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36 lines
1.3 KiB
C++
36 lines
1.3 KiB
C++
// $Id: fastaFormat.h 962 2006-11-07 15:13:34Z privmane $
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#ifndef ___FASTA_FORMAT
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#define ___FASTA_FORMAT
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#include "sequenceContainer.h"
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class fastaFormat{
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public:
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static sequenceContainer read(istream &infile, const alphabet* alph);
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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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static void write(ostream &out, const sequenceContainer& sd);
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};
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#endif
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/* EXAMPLE OF FASTA FORMAT:
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>Langur
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KIFERCELARTLKKLGLDGYKGVSLANWVCLAKWESGYNTEATNYNPGDESTDYGIFQINSRYWCNNGKPGAVDACHISCSALLQNNIADAVACAKRVVSDQGIRAWVAWRNHCQNKDVSQYVKGCGV
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>Baboon
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KIFERCELARTLKRLGLDGYRGISLANWVCLAKWESDYNTQATNYNPGDQSTDYGIFQINSHYWCNDGKPGAVNACHISCNALLQDNITDAVACAKRVVSDQGIRAWVAWRNHCQNRDVSQYVQGCGV
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>Human
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KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKPGAVNACHLSCSALLQDNIADAVACAKRVVRDQGIRAWVAWRNRCQNRDVRQYVQGCGV
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>Rat
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KTYERCEFARTLKRNGMSGYYGVSLADWVCLAQHESNYNTQARNYDPGDQSTDYGIFQINSRYWCNDGKPRAKNACGIPCSALLQDDITQAIQCAKRVVRDQGIRAWVAWQRHCKNRDLSGYIRNCGV
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>Cow
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KVFERCELARTLKKLGLDGYKGVSLANWLCLTKWESSYNTKATNYNPSSESTDYGIFQINSKWWCNDGKPNAVDGCHVSCSELMENDIAKAVACAKKIVSEQGITAWVAWKSHCRDHDVSSYVEGCTL
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>Horse
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KVFSKCELAHKLKAQEMDGFGGYSLANWVCMAEYESNFNTRAFNGKNANGSSDYGLFQLNNKWWCKDNKRSSSNACNIMCSKLLDENIDDDISCAKRVVRDKGMSAWKAWVKHCKDKDLSEYLASCNL
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*/
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