Ion (computational omics utilities 4.5.7 API)

java.lang.Object
- com.compomics.util.experiment.personalization.ExperimentObject
- - com.compomics.util.experiment.biology.Ion

All Implemented Interfaces:

Serializable, Cloneable

Direct Known Subclasses:

ElementaryIon, Glycan, ImmoniumIon, PeptideFragmentIon, PrecursorIon, RelatedIon, ReporterIon, TagFragmentIon
```
public abstract class Ion
extends ExperimentObject
```
This class models an ion.

Author:

Marc Vaudel

See Also:

Serialized Form

Nested Class Summary

Nested Classes
Modifier and Type Class and Description

static class Ion.IonType
An enumerator of the supported ion types.

Nested Classes
Modifier and Type	Class and Description
`static class`	`Ion.IonType` An enumerator of the supported ion types.

Field Summary

Fields
Modifier and Type	Field and Description
`protected AtomChain`	`atomChain` The atomic composition of the ion.
`protected Double`	`theoreticMass` The theoretic mass.
`protected Ion.IonType`	`type` Type of ion.

Constructor Summary

Constructors
Constructor and Description

Ion()

Constructors
Constructor and Description
`Ion()`

Method Summary

All Methods Static Methods Instance Methods Abstract Methods Concrete Methods
Modifier and Type	Method and Description
`AtomChain`	`getAtomicComposition()` Returns the atomic composition.
`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, from the atomic composition if available, from the theoreticMass field otherwise.
`double`	`getTheoreticMz(int chargeValue)` Returns the theoretic m/z of an ion at a given charge state.
`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.
`boolean`	`hasNeutralLosses()` Indicates whether the ion has a neutral loss.
`abstract boolean`	`isSameAs(Ion anotherIon)` Returns a boolean indicating whether the ion is the same as another ion.
`void`	`setAtomicComposition(AtomChain atomChain)` Returns the atomic composition.
`void`	`setTheoreticMass(double theoreticMass)` Sets a new theoretic mass.

Methods inherited from class com.compomics.util.experiment.personalization.ExperimentObject
addUrParam, getParameterKey, getUrParam

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - type
```
protected Ion.IonType type
```
    Type of ion.
  - theoreticMass
```
protected Double theoreticMass
```
    The theoretic mass.
  - atomChain
```
protected AtomChain atomChain
```
    The atomic composition of the ion.
- Constructor Detail
  - Ion
```
public Ion()
```
- Method Detail
  - getName
```
public abstract String getName()
```
    Returns the name of the ion. The name should be short enough to be displayed on a spectrum.
    
    Returns:
    
    the name of the ion
  - getPrideCvTerm
```
public abstract CvTerm getPrideCvTerm()
```
    Returns the pride cv term adapted to the fragment ion. null if none corresponding.
    
    Returns:
    
    the pride cv term adapted to the fragment ion. null if none corresponding
  - getSubType
```
public abstract int getSubType()
```
    Returns the ion subtype.
    
    Returns:
    
    the ion subtype as integer
  - getSubTypeAsString
```
public abstract String getSubTypeAsString()
```
    Returns the subtype as string.
    
    Returns:
    
    the subtype as string
  - getPossibleSubtypes
```
public static ArrayList<Integer> getPossibleSubtypes(Ion.IonType ionType)
```
    Returns an arraylist of possible subtypes.
    
    Parameters:
    
    ionType - an arraylist of possible subtypes
    
    Returns:
    
    an arraylist of possible subtypes
  - getNeutralLosses
```
public abstract ArrayList<NeutralLoss> getNeutralLosses()
```
    Returns the possible neutral losses of this ion type. An empty list if none.
    
    Returns:
    
    the possible neutral losses of this ion type
  - hasNeutralLosses
```
public boolean hasNeutralLosses()
```
    Indicates whether the ion has a neutral loss.
    
