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

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.SpectrumIdentificationItem
All Implemented Interfaces:
Serializable, CvParamListCapable, ParamGroupCapable

public class SpectrumIdentificationItem
extends Identifiable
implements Serializable, ParamGroupCapable

An identification of a single (poly)peptide, resulting from querying an input spectra, along with the set of confidence values for that identification. PeptideEvidence elements should be given for all mappings of the corresponding Peptide sequence within protein sequences. TODO marshalling/ persistor add validation to check for case where someone gets peptide/massTable/sample and changes its id without updating ref id in SpectrumIdentificationItem and other such clases. NOTE: There is no setter method for the peptideRef/massTableRef/sampleRef. This simplifies keeping the peptide/massTable/sample object reference and peptideRef/massTableRef/sampleRef synchronized. TODO: write an adaptor for changing List to List

Java class for SpectrumIdentificationItemType complex type.

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

 <complexType name="SpectrumIdentificationItemType">
   <complexContent>
     <extension base="{http://psidev.info/psi/pi/mzIdentML/1.1}IdentifiableType">
       <sequence>
         <element name="PeptideEvidenceRef" type="{http://psidev.info/psi/pi/mzIdentML/1.1}PeptideEvidenceRefType" maxOccurs="unbounded"/>
         <element name="Fragmentation" type="{http://psidev.info/psi/pi/mzIdentML/1.1}FragmentationType" minOccurs="0"/>
         <group ref="{http://psidev.info/psi/pi/mzIdentML/1.1}ParamGroup" maxOccurs="unbounded" minOccurs="0"/>
       </sequence>
       <attribute name="chargeState" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
       <attribute name="experimentalMassToCharge" use="required" type="{http://www.w3.org/2001/XMLSchema}double" />
       <attribute name="calculatedMassToCharge" type="{http://www.w3.org/2001/XMLSchema}double" />
       <attribute name="calculatedPI" type="{http://www.w3.org/2001/XMLSchema}float" />
       <attribute name="peptide_ref" type="{http://www.w3.org/2001/XMLSchema}string" />
       <attribute name="rank" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
       <attribute name="passThreshold" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
       <attribute name="massTable_ref" type="{http://www.w3.org/2001/XMLSchema}string" />
       <attribute name="sample_ref" type="{http://www.w3.org/2001/XMLSchema}string" />
     </extension>
   </complexContent>
 </complexType>
 

See Also:
Serialized Form

Field Summary
protected  Double calculatedMassToCharge
           
protected  Float calculatedPI
           
protected  int chargeState
           
protected  double experimentalMassToCharge
           
protected  Fragmentation fragmentation
           
protected  MassTable massTable
           
protected  String massTableRef
           
protected  List<AbstractParam> paramGroup
           
protected  boolean passThreshold
           
protected  Peptide peptide
           
protected  List<PeptideEvidenceRef> peptideEvidenceRef
           
protected  String peptideRef
           
protected  int rank
           
protected  Sample sample
           
protected  String sampleRef
           
 
Fields inherited from class uk.ac.ebi.jmzidml.model.mzidml.Identifiable
id, name
 
Constructor Summary
SpectrumIdentificationItem()
           
 
Method Summary
 Double getCalculatedMassToCharge()
          Gets the value of the calculatedMassToCharge property.
 Float getCalculatedPI()
          Gets the value of the calculatedPI property.
 int getChargeState()
          Gets the value of the chargeState property.
 List<CvParam> getCvParam()
          Get the cv params for SpectrumIdentification
 double getExperimentalMassToCharge()
          Gets the value of the experimentalMassToCharge property.
 Fragmentation getFragmentation()
          Gets the value of the fragmentation property.
 MassTable getMassTable()
           
 String getMassTableRef()
          Gets the value of the massTableRef property.
 List<AbstractParam> getParamGroup()
          Scores or attributes associated with the SpectrumIdentificationItem e.g.
 Peptide getPeptide()
           
 List<PeptideEvidenceRef> getPeptideEvidenceRef()
          Gets the value of the peptideEvidenceRef property.
 String getPeptideRef()
          Gets the value of the peptideRef property.
 int getRank()
          Gets the value of the rank property.
 Sample getSample()
           
