| [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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|  | 206 | #if BOOST_VERSION >= 106300 | 
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|  | 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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|  | 226 | #else | 
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|  | 227 | template <typename T> | 
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|  | 228 | po::typed_value<T>* implicit_value(const T& value) | 
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|  | 229 | { | 
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|  | 230 | return new po::typed_value<T>()->implicit_value(value); | 
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|  | 231 | } | 
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|  | 232 | #endif | 
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|  | 233 |  | 
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|  | 234 |  | 
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| [e4afb4] | 235 | /** Adds an Action or Option to the CommandLineParser. | 
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|  | 236 | * Note that Action is derived from Option(Trait) | 
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|  | 237 | * | 
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|  | 238 | * This ugly switch function is necessary because of the compile-time problem: | 
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|  | 239 | * po::value<T> has to be instantiated at compile-time however we do know the type not until run-time. | 
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|  | 240 | * Not even a templated function like po::value<T> getProgramOptionValuefromType() does help, specialized | 
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|  | 241 | * to each available type, as the signatures of all the functions differ. Hence, they cannot not put into | 
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|  | 242 | * one type_info -> po::value<T> map ... | 
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|  | 243 | * | 
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|  | 244 | * \param *currentOption pointer to Action/Option to add | 
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|  | 245 | * \param *OptionList program_options list to add to | 
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| [7912e9] | 246 | * \param _DefaultAsImplicit whether to add a default value as default_value or | 
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|  | 247 | *        as implicit_value (default = option token present or not, implicit = | 
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|  | 248 | option token present but not necessarily followed by argument) | 
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| [e4afb4] | 249 | */ | 
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| [7912e9] | 250 | void CommandLineParser::AddOptionToParser( | 
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|  | 251 | const OptionTrait * const currentOption, | 
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|  | 252 | po::options_description* OptionList, | 
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|  | 253 | const bool _DefaultAsImplicit) | 
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| [e4afb4] | 254 | { | 
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|  | 255 | // check whether dynamic_cast in Init() suceeded | 
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|  | 256 | ASSERT(currentOption != NULL, "CommandLineParser::AddOptionToParser() - currentOption is NULL!"); | 
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|  | 257 | // add other options | 
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| [ec098d] | 258 | //  std::cout << "Adding Action " << currentOption->getName() << " with type " | 
