org.geworkbench.components.parsers.sequences
Class SequenceFileFormat

java.lang.Object
  org.geworkbench.components.parsers.FileFormat
      org.geworkbench.components.parsers.microarray.DataSetFileFormat
          org.geworkbench.components.parsers.sequences.SequenceFileFormat

public class SequenceFileFormat
extends DataSetFileFormat

Title: SequenceFileFormat

Description: SequenceFileFormat

Copyright: Copyright (c) 2003

Company: Califano Lab

Version:

1.0

Author:

Saroja Hanasoge

Nested Class Summary

class

SequenceFileFormat.FASTAFilter Defines a FileFilter to be used when the user is prompted to select Affymetrix input files.

Field Summary

Fields inherited from class org.geworkbench.components.parsers.FileFormat

formatName

Constructor Summary

SequenceFileFormat()

Method Summary

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

Methods inherited from class org.geworkbench.components.parsers.microarray.DataSetFileFormat

getDataFile

Methods inherited from class org.geworkbench.components.parsers.FileFormat

getFormatName, getMArraySet

Methods inherited from class java.lang.Object

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

Constructor Detail

SequenceFileFormat

public SequenceFileFormat()

Method Detail

getResource

public Resource getResource(java.io.File file)

Description copied from class: FileFormat

Return a Resource object for the designated file.

Specified by:

getResource in class FileFormat

Returns:

getFileExtensions

public java.lang.String[] getFileExtensions()

Description copied from class: FileFormat

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

Specified by:

getFileExtensions in class FileFormat

Returns:

checkFormat

public boolean checkFormat(java.io.File file)

Description copied from class: FileFormat

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

Specified by:

checkFormat in class FileFormat

Parameters:

file - File to check.

Returns:

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

getDataFile

public DSDataSet getDataFile(java.io.File file)
                      throws InputFileFormatException

Specified by:

getDataFile in class DataSetFileFormat

Throws:

InputFileFormatException

getDataFile

public DSDataSet getDataFile(java.io.File[] files)

Specified by:

getDataFile in class DataSetFileFormat

getMArraySet

public DSMicroarraySet getMArraySet(java.io.File file)

Description copied from class: FileFormat

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

Specified by:

getMArraySet in class FileFormat

Parameters:

file - The file containing the input data.

Returns:

The corresponding MicroarraySet object.

getOptions

public java.util.List getOptions()

getFileFilter

public javax.swing.filechooser.FileFilter getFileFilter()

Overrides:

getFileFilter in class FileFormat

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.