com.compomics.util.experiment.biology.ions
Class PeptideFragmentIon

java.lang.Object
  extended by com.compomics.util.experiment.personalization.ExperimentObject
      extended by com.compomics.util.experiment.biology.Ion
          extended by com.compomics.util.experiment.biology.ions.PeptideFragmentIon
All Implemented Interfaces:
Serializable, Cloneable

public class PeptideFragmentIon
extends Ion

This class models a peptide fragment ion. Created by IntelliJ IDEA. User: Marc Date: Jun 18, 2010 Time: 8:58:02 AM

See Also:
Serialized Form

Nested Class Summary
static class PeptideFragmentIon.PeptideFragmentIonType
          An enumerator of the supported fragment ion types.
 
Field Summary
 
Fields inherited from class com.compomics.util.experiment.biology.Ion
ELEMENTARY_ION, familyType, GLYCON_FRAGMENT, PEPTIDE_FRAGMENT, REPORTER_ION, theoreticMass
 
Constructor Summary
PeptideFragmentIon(PeptideFragmentIon.PeptideFragmentIonType type, double mass)
          Construction for a peptide fragment.
PeptideFragmentIon(PeptideFragmentIon.PeptideFragmentIonType type, int number, double mass)
          Construction for a peptide fragment.
PeptideFragmentIon(PeptideFragmentIon.PeptideFragmentIonType type, int number, double mass, ArrayList<NeutralLoss> neutralLosses)
          Construction for a peptide fragment with neutral loss.
PeptideFragmentIon(PeptideFragmentIon.PeptideFragmentIonType type, String residue, double mass)
          Construction for a peptide fragment.
 
Method Summary
 String getIonType()
          Returns the ion type (a, b, c, x, y, z) as a string.
 String getNeutralLoss()
          Returns the neutral loss (if any), the empty string if no loss.
 ArrayList<NeutralLoss> getNeutralLosses()
          Returns the neutral losses for this fragment ion
 int getNumber()
          Returns the number of the fragment in the sequence
 PeptideFragmentIon.PeptideFragmentIonType getType()
          Getter for the ion type
 String toString()
           
 
Methods inherited from class com.compomics.util.experiment.biology.Ion
getIonFamilyType, proton
 
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, wait, wait, wait
 

Constructor Detail

PeptideFragmentIon

public PeptideFragmentIon(PeptideFragmentIon.PeptideFragmentIonType type,
                          double mass)
Construction for a peptide fragment.

Parameters:
type - the type of ion according to static fields
mass - the ion mass

PeptideFragmentIon

public PeptideFragmentIon(PeptideFragmentIon.PeptideFragmentIonType type,
                          int number,
                          double mass,
                          ArrayList<NeutralLoss> neutralLosses)
Construction for a peptide fragment with neutral loss.

Parameters:
type - the type of ion according to static fields
mass - the ion mass (accounting for neutral losses)
number - the ion number
neutralLosses - List of neutral losses detected

PeptideFragmentIon

public PeptideFragmentIon(PeptideFragmentIon.PeptideFragmentIonType type,
                          int number,
                          double mass)
Construction for a peptide fragment.

Parameters:
type - the type of ion according to static fields
number - the ion number
mass - the ion mass

PeptideFragmentIon

public PeptideFragmentIon(PeptideFragmentIon.PeptideFragmentIonType type,
                          String residue,
                          double mass)
Construction for a peptide fragment.

Parameters:
type - the type of ion according to static fields
number - the ion number
mass - the ion mass
Method Detail

getType

public PeptideFragmentIon.PeptideFragmentIonType getType()
Getter for the ion type

Returns:
the ion type

getNumber

public int getNumber()
Returns the number of the fragment in the sequence

Returns:
the number of the fragment in the sequence

getIonType

public String getIonType()
Returns the ion type (a, b, c, x, y, z) as a string.

Returns:
the ion type as a string.

getNeutralLoss

public String getNeutralLoss()
Returns the neutral loss (if any), the empty string if no loss.

Returns:
the neutral loss

getNeutralLosses

public ArrayList<NeutralLoss> getNeutralLosses()
Returns the neutral losses for this fragment ion

Returns:
a list of neutral losses

toString

public String toString()
Overrides:
toString in class Object


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