uk.ac.ebi.adfconverter.tools.filestructure
Class FileStructureDescription

java.lang.Object
  uk.ac.ebi.adfconverter.tools.filestructure.FileStructureDescription

public class FileStructureDescription

extends java.lang.Object

class used to manipulated the data/ tabular file structure description contained in an XML file

Since:

14 sept. 2004

Version:

1

Author:

Pierre MARGUERITE

Constructor Summary

FileStructureDescription()
default Constructor

Method Summary

CorrectableHeaderItem	createItem(ItemType itemType) Create a correctableHeaderITem corresponding to a itemType
CorrectableHeaderItem	createItem(java.lang.String type) Create an item object of a given type.
CorrectableHeaderItem	createItem(java.lang.String type, int columnNumber) Create a CorrectableHeaderItem object with a given type
FileType	FileType(java.lang.String filename) Retrieves the FileType associated to a given filename in the file structure definition.
CorrectableHeaderItem	getAssociatedSimpleMicroArrayLayoutItem(CorrectableHeaderItem item) Retrieves the associated Simple Microarray layout item associated to a given item in the structure definition.
CorrectableHeaderItem	getAssociatedSimpleMicroArrayLayoutItem(CorrectableHeaderItem item, int columnNumber) Retrieves the associated Simple Microarray layout item associated to a given item in the structure definition.
DataType	getDataType(java.lang.String dataName) Retrieves the DataType object with a given dataname.
FileType	getFileType() Retrieves the fileType attribut
HeaderType	getHeaderType() Retrieves the headerType attribut
DataType	getNextDataType() Retrieves the next DataType object in the structure definition
FileType	getNextFileType() Retrieves the next FileType object from the structure definition (XML)
TableType	getNextTable() Retrieves the next table object in the structure definition hierarchy/tree
DataType	getPreviousData() Retrieves the previous DataType object in the structure definition
TableType	getPreviousTable() Retrieves the previous table object in the structure definition hierarchy/tree
TableType	getTableType(java.lang.String tableName) Retrieves the TableType object with a given name.
void	openStructure(java.lang.String _structureFile) Open a file structure
void	setCurrentHeaderType(HeaderType _headerType) Set the current HeaderType object.

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

FileStructureDescription

public FileStructureDescription()

default Constructor

Method Detail

createItem

public CorrectableHeaderItem createItem(ItemType itemType)

Create a correctableHeaderITem corresponding to a itemType

Parameters:

itemType - the itemType describing an header item

Returns:

a corresponding correctableHeaderITem , if the itemType is correct,. null otherwise

createItem

public CorrectableHeaderItem createItem(java.lang.String type)
                                 throws IncorrectFileStructure

Create an item object of a given type.

Parameters:

type - the type of the item to create

Returns:

the created item of the given type

Throws:

IncorrectFileStructure - if the structure definition is incorrect.

createItem

public CorrectableHeaderItem createItem(java.lang.String type,
                                        int columnNumber)
                                 throws IncorrectFileStructure

Create a CorrectableHeaderItem object with a given type

Parameters:

type - the type of the item to createz

columnNumber - the column of the item in the file header

Returns:

a CorrectableHeaderItem object with the given type, if the type has been retrieved from the file structure description. null, otherwise

Throws:

IncorrectFileStructure - if description file is incorrect

FileType

public FileType FileType(java.lang.String filename)

Retrieves the FileType associated to a given filename in the file structure definition.

Parameters:

filename - the filename to which the associated FileType is looked for.

Returns:

the FileType object associated to the filename, if existing. null otherwise

getAssociatedSimpleMicroArrayLayoutItem

public CorrectableHeaderItem getAssociatedSimpleMicroArrayLayoutItem(CorrectableHeaderItem item)
                                                              throws IncorrectFileStructure

Retrieves the associated Simple Microarray layout item associated to a given item in the structure definition. only currently useable with ADF definition

Parameters:

item - the item to which the associated item is looked for

Returns:

a corresponding correctableHeaderITem , if the associated item exists. null, otherwise.

Throws:

IncorrectFileStructure - if the structure definition is incorrect.

getAssociatedSimpleMicroArrayLayoutItem

public CorrectableHeaderItem getAssociatedSimpleMicroArrayLayoutItem(CorrectableHeaderItem item,
                                                                     int columnNumber)
                                                              throws IncorrectFileStructure

Retrieves the associated Simple Microarray layout item associated to a given item in the structure definition. only currently useable with ADF definition

Parameters:

item - the item to which the associated item is looked for

columnNumber - the item column../not used...

Returns:

a corresponding correctableHeaderITem , if the associated item exists. null, otherwise.

Throws:

IncorrectFileStructure - if the structure definition is incorrect.

getDataType

public DataType getDataType(java.lang.String dataName)
                     throws IncorrectFileStructure

Retrieves the DataType object with a given dataname.

Parameters:

dataName - the dataname of the DataType looked for.

Returns:

the DataType object with the given data name.

Throws:

IncorrectFileStructure - if the structure definition file /xml tree, is incorrect

getFileType

public FileType getFileType()

Retrieves the fileType attribut

Returns:

Returns the fileType.

getHeaderType

public HeaderType getHeaderType()
                         throws IncorrectFileStructure

Retrieves the headerType attribut

Returns:

Returns the headerType.

Throws:

IncorrectFileStructure - the structure definition is incorrect.

getNextDataType

public DataType getNextDataType()
                         throws IncorrectFileStructure

Retrieves the next DataType object in the structure definition

Returns:

the next DataType object, if existing. null, otherwise

Throws:

IncorrectFileStructure - if the file structure definition file is incorrect.

getNextFileType

public FileType getNextFileType()

Retrieves the next FileType object from the structure definition (XML)

Returns:

the next FileType object, if existing. null, otherwise.

getNextTable

public TableType getNextTable()
                       throws IncorrectFileStructure

Retrieves the next table object in the structure definition hierarchy/tree

Returns:

the next TableType object, if existing. null, otherwise.

Throws:

IncorrectFileStructure - if the structur definition is incorrect.

getPreviousData

public DataType getPreviousData()
                         throws IncorrectFileStructure

Retrieves the previous DataType object in the structure definition

Returns:

the previous DataType object, if existing. null, otherwise

Throws:

IncorrectFileStructure - if the file structure definition file is incorrect.

getPreviousTable

public TableType getPreviousTable()
                           throws IncorrectFileStructure

Retrieves the previous table object in the structure definition hierarchy/tree

Returns:

the previous TableType object, if existing. null, otherwise.

Throws:

IncorrectFileStructure - if the structur definition is incorrect.

getTableType

public TableType getTableType(java.lang.String tableName)
                       throws IncorrectFileStructure

Retrieves the TableType object with a given name.

Parameters:

tableName - the name of the table looked for.

Returns:

the TableType with the given name.

Throws:

IncorrectFileStructure - the structure definition is incorrect.

openStructure

public void openStructure(java.lang.String _structureFile)
                   throws java.io.IOException

Open a file structure

Parameters:

_structureFile - the XML file contained a data file description

Throws:

java.io.IOException - if an error occurs file access

setCurrentHeaderType

public void setCurrentHeaderType(HeaderType _headerType)

Set the current HeaderType object.

Parameters:

_headerType - the HeaderType object to set as current.