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tim |
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/* |
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* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
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* |
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* The University of Notre Dame grants you ("Licensee") a |
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* non-exclusive, royalty free, license to use, modify and |
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* redistribute this software in source and binary code form, provided |
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* that the following conditions are met: |
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* |
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* 1. Acknowledgement of the program authors must be made in any |
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* publication of scientific results based in part on use of the |
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* program. An acceptable form of acknowledgement is citation of |
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* the article in which the program was described (Matthew |
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* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
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* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
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* Parallel Simulation Engine for Molecular Dynamics," |
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* J. Comput. Chem. 26, pp. 252-271 (2005)) |
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* |
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* 2. Redistributions of source code must retain the above copyright |
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* notice, this list of conditions and the following disclaimer. |
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* |
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* 3. Redistributions in binary form must reproduce the above copyright |
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* notice, this list of conditions and the following disclaimer in the |
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* documentation and/or other materials provided with the |
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* distribution. |
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* |
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* This software is provided "AS IS," without a warranty of any |
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* kind. All express or implied conditions, representations and |
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* warranties, including any implied warranty of merchantability, |
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* fitness for a particular purpose or non-infringement, are hereby |
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* excluded. The University of Notre Dame and its licensors shall not |
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* be liable for any damages suffered by licensee as a result of |
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* using, modifying or distributing the software or its |
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* derivatives. In no event will the University of Notre Dame or its |
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* licensors be liable for any lost revenue, profit or data, or for |
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* direct, indirect, special, consequential, incidental or punitive |
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* damages, however caused and regardless of the theory of liability, |
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* arising out of the use of or inability to use software, even if the |
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* University of Notre Dame has been advised of the possibility of |
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* such damages. |
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*/ |
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tim |
283 |
#include <stack> |
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tim |
277 |
#include "selection/SelectionEvaluator.hpp" |
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tim |
283 |
#include "primitives/Atom.hpp" |
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#include "primitives/DirectionalAtom.hpp" |
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#include "primitives/RigidBody.hpp" |
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#include "primitives/Molecule.hpp" |
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tim |
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namespace oopse { |
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tim |
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SelectionEvaluator::SelectionEvaluator(SimInfo* si) : info(si), nameFinder(info), distanceFinder(info), isLoaded_(false){ |
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nStuntDouble = info->getNGlobalAtoms() + info->getNRigidBodies(); |
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tim |
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} |
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tim |
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bool SelectionEvaluator::loadScript(const std::string& filename, const std::string& script) { |
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tim |
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clearDefinitionsAndLoadPredefined(); |
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tim |
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this->filename = filename; |
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this->script = script; |
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if (! compiler.compile(filename, script)) { |
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error = true; |
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errorMessage = compiler.getErrorMessage(); |
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tim |
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std::cerr << "SelectionCompiler Error: " << errorMessage << std::endl; |
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tim |
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return false; |
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} |
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pc = 0; |
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aatoken = compiler.getAatokenCompiled(); |
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linenumbers = compiler.getLineNumbers(); |
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lineIndices = compiler.getLineIndices(); |
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tim |
288 |
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std::vector<std::vector<Token> >::const_iterator i; |
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isDynamic_ = false; |
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for (i = aatoken.begin(); i != aatoken.end(); ++i) { |
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if (containDynamicToken(*i)) { |
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isDynamic_ = true; |
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break; |
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} |
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} |
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isLoaded_ = true; |
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tim |
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return true; |
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tim |
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} |
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tim |
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|
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void SelectionEvaluator::clearState() { |
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tim |
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//for (int i = scriptLevelMax; --i >= 0; ) |
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// stack[i].clear(); |
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//scriptLevel = 0; |
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tim |
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error = false; |
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tim |
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errorMessage = ""; |
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tim |
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} |
