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github.com/HUPO-PSI/mzML
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Functions
679 in github.com/HUPO-PSI/mzML
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Functions
679
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Types & classes
91
↓ 1 callers
Method
setRef
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 callers
Method
setRef
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 callers
Method
setSampleRef
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 callers
Method
setScanNumber
Sets the value of the scanNumber property.
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/SpectrumType.java:290
↓ 1 callers
Method
setSchemaUri
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 callers
Method
setSkipValidation
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 callers
Method
setSoftwareRef
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 callers
Method
setSourceFileLocation
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 callers
Method
setSourceFileName
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 callers
Method
setSourceFileRef
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 callers
Method
setSourceFileRef
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 callers
Method
setSpectrumRef
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 callers
Method
setSpectrumRef
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 callers
Method
setSpectrumType
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 callers
Method
setTimeStamp
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 callers
Method
setType
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 callers
Method
setType
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 callers
Method
setURI
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 callers
Method
setUnitAccession
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 callers
Method
setUnitName
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 callers
Method
setValue
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 callers
Method
setValue
Set the value produced by worker thread
validator/src/main/java/psidev/psi/ms/swingworker/SwingWorker.java:57
↓ 1 callers
Method
setVersion
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 callers
Method
setVersion
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 callers
Method
setVersion
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 callers
Method
showExtendedReportDialog
(int messageNumber)
validator/src/main/java/psidev/psi/ms/MzMLValidatorGUI.java:682
↓ 1 callers
Method
showMessages
(Collection<ValidatorMessage> aMessages)
validator/src/main/java/psidev/psi/ms/MzMLValidatorGUI.java:764
↓ 1 callers
Method
skipValidation
()
validator/src/main/java/psidev/psi/ms/MzMLValidatorGUI.java:859
↓ 1 callers
Method
storeAsTemporaryFile
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 callers
Method
updateDoneCount
()
validator/src/main/java/psidev/psi/ms/MzMLValidator.java:1065
↓ 1 callers
Method
updateRulesToSkipByCvMappingRuleResult
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 callers
Method
updateRulesToSkipByObjectRuleResult
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 callers
Method
validationDone
()
validator/src/main/java/psidev/psi/ms/MzMLValidatorGUI.java:627
Method
AcquisitionListType
()
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/AcquisitionListType.java:71
Method
AcquisitionParametersFileRefObjectRule
()
validator/src/main/java/psidev/psi/ms/object_rules/AcquisitionParametersFileRefObjectRule.java:35
Method
AcquisitionType
()
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/AcquisitionType.java:62
Method
BinaryDataArrayType
()
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/BinaryDataArrayType.java:68
Method
CVListType
()
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/CVListType.java:65
Method
CVParamType
()
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/CVParamType.java:70
Method
CVType
()
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/CVType.java:63
Method
ClusteredContext
(String context)
validator/src/main/java/psidev/psi/ms/ClusteredContext.java:16
Method
ComponentListType
()
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/ComponentListType.java:77
Method
ComponentType
()
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/ComponentType.java:56
Method
ContactType
()
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/ContactType.java:57
Method
DataProcessingListType
()
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/DataProcessingListType.java:65
Method
DataProcessingType
()
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/DataProcessingType.java:76
Method
ExplicitAcquisitionParametersObjectRule
()
validator/src/main/java/psidev/psi/ms/object_rules/ExplicitAcquisitionParametersObjectRule.java:45
Method
ExtendedValidatorReport
(Collection<ObjectRule> objectRules)
validator/src/main/java/psidev/psi/ms/ExtendedValidatorReport.java:23
Method
FileChecksumType
()
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/FileChecksumType.java:59
Method
FileDescriptionType
()
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/FileDescriptionType.java:67
Method
InnerIteratorSync
(Iterator<T> aIterator)
validator/src/main/java/psidev/psi/ms/MzMLValidator.java:1045
Method
InnerSpecValidator
