Index (ADF MAGE-ML Tool)

Overview

Package

Class

Use

Tree

Index

Help

PREV NEXT

FRAMES NO FRAMES

A C D E F G H I J L M N O P R S T U V W X _

A

ADFBioSequence - class uk.ac.ebi.adfconverter.data.adf.ADFBioSequence.: This class represents a BioSequence, from ADF data, in the tool.
ADFBioSequence() - Constructor for class uk.ac.ebi.adfconverter.data.adf.ADFBioSequence: Default Constructor of an ADFBioSequence object.
ADFBioSequence(int) - Constructor for class uk.ac.ebi.adfconverter.data.adf.ADFBioSequence: Constructor of an ADFBioSequence object with a maximum capacity
ADFCconverterGUI - class uk.ac.ebi.adfconverter.usermode.gui.ADFCconverterGUI.
ADFCconverterGUI() - Constructor for class uk.ac.ebi.adfconverter.usermode.gui.ADFCconverterGUI
ADFChecker - class uk.ac.ebi.adfconverter.tools.checker.ADFChecker.: Class for file strcuture checking will check file structure and data contained in a file
ADFChecker() - Constructor for class uk.ac.ebi.adfconverter.tools.checker.ADFChecker: Default Constructor of FileChecker inits sub tables
ADFChecker(File) - Constructor for class uk.ac.ebi.adfconverter.tools.checker.ADFChecker: Constructor of FileChecker
ADFCompositeSequence - class uk.ac.ebi.adfconverter.data.adf.ADFCompositeSequence.: This class represents a CompositeSequence, from ADF data, in the tool.
ADFCompositeSequence() - Constructor for class uk.ac.ebi.adfconverter.data.adf.ADFCompositeSequence: Default ADFCompositeSequence class Constructor Inits associated biosequence, reporter, composite sequence and group lists
ADFCompositeSequence(int) - Constructor for class uk.ac.ebi.adfconverter.data.adf.ADFCompositeSequence: ADFCompositeSequence class Constructor with a given capacity (to limit memory usage) Inits associated biosequence, reporter, composite sequence and group lists
ADFCompositeSequenceGroup - class uk.ac.ebi.adfconverter.data.adf.ADFCompositeSequenceGroup.: This class represents a group of ADFCompositeSequences.
ADFCompositeSequenceGroup() - Constructor for class uk.ac.ebi.adfconverter.data.adf.ADFCompositeSequenceGroup: Default Constructor
ADFCompositeSequenceGroup(String, CorrectableHeaderItem) - Constructor for class uk.ac.ebi.adfconverter.data.adf.ADFCompositeSequenceGroup: Constructor of an ADFCompositeSequenceGroup object, with a given name and the corresponding item from the ADF file.
ADFConverterCommandLine - class uk.ac.ebi.adfconverter.usermode.commandline.ADFConverterCommandLine.: Created on 12 sept. 2004 Class to access to the ADFConverter tool (the Library) by command line.
ADFConverterCommandLine() - Constructor for class uk.ac.ebi.adfconverter.usermode.commandline.ADFConverterCommandLine
ADFConverterConfiguration - class uk.ac.ebi.adfconverter.common.configuration.ADFConverterConfiguration.: Allows the configuration of ADFConverter from an external file All option values admit variable substitution.
ADFConverterConfiguration() - Constructor for class uk.ac.ebi.adfconverter.common.configuration.ADFConverterConfiguration: Constructor of the ADFConverterConfiguration init list of mandatory properties
ADFConverterFileReader - interface uk.ac.ebi.adfconverter.common.tools.file.reader.ADFConverterFileReader.: Interface for all file format classes used in reading data
ADFConverterFileReaderImpl - class uk.ac.ebi.adfconverter.common.tools.file.reader.ADFConverterFileReaderImpl.: Interface for all file format classes used in reading data
ADFConverterFileReaderImpl(String) - Constructor for class uk.ac.ebi.adfconverter.common.tools.file.reader.ADFConverterFileReaderImpl: Create an instance of a file reader for a give file
ADFConverterFileReaderImpl(String, String) - Constructor for class uk.ac.ebi.adfconverter.common.tools.file.reader.ADFConverterFileReaderImpl: Create an instance of a file reader for a give file with a given Java character encoding
ADFConverterFileReaderImpl(File) - Constructor for class uk.ac.ebi.adfconverter.common.tools.file.reader.ADFConverterFileReaderImpl: Create an instance of a file reader for a give file
ADFConverterFileReaderImpl(File, String) - Constructor for class uk.ac.ebi.adfconverter.common.tools.file.reader.ADFConverterFileReaderImpl: Create an instance of a file reader for a give file with a given Java character encoding
ADFConverterFileWriter - interface uk.ac.ebi.adfconverter.common.tools.file.writer.ADFConverterFileWriter.: Interface for all file format classes used in writing data
ADFConverterFileWriterImpl - class uk.ac.ebi.adfconverter.common.tools.file.writer.ADFConverterFileWriterImpl.: Interface for all file format classes used in writing data
ADFConverterFileWriterImpl(File) - Constructor for class uk.ac.ebi.adfconverter.common.tools.file.writer.ADFConverterFileWriterImpl: Create an instance of a file writer for a give file
ADFConverterFileWriterImpl(File, String) - Constructor for class uk.ac.ebi.adfconverter.common.tools.file.writer.ADFConverterFileWriterImpl: Create an instance of a file writer for a give file with a given Java character encoding
ADFConverterLibrary - class uk.ac.ebi.adfconverter.library.ADFConverterLibrary.: This class is a library, it gathers methods to treat data file (MAGE-ML & ADF) It offers tool initialisation methods, data file treatment, ADF checking and conversion, MAGE-ML checking and conversion.
ADFConverterLibrary(String, Properties) - Constructor for class uk.ac.ebi.adfconverter.library.ADFConverterLibrary: Contructor for the ADFConverterLibrary class Inits the application
ADFConverterLogger - interface uk.ac.ebi.adfconverter.common.tools.log.ADFConverterLogger.: Interface of tool log.
ADFConverterLoggerImpl - class uk.ac.ebi.adfconverter.common.tools.log.ADFConverterLoggerImpl.: Implements tool logger using Log4J API.
ADFConverterLoggerImpl() - Constructor for class uk.ac.ebi.adfconverter.common.tools.log.ADFConverterLoggerImpl: Constructor of the ADFConverterLoggerImpl class Inits list of used log (as hashtable)
ADFConverterLoggerImpl(String) - Constructor for class uk.ac.ebi.adfconverter.common.tools.log.ADFConverterLoggerImpl: Constructor Should be removed for optimisation
ADFConverterLoggerImpl(Class) - Constructor for class uk.ac.ebi.adfconverter.common.tools.log.ADFConverterLoggerImpl: Constructor of the ADFConverterLoggerImpl class for a given class object should be removed
ADFConverterLoggerImpl(File) - Constructor for class uk.ac.ebi.adfconverter.common.tools.log.ADFConverterLoggerImpl: Constructor of the ADFConverterLoggerImpl class for a given treated file
ADFConverterLoggerImpl(Class, File) - Constructor for class uk.ac.ebi.adfconverter.common.tools.log.ADFConverterLoggerImpl: Constructor of the ADFConverterLoggerImpl class for a given class object and a given file object should be removed
ADFConverterNetwork - class uk.ac.ebi.adfconverter.tools.networking.ADFConverterNetwork.: This class handles network connection.
ADFConverterNetwork() - Constructor for class uk.ac.ebi.adfconverter.tools.networking.ADFConverterNetwork: Constructor
ADFConverterSendMail - class uk.ac.ebi.adfconverter.common.tools.net.mail.ADFConverterSendMail.: Class to send e-mail.
ADFConverterSendMail(String) - Constructor for class uk.ac.ebi.adfconverter.common.tools.net.mail.ADFConverterSendMail: Constructor of the ADFConverterSendMail class.
ADFConverterSendMail(String, String, String) - Constructor for class uk.ac.ebi.adfconverter.common.tools.net.mail.ADFConverterSendMail: Constructor of the ADFConverterSendMail class.
ADFDesignElement - class uk.ac.ebi.adfconverter.data.adf.ADFDesignElement.: Class Representing a Design element from ADF in the tool Each ADFDesignElement has associated biosequences
ADFDesignElement() - Constructor for class uk.ac.ebi.adfconverter.data.adf.ADFDesignElement: Default Constructor Inits associated biosequence group lists
ADFDesignElement(int) - Constructor for class uk.ac.ebi.adfconverter.data.adf.ADFDesignElement: Constructor with a default object capacity
ADFExporter - class uk.ac.ebi.adfconverter.tools.exporter.ADFExporter.: Class used to export ADF data objects in ADF files (One workbook or 2-3 plain text files)
ADFExporter(Properties) - Constructor for class uk.ac.ebi.adfconverter.tools.exporter.ADFExporter: Constructor for class initialisation init the default output file format, if not specified
ADFExporter(String) - Constructor for class uk.ac.ebi.adfconverter.tools.exporter.ADFExporter: Constructor of th ADF exporter init unMoveable Items Do nothing
ADFExporterInitException - exception uk.ac.ebi.adfconverter.tools.exporter.exceptions.ADFExporterInitException.: Signals an error during the initialisation of the ADF Exporter.
ADFExporterInitException() - Constructor for class uk.ac.ebi.adfconverter.tools.exporter.exceptions.ADFExporterInitException: Exception if the file structure description file is incorrect with no specified element
ADFFeature - class uk.ac.ebi.adfconverter.data.adf.ADFFeature.: Class Representing a Design element from ADF in the tool Each ADFFeature has always an associated Reporter.
ADFFeature() - Constructor for class uk.ac.ebi.adfconverter.data.adf.ADFFeature: Default ADFFeature Constructor
ADFFeature(int) - Constructor for class uk.ac.ebi.adfconverter.data.adf.ADFFeature: ADFFeature Constructor with a default capacity
ADFFeature(ADFReporter) - Constructor for class uk.ac.ebi.adfconverter.data.adf.ADFFeature: ADFFeature Constructor with an associated reporter
ADFGroup - class uk.ac.ebi.adfconverter.data.adf.ADFGroup.: Class representing a Group in ADF Super class for ADFReporterGroup and ADFCompositeSequenceGroup
ADFGroup() - Constructor for class uk.ac.ebi.adfconverter.data.adf.ADFGroup: Default Constructor with no group name or header item corresponding to the group
ADFGroup(String, CorrectableHeaderItem) - Constructor for class uk.ac.ebi.adfconverter.data.adf.ADFGroup: ADFGroup class Constructor with a given group name and an associated headeritem
ADFJava - class uk.ac.ebi.adfconverter.data.adf.ADFJava.: Root Object representing an ADF file/data set.s Composed of an header part, several features, reporters and CompositeSequences(optional) data The internal ADF representation is based on the ADF file structure.
ADFJava() - Constructor for class uk.ac.ebi.adfconverter.data.adf.ADFJava: Default ADFJava Constructor Inits associated tables
ADFJava(CorrectableDataTable) - Constructor for class uk.ac.ebi.adfconverter.data.adf.ADFJava: testing purpose
ADFJava(CorrectableDataTable, CorrectableDataTable, CorrectableDataTable, CorrectableDataTable, CorrectableDataTable, Hashtable, Hashtable) - Constructor for class uk.ac.ebi.adfconverter.data.adf.ADFJava: ADFJava class Constructor with associated elements (header, feature, reporter, CompositeSequence biosequence, and group lists.
ADFReporter - class uk.ac.ebi.adfconverter.data.adf.ADFReporter.: This class represents an ADF reporter in the tool.
ADFReporter() - Constructor for class uk.ac.ebi.adfconverter.data.adf.ADFReporter: Default ADFReporter class Constructor; Inits associated objects lists ( biosequences, CompositeSequence, groups)
ADFReporter(int) - Constructor for class uk.ac.ebi.adfconverter.data.adf.ADFReporter: ADFReporter Constructor with a given row capacity (maximal number of data) Inits associated objects lists ( biosequences, CompositeSequence, groups)
ADFReporterGroup - class uk.ac.ebi.adfconverter.data.adf.ADFReporterGroup.: the class represents an ADF Reporter Group, a set of reporters with a same characteritics.
ADFReporterGroup() - Constructor for class uk.ac.ebi.adfconverter.data.adf.ADFReporterGroup: Default ADFReporterGroup class constructor
ADFReporterGroup(String, CorrectableHeaderItem) - Constructor for class uk.ac.ebi.adfconverter.data.adf.ADFReporterGroup: ADFReporterGroup class Constructor with a group name and an associated ADF header item
ADFToMAGEConverter - class uk.ac.ebi.adfconverter.tools.converter.ADFToMAGEConverter.: Convert ADF data in MAGE objects.
ADFToMAGEConverter() - Constructor for class uk.ac.ebi.adfconverter.tools.converter.ADFToMAGEConverter: Constructor of the ADFToMAGEConvert class inits list of contract attributes
ADFToMAGEConverter(Properties) - Constructor for class uk.ac.ebi.adfconverter.tools.converter.ADFToMAGEConverter: Constructor of the ADFToMAGEConvert class with additional properties for the converter for class initialisation
AbstractFileChecker - class uk.ac.ebi.adfconverter.tools.checker.AbstractFileChecker.: Abstract class for file checking.
AbstractFileChecker() - Constructor for class uk.ac.ebi.adfconverter.tools.checker.AbstractFileChecker: Constructor
AbstractUnmarshallingEventHandlerImpl - class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.AbstractUnmarshallingEventHandlerImpl.: Convenient default implementation of com.sun.xml.bind.unmarshaller.UnmarshallingEventHandler to minimize code generation.
AbstractUnmarshallingEventHandlerImpl(UnmarshallingContext, String) - Constructor for class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.AbstractUnmarshallingEventHandlerImpl
AppliError(String) - Method in interface uk.ac.ebi.adfconverter.common.tools.log.ADFConverterLogger: Reports an error message to the application log
AppliError(String, Throwable) - Method in interface uk.ac.ebi.adfconverter.common.tools.log.ADFConverterLogger: Reports a error message to the application log with throwable object rise (often an exception)
AppliError(String) - Method in class uk.ac.ebi.adfconverter.common.tools.log.ADFConverterLoggerImpl: Logs an error message into the tool logger
AppliError(String, Throwable) - Method in class uk.ac.ebi.adfconverter.common.tools.log.ADFConverterLoggerImpl: Logs an error message into the tool logger and reports an exception
AppliFatal(String) - Method in interface uk.ac.ebi.adfconverter.common.tools.log.ADFConverterLogger: Reports an fatal message to the application log
AppliFatal(String, Throwable) - Method in interface uk.ac.ebi.adfconverter.common.tools.log.ADFConverterLogger: Reports a fatal message to the application log with throwable object rise (often an exception)
AppliFatal(String) - Method in class uk.ac.ebi.adfconverter.common.tools.log.ADFConverterLoggerImpl: Logs an fatal message into the tool logger
AppliFatal(String, Throwable) - Method in class uk.ac.ebi.adfconverter.common.tools.log.ADFConverterLoggerImpl: Logs an fatal message into the tool logger and reports an exception
AppliInfo(String) - Method in interface uk.ac.ebi.adfconverter.common.tools.log.ADFConverterLogger: Reports an info message to the application log
AppliInfo(String, Throwable) - Method in interface uk.ac.ebi.adfconverter.common.tools.log.ADFConverterLogger: Reports a info message to the application log with throwable object rise (often an exception)
AppliInfo(String) - Method in class uk.ac.ebi.adfconverter.common.tools.log.ADFConverterLoggerImpl: Logs an info message into the tool logger and reports an exception
AppliInfo(String, Throwable) - Method in class uk.ac.ebi.adfconverter.common.tools.log.ADFConverterLoggerImpl: Logs an info message into the tool logger and reports an exception
AppliWarn(String) - Method in interface uk.ac.ebi.adfconverter.common.tools.log.ADFConverterLogger: Reports an warn message to the application log
AppliWarn(String, Throwable) - Method in interface uk.ac.ebi.adfconverter.common.tools.log.ADFConverterLogger: Reports a warn message to the application log with throwable object rise (often an exception)
AppliWarn(String) - Method in class uk.ac.ebi.adfconverter.common.tools.log.ADFConverterLoggerImpl: Logs an warn message into the tool logger and reports an exception
AppliWarn(String, Throwable) - Method in class uk.ac.ebi.adfconverter.common.tools.log.ADFConverterLoggerImpl: Logs an warn message into the tool logger and reports an exception
Applidebug(String) - Method in interface uk.ac.ebi.adfconverter.common.tools.log.ADFConverterLogger: reports a message to the application level at debug level
Applidebug(String, Throwable) - Method in interface uk.ac.ebi.adfconverter.common.tools.log.ADFConverterLogger: Reports a debug message to the application log with throwable object rise (often an exception)
Applidebug(String) - Method in class uk.ac.ebi.adfconverter.common.tools.log.ADFConverterLoggerImpl: Logs a debug message into the tool logger
Applidebug(String, Throwable) - Method in class uk.ac.ebi.adfconverter.common.tools.log.ADFConverterLoggerImpl: Logs a debug message into the tool logger and reports an exception
accept(File, String) - Method in class uk.ac.ebi.adfconverter.library.DirectoryFilter: retrieved if a file accepted by the filter.
accept(File, String) - Method in class uk.ac.ebi.adfconverter.library.FileFilter: retrieved if a file accepted by the filter.
accept(File, String) - Method in class uk.ac.ebi.adfconverter.library.NameFilter: retrieved if a file accepted by the filter.
add(String) - Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.DataRow: Adds a String datum to the next location in the Row
add(StringBuffer) - Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.DataRow: Adds a StringBuffer datum to the next location in the row
add(DataBuffer) - Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.DataRow: Adds a DataBuffer datum to the next location in the row
add(StringBuffer, int) - Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.DataRow: Adds a StringBuffer datum at a given position in the current row stores as DataBuffer
add(String, int) - Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.DataRow: Adds a String datum at a given position in the current row stores as DataBuffer
add(DataBuffer, int) - Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.DataRow: Adds a databuffer datum at a given position in the current row
addApprouvedDBFile(String) - Static method in class uk.ac.ebi.adfconverter.tools.checker.DatabaseChecker: DBFileStructureDescriptionFileName is the same of all DBfile loaded duriing execution
addBioSequence(ADFBioSequence) - Method in class uk.ac.ebi.adfconverter.data.adf.ADFDesignElement: sets biosequences associated to the reporter
addCompositeSequence(ADFCompositeSequence) - Method in class uk.ac.ebi.adfconverter.data.adf.ADFCompositeSequence: add an associated compositeSequence to the current CompositeSequence
addCompositeSequencegroup(ADFCompositeSequenceGroup) - Method in class uk.ac.ebi.adfconverter.data.adf.ADFCompositeSequence: add CompositeSequenceGroup associated to the compositeSequence
addCompositeSequences(ADFCompositeSequence) - Method in class uk.ac.ebi.adfconverter.data.adf.ADFReporter: sets a compositeSequence associated to the reporter
addEmpty() - Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.DataRow: Adds an empty item (spacer)
addExtension(String) - Method in class uk.ac.ebi.adfconverter.library.FileFilter: Adds authorise file extension
addItem(CorrectableHeaderItem, int) - Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.CorrectableDataTableHeader: Adds an item to the header list
addItem(CorrectableHeaderItem) - Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.CorrectableDataTableHeader: Adds an item to the header list
addItem(HeaderItem, int) - Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.DataTableHeader: Adds an item to the header list
addItem(HeaderItem) - Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.DataTableHeader: Adds an item to the header list for convenience
addItem(String) - Method in class uk.ac.ebi.adfconverter.usermode.gui.visualisation.DataVisualisationTable: Adds an empty column with a given name to the table
addItem(String, Object[]) - Method in class uk.ac.ebi.adfconverter.usermode.gui.visualisation.DataVisualisationTable: Adds an column with a given name to the table
addName(String) - Method in class uk.ac.ebi.adfconverter.library.NameFilter: Add a fime name filter
addPatcher(Runnable) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.SAXUnmarshallerHandlerImpl
addPatcher(Runnable) - Method in interface uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.UnmarshallingContext: Adds a job that will be executed at the last of the unmarshalling.
addProperty(String, String) - Static method in class uk.ac.ebi.adfconverter.common.configuration.ADFConverterConfiguration: Adds a property to the configuration
addReporter(ADFReporter) - Method in class uk.ac.ebi.adfconverter.data.adf.ADFCompositeSequence: Associates a reporter to the current object
addRow(DataRow) - Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.DataTable: Adds a datarow in the table
addToIdTable(String) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.SAXUnmarshallerHandlerImpl
addToIdTable(String) - Method in interface uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.UnmarshallingContext: Adds the object which is currently being unmarshalled to the ID table.
addValue(float) - Method in class uk.ac.ebi.adfconverter.tools.monitor.MemMonitor.Data
adfHandler(File, boolean, boolean) - Method in class uk.ac.ebi.adfconverter.library.ADFConverterLibrary: Manages ADF - file or directory For checking only or checking and conversion
append(DataBuffer) - Method in class uk.ac.ebi.adfconverter.common.data.DataBuffer: Appends the DataBuffer to the current one Add the String og the databuffer to the end of the current one
append(String) - Method in class uk.ac.ebi.adfconverter.common.data.DataBuffer: Appends the DataBuffer to the current one Add the String og the databuffer to the end of the current one
append(char) - Method in class uk.ac.ebi.adfconverter.common.data.DataBuffer: Appends a char to the current one Add the char og the databuffer to the end of the current one
append(char[]) - Method in class uk.ac.ebi.adfconverter.common.data.DataBuffer: Appends a char array to the current one Add the char array og the databuffer to the end of the current one
application - Variable in class uk.ac.ebi.adfconverter.data.adf.ADFJava: application representation the microarray application, the experiment is used for.
assignFirstValue(MGEDOntologyEntry) - Method in class uk.ac.ebi.adfconverter.tools.checker.ontology.MGEDOntologyChecker: Assign first value to current entry if assignable
availableElement() - Method in class uk.ac.ebi.adfconverter.tools.checker.Cardinality: Infocates if an element can still be add

