BALL::Mutator Class Reference

#include <BALL/STRUCTURE/mutator.h>

Inheritance diagram for BALL::Mutator:

Public Types
enum	MutatorOptions { NONE = 0, OPTIMIZE = 1 }

Public Member Functions
	Mutator (FragmentDB *db=0)
virtual	~Mutator ()
void	setFragmentDB (FragmentDB *db)
virtual void	setup ()
virtual void	addMutation (Index i, const String &new_frag_name)=0
virtual void	clearMutations ()=0
void	mutate (MutatorOptions opts=NONE)
virtual bool	optimize ()=0

Protected Member Functions
virtual void	mutate_impl_ (MutatorOptions opts)=0

Protected Attributes
FragmentDB *	db_

Private Member Functions
void	freeDB_ ()

Private Attributes
bool	keep_db_

Detailed Description

Definition at line 12 of file mutator.h.

Member Enumeration Documentation

enum BALL::Mutator::MutatorOptions

This enum is used in order to finetune the behaviour of the mutate method. Currently it only offers control over the automatic use of the optimizer after successfully mutating.

Enumerator
NONE
OPTIMIZE

Definition at line 20 of file mutator.h.

Constructor & Destructor Documentation

BALL::Mutator::Mutator

(

FragmentDB *

db = 0

)

The default constructor can be used to pass a FragmentDB instance to the Mutator. If 0 is passed, a default FragmentDB is instanciated once setup() has been called

virtual BALL::Mutator::~Mutator ( )

virtual

Member Function Documentation

virtual void BALL::Mutator::addMutation ( Index  i, const String &  new_frag_name  )

pure virtual

Adds a mutation to the list of scheduled mutations. Note that it is usually not advisable to conduct too many changes on your structure, as with a growing number mutations results become more and more unreliable.

Exceptions

NotInitialized

This exception is thrown whenever the Mutator needs further information. Usually the Molecule which to mutate needs to be supplied.

Implemented in BALL::DNAMutator.

virtual void BALL::Mutator::clearMutations ( )

pure virtual

Clear the list of scheduled mutations

Implemented in BALL::DNAMutator.

void BALL::Mutator::freeDB_ ( )

private

void BALL::Mutator::mutate

(

MutatorOptions

opts = NONE

)

Apply the list of scheduled mutations.

Note

This will modify your original structure and most likely render iterators and pointers invalid.

virtual void BALL::Mutator::mutate_impl_ ( MutatorOptions  opts )

protectedpure virtual

Implemented in BALL::DNAMutator.

virtual bool BALL::Mutator::optimize ( )

pure virtual

Optimize the structure that was obtained during minimization

Implemented in BALL::DNAMutator.

void BALL::Mutator::setFragmentDB

(

FragmentDB *

db

)

virtual void BALL::Mutator::setup ( )

virtual

Calling this method explicitly circumvents lazy loading of the FragmentDB. This method has no effect if mutate has already been called or if valid instances of the fragmentDB has been passed via the constructor.

Warning

If you called setup() and then set the FragmentDB to NULL via setFragmentDB() you will need to call setup() again in order to prevent lazy loading.

Reimplemented in BALL::DNAMutator.

Member Data Documentation

FragmentDB* BALL::Mutator::db_

protected

Definition at line 78 of file mutator.h.

bool BALL::Mutator::keep_db_

private

Definition at line 83 of file mutator.h.