| [e4afb4] | 1 | /*
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 | 2 |  * Project: MoleCuilder
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 | 3 |  * Description: creates and alters molecular systems
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| [0aa122] | 4 |  * Copyright (C)  2010-2012 University of Bonn. All rights reserved.
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| [94d5ac6] | 5 |  * 
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 | 6 |  *
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 | 7 |  *   This file is part of MoleCuilder.
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 | 8 |  *
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 | 9 |  *    MoleCuilder is free software: you can redistribute it and/or modify
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 | 10 |  *    it under the terms of the GNU General Public License as published by
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 | 11 |  *    the Free Software Foundation, either version 2 of the License, or
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 | 12 |  *    (at your option) any later version.
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 | 13 |  *
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 | 14 |  *    MoleCuilder is distributed in the hope that it will be useful,
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 | 15 |  *    but WITHOUT ANY WARRANTY; without even the implied warranty of
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 | 16 |  *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
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 | 17 |  *    GNU General Public License for more details.
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 | 18 |  *
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 | 19 |  *    You should have received a copy of the GNU General Public License
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 | 20 |  *    along with MoleCuilder.  If not, see <http://www.gnu.org/licenses/>.
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| [e4afb4] | 21 |  */
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 | 22 | 
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 | 23 | /*
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 | 24 |  * CommandLineParser.cpp
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 | 25 |  *
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 | 26 |  *  Created on: May 8, 2010
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 | 27 |  *      Author: heber
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 | 28 |  */
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 | 29 | 
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 | 30 | // include config.h
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 | 31 | #ifdef HAVE_CONFIG_H
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 | 32 | #include <config.h>
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 | 33 | #endif
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 | 34 | 
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| [9eb71b3] | 35 | //#include "CodePatterns/MemDebug.hpp"
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| [e4afb4] | 36 | 
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| [b56827] | 37 | #include <boost/algorithm/string.hpp>
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| [e4afb4] | 38 | #include <boost/filesystem.hpp>
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| [15d21e] | 39 | #include <boost/lexical_cast.hpp>
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 | 40 | #include <boost/program_options/option.hpp>
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 | 41 | #include <boost/program_options/value_semantic.hpp>
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| [e4afb4] | 42 | #include <boost/program_options.hpp>
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 | 43 | #include <fstream>
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 | 44 | #include <iostream>
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| [5a8f38] | 45 | #include <set>
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| [e4afb4] | 46 | #include <map>
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 | 47 | 
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 | 48 | #include "Actions/Action.hpp"
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| [628577] | 49 | #include "Actions/ActionQueue.hpp"
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| [3139b2] | 50 | #include "Actions/ActionTrait.hpp"
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| [e4afb4] | 51 | #include "Actions/OptionRegistry.hpp"
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 | 52 | #include "Actions/OptionTrait.hpp"
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 | 53 | #include "Actions/Values.hpp"
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| [ad011c] | 54 | #include "CodePatterns/Log.hpp"
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 | 55 | #include "CodePatterns/Verbose.hpp"
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| [e4afb4] | 56 | #include "CommandLineParser.hpp"
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| [3a21a7] | 57 | #include "CommandLineParser_validate.hpp"
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| [33e801] | 58 | #include "Parameters/Specifics/KeyValuePair.hpp"
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| [11d433] | 59 | #include "World.hpp"
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| [e4afb4] | 60 | 
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| [ad011c] | 61 | #include "CodePatterns/Singleton_impl.hpp"
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| [e4afb4] | 62 | 
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| [ce7fdc] | 63 | using namespace MoleCuilder;
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 | 64 | 
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| [e4afb4] | 65 | class element;
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 | 66 | 
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 | 67 | /** Constructor of class CommandLineParser.
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 | 68 |  *
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 | 69 |  */
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 | 70 | CommandLineParser::CommandLineParser() :
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 | 71 |   analysis("Analysis options"),
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 | 72 |   atom("Atom options"),
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| [f63e41] | 73 |   bond("Bond options"),
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| [e4afb4] | 74 |   command("Command options"),
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| [a88452] | 75 |   fill("fill options"),
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| [4dc309] | 76 |   shape("shape options"),
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| [e4afb4] | 77 |   fragmentation("Fragmentation options"),
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| [987145] | 78 |   geometry("Geometry options"),
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| [d09093] | 79 |   graph("Graph options"),
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| [e4afb4] | 80 |   molecule("Molecule options"),
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| [d09093] | 81 |   options("Secondary options"),
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| [e4afb4] | 82 |   parser("Parser options"),
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| [f5724f] | 83 |   potential("Potential options"),
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| [e4afb4] | 84 |   selection("Selection options"),
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 | 85 |   tesselation("Tesselation options"),
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| [d09093] | 86 |   world("World options")
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| [e4afb4] | 87 | {
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 | 88 |   // put all options lists into a lookup
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 | 89 |   CmdParserLookup["analysis"] = &analysis;
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 | 90 |   CmdParserLookup["atom"] = &atom;
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| [f63e41] | 91 |   CmdParserLookup["bond"] = &bond;
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| [e4afb4] | 92 |   CmdParserLookup["command"] = &command;
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 | 93 |   CmdParserLookup["edit"] = &edit;
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| [a88452] | 94 |   CmdParserLookup["fill"] = &fill;
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| [4dc309] | 95 |   CmdParserLookup["shape"] = &shape;
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| [e4afb4] | 96 |   CmdParserLookup["fragmentation"] = &fragmentation;
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| [987145] | 97 |   CmdParserLookup["geometry"] = &geometry;
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| [d09093] | 98 |   CmdParserLookup["graph"] = &graph;
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 | 99 |   CmdParserLookup["options"] = &options;
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| [e4afb4] | 100 |   CmdParserLookup["molecule"] = &molecule;
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 | 101 |   CmdParserLookup["parser"] = &parser;
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| [f5724f] | 102 |   CmdParserLookup["potential"] = &potential;
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| [e4afb4] | 103 |   CmdParserLookup["selection"] = &selection;
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 | 104 |   CmdParserLookup["tesselation"] = &tesselation;
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 | 105 |   CmdParserLookup["world"] = &world;
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 | 106 | }
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 | 107 | 
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 | 108 | /** Destructor of class CommandLineParser.
