org.biolegato.gdesupport.formats
Class FastAFile

java.lang.Object
  javax.swing.filechooser.FileFilter
      org.biolegato.gdesupport.formats.DataFormat
          org.biolegato.gdesupport.formats.FastAFile

public class FastAFile
extends DataFormat

FastA file format parser. NOTE: this parser will automatically detect whether the sequence is protein, RNA or DNA.

Author:

Graham Alvare, Brian Fristensky

Constructor Summary

FastAFile()
Creates a new instance of FastAFile

Method Summary

boolean	accept(java.io.File file) Determines whether or not a specified file is of type GenBank file (based on extension).
java.lang.String	getDescription() Returns a description of the file format that can be displayed to the user.
java.lang.String	getName() Obtains the internal name of the file format (this is great for hashtables storage and searching).
boolean	isFormat(java.io.Reader test) Used to auto-detect Bio Legato formats
Cell[]	translateFrom(java.io.BufferedReader data) Translates data in the FastA file format to sequence objecte
java.lang.String	translateTo(Cell seq) Translates a sequence into the FastA file format.

Methods inherited from class org.biolegato.gdesupport.formats.DataFormat

addFormats, auto, auto, auto, getFormat, readFile, writeFile

Methods inherited from class java.lang.Object

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

Constructor Detail

FastAFile

public FastAFile()

Creates a new instance of FastAFile

Method Detail

translateTo

public java.lang.String translateTo(Cell seq)

Translates a sequence into the FastA file format.

Specified by:

translateTo in class DataFormat

Parameters:

seq - the sequence to translate

Returns:

the resulting string

translateFrom

public Cell[] translateFrom(java.io.BufferedReader data)
                     throws java.io.IOException

Translates data in the FastA file format to sequence objecte

Specified by:

translateFrom in class DataFormat

Parameters:

data - the buffered reader to parse

Returns:

the translated sequences

Throws:

java.io.IOException - any exeptions that occur while reading the stream are passed

accept

public boolean accept(java.io.File file)

Determines whether or not a specified file is of type GenBank file (based on extension). Currently the only extensions supported are ".wrp", ".fasta", and ".fsa".

Specified by:

accept in class javax.swing.filechooser.FileFilter

Parameters:

file - the file to test

Returns:

true if the file is of type FastA file (otherwise false)

See Also:

FileFilter.accept(java.io.File)

getName

public java.lang.String getName()

Obtains the internal name of the file format (this is great for hashtables storage and searching).

Overrides:

getName in class DataFormat

Returns:

the name of the file format

getDescription

public java.lang.String getDescription()

Returns a description of the file format that can be displayed to the user.

Specified by:

getDescription in class javax.swing.filechooser.FileFilter

Returns:

the string description of the file format

See Also:

FileFilter.getDescription()

isFormat

public boolean isFormat(java.io.Reader test)

Used to auto-detect Bio Legato formats

Specified by:

isFormat in class DataFormat

Parameters:

test - the reader to parse data from

Returns:

whether or not the format is correct