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java.lang.Objectcom.compomics.util.experiment.personalization.ExperimentObject
com.compomics.util.experiment.biology.Peptide
public class Peptide
This class models a peptide.
Created by IntelliJ IDEA. User: Marc Date: Jun 18, 2010 Time: 8:56:40 AM
Constructor Summary | |
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Peptide()
Constructor for the peptide |
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Peptide(String aSequence,
Double mass,
ArrayList<Protein> parentProteins,
ArrayList<ModificationMatch> modifications)
Constructor for the peptide |
Method Summary | |
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void |
addFragmentIon(PeptideFragmentIon fragment)
method to add a fragmentIon |
void |
addModificationMatch(ModificationMatch modificationMatch)
Adds a modification match |
void |
clearModificationMAtches()
Clears the list of imported modification matches |
Iterator<PeptideFragmentIon> |
fragmentIterator()
Method which returns an iterator on the fragment ions |
String |
getKey()
Returns the index of a peptide. index = SEQUENCE_mod1_mod2 with modifications ordered alphabetically. |
Double |
getMass()
getter for the mass |
ArrayList<ModificationMatch> |
getModificationMatches()
getter for the modifications carried by this peptide |
int |
getNMissedCleavages()
This methods evaluates the number of missed cleavages |
ArrayList<Protein> |
getParentProteins()
Getter for the parent proteins |
String |
getSequence()
getter for the sequence |
boolean |
isSameAs(Peptide anOtherPeptide)
a method which compares to peptides. |
void |
setParentProteins(ArrayList<Protein> parentProteins)
Sets the parent proteins |
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, toString, wait, wait, wait |
Constructor Detail |
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public Peptide()
public Peptide(String aSequence, Double mass, ArrayList<Protein> parentProteins, ArrayList<ModificationMatch> modifications)
aSequence
- The peptide sequencemass
- The peptide massparentProteins
- The parent proteinsmodifications
- The PTM of this peptideMethod Detail |
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public Double getMass()
public ArrayList<ModificationMatch> getModificationMatches()
public void clearModificationMAtches()
public void addModificationMatch(ModificationMatch modificationMatch)
modificationMatch
- the modification match to addpublic String getSequence()
public void addFragmentIon(PeptideFragmentIon fragment)
fragment
- a fragment ion of this peptidepublic Iterator<PeptideFragmentIon> fragmentIterator()
public ArrayList<Protein> getParentProteins()
public void setParentProteins(ArrayList<Protein> parentProteins)
parentProteins
- the parent proteins as listpublic int getNMissedCleavages()
public String getKey()
public boolean isSameAs(Peptide anOtherPeptide)
anOtherPeptide
- an other peptide
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