|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Objectuk.ac.ebi.jmzidml.model.MzIdentMLObject
uk.ac.ebi.jmzidml.model.mzidml.Identifiable
uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationProtocol
public class SpectrumIdentificationProtocol
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>
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 |
---|
protected Param searchType
protected ParamList additionalSearchParams
protected ModificationParams modificationParams
protected Enzymes enzymes
protected List<MassTable> massTable
protected Tolerance fragmentTolerance
protected Tolerance parentTolerance
protected ParamList threshold
protected DatabaseFilters databaseFilters
protected DatabaseTranslation databaseTranslation
protected String analysisSoftwareRef
protected AnalysisSoftware analysisSoftware
Constructor Detail |
---|
public SpectrumIdentificationProtocol()
Method Detail |
---|
public AnalysisSoftware getAnalysisSoftware()
public void setAnalysisSoftware(AnalysisSoftware analysisSoftware)
public Param getSearchType()
Param
public void setSearchType(Param value)
value
- allowed object is
Param
public ParamList getAdditionalSearchParams()
ParamList
public void setAdditionalSearchParams(ParamList value)
value
- allowed object is
ParamList
public ModificationParams getModificationParams()
ModificationParams
public void setModificationParams(ModificationParams value)
value
- allowed object is
ModificationParams
public Enzymes getEnzymes()
Enzymes
public void setEnzymes(Enzymes value)
value
- allowed object is
Enzymes
public List<MassTable> getMassTable()
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
public Tolerance getFragmentTolerance()
Tolerance
public void setFragmentTolerance(Tolerance value)
value
- allowed object is
Tolerance
public Tolerance getParentTolerance()
Tolerance
public void setParentTolerance(Tolerance value)
value
- allowed object is
Tolerance
public ParamList getThreshold()
ParamList
public void setThreshold(ParamList value)
value
- allowed object is
ParamList
public DatabaseFilters getDatabaseFilters()
DatabaseFilters
public void setDatabaseFilters(DatabaseFilters value)
value
- allowed object is
DatabaseFilters
public DatabaseTranslation getDatabaseTranslation()
DatabaseTranslation
public void setDatabaseTranslation(DatabaseTranslation value)
value
- allowed object is
DatabaseTranslation
public String getAnalysisSoftwareRef()
String
|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |