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Functions679 in github.com/HUPO-PSI/mzML

↓ 1 callersMethodsetRef
Sets the value of the ref property. @param value allowed object is {@link String }
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/InstrumentSoftwareRefType.java:126
↓ 1 callersMethodsetRef
Sets the value of the ref property. @param value allowed object is {@link String }
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/ParamGroupRefType.java:178
↓ 1 callersMethodsetSampleRef
Sets the value of the sampleRef property. @param value allowed object is {@link String }
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/RunType.java:298
↓ 1 callersMethodsetScanNumber
Sets the value of the scanNumber property.
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/SpectrumType.java:290
↓ 1 callersMethodsetSchemaUri
Use this to overwrite default schema location and specify your own schema to validate against. Note: to be able to validate both indexed and non-index
validator/src/main/java/psidev/psi/ms/MzMLValidator.java:194
↓ 1 callersMethodsetSkipValidation
Flag to specify if a schema validation is to be performed. @param skipValidation set to true if the schema validation step should be skipp
validator/src/main/java/psidev/psi/ms/MzMLValidator.java:214
↓ 1 callersMethodsetSoftwareRef
Sets the value of the softwareRef property. @param value allowed object is {@link String }
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/DataProcessingType.java:212
↓ 1 callersMethodsetSourceFileLocation
Sets the value of the sourceFileLocation property. @param value allowed object is {@link String }
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/SourceFileType.java:186
↓ 1 callersMethodsetSourceFileName
Sets the value of the sourceFileName property. @param value allowed object is {@link String }
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/SourceFileType.java:210
↓ 1 callersMethodsetSourceFileRef
Sets the value of the sourceFileRef property. @param value allowed object is {@link String }
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/SpectrumType.java:314
↓ 1 callersMethodsetSourceFileRef
Sets the value of the sourceFileRef property. @param value allowed object is {@link String }
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/AcquisitionType.java:161
↓ 1 callersMethodsetSpectrumRef
Sets the value of the spectrumRef property. @param value allowed object is {@link String }
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/PrecursorType.java:204
↓ 1 callersMethodsetSpectrumRef
Sets the value of the spectrumRef property. @param value allowed object is {@link String }
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/AcquisitionType.java:185
↓ 1 callersMethodsetSpectrumType
Sets the value of the spectrumType property. @param value allowed object is {@link String }
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/AcquisitionListType.java:236
↓ 1 callersMethodsetTimeStamp
Sets the value of the timeStamp property. @param value allowed object is {@link XMLGregorianCalendar }
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/RunType.java:322
↓ 1 callersMethodsetType
Sets the value of the type property. @param value allowed object is {@link String }
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/UserParamType.java:166
↓ 1 callersMethodsetType
Sets the value of the type property. @param value allowed object is {@link String }
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/FileChecksumType.java:162
↓ 1 callersMethodsetURI
Sets the value of the uri property. @param value allowed object is {@link String }
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/CVType.java:149
↓ 1 callersMethodsetUnitAccession
Sets the value of the unitAccession property. @param value allowed object is {@link String }
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/CVParamType.java:239
↓ 1 callersMethodsetUnitName
Sets the value of the unitName property. @param value allowed object is {@link String }
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/CVParamType.java:263
↓ 1 callersMethodsetValue
Sets the value of the value property. @param value allowed object is {@link String }
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/UserParamType.java:190
↓ 1 callersMethodsetValue
Set the value produced by worker thread
validator/src/main/java/psidev/psi/ms/swingworker/SwingWorker.java:57
↓ 1 callersMethodsetVersion
Sets the value of the version property. @param value allowed object is {@link String }
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/CVType.java:221
↓ 1 callersMethodsetVersion
Sets the value of the version property. @param value allowed object is {@link String }
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/SoftwareListType.java:551
↓ 1 callersMethodsetVersion
Sets the value of the version property. @param value allowed object is {@link String }
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/MzMLType.java:472
↓ 1 callersMethodshowExtendedReportDialog
(int messageNumber)
validator/src/main/java/psidev/psi/ms/MzMLValidatorGUI.java:682
↓ 1 callersMethodshowMessages
(Collection<ValidatorMessage> aMessages)
validator/src/main/java/psidev/psi/ms/MzMLValidatorGUI.java:764
↓ 1 callersMethodskipValidation
()
validator/src/main/java/psidev/psi/ms/MzMLValidatorGUI.java:859
↓ 1 callersMethodstoreAsTemporaryFile
Store the content of the given input stream into a temporary file and return its descriptor. @param is the input stream to store. @return
validator/src/main/java/psidev/psi/ms/MzMLValidator.java:250
↓ 1 callersMethodupdateDoneCount
()
validator/src/main/java/psidev/psi/ms/MzMLValidator.java:1065
↓ 1 callersMethodupdateRulesToSkipByCvMappingRuleResult
Check if it is necessary to add some rules to skip since the result of the execution of a cvRule @param rule @param valid if the rule has
validator/src/main/java/psidev/psi/ms/rulefilter/RuleFilterManager.java:364
↓ 1 callersMethodupdateRulesToSkipByObjectRuleResult
Check if it is necessary to add some rules to skip since the result of the execution of a object rule @param rule @param valid if the rule
validator/src/main/java/psidev/psi/ms/rulefilter/RuleFilterManager.java:387
↓ 1 callersMethodvalidationDone
()
validator/src/main/java/psidev/psi/ms/MzMLValidatorGUI.java:627
MethodAcquisitionListType
()
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/AcquisitionListType.java:71
MethodAcquisitionParametersFileRefObjectRule
()
validator/src/main/java/psidev/psi/ms/object_rules/AcquisitionParametersFileRefObjectRule.java:35
MethodAcquisitionType
()
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/AcquisitionType.java:62
MethodBinaryDataArrayType
()
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/BinaryDataArrayType.java:68
MethodCVListType
()
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/CVListType.java:65
MethodCVParamType
()
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/CVParamType.java:70
MethodCVType
()
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/CVType.java:63
MethodClusteredContext
(String context)
validator/src/main/java/psidev/psi/ms/ClusteredContext.java:16
MethodComponentListType
()
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/ComponentListType.java:77
MethodComponentType
()
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/ComponentType.java:56
MethodContactType
()
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/ContactType.java:57
MethodDataProcessingListType
()
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/DataProcessingListType.java:65
MethodDataProcessingType
()
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/DataProcessingType.java:76
MethodExplicitAcquisitionParametersObjectRule
()
validator/src/main/java/psidev/psi/ms/object_rules/ExplicitAcquisitionParametersObjectRule.java:45
MethodExtendedValidatorReport
(Collection<ObjectRule> objectRules)
validator/src/main/java/psidev/psi/ms/ExtendedValidatorReport.java:23
MethodFileChecksumType
()
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/FileChecksumType.java:59
MethodFileDescriptionType
()
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/FileDescriptionType.java:67
MethodInnerIteratorSync
(Iterator<T> aIterator)
validator/src/main/java/psidev/psi/ms/MzMLValidator.java:1045
MethodInnerSpecValidator
(InnerIteratorSync<T> aIterator, InnerLock aLock, int aNumber)
validator/src/main/java/psidev/psi/ms/MzMLValidator.java:1093
MethodInstrumentConfigurationObjectRule
()
validator/src/main/java/psidev/psi/ms/object_rules/InstrumentConfigurationObjectRule.java:44
MethodInstrumentListType
()
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/InstrumentListType.java:65
MethodInstrumentSoftwareRefType
()
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/InstrumentSoftwareRefType.java:52
MethodInstrumentType
()
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/InstrumentType.java:67
MethodLaserWavelengthObjectRule
()
validator/src/main/java/psidev/psi/ms/object_rules/LaserWavelengthObjectRule.java:32
MethodMaldiOrEsiCondition
(String option)
validator/src/main/java/psidev/psi/ms/rulefilter/MaldiOrEsiCondition.java:11
MethodMandatoryElementsObjectRule
(OntologyManager ontologyManager)
validator/src/main/java/psidev/psi/ms/object_rules/MandatoryElementsObjectRule.java:19
MethodMassSpectraOrParameterFileInSourceFileListObjectRule
()
validator/src/main/java/psidev/psi/ms/object_rules/MassSpectraOrParameterFileInSourceFileListObjectRule.java:43
