source: src/Parser/FormatParser_Parameters.cpp@ b11f5e

Action_Thermostats Add_AtomRandomPerturbation Add_FitFragmentPartialChargesAction Add_RotateAroundBondAction Add_SelectAtomByNameAction Added_ParseSaveFragmentResults AddingActions_SaveParseParticleParameters Adding_Graph_to_ChangeBondActions Adding_MD_integration_tests Adding_ParticleName_to_Atom Adding_StructOpt_integration_tests AtomFragments Automaking_mpqc_open AutomationFragmentation_failures Candidate_v1.5.4 Candidate_v1.6.0 Candidate_v1.6.1 ChangeBugEmailaddress ChangingTestPorts ChemicalSpaceEvaluator CombiningParticlePotentialParsing Combining_Subpackages Debian_Package_split Debian_package_split_molecuildergui_only Disabling_MemDebug Docu_Python_wait EmpiricalPotential_contain_HomologyGraph EmpiricalPotential_contain_HomologyGraph_documentation Enable_parallel_make_install Enhance_userguide Enhanced_StructuralOptimization Enhanced_StructuralOptimization_continued Example_ManyWaysToTranslateAtom Exclude_Hydrogens_annealWithBondGraph FitPartialCharges_GlobalError Fix_BoundInBox_CenterInBox_MoleculeActions Fix_ChargeSampling_PBC Fix_ChronosMutex Fix_FitPartialCharges Fix_FitPotential_needs_atomicnumbers Fix_ForceAnnealing Fix_IndependentFragmentGrids Fix_ParseParticles Fix_ParseParticles_split_forward_backward_Actions Fix_PopActions Fix_QtFragmentList_sorted_selection Fix_Restrictedkeyset_FragmentMolecule Fix_StatusMsg Fix_StepWorldTime_single_argument Fix_Verbose_Codepatterns Fix_fitting_potentials Fixes ForceAnnealing_goodresults ForceAnnealing_oldresults ForceAnnealing_tocheck ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_continued ForceAnnealing_with_BondGraph_continued_betteresults ForceAnnealing_with_BondGraph_contraction-expansion FragmentAction_writes_AtomFragments FragmentMolecule_checks_bonddegrees GeometryObjects Gui_Fixes Gui_displays_atomic_force_velocity ImplicitCharges IndependentFragmentGrids IndependentFragmentGrids_IndividualZeroInstances IndependentFragmentGrids_IntegrationTest IndependentFragmentGrids_Sole_NN_Calculation JobMarket_RobustOnKillsSegFaults JobMarket_StableWorkerPool JobMarket_unresolvable_hostname_fix MoreRobust_FragmentAutomation ODR_violation_mpqc_open PartialCharges_OrthogonalSummation PdbParser_setsAtomName PythonUI_with_named_parameters QtGui_reactivate_TimeChanged_changes Recreated_GuiChecks Rewrite_FitPartialCharges RotateToPrincipalAxisSystem_UndoRedo SaturateAtoms_findBestMatching SaturateAtoms_singleDegree StoppableMakroAction Subpackage_CodePatterns Subpackage_JobMarket Subpackage_LinearAlgebra Subpackage_levmar Subpackage_mpqc_open Subpackage_vmg Switchable_LogView ThirdParty_MPQC_rebuilt_buildsystem TrajectoryDependenant_MaxOrder TremoloParser_IncreasedPrecision TremoloParser_MultipleTimesteps TremoloParser_setsAtomName Ubuntu_1604_changes stable
Last change on this file since b11f5e was 94d5ac6, checked in by Frederik Heber <heber@…>, 12 years ago

FIX: As we use GSL internally, we are as of now required to use GPL v2 license.

  • GNU Scientific Library is used at every place in the code, especially the sub-package LinearAlgebra is based on it which in turn is used really everywhere in the remainder of MoleCuilder. Hence, we have to use the GPL license for the whole of MoleCuilder. In effect, GPL's COPYING was present all along and stated the terms of the GPL v2 license.
  • Hence, I added the default GPL v2 disclaimer to every source file and removed the note about a (actually missing) LICENSE file.
