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

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.MzIdentML
All Implemented Interfaces:
Serializable

public class MzIdentML
extends Identifiable
implements Serializable

The upper-most hierarchy level of mzIdentML with sub-containers for example describing software, protocols and search results (spectrum identifications or protein detection results).

Java class for MzIdentMLType complex type.

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

 <complexType name="MzIdentMLType">
   <complexContent>
     <extension base="{http://psidev.info/psi/pi/mzIdentML/1.1}IdentifiableType">
       <sequence>
         <element name="cvList" type="{http://psidev.info/psi/pi/mzIdentML/1.1}CVListType"/>
         <element name="AnalysisSoftwareList" type="{http://psidev.info/psi/pi/mzIdentML/1.1}AnalysisSoftwareListType" minOccurs="0"/>
         <element name="Provider" type="{http://psidev.info/psi/pi/mzIdentML/1.1}ProviderType" minOccurs="0"/>
         <element name="AuditCollection" type="{http://psidev.info/psi/pi/mzIdentML/1.1}AuditCollectionType" minOccurs="0"/>
         <element name="AnalysisSampleCollection" type="{http://psidev.info/psi/pi/mzIdentML/1.1}AnalysisSampleCollectionType" minOccurs="0"/>
         <element name="SequenceCollection" type="{http://psidev.info/psi/pi/mzIdentML/1.1}SequenceCollectionType" minOccurs="0"/>
         <element name="AnalysisCollection" type="{http://psidev.info/psi/pi/mzIdentML/1.1}AnalysisCollectionType"/>
         <element name="AnalysisProtocolCollection" type="{http://psidev.info/psi/pi/mzIdentML/1.1}AnalysisProtocolCollectionType"/>
         <element name="DataCollection" type="{http://psidev.info/psi/pi/mzIdentML/1.1}DataCollectionType"/>
         <element name="BibliographicReference" type="{http://psidev.info/psi/pi/mzIdentML/1.1}BibliographicReferenceType" maxOccurs="unbounded" minOccurs="0"/>
       </sequence>
       <attribute name="creationDate" type="{http://www.w3.org/2001/XMLSchema}dateTime" />
       <attribute name="version" use="required" type="{http://psidev.info/psi/pi/mzIdentML/1.1}versionRegex" />
     </extension>
   </complexContent>
 </complexType>
 

See Also:
Serialized Form

Field Summary
protected  AnalysisCollection analysisCollection
           
protected  AnalysisProtocolCollection analysisProtocolCollection
           
protected  AnalysisSampleCollection analysisSampleCollection
           
protected  AnalysisSoftwareList analysisSoftwareList
           
protected  AuditCollection auditCollection
           
protected  List<BibliographicReference> bibliographicReference
           
protected  Calendar creationDate
           
protected  CvList cvList
           
protected  DataCollection dataCollection
           
protected  Provider provider
           
protected  SequenceCollection sequenceCollection
           
protected  String version
           
 
Fields inherited from class uk.ac.ebi.jmzidml.model.mzidml.Identifiable
id, name
 
Constructor Summary
MzIdentML()
           
 
Method Summary
 AnalysisCollection getAnalysisCollection()
          Gets the value of the analysisCollection property.
 AnalysisProtocolCollection getAnalysisProtocolCollection()
          Gets the value of the analysisProtocolCollection property.
 AnalysisSampleCollection getAnalysisSampleCollection()
          Gets the value of the analysisSampleCollection property.
 AnalysisSoftwareList getAnalysisSoftwareList()
          Gets the value of the analysisSoftwareList property.
 AuditCollection getAuditCollection()
          Gets the value of the auditCollection property.
 List<BibliographicReference> getBibliographicReference()
          Gets the value of the bibliographicReference property.
 Calendar getCreationDate()
          Gets the value of the creationDate property.
 CvList getCvList()
          Gets the value of the cvList property.
 DataCollection getDataCollection()
          Gets the value of the dataCollection property.
 Provider getProvider()
          Gets the value of the provider property.
 SequenceCollection getSequenceCollection()
          Gets the value of the sequenceCollection property.
 String getVersion()
          Gets the value of the version property.
 void setAnalysisCollection(AnalysisCollection value)
          Sets the value of the analysisCollection property.
 void setAnalysisProtocolCollection(AnalysisProtocolCollection value)
          Sets the value of the analysisProtocolCollection property.
 void setAnalysisSampleCollection(AnalysisSampleCollection value)
          Sets the value of the analysisSampleCollection property.
 void setAnalysisSoftwareList(AnalysisSoftwareList value)
          Sets the value of the analysisSoftwareList property.
 void setAuditCollection(AuditCollection value)
          Sets the value of the auditCollection property.
 void setCreationDate(Calendar value)
          Sets the value of the creationDate property.
 void setCvList(CvList value)
          Sets the value of the cvList property.
 void setDataCollection(DataCollection value)
          Sets the value of the dataCollection property.
 void setProvider(Provider value)
          Sets the value of the provider property.
 void setSequenceCollection(SequenceCollection value)
          Sets the value of the sequenceCollection property.
 void setVersion(String value)
          Sets the value of the version 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

