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java.lang.Objectuk.ac.ebi.jmzidml.model.MzIdentMLObject
uk.ac.ebi.jmzidml.model.mzidml.Identifiable
uk.ac.ebi.jmzidml.model.mzidml.ProtocolApplication
uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentification
public class SpectrumIdentification
An Analysis which tries to identify peptides in input spectra, referencing the database searched, the input spectra, the output results and the protocol that is run. TODO marshalling/ persistor add validation to check for case where someone gets spectrumIdentificationList/spectrumIdentificationProtocol and changes its id without updating ref id in SpectrumIdentification and other such clases.
NOTE: There is no setter method for the spectrumIdentificationListRef/spectrumIdentificationProtocolRef. This simplifies keeping the spectrumIdentificationList/spectrumIdentificationProtocol object reference and spectrumIdentificationListRef/spectrumIdentificationProtocolRef synchronized.Java class for SpectrumIdentificationType complex type.
The following schema fragment specifies the expected content contained within this class.
<complexType name="SpectrumIdentificationType"> <complexContent> <extension base="{http://psidev.info/psi/pi/mzIdentML/1.1}ProtocolApplicationType"> <sequence> <element name="InputSpectra" type="{http://psidev.info/psi/pi/mzIdentML/1.1}InputSpectraType" maxOccurs="unbounded"/> <element name="SearchDatabaseRef" type="{http://psidev.info/psi/pi/mzIdentML/1.1}SearchDatabaseRefType" maxOccurs="unbounded"/> </sequence> <attribute name="spectrumIdentificationProtocol_ref" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /> <attribute name="spectrumIdentificationList_ref" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /> </extension> </complexContent> </complexType>
Field Summary | |
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protected List<InputSpectra> |
inputSpectra
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protected List<SearchDatabaseRef> |
searchDatabaseRef
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protected SpectrumIdentificationList |
spectrumIdentificationList
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protected String |
spectrumIdentificationListRef
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protected SpectrumIdentificationProtocol |
spectrumIdentificationProtocol
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protected String |
spectrumIdentificationProtocolRef
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Fields inherited from class uk.ac.ebi.jmzidml.model.mzidml.ProtocolApplication |
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activityDate |
Fields inherited from class uk.ac.ebi.jmzidml.model.mzidml.Identifiable |
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id, name |
Constructor Summary | |
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SpectrumIdentification()
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Method Summary | |
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List<InputSpectra> |
getInputSpectra()
Gets the value of the inputSpectra property. |
List<SearchDatabaseRef> |
getSearchDatabaseRef()
Gets the value of the searchDatabaseRef property. |
SpectrumIdentificationList |
getSpectrumIdentificationList()
|
String |
getSpectrumIdentificationListRef()
Gets the value of the spectrumIdentificationListRef property. |
SpectrumIdentificationProtocol |
getSpectrumIdentificationProtocol()
|
String |
getSpectrumIdentificationProtocolRef()
Gets the value of the spectrumIdentificationProtocolRef property. |
void |
setSpectrumIdentificationList(SpectrumIdentificationList spectrumIdentificationList)
|
void |
setSpectrumIdentificationProtocol(SpectrumIdentificationProtocol spectrumIdentificationProtocol)
|
Methods inherited from class uk.ac.ebi.jmzidml.model.mzidml.ProtocolApplication |
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getActivityDate, setActivityDate |
Methods inherited from class uk.ac.ebi.jmzidml.model.mzidml.Identifiable |
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getId, getName, setId, setName |
Methods inherited from class uk.ac.ebi.jmzidml.model.MzIdentMLObject |
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getHid |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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protected List<InputSpectra> inputSpectra
protected List<SearchDatabaseRef> searchDatabaseRef
protected String spectrumIdentificationProtocolRef
protected String spectrumIdentificationListRef
protected SpectrumIdentificationList spectrumIdentificationList
protected SpectrumIdentificationProtocol spectrumIdentificationProtocol
Constructor Detail |
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public SpectrumIdentification()
Method Detail |
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public SpectrumIdentificationProtocol getSpectrumIdentificationProtocol()
public void setSpectrumIdentificationProtocol(SpectrumIdentificationProtocol spectrumIdentificationProtocol)
public SpectrumIdentificationList getSpectrumIdentificationList()
public void setSpectrumIdentificationList(SpectrumIdentificationList spectrumIdentificationList)
public List<InputSpectra> getInputSpectra()
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 inputSpectra property.
For example, to add a new item, do as follows:
getInputSpectra().add(newItem);
Objects of the following type(s) are allowed in the list
InputSpectra
public List<SearchDatabaseRef> getSearchDatabaseRef()
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 searchDatabaseRef property.
For example, to add a new item, do as follows:
getSearchDatabaseRef().add(newItem);
Objects of the following type(s) are allowed in the list
SearchDatabaseRef
public String getSpectrumIdentificationProtocolRef()
String
public String getSpectrumIdentificationListRef()
String
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