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github.com/HUPO-PSI/mzML
/ functions
Functions
679 in github.com/HUPO-PSI/mzML
⨍
Functions
679
◇
Types & classes
91
↓ 34 callers
Method
getId
Gets the value of the id property. @return possible object is {@link String }
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/RunType.java:238
↓ 33 callers
Method
getId
Gets the value of the id property. @return possible object is {@link String }
validator/src/main/java/psidev/psi/ms/rulefilter/jaxb/UserOption.java:152
↓ 27 callers
Method
getCvParam
Gets the value of the cvParam property. <p> This accessor method returns a reference to the live list, not a snapshot. Therefore any modification you
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/ParamGroupType.java:205
↓ 21 callers
Method
checkAccessionsInCVParams
Check if any of the cvParams is one of the accessions @param cvParams @param accessions @return The list of {@link CVParam} found, or an empty list i
validator/src/main/java/psidev/psi/ms/object_rules/util/ObjectRuleUtil.java:17
↓ 21 callers
Method
getValue
Get the value produced by the worker thread, or null if it hasn't been constructed yet.
validator/src/main/java/psidev/psi/ms/swingworker/SwingWorker.java:50
↓ 20 callers
Method
get
Return the value created by the <code>construct</code> method. Returns null if either the constructing thread or the current thread was interrupted be
validator/src/main/java/psidev/psi/ms/swingworker/SwingWorker.java:92
↓ 15 callers
Method
getLevel
()
validator/src/main/java/psidev/psi/ms/MzMLValidatorGUI.java:842
↓ 15 callers
Method
getMessage
(String sourceFileId, boolean massSpectrometerFileTypeFormatError, boolean dataFileChecksumTypeError, bo
validator/src/main/java/psidev/psi/ms/object_rules/MassSpectraOrParameterFileInSourceFileListObjectRule.java:109
↓ 15 callers
Method
toString
()
validator/src/main/java/psidev/psi/ms/ClusteredContext.java:32
↓ 14 callers
Method
clear
()
validator/src/main/java/psidev/psi/ms/swingworker/SwingWorker.java:41
↓ 13 callers
Method
getName
()
validator/src/main/java/psidev/psi/ms/ValidationType.java:11
↓ 13 callers
Method
getProperty
(String propertyName)
validator/src/main/java/psidev/psi/ms/MzMLValidatorGUI.java:606
↓ 12 callers
Method
getCvMappingRuleToSkip
Gets the value of the cvMappingRuleToSkip property. <p> This accessor method returns a reference to the live list, not a snapshot. Therefore any modi
validator/src/main/java/psidev/psi/ms/rulefilter/jaxb/UserOption.java:79
↓ 12 callers
Method
printError
(String aMessage)
validator/src/main/java/psidev/psi/ms/MzMLValidator.java:1135
↓ 11 callers
Method
getObjectRuleToSkip
Gets the value of the objectRuleToSkip property. <p> This accessor method returns a reference to the live list, not a snapshot. Therefore any modific
validator/src/main/java/psidev/psi/ms/rulefilter/jaxb/UserOption.java:108
↓ 10 callers
Method
isValid
Gets the value of the valid property.
