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

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.ProtocolApplication
              extended by uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentification
All Implemented Interfaces:
Serializable

public class SpectrumIdentification
extends ProtocolApplication
implements Serializable

An Analysis which tries to identify peptides in input spectra, referencing the database searched, the input spectra, the output results and the protocol that is run. TODO marshalling/ persistor add validation to check for case where someone gets spectrumIdentificationList/spectrumIdentificationProtocol and changes its id without updating ref id in SpectrumIdentification and other such clases.

NOTE: There is no setter method for the spectrumIdentificationListRef/spectrumIdentificationProtocolRef. This simplifies keeping the spectrumIdentificationList/spectrumIdentificationProtocol object reference and spectrumIdentificationListRef/spectrumIdentificationProtocolRef synchronized.

Java class for SpectrumIdentificationType complex type.

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

 <complexType name="SpectrumIdentificationType">
   <complexContent>
     <extension base="{http://psidev.info/psi/pi/mzIdentML/1.1}ProtocolApplicationType">
       <sequence>
         <element name="InputSpectra" type="{http://psidev.info/psi/pi/mzIdentML/1.1}InputSpectraType" maxOccurs="unbounded"/>
         <element name="SearchDatabaseRef" type="{http://psidev.info/psi/pi/mzIdentML/1.1}SearchDatabaseRefType" maxOccurs="unbounded"/>
       </sequence>
       <attribute name="spectrumIdentificationProtocol_ref" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
       <attribute name="spectrumIdentificationList_ref" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
     </extension>
   </complexContent>
 </complexType>
 

See Also:
Serialized Form

Field Summary
protected  List<InputSpectra> inputSpectra
           
protected  List<SearchDatabaseRef> searchDatabaseRef
           
protected  SpectrumIdentificationList spectrumIdentificationList
           
protected  String spectrumIdentificationListRef
           
protected  SpectrumIdentificationProtocol spectrumIdentificationProtocol
           
protected  String spectrumIdentificationProtocolRef
           
 
Fields inherited from class uk.ac.ebi.jmzidml.model.mzidml.ProtocolApplication
activityDate
 
Fields inherited from class uk.ac.ebi.jmzidml.model.mzidml.Identifiable
id, name
 
Constructor Summary
SpectrumIdentification()
           
 
Method Summary
 List<InputSpectra> getInputSpectra()
          Gets the value of the inputSpectra property.
 List<SearchDatabaseRef> getSearchDatabaseRef()
          Gets the value of the searchDatabaseRef property.
 SpectrumIdentificationList getSpectrumIdentificationList()
           
 String getSpectrumIdentificationListRef()
          Gets the value of the spectrumIdentificationListRef property.
 SpectrumIdentificationProtocol getSpectrumIdentificationProtocol()
           
 String getSpectrumIdentificationProtocolRef()
          Gets the value of the spectrumIdentificationProtocolRef property.
 void setSpectrumIdentificationList(SpectrumIdentificationList spectrumIdentificationList)
           
 void setSpectrumIdentificationProtocol(SpectrumIdentificationProtocol spectrumIdentificationProtocol)
           
 
Methods inherited from class uk.ac.ebi.jmzidml.model.mzidml.ProtocolApplication
getActivityDate, setActivityDate
 
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

inputSpectra

protected List<InputSpectra> inputSpectra

searchDatabaseRef

protected List<SearchDatabaseRef> searchDatabaseRef

spectrumIdentificationProtocolRef

protected String spectrumIdentificationProtocolRef

spectrumIdentificationListRef

protected String spectrumIdentificationListRef

spectrumIdentificationList

protected SpectrumIdentificationList spectrumIdentificationList

spectrumIdentificationProtocol

protected SpectrumIdentificationProtocol spectrumIdentificationProtocol
Constructor Detail

SpectrumIdentification

public SpectrumIdentification()
Method Detail

getSpectrumIdentificationProtocol

public SpectrumIdentificationProtocol getSpectrumIdentificationProtocol()

setSpectrumIdentificationProtocol

public void setSpectrumIdentificationProtocol(SpectrumIdentificationProtocol spectrumIdentificationProtocol)

getSpectrumIdentificationList

public SpectrumIdentificationList getSpectrumIdentificationList()

setSpectrumIdentificationList

public void setSpectrumIdentificationList(SpectrumIdentificationList spectrumIdentificationList)

getInputSpectra

public List<InputSpectra> getInputSpectra()
Gets the value of the inputSpectra 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 inputSpectra property.

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

    getInputSpectra().add(newItem);
 

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


getSearchDatabaseRef

public List<SearchDatabaseRef> getSearchDatabaseRef()
Gets the value of the searchDatabaseRef 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 searchDatabaseRef property.

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

    getSearchDatabaseRef().add(newItem);
 

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


getSpectrumIdentificationProtocolRef

public String getSpectrumIdentificationProtocolRef()
Gets the value of the spectrumIdentificationProtocolRef property.

Returns:
possible object is String

getSpectrumIdentificationListRef

public String getSpectrumIdentificationListRef()
Gets the value of the spectrumIdentificationListRef property.

Returns:
possible object is String


Copyright © 2012. All Rights Reserved.