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 | 109 |  *
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 | 110 |  */
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 | 111 | CommandLineParser::~CommandLineParser()
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 | 112 | {}
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 | 113 | 
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 | 114 | /** Initializes command arguments to accept.
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 | 115 |  * Goes through ActionRegistry and puts all actions therein into the map.
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 | 116 |  */
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 | 117 | void CommandLineParser::InitializeCommandArguments()
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 | 118 | {
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| [5a8f38] | 119 |   // we need a list of already added options, otherwise we get ambigious exceptions
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 | 120 |   std::set<std::string> AlreadyAddedOptionNames;
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 | 121 | 
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| [e4afb4] | 122 |   bool ActionAlreadyAdded_flag = false;
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| [690741] | 123 |   ActionQueue &AQ = ActionQueue::getInstance();
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 | 124 |   ActionQueue::ActionTokens_t tokens = AQ.getListOfActions();
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 | 125 |   for (ActionQueue::ActionTokens_t::const_iterator iter = tokens.begin();
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 | 126 |       iter != tokens.end(); ++iter) {
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 | 127 |     const ActionTrait &CurrentTrait = AQ.getActionsTrait(*iter);
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| [e4afb4] | 128 |     ActionAlreadyAdded_flag = false;
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 | 129 |     //std::cout << "Current Action to initialize is: " << actioniter->first << std::endl;
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 | 130 | 
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| [690741] | 131 |     for (ActionTrait::options_const_iterator optioniter = CurrentTrait.getBeginIter();
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 | 132 |         optioniter != CurrentTrait.getEndIter();
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| [e4afb4] | 133 |         ++optioniter) {
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| [690741] | 134 |       if (optioniter->first == *iter)
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| [e4afb4] | 135 |         ActionAlreadyAdded_flag = true;
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 | 136 |       ASSERT( OptionRegistry::getInstance().isOptionPresentByName(optioniter->first),
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| [5a8f38] | 137 |           "CommandLineParser::Init() - Option "+optioniter->first+" not present in OptionRegistry." );
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| [e4afb4] | 138 |       const OptionTrait* const currentOption = OptionRegistry::getInstance().getOptionByName(optioniter->first);
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 | 139 | 
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| [5a8f38] | 140 |       if (AlreadyAddedOptionNames.find(optioniter->first) == AlreadyAddedOptionNames.end()) {
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 | 141 |         // add the option
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 | 142 | //        std::cout << "Registering Option "
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 | 143 | //            << currentOption->getName()
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 | 144 | //            << " with type '" << currentOption->getTypeName() << "' "
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 | 145 | //            << " with description '" << currentOption->getDescription() << "' ";
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 | 146 | //        if (currentOption->hasShortForm())
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 | 147 | //          std::cout << ", with short form " << currentOption->getShortForm();
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 | 148 | //        else
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 | 149 | //          std::cout << ", with no short form ";
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 | 150 | //        if (currentOption->hasDefaultValue())
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 | 151 | //          std::cout << ", with default value " << currentOption->getDefaultValue();
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 | 152 | //        else
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 | 153 | //          std::cout << ", with no default value ";
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 | 154 | //        std::cout << std::endl;
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 | 155 | 
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| [7912e9] | 156 |         AddOptionToParser(currentOption, (CmdParserLookup["options"]),
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 | 157 |             (optioniter->first == *iter) ?
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 | 158 |                 true : false);
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| [5a8f38] | 159 | 
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 | 160 |         AlreadyAddedOptionNames.insert(optioniter->first);
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 | 161 |       } else {
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 | 162 | //        std::cout << "Option " << currentOption->getName() << " already registered." << std::endl;
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 | 163 |       }
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| [e4afb4] | 164 |     }
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 | 165 | 
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 | 166 |     if (!ActionAlreadyAdded_flag) {
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 | 167 |       // add the action
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| [ad7270] | 168 | //      std::cout << "Registering Action "
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 | 169 | //          << currentAction->Traits.getName()
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 | 170 | //          << " in menu " << currentAction->Traits.getMenuName()
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 | 171 | //          << " with type '" << currentAction->Traits.getTypeName() << "' "
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 | 172 | //          << " with description '" << currentAction->Traits.getDescription() << "' ";
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 | 173 | //      if (currentAction->Traits.hasShortForm())
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 | 174 | //        std::cout << ", with short form " << currentAction->Traits.getShortForm();
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 | 175 | //      else
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 | 176 | //        std::cout << ", with no short form ";
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 | 177 | //      if (currentAction->Traits.hasDefaultValue())
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 | 178 | //        std::cout << ", with default value " << currentAction->Traits.getDefaultValue();
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 | 179 | //      else
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 | 180 | //        std::cout << ", with no default value ";
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 | 181 | //      std::cout  << std::endl;
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| [e4afb4] | 182 | 
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| [690741] | 183 |       ASSERT(CmdParserLookup.find(CurrentTrait.getMenuName()) != CmdParserLookup.end(),
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| [e4afb4] | 184 |           "CommandLineParser: boost::program_options::options_description for this Action not present.");
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| [7912e9] | 185 |       AddOptionToParser(
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 | 186 |           dynamic_cast<const OptionTrait * const>(&CurrentTrait),
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 | 187 |           (CmdParserLookup[CurrentTrait.getMenuName()]),
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 | 188 |           false);
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| [e4afb4] | 189 |     }
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 | 190 |   }
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 | 191 |   // note: positioning is not important on the command line
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 | 192 | }
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 | 193 | 
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| [b56827] | 194 | /**
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 | 195 |  * This is a fix by Benedek Thaler given on the boost mailing list to get back
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 | 196 |  * to the old behavior before the breaking change in 1.63 for
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 | 197 |  * boost::program_options.
