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48 lines
1.3 KiB
C++
48 lines
1.3 KiB
C++
// $Id: molphyFormat.h 962 2006-11-07 15:13:34Z privmane $
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#ifndef ___MOLPHY_FORMAT
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#define ___MOLPHY_FORMAT
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#include "sequenceContainer.h"
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class molphyFormat{
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public:
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static sequenceContainer read(istream &infile, const alphabet* alph);
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static void write(ostream &out, const sequenceContainer& sd);
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//readUnAligned: the input sequences do not need to be aligned (not all sequences are the same length).
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static sequenceContainer readUnAligned(istream &infile, const alphabet* alph);
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};
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#endif
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/* EXAMPLE OF MOLPHY FORMAT:
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6 128
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Langur
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KIFERCELARTLKKLGLDGYKGVSLANWVCLAKWESGYNTEATNYNPGDESTDYGIFQIN
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SRYWCNNGKPGAVDACHISCSALLQNNIADAVACAKRVVSDQGIRAWVAWRNHCQNKDVS
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QYVKGCGV
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Baboon
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KIFERCELARTLKRLGLDGYRGISLANWVCLAKWESDYNTQATNYNPGDQSTDYGIFQIN
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SHYWCNDGKPGAVNACHISCNALLQDNITDAVACAKRVVSDQGIRAWVAWRNHCQNRDVS
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QYVQGCGV
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Human
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KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQIN
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SRYWCNDGKPGAVNACHLSCSALLQDNIADAVACAKRVVRDQGIRAWVAWRNRCQNRDVR
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QYVQGCGV
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Rat
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KTYERCEFARTLKRNGMSGYYGVSLADWVCLAQHESNYNTQARNYDPGDQSTDYGIFQIN
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SRYWCNDGKPRAKNACGIPCSALLQDDITQAIQCAKRVVRDQGIRAWVAWQRHCKNRDLS
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GYIRNCGV
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Cow
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KVFERCELARTLKKLGLDGYKGVSLANWLCLTKWESSYNTKATNYNPSSESTDYGIFQIN
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SKWWCNDGKPNAVDGCHVSCSELMENDIAKAVACAKKIVSEQGITAWVAWKSHCRDHDVS
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SYVEGCTL
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Horse
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KVFSKCELAHKLKAQEMDGFGGYSLANWVCMAEYESNFNTRAFNGKNANGSSDYGLFQLN
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NKWWCKDNKRSSSNACNIMCSKLLDENIDDDISCAKRVVRDKGMSAWKAWVKHCKDKDLS
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EYLASCNL
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*/
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