JAligner

jaligner.formats
Class FASTA

java.lang.Object
  extended byjaligner.formats.Format
      extended byjaligner.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

JAligner

Ahmed Moustafa (ahmed@users.sf.net)SourceForge.net
The source code of JAligner is licensed under The GNU General Public License (GPL)