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
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
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
SpectrumIdentificationItem
public SpectrumIdentificationItem()
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.
Copyright © 2012. All Rights Reserved.