Package org.biojava.nbio.aaproperties.xml

Class ModifiedAminoAcidCompoundSet

java.lang.Object

org.biojava.nbio.aaproperties.xml.ModifiedAminoAcidCompoundSet

All Implemented Interfaces:

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

public class ModifiedAminoAcidCompoundSet
extends Object
implements org.biojava.nbio.core.sequence.template.CompoundSet<org.biojava.nbio.core.sequence.compound.AminoAcidCompound>

Constructor Summary

Constructors

Constructor	Description
ModifiedAminoAcidCompoundSet(List<AminoAcidComposition> aaList, Map<Character,Double> aaSymbol2MolecularWeight)

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()
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

ModifiedAminoAcidCompoundSet

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

Method Detail

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>

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>

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>

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>