Package org.biojava.nbio.aaproperties.xml

Class ModifiedAminoAcidCompoundSet

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 Detail

ModifiedAminoAcidCompoundSet

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

Method Detail

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>