src/io/SectionParserManager.cpp

/*
 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
 * [4]  Vardeman & Gezelter, in progress (2009).                        
 */
#include <algorithm> 
#include <stack>
#include <cstdio>
#include "io/SectionParserManager.hpp"
#include "utils/Trim.hpp"
#include "utils/simError.h"

namespace OpenMD {

  SectionParserManager::~SectionParserManager() {
    SectionParserManager::iterator i;
    for (i = sectionParsers_.begin(); i != sectionParsers_.end(); ++i) {
      delete (i->sectionParser);
    }
    sectionParsers_.clear();
  }

  void SectionParserManager::parse(std::istream& input, ForceField& ff) {

    //reset active flags
    SectionParserManager::iterator i;
    for (i = sectionParsers_.begin(); i != sectionParsers_.end(); ++i) {
      i->isActive = false;
    }

    const int bufferSize = 65535;
    char buffer[bufferSize];
    int lineNo = 0;
    std::stack<std::string> sectionNameStack;
    //scan through the input stream and find section names        
    while(input.getline(buffer, bufferSize)) {
      ++lineNo;
        
      std::string line = trimLeftCopy(buffer);
      //a line begins with "//" is a comment line
      if ( line.empty() || (line.size() >= 2 && line[0] == '/' 
                            && line[1] == '/') ) {
        continue;
      } else {        
        StringTokenizer tokenizer(line);
        if (tokenizer.countTokens() < 2) {
          continue;
        } else {
          std::string keyword = tokenizer.nextToken();

          if (keyword == "begin") {
            std::string section = tokenizer.nextToken();
            sectionNameStack.push(section);
 
            i = std::find_if(sectionParsers_.begin(), sectionParsers_.end(),
                       SameSectionParserFunctor(section));
            if (i == sectionParsers_.end()){
              sprintf(painCave.errMsg, 
                "SectionParserManager Error: Can not find corresponding "
                "section parser for %s\n",
                section.c_str());
              painCave.isFatal = 1;
              simError();                        
            } else {
              if (i->isActive) {
          sprintf(painCave.errMsg, "SectionParserManager Error:find multiple %s "
                  "section\n",
                  section.c_str());
          painCave.isFatal = 1;
          simError();                        
              } else {                         
          i->isActive = true;
          i->lineNo = lineNo;
          i->offset = input.tellg();
              }
            }
          } else if (keyword == "end") {
            std::string section = tokenizer.nextToken();
            if (sectionNameStack.top() == section) {
              sectionNameStack.pop();
            } else {
              sprintf(painCave.errMsg, "SectionParserManager Error: begin %s and end %s does not match at line %d\n",
                sectionNameStack.top().c_str(), section.c_str(), lineNo);
              painCave.isFatal = 1;
              simError();
            }
      
          } else {
            continue;
          }
        }
      }
      
    }
    
    if (!sectionNameStack.empty()) {
      sprintf(painCave.errMsg, "SectionParserManager Error: stack is not empty\n");
      painCave.isFatal = 1;
      simError();
    }
    
    //invoke parser
    for (i = sectionParsers_.begin(); i != sectionParsers_.end(); ++i) {
      if (i->isActive) {
        //C++ standard does not guarantee seekg  reset EOF, in that case, seekg will fail
        //It is always a good idea to call clear() before seek
        input.clear();            
        input.seekg(i->offset);
        (i->sectionParser)->parse(input, ff, i->lineNo);
        (i->sectionParser)->validateSection();
      }
    }
    
  }
  
  void SectionParserManager::push_front(SectionParser* sp) {
    SectionParserManager::iterator i;
    i = findSectionParser(sp->getSectionName());
    if (i != sectionParsers_.end()) {
      std::cerr << sp->getSectionName() << " section parser already exists" 
      << std::endl;
      return;
    }
    
