org.biojava.nbio.aaproperties.xml.CaseFreeAminoAcidCompoundSet

All Implemented Interfaces:: CompoundSet<AminoAcidCompound>

public class CaseFreeAminoAcidCompoundSet extends Object implements CompoundSet<AminoAcidCompound>

Set of proteinogenic amino acids. Molecular weights are recorded in daltons (Da) as residues of a chain; monomers outside of a chain would likely have an additional mass of 18.01524 Da contributed by an associated water molecule. Currently we have different symbols to handle inserts so not as clean as it should be

Author:: Richard Holland, Scooter Willis, Mark Chapman

Constructor Summary

Constructors

Constructor

Description

CaseFreeAminoAcidCompoundSet()
Method Summary

Modifier and Type

Method

Description

boolean

compoundsEquivalent(AminoAcidCompound compoundOne, AminoAcidCompound compoundTwo)

List<AminoAcidCompound>

getAllCompounds()

static CaseFreeAminoAcidCompoundSet

getAminoAcidCompoundSet()

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
- CaseFreeAminoAcidCompoundSet
  
  public CaseFreeAminoAcidCompoundSet()
Method Details
- getStringForCompound
  
  public String getStringForCompound(AminoAcidCompound compound)
  
  Specified by:
  
  getStringForCompound 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>
- 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>
- getAminoAcidCompoundSet
  
  public static CaseFreeAminoAcidCompoundSet getAminoAcidCompoundSet()
- 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 CaseFreeAminoAcidCompoundSet

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Details

CaseFreeAminoAcidCompoundSet

Method Details

getStringForCompound

getCompoundForString

getMaxSingleCompoundStringLength

isCompoundStringLengthEqual

getAminoAcidCompoundSet

compoundsEquivalent

getEquivalentCompounds

hasCompound

getAllCompounds

isComplementable

isValidSequence