C

Cardinality - class uk.ac.ebi.adfconverter.tools.checker.Cardinality.: Class for checking item or field cardinality in a table.
Cardinality(String, int) - Constructor for class uk.ac.ebi.adfconverter.tools.checker.Cardinality: Constructor of a cardinality Object with a given lower bound
Cardinality(String, int, int) - Constructor for class uk.ac.ebi.adfconverter.tools.checker.Cardinality: Constructor of a cardinality Object with a given lower bound
CardinalityType - interface uk.ac.ebi.adfconverter.tools.checker.data.CardinalityType.: Cardinality of an item or value in a field Represent by a minimal occur and a maximal Java content class for CardinalityType complex type.
CardinalityTypeImpl - class uk.ac.ebi.adfconverter.tools.checker.data.impl.CardinalityTypeImpl.
CardinalityTypeImpl() - Constructor for class uk.ac.ebi.adfconverter.tools.checker.data.impl.CardinalityTypeImpl
CardinalityTypeImpl.Unmarshaller - class uk.ac.ebi.adfconverter.tools.checker.data.impl.CardinalityTypeImpl.Unmarshaller.
CardinalityTypeImpl.Unmarshaller(UnmarshallingContext) - Constructor for class uk.ac.ebi.adfconverter.tools.checker.data.impl.CardinalityTypeImpl.Unmarshaller
CheckRuleType - interface uk.ac.ebi.adfconverter.tools.checker.data.CheckRuleType.: Rule for checking: using pattern to identify items Java content class for CheckRuleType complex type.
CheckRuleTypeImpl - class uk.ac.ebi.adfconverter.tools.checker.data.impl.CheckRuleTypeImpl.
CheckRuleTypeImpl() - Constructor for class uk.ac.ebi.adfconverter.tools.checker.data.impl.CheckRuleTypeImpl
CheckRuleTypeImpl.Unmarshaller - class uk.ac.ebi.adfconverter.tools.checker.data.impl.CheckRuleTypeImpl.Unmarshaller.
CheckRuleTypeImpl.Unmarshaller(UnmarshallingContext) - Constructor for class uk.ac.ebi.adfconverter.tools.checker.data.impl.CheckRuleTypeImpl.Unmarshaller
CheckTables(DataTable, DataTable, DataTable, boolean, boolean) - Method in class uk.ac.ebi.adfconverter.tools.checker.ADFChecker: Check an ADF.
CheckerPREFIX - Static variable in class uk.ac.ebi.adfconverter.common.configuration.ADFConverterConfiguration: Definition of the adfconverter property name sub prefix for the checker module: checker.
ConfigurationMissingConfException - exception uk.ac.ebi.adfconverter.common.configuration.exceptions.ConfigurationMissingConfException.: Signals an error of application configuration.
ConfigurationMissingConfException() - Constructor for class uk.ac.ebi.adfconverter.common.configuration.exceptions.ConfigurationMissingConfException: class Constructor
ConstraintType - interface uk.ac.ebi.adfconverter.tools.checker.data.ConstraintType.: Java content class for ConstraintType complex type.
ConstraintTypeImpl - class uk.ac.ebi.adfconverter.tools.checker.data.impl.ConstraintTypeImpl.
ConstraintTypeImpl() - Constructor for class uk.ac.ebi.adfconverter.tools.checker.data.impl.ConstraintTypeImpl
ConstraintTypeImpl.Unmarshaller - class uk.ac.ebi.adfconverter.tools.checker.data.impl.ConstraintTypeImpl.Unmarshaller.
ConstraintTypeImpl.Unmarshaller(UnmarshallingContext) - Constructor for class uk.ac.ebi.adfconverter.tools.checker.data.impl.ConstraintTypeImpl.Unmarshaller
ContentHandlerAdaptor - class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.ContentHandlerAdaptor.: Receives SAX2 events and send the equivalent events to com.sun.xml.bind.serializer.XMLSerializer
ContentHandlerAdaptor(XMLSerializer) - Constructor for class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.ContentHandlerAdaptor
ConvertRegex - class uk.ac.ebi.adfconverter.common.tools.regex.ConvertRegex.: This class convert a String in a Java regular expression.
ConvertRegex() - Constructor for class uk.ac.ebi.adfconverter.common.tools.regex.ConvertRegex
ConvertToMAGE(ADFJava) - Method in class uk.ac.ebi.adfconverter.tools.converter.ADFToMAGEConverter: Method for ADF to MAGE object conversion First step before the MAGE-ML
CorrectableDataTable - class uk.ac.ebi.adfconverter.common.data.tabulardata.CorrectableDataTable.: Object representing a collection of dataRow
CorrectableDataTable() - Constructor for class uk.ac.ebi.adfconverter.common.data.tabulardata.CorrectableDataTable: Creates a new CorrectableDataTable instance.
CorrectableDataTable(File) - Constructor for class uk.ac.ebi.adfconverter.common.data.tabulardata.CorrectableDataTable: Creates a new CorrectableDataTable instance.
CorrectableDataTable(String, File) - Constructor for class uk.ac.ebi.adfconverter.common.data.tabulardata.CorrectableDataTable: Creates a new CorrectableDataTable instance.
CorrectableDataTableHeader - class uk.ac.ebi.adfconverter.common.data.tabulardata.CorrectableDataTableHeader.: This Class represents the list of data table headers which can be modify
CorrectableDataTableHeader() - Constructor for class uk.ac.ebi.adfconverter.common.data.tabulardata.CorrectableDataTableHeader: Constructor of the headerItem class
CorrectableDataTableHeader(int) - Constructor for class uk.ac.ebi.adfconverter.common.data.tabulardata.CorrectableDataTableHeader: Constructor of the headerItem class with an initial capacity for the header list
CorrectableDataTablePool - class uk.ac.ebi.adfconverter.common.util.pool.CorrectableDataTablePool.: Pool class for CorrectableDataTable objects Contains a list of available tables.
CorrectableDataTablePool() - Constructor for class uk.ac.ebi.adfconverter.common.util.pool.CorrectableDataTablePool
CorrectableHeaderItem - class uk.ac.ebi.adfconverter.common.data.tabulardata.CorrectableHeaderItem.: This class represents an header item of a data table which can be use for correct table following a structure
CorrectableHeaderItem() - Constructor for class uk.ac.ebi.adfconverter.common.data.tabulardata.CorrectableHeaderItem: Class contructor : creates an instance without name of item or column number name and column number must be set later
CorrectableHeaderItem(String, int) - Constructor for class uk.ac.ebi.adfconverter.common.data.tabulardata.CorrectableHeaderItem: Class contructor : creates an instance with a given name of item
CorrectableHeaderItem(String, String, int) - Constructor for class uk.ac.ebi.adfconverter.common.data.tabulardata.CorrectableHeaderItem: Class contructor : creates an instance with a given name of item
CorrectableHeaderItem(String, String, String, int) - Constructor for class uk.ac.ebi.adfconverter.common.data.tabulardata.CorrectableHeaderItem: Class contructor : creates an instance with a given name of item
CorrectableHeaderItem(String, String, String, int, String) - Constructor for class uk.ac.ebi.adfconverter.common.data.tabulardata.CorrectableHeaderItem: Class contructor : creates an instance with a given name of item
CorrectableHeaderItem(HeaderItem, String, String, int) - Constructor for class uk.ac.ebi.adfconverter.common.data.tabulardata.CorrectableHeaderItem: Class contructor : creates an instance with a given name of item
CorrectableHeaderItem(CorrectableHeaderItem, String, String) - Constructor for class uk.ac.ebi.adfconverter.common.data.tabulardata.CorrectableHeaderItem: Class contructor : creates an instance with a given name of item
CorrectableHeaderItemPool - class uk.ac.ebi.adfconverter.common.util.pool.CorrectableHeaderItemPool.: Pool class for CorrectableHeaderItem objects Contains a list of available tables.
CorrectableHeaderItemPool() - Constructor for class uk.ac.ebi.adfconverter.common.util.pool.CorrectableHeaderItemPool
castToValidatableObject(Object) - Method in interface uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.GrammarInfo
castToValidatableObject(Object) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.GrammarInfoImpl
castToXMLSerializable(Object) - Method in interface uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.GrammarInfo
castToXMLSerializable(Object) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.GrammarInfoImpl
characters(char[], int, int) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.ContentHandlerAdaptor
characters(char[], int, int) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.SAXUnmarshallerHandlerImpl
check(String, boolean, boolean, boolean, boolean) - Method in class uk.ac.ebi.adfconverter.library.ADFConverterLibrary: Check a file following its name (file extension)
check(File, boolean, boolean) - Method in class uk.ac.ebi.adfconverter.tools.checker.ADFChecker: Check an ADF.
check(File, boolean, boolean) - Method in class uk.ac.ebi.adfconverter.tools.checker.OptimizedADFChecker: Check an ADF.
checkADF(File, boolean, boolean, boolean, boolean) - Method in class uk.ac.ebi.adfconverter.library.ADFConverterLibrary: Check and convert in MAGE-ML a ADF following its name or its ADF adh file
checkADFDirectory(File, boolean, boolean, boolean, boolean) - Method in class uk.ac.ebi.adfconverter.library.ADFConverterLibrary: Check and convert in MAGE-ML a ADF following its name or its ADF adh file
checkADFFile(File, boolean, boolean, boolean, boolean) - Method in class uk.ac.ebi.adfconverter.library.ADFConverterLibrary: Check and convert in MAGE-ML a ADF following its name or its ADF adh file
checkAndConvert(String, boolean, boolean, boolean) - Method in class uk.ac.ebi.adfconverter.library.ADFConverterLibrary: Check a file following its name (file extension)
checkAndConvertADF(File, boolean, boolean, boolean) - Method in class uk.ac.ebi.adfconverter.library.ADFConverterLibrary: Check and convert in MAGE-ML a ADF following its name or its ADF adh file
checkAndConvertADFDirectory(File, boolean, boolean, boolean) - Method in class uk.ac.ebi.adfconverter.library.ADFConverterLibrary: Check and convert in MAGE-ML a ADF following its name or its ADF adh file
checkAndConvertADFFile(File, boolean, boolean, boolean) - Method in class uk.ac.ebi.adfconverter.library.ADFConverterLibrary: Check and convert in MAGE-ML a ADF following its name or its ADF adh file
checkAndCurateADF(File, boolean, boolean) - Method in class uk.ac.ebi.adfconverter.tools.checker.ADFChecker: Check if an ADF is correct and retrieves the ADFJava object
checkAndCurateADF(File, boolean, boolean) - Method in class uk.ac.ebi.adfconverter.tools.checker.OptimizedADFChecker: Check if an ADF is correct and retrieves the ADFJava object
checkCurrentRowFieldDependance(Hashtable) - Method in class uk.ac.ebi.adfconverter.tools.checker.FileChecker: Checks dependances between fields of a row.
checkCurrentRowFieldDependance(Hashtable) - Method in class uk.ac.ebi.adfconverter.tools.checker.OptimizedFileChecker: Checks dependances between fields of a row.
checkDBAccNumber(ADFConverterLogger, String, String) - Static method in class uk.ac.ebi.adfconverter.tools.checker.DatabaseChecker: Checks if an Accession is correct (regex matching) according to the database tag additional information will be added during MAGE object creation
checkDBTag(ADFConverterLogger, DataBuffer, boolean, ArrayList, boolean) - Static method in class uk.ac.ebi.adfconverter.tools.checker.DatabaseChecker: Checks if a DB tag is an approved Databases or a userdefined one.
checkDataTable(DataTable, HeaderType, boolean, boolean, boolean) - Method in class uk.ac.ebi.adfconverter.tools.checker.FileChecker: * checks a data table against a structure file
checkDocument(File, String, boolean, boolean, boolean) - Method in class uk.ac.ebi.adfconverter.tools.checker.OptimizedFileChecker: Checks a file against a document structure (contains in a XML file)
checkFile(File, FileType, boolean, boolean, boolean) - Method in class uk.ac.ebi.adfconverter.tools.checker.FileChecker: Checks a data file .
checkFile(File, String, boolean, boolean, boolean) - Method in class uk.ac.ebi.adfconverter.tools.checker.OptimizedFileChecker
checkFile(File, String, String, boolean, boolean, boolean) - Method in class uk.ac.ebi.adfconverter.tools.checker.OptimizedFileChecker
checkFileAndCurate(File, FileType, boolean, boolean) - Method in class uk.ac.ebi.adfconverter.tools.checker.FileChecker: Checks and curates a data file.
checkFileAndCurate(File, String, boolean, boolean) - Method in class uk.ac.ebi.adfconverter.tools.checker.OptimizedFileChecker: Checks and curates a data file.
checkFileAndCurate(File, String, String, boolean, boolean) - Method in class uk.ac.ebi.adfconverter.tools.checker.OptimizedFileChecker: Checks and curates a data file.
checkFileData(File, String, String, boolean, boolean, boolean) - Method in class uk.ac.ebi.adfconverter.tools.checker.OptimizedFileChecker
checkMAGEML(File, boolean, boolean, boolean) - Method in class uk.ac.ebi.adfconverter.library.ADFConverterLibrary: Check / check & convert a MAGE-ML file
checkOntologyEntry(ADFConverterLogger, Extendable, OntologyEntry, String) - Method in class uk.ac.ebi.adfconverter.tools.checker.ontology.MGEDOntologyChecker: Check the ontology term in a an OntologyEntry
checkTableAndCurate(DataTable, HeaderType, boolean, boolean) - Method in class uk.ac.ebi.adfconverter.tools.checker.FileChecker: checks a data table against a structure file and returns the corrected/curated (if needed) data table
checkVerticalDataTable(DataTable, HeaderType, boolean, boolean, boolean) - Method in class uk.ac.ebi.adfconverter.tools.checker.OptimizedFileChecker: checks a vertical data table against a structure file The whole table is checked ( not row by row)
checkontologyTerm(ADFConverterLogger, String, DataBuffer) - Method in class uk.ac.ebi.adfconverter.tools.checker.ontology.MGEDOntologyChecker: Check if a term belong to the MGED ontology
childAsAttributes(JAXBObject, String) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.MSVValidator
childAsAttributes(JAXBObject, String) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.SAXMarshaller
childAsAttributes(JAXBObject, String) - Method in interface uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.XMLSerializer: This method is called when an JAXBObject object is found while the marshaller is in the "attribute" mode (i.e. marshalling attributes of an element)
childAsBody(JAXBObject, String) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.MSVValidator
childAsBody(JAXBObject, String) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.SAXMarshaller
childAsBody(JAXBObject, String) - Method in interface uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.XMLSerializer: This method is called when an JAXBObject object is found while the marshaller is in the "element" mode (i.e. marshalling a content model of an element)
childAsURIs(JAXBObject, String) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.MSVValidator
childAsURIs(JAXBObject, String) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.SAXMarshaller
childAsURIs(JAXBObject, String) - Method in interface uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.XMLSerializer: This method is called when an JAXBObject object is found while the marshaller is in the "URI" mode.
clean() - Static method in class uk.ac.ebi.adfconverter.common.util.pool.CorrectableDataTablePool: Cleans the pool
clean() - Static method in class uk.ac.ebi.adfconverter.common.util.pool.CorrectableHeaderItemPool: Cleans the pool
clean() - Static method in class uk.ac.ebi.adfconverter.common.util.pool.DataBufferPool: Cleans the pool
clean() - Static method in class uk.ac.ebi.adfconverter.common.util.pool.DataRowPool: Cleans the pool
clean() - Static method in class uk.ac.ebi.adfconverter.common.util.pool.DataTablePool: Cleans the pool
clean() - Static method in class uk.ac.ebi.adfconverter.common.util.pool.HeaderItemPool: Cleans the pool
clean() - Static method in class uk.ac.ebi.adfconverter.common.util.pool.StringBufferPool: Cleans the pool
clean() - Static method in class uk.ac.ebi.adfconverter.common.util.pool.StringPool: Cleans the pool
clean() - Method in class uk.ac.ebi.adfconverter.library.ADFConverterLibrary: Cleans th application (memory) Calls garbage collector
clear() - Method in class uk.ac.ebi.adfconverter.common.data.DataBuffer: Clears the current object
clear() - Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.CorrectableDataTable: Clears the current object, the datatable.
clear() - Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.CorrectableHeaderItem: Clears th CorrectableHeaderItem object
clear() - Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.DataRow: Remove the content of DataRow.
clear() - Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.DataTable: cleans memory used when the header is not needed anymore
clear() - Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.DataTableHeader: cleans memory used when the header is not needed anymore
clear() - Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.HeaderItem: Clears the object
clear() - Method in class uk.ac.ebi.adfconverter.common.tools.file.reader.ADFConverterFileReaderImpl: Clear the current object.
clear() - Method in class uk.ac.ebi.adfconverter.common.tools.file.writer.ADFConverterFileWriterImpl: Finalization method that closes the file descriptor.
clear() - Method in class uk.ac.ebi.adfconverter.common.tools.file.writer.PlainTextDataFileWriter: Finalization method that closes the file descriptor.
clear() - Method in class uk.ac.ebi.adfconverter.common.tools.file.writer.PlainTextFileWriter: Finalization method that closes the file descriptor.
clear() - Method in class uk.ac.ebi.adfconverter.data.adf.ADFJava: Clear the object
clear() - Method in class uk.ac.ebi.adfconverter.tools.checker.ADFChecker: clear the object / memory
clear() - Method in class uk.ac.ebi.adfconverter.tools.checker.OptimizedADFChecker: clear the object / memory
close() - Method in class uk.ac.ebi.adfconverter.common.tools.file.reader.DataFileReader: Closes file access/ reading
close() - Method in class uk.ac.ebi.adfconverter.common.tools.file.reader.DataFileReaderIntf: Closes file access/ reading
closeFile() - Method in interface uk.ac.ebi.adfconverter.common.tools.file.reader.ADFConverterFileReader: Closes a data text file.
closeFile() - Method in class uk.ac.ebi.adfconverter.common.tools.file.reader.ADFConverterFileReaderImpl: Closes a data text file.
closeFile() - Method in interface uk.ac.ebi.adfconverter.common.tools.file.reader.DataReader: Closes a data text file.
closeFile() - Method in class uk.ac.ebi.adfconverter.common.tools.file.reader.PlainTextDataFileReader: Closes a data text file.
closeFile() - Method in class uk.ac.ebi.adfconverter.common.tools.file.reader.PlainTextFileReader: Closes a data text file.
closeFile() - Method in class uk.ac.ebi.adfconverter.common.tools.file.reader.WorkBookFileReaderjxl: Closes a data text file.
closeFile() - Method in interface uk.ac.ebi.adfconverter.common.tools.file.writer.ADFConverterFileWriter: Closes a data text file
closeFile() - Method in class uk.ac.ebi.adfconverter.common.tools.file.writer.ADFConverterFileWriterImpl: Closes a data text file.
closeFile() - Method in interface uk.ac.ebi.adfconverter.common.tools.file.writer.DataWriter: Closes a data text file.
closeFile() - Method in class uk.ac.ebi.adfconverter.common.tools.file.writer.PlainTextDataFileWriter: Closes a data text file.
closeFile() - Method in class uk.ac.ebi.adfconverter.common.tools.file.writer.PlainTextFileWriter: Closes a data text file.
closeFile() - Method in class uk.ac.ebi.adfconverter.common.tools.file.writer.WorkBookFileWriterjxl: Closes a data workbook file.
commonPREFIX - Static variable in class uk.ac.ebi.adfconverter.common.configuration.ADFConverterConfiguration: Definition of the adfconverter property name sub prefix for the common module: common.
compositeFileExtension - Static variable in class uk.ac.ebi.adfconverter.data.adf.ADFJava: compositeFileExtension: default CompositeSequence text file extension
concat(DataBuffer) - Method in class uk.ac.ebi.adfconverter.common.data.DataBuffer: Concats the current DataBuffer with another databuffer
consumeAttribute(int) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.SAXUnmarshallerHandlerImpl
consumeAttribute(int) - Method in interface uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.UnmarshallingContext: Fires an attribute event for the specified attribute, and marks the attribute as "used".
contains(DataRow) - Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.DataTable: retrieves if a row is already contained in the table
contains(HeaderItem) - Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.DataTableHeader: retrieves an item is already in this header
containsHeader(boolean) - Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.CorrectableDataTable: Sets the indicator for header row.
containsHeader() - Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.CorrectableDataTable: Checks if header indicator has been turned on using CorrectableDataTable.containsHeader(boolean). .
containsHeader(boolean) - Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.DataTable: Sets the indicator for header row.
containsHeader() - Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.DataTable: Checks if header indicator has been turned on using DataTable.containsHeader(boolean). .
containsHeader(boolean) - Method in class uk.ac.ebi.adfconverter.common.tools.file.reader.DataFileReaderIntf: Sets the indicator for header row.
containsHeader() - Method in class uk.ac.ebi.adfconverter.common.tools.file.reader.DataFileReaderIntf: Checks if header indicator has been turned on using DataFileReaderIntf.containsHeader(boolean). .
containsHeader(boolean) - Method in class uk.ac.ebi.adfconverter.common.tools.file.writer.DataFileWriter: Sets the indicator for header row.
context - Variable in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.AbstractUnmarshallingEventHandlerImpl
conversionPREFIX - Static variable in class uk.ac.ebi.adfconverter.common.configuration.ADFConverterConfiguration: Definition of the adfconverter property name sub prefix for the conversion module: converter.
convert2Regex(String) - Static method in class uk.ac.ebi.adfconverter.common.tools.regex.ConvertRegex: Converts String to regex.
convert2Regex(String) - Static method in class uk.ac.ebi.adfconverter.tools.checker.FileChecker: Characters // x The character x // \\ The backslash character // \0n The character with octal value 0n (0 <= n <= 7) // \0nn The character with octal value 0nn (0 <= n <= 7) // \0mnn The character with octal value 0mnn (0 <= m <= 3, 0 <= n <= 7) // \xhh The character with hexadecimal value 0xhh //// \ uhhhh The character with hexadecimal value 0xhhhh // \t The tab character (' ') // \n The newline (line feed) character (' ') // \r The carriage-return character (' ') // \f The form-feed character (' ') // \a The alert (bell) character ('') // \e The escape character ('') // \cx The control character corresponding to x // Character classes // [abc] a, b, or c (simple class) // [^abc] Any character except a, b, or c (negation) // [a-zA-Z] a through z or A through Z, inclusive (range) // [a-d[m-p]] a through d, or m through p: [a-dm-p] (union) // [a-z&&[def]] d, e, or f (intersection) // [a-z&&[^bc]] a through z, except for b and c: [ad-z] (subtraction) // [a-z&&[^m-p]] a through z, and not m through p: [a-lq-z](subtraction) // Predefined character classes // .
convert2Regex(String) - Static method in class uk.ac.ebi.adfconverter.tools.checker.OptimizedFileChecker: Characters // x The character x // \\ The backslash character // \0n The character with octal value 0n (0 <= n <= 7) // \0nn The character with octal value 0nn (0 <= n <= 7) // \0mnn The character with octal value 0mnn (0 <= m <= 3, 0 <= n <= 7) // \xhh The character with hexadecimal value 0xhh //// \ uhhhh The character with hexadecimal value 0xhhhh // \t The tab character (' ') // \n The newline (line feed) character (' ') // \r The carriage-return character (' ') // \f The form-feed character (' ') // \a The alert (bell) character ('') // \e The escape character ('') // \cx The control character corresponding to x // Character classes // [abc] a, b, or c (simple class) // [^abc] Any character except a, b, or c (negation) // [a-zA-Z] a through z or A through Z, inclusive (range) // [a-d[m-p]] a through d, or m through p: [a-dm-p] (union) // [a-z&&[def]] d, e, or f (intersection) // [a-z&&[^bc]] a through z, except for b and c: [ad-z] (subtraction) // [a-z&&[^m-p]] a through z, and not m through p: [a-lq-z](subtraction) // Predefined character classes // .
convertCurrentADF() - Method in class uk.ac.ebi.adfconverter.library.ADFConverterLibrary: Converts the current checked and correct ADF in MAGEObject.
convertHeader(PhysicalArrayDesign) - Method in class uk.ac.ebi.adfconverter.tools.converter.MAGEToADFConverter: Retrieves a ADF header data from a Physical ArrayDesign Add data to the current ADFJava object corresponding to the mage data.
convertLine(String) - Static method in class uk.ac.ebi.adfconverter.common.tools.file.converter.DelimiterLineConverter: Splits a String (file data line) following the current delimiter characters and the current escape characters
convertLine(DataBuffer) - Static method in class uk.ac.ebi.adfconverter.common.tools.file.converter.DelimiterLineConverter: Splits a String (file data line) following the current delimiter and the current escape characters
convertLine(String, int) - Static method in class uk.ac.ebi.adfconverter.common.tools.file.converter.DelimiterLineConverter: Splits a String (file data line) following the current delimiter and the current escape characters, with a limited number of exporting token in output DataRow
convertLine(DataBuffer, int) - Static method in class uk.ac.ebi.adfconverter.common.tools.file.converter.DelimiterLineConverter: Splits a String (file data line) following the current delimiter and the current escape characters, with a limited number of exporting token in output DataRow
convertLine(DataBuffer) - Method in interface uk.ac.ebi.adfconverter.common.tools.file.converter.TextLineConverter: Converts a line of data into a DataRow object which contains each data item in individual cells.
convertLine(DataBuffer, int) - Method in interface uk.ac.ebi.adfconverter.common.tools.file.converter.TextLineConverter: Converts a line of data into a DataRow object which contains each data item in individual cells.
convertLine(String) - Method in interface uk.ac.ebi.adfconverter.common.tools.file.converter.TextLineConverter: Converts a line of data into a DataRow object which contains each data item in individual cells.
convertLine(String, int) - Method in interface uk.ac.ebi.adfconverter.common.tools.file.converter.TextLineConverter: Converts a line of data into a DataRow object which contains each data item in individual cells.
convertToADF(File) - Method in class uk.ac.ebi.adfconverter.tools.converter.MAGEToADFConverter: Converts data from a MAGE-ML file to ADFJava.
copy(String, String) - Static method in class uk.ac.ebi.adfconverter.common.tools.file.copier.FileCopy: Static method copying a file with a given file path to file with a specified path
copy(File, File) - Static method in class uk.ac.ebi.adfconverter.common.tools.file.copier.FileCopy: *Static method copying a file as another one (rename, move)
create(Grammar, SAXUnmarshallerHandler, Locator) - Static method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.ValidatingUnmarshaller: Creates a new instance of ValidatingUnmarshaller.
createCardinalityType() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.ObjectFactory: Create an instance of CardinalityType
createCheckRuleType() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.ObjectFactory: Create an instance of CheckRuleType
createCompositeSequence(ADFReporter) - Method in class uk.ac.ebi.adfconverter.tools.checker.ADFChecker: In case of simple microarray layout, create the composite sequence associated to the reporter Data, are simply copy from reporter to compositeSequence
createCompositeSequence(ADFReporter) - Method in class uk.ac.ebi.adfconverter.tools.checker.OptimizedADFChecker: In case of simple microarray layout, create the composite sequence associated to the reporter Data, are simply copy from reporter to compositeSequence
createCompositeSequence(ADFReporter) - Method in class uk.ac.ebi.adfconverter.tools.converter.MAGEToADFConverter: In case of simple microarray layout, create the composite sequence associated to the reporter Data, are simply copy from reporter to compositeSequence
createConstraintType() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.ObjectFactory: Create an instance of ConstraintType
createDataType() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.ObjectFactory: Create an instance of DataType
createDataTypeTablesType() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.ObjectFactory: Create an instance of DataTypeTablesType
createDocumentStructure() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.ObjectFactory: Create an instance of DocumentStructure
createDocumentStructureType() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.ObjectFactory: Create an instance of DocumentStructureType
createDocumentStructureTypeFilesType() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.ObjectFactory: Create an instance of DocumentStructureTypeFilesType
createFieldType() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.ObjectFactory: Create an instance of FieldType
createFieldTypeConstraintsType() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.ObjectFactory: Create an instance of FieldTypeConstraintsType
createFileType() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.ObjectFactory: Create an instance of FileType
createFileTypeDataSetType() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.ObjectFactory: Create an instance of FileTypeDataSetType
createFiler() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.ObjectFactory: Create an instance of Filer
createHeader() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.ObjectFactory: Create an instance of Header
createHeaderType() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.ObjectFactory: Create an instance of HeaderType
createHeaderTypeItemsType() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.ObjectFactory: Create an instance of HeaderTypeItemsType
createItem(ItemType) - Method in class uk.ac.ebi.adfconverter.tools.filestructure.FileStructureDescription: Create a correctableHeaderITem corresponding to a itemType
createItem(String) - Method in class uk.ac.ebi.adfconverter.tools.filestructure.FileStructureDescription: Create an item object of a given type.
createItem(String, int) - Method in class uk.ac.ebi.adfconverter.tools.filestructure.FileStructureDescription: Create a CorrectableHeaderItem object with a given type
createItemTemp() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.ObjectFactory: Create an instance of ItemTemp
createItemType() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.ObjectFactory: Create an instance of ItemType
createItemTypeFieldDependenceType() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.ObjectFactory: Create an instance of ItemTypeFieldDependenceType
createItemTypeRelaxCheckRulesType() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.ObjectFactory: Create an instance of ItemTypeRelaxCheckRulesType
createItemTypeSubNamesType() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.ObjectFactory: Create an instance of ItemTypeSubNamesType
createLocationType() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.ObjectFactory: Create an instance of LocationType
createLocationTypePreviousColumnsType() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.ObjectFactory: Create an instance of LocationTypePreviousColumnsType
createMarshaller() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.DefaultJAXBContextImpl: Create a Marshaller object that can be used to convert a java content-tree into XML data.
createOntologyEntry(String, String) - Method in class uk.ac.ebi.adfconverter.tools.checker.ontology.MGEDOntologyChecker: Creates an ontology entry object
createRawValidator() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.CardinalityTypeImpl
createRawValidator() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.CheckRuleTypeImpl
createRawValidator() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ConstraintTypeImpl
createRawValidator() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.DataTypeImpl.TablesTypeImpl
createRawValidator() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.DataTypeImpl
createRawValidator() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.DocumentStructureImpl
createRawValidator() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.DocumentStructureTypeImpl.FilesTypeImpl
createRawValidator() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.DocumentStructureTypeImpl
createRawValidator() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.FieldTypeImpl.ConstraintsTypeImpl
createRawValidator() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.FieldTypeImpl
createRawValidator() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.FileTypeImpl.DataSetTypeImpl
createRawValidator() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.FileTypeImpl
createRawValidator() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.FilerImpl
createRawValidator() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.HeaderImpl
createRawValidator() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.HeaderTypeImpl.ItemsTypeImpl
createRawValidator() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.HeaderTypeImpl
createRawValidator() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTempImpl
createRawValidator() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTypeImpl.FieldDependenceTypeImpl
createRawValidator() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTypeImpl.RelaxCheckRulesTypeImpl
createRawValidator() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTypeImpl.SubNamesTypeImpl
createRawValidator() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTypeImpl
createRawValidator() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.LocationTypeImpl.PreviousColumnsTypeImpl
createRawValidator() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.LocationTypeImpl
createRawValidator() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.SubNameTypeImpl.ConstraintsTypeImpl
createRawValidator() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.SubNameTypeImpl
createRawValidator() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.TableTypeImpl
createRawValidator() - Method in interface uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.ValidatableObject: Gets the schema fragment associated with this class.
createSubNameType() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.ObjectFactory: Create an instance of SubNameType
createSubNameTypeConstraintsType() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.ObjectFactory: Create an instance of SubNameTypeConstraintsType
createTableType() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.ObjectFactory: Create an instance of TableType
createUnmarshaller(UnmarshallingContext) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.CardinalityTypeImpl
createUnmarshaller(UnmarshallingContext) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.CheckRuleTypeImpl
createUnmarshaller(UnmarshallingContext) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ConstraintTypeImpl
createUnmarshaller(UnmarshallingContext) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.DataTypeImpl.TablesTypeImpl
createUnmarshaller(UnmarshallingContext) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.DataTypeImpl
createUnmarshaller(UnmarshallingContext) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.DocumentStructureImpl
createUnmarshaller(UnmarshallingContext) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.DocumentStructureTypeImpl.FilesTypeImpl
createUnmarshaller(UnmarshallingContext) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.DocumentStructureTypeImpl
createUnmarshaller(UnmarshallingContext) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.FieldTypeImpl.ConstraintsTypeImpl
createUnmarshaller(UnmarshallingContext) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.FieldTypeImpl
createUnmarshaller(UnmarshallingContext) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.FileTypeImpl.DataSetTypeImpl
createUnmarshaller(UnmarshallingContext) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.FileTypeImpl
createUnmarshaller(UnmarshallingContext) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.FilerImpl
createUnmarshaller(UnmarshallingContext) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.HeaderImpl
createUnmarshaller(UnmarshallingContext) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.HeaderTypeImpl.ItemsTypeImpl
createUnmarshaller(UnmarshallingContext) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.HeaderTypeImpl
createUnmarshaller(UnmarshallingContext) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTempImpl
createUnmarshaller(UnmarshallingContext) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTypeImpl.FieldDependenceTypeImpl
createUnmarshaller(UnmarshallingContext) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTypeImpl.RelaxCheckRulesTypeImpl
createUnmarshaller(UnmarshallingContext) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTypeImpl.SubNamesTypeImpl
createUnmarshaller(UnmarshallingContext) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTypeImpl
createUnmarshaller(UnmarshallingContext) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.LocationTypeImpl.PreviousColumnsTypeImpl
createUnmarshaller(UnmarshallingContext) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.LocationTypeImpl
createUnmarshaller(UnmarshallingContext) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.SubNameTypeImpl.ConstraintsTypeImpl
createUnmarshaller(UnmarshallingContext) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.SubNameTypeImpl
createUnmarshaller(UnmarshallingContext) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.TableTypeImpl
createUnmarshaller() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.DefaultJAXBContextImpl: Create an Unmarshaller object that can be used to convert XML data into a java content-tree.
createUnmarshaller(String, String, UnmarshallingContext) - Method in interface uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.GrammarInfo: Creates an unmarshaller that can unmarshal a given element.
createUnmarshaller(String, String, UnmarshallingContext) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.GrammarInfoImpl
createUnmarshaller(UnmarshallingContext) - Method in interface uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.UnmarshallableObject: Creates an unmarshaller that will unmarshall this object.
createValidator() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.DefaultJAXBContextImpl: Create a Validator object that can be used to validate a java content-tree.
createWriter(Writer, String) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.MarshallerImpl
createWriter(Writer) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.MarshallerImpl
createWriter(OutputStream) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.MarshallerImpl
createWriter(OutputStream, String) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.MarshallerImpl

