java.lang.Object

org.biojava.nbio.aaproperties.xml.ModifiedAminoAcidCompoundSet

All Implemented Interfaces:: CompoundSet<AminoAcidCompound>

public class ModifiedAminoAcidCompoundSet extends Object implements CompoundSet<AminoAcidCompound>

Constructor Summary

Constructors

Constructor

Description

ModifiedAminoAcidCompoundSet(List<AminoAcidComposition> aaList, Map<Character,Double> aaSymbol2MolecularWeight)
Method Summary

Modifier and Type

Method

Description

boolean

compoundsEquivalent(AminoAcidCompound compoundOne, AminoAcidCompound compoundTwo)

List<AminoAcidCompound>

getAllCompounds()

AminoAcidCompound

getCompoundForString(String string)

Return null if not recognised.

Set<AminoAcidCompound>

getEquivalentCompounds(AminoAcidCompound compound)

int

getMaxSingleCompoundStringLength()

Returns the maximum size of a compound String this set holds

String

getStringForCompound(AminoAcidCompound compound)

boolean

hasCompound(AminoAcidCompound compound)

boolean

isComplementable()

boolean

isCompoundStringLengthEqual()

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

boolean

isValidSequence(Sequence<AminoAcidCompound> sequence)

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details
- ModifiedAminoAcidCompoundSet
  
  public ModifiedAminoAcidCompoundSet(List<AminoAcidComposition> aaList, Map<Character,Double> aaSymbol2MolecularWeight)
Method Details
- getMaxSingleCompoundStringLength
  
  public int getMaxSingleCompoundStringLength()
  
  Description copied from interface: CompoundSet
  
  Returns the maximum size of a compound String this set holds
  
  Specified by:
  
  getMaxSingleCompoundStringLength in interface CompoundSet<AminoAcidCompound>
- isCompoundStringLengthEqual
  
  public boolean isCompoundStringLengthEqual()
  
  Description copied from interface: CompoundSet
  
  Returns true if all String representations of Compounds are of the same length.
  
  Specified by:
  
  isCompoundStringLengthEqual in interface CompoundSet<AminoAcidCompound>
- getCompoundForString
  
  public AminoAcidCompound getCompoundForString(String string)
  
  Description copied from interface: CompoundSet
  
  Return null if not recognised. Throw IllegalArgumentException if string is longer than maximum allowed by CompoundSet.getStringForCompound(Compound).
  
  Specified by:
  
  getCompoundForString in interface CompoundSet<AminoAcidCompound>
- getStringForCompound
  
  public String getStringForCompound(AminoAcidCompound compound)
  
  Specified by:
  
  getStringForCompound in interface CompoundSet<AminoAcidCompound>
- compoundsEquivalent
  
  public boolean compoundsEquivalent(AminoAcidCompound compoundOne, AminoAcidCompound compoundTwo)
  
  Specified by:
  
  compoundsEquivalent in interface CompoundSet<AminoAcidCompound>
- getEquivalentCompounds
  
  public Set<AminoAcidCompound> getEquivalentCompounds(AminoAcidCompound compound)
  
  Specified by:
  
  getEquivalentCompounds in interface CompoundSet<AminoAcidCompound>
- hasCompound
  
  public boolean hasCompound(AminoAcidCompound compound)
  
  Specified by:
  
  hasCompound in interface CompoundSet<AminoAcidCompound>
- getAllCompounds
  
  public List<AminoAcidCompound> getAllCompounds()
  
  Specified by:
  
  getAllCompounds in interface CompoundSet<AminoAcidCompound>
- isComplementable
  
  public boolean isComplementable()
  
  Specified by:
  
  isComplementable in interface CompoundSet<AminoAcidCompound>
- isValidSequence
  
  public boolean isValidSequence(Sequence<AminoAcidCompound> sequence)
  
  Specified by:
  
  isValidSequence in interface CompoundSet<AminoAcidCompound>

Class ModifiedAminoAcidCompoundSet

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Details

ModifiedAminoAcidCompoundSet

Method Details

getMaxSingleCompoundStringLength

isCompoundStringLengthEqual

getCompoundForString

getStringForCompound

compoundsEquivalent

getEquivalentCompounds

hasCompound

getAllCompounds

isComplementable

isValidSequence