    SectionParserContext context;
    
    if (sectionParsers_.empty()) {
      context.priority = beginPriority_;
    } else {
      context.priority = sectionParsers_.front().priority - priorityDifference_;
    }
    
    context.sectionParser = sp;
    context.lineNo = 0;
    context.offset = 0;
    context.isActive = false;

    sectionParsers_.push_front(context);
  }

  void SectionParserManager::push_back(SectionParser* sp) {
    SectionParserManager::iterator i;
    i = findSectionParser(sp->getSectionName());
    if (i != sectionParsers_.end()) {
      std::cerr << sp->getSectionName() << " section parser already exists" 
      << std::endl;
      return;
    }

    SectionParserContext context;    
    if (sectionParsers_.empty()) {
      context.priority = beginPriority_;
    } else {
      context.priority = sectionParsers_.back().priority + priorityDifference_;
    }

    context.sectionParser = sp;
    context.lineNo = 0;
    context.offset = 0;
    context.isActive = false;

    sectionParsers_.push_back(context);

  }

  void SectionParserManager::insert(SectionParser* sp, int priority) {
    SectionParserManager::iterator i;
    i = findSectionParser(sp->getSectionName());
    if (i != sectionParsers_.end()) {
      std::cerr << sp->getSectionName() << " section parser already exists" 
      << std::endl;
    }

    SectionParserContext context;    
    context.priority = priority;
    context.sectionParser = sp;
    context.lineNo = 0;
    context.offset = 0;
    context.isActive = false;

    if (sectionParsers_.empty()) {
      sectionParsers_.push_back(context);
    } else {

      for (i = sectionParsers_.begin(); i != sectionParsers_.end(); ++i) {
        if (i->priority == priority) {
          std::cerr << "Priority " << priority << " already used" << std::endl;
          return;
        } else if (i->priority > priority) {
          sectionParsers_.insert(i, context);
          break;
        }
            
      }
    }

  }


  SectionParserManager::iterator SectionParserManager::findSectionParser(const std::string& sectionName) {
    SectionParserManager::iterator i;
    for (i = sectionParsers_.begin(); i != sectionParsers_.end(); ++i) {
      if (i->sectionParser->getSectionName() == sectionName) {
        break;
      }
    }

