mirror of
http://43.156.76.180:8026/YuuMJ/EukPhylo.git
synced 2025-12-28 07:20:25 +08:00
48 lines
1.7 KiB
C++
48 lines
1.7 KiB
C++
// $Id: phylipFormat.h 1812 2007-03-01 09:29:12Z adist $
|
|
|
|
#ifndef ___PHYLIP_FORMAT
|
|
#define ___PHYLIP_FORMAT
|
|
|
|
#include "definitions.h"
|
|
#include "sequenceContainer.h"
|
|
|
|
class phylipFormat {
|
|
public:
|
|
static sequenceContainer read(istream &infile, const alphabet* alph);
|
|
static void write(ostream &out, const sequenceContainer& sd,
|
|
const int numOfPositionInLine = 50,
|
|
const int spaceEvery = 10);
|
|
//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 PHYLIP FORMAT (interleaved):
|
|
|
|
6 128
|
|
Langur KIFERCELAR TLKKLGLDGY KGVSLANWVC LAKWESGYNT EATNYNPGDE
|
|
Baboon KIFERCELAR TLKRLGLDGY RGISLANWVC LAKWESDYNT QATNYNPGDQ
|
|
Human KVFERCELAR TLKRLGMDGY RGISLANWMC LAKWESGYNT RATNYNAGDR
|
|
Rat KTYERCEFAR TLKRNGMSGY YGVSLADWVC LAQHESNYNT QARNYDPGDQ
|
|
Cow KVFERCELAR TLKKLGLDGY KGVSLANWLC LTKWESSYNT KATNYNPSSE
|
|
Horse KVFSKCELAH KLKAQEMDGF GGYSLANWVC MAEYESNFNT RAFNGKNANG
|
|
|
|
STDYGIFQIN SRYWCNNGKP GAVDACHISC SALLQNNIAD AVACAKRVVS
|
|
STDYGIFQIN SHYWCNDGKP GAVNACHISC NALLQDNITD AVACAKRVVS
|
|
STDYGIFQIN SRYWCNDGKP GAVNACHLSC SALLQDNIAD AVACAKRVVR
|
|
STDYGIFQIN SRYWCNDGKP RAKNACGIPC SALLQDDITQ AIQCAKRVVR
|
|
STDYGIFQIN SKWWCNDGKP NAVDGCHVSC SELMENDIAK AVACAKKIVS
|
|
SSDYGLFQLN NKWWCKDNKR SSSNACNIMC SKLLDENIDD DISCAKRVVR
|
|
|
|
DQGIRAWVAW RNHCQNKDVS QYVKGCGV
|
|
DQGIRAWVAW RNHCQNRDVS QYVQGCGV
|
|
DQGIRAWVAW RNRCQNRDVR QYVQGCGV
|
|
DQGIRAWVAW QRHCKNRDLS GYIRNCGV
|
|
EQGITAWVAW KSHCRDHDVS SYVEGCTL
|
|
DKGMSAWKAW VKHCKDKDLS EYLASCNL
|
|
|
|
|
|
*/
|
|
|