Package org.biojava.nbio.aaproperties.xml

Class CaseFreeAminoAcidCompoundSet

java.lang.Object

org.biojava.nbio.aaproperties.xml.CaseFreeAminoAcidCompoundSet

All Implemented Interfaces:

org.biojava.nbio.core.sequence.template.CompoundSet<org.biojava.nbio.core.sequence.compound.AminoAcidCompound>

public class CaseFreeAminoAcidCompoundSet
extends Object
implements org.biojava.nbio.core.sequence.template.CompoundSet<org.biojava.nbio.core.sequence.compound.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(org.biojava.nbio.core.sequence.compound.AminoAcidCompound compoundOne, org.biojava.nbio.core.sequence.compound.AminoAcidCompound compoundTwo)
List<org.biojava.nbio.core.sequence.compound.AminoAcidCompound>	getAllCompounds()
static CaseFreeAminoAcidCompoundSet	getAminoAcidCompoundSet()
org.biojava.nbio.core.sequence.compound.AminoAcidCompound	getCompoundForString(String string)
Set<org.biojava.nbio.core.sequence.compound.AminoAcidCompound>	getEquivalentCompounds(org.biojava.nbio.core.sequence.compound.AminoAcidCompound compound)
int	getMaxSingleCompoundStringLength()
String	getStringForCompound(org.biojava.nbio.core.sequence.compound.AminoAcidCompound compound)
boolean	hasCompound(org.biojava.nbio.core.sequence.compound.AminoAcidCompound compound)
boolean	isComplementable()
boolean	isCompoundStringLengthEqual()
boolean	isValidSequence(org.biojava.nbio.core.sequence.template.Sequence<org.biojava.nbio.core.sequence.compound.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(org.biojava.nbio.core.sequence.compound.AminoAcidCompound compound)

Specified by:

getStringForCompound in interface org.biojava.nbio.core.sequence.template.CompoundSet<org.biojava.nbio.core.sequence.compound.AminoAcidCompound>

getCompoundForString

public org.biojava.nbio.core.sequence.compound.AminoAcidCompound getCompoundForString(String string)

Specified by:

getCompoundForString in interface org.biojava.nbio.core.sequence.template.CompoundSet<org.biojava.nbio.core.sequence.compound.AminoAcidCompound>

getMaxSingleCompoundStringLength

public int getMaxSingleCompoundStringLength()

Specified by:

getMaxSingleCompoundStringLength in interface org.biojava.nbio.core.sequence.template.CompoundSet<org.biojava.nbio.core.sequence.compound.AminoAcidCompound>

isCompoundStringLengthEqual

public boolean isCompoundStringLengthEqual()

Specified by:

isCompoundStringLengthEqual in interface org.biojava.nbio.core.sequence.template.CompoundSet<org.biojava.nbio.core.sequence.compound.AminoAcidCompound>

getAminoAcidCompoundSet

public static CaseFreeAminoAcidCompoundSet getAminoAcidCompoundSet()

compoundsEquivalent

public boolean compoundsEquivalent(org.biojava.nbio.core.sequence.compound.AminoAcidCompound compoundOne,
                                   org.biojava.nbio.core.sequence.compound.AminoAcidCompound compoundTwo)

Specified by:

compoundsEquivalent in interface org.biojava.nbio.core.sequence.template.CompoundSet<org.biojava.nbio.core.sequence.compound.AminoAcidCompound>

getEquivalentCompounds

public Set<org.biojava.nbio.core.sequence.compound.AminoAcidCompound> getEquivalentCompounds(org.biojava.nbio.core.sequence.compound.AminoAcidCompound compound)

Specified by:

getEquivalentCompounds in interface org.biojava.nbio.core.sequence.template.CompoundSet<org.biojava.nbio.core.sequence.compound.AminoAcidCompound>

hasCompound

public boolean hasCompound(org.biojava.nbio.core.sequence.compound.AminoAcidCompound compound)

Specified by:

hasCompound in interface org.biojava.nbio.core.sequence.template.CompoundSet<org.biojava.nbio.core.sequence.compound.AminoAcidCompound>

getAllCompounds

public List<org.biojava.nbio.core.sequence.compound.AminoAcidCompound> getAllCompounds()

Specified by:

getAllCompounds in interface org.biojava.nbio.core.sequence.template.CompoundSet<org.biojava.nbio.core.sequence.compound.AminoAcidCompound>

isComplementable

public boolean isComplementable()

Specified by:

isComplementable in interface org.biojava.nbio.core.sequence.template.CompoundSet<org.biojava.nbio.core.sequence.compound.AminoAcidCompound>

isValidSequence

public boolean isValidSequence(org.biojava.nbio.core.sequence.template.Sequence<org.biojava.nbio.core.sequence.compound.AminoAcidCompound> sequence)

Specified by:

isValidSequence in interface org.biojava.nbio.core.sequence.template.CompoundSet<org.biojava.nbio.core.sequence.compound.AminoAcidCompound>