Uses of Class
com.compomics.util.experiment.biology.atoms.AtomChain

Packages that use AtomChain

Package	Description
com.compomics.util.experiment.biology.aminoacids	The amino acid classes.
com.compomics.util.experiment.biology.atoms	The atom classes.
com.compomics.util.experiment.biology.ions	Experiment classes related to ions.
com.compomics.util.experiment.biology.ions.impl	Ion implementations.
com.compomics.util.experiment.biology.modifications
com.compomics.util.gui.atoms	Atoms GUI dialogs.

Uses of AtomChain in com.compomics.util.experiment.biology.aminoacids

Fields in com.compomics.util.experiment.biology.aminoacids declared as AtomChain

Modifier and Type	Field	Description
protected AtomChain	AminoAcid.monoisotopicAtomChain	The monoisotopic atom chain.

Methods in com.compomics.util.experiment.biology.aminoacids that return AtomChain

Modifier and Type	Method	Description
AtomChain	AminoAcid.getMonoisotopicAtomChain()	Returns the monoisotopic atom chain representing this amino acid.

Uses of AtomChain in com.compomics.util.experiment.biology.atoms

Methods in com.compomics.util.experiment.biology.atoms that return AtomChain

Modifier and Type	Method	Description
AtomChain	AtomChain.clone()
static AtomChain	AtomChain.getAtomChain(String atomChainAsString)	Returns an atom chain from the input as string.

Methods in com.compomics.util.experiment.biology.atoms with parameters of type AtomChain

Modifier and Type	Method	Description
boolean	AtomChain.isSameCompositionAs(AtomChain anotherChain)	Indicates whether two atom chains are of the same composition by comparing their string and type.

Uses of AtomChain in com.compomics.util.experiment.biology.ions

Fields in com.compomics.util.experiment.biology.ions declared as AtomChain

Modifier and Type	Field	Description
protected AtomChain	Ion.atomChain	The atomic composition of the ion.

Methods in com.compomics.util.experiment.biology.ions that return AtomChain

Modifier and Type	Method	Description
AtomChain	Ion.getAtomicComposition()	Returns the atomic composition.
AtomChain	NeutralLoss.getComposition()	The composition of the loss.

Methods in com.compomics.util.experiment.biology.ions with parameters of type AtomChain

Modifier and Type	Method	Description
void	Ion.setAtomicComposition(AtomChain atomChain)	Returns the atomic composition.
void	NeutralLoss.setComposition(AtomChain composition)	Sets the composition of the neutral loss.

Constructors in com.compomics.util.experiment.biology.ions with parameters of type AtomChain

Modifier	Constructor	Description
	NeutralLoss(String name, AtomChain composition, boolean fixed)	Constructor for a user defined neutral loss.
	NeutralLoss(String name, AtomChain composition, boolean fixed, char[] aminoAcids)	Constructor for a user defined neutral loss.
	NeutralLoss(String name, AtomChain composition, boolean fixed, char[] aminoAcids, boolean save)	Constructor for a user defined neutral loss.

Uses of AtomChain in com.compomics.util.experiment.biology.ions.impl

Constructors in com.compomics.util.experiment.biology.ions.impl with parameters of type AtomChain

Modifier	Constructor	Description
	RelatedIon(AminoAcid aminoAcidTarget, AtomChain atomChain, int subType)	Constructor for a related ion.
	RelatedIon(AminoAcid aminoAcidTarget, AtomChain atomChain, int subType, boolean save)	Constructor for a related ion.
	ReporterIon(String name, AtomChain atomChain)	Constructor for a user-defined reporter ion.
	ReporterIon(String name, AtomChain atomChain, boolean save)	Constructor for a user-defined reporter ion.

Uses of AtomChain in com.compomics.util.experiment.biology.modifications

Methods in com.compomics.util.experiment.biology.modifications that return AtomChain

Modifier and Type	Method	Description
AtomChain	Modification.getAtomChainAdded()	Returns the atom chain added.
AtomChain	Modification.getAtomChainRemoved()	Returns the atom chain removed.

Methods in com.compomics.util.experiment.biology.modifications with parameters of type AtomChain

Modifier and Type	Method	Description
void	Modification.setAtomChainAdded(AtomChain atomChainAdded)	Sets the atom chain added.
void	Modification.setAtomChainRemoved(AtomChain atomChainRemoved)	Sets the atom chain removed.

Constructors in com.compomics.util.experiment.biology.modifications with parameters of type AtomChain

Modifier	Constructor	Description
	Modification(ModificationType modificationType, String name, String shortName, AtomChain atomChainAdded, AtomChain atomChainRemoved, AminoAcidPattern aminoAcidPattern, ModificationCategory category)	Constructor for a reference modification.
	Modification(ModificationType modificationType, String name, String shortName, AtomChain atomChainAdded, AtomChain atomChainRemoved, AminoAcidPattern aminoAcidPattern, CvTerm unimodCvTerm, CvTerm psiModCvTerm, ModificationCategory category)	Constructor for a reference modification.

Uses of AtomChain in com.compomics.util.gui.atoms

Methods in com.compomics.util.gui.atoms that return AtomChain

Modifier and Type	Method	Description
AtomChain	AtomChainDialog.getAtomChainAdded()	Returns the added atom chain as edited by the user.
AtomChain	AtomChainDialog.getAtomChainRemoved()	Returns the removed atom chain as edited by the user.

Constructors in com.compomics.util.gui.atoms with parameters of type AtomChain

Modifier	Constructor	Description
	AtomChainDialog(Frame parent, AtomChain atomChainAdded, AtomChain atomChainRemoved, boolean onlyAddition)	Creates a new dialog.
	AtomChainDialog(JDialog parent, AtomChain atomChainAdded, AtomChain atomChainRemoved, boolean onlyAddition)	Creates a new dialog.