AFLPcore
Class ImportFilter

java.lang.Object
  |
  +--AFLPcore.Operation
        |
        +--AFLPcore.ImportFilter

Direct Known Subclasses:

ABI3x00Filter, ABILaneFilter, CEQLaneFilter, SCFFilter

public abstract class ImportFilter

extends Operation

This is an abstract class that should be extended to create filters that read data from files. The data files should be of two basic types, gel or lane. A lane file would contain only data for a single lane. A gel file would contain the entire gel In that case, the lanes would have to be tracked and extracted, and then reassembled into a Gel. The filter should size the data using a size standard if neccessary. Support for this may be added elsewhere in the program, in which case, the filter could simply call the approriate methods. Obviously a filter cannot implement both readLane and readGel, so for the one that is not supported, null should be returned. The class ImportMgr can be used to track the different filters. By adding the filters to it, one should be able to have a program that read several different file types.

See Also:

Operation, Lane, Gel, SizeFunction, ImportMgr

Field Summary

protected int	filetype
int	GEL constant to determine type of file filter is used on
int	LANE constant to determine type of file filter is used on

Fields inherited from class AFLPcore.Operation

descript, helpFile, name, options

Constructor Summary

ImportFilter()

Method Summary

abstract int	getFileType() Returns the type of input file supported by this filter, options are ImportFilter.LANE or ImportFilter.GEL.
abstract Gel	readGel(java.io.File inputFile) This is the method that is called to preform the actual reading of the file.
abstract Lane[]	readLane(java.io.File inputFile) This is the method that is called to preform the actual reading of the file.

Methods inherited from class AFLPcore.Operation

getDescription, getHelpFile, getName, getOptions, setOptions

Methods inherited from class java.lang.Object

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

Field Detail

LANE

public final int LANE

constant to determine type of file filter is used on

GEL

public final int GEL

constant to determine type of file filter is used on

filetype

protected int filetype

Constructor Detail

ImportFilter

public ImportFilter()

Method Detail

getFileType

public abstract int getFileType()

Returns the type of input file supported by this filter, options are ImportFilter.LANE or ImportFilter.GEL. This information should be used by the caller to determine which method to call readLane or readGel.

Returns:

either constant GEL or LANE, as described above.

readLane

public abstract Lane[] readLane(java.io.File inputFile)
                         throws java.io.IOException

This is the method that is called to preform the actual reading of the file. The data in the file represents data from a gel. If the filter has any options to be selected, they should be set using the get/setOptions methods. This method should check to see that the options are appropriate before continuing. Note that a filter will only work on one type of data file, gel or lane. Therefore, one of the methods readLane or readGel, will not apply to the filter. For the one that does not apply, null should be returned.

Parameters:

inputFile - The file that contains the lane data.

Returns:

a Lane object with all of the appropriate information. It will return null if the filter reads gels instead of lanes.

Throws:

java.io.IOException - If an error is encountered in the file, then this exception will be thrown

readGel

public abstract Gel readGel(java.io.File inputFile)
                     throws java.io.IOException

This is the method that is called to preform the actual reading of the file. The data in the file represents data from a gel. If the filter has any options to be selected, tose should be set using the get/setOptions methods. This method should check to see that the options are appropriate before continuing. Note that a filter will only work on one type of data file, gel or lane. Therefore, one of the methods readLane or readGel, will not apply to the filter. For the one that does not apply, null should be returned.

Parameters:

inputFile - The file that contains the gel data.

Returns:

a Lane object with all of the appropriate information. It will return null if the filter reads lanes instead of gels.

Throws:

java.io.IOException - If an error is encountered in the file, then this exception will be thrown