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bool SelectionEvaluator::loadScriptString(const std::string& script) { |
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clearState(); |
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tim |
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return loadScript("", script); |
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tim |
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} |
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bool SelectionEvaluator::loadScriptFile(const std::string& filename) { |
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clearState(); |
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return loadScriptFileInternal(filename); |
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} |
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tim |
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bool SelectionEvaluator::loadScriptFileInternal(const std::string & filename) { |
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tim |
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ifstream ifs(filename.c_str()); |
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if (!ifs.is_open()) { |
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return false; |
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} |
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const int bufferSize = 65535; |
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char buffer[bufferSize]; |
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std::string script; |
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while(ifs.getline(buffer, bufferSize)) { |
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script += buffer; |
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} |
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return loadScript(filename, script); |
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tim |
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} |
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tim |
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void SelectionEvaluator::instructionDispatchLoop(BitSet& bs){ |
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tim |
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while ( pc < aatoken.size()) { |
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tim |
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statement = aatoken[pc++]; |
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tim |
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statementLength = statement.size(); |
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tim |
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Token token = statement[0]; |
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switch (token.tok) { |
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tim |
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case Token::define: |
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tim |
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define(); |
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break; |
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tim |
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case Token::select: |
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tim |
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select(bs); |
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tim |
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break; |
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default: |
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unrecognizedCommand(token); |
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return; |
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} |
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} |
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tim |
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tim |
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} |
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tim |
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BitSet SelectionEvaluator::expression(const std::vector<Token>& code, int pcStart) { |
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tim |
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BitSet bs; |
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tim |
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std::stack<BitSet> stack; |
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tim |
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for (int pc = pcStart; pc < code.size(); ++pc) { |
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tim |
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Token instruction = code[pc]; |
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tim |
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tim |
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switch (instruction.tok) { |
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tim |
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case Token::expressionBegin: |
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tim |
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break; |
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tim |
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case Token::expressionEnd: |
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tim |
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break; |
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tim |
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case Token::all: |
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tim |
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bs = BitSet(nStuntDouble); |
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bs.setAll(); |
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stack.push(bs); |
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tim |
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break; |
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tim |
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case Token::none: |
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tim |
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bs = BitSet(nStuntDouble); |
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stack.push(bs); |
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tim |
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break; |
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tim |
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case Token::opOr: |
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tim |
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bs = stack.top(); |
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stack.pop(); |
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stack.top() |= bs; |
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tim |
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break; |
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tim |
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case Token::opAnd: |
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tim |
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bs = stack.top(); |
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stack.pop(); |
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stack.top() &= bs; |
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tim |
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break; |
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tim |
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case Token::opNot: |
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tim |
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stack.top().flip(); |
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tim |
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break; |
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tim |
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case Token::within: |
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tim |
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withinInstruction(instruction, stack.top()); |
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tim |
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break; |
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tim |
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//case Token::selected: |
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// stack.push(getSelectionSet()); |
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// break; |
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tim |
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case Token::name: |
