source: src/UIElements/CommandLineUI/CommandLineDialog.cpp@ bd2390

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Last change on this file since bd2390 was bd2390, checked in by Frederik Heber <heber@…>, 14 years ago

BUGFIX: new boost::filesystem led to non-parsing of files.

  • BUGFIX: MapOfActions::TypeMap is not only important for set/queryCurrentValue but also for CommandLineParser.
    • CommandLineDialog::FileCommandLineQuery::handle() expects boost::filesystem::path
    • new validate for boost::filesystem::path
    • AddOptionsToParser was missing case for enum File
    • no enum File in TypeEnumMap
  • BUGFIX: InputAction
    • now setting prefix for all parsers even if filename nor present
    • now always setting name of last inserted molecule in World::getInstance().getMolecules()
    • not returning Action::failure when not present, only when not has_filename()
  • BUGFIX: PdbParser and TremoloParser were not inserting, but only creating a new molecule
  • BUGFIX: TremoloParser::load() nad no ASSET(false) as it's not implemented.
  • BUGFIX: as molId of 0 may occur, PdbParser::save() prints -1 for homeless atoms now
  • TESTFIX: Simple_configuration/2/test.pdb has molnr of 0 instead of former 1 (see above)
  • Property mode set to 100644
File size: 16.7 KB
Line 
1/*
2 * Project: MoleCuilder
3 * Description: creates and alters molecular systems
4 * Copyright (C) 2010 University of Bonn. All rights reserved.
5 * Please see the LICENSE file or "Copyright notice" in builder.cpp for details.
6 */
7
8/*
9 * CommandLineDialog.cpp
10 *
11 * Created on: May 8, 2010
12 * Author: heber
13 */
14
15// include config.h
16#ifdef HAVE_CONFIG_H
17#include <config.h>
18#endif
19
20#include "Helpers/MemDebug.hpp"
21
22#include <iostream>
23#include <vector>
24
25#include <Descriptors/AtomDescriptor.hpp>
26#include <Descriptors/AtomIdDescriptor.hpp>
27#include <Descriptors/MoleculeDescriptor.hpp>
28#include <Descriptors/MoleculeIdDescriptor.hpp>
29#include "CommandLineUI/CommandLineDialog.hpp"
30
31#include "Actions/Values.hpp"
32
33#include "element.hpp"
34#include "periodentafel.hpp"
35#include "CommandLineParser.hpp"
36#include "defs.hpp"
37#include "Helpers/Log.hpp"
38#include "LinearAlgebra/Matrix.hpp"
39#include "periodentafel.hpp"
40#include "Helpers/Verbose.hpp"
41#include "World.hpp"
42#include "Box.hpp"
43
44#include "atom.hpp"
45#include "element.hpp"
46#include "molecule.hpp"
47#include "LinearAlgebra/Vector.hpp"
48
49using namespace std;
50
51
52CommandLineDialog::CommandLineDialog()
53{
54}
55
56CommandLineDialog::~CommandLineDialog()
57{
58}
59
60
61void CommandLineDialog::queryEmpty(const char* title, string _description){
62 registerQuery(new EmptyCommandLineQuery(title, _description));
63}
64
65void CommandLineDialog::queryInt(const char* title, string _description){
66 registerQuery(new IntCommandLineQuery(title, _description));
67}
68
69void CommandLineDialog::queryInts(const char* title, string _description){
70 registerQuery(new IntsCommandLineQuery(title, _description));
71}
72
73void CommandLineDialog::queryBoolean(const char* title, string _description){
74 registerQuery(new BooleanCommandLineQuery(title, _description));
75}
76
77void CommandLineDialog::queryDouble(const char* title, string _description){
78 registerQuery(new DoubleCommandLineQuery(title, _description));
79}
80
81void CommandLineDialog::queryDoubles(const char* title, string _description){
82 registerQuery(new DoublesCommandLineQuery(title, _description));
83}
84
85void CommandLineDialog::queryString(const char* title, string _description){
86 registerQuery(new StringCommandLineQuery(title, _description));
87}
88
89void CommandLineDialog::queryStrings(const char* title, string _description){
90 registerQuery(new StringsCommandLineQuery(title, _description));
91}
92
93void CommandLineDialog::queryAtom(const char* title, string _description) {
94 registerQuery(new AtomCommandLineQuery(title, _description));
95}
96
97void CommandLineDialog::queryAtoms(const char* title, string _description) {
98 registerQuery(new AtomsCommandLineQuery(title, _description));
99}
100
101void CommandLineDialog::queryMolecule(const char* title, string _description) {
102 registerQuery(new MoleculeCommandLineQuery(title, _description));
103}
104
105void CommandLineDialog::queryMolecules(const char* title, string _description) {
106 registerQuery(new MoleculesCommandLineQuery(title, _description));
107}
108
109void CommandLineDialog::queryVector(const char* title, bool check, string _description) {
110 registerQuery(new VectorCommandLineQuery(title,check, _description));
111}
112
113void CommandLineDialog::queryVectors(const char* title, bool check, string _description) {
114 registerQuery(new VectorsCommandLineQuery(title,check, _description));
115}
116
117void CommandLineDialog::queryBox(const char* title, string _description) {
118 registerQuery(new BoxCommandLineQuery(title,_description));
119}
120
121void CommandLineDialog::queryElement(const char* title, string _description){
122 registerQuery(new ElementCommandLineQuery(title, _description));
123}
124
125void CommandLineDialog::queryElements(const char* title, string _description){
