ell::S_Explicit Class Reference
#include <S_Explicit.hh>
Inheritance diagram for ell::S_Explicit:
Detailed Description
An explicit energy landscape representation using a graph representation as the underlying data structure.
Definition at line 16 of file S_Explicit.hh.
Public Types | |
| typedef biu::VirtualList< State > | NeighborList |
| typedef std::auto_ptr< NeighborList > | NeighborListPtr |
Public Member Functions | |
| virtual State * | applyNeighborChange (const size_t index, State *const copy) const |
| virtual S_Explicit * | clone (State *toFill=NULL) const |
| virtual CSequence & | compress (CSequence &toFill) const |
| virtual CSequence | compress (void) const |
| virtual State * | fromString (const std::string &stringRep) const |
| virtual double | getEnergy () const |
| virtual const std::string & | getID (void) const |
| virtual unsigned int | getMinimalDistance (const State &state2) const |
| virtual State * | getNeighbor (const size_t index, State *neigh) const |
| virtual NeighborListPtr | getNeighborList () const |
| virtual size_t | getNeighborNumber (void) const |
| virtual State * | getRandomNeighbor (State *inPlaceNeigh=NULL) const |
| virtual NeighborListPtr | getRandomNeighborList () const |
| virtual bool | operator!= (const State &state2) const |
| virtual bool | operator< (const State &state2) const |
| virtual bool | operator== (const State &state2) const |
| S_Explicit (const LandscapeGraph *lg, const size_t nodeIndex) | |
| virtual std::string & | toString (std::string &toFill) const |
| virtual std::string | toString () const |
| virtual State * | uncompress (const CSequence &cseq) |
| virtual State * | uncompress (const CSequence &cseq, State *toFill) const |
| virtual State * | undoNeighborChange (const size_t index, State *const neigh) const |
| virtual | ~S_Explicit () |
Static Public Member Functions | |
| static bool | less (const State *s1, const State *s2) |
Static Public Attributes | |
| static const std::string | ID |
Protected Attributes | |
| const LandscapeGraph * | lg |
| size_t | nodeIndex |
| size_t | sRepLength |
Static Protected Attributes | |
| static const biu::Alphabet | numberAlph |
Data Structures | |
| class | LandscapeGraph |
Member Typedef Documentation
typedef biu::VirtualList<State> ell::State::NeighborList [inherited] |
typedef std::auto_ptr<NeighborList> ell::State::NeighborListPtr [inherited] |
Constructor & Destructor Documentation
| ell::S_Explicit::S_Explicit | ( | const LandscapeGraph * | lg, | |
| const size_t | nodeIndex | |||
| ) |
Constructs a state that represents the node of the given index of the explicite landscape representation. The neighbors of the node are defined by the adjacent nodes in the LandscapeGraph.
- Parameters:
-
lg the landscape graph representing the energy landscape nodeIndex the index of the node this state is representing
Definition at line 14 of file S_Explicit.cc.
| ell::S_Explicit::~S_Explicit | ( | ) | [virtual] |
Member Function Documentation
| State * ell::S_Explicit::applyNeighborChange | ( | const size_t | index, | |
| State *const | copy | |||
| ) | const [virtual] |
Applies the necessary changes to a given state to get the neighbor. Note: @copy is expected to be a copy (i.e. *this == *copy) and therefore direct changes are possible and != NULL.
- Parameters:
-
index the neighbor to generate copy a copy of *this the changes should be applied to
- Returns:
- copy = the neighbor state of the given index or NULL if the index is out of range
Implements ell::IterableNeighbors.
Definition at line 356 of file S_Explicit.cc.
| S_Explicit * ell::S_Explicit::clone | ( | State * | toFill = NULL |
) | const [virtual] |
Returns a pointer to a clone of the current state.
- Returns:
- a pointer to a copy of this state, if toFill is != NULL the return value corresponds to the updated state pointed to by toFill, otherwise a new object is created !!!
Implements ell::State.
Definition at line 119 of file S_Explicit.cc.
Access to a compressed sequence representation of the state.
- Parameters:
-
toFill a data structure to write the compressed representation too
- Returns:
- the compressed sequence representation
Implements ell::State.
Definition at line 232 of file S_Explicit.cc.
| CSequence ell::S_Explicit::compress | ( | void | ) | const [virtual] |
Access to a compressed sequence representation of the state.
- Returns:
- the compressed sequence representation
Implements ell::State.
Definition at line 220 of file S_Explicit.cc.
| State * ell::S_Explicit::fromString | ( | const std::string & | stringRep | ) | const [virtual] |
Returns a new State based on the current state. The new state differs only by the information given by stringRep.
Implements ell::State.
Definition at line 141 of file S_Explicit.cc.
| double ell::S_Explicit::getEnergy | ( | ) | const [virtual] |
Returns the state specific energy.
Implements ell::State.
Definition at line 98 of file S_Explicit.cc.
| const std::string & ell::S_Explicit::getID | ( | void | ) | const [virtual] |
Access to a State subclass specific ID string to identify instances of this class.
- Returns:
- the subclass specific ID string
Implements ell::State.
