Class RelatedIon
java.lang.Object
com.compomics.util.experiment.personalization.ExperimentObject
com.compomics.util.experiment.biology.ions.Ion
com.compomics.util.experiment.biology.ions.impl.RelatedIon
- All Implemented Interfaces:
Serializable
public class RelatedIon extends Ion
Represents a related ion, i.e., an ion that is related to a given amino acid,
and is its own factory.
- Author:
- Harald Barsnes, 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 RelatedIon
RELATED_C_1
Related ion for C.static RelatedIon
RELATED_C_2
Related ion for C.static RelatedIon
RELATED_D_1
Related ion for D.static RelatedIon
RELATED_E_1
Related ion for E.static RelatedIon
RELATED_F_1
Related ion for F.static RelatedIon
RELATED_H_1
Related ion for H (C4H5N2).static RelatedIon
RELATED_H_2
Related ion for H.static RelatedIon
RELATED_K_1
Related ion for K.static RelatedIon
RELATED_K_2
Related ion for K.static RelatedIon
RELATED_K_3
Related ion for K.static RelatedIon
RELATED_M_1
Related ion for M (C2H4S).static RelatedIon
RELATED_N_1
Related ion for N.static RelatedIon
RELATED_Q_1
Related ion for Q.static RelatedIon
RELATED_Q_2
Related ion for Q.static RelatedIon
RELATED_R_1
Related ion for R.static RelatedIon
RELATED_R_2
Related ion for R.static RelatedIon
RELATED_R_3
Related ion for R.static RelatedIon
RELATED_R_4
Related ion for R (C5H10N2O).static RelatedIon
RELATED_W_1
Related ion for W (C9H7N).static RelatedIon
RELATED_Y_1
Related ion for Y (C7H7O).Fields inherited from class com.compomics.util.experiment.biology.ions.Ion
atomChain, theoreticMass, theoreticMass1, type
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Constructor Summary
Constructors Constructor Description RelatedIon()
Empty default constructorRelatedIon(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. -
Method Summary
Modifier and Type Method Description 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.static ArrayList<RelatedIon>
getRelatedIons(char aa)
Returns the list of related ions for the given amino acid.static ArrayList<RelatedIon>
getRelatedIons(AminoAcid aminoAcidTarget)
Returns the list of related ions for the given amino acid.int
getSubType()
Returns the ion subtype.String
getSubTypeAsString()
Returns the subtype as string.boolean
isSameAs(RelatedIon anotherRelatedIon)
Compares the current related ion with another one based on their composition.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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RELATED_R_1
Related ion for R. Cyanamid and ammonia loss from immonium ion (C4H7N). -
RELATED_R_2
Related ion for R. Cyanamid loss from immonium ion (C4H10N2). -
RELATED_R_3
Related ion for R. Ammonia loss from immonium ion (C5H9N3). -
RELATED_R_4
Related ion for R (C5H10N2O). -
RELATED_N_1
Related ion for N. Ammonia loss from immonium ion (C3H3NO). -
RELATED_D_1
Related ion for D. water loss from immonium ion (C3H3NO). -
RELATED_C_1
Related ion for C. Carbamidomethylated immonium ion (C4H8N2SO). -
RELATED_C_2
Related ion for C. Carbamidomethylated and ammonia loss from immonium ion (C4H5NSO). -
RELATED_E_1
Related ion for E. Water loss from immonium ion (C4H5NO). -
RELATED_Q_1
Related ion for Q. Ammonia loss from immonium ion (C4H5NO). -
RELATED_Q_2
Related ion for Q. Internal b-ion (C5H8N2O2). -
RELATED_H_1
Related ion for H (C4H5N2). -
RELATED_H_2
Related ion for H. Internal b-ion (C6H7N3O). -
RELATED_K_1
Related ion for K. Ammonia loss from immonium ion (C5H9N). -
RELATED_K_2
Related ion for K. Ammonia loss from internal b-ion (C6H9NO). -
RELATED_K_3
Related ion for K. Internal b-ion (C6H12N2O). -
RELATED_M_1
Related ion for M (C2H4S). -
RELATED_F_1
Related ion for F. Tropylium ion (C7H6). -
RELATED_W_1
Related ion for W (C9H7N). -
RELATED_Y_1
Related ion for Y (C7H7O).
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Constructor Details
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RelatedIon
public RelatedIon()Empty default constructor -
RelatedIon
Constructor for a related ion.- Parameters:
aminoAcidTarget
- the amino acid targetatomChain
- the atomic composition of this ionsubType
- the ion subtype
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RelatedIon
Constructor for a related ion.- Parameters:
aminoAcidTarget
- the amino acid targetatomChain
- the atomic composition of this ionsubType
- the ion subtypesave
- if true the related ion will be saved in the static map for later reuse
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Method Details
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getRelatedIons
Returns the list of related ions for the given amino acid.- Parameters:
aa
- the amino acid target single letter code- Returns:
- the list of related ions for the given amino acid
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getRelatedIons
Returns the list of related ions for the given amino acid.- Parameters:
aminoAcidTarget
- the amino acid target- Returns:
- the list of related ions for the given amino acid
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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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isSameAs
Compares the current related ion with another one based on their composition.- Parameters:
anotherRelatedIon
- the other related ion- Returns:
- a boolean indicating whether compositions are equal
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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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