jaligner.formats
Class CLUSTAL

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