Package | Description |
---|---|
com.compomics.util.experiment.biology |
Experiment classes related to biological entities.
|
com.compomics.util.experiment.biology.ions |
Experiment classes related to ions.
|
com.compomics.util.gui.atoms |
Atoms GUI dialogs.
|
Modifier and Type | Field and Description |
---|---|
protected AtomChain |
Ion.atomChain
The atomic composition of the ion.
|
protected AtomChain |
AminoAcid.monoisotopicAtomChain
The monoisotopic atom chain.
|
Modifier and Type | Method and Description |
---|---|
AtomChain |
AtomChain.clone() |
AtomChain |
PTM.getAtomChainAdded()
Returns the atom chain added.
|
AtomChain |
PTM.getAtomChainRemoved()
Returns the atom chain removed.
|
AtomChain |
Ion.getAtomicComposition()
Returns the atomic composition.
|
AtomChain |
NeutralLoss.getComposition()
The composition of the loss.
|
AtomChain |
AminoAcid.getMonoisotopicAtomChain()
Returns the monoisotopic atom chain representing this amino acid.
|
Modifier and Type | Method and Description |
---|---|
boolean |
AtomChain.isSameCompositionAs(AtomChain anotherChain)
Indicates whether two atom chains are of the same composition by
comparing their string and type.
|
void |
PTM.setAtomChainAdded(AtomChain atomChainAdded)
Sets the atom chain added.
|
void |
PTM.setAtomChainRemoved(AtomChain atomChainRemoved)
Sets the atom chain removed.
|
void |
Ion.setAtomicComposition(AtomChain atomChain)
Returns the atomic composition.
|
void |
NeutralLoss.setComposition(AtomChain composition)
Sets the composition of the neutral loss.
|
Constructor and Description |
---|
NeutralLoss(String name,
AtomChain composition,
boolean fixed)
Constructor for a user defined neutral loss.
|
NeutralLoss(String name,
AtomChain composition,
boolean fixed,
boolean save)
Constructor for a user defined neutral loss.
|
PTM(int type,
String name,
String shortName,
AtomChain atomChainAdded,
AtomChain atomChainRemoved,
AminoAcidPattern aminoAcidPattern)
Constructor for a reference modification.
|
PTM(int type,
String name,
String shortName,
AtomChain atomChainAdded,
AtomChain atomChainRemoved,
AminoAcidPattern aminoAcidPattern,
CvTerm cvTerm)
Constructor for a reference modification.
|
Constructor and 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.
|
Modifier and Type | Method and 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.
|
Constructor and 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.
|
Copyright © 2016. All rights reserved.