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|  | 259 | //      << currentOption->getType()->name() << ", " << (currentOption->hasDefaultValue() ? "with" : "without") | 
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|  | 260 | //      << " default value, and KeyandShortform " << currentOption->getKeyAndShortForm() | 
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|  | 261 | //      << " to CommandLineParser." << std::endl; | 
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| [e4afb4] | 262 | switch(TypeToEnums.getEnumforType(currentOption->getType())) { | 
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|  | 263 | default: | 
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|  | 264 | case TypeEnumContainer::NoneType: | 
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|  | 265 | OptionList->add_options() | 
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|  | 266 | (currentOption->getKeyAndShortForm().c_str(), currentOption->getDescription().c_str()) | 
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|  | 267 | ; | 
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|  | 268 | break; | 
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|  | 269 | case TypeEnumContainer::BooleanType: | 
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|  | 270 | OptionList->add_options() | 
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|  | 271 | (currentOption->getKeyAndShortForm().c_str(), | 
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|  | 272 | currentOption->hasDefaultValue() ? | 
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| [7912e9] | 273 | (_DefaultAsImplicit ? | 
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| [b56827] | 274 | implicit_value(bool(boost::lexical_cast<int>(currentOption->getDefaultValue().c_str()))) : | 
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| [7912e9] | 275 | po::value < bool >()->default_value(boost::lexical_cast<int>(currentOption->getDefaultValue().c_str()))) : | 
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| [e4afb4] | 276 | po::value < bool >(), | 
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|  | 277 | currentOption->getDescription().c_str()) | 
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|  | 278 | ; | 
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|  | 279 | break; | 
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|  | 280 | case TypeEnumContainer::FileType: | 
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|  | 281 | OptionList->add_options() | 
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|  | 282 | (currentOption->getKeyAndShortForm().c_str(), | 
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|  | 283 | //            currentOption->hasDefaultValue() ? | 
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|  | 284 | //                  po::value < boost::filesystem::path >()->default_value(boost::lexical_cast<boost::filesystem::path>(currentOption->getDefaultValue().c_str())) : | 
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|  | 285 | po::value < boost::filesystem::path >(), | 
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|  | 286 | currentOption->getDescription().c_str()) | 
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|  | 287 | ; | 
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|  | 288 | break; | 
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|  | 289 | case TypeEnumContainer::ListOfFilesType: | 
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|  | 290 | OptionList->add_options() | 
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|  | 291 | (currentOption->getKeyAndShortForm().c_str(), | 
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|  | 292 | //            currentOption->hasDefaultValue() ? | 