    return i;
  }

}
Revision:	1401
Committed:	Wed Jan 6 21:06:59 2010 UTC (15 years, 9 months ago) by jmarr
File size:	8091 byte(s)
Log Message:	Added missing cstdio include lines for gcc 4.4 compatibility
#	User	Rev	Content
1	gezelter	507	/*
2	gezelter	246	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3			*
4			* The University of Notre Dame grants you ("Licensee") a
5			* non-exclusive, royalty free, license to use, modify and
6			* redistribute this software in source and binary code form, provided
7			* that the following conditions are met:
8			*
9	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	gezelter	246	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	gezelter	246	* notice, this list of conditions and the following disclaimer in the
14			* documentation and/or other materials provided with the
15			* distribution.
16			*
17			* This software is provided "AS IS," without a warranty of any
18			* kind. All express or implied conditions, representations and
19			* warranties, including any implied warranty of merchantability,
20			* fitness for a particular purpose or non-infringement, are hereby
21			* excluded. The University of Notre Dame and its licensors shall not
22			* be liable for any damages suffered by licensee as a result of
23			* using, modifying or distributing the software or its
24			* derivatives. In no event will the University of Notre Dame or its
25			* licensors be liable for any lost revenue, profit or data, or for
26			* direct, indirect, special, consequential, incidental or punitive
27			* damages, however caused and regardless of the theory of liability,
28			* arising out of the use of or inability to use software, even if the
29			* University of Notre Dame has been advised of the possibility of
30			* such damages.
31	gezelter	1390	*
32			* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your
33			* research, please cite the appropriate papers when you publish your
34			* work. Good starting points are:
35			*
36			* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37			* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38			* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39			* [4] Vardeman & Gezelter, in progress (2009).
40	gezelter	246	*/
41			#include <algorithm>
42	tim	413	#include <stack>
43	jmarr	1401	#include <cstdio>
44	gezelter	246	#include "io/SectionParserManager.hpp"
45			#include "utils/Trim.hpp"
46	tim	413	#include "utils/simError.h"
47	gezelter	246
48	gezelter	1390	namespace OpenMD {
49	gezelter	246
50	gezelter	507	SectionParserManager::~SectionParserManager() {
51	gezelter	246	SectionParserManager::iterator i;
52			for (i = sectionParsers_.begin(); i != sectionParsers_.end(); ++i) {
53	gezelter	507	delete (i->sectionParser);
54	gezelter	246	}
55			sectionParsers_.clear();
56	gezelter	507	}
57	gezelter	246
58	gezelter	507	void SectionParserManager::parse(std::istream& input, ForceField& ff) {
59	gezelter	246
60			//reset active flags
61			SectionParserManager::iterator i;
62			for (i = sectionParsers_.begin(); i != sectionParsers_.end(); ++i) {
63	gezelter	507	i->isActive = false;
64	gezelter	246	}
65
66			const int bufferSize = 65535;
67			char buffer[bufferSize];
68			int lineNo = 0;
69	tim	413	std::stack<std::string> sectionNameStack;
70	gezelter	246	//scan through the input stream and find section names
71			while(input.getline(buffer, bufferSize)) {
72	gezelter	507	++lineNo;
73	gezelter	246
74	gezelter	507	std::string line = trimLeftCopy(buffer);
75			//a line begins with "//" is a comment line
76	chrisfen	514	if ( line.empty() \|\| (line.size() >= 2 && line[0] == '/'
77			&& line[1] == '/') ) {
78	gezelter	507	continue;
79			} else {
80			StringTokenizer tokenizer(line);
81			if (tokenizer.countTokens() < 2) {
82			continue;
83			} else {
84			std::string keyword = tokenizer.nextToken();
85	gezelter	246
86	gezelter	507	if (keyword == "begin") {
87			std::string section = tokenizer.nextToken();
88			sectionNameStack.push(section);
89	chrisfen	514
90			i = std::find_if(sectionParsers_.begin(), sectionParsers_.end(),
91			SameSectionParserFunctor(section));
92	gezelter	507	if (i == sectionParsers_.end()){
93	chrisfen	514	sprintf(painCave.errMsg,
94			"SectionParserManager Error: Can not find corresponding "
95			"section parser for %s\n",
96			section.c_str());
97	gezelter	507	painCave.isFatal = 1;
98			simError();
99			} else {
100			if (i->isActive) {
101	chrisfen	514	sprintf(painCave.errMsg, "SectionParserManager Error:find multiple %s "
102			"section\n",
103			section.c_str());
104			painCave.isFatal = 1;
105			simError();
106	gezelter	507	} else {
107	chrisfen	514	i->isActive = true;
