Package org.biojava.nbio.core.sequence.template

Class AbstractCompoundTranslator<F extends Compound,T extends Compound>

java.lang.Object

org.biojava.nbio.core.sequence.template.AbstractCompoundTranslator<F,T>

All Implemented Interfaces:

CompoundTranslator<F,T>

Direct Known Subclasses:

DNAToRNATranslator, RNAToAminoAcidTranslator

public abstract class AbstractCompoundTranslator<F extends Compound,T extends Compound>
extends java.lang.Object
implements CompoundTranslator<F,T>

Constructor Summary

Constructors

Constructor	Description
AbstractCompoundTranslator(SequenceCreatorInterface<T> creator, CompoundSet<F> fromCompoundSet, CompoundSet<T> toCompoundSet)

Method Summary

Modifier and Type	Method	Description
protected void	addCompounds(F source, T... targets)
protected void	addCompoundsToList(java.util.List<T> compounds, java.util.List<java.util.List<T>> workingList)
protected void	addCompoundToLists(java.util.List<java.util.List<T>> list, T compound)
protected void	addStrings(java.lang.String source, java.lang.String... targets)
Sequence<T>	createSequence(Sequence<F> originalSequence)
java.util.List<Sequence<T>>	createSequences(Sequence<F> originalSequence)
SequenceCreatorInterface<T>	getCreator()
CompoundSet<F>	getFromCompoundSet()
CompoundSet<T>	getToCompoundSet()
protected abstract void	postProcessCompoundLists(java.util.List<java.util.List<T>> compoundLists)
T	translate(F fromCompound)
java.util.List<T>	translateMany(F fromCompound)
protected java.util.List<Sequence<T>>	workingListToSequences(java.util.List<java.util.List<T>> workingList)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

AbstractCompoundTranslator

public AbstractCompoundTranslator(SequenceCreatorInterface<T> creator,
                                  CompoundSet<F> fromCompoundSet,
                                  CompoundSet<T> toCompoundSet)

Method Detail

getCreator

public SequenceCreatorInterface<T> getCreator()

getFromCompoundSet

public CompoundSet<F> getFromCompoundSet()

getToCompoundSet

public CompoundSet<T> getToCompoundSet()

addStrings

protected void addStrings(java.lang.String source,
                          java.lang.String... targets)

addCompounds

protected void addCompounds(F source,
                            T... targets)

translateMany

public java.util.List<T> translateMany(F fromCompound)

Specified by:

translateMany in interface CompoundTranslator<F extends Compound,T extends Compound>

translate

public T translate(F fromCompound)

Specified by:

translate in interface CompoundTranslator<F extends Compound,T extends Compound>

createSequences

public java.util.List<Sequence<T>> createSequences(Sequence<F> originalSequence)

Specified by:

createSequences in interface CompoundTranslator<F extends Compound,T extends Compound>

postProcessCompoundLists

protected abstract void postProcessCompoundLists(java.util.List<java.util.List<T>> compoundLists)

addCompoundsToList

protected void addCompoundsToList(java.util.List<T> compounds,
                                  java.util.List<java.util.List<T>> workingList)

workingListToSequences

protected java.util.List<Sequence<T>> workingListToSequences(java.util.List<java.util.List<T>> workingList)

addCompoundToLists

protected void addCompoundToLists(java.util.List<java.util.List<T>> list,
                                  T compound)

createSequence

public Sequence<T> createSequence(Sequence<F> originalSequence)

Specified by:

createSequence in interface CompoundTranslator<F extends Compound,T extends Compound>