Modifier and Type | Method and Description |
---|---|
static List<CvParam> |
DataAccessUtilities.getCvParam(ParamGroup paramGroup,
String cvLabel,
String accession)
Get cv param by accession number and cv label.
|
static List<CvParam> |
DataAccessUtilities.getCvParam(String name,
String cvLabel,
String accession,
String value)
Create a List of Cv Params
|
Modifier and Type | Method and Description |
---|---|
static CvParam |
PrideXmlTransformer.transformCvParam(uk.ac.ebi.pride.jaxb.model.CvParam rawCvParam)
Transform a cv parameter from pride xml format to core data model format.
|
static CvParam |
MzMLTransformer.transformDateToCvParam(Date creationDate) |
static CvParam |
MzIdentMLTransformer.transformDateToCvParam(Date creationDate) |
static CvParam |
MzXmlTransformer.transformDurationToCvParam(Duration startDate,
uk.ac.ebi.pride.utilities.term.CvTermReference msScanDate) |
Modifier and Type | Method and Description |
---|---|
static List<CvParam> |
PrideXmlTransformer.transformCvParams(List<uk.ac.ebi.pride.jaxb.model.CvParam> rawCvParams)
Convert a list of cv params
|
Modifier and Type | Class and Description |
---|---|
class |
IonType
IonType defines the index of fragmentation ions being reported,
importing a CV term for the type of ion e.g.
|
Modifier and Type | Method and Description |
---|---|
CvParam |
QuantitativeSample.getCellLine(int index)
Get cell line cv param of a sub sample with given index
|
CvParam |
QuantitativeSample.getDescription(int index)
Get description cv param of a sub sample with given index
|
CvParam |
QuantitativeSample.getDisease(int index)
Get disease cv param of a sub sample with given index
|
CvParam |
SourceFile.getFileFormat() |
CvParam |
ExternalData.getFileFormat() |
CvParam |
QuantitativeSample.getGOTerm(int index)
Get GO cv param of a sub sample with given index
|
CvParam |
Assay.getReagent() |
CvParam |
QuantitativeSample.getReagent(int index)
Get reagent cv param of a sub sample with given index
|
CvParam |
Provider.getRole() |
CvParam |
ContactRole.getRole() |
CvParam |
QuantitativeSample.getSpecies(int index)
Get the species information of sub sample with given index
|
CvParam |
SpectraData.getSpectrumIdFormat() |
CvParam |
QuantitativeSample.getTissue(int index)
Get tissue cv param of a sub sample with given index
|
Modifier and Type | Method and Description |
---|---|
Map<Contact,CvParam> |
Sample.getContactRoles() |
List<CvParam> |
SearchModification.getCvParams() |
List<CvParam> |
ParamGroup.getCvParams()
This method return a List of CvParam, the result List in a new Instance
of the current List of CvParam
|
List<CvParam> |
SearchDataBase.getDescription() |
List<CvParam> |
SpectrumIdentificationProtocol.getFragmentTolerance() |
List<CvParam> |
SpectrumIdentificationProtocol.getParentTolerance() |
List<CvParam> |
SearchModification.getSpecificityRules() |
Modifier and Type | Method and Description |
---|---|
void |
ParamGroup.addCvParam(CvParam cv) |
void |
ParamGroup.removeCvParam(CvParam cv) |
void |
QuantitativeSample.setCellLine(CvParam cvParam)
Add cell line information to a subsample
|
void |
QuantitativeSample.setCellLine(int index,
CvParam cvParam)
Add cell line information to a subsample
|
void |
QuantitativeSample.setDescription(CvParam cvParam)
Add description to a subsample
|
void |
QuantitativeSample.setDescription(int index,
CvParam cvParam)
Add description to a subsample
|
void |
QuantitativeSample.setDisease(CvParam cvParam)
Add disease information to a subsample
|
void |
QuantitativeSample.setDisease(int index,
CvParam cvParam)
Add disease information to a subsample
|
void |
SourceFile.setFileFormat(CvParam fileFormat) |
void |
ExternalData.setFileFormat(CvParam fileFormat) |
void |
QuantitativeSample.setGOTerm(CvParam cvParam)
Add GO information to a subsample
|
void |
QuantitativeSample.setGOTerm(int index,
CvParam cvParam)
Add GO information to a subsample
|
void |
QuantitativeSample.setReagent(CvParam cvParam)
Add reagent information to a subsample