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 | 198 |  *
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 | 199 |  * The problem is that for an implicit value "-a foo" will not recognize the
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 | 200 |  * value for "a". It now needs to read "-a=foo" to store the value "foo" for
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 | 201 |  * the action "a". This broke our behavior for all action that have same-named
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 | 202 |  * options.
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 | 203 |  *
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 | 204 |  * See https://lists.boost.org/Archives/boost/2017/01/232272.php
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 | 205 |  */
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| [30def8] | 206 | #if BOOST_VERSION >= 106300 and BOOST_VERSION < 106900
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| [b56827] | 207 | template <typename T>
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 | 208 | struct greedy_implicit_value : public po::typed_value<T>
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 | 209 | {
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 | 210 |   using base = po::typed_value<T>;
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 | 211 | 
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 | 212 |   greedy_implicit_value(const T& value) : base(nullptr)
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 | 213 |   {
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 | 214 |     base::implicit_value(value);
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 | 215 |   }
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 | 216 | 
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 | 217 |   bool adjacent_tokens_only() const override { return false; }
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 | 218 | unsigned max_tokens() const override { return 1; }
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 | 219 | };
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 | 220 | 
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 | 221 | template <typename T>
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 | 222 | po::typed_value<T>* implicit_value(const T& value)
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 | 223 | {
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 | 224 |   return new greedy_implicit_value<T>(value);
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 | 225 | }
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| [30def8] | 226 | #endif
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 | 227 | #if BOOST_VERSION < 106300
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| [b56827] | 228 | template <typename T>
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 | 229 | po::typed_value<T>* implicit_value(const T& value)
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 | 230 | {
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 | 231 |   return new po::typed_value<T>()->implicit_value(value);
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 | 232 | }
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 | 233 | #endif
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| [30def8] | 234 | #if BOOST_VERSION >= 106900
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 | 235 | template <typename T>
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 | 236 | po::typed_value<T>* implicit_value(const T& value)
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 | 237 | {
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 | 238 |   return (new po::typed_value<T>(NULL))->implicit_value(value);
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 | 239 | }
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 | 240 | #endif
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| [b56827] | 241 | 
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 | 242 | 
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| [e4afb4] | 243 | /** Adds an Action or Option to the CommandLineParser.
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 | 244 |  * Note that Action is derived from Option(Trait)
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 | 245 |  *
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 | 246 |  * This ugly switch function is necessary because of the compile-time problem:
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 | 247 |  * po::value<T> has to be instantiated at compile-time however we do know the type not until run-time.
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 | 248 |  * Not even a templated function like po::value<T> getProgramOptionValuefromType() does help, specialized
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 | 249 |  * to each available type, as the signatures of all the functions differ. Hence, they cannot not put into
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 | 250 |  * one type_info -> po::value<T> map ...
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 | 251 |  *
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 | 252 |  * \param *currentOption pointer to Action/Option to add
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 | 253 |  * \param *OptionList program_options list to add to
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| [7912e9] | 254 |  * \param _DefaultAsImplicit whether to add a default value as default_value or
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 | 255 |  *        as implicit_value (default = option token present or not, implicit =
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 | 256 |           option token present but not necessarily followed by argument)
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| [e4afb4] | 257 |  */
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| [7912e9] | 258 | void CommandLineParser::AddOptionToParser(
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 | 259 |     const OptionTrait * const currentOption, 
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 | 260 |     po::options_description* OptionList,
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 | 261 |     const bool _DefaultAsImplicit)
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| [e4afb4] | 262 | {
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 | 263 |   // check whether dynamic_cast in Init() suceeded
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 | 264 |   ASSERT(currentOption != NULL, "CommandLineParser::AddOptionToParser() - currentOption is NULL!");
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 | 265 |   // add other options
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| [ec098d] | 266 | //  std::cout << "Adding Action " << currentOption->getName() << " with type "
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 | 267 | //      << currentOption->getType()->name() << ", " << (currentOption->hasDefaultValue() ? "with" : "without")
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 | 268 | //      << " default value, and KeyandShortform " << currentOption->getKeyAndShortForm()
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 | 269 | //      << " to CommandLineParser." << std::endl;
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| [e4afb4] | 270 |   switch(TypeToEnums.getEnumforType(currentOption->getType())) {
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 | 271 |     default:
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 | 272 |     case TypeEnumContainer::NoneType:
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 | 273 |       OptionList->add_options()
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 | 274 |         (currentOption->getKeyAndShortForm().c_str(), currentOption->getDescription().c_str())
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 | 275 |         ;
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 | 276 |       break;
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 | 277 |     case TypeEnumContainer::BooleanType:
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 | 278 |       OptionList->add_options()
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 | 279 |         (currentOption->getKeyAndShortForm().c_str(),
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 | 280 |             currentOption->hasDefaultValue() ?
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| [7912e9] | 281 |                   (_DefaultAsImplicit ? 
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| [b56827] | 282 |                       implicit_value(bool(boost::lexical_cast<int>(currentOption->getDefaultValue().c_str()))) :
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| [7912e9] | 283 |                       po::value < bool >()->default_value(boost::lexical_cast<int>(currentOption->getDefaultValue().c_str()))) :
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| [e4afb4] | 284 |                   po::value < bool >(),
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 | 285 |                   currentOption->getDescription().c_str())
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 | 286 |         ;
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 | 287 |       break;
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 | 288 |     case TypeEnumContainer::FileType:
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 | 289 |       OptionList->add_options()
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 | 290 |         (currentOption->getKeyAndShortForm().c_str(),
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 | 291 | //            currentOption->hasDefaultValue() ?