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tim |
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stack.push(nameInstruction(boost::any_cast<std::string>(instruction.value))); |
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tim |
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break; |
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tim |
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case Token::index: |
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stack.push(indexInstruction(instruction.value)); |
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tim |
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break; |
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case Token::identifier: |
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tim |
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stack.push(lookupValue(boost::any_cast<std::string>(instruction.value))); |
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tim |
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break; |
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case Token::opLT: |
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case Token::opLE: |
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case Token::opGE: |
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case Token::opGT: |
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case Token::opEQ: |
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case Token::opNE: |
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tim |
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stack.push(comparatorInstruction(instruction)); |
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tim |
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break; |
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default: |
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unrecognizedExpression(); |
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} |
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} |
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tim |
283 |
if (stack.size() != 1) |
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tim |
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evalError("atom expression compiler error - stack over/underflow"); |
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tim |
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return stack.top(); |
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tim |
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} |
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tim |
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BitSet SelectionEvaluator::comparatorInstruction(const Token& instruction) { |
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tim |
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int comparator = instruction.tok; |
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int property = instruction.intValue; |
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tim |
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float comparisonValue = boost::any_cast<float>(instruction.value); |
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float propertyValue; |
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BitSet bs(nStuntDouble); |
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tim |
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bs.clearAll(); |
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tim |
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SimInfo::MoleculeIterator mi; |
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Molecule* mol; |
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Molecule::AtomIterator ai; |
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Atom* atom; |
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Molecule::RigidBodyIterator rbIter; |
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RigidBody* rb; |
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for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) { |
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tim |
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tim |
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for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
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compareProperty(atom, bs, property, comparator, comparisonValue); |
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} |
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//change the positions of atoms which belong to the rigidbodies |
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for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
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compareProperty(rb, bs, property, comparator, comparisonValue); |
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} |
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tim |
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} |
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tim |
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return bs; |
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} |
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tim |
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tim |
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void SelectionEvaluator::compareProperty(StuntDouble* sd, BitSet& bs, int property, int comparator, float comparisonValue) { |
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double propertyValue; |
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switch (property) { |
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case Token::mass: |
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propertyValue = sd->getMass(); |
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break; |
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case Token::charge: |
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return; |
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//break; |
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case Token::dipole: |
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return; |
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//break; |
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default: |
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unrecognizedAtomProperty(property); |
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} |
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bool match = false; |
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switch (comparator) { |
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case Token::opLT: |
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match = propertyValue < comparisonValue; |
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break; |
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case Token::opLE: |
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match = propertyValue <= comparisonValue; |
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break; |
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case Token::opGE: |
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match = propertyValue >= comparisonValue; |
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break; |
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case Token::opGT: |
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match = propertyValue > comparisonValue; |
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break; |
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case Token::opEQ: |
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match = propertyValue == comparisonValue; |
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break; |
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case Token::opNE: |
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match = propertyValue != comparisonValue; |
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break; |
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} |
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if (match) |
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bs.setBitOn(sd->getGlobalIndex()); |
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} |
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void SelectionEvaluator::withinInstruction(const Token& instruction, BitSet& bs){ |
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tim |
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tim |
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boost::any withinSpec = instruction.value; |
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tim |
295 |
float distance; |
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tim |
282 |
if (withinSpec.type() == typeid(float)){ |
