X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=website%2Farchive%2Fbinaries%2Fmac%2Fsrc%2Fclustalw%2Fsrc%2FfileInput%2FPearsonFileParser.h;fp=website%2Farchive%2Fbinaries%2Fmac%2Fsrc%2Fclustalw%2Fsrc%2FfileInput%2FPearsonFileParser.h;h=d298eef17fd57d8b46b466d461df52f1a24f971e;hb=dbde3fb6f00b9bb770343631a517c0e599db8528;hp=0000000000000000000000000000000000000000;hpb=85f830bbd51a7277994bd4233141016304e210c9;p=jabaws.git diff --git a/website/archive/binaries/mac/src/clustalw/src/fileInput/PearsonFileParser.h b/website/archive/binaries/mac/src/clustalw/src/fileInput/PearsonFileParser.h new file mode 100644 index 0000000..d298eef --- /dev/null +++ b/website/archive/binaries/mac/src/clustalw/src/fileInput/PearsonFileParser.h @@ -0,0 +1,43 @@ +/** + * Author: Mark Larkin + * + * Copyright (c) 2007 Des Higgins, Julie Thompson and Toby Gibson. + */ +/** + * This file is for parsing pearson format files. + * CHANGE: + */ +#ifndef PEARSONFILEPARSER_H +#define PEARSONFILEPARSER_H + +#include +#include "FileParser.h" + +namespace clustalw +{ +using namespace std; + +class PearsonFileParser : public FileParser +{ + public: + /* Functions */ + PearsonFileParser(string filePath); + virtual vector getSeqRange(int firstSeq, int num, string *offendingSeq=NULL); + virtual Sequence getSeq(int seqNum, string *offendingSeq=NULL); + virtual int countSeqs(); + virtual void getSecStructure(vector& gapPenaltyMask, + vector& secStructMask, string& secStructName, + int &structPenalties, int length); + + /* Attributes */ + + private: + /* Functions */ + + /* Attributes */ + string fileName; +}; + +} +#endif +