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 | 292 | //                  po::value < boost::filesystem::path >()->default_value(boost::lexical_cast<boost::filesystem::path>(currentOption->getDefaultValue().c_str())) :
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 | 293 |                   po::value < boost::filesystem::path >(),
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 | 294 |                   currentOption->getDescription().c_str())
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 | 295 |         ;
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 | 296 |       break;
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 | 297 |     case TypeEnumContainer::ListOfFilesType:
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 | 298 |       OptionList->add_options()
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 | 299 |         (currentOption->getKeyAndShortForm().c_str(),
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 | 300 | //            currentOption->hasDefaultValue() ?
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 | 301 | //                  po::value < std::vector<boost::filesystem::path> >()->default_value(boost::lexical_cast< std::vector<boost::filesystem::path> >(currentOption->getDefaultValue().c_str())) :
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 | 302 |                   po::value < std::vector<boost::filesystem::path> >()->multitoken(),
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 | 303 |                   currentOption->getDescription().c_str())
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 | 304 |         ;
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 | 305 |       break;
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 | 306 |     case TypeEnumContainer::IntegerType:
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 | 307 |       OptionList->add_options()
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 | 308 |         (currentOption->getKeyAndShortForm().c_str(),
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 | 309 |             currentOption->hasDefaultValue() ?
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| [7912e9] | 310 |                   (_DefaultAsImplicit ? 
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| [b56827] | 311 |                       implicit_value(boost::lexical_cast<int>(currentOption->getDefaultValue().c_str())) :
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| [7912e9] | 312 |                       po::value < int >()->default_value(boost::lexical_cast<int>(currentOption->getDefaultValue().c_str()))) :
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| [e4afb4] | 313 |                   po::value < int >(),
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 | 314 |                   currentOption->getDescription().c_str())
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 | 315 |         ;
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 | 316 |       break;
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 | 317 |     case TypeEnumContainer::ListOfIntegersType:
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 | 318 |       OptionList->add_options()
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 | 319 |         (currentOption->getKeyAndShortForm().c_str(),
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 | 320 | //            currentOption->hasDefaultValue() ?
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 | 321 | //                  po::value < std::vector<int> >()->default_value(boost::lexical_cast< std::vector<int> >(currentOption->getDefaultValue().c_str())) :
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 | 322 |                   po::value < std::vector<int> >()->multitoken(),
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 | 323 |                   currentOption->getDescription().c_str())
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 | 324 |         ;
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 | 325 |       break;
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| [838cd0] | 326 |     case TypeEnumContainer::UnsignedIntegerType:
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 | 327 |       OptionList->add_options()
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 | 328 |         (currentOption->getKeyAndShortForm().c_str(),
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 | 329 |             currentOption->hasDefaultValue() ?
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| [7912e9] | 330 |                   (_DefaultAsImplicit ? 
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| [b56827] | 331 |                       implicit_value(boost::lexical_cast<unsigned int>(currentOption->getDefaultValue().c_str())) :
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| [7912e9] | 332 |                       po::value < unsigned int >()->default_value(boost::lexical_cast<unsigned int>(currentOption->getDefaultValue().c_str()))) :
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| [838cd0] | 333 |                   po::value < unsigned int >(),
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 | 334 |                   currentOption->getDescription().c_str())
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 | 335 |         ;
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 | 336 |       break;
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| [12948c] | 337 |     case TypeEnumContainer::ListOfUnsignedIntegersType:
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 | 338 |       OptionList->add_options()
 | 
|---|
 | 339 |         (currentOption->getKeyAndShortForm().c_str(),
 | 
|---|
 | 340 | //            currentOption->hasDefaultValue() ?
 | 
|---|
 | 341 | //                  po::value < std::vector<unsigned int> >()->default_value(boost::lexical_cast< std::vector<unsigned int> >(currentOption->getDefaultValue().c_str())) :
 | 
|---|
 | 342 |                   po::value < std::vector<unsigned int> >()->multitoken(),
 | 
|---|
 | 343 |                   currentOption->getDescription().c_str())
 | 
|---|
 | 344 |         ;
 | 
|---|
 | 345 |       break;
 | 
|---|
| [e4afb4] | 346 |     case TypeEnumContainer::DoubleType:
 | 
|---|
 | 347 |       OptionList->add_options()
 | 
|---|
 | 348 |         (currentOption->getKeyAndShortForm().c_str(),
 | 
|---|
 | 349 |             currentOption->hasDefaultValue() ?
 | 
|---|
| [7912e9] | 350 |                   (_DefaultAsImplicit ? 
 | 
|---|
| [b56827] | 351 |                       implicit_value(boost::lexical_cast<double>(currentOption->getDefaultValue().c_str())) :
 | 
|---|
| [7912e9] | 352 |                       po::value < double >()->default_value(boost::lexical_cast<double>(currentOption->getDefaultValue().c_str()))) :
 | 
|---|
| [e4afb4] | 353 |                   po::value < double >(),
 | 
|---|
 | 354 |                   currentOption->getDescription().c_str())
 | 
|---|
 | 355 |         ;
 | 
|---|
 | 356 |       break;
 | 
|---|
 | 357 |     case TypeEnumContainer::ListOfDoublesType:
 | 
|---|
 | 358 |       OptionList->add_options()
 | 
|---|
 | 359 |         (currentOption->getKeyAndShortForm().c_str(),
 | 
|---|
 | 360 | //            currentOption->hasDefaultValue() ?