(InnerIteratorSync<T> aIterator, InnerLock aLock, int aNumber)
validator/src/main/java/psidev/psi/ms/MzMLValidator.java:1093
Method
InstrumentConfigurationObjectRule
()
validator/src/main/java/psidev/psi/ms/object_rules/InstrumentConfigurationObjectRule.java:44
Method
InstrumentListType
()
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/InstrumentListType.java:65
Method
InstrumentSoftwareRefType
()
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/InstrumentSoftwareRefType.java:52
Method
InstrumentType
()
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/InstrumentType.java:67
Method
LaserWavelengthObjectRule
()
validator/src/main/java/psidev/psi/ms/object_rules/LaserWavelengthObjectRule.java:32
Method
MaldiOrEsiCondition
(String option)
validator/src/main/java/psidev/psi/ms/rulefilter/MaldiOrEsiCondition.java:11
Method
MandatoryElementsObjectRule
(OntologyManager ontologyManager)
validator/src/main/java/psidev/psi/ms/object_rules/MandatoryElementsObjectRule.java:19
Method
MassSpectraOrParameterFileInSourceFileListObjectRule
()
validator/src/main/java/psidev/psi/ms/object_rules/MassSpectraOrParameterFileInSourceFileListObjectRule.java:43
Method
MatrixSolutionObjectRule
()
validator/src/main/java/psidev/psi/ms/object_rules/MatrixSolutionObjectRule.java:33
Method
MzMLType
()
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/MzMLType.java:94
Method
MzMLValidationErrorHandler
()
validator/src/main/java/psidev/psi/ms/MzMLValidationErrorHandler.java:22
Method
MzMLValidator
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
Method
MzMLValidatorGUI
Creates new form MzMLValidatorGUI
validator/src/main/java/psidev/psi/ms/MzMLValidatorGUI.java:56
Method
ObjectFactory
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
Method
ObjectFactory
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
Method
OtherSourceObjectRule
()
validator/src/main/java/psidev/psi/ms/object_rules/OtherSourceObjectRule.java:43
Method
ParamGroupRefType
()
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/ParamGroupRefType.java:56
Method
ParamGroupType
()
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/ParamGroupType.java:70
Method
ParameterFileInSourceFileListObjectRule
()
validator/src/main/java/psidev/psi/ms/object_rules/ParameterFileInSourceFileListObjectRule.java:38
Method
PrecursorListType
()
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/PrecursorListType.java:65
Method
PrecursorType
()
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/PrecursorType.java:66
Method
ProcessingMethod
()
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/DataProcessingType.java:246
Method
ReferenceableParamGroupListType
()
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/ReferenceableParamGroupListType.java:65
Method
ReferenceableParamGroupType
()
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/ReferenceableParamGroupType.java:56
Method
RuleFilterManager
(File xmlFile)
validator/src/main/java/psidev/psi/ms/rulefilter/RuleFilterManager.java:45
Method
RunType
()
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/RunType.java:95
Method
SampleListType
()
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/SampleListType.java:65
Method
SampleType
()
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/SampleType.java:59
Method
Scan
()
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/SpectrumDescriptionType.java:293
Method
SelectionWindow
()
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/SpectrumDescriptionType.java:561
Method
SelectionWindowList
()
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/SpectrumDescriptionType.java:425
Method
Software
()
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/SoftwareListType.java:247
Method
SoftwareListObjectRule
()
validator/src/main/java/psidev/psi/ms/object_rules/SoftwareListObjectRule.java:44
Method
SoftwareListType
()
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/SoftwareListType.java:87
Method
SoftwareParam
()
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/SoftwareListType.java:393
Method
SourceFileListType
()
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/SourceFileListType.java:65
Method
SourceFileRef
()
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/RunType.java:509
Method
SourceFileRefList
()
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/RunType.java:369
Method
SourceFileType
()
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/SourceFileType.java:71
Method
SpectrumDescriptionType
()
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/SpectrumDescriptionType.java:95
Method
SpectrumListType
()
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/SpectrumListType.java:65
Method
SpectrumObjectRule
()
validator/src/main/java/psidev/psi/ms/object_rules/SpectrumObjectRule.java:56
Method
SpectrumType
()
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/SpectrumType.java:78
Method
SwingWorker
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
Method
TemplateObjectRule
()
validator/src/main/java/psidev/psi/ms/object_rules/TemplateObjectRule.java:19
Method
ThreadVar
(Thread t)
validator/src/main/java/psidev/psi/ms/swingworker/SwingWorker.java:39
Method
UserParamType
()
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/UserParamType.java:60
Method
ValidationType
(String name)
validator/src/main/java/psidev/psi/ms/ValidationType.java:7
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