JAligner

jaligner.formats
Class CLUSTAL

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

public class CLUSTAL
extends Format

CLUSTAL format. Example:

 
 CLUSTAL_FORMAT W(1.60) multiple sequence alignment


 JC2395          NVSDVNLNK---YIWRTAEKMK---ICDAKKFARQHKIPESKIDEIEHNSPQDAAE----
 KPEL_DROME      MAIRLLPLPVRAQLCAHLDAL-----DVWQQLATAVKLYPDQVEQISSQKQRGRS-----
 FASA_MOUSE      NASNLSLSK---YIPRIAEDMT---IQEAKKFARENNIKEGKIDEIMHDSIQDTAE----


 JC2395          -------------------------QKIQLLQCWYQSHGKT--GACQALIQGLRKANRCD
 KPEL_DROME      -------------------------ASNEFLNIWGGQYN----HTVQTLFALFKKLKLHN
 FASA_MOUSE      -------------------------QKVQLLLCWYQSHGKS--DAYQDLIKGLKKAECRR


 JC2395          IAEEIQAM
 KPEL_DROME      AMRLIKDY
 FASA_MOUSE      TLDKFQDM
 
 

Author:
Ahmed Moustafa (ahmed@users.sf.net)

Constructor Summary
CLUSTAL()
          Constructor
 
Method Summary
 java.lang.String format(Alignment alignment)
          Returns CLUSTAL format of the alignment
 java.lang.String format(java.lang.String[] names, java.lang.String[] sequences)
          Returns CLUSTAL format
 
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

CLUSTAL

public CLUSTAL()
Constructor

Method Detail

format

public java.lang.String format(java.lang.String[] names,
                               java.lang.String[] sequences)
Returns CLUSTAL format

Parameters:
names - array of the names of the sequences.
sequences - array of the sequences

format

public java.lang.String format(Alignment alignment)
Returns CLUSTAL format of the alignment

Specified by:
format in class Format
Parameters:
alignment - (Alignment)
Returns:
CLUSTAL format of the 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)