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|  | 293 | //                  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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|  | 294 | po::value < std::vector<boost::filesystem::path> >()->multitoken(), | 
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|  | 295 | currentOption->getDescription().c_str()) | 
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|  | 296 | ; | 
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|  | 297 | break; | 
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|  | 298 | case TypeEnumContainer::IntegerType: | 
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|  | 299 | OptionList->add_options() | 
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|  | 300 | (currentOption->getKeyAndShortForm().c_str(), | 
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|  | 301 | currentOption->hasDefaultValue() ? | 
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| [7912e9] | 302 | (_DefaultAsImplicit ? | 
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| [b56827] | 303 | implicit_value(boost::lexical_cast<int>(currentOption->getDefaultValue().c_str())) : | 
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| [7912e9] | 304 | po::value < int >()->default_value(boost::lexical_cast<int>(currentOption->getDefaultValue().c_str()))) : | 
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| [e4afb4] | 305 | po::value < int >(), | 
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|  | 306 | currentOption->getDescription().c_str()) | 
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|  | 307 | ; | 
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|  | 308 | break; | 
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|  | 309 | case TypeEnumContainer::ListOfIntegersType: | 
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|  | 310 | OptionList->add_options() | 
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|  | 311 | (currentOption->getKeyAndShortForm().c_str(), | 
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|  | 312 | //            currentOption->hasDefaultValue() ? | 
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|  | 313 | //                  po::value < std::vector<int> >()->default_value(boost::lexical_cast< std::vector<int> >(currentOption->getDefaultValue().c_str())) : | 
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|  | 314 | po::value < std::vector<int> >()->multitoken(), | 
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|  | 315 | currentOption->getDescription().c_str()) | 
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|  | 316 | ; | 
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|  | 317 | break; | 
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| [838cd0] | 318 | case TypeEnumContainer::UnsignedIntegerType: | 
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|  | 319 | OptionList->add_options() | 
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|  | 320 | (currentOption->getKeyAndShortForm().c_str(), | 
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|  | 321 | currentOption->hasDefaultValue() ? | 
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| [7912e9] | 322 | (_DefaultAsImplicit ? | 
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| [b56827] | 323 | implicit_value(boost::lexical_cast<unsigned int>(currentOption->getDefaultValue().c_str())) : | 
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| [7912e9] | 324 | po::value < unsigned int >()->default_value(boost::lexical_cast<unsigned int>(currentOption->getDefaultValue().c_str()))) : | 
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| [838cd0] | 325 | po::value < unsigned int >(), | 
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|  | 326 | currentOption->getDescription().c_str()) | 
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|  | 327 | ; | 
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|  | 328 | break; | 
