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java.lang.Objectcom.compomics.util.experiment.personalization.ExperimentObject
com.compomics.util.experiment.biology.Ion
com.compomics.util.experiment.biology.ions.PeptideFragmentIon
public class PeptideFragmentIon
This class models a peptide fragment ion. Created by IntelliJ IDEA. User: Marc Date: Jun 18, 2010 Time: 8:58:02 AM
Nested Class Summary | |
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static class |
PeptideFragmentIon.PeptideFragmentIonType
An enumerator of the supported fragment ion types. |
Field Summary |
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Fields inherited from class com.compomics.util.experiment.biology.Ion |
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ELEMENTARY_ION, familyType, GLYCON_FRAGMENT, PEPTIDE_FRAGMENT, REPORTER_ION, theoreticMass |
Constructor Summary | |
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PeptideFragmentIon(PeptideFragmentIon.PeptideFragmentIonType type,
double mass)
Construction for a peptide fragment. |
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PeptideFragmentIon(PeptideFragmentIon.PeptideFragmentIonType type,
int number,
double mass)
Construction for a peptide fragment. |
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PeptideFragmentIon(PeptideFragmentIon.PeptideFragmentIonType type,
int number,
double mass,
ArrayList<NeutralLoss> neutralLosses)
Construction for a peptide fragment with neutral loss. |
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PeptideFragmentIon(PeptideFragmentIon.PeptideFragmentIonType type,
String residue,
double mass)
Construction for a peptide fragment. |
Method Summary | |
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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()
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Methods inherited from class com.compomics.util.experiment.biology.Ion |
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getIonFamilyType, proton |
Methods inherited from class com.compomics.util.experiment.personalization.ExperimentObject |
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addUrParam, getUrParam |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Constructor Detail |
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public PeptideFragmentIon(PeptideFragmentIon.PeptideFragmentIonType type, double mass)
type
- the type of ion according to static fieldsmass
- the ion masspublic PeptideFragmentIon(PeptideFragmentIon.PeptideFragmentIonType type, int number, double mass, ArrayList<NeutralLoss> neutralLosses)
type
- the type of ion according to static fieldsmass
- the ion mass (accounting for neutral losses)number
- the ion numberneutralLosses
- List of neutral losses detectedpublic PeptideFragmentIon(PeptideFragmentIon.PeptideFragmentIonType type, int number, double mass)
type
- the type of ion according to static fieldsnumber
- the ion numbermass
- the ion masspublic PeptideFragmentIon(PeptideFragmentIon.PeptideFragmentIonType type, String residue, double mass)
type
- the type of ion according to static fieldsnumber
- the ion numbermass
- the ion massMethod Detail |
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public PeptideFragmentIon.PeptideFragmentIonType getType()
public int getNumber()
public String getIonType()
public String getNeutralLoss()
public ArrayList<NeutralLoss> getNeutralLosses()
public String toString()
toString
in class Object
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