 | 
|---|
 | 361 | //                  po::value < std::vector<double> >()->default_value(boost::lexical_cast< std::vector<double> >(currentOption->getDefaultValue().c_str())) :
 | 
|---|
 | 362 |                   po::value < std::vector<double> >()->multitoken(),
 | 
|---|
 | 363 |                   currentOption->getDescription().c_str())
 | 
|---|
 | 364 |         ;
 | 
|---|
 | 365 |       break;
 | 
|---|
 | 366 |     case TypeEnumContainer::StringType:
 | 
|---|
 | 367 |       OptionList->add_options()
 | 
|---|
 | 368 |         (currentOption->getKeyAndShortForm().c_str(),
 | 
|---|
 | 369 |             currentOption->hasDefaultValue() ?
 | 
|---|
| [7912e9] | 370 |                   (_DefaultAsImplicit ? 
 | 
|---|
| [b56827] | 371 |                       implicit_value(currentOption->getDefaultValue()) :
 | 
|---|
| [7912e9] | 372 |                       po::value < std::string >()->default_value(currentOption->getDefaultValue())) :
 | 
|---|
| [e4afb4] | 373 |                   po::value < std::string >(),
 | 
|---|
 | 374 |                   currentOption->getDescription().c_str())
 | 
|---|
 | 375 |         ;
 | 
|---|
 | 376 |       break;
 | 
|---|
 | 377 |     case TypeEnumContainer::ListOfStringsType:
 | 
|---|
 | 378 |       OptionList->add_options()
 | 
|---|
 | 379 |         (currentOption->getKeyAndShortForm().c_str(),
 | 
|---|
 | 380 | //            currentOption->hasDefaultValue() ?
 | 
|---|
 | 381 | //                  po::value < std::vector<std::string> >()->default_value(boost::lexical_cast< std::vector<std::string> >(currentOption->getDefaultValue().c_str())) :
 | 
|---|
 | 382 |                   po::value < std::vector<std::string> >()->multitoken(),
 | 
|---|
 | 383 |                   currentOption->getDescription().c_str())
 | 
|---|
 | 384 |         ;
 | 
|---|
 | 385 |       break;
 | 
|---|
 | 386 |     case TypeEnumContainer::VectorType:
 | 
|---|
 | 387 |       OptionList->add_options()
 | 
|---|
 | 388 |         (currentOption->getKeyAndShortForm().c_str(),
 | 
|---|
 | 389 | //            currentOption->hasDefaultValue() ?
 | 
|---|
 | 390 | //                  po::value < VectorValue >()->default_value(boost::lexical_cast<VectorValue>(currentOption->getDefaultValue().c_str())) :
 | 
|---|
 | 391 |                   po::value < VectorValue >(),
 | 
|---|
 | 392 |                   currentOption->getDescription().c_str())
 | 
|---|
 | 393 |         ;
 | 
|---|
 | 394 |       break;
 | 
|---|
 | 395 |     case TypeEnumContainer::ListOfVectorsType:
 | 
|---|
 | 396 |       OptionList->add_options()
 | 
|---|
 | 397 |         (currentOption->getKeyAndShortForm().c_str(),
 | 
|---|
 | 398 | //            currentOption->hasDefaultValue() ?
 | 
|---|
 | 399 | //                  po::value < std::vector<VectorValue> >()->default_value(boost::lexical_cast< std::vector<VectorValue> >(currentOption->getDefaultValue().c_str())) :
 | 
|---|
 | 400 |                   po::value < std::vector<VectorValue> >()->multitoken(),
 | 
|---|
 | 401 |                   currentOption->getDescription().c_str())
 | 
|---|
 | 402 |         ;
 | 
|---|
 | 403 |       break;
 | 
|---|
 | 404 |     case TypeEnumContainer::MoleculeType:
 | 
|---|
 | 405 |       OptionList->add_options()
 | 
|---|
 | 406 |         (currentOption->getKeyAndShortForm().c_str(),
 | 
|---|
 | 407 | //            currentOption->hasDefaultValue() ?
 | 
|---|
 | 408 | //                  po::value < const molecule * >()->default_value(boost::lexical_cast<const molecule *>(currentOption->getDefaultValue().c_str())) :
 | 
|---|
 | 409 |                   po::value < int >(),
 | 
|---|
 | 410 |                   currentOption->getDescription().c_str())
 | 
|---|
 | 411 |         ;
 | 
|---|
 | 412 |       break;
 | 
|---|
 | 413 |     case TypeEnumContainer::ListOfMoleculesType:
 | 
|---|
 | 414 |       OptionList->add_options()
 | 
|---|
 | 415 |         (currentOption->getKeyAndShortForm().c_str(),
 | 
|---|
 | 416 | //            currentOption->hasDefaultValue() ?
 | 
|---|
 | 417 | //                  po::value < std::vector<const molecule *> >()->default_value(boost::lexical_cast< std::vector<const molecule *> >(currentOption->getDefaultValue().c_str())) :
 | 
|---|
 | 418 |                   po::value < std::vector<int> >()->multitoken(),
 | 
|---|
 | 419 |                   currentOption->getDescription().c_str())
 | 
|---|
 | 420 |         ;
 | 
|---|
 | 421 |       break;
 | 
|---|
 | 422 |     case TypeEnumContainer::AtomType:
 | 
|---|
 | 423 |       OptionList->add_options()
 | 
|---|
 | 424 |         (currentOption->getKeyAndShortForm().c_str(),
 | 
|---|
 | 425 |             currentOption->hasDefaultValue() ?
 | 
|---|
| [7912e9] | 426 |                   (_DefaultAsImplicit ? 
