org.geworkbench.components.parsers
Class FileFormat

java.lang.Object
  org.geworkbench.components.parsers.FileFormat

Direct Known Subclasses:

DataSetFileFormat

public abstract class FileFormat
extends java.lang.Object

Version:

$Id: FileFormat.java,v 1.4 2009-10-07 15:38:48 my2248 Exp $ Base class for reading input data files complying to a desired format. Support for any given microarray data format (e.g., Affymetrix MAS 5, GenePix, etc), can be provide as follows:

• Create a new concrete class extending FileFormat and provide method implementations approrpriate for the new format.
• In the configuration file of the application, list an object of the new concrete class as a plugin associated with the extension point titled "input-format".

Author:

my2248

Field Summary

protected java.lang.String

formatName The display name of the format.

Constructor Summary

FileFormat()

Method Summary

abstract boolean	checkFormat(java.io.File file) Checks if the contents of the designated file conform to the format.
abstract java.lang.String[]	getFileExtensions() Return the list of extensions (if any) for the files following this format.
javax.swing.filechooser.FileFilter	getFileFilter()
java.lang.String	getFormatName()
abstract DSDataSet	getMArraySet(java.io.File file) Generates and returns a MicrorarrauSet from the designated argument.
void	getMArraySet(java.io.File file, CSExprMicroarraySet maSet) Generates and returns a MicrorarraySet from the designated argument.
abstract Resource	getResource(java.io.File file) Return a Resource object for the designated file.

Methods inherited from class java.lang.Object

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

Field Detail

formatName

protected java.lang.String formatName

The display name of the format.

Constructor Detail

FileFormat

public FileFormat()

Method Detail

getFormatName

public java.lang.String getFormatName()

Returns:

The format name.

checkFormat

public abstract boolean checkFormat(java.io.File file)
                             throws java.io.InterruptedIOException

Checks if the contents of the designated file conform to the format.

Parameters:

file - File to check.

Returns:

True or false, depending on if the argument is well formed according to the format or not.

Throws:

java.io.InterruptedIOException

getResource

public abstract Resource getResource(java.io.File file)

Return a Resource object for the designated file.

Parameters:

file -

Returns:

getMArraySet

public abstract DSDataSet getMArraySet(java.io.File file)
                                throws InputFileFormatException,
                                       java.io.InterruptedIOException

Generates and returns a MicrorarrauSet from the designated argument. In file does not conform to the format, returns null.

Parameters:

file - The file containing the input data.

Returns:

The corresponding MicroarraySet object.

Throws:

InputFileFormatException

java.io.InterruptedIOException

getMArraySet

public void getMArraySet(java.io.File file,
                         CSExprMicroarraySet maSet)
                  throws InputFileFormatException,
                         java.io.InterruptedIOException

Generates and returns a MicrorarraySet from the designated argument. In file does not conform to the format, returns null.

Parameters:

file - The file containing the input data.

maSet - The set to load the data in

Throws:

InputFileFormatException

java.io.InterruptedIOException

getFileExtensions

public abstract java.lang.String[] getFileExtensions()

Return the list of extensions (if any) for the files following this format.

Returns:

getFileFilter

public javax.swing.filechooser.FileFilter getFileFilter()

Returns:

An (optional) FileFilter to be used in gating the files offered to the user for selection. Useful, e.g., when the files of the format at hand have predefined extensions.