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

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.SpectrumIdentificationProtocol
All Implemented Interfaces:
Serializable, ParamCapable, ParamListCapable

public class SpectrumIdentificationProtocol
extends Identifiable
implements Serializable, ParamListCapable, ParamCapable

The parameters and settings of a SpectrumIdentification analysis.

Java class for SpectrumIdentificationProtocolType complex type.

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

 <complexType name="SpectrumIdentificationProtocolType">
   <complexContent>
     <extension base="{http://psidev.info/psi/pi/mzIdentML/1.1}IdentifiableType">
       <sequence>
         <element name="SearchType" type="{http://psidev.info/psi/pi/mzIdentML/1.1}ParamType"/>
         <element name="AdditionalSearchParams" type="{http://psidev.info/psi/pi/mzIdentML/1.1}ParamListType" minOccurs="0"/>
         <element name="ModificationParams" type="{http://psidev.info/psi/pi/mzIdentML/1.1}ModificationParamsType" minOccurs="0"/>
         <element name="Enzymes" type="{http://psidev.info/psi/pi/mzIdentML/1.1}EnzymesType" minOccurs="0"/>
         <element name="MassTable" type="{http://psidev.info/psi/pi/mzIdentML/1.1}MassTableType" maxOccurs="unbounded" minOccurs="0"/>
         <element name="FragmentTolerance" type="{http://psidev.info/psi/pi/mzIdentML/1.1}ToleranceType" minOccurs="0"/>
         <element name="ParentTolerance" type="{http://psidev.info/psi/pi/mzIdentML/1.1}ToleranceType" minOccurs="0"/>
         <element name="Threshold" type="{http://psidev.info/psi/pi/mzIdentML/1.1}ParamListType"/>
         <element name="DatabaseFilters" type="{http://psidev.info/psi/pi/mzIdentML/1.1}DatabaseFiltersType" minOccurs="0"/>
         <element name="DatabaseTranslation" type="{http://psidev.info/psi/pi/mzIdentML/1.1}DatabaseTranslationType" minOccurs="0"/>
       </sequence>
       <attribute name="analysisSoftware_ref" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
     </extension>
   </complexContent>
 </complexType>
 

See Also:
Serialized Form

Field Summary
protected  ParamList additionalSearchParams
           
protected  AnalysisSoftware analysisSoftware
           
protected  String analysisSoftwareRef
           
protected  DatabaseFilters databaseFilters
           
protected  DatabaseTranslation databaseTranslation
           
protected  Enzymes enzymes
           
protected  Tolerance fragmentTolerance
           
protected  List<MassTable> massTable
           
protected  ModificationParams modificationParams
           
protected  Tolerance parentTolerance
           
protected  Param searchType
           
protected  ParamList threshold
           
 
Fields inherited from class uk.ac.ebi.jmzidml.model.mzidml.Identifiable
id, name
 
Constructor Summary
SpectrumIdentificationProtocol()
           
 
Method Summary
 ParamList getAdditionalSearchParams()
          Gets the value of the additionalSearchParams property.
 AnalysisSoftware getAnalysisSoftware()
           
 String getAnalysisSoftwareRef()
          Gets the value of the analysisSoftwareRef property.
 DatabaseFilters getDatabaseFilters()
          Gets the value of the databaseFilters property.
 DatabaseTranslation getDatabaseTranslation()
          Gets the value of the databaseTranslation property.
 Enzymes getEnzymes()
          Gets the value of the enzymes property.
 Tolerance getFragmentTolerance()
          Gets the value of the fragmentTolerance property.
 List<MassTable> getMassTable()
          Gets the value of the massTable property.
 ModificationParams getModificationParams()
          Gets the value of the modificationParams property.
 Tolerance getParentTolerance()
          Gets the value of the parentTolerance property.
 Param getSearchType()
          Gets the value of the searchType property.
 ParamList getThreshold()
          Gets the value of the threshold property.
 void setAdditionalSearchParams(ParamList value)
          Sets the value of the additionalSearchParams property.
 void setAnalysisSoftware(AnalysisSoftware analysisSoftware)
           
