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