 | 
|---|
| [b56827] | 427 |                       implicit_value(boost::lexical_cast<int>(currentOption->getDefaultValue().c_str())) :
 | 
|---|
| [7912e9] | 428 |                       po::value < int >()->default_value(boost::lexical_cast<int>(currentOption->getDefaultValue().c_str()))) :
 | 
|---|
| [e4afb4] | 429 |                   po::value < int >(),
 | 
|---|
 | 430 |                   currentOption->getDescription().c_str())
 | 
|---|
 | 431 |         ;
 | 
|---|
 | 432 |       break;
 | 
|---|
 | 433 |     case TypeEnumContainer::ListOfAtomsType:
 | 
|---|
 | 434 |       OptionList->add_options()
 | 
|---|
 | 435 |         (currentOption->getKeyAndShortForm().c_str(),
 | 
|---|
 | 436 | //            currentOption->hasDefaultValue() ?
 | 
|---|
 | 437 | //                  po::value < std::vector<const atom *> >()->default_value(boost::lexical_cast< std::vector<const atom *> >(currentOption->getDefaultValue().c_str())) :
 | 
|---|
 | 438 |                   po::value < std::vector<int> >()->multitoken(),
 | 
|---|
 | 439 |                   currentOption->getDescription().c_str())
 | 
|---|
 | 440 |         ;
 | 
|---|
 | 441 |       break;
 | 
|---|
 | 442 |     case TypeEnumContainer::ElementType:
 | 
|---|
 | 443 |       OptionList->add_options()
 | 
|---|
 | 444 |         (currentOption->getKeyAndShortForm().c_str(),
 | 
|---|
 | 445 | //            currentOption->hasDefaultValue() ?
 | 
|---|
 | 446 | //                  po::value < const element * >()->default_value(boost::lexical_cast<const element *>(currentOption->getDefaultValue().c_str())) :
 | 
|---|
| [2f429e] | 447 |                   po::value < std::string >(),
 | 
|---|
| [e4afb4] | 448 |                   currentOption->getDescription().c_str())
 | 
|---|
 | 449 |         ;
 | 
|---|
 | 450 |       break;
 | 
|---|
 | 451 |     case TypeEnumContainer::ListOfElementsType:
 | 
|---|
 | 452 |       OptionList->add_options()
 | 
|---|
 | 453 |         (currentOption->getKeyAndShortForm().c_str(),
 | 
|---|
 | 454 | //            currentOption->hasDefaultValue() ?
 | 
|---|
 | 455 | //                  po::value < std::vector<const element *> >()->default_value(boost::lexical_cast< std::vector<const element *> >(currentOption->getDefaultValue().c_str())) :
 | 
|---|
| [2f429e] | 456 |                   po::value < std::vector<std::string> >()->multitoken(),
 | 
|---|
| [e4afb4] | 457 |                   currentOption->getDescription().c_str())
 | 
|---|
 | 458 |         ;
 | 
|---|
 | 459 |       break;
 | 
|---|
| [7d9416] | 460 |     case TypeEnumContainer::RealSpaceMatrixType:
 | 
|---|
 | 461 |       OptionList->add_options()
 | 
|---|
 | 462 |         (currentOption->getKeyAndShortForm().c_str(),
 | 
|---|
 | 463 | //            currentOption->hasDefaultValue() ?
 | 
|---|
 | 464 | //                  po::value < RealSpaceMatrixValue >()->default_value(boost::lexical_cast<BoxValue>(currentOption->getDefaultValue().c_str())) :
 | 
|---|
 | 465 |                   po::value < RealSpaceMatrixValue >(),
 | 
|---|
 | 466 |                   currentOption->getDescription().c_str())
 | 
|---|
 | 467 |         ;
 | 
|---|
 | 468 |       break;
 | 
|---|
| [33e801] | 469 |     case TypeEnumContainer::KeyValueType:
 | 
|---|
 | 470 |       OptionList->add_options()
 | 
|---|
 | 471 |         (currentOption->getKeyAndShortForm().c_str(),
 | 
|---|
 | 472 |             currentOption->hasDefaultValue() ?
 | 
|---|
 | 473 |                   (_DefaultAsImplicit ?
 | 
|---|
| [b56827] | 474 |                       implicit_value(boost::lexical_cast< KeyValuePair >(currentOption->getDefaultValue().c_str())) :
 | 
|---|
| [33e801] | 475 |                       po::value < KeyValuePair >()->default_value(boost::lexical_cast< KeyValuePair >(currentOption->getDefaultValue().c_str()))) :
 | 
|---|
 | 476 |                   po::value < KeyValuePair >(),
 | 
|---|
 | 477 |                   currentOption->getDescription().c_str())
 | 
|---|
 | 478 |         ;
 | 
|---|
 | 479 |       break;
 | 
|---|
 | 480 |     case TypeEnumContainer::ListOfKeyValuesType:
 | 
|---|
 | 481 |       OptionList->add_options()
 | 
|---|
 | 482 |         (currentOption->getKeyAndShortForm().c_str(),
 | 
|---|
 | 483 | //            currentOption->hasDefaultValue() ?
 | 
|---|
 | 484 | //                  po::value < std::vector<KeyValuePair> >()->default_value(boost::lexical_cast< std::vector<KeyValuePair> >(currentOption->getDefaultValue().c_str())) :
 | 
|---|
 | 485 |                   po::value < std::vector<KeyValuePair> >()->multitoken(),
 | 
|---|
 | 486 |                   currentOption->getDescription().c_str())
 | 
|---|
 | 487 |         ;
 | 
|---|
 | 488 |       break;
 | 
|---|
| [e4afb4] | 489 |   }
 | 
|---|
 | 490 | }
 | 
|---|
 | 491 | 
 | 
|---|
 | 492 | /** States whether there are command line arguments.
