net.sourceforge.cilib.bioinf.rnaprediction
Class RNAConformation

java.lang.Object
  net.sourceforge.cilib.type.types.container.Set<RNAStem>
      net.sourceforge.cilib.bioinf.rnaprediction.RNAConformation

All Implemented Interfaces:

Serializable, Iterable<RNAStem>, StructuredType<RNAStem>, Randomizable, Type, Cloneable

public class RNAConformation
extends Set<RNAStem>

See Also:

Serialized Form

Constructor Summary

RNAConformation()
Create an instance of a RNAConformation.

Method Summary

boolean	contains(NucleotidePair pair) Determine if the current RNAConformation contains the provided NucleotidePair.
boolean	equals(Object other) Compare the specified object with this type for equality.
char[]	getCharRepresentation() Get the character representation of the current RNAConformation.
RNAConformation	getClone() Create a cloned copy of the current object and return it.
int	getNumOfPairs() Get the number of pairs within this RNAConformation.
int	hashCode() Returns the hash code value for this list.
void	isInvalid() Determine if the current RNAConformation is valid.
int	length() Get the length of the current RNAConformation.

Methods inherited from class net.sourceforge.cilib.type.types.container.Set

accept, add, addAll, clear, contains, getDimension, getRepresentation, isEmpty, isInsideBounds, iterator, randomise, randomize, remove, remove, removeAll, reset, size, toArray, toArray, toString

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Constructor Detail

RNAConformation

public RNAConformation()

Create an instance of a RNAConformation.

Method Detail

length

public int length()

Get the length of the current RNAConformation.

Returns:

The length of the RNAConformation.

getCharRepresentation

public char[] getCharRepresentation()

Get the character representation of the current RNAConformation.

Returns:

The RNAConformation represented by a character array.

getClone

public RNAConformation getClone()

Create a cloned copy of the current object and return it. In general the created copy will be a deep copy of the provided instance. As a result this operation an be quite expensive if used incorrectly.

Specified by:

getClone in interface StructuredType<RNAStem>

Specified by:

getClone in interface Type

Specified by:

getClone in interface Cloneable

Overrides:

getClone in class Set<RNAStem>

Returns:

An exact clone of the current object instance.

See Also:

Object.clone()

equals

public boolean equals(Object other)

Description copied from class: Set

Compare the specified object with this type for equality. Returns true if and only if the specified object is also an instance of the same type.

Specified by:

equals in interface Type

Overrides:

equals in class Set<RNAStem>

Parameters:

other - The object to compare.

Returns:

true if equality exists, false otherwise.

See Also:

Object.equals(Object)

hashCode

public int hashCode()

Description copied from class: Set

Returns the hash code value for this list. The hash code of a list is defined to be the result of the following calculation:

  int hashCode = 7;
  Iterator<E> i = list.iterator();
  while (i.hasNext()) {
      E obj = i.next();
      hashCode = 31*hashCode + (obj==null ? 0 : obj.hashCode());
  }
 

This ensures that type1.equals(type2) implies that type1.hashCode()==type2.hashCode() for any two types, type1 and type2, as required by the general contract of Object.hashCode().

Specified by:

hashCode in interface Type

Overrides:

hashCode in class Set<RNAStem>

Returns:

the hash code value for this list

See Also:

Object.equals(Object), Type.equals(Object)

isInvalid

public void isInvalid()

Determine if the current RNAConformation is valid.

Throws:

RuntimeException - if an invalid confirmation is created.

contains

public boolean contains(NucleotidePair pair)

Determine if the current RNAConformation contains the provided NucleotidePair.

Parameters:

pair - The NucleotidePair to test.

Returns:

true if the RNAConformation contains the NucleotidePair, false otherwise.

getNumOfPairs

public int getNumOfPairs()

Get the number of pairs within this RNAConformation.

Returns:

The number of pairs.