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| [12948c] | 329 | case TypeEnumContainer::ListOfUnsignedIntegersType: | 
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|  | 330 | OptionList->add_options() | 
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|  | 331 | (currentOption->getKeyAndShortForm().c_str(), | 
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|  | 332 | //            currentOption->hasDefaultValue() ? | 
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|  | 333 | //                  po::value < std::vector<unsigned int> >()->default_value(boost::lexical_cast< std::vector<unsigned int> >(currentOption->getDefaultValue().c_str())) : | 
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|  | 334 | po::value < std::vector<unsigned int> >()->multitoken(), | 
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|  | 335 | currentOption->getDescription().c_str()) | 
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|  | 336 | ; | 
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|  | 337 | break; | 
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| [e4afb4] | 338 | case TypeEnumContainer::DoubleType: | 
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|  | 339 | OptionList->add_options() | 
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|  | 340 | (currentOption->getKeyAndShortForm().c_str(), | 
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|  | 341 | currentOption->hasDefaultValue() ? | 
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| [7912e9] | 342 | (_DefaultAsImplicit ? | 
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| [b56827] | 343 | implicit_value(boost::lexical_cast<double>(currentOption->getDefaultValue().c_str())) : | 
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| [7912e9] | 344 | po::value < double >()->default_value(boost::lexical_cast<double>(currentOption->getDefaultValue().c_str()))) : | 
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| [e4afb4] | 345 | po::value < double >(), | 
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|  | 346 | currentOption->getDescription().c_str()) | 
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|  | 347 | ; | 
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|  | 348 | break; | 
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|  | 349 | case TypeEnumContainer::ListOfDoublesType: | 
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|  | 350 | OptionList->add_options() | 
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|  | 351 | (currentOption->getKeyAndShortForm().c_str(), | 
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|  | 352 | //            currentOption->hasDefaultValue() ? | 
|---|
|  | 353 | //                  po::value < std::vector<double> >()->default_value(boost::lexical_cast< std::vector<double> >(currentOption->getDefaultValue().c_str())) : | 
|---|
|  | 354 | po::value < std::vector<double> >()->multitoken(), | 
|---|
|  | 355 | currentOption->getDescription().c_str()) | 
|---|
|  | 356 | ; | 
|---|
|  | 357 | break; | 
|---|
|  | 358 | case TypeEnumContainer::StringType: | 
|---|
|  | 359 | OptionList->add_options() | 
|---|
|  | 360 | (currentOption->getKeyAndShortForm().c_str(), | 
|---|
|  | 361 | currentOption->hasDefaultValue() ? | 
|---|
| [7912e9] | 362 | (_DefaultAsImplicit ? | 
|---|
| [b56827] | 363 | implicit_value(currentOption->getDefaultValue()) : | 
|---|
| [7912e9] | 364 | po::value < std::string >()->default_value(currentOption->getDefaultValue())) : | 
|---|
| [e4afb4] | 365 | po::value < std::string >(), | 
|---|
|  | 366 | currentOption->getDescription().c_str()) | 
|---|
|  | 367 | ; | 
|---|
|  | 368 | break; | 
|---|
|  | 369 | case TypeEnumContainer::ListOfStringsType: | 
|---|
|  | 370 | OptionList->add_options() | 
|---|
|  | 371 | (currentOption->getKeyAndShortForm().c_str(), | 
|---|
|  | 372 | //            currentOption->hasDefaultValue() ? | 
