org.biojava.nbio.core.sequence.compound

Class NucleotideCompound

java.lang.Object

org.biojava.nbio.core.sequence.template.AbstractCompound

org.biojava.nbio.core.sequence.compound.NucleotideCompound

All Implemented Interfaces:

ComplementCompound, Compound

public class NucleotideCompound
extends AbstractCompound
implements ComplementCompound

Author:

Scooter Willis, Andy Yates

Constructor Summary

Constructors

Constructor and Description
NucleotideCompound(String base, CompoundSet<NucleotideCompound> compoundSet, String complementStr)
NucleotideCompound(String base, CompoundSet<NucleotideCompound> compoundSet, String complementStr, NucleotideCompound[] constituents)

Method Summary

Modifier and Type	Method and Description
boolean	equals(Object obj)
boolean	equalsIgnoreCase(Compound compound)
ComplementCompound	getComplement()
Set<NucleotideCompound>	getConsituents() Deprecated. replaced with getConstituents() due to typographical error
Set<NucleotideCompound>	getConstituents()
String	getShortName()
int	hashCode()
boolean	isAmbiguous()

Methods inherited from class org.biojava.nbio.core.sequence.template.AbstractCompound

getBase, getDescription, getLongName, getMolecularWeight, getUpperedBase, setDescription, setLongName, setMolecularWeight, setShortName, toString

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.biojava.nbio.core.sequence.template.Compound

getDescription, getLongName, getMolecularWeight, setDescription, setLongName, setMolecularWeight, setShortName

Constructor Detail

NucleotideCompound

public NucleotideCompound(String base,
                          CompoundSet<NucleotideCompound> compoundSet,
                          String complementStr)

NucleotideCompound

public NucleotideCompound(String base,
                          CompoundSet<NucleotideCompound> compoundSet,
                          String complementStr,
                          NucleotideCompound[] constituents)

Method Detail

getShortName

public String getShortName()

Specified by:

getShortName in interface Compound

Overrides:

getShortName in class AbstractCompound

getComplement

public ComplementCompound getComplement()

Specified by:

getComplement in interface ComplementCompound

equals

public boolean equals(Object obj)

Overrides:

equals in class AbstractCompound

hashCode

public int hashCode()

Overrides:

hashCode in class AbstractCompound

equalsIgnoreCase

public boolean equalsIgnoreCase(Compound compound)

Specified by:

equalsIgnoreCase in interface Compound

Overrides:

equalsIgnoreCase in class AbstractCompound

getConstituents

public Set<NucleotideCompound> getConstituents()

getConsituents

@Deprecated
public Set<NucleotideCompound> getConsituents()

Deprecated. replaced with getConstituents() due to typographical error

isAmbiguous

public boolean isAmbiguous()