org.geworkbench.components.parsers
Class ExpressionFileFormat

java.lang.Object
  extended by org.geworkbench.components.parsers.FileFormat
      extended by org.geworkbench.components.parsers.microarray.DataSetFileFormat
          extended by org.geworkbench.components.parsers.ExpressionFileFormat

public class ExpressionFileFormat
extends DataSetFileFormat

Title: Sequence and Pattern Plugin

Description:

Copyright: Copyright (c) 2003

Company:

Version:
1.0

Field Summary
 
Fields inherited from class org.geworkbench.components.parsers.FileFormat
formatName
 
Constructor Summary
ExpressionFileFormat()
           
 
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)
          getDataFile
 DSDataSet getDataFile(java.io.File file, java.lang.String compatibilityLabel)
           
 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.
 void getMArraySet(java.io.File file, CSExprMicroarraySet maSet)
          Generates and returns a MicrorarraySet 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.FileFormat
getFormatName
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

ExpressionFileFormat

public ExpressionFileFormat()
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,
                             java.lang.String compatibilityLabel)
                      throws InputFileFormatException
Overrides:
getDataFile in class DataSetFileFormat
Throws:
InputFileFormatException

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.

getMArraySet

public void getMArraySet(java.io.File file,
                         CSExprMicroarraySet maSet)
Description copied from class: FileFormat
Generates and returns a MicrorarraySet from the designated argument. In file does not conform to the format, returns null.

Overrides:
getMArraySet in class FileFormat
Parameters:
file - The file containing the input data.
maSet - The set to load the data in

getDataFile

public DSDataSet getDataFile(java.io.File file)
Specified by:
getDataFile in class DataSetFileFormat

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.

getDataFile

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

Specified by:
getDataFile in class DataSetFileFormat
Parameters:
files - File[]
Returns:
DataSet