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|  | 373 | //                  po::value < std::vector<std::string> >()->default_value(boost::lexical_cast< std::vector<std::string> >(currentOption->getDefaultValue().c_str())) : | 
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|  | 374 | po::value < std::vector<std::string> >()->multitoken(), | 
|---|
|  | 375 | currentOption->getDescription().c_str()) | 
|---|
|  | 376 | ; | 
|---|
|  | 377 | break; | 
|---|
|  | 378 | case TypeEnumContainer::VectorType: | 
|---|
|  | 379 | OptionList->add_options() | 
|---|
|  | 380 | (currentOption->getKeyAndShortForm().c_str(), | 
|---|
|  | 381 | //            currentOption->hasDefaultValue() ? | 
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|  | 382 | //                  po::value < VectorValue >()->default_value(boost::lexical_cast<VectorValue>(currentOption->getDefaultValue().c_str())) : | 
|---|
|  | 383 | po::value < VectorValue >(), | 
|---|
|  | 384 | currentOption->getDescription().c_str()) | 
|---|
|  | 385 | ; | 
|---|
|  | 386 | break; | 
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|  | 387 | case TypeEnumContainer::ListOfVectorsType: | 
|---|
|  | 388 | OptionList->add_options() | 
|---|
|  | 389 | (currentOption->getKeyAndShortForm().c_str(), | 
|---|
|  | 390 | //            currentOption->hasDefaultValue() ? | 
|---|
|  | 391 | //                  po::value < std::vector<VectorValue> >()->default_value(boost::lexical_cast< std::vector<VectorValue> >(currentOption->getDefaultValue().c_str())) : | 
|---|
|  | 392 | po::value < std::vector<VectorValue> >()->multitoken(), | 
|---|
|  | 393 | currentOption->getDescription().c_str()) | 
|---|
|  | 394 | ; | 
|---|
|  | 395 | break; | 
|---|
|  | 396 | case TypeEnumContainer::MoleculeType: | 
|---|
|  | 397 | OptionList->add_options() | 
|---|
|  | 398 | (currentOption->getKeyAndShortForm().c_str(), | 
|---|
|  | 399 | //            currentOption->hasDefaultValue() ? | 
|---|
|  | 400 | //                  po::value < const molecule * >()->default_value(boost::lexical_cast<const molecule *>(currentOption->getDefaultValue().c_str())) : | 
|---|
|  | 401 | po::value < int >(), | 
|---|
|  | 402 | currentOption->getDescription().c_str()) | 
|---|
|  | 403 | ; | 
|---|
|  | 404 | break; | 
|---|
|  | 405 | case TypeEnumContainer::ListOfMoleculesType: | 
|---|
|  | 406 | OptionList->add_options() | 
|---|
|  | 407 | (currentOption->getKeyAndShortForm().c_str(), | 
|---|
|  | 408 | //            currentOption->hasDefaultValue() ? | 
|---|
|  | 409 | //                  po::value < std::vector<const molecule *> >()->default_value(boost::lexical_cast< std::vector<const molecule *> >(currentOption->getDefaultValue().c_str())) : | 
|---|
|  | 410 | po::value < std::vector<int> >()->multitoken(), | 
|---|
|  | 411 | currentOption->getDescription().c_str()) | 
|---|
|  | 412 | ; | 
|---|
|  | 413 | break; | 
|---|
|  | 414 | case TypeEnumContainer::AtomType: | 
|---|
|  | 415 | OptionList->add_options() | 
|---|
|  | 416 | (currentOption->getKeyAndShortForm().c_str(), | 
|---|
|  | 417 | currentOption->hasDefaultValue() ? | 
|---|
| [7912e9] | 418 | (_DefaultAsImplicit ? | 
|---|
| [b56827] | 419 | implicit_value(boost::lexical_cast<int>(currentOption->getDefaultValue().c_str())) : | 
|---|
| [7912e9] | 420 | po::value < int >()->default_value(boost::lexical_cast<int>(currentOption->getDefaultValue().c_str()))) : | 
|---|
| [e4afb4] | 421 | po::value < int >(), | 
|---|
|  | 422 | currentOption->getDescription().c_str()) | 
|---|
|  | 423 | ; | 
|---|
|  | 424 | break; | 
|---|
|  | 425 | case TypeEnumContainer::ListOfAtomsType: | 
|---|
|  | 426 | OptionList->add_options() | 
|---|
|  | 427 | (currentOption->getKeyAndShortForm().c_str(), | 
|---|
|  | 428 | //            currentOption->hasDefaultValue() ? | 
|---|
