net.sourceforge.cilib.bioinf.rnaprediction
Class RNAStem

java.lang.Object
  net.sourceforge.cilib.bioinf.rnaprediction.RNAStem

All Implemented Interfaces:

Serializable, Comparable<RNAStem>, Iterable<NucleotidePair>, Collection<NucleotidePair>, Type, Cloneable

public class RNAStem
extends Object
implements Type, Comparable<RNAStem>, Collection<NucleotidePair>

Author:

mneethling

See Also:

Serialized Form

Constructor Summary

RNAStem()

RNAStem(ArrayList<NucleotidePair> basePairs)

Method Summary

boolean	add(NucleotidePair o)
boolean	addAll(Collection<? extends NucleotidePair> c)
void	clear()
int	compareTo(RNAStem o)
boolean	conflictsWith(RNAStem otherstem) Uses the StemConflictTable Singleton class to look up conflicts quicker.
boolean	contains(Object o)
boolean	containsAll(Collection<?> c)
boolean	equals(Object other) Compare the specified object with this type for equality.
RNAStem	getClone() Create a cloned copy of the current object and return it.
ArrayList<RNAStem>	getConflictingStems()
int	getId()
int	getIndex()
int	getLength()
int	hashCode() Returns the hash code value for this list.
boolean	isEmpty()
Iterator<NucleotidePair>	iterator()
boolean	remove(Object o)
boolean	removeAll(Collection<?> c)
boolean	retainAll(Collection<?> c)
void	setConflictingStems(ArrayList<RNAStem> conflicts)
void	setIndex(int index)
int	size()
boolean	slowConflictsWith(RNAStem otherstem) returns true if the stems fail all of four tests.
Object[]	toArray()
<T> T[]	toArray(T[] a)
String	toString()

Methods inherited from class java.lang.Object

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

Constructor Detail

RNAStem

public RNAStem()

RNAStem

public RNAStem(ArrayList<NucleotidePair> basePairs)

Method Detail

getId

public int getId()

getIndex

public int getIndex()

Returns:

Returns the index.

setIndex

public void setIndex(int index)

Parameters:

index - The index to set.

equals

public boolean equals(Object other)

Description copied from interface: Type

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 Collection<NucleotidePair>

Specified by:

equals in interface Type

Overrides:

equals in class Object

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 interface: Type

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 Collection<NucleotidePair>

Specified by:

hashCode in interface Type

Overrides:

hashCode in class Object

Returns:

the hash code value for this list

See Also:

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

getLength

public int getLength()

size

public int size()

Specified by:

size in interface Collection<NucleotidePair>

isEmpty

public boolean isEmpty()

Specified by:

isEmpty in interface Collection<NucleotidePair>

contains

public boolean contains(Object o)

Specified by:

contains in interface Collection<NucleotidePair>

toArray

public Object[] toArray()

Specified by:

toArray in interface Collection<NucleotidePair>

remove

public boolean remove(Object o)

Specified by:

remove in interface Collection<NucleotidePair>

clear

public void clear()

Specified by:

clear in interface Collection<NucleotidePair>

conflictsWith

public boolean conflictsWith(RNAStem otherstem)

Uses the StemConflictTable Singleton class to look up conflicts quicker.

Parameters:

otherstem -

Returns:

slowConflictsWith

public boolean slowConflictsWith(RNAStem otherstem)

returns true if the stems fail all of four tests.

Parameters:

stem -

Returns:

add

public boolean add(NucleotidePair o)

Specified by:

add in interface Collection<NucleotidePair>

compareTo

public int compareTo(RNAStem o)

Specified by:

compareTo in interface Comparable<RNAStem>

addAll

public boolean addAll(Collection<? extends NucleotidePair> c)

Specified by:

addAll in interface Collection<NucleotidePair>

removeAll

public boolean removeAll(Collection<?> c)

Specified by:

removeAll in interface Collection<NucleotidePair>

retainAll

public boolean retainAll(Collection<?> c)

Specified by:

retainAll in interface Collection<NucleotidePair>

toArray

public <T> T[] toArray(T[] a)

Specified by:

toArray in interface Collection<NucleotidePair>

iterator

public Iterator<NucleotidePair> iterator()

Specified by:

iterator in interface Iterable<NucleotidePair>

Specified by:

iterator in interface Collection<NucleotidePair>

containsAll

public boolean containsAll(Collection<?> c)

Specified by:

containsAll in interface Collection<NucleotidePair>

setConflictingStems

public void setConflictingStems(ArrayList<RNAStem> conflicts)

getConflictingStems

public ArrayList<RNAStem> getConflictingStems()

getClone

public RNAStem getClone()

Description copied from interface: Type

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 Type

Specified by:

getClone in interface Cloneable

Returns:

An exact clone of the current object instance.

See Also:

Object.clone()

toString

public String toString()

Overrides:

toString in class Object