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43 lines
1.4 KiB
C++
43 lines
1.4 KiB
C++
// $Id: maseFormat.h 962 2006-11-07 15:13:34Z privmane $
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#ifndef ___MASE_FORMAT
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#define ___MASE_FORMAT
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#include "sequenceContainer.h"
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class maseFormat{
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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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;;this is the place for general remarks.
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;here we put sequence specific remark.
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Langur
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KIFERCELARTLKKLGLDGYKGVSLANWVCLAKWESGYNTEATNYNPGDESTDYGIFQINSRYWCNNGKPGAVDACHISCSALLQNNIADAVACAKRVVSDQGIRAWVAWRNHCQNKDVSQYVKGCGV
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;
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Baboon
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KIFERCELARTLKRLGLDGYRGISLANWVCLAKWESDYNTQATNYNPGDQSTDYGIFQINSHYWCNDGKPGAVNACHISCNALLQDNITDAVACAKRVVSDQGIRAWVAWRNHCQNRDVSQYVQGCGV
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;
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Human
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KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKPGAVNACHLSCSALLQDNIADAVACAKRVVRDQGIRAWVAWRNRCQNRDVRQYVQGCGV
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;
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Rat
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KTYERCEFARTLKRNGMSGYYGVSLADWVCLAQHESNYNTQARNYDPGDQSTDYGIFQINSRYWCNDGKPRAKNACGIPCSALLQDDITQAIQCAKRVVRDQGIRAWVAWQRHCKNRDLSGYIRNCGV
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;
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Cow
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KVFERCELARTLKKLGLDGYKGVSLANWLCLTKWESSYNTKATNYNPSSESTDYGIFQINSKWWCNDGKPNAVDGCHVSCSELMENDIAKAVACAKKIVSEQGITAWVAWKSHCRDHDVSSYVEGCTL
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;
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Horse
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KVFSKCELAHKLKAQEMDGFGGYSLANWVCMAEYESNFNTRAFNGKNANGSSDYGLFQLNNKWWCKDNKRSSSNACNIMCSKLLDENIDDDISCAKRVVRDKGMSAWKAWVKHCKDKDLSEYLASCNL
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*/
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