D

DUMMY_ELEMENT_NS - Static variable in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.MSVValidator: namespace URI of dummy elements.
DataBuffer - class uk.ac.ebi.adfconverter.common.data.DataBuffer.: ADF MAGE-TOOL - MicroArray Informatics Team / European Bioinformatics Institute (EBI) ArrayExpress License: ============================================================================== Copyright (c) 2002 The European Bioinformatics Institute.
DataBuffer() - Constructor for class uk.ac.ebi.adfconverter.common.data.DataBuffer: Constructor of DataBuffer class sets by default internalString to "", empty string
DataBuffer(String) - Constructor for class uk.ac.ebi.adfconverter.common.data.DataBuffer: Constructor with a given string
DataBufferPool - class uk.ac.ebi.adfconverter.common.util.pool.DataBufferPool.: Pool class for DataBufferPool objects Contains a list of available tables.
DataBufferPool() - Constructor for class uk.ac.ebi.adfconverter.common.util.pool.DataBufferPool
DataDisplay - class uk.ac.ebi.adfconverter.usermode.gui.visualisation.DataDisplay.: Dat display test
DataDisplay() - Constructor for class uk.ac.ebi.adfconverter.usermode.gui.visualisation.DataDisplay
DataFileReader - class uk.ac.ebi.adfconverter.common.tools.file.reader.DataFileReader.: This class converts data from a file in a DataTable in Java, for manipulation
DataFileReader(File) - Constructor for class uk.ac.ebi.adfconverter.common.tools.file.reader.DataFileReader: constructor for converting a data file in data table in memory
DataFileReader(File, boolean) - Constructor for class uk.ac.ebi.adfconverter.common.tools.file.reader.DataFileReader: constructor for converting a data file in data table in memory
DataFileReaderIntf - class uk.ac.ebi.adfconverter.common.tools.file.reader.DataFileReaderIntf.: This class converts data from a file in a DataTable in Java, for manipulation
DataFileReaderIntf(File) - Constructor for class uk.ac.ebi.adfconverter.common.tools.file.reader.DataFileReaderIntf: constructor for converting a data file in data table in memory
DataFileReaderIntf(File, boolean) - Constructor for class uk.ac.ebi.adfconverter.common.tools.file.reader.DataFileReaderIntf: constructor for converting a data file in data table in memory
DataFileWriter - class uk.ac.ebi.adfconverter.common.tools.file.writer.DataFileWriter.: This class converts data in memory in a file for output
DataFileWriter(File) - Constructor for class uk.ac.ebi.adfconverter.common.tools.file.writer.DataFileWriter: constructor for converting a data table in a data file
DataFileWriter(File, boolean) - Constructor for class uk.ac.ebi.adfconverter.common.tools.file.writer.DataFileWriter: constructor for converting a data table in data file in memory
DataReader - interface uk.ac.ebi.adfconverter.common.tools.file.reader.DataReader.: Interface for all file format classes used in reading data
DataRow - class uk.ac.ebi.adfconverter.common.data.tabulardata.DataRow.: Object representing collection of data items contained within one line of the data file
DataRow() - Constructor for class uk.ac.ebi.adfconverter.common.data.tabulardata.DataRow: Creates a new DataRow instance.
DataRow(int) - Constructor for class uk.ac.ebi.adfconverter.common.data.tabulardata.DataRow: Creates a new DataRow instance.
DataRow(NumberFormat) - Constructor for class uk.ac.ebi.adfconverter.common.data.tabulardata.DataRow: Creates a new DataRow instance.
DataRowPool - class uk.ac.ebi.adfconverter.common.util.pool.DataRowPool.: Pool class for DataRowPool objects Contains a list of available tables.
DataRowPool() - Constructor for class uk.ac.ebi.adfconverter.common.util.pool.DataRowPool
DataTable - class uk.ac.ebi.adfconverter.common.data.tabulardata.DataTable.: Object representing collection of dataRow
DataTable() - Constructor for class uk.ac.ebi.adfconverter.common.data.tabulardata.DataTable: Creates a new DataTable instance.
DataTable(File) - Constructor for class uk.ac.ebi.adfconverter.common.data.tabulardata.DataTable: Creates a new DataTable instance.
DataTable(String, File) - Constructor for class uk.ac.ebi.adfconverter.common.data.tabulardata.DataTable: Creates a new DataTable instance.
DataTableHeader - class uk.ac.ebi.adfconverter.common.data.tabulardata.DataTableHeader.: This Class represents the list of data table headers
DataTableHeader() - Constructor for class uk.ac.ebi.adfconverter.common.data.tabulardata.DataTableHeader: Constructor of the headerItem class
DataTableHeader(int) - Constructor for class uk.ac.ebi.adfconverter.common.data.tabulardata.DataTableHeader: Constructor of the headerItem class with an initial capacity for the header list
DataTableModel - class uk.ac.ebi.adfconverter.usermode.gui.visualisation.DataTableModel.: Describe class DataTableModel here.
DataTableModel() - Constructor for class uk.ac.ebi.adfconverter.usermode.gui.visualisation.DataTableModel: Creates a new emptyTableModel instance.
DataTableModel(DataTable) - Constructor for class uk.ac.ebi.adfconverter.usermode.gui.visualisation.DataTableModel: Creates a new TableModel instance.
DataTablePool - class uk.ac.ebi.adfconverter.common.util.pool.DataTablePool.: Pool class for DataTablePool objects Contains a list of available tables.
DataTablePool() - Constructor for class uk.ac.ebi.adfconverter.common.util.pool.DataTablePool
DataType - interface uk.ac.ebi.adfconverter.tools.checker.data.DataType.: structure of data: can be composed of several table Java content class for DataType complex type.
DataType.TablesType - interface uk.ac.ebi.adfconverter.tools.checker.data.DataType.TablesType.: Java content class for anonymous complex type.
DataTypeImpl - class uk.ac.ebi.adfconverter.tools.checker.data.impl.DataTypeImpl.
DataTypeImpl() - Constructor for class uk.ac.ebi.adfconverter.tools.checker.data.impl.DataTypeImpl
DataTypeImpl.TablesTypeImpl - class uk.ac.ebi.adfconverter.tools.checker.data.impl.DataTypeImpl.TablesTypeImpl.
DataTypeImpl.TablesTypeImpl() - Constructor for class uk.ac.ebi.adfconverter.tools.checker.data.impl.DataTypeImpl.TablesTypeImpl
DataTypeImpl.TablesTypeImpl.Unmarshaller - class uk.ac.ebi.adfconverter.tools.checker.data.impl.DataTypeImpl.TablesTypeImpl.Unmarshaller.
DataTypeImpl.TablesTypeImpl.Unmarshaller(UnmarshallingContext) - Constructor for class uk.ac.ebi.adfconverter.tools.checker.data.impl.DataTypeImpl.TablesTypeImpl.Unmarshaller
DataTypeImpl.Unmarshaller - class uk.ac.ebi.adfconverter.tools.checker.data.impl.DataTypeImpl.Unmarshaller.
DataTypeImpl.Unmarshaller(UnmarshallingContext) - Constructor for class uk.ac.ebi.adfconverter.tools.checker.data.impl.DataTypeImpl.Unmarshaller
DataVisualisationTable - class uk.ac.ebi.adfconverter.usermode.gui.visualisation.DataVisualisationTable.
DataVisualisationTable() - Constructor for class uk.ac.ebi.adfconverter.usermode.gui.visualisation.DataVisualisationTable
DataVisualisationTable(DataTable) - Constructor for class uk.ac.ebi.adfconverter.usermode.gui.visualisation.DataVisualisationTable
DataWriter - interface uk.ac.ebi.adfconverter.common.tools.file.writer.DataWriter.: Interface for all file format classes used in reading data
DatabaseChecker - class uk.ac.ebi.adfconverter.tools.checker.DatabaseChecker.: Checking for database stuff will check database tags and database accesion number In Approved db file structure, the item name are: DB tag item - DBTag database link item - URI$ database name - DBName regex - ACCRegex
DatabaseChecker() - Constructor for class uk.ac.ebi.adfconverter.tools.checker.DatabaseChecker: Default Constructor with a default DatabaseChecker with a default DB file path: etc/checking/public_DB_Accnos.xls
DatabaseChecker(String, String, String, boolean) - Constructor for class uk.ac.ebi.adfconverter.tools.checker.DatabaseChecker: Constructor with a given approved DB file, approved DB file structure xml file,and the separator between DB name and web link retrieved from workbook
DefaultJAXBContextImpl - class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.DefaultJAXBContextImpl.: This class provides the default implementation of JAXBContext.
DefaultJAXBContextImpl(String, ClassLoader) - Constructor for class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.DefaultJAXBContextImpl: This is the constructor used by javax.xml.bind.FactoryFinder which bootstraps the RI.
DefaultJAXBContextImpl(GrammarInfo) - Constructor for class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.DefaultJAXBContextImpl: This constructor is used by the default no-arg constructor in the generated JAXBContextImpl objects.
DelimiterLineConverter - class uk.ac.ebi.adfconverter.common.tools.file.converter.DelimiterLineConverter.: DelimiterLineConverter is configurable data format that uses any simple delimiter and escape sequence scheme to encode data into a text file.
DelimiterLineConverter(String, String) - Constructor for class uk.ac.ebi.adfconverter.common.tools.file.converter.DelimiterLineConverter: Creates a new instance of DelimiterLineConverter with specified delimiter and escape sequence.
DelimiterLineConverter(String) - Constructor for class uk.ac.ebi.adfconverter.common.tools.file.converter.DelimiterLineConverter: Creates a new instance of DelimiterLineConverter with specified delimiter and escape sequence.
DirectoryFilter - class uk.ac.ebi.adfconverter.library.DirectoryFilter.: implements java.io.FilenameFilter interface.
DirectoryFilter() - Constructor for class uk.ac.ebi.adfconverter.library.DirectoryFilter: Default contructor of a filter for subdirectory
DiskUtil - class uk.ac.ebi.adfconverter.common.tools.file.filesystem.DiskUtil.: Retrieves available disk space for Windows operating system or Linux operating system
DiskUtil() - Constructor for class uk.ac.ebi.adfconverter.common.tools.file.filesystem.DiskUtil
DocumentStructure - interface uk.ac.ebi.adfconverter.tools.checker.data.DocumentStructure.: data structure in a or several files Java content class for documentStructure element declaration.
DocumentStructureImpl - class uk.ac.ebi.adfconverter.tools.checker.data.impl.DocumentStructureImpl.
DocumentStructureImpl() - Constructor for class uk.ac.ebi.adfconverter.tools.checker.data.impl.DocumentStructureImpl
DocumentStructureImpl.Unmarshaller - class uk.ac.ebi.adfconverter.tools.checker.data.impl.DocumentStructureImpl.Unmarshaller.
DocumentStructureImpl.Unmarshaller(UnmarshallingContext) - Constructor for class uk.ac.ebi.adfconverter.tools.checker.data.impl.DocumentStructureImpl.Unmarshaller
DocumentStructureType - interface uk.ac.ebi.adfconverter.tools.checker.data.DocumentStructureType.: definition of a data document: can contain several data table (in several files) Java content class for documentStructureType complex type.
DocumentStructureType.FilesType - interface uk.ac.ebi.adfconverter.tools.checker.data.DocumentStructureType.FilesType.: Java content class for anonymous complex type.
DocumentStructureTypeImpl - class uk.ac.ebi.adfconverter.tools.checker.data.impl.DocumentStructureTypeImpl.
DocumentStructureTypeImpl() - Constructor for class uk.ac.ebi.adfconverter.tools.checker.data.impl.DocumentStructureTypeImpl
DocumentStructureTypeImpl.FilesTypeImpl - class uk.ac.ebi.adfconverter.tools.checker.data.impl.DocumentStructureTypeImpl.FilesTypeImpl.
DocumentStructureTypeImpl.FilesTypeImpl() - Constructor for class uk.ac.ebi.adfconverter.tools.checker.data.impl.DocumentStructureTypeImpl.FilesTypeImpl
DocumentStructureTypeImpl.FilesTypeImpl.Unmarshaller - class uk.ac.ebi.adfconverter.tools.checker.data.impl.DocumentStructureTypeImpl.FilesTypeImpl.Unmarshaller.
DocumentStructureTypeImpl.FilesTypeImpl.Unmarshaller(UnmarshallingContext) - Constructor for class uk.ac.ebi.adfconverter.tools.checker.data.impl.DocumentStructureTypeImpl.FilesTypeImpl.Unmarshaller
DocumentStructureTypeImpl.Unmarshaller - class uk.ac.ebi.adfconverter.tools.checker.data.impl.DocumentStructureTypeImpl.Unmarshaller.
DocumentStructureTypeImpl.Unmarshaller(UnmarshallingContext) - Constructor for class uk.ac.ebi.adfconverter.tools.checker.data.impl.DocumentStructureTypeImpl.Unmarshaller
debug(String) - Method in interface uk.ac.ebi.adfconverter.common.tools.log.ADFConverterLogger: Reports message at debug
debug(String) - Method in class uk.ac.ebi.adfconverter.common.tools.log.ADFConverterLoggerImpl: Logs a debug message into the current logger
declareNamespace(String, String, boolean) - Method in interface uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.NamespaceContext2: Declares a new namespace binding within the current context.
declareNamespace(String, String, boolean) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.NamespaceContextImpl
decompress(File) - Static method in class uk.ac.ebi.adfconverter.common.tools.file.archives.Untar: Decompress a Tar file.
decompress(File) - Static method in class uk.ac.ebi.adfconverter.common.tools.file.archives.Unzip: Decompress a Zip file.
doConfigure(String, boolean) - Static method in class uk.ac.ebi.adfconverter.common.configuration.ADFConverterConfiguration: Read configuration from a file.
doConfigure(Properties) - Static method in class uk.ac.ebi.adfconverter.common.configuration.ADFConverterConfiguration: Read configuration options from properties.
doConfigure(URL) - Static method in class uk.ac.ebi.adfconverter.common.configuration.ADFConverterConfiguration: Read configuration options from url configURL.
doOverwrite(boolean) - Method in class uk.ac.ebi.adfconverter.common.tools.file.writer.DataFileWriter: Sets, if file exists, if the writer over write the existing file

E

ErrorHandlerAdaptor - class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.ErrorHandlerAdaptor.: Receives errors through ErrorHandler and reports to the SAXUnmarshallerHandler.
ErrorHandlerAdaptor(SAXUnmarshallerHandler, Locator) - Constructor for class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.ErrorHandlerAdaptor
ErrorInitLog - exception uk.ac.ebi.adfconverter.common.tools.log.exceptions.ErrorInitLog.: Signals an error of application logger.
ErrorInitLog() - Constructor for class uk.ac.ebi.adfconverter.common.tools.log.exceptions.ErrorInitLog
eatAttribute(int) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.SAXUnmarshallerHandlerImpl
eatAttribute(int) - Method in interface uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.UnmarshallingContext: Marks the attribute as "used" and return the value of the attribute.
endAttribute() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.MSVValidator
endAttribute() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.SAXMarshaller
endAttribute() - Method in interface uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.XMLSerializer
endAttributes() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.MSVValidator
endAttributes() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.SAXMarshaller: Switches to the "marshal child texts/elements" mode.
endAttributes() - Method in interface uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.XMLSerializer: Switches to the mode to marshal child texts/elements.
endDocument() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.ContentHandlerAdaptor
endDocument() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.SAXUnmarshallerHandlerImpl
endElement(String, String, String) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.ContentHandlerAdaptor
endElement() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.MSVValidator
endElement() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.NamespaceContextImpl: Ends the current element context and gets back to the parent context.
endElement() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.SAXMarshaller: Ends marshalling of an element.
endElement(String, String, String) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.SAXUnmarshallerHandlerImpl
endElement() - Method in interface uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.XMLSerializer: Ends marshalling of an element.
endNamespaceDecls() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.MSVValidator
endNamespaceDecls() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.NamespaceContextImpl: Reconciles the namespace URI/prefix mapping requests since the last startElement method invocation and finalizes them.
endNamespaceDecls() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.SAXMarshaller
endNamespaceDecls() - Method in interface uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.XMLSerializer: Switches to the mode to marshal attribute values.
endPrefixMapping(String) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.ContentHandlerAdaptor
endPrefixMapping(String) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.SAXUnmarshallerHandlerImpl
enterAttribute(String, String, String) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.CardinalityTypeImpl.Unmarshaller
enterAttribute(String, String, String) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.CheckRuleTypeImpl.Unmarshaller
enterAttribute(String, String, String) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ConstraintTypeImpl.Unmarshaller
enterAttribute(String, String, String) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.DataTypeImpl.TablesTypeImpl.Unmarshaller
enterAttribute(String, String, String) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.DataTypeImpl.Unmarshaller
enterAttribute(String, String, String) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.DocumentStructureImpl.Unmarshaller
enterAttribute(String, String, String) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.DocumentStructureTypeImpl.FilesTypeImpl.Unmarshaller
enterAttribute(String, String, String) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.DocumentStructureTypeImpl.Unmarshaller
enterAttribute(String, String, String) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.FieldTypeImpl.ConstraintsTypeImpl.Unmarshaller
enterAttribute(String, String, String) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.FieldTypeImpl.Unmarshaller
enterAttribute(String, String, String) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.FileTypeImpl.DataSetTypeImpl.Unmarshaller
enterAttribute(String, String, String) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.FileTypeImpl.Unmarshaller
enterAttribute(String, String, String) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.FilerImpl.Unmarshaller
enterAttribute(String, String, String) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.HeaderImpl.Unmarshaller
enterAttribute(String, String, String) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.HeaderTypeImpl.ItemsTypeImpl.Unmarshaller
enterAttribute(String, String, String) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.HeaderTypeImpl.Unmarshaller
enterAttribute(String, String, String) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTempImpl.Unmarshaller
enterAttribute(String, String, String) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTypeImpl.FieldDependenceTypeImpl.Unmarshaller
enterAttribute(String, String, String) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTypeImpl.RelaxCheckRulesTypeImpl.Unmarshaller
enterAttribute(String, String, String) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTypeImpl.SubNamesTypeImpl.Unmarshaller
enterAttribute(String, String, String) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTypeImpl.Unmarshaller
enterAttribute(String, String, String) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.LocationTypeImpl.PreviousColumnsTypeImpl.Unmarshaller
enterAttribute(String, String, String) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.LocationTypeImpl.Unmarshaller
enterAttribute(String, String, String) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.SubNameTypeImpl.ConstraintsTypeImpl.Unmarshaller
enterAttribute(String, String, String) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.SubNameTypeImpl.Unmarshaller
enterAttribute(String, String, String) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.TableTypeImpl.Unmarshaller
enterAttribute(String, String, String) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.AbstractUnmarshallingEventHandlerImpl
enterAttribute(String, String, String) - Method in interface uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.UnmarshallingEventHandler
enterAttribute(String, String, String) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.UnmarshallingEventHandlerAdaptor
enterElement(String, String, String, Attributes) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.CardinalityTypeImpl.Unmarshaller
enterElement(String, String, String, Attributes) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.CheckRuleTypeImpl.Unmarshaller
enterElement(String, String, String, Attributes) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ConstraintTypeImpl.Unmarshaller
enterElement(String, String, String, Attributes) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.DataTypeImpl.TablesTypeImpl.Unmarshaller
enterElement(String, String, String, Attributes) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.DataTypeImpl.Unmarshaller
enterElement(String, String, String, Attributes) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.DocumentStructureImpl.Unmarshaller
enterElement(String, String, String, Attributes) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.DocumentStructureTypeImpl.FilesTypeImpl.Unmarshaller
enterElement(String, String, String, Attributes) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.DocumentStructureTypeImpl.Unmarshaller
enterElement(String, String, String, Attributes) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.FieldTypeImpl.ConstraintsTypeImpl.Unmarshaller
enterElement(String, String, String, Attributes) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.FieldTypeImpl.Unmarshaller
enterElement(String, String, String, Attributes) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.FileTypeImpl.DataSetTypeImpl.Unmarshaller
enterElement(String, String, String, Attributes) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.FileTypeImpl.Unmarshaller
enterElement(String, String, String, Attributes) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.FilerImpl.Unmarshaller
enterElement(String, String, String, Attributes) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.HeaderImpl.Unmarshaller
enterElement(String, String, String, Attributes) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.HeaderTypeImpl.ItemsTypeImpl.Unmarshaller
enterElement(String, String, String, Attributes) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.HeaderTypeImpl.Unmarshaller
enterElement(String, String, String, Attributes) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTempImpl.Unmarshaller
enterElement(String, String, String, Attributes) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTypeImpl.FieldDependenceTypeImpl.Unmarshaller
enterElement(String, String, String, Attributes) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTypeImpl.RelaxCheckRulesTypeImpl.Unmarshaller
enterElement(String, String, String, Attributes) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTypeImpl.SubNamesTypeImpl.Unmarshaller
enterElement(String, String, String, Attributes) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTypeImpl.Unmarshaller
enterElement(String, String, String, Attributes) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.LocationTypeImpl.PreviousColumnsTypeImpl.Unmarshaller
enterElement(String, String, String, Attributes) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.LocationTypeImpl.Unmarshaller
enterElement(String, String, String, Attributes) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.SubNameTypeImpl.ConstraintsTypeImpl.Unmarshaller
enterElement(String, String, String, Attributes) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.SubNameTypeImpl.Unmarshaller
enterElement(String, String, String, Attributes) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.TableTypeImpl.Unmarshaller
enterElement(String, String, String, Attributes) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.AbstractUnmarshallingEventHandlerImpl
enterElement(String, String, String, Attributes) - Method in interface uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.UnmarshallingEventHandler
enterElement(String, String, String, Attributes) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.UnmarshallingEventHandlerAdaptor
equals(Object) - Method in class uk.ac.ebi.adfconverter.common.data.DataBuffer: Compares the current string to an object must be a DataBuffer or a String Compare the associated internal String
equals(Object) - Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.CorrectableHeaderItem: Compares the object with another one mainly for searching in the headerlist
equals(Object) - Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.DataRow: checks if the current object is equal to another one (which is supposed to be a DataRow object)
equals(Object) - Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.HeaderItem: Compares the object with another one mainly for searching in the headerlist
equalsIgnoreCase(Object) - Method in class uk.ac.ebi.adfconverter.common.data.DataBuffer: Compares the current string to an object must be a DataBuffer or a String Compare the associated internal String Case insensitive
error(String) - Method in interface uk.ac.ebi.adfconverter.common.tools.log.ADFConverterLogger: Reports an error message to the current log.
error(String) - Method in class uk.ac.ebi.adfconverter.common.tools.log.ADFConverterLoggerImpl: Logs an errormessage into the current logger
error(SAXParseException) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.ErrorHandlerAdaptor
export(ADFJava, boolean) - Static method in class uk.ac.ebi.adfconverter.tools.exporter.ADFExporter: Export a ADFJava object in ADF files
export(ADFJava, int, boolean) - Static method in class uk.ac.ebi.adfconverter.tools.exporter.ADFExporter: Export a ADFJava object in ADF files By default, the ADF is export as plain text file
export(File, MAGEJava) - Static method in class uk.ac.ebi.adfconverter.tools.exporter.MAGEMLExporter: Export a MAGEJava object in a MAGE-ML file create a temporay file in the temp directory (can be an issue), before obtaining a pretty and well form MAGE-File
exportCurrentMAGEML() - Method in class uk.ac.ebi.adfconverter.library.ADFConverterLibrary: export the current checked and correct ADF in MAGE-ML.
exportIdentifier(File) - Method in class uk.ac.ebi.adfconverter.tools.converter.ADFToMAGEConverter: Export identifiers to a file.
exporterPREFIX - Static variable in class uk.ac.ebi.adfconverter.common.configuration.ADFConverterConfiguration: Definition of the adfconverter property name sub prefix for exporter module: exporter.

F

Fetch - class uk.ac.ebi.adfconverter.common.tools.net.update.Fetch.
Fetch() - Constructor for class uk.ac.ebi.adfconverter.common.tools.net.update.Fetch
FieldType - interface uk.ac.ebi.adfconverter.tools.checker.data.FieldType.: Specifies the field value type and constraints Java content class for FieldType complex type.
FieldType.ConstraintsType - interface uk.ac.ebi.adfconverter.tools.checker.data.FieldType.ConstraintsType.: Java content class for anonymous complex type.
FieldTypeImpl - class uk.ac.ebi.adfconverter.tools.checker.data.impl.FieldTypeImpl.
FieldTypeImpl() - Constructor for class uk.ac.ebi.adfconverter.tools.checker.data.impl.FieldTypeImpl
FieldTypeImpl.ConstraintsTypeImpl - class uk.ac.ebi.adfconverter.tools.checker.data.impl.FieldTypeImpl.ConstraintsTypeImpl.
FieldTypeImpl.ConstraintsTypeImpl() - Constructor for class uk.ac.ebi.adfconverter.tools.checker.data.impl.FieldTypeImpl.ConstraintsTypeImpl
FieldTypeImpl.ConstraintsTypeImpl.Unmarshaller - class uk.ac.ebi.adfconverter.tools.checker.data.impl.FieldTypeImpl.ConstraintsTypeImpl.Unmarshaller.
FieldTypeImpl.ConstraintsTypeImpl.Unmarshaller(UnmarshallingContext) - Constructor for class uk.ac.ebi.adfconverter.tools.checker.data.impl.FieldTypeImpl.ConstraintsTypeImpl.Unmarshaller
FieldTypeImpl.Unmarshaller - class uk.ac.ebi.adfconverter.tools.checker.data.impl.FieldTypeImpl.Unmarshaller.
FieldTypeImpl.Unmarshaller(UnmarshallingContext) - Constructor for class uk.ac.ebi.adfconverter.tools.checker.data.impl.FieldTypeImpl.Unmarshaller
FileChecker - class uk.ac.ebi.adfconverter.tools.checker.FileChecker.: Class for file strcuture checking will check file structure and data contained in a file
FileChecker() - Constructor for class uk.ac.ebi.adfconverter.tools.checker.FileChecker: Default Constructor of FileChecker
FileChecker(String) - Constructor for class uk.ac.ebi.adfconverter.tools.checker.FileChecker: Constructor of FileChecker with a given structure file
FileChecking - class uk.ac.ebi.adfconverter.usermode.gui.check.FileChecking.: Dat display test
FileChecking() - Constructor for class uk.ac.ebi.adfconverter.usermode.gui.check.FileChecking
FileCopy - class uk.ac.ebi.adfconverter.common.tools.file.copier.FileCopy.
FileCopy() - Constructor for class uk.ac.ebi.adfconverter.common.tools.file.copier.FileCopy
FileCopyException - exception uk.ac.ebi.adfconverter.common.tools.file.copier.exceptions.FileCopyException.
FileCopyException(String) - Constructor for class uk.ac.ebi.adfconverter.common.tools.file.copier.exceptions.FileCopyException: Constructor for the FileCopyException class creates a FileCopyException object with a givn message
FileFilter - class uk.ac.ebi.adfconverter.library.FileFilter.: implements java.io.FilenameFilter interface.
FileFilter() - Constructor for class uk.ac.ebi.adfconverter.library.FileFilter: contructor of a filter to filtre only file without extension
FileFilter(String[]) - Constructor for class uk.ac.ebi.adfconverter.library.FileFilter: contructor of a filter to filtre on ly file with the given extensio
FileFormatDescription - class uk.ac.ebi.adfconverter.common.tools.file.description.FileFormatDescription.: This interface the file type of a file (not simply the extension - I hope)
FileFormatDescription() - Constructor for class uk.ac.ebi.adfconverter.common.tools.file.description.FileFormatDescription
FileStructureDescription - class uk.ac.ebi.adfconverter.tools.filestructure.FileStructureDescription.: class used to manipulated the data/ tabular file structure description contained in an XML file
FileStructureDescription() - Constructor for class uk.ac.ebi.adfconverter.tools.filestructure.FileStructureDescription: default Constructor
FileType - interface uk.ac.ebi.adfconverter.tools.checker.data.FileType.: definition of a file Java content class for FileType complex type.
FileType(String) - Method in class uk.ac.ebi.adfconverter.tools.filestructure.FileStructureDescription: Retrieves the FileType associated to a given filename in the file structure definition.
FileType.DataSetType - interface uk.ac.ebi.adfconverter.tools.checker.data.FileType.DataSetType.: Java content class for anonymous complex type.
FileTypeImpl - class uk.ac.ebi.adfconverter.tools.checker.data.impl.FileTypeImpl.
FileTypeImpl() - Constructor for class uk.ac.ebi.adfconverter.tools.checker.data.impl.FileTypeImpl
FileTypeImpl.DataSetTypeImpl - class uk.ac.ebi.adfconverter.tools.checker.data.impl.FileTypeImpl.DataSetTypeImpl.
FileTypeImpl.DataSetTypeImpl() - Constructor for class uk.ac.ebi.adfconverter.tools.checker.data.impl.FileTypeImpl.DataSetTypeImpl
FileTypeImpl.DataSetTypeImpl.Unmarshaller - class uk.ac.ebi.adfconverter.tools.checker.data.impl.FileTypeImpl.DataSetTypeImpl.Unmarshaller.
FileTypeImpl.DataSetTypeImpl.Unmarshaller(UnmarshallingContext) - Constructor for class uk.ac.ebi.adfconverter.tools.checker.data.impl.FileTypeImpl.DataSetTypeImpl.Unmarshaller
FileTypeImpl.Unmarshaller - class uk.ac.ebi.adfconverter.tools.checker.data.impl.FileTypeImpl.Unmarshaller.
FileTypeImpl.Unmarshaller(UnmarshallingContext) - Constructor for class uk.ac.ebi.adfconverter.tools.checker.data.impl.FileTypeImpl.Unmarshaller
Filer - interface uk.ac.ebi.adfconverter.tools.checker.data.Filer.: data file strucuture definition Java content class for filer element declaration.
FilerImpl - class uk.ac.ebi.adfconverter.tools.checker.data.impl.FilerImpl.
FilerImpl() - Constructor for class uk.ac.ebi.adfconverter.tools.checker.data.impl.FilerImpl
FilerImpl.Unmarshaller - class uk.ac.ebi.adfconverter.tools.checker.data.impl.FilerImpl.Unmarshaller.
FilerImpl.Unmarshaller(UnmarshallingContext) - Constructor for class uk.ac.ebi.adfconverter.tools.checker.data.impl.FilerImpl.Unmarshaller
fatal(String) - Method in interface uk.ac.ebi.adfconverter.common.tools.log.ADFConverterLogger: Reports an fatal message to the current log.
fatal(String) - Method in class uk.ac.ebi.adfconverter.common.tools.log.ADFConverterLoggerImpl: Logs a fatal message into the current logger
fatalError(SAXParseException) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.ErrorHandlerAdaptor
fetch(String) - Static method in class uk.ac.ebi.adfconverter.common.tools.net.update.Fetch
fetchimage(String, Component) - Static method in class uk.ac.ebi.adfconverter.common.tools.net.update.Fetch
finalize() - Method in class uk.ac.ebi.adfconverter.common.tools.file.reader.ADFConverterFileReaderImpl: Finalization method that closes the file descriptor.
format(DataRow) - Static method in class uk.ac.ebi.adfconverter.common.tools.file.converter.DelimiterLineConverter: Format a DataRow following the current delimiter for output
format(DataTableHeader) - Static method in class uk.ac.ebi.adfconverter.common.tools.file.converter.DelimiterLineConverter: Format a DataHeaderRow following the current delimiter for output
format(DataRow) - Method in interface uk.ac.ebi.adfconverter.common.tools.file.converter.TextLineConverter: Formats the data contained in the DataRow object into a line of data following the text file format.
format(DataTableHeader) - Method in interface uk.ac.ebi.adfconverter.common.tools.file.converter.TextLineConverter: Formats the header item list object into a line of data following the text file format.

