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

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

All Implemented Interfaces:

ADFConverterFileReader

Direct Known Subclasses:

PlainTextFileReader, WorkBookFileReaderjxl

public abstract class ADFConverterFileReaderImpl

extends java.lang.Object

implements ADFConverterFileReader

Interface for all file format classes used in reading data

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

ADFConverterFileReaderImpl(java.io.File datafile)
Create an instance of a file reader for a give file

ADFConverterFileReaderImpl(java.io.File datafile, java.lang.String enc)
Create an instance of a file reader for a give file with a given Java character encoding

ADFConverterFileReaderImpl(java.lang.String datafilename)
Create an instance of a file reader for a give file

ADFConverterFileReaderImpl(java.lang.String datafilename, java.lang.String enc)
Create an instance of a file reader for a give file with a given Java character encoding

Method Summary

void	clear() Clear the current object.
abstract void	closeFile() Closes a data text file.
void	finalize() Finalization method that closes the file descriptor.
abstract DataBuffer	getLine() Retrieves a line from a data file Only when termination requirements have been met, the method should return a String object.
int	getLineNumber() Retrieves the line number of current line in the data file
abstract void	openFile() Opens a data file for reading or writing

Methods inherited from class java.lang.Object

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

Constructor Detail

ADFConverterFileReaderImpl

public ADFConverterFileReaderImpl(java.io.File datafile)

Create an instance of a file reader for a give file

Parameters:

datafile - a file to read

ADFConverterFileReaderImpl

public ADFConverterFileReaderImpl(java.io.File datafile,
                                  java.lang.String enc)

Create an instance of a file reader for a give file with a given Java character encoding

Parameters:

datafile - a file to read

enc - a specific Java character encoding for writing

ADFConverterFileReaderImpl

public ADFConverterFileReaderImpl(java.lang.String datafilename)

Create an instance of a file reader for a give file

Parameters:

datafilename - a file to read

ADFConverterFileReaderImpl

public ADFConverterFileReaderImpl(java.lang.String datafilename,
                                  java.lang.String enc)

Create an instance of a file reader for a give file with a given Java character encoding

Parameters:

datafilename - a file to read

enc - a specific Java character encoding for writing

Method Detail

clear

public void clear()

Clear the current object. close the file

closeFile

public abstract void closeFile()

Closes a data text file.

Specified by:

closeFile in interface ADFConverterFileReader

finalize

public void finalize()

Finalization method that closes the file descriptor. This would work only if JVM is current (1.3 or later?).

getLine

public abstract DataBuffer getLine()
                            throws java.io.IOException

Retrieves a line from a data file Only when termination requirements have been met, the method should return a String object.

Specified by:

getLine in interface ADFConverterFileReader

Returns:

line containing data items in one String

Throws:

java.io.IOException - if an error occurs

getLineNumber

public int getLineNumber()

Retrieves the line number of current line in the data file

Specified by:

getLineNumber in interface ADFConverterFileReader

Returns:

the current line number

openFile

public abstract void openFile()
                       throws java.io.IOException

Opens a data file for reading or writing

Specified by:

openFile in interface ADFConverterFileReader

Throws:

java.io.IOException - if an error occurs