Interface CompoundSet<C extends Compound>
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- All Known Implementing Classes:
 ABITracerCompoundSet,AbstractCompoundSet,AbstractNucleotideCompoundSet,AmbiguityDNACompoundSet,AmbiguityDNARNAHybridCompoundSet,AmbiguityRNACompoundSet,AminoAcidCompoundSet,CaseFreeAminoAcidCompoundSet,DNACompoundSet,ModifiedAminoAcidCompoundSet,RNACompoundSet
public interface CompoundSet<C extends Compound>
 
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Method Summary
All Methods Instance Methods Abstract Methods Modifier and Type Method Description booleancompoundsEquivalent(C compoundOne, C compoundTwo)List<C>getAllCompounds()CgetCompoundForString(String string)Return null if not recognised.Set<C>getEquivalentCompounds(C compound)intgetMaxSingleCompoundStringLength()Returns the maximum size of a compound String this set holdsStringgetStringForCompound(C compound)booleanhasCompound(C compound)booleanisComplementable()booleanisCompoundStringLengthEqual()Returns true if all String representations of Compounds are of the same length.booleanisValidSequence(Sequence<C> sequence) 
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Method Detail
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getMaxSingleCompoundStringLength
int getMaxSingleCompoundStringLength()
Returns the maximum size of a compound String this set holds 
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isCompoundStringLengthEqual
boolean isCompoundStringLengthEqual()
Returns true if all String representations of Compounds are of the same length. 
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getCompoundForString
C getCompoundForString(String string)
Return null if not recognised. Throw IllegalArgumentException if string is longer than maximum allowed bygetStringForCompound(Compound). 
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getStringForCompound
String getStringForCompound(C compound)
 
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compoundsEquivalent
boolean compoundsEquivalent(C compoundOne, C compoundTwo)
 
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isValidSequence
boolean isValidSequence(Sequence<C> sequence)
 
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getEquivalentCompounds
Set<C> getEquivalentCompounds(C compound)
 
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hasCompound
boolean hasCompound(C compound)
 
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getAllCompounds
List<C> getAllCompounds()
 
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isComplementable
boolean isComplementable()
 
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