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

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.SpectrumIdentificationResult
All Implemented Interfaces:
Serializable, CvParamListCapable, ParamGroupCapable

public class SpectrumIdentificationResult
extends Identifiable
implements Serializable, ParamGroupCapable

All identifications made from searching one spectrum. For PMF data, all peptide identifications will be listed underneath as SpectrumIdentificationItems. For MS/MS data, there will be ranked SpectrumIdentificationItems corresponding to possible different peptide IDs.

Java class for SpectrumIdentificationResultType complex type.

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

 <complexType name="SpectrumIdentificationResultType">
   <complexContent>
     <extension base="{http://psidev.info/psi/pi/mzIdentML/1.1}IdentifiableType">
       <sequence>
         <element name="SpectrumIdentificationItem" type="{http://psidev.info/psi/pi/mzIdentML/1.1}SpectrumIdentificationItemType" maxOccurs="unbounded"/>
         <group ref="{http://psidev.info/psi/pi/mzIdentML/1.1}ParamGroup" maxOccurs="unbounded" minOccurs="0"/>
       </sequence>
       <attribute name="spectrumID" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
       <attribute name="spectraData_ref" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
     </extension>
   </complexContent>
 </complexType>
 

See Also:
Serialized Form

Field Summary
protected  List<AbstractParam> paramGroup
           
protected  SpectraData spectraData
           
protected  String spectraDataRef
           
protected  String spectrumID
           
protected  List<SpectrumIdentificationItem> spectrumIdentificationItem
           
 
Fields inherited from class uk.ac.ebi.jmzidml.model.mzidml.Identifiable
id, name
 
Constructor Summary
SpectrumIdentificationResult()
           
 
Method Summary
 List<CvParam> getCvParam()
          Get the cvparams for spectrumidentificationresult
 List<AbstractParam> getParamGroup()
          Scores or parameters associated with the SpectrumIdentificationResult (i.e the set of SpectrumIdentificationItems derived from one spectrum) e.g.
 SpectraData getSpectraData()
           
 String getSpectraDataRef()
          Gets the value of the spectraDataRef property.
 String getSpectrumID()
          Gets the value of the spectrumID property.
 List<SpectrumIdentificationItem> getSpectrumIdentificationItem()
          Gets the value of the spectrumIdentificationItem property.
 List<UserParam> getUserParam()
          Get the userparams for spectrumidentificationresult
 void setSpectraData(SpectraData spectraData)
           
 void setSpectrumID(String value)
          Sets the value of the spectrumID 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

spectrumIdentificationItem

protected List<SpectrumIdentificationItem> spectrumIdentificationItem

paramGroup

protected List<AbstractParam> paramGroup

spectrumID

protected String spectrumID

spectraDataRef

protected String spectraDataRef

spectraData

protected SpectraData spectraData
Constructor Detail

SpectrumIdentificationResult

public SpectrumIdentificationResult()
Method Detail

getSpectraData

public SpectraData getSpectraData()

setSpectraData

public void setSpectraData(SpectraData spectraData)

getSpectrumIdentificationItem

public List<SpectrumIdentificationItem> getSpectrumIdentificationItem()
Gets the value of the spectrumIdentificationItem 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 spectrumIdentificationItem property.

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

    getSpectrumIdentificationItem().add(newItem);
 

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


getParamGroup

public List<AbstractParam> getParamGroup()
Scores or parameters associated with the SpectrumIdentificationResult (i.e the set of SpectrumIdentificationItems derived from one spectrum) e.g. the number of peptide sequences within the parent tolerance for this spectrum. 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


getSpectrumID

public String getSpectrumID()
Gets the value of the spectrumID property.

Returns:
possible object is String

setSpectrumID

public void setSpectrumID(String value)
Sets the value of the spectrumID property.

Parameters:
value - allowed object is String

getSpectraDataRef

public String getSpectraDataRef()
Gets the value of the spectraDataRef property.

Returns:
possible object is String

getCvParam

public List<CvParam> getCvParam()
Get the cvparams for spectrumidentificationresult

Specified by:
getCvParam in interface CvParamListCapable
Specified by:
getCvParam in interface ParamGroupCapable
Returns:

getUserParam

public List<UserParam> getUserParam()
Get the userparams for spectrumidentificationresult

Specified by:
getUserParam in interface ParamGroupCapable
Returns:


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