prosite.cpp
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- /*
- * ===========================================================================
- * PRODUCTION $Log: prosite.cpp,v $
- * PRODUCTION Revision 1000.2 2004/06/01 20:55:35 gouriano
- * PRODUCTION PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.4
- * PRODUCTION
- * ===========================================================================
- */
- /* $Id: prosite.cpp,v 1000.2 2004/06/01 20:55:35 gouriano Exp $
- * ===========================================================================
- *
- * PUBLIC DOMAIN NOTICE
- * National Center for Biotechnology Information
- *
- * This software/database is a "United States Government Work" under the
- * terms of the United States Copyright Act. It was written as part of
- * the author's official duties as a United States Government employee and
- * thus cannot be copyrighted. This software/database is freely available
- * to the public for use. The National Library of Medicine and the U.S.
- * Government have not placed any restriction on its use or reproduction.
- *
- * Although all reasonable efforts have been taken to ensure the accuracy
- * and reliability of the software and data, the NLM and the U.S.
- * Government do not and cannot warrant the performance or results that
- * may be obtained by using this software or data. The NLM and the U.S.
- * Government disclaim all warranties, express or implied, including
- * warranties of performance, merchantability or fitness for any particular
- * purpose.
- *
- * Please cite the author in any work or product based on this material.
- *
- * ===========================================================================
- *
- * Authors: Josh Cherry
- *
- * File Description: Class for handling prosite-format pattern databases
- *
- */
- #include <ncbi_pch.hpp>
- #include "prosite_entry.hpp"
- #include "prosite.hpp"
- BEGIN_NCBI_SCOPE
- // this function reads a stream in the format of prosite.dat and
- // APPENDS prosite entries to the vector of entries it's handed
- void CProsite::ReadEntries(istream& input, vector<CPrositeEntry>& entries)
- {
- string line;
- CPrositeEntry entry;
- char buffer[4096];
- while (input.getline(buffer, 4096)) {
- line = buffer;
- string ltype = line.substr(0, 2);
- if (ltype == "ID") {
- entry.SetId(line.substr(5));
- } else if (ltype == "DE") {
- entry.SetDesc(line.substr(5));
- } else if (ltype == "DO") {
- entry.SetDoc(line.substr(5));
- } else if (ltype == "AC") {
- entry.SetAccession(line.substr(5));
- } else if (ltype == "PA") {
- entry.SetPattern() += line.substr(5);
- } else if (ltype == "CC") {
- if (line.length() >= 5) {
- if (line.substr(5) == "/SKIP-FLAG=TRUE;") {
- entry.SetSkipFlag(1);
- }
- }
- } else if (ltype == "//") {
- if (!entry.GetPattern().empty()) {
- // get rid of the ending '.' in pattern
- string& pa = entry.SetPattern();
- pa.erase(pa.length() - 1);
- // save the entry
- entries.push_back(entry);
- }
- entry.Reset();
- }
- }
- }
- string CProsite::PSPatternToPCRE(const string& pat)
- {
- list<string> l;
- string re;
- // get elements between the -'s
- NStr::Split(pat, "-", l);
- ITERATE (list<string>, iter, l) {
- re += x_ElementConvert(*iter);
- }
- return re;
- }
- string CProsite::x_ElementConvert(const string& el)
- {
- string rv;
- for(unsigned int i = 0; i < el.length(); i++) {
- switch (char ch = el[i]) {
- case '{':
- rv += "[^";
- break;
- case '}':
- rv += ']';
- break;
- case '(':
- rv += '{';
- break;
- case ')':
- rv += '}';
- break;
- case 'x': case 'X':
- rv += '.';
- break;
- case '<':
- rv += '^';
- break;
- case '>':
- rv += '$';
- break;
- default:
- rv += ch;
- }
- }
- return rv;
- }
- END_NCBI_SCOPE
- /*
- * ===========================================================================
- * $Log: prosite.cpp,v $
- * Revision 1000.2 2004/06/01 20:55:35 gouriano
- * PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.4
- *
- * Revision 1.4 2004/05/21 22:27:47 gorelenk
- * Added PCH ncbi_pch.hpp
- *
- * Revision 1.3 2004/01/27 18:38:07 dicuccio
- * Code clean-up. Use standard names for plugins. Removed unnecessary #includes
- *
- * Revision 1.2 2003/08/15 20:24:47 jcherry
- * Sped up reading of prosite data file
- *
- * Revision 1.1 2003/08/04 20:05:45 jcherry
- * Initial version
- *
- * ===========================================================================
- */