uk.ac.ebi.adfconverter.common.tools.file.reader
Class DataFileReaderIntf

java.lang.Object
  uk.ac.ebi.adfconverter.common.tools.file.reader.DataFileReaderIntf

Direct Known Subclasses:

DataFileReader

public abstract class DataFileReaderIntf

extends java.lang.Object

This class converts data from a file in a DataTable in Java, for manipulation

Version:

1 ADF MAGE-TOOL - MicroArray Informatics Team / European Bioinformatics Institute (EBI) ArrayExpress License: ============================================================================== Copyright (c) 2002 The European Bioinformatics Institute. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. 3. The name ArrayExpress must not be used to endorse or promote products derived from this software without prior written permission. For written permission, please contact arrayexpress@ebi.ac.uk 4. Products derived from this software may not be called "ArrayExpress" nor may "ArrayExpress" appear in their names without prior written permission of the ArrayExpress developers. 5. Redistributions of any form whatsoever must retain the following acknowledgment: "This product includes software developed by ArrayExpress (http://www.ebi.ac.uk/arrayexpress)" THIS SOFTWARE IS PROVIDED BY THE ARRAYEXPRESS GROUP ``AS IS'' AND ANY EXPRESSED OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE ARRAYEXPRESS GROUP OR ITS CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. The European Bioinformatics Institute may publish revised and/or new versions of this license with new releases of ArrayExpress software. ==============================================================================

Author:

Pierre MARGUERITE

See Also:

DataTable

Constructor Summary

DataFileReaderIntf(java.io.File aFile)
constructor for converting a data file in data table in memory

DataFileReaderIntf(java.io.File aFile, boolean hasHeader)
constructor for converting a data file in data table in memory

Method Summary

abstract void	close() Closes file access/ reading
boolean	containsHeader() Checks if header indicator has been turned on using containsHeader(boolean). .
void	containsHeader(boolean _header) Sets the indicator for header row.
abstract DataTable	getData() Retrieves data from file
abstract DataTable	getData(int fileFormat) Retrieves data from file in a given file format, specifying file format type
abstract DataTable	getData(java.lang.String enc, java.lang.String delimiter, java.lang.String escape, int orientation, int type) Retrieves data from file with a specific character encoding
java.io.File	getFile() Retrieves the file associated/red by the reader
abstract DataRow	getHorizontalDataRow() Retrieves the next datarow in the horizontal datable.
abstract DataTable	getHorizontalDataTable(java.lang.String enc, java.lang.String delimiter, java.lang.String escape) Retrieves data from file with a specific character encoding in a vertical orientation of data
abstract DataTable	getHorizontalDataTable(java.lang.String enc, java.lang.String delimiter, java.lang.String escape, int type) Retrieves data from file with a specific character encoding in a horizontal orientation of data
abstract DataTableHeader	getHorizontalHeader() Retrieves the header of a horizontal data table contained in a file
abstract DataTable	getVerticalDataTable(java.lang.String enc, java.lang.String delimiter, java.lang.String escape) Retrieves data from file with a specific character encoding in a vertical orientation of data
abstract DataTable	getVerticalDataTable(java.lang.String enc, java.lang.String delimiter, java.lang.String escape, int type) Retrieves data from file with a specific character encoding in a vertical orientation of data
abstract boolean	open(java.lang.String enc, java.lang.String delimiter, java.lang.String escape, int type) Open a data file with a given character encoding , delimiter and escape strings , file orientation and file type
void	setSheet(int sheetNumber) For Microsoft excel workbook, set the sheet to read
void	setSheet(java.lang.String sheetName) For Microsoft excel workbook, set the sheet to read

Methods inherited from class java.lang.Object

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

Constructor Detail

DataFileReaderIntf

public DataFileReaderIntf(java.io.File aFile)

constructor for converting a data file in data table in memory

Parameters:

aFile - a file object of a file containing data

DataFileReaderIntf

public DataFileReaderIntf(java.io.File aFile,
                          boolean hasHeader)

constructor for converting a data file in data table in memory

Parameters:

aFile - a file object of a file containing data

hasHeader - a boolean indicating if the first row is considered as the table header

Method Detail

close

public abstract void close()

Closes file access/ reading

containsHeader

public boolean containsHeader()

Checks if header indicator has been turned on using containsHeader(boolean). .

Returns:

True, if table header indicator has been set to true. False, otherwise.

containsHeader

public void containsHeader(boolean _header)

Sets the indicator for header row.

Parameters:

_header - True if the table contains a header row. False, otherwise.

getData

public abstract DataTable getData()
                           throws java.io.IOException,
                                  IncorrectFile,
                                  IncorrectDataFile

Retrieves data from file

Returns:

the data contained in the data file as DataTable

Throws:

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

IncorrectFile - if the opened file is incorrect (not as expected)

IncorrectDataFile - if the opened data file is incorrect.(incorrect data type, incorrect file structure)

getData

public abstract DataTable getData(int fileFormat)
                           throws java.io.IOException,
                                  IncorrectFile,
                                  IncorrectDataFile

Retrieves data from file in a given file format, specifying file format type

Parameters:

fileFormat - the file format

Returns:

the data contained in the data file as DataTable

Throws:

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

IncorrectFile - if the opened file is incorrect (not as expected)