G

GetURLInfo - class uk.ac.ebi.adfconverter.common.tools.net.update.GetURLInfo.
GetURLInfo() - Constructor for class uk.ac.ebi.adfconverter.common.tools.net.update.GetURLInfo
GrammarInfo - interface uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.GrammarInfo.: Keeps the information about the grammar as a whole.
GrammarInfoImpl - class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.GrammarInfoImpl.: Keeps the information about the grammar as a whole.
GrammarInfoImpl(Map, Map, Class) - Constructor for class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.GrammarInfoImpl
generateIdentifier(String) - Method in class uk.ac.ebi.adfconverter.tools.converter.IdentifierGenerater.MAGEIdentifierGenerator: Generates a new identifier for a given objectType following the rules given in the configuration file.
generateIdentifier(String, Hashtable) - Method in class uk.ac.ebi.adfconverter.tools.converter.IdentifierGenerater.MAGEIdentifierGenerator: Generates a new identifier for a given objectType following the rules given in the configuration file.
getADFFile() - Method in class uk.ac.ebi.adfconverter.data.adf.ADFJava: retrieves the ADF associated to the object
getAllDeclaredPrefixes() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.SAXUnmarshallerHandlerImpl
getAllDeclaredPrefixes() - Method in interface uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.UnmarshallingContext: Returns a list of all in-scope prefixes.
getApplication() - Method in class uk.ac.ebi.adfconverter.data.adf.ADFJava: retrieves the application of the microarray layout
getApplicationLogger(String) - Method in class uk.ac.ebi.adfconverter.common.tools.log.ADFConverterLoggerImpl: Retrieves tool logger
getAssociatedItem() - Method in class uk.ac.ebi.adfconverter.data.adf.ADFGroup: Retrieves the associated Item
getAssociatedSimpleMicroArrayLayoutItem(CorrectableHeaderItem) - Method in class uk.ac.ebi.adfconverter.tools.filestructure.FileStructureDescription: Retrieves the associated Simple Microarray layout item associated to a given item in the structure definition.
getAssociatedSimpleMicroArrayLayoutItem(CorrectableHeaderItem, int) - Method in class uk.ac.ebi.adfconverter.tools.filestructure.FileStructureDescription: Retrieves the associated Simple Microarray layout item associated to a given item in the structure definition.
getAttribute(String, String) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.SAXUnmarshallerHandlerImpl
getAttribute(String, String) - Method in interface uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.UnmarshallingContext: Gets the index of the attribute with the specified name.
getAuthorisedADFExtension() - Static method in class uk.ac.ebi.adfconverter.data.adf.ADFJava: Retrieves the list of possible file extensions for ADF
getAvailableNumber() - Method in class uk.ac.ebi.adfconverter.tools.checker.Cardinality: Retrieves the number of still available element
getBaseUri() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.MSVValidator
getBaseUri() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.SAXUnmarshallerHandlerImpl
getBaseUri() - Method in interface uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.UnmarshallingContext
getBioSequences() - Method in class uk.ac.ebi.adfconverter.data.adf.ADFDesignElement: retrieves biosequences associated to the reporter
getBiosequencesTable() - Method in class uk.ac.ebi.adfconverter.data.adf.ADFJava: retrieves the ADF biosequences table
getCardinality() - Method in interface uk.ac.ebi.adfconverter.tools.checker.data.ItemType: Cardinality of the item in the table header (how many time it is supposed to be present in the header)
getCardinality() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTypeImpl
getCheckerProperty(String) - Static method in class uk.ac.ebi.adfconverter.common.configuration.ADFConverterConfiguration: Retrieves a Checker configuration property value
getColumNumber() - Method in interface uk.ac.ebi.adfconverter.tools.checker.data.LocationType: Gets the value of the columNumber property.
getColumNumber() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.LocationTypeImpl
getColumnClass(int) - Method in class uk.ac.ebi.adfconverter.usermode.gui.visualisation.DataTableModel: Describe getColumnClass method here.
getColumnCount() - Method in class uk.ac.ebi.adfconverter.usermode.gui.visualisation.DataTableModel: Describe getColumnCount method here.
getColumnName(int) - Method in class uk.ac.ebi.adfconverter.usermode.gui.visualisation.DataTableModel: Describe getColumnName method here.
getColumnNumber() - Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.HeaderItem: retrieves the column number of the item
getCommonProperty(String) - Static method in class uk.ac.ebi.adfconverter.common.configuration.ADFConverterConfiguration: Retrieves a commom configuration property value
getCompositeSequenceList() - Method in class uk.ac.ebi.adfconverter.data.adf.ADFJava: retrieves the ADF Composite Sequence List
getCompositeSequenceTable() - Method in class uk.ac.ebi.adfconverter.data.adf.ADFJava: retrieves the ADF compositeSequences table
getCompositeSequencegroups() - Method in class uk.ac.ebi.adfconverter.data.adf.ADFCompositeSequence: retrieves CompositeSequenceGroup associated to the compositeSequence
getCompositeSequences() - Method in class uk.ac.ebi.adfconverter.data.adf.ADFCompositeSequence: retrieves compositeSequences associated to the compositeSequence
getCompositeSequences() - Method in class uk.ac.ebi.adfconverter.data.adf.ADFReporter: retrieves compositeSequences associated to the reporter
getConstraint() - Method in interface uk.ac.ebi.adfconverter.tools.checker.data.FieldType.ConstraintsType: Gets the value of the Constraint property.
getConstraint() - Method in interface uk.ac.ebi.adfconverter.tools.checker.data.SubNameType.ConstraintsType: Gets the value of the Constraint property.
getConstraint() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.FieldTypeImpl.ConstraintsTypeImpl
getConstraint() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.SubNameTypeImpl.ConstraintsTypeImpl
getConstraints() - Method in interface uk.ac.ebi.adfconverter.tools.checker.data.FieldType: Gets the value of the constraints property.
getConstraints() - Method in interface uk.ac.ebi.adfconverter.tools.checker.data.SubNameType: Gets the value of the constraints property.
getConstraints() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.FieldTypeImpl
getConstraints() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.SubNameTypeImpl
getConversionProperties() - Static method in class uk.ac.ebi.adfconverter.common.configuration.ADFConverterConfiguration: Retrieves all properties for the converter
getConversionProperty(String) - Static method in class uk.ac.ebi.adfconverter.common.configuration.ADFConverterConfiguration: Retrieves a Conversion configuration property value
getCuratedTable() - Method in class uk.ac.ebi.adfconverter.tools.checker.FileChecker: Retrieves the curated data table for the current data file
getCuratedTable() - Method in class uk.ac.ebi.adfconverter.tools.checker.OptimizedFileChecker: Retrieves the curated data table for the current data file
getCuratedValue() - Method in interface uk.ac.ebi.adfconverter.tools.checker.data.ConstraintType: Gets the value of the curatedValue property.
getCuratedValue() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ConstraintTypeImpl
getCurrentHandler() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.SAXUnmarshallerHandlerImpl
getCurrentHandler() - Method in interface uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.UnmarshallingContext: Gets the current handler.
getDBComment(String) - Static method in class uk.ac.ebi.adfconverter.tools.checker.DatabaseChecker: retrieves the comment for a given DBTag
getDBName(String) - Static method in class uk.ac.ebi.adfconverter.tools.checker.DatabaseChecker: retrieves the database name for a given DBTag
getDBURI(String) - Static method in class uk.ac.ebi.adfconverter.tools.checker.DatabaseChecker: retrieves the URI for a given DBTag
getData() - Method in class uk.ac.ebi.adfconverter.common.tools.file.reader.DataFileReader: Retrieves data from file
getData(int) - Method in class uk.ac.ebi.adfconverter.common.tools.file.reader.DataFileReader: Retrieves data from file in a given file format, specifying file format type
getData(String, String, String, int, int) - Method in class uk.ac.ebi.adfconverter.common.tools.file.reader.DataFileReader: Retrieves data from file with a specific character encoding
getData() - Method in class uk.ac.ebi.adfconverter.common.tools.file.reader.DataFileReaderIntf: Retrieves data from file
getData(int) - Method in class uk.ac.ebi.adfconverter.common.tools.file.reader.DataFileReaderIntf: Retrieves data from file in a given file format, specifying file format type
getData(String, String, String, int, int) - Method in class uk.ac.ebi.adfconverter.common.tools.file.reader.DataFileReaderIntf: Retrieves data from file with a specific character encoding
getData() - Method in interface uk.ac.ebi.adfconverter.tools.checker.data.FileType.DataSetType: Gets the value of the Data property.
getData() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.FileTypeImpl.DataSetTypeImpl
getDataBuffer(int) - Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.DataRow: Retrieves the DataBuffer value contained in the specified location.
getDataBuffer(String) - Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.DataRow: Retrieves the DataBuffer value located under specified column label.
getDataBuffer(int, String) - Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.DataRow: Retrieves the String value contained in the specified location or defaultVal if it does not.
getDataBuffer(String, String) - Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.DataRow: Retrieves the String value contained under the specified column label.
getDataDelimiter() - Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.CorrectableHeaderItem: Retrieves the value delimiter of the item
getDataDelimiter() - Method in interface uk.ac.ebi.adfconverter.tools.checker.data.TableType: Gets the value of the dataDelimiter property.
getDataDelimiter() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.TableTypeImpl
getDataFileType() - Method in class uk.ac.ebi.adfconverter.common.tools.file.description.FileFormatDescription: Retrieves the the file format
getDataFileType() - Method in class uk.ac.ebi.adfconverter.common.tools.file.description.SimpleFileFormatDescription: Retrieves the the file format
getDataFormat() - Method in interface uk.ac.ebi.adfconverter.tools.checker.data.DataType: Gets the value of the dataFormat property.
getDataFormat() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.DataTypeImpl
getDataLine(Integer) - Method in interface uk.ac.ebi.adfconverter.common.tools.file.reader.DataReader: Retrieves a line from a data file Only when termination requirements have been met, the method should return a DataRow/code> object.
getDataLine(Integer) - Method in class uk.ac.ebi.adfconverter.common.tools.file.reader.PlainTextDataFileReader: Retrieves a line from a data file Only when termination requirements have been met, the method should return a String object.
getDataLine(Integer) - Method in class uk.ac.ebi.adfconverter.common.tools.file.reader.WorkBookFileReaderjxl: Retrieves a data row from a data file Only when termination requirements have been met, the method should return a DataRow object.
getDataSet() - Method in interface uk.ac.ebi.adfconverter.tools.checker.data.FileType: set of data contained in a file or spreadsheet
getDataSet() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.FileTypeImpl
getDataType(String) - Method in class uk.ac.ebi.adfconverter.tools.filestructure.FileStructureDescription: Retrieves the DataType object with a given dataname.
getDate(int, String) - Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.DataRow: Retrieves the date using the specified pattern to parse the date.
getDate(String, String) - Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.DataRow: Retrieves the date corresponding to the specified column label.
getDefaultImplementation(Class) - Method in interface uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.GrammarInfo: Gets the default implementation for the given public content interface.
getDefaultImplementation(Class) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.GrammarInfoImpl
getDescription() - Method in interface uk.ac.ebi.adfconverter.tools.checker.data.CheckRuleType: description of the rule, will be displayed in the tool
getDescription() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.CheckRuleTypeImpl
getDim(Object[][]) - Static method in class uk.ac.ebi.adfconverter.usermode.gui.visualisation.DataTableModel: Describe getDim method here.
getDouble(int) - Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.DataRow: Retrieves the double value of the datum contained in the specified location.
getDouble(String) - Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.DataRow: Retrieve the double value contained in data cell corresponding to the specified column label
getDouble(int, double) - Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.DataRow: Retrieves the double value of the datum contained in the specified location.
getDouble(int, DecimalFormat, double) - Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.DataRow: Retrieves the double value at specified location parsed using format.
getDouble(String, double) - Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.DataRow: Retrieve the double value contained in data cell corresponding to the specified column label.
getElement() - Method in interface uk.ac.ebi.adfconverter.tools.checker.data.ItemType: Gets the value of the element property.
getElement() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTypeImpl
getElementNumber() - Method in class uk.ac.ebi.adfconverter.tools.checker.Cardinality: Retrieves the number of already found element
getEnc() - Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.DataTable: Retrieves characters encoding
getEventHandler() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.ValidatorImpl
getExactName() - Method in interface uk.ac.ebi.adfconverter.tools.checker.data.ItemType: exact name, according to the specification, that should have the item
getExactName() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTypeImpl
getExporterProperties() - Static method in class uk.ac.ebi.adfconverter.common.configuration.ADFConverterConfiguration: Retrieves the properties corresponding to the exporter module
getExtension() - Method in interface uk.ac.ebi.adfconverter.tools.checker.data.FileType: Gets the value of the extension property.
getExtension() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.FileTypeImpl
getFeatureTable() - Method in class uk.ac.ebi.adfconverter.data.adf.ADFJava: retrieves the ADF feature table
getFieldCardinality() - Method in interface uk.ac.ebi.adfconverter.tools.checker.data.ItemType: Cardinality of associated field in the table (how many time it is supposed to be present in a row)
getFieldCardinality() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTypeImpl
getFieldDependence() - Method in interface uk.ac.ebi.adfconverter.tools.checker.data.ItemType: defines dependance between field
getFieldDependence() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTypeImpl
getFieldType() - Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.CorrectableHeaderItem: Retrieves the fieldtype of the item
getFieldValueType() - Method in interface uk.ac.ebi.adfconverter.tools.checker.data.ItemType: characterics of associated fields
getFieldValueType() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTypeImpl
getFile() - Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.DataTable: Gets the data file.
getFile() - Method in class uk.ac.ebi.adfconverter.common.tools.file.reader.DataFileReaderIntf: Retrieves the file associated/red by the reader
getFile() - Method in interface uk.ac.ebi.adfconverter.tools.checker.data.DocumentStructureType.FilesType: Gets the value of the File property.
getFile() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.DocumentStructureTypeImpl.FilesTypeImpl
getFileExtension() - Method in class uk.ac.ebi.adfconverter.common.tools.file.description.FileFormatDescription: Retrieves the the file format
getFileExtension() - Method in class uk.ac.ebi.adfconverter.common.tools.file.description.SimpleFileFormatDescription: Retrieves the the file extension
getFileFormat(String) - Static method in class uk.ac.ebi.adfconverter.common.data.tabulardata.DataTable: retrieves file format from strong
getFileFormat() - Method in class uk.ac.ebi.adfconverter.common.tools.file.description.SimpleFileFormatDescription: Retrieves the fileformat of the file as String
getFileFormat() - Method in interface uk.ac.ebi.adfconverter.tools.checker.data.FileType: Gets the value of the fileFormat property.
getFileFormat() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.FileTypeImpl
getFileName() - Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.DataTable: Gets the fileName.
getFilePath() - Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.DataTable: Gets the filepath.
getFileStructure(String, String) - Method in class uk.ac.ebi.adfconverter.tools.checker.FileChecker: Retrieves the FileType object from the XML file describing the file structure
getFileType() - Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.DataTable: Retrieves the file type but DataTable is correct. do not depend of this orientation For convience
getFileType() - Method in class uk.ac.ebi.adfconverter.tools.filestructure.FileStructureDescription: Retrieves the fileType attribut
getFiles() - Method in interface uk.ac.ebi.adfconverter.tools.checker.data.DocumentStructureType: set of one or sereral data files
getFiles() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.DocumentStructureTypeImpl
getFirstItemColumnByType(String) - Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.CorrectableDataTableHeader: retrieve the column of the first item in the header list with a given type
getFormat() - Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.DataTable: Gets the file format.
getFreeSpace(String) - Static method in class uk.ac.ebi.adfconverter.common.tools.file.filesystem.DiskUtil: Retrieves available free space on a hard drive following a file path
getGrammar() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.DefaultJAXBContextImpl: Loads a grammar object for the unmarshal-time validation.
getGrammar() - Method in interface uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.GrammarInfo: Gets the MSV AGM which can be used to validate XML during marshalling/unmarshalling.
getGrammar() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.GrammarInfoImpl: Gets the MSV AGM which can be used to validate XML during marshalling/unmarshalling.
getGrammarInfo() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.DefaultJAXBContextImpl
getGrammarInfo() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.SAXUnmarshallerHandlerImpl
getGrammarInfo() - Method in interface uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.UnmarshallingContext: Obtains a reference to the current grammar info.
getGroups() - Method in class uk.ac.ebi.adfconverter.data.adf.ADFDesignElement: retrieves Group associated to the design element
getHeader() - Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.CorrectableDataTable: Retrieves table header
getHeader() - Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.DataTable: Retrieves table header
getHeader() - Method in interface uk.ac.ebi.adfconverter.tools.checker.data.TableType: Gets the value of the header property.
getHeader() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.TableTypeImpl
getHeaderIndex() - Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.DataRow: Method for DataFile to get the shared instance of a Hashtable that contains column label to index reference.
getHeaderStructure(String, String) - Method in class uk.ac.ebi.adfconverter.tools.checker.FileChecker: Retrieves the HeaderType object corresponding to a given header structure
getHeaderTable() - Method in class uk.ac.ebi.adfconverter.data.adf.ADFJava: retrieves the ADF header table
getHeaderType() - Method in class uk.ac.ebi.adfconverter.tools.filestructure.FileStructureDescription: Retrieves the headerType attribut
getHorizontalDataRow() - Method in class uk.ac.ebi.adfconverter.common.tools.file.reader.DataFileReader: Retrieves the next datarow in the horizontal datable.
getHorizontalDataRow() - Method in class uk.ac.ebi.adfconverter.common.tools.file.reader.DataFileReaderIntf: Retrieves the next datarow in the horizontal datable.
getHorizontalDataTable(String, String, String) - Method in class uk.ac.ebi.adfconverter.common.tools.file.reader.DataFileReader: Retrieves data from file with a specific character encoding in a vertical orientation of data
getHorizontalDataTable(String, String, String, int) - Method in class uk.ac.ebi.adfconverter.common.tools.file.reader.DataFileReader: Retrieves data from file with a specific character encoding in a horizontal orientation of data
getHorizontalDataTable(String, String, String) - Method in class uk.ac.ebi.adfconverter.common.tools.file.reader.DataFileReaderIntf: Retrieves data from file with a specific character encoding in a vertical orientation of data
getHorizontalDataTable(String, String, String, int) - Method in class uk.ac.ebi.adfconverter.common.tools.file.reader.DataFileReaderIntf: Retrieves data from file with a specific character encoding in a horizontal orientation of data
getHorizontalHeader() - Method in class uk.ac.ebi.adfconverter.common.tools.file.reader.DataFileReader: Retrieves the header of a horizontal data table contained in a file
getHorizontalHeader() - Method in class uk.ac.ebi.adfconverter.common.tools.file.reader.DataFileReaderIntf: Retrieves the header of a horizontal data table contained in a file
getHorizontalOrientation() - Static method in class uk.ac.ebi.adfconverter.common.data.tabulardata.DataTable: retrieves Horizontal table orientation format
getIdentifierProperties() - Static method in class uk.ac.ebi.adfconverter.common.configuration.ADFConverterConfiguration: Retrieves all properties of the identifier generation
getInitialName() - Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.CorrectableHeaderItem: Retrieves the initial name of the item
getInnerValueFieldSeparator() - Method in interface uk.ac.ebi.adfconverter.tools.checker.data.ItemType: innerseparator of values in a field, if a value can contained several data
getInnerValueFieldSeparator() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTypeImpl
getInt(int) - Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.DataRow: Retrieves the int value of the datum contained in the specified location.
getInt(String) - Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.DataRow: Retrieves the int value of the datum contained under specified column label.
getInt(int, int) - Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.DataRow: Retrieves the int value of the datum contained in the specified location.
getInt(int, DecimalFormat, int) - Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.DataRow: Retrieves the int value at specified location parsed using format.
getInt(String, int) - Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.DataRow: Retrieves the int value under the specified column label.
getItem(int) - Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.DataTableHeader: retrieve an item from the header list at a given position
getItem(String) - Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.DataTableHeader: retrieve an item from the header list by a given name
getItem() - Static method in class uk.ac.ebi.adfconverter.common.util.pool.CorrectableDataTablePool: Retrieved a previous initialised/ created object from the pool.
getItem() - Static method in class uk.ac.ebi.adfconverter.common.util.pool.CorrectableHeaderItemPool: Retrieved a previous initialised/ created object from the pool.
getItem() - Static method in class uk.ac.ebi.adfconverter.common.util.pool.DataTablePool: Retrieved a previous initialised/ created object from the pool.
getItem() - Static method in class uk.ac.ebi.adfconverter.common.util.pool.HeaderItemPool: Retrieved a previous initialised/ created object from the pool.
getItem() - Method in interface uk.ac.ebi.adfconverter.tools.checker.data.HeaderType.ItemsType: Gets the value of the Item property.
getItem() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.HeaderTypeImpl.ItemsTypeImpl
getItemColumn(HeaderItem) - Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.DataTableHeader: retrieve the position of an item
getItemColumnByFieldType(String) - Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.CorrectableDataTableHeader: retrieve all items from the header list with a given field type
getItemColumnByLabel(String) - Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.DataTableHeader: retrieve the position of an item by its label
getItemColumnByType(String) - Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.CorrectableDataTableHeader: retrieve all items from the header list with a given type
getItemType() - Method in interface uk.ac.ebi.adfconverter.tools.checker.data.ItemType: name of the item type
getItemType() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTypeImpl
getItemref() - Method in interface uk.ac.ebi.adfconverter.tools.checker.data.ItemType.FieldDependenceType: Gets the value of the Itemref property.
getItemref() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTypeImpl.FieldDependenceTypeImpl
getItems() - Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.DataTableHeader: Retrieves the list of items contained in the header .
getItems() - Method in interface uk.ac.ebi.adfconverter.tools.checker.data.HeaderType: set of header items, describing the table structure
getItems() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.HeaderTypeImpl
getItemsByLabel(String) - Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.CorrectableDataTableHeader: retrieve all items from the header list with a given label
getLine() - Method in interface uk.ac.ebi.adfconverter.common.tools.file.reader.ADFConverterFileReader: Retrieves a line from a data file Only when termination requirements have been met, the method should return a String object.
getLine() - Method in class uk.ac.ebi.adfconverter.common.tools.file.reader.ADFConverterFileReaderImpl: Retrieves a line from a data file Only when termination requirements have been met, the method should return a String object.
getLine() - Method in class uk.ac.ebi.adfconverter.common.tools.file.reader.PlainTextFileReader: Retrieves a line from a data file Only when termination requirements have been met, the method should return a String object.
getLine() - Method in class uk.ac.ebi.adfconverter.common.tools.file.reader.WorkBookFileReaderjxl: Retrieves a line from a data file Only when termination requirements have been met, the method should return a String object.
getLineNumber() - Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.DataRow: Retrieve dataRow Line number in the data file
getLineNumber() - Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.DataTableHeader: Retrieves the line number of the header in the data file.
getLineNumber() - Method in interface uk.ac.ebi.adfconverter.common.tools.file.reader.ADFConverterFileReader: Retrieves the line number of current line in the data file
getLineNumber() - Method in class uk.ac.ebi.adfconverter.common.tools.file.reader.ADFConverterFileReaderImpl: Retrieves the line number of current line in the data file
getLineNumber() - Method in interface uk.ac.ebi.adfconverter.common.tools.file.reader.DataReader: Retrieves the line number of current line in the data file
getLocation() - Method in interface uk.ac.ebi.adfconverter.tools.checker.data.ItemType: Location of the item in the header
getLocation() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTypeImpl
getLocator() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.SAXUnmarshallerHandlerImpl
getLocator() - Method in interface uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.UnmarshallingContext: Gets the current source location information.
getLoggerProperties() - Static method in class uk.ac.ebi.adfconverter.common.configuration.ADFConverterConfiguration: Retrieves all properties corresponding to the logging module
getLowerBound() - Method in interface uk.ac.ebi.adfconverter.tools.checker.data.CardinalityType: Gets the value of the lowerBound property.
getLowerBound() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.CardinalityTypeImpl
getMAGEobj() - Method in class uk.ac.ebi.adfconverter.common.tools.file.reader.MAGEReader: Retrieves the MAGE object obtained from MAGE-ML file
getMessage() - Method in class uk.ac.ebi.adfconverter.library.exceptions.LibraryException: Returns the message of the exception
getMissingElement() - Method in class uk.ac.ebi.adfconverter.tools.checker.exceptions.IncorrectFileStructure: Retrieves the name of the missing element in the structure
getName() - Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.HeaderItem: retrieves the name of the item
getName() - Method in class uk.ac.ebi.adfconverter.data.adf.ADFGroup: returns the name of the group
getName() - Method in class uk.ac.ebi.adfconverter.tools.checker.Cardinality: Retrieves the name of the element
getName() - Method in interface uk.ac.ebi.adfconverter.tools.checker.data.DataType: Gets the value of the name property.
getName() - Method in interface uk.ac.ebi.adfconverter.tools.checker.data.FileType: Gets the value of the name property.
getName() - Method in interface uk.ac.ebi.adfconverter.tools.checker.data.ItemType: Gets the value of the name property.
getName() - Method in interface uk.ac.ebi.adfconverter.tools.checker.data.TableType: Gets the value of the name property.
getName() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.DataTypeImpl
getName() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.FileTypeImpl
getName() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTypeImpl
getName() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.TableTypeImpl
getNamespaceContext() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.MSVValidator
getNamespaceContext() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.SAXMarshaller
getNamespaceContext() - Method in interface uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.XMLSerializer: Obtains a namespace context object, which is used to declare/obtain namespace bindings.
getNamespacePrefixMapper() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.NamespaceContextImpl
getNamespaceURI(String) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.NamespaceContextImpl: Obtains the namespace URI currently associated to the given prefix.
getNamespaceURI(String) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.SAXUnmarshallerHandlerImpl
getNetworkProperty(String) - Static method in class uk.ac.ebi.adfconverter.common.configuration.ADFConverterConfiguration: Retrieves a Conversion configuration property value
getNewlyDeclaredPrefixes() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.SAXUnmarshallerHandlerImpl
getNewlyDeclaredPrefixes() - Method in interface uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.UnmarshallingContext: Returns a list of prefixes newly declared on this element.
getNextDataType() - Method in class uk.ac.ebi.adfconverter.tools.filestructure.FileStructureDescription: Retrieves the next DataType object in the structure definition
getNextFileType() - Method in class uk.ac.ebi.adfconverter.tools.filestructure.FileStructureDescription: Retrieves the next FileType object from the structure definition (XML)
getNextTable() - Method in class uk.ac.ebi.adfconverter.tools.filestructure.FileStructureDescription: Retrieves the next table object in the structure definition hierarchy/tree
getObjectFromId(String) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.SAXUnmarshallerHandlerImpl
getObjectFromId(String) - Method in interface uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.UnmarshallingContext: Looks up the ID table and gets associated object.
getOrientation() - Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.DataTable: Retrieves the orientation of data in file but DataTable is correct. do not depend of this orientation For convience
getOrientation() - Method in interface uk.ac.ebi.adfconverter.tools.checker.data.TableType: Gets the value of the orientation property.
getOrientation() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.TableTypeImpl
getPrefix(String) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.NamespaceContextImpl
getPrefix(String) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.SAXUnmarshallerHandlerImpl
getPrefixDelimiter() - Method in interface uk.ac.ebi.adfconverter.tools.checker.data.SubNameType: Gets the value of the prefixDelimiter property.
getPrefixDelimiter() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.SubNameTypeImpl
getPrefixSubName() - Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.CorrectableHeaderItem: Retreives the prefix delimiter for subname
getPrefixes(String) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.NamespaceContextImpl
getPrefixes(String) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.SAXUnmarshallerHandlerImpl
getPreviousColumn() - Method in interface uk.ac.ebi.adfconverter.tools.checker.data.LocationType.PreviousColumnsType: Gets the value of the PreviousColumn property.
getPreviousColumn() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.LocationTypeImpl.PreviousColumnsTypeImpl
getPreviousColumns() - Method in interface uk.ac.ebi.adfconverter.tools.checker.data.LocationType: Gets the value of the previousColumns property.
getPreviousColumns() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.LocationTypeImpl
getPreviousData() - Method in class uk.ac.ebi.adfconverter.tools.filestructure.FileStructureDescription: Retrieves the previous DataType object in the structure definition
getPreviousTable() - Method in class uk.ac.ebi.adfconverter.tools.filestructure.FileStructureDescription: Retrieves the previous table object in the structure definition hierarchy/tree
getPrimaryInterface() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.CardinalityTypeImpl
getPrimaryInterface() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.CheckRuleTypeImpl
getPrimaryInterface() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ConstraintTypeImpl
getPrimaryInterface() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.DataTypeImpl.TablesTypeImpl
getPrimaryInterface() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.DataTypeImpl
getPrimaryInterface() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.DocumentStructureImpl
getPrimaryInterface() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.DocumentStructureTypeImpl.FilesTypeImpl
getPrimaryInterface() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.DocumentStructureTypeImpl
getPrimaryInterface() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.FieldTypeImpl.ConstraintsTypeImpl
getPrimaryInterface() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.FieldTypeImpl
getPrimaryInterface() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.FileTypeImpl.DataSetTypeImpl
getPrimaryInterface() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.FileTypeImpl
getPrimaryInterface() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.FilerImpl
getPrimaryInterface() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.HeaderImpl
getPrimaryInterface() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.HeaderTypeImpl.ItemsTypeImpl
getPrimaryInterface() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.HeaderTypeImpl
getPrimaryInterface() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTempImpl
getPrimaryInterface() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTypeImpl.FieldDependenceTypeImpl
getPrimaryInterface() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTypeImpl.RelaxCheckRulesTypeImpl
getPrimaryInterface() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTypeImpl.SubNamesTypeImpl
getPrimaryInterface() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTypeImpl
getPrimaryInterface() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.LocationTypeImpl.PreviousColumnsTypeImpl
getPrimaryInterface() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.LocationTypeImpl
getPrimaryInterface() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.SubNameTypeImpl.ConstraintsTypeImpl
getPrimaryInterface() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.SubNameTypeImpl
getPrimaryInterface() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.TableTypeImpl
getPrimaryInterface() - Method in interface uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.ValidatableObject: Gets the main interface that this object implements.
getProbePoints() - Method in interface uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.GrammarInfo: Return the probe points for this GrammarInfo, which are used to detect {namespaceURI,localName} collisions across the GrammarInfo's on the schemaPath.
getProbePoints() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.GrammarInfoImpl
getProperty(String) - Static method in class uk.ac.ebi.adfconverter.common.configuration.ADFConverterConfiguration: Retrieves a configuration property value
getProperty(String) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.ObjectFactory: Get the specified property.
getProperty(String) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.DefaultJAXBContextImpl: There are no required properties, so simply throw an exception.
getProperty(String) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.MarshallerImpl
getProperty(String) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.ValidatorImpl: There are no required properties, so simply throw an exception.
getRegex() - Method in interface uk.ac.ebi.adfconverter.tools.checker.data.CheckRuleType: regulax expression used for identification
getRegex() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.CheckRuleTypeImpl
getRelaxCheck() - Method in interface uk.ac.ebi.adfconverter.tools.checker.data.ItemType.RelaxCheckRulesType: Gets the value of the RelaxCheck property.
getRelaxCheck() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTypeImpl.RelaxCheckRulesTypeImpl
getRelaxCheckRules() - Method in interface uk.ac.ebi.adfconverter.tools.checker.data.ItemType: list of relax rules: relax checking mode, the different possibilities for the item
getRelaxCheckRules() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTypeImpl
getReporter() - Method in class uk.ac.ebi.adfconverter.data.adf.ADFFeature: Retrieves the associated Reporter
getReporterGroupList() - Method in class uk.ac.ebi.adfconverter.data.adf.ADFJava: retrieves the ADF Reporter Group List
getReporterTable() - Method in class uk.ac.ebi.adfconverter.data.adf.ADFJava: retrieves the ADF reporter table * @return the associated ADF reporter table
getReportergroups() - Method in class uk.ac.ebi.adfconverter.data.adf.ADFReporter: retrieves ReporterGroup associated to the reporter
getReporters() - Method in class uk.ac.ebi.adfconverter.data.adf.ADFCompositeSequence: retrieves reporters associated to the compositeSequence
getResult() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.SAXUnmarshallerHandlerImpl
getResult() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.ValidatingUnmarshaller
getRootElement(String, String) - Method in interface uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.GrammarInfo: Creates an instance for the root element.
getRootElement(String, String) - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.GrammarInfoImpl
getRow(int) - Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.DataTable: gets a datarow in the table
getRow() - Static method in class uk.ac.ebi.adfconverter.common.util.pool.DataRowPool: Retrieved a previous initialised/ created object from the pool.
getRowCount() - Method in class uk.ac.ebi.adfconverter.usermode.gui.visualisation.DataTableModel: Describe getRowCount method here.
getRows() - Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.DataTable: Retrieves the list of rows found in the data file.
getRule() - Method in interface uk.ac.ebi.adfconverter.tools.checker.data.ConstraintType: Gets the value of the rule property.
getRule() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ConstraintTypeImpl
getSheetNumber() - Method in interface uk.ac.ebi.adfconverter.tools.checker.data.TableType: Gets the value of the sheetNumber property.
getSheetNumber() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.TableTypeImpl
getSimpleMicroarrayLayoutRelatedItem() - Method in interface uk.ac.ebi.adfconverter.tools.checker.data.ItemType: Gets the value of the simpleMicroarrayLayoutRelatedItem property.
getSimpleMicroarrayLayoutRelatedItem() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTypeImpl
getStrictCheck() - Method in interface uk.ac.ebi.adfconverter.tools.checker.data.ItemType: a unique rule, exactly matching the specification
getStrictCheck() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTypeImpl
getString() - Method in class uk.ac.ebi.adfconverter.common.data.DataBuffer: Retrieves the internalString attribut
getString(int) - Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.DataRow: Retrieves the String value contained in the specified location.
getString(String) - Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.DataRow: Retrieves the String value located under specified column label.
getString(int, String) - Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.DataRow: Retrieves the String value contained in the specified location or defaultVal if it does not.
getString(String, String) - Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.DataRow: Retrieves the String value contained under the specified column label.
getString() - Static method in class uk.ac.ebi.adfconverter.common.util.pool.DataBufferPool: Retrieved a previous initialised/ created object from the pool.
getString() - Static method in class uk.ac.ebi.adfconverter.common.util.pool.StringBufferPool: Retrieved a previous initialised/ created object from the pool.
getString() - Static method in class uk.ac.ebi.adfconverter.common.util.pool.StringPool: Returns a String object not used.
getStringBuffer(int) - Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.DataRow: Retrieves the StringBuffer value contained in the specified location.
getStringBuffer(String) - Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.DataRow: Retrieves the StringBuffer value located under specified column label.
getStringBuffer(int, StringBuffer) - Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.DataRow: Retrieves the String value contained in the specified location or defaultVal if it does not.
getStringBuffer(String, StringBuffer) - Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.DataRow: Retrieves the String value contained under the specified column label.
getStringChecking() - Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.DataRow: Retrieves the stringChecking attribut
getStructureFileName() - Method in class uk.ac.ebi.adfconverter.tools.checker.exceptions.IncorrectFileStructure: Retrieves the path to the used structure file
getSubName() - Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.CorrectableHeaderItem: Retrieves the subname of the item
getSubName() - Method in interface uk.ac.ebi.adfconverter.tools.checker.data.ItemType.SubNamesType: Gets the value of the SubName property.
getSubName() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTypeImpl.SubNamesTypeImpl
getSubNames() - Method in interface uk.ac.ebi.adfconverter.tools.checker.data.ItemType: Gets the value of the subNames property.
getSubNames() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTypeImpl
getSuffixDelimiter() - Method in interface uk.ac.ebi.adfconverter.tools.checker.data.SubNameType: Gets the value of the suffixDelimiter property.
getSuffixDelimiter() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.SubNameTypeImpl
getSuffixSubName() - Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.CorrectableHeaderItem: Retrieves the suffix delimiter for subname
getTable(String) - Method in class uk.ac.ebi.adfconverter.data.adf.ADFJava: Retrieves a table following a given name
getTable() - Method in interface uk.ac.ebi.adfconverter.tools.checker.data.DataType.TablesType: Gets the value of the Table property.
getTable() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.DataTypeImpl.TablesTypeImpl
getTableDelimiter() - Method in interface uk.ac.ebi.adfconverter.tools.checker.data.DataType: Gets the value of the tableDelimiter property.
getTableDelimiter() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.DataTypeImpl
getTableOrientationFormat(String) - Static method in class uk.ac.ebi.adfconverter.common.data.tabulardata.DataTable: retrieves file format from string
getTableType(String) - Method in class uk.ac.ebi.adfconverter.tools.filestructure.FileStructureDescription: Retrieves the TableType object with a given name.
getTables() - Method in interface uk.ac.ebi.adfconverter.tools.checker.data.DataType: set of data tables (at least one)
getTables() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.DataTypeImpl
getTextFile() - Static method in class uk.ac.ebi.adfconverter.common.data.tabulardata.DataTable: retrieves text file format
getTracer() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.SAXUnmarshallerHandlerImpl
getTracer() - Method in interface uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.UnmarshallingContext: Gets a tracer object.
getType() - Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.CorrectableHeaderItem: Retrieves the type of the item
getType() - Method in interface uk.ac.ebi.adfconverter.tools.checker.data.SubNameType: Gets the value of the type property.
getType() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.SubNameTypeImpl
getTypeName() - Method in interface uk.ac.ebi.adfconverter.tools.checker.data.FieldType: Gets the value of the typeName property.
getTypeName() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.FieldTypeImpl
getUnconsumedAttributes() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.SAXUnmarshallerHandlerImpl
getUnconsumedAttributes() - Method in interface uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.UnmarshallingContext: Gets all the unconsumed attributes.
getUnknownFileFormat() - Static method in class uk.ac.ebi.adfconverter.common.data.tabulardata.DataTable: retrieves unknown file format
getUnmarshallerHandler() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.UnmarshallerImpl
getUpperBound() - Method in interface uk.ac.ebi.adfconverter.tools.checker.data.CardinalityType: Gets the value of the upperBound property.
getUpperBound() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.CardinalityTypeImpl
getValueAt(int, int) - Method in class uk.ac.ebi.adfconverter.usermode.gui.visualisation.DataTableModel: Describe getValueAt method here.
getValueDelimiter() - Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.CorrectableHeaderItem: Retrieves the inner value delimiter of the item
getValueFieldSeparator() - Method in interface uk.ac.ebi.adfconverter.tools.checker.data.ItemType: separator of values in a field, if multiplicity possible
getValueFieldSeparator() - Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTypeImpl
getVerticalDataTable(String, String, String) - Method in class uk.ac.ebi.adfconverter.common.tools.file.reader.DataFileReader: Retrieves data from file with a specific character encoding in a vertical orientation of data
getVerticalDataTable(String, String, String, int) - Method in class uk.ac.ebi.adfconverter.common.tools.file.reader.DataFileReader: Retrieves data from file with a specific character encoding in a vertical orientation of data
getVerticalDataTable(String, String, String) - Method in class uk.ac.ebi.adfconverter.common.tools.file.reader.DataFileReaderIntf: Retrieves data from file with a specific character encoding in a vertical orientation of data
getVerticalDataTable(String, String, String, int) - Method in class uk.ac.ebi.adfconverter.common.tools.file.reader.DataFileReaderIntf: Retrieves data from file with a specific character encoding in a vertical orientation of data
getVerticalOrientation() - Static method in class uk.ac.ebi.adfconverter.common.data.tabulardata.DataTable: retrieves vertical table orientation format
getWorkBookFile() - Static method in class uk.ac.ebi.adfconverter.common.data.tabulardata.DataTable: retrieves workbook file format
getlowerBound() - Method in class uk.ac.ebi.adfconverter.tools.checker.Cardinality: Retrieves the lower bound
getupperBound() - Method in class uk.ac.ebi.adfconverter.tools.checker.Cardinality: Retrieves the upper bound
grammarInfo - Static variable in class uk.ac.ebi.adfconverter.tools.checker.data.ObjectFactory




