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 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(List<T> compounds, List<List<T>> workingList)

protected void

addCompoundToLists(List<List<T>> list, T compound)

protected void

addStrings(String source, String... targets)

Sequence<T>

createSequence(Sequence<F> originalSequence)

List<Sequence<T>>

createSequences(Sequence<F> originalSequence)

SequenceCreatorInterface<T>

getCreator()

CompoundSet<F>

getFromCompoundSet()

CompoundSet<T>

getToCompoundSet()

protected abstract void

postProcessCompoundLists(List<List<T>> compoundLists)

T

translate(F fromCompound)

List<T>

translateMany(F fromCompound)

protected List<Sequence<T>>

workingListToSequences(List<List<T>> workingList)

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details
- AbstractCompoundTranslator
  
  public AbstractCompoundTranslator(SequenceCreatorInterface<T> creator, CompoundSet<F> fromCompoundSet, CompoundSet<T> toCompoundSet)
Method Details
- getCreator
  
  public SequenceCreatorInterface<T> getCreator()
- getFromCompoundSet
  
  public CompoundSet<F> getFromCompoundSet()
- getToCompoundSet
  
  public CompoundSet<T> getToCompoundSet()
- addStrings
  
  protected void addStrings(String source, String... targets)
- addCompounds
  
  protected void addCompounds(F source, T... targets)
- translateMany
  
  public 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 List<Sequence<T>> createSequences(Sequence<F> originalSequence)
  
  Specified by:
  
  createSequences in interface CompoundTranslator<F extends Compound,T extends Compound>
- postProcessCompoundLists
  
  protected abstract void postProcessCompoundLists(List<List<T>> compoundLists)
- addCompoundsToList
  
  protected void addCompoundsToList(List<T> compounds, List<List<T>> workingList)
- workingListToSequences
  
  protected List<Sequence<T>> workingListToSequences(List<List<T>> workingList)
- addCompoundToLists
  
  protected void addCompoundToLists(List<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>

Class AbstractCompoundTranslator<F extends Compound,T extends Compound>

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Details

AbstractCompoundTranslator

Method Details

getCreator

getFromCompoundSet

getToCompoundSet

addStrings

addCompounds

translateMany

translate

createSequences

postProcessCompoundLists

addCompoundsToList

workingListToSequences

addCompoundToLists

createSequence