Definition at line 34 of file S_Explicit.cc.
| unsigned int ell::S_Explicit::getMinimalDistance | ( | const State & | state2 | ) | const [virtual] |
Returns the minimal number of steps via valid neighbored states from this to another valid State.
- Parameters:
-
state2 the State to reach
Implements ell::State.
Definition at line 110 of file S_Explicit.cc.
Access to a specific neighbor.
- Parameters:
-
index the index of the neighbor in [0, getNeighborNumber()) neigh if != NULL this state should be converted into the neighbor otherwise a new one is created and returned
- Returns:
- the new neighbor state or NULL if the index is >= getNeighborNumber()
Implements ell::IterableNeighbors.
Definition at line 300 of file S_Explicit.cc.
| State::NeighborListPtr ell::S_Explicit::getNeighborList | ( | ) | const [virtual] |
Returns a virtual list of all VALID neighbored states in the energy landscape in a specific order.
Implements ell::State.
Definition at line 186 of file S_Explicit.cc.
| size_t ell::S_Explicit::getNeighborNumber | ( | void | ) | const [virtual] |
How many neighbor indices are accessible.
- Returns:
- the number of neighbors
Implements ell::IterableNeighbors.
Definition at line 42 of file S_Explicit.cc.
Returns a VALID random neighbored state. If a state is given, this is changed to a neighbor.
Implements ell::State.
Definition at line 205 of file S_Explicit.cc.
| State::NeighborListPtr ell::S_Explicit::getRandomNeighborList | ( | ) | const [virtual] |
Returns a virtual list of all VALID neighbored states in the energy landscape in a random order. If a state is given, this is changed to a neighbor.
Implements ell::State.
Definition at line 196 of file S_Explicit.cc.
Comparison function that compares two State pointer based on the less than operator '<' of the first State. The function can be used in STL algorithms, e.g. if only State pointer are stored but the ordering should be based on the object order.
- Parameters:
-
s1 the State pointer of the object that is asked to be smaller (!=NULL) s2 the State pointer of the object that is asked to be bigger (!=NULL)
- Returns:
- s1->operator <(*s1);
Reimplemented from ell::State.
| bool ell::S_Explicit::operator!= | ( | const State & | state2 | ) | const [virtual] |
| bool ell::S_Explicit::operator< | ( | const State & | state2 | ) | const [virtual] |
Implements a unique order on states based on their energy and string representation. A state is smaller than another one iff it has smaller energy or it has equal energy and a lexicographically smaller string representation (tie breaker).
This function will be overwritten to achive a better performance than calling getEnergy() and getString().
If the energy function is non-degenerate the string comparison is obsolete.
- Parameters:
-
state2 the State object to compare to
- Returns:
- true if this state is smaller than state2 according to the unique order of the states
Reimplemented from ell::State.
Definition at line 83 of file S_Explicit.cc.
| bool ell::S_Explicit::operator== | ( | const State & | state2 | ) | const [virtual] |
| std::string & ell::S_Explicit::toString | ( | std::string & | toFill | ) | const [virtual] |
Fill the given string with a specific std::string representation of this State.
- Parameters:
-
toFill the string to overwrite
- Returns:
- the changed toFill in parameter
Implements ell::State.
Definition at line 172 of file S_Explicit.cc.
| std::string ell::S_Explicit::toString | ( | ) | const [virtual] |
Returns a specific std::string representation of this State.
Implements ell::State.
Definition at line 157 of file S_Explicit.cc.
Uncompresses a compressed sequencce representation into a this State object.
- Parameters:
-
cseq the compressed sequence representation of a state
- Returns:
- this or NULL in error case
Implements ell::State.
Definition at line 275 of file S_Explicit.cc.
Uncompresses a compressed sequencce representation into a new State object.
- Parameters:
-
cseq the compressed sequence representation of a state toFill a state object to uncompress too or NULL if a new object has to be created
- Returns:
- new State object that is encoded in cseq or NULL in error case.
Implements ell::State.
Definition at line 248 of file S_Explicit.cc.
| State * ell::S_Explicit::undoNeighborChange | ( | const size_t | index, | |
| State *const | neigh | |||
| ) | const [virtual] |
Undo the changes done to this state to generate the given neighbor. The goal is to do less operations than doing a full copy like (*neigh = *this).
- Parameters:
-
index the neighbor index that was applied last [ 0, getNeighborNumber() ) neigh the state resulting from the last changes
- Returns:
- the copy of this object via undoing the last changes in neigh or NULL if neigh == NULL
Implements ell::IterableNeighbors.
Definition at line 333 of file S_Explicit.cc.
Field Documentation
const std::string ell::S_Explicit::ID [static] |
const LandscapeGraph* ell::S_Explicit::lg [protected] |
size_t ell::S_Explicit::nodeIndex [protected] |
const biu::Alphabet ell::S_Explicit::numberAlph [static, protected] |
size_t ell::S_Explicit::sRepLength [protected] |
length of all string representations of states of this landscape.
Definition at line 41 of file S_Explicit.hh.
The documentation for this class was generated from the following files:
- src/ell/S_Explicit.hh
- src/ell/S_Explicit.cc