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tim |
295 |
distance = boost::any_cast<float>(withinSpec); |
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} else if (withinSpec.type() == typeid(int)) { |
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distance = boost::any_cast<int>(withinSpec); |
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} else { |
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evalError("casting error in withinInstruction"); |
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bs.clearAll(); |
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tim |
278 |
} |
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tim |
282 |
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tim |
295 |
bs = distanceFinder.find(bs, distance); |
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tim |
278 |
} |
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tim |
283 |
void SelectionEvaluator::define() { |
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tim |
282 |
assert(statement.size() >= 3); |
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std::string variable = boost::any_cast<std::string>(statement[1].value); |
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tim |
283 |
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tim |
281 |
variables.insert(std::make_pair(variable, expression(statement, 2))); |
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tim |
278 |
} |
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tim |
283 |
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tim |
282 |
/** @todo */ |
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void SelectionEvaluator::predefine(const std::string& script) { |
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tim |
278 |
|
| 310 |
tim |
282 |
if (compiler.compile("#predefine", script)) { |
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std::vector<std::vector<Token> > aatoken = compiler.getAatokenCompiled(); |
| 312 |
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if (aatoken.size() != 1) { |
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evalError("predefinition does not have exactly 1 command:" |
| 314 |
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+ script); |
| 315 |
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return; |
| 316 |
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} |
| 317 |
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std::vector<Token> statement = aatoken[0]; |
| 318 |
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if (statement.size() > 2) { |
| 319 |
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int tok = statement[1].tok; |
| 320 |
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if (tok == Token::identifier || (tok & Token::predefinedset) == Token::predefinedset) { |
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tim |
283 |
std::string variable = boost::any_cast<std::string>(statement[1].value); |
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tim |
282 |
variables.insert(std::make_pair(variable, statement)); |
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} else { |
| 325 |
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evalError("invalid variable name:" + script); |
| 326 |
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} |
| 327 |
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}else { |
| 328 |
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evalError("bad predefinition length:" + script); |
| 329 |
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} |
| 330 |
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| 332 |
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} else { |
| 333 |
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evalError("predefined set compile error:" + script + |
| 334 |
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"\ncompile error:" + compiler.getErrorMessage()); |
| 335 |
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} |
| 336 |
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| 337 |
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} |
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| 339 |
tim |
288 |
void SelectionEvaluator::select(BitSet& bs){ |
| 340 |
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bs = expression(statement, 1); |
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tim |
282 |
} |
| 342 |
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| 343 |
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BitSet SelectionEvaluator::lookupValue(const std::string& variable){ |
| 344 |
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| 345 |
tim |
295 |
BitSet bs(nStuntDouble); |
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tim |
282 |
std::map<std::string, boost::any>::iterator i = variables.find(variable); |
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tim |
295 |
|
| 348 |
tim |
282 |
if (i != variables.end()) { |
| 349 |
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if (i->second.type() == typeid(BitSet)) { |
| 350 |
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return boost::any_cast<BitSet>(i->second); |
| 351 |
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} else if (i->second.type() == typeid(std::vector<Token>)){ |
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tim |
295 |
bs = expression(boost::any_cast<std::vector<Token> >(i->second), 2); |
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tim |
282 |
i->second = bs; /**@todo fixme */ |
| 354 |
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return bs; |
| 355 |
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} |
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tim |
283 |
} else { |
| 357 |
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unrecognizedIdentifier(variable); |
| 358 |
tim |
282 |
} |
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tim |
295 |
|
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return bs; |
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tim |
282 |
} |
| 362 |
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tim |
283 |
BitSet SelectionEvaluator::nameInstruction(const std::string& name){ |
| 364 |
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tim |
295 |
return nameFinder.match(name); |
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tim |
288 |
|
| 367 |
tim |
283 |
} |
| 368 |
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tim |
288 |
bool SelectionEvaluator::containDynamicToken(const std::vector<Token>& tokens){ |
| 370 |
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std::vector<Token>::const_iterator i; |
| 371 |
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for (i = tokens.begin(); i != tokens.end(); ++i) { |
| 372 |
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if (i->tok & Token::dynamic) { |
| 373 |
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return true; |
| 374 |
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} |
| 375 |
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} |
| 376 |
tim |
283 |
|
| 377 |
tim |
288 |
return false; |
| 378 |
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} |
| 379 |
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| 380 |
|
|
void SelectionEvaluator::clearDefinitionsAndLoadPredefined() { |
| 381 |
|
|
variables.clear(); |
| 382 |
|
|
//load predefine |
| 383 |
|
|
//predefine(); |
| 384 |
tim |
282 |
} |
| 385 |
tim |
288 |
|
| 386 |
|
|
BitSet SelectionEvaluator::evaluate() { |
| 387 |
|
|
BitSet bs(nStuntDouble); |
| 388 |
|
|
if (isLoaded_) { |
| 389 |
tim |
298 |
pc = 0; |
| 390 |
tim |
288 |
instructionDispatchLoop(bs); |
| 391 |
|
|
} |
| 392 |
|
|
|
| 393 |
|
|
return bs; |
| 394 |
|
|
} |
| 395 |
tim |
295 |
|
| 396 |
|
|
BitSet SelectionEvaluator::indexInstruction(const boost::any& value) { |
| 397 |
|
|
BitSet bs(nStuntDouble); |
| 398 |
|
|
|
| 399 |
|
|
if (value.type() == typeid(int)) { |
| 400 |
|
|
int index = boost::any_cast<int>(value); |
| 401 |
|
|
if (index < 0 || index >= bs.size()) { |
| 402 |
|
|
invalidIndex(index); |
| 403 |
|
|
} else { |
| 404 |
|
|
bs.setBitOn(index); |
| 405 |
|
|
} |
| 406 |
|
|
} else if (value.type() == typeid(std::pair<int, int>)) { |
| 407 |
|
|
std::pair<int, int> indexRange= boost::any_cast<std::pair<int, int> >(value); |
| 408 |
|
|
assert(indexRange.first <= indexRange.second); |
| 409 |
|
|
if (indexRange.first < 0 || indexRange.second >= bs.size()) { |
| 410 |
|
|
invalidIndexRange(indexRange); |
| 411 |
|
|
}else { |
| 412 |
|
|
bs.setRangeOn(indexRange.first, indexRange.second); |
| 413 |
|
|
} |
| 414 |
|
|
} |
| 415 |
|
|
|
| 416 |
|
|
return bs; |
| 417 |
|
|
} |
| 418 |
|
|
|
| 419 |
tim |
288 |
//BitSet SelectionEvaluator::evaluate(int frameNo) { |
| 420 |
|
|
// |
| 421 |
|
|
//} |
| 422 |
|
|
|
| 423 |
|
|
} |