|  | 429 | //                  po::value < std::vector<const atom *> >()->default_value(boost::lexical_cast< std::vector<const atom *> >(currentOption->getDefaultValue().c_str())) : | 
|---|
|  | 430 | po::value < std::vector<int> >()->multitoken(), | 
|---|
|  | 431 | currentOption->getDescription().c_str()) | 
|---|
|  | 432 | ; | 
|---|
|  | 433 | break; | 
|---|
|  | 434 | case TypeEnumContainer::ElementType: | 
|---|
|  | 435 | OptionList->add_options() | 
|---|
|  | 436 | (currentOption->getKeyAndShortForm().c_str(), | 
|---|
|  | 437 | //            currentOption->hasDefaultValue() ? | 
|---|
|  | 438 | //                  po::value < const element * >()->default_value(boost::lexical_cast<const element *>(currentOption->getDefaultValue().c_str())) : | 
|---|
| [2f429e] | 439 | po::value < std::string >(), | 
|---|
| [e4afb4] | 440 | currentOption->getDescription().c_str()) | 
|---|
|  | 441 | ; | 
|---|
|  | 442 | break; | 
|---|
|  | 443 | case TypeEnumContainer::ListOfElementsType: | 
|---|
|  | 444 | OptionList->add_options() | 
|---|
|  | 445 | (currentOption->getKeyAndShortForm().c_str(), | 
|---|
|  | 446 | //            currentOption->hasDefaultValue() ? | 
|---|
|  | 447 | //                  po::value < std::vector<const element *> >()->default_value(boost::lexical_cast< std::vector<const element *> >(currentOption->getDefaultValue().c_str())) : | 
|---|
| [2f429e] | 448 | po::value < std::vector<std::string> >()->multitoken(), | 
|---|
| [e4afb4] | 449 | currentOption->getDescription().c_str()) | 
|---|
|  | 450 | ; | 
|---|
|  | 451 | break; | 
|---|
| [7d9416] | 452 | case TypeEnumContainer::RealSpaceMatrixType: | 
|---|
|  | 453 | OptionList->add_options() | 
|---|
|  | 454 | (currentOption->getKeyAndShortForm().c_str(), | 
|---|
|  | 455 | //            currentOption->hasDefaultValue() ? | 
|---|
|  | 456 | //                  po::value < RealSpaceMatrixValue >()->default_value(boost::lexical_cast<BoxValue>(currentOption->getDefaultValue().c_str())) : | 
|---|
|  | 457 | po::value < RealSpaceMatrixValue >(), | 
|---|
|  | 458 | currentOption->getDescription().c_str()) | 
|---|
|  | 459 | ; | 
|---|
|  | 460 | break; | 
|---|
| [33e801] | 461 | case TypeEnumContainer::KeyValueType: | 
|---|
|  | 462 | OptionList->add_options() | 
|---|
|  | 463 | (currentOption->getKeyAndShortForm().c_str(), | 
|---|
|  | 464 | currentOption->hasDefaultValue() ? | 
|---|
|  | 465 | (_DefaultAsImplicit ? | 
|---|
| [b56827] | 466 | implicit_value(boost::lexical_cast< KeyValuePair >(currentOption->getDefaultValue().c_str())) : | 
|---|
| [33e801] | 467 | po::value < KeyValuePair >()->default_value(boost::lexical_cast< KeyValuePair >(currentOption->getDefaultValue().c_str()))) : | 
|---|
|  | 468 | po::value < KeyValuePair >(), | 
|---|
|  | 469 | currentOption->getDescription().c_str()) | 
|---|
|  | 470 | ; | 
|---|
|  | 471 | break; | 
|---|
|  | 472 | case TypeEnumContainer::ListOfKeyValuesType: | 
|---|
|  | 473 | OptionList->add_options() | 
|---|
|  | 474 | (currentOption->getKeyAndShortForm().c_str(), | 
|---|
|  | 475 | //            currentOption->hasDefaultValue() ? | 
|---|
|  | 476 | //                  po::value < std::vector<KeyValuePair> >()->default_value(boost::lexical_cast< std::vector<KeyValuePair> >(currentOption->getDefaultValue().c_str())) : | 
|---|
|  | 477 | po::value < std::vector<KeyValuePair> >()->multitoken(), | 
|---|
|  | 478 | currentOption->getDescription().c_str()) | 
|---|
|  | 479 | ; | 
|---|
|  | 480 | break; | 
|---|
| [e4afb4] | 481 | } | 
|---|
|  | 482 | } | 
|---|
|  | 483 |  | 
|---|
|  | 484 | /** States whether there are command line arguments. | 
|---|
|  | 485 | * \return true - there are none, false - there is at least one command line argument | 
|---|
|  | 486 | */ | 
|---|
|  | 487 | bool CommandLineParser::isEmpty() | 
|---|
|  | 488 | { | 
|---|
|  | 489 | return vm.empty(); | 
|---|
|  | 490 | } | 
|---|
|  | 491 |  | 
|---|
|  | 492 | /** Sets the options. | 