    Returns:
    
    a boolean indicating whether the ion has a neutral loss
  - isSameAs
```
public abstract boolean isSameAs(Ion anotherIon)
```
    Returns a boolean indicating whether the ion is the same as another ion.
    
    Parameters:
    
    anotherIon - the other ion
    
    Returns:
    
    a boolean indicating whether the ion is the same as another ion
  - getNeutralLossesAsString
```
public String getNeutralLossesAsString()
```
    Returns the neutral loss (if any), the empty string if no loss.
    
    Returns:
    
    the neutral loss
  - getNeutralLossesAsString
```
public static String getNeutralLossesAsString(ArrayList<NeutralLoss> neutralLosses)
```
    Returns the neutral loss (if any), the empty string if no loss.
    
    Parameters:
    
    neutralLosses - the neutral loss (if any)
    
    Returns:
    
    the neutral loss
  - getTheoreticMass
```
public Double getTheoreticMass()
```
    Returns the theoretic mass, from the atomic composition if available, from the theoreticMass field otherwise.
    
    Returns:
    
    the theoretic mass
  - getAtomicComposition
```
public AtomChain getAtomicComposition()
```
    Returns the atomic composition.
    
    Returns:
    
    the atomic composition
  - setAtomicComposition
```
public void setAtomicComposition(AtomChain atomChain)
```
    Returns the atomic composition.
    
    Parameters:
    
    atomChain - the atomic composition
  - getTheoreticMz
```
public double getTheoreticMz(int chargeValue)
```
    Returns the theoretic m/z of an ion at a given charge state.
    
    Parameters:
    
    chargeValue - the value of the carried charge
    
    Returns:
    
    the theoretic m/z.
  - setTheoreticMass
```
public void setTheoreticMass(double theoreticMass)
```
    Sets a new theoretic mass.
    
    Parameters:
    
    theoreticMass - a new theoretic mass
  - getType
```
public Ion.IonType getType()
```
    Returns the ion type.
    
    Returns:
    
    the ion type
  - getImplementedIonTypes
```
public static ArrayList<Ion.IonType> getImplementedIonTypes()
```
    Returns the implemented ion types.
    
    Returns:
    
    the implemented ion types
  - getTypeAsString
```
public String getTypeAsString()
```
    Returns the type of ion as string.
    
    Returns:
    
    the type of ion as string
  - getTypeAsString
```
public static String getTypeAsString(Ion.IonType type)
```
    Returns the type of ion as string.
    
    Parameters:
    
    type - the type of ion as string
    
    Returns:
    
    the type of ion as string
  - getGenericIon
```
public static Ion getGenericIon(Ion.IonType ionType,
                                int subType,
                                ArrayList<NeutralLoss> neutralLosses)
```
    Convenience method returning a generic ion based on the given ion type.
    
    Parameters:
    
    ionType - the ion type
    
    subType - the ion subtype
    
    neutralLosses - the neutral losses. Null list if none.
    
    Returns:
    
    a generic ion
  - getGenericIon
```
public static Ion getGenericIon(Ion.IonType ionType,
                                int subType)
```
    Convenience method returning a generic ion based on the given ion type without neutral losses.
    
    Parameters:
    
    ionType - the ion type
    
    subType - the ion subtype
    
    Returns:
    
    a generic ion

Class Ion

Nested Class Summary

Field Summary

Constructor Summary

Method Summary

Methods inherited from class com.compomics.util.experiment.personalization.ExperimentObject

Methods inherited from class java.lang.Object

Field Detail

type

theoreticMass

atomChain

Constructor Detail

Ion

Method Detail

getName

getPrideCvTerm

getSubType

getSubTypeAsString

getPossibleSubtypes

getNeutralLosses

hasNeutralLosses

isSameAs

getNeutralLossesAsString

getNeutralLossesAsString

getTheoreticMass

getAtomicComposition

setAtomicComposition

getTheoreticMz

setTheoreticMass

getType

getImplementedIonTypes

getTypeAsString

getTypeAsString

getGenericIon

getGenericIon