H

HORIZONTALTABLE - 
Static variable in class uk.ac.ebi.adfconverter.common.data.tabulardata.DataTable
Horizontal  table orientation
Header - interface uk.ac.ebi.adfconverter.tools.checker.data.Header.
list of header item of data table contained in a file
 Java content class for header element declaration.
 
HeaderImpl - class uk.ac.ebi.adfconverter.tools.checker.data.impl.HeaderImpl.
 
HeaderImpl() - 
Constructor for class uk.ac.ebi.adfconverter.tools.checker.data.impl.HeaderImpl
 
HeaderImpl.Unmarshaller - class uk.ac.ebi.adfconverter.tools.checker.data.impl.HeaderImpl.Unmarshaller.
 
HeaderImpl.Unmarshaller(UnmarshallingContext) - 
Constructor for class uk.ac.ebi.adfconverter.tools.checker.data.impl.HeaderImpl.Unmarshaller
 
HeaderItem - class uk.ac.ebi.adfconverter.common.data.tabulardata.HeaderItem.
This class represents an header item of a data table
HeaderItem() - 
Constructor for class uk.ac.ebi.adfconverter.common.data.tabulardata.HeaderItem
Class contructor : creates an instance 
 
 for convenience (empty constructor)
HeaderItem(String) - 
Constructor for class uk.ac.ebi.adfconverter.common.data.tabulardata.HeaderItem
Class contructor : creates an instance 
 with a given name of item
HeaderItem(String, int) - 
Constructor for class uk.ac.ebi.adfconverter.common.data.tabulardata.HeaderItem
Class contructor : creates an instance 
 with a given name of item and a given column number
HeaderItemPool - class uk.ac.ebi.adfconverter.common.util.pool.HeaderItemPool.
Pool class for HeaderItemPool objects
 
 Contains a list of available tables. 
 
HeaderItemPool() - 
Constructor for class uk.ac.ebi.adfconverter.common.util.pool.HeaderItemPool
 
HeaderType - interface uk.ac.ebi.adfconverter.tools.checker.data.HeaderType.
Header list Structure: contains item
 Java content class for headerType complex type.
 
HeaderType.ItemsType - interface uk.ac.ebi.adfconverter.tools.checker.data.HeaderType.ItemsType.
Java content class for anonymous complex type.
 
HeaderTypeImpl - class uk.ac.ebi.adfconverter.tools.checker.data.impl.HeaderTypeImpl.
 
HeaderTypeImpl() - 
Constructor for class uk.ac.ebi.adfconverter.tools.checker.data.impl.HeaderTypeImpl
 
HeaderTypeImpl.ItemsTypeImpl - class uk.ac.ebi.adfconverter.tools.checker.data.impl.HeaderTypeImpl.ItemsTypeImpl.
 
HeaderTypeImpl.ItemsTypeImpl() - 
Constructor for class uk.ac.ebi.adfconverter.tools.checker.data.impl.HeaderTypeImpl.ItemsTypeImpl
 
HeaderTypeImpl.ItemsTypeImpl.Unmarshaller - class uk.ac.ebi.adfconverter.tools.checker.data.impl.HeaderTypeImpl.ItemsTypeImpl.Unmarshaller.
 
HeaderTypeImpl.ItemsTypeImpl.Unmarshaller(UnmarshallingContext) - 
Constructor for class uk.ac.ebi.adfconverter.tools.checker.data.impl.HeaderTypeImpl.ItemsTypeImpl.Unmarshaller
 
HeaderTypeImpl.Unmarshaller - class uk.ac.ebi.adfconverter.tools.checker.data.impl.HeaderTypeImpl.Unmarshaller.
 
HeaderTypeImpl.Unmarshaller(UnmarshallingContext) - 
Constructor for class uk.ac.ebi.adfconverter.tools.checker.data.impl.HeaderTypeImpl.Unmarshaller
 
handleEvent(ValidationEvent, boolean) - 
Method in interface uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.SAXUnmarshallerHandler
Reports an error to the user, and asks if s/he wants
 to recover. 
handleEvent(ValidationEvent, boolean) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.SAXUnmarshallerHandlerImpl
 
handleEvent(ValidationEvent, boolean) - 
Method in interface uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.UnmarshallingContext
Reports an error to the user, and asks if s/he wants
 to recover. 
handleEvent(ValidationEvent, boolean) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.ValidatingUnmarshaller
 
handlePrintConversionException(Object, Exception, XMLSerializer) - 
Static method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.Util
Reports a print conversion error while marshalling.
handleText(String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.CardinalityTypeImpl.Unmarshaller
 
handleText(String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.CheckRuleTypeImpl.Unmarshaller
 
handleText(String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ConstraintTypeImpl.Unmarshaller
 
handleText(String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.DataTypeImpl.TablesTypeImpl.Unmarshaller
 
handleText(String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.DataTypeImpl.Unmarshaller
 
handleText(String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.DocumentStructureImpl.Unmarshaller
 
handleText(String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.DocumentStructureTypeImpl.FilesTypeImpl.Unmarshaller
 
handleText(String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.DocumentStructureTypeImpl.Unmarshaller
 
handleText(String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.FieldTypeImpl.ConstraintsTypeImpl.Unmarshaller
 
handleText(String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.FieldTypeImpl.Unmarshaller
 
handleText(String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.FileTypeImpl.DataSetTypeImpl.Unmarshaller
 
handleText(String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.FileTypeImpl.Unmarshaller
 
handleText(String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.FilerImpl.Unmarshaller
 
handleText(String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.HeaderImpl.Unmarshaller
 
handleText(String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.HeaderTypeImpl.ItemsTypeImpl.Unmarshaller
 
handleText(String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.HeaderTypeImpl.Unmarshaller
 
handleText(String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTempImpl.Unmarshaller
 
handleText(String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTypeImpl.FieldDependenceTypeImpl.Unmarshaller
 
handleText(String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTypeImpl.RelaxCheckRulesTypeImpl.Unmarshaller
 
handleText(String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTypeImpl.SubNamesTypeImpl.Unmarshaller
 
handleText(String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTypeImpl.Unmarshaller
 
handleText(String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.LocationTypeImpl.PreviousColumnsTypeImpl.Unmarshaller
 
handleText(String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.LocationTypeImpl.Unmarshaller
 
handleText(String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.SubNameTypeImpl.ConstraintsTypeImpl.Unmarshaller
 
handleText(String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.SubNameTypeImpl.Unmarshaller
 
handleText(String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.TableTypeImpl.Unmarshaller
 
handleTypeMismatchError(XMLSerializer, Object, String, Object) - 
Static method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.Util
Reports that the type of an object in a property is unexpected.
hasNext() - 
Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.DataTable
retrieves if there a next row after the current one
headerFileExtension - 
Static variable in class uk.ac.ebi.adfconverter.data.adf.ADFJava
adfFile: default header text file extension
horizontalToVerticalTable(DataTable) - 
Method in class uk.ac.ebi.adfconverter.common.tools.file.reader.DataFileReader
ConvertTable from table obtained from
 a file in the correct data orientation
horizontalToVerticalTable(DataTable) - 
Method in class uk.ac.ebi.adfconverter.common.tools.file.writer.DataFileWriter
ConvertTable from a given table  
 in the correct data orientation



I

IncorrectADFCheckerInitException - exception uk.ac.ebi.adfconverter.tools.checker.exceptions.IncorrectADFCheckerInitException.
Signals an error of database checking initialisation.
 
IncorrectADFCheckerInitException() - 
Constructor for class uk.ac.ebi.adfconverter.tools.checker.exceptions.IncorrectADFCheckerInitException
 
IncorrectADFFile - exception uk.ac.ebi.adfconverter.tools.checker.exceptions.IncorrectADFFile.
Signals during the ADF Header data checking.
 
IncorrectADFFile() - 
Constructor for class uk.ac.ebi.adfconverter.tools.checker.exceptions.IncorrectADFFile
Default IncorrectADFFile class Constructor
IncorrectADFFile(String) - 
Constructor for class uk.ac.ebi.adfconverter.tools.checker.exceptions.IncorrectADFFile
IncorrectADFFile exception Constructor with  the name of the incorrect file
IncorrectADFHeaderFile - exception uk.ac.ebi.adfconverter.tools.checker.exceptions.IncorrectADFHeaderFile.
Signals during the ADF Header data checking.
 
IncorrectADFHeaderFile() - 
Constructor for class uk.ac.ebi.adfconverter.tools.checker.exceptions.IncorrectADFHeaderFile
IncorrectADFHeaderFile class default Constructor
IncorrectADFHeaderFile(String) - 
Constructor for class uk.ac.ebi.adfconverter.tools.checker.exceptions.IncorrectADFHeaderFile
IncorrectADFHeaderFile class Constructor with the incorrect file path
IncorrectDataBaseInit - exception uk.ac.ebi.adfconverter.tools.checker.exceptions.IncorrectDataBaseInit.
Signals an error of database checking initialisation.
 
IncorrectDataBaseInit() - 
Constructor for class uk.ac.ebi.adfconverter.tools.checker.exceptions.IncorrectDataBaseInit
 
IncorrectDataFile - exception uk.ac.ebi.adfconverter.common.tools.file.reader.exceptions.IncorrectDataFile.
Signals an error of file reader.
 
IncorrectDataFile() - 
Constructor for class uk.ac.ebi.adfconverter.common.tools.file.reader.exceptions.IncorrectDataFile
Constructor of the IncorrectDataFile class
 default constructor , without associated incorrect file
IncorrectDataFile(String) - 
Constructor for class uk.ac.ebi.adfconverter.common.tools.file.reader.exceptions.IncorrectDataFile
Constructor of the IncorrectDataFile class,
 with the name of the incorrect file
IncorrectDataTableException - exception uk.ac.ebi.adfconverter.common.data.tabulardata.exceptions.IncorrectDataTableException.
Signals an error of data table.
 
IncorrectDataTableException() - 
Constructor for class uk.ac.ebi.adfconverter.common.data.tabulardata.exceptions.IncorrectDataTableException
Constructor of the IncorrectDataTableException class
 creates a default exception object
IncorrectDataTableException(String) - 
Constructor for class uk.ac.ebi.adfconverter.common.data.tabulardata.exceptions.IncorrectDataTableException
Constructor of the IncorrectDataTableException class
 with an associated fileName.
 
IncorrectFile - exception uk.ac.ebi.adfconverter.common.tools.file.reader.exceptions.IncorrectFile.
Signals an error of file reader.
 
IncorrectFile() - 
Constructor for class uk.ac.ebi.adfconverter.common.tools.file.reader.exceptions.IncorrectFile
contructor IncorrectFile Exception
 default one, currently empty
IncorrectFile(String) - 
Constructor for class uk.ac.ebi.adfconverter.common.tools.file.reader.exceptions.IncorrectFile
contructor IncorrectFile Exception with a name of the incorrect file
IncorrectFileStructure - exception uk.ac.ebi.adfconverter.tools.checker.exceptions.IncorrectFileStructure.
Signals an error of file reader.
 
IncorrectFileStructure() - 
Constructor for class uk.ac.ebi.adfconverter.tools.checker.exceptions.IncorrectFileStructure
Exception if the file structure description file is
 incorrect with no specified element
IncorrectFileStructure(String) - 
Constructor for class uk.ac.ebi.adfconverter.tools.checker.exceptions.IncorrectFileStructure
Exception if the file structure description file is
 incorrect with no specified element
IncorrectFileStructure(String, String) - 
Constructor for class uk.ac.ebi.adfconverter.tools.checker.exceptions.IncorrectFileStructure
Exception if the file structure description file is
 incorrect with a  specified structure element
IncorrectOntologyException - exception uk.ac.ebi.adfconverter.tools.checker.ontology.exceptions.IncorrectOntologyException.
Signals an error of file reader.
 
IncorrectOntologyException() - 
Constructor for class uk.ac.ebi.adfconverter.tools.checker.ontology.exceptions.IncorrectOntologyException
 
IncorrectOntologyFileException - exception uk.ac.ebi.adfconverter.tools.checker.ontology.exceptions.IncorrectOntologyFileException.
Signals an error of file reader.
 
IncorrectOntologyFileException() - 
Constructor for class uk.ac.ebi.adfconverter.tools.checker.ontology.exceptions.IncorrectOntologyFileException
 
IncorrectSubNameException - exception uk.ac.ebi.adfconverter.tools.checker.exceptions.IncorrectSubNameException.
Signals an error during data checking.
 
 
IncorrectSubNameException() - 
Constructor for class uk.ac.ebi.adfconverter.tools.checker.exceptions.IncorrectSubNameException
 
InitNextItem() - 
Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.DataTableHeader
initialised the parsing of item list
 Starts at the begin of the list
InitNextRow() - 
Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.DataTable
initialised the parsing of row list
 Starts at the begin of the list
IsSimpleMicroArrayLayout - 
Variable in class uk.ac.ebi.adfconverter.tools.converter.MAGEToADFConverter
 
ItemTemp - interface uk.ac.ebi.adfconverter.tools.checker.data.ItemTemp.
Java content class for itemTemp element declaration.
 
ItemTempImpl - class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTempImpl.
 
ItemTempImpl() - 
Constructor for class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTempImpl
 
ItemTempImpl.Unmarshaller - class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTempImpl.Unmarshaller.
 
ItemTempImpl.Unmarshaller(UnmarshallingContext) - 
Constructor for class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTempImpl.Unmarshaller
 
ItemType - interface uk.ac.ebi.adfconverter.tools.checker.data.ItemType.
an header item with characteristic of it for checking
 Java content class for ItemType complex type.
 
ItemType.FieldDependenceType - interface uk.ac.ebi.adfconverter.tools.checker.data.ItemType.FieldDependenceType.
Java content class for anonymous complex type.
 
ItemType.RelaxCheckRulesType - interface uk.ac.ebi.adfconverter.tools.checker.data.ItemType.RelaxCheckRulesType.
Java content class for anonymous complex type.
 
ItemType.SubNamesType - interface uk.ac.ebi.adfconverter.tools.checker.data.ItemType.SubNamesType.
Java content class for anonymous complex type.
 
ItemTypeImpl - class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTypeImpl.
 
ItemTypeImpl() - 
Constructor for class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTypeImpl
 
ItemTypeImpl.FieldDependenceTypeImpl - class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTypeImpl.FieldDependenceTypeImpl.
 
ItemTypeImpl.FieldDependenceTypeImpl() - 
Constructor for class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTypeImpl.FieldDependenceTypeImpl
 
ItemTypeImpl.FieldDependenceTypeImpl.Unmarshaller - class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTypeImpl.FieldDependenceTypeImpl.Unmarshaller.
 
ItemTypeImpl.FieldDependenceTypeImpl.Unmarshaller(UnmarshallingContext) - 
Constructor for class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTypeImpl.FieldDependenceTypeImpl.Unmarshaller
 
ItemTypeImpl.RelaxCheckRulesTypeImpl - class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTypeImpl.RelaxCheckRulesTypeImpl.
 
ItemTypeImpl.RelaxCheckRulesTypeImpl() - 
Constructor for class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTypeImpl.RelaxCheckRulesTypeImpl
 
ItemTypeImpl.RelaxCheckRulesTypeImpl.Unmarshaller - class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTypeImpl.RelaxCheckRulesTypeImpl.Unmarshaller.
 
ItemTypeImpl.RelaxCheckRulesTypeImpl.Unmarshaller(UnmarshallingContext) - 
Constructor for class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTypeImpl.RelaxCheckRulesTypeImpl.Unmarshaller
 
ItemTypeImpl.SubNamesTypeImpl - class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTypeImpl.SubNamesTypeImpl.
 
ItemTypeImpl.SubNamesTypeImpl() - 
Constructor for class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTypeImpl.SubNamesTypeImpl
 
ItemTypeImpl.SubNamesTypeImpl.Unmarshaller - class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTypeImpl.SubNamesTypeImpl.Unmarshaller.
 
ItemTypeImpl.SubNamesTypeImpl.Unmarshaller(UnmarshallingContext) - 
Constructor for class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTypeImpl.SubNamesTypeImpl.Unmarshaller
 
ItemTypeImpl.Unmarshaller - class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTypeImpl.Unmarshaller.
 
