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java.lang.Objectcom.compomics.util.experiment.personalization.ExperimentObject
com.compomics.util.experiment.biology.Ion
public abstract class Ion
This class models an ion. Created by IntelliJ IDEA. User: Marc Date: Jun 18, 2010 Time: 8:57:33 AM
Nested Class Summary | |
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static class |
Ion.IonType
An enumerator of the supported ion types. |
Field Summary | |
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protected double |
theoreticMass
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protected Ion.IonType |
type
Type of ion. |
Constructor Summary | |
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Ion()
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Method Summary | |
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static Ion |
getGenericIon(Ion.IonType ionType,
int subType)
Convenience method returning a generic ion based on the given ion type without neutral losses. |
static Ion |
getGenericIon(Ion.IonType ionType,
int subType,
ArrayList<NeutralLoss> neutralLosses)
Convenience method returning a generic ion based on the given ion type. |
static ArrayList<Ion.IonType> |
getImplementedIonTypes()
Returns the implemented ion types. |
abstract String |
getName()
Returns the name of the ion. |
abstract ArrayList<NeutralLoss> |
getNeutralLosses()
Returns the possible neutral losses of this ion type. |
String |
getNeutralLossesAsString()
Returns the neutral loss (if any), the empty string if no loss. |
static String |
getNeutralLossesAsString(ArrayList<NeutralLoss> neutralLosses)
Returns the neutral loss (if any), the empty string if no loss. |
static ArrayList<Integer> |
getPossibleSubtypes(Ion.IonType ionType)
Returns an arraylist of possible subtypes. |
abstract CvTerm |
getPrideCvTerm()
Returns the pride cv term adapted to the fragment ion. |
abstract int |
getSubType()
Returns the ion subtype. |
abstract String |
getSubTypeAsString()
Returns the subtype as string. |
double |
getTheoreticMass()
Returns the theoretic mass. |
Ion.IonType |
getType()
Returns the ion type. |
String |
getTypeAsString()
Returns the type of ion as string. |
static String |
getTypeAsString(Ion.IonType type)
Returns the type of ion as string. |
abstract boolean |
isSameAs(Ion anotherIon)
Returns a boolean indicating whether the ion is the same as another ion. |
void |
setTheoreticMass(double theoreticMass)
Sets a new theoretic mass. |
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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protected Ion.IonType type
protected double theoreticMass
Constructor Detail |
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public Ion()
Method Detail |
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public abstract String getName()
public abstract CvTerm getPrideCvTerm()
public abstract int getSubType()
public abstract String getSubTypeAsString()
public static ArrayList<Integer> getPossibleSubtypes(Ion.IonType ionType)
ionType
- an arraylist of possible subtypes
public abstract ArrayList<NeutralLoss> getNeutralLosses()
public abstract boolean isSameAs(Ion anotherIon)
anotherIon
- the other ion
public String getNeutralLossesAsString()
public static String getNeutralLossesAsString(ArrayList<NeutralLoss> neutralLosses)
neutralLosses
- the neutral loss (if any)
public double getTheoreticMass()
public void setTheoreticMass(double theoreticMass)
theoreticMass
- a new theoretic masspublic Ion.IonType getType()
public static ArrayList<Ion.IonType> getImplementedIonTypes()
public String getTypeAsString()
public static String getTypeAsString(Ion.IonType type)
type
- the type of ion as string
public static Ion getGenericIon(Ion.IonType ionType, int subType, ArrayList<NeutralLoss> neutralLosses)
ionType
- the ion typesubType
- the ion subtypeneutralLosses
- the neutral losses. An empty or null list if none.
public static Ion getGenericIon(Ion.IonType ionType, int subType)
ionType
- the ion typesubType
- the ion subtype
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