// $Id: molphyFormat.h 962 2006-11-07 15:13:34Z privmane $

#ifndef ___MOLPHY_FORMAT
#define ___MOLPHY_FORMAT

#include "sequenceContainer.h"

class molphyFormat{
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 MOLPHY FORMAT:

6 128
Langur
KIFERCELARTLKKLGLDGYKGVSLANWVCLAKWESGYNTEATNYNPGDESTDYGIFQIN
SRYWCNNGKPGAVDACHISCSALLQNNIADAVACAKRVVSDQGIRAWVAWRNHCQNKDVS
QYVKGCGV
Baboon
KIFERCELARTLKRLGLDGYRGISLANWVCLAKWESDYNTQATNYNPGDQSTDYGIFQIN
SHYWCNDGKPGAVNACHISCNALLQDNITDAVACAKRVVSDQGIRAWVAWRNHCQNRDVS
QYVQGCGV
Human
KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQIN
SRYWCNDGKPGAVNACHLSCSALLQDNIADAVACAKRVVRDQGIRAWVAWRNRCQNRDVR
QYVQGCGV
Rat
KTYERCEFARTLKRNGMSGYYGVSLADWVCLAQHESNYNTQARNYDPGDQSTDYGIFQIN
SRYWCNDGKPRAKNACGIPCSALLQDDITQAIQCAKRVVRDQGIRAWVAWQRHCKNRDLS
GYIRNCGV
Cow
KVFERCELARTLKKLGLDGYKGVSLANWLCLTKWESSYNTKATNYNPSSESTDYGIFQIN
SKWWCNDGKPNAVDGCHVSCSELMENDIAKAVACAKKIVSEQGITAWVAWKSHCRDHDVS
SYVEGCTL
Horse
KVFSKCELAHKLKAQEMDGFGGYSLANWVCMAEYESNFNTRAFNGKNANGSSDYGLFQLN
NKWWCKDNKRSSSNACNIMCSKLLDENIDDDISCAKRVVRDKGMSAWKAWVKHCKDKDLS
EYLASCNL

*/