BALL
1.5.0
include
BALL
STRUCTURE
mutator.h
Go to the documentation of this file.
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#ifndef BALL_STRUCTURE_MUTATOR_H
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#define BALL_STRUCTURE_MUTATOR_H
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#include <
BALL/COMMON/debug.h
>
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#include <
BALL/COMMON/global.h
>
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namespace
BALL
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{
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class
String;
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class
FragmentDB;
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class
BALL_EXPORT
Mutator
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{
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public
:
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enum
MutatorOptions
{ NONE = 0, OPTIMIZE = 1 };
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Mutator
(
FragmentDB
*
db
= 0);
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virtual
~Mutator
();
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/*
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* Set a new FragmentDB instance that shall be used to obtain
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* the new bases. If 0 is passed, a default instance will be automatically
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* created when calling DNAMutator::mutate(). The passed instance will
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* <b>not</b> be deleted upon destruction.
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*/
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void
setFragmentDB
(
FragmentDB
*
db
);
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virtual
void
setup
();
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virtual
void
addMutation
(
Index
i,
const
String
& new_frag_name) = 0;
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virtual
void
clearMutations
() = 0;
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void
mutate
(
MutatorOptions
opts = NONE);
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virtual
bool
optimize
() = 0;
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protected
:
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FragmentDB
*
db_
;
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virtual
void
mutate_impl_
(
MutatorOptions
opts) = 0;
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private
:
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bool
keep_db_;
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void
freeDB_();
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};
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}
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#endif //BALL_STRUCTURE_MUTATOR_H
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BALL::Mutator::setup
virtual void setup()
BALL_EXPORT
#define BALL_EXPORT
Definition:
COMMON/global.h:50
global.h
BALL::Mutator::clearMutations
virtual void clearMutations()=0
BALL::Mutator::addMutation
virtual void addMutation(Index i, const String &new_frag_name)=0
BALL::Mutator::db_
FragmentDB * db_
Definition:
mutator.h:78
BALL::Mutator::Mutator
Mutator(FragmentDB *db=0)
BALL::Mutator::MutatorOptions
MutatorOptions
Definition:
mutator.h:20
db
db
Definition:
GAFFTypeProcessor.h:74
BALL::String
Definition:
string.h:57
BALL::Mutator::mutate_impl_
virtual void mutate_impl_(MutatorOptions opts)=0
BALL
Definition:
constants.h:13
BALL::Mutator::~Mutator
virtual ~Mutator()
BALL::Mutator
Definition:
mutator.h:13
BALL_INDEX_TYPE
BALL::FragmentDB
Definition:
fragmentDB.h:45
BALL::Mutator::setFragmentDB
void setFragmentDB(FragmentDB *db)
BALL::Mutator::optimize
virtual bool optimize()=0
debug.h
BALL::Mutator::mutate
void mutate(MutatorOptions opts=NONE)
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