Class Glycan
java.lang.Object
com.compomics.util.experiment.personalization.ExperimentObject
com.compomics.util.experiment.biology.ions.Ion
com.compomics.util.experiment.biology.ions.impl.Glycan
- All Implemented Interfaces:
Serializable
public class Glycan extends Ion
This class represents a glycan.
- Author:
- Marc Vaudel
- See Also:
- Serialized Form
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Nested Class Summary
Nested classes/interfaces inherited from class com.compomics.util.experiment.biology.ions.Ion
Ion.IonType
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Field Summary
Fields Modifier and Type Field Description static int
DEUTEROACETYLATED_MASS
Final index for deuteroacetylated masses.static int
DEUTEROMETHYLATED_MASS
Final index for deuteromethylated masses.static int
PERACETYLATED_MASS
Final index for peracetylated masses.static int
PERMETHYLATED_MASS
Final index for permethylated masses.static int
UNDERIVATED_MASS
Final index for underivated masses.Fields inherited from class com.compomics.util.experiment.biology.ions.Ion
atomChain, theoreticMass, theoreticMass1, type
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Constructor Summary
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Method Summary
Modifier and Type Method Description void
addMass(int massType, double value)
Add a mass for this glycan.double
getMass(int aType)
Get the glycan mass.String
getName()
Returns the name of the ion.NeutralLoss[]
getNeutralLosses()
Returns the possible neutral losses of this ion type.static int[]
getPossibleSubtypes()
Returns the possible subtypes.CvTerm
getPrideCvTerm()
Returns the CV term adapted to the fragment ion.CvTerm
getPsiMsCvTerm()
Returns the CV term adapted to the fragment ion.int
getSubType()
Returns the ion subtype.String
getSubTypeAsString()
Returns the subtype as string.boolean
isSameAs(Ion anotherIon)
Returns a boolean indicating whether the ion is the same as another ion.Methods inherited from class com.compomics.util.experiment.biology.ions.Ion
getAtomicComposition, getGenericIon, getGenericIon, getImplementedIonTypes, getNeutralLossesAsString, getNeutralLossesAsString, getPossibleSubtypes, getPossibleSubtypesAsSet, getTheoreticMass, getTheoreticMz, getType, getTypeAsString, getTypeAsString, hasNeutralLosses, setAtomicComposition, setTheoreticMass
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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UNDERIVATED_MASS
public static final int UNDERIVATED_MASSFinal index for underivated masses.- See Also:
- Constant Field Values
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PERMETHYLATED_MASS
public static final int PERMETHYLATED_MASSFinal index for permethylated masses.- See Also:
- Constant Field Values
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DEUTEROMETHYLATED_MASS
public static final int DEUTEROMETHYLATED_MASSFinal index for deuteromethylated masses.- See Also:
- Constant Field Values
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PERACETYLATED_MASS
public static final int PERACETYLATED_MASSFinal index for peracetylated masses.- See Also:
- Constant Field Values
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DEUTEROACETYLATED_MASS
public static final int DEUTEROACETYLATED_MASSFinal index for deuteroacetylated masses.- See Also:
- Constant Field Values
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Constructor Details
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Method Details
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addMass
public void addMass(int massType, double value)Add a mass for this glycan.- Parameters:
massType
- mass type indexed according to the static fieldvalue
- Value of the mass
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getMass
public double getMass(int aType)Get the glycan mass.- Parameters:
aType
- Type of mass requested indexed according to static int.- Returns:
- the requested mass
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getName
Description copied from class:Ion
Returns the name of the ion. The name should be short enough to be displayed on a spectrum. -
getPrideCvTerm
Description copied from class:Ion
Returns the CV term adapted to the fragment ion. Null if none corresponding.- Specified by:
getPrideCvTerm
in classIon
- Returns:
- the CV term adapted to the fragment ion. Null if none corresponding
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getPsiMsCvTerm
Description copied from class:Ion
Returns the CV term adapted to the fragment ion. Null if none corresponding.- Specified by:
getPsiMsCvTerm
in classIon
- Returns:
- the CV term adapted to the fragment ion. Null if none corresponding
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getSubType
public int getSubType()Description copied from class:Ion
Returns the ion subtype.- Specified by:
getSubType
in classIon
- Returns:
- the ion subtype as integer
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getSubTypeAsString
Description copied from class:Ion
Returns the subtype as string.- Specified by:
getSubTypeAsString
in classIon
- Returns:
- the subtype as string
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getPossibleSubtypes
public static int[] getPossibleSubtypes()Returns the possible subtypes.- Returns:
- the possible subtypes
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getNeutralLosses
Description copied from class:Ion
Returns the possible neutral losses of this ion type. An empty list if none.- Specified by:
getNeutralLosses
in classIon
- Returns:
- the possible neutral losses of this ion type
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isSameAs
Description copied from class:Ion
Returns a boolean indicating whether the ion is the same as another ion.
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