|---|
|  | 493 | * \param _argc arg count from main() | 
|---|
|  | 494 | * \param **_argv argument array from main() | 
|---|
|  | 495 | */ | 
|---|
|  | 496 | void CommandLineParser::setOptions(int _argc, char **_argv) | 
|---|
|  | 497 | { | 
|---|
|  | 498 | argc = _argc; | 
|---|
|  | 499 | argv = _argv; | 
|---|
|  | 500 | config_file_options.add(options); | 
|---|
| [c6e5eb] | 501 | // append all option_descriptions to both cmdline_options and visible | 
|---|
|  | 502 | for (CmdParserLookupMap::iterator iter = CmdParserLookup.begin(); | 
|---|
|  | 503 | iter != CmdParserLookup.end(); | 
|---|
|  | 504 | ++iter) { | 
|---|
|  | 505 | cmdline_options.add(*(iter->second)); | 
|---|
|  | 506 | visible.add(*(iter->second)); | 
|---|
|  | 507 | } | 
|---|
| [e4afb4] | 508 | } | 
|---|
|  | 509 |  | 
|---|
| [15d21e] | 510 | /** This is due to the answer by Aleksey Vitebskiy | 
|---|
|  | 511 | * in http://stackoverflow.com/questions/4107087/accepting-negative-doubles-with-boostprogram-options | 
|---|
|  | 512 | * | 
|---|
|  | 513 | */ | 
|---|
|  | 514 | std::vector<po::option> ignore_numbers(std::vector<std::string>& args) | 
|---|
|  | 515 | { | 
|---|
|  | 516 | std::vector<po::option> result; | 
|---|
|  | 517 | int pos = 0; | 
|---|
|  | 518 | while(!args.empty()) { | 
|---|
|  | 519 | const std::string& arg = args[0]; | 
|---|
|  | 520 | bool isNumber = true; | 
|---|
|  | 521 | try { | 
|---|
|  | 522 | boost::lexical_cast<double>(arg); | 
|---|
|  | 523 | } catch(boost::bad_lexical_cast) { | 
|---|
|  | 524 | isNumber = false; | 
|---|
|  | 525 | } | 
|---|
|  | 526 | if (isNumber) { | 
|---|
|  | 527 | result.push_back(po::option()); | 
|---|
|  | 528 | po::option& opt = result.back(); | 
|---|
|  | 529 |  | 
|---|
|  | 530 | opt.position_key = pos++; | 
|---|
|  | 531 | opt.value.push_back(arg); | 
|---|
|  | 532 | opt.original_tokens.push_back(arg); | 
|---|
|  | 533 |  | 
|---|
|  | 534 | args.erase(args.begin()); | 
|---|
|  | 535 | } else { | 
|---|
|  | 536 | break; | 
|---|
|  | 537 | } | 
|---|
|  | 538 | } | 
|---|
|  | 539 |  | 
|---|
|  | 540 | return result; | 
|---|
|  | 541 | } | 
|---|
|  | 542 |  | 
|---|
| [e4afb4] | 543 | /** Parses the command line arguments. | 
|---|
|  | 544 | * Calls program_options::store() and program_options::notify() | 
|---|
| [06b5df] | 545 | * | 
|---|
|  | 546 | * @return true - all is ok, false - command-line options could not be parsed | 
|---|
|  | 547 | *         correctly | 
|---|
| [e4afb4] | 548 | */ | 
|---|
| [06b5df] | 549 | bool CommandLineParser::Parse() | 
|---|
| [e4afb4] | 550 | { | 
|---|
| [06b5df] | 551 | bool status = true; | 
|---|
| [11d433] | 552 | try { | 
|---|
| [15d21e] | 553 | po::store(po::command_line_parser(argc,argv).extra_style_parser(&ignore_numbers).options(cmdline_options).run(), vm); | 
|---|
| [11d433] | 554 | } catch (std::exception &e) { | 
|---|
| [7912e9] | 555 | std::cerr << "Something went wrong with parsing the command-line arguments: " | 
|---|
|  | 556 | << e.what() << std::endl; | 
|---|
| [11d433] | 557 | World::getInstance().setExitFlag(134); | 
|---|
|  | 558 | #ifdef HAVE_ACTION_THREAD | 
|---|
|  | 559 | // force action queue to stop thread | 
|---|
|  | 560 | ActionQueue::getInstance().stop(); | 
|---|
| [601ef8] | 561 | ActionQueue::getInstance().clearTempQueue(); | 
|---|
| [11d433] | 562 | #endif | 
|---|
|  | 563 | ActionQueue::getInstance().clearQueue(); | 
|---|
| [06b5df] | 564 | status = false; | 
|---|
|  | 565 | } | 
|---|
|  | 566 | if (status) { | 
|---|
|  | 567 | std::ifstream input; | 
|---|
|  | 568 | input.open("example.cfg"); | 
|---|
|  | 569 | if (!input.fail()) | 
|---|
|  | 570 | po::store(po::parse_config_file(input, config_file_options), vm); | 
|---|
|  | 571 | input.close(); | 
|---|
|  | 572 | po::notify(vm); | 
|---|
| [11d433] | 573 | } | 
|---|
| [06b5df] | 574 | return status; | 
|---|
| [e4afb4] | 575 | } | 
