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

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.ProteinDetection
All Implemented Interfaces:
Serializable

public class ProteinDetection
extends ProtocolApplication
implements Serializable

An Analysis which assembles a set of peptides (e.g. from a spectra search analysis) to proteins. TODO marshalling/ persistor add validation to check for case where someone gets proteinDetectionList/proteinDetectionProtocol and changes its id without updating ref id in ProteinDetection and other such clases. NOTE: There is no setter method for the proteinDetectionListRef/proteinDetectionProtocolRef. This simplifies keeping the proteinDetectionList/proteinDetectionProtocol object reference and proteinDetectionListRef/proteinDetectionProtocolRef synchronized.

Java class for ProteinDetectionType complex type.

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

 <complexType name="ProteinDetectionType">
   <complexContent>
     <extension base="{http://psidev.info/psi/pi/mzIdentML/1.1}ProtocolApplicationType">
       <sequence>
         <element name="InputSpectrumIdentifications" type="{http://psidev.info/psi/pi/mzIdentML/1.1}InputSpectrumIdentificationsType" maxOccurs="unbounded"/>
       </sequence>
       <attribute name="proteinDetectionList_ref" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
       <attribute name="proteinDetectionProtocol_ref" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
     </extension>
   </complexContent>
 </complexType>
 

See Also:
Serialized Form

Field Summary
protected  List<InputSpectrumIdentifications> inputSpectrumIdentifications
           
protected  ProteinDetectionList proteinDetectionList
           
protected  String proteinDetectionListRef
           
protected  ProteinDetectionProtocol proteinDetectionProtocol
           
protected  String proteinDetectionProtocolRef
           
 
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
ProteinDetection()
           
 
Method Summary
 List<InputSpectrumIdentifications> getInputSpectrumIdentifications()
          Gets the value of the inputSpectrumIdentifications property.
 ProteinDetectionList getProteinDetectionList()
           
 String getProteinDetectionListRef()
          Gets the value of the proteinDetectionListRef property.
 ProteinDetectionProtocol getProteinDetectionProtocol()
           
 String getProteinDetectionProtocolRef()
          Gets the value of the proteinDetectionProtocolRef property.
 void setProteinDetectionList(ProteinDetectionList proteinDetectionList)
           
 void setProteinDetectionProtocol(ProteinDetectionProtocol proteinDetectionProtocol)
           
 
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

inputSpectrumIdentifications

protected List<InputSpectrumIdentifications> inputSpectrumIdentifications

proteinDetectionListRef

protected String proteinDetectionListRef

proteinDetectionProtocolRef

protected String proteinDetectionProtocolRef

proteinDetectionList

protected ProteinDetectionList proteinDetectionList

proteinDetectionProtocol

protected ProteinDetectionProtocol proteinDetectionProtocol
Constructor Detail

ProteinDetection

public ProteinDetection()
Method Detail

getProteinDetectionList

public ProteinDetectionList getProteinDetectionList()

setProteinDetectionList

public void setProteinDetectionList(ProteinDetectionList proteinDetectionList)

getProteinDetectionProtocol

public ProteinDetectionProtocol getProteinDetectionProtocol()

setProteinDetectionProtocol

public void setProteinDetectionProtocol(ProteinDetectionProtocol proteinDetectionProtocol)

getInputSpectrumIdentifications

public List<InputSpectrumIdentifications> getInputSpectrumIdentifications()
Gets the value of the inputSpectrumIdentifications 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 inputSpectrumIdentifications property.

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

    getInputSpectrumIdentifications().add(newItem);
 

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


getProteinDetectionListRef

public String getProteinDetectionListRef()
Gets the value of the proteinDetectionListRef property.

Returns:
possible object is String

getProteinDetectionProtocolRef

public String getProteinDetectionProtocolRef()
Gets the value of the proteinDetectionProtocolRef property.

Returns:
possible object is String


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