 | 
|---|
 | 493 |  * \return true - there are none, false - there is at least one command line argument
 | 
|---|
 | 494 |  */
 | 
|---|
 | 495 | bool CommandLineParser::isEmpty()
 | 
|---|
 | 496 | {
 | 
|---|
 | 497 |   return vm.empty();
 | 
|---|
 | 498 | }
 | 
|---|
 | 499 | 
 | 
|---|
 | 500 | /** Sets the options.
 | 
|---|
 | 501 |  * \param _argc arg count from main()
 | 
|---|
 | 502 |  * \param **_argv argument array from main()
 | 
|---|
 | 503 |  */
 | 
|---|
 | 504 | void CommandLineParser::setOptions(int _argc, char **_argv)
 | 
|---|
 | 505 | {
 | 
|---|
 | 506 |   argc = _argc;
 | 
|---|
 | 507 |   argv = _argv;
 | 
|---|
 | 508 |   config_file_options.add(options);
 | 
|---|
| [c6e5eb] | 509 |   // append all option_descriptions to both cmdline_options and visible
 | 
|---|
 | 510 |   for (CmdParserLookupMap::iterator iter = CmdParserLookup.begin();
 | 
|---|
 | 511 |       iter != CmdParserLookup.end();
 | 
|---|
 | 512 |       ++iter) {
 | 
|---|
 | 513 |     cmdline_options.add(*(iter->second));
 | 
|---|
 | 514 |     visible.add(*(iter->second));
 | 
|---|
 | 515 |   }
 | 
|---|
| [e4afb4] | 516 | }
 | 
|---|
 | 517 | 
 | 
|---|
| [15d21e] | 518 | /** This is due to the answer by Aleksey Vitebskiy
 | 
|---|
 | 519 |  * in http://stackoverflow.com/questions/4107087/accepting-negative-doubles-with-boostprogram-options
 | 
|---|
 | 520 |  *
 | 
|---|
 | 521 |  */
 | 
|---|
 | 522 | std::vector<po::option> ignore_numbers(std::vector<std::string>& args)
 | 
|---|
 | 523 | {
 | 
|---|
 | 524 |     std::vector<po::option> result;
 | 
|---|
 | 525 |     int pos = 0;
 | 
|---|
 | 526 |     while(!args.empty()) {
 | 
|---|
 | 527 |         const std::string& arg = args[0];
 | 
|---|
 | 528 |         bool isNumber = true;
 | 
|---|
 | 529 |         try {
 | 
|---|
 | 530 |           boost::lexical_cast<double>(arg);
 | 
|---|
 | 531 |         } catch(boost::bad_lexical_cast) {
 | 
|---|
 | 532 |           isNumber = false;
 | 
|---|
 | 533 |         }
 | 
|---|
 | 534 |         if (isNumber) {
 | 
|---|
 | 535 |             result.push_back(po::option());
 | 
|---|
 | 536 |             po::option& opt = result.back();
 | 
|---|
 | 537 | 
 | 
|---|
 | 538 |             opt.position_key = pos++;
 | 
|---|
 | 539 |             opt.value.push_back(arg);
 | 
|---|
 | 540 |             opt.original_tokens.push_back(arg);
 | 
|---|
 | 541 | 
 | 
|---|
 | 542 |             args.erase(args.begin());
 | 
|---|
 | 543 |         } else {
 | 
|---|
 | 544 |             break;
 | 
|---|
 | 545 |         }
 | 
|---|
 | 546 |     }
 | 
|---|
 | 547 | 
 | 
|---|
 | 548 |     return result;
 | 
|---|
 | 549 | }
 | 
|---|
 | 550 | 
 | 
|---|
| [e4afb4] | 551 | /** Parses the command line arguments.
 | 
|---|
 | 552 |  * Calls program_options::store() and program_options::notify()
 | 
|---|
| [06b5df] | 553 |  *
 | 
|---|
 | 554 |  * @return true - all is ok, false - command-line options could not be parsed 
 | 
|---|
 | 555 |  *         correctly
 | 
|---|
| [e4afb4] | 556 |  */
 | 
|---|
| [06b5df] | 557 | bool CommandLineParser::Parse()
 | 
|---|
| [e4afb4] | 558 | {
 | 
|---|
| [06b5df] | 559 |   bool status = true;
 | 
|---|
| [11d433] | 560 |   try {
 | 
|---|
| [15d21e] | 561 |     po::store(po::command_line_parser(argc,argv).extra_style_parser(&ignore_numbers).options(cmdline_options).run(), vm);
 | 
|---|
| [11d433] | 562 |   } catch (std::exception &e) {
 | 
|---|
| [7912e9] | 563 |     std::cerr << "Something went wrong with parsing the command-line arguments: " 
 | 
|---|
 | 564 |         << e.what() << std::endl;
 | 
|---|
| [11d433] | 565 |     World::getInstance().setExitFlag(134);
 | 
|---|
 | 566 | #ifdef HAVE_ACTION_THREAD
 | 
|---|
 | 567 |     // force action queue to stop thread
 | 
|---|
 | 568 |     ActionQueue::getInstance().stop();
 | 
|---|
| [601ef8] | 569 |     ActionQueue::getInstance().clearTempQueue();
 | 
|---|
| [11d433] | 570 | #endif
 | 
|---|
 | 571 |     ActionQueue::getInstance().clearQueue();
 | 
|---|
| [06b5df] | 572 |     status = false;
 | 
|---|
 | 573 |   }
 | 
|---|
 | 574 |   if (status) {
 | 
|---|
 | 575 |     std::ifstream input;
 | 
|---|
 | 576 |     input.open("example.cfg");
 | 
|---|
 | 577 |     if (!input.fail())
 | 
|---|
 | 578 |       po::store(po::parse_config_file(input, config_file_options), vm);
 | 
|---|
 | 579 |     input.close();
 | 
|---|
 | 580 |     po::notify(vm);
 | 
|---|
| [11d433] | 581 |   }
 | 
|---|
| [06b5df] | 582 |   return status;
 | 
|---|
| [e4afb4] | 583 | }
 | 
|---|
 | 584 | 
 | 
|---|
 | 585 | /** Scan the argument list for -a or --arguments and store their order for later use.