ItemTypeImpl.Unmarshaller(UnmarshallingContext) - 
Constructor for class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTypeImpl.Unmarshaller
 
identifierPREFIX - 
Static variable in class uk.ac.ebi.adfconverter.common.configuration.ADFConverterConfiguration
Definition of the adfconverter property name sub prefix for the identifier submodule
  (for identifier generation): 
 identifier.
ignorableWhitespace(char[], int, int) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.ContentHandlerAdaptor
 
ignorableWhitespace(char[], int, int) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.SAXUnmarshallerHandlerImpl
 
info(String) - 
Method in interface uk.ac.ebi.adfconverter.common.tools.log.ADFConverterLogger
Reports an info message to the current log.
info(String) - 
Method in class uk.ac.ebi.adfconverter.common.tools.log.ADFConverterLoggerImpl
Logs a info message into the current logger
init() - 
Static method in class uk.ac.ebi.adfconverter.common.util.pool.CorrectableDataTablePool
Inits the pool.
 
init() - 
Static method in class uk.ac.ebi.adfconverter.common.util.pool.CorrectableHeaderItemPool
Inits the pool.
 
init() - 
Static method in class uk.ac.ebi.adfconverter.common.util.pool.DataBufferPool
Inits the pool.
 
init() - 
Static method in class uk.ac.ebi.adfconverter.common.util.pool.DataRowPool
Inits the pool.
 
init() - 
Static method in class uk.ac.ebi.adfconverter.common.util.pool.DataTablePool
Inits the pool.
 
init() - 
Static method in class uk.ac.ebi.adfconverter.common.util.pool.HeaderItemPool
Inits the pool.
 
init() - 
Static method in class uk.ac.ebi.adfconverter.common.util.pool.StringBufferPool
Inits the pool.
 
init() - 
Static method in class uk.ac.ebi.adfconverter.common.util.pool.StringPool
Initialises the pool.
 
init() - 
Method in class uk.ac.ebi.adfconverter.tools.checker.Cardinality
init the cardinality.
 
isCellEditable(int, int) - 
Method in class uk.ac.ebi.adfconverter.usermode.gui.visualisation.DataTableModel
 
isEmpty() - 
Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.DataRow
Tests if this row has no elements.
isEmpty() - 
Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.DataTable
Retrieves if the table is empty
isErasable(boolean) - 
Method in interface uk.ac.ebi.adfconverter.common.tools.file.writer.ADFConverterFileWriter
Sets if a file should be overwritten,
 	if it exists
isErasable(boolean) - 
Method in class uk.ac.ebi.adfconverter.common.tools.file.writer.ADFConverterFileWriterImpl
Sets if a file should be overwritten,
 	if it exists
isErasable(boolean) - 
Method in interface uk.ac.ebi.adfconverter.common.tools.file.writer.DataWriter
Sets if a file should be overwritten,
 	if it exists
isHaveHeader() - 
Method in interface uk.ac.ebi.adfconverter.tools.checker.data.TableType
Gets the value of the haveHeader property.
isHaveHeader() - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.TableTypeImpl
 
isMandatory() - 
Method in interface uk.ac.ebi.adfconverter.tools.checker.data.FileType
Gets the value of the mandatory property.
isMandatory() - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.FileTypeImpl
 
isMultiplicity() - 
Method in interface uk.ac.ebi.adfconverter.tools.checker.data.ItemType
if multiplicity of values in a associatd field
isMultiplicity() - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTypeImpl
 
isNotation(String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.MSVValidator
 
isNotation(String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.SAXUnmarshallerHandlerImpl
 
isNotation(String) - 
Method in interface uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.UnmarshallingContext
 
isProduction() - 
Static method in class uk.ac.ebi.adfconverter.common.tools.log.ADFConverterLoggerImpl
Retrieves the  isProduction attribut
isUnparsedEntity(String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.MSVValidator
 
isUnparsedEntity(String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.SAXUnmarshallerHandlerImpl
 
isUnparsedEntity(String) - 
Method in interface uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.UnmarshallingContext
 
iterateDeclaredPrefixes(PrefixCallback) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.NamespaceContextImpl
Iterates all newly declared namespace prefixes for this element.



J

JAXBVersion - class uk.ac.ebi.adfconverter.tools.checker.data.impl.JAXBVersion.
 
JAXBVersion() - 
Constructor for class uk.ac.ebi.adfconverter.tools.checker.data.impl.JAXBVersion
 



L

LibraryException - exception uk.ac.ebi.adfconverter.library.exceptions.LibraryException.
Reports during the library execution
LibraryException(Exception) - 
Constructor for class uk.ac.ebi.adfconverter.library.exceptions.LibraryException
Constructor  of the ADFConverterLibraryException class
LocationType - interface uk.ac.ebi.adfconverter.tools.checker.data.LocationType.
type of the field value : : a free text, a controlled vocabulary, a date...
 
LocationType.PreviousColumnsType - interface uk.ac.ebi.adfconverter.tools.checker.data.LocationType.PreviousColumnsType.
Java content class for anonymous complex type.
 
LocationTypeImpl - class uk.ac.ebi.adfconverter.tools.checker.data.impl.LocationTypeImpl.
 
LocationTypeImpl() - 
Constructor for class uk.ac.ebi.adfconverter.tools.checker.data.impl.LocationTypeImpl
 
LocationTypeImpl.PreviousColumnsTypeImpl - class uk.ac.ebi.adfconverter.tools.checker.data.impl.LocationTypeImpl.PreviousColumnsTypeImpl.
 
LocationTypeImpl.PreviousColumnsTypeImpl() - 
Constructor for class uk.ac.ebi.adfconverter.tools.checker.data.impl.LocationTypeImpl.PreviousColumnsTypeImpl
 
LocationTypeImpl.PreviousColumnsTypeImpl.Unmarshaller - class uk.ac.ebi.adfconverter.tools.checker.data.impl.LocationTypeImpl.PreviousColumnsTypeImpl.Unmarshaller.
 
LocationTypeImpl.PreviousColumnsTypeImpl.Unmarshaller(UnmarshallingContext) - 
Constructor for class uk.ac.ebi.adfconverter.tools.checker.data.impl.LocationTypeImpl.PreviousColumnsTypeImpl.Unmarshaller
 
LocationTypeImpl.Unmarshaller - class uk.ac.ebi.adfconverter.tools.checker.data.impl.LocationTypeImpl.Unmarshaller.
 
LocationTypeImpl.Unmarshaller(UnmarshallingContext) - 
Constructor for class uk.ac.ebi.adfconverter.tools.checker.data.impl.LocationTypeImpl.Unmarshaller
 
leaveAttribute(String, String, String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.CardinalityTypeImpl.Unmarshaller
 
leaveAttribute(String, String, String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.CheckRuleTypeImpl.Unmarshaller
 
leaveAttribute(String, String, String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ConstraintTypeImpl.Unmarshaller
 
leaveAttribute(String, String, String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.DataTypeImpl.TablesTypeImpl.Unmarshaller
 
leaveAttribute(String, String, String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.DataTypeImpl.Unmarshaller
 
leaveAttribute(String, String, String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.DocumentStructureImpl.Unmarshaller
 
leaveAttribute(String, String, String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.DocumentStructureTypeImpl.FilesTypeImpl.Unmarshaller
 
leaveAttribute(String, String, String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.DocumentStructureTypeImpl.Unmarshaller
 
leaveAttribute(String, String, String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.FieldTypeImpl.ConstraintsTypeImpl.Unmarshaller
 
leaveAttribute(String, String, String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.FieldTypeImpl.Unmarshaller
 
leaveAttribute(String, String, String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.FileTypeImpl.DataSetTypeImpl.Unmarshaller
 
leaveAttribute(String, String, String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.FileTypeImpl.Unmarshaller
 
leaveAttribute(String, String, String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.FilerImpl.Unmarshaller
 
leaveAttribute(String, String, String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.HeaderImpl.Unmarshaller
 
leaveAttribute(String, String, String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.HeaderTypeImpl.ItemsTypeImpl.Unmarshaller
 
leaveAttribute(String, String, String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.HeaderTypeImpl.Unmarshaller
 
leaveAttribute(String, String, String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTempImpl.Unmarshaller
 
leaveAttribute(String, String, String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTypeImpl.FieldDependenceTypeImpl.Unmarshaller
 
leaveAttribute(String, String, String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTypeImpl.RelaxCheckRulesTypeImpl.Unmarshaller
 
leaveAttribute(String, String, String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTypeImpl.SubNamesTypeImpl.Unmarshaller
 
leaveAttribute(String, String, String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTypeImpl.Unmarshaller
 
leaveAttribute(String, String, String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.LocationTypeImpl.PreviousColumnsTypeImpl.Unmarshaller
 
leaveAttribute(String, String, String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.LocationTypeImpl.Unmarshaller
 
leaveAttribute(String, String, String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.SubNameTypeImpl.ConstraintsTypeImpl.Unmarshaller
 
leaveAttribute(String, String, String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.SubNameTypeImpl.Unmarshaller
 
leaveAttribute(String, String, String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.TableTypeImpl.Unmarshaller
 
leaveAttribute(String, String, String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.AbstractUnmarshallingEventHandlerImpl
 
leaveAttribute(String, String, String) - 
Method in interface uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.UnmarshallingEventHandler
 
leaveAttribute(String, String, String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.UnmarshallingEventHandlerAdaptor
 
leaveChild(int) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.AbstractUnmarshallingEventHandlerImpl
 
leaveChild(int) - 
Method in interface uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.UnmarshallingEventHandler
 
leaveChild(int) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.UnmarshallingEventHandlerAdaptor
 
leaveElement(String, String, String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.CardinalityTypeImpl.Unmarshaller
 
leaveElement(String, String, String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.CheckRuleTypeImpl.Unmarshaller
 
leaveElement(String, String, String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ConstraintTypeImpl.Unmarshaller
 
leaveElement(String, String, String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.DataTypeImpl.TablesTypeImpl.Unmarshaller
 
leaveElement(String, String, String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.DataTypeImpl.Unmarshaller
 
leaveElement(String, String, String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.DocumentStructureImpl.Unmarshaller
 
leaveElement(String, String, String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.DocumentStructureTypeImpl.FilesTypeImpl.Unmarshaller
 
leaveElement(String, String, String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.DocumentStructureTypeImpl.Unmarshaller
 
leaveElement(String, String, String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.FieldTypeImpl.ConstraintsTypeImpl.Unmarshaller
 
leaveElement(String, String, String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.FieldTypeImpl.Unmarshaller
 
leaveElement(String, String, String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.FileTypeImpl.DataSetTypeImpl.Unmarshaller
 
leaveElement(String, String, String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.FileTypeImpl.Unmarshaller
 
leaveElement(String, String, String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.FilerImpl.Unmarshaller
 
leaveElement(String, String, String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.HeaderImpl.Unmarshaller
 
leaveElement(String, String, String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.HeaderTypeImpl.ItemsTypeImpl.Unmarshaller
 
leaveElement(String, String, String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.HeaderTypeImpl.Unmarshaller
 
leaveElement(String, String, String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTempImpl.Unmarshaller
 
leaveElement(String, String, String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTypeImpl.FieldDependenceTypeImpl.Unmarshaller
 
leaveElement(String, String, String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTypeImpl.RelaxCheckRulesTypeImpl.Unmarshaller
 
leaveElement(String, String, String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTypeImpl.SubNamesTypeImpl.Unmarshaller
 
leaveElement(String, String, String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTypeImpl.Unmarshaller
 
leaveElement(String, String, String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.LocationTypeImpl.PreviousColumnsTypeImpl.Unmarshaller
 
leaveElement(String, String, String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.LocationTypeImpl.Unmarshaller
 
leaveElement(String, String, String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.SubNameTypeImpl.ConstraintsTypeImpl.Unmarshaller
 
leaveElement(String, String, String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.SubNameTypeImpl.Unmarshaller
 
leaveElement(String, String, String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.TableTypeImpl.Unmarshaller
 
leaveElement(String, String, String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.AbstractUnmarshallingEventHandlerImpl
 
leaveElement(String, String, String) - 
Method in interface uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.UnmarshallingEventHandler
 
leaveElement(String, String, String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.UnmarshallingEventHandlerAdaptor
 
length() - 
Method in class uk.ac.ebi.adfconverter.common.data.DataBuffer
Retrieves the length of the DataBuffer
loggerPREFIX - 
Static variable in class uk.ac.ebi.adfconverter.common.configuration.ADFConverterConfiguration
Definition of the adfconverter property name sub prefix for logging module: 
 logger.



M

MAGEIdentifierGenerator - class uk.ac.ebi.adfconverter.tools.converter.IdentifierGenerater.MAGEIdentifierGenerator.
This class handles MAGE identifier generation.
 
MAGEIdentifierGenerator() - 
Constructor for class uk.ac.ebi.adfconverter.tools.converter.IdentifierGenerater.MAGEIdentifierGenerator
Default Contructor for generator use
 Inits as well the MGED ontology Checker by providing an Database MAGE Identifier
MAGEIdentifierGenerator(Properties) - 
Constructor for class uk.ac.ebi.adfconverter.tools.converter.IdentifierGenerater.MAGEIdentifierGenerator
Constructor
 Inits generator with rules 
 Inits as well the MGED ontology Checker by providing an Database MAGE Identifier
MAGEMLExporter - class uk.ac.ebi.adfconverter.tools.exporter.MAGEMLExporter.
Class used to export MAGE objects in a MAGE-ML file
 
 Due to the JAVA MAGEstk, a temporary file is created first and this file is red to 
 obtain a "pretty" xml file with header, doctype and indentation
MAGEMLExporter(String, String, String) - 
Constructor for class uk.ac.ebi.adfconverter.tools.exporter.MAGEMLExporter
Constructor of th MAGE-ML exporter
 specified the dtd file for all MAGE-ML file
 
 THe user can specified a doctype a system one (local file system)
 or public one (web).
 
MAGEMLExporterInitException - exception uk.ac.ebi.adfconverter.tools.exporter.exceptions.MAGEMLExporterInitException.
Signals an error during the initialisation of 
 the MAGE ML Exporter.
MAGEMLExporterInitException() - 
Constructor for class uk.ac.ebi.adfconverter.tools.exporter.exceptions.MAGEMLExporterInitException
Exception if the file structure description file is
 incorrect with no specified element
MAGEReader - class uk.ac.ebi.adfconverter.common.tools.file.reader.MAGEReader.
Class for MAGE-ML file reading
 
 Based on the MAGEReader From MAGEstk by  Kjell Petersen
MAGEReader() - 
Constructor for class uk.ac.ebi.adfconverter.common.tools.file.reader.MAGEReader
Creates a new instance of MAGEReader
MAGEReader(File) - 
Constructor for class uk.ac.ebi.adfconverter.common.tools.file.reader.MAGEReader
Creates a new instance of MAGEReader
MAGEToADFConverter - class uk.ac.ebi.adfconverter.tools.converter.MAGEToADFConverter.
Convert MAGE data file) in ADF objects   
 This class converts a MAGE-OM object  (MAGEJava) to an ADFJava object.
 
MAGEToADFConverter() - 
Constructor for class uk.ac.ebi.adfconverter.tools.converter.MAGEToADFConverter
Default MAGEToADFConverter Constructor 

inits organization list
MAGEToADFConverter(Properties) - 
Constructor for class uk.ac.ebi.adfconverter.tools.converter.MAGEToADFConverter
MAGEToADFConverter Constructor 
 inits the converter with a list of properties
MGEDOntologyChecker - class uk.ac.ebi.adfconverter.tools.checker.ontology.MGEDOntologyChecker.
Check if a term is in the MGED ontology
 using Ontology helper from MAGEstk (read daml file)

From TestMOE of MAGESTK
MGEDOntologyChecker() - 
Constructor for class uk.ac.ebi.adfconverter.tools.checker.ontology.MGEDOntologyChecker
Creates a new instance of testMGEDOE
MGEDOntologyChecker(String) - 
Constructor for class uk.ac.ebi.adfconverter.tools.checker.ontology.MGEDOntologyChecker
Creates a new instance of MGEDOntologyChecker
MGEDOntologyChecker(String, File, String, boolean) - 
Constructor for class uk.ac.ebi.adfconverter.tools.checker.ontology.MGEDOntologyChecker
Creates a new instance of MGEDOntologyChecker
MSVValidator - class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.MSVValidator.
XMLSerializer that calls the native interface of MSV and performs validation.
 
MarshallerImpl - class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.MarshallerImpl.
Implementation of Marshaller interface for JAXB RI.
MarshallerImpl(DefaultJAXBContextImpl) - 
Constructor for class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.MarshallerImpl
 
MemMonitor - class uk.ac.ebi.adfconverter.tools.monitor.MemMonitor.
Monitors heap size, allocation size, change in allocation,
   change in heap size, and detects garbage collection (when the
   allocation size decreases). 
MemMonitor() - 
Constructor for class uk.ac.ebi.adfconverter.tools.monitor.MemMonitor
 
MemMonitor.Data - class uk.ac.ebi.adfconverter.tools.monitor.MemMonitor.Data.
The Data class contains info on a series of float values.
       
MemMonitor.Data() - 
Constructor for class uk.ac.ebi.adfconverter.tools.monitor.MemMonitor.Data
 
MyFrame - class uk.ac.ebi.adfconverter.usermode.gui.MyFrame.
Environment for frame managing
 adds frame to the static JDesktopPane
MyFrame(JDesktopPane) - 
Constructor for class uk.ac.ebi.adfconverter.usermode.gui.MyFrame
Constructor of MyFrame class

 add the desktop desktop, where future frame will display

MyFrame(JComponent) - 
Constructor for class uk.ac.ebi.adfconverter.usermode.gui.MyFrame
Constructor of MyFrame class

 displays a frame including a given JComponent p

MyFrame(JComponent, String) - 
Constructor for class uk.ac.ebi.adfconverter.usermode.gui.MyFrame
Constructor of MyFrame class

 displays a frame, with a given name name,  including a given JComponent p

MyFrame(JComponent, String, int, int) - 
Constructor for class uk.ac.ebi.adfconverter.usermode.gui.MyFrame
Constructor of MyFrame class

 displays a frame, with a given name name 
 and a size (width,heigth),  including a given JComponent p

MyFrame(JComponent, String, ImageIcon) - 
Constructor for class uk.ac.ebi.adfconverter.usermode.gui.MyFrame
Constructor of MyFrame class

 displays a frame, with a given name name
 and an ImageIcon for left corner,  including a given JComponent p

MyFrame(JComponent, String, ImageIcon, int, int) - 
Constructor for class uk.ac.ebi.adfconverter.usermode.gui.MyFrame
Constructor of MyFrame class

 displays a frame, with a given name name, 
  an ImageIcon for left corner  and a size (width,heigth),
  including a given JComponent p

main(String[]) - 
Static method in class uk.ac.ebi.adfconverter.common.tools.file.copier.FileCopy
main method, testing purpose
main(String[]) - 
Static method in class uk.ac.ebi.adfconverter.common.tools.file.filesystem.DiskUtil
Test method
 testing purpose only
main(String[]) - 
Static method in class uk.ac.ebi.adfconverter.common.tools.net.update.Fetch
 
main(String[]) - 
Static method in class uk.ac.ebi.adfconverter.common.tools.net.update.GetURLInfo
 
main(String[]) - 
Static method in class uk.ac.ebi.adfconverter.library.FileFilter
for testing purpose
  retrieves file in the current directory with a given file extension
main(String[]) - 
Static method in class uk.ac.ebi.adfconverter.tools.checker.OptimizedADFChecker
 
main(String[]) - 
Static method in class uk.ac.ebi.adfconverter.tools.checker.OptimizedFileChecker
 
main(String[]) - 
Static method in class uk.ac.ebi.adfconverter.usermode.commandline.ADFConverterCommandLine
Main method the ADF converter launch by command-line
main(String[]) - 
Static method in class uk.ac.ebi.adfconverter.usermode.gui.test1
 
marshal(Object, Result) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.MarshallerImpl
 
minimumAchieve() - 
Method in class uk.ac.ebi.adfconverter.tools.checker.Cardinality
indicates if the minimal number of the element 
 has been achieved



N

NameFilter - class uk.ac.ebi.adfconverter.library.NameFilter.
implements java.io.FilenameFilter interface.
 
NameFilter() - 
Constructor for class uk.ac.ebi.adfconverter.library.NameFilter
contructor of a filter
NameFilter(String[]) - 
Constructor for class uk.ac.ebi.adfconverter.library.NameFilter
contructor of a filter following an array of file name
NamespaceContext2 - interface uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.NamespaceContext2.
Maintains namespace<->prefix bindings.
 
 
NamespaceContextImpl - class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.NamespaceContextImpl.
Implementation of the NamespaceContext2.
 
 
NamespaceContextImpl(NamespacePrefixMapper) - 
Constructor for class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.NamespaceContextImpl
 
networkPREFIX - 
Static variable in class uk.ac.ebi.adfconverter.common.configuration.ADFConverterConfiguration
Definition of the adfconverter property name sub prefix for network module: 
 network.
newElement() - 
Method in class uk.ac.ebi.adfconverter.tools.checker.Cardinality
To count when a new element has been bound and 
 update for still available elements
newInstance(Class) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.ObjectFactory
Create an instance of the specified Java content interface.
newInstance(Class) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.DefaultJAXBContextImpl
Create an instance of the specified Java content interface.
nextItem() - 
Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.DataTableHeader
Retrieves the next item in the list
nextRow() - 
Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.DataTable
Retrieves the next Row in the list



O

ObjectFactory - class uk.ac.ebi.adfconverter.tools.checker.data.ObjectFactory.
This object contains factory methods for each 
 Java content interface and Java element interface 
 generated in the uk.ac.ebi.adfconverter.tools.checker.data package. 
 
ObjectFactory() - 
Constructor for class uk.ac.ebi.adfconverter.tools.checker.data.ObjectFactory
Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: uk.ac.ebi.adfconverter.tools.checker.data
OptimizedADFChecker - class uk.ac.ebi.adfconverter.tools.checker.OptimizedADFChecker.
Class for file strcuture checking
 will check file structure and data contained in a file
OptimizedADFChecker() - 
Constructor for class uk.ac.ebi.adfconverter.tools.checker.OptimizedADFChecker
Default Constructor of FileChecker 
 inits sub tables
OptimizedADFChecker(File, boolean) - 
Constructor for class uk.ac.ebi.adfconverter.tools.checker.OptimizedADFChecker
Constructor of FileChecker
OptimizedFileChecker - class uk.ac.ebi.adfconverter.tools.checker.OptimizedFileChecker.
Checks data tables in an optimized way ( memory, CPU)
 Data tables are checked row by row.
OptimizedFileChecker() - 
Constructor for class uk.ac.ebi.adfconverter.tools.checker.OptimizedFileChecker
Constructor
onID(IdentifiableObject, String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.MSVValidator
 
onID(IdentifiableObject, String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.SAXMarshaller
 
onID(IdentifiableObject, String) - 
Method in interface uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.XMLSerializer
Notifies the serializer that an ID value has just marshalled.
 
 
onIDREF(IdentifiableObject) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.MSVValidator
 
onIDREF(IdentifiableObject) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.SAXMarshaller
 
onIDREF(IdentifiableObject) - 
Method in interface uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.XMLSerializer
Notifies the serializer that an IDREF value has just marshalled.
 
 
onPrefixMapping(String, String) - 
Method in interface uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.PrefixCallback
 
open(String, String, String, int) - 
Method in class uk.ac.ebi.adfconverter.common.tools.file.reader.DataFileReader
Open a data file with a given character encoding , delimiter and escape strings , file orientation and file type
open(String, String, String, int) - 
Method in class uk.ac.ebi.adfconverter.common.tools.file.reader.DataFileReaderIntf
Open a data file with a given character encoding , delimiter and escape strings , file orientation and file type
openFile() - 
Method in interface uk.ac.ebi.adfconverter.common.tools.file.reader.ADFConverterFileReader
Opens the data file for reading or writing
openFile() - 
Method in class uk.ac.ebi.adfconverter.common.tools.file.reader.ADFConverterFileReaderImpl
Opens a data file for reading or writing
openFile() - 
Method in interface uk.ac.ebi.adfconverter.common.tools.file.reader.DataReader
Opens a data file for reading or writing
openFile() - 
Method in class uk.ac.ebi.adfconverter.common.tools.file.reader.PlainTextDataFileReader
Opens a data file for reading or writing
openFile() - 
Method in class uk.ac.ebi.adfconverter.common.tools.file.reader.PlainTextFileReader
Opens a data file for reading or writing
openFile() - 
Method in class uk.ac.ebi.adfconverter.common.tools.file.reader.WorkBookFileReaderjxl
Opens a data file for reading or writing

 By default, opens the first sheet of the workbook
openFile() - 
Method in interface uk.ac.ebi.adfconverter.common.tools.file.writer.ADFConverterFileWriter
Opens a data file for  writing
openFile() - 
Method in class uk.ac.ebi.adfconverter.common.tools.file.writer.ADFConverterFileWriterImpl
Opens a data file for reading or writing
openFile() - 
Method in interface uk.ac.ebi.adfconverter.common.tools.file.writer.DataWriter
Opens a data file for reading or writing
openFile() - 
Method in class uk.ac.ebi.adfconverter.common.tools.file.writer.PlainTextDataFileWriter
Opens a data file for reading or writing
openFile() - 
Method in class uk.ac.ebi.adfconverter.common.tools.file.writer.PlainTextFileWriter
Opens a data file for reading or writing
openFile() - 
Method in class uk.ac.ebi.adfconverter.common.tools.file.writer.WorkBookFileWriterjxl
Opens a data file for writing

 By default, opens the fisrt sheet of the workbook
openStructure(String) - 
Method in class uk.ac.ebi.adfconverter.tools.filestructure.FileStructureDescription
Open a file structure
owner() - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.CardinalityTypeImpl.Unmarshaller
 
owner() - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.CheckRuleTypeImpl.Unmarshaller
 
owner() - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ConstraintTypeImpl.Unmarshaller
 
owner() - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.DataTypeImpl.TablesTypeImpl.Unmarshaller
 
owner() - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.DataTypeImpl.Unmarshaller
 
owner() - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.DocumentStructureImpl.Unmarshaller
 
owner() - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.DocumentStructureTypeImpl.FilesTypeImpl.Unmarshaller
 
owner() - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.DocumentStructureTypeImpl.Unmarshaller
 
owner() - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.FieldTypeImpl.ConstraintsTypeImpl.Unmarshaller
 
owner() - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.FieldTypeImpl.Unmarshaller
 
owner() - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.FileTypeImpl.DataSetTypeImpl.Unmarshaller
 
owner() - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.FileTypeImpl.Unmarshaller
 
owner() - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.FilerImpl.Unmarshaller
 
owner() - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.HeaderImpl.Unmarshaller
 
owner() - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.HeaderTypeImpl.ItemsTypeImpl.Unmarshaller
 
owner() - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.HeaderTypeImpl.Unmarshaller
 
owner() - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTempImpl.Unmarshaller
 
owner() - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTypeImpl.FieldDependenceTypeImpl.Unmarshaller
 
owner() - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTypeImpl.RelaxCheckRulesTypeImpl.Unmarshaller
 
owner() - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTypeImpl.SubNamesTypeImpl.Unmarshaller
 
owner() - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTypeImpl.Unmarshaller
 
owner() - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.LocationTypeImpl.PreviousColumnsTypeImpl.Unmarshaller
 
owner() - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.LocationTypeImpl.Unmarshaller
 
owner() - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.SubNameTypeImpl.ConstraintsTypeImpl.Unmarshaller
 
owner() - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.SubNameTypeImpl.Unmarshaller
 
owner() - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.TableTypeImpl.Unmarshaller
 
owner() - 
Method in interface uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.UnmarshallingEventHandler
Returns the content-tree object for which this unmarshaller
 is working for.
owner() - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.UnmarshallingEventHandlerAdaptor
 



P

PREFIX - 
Static variable in class uk.ac.ebi.adfconverter.common.configuration.ADFConverterConfiguration
Definition of the adfconverter property name prefix: 
 adfconverter.
PlainTextDataFileReader - class uk.ac.ebi.adfconverter.common.tools.file.reader.PlainTextDataFileReader.
Interface for all file format classes used in reading
 data
PlainTextDataFileReader(File) - 
Constructor for class uk.ac.ebi.adfconverter.common.tools.file.reader.PlainTextDataFileReader
Constructor for reader of data contained in tabular file
PlainTextDataFileReader(File, String) - 
Constructor for class uk.ac.ebi.adfconverter.common.tools.file.reader.PlainTextDataFileReader
Constructor for reader of data contained in tabular file
PlainTextDataFileReader(File, String, String, String) - 
Constructor for class uk.ac.ebi.adfconverter.common.tools.file.reader.PlainTextDataFileReader
Constructor of the class,
 Set a text file to read, an character encoding,
 an data delimiter and an escape character
PlainTextDataFileWriter - class uk.ac.ebi.adfconverter.common.tools.file.writer.PlainTextDataFileWriter.
Interface for all file format classes used in writing
 data
PlainTextDataFileWriter(File) - 
Constructor for class uk.ac.ebi.adfconverter.common.tools.file.writer.PlainTextDataFileWriter
Create an instance of a file writer for a give file
PlainTextDataFileWriter(File, String) - 
Constructor for class uk.ac.ebi.adfconverter.common.tools.file.writer.PlainTextDataFileWriter
Create an instance of a file writer for a give file with a given Java character encoding
PlainTextDataFileWriter(File, String, String, String) - 
Constructor for class uk.ac.ebi.adfconverter.common.tools.file.writer.PlainTextDataFileWriter
Create an instance of a file writer for a give file with a given Java character encoding
PlainTextFileReader - class uk.ac.ebi.adfconverter.common.tools.file.reader.PlainTextFileReader.
Interface for all file format classes used in reading
 data
PlainTextFileReader(File) - 
Constructor for class uk.ac.ebi.adfconverter.common.tools.file.reader.PlainTextFileReader
Contructor for reader of a given plain text file
PlainTextFileReader(File, String) - 
Constructor for class uk.ac.ebi.adfconverter.common.tools.file.reader.PlainTextFileReader
Contructor for reader of a given plain text file
  following a given encoding
PlainTextFileWriter - class uk.ac.ebi.adfconverter.common.tools.file.writer.PlainTextFileWriter.
Interface for all file format classes used in writing
 data
PlainTextFileWriter(File) - 
Constructor for class uk.ac.ebi.adfconverter.common.tools.file.writer.PlainTextFileWriter
Create an instance of a file writer for a give file
PlainTextFileWriter(File, String) - 
Constructor for class uk.ac.ebi.adfconverter.common.tools.file.writer.PlainTextFileWriter
Create an instance of a file writer for a give file with a given Java character encoding
PrefixCallback - interface uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.PrefixCallback.
 
popAttributes() - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.SAXUnmarshallerHandlerImpl
 
popAttributes() - 
Method in interface uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.UnmarshallingContext
Discards the previously stored attribute set.
 
popContentHandler() - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.SAXUnmarshallerHandlerImpl
 
popContentHandler() - 
Method in interface uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.UnmarshallingContext
Pops a content handler from the stack and registers
 it as the current content handler.
 
 
postMail(String[], String, String, String) - 
Method in class uk.ac.ebi.adfconverter.common.tools.net.mail.ADFConverterSendMail
Sends an email to a list of recipients.
printinfo(URLConnection) - 
Static method in class uk.ac.ebi.adfconverter.common.tools.net.update.GetURLInfo
 
processingInstruction(String, String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.ContentHandlerAdaptor
 
processingInstruction(String, String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.SAXUnmarshallerHandlerImpl
 
pushAttributes(Attributes, boolean) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.SAXUnmarshallerHandlerImpl
 
pushAttributes(Attributes, boolean) - 
Method in interface uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.UnmarshallingContext
Stores a new attribute set.
 
pushContentHandler(UnmarshallingEventHandler, int) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.SAXUnmarshallerHandlerImpl
 
pushContentHandler(UnmarshallingEventHandler, int) - 
Method in interface uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.UnmarshallingContext
Pushes the current content handler into the stack
 and registers the newly specified content handler so
 that it can receive SAX events.