  • also, I added a help-redistribute action which again gives the disclaimer of the GPL v2.
  • also, I changed in the disclaimer that is printed at every program start in builder_init.cpp.
  • TEST: Added check on GPL statement present in every module to test CodeChecks project-disclaimer.
  • Property mode set to 100644
File size: 7.0 KB
Line 
1/*
2 * Project: MoleCuilder
3 * Description: creates and alters molecular systems
4 * Copyright (C) 2010-2012 University of Bonn. All rights reserved.
5 *
6 *
7 * This file is part of MoleCuilder.
8 *
9 * MoleCuilder is free software: you can redistribute it and/or modify
10 * it under the terms of the GNU General Public License as published by
11 * the Free Software Foundation, either version 2 of the License, or
12 * (at your option) any later version.
13 *
14 * MoleCuilder is distributed in the hope that it will be useful,
15 * but WITHOUT ANY WARRANTY; without even the implied warranty of
16 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
17 * GNU General Public License for more details.
18 *
19 * You should have received a copy of the GNU General Public License
20 * along with MoleCuilder. If not, see <http://www.gnu.org/licenses/>.
21 */
22
23/*
24 * FormatParser_Parameters.cpp
25 *
26 * Created on: Sep 30, 2011
27 * Author: heber
28 */
29
30// include config.h
31#ifdef HAVE_CONFIG_H
32#include <config.h>
33#endif
34
35#include "CodePatterns/MemDebug.hpp"
36
37#include <iostream>
38#include <boost/algorithm/string.hpp>
39#include <boost/tokenizer.hpp>
40#include <sstream>
41#include <string>
42
43#include "CodePatterns/Assert.hpp"
44#include "CodePatterns/Log.hpp"
45
46#include "Parameters/ParameterAsString.hpp"
47#include "FormatParser_Parameters.hpp"
48
49/** Constructor of class FormatParser_Parameters.
50 *
51 * \note we make sure that storage is always present
52 *
53 */
54FormatParser_Parameters::FormatParser_Parameters() :
55 storage(new ParameterStorage)
56{}
57
58/** Copy constructor of class FormatParser_Parameters.
59 *
60 * @param _parameters instance to copy from
61 */
62FormatParser_Parameters::FormatParser_Parameters(const FormatParser_Parameters &_parameters) :
63 storage(new ParameterStorage(*_parameters.storage))
64{}
65
66
67/** Destructor of class FormatParser_Parameters.
68 *
69 */
70FormatParser_Parameters::~FormatParser_Parameters()
71{
72 delete storage;
73}
74
75/** Implements the Parameter::clone() function.
76 *
77 * @return another instance with an identical copy of each parameter in \a storage
78 */
79FormatParser_Parameters* FormatParser_Parameters::clone() const
80{
81 return (new FormatParser_Parameters(*this));
82}
83
84/** This makes this instance a clone of \a _instance.
85 *
86 * \note This is basically the other way round to clone().
87 *
88 * @param _instance instance to clone from
89 */
90void FormatParser_Parameters::makeClone(const FormatParser_Parameters &_instance)
91{
92 // we simply remove storage
93 delete storage;
94 // and clone the one from _instance
95 storage = new ParameterStorage(*_instance.storage);
96}
97
98/** Adds a parameter to \a storage.
99 *
100 * This just eases use, saves some typing and is more clear as to what is done.
101 *
102 * @param instance parameter to add
103 */
104void FormatParser_Parameters::appendParameter(ParameterAsString *instance)
105{
106 storage->registerInstance(instance);
107}
108
109/** Checks for presence of a parameter in \a storage.
110 *
111 * This just eases use, saves some typing and is more clear as to what is done.
112 *
113 * @return true - parameter by this \a _name is present in storage, false - else
114 */
115bool FormatParser_Parameters::haveParameter(const std::string &_name) const
116{
117 return storage->isPresentByName(_name);
118}
119
120/** Gets a parameter from \a storage.
121 *
122 * This just eases use, saves some typing and is more clear as to what is done.
123 *
124 * @return pointer to instance with this \a _name
125 */
126ParameterAsString *FormatParser_Parameters::getParameter(const std::string &_name) const
127{
128 return storage->getByName(_name);
129}
130
131/** Output operator for the contents of FormatParser_Parameters::params.