validator/src/main/java/psidev/psi/ms/rulefilter/jaxb/ObjectRuleCondition.java:143
↓ 8 callers
Method
getObjectRulesInvalid
()
validator/src/main/java/psidev/psi/ms/ExtendedValidatorReport.java:36
↓ 8 callers
Method
getReferences
Gets the value of the references property. @return possible object is {@link References }
validator/src/main/java/psidev/psi/ms/rulefilter/jaxb/RuleFilter.java:139
↓ 7 callers
Method
setProgress
(int value, String message)
validator/src/main/java/psidev/psi/ms/MzMLValidatorGUI.java:875
↓ 6 callers
Method
checkElementCvMapping
(String xpath, Class clazz)
validator/src/main/java/psidev/psi/ms/MzMLValidator.java:902
↓ 6 callers
Method
getCvMappingRuleConditions
Gets the value of the cvMappingRuleConditions property. @return possible object is {@link CvMappingRuleConditions }
validator/src/main/java/psidev/psi/ms/rulefilter/jaxb/RuleFilter.java:115
↓ 6 callers
Method
getObjectRuleConditions
Gets the value of the objectRuleConditions property. @return possible object is {@link ObjectRuleConditions }
validator/src/main/java/psidev/psi/ms/rulefilter/jaxb/RuleFilter.java:91
↓ 6 callers
Method
getRulesToSkipRef
Gets the value of the rulesToSkipRef property. <p> This accessor method returns a reference to the live list, not a snapshot. Therefore any modificat
validator/src/main/java/psidev/psi/ms/rulefilter/jaxb/UserOption.java:137
↓ 6 callers
Method
next
()
validator/src/main/java/psidev/psi/ms/MzMLValidator.java:1049
↓ 5 callers
Method
addMessages
(Collection<ValidatorMessage> aNewMessages, MessageLevel aLevel)
validator/src/main/java/psidev/psi/ms/MzMLValidator.java:1154
↓ 5 callers
Method
addValidatorMessage
(String ruleId, ValidatorMessage validatorMessage, MessageLevel msgLevel)
validator/src/main/java/psidev/psi/ms/MzMLValidator.java:968
↓ 5 callers
Method
checkElementObjectRule
(String xpath, Class clazz)
validator/src/main/java/psidev/psi/ms/MzMLValidator.java:920
↓ 5 callers
Method
getCvMappingRulesToSkip
Gets the list of identifiers of cv mapping rules to skip @return
validator/src/main/java/psidev/psi/ms/rulefilter/RuleFilterManager.java:352
↓ 5 callers
Method
getID
()
validator/src/main/java/psidev/psi/ms/rulefilter/MaldiOrEsiCondition.java:7
↓ 5 callers
Method
getMessageCollection
()
validator/src/main/java/psidev/psi/ms/MzMLValidator.java:794
↓ 5 callers
Method
getOption
()
validator/src/main/java/psidev/psi/ms/rulefilter/MaldiOrEsiCondition.java:15
↓ 5 callers
Method
getReferencedRules
Gets the value of the referencedRules property. <p> This accessor method returns a reference to the live list, not a snapshot. Therefore any modifica
validator/src/main/java/psidev/psi/ms/rulefilter/jaxb/References.java:71
↓ 5 callers
Method
getSoftware
Gets the value of the software property. <p> This accessor method returns a reference to the live list, not a snapshot. Therefore any modification yo
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/SoftwareListType.java:168
↓ 5 callers
Method
getSourceFile
Gets the value of the sourceFile property. <p> This accessor method returns a reference to the live list, not a snapshot. Therefore any modification
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/SourceFileListType.java:146
↓ 5 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/CVParamType.java:287
↓ 4 callers
Method
create
(Node node)
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/RunType.java:133
↓ 4 callers
Method
extractResource
Extracts a resource using the classloader of {@code Resources} to locate the resource given by {@code resourcePath}. The extracted resource will be pl
validator/src/main/java/psidev/psi/ms/Resources.java:31
↓ 4 callers
Method
getObjectRuleById
Search for a rule in a collection of rules @param ruleId @param map @return
validator/src/main/java/psidev/psi/ms/ExtendedValidatorReport.java:161
↓ 4 callers
Method
getObjectRulesNotChecked
()
validator/src/main/java/psidev/psi/ms/ExtendedValidatorReport.java:28
↓ 4 callers
Method
getObjectRulesValid
()