 String getSampleRef()
          Gets the value of the sampleRef property.
 List<UserParam> getUserParam()
          Get the user params for SpectrumIdentification
 boolean isPassThreshold()
          Gets the value of the passThreshold property.
 void setCalculatedMassToCharge(Double value)
          Sets the value of the calculatedMassToCharge property.
 void setCalculatedPI(Float value)
          Sets the value of the calculatedPI property.
 void setChargeState(int value)
          Sets the value of the chargeState property.
 void setExperimentalMassToCharge(double value)
          Sets the value of the experimentalMassToCharge property.
 void setFragmentation(Fragmentation value)
          Sets the value of the fragmentation property.
 void setMassTable(MassTable massTable)
           
 void setPassThreshold(boolean value)
          Sets the value of the passThreshold property.
 void setPeptide(Peptide peptide)
           
 void setRank(int value)
          Sets the value of the rank property.
 void setSample(Sample sample)
           
 
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

peptideEvidenceRef

protected List<PeptideEvidenceRef> peptideEvidenceRef

fragmentation

protected Fragmentation fragmentation

paramGroup

protected List<AbstractParam> paramGroup

chargeState

protected int chargeState

experimentalMassToCharge

protected double experimentalMassToCharge

calculatedMassToCharge

protected Double calculatedMassToCharge

calculatedPI

protected Float calculatedPI

peptideRef

protected String peptideRef

rank

protected int rank

passThreshold

protected boolean passThreshold

massTableRef

protected String massTableRef

sampleRef

protected String sampleRef

peptide

protected Peptide peptide

massTable

protected MassTable massTable

sample

protected Sample sample
Constructor Detail

SpectrumIdentificationItem

public SpectrumIdentificationItem()
Method Detail

getPeptide

public Peptide getPeptide()

setPeptide

public void setPeptide(Peptide peptide)

getMassTable

public MassTable getMassTable()

setMassTable

public void setMassTable(MassTable massTable)

getSample

public Sample getSample()

setSample

public void setSample(Sample sample)

getPeptideEvidenceRef

public List<PeptideEvidenceRef> getPeptideEvidenceRef()
Gets the value of the peptideEvidenceRef 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 peptideEvidenceRef property.

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

    getPeptideEvidenceRef().add(newItem);
 

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


getFragmentation

public Fragmentation getFragmentation()
Gets the value of the fragmentation property.

Returns:
possible object is Fragmentation

setFragmentation

public void setFragmentation(Fragmentation value)
Sets the value of the fragmentation property.

Parameters:
value - allowed object is Fragmentation

getParamGroup

public List<AbstractParam> getParamGroup()
Scores or attributes associated with the SpectrumIdentificationItem e.g. e-value, p-value, score.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


getChargeState

public int getChargeState()
Gets the value of the chargeState property.


setChargeState

public void setChargeState(int value)
Sets the value of the chargeState property.


getExperimentalMassToCharge

public double getExperimentalMassToCharge()
Gets the value of the experimentalMassToCharge property.


setExperimentalMassToCharge

public void setExperimentalMassToCharge(double value)
Sets the value of the experimentalMassToCharge property.


getCalculatedMassToCharge

public Double getCalculatedMassToCharge()
Gets the value of the calculatedMassToCharge property.

Returns:
possible object is Double

setCalculatedMassToCharge

public void setCalculatedMassToCharge(Double value)
Sets the value of the calculatedMassToCharge property.

Parameters:
value - allowed object is Double

getCalculatedPI

public Float getCalculatedPI()
Gets the value of the calculatedPI property.

Returns:
possible object is Float

setCalculatedPI

public void setCalculatedPI(Float value)
Sets the value of the calculatedPI property.

Parameters:
value - allowed object is Float

getPeptideRef

public String getPeptideRef()
Gets the value of the peptideRef property.

Returns:
possible object is String

getRank

public int getRank()
Gets the value of the rank property.


setRank

public void setRank(int value)
Sets the value of the rank property.


isPassThreshold

public boolean isPassThreshold()
Gets the value of the passThreshold property.


setPassThreshold

public void setPassThreshold(boolean value)
Sets the value of the passThreshold property.


getMassTableRef

public String getMassTableRef()
Gets the value of the massTableRef property.

Returns:
possible object is String

getSampleRef

public String getSampleRef()
Gets the value of the sampleRef property.

Returns:
possible object is String

getCvParam

public List<CvParam> getCvParam()
Get the cv params for SpectrumIdentification

Specified by:
getCvParam in interface CvParamListCapable
Specified by:
getCvParam in interface ParamGroupCapable
Returns:
List A FacadeList providing a CvParam view of the underlying param list.

getUserParam

public List<UserParam> getUserParam()
Get the user params for SpectrumIdentification

Specified by:
getUserParam in interface ParamGroupCapable
Returns:
List A FacadeList providing a UserParam view of the underlying param list.


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