Class Atom
java.lang.Object
com.compomics.util.experiment.personalization.ExperimentObject
com.compomics.util.experiment.biology.atoms.Atom
- All Implemented Interfaces:
Serializable
- Direct Known Subclasses:
Calcium
,Carbon
,Copper
,Fluorine
,Helium
,Hydrogen
,Iodine
,Iron
,Lithium
,Magnesium
,Nitrogen
,Oxygen
,Phosphorus
,Potassium
,Selenium
,Sodium
,Sulfur
,Zinc
public abstract class Atom extends ExperimentObject
This interface contains information about atoms.
- Author:
- Marc Vaudel, Harald Barsnes
- See Also:
- Serialized Form
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Field Summary
Fields Modifier and Type Field Description static Atom
C
The carbon atom.static Atom
Ca
The Calcium atom.static Atom
Cu
The Copper atom.static Atom
F
The Fluorine atom.static Atom
Fe
The Iron atom.static Atom
H
The hydrogen atom.static Atom
He
The helium atom.static Atom
I
The Iodine atom.protected HashMap<Integer,Double>
isotopeMap
Map of the isotope masses relative to the monoisotopic peak (+1 for carbon 13).static Atom
K
The Potassium atom.protected String
letter
The symbol for the atom.static Atom
Li
The phosphorus atom.static Atom
Mg
The Magnesium atom.protected double
monoisotopicMass
The monoisotopic mass.static Atom
N
The nitrogen atom.static Atom
Na
The sodium atom.protected String
name
The name of the atom.static Atom
O
The oxygen atom.static Atom
P
The phosphorus atom.protected HashMap<Integer,Double>
representativeComposition
Map of the isotope representative composition of the stable isotopes.static Atom
S
The sulfur atom.static Atom
Se
The selenium atom.static Atom
Zn
The Zinc atom. -
Constructor Summary
Constructors Constructor Description Atom()
Empty default constructor -
Method Summary
Modifier and Type Method Description static Atom
getAtom(String shortName)
Returns the atom corresponding to the given short name.double
getDifferenceToMonoisotopic(int isotopeNumber)
Returns the mass difference between the given isotope and the monoisotopic mass.static String[]
getImplementedAtoms(boolean includeSelect)
Returns an array of implemented atoms indicated by their short name.ArrayList<Integer>
getImplementedIsotopes()
returns an unsorted list of isotopes for which a mass is available relative to the monoisotopic peak (+1 for carbon 13).Double
getIsotopeMass(int isotopeNumber)
Returns the mass corresponding to the given isotope number.String
getLetter()
Returns the symbol for the atom.double
getMonoisotopicMass()
Returns the monoisotopic mass.String
getName()
Returns the name of the atom.String
toString()
Methods inherited from class com.compomics.util.experiment.personalization.ExperimentObject
addUrParam, asLong, clearParametersMap, getId, getUrParam, getUrParams, removeUrParam, setId, setUrParams
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Field Details
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H
The hydrogen atom. -
N
The nitrogen atom. -
O
The oxygen atom. -
C
The carbon atom. -
S
The sulfur atom. -
P
The phosphorus atom. -
He
The helium atom. -
Li
The phosphorus atom. -
Na
The sodium atom. -
Se
The selenium atom. -
I
The Iodine atom. -
F
The Fluorine atom. -
Fe
The Iron atom. -
K
The Potassium atom. -
Ca
The Calcium atom. -
Zn
The Zinc atom. -
Mg
The Magnesium atom. -
Cu
The Copper atom. -
monoisotopicMass
protected double monoisotopicMassThe monoisotopic mass. Access is faster then querying the isotope map. -
isotopeMap
Map of the isotope masses relative to the monoisotopic peak (+1 for carbon 13). -
representativeComposition
Map of the isotope representative composition of the stable isotopes. -
name
The name of the atom. -
letter
The symbol for the atom.
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Constructor Details
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Atom
public Atom()Empty default constructor
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Method Details
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getImplementedAtoms
Returns an array of implemented atoms indicated by their short name.- Parameters:
includeSelect
- if true, the first item is set to '- Select -'- Returns:
- an array of implemented atoms
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getAtom
Returns the atom corresponding to the given short name.- Parameters:
shortName
- the short name of the atom- Returns:
- the atom corresponding to the given short name
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getMonoisotopicMass
public double getMonoisotopicMass()Returns the monoisotopic mass.- Returns:
- the monoisotopic mass in Da
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getName
Returns the name of the atom.- Returns:
- the name of the atom
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getLetter
Returns the symbol for the atom.- Returns:
- the symbol for the atom
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getImplementedIsotopes
returns an unsorted list of isotopes for which a mass is available relative to the monoisotopic peak (+1 for carbon 13).- Returns:
- a list of isotopes for which a mass is available
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getIsotopeMass
Returns the mass corresponding to the given isotope number. Null if not found.- Parameters:
isotopeNumber
- the isotope number of interest relative to the monoisotopic peak (+1 for carbon 13).- Returns:
- the corresponding mass
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getDifferenceToMonoisotopic
public double getDifferenceToMonoisotopic(int isotopeNumber)Returns the mass difference between the given isotope and the monoisotopic mass.- Parameters:
isotopeNumber
- the isotope number relative to the monoisotopic peak (+1 for carbon 13)- Returns:
- the mass difference between the given isotope and the monoisotopic mass
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toString
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