validator/src/main/java/psidev/psi/ms/ExtendedValidatorReport.java:32
↓ 4 callers
Method
getPrecursorList
Gets the value of the precursorList property. @return possible object is {@link PrecursorListType }
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/SpectrumDescriptionType.java:198
↓ 4 callers
Method
getRef
Gets the value of the ref property. @return possible object is {@link String }
validator/src/main/java/psidev/psi/ms/rulefilter/jaxb/RulesToSkipRef.java:51
↓ 4 callers
Method
getTotalCvRules
()
validator/src/main/java/psidev/psi/ms/ExtendedValidatorReport.java:270
↓ 4 callers
Method
getUserParam
Gets the value of the userParam property. <p> This accessor method returns a reference to the live list, not a snapshot. Therefore any modification y
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/ParamGroupType.java:234
↓ 4 callers
Method
isMIAPEValidationSelected
()
validator/src/main/java/psidev/psi/ms/MzMLValidatorGUI.java:601
↓ 4 callers
Method
printCvMappingRules
(StringBuilder sb, String header, Collection<CvRule> rules)
validator/src/main/java/psidev/psi/ms/ExtendedValidatorReport.java:213
↓ 3 callers
Method
clusterByMessagesAndRules
Clusters the ValidatorMessages @param messages @return
validator/src/main/java/psidev/psi/ms/MzMLValidator.java:672
↓ 3 callers
Method
create
(Node node)
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/SpectrumDescriptionType.java:132
↓ 3 callers
Method
enableRadioButtons
(boolean b)
validator/src/main/java/psidev/psi/ms/MzMLValidatorGUI.java:424
↓ 3 callers
Method
getAccession
Gets the value of the accession property. @return possible object is {@link String }
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/MzMLType.java:412
↓ 3 callers
Method
getCVMappingRulesToSkipByUserOptions
Look for the chosen options in the rule filter file and returns a list with the identifiers of the rules to exclude @param selectedOptions
validator/src/main/java/psidev/psi/ms/rulefilter/RuleFilterManager.java:99
↓ 3 callers
Method
getCvMappingRuleCondition
Gets the value of the cvMappingRuleCondition property. <p> This accessor method returns a reference to the live list, not a snapshot. Therefore any m
validator/src/main/java/psidev/psi/ms/rulefilter/jaxb/CvMappingRuleConditions.java:71
↓ 3 callers
Method
getId
()
validator/src/main/java/psidev/psi/ms/object_rules/InstrumentConfigurationObjectRule.java:152
↓ 3 callers
Method
getMandatoryElements
Gets a list of mandatory elements @return
validator/src/main/java/psidev/psi/ms/rulefilter/RuleFilterManager.java:71
↓ 3 callers
Method
getObjectRuleCondition
Gets the value of the objectRuleCondition property. <p> This accessor method returns a reference to the live list, not a snapshot. Therefore any modi
validator/src/main/java/psidev/psi/ms/rulefilter/jaxb/ObjectRuleConditions.java:71
↓ 3 callers
Method
getObjectRulesToSkip
(UserCondition condition, String optionId)
validator/src/main/java/psidev/psi/ms/rulefilter/RuleFilterManager.java:185
↓ 3 callers
Method
getPrecursor
Gets the value of the precursor property. <p> This accessor method returns a reference to the live list, not a snapshot. Therefore any modification y
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/PrecursorListType.java:145
↓ 3 callers
Method
getSourceFileRef
Gets the value of the sourceFileRef property. @return possible object is {@link String }
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/SpectrumType.java:302
↓ 3 callers
Method
getUserOption
Gets the value of the userOption property. <p> This accessor method returns a reference to the live list, not a snapshot. Therefore any modification
validator/src/main/java/psidev/psi/ms/rulefilter/jaxb/UserCondition.java:75
↓ 3 callers
Method
printObjectRules
(StringBuilder sb, String header, Collection<ObjectRule> rules)
validator/src/main/java/psidev/psi/ms/ExtendedValidatorReport.java:222
↓ 3 callers
Method
startValidation
Starts the validation of a mzML file @param mzMLFile File with the mzML file to validate. @return Collection with validator messages.