132 *
133 * @param ost output stream
134 * @param params reference to FormatParser_Parameters containing params.
135 * @return reference to output stream for concatenation
136 */
137std::ostream & operator << (std::ostream& ost, const FormatParser_Parameters &params)
138{
139 // this is ugly, but with boost::any to safeguard const-ness is plain impossible
140 std::ostringstream output;
141 ASSERT(params.storage != NULL,
142 "operator<<(FormatParser_Parameters) - storage is NULL.");
143 for (ParameterStorage::const_iterator iter = params.storage->getBeginIter();
144 iter != params.storage->getEndIter();
145 ++iter)
146 if (!iter->second->getAsString().empty())
147 output << iter->first << "=" << iter->second->getAsString() << ";";
148 ost << output.str();
149 return ost;
150}
151
152/** Input operator for a list of parameters to place into \a params.
153 *
154 * @param ist input stream
155 * @param params parameters to parse into
156 * @return input stream for concatenation
157 */
158std::istream & operator >> (std::istream& ist, FormatParser_Parameters &params)
159{
160 typedef boost::tokenizer<boost::char_separator<char> >
161 tokenizer;
162 boost::char_separator<char> semicolonsep(";");
163 boost::char_separator<char> equalitysep("=");
164 boost::char_separator<char> ticksep("\"");
165 std::string line;
166 std::getline( ist, line );
167 //LOG(0, "INFO: full line of parameters is '" << line << "'");
168 tokenizer tokens(line, semicolonsep);
169 ASSERT(tokens.begin() != tokens.end(),
170 "operator<< on FormatParser_Parameters - empty string, need at least ';' in line "+line+"!");
171 for (tokenizer::iterator tok_iter = tokens.begin();
172 tok_iter != tokens.end(); ++tok_iter) {
173 //LOG(2, "INFO: (key,value) pair is: " << *tok_iter << ".");
174 tokenizer paramtokens(*tok_iter, equalitysep);
175 if (paramtokens.begin() != paramtokens.end()) {
176 tokenizer::iterator tok_paramiter = paramtokens.begin();
177 ASSERT(tok_paramiter != paramtokens.end(),
178 "operator<< on FormatParser_Parameters - missing value before ' =' in token "+*tok_iter+"!");
179 tokenizer::iterator tok_valueiter = tok_paramiter;
180 tokenizer::iterator tok_checkiter = ++tok_valueiter;
181 ASSERT(tok_valueiter != paramtokens.end(),
182 "operator<< on FormatParser_Parameters - missing value after ' =' in token "+*tok_iter+"!");
183 ++tok_checkiter;
184 ASSERT(tok_checkiter == paramtokens.end(),
185 "operator<< on FormatParser_Parameters - still more tokens after ' =' in token "+*tok_iter+":"
186 +*tok_checkiter+"!");
187 LOG(3, "INFO: key is '" << *tok_paramiter << "', value is '" << *tok_valueiter << "'.");
188 // TODO: throw exception instead of ASSERT
189 std::string key(*tok_paramiter);
190 std::string value(*tok_valueiter);
191 boost::trim(key);
192 boost::trim(value);
193 tokenizer ticklesstokens(value, ticksep);
194 ASSERT(ticklesstokens.begin() != ticklesstokens.end(),
195 "operator<< on FormatParser_Parameters - no tokens present after removing ticks in token "+*tok_valueiter+"!");
196 std::stringstream valuestream(*(ticklesstokens.begin()));
197 //LOG(2, "INFO: Token pair is " << key << "," << valuestream.str());
198
199 // TODO: throw exception instead of DoeLog()
200 ASSERT(params.haveParameter(key),
201 "operator >> on FormatParser_Parameters - unknown parameter name '"
202 +key+"' with value "+valuestream.str()+"!");
203 if (params.haveParameter(key)) {
204 ParameterAsString *instance = params.getParameter(key);
205 instance->setAsString(valuestream.str());
206 }
207 } else {
208 ist.setstate(std::ios::eofbit);
209 }
210 }
211 return ist;
212}
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