cvList

protected CvList cvList

analysisSoftwareList

protected AnalysisSoftwareList analysisSoftwareList

provider

protected Provider provider

auditCollection

protected AuditCollection auditCollection

analysisSampleCollection

protected AnalysisSampleCollection analysisSampleCollection

sequenceCollection

protected SequenceCollection sequenceCollection

analysisCollection

protected AnalysisCollection analysisCollection

analysisProtocolCollection

protected AnalysisProtocolCollection analysisProtocolCollection

dataCollection

protected DataCollection dataCollection

bibliographicReference

protected List<BibliographicReference> bibliographicReference

creationDate

protected Calendar creationDate

version

protected String version
Constructor Detail

MzIdentML

public MzIdentML()
Method Detail

getCvList

public CvList getCvList()
Gets the value of the cvList property.

Returns:
possible object is CvList

setCvList

public void setCvList(CvList value)
Sets the value of the cvList property.

Parameters:
value - allowed object is CvList

getAnalysisSoftwareList

public AnalysisSoftwareList getAnalysisSoftwareList()
Gets the value of the analysisSoftwareList property.

Returns:
possible object is AnalysisSoftwareList

setAnalysisSoftwareList

public void setAnalysisSoftwareList(AnalysisSoftwareList value)
Sets the value of the analysisSoftwareList property.

Parameters:
value - allowed object is AnalysisSoftwareList

getProvider

public Provider getProvider()
Gets the value of the provider property.

Returns:
possible object is Provider

setProvider

public void setProvider(Provider value)
Sets the value of the provider property.

Parameters:
value - allowed object is Provider

getAuditCollection

public AuditCollection getAuditCollection()
Gets the value of the auditCollection property.

Returns:
possible object is AuditCollection

setAuditCollection

public void setAuditCollection(AuditCollection value)
Sets the value of the auditCollection property.

Parameters:
value - allowed object is AuditCollection

getAnalysisSampleCollection

public AnalysisSampleCollection getAnalysisSampleCollection()
Gets the value of the analysisSampleCollection property.

Returns:
possible object is AnalysisSampleCollection

setAnalysisSampleCollection

public void setAnalysisSampleCollection(AnalysisSampleCollection value)
Sets the value of the analysisSampleCollection property.

Parameters:
value - allowed object is AnalysisSampleCollection

getSequenceCollection

public SequenceCollection getSequenceCollection()
Gets the value of the sequenceCollection property.

Returns:
possible object is SequenceCollection

setSequenceCollection

public void setSequenceCollection(SequenceCollection value)
Sets the value of the sequenceCollection property.

Parameters:
value - allowed object is SequenceCollection

getAnalysisCollection

public AnalysisCollection getAnalysisCollection()
Gets the value of the analysisCollection property.

Returns:
possible object is AnalysisCollection

setAnalysisCollection

public void setAnalysisCollection(AnalysisCollection value)
Sets the value of the analysisCollection property.

Parameters:
value - allowed object is AnalysisCollection

getAnalysisProtocolCollection

public AnalysisProtocolCollection getAnalysisProtocolCollection()
Gets the value of the analysisProtocolCollection property.

Returns:
possible object is AnalysisProtocolCollection

setAnalysisProtocolCollection

public void setAnalysisProtocolCollection(AnalysisProtocolCollection value)
Sets the value of the analysisProtocolCollection property.

Parameters:
value - allowed object is AnalysisProtocolCollection

getDataCollection

public DataCollection getDataCollection()
Gets the value of the dataCollection property.

Returns:
possible object is DataCollection

setDataCollection

public void setDataCollection(DataCollection value)
Sets the value of the dataCollection property.

Parameters:
value - allowed object is DataCollection

getBibliographicReference

public List<BibliographicReference> getBibliographicReference()
Gets the value of the bibliographicReference 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 bibliographicReference property.

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

    getBibliographicReference().add(newItem);
 

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


getCreationDate

public Calendar getCreationDate()
Gets the value of the creationDate property.

Returns:
possible object is String

setCreationDate

public void setCreationDate(Calendar value)
Sets the value of the creationDate property.

Parameters:
value - allowed object is String

getVersion

public String getVersion()
Gets the value of the version property.

Returns:
possible object is String

setVersion

public void setVersion(String value)
Sets the value of the version property.

Parameters:
value - allowed object is String


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