|
void |
Assay.setReagent(CvParam reagent) |
void |
QuantitativeSample.setReagent(int index,
CvParam cvParam)
Add reagent information to a subsample
|
void |
Provider.setRole(CvParam role) |
void |
ContactRole.setRole(CvParam role) |
void |
QuantitativeSample.setSpecies(CvParam cvParam)
Add species information to a subsample
|
void |
QuantitativeSample.setSpecies(int index,
CvParam cvParam)
Add species information to a subsample
|
void |
SpectraData.setSpectrumIdFormat(CvParam spectrumIdFormat) |
void |
QuantitativeSample.setTissue(CvParam cvParam)
Add tissue information to a subsample
|
void |
QuantitativeSample.setTissue(int index,
CvParam cvParam)
Add tissue information to a subsample
|
Modifier and Type | Method and Description |
---|---|
void |
ParamGroup.addCvParams(List<CvParam> cvs) |
void |
ParamGroup.removeCvParams(List<CvParam> cvs) |
void |
Sample.setContactRoles(Map<Contact,CvParam> contactRoles) |
void |
SearchModification.setCvParams(List<CvParam> cvParams) |
void |
ParamGroup.setCvParams(List<CvParam> cvs) |
void |
SearchDataBase.setDescription(List<CvParam> description) |
void |
SpectrumIdentificationProtocol.setFragmentTolerance(List<CvParam> fragmentTolerance) |
void |
SpectrumIdentificationProtocol.setParentTolerance(List<CvParam> parentTolerance) |
void |
SearchModification.setSpecificityRules(List<CvParam> specificityRules) |
Constructor and Description |
---|
Assay(ParamGroup params,
Comparable id,
String name,
Sample sample,
CvParam reagent) |
ContactRole(Contact contact,
CvParam role) |
ExternalData(String id,
String name,
String location,
CvParam fileFormat,
String externalFormatDocumentationURI)
Constructor of External Data Objects
|
ParamGroup(CvParam cvParam,
UserParam userParam) |
Provider(Comparable id,
String name,
Software software,
Contact contact,
CvParam role) |
SearchDataBase(String id,
String name,
String location,
CvParam fileFormat,
String externalFormatDocumentationURI,
String version,
String releaseDate,
int numDatabaseSequence,
long numDatabaseResidue,
ParamGroup nameDatabase,
List<CvParam> description) |
SourceFile(ParamGroup params,
String id,
String name,
String path,
CvParam fileFormat,
String externalFormatDocumentationURI) |
SpectraData(String id,
String name,
String location,
CvParam fileFormat,
String externalFormatDocumentationURI,
CvParam spectrumIdFormat) |
Constructor and Description |
---|
ParamGroup(List<CvParam> cvParams,
List<UserParam> userParams)
Constructor
|
PeptideSequence(List<CvParam> cvParams,
List<UserParam> userParams,
String id,
String name,
String sequence,
List<Modification> modifications) |
PeptideSequence(List<CvParam> cvParams,
List<UserParam> userParams,
String id,
String name,
String sequence,
List<Modification> modifications,
List<SubstitutionModification> substitutionModifications) |
Quantification(Quantification.Type type,
List<CvParam> cvParamList) |
Reference(List<CvParam> cvParams,
List<UserParam> userParams,
String id,
String name,
String fullReference) |
Reference(List<CvParam> cvParams,
List<UserParam> userParams,
String id,
String name,
String doi,
String title,
String pages,
String issue,
String volume,
String year,
String editor,
String publisher,
String publication,
String authors,
String fullReference) |
Sample(ParamGroup params,
String id,
String name,
List<Sample> subSamples,
Map<Contact,CvParam> contactRoles) |
SearchDataBase(String id,
String name,
String location,
CvParam fileFormat,
String externalFormatDocumentationURI,
String version,
String releaseDate,
int numDatabaseSequence,
long numDatabaseResidue,
ParamGroup nameDatabase,
List<CvParam> description) |
SearchModification(boolean fixedMod,
double massDelta,
List<String> specificities,
List<CvParam> specificityRules,
List<CvParam> cvParams) |
SearchModification(boolean fixedMod,
double massDelta,
List<String> specificities,
List<CvParam> specificityRules,
List<CvParam> cvParams) |
SpectrumIdentificationProtocol(Comparable id,
String name,