R

readFile(File) - 
Method in class uk.ac.ebi.adfconverter.common.tools.file.reader.MAGEReader
Reads a MAGE-ML File  (converts it in MAGE Object)
recognize(String, String) - 
Method in interface uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.GrammarInfo
Returns true if the invocation of the createUnmarshaller method
 will return a non-null value for the given name pair.
recognize(String, String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.GrammarInfoImpl
 
removeItem(CorrectableHeaderItem) - 
Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.CorrectableDataTableHeader
Removes an given item from the header list
removeItem(int) - 
Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.CorrectableDataTableHeader
Removes an item at a given position from the header list
removeItem(HeaderItem) - 
Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.DataTableHeader
Removes an given item from the header list
removeItem(int) - 
Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.DataTableHeader
Removes an item at a given position from the header list
removeProperty(String) - 
Static method in class uk.ac.ebi.adfconverter.common.configuration.ADFConverterConfiguration
Removes a property from configuration property list
removeRow(int) - 
Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.DataTable
removes a datarow in the table
 at a given position
removeRow(DataRow) - 
Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.DataTable
removes a datarow in the table
 at a given position
reportError(ValidationEvent) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.MSVValidator
 
reportError(ValidationEvent) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.SAXMarshaller
 
reportError(ValidationEvent) - 
Method in interface uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.XMLSerializer
Errors detected by the XMLSerializable should be either thrown
 as SAXException or reported through this method.
 
 
reportMissingObjectError(String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.MSVValidator
 
reportMissingObjectError(String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.SAXMarshaller
 
reporterFileExtension - 
Static variable in class uk.ac.ebi.adfconverter.data.adf.ADFJava
reporterFileExtension: default feature reporter text file extension
resolveNamespacePrefix(String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.MSVValidator
 
resolveNamespacePrefix(String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.SAXUnmarshallerHandlerImpl
 
resolveNamespacePrefix(String) - 
Method in interface uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.UnmarshallingContext
 
returnItem(CorrectableDataTable) - 
Static method in class uk.ac.ebi.adfconverter.common.util.pool.CorrectableDataTablePool
Returns a no more needed CorrectableDataTable object to the pool for reuse.
returnItem(CorrectableHeaderItem) - 
Static method in class uk.ac.ebi.adfconverter.common.util.pool.CorrectableHeaderItemPool
Returns a no more needed  object to the pool for reuse.
returnItem(DataTable) - 
Static method in class uk.ac.ebi.adfconverter.common.util.pool.DataTablePool
Returns a no more needed  object to the pool for reuse.
returnItem(HeaderItem) - 
Static method in class uk.ac.ebi.adfconverter.common.util.pool.HeaderItemPool
Returns a no more needed  object to the pool for reuse.
returnRow(DataRow) - 
Static method in class uk.ac.ebi.adfconverter.common.util.pool.DataRowPool
Returns a no more needed  object to the pool for reuse.
returnString(DataBuffer) - 
Static method in class uk.ac.ebi.adfconverter.common.util.pool.DataBufferPool
Returns a no more needed  object to the pool for reuse.
returnString(StringBuffer) - 
Static method in class uk.ac.ebi.adfconverter.common.util.pool.StringBufferPool
Returns a no more needed  object to the pool for reuse.
returnString(String) - 
Static method in class uk.ac.ebi.adfconverter.common.util.pool.StringPool
Freed a String previously used
rulePREFIX - 
Static variable in class uk.ac.ebi.adfconverter.common.configuration.ADFConverterConfiguration
Definition of the adfconverter property name sub prefix for identifier generation rules: 
 rule.



S

SAXMarshaller - class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.SAXMarshaller.
XMLSerializer that produces SAX2 events.
 
 
SAXMarshaller(ContentHandler, NamespacePrefixMapper, MarshallerImpl) - 
Constructor for class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.SAXMarshaller
Creates a marshalling context by designating the ContentHandler
 that receives generated SAX2 events.
SAXUnmarshallerHandler - interface uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.SAXUnmarshallerHandler.
Unified event handler that processes
 both the SAX events and error events.
 
 
SAXUnmarshallerHandlerImpl - class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.SAXUnmarshallerHandlerImpl.
Implementation of UnmarshallerHandler.
 
 
SAXUnmarshallerHandlerImpl(UnmarshallerImpl, GrammarInfo) - 
Constructor for class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.SAXUnmarshallerHandlerImpl
 
SeveralTablesVisualisation - class uk.ac.ebi.adfconverter.usermode.gui.visualisation.SeveralTablesVisualisation.
 
SeveralTablesVisualisation(ArrayList) - 
Constructor for class uk.ac.ebi.adfconverter.usermode.gui.visualisation.SeveralTablesVisualisation
 
SimpleFileFormatDescription - class uk.ac.ebi.adfconverter.common.tools.file.description.SimpleFileFormatDescription.
This class is used to describe a file. it returns the file extension and the
 file format
SimpleFileFormatDescription(File) - 
Constructor for class uk.ac.ebi.adfconverter.common.tools.file.description.SimpleFileFormatDescription
the constructor initialises the file to describe
StringBufferPool - class uk.ac.ebi.adfconverter.common.util.pool.StringBufferPool.
Pool class for StringBufferPool objects
 
 Contains a list of available tables. 
 
StringBufferPool() - 
Constructor for class uk.ac.ebi.adfconverter.common.util.pool.StringBufferPool
 
StringPool - class uk.ac.ebi.adfconverter.common.util.pool.StringPool.
Pool for String objects.
 
StringPool() - 
Constructor for class uk.ac.ebi.adfconverter.common.util.pool.StringPool
 
SubNameType - interface uk.ac.ebi.adfconverter.tools.checker.data.SubNameType.
Definition for the subname of the item
 Java content class for SubNameType complex type.
 
SubNameType.ConstraintsType - interface uk.ac.ebi.adfconverter.tools.checker.data.SubNameType.ConstraintsType.
list of constraints, that should match the  item subname
 Java content class for anonymous complex type.
 
SubNameTypeImpl - class uk.ac.ebi.adfconverter.tools.checker.data.impl.SubNameTypeImpl.
 
SubNameTypeImpl() - 
Constructor for class uk.ac.ebi.adfconverter.tools.checker.data.impl.SubNameTypeImpl
 
SubNameTypeImpl.ConstraintsTypeImpl - class uk.ac.ebi.adfconverter.tools.checker.data.impl.SubNameTypeImpl.ConstraintsTypeImpl.
 
SubNameTypeImpl.ConstraintsTypeImpl() - 
Constructor for class uk.ac.ebi.adfconverter.tools.checker.data.impl.SubNameTypeImpl.ConstraintsTypeImpl
 
SubNameTypeImpl.ConstraintsTypeImpl.Unmarshaller - class uk.ac.ebi.adfconverter.tools.checker.data.impl.SubNameTypeImpl.ConstraintsTypeImpl.Unmarshaller.
 
SubNameTypeImpl.ConstraintsTypeImpl.Unmarshaller(UnmarshallingContext) - 
Constructor for class uk.ac.ebi.adfconverter.tools.checker.data.impl.SubNameTypeImpl.ConstraintsTypeImpl.Unmarshaller
 
SubNameTypeImpl.Unmarshaller - class uk.ac.ebi.adfconverter.tools.checker.data.impl.SubNameTypeImpl.Unmarshaller.
 
SubNameTypeImpl.Unmarshaller(UnmarshallingContext) - 
Constructor for class uk.ac.ebi.adfconverter.tools.checker.data.impl.SubNameTypeImpl.Unmarshaller
 
serializeAttributes(XMLSerializer) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.CardinalityTypeImpl
 
serializeAttributes(XMLSerializer) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.CheckRuleTypeImpl
 
serializeAttributes(XMLSerializer) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ConstraintTypeImpl
 
serializeAttributes(XMLSerializer) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.DataTypeImpl.TablesTypeImpl
 
serializeAttributes(XMLSerializer) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.DataTypeImpl
 
serializeAttributes(XMLSerializer) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.DocumentStructureImpl
 
serializeAttributes(XMLSerializer) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.DocumentStructureTypeImpl.FilesTypeImpl
 
serializeAttributes(XMLSerializer) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.DocumentStructureTypeImpl
 
serializeAttributes(XMLSerializer) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.FieldTypeImpl.ConstraintsTypeImpl
 
serializeAttributes(XMLSerializer) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.FieldTypeImpl
 
serializeAttributes(XMLSerializer) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.FileTypeImpl.DataSetTypeImpl
 
serializeAttributes(XMLSerializer) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.FileTypeImpl
 
serializeAttributes(XMLSerializer) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.FilerImpl
 
serializeAttributes(XMLSerializer) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.HeaderImpl
 
serializeAttributes(XMLSerializer) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.HeaderTypeImpl.ItemsTypeImpl
 
serializeAttributes(XMLSerializer) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.HeaderTypeImpl
 
serializeAttributes(XMLSerializer) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTempImpl
 
serializeAttributes(XMLSerializer) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTypeImpl.FieldDependenceTypeImpl
 
serializeAttributes(XMLSerializer) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTypeImpl.RelaxCheckRulesTypeImpl
 
serializeAttributes(XMLSerializer) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTypeImpl.SubNamesTypeImpl
 
serializeAttributes(XMLSerializer) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTypeImpl
 
serializeAttributes(XMLSerializer) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.LocationTypeImpl.PreviousColumnsTypeImpl
 
serializeAttributes(XMLSerializer) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.LocationTypeImpl
 
serializeAttributes(XMLSerializer) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.SubNameTypeImpl.ConstraintsTypeImpl
 
serializeAttributes(XMLSerializer) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.SubNameTypeImpl
 
serializeAttributes(XMLSerializer) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.TableTypeImpl
 
serializeAttributes(XMLSerializer) - 
Method in interface uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.XMLSerializable
Serializes attributes into the specified target.
serializeBody(XMLSerializer) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.CardinalityTypeImpl
 
serializeBody(XMLSerializer) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.CheckRuleTypeImpl
 
serializeBody(XMLSerializer) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ConstraintTypeImpl
 
serializeBody(XMLSerializer) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.DataTypeImpl.TablesTypeImpl
 
serializeBody(XMLSerializer) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.DataTypeImpl
 
serializeBody(XMLSerializer) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.DocumentStructureImpl
 
serializeBody(XMLSerializer) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.DocumentStructureTypeImpl.FilesTypeImpl
 
serializeBody(XMLSerializer) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.DocumentStructureTypeImpl
 
serializeBody(XMLSerializer) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.FieldTypeImpl.ConstraintsTypeImpl
 
serializeBody(XMLSerializer) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.FieldTypeImpl
 
serializeBody(XMLSerializer) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.FileTypeImpl.DataSetTypeImpl
 
serializeBody(XMLSerializer) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.FileTypeImpl
 
serializeBody(XMLSerializer) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.FilerImpl
 
serializeBody(XMLSerializer) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.HeaderImpl
 
serializeBody(XMLSerializer) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.HeaderTypeImpl.ItemsTypeImpl
 
serializeBody(XMLSerializer) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.HeaderTypeImpl
 
serializeBody(XMLSerializer) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTempImpl
 
serializeBody(XMLSerializer) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTypeImpl.FieldDependenceTypeImpl
 
serializeBody(XMLSerializer) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTypeImpl.RelaxCheckRulesTypeImpl
 
serializeBody(XMLSerializer) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTypeImpl.SubNamesTypeImpl
 
serializeBody(XMLSerializer) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTypeImpl
 
serializeBody(XMLSerializer) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.LocationTypeImpl.PreviousColumnsTypeImpl
 
serializeBody(XMLSerializer) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.LocationTypeImpl
 
serializeBody(XMLSerializer) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.SubNameTypeImpl.ConstraintsTypeImpl
 
serializeBody(XMLSerializer) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.SubNameTypeImpl
 
serializeBody(XMLSerializer) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.TableTypeImpl
 
serializeBody(XMLSerializer) - 
Method in interface uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.XMLSerializable
Serializes child elements and texts into the specified target.
serializeURIs(XMLSerializer) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.CardinalityTypeImpl
 
serializeURIs(XMLSerializer) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.CheckRuleTypeImpl
 
serializeURIs(XMLSerializer) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ConstraintTypeImpl
 
serializeURIs(XMLSerializer) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.DataTypeImpl.TablesTypeImpl
 
serializeURIs(XMLSerializer) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.DataTypeImpl
 
serializeURIs(XMLSerializer) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.DocumentStructureImpl
 
serializeURIs(XMLSerializer) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.DocumentStructureTypeImpl.FilesTypeImpl
 
serializeURIs(XMLSerializer) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.DocumentStructureTypeImpl
 
serializeURIs(XMLSerializer) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.FieldTypeImpl.ConstraintsTypeImpl
 
serializeURIs(XMLSerializer) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.FieldTypeImpl
 
serializeURIs(XMLSerializer) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.FileTypeImpl.DataSetTypeImpl
 
serializeURIs(XMLSerializer) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.FileTypeImpl
 
serializeURIs(XMLSerializer) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.FilerImpl
 
serializeURIs(XMLSerializer) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.HeaderImpl
 
serializeURIs(XMLSerializer) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.HeaderTypeImpl.ItemsTypeImpl
 
serializeURIs(XMLSerializer) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.HeaderTypeImpl
 
serializeURIs(XMLSerializer) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTempImpl
 
serializeURIs(XMLSerializer) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTypeImpl.FieldDependenceTypeImpl
 
serializeURIs(XMLSerializer) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTypeImpl.RelaxCheckRulesTypeImpl
 
serializeURIs(XMLSerializer) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTypeImpl.SubNamesTypeImpl
 
serializeURIs(XMLSerializer) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTypeImpl
 
serializeURIs(XMLSerializer) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.LocationTypeImpl.PreviousColumnsTypeImpl
 
serializeURIs(XMLSerializer) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.LocationTypeImpl
 
serializeURIs(XMLSerializer) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.SubNameTypeImpl.ConstraintsTypeImpl
 
serializeURIs(XMLSerializer) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.SubNameTypeImpl
 
serializeURIs(XMLSerializer) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.TableTypeImpl
 
serializeURIs(XMLSerializer) - 
Method in interface uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.XMLSerializable
Declares all the namespace URIs this object is using at
 its top-level scope into the specified target.
setAppend(boolean) - 
Method in interface uk.ac.ebi.adfconverter.common.tools.file.writer.ADFConverterFileWriter
sets if the write writes at the end of the file or 
 overwrite it
setAppend(boolean) - 
Method in class uk.ac.ebi.adfconverter.common.tools.file.writer.ADFConverterFileWriterImpl
sets if the write writes at the end of the file or 
 overwrite it
setAppend(boolean) - 
Method in interface uk.ac.ebi.adfconverter.common.tools.file.writer.DataWriter
sets if the write writes at the end of the file or 
 overwrite it
setAssociatedItem(CorrectableHeaderItem) - 
Method in class uk.ac.ebi.adfconverter.data.adf.ADFGroup
Sets associatedItem attribut
setCardinality(CardinalityType) - 
Method in interface uk.ac.ebi.adfconverter.tools.checker.data.ItemType
Cardinality of the item in the table header (how many time it is supposed to be present in the header)
setCardinality(CardinalityType) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTypeImpl
 
setColumNumber(int) - 
Method in interface uk.ac.ebi.adfconverter.tools.checker.data.LocationType
Sets the value of the columNumber property.
setColumNumber(int) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.LocationTypeImpl
 
setConstraints(FieldType.ConstraintsType) - 
Method in interface uk.ac.ebi.adfconverter.tools.checker.data.FieldType
Sets the value of the constraints property.
setConstraints(SubNameType.ConstraintsType) - 
Method in interface uk.ac.ebi.adfconverter.tools.checker.data.SubNameType
Sets the value of the constraints property.
setConstraints(FieldType.ConstraintsType) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.FieldTypeImpl
 
setConstraints(SubNameType.ConstraintsType) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.SubNameTypeImpl
 
setCuratedValue(String) - 
Method in interface uk.ac.ebi.adfconverter.tools.checker.data.ConstraintType
Sets the value of the curatedValue property.
setCuratedValue(String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ConstraintTypeImpl
 
setCurrentHeaderType(HeaderType) - 
Method in class uk.ac.ebi.adfconverter.tools.filestructure.FileStructureDescription
Set the current HeaderType object.
setData(DataTable) - 
Method in class uk.ac.ebi.adfconverter.usermode.gui.visualisation.DataTableModel
Describe setData method here.
setData(DataTable) - 
Method in class uk.ac.ebi.adfconverter.usermode.gui.visualisation.DataVisualisationTable
 
setDataDelimiter(String) - 
Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.CorrectableHeaderItem
sets the datadelimiter of the item 
 in case of multiple values in the field
setDataDelimiter(String) - 
Method in interface uk.ac.ebi.adfconverter.tools.checker.data.TableType
Sets the value of the dataDelimiter property.
setDataDelimiter(String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.TableTypeImpl
 
setDataFormat(String) - 
Method in interface uk.ac.ebi.adfconverter.tools.checker.data.DataType
Sets the value of the dataFormat property.
setDataFormat(String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.DataTypeImpl
 
setDataSet(FileType.DataSetType) - 
Method in interface uk.ac.ebi.adfconverter.tools.checker.data.FileType
set of data contained in a file or spreadsheet
setDataSet(FileType.DataSetType) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.FileTypeImpl
 
setDelimiter(String) - 
Static method in class uk.ac.ebi.adfconverter.common.tools.file.converter.DelimiterLineConverter
Sets delimiter attribut
setDelimiter(String) - 
Method in class uk.ac.ebi.adfconverter.common.tools.file.reader.PlainTextDataFileReader
sets the delimiter character used in
 the data  to delimit data
setDelimiter(String) - 
Method in class uk.ac.ebi.adfconverter.common.tools.file.writer.PlainTextDataFileWriter
sets the delimiter character used in
 the data  to delimit data
setDescription(String) - 
Method in interface uk.ac.ebi.adfconverter.tools.checker.data.CheckRuleType
description of the rule, will be displayed in the tool
setDescription(String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.CheckRuleTypeImpl
 
setDocumentLocator(Locator) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.ContentHandlerAdaptor
 
setDocumentLocator(Locator) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.SAXUnmarshallerHandlerImpl
 
setElement(String) - 
Method in interface uk.ac.ebi.adfconverter.tools.checker.data.ItemType
Sets the value of the element property.
setElement(String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTypeImpl
 
setEscape(String) - 
Static method in class uk.ac.ebi.adfconverter.common.tools.file.converter.DelimiterLineConverter
Sets escape attribut
setEscape(String) - 
Method in class uk.ac.ebi.adfconverter.common.tools.file.reader.PlainTextDataFileReader
sets the escape character used in
 the data  to delimit data
setEscape(String) - 
Method in class uk.ac.ebi.adfconverter.common.tools.file.writer.PlainTextDataFileWriter
sets the escape character used in
 the data  to delimit data
setEventHandler(ValidationEventHandler) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.ValidatorImpl
 
setExactName(String) - 
Method in interface uk.ac.ebi.adfconverter.tools.checker.data.ItemType
exact name, according to the specification, that should have the item
setExactName(String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTypeImpl
 
setExtension(String) - 
Method in interface uk.ac.ebi.adfconverter.tools.checker.data.FileType
Sets the value of the extension property.
setExtension(String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.FileTypeImpl
 
setFieldCardinality(CardinalityType) - 
Method in interface uk.ac.ebi.adfconverter.tools.checker.data.ItemType
Cardinality of associated field in the table  (how many time it is supposed to be present in a row)
setFieldCardinality(CardinalityType) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTypeImpl
 
setFieldDependence(ItemType.FieldDependenceType) - 
Method in interface uk.ac.ebi.adfconverter.tools.checker.data.ItemType
defines dependance between field
setFieldDependence(ItemType.FieldDependenceType) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTypeImpl
 
setFieldType(String) - 
Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.CorrectableHeaderItem
sets the field type of the item
setFieldValueType(FieldType) - 
Method in interface uk.ac.ebi.adfconverter.tools.checker.data.ItemType
characterics of associated fields
setFieldValueType(FieldType) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTypeImpl
 
setFile(File) - 
Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.DataTable
Sets file attribut
setFileFormat(String) - 
Method in interface uk.ac.ebi.adfconverter.tools.checker.data.FileType
Sets the value of the fileFormat property.
setFileFormat(String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.FileTypeImpl
 
setFileName(String) - 
Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.DataTable
Sets the file name.
setFileType(int) - 
Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.DataTable
set the type of the file where was the data
 use when saving dataTable
 for convenience
setFiles(DocumentStructureType.FilesType) - 
Method in interface uk.ac.ebi.adfconverter.tools.checker.data.DocumentStructureType
set of one or sereral data files
setFiles(DocumentStructureType.FilesType) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.DocumentStructureTypeImpl
 
setFormat(TextLineConverter) - 
Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.DataTable
Sets the file format.
setGroups(ADFReporterGroup) - 
Method in class uk.ac.ebi.adfconverter.data.adf.ADFDesignElement
sets a  group associated to
 the design element
setHaveHeader(boolean) - 
Method in interface uk.ac.ebi.adfconverter.tools.checker.data.TableType
Sets the value of the haveHeader property.
setHaveHeader(boolean) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.TableTypeImpl
 
setHeader(CorrectableDataTableHeader) - 
Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.CorrectableDataTable
sets the header of the table
setHeader(DataTableHeader) - 
Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.DataTable
sets the header of the table
setHeader(HeaderType) - 
Method in interface uk.ac.ebi.adfconverter.tools.checker.data.TableType
Sets the value of the header property.
setHeader(HeaderType) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.TableTypeImpl
 
setHeaderIndex(DataTableHeader) - 
Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.DataRow
Method for DataFile to set the shared
 instance of a Hashtable that contains
 column label to index reference.
setIdentifierRule(String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.ontology.MGEDOntologyChecker
Set the database identifier generation rule.
setInnerValueFieldSeparator(String) - 
Method in interface uk.ac.ebi.adfconverter.tools.checker.data.ItemType
innerseparator of values in a field, if a value can contained several data
setInnerValueFieldSeparator(String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTypeImpl
 
setItemType(String) - 
Method in interface uk.ac.ebi.adfconverter.tools.checker.data.ItemType
name  of the item type
setItemType(String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTypeImpl
 
setItems(HeaderType.ItemsType) - 
Method in interface uk.ac.ebi.adfconverter.tools.checker.data.HeaderType
set of header items, describing  the table structure
setItems(HeaderType.ItemsType) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.HeaderTypeImpl
 
setLineNumber(int) - 
Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.DataRow
sets dataRow Line number in the data file
setLineNumber(int) - 
Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.DataTableHeader
Sets the line number of the header in the data file
setLocation(LocationType) - 
Method in interface uk.ac.ebi.adfconverter.tools.checker.data.ItemType
Location of the item in the header
setLocation(LocationType) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTypeImpl
 
setLoggingLevel(String) - 
Method in class uk.ac.ebi.adfconverter.common.tools.log.ADFConverterLoggerImpl
Sets treated file logger log level following level name string.
 
setLowerBound(BigInteger) - 
Method in interface uk.ac.ebi.adfconverter.tools.checker.data.CardinalityType
Sets the value of the lowerBound property.
setLowerBound(BigInteger) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.CardinalityTypeImpl
 
setMandatory(boolean) - 
Method in interface uk.ac.ebi.adfconverter.tools.checker.data.FileType
Sets the value of the mandatory property.
setMandatory(boolean) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.FileTypeImpl
 
setMultiplicity(boolean) - 
Method in interface uk.ac.ebi.adfconverter.tools.checker.data.ItemType
if multiplicity of values in a associatd field
setMultiplicity(boolean) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTypeImpl
 
setName(String) - 
Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.CorrectableHeaderItem
Sets the name of the item
setName(String) - 
Method in class uk.ac.ebi.adfconverter.data.adf.ADFGroup
Sets name attribut
setName(String) - 
Method in interface uk.ac.ebi.adfconverter.tools.checker.data.DataType
Sets the value of the name property.
setName(String) - 
Method in interface uk.ac.ebi.adfconverter.tools.checker.data.FileType
Sets the value of the name property.
setName(String) - 
Method in interface uk.ac.ebi.adfconverter.tools.checker.data.ItemType
Sets the value of the name property.
setName(String) - 
Method in interface uk.ac.ebi.adfconverter.tools.checker.data.TableType
Sets the value of the name property.
setName(String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.DataTypeImpl
 
setName(String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.FileTypeImpl
 
setName(String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTypeImpl
 
setName(String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.TableTypeImpl
 
setOrientation(int) - 
Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.DataTable
Indicates the orientation of data
 but DataTable is correct. do not depend of this orientation
 For convience
setOrientation(String) - 
Method in interface uk.ac.ebi.adfconverter.tools.checker.data.TableType
Sets the value of the orientation property.
setOrientation(String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.TableTypeImpl
 
setPrefixDelimiter(String) - 
Method in interface uk.ac.ebi.adfconverter.tools.checker.data.SubNameType
Sets the value of the prefixDelimiter property.
setPrefixDelimiter(String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.SubNameTypeImpl
 
setPrefixSubName(String) - 
Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.CorrectableHeaderItem
Set the prefix delimiter for subname
setPreviousColumns(LocationType.PreviousColumnsType) - 
Method in interface uk.ac.ebi.adfconverter.tools.checker.data.LocationType
Sets the value of the previousColumns property.
setPreviousColumns(LocationType.PreviousColumnsType) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.LocationTypeImpl
 
setProperty(String, Object) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.ObjectFactory
Set the specified property. 
setProperty(String, Object) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.DefaultJAXBContextImpl
There are no required properties, so simply throw an exception.  
setProperty(String, Object) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.MarshallerImpl
 
setProperty(String, Object) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.ValidatorImpl
There are no required properties, so simply throw an exception.  
setRegex(String) - 
Method in interface uk.ac.ebi.adfconverter.tools.checker.data.CheckRuleType
regulax expression used for identification
setRegex(String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.CheckRuleTypeImpl
 
setRelaxCheckRules(ItemType.RelaxCheckRulesType) - 
Method in interface uk.ac.ebi.adfconverter.tools.checker.data.ItemType
list of  relax rules: relax checking mode,  the different possibilities for the item
setRelaxCheckRules(ItemType.RelaxCheckRulesType) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTypeImpl
 
setReporter(ADFReporter) - 
Method in class uk.ac.ebi.adfconverter.data.adf.ADFFeature
sets the relation between a feature and a reporter
setReportergroups(ADFReporterGroup) - 
Method in class uk.ac.ebi.adfconverter.data.adf.ADFReporter
sets a  ReporterGroup associated to
 the reporter
setRootLogger(Properties) - 
Method in class uk.ac.ebi.adfconverter.common.tools.log.ADFConverterLoggerImpl
Sets root logger.
 