 void setDatabaseFilters(DatabaseFilters value)
          Sets the value of the databaseFilters property.
 void setDatabaseTranslation(DatabaseTranslation value)
          Sets the value of the databaseTranslation property.
 void setEnzymes(Enzymes value)
          Sets the value of the enzymes property.
 void setFragmentTolerance(Tolerance value)
          Sets the value of the fragmentTolerance property.
 void setModificationParams(ModificationParams value)
          Sets the value of the modificationParams property.
 void setParentTolerance(Tolerance value)
          Sets the value of the parentTolerance property.
 void setSearchType(Param value)
          Sets the value of the searchType property.
 void setThreshold(ParamList value)
          Sets the value of the threshold 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

searchType

protected Param searchType

additionalSearchParams

protected ParamList additionalSearchParams

modificationParams

protected ModificationParams modificationParams

enzymes

protected Enzymes enzymes

massTable

protected List<MassTable> massTable

fragmentTolerance

protected Tolerance fragmentTolerance

parentTolerance

protected Tolerance parentTolerance

threshold

protected ParamList threshold

databaseFilters

protected DatabaseFilters databaseFilters

databaseTranslation

protected DatabaseTranslation databaseTranslation

analysisSoftwareRef

protected String analysisSoftwareRef

analysisSoftware

protected AnalysisSoftware analysisSoftware
Constructor Detail

SpectrumIdentificationProtocol

public SpectrumIdentificationProtocol()
Method Detail

getAnalysisSoftware

public AnalysisSoftware getAnalysisSoftware()

setAnalysisSoftware

public void setAnalysisSoftware(AnalysisSoftware analysisSoftware)

getSearchType

public Param getSearchType()
Gets the value of the searchType property.

Returns:
possible object is Param

setSearchType

public void setSearchType(Param value)
Sets the value of the searchType property.

Parameters:
value - allowed object is Param

getAdditionalSearchParams

public ParamList getAdditionalSearchParams()
Gets the value of the additionalSearchParams property.

Returns:
possible object is ParamList

setAdditionalSearchParams

public void setAdditionalSearchParams(ParamList value)
Sets the value of the additionalSearchParams property.

Parameters:
value - allowed object is ParamList

getModificationParams

public ModificationParams getModificationParams()
Gets the value of the modificationParams property.

Returns:
possible object is ModificationParams

setModificationParams

public void setModificationParams(ModificationParams value)
Sets the value of the modificationParams property.

Parameters:
value - allowed object is ModificationParams

getEnzymes

public Enzymes getEnzymes()
Gets the value of the enzymes property.

Returns:
possible object is Enzymes

setEnzymes

public void setEnzymes(Enzymes value)
Sets the value of the enzymes property.

Parameters:
value - allowed object is Enzymes

getMassTable

public List<MassTable> getMassTable()
Gets the value of the massTable 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 massTable property.

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

    getMassTable().add(newItem);
 

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


getFragmentTolerance

public Tolerance getFragmentTolerance()
Gets the value of the fragmentTolerance property.

Returns:
possible object is Tolerance

setFragmentTolerance

public void setFragmentTolerance(Tolerance value)
Sets the value of the fragmentTolerance property.

Parameters:
value - allowed object is Tolerance

getParentTolerance

public Tolerance getParentTolerance()
Gets the value of the parentTolerance property.

Returns:
possible object is Tolerance

setParentTolerance

public void setParentTolerance(Tolerance value)
Sets the value of the parentTolerance property.

Parameters:
value - allowed object is Tolerance

getThreshold

public ParamList getThreshold()
Gets the value of the threshold property.

Returns:
possible object is ParamList

setThreshold

public void setThreshold(ParamList value)
Sets the value of the threshold property.

Parameters:
value - allowed object is ParamList

getDatabaseFilters

public DatabaseFilters getDatabaseFilters()
Gets the value of the databaseFilters property.

Returns:
possible object is DatabaseFilters

setDatabaseFilters

public void setDatabaseFilters(DatabaseFilters value)
Sets the value of the databaseFilters property.

Parameters:
value - allowed object is DatabaseFilters

getDatabaseTranslation

public DatabaseTranslation getDatabaseTranslation()
Gets the value of the databaseTranslation property.

Returns:
possible object is DatabaseTranslation

setDatabaseTranslation

public void setDatabaseTranslation(DatabaseTranslation value)
Sets the value of the databaseTranslation property.

Parameters:
value - allowed object is DatabaseTranslation

getAnalysisSoftwareRef

public String getAnalysisSoftwareRef()
Gets the value of the analysisSoftwareRef property.

Returns:
possible object is String


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