org.biojava3.core.sequence.template
Interface CompoundSet<C extends Compound>

All Known Implementing Classes:
AbstractCompoundSet, AbstractNucleotideCompoundSet, AmbiguityDNACompoundSet, AmbiguityRNACompoundSet, AminoAcidCompoundSet, CaseFreeAminoAcidCompoundSet, DNACompoundSet, ModifiedAminoAcidCompoundSet, RNACompoundSet

public interface CompoundSet<C extends Compound>


Method Summary
 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.
 void verifySequence(Sequence<C> sequence)
           
 

Method Detail

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)

verifySequence

void verifySequence(Sequence<C> sequence)
                    throws CompoundNotFoundError
Throws:
CompoundNotFoundError

getEquivalentCompounds

Set<C> getEquivalentCompounds(C compound)

hasCompound

boolean hasCompound(C compound)

getAllCompounds

List<C> getAllCompounds()

isComplementable

boolean isComplementable()