MethodMatrixSolutionObjectRule
()
validator/src/main/java/psidev/psi/ms/object_rules/MatrixSolutionObjectRule.java:33
MethodMzMLType
()
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/MzMLType.java:94
MethodMzMLValidationErrorHandler
()
validator/src/main/java/psidev/psi/ms/MzMLValidationErrorHandler.java:22
MethodMzMLValidator
Constructor to initialise the validator with the custom ontology and cv-mapping without object rule settings. Note: this constructor will try to load
validator/src/main/java/psidev/psi/ms/MzMLValidator.java:114
MethodMzMLValidatorGUI
Creates new form MzMLValidatorGUI
validator/src/main/java/psidev/psi/ms/MzMLValidatorGUI.java:56
MethodObjectFactory
Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: psidev.psi.ms.rulefilter.jaxb
validator/src/main/java/psidev/psi/ms/rulefilter/jaxb/ObjectFactory.java:36
MethodObjectFactory
Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: psidev.psi.ms.mzml.mapping.jaxb
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/ObjectFactory.java:43
MethodOtherSourceObjectRule
()
validator/src/main/java/psidev/psi/ms/object_rules/OtherSourceObjectRule.java:43
MethodParamGroupRefType
()
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/ParamGroupRefType.java:56
MethodParamGroupType
()
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/ParamGroupType.java:70
MethodParameterFileInSourceFileListObjectRule
()
validator/src/main/java/psidev/psi/ms/object_rules/ParameterFileInSourceFileListObjectRule.java:38
MethodPrecursorListType
()
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/PrecursorListType.java:65
MethodPrecursorType
()
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/PrecursorType.java:66
MethodProcessingMethod
()
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/DataProcessingType.java:246
MethodReferenceableParamGroupListType
()
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/ReferenceableParamGroupListType.java:65
MethodReferenceableParamGroupType
()
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/ReferenceableParamGroupType.java:56
MethodRuleFilterManager
(File xmlFile)
validator/src/main/java/psidev/psi/ms/rulefilter/RuleFilterManager.java:45
MethodRunType
()
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/RunType.java:95
MethodSampleListType
()
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/SampleListType.java:65
MethodSampleType
()
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/SampleType.java:59
MethodScan
()
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/SpectrumDescriptionType.java:293
MethodSelectionWindow
()
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/SpectrumDescriptionType.java:561
MethodSelectionWindowList
()
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/SpectrumDescriptionType.java:425
MethodSoftware
()
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/SoftwareListType.java:247
MethodSoftwareListObjectRule
()
validator/src/main/java/psidev/psi/ms/object_rules/SoftwareListObjectRule.java:44
MethodSoftwareListType
()
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/SoftwareListType.java:87
MethodSoftwareParam
()
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/SoftwareListType.java:393
MethodSourceFileListType
()
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/SourceFileListType.java:65
MethodSourceFileRef
()
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/RunType.java:509
MethodSourceFileRefList
()
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/RunType.java:369
MethodSourceFileType
()
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/SourceFileType.java:71
MethodSpectrumDescriptionType
()
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/SpectrumDescriptionType.java:95
MethodSpectrumListType
()
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/SpectrumListType.java:65
MethodSpectrumObjectRule
()
validator/src/main/java/psidev/psi/ms/object_rules/SpectrumObjectRule.java:56
MethodSpectrumType
()
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/SpectrumType.java:78
MethodSwingWorker
Start a thread that will call the <code>construct</code> method and then exit.
validator/src/main/java/psidev/psi/ms/swingworker/SwingWorker.java:113
MethodTemplateObjectRule
()
validator/src/main/java/psidev/psi/ms/object_rules/TemplateObjectRule.java:19
MethodThreadVar
(Thread t)
validator/src/main/java/psidev/psi/ms/swingworker/SwingWorker.java:39
MethodUserParamType
()
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/UserParamType.java:60
MethodValidationType
(String name)
validator/src/main/java/psidev/psi/ms/ValidationType.java:7
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