jaligner.formats
Class FASTA

java.lang.Object
  jaligner.formats.Format
      jaligner.formats.FASTA

public class FASTA

extends Format

FASTA format.

Author:

Ahmed Moustafa (ahmed@users.sf.net)

Constructor Summary

FASTA()
Constructor for FASTA.

Method Summary

java.lang.String	format(Alignment alignment) Formats alignment
java.lang.String	format(Sequence sequence) Returns the name, description and sequence combined in one string.

Methods inherited from class jaligner.formats.Format

getId, setId

Methods inherited from class java.lang.Object

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

Constructor Detail

FASTA

public FASTA()

Constructor for FASTA.

Method Detail

format

public java.lang.String format(Sequence sequence)

Returns the name, description and sequence combined in one string. The length of each line in the sequence is FASTA.LINE_LENGTH

Returns:

String

format

public java.lang.String format(Alignment alignment)

Description copied from class: Format

Formats alignment

Specified by:

format in class Format

Parameters:

alignment -

Returns:

FASTA format of the input alignment

See Also:

Alignment