CompoundSet

All Known Implementing Classes:: AbstractCompoundSet, AbstractNucleotideCompoundSet, AmbiguityDNACompoundSet, AmbiguityRNACompoundSet, AminoAcidCompoundSet, DNACompoundSet, 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.

void

verifySequence(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)
- 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()