IncorrectDataFile - if the opened data file is incorrect.(incorrect data type, incorrect file structure)

getData

public abstract DataTable getData(java.lang.String enc,
                                  java.lang.String delimiter,
                                  java.lang.String escape,
                                  int orientation,
                                  int type)
                           throws java.io.IOException,
                                  IncorrectFile,
                                  IncorrectDataFile

Retrieves data from file with a specific character encoding

Parameters:

enc - a character encoding

delimiter - the delimiter string in a row (line)

escape - the escape string of a row in the file

type - the type of the data file

Returns:

the retrieved data table from the data file

Throws:

java.io.IOException

IncorrectFile

IncorrectDataFile

See Also:

authorizes file format
Description of Data Content Typical Filename Extensions MIME type/subtype Text and Text-Related Types HTML text data (RFC 1866) html htm text/html Plain text: documents; program listings txt c c++ pl cc h text/plain Excel spreadsheet (Microsoft) xls, xlc, xll, xlm, xlw application/vnd.ms-excel application/x-msexcel application/ms-excel application/msexcel application/x-excel *

getFile

public java.io.File getFile()

Retrieves the file associated/red by the reader

Returns:

the associated file. null, if the file is incorrect

getHorizontalDataRow

public abstract DataRow getHorizontalDataRow()
                                      throws java.io.IOException,
                                             IncorrectDataFile

Retrieves the next datarow in the horizontal datable. Must be call after calling once open method

Returns:

the next retrieved DataRow, if existing. null, otherwise.

Throws:

java.io.IOException

IncorrectDataFile

getHorizontalDataTable

public abstract DataTable getHorizontalDataTable(java.lang.String enc,
                                                 java.lang.String delimiter,
                                                 java.lang.String escape)
                                          throws java.io.IOException,
                                                 IncorrectFile,
                                                 IncorrectDataFile

Retrieves data from file with a specific character encoding in a vertical orientation of data

Parameters:

enc - a character encoding

delimiter - the delimiter string in a row (line)

escape - the escape string of a row in the file

Returns:

contained data as DataTable (each table is in correct composition - accessible as horizontal table)

Throws:

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

IncorrectFile - if the opened file is incorrect (not as expected)

IncorrectDataFile - if the opened data file is incorrect.(incorrect data type,

getHorizontalDataTable

public abstract DataTable getHorizontalDataTable(java.lang.String enc,
                                                 java.lang.String delimiter,
                                                 java.lang.String escape,
                                                 int type)
                                          throws java.io.IOException,
                                                 IncorrectFile,
                                                 IncorrectDataFile

Retrieves data from file with a specific character encoding in a horizontal orientation of data

Parameters:

enc - a character encoding

delimiter - the delimiter string in a row (line)

escape - the escape string of a row in the file

type - the type of the data file

Returns:

contained data as DataTable (each table is in correct composition - accessible as horizontal table)

Throws:

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

IncorrectFile - if the opened file is incorrect (not as expected)

IncorrectDataFile - if the opened data file is incorrect.(incorrect data type,

See Also:

DataTable

getHorizontalHeader

public abstract DataTableHeader getHorizontalHeader()
                                             throws java.io.IOException,
                                                    IncorrectDataFile

Retrieves the header of a horizontal data table contained in a file

Returns:

the retrieved DataTableHeader, if the table contains an header. null, otherwise.

Throws:

java.io.IOException

IncorrectDataFile

getVerticalDataTable

public abstract DataTable getVerticalDataTable(java.lang.String enc,
                                               java.lang.String delimiter,
                                               java.lang.String escape)
                                        throws java.io.IOException,
                                               IncorrectFile,
                                               IncorrectDataFile

Retrieves data from file with a specific character encoding in a vertical orientation of data

Parameters:

enc - a character encoding

delimiter - the delimiter string in a row (line)

escape - the escape string of a row in the file

Returns:

contained data as DataTable (each table is in correct composition - accessible as horizontal table)

Throws:

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

IncorrectFile - if the opened file is incorrect (not as expected)

IncorrectDataFile - if the opened data file is incorrect.(incorrect data type,

getVerticalDataTable

public abstract DataTable getVerticalDataTable(java.lang.String enc,
                                               java.lang.String delimiter,
                                               java.lang.String escape,
                                               int type)
                                        throws java.io.IOException,
                                               IncorrectFile,
                                               IncorrectDataFile

Retrieves data from file with a specific character encoding in a vertical orientation of data

Parameters:

enc - a character encoding

delimiter - the delimiter string in a row (line)

escape - the escape string of a row in the file

type - the type of the data file

Returns:

contained data as DataTable (each table is in correct composition - accessible as horizontal table)

Throws:

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

IncorrectFile - if the opened file is incorrect (not as expected)

IncorrectDataFile - if the opened data file is incorrect.(incorrect data type,

See Also:

DataTable

open

public abstract boolean open(java.lang.String enc,
                             java.lang.String delimiter,
                             java.lang.String escape,
                             int type)

Open a data file with a given character encoding , delimiter and escape strings , file orientation and file type

Parameters:

enc -

delimiter -

escape -

type -

Returns:

true, if the file is opened correctly.

See Also:

DataTable

setSheet

public void setSheet(int sheetNumber)

For Microsoft excel workbook, set the sheet to read

Parameters:

sheetNumber - the sheet number to read

setSheet

public void setSheet(java.lang.String sheetName)

For Microsoft excel workbook, set the sheet to read

Parameters:

sheetName - the sheet name to read