108			i->lineNo = lineNo;
109			i->offset = input.tellg();
110	gezelter	507	}
111			}
112			} else if (keyword == "end") {
113			std::string section = tokenizer.nextToken();
114			if (sectionNameStack.top() == section) {
115			sectionNameStack.pop();
116			} else {
117			sprintf(painCave.errMsg, "SectionParserManager Error: begin %s and end %s does not match at line %d\n",
118	chrisfen	514	sectionNameStack.top().c_str(), section.c_str(), lineNo);
119	gezelter	507	painCave.isFatal = 1;
120			simError();
121			}
122	chrisfen	514
123	gezelter	507	} else {
124			continue;
125			}
126			}
127			}
128	chrisfen	514
129	gezelter	246	}
130	chrisfen	514
131	tim	413	if (!sectionNameStack.empty()) {
132	gezelter	507	sprintf(painCave.errMsg, "SectionParserManager Error: stack is not empty\n");
133			painCave.isFatal = 1;
134			simError();
135	tim	413	}
136	chrisfen	514
137	gezelter	246	//invoke parser
138			for (i = sectionParsers_.begin(); i != sectionParsers_.end(); ++i) {
139	gezelter	507	if (i->isActive) {
140	chrisfen	514	//C++ standard does not guarantee seekg reset EOF, in that case, seekg will fail
141			//It is always a good idea to call clear() before seek
142			input.clear();
143			input.seekg(i->offset);
144			(i->sectionParser)->parse(input, ff, i->lineNo);
145	tim	749	(i->sectionParser)->validateSection();
146	gezelter	507	}
147	gezelter	246	}
148
149	gezelter	507	}
150	chrisfen	514
151	gezelter	507	void SectionParserManager::push_front(SectionParser* sp) {
152	gezelter	246	SectionParserManager::iterator i;
153			i = findSectionParser(sp->getSectionName());
154			if (i != sectionParsers_.end()) {
155	gezelter	1277	std::cerr << sp->getSectionName() << " section parser already exists"
156	chrisfen	514	<< std::endl;
157	gezelter	507	return;
158	gezelter	246	}
159
160			SectionParserContext context;
161
162			if (sectionParsers_.empty()) {
163	gezelter	507	context.priority = beginPriority_;
164	gezelter	246	} else {
165	gezelter	507	context.priority = sectionParsers_.front().priority - priorityDifference_;
166	gezelter	246	}
167	chrisfen	514
168	gezelter	246	context.sectionParser = sp;
169			context.lineNo = 0;
170			context.offset = 0;
171			context.isActive = false;
172
173			sectionParsers_.push_front(context);
174	gezelter	507	}
175	gezelter	246
176	gezelter	507	void SectionParserManager::push_back(SectionParser* sp) {
177	gezelter	246	SectionParserManager::iterator i;
178			i = findSectionParser(sp->getSectionName());
179			if (i != sectionParsers_.end()) {
180	gezelter	1277	std::cerr << sp->getSectionName() << " section parser already exists"
181	chrisfen	514	<< std::endl;
182	gezelter	507	return;
183	gezelter	246	}
184
185			SectionParserContext context;
186			if (sectionParsers_.empty()) {
187	gezelter	507	context.priority = beginPriority_;
188	gezelter	246	} else {
189	gezelter	507	context.priority = sectionParsers_.back().priority + priorityDifference_;
190	gezelter	246	}
191
192			context.sectionParser = sp;
193			context.lineNo = 0;
194			context.offset = 0;
195			context.isActive = false;
196
197			sectionParsers_.push_back(context);
198
199	gezelter	507	}
200	gezelter	246
201	gezelter	507	void SectionParserManager::insert(SectionParser* sp, int priority) {
202	gezelter	246	SectionParserManager::iterator i;
203			i = findSectionParser(sp->getSectionName());
204			if (i != sectionParsers_.end()) {
205	gezelter	1277	std::cerr << sp->getSectionName() << " section parser already exists"
206	chrisfen	514	<< std::endl;
207	gezelter	246	}
208
209			SectionParserContext context;
210			context.priority = priority;
211			context.sectionParser = sp;
212			context.lineNo = 0;
213			context.offset = 0;
214			context.isActive = false;
215
216			if (sectionParsers_.empty()) {
217	gezelter	507	sectionParsers_.push_back(context);
218	gezelter	246	} else {
219
220	gezelter	507	for (i = sectionParsers_.begin(); i != sectionParsers_.end(); ++i) {
221			if (i->priority == priority) {
222			std::cerr << "Priority " << priority << " already used" << std::endl;
223			return;
224			} else if (i->priority > priority) {
225			sectionParsers_.insert(i, context);
226			break;
227			}
228	gezelter	246
229	gezelter	507	}
230	gezelter	246	}
231
232	gezelter	507	}
233	gezelter	246
234
235	gezelter	507	SectionParserManager::iterator SectionParserManager::findSectionParser(const std::string& sectionName) {
236	gezelter	246	SectionParserManager::iterator i;
237			for (i = sectionParsers_.begin(); i != sectionParsers_.end(); ++i) {
238	gezelter	507	if (i->sectionParser->getSectionName() == sectionName) {
239	chrisfen	514	break;
240	gezelter	507	}
241	gezelter	246	}
242
243			return i;
244	gezelter	507	}
245	gezelter	246
246			}