uk.ac.ebi.jmzidml.model.mzidml
Class Peptide

java.lang.Object
  extended by uk.ac.ebi.jmzidml.model.MzIdentMLObject
      extended by uk.ac.ebi.jmzidml.model.mzidml.Identifiable
          extended by uk.ac.ebi.jmzidml.model.mzidml.Peptide
All Implemented Interfaces:
Serializable, CvParamListCapable, ParamGroupCapable

public class Peptide
extends Identifiable
implements Serializable, ParamGroupCapable

One (poly)peptide (a sequence with modifications). The combination of Peptide sequence and modifications must be unique in the file.

Java class for PeptideType complex type.

The following schema fragment specifies the expected content contained within this class.

 <complexType name="PeptideType">
   <complexContent>
     <extension base="{http://psidev.info/psi/pi/mzIdentML/1.1}IdentifiableType">
       <sequence>
         <element name="PeptideSequence" type="{http://psidev.info/psi/pi/mzIdentML/1.1}sequence"/>
         <element name="Modification" type="{http://psidev.info/psi/pi/mzIdentML/1.1}ModificationType" maxOccurs="unbounded" minOccurs="0"/>
         <element name="SubstitutionModification" type="{http://psidev.info/psi/pi/mzIdentML/1.1}SubstitutionModificationType" maxOccurs="unbounded" minOccurs="0"/>
         <group ref="{http://psidev.info/psi/pi/mzIdentML/1.1}ParamGroup" maxOccurs="unbounded" minOccurs="0"/>
       </sequence>
     </extension>
   </complexContent>
 </complexType>
 

See Also:
Serialized Form

Field Summary
protected  List<Modification> modification
           
protected  List<AbstractParam> paramGroup
           
protected  String peptideSequence
           
protected  List<SubstitutionModification> substitutionModification
           
 
Fields inherited from class uk.ac.ebi.jmzidml.model.mzidml.Identifiable
id, name
 
Constructor Summary
Peptide()
           
 
Method Summary
 List<CvParam> getCvParam()
           
 List<Modification> getModification()
          Gets the value of the modification property.
 List<AbstractParam> getParamGroup()
          Additional descriptors of this peptide sequence Gets the value of the paramGroup property.
 String getPeptideSequence()
          Gets the value of the peptideSequence property.
 List<SubstitutionModification> getSubstitutionModification()
          Gets the value of the substitutionModification property.
 List<UserParam> getUserParam()
           
 void setPeptideSequence(String value)
          Sets the value of the peptideSequence property.
 
Methods inherited from class uk.ac.ebi.jmzidml.model.mzidml.Identifiable
getId, getName, setId, setName
 
Methods inherited from class uk.ac.ebi.jmzidml.model.MzIdentMLObject
getHid
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

peptideSequence

protected String peptideSequence

modification

protected List<Modification> modification

substitutionModification

protected List<SubstitutionModification> substitutionModification

paramGroup

protected List<AbstractParam> paramGroup
Constructor Detail

Peptide

public Peptide()
Method Detail

getPeptideSequence

public String getPeptideSequence()
Gets the value of the peptideSequence property.

Returns:
possible object is String

setPeptideSequence

public void setPeptideSequence(String value)
Sets the value of the peptideSequence property.

Parameters:
value - allowed object is String

getModification

public List<Modification> getModification()
Gets the value of the modification property.

This accessor method returns a reference to the live list, not a snapshot. Therefore any modification you make to the returned list will be present inside the JAXB object. This is why there is not a set method for the modification property.

For example, to add a new item, do as follows:

    getModification().add(newItem);
 

Objects of the following type(s) are allowed in the list Modification


getSubstitutionModification

public List<SubstitutionModification> getSubstitutionModification()
Gets the value of the substitutionModification property.

This accessor method returns a reference to the live list, not a snapshot. Therefore any modification you make to the returned list will be present inside the JAXB object. This is why there is not a set method for the substitutionModification property.

For example, to add a new item, do as follows:

    getSubstitutionModification().add(newItem);
 

Objects of the following type(s) are allowed in the list SubstitutionModification


getParamGroup

public List<AbstractParam> getParamGroup()
Additional descriptors of this peptide sequence Gets the value of the paramGroup property.

This accessor method returns a reference to the live list, not a snapshot. Therefore any modification you make to the returned list will be present inside the JAXB object. This is why there is not a set method for the paramGroup property.

For example, to add a new item, do as follows:

    getParamGroup().add(newItem);
 

Objects of the following type(s) are allowed in the list CvParam UserParam


getCvParam

public List<CvParam> getCvParam()
Specified by:
getCvParam in interface CvParamListCapable
Specified by:
getCvParam in interface ParamGroupCapable
Returns:
A List of CvParam objects.

getUserParam

public List<UserParam> getUserParam()
Specified by:
getUserParam in interface ParamGroupCapable


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