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

Interface CompoundSet<C extends Compound>

All Known Implementing Classes:

ABITracerCompoundSet, AbstractCompoundSet, AbstractNucleotideCompoundSet, AmbiguityDNACompoundSet, AmbiguityDNARNAHybridCompoundSet, AmbiguityRNACompoundSet, AminoAcidCompoundSet, CaseFreeAminoAcidCompoundSet, DNACompoundSet, ModifiedAminoAcidCompoundSet, RNACompoundSet

public interface CompoundSet<C extends Compound>

Method Summary

Modifier and Type	Method	Description
boolean	compoundsEquivalent(C compoundOne, C compoundTwo)
List<C>	getAllCompounds()
C	getCompoundForString(String string)	Return null if not recognised.
Set<C>	getEquivalentCompounds(C compound)
int	getMaxSingleCompoundStringLength()	Returns the maximum size of a compound String this set holds
String	getStringForCompound(C compound)
boolean	hasCompound(C compound)
boolean	isComplementable()
boolean	isCompoundStringLengthEqual()	Returns true if all String representations of Compounds are of the same length.
boolean	isValidSequence(Sequence<C> sequence)

Method Details

getMaxSingleCompoundStringLength

int getMaxSingleCompoundStringLength()

Returns the maximum size of a compound String this set holds

isCompoundStringLengthEqual

boolean isCompoundStringLengthEqual()

Returns true if all String representations of Compounds are of the same length.

getCompoundForString

C getCompoundForString(String string)

Return null if not recognised. Throw IllegalArgumentException if string is longer than maximum allowed by getStringForCompound(Compound).

getStringForCompound

String getStringForCompound(C compound)

compoundsEquivalent

boolean compoundsEquivalent(C compoundOne,
 C compoundTwo)

isValidSequence

boolean isValidSequence(Sequence<C> sequence)

getEquivalentCompounds

Set<C> getEquivalentCompounds(C compound)

hasCompound

boolean hasCompound(C compound)

getAllCompounds

List<C> getAllCompounds()

isComplementable

boolean isComplementable()