validator/src/main/java/psidev/psi/ms/MzMLValidator.java:517
↓ 2 callers
Method
addCvMappingRulesToSkip
Add a collection of cv mapping rules identifiers to the list of cv mapping rules to skip @param cvMappingRulesIdentifiers
validator/src/main/java/psidev/psi/ms/rulefilter/RuleFilterManager.java:302
↓ 2 callers
Method
addObjectRulesToSkip
Add a collection of object rules identifiers to the list of object rules to skip @param objectRulesIdentifiers
validator/src/main/java/psidev/psi/ms/rulefilter/RuleFilterManager.java:314
↓ 2 callers
Method
canCheck
(Object o)
validator/src/main/java/psidev/psi/ms/object_rules/SpectrumObjectRule.java:67
↓ 2 callers
Method
check
(Spectrum spectrum)
validator/src/main/java/psidev/psi/ms/object_rules/SpectrumObjectRule.java:71
↓ 2 callers
Method
checkCvMapping
(Collection<?> collection, String xPath)
validator/src/main/java/psidev/psi/ms/MzMLValidator.java:939
↓ 2 callers
Method
create
(Node node)
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/PrecursorType.java:104
↓ 2 callers
Method
create
(Node node)
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/SpectrumListType.java:103
↓ 2 callers
Method
create
(Node node)
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/CVType.java:101
↓ 2 callers
Method
create
(Node node)
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/SoftwareListType.java:125
↓ 2 callers
Method
create
(Node node)
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/SoftwareListType.java:285
↓ 2 callers
Method
create
(Node node)
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/SoftwareListType.java:431
↓ 2 callers
Method
create
(Node node)
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/SourceFileListType.java:103
↓ 2 callers
Method
create
(Node node)
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/RunType.java:407
↓ 2 callers
Method
create
(Node node)
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/RunType.java:547
↓ 2 callers
Method
create
(Node node)
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/PrecursorListType.java:103
↓ 2 callers
Method
create
(Node node)
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/InstrumentSoftwareRefType.java:90
↓ 2 callers
Method
create
(Node node)
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/SampleListType.java:103
↓ 2 callers
Method
create
(Node node)
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/ParamGroupRefType.java:138
↓ 2 callers
Method
create
(Node node)
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/SpectrumType.java:116
↓ 2 callers
Method
create
(Node node)
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/BinaryDataArrayType.java:106
↓ 2 callers
Method
create
(Node node)
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/InstrumentListType.java:103
↓ 2 callers
Method
create
(Node node)
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/SourceFileType.java:109
↓ 2 callers
Method
create
(Node node)
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/CVListType.java:103
↓ 2 callers
Method
create
(Node node)
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/AcquisitionType.java:100
↓ 2 callers
Method
create
(Node node)
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/MzMLType.java:132
↓ 2 callers
Method
create
(Node node)
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/InstrumentType.java:105
↓ 2 callers
Method
create
(Node node)
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/SpectrumDescriptionType.java:331
↓ 2 callers
Method
create
(Node node)
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/SpectrumDescriptionType.java:463
↓ 2 callers
Method
create
(Node node)
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/SpectrumDescriptionType.java:599
↓ 2 callers
Method
create
(Node node)
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/AcquisitionListType.java:109
↓ 2 callers
Method
create
(Node node)
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/CVParamType.java:107
↓ 2 callers
Method
create
(Node node)
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/DataProcessingListType.java:103
↓ 2 callers
Method
create
(Node node)
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/ComponentType.java:100
↓ 2 callers
Method
create
(Node node)
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/UserParamType.java:98
↓ 2 callers
Method
create
(Node node)
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/ComponentListType.java:115
↓ 2 callers
Method
create
(Node node)
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/FileChecksumType.java:97
↓ 2 callers
Method
create
(Node node)
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/DataProcessingType.java:114
↓ 2 callers
Method
create
(Node node)
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/DataProcessingType.java:284
↓ 2 callers
Method
create
(Node node)
validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/ReferenceableParamGroupType.java:94
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