &biosource)
 
bool x_FixupOrganismNames (objects::CBioSource &biosource)
 
bool x_SplittingQualifiersAtCommas (objects::CBioSource &biosource)
 
bool x_SplittingStructCollections (objects::CBioSource &biosource)
 
bool x_TrimmingOrganismNames (objects::CBioSource &biosource)
 
void x_ParseStrainSerotype (CCmdComposite *composite)
 
void x_ParseStrainSerotype (CCmdComposite *composite, bool overwrite)
 
void x_TestEntryForParsing (const objects::CSeq_entry &se, int &count)
 
void x_TestBiosourceForParsing (const objects::CBioSource &biosource, int &count)
 
bool x_IsParsableInfluenzaVirusName (const objects::CBioSource &biosource, string &strain, string &serotype)
 
int x_GetStrainSerotypeConflicts (const objects::CBioSource &biosource, const string &strain, const string &serotype)
 
void x_ParseEntry (CCmdComposite *composite, bool update)
 
void x_ParseDescriptors (const objects::CSeq_entry &se, CCmdComposite *composite, bool update)
 
bool x_ParseBiosource (objects::CBioSource &biosource, bool update)
 
bool x_UpdateStrainSerotype (objects::CBioSource &biosource, const string &strain, const string &serotype, bool update)
 

Private Attributes

ECommandInfluenza m_Type
 
bool m_Parsable { false }
 

Friends

CRef< CCmdCompositeTestCStrainSerotypeInfluenza_Parse (CStrainSerotypeInfluenza &parser, objects::CSeq_entry_Handle tse, const string &title, bool overwrite)
 

Additional Inherited Members

- Protected Member Functions inherited from IModifyBiosourceQuals
void x_ApplyToSeqAndFeat (CCmdComposite *composite)
 
void x_ApplyToDescriptors (const objects::CSeq_entry &se, CCmdComposite *composite)
 
CRef< CCmdCompositex_GetCommand (objects::CSeq_entry_Handle tse, const string &title)
 
- Protected Attributes inherited from IModifyBiosourceQuals
objects::CSeq_entry_Handle m_Seh
 

Detailed Description

Definition at line 37 of file strain_serotype_influenza.hpp.

Member Enumeration Documentation

◆ ECommandInfluenza

Enumerator
eCommandInfluenza_parse 
eCommandInfluenza_add 
eCommandInfluenza_fixup 
eCommandSplitQualsAtCommas 
eCommandSplitStructuredCollections 
eCommandTrimOrganismNames 

Definition at line 40 of file strain_serotype_influenza.hpp.

Constructor & Destructor Documentation

◆ CStrainSerotypeInfluenza()

CStrainSerotypeInfluenza::CStrainSerotypeInfluenza ( ECommandInfluenza  type)
inline

Definition at line 49 of file strain_serotype_influenza.hpp.

Member Function Documentation

◆ GetCommand()

CRef< CCmdComposite > CStrainSerotypeInfluenza::GetCommand ( objects::CSeq_entry_Handle  tse,
const string title 
)

◆ x_AddToInfluenzaNames()

bool CStrainSerotypeInfluenza::x_AddToInfluenzaNames ( objects::CBioSource &  biosource)
private

◆ x_ApplyToBioSource()

bool CStrainSerotypeInfluenza::x_ApplyToBioSource ( objects::CBioSource &  biosource)
privatevirtual

◆ x_FixupOrganismNames()

bool CStrainSerotypeInfluenza::x_FixupOrganismNames ( objects::CBioSource &  biosource)
private

◆ x_GetStrainSerotypeConflicts()

int CStrainSerotypeInfluenza::x_GetStrainSerotypeConflicts ( const objects::CBioSource &  biosource,
const string strain,
const string serotype 
)
private

◆ x_IsParsableInfluenzaVirusName()

bool CStrainSerotypeInfluenza::x_IsParsableInfluenzaVirusName ( const objects::CBioSource &  biosource,
string strain,
string serotype 
)
private

◆ x_ParseBiosource()

bool CStrainSerotypeInfluenza::x_ParseBiosource ( objects::CBioSource &  biosource,
bool  update 
)
private

◆ x_ParseDescriptors()

void CStrainSerotypeInfluenza::x_ParseDescriptors ( const objects::CSeq_entry &  se,
CCmdComposite composite,
bool  update 
)
private

◆ x_ParseEntry()

void CStrainSerotypeInfluenza::x_ParseEntry ( CCmdComposite composite,
bool  update 
)
private

◆ x_ParseStrainSerotype() [1/2]

void CStrainSerotypeInfluenza::x_ParseStrainSerotype ( CCmdComposite composite)
private

◆ x_ParseStrainSerotype() [2/2]

void CStrainSerotypeInfluenza::x_ParseStrainSerotype ( CCmdComposite composite,
bool  overwrite 
)
private

◆ x_SplittingQualifiersAtCommas()

bool CStrainSerotypeInfluenza::x_SplittingQualifiersAtCommas ( objects::CBioSource &  biosource)
private

◆ x_SplittingStructCollections()

bool CStrainSerotypeInfluenza::x_SplittingStructCollections ( objects::CBioSource &  biosource)
private

◆ x_TestBiosourceForParsing()

void CStrainSerotypeInfluenza::x_TestBiosourceForParsing ( const objects::CBioSource &  biosource,
int count 
)
private

◆ x_TestEntryForParsing()

void CStrainSerotypeInfluenza::x_TestEntryForParsing ( const objects::CSeq_entry &  se,
int count 
)
private

◆ x_TrimmingOrganismNames()

bool CStrainSerotypeInfluenza::x_TrimmingOrganismNames ( objects::CBioSource &  biosource)
private

◆ x_UpdateStrainSerotype()

bool CStrainSerotypeInfluenza::x_UpdateStrainSerotype ( objects::CBioSource &  biosource,
const string strain,
const string serotype,
bool  update 
)
private

Friends And Related Function Documentation

◆ TestCStrainSerotypeInfluenza_Parse

CRef<CCmdComposite> TestCStrainSerotypeInfluenza_Parse ( CStrainSerotypeInfluenza parser,
objects::CSeq_entry_Handle  tse,
const string title,
bool  overwrite 
)
friend

Member Data Documentation

◆ m_Parsable

bool CStrainSerotypeInfluenza::m_Parsable { false }
private

◆ m_Type

ECommandInfluenza CStrainSerotypeInfluenza::m_Type
private

Definition at line 81 of file strain_serotype_influenza.hpp.

Referenced by GetCommand(), and x_ApplyToBioSource().


The documentation for this class was generated from the following files:
Modified on Sun Apr 14 05:25:03 2024 by modify_doxy.py rev. 669887