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48 lines
1.6 KiB
C++
48 lines
1.6 KiB
C++
// $Id: clustalFormat.h 962 2006-11-07 15:13:34Z privmane $
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#ifndef ___CLUSTAL_FORMAT
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#define ___CLUSTAL_FORMAT
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#include "sequenceContainer.h"
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class clustalFormat{
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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 THE FORMAT:
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CLUSTAL V
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Langur KIFERCELARTLKKLGLDGYKGVSLANWVCLAKWESGYNTEATNYNPGDESTDYGIFQIN
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Baboon KIFERCELARTLKRLGLDGYRGISLANWVCLAKWESDYNTQATNYNPGDQSTDYGIFQIN
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Human KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQIN
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Rat KTYERCEFARTLKRNGMSGYYGVSLADWVCLAQHESNYNTQARNYDPGDQSTDYGIFQIN
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Cow KVFERCELARTLKKLGLDGYKGVSLANWLCLTKWESSYNTKATNYNPSSESTDYGIFQIN
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Horse KVFSKCELAHKLKAQEMDGFGGYSLANWVCMAEYESNFNTRAFNGKNANGSSDYGLFQLN
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Langur SRYWCNNGKPGAVDACHISCSALLQNNIADAVACAKRVVSDQGIRAWVAWRNHCQNKDVS
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Baboon SHYWCNDGKPGAVNACHISCNALLQDNITDAVACAKRVVSDQGIRAWVAWRNHCQNRDVS
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Human SRYWCNDGKPGAVNACHLSCSALLQDNIADAVACAKRVVRDQGIRAWVAWRNRCQNRDVR
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Rat SRYWCNDGKPRAKNACGIPCSALLQDDITQAIQCAKRVVRDQGIRAWVAWQRHCKNRDLS
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Cow SKWWCNDGKPNAVDGCHVSCSELMENDIAKAVACAKKIVSEQGITAWVAWKSHCRDHDVS
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Horse NKWWCKDNKRSSSNACNIMCSKLLDENIDDDISCAKRVVRDKGMSAWKAWVKHCKDKDLS
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Langur QYVKGCGV
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Baboon QYVQGCGV
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Human QYVQGCGV
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Rat GYIRNCGV
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Cow SYVEGCTL
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Horse EYLASCNL
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*/
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