 | 
|---|
 | 586 |  */
 | 
|---|
 | 587 | void CommandLineParser::scanforSequenceOfArguments()
 | 
|---|
 | 588 | {
 | 
|---|
| [3a21a7] | 589 |   std::map <std::string, std::string> ShortFormToActionMap = getShortFormToActionMap();
 | 
|---|
| [47d041] | 590 |   LOG(0, "Scanning command line arguments and recognizing Actions.");
 | 
|---|
| [e4afb4] | 591 |   // go through all arguments
 | 
|---|
 | 592 |   for (int i=1;i<argc;i++) {
 | 
|---|
| [47d041] | 593 |     LOG(2, "Checking on " << argv[i]);
 | 
|---|
| [e4afb4] | 594 |     // check whether they
 | 
|---|
 | 595 |     if (argv[i][0] == '-') { // .. begin with -
 | 
|---|
| [47d041] | 596 |       LOG(2, "Possible argument: " << argv[i]);
 | 
|---|
| [e4afb4] | 597 |       if (argv[i][1] == '-') { // .. or --
 | 
|---|
| [47d041] | 598 |         LOG(1, "Putting " << argv[i] << " into the sequence.");
 | 
|---|
| [b56827] | 599 |         std::vector<std::string> fields;
 | 
|---|
 | 600 |         boost::split(fields, argv[i], boost::is_any_of("="));
 | 
|---|
 | 601 |         SequenceOfActions.push_back(&(fields[0][2]));
 | 
|---|
| [e4afb4] | 602 |         //  .. and check that next letter is not numeric, if so insert
 | 
|---|
 | 603 |       } else if (((argv[i][1] < '0') || (argv[i][1] > '9')) && ((argv[i][1] != '.'))) {
 | 
|---|
| [3a21a7] | 604 |         std::map <std::string, std::string>::iterator iter = ShortFormToActionMap.find(&(argv[i][1]));
 | 
|---|
| [e4afb4] | 605 |         if (iter != ShortFormToActionMap.end()) {
 | 
|---|
| [47d041] | 606 |           LOG(1, "Putting " << iter->second << " for " << iter->first << " into the sequence.");
 | 
|---|
| [e4afb4] | 607 |           SequenceOfActions.push_back(iter->second);
 | 
|---|
 | 608 |         }
 | 
|---|
 | 609 |       }
 | 
|---|
 | 610 |     }
 | 
|---|
 | 611 |   }
 | 
|---|
 | 612 | }
 | 
|---|
 | 613 | 
 | 
|---|
 | 614 | /** Makes the Parser parse the command line options with current known options.
 | 
|---|
 | 615 |  * \param _argc arg count from main()
 | 
|---|
 | 616 |  * \param **_argv argument array from main()
 | 
|---|
 | 617 |  */
 | 
|---|
 | 618 | void CommandLineParser::Run(int _argc, char **_argv)
 | 
|---|
 | 619 | {
 | 
|---|
 | 620 |   setOptions(_argc,_argv);
 | 
|---|
| [06b5df] | 621 |   const bool status = Parse();
 | 
|---|
 | 622 |   if (status)
 | 
|---|
 | 623 |     scanforSequenceOfArguments();
 | 
|---|
| [e4afb4] | 624 | }
 | 
|---|
 | 625 | 
 | 
|---|
 | 626 | /** Go through all Actions and create a map from short form to their token.
 | 
|---|
 | 627 |  * \return map from Action's ShortForm to token.
 | 
|---|
 | 628 |  */
 | 
|---|
| [2a0a9e3] | 629 | std::map <std::string, std::string> CommandLineParser::getShortFormToActionMap() const
 | 
|---|
| [e4afb4] | 630 | {
 | 
|---|
| [3a21a7] | 631 |   std::map <std::string, std::string> result;
 | 
|---|
| [e4afb4] | 632 | 
 | 
|---|
| [690741] | 633 |   ActionQueue &AQ = ActionQueue::getInstance();
 | 
|---|
 | 634 |   ActionQueue::ActionTokens_t tokens = AQ.getListOfActions();
 | 
|---|
 | 635 |   for (ActionQueue::ActionTokens_t::const_iterator iter = tokens.begin();
 | 
|---|
 | 636 |       iter != tokens.end(); ++iter) {
 | 
|---|
 | 637 |     const ActionTrait &CurrentTrait = AQ.getActionsTrait(*iter);
 | 
|---|
 | 638 |     if (CurrentTrait.hasShortForm()) {
 | 
|---|
 | 639 |       ASSERT(result.find(CurrentTrait.getShortForm()) == result.end(),
 | 
|---|
 | 640 |           "Short form "+toString(CurrentTrait.getShortForm())+
 | 
|---|
 | 641 |           " for action "+toString(*iter)+" already present from "+
 | 
|---|
 | 642 |           std::string(result[CurrentTrait.getShortForm()])+"!");
 | 
|---|
 | 643 |       result[CurrentTrait.getShortForm()] = *iter;
 | 
|---|
| [e4afb4] | 644 |     }
 | 
|---|
| [690741] | 645 |   }
 | 
|---|
| [e4afb4] | 646 | 
 | 
|---|
 | 647 |   return result;
 | 
|---|
 | 648 | }
 | 
|---|
 | 649 | 
 | 
|---|
 | 650 | CONSTRUCT_SINGLETON(CommandLineParser)
 | 
|---|