- java.lang.Object
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- org.biojava.nbio.core.sequence.template.AbstractCompoundTranslator<F,T>
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- 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>
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Constructor Summary
Constructors Constructor Description AbstractCompoundTranslator(SequenceCreatorInterface<T> creator, CompoundSet<F> fromCompoundSet, CompoundSet<T> toCompoundSet)
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Method Summary
All Methods Instance Methods Abstract Methods Concrete Methods 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)
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Constructor Detail
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AbstractCompoundTranslator
public AbstractCompoundTranslator(SequenceCreatorInterface<T> creator, CompoundSet<F> fromCompoundSet, CompoundSet<T> toCompoundSet)
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Method Detail
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getCreator
public SequenceCreatorInterface<T> getCreator()
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getFromCompoundSet
public CompoundSet<F> getFromCompoundSet()
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getToCompoundSet
public CompoundSet<T> getToCompoundSet()
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addStrings
protected void addStrings(java.lang.String source, java.lang.String... targets)
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translateMany
public java.util.List<T> translateMany(F fromCompound)
- Specified by:
translateMany
in interfaceCompoundTranslator<F extends Compound,T extends Compound>
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createSequences
public java.util.List<Sequence<T>> createSequences(Sequence<F> originalSequence)
- Specified by:
createSequences
in interfaceCompoundTranslator<F extends Compound,T extends Compound>
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postProcessCompoundLists
protected abstract void postProcessCompoundLists(java.util.List<java.util.List<T>> compoundLists)
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addCompoundsToList
protected void addCompoundsToList(java.util.List<T> compounds, java.util.List<java.util.List<T>> workingList)
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workingListToSequences
protected java.util.List<Sequence<T>> workingListToSequences(java.util.List<java.util.List<T>> workingList)
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addCompoundToLists
protected void addCompoundToLists(java.util.List<java.util.List<T>> list, T compound)
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createSequence
public Sequence<T> createSequence(Sequence<F> originalSequence)
- Specified by:
createSequence
in interfaceCompoundTranslator<F extends Compound,T extends Compound>
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