|---|
|  | 576 |  | 
|---|
|  | 577 | /** Scan the argument list for -a or --arguments and store their order for later use. | 
|---|
|  | 578 | */ | 
|---|
|  | 579 | void CommandLineParser::scanforSequenceOfArguments() | 
|---|
|  | 580 | { | 
|---|
| [3a21a7] | 581 | std::map <std::string, std::string> ShortFormToActionMap = getShortFormToActionMap(); | 
|---|
| [47d041] | 582 | LOG(0, "Scanning command line arguments and recognizing Actions."); | 
|---|
| [e4afb4] | 583 | // go through all arguments | 
|---|
|  | 584 | for (int i=1;i<argc;i++) { | 
|---|
| [47d041] | 585 | LOG(2, "Checking on " << argv[i]); | 
|---|
| [e4afb4] | 586 | // check whether they | 
|---|
|  | 587 | if (argv[i][0] == '-') { // .. begin with - | 
|---|
| [47d041] | 588 | LOG(2, "Possible argument: " << argv[i]); | 
|---|
| [e4afb4] | 589 | if (argv[i][1] == '-') { // .. or -- | 
|---|
| [47d041] | 590 | LOG(1, "Putting " << argv[i] << " into the sequence."); | 
|---|
| [b56827] | 591 | std::vector<std::string> fields; | 
|---|
|  | 592 | boost::split(fields, argv[i], boost::is_any_of("=")); | 
|---|
|  | 593 | SequenceOfActions.push_back(&(fields[0][2])); | 
|---|
| [e4afb4] | 594 | //  .. and check that next letter is not numeric, if so insert | 
|---|
|  | 595 | } else if (((argv[i][1] < '0') || (argv[i][1] > '9')) && ((argv[i][1] != '.'))) { | 
|---|
| [3a21a7] | 596 | std::map <std::string, std::string>::iterator iter = ShortFormToActionMap.find(&(argv[i][1])); | 
|---|
| [e4afb4] | 597 | if (iter != ShortFormToActionMap.end()) { | 
|---|
| [47d041] | 598 | LOG(1, "Putting " << iter->second << " for " << iter->first << " into the sequence."); | 
|---|
| [e4afb4] | 599 | SequenceOfActions.push_back(iter->second); | 
|---|
|  | 600 | } | 
|---|
|  | 601 | } | 
|---|
|  | 602 | } | 
|---|
|  | 603 | } | 
|---|
|  | 604 | } | 
|---|
|  | 605 |  | 
|---|
|  | 606 | /** Makes the Parser parse the command line options with current known options. | 
|---|
|  | 607 | * \param _argc arg count from main() | 
|---|
|  | 608 | * \param **_argv argument array from main() | 
|---|
|  | 609 | */ | 
|---|
|  | 610 | void CommandLineParser::Run(int _argc, char **_argv) | 
|---|
|  | 611 | { | 
|---|
|  | 612 | setOptions(_argc,_argv); | 
|---|
| [06b5df] | 613 | const bool status = Parse(); | 
|---|
|  | 614 | if (status) | 
|---|
|  | 615 | scanforSequenceOfArguments(); | 
|---|
| [e4afb4] | 616 | } | 
|---|
|  | 617 |  | 
|---|
|  | 618 | /** Go through all Actions and create a map from short form to their token. | 
|---|
|  | 619 | * \return map from Action's ShortForm to token. | 
|---|
|  | 620 | */ | 
|---|
| [2a0a9e3] | 621 | std::map <std::string, std::string> CommandLineParser::getShortFormToActionMap() const | 
|---|
| [e4afb4] | 622 | { | 
|---|
| [3a21a7] | 623 | std::map <std::string, std::string> result; | 
|---|
| [e4afb4] | 624 |  | 
|---|
| [690741] | 625 | ActionQueue &AQ = ActionQueue::getInstance(); | 
|---|
|  | 626 | ActionQueue::ActionTokens_t tokens = AQ.getListOfActions(); | 
|---|
|  | 627 | for (ActionQueue::ActionTokens_t::const_iterator iter = tokens.begin(); | 
|---|
|  | 628 | iter != tokens.end(); ++iter) { | 
|---|
|  | 629 | const ActionTrait &CurrentTrait = AQ.getActionsTrait(*iter); | 
|---|
|  | 630 | if (CurrentTrait.hasShortForm()) { | 
|---|
|  | 631 | ASSERT(result.find(CurrentTrait.getShortForm()) == result.end(), | 
|---|
|  | 632 | "Short form "+toString(CurrentTrait.getShortForm())+ | 
|---|
|  | 633 | " for action "+toString(*iter)+" already present from "+ | 
|---|
|  | 634 | std::string(result[CurrentTrait.getShortForm()])+"!"); | 
|---|
|  | 635 | result[CurrentTrait.getShortForm()] = *iter; | 
|---|
| [e4afb4] | 636 | } | 
|---|
| [690741] | 637 | } | 
|---|
| [e4afb4] | 638 |  | 
|---|
|  | 639 | return result; | 
|---|
|  | 640 | } | 
|---|
|  | 641 |  | 
|---|
|  | 642 | CONSTRUCT_SINGLETON(CommandLineParser) | 
|---|