org.biolegato.gdesupport.files
Class FastAFile

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

public class FastAFile
extends DataFormat

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

Author:

Graham Alvare, Brian Fristensky

Field Summary

Fields inherited from class org.biolegato.gdesupport.files.DataFormat

FASTA, FORMAT_LIST, GDEFILE, GDEFLAT, GENBANK

Constructor Summary

FastAFile()
Creates a new instance of FastAFile

Method Summary

boolean	accept(java.io.File file) Determines whether 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.
boolean	isFormat(java.io.Reader test) Used to auto-detect Bio Legato formats
void	translateFrom(Dataset datamodel, java.io.BufferedReader data) Translates data in the FastA file format to sequence objects
void	translateTo(java.lang.Appendable result, Seq seq, int offset, int length) Translates a sequence into the FastA file format.

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

autodetect, getFormat, getName, readFile, readFile, writeAll

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 void translateTo(java.lang.Appendable result,
                        Seq seq,
                        int offset,
                        int length)
                 throws java.io.IOException

Translates a sequence into the FastA file format.

Specified by:

translateTo in class DataFormat

Parameters:

result - the destination for the translated sequence

seq - the sequence to translate

Throws:

java.io.IOException

translateFrom

public void translateFrom(Dataset datamodel,
                          java.io.BufferedReader data)
                   throws java.io.IOException

Translates data in the FastA file format to sequence objects

Specified by:

translateFrom in class DataFormat

Parameters:

datamodel - the location to store the translated sequences

data - the buffered reader to parse

Throws:

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

accept

public boolean accept(java.io.File file)

Determines whether 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)

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 the format is correct