// $Id: nexusFormat.h 5158 2008-11-06 17:44:08Z itaymay $

#ifndef ___NEXUS_FORMAT
#define ___NEXUS_FORMAT

#include "sequenceContainer.h"

class nexusFormat{
public:
	static sequenceContainer read(istream &infile, const alphabet* alph);
	static void write(ostream &out, const sequenceContainer& sd);
	//readUnAligned: the input sequences do not need to be aligned (not all sequences are the same length).
	static sequenceContainer readUnAligned(istream &infile, const alphabet* alph);
};

#endif

/* EXAMPLE OF THE FORMAT:
#NEXUS

begin data;
	dimensions ntax=6 nchar=128;
	format datatype=Protein gap=-;
	matrix
	Horse	KVFSKCELAHKLKAQEMDGFGGYSLANWVCMAEYESNFNTRAFNGKNANGSSDYGLFQLNNKWWCKDNKRSSSNACNIMCSKLLDENIDDDISCAKRVVRDKGMSAWKAWVKHCKDKDLSEYLASCNL
	Langur	KIFERCELARTLKKLGLDGYKGVSLANWVCLAKWESGYNTEATNYNPGDESTDYGIFQINSRYWCNNGKPGAVDACHISCSALLQNNIADAVACAKRVVSDQGIRAWVAWRNHCQNKDVSQYVKGCGV
	Human	KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKPGAVNACHLSCSALLQDNIADAVACAKRVVRDQGIRAWVAWRNRCQNRDVRQYVQGCGV
	Rat	    KTYERCEFARTLKRNGMSGYYGVSLADWVCLAQHESNYNTQARNYDPGDQSTDYGIFQINSRYWCNDGKPRAKNACGIPCSALLQDDITQAIQCAKRVVRDQGIRAWVAWQRHCKNRDLSGYIRNCGV
	Cow	    KVFERCELARTLKKLGLDGYKGVSLANWLCLTKWESSYNTKATNYNPSSESTDYGIFQINSKWWCNDGKPNAVDGCHVSCSELMENDIAKAVACAKKIVSEQGITAWVAWKSHCRDHDVSSYVEGCTL
	Baboon	KIFERCELARTLKRLGLDGYRGISLANWVCLAKWESDYNTQATNYNPGDQSTDYGIFQINSHYWCNDGKPGAVNACHISCNALLQDNITDAVACAKRVVSDQGIRAWVAWRNHCQNRDVSQYVQGCGV
	;
end;

NOTE!!!!
The seqeunces can also be ordered in an "interleaved" way:
Horse	KVFSKCELAHKLKAQEMDGFGGYSLANWVCMAEYESNFNTRAFNGKNANGS
Langur	KIFERCELARTLKKLGLDGYKGVSLANWVCLAKWESGYNTEATNYNPGDES

Horse	SDYGLFQLNNKWWCKDNKRSSSNACNIMCSKLLDENIDDDISCAKRVVRDKGMSAWKAWVKHCKDKDLSEYLASCNL
Langur	TDYGIFQINSRYWCNNGKPGAVDACHISCSALLQNNIADAVACAKRVVSDQGIRAWVAWRNHCQNKDVSQYVKGCGV
*/