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java.lang.Objectcom.compomics.util.experiment.personalization.ExperimentObject
com.compomics.util.experiment.biology.Ion
com.compomics.util.experiment.biology.ions.ImmoniumIon
public class ImmoniumIon
Represents an immonium ion.
Nested Class Summary |
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Nested classes/interfaces inherited from class com.compomics.util.experiment.biology.Ion |
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Ion.IonType |
Field Summary | |
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static int |
ALANINE
Subtype int for an alanine immonium ion. |
static int |
ARGININE
Subtype int for an arginine immonium ion. |
static int |
ASPARAGINE
Subtype int for an asparagine immonium ion. |
static int |
ASPARTIC_ACID
Subtype int for an aspartic acid immonium ion. |
static int |
CYSTEINE
Subtype int for a cysteine immonium ion. |
static int |
GLUTAMIC_ACID
Subtype int for a glutamic acid immonium ion. |
static int |
GLUTAMINE
Subtype int for a glutamine immonium ion. |
static int |
GLYCINE
Subtype int for a glycine immonium ion. |
static int |
HISTIDINE
Subtype int for an histidine immonium ion. |
static int |
ISOLEUCINE
Subtype int for an isoleucine immonium ion. |
static int |
LEUCINE
Subtype int for a leucine immonium ion. |
static int |
LYSINE
Subtype int for a lysine immonium ion. |
static int |
METHIONINE
Subtype int for a methionine immonium ion. |
static int |
PHENYLALANINE
Subtype int for a phenylananine immonium ion. |
static int |
PROLINE
Subtype int for a proline immonium ion. |
static int |
SELENOCYSTEINE
Subtype int for a selenocysteine immonium ion. |
static int |
SERINE
Subtype int for a serine immonium ion. |
static int |
THREONINE
Subtype int for a threonine immonium ion. |
static int |
TRYPTOPHAN
Subtype int for a tryptophan immonium ion. |
static int |
TYROSINE
Subtype int for a tyrosine immonium ion. |
static int |
VALINE
Subtype int for a valine immonium ion. |
Fields inherited from class com.compomics.util.experiment.biology.Ion |
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theoreticMass, type |
Constructor Summary | |
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ImmoniumIon(char residue)
Constructor for an immonium ion. |
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ImmoniumIon(int subType)
Constructor for an immonium ion. |
Method Summary | |
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String |
getName()
Returns the name of the ion. |
ArrayList<NeutralLoss> |
getNeutralLosses()
Returns the possible neutral losses of this ion type. |
static ArrayList<Integer> |
getPossibleSubtypes()
Returns an arraylist of possible subtypes. |
CvTerm |
getPrideCvTerm()
Returns the pride cv term adapted to the fragment ion. |
static char |
getResidue(int subtype)
Returns the amino acid of the immonium ion based on the subtype index. |
int |
getSubType()
Returns the ion subtype. |
static int |
getSubtype(char residue)
Returns the subtype identifier based on the amino acid one letter symbol. |
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.Ion |
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getGenericIon, getGenericIon, getImplementedIonTypes, getNeutralLossesAsString, getNeutralLossesAsString, getPossibleSubtypes, getTheoreticMass, getType, getTypeAsString, getTypeAsString, setTheoreticMass |
Methods inherited from class com.compomics.util.experiment.personalization.ExperimentObject |
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addUrParam, getParameterKey, getUrParam |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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public static final int ALANINE
public static final int ARGININE
public static final int ASPARAGINE
public static final int ASPARTIC_ACID
public static final int CYSTEINE
public static final int GLUTAMIC_ACID
public static final int GLUTAMINE
public static final int GLYCINE
public static final int HISTIDINE
public static final int ISOLEUCINE
public static final int LEUCINE
public static final int LYSINE
public static final int METHIONINE
public static final int PHENYLALANINE
public static final int PROLINE
public static final int SELENOCYSTEINE
public static final int SERINE
public static final int THREONINE
public static final int TRYPTOPHAN
public static final int TYROSINE
public static final int VALINE
Constructor Detail |
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public ImmoniumIon(char residue)
residue
- the type of immonium ion as charpublic ImmoniumIon(int subType)
subType
- the type of immonium ion as integer as indexed by the
static fieldsMethod Detail |
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public static char getResidue(int subtype)
subtype
- the subtype index from the static fields
public static int getSubtype(char residue)
residue
- the amino acid as char
public String getName()
Ion
getName
in class Ion
public CvTerm getPrideCvTerm()
Ion
getPrideCvTerm
in class Ion
public int getSubType()
Ion
getSubType
in class Ion
public String getSubTypeAsString()
Ion
getSubTypeAsString
in class Ion
public static ArrayList<Integer> getPossibleSubtypes()
public ArrayList<NeutralLoss> getNeutralLosses()
Ion
getNeutralLosses
in class Ion
public boolean isSameAs(Ion anotherIon)
Ion
isSameAs
in class Ion
anotherIon
- the other ion
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