Uses of Class
uk.ac.ebi.adfconverter.tools.checker.exceptions.IncorrectFileStructure

Packages that use IncorrectFileStructure

uk.ac.ebi.adfconverter.tools.checker
uk.ac.ebi.adfconverter.tools.converter
uk.ac.ebi.adfconverter.tools.filestructure

Uses of IncorrectFileStructure in uk.ac.ebi.adfconverter.tools.checker

Methods in uk.ac.ebi.adfconverter.tools.checker that throw IncorrectFileStructure

CorrectableDataTable	OptimizedFileChecker.checkFileAndCurate(java.io.File checkFile, java.lang.String fileStructure, boolean strictMode, boolean stepByStepMode) Checks and curates a data file.
CorrectableDataTable	OptimizedFileChecker.checkFileAndCurate(java.io.File checkFile, java.lang.String fileStructure, java.lang.String structureName, boolean strictMode, boolean stepByStepMode) Checks and curates a data file.
boolean	OptimizedFileChecker.checkVerticalDataTable(DataTable dataTable, HeaderType header, boolean strictMode, boolean doCuration, boolean stepByStepMode) checks a vertical data table against a structure file The whole table is checked ( not row by row)
boolean	OptimizedADFChecker.check(java.io.File _ADFFile, boolean strictMode, boolean stepByStepMode) Check an ADF.
ADFJava	OptimizedADFChecker.checkAndCurateADF(java.io.File _ADFFile, boolean strictMode, boolean stepByStepMode) Check if an ADF is correct and retrieves the ADFJava object
void	OptimizedADFChecker.createCompositeSequence(ADFReporter reporter) In case of simple microarray layout, create the composite sequence associated to the reporter Data, are simply copy from reporter to compositeSequence
CorrectableDataTable	FileChecker.checkFileAndCurate(java.io.File checkFile, FileType fileStructure, boolean strictMode, boolean stepByStepMode) Checks and curates a data file.
boolean	FileChecker.checkFile(java.io.File checkFile, FileType fileStructure, boolean strictMode, boolean doCuration, boolean stepByStepMode) Checks a data file .
CorrectableDataTable	FileChecker.checkTableAndCurate(DataTable table, HeaderType headerStructure, boolean strictMode, boolean stepByStepMode) checks a data table against a structure file and returns the corrected/curated (if needed) data table
boolean	FileChecker.checkDataTable(DataTable dataTable, HeaderType header, boolean strictMode, boolean doCuration, boolean stepByStepMode) * checks a data table against a structure file
boolean	ADFChecker.check(java.io.File _ADFFile, boolean strictMode, boolean stepByStepMode) Check an ADF.
ADFJava	ADFChecker.checkAndCurateADF(java.io.File _ADFFile, boolean strictMode, boolean stepByStepMode) Check if an ADF is correct and retrieves the ADFJava object
boolean	ADFChecker.CheckTables(DataTable headerTable, DataTable featureReporterTable, DataTable compositeSequenceTable, boolean strictMode, boolean stepByStepMode) Check an ADF.

Uses of IncorrectFileStructure in uk.ac.ebi.adfconverter.tools.converter

Methods in uk.ac.ebi.adfconverter.tools.converter that throw IncorrectFileStructure

ADFJava	MAGEToADFConverter.convertToADF(java.io.File magefile) Converts data from a MAGE-ML file to ADFJava.
void	MAGEToADFConverter.convertHeader(PhysicalArrayDesign mageobj) Retrieves a ADF header data from a Physical ArrayDesign Add data to the current ADFJava object corresponding to the mage data.
ADFCompositeSequence	MAGEToADFConverter.createCompositeSequence(ADFReporter reporter) In case of simple microarray layout, create the composite sequence associated to the reporter Data, are simply copy from reporter to compositeSequence

Uses of IncorrectFileStructure in uk.ac.ebi.adfconverter.tools.filestructure

Methods in uk.ac.ebi.adfconverter.tools.filestructure that throw IncorrectFileStructure

DataType	FileStructureDescription.getNextDataType() Retrieves the next DataType object in the structure definition
DataType	FileStructureDescription.getPreviousData() Retrieves the previous DataType object in the structure definition
DataType	FileStructureDescription.getDataType(java.lang.String dataName) Retrieves the DataType object with a given dataname.
TableType	FileStructureDescription.getNextTable() Retrieves the next table object in the structure definition hierarchy/tree
TableType	FileStructureDescription.getPreviousTable() Retrieves the previous table object in the structure definition hierarchy/tree
TableType	FileStructureDescription.getTableType(java.lang.String tableName) Retrieves the TableType object with a given name.
HeaderType	FileStructureDescription.getHeaderType() Retrieves the headerType attribut
CorrectableHeaderItem	FileStructureDescription.getAssociatedSimpleMicroArrayLayoutItem(CorrectableHeaderItem item) Retrieves the associated Simple Microarray layout item associated to a given item in the structure definition.
CorrectableHeaderItem	FileStructureDescription.getAssociatedSimpleMicroArrayLayoutItem(CorrectableHeaderItem item, int columnNumber) Retrieves the associated Simple Microarray layout item associated to a given item in the structure definition.
CorrectableHeaderItem	FileStructureDescription.createItem(java.lang.String type) Create an item object of a given type.
CorrectableHeaderItem	FileStructureDescription.createItem(java.lang.String type, int columnNumber) Create a CorrectableHeaderItem object with a given type