Software analysisSoftware,
ParamGroup analysisParam,
ParamGroup threshold,
ParamGroup searchType,
List<SearchModification> searchModifications,
boolean enzymeIndependent,
List<Enzyme> enzymes,
List<MassTable> massTables,
List<CvParam> fragmentTolerance,
List<CvParam> parentTolerance,
List<Filter> filters,
DataBaseTranslation dataBaseTranslation) |
SpectrumIdentificationProtocol(Comparable id,
String name,
Software analysisSoftware,
ParamGroup analysisParam,
ParamGroup threshold,
ParamGroup searchType,
List<SearchModification> searchModifications,
boolean enzymeIndependent,
List<Enzyme> enzymes,
List<MassTable> massTables,
List<CvParam> fragmentTolerance,
List<CvParam> parentTolerance,
List<Filter> filters,
DataBaseTranslation dataBaseTranslation) |
SpectrumIdentificationProtocol(ParamGroup analysisParam,
Comparable id,
String name,
Software analysisSoftware,
ParamGroup threshold,
ParamGroup searchType,
List<SearchModification> searchModifications,
boolean enzymeIndependent,
List<Enzyme> enzymes,
List<MassTable> massTables,
List<CvParam> fragmentTolerance,
List<CvParam> parentTolerance,
List<Filter> filters,
DataBaseTranslation dataBaseTranslation) |
SpectrumIdentificationProtocol(ParamGroup analysisParam,
Comparable id,
String name,
Software analysisSoftware,
ParamGroup threshold,
ParamGroup searchType,
List<SearchModification> searchModifications,
boolean enzymeIndependent,
List<Enzyme> enzymes,
List<MassTable> massTables,
List<CvParam> fragmentTolerance,
List<CvParam> parentTolerance,
List<Filter> filters,
DataBaseTranslation dataBaseTranslation) |
Modifier and Type | Method and Description |
---|---|
protected String |
MzIdentMLMzTabConverter.getDatabaseName(List<CvParam> databaseName,
List<UserParam> userParam) |
protected String |
MzIdentMLMzTabConverter.getDescriptionFromCVParams(List<CvParam> cvParams) |
Modifier and Type | Method and Description |
---|---|
static CvParam |
MzTabUtils.convertParamToCvParam(uk.ac.ebi.pride.jmztab.model.Param param) |
static CvParam |
PRIDEUtils.convertSoftwareNameToCvPram(String name,
String version)
Conversion from PRIDE Software to CVParam using a general CVTerm like Analysis Software
|
static CvParam |
CvUtilities.getCVTermFromCvReference(uk.ac.ebi.pride.utilities.term.CvTermReference cvTerm,
String value) |
static CvParam |
MzIdentMLUtils.getFileFormatMGFTitle()
This CvParam override the current File format CVparam for those files that are native wiff but are mgf using title reference.
|
static CvParam |
CvUtilities.getQuantTermFromQuantReference(uk.ac.ebi.pride.utilities.term.QuantCvTermReference quantTerm,
String value) |
static CvParam |
MzIdentMLUtils.getSpectrumIdFormatMGFTitle() |
static CvParam |
MzTabUtils.parseQuantitationReagentCvParam(uk.ac.ebi.pride.jmztab.model.Param quantificationReagent)
Param for the reagent to retrieve the PRIDE Term for that, is important that most of the fields can be null, for
that reason we look through all the the information looking for patterns.
|
Modifier and Type | Method and Description |
---|---|
static List<CvParam> |
MzTabUtils.convertParamToCvParam(List<uk.ac.ebi.pride.jmztab.model.Param> params) |
Modifier and Type | Method and Description |
---|---|
static uk.ac.ebi.pride.jmztab.model.CVParam |
MzTabUtils.convertCvParamToCVParam(CvParam cvParam)
This function takes the value of a CVParam and retrieve the corresponding CVParam
|
static uk.ac.ebi.pride.jmztab.model.CVParam |
MzTabUtils.convertCvParamToCVParam(CvParam cvParam,
Double mass)
This function takes the value of a CVParam and retrieve the corresponding CVParam
|
Modifier and Type | Method and Description |
---|---|
static List<uk.ac.ebi.pride.jmztab.utils.convert.SearchEngineParam> |
MzIdentMLUtils.getSearchEngineCvTermReferences(List<CvParam> cvParams)
Search and find a list of search engine types from input parameter group.
|
static String |
CvUtilities.getValueFromParmGroup(List<CvParam> cvParams,
String accession) |
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