jaligner.formats.CLUSTAL Class Reference

Inheritance diagram for jaligner.formats.CLUSTAL:

Collaboration diagram for jaligner.formats.CLUSTAL:

Public Member Functions
	CLUSTAL ()
String	format (String[] names, String[] sequences)
String	format (Alignment alignment)
Public Member Functions inherited from jaligner.formats.Format
abstract String	format (Alignment alignment)
void	setId (String id)
String	getId ()

Detailed Description

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.nosp@m.@use.nosp@m.rs.sf.nosp@m..net)

Constructor & Destructor Documentation

jaligner.formats.CLUSTAL.CLUSTAL

(

)

Constructor

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Member Function Documentation

String jaligner.formats.CLUSTAL.format	(	String[]	names,
		String[]	sequences
	)

Returns CLUSTAL format

Parameters

names	array of the names of the sequences.
sequences	array of the sequences

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String jaligner.formats.CLUSTAL.format

(

Alignment

alignment

)

Returns CLUSTAL format of the alignment

Parameters

alignment

(Alignment)

Returns

CLUSTAL format of the alignment

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The documentation for this class was generated from the following file:

• java/jaligner/formats/CLUSTAL.java