Package org.biojava.nbio.aaproperties.xml

Class CaseFreeAminoAcidCompoundSet

java.lang.Object

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 Detail

CaseFreeAminoAcidCompoundSet

public CaseFreeAminoAcidCompoundSet()

Method Detail

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>