setRule(CheckRuleType) - 
Method in interface uk.ac.ebi.adfconverter.tools.checker.data.ConstraintType
Sets the value of the rule property.
setRule(CheckRuleType) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ConstraintTypeImpl
 
setSheet(String) - 
Method in class uk.ac.ebi.adfconverter.common.tools.file.reader.DataFileReaderIntf
For Microsoft excel workbook, set the sheet to read
setSheet(int) - 
Method in class uk.ac.ebi.adfconverter.common.tools.file.reader.DataFileReaderIntf
For Microsoft excel workbook, set the sheet to read
setSheet(String) - 
Method in class uk.ac.ebi.adfconverter.common.tools.file.reader.WorkBookFileReaderjxl
Sets in which sheet of the workbook, is supposed to be read
setSheet(int) - 
Method in class uk.ac.ebi.adfconverter.common.tools.file.reader.WorkBookFileReaderjxl
Sets in which sheet of the wookbook, is supposed to be read
setSheet(String) - 
Method in class uk.ac.ebi.adfconverter.common.tools.file.writer.WorkBookFileWriterjxl
Sets in which sheet of the wookbook, is supposed to be read
setSheet(int) - 
Method in class uk.ac.ebi.adfconverter.common.tools.file.writer.WorkBookFileWriterjxl
Sets in which sheet of the wookbook, is supposed to be read
setSheet(String, int) - 
Method in class uk.ac.ebi.adfconverter.common.tools.file.writer.WorkBookFileWriterjxl
Sets in which sheet of the wookbook, is supposed to be read
setSheetNumber(int) - 
Method in interface uk.ac.ebi.adfconverter.tools.checker.data.TableType
Sets the value of the sheetNumber property.
setSheetNumber(int) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.TableTypeImpl
 
setSimpleMicroarrayLayoutRelatedItem(Object) - 
Method in interface uk.ac.ebi.adfconverter.tools.checker.data.ItemType
Sets the value of the simpleMicroarrayLayoutRelatedItem property.
setSimpleMicroarrayLayoutRelatedItem(Object) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTypeImpl
 
setStrictCheck(CheckRuleType) - 
Method in interface uk.ac.ebi.adfconverter.tools.checker.data.ItemType
a unique rule, exactly matching the specification
setStrictCheck(CheckRuleType) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTypeImpl
 
setString(String) - 
Method in class uk.ac.ebi.adfconverter.common.data.DataBuffer
Create a new DataBuffer
setSubName(String) - 
Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.CorrectableHeaderItem
sets the subname of the item
setSubNames(ItemType.SubNamesType) - 
Method in interface uk.ac.ebi.adfconverter.tools.checker.data.ItemType
Sets the value of the subNames property.
setSubNames(ItemType.SubNamesType) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTypeImpl
 
setSuffixDelimiter(String) - 
Method in interface uk.ac.ebi.adfconverter.tools.checker.data.SubNameType
Sets the value of the suffixDelimiter property.
setSuffixDelimiter(String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.SubNameTypeImpl
 
setSuffixSubName(String) - 
Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.CorrectableHeaderItem
Set the suffix delimiter for subname
setTableDelimiter(String) - 
Method in interface uk.ac.ebi.adfconverter.tools.checker.data.DataType
Sets the value of the tableDelimiter property.
setTableDelimiter(String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.DataTypeImpl
 
setTables(DataType.TablesType) - 
Method in interface uk.ac.ebi.adfconverter.tools.checker.data.DataType
set of data tables (at least one)
setTables(DataType.TablesType) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.DataTypeImpl
 
setTracer(Tracer) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.SAXUnmarshallerHandlerImpl
 
setType(String) - 
Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.CorrectableHeaderItem
Sets the type of the item
setType(String) - 
Method in interface uk.ac.ebi.adfconverter.tools.checker.data.SubNameType
Sets the value of the type property.
setType(String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.SubNameTypeImpl
 
setTypeName(String) - 
Method in interface uk.ac.ebi.adfconverter.tools.checker.data.FieldType
Sets the value of the typeName property.
setTypeName(String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.FieldTypeImpl
 
setUpperBound(int) - 
Method in interface uk.ac.ebi.adfconverter.tools.checker.data.CardinalityType
Sets the value of the upperBound property.
setUpperBound(int) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.CardinalityTypeImpl
 
setValidating(boolean) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.UnmarshallerImpl
 
setValueAt(Object, int, int) - 
Method in class uk.ac.ebi.adfconverter.usermode.gui.visualisation.DataTableModel
Don't need to implement this method unless your table's
 data can change.
setValueDelimiter(String) - 
Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.CorrectableHeaderItem
sets the valuedelimiter of the item 
 in case of multiple component of a value
setValueFieldSeparator(String) - 
Method in interface uk.ac.ebi.adfconverter.tools.checker.data.ItemType
separator of values in a field, if multiplicity possible
setValueFieldSeparator(String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTypeImpl
 
sheetExists(String) - 
Method in class uk.ac.ebi.adfconverter.common.tools.file.reader.WorkBookFileReaderjxl
Tests if a sheet with a given name exists in the workbook
sheetExists(int) - 
Method in class uk.ac.ebi.adfconverter.common.tools.file.reader.WorkBookFileReaderjxl
Tests if a sheet at a given position exists in the workbook
size() - 
Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.DataRow
Retrieves the number of location in row.
size() - 
Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.DataTable
Retrieves the table size
size() - 
Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.DataTableHeader
Retrieves the header items number
skippedEntity(String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.ContentHandlerAdaptor
 
skippedEntity(String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.SAXUnmarshallerHandlerImpl
 
sortADF(String) - 
Method in class uk.ac.ebi.adfconverter.library.ADFConverterLibrary
sorts ADF in a directory.
 
 
startAttribute(String, String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.MSVValidator
 
startAttribute(String, String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.SAXMarshaller
Starts marshalling of an attribute.
 
 
startAttribute(String, String) - 
Method in interface uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.XMLSerializer
Starts marshalling of an attribute.
 
 
startDocument() - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.ContentHandlerAdaptor
 
startDocument() - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.SAXUnmarshallerHandlerImpl
 
startElement(String, String, String, Attributes) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.ContentHandlerAdaptor
 
startElement(String, String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.MSVValidator
 
startElement() - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.NamespaceContextImpl
Sets the current bindings aside and starts a new element context.
 
 
startElement(String, String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.SAXMarshaller
Starts marshalling of an element.
 
startElement(String, String, String, Attributes) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.SAXUnmarshallerHandlerImpl
 
startElement(String, String, String, Attributes) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.ValidatingUnmarshaller
 
startElement(String, String) - 
Method in interface uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.XMLSerializer
Starts marshalling of an element.
 
startPrefixMapping(String, String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.ContentHandlerAdaptor
 
startPrefixMapping(String, String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.SAXUnmarshallerHandlerImpl
 
state - 
Variable in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.AbstractUnmarshallingEventHandlerImpl
Current state of this automaton.



T

TEXTFILE - 
Static variable in class uk.ac.ebi.adfconverter.common.data.tabulardata.DataTable
TEXT file type
TableType - interface uk.ac.ebi.adfconverter.tools.checker.data.TableType.
structure of datatable: can have a header
 Java content class for tableType complex type.
 
TableTypeImpl - class uk.ac.ebi.adfconverter.tools.checker.data.impl.TableTypeImpl.
 
TableTypeImpl() - 
Constructor for class uk.ac.ebi.adfconverter.tools.checker.data.impl.TableTypeImpl
 
TableTypeImpl.Unmarshaller - class uk.ac.ebi.adfconverter.tools.checker.data.impl.TableTypeImpl.Unmarshaller.
 
TableTypeImpl.Unmarshaller(UnmarshallingContext) - 
Constructor for class uk.ac.ebi.adfconverter.tools.checker.data.impl.TableTypeImpl.Unmarshaller
 
TextLineConverter - interface uk.ac.ebi.adfconverter.common.tools.file.converter.TextLineConverter.
Interface for converting file line in data
takeSample() - 
Method in class uk.ac.ebi.adfconverter.tools.monitor.MemMonitor
Takes a sample of the current memory state.
test1 - class uk.ac.ebi.adfconverter.usermode.gui.test1.
 
test1() - 
Constructor for class uk.ac.ebi.adfconverter.usermode.gui.test1
 
testAssigningValues(Vector) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.ontology.MGEDOntologyChecker
Tests if Ontoloy class entries are correct
testInitOfMGEDOE(Vector) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.ontology.MGEDOntologyChecker
 
text(String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.AbstractUnmarshallingEventHandlerImpl
 
text(String, String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.MSVValidator
 
text(String, String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.SAXMarshaller
Marshalls text.
 
 
text(String) - 
Method in interface uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.UnmarshallingEventHandler
 
text(String) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.UnmarshallingEventHandlerAdaptor
 
text(String, String) - 
Method in interface uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.XMLSerializer
Marshalls text.
 
 
toArrayList() - 
Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.DataRow
Converts the row of data into an arrayList
toByteFormat(float) - 
Static method in class uk.ac.ebi.adfconverter.tools.monitor.MemMonitor
Convert number of bytes to string representing bytes,
       kilobytes, megabytes, etc.
toCharArray() - 
Method in class uk.ac.ebi.adfconverter.common.data.DataBuffer
retrieves the object as char array
toLowerCase() - 
Method in class uk.ac.ebi.adfconverter.common.data.DataBuffer
Retrieves the databuffer in lower case
toString() - 
Method in class uk.ac.ebi.adfconverter.common.data.DataBuffer
Retrieves the DataBuffer as String
toString() - 
Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.CorrectableDataTable
represents the table as String
toString() - 
Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.CorrectableHeaderItem
Transforms object in String
toString() - 
Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.DataRow
For debugging purpose.
 
toString() - 
Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.DataTable
represents the table as String
toString() - 
Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.DataTableHeader
For debugging purpose.
 
toString() - 
Method in class uk.ac.ebi.adfconverter.common.data.tabulardata.HeaderItem
Transforms object in String
toString() - 
Method in class uk.ac.ebi.adfconverter.common.tools.file.reader.exceptions.IncorrectFile
represents the exception as string
toString() - 
Method in class uk.ac.ebi.adfconverter.data.adf.ADFDesignElement
Represents the group as String 
  (non-Javadoc)
toString() - 
Method in class uk.ac.ebi.adfconverter.data.adf.ADFGroup
Retrieves the current ADFGroup as String
toString() - 
Method in class uk.ac.ebi.adfconverter.tools.checker.Cardinality
Represents the cardinality as String
toString() - 
Method in class uk.ac.ebi.adfconverter.tools.monitor.MemMonitor.Data
 
toString() - 
Method in class uk.ac.ebi.adfconverter.tools.monitor.MemMonitor
 
toUpperCase() - 
Method in class uk.ac.ebi.adfconverter.common.data.DataBuffer
Retrieves the databuffer in upper case



U

UNKNOWNFILE - 
Static variable in class uk.ac.ebi.adfconverter.common.data.tabulardata.DataTable
UNKNOWN File type
UnknownStructure - exception uk.ac.ebi.adfconverter.tools.checker.exceptions.UnknownStructure.
Signals an error of unkwonn file structure.
 
UnknownStructure() - 
Constructor for class uk.ac.ebi.adfconverter.tools.checker.exceptions.UnknownStructure
 
UnmarshallableObject - interface uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.UnmarshallableObject.
Generated classes have to implement this interface for it
 to be unmarshallable.
UnmarshallerImpl - class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.UnmarshallerImpl.
Default Unmarshall implementation.
 
 
UnmarshallerImpl(DefaultJAXBContextImpl, GrammarInfo) - 
Constructor for class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.UnmarshallerImpl
 
UnmarshallingContext - interface uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.UnmarshallingContext.
Methods exposed by the unmarshalling coordinator object
 to the generated code.
 
 
UnmarshallingEventHandler - interface uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.UnmarshallingEventHandler.
Implemented by the generated code to unmarshall an object
 from unmarshaller events.
 
 
UnmarshallingEventHandlerAdaptor - class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.UnmarshallingEventHandlerAdaptor.
Redirects events to another SAX ContentHandler.
 
 
UnmarshallingEventHandlerAdaptor(UnmarshallingContext, ContentHandler) - 
Constructor for class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.UnmarshallingEventHandlerAdaptor
 
Untar - class uk.ac.ebi.adfconverter.common.tools.file.archives.Untar.
Uncompress a tar file
Untar() - 
Constructor for class uk.ac.ebi.adfconverter.common.tools.file.archives.Untar
 
Unzip - class uk.ac.ebi.adfconverter.common.tools.file.archives.Unzip.
Uncompress a gzip/zip file
 or a tgz file to tar
Unzip() - 
Constructor for class uk.ac.ebi.adfconverter.common.tools.file.archives.Unzip
 
Util - class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.Util.
 
Util() - 
Constructor for class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.Util
 
uk.ac.ebi.adfconverter.common.configuration - package uk.ac.ebi.adfconverter.common.configuration
 
uk.ac.ebi.adfconverter.common.configuration.exceptions - package uk.ac.ebi.adfconverter.common.configuration.exceptions
 
uk.ac.ebi.adfconverter.common.data - package uk.ac.ebi.adfconverter.common.data
 
uk.ac.ebi.adfconverter.common.data.tabulardata - package uk.ac.ebi.adfconverter.common.data.tabulardata
 
uk.ac.ebi.adfconverter.common.data.tabulardata.exceptions - package uk.ac.ebi.adfconverter.common.data.tabulardata.exceptions
 
uk.ac.ebi.adfconverter.common.tools.file.archives - package uk.ac.ebi.adfconverter.common.tools.file.archives
 
uk.ac.ebi.adfconverter.common.tools.file.converter - package uk.ac.ebi.adfconverter.common.tools.file.converter
 
uk.ac.ebi.adfconverter.common.tools.file.copier - package uk.ac.ebi.adfconverter.common.tools.file.copier
 
uk.ac.ebi.adfconverter.common.tools.file.copier.exceptions - package uk.ac.ebi.adfconverter.common.tools.file.copier.exceptions
 
uk.ac.ebi.adfconverter.common.tools.file.description - package uk.ac.ebi.adfconverter.common.tools.file.description
 
uk.ac.ebi.adfconverter.common.tools.file.filesystem - package uk.ac.ebi.adfconverter.common.tools.file.filesystem
 
uk.ac.ebi.adfconverter.common.tools.file.reader - package uk.ac.ebi.adfconverter.common.tools.file.reader
 
uk.ac.ebi.adfconverter.common.tools.file.reader.exceptions - package uk.ac.ebi.adfconverter.common.tools.file.reader.exceptions
 
uk.ac.ebi.adfconverter.common.tools.file.writer - package uk.ac.ebi.adfconverter.common.tools.file.writer
 
uk.ac.ebi.adfconverter.common.tools.log - package uk.ac.ebi.adfconverter.common.tools.log
 
uk.ac.ebi.adfconverter.common.tools.log.exceptions - package uk.ac.ebi.adfconverter.common.tools.log.exceptions
 
uk.ac.ebi.adfconverter.common.tools.net.mail - package uk.ac.ebi.adfconverter.common.tools.net.mail
 
uk.ac.ebi.adfconverter.common.tools.net.update - package uk.ac.ebi.adfconverter.common.tools.net.update
 
uk.ac.ebi.adfconverter.common.tools.regex - package uk.ac.ebi.adfconverter.common.tools.regex
 
uk.ac.ebi.adfconverter.common.util.pool - package uk.ac.ebi.adfconverter.common.util.pool
 
uk.ac.ebi.adfconverter.data.adf - package uk.ac.ebi.adfconverter.data.adf
 
uk.ac.ebi.adfconverter.library - package uk.ac.ebi.adfconverter.library
 
uk.ac.ebi.adfconverter.library.exceptions - package uk.ac.ebi.adfconverter.library.exceptions
 
uk.ac.ebi.adfconverter.tools.checker - package uk.ac.ebi.adfconverter.tools.checker
 
uk.ac.ebi.adfconverter.tools.checker.data - package uk.ac.ebi.adfconverter.tools.checker.data
 
uk.ac.ebi.adfconverter.tools.checker.data.impl - package uk.ac.ebi.adfconverter.tools.checker.data.impl
 
uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime - package uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime
 
uk.ac.ebi.adfconverter.tools.checker.exceptions - package uk.ac.ebi.adfconverter.tools.checker.exceptions
 
uk.ac.ebi.adfconverter.tools.checker.ontology - package uk.ac.ebi.adfconverter.tools.checker.ontology
 
uk.ac.ebi.adfconverter.tools.checker.ontology.exceptions - package uk.ac.ebi.adfconverter.tools.checker.ontology.exceptions
 
uk.ac.ebi.adfconverter.tools.converter - package uk.ac.ebi.adfconverter.tools.converter
 
uk.ac.ebi.adfconverter.tools.converter.IdentifierGenerater - package uk.ac.ebi.adfconverter.tools.converter.IdentifierGenerater
 
uk.ac.ebi.adfconverter.tools.exporter - package uk.ac.ebi.adfconverter.tools.exporter
 
uk.ac.ebi.adfconverter.tools.exporter.exceptions - package uk.ac.ebi.adfconverter.tools.exporter.exceptions
 
uk.ac.ebi.adfconverter.tools.filestructure - package uk.ac.ebi.adfconverter.tools.filestructure
 
uk.ac.ebi.adfconverter.tools.monitor - package uk.ac.ebi.adfconverter.tools.monitor
 
uk.ac.ebi.adfconverter.tools.networking - package uk.ac.ebi.adfconverter.tools.networking
 
uk.ac.ebi.adfconverter.usermode.commandline - package uk.ac.ebi.adfconverter.usermode.commandline
 
uk.ac.ebi.adfconverter.usermode.gui - package uk.ac.ebi.adfconverter.usermode.gui
 
uk.ac.ebi.adfconverter.usermode.gui.check - package uk.ac.ebi.adfconverter.usermode.gui.check
 
uk.ac.ebi.adfconverter.usermode.gui.visualisation - package uk.ac.ebi.adfconverter.usermode.gui.visualisation
 
unmarshal(Node) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.UnmarshallerImpl
 



V

VERTICALTABLE - 
Static variable in class uk.ac.ebi.adfconverter.common.data.tabulardata.DataTable
Vertical  table orientation
ValidatableObject - interface uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.ValidatableObject.
This interface is implemented by generated classes
 to indicate that the class supports validation.
ValidatingUnmarshaller - class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.ValidatingUnmarshaller.
Filter implementation of SAXUnmarshallerHandler.
 
 
ValidatorImpl - class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.ValidatorImpl.
Validator implementation of JAXB RI.
ValidatorImpl(DefaultJAXBContextImpl) - 
Constructor for class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.ValidatorImpl
 
validate(DefaultJAXBContextImpl, ValidationContext, ValidatableObject) - 
Static method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.MSVValidator
Validates the specified object and reports any error to the context.
validate(Object) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.ValidatorImpl
 
validateRoot(Object) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.ValidatorImpl
 
version - 
Static variable in class uk.ac.ebi.adfconverter.tools.checker.data.ObjectFactory
 
version - 
Static variable in class uk.ac.ebi.adfconverter.tools.checker.data.impl.CardinalityTypeImpl
 
version - 
Static variable in class uk.ac.ebi.adfconverter.tools.checker.data.impl.CheckRuleTypeImpl
 
version - 
Static variable in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ConstraintTypeImpl
 
version - 
Static variable in class uk.ac.ebi.adfconverter.tools.checker.data.impl.DataTypeImpl.TablesTypeImpl
 
version - 
Static variable in class uk.ac.ebi.adfconverter.tools.checker.data.impl.DataTypeImpl
 
version - 
Static variable in class uk.ac.ebi.adfconverter.tools.checker.data.impl.DocumentStructureImpl
 
version - 
Static variable in class uk.ac.ebi.adfconverter.tools.checker.data.impl.DocumentStructureTypeImpl.FilesTypeImpl
 
version - 
Static variable in class uk.ac.ebi.adfconverter.tools.checker.data.impl.DocumentStructureTypeImpl
 
version - 
Static variable in class uk.ac.ebi.adfconverter.tools.checker.data.impl.FieldTypeImpl.ConstraintsTypeImpl
 
version - 
Static variable in class uk.ac.ebi.adfconverter.tools.checker.data.impl.FieldTypeImpl
 
version - 
Static variable in class uk.ac.ebi.adfconverter.tools.checker.data.impl.FileTypeImpl.DataSetTypeImpl
 
version - 
Static variable in class uk.ac.ebi.adfconverter.tools.checker.data.impl.FileTypeImpl
 
version - 
Static variable in class uk.ac.ebi.adfconverter.tools.checker.data.impl.FilerImpl
 
version - 
Static variable in class uk.ac.ebi.adfconverter.tools.checker.data.impl.HeaderImpl
 
version - 
Static variable in class uk.ac.ebi.adfconverter.tools.checker.data.impl.HeaderTypeImpl.ItemsTypeImpl
 
version - 
Static variable in class uk.ac.ebi.adfconverter.tools.checker.data.impl.HeaderTypeImpl
 
version - 
Static variable in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTempImpl
 
version - 
Static variable in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTypeImpl.FieldDependenceTypeImpl
 
version - 
Static variable in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTypeImpl.RelaxCheckRulesTypeImpl
 
version - 
Static variable in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTypeImpl.SubNamesTypeImpl
 
version - 
Static variable in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTypeImpl
 
version - 
Static variable in class uk.ac.ebi.adfconverter.tools.checker.data.impl.JAXBVersion
 
version - 
Static variable in class uk.ac.ebi.adfconverter.tools.checker.data.impl.LocationTypeImpl.PreviousColumnsTypeImpl
 
version - 
Static variable in class uk.ac.ebi.adfconverter.tools.checker.data.impl.LocationTypeImpl
 
version - 
Static variable in class uk.ac.ebi.adfconverter.tools.checker.data.impl.SubNameTypeImpl.ConstraintsTypeImpl
 
version - 
Static variable in class uk.ac.ebi.adfconverter.tools.checker.data.impl.SubNameTypeImpl
 
version - 
Static variable in class uk.ac.ebi.adfconverter.tools.checker.data.impl.TableTypeImpl
 



W

WORKBOOKFILE - 
Static variable in class uk.ac.ebi.adfconverter.common.data.tabulardata.DataTable
WORKBOOK File type
WorkBookFileReaderjxl - class uk.ac.ebi.adfconverter.common.tools.file.reader.WorkBookFileReaderjxl.
Interface for all file format classes used in reading
 data
WorkBookFileReaderjxl(File) - 
Constructor for class uk.ac.ebi.adfconverter.common.tools.file.reader.WorkBookFileReaderjxl
Default Constructor for workbook reading
WorkBookFileReaderjxl(File, String) - 
Constructor for class uk.ac.ebi.adfconverter.common.tools.file.reader.WorkBookFileReaderjxl
Constructor for workbook reading with a specific encoding
WorkBookFileWriterjxl - class uk.ac.ebi.adfconverter.common.tools.file.writer.WorkBookFileWriterjxl.
Interface for all file format classes used in data writing
WorkBookFileWriterjxl(File) - 
Constructor for class uk.ac.ebi.adfconverter.common.tools.file.writer.WorkBookFileWriterjxl
WorkBookFileWriterjxl class Constructor. 
WorkBookFileWriterjxl(File, String) - 
Constructor for class uk.ac.ebi.adfconverter.common.tools.file.writer.WorkBookFileWriterjxl
WorkBookFileWriterjxl class Constructor. 
WriteConfiguration() - 
Static method in class uk.ac.ebi.adfconverter.common.configuration.ADFConverterConfiguration
Writes the current configuration in the configuration file
warn(String) - 
Method in interface uk.ac.ebi.adfconverter.common.tools.log.ADFConverterLogger
Reports an warn message to the current log.
warn(String) - 
Method in class uk.ac.ebi.adfconverter.common.tools.log.ADFConverterLoggerImpl
Logs a warn message into the current logger
warning(SAXParseException) - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.ErrorHandlerAdaptor
 
workbookFileExtension - 
Static variable in class uk.ac.ebi.adfconverter.data.adf.ADFJava
workbookFileExtension: default Microsoft Excel Workbook file extension
writeData(DataTable) - 
Method in class uk.ac.ebi.adfconverter.common.tools.file.writer.DataFileWriter
Writes data in file
writeData(DataTable, String, String, String, int, int) - 
Method in class uk.ac.ebi.adfconverter.common.tools.file.writer.DataFileWriter
write data into file with a specific character encoding
writeDataLine(DataRow) - 
Method in interface uk.ac.ebi.adfconverter.common.tools.file.writer.DataWriter

 Write a data row in a file 
 Only when termination requirements have been met, the method should return a
 DataRow/code> object.
 
writeDataLine(DataRow) - 
Method in class uk.ac.ebi.adfconverter.common.tools.file.writer.PlainTextDataFileWriter
Write a data row in a file
writeDataLine(DataRow) - 
Method in class uk.ac.ebi.adfconverter.common.tools.file.writer.WorkBookFileWriterjxl

 Write a data row in a data file  
 
writeHeaderLine(DataTableHeader) - 
Method in interface uk.ac.ebi.adfconverter.common.tools.file.writer.DataWriter

 Write table header into a line  
 Only when termination requirements have been met, the method should return a
 DataRow/code> object.
 
writeHeaderLine(DataTableHeader) - 
Method in class uk.ac.ebi.adfconverter.common.tools.file.writer.PlainTextDataFileWriter
Write a table header in a file
writeHeaderLine(DataTableHeader) - 
Method in class uk.ac.ebi.adfconverter.common.tools.file.writer.WorkBookFileWriterjxl
Write a table header in a file
writeHorizontalDataTable(DataTable, String, String, String) - 
Method in class uk.ac.ebi.adfconverter.common.tools.file.writer.DataFileWriter
Writes data into a file with a specific character encoding
  in a Horizontal orientation of data
writeHorizontalDataTable(DataTable, String, String, String, int) - 
Method in class uk.ac.ebi.adfconverter.common.tools.file.writer.DataFileWriter
Retrieves data from file with a specific character encoding
  in a horizontal  orientation of data
writeLine(DataBuffer) - 
Method in interface uk.ac.ebi.adfconverter.common.tools.file.writer.ADFConverterFileWriter

 Write a line in a data file  

 
writeLine(DataBuffer) - 
Method in class uk.ac.ebi.adfconverter.common.tools.file.writer.ADFConverterFileWriterImpl

 Write a line in a data file.
 
writeLine(DataBuffer) - 
Method in class uk.ac.ebi.adfconverter.common.tools.file.writer.PlainTextFileWriter

 Retrieves a line from a data file  
 Only when termination requirements have been met, the method should return a
 String object.
 
writeLine(DataBuffer) - 
Method in class uk.ac.ebi.adfconverter.common.tools.file.writer.WorkBookFileWriterjxl

 Write a line ina data file  
 Only when termination requirements have been met, the method should return a
 String object.
 
writeVerticalDataTable(DataTable, String, String, String) - 
Method in class uk.ac.ebi.adfconverter.common.tools.file.writer.DataFileWriter
Write a  data into a  file with a specific character encoding
  in a vertical orientation of data
writeVerticalDataTable(DataTable, String, String, String, int) - 
Method in class uk.ac.ebi.adfconverter.common.tools.file.writer.DataFileWriter
Write  data into a  file with a specific character encoding
  in a vertical orientation of data



X

XMLSerializable - interface uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.XMLSerializable.
For a generated class to be serializable, it has to
 implement this interface.
XMLSerializer - interface uk.ac.ebi.adfconverter.tools.checker.data.impl.runtime.XMLSerializer.
Receives XML serialization event
 
 
 This object coordinates the overall marshalling efforts across different
 content-tree objects and different target formats.
 
 


_

____jaxb____getId() - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTypeImpl
 
____jaxb_ri____getLocalName() - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.DocumentStructureImpl
 
____jaxb_ri____getLocalName() - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.FilerImpl
 
____jaxb_ri____getLocalName() - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.HeaderImpl
 
____jaxb_ri____getLocalName() - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTempImpl
 
____jaxb_ri____getNamespaceURI() - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.DocumentStructureImpl
 
____jaxb_ri____getNamespaceURI() - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.FilerImpl
 
____jaxb_ri____getNamespaceURI() - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.HeaderImpl
 
____jaxb_ri____getNamespaceURI() - 
Method in class uk.ac.ebi.adfconverter.tools.checker.data.impl.ItemTempImpl
 


A C D E F G H I J L M N O P R S T U V W X _ 









  
      Overview 
      Package 
      Class 
      Use 
      Tree 
    Index 
      Help 
  









 PREV 
 NEXT

  FRAMES   
 NO FRAMES   
 









European Bioinformatics InstituteMicroarray Informatics Team