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44 lines
1.8 KiB
C++
44 lines
1.8 KiB
C++
// $Id: nexusFormat.h 5158 2008-11-06 17:44:08Z itaymay $
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#ifndef ___NEXUS_FORMAT
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#define ___NEXUS_FORMAT
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#include "sequenceContainer.h"
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class nexusFormat{
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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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#NEXUS
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begin data;
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dimensions ntax=6 nchar=128;
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format datatype=Protein gap=-;
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matrix
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Horse KVFSKCELAHKLKAQEMDGFGGYSLANWVCMAEYESNFNTRAFNGKNANGSSDYGLFQLNNKWWCKDNKRSSSNACNIMCSKLLDENIDDDISCAKRVVRDKGMSAWKAWVKHCKDKDLSEYLASCNL
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Langur KIFERCELARTLKKLGLDGYKGVSLANWVCLAKWESGYNTEATNYNPGDESTDYGIFQINSRYWCNNGKPGAVDACHISCSALLQNNIADAVACAKRVVSDQGIRAWVAWRNHCQNKDVSQYVKGCGV
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Human KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKPGAVNACHLSCSALLQDNIADAVACAKRVVRDQGIRAWVAWRNRCQNRDVRQYVQGCGV
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Rat KTYERCEFARTLKRNGMSGYYGVSLADWVCLAQHESNYNTQARNYDPGDQSTDYGIFQINSRYWCNDGKPRAKNACGIPCSALLQDDITQAIQCAKRVVRDQGIRAWVAWQRHCKNRDLSGYIRNCGV
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Cow KVFERCELARTLKKLGLDGYKGVSLANWLCLTKWESSYNTKATNYNPSSESTDYGIFQINSKWWCNDGKPNAVDGCHVSCSELMENDIAKAVACAKKIVSEQGITAWVAWKSHCRDHDVSSYVEGCTL
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Baboon KIFERCELARTLKRLGLDGYRGISLANWVCLAKWESDYNTQATNYNPGDQSTDYGIFQINSHYWCNDGKPGAVNACHISCNALLQDNITDAVACAKRVVSDQGIRAWVAWRNHCQNRDVSQYVQGCGV
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;
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end;
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NOTE!!!!
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The seqeunces can also be ordered in an "interleaved" way:
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Horse KVFSKCELAHKLKAQEMDGFGGYSLANWVCMAEYESNFNTRAFNGKNANGS
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Langur KIFERCELARTLKKLGLDGYKGVSLANWVCLAKWESGYNTEATNYNPGDES
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Horse SDYGLFQLNNKWWCKDNKRSSSNACNIMCSKLLDENIDDDISCAKRVVRDKGMSAWKAWVKHCKDKDLSEYLASCNL
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Langur TDYGIFQINSRYWCNNGKPGAVDACHISCSALLQNNIADAVACAKRVVSDQGIRAWVAWRNHCQNKDVSQYVKGCGV
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*/
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