126 registerQuery(new ElementsCommandLineQuery(title, _description));
127}
128
129void CommandLineDialog::queryFile(const char* title, string _description){
130 registerQuery(new FileCommandLineQuery(title, _description));
131}
132
133/************************** Query Infrastructure ************************/
134
135CommandLineDialog::EmptyCommandLineQuery::EmptyCommandLineQuery(string title, string _description) :
136 Dialog::EmptyQuery(title, _description)
137{}
138
139CommandLineDialog::EmptyCommandLineQuery::~EmptyCommandLineQuery() {}
140
141bool CommandLineDialog::EmptyCommandLineQuery::handle() {
142 cout << "Message of " << getTitle() << ":\n" << getDescription() << "\n";
143 return true;
144}
145
146CommandLineDialog::IntCommandLineQuery::IntCommandLineQuery(string title, string _description) :
147 Dialog::IntQuery(title, _description)
148{}
149
150CommandLineDialog::IntCommandLineQuery::~IntCommandLineQuery() {}
151
152bool CommandLineDialog::IntCommandLineQuery::handle() {
153 if (CommandLineParser::getInstance().vm.count(getTitle())) {
154 tmp = CommandLineParser::getInstance().vm[getTitle()].as<int>();
155 return true;
156 } else {
157 DoeLog(1) && (eLog() << Verbose(1) << "CommandLineUI parsing error: Missing integer for " << getTitle() << "." << endl);
158 return false;
159 }
160}
161
162CommandLineDialog::IntsCommandLineQuery::IntsCommandLineQuery(string title, string _description) :
163 Dialog::IntsQuery(title, _description)
164{}
165
166CommandLineDialog::IntsCommandLineQuery::~IntsCommandLineQuery() {}
167
168bool CommandLineDialog::IntsCommandLineQuery::handle() {
169 if (CommandLineParser::getInstance().vm.count(getTitle())) {
170 tmp = CommandLineParser::getInstance().vm[getTitle()].as< std::vector<int> >();
171 return true;
172 } else {
173 DoeLog(1) && (eLog() << Verbose(1) << "CommandLineUI parsing error: Missing integers for " << getTitle() << "." << endl);
174 return false;
175 }
176}
177
178CommandLineDialog::BooleanCommandLineQuery::BooleanCommandLineQuery(string title, string _description) :
179 Dialog::BooleanQuery(title, _description)
180{}
181
182CommandLineDialog::BooleanCommandLineQuery::~BooleanCommandLineQuery() {}
183
184bool CommandLineDialog::BooleanCommandLineQuery::handle() {
185 if (CommandLineParser::getInstance().vm.count(getTitle())) {
186 tmp = CommandLineParser::getInstance().vm[getTitle()].as<bool>();
187 return true;
188 } else {
189 DoeLog(1) && (eLog() << Verbose(1) << "CommandLineUI parsing error: Missing boolean for " << getTitle() << "." << endl);
190 return false;
191 }
192}
193
194CommandLineDialog::StringCommandLineQuery::StringCommandLineQuery(string title, string _description) :
195 Dialog::StringQuery(title, _description)
196{}
197
198CommandLineDialog::StringCommandLineQuery::~StringCommandLineQuery() {}
199
200bool CommandLineDialog::StringCommandLineQuery::handle() {
201 if (CommandLineParser::getInstance().vm.count(getTitle())) {
202 tmp = CommandLineParser::getInstance().vm[getTitle()].as<string>();
203 return true;
204 } else {
205 DoeLog(1) && (eLog() << Verbose(1) << "CommandLineUI parsing error: Missing string for " << getTitle() << "." << endl);
206 return false;
207 }
208}
209
210CommandLineDialog::StringsCommandLineQuery::StringsCommandLineQuery(string title, string _description) :
211 Dialog::StringsQuery(title, _description)
212{}
213
214CommandLineDialog::StringsCommandLineQuery::~StringsCommandLineQuery() {}
215
216bool CommandLineDialog::StringsCommandLineQuery::handle() {
217 if (CommandLineParser::getInstance().vm.count(getTitle())) {
218 tmp = CommandLineParser::getInstance().vm[getTitle()].as< vector<string> >();
219 return true;
220 } else {
221 DoeLog(1) && (eLog() << Verbose(1) << "CommandLineUI parsing error: Missing strings for " << getTitle() << "." << endl);
222 return false;
223 }
224}
225
226CommandLineDialog::DoubleCommandLineQuery::DoubleCommandLineQuery(string title, string _description) :
227 Dialog::DoubleQuery(title, _description)
228{}
229
230CommandLineDialog::DoubleCommandLineQuery::~DoubleCommandLineQuery() {}
231
232bool CommandLineDialog::DoubleCommandLineQuery::handle() {
233 if (CommandLineParser::getInstance().vm.count(getTitle())) {
234 tmp = CommandLineParser::getInstance().vm[getTitle()].as<double>();
235 return true;
236 } else {
237 DoeLog(1) && (eLog() << Verbose(1) << "CommandLineUI parsing error: Missing double for " << getTitle() << "." << endl);
238 return false;
239 }
240}
241
242CommandLineDialog::DoublesCommandLineQuery::DoublesCommandLineQuery(string title, string _description) :
243 Dialog::DoublesQuery(title, _description)
244{}
245
246CommandLineDialog::DoublesCommandLineQuery::~DoublesCommandLineQuery() {}
247
248bool CommandLineDialog::DoublesCommandLineQuery::handle() {
249 if (CommandLineParser::getInstance().vm.count(getTitle())) {
250 tmp = CommandLineParser::getInstance().vm[getTitle()].as< std::vector<double> >();
251 return true;
252 } else {
253 DoeLog(1) && (eLog() << Verbose(1) << "CommandLineUI parsing error: Missing doubles for " << getTitle() << "." << endl);
254 return false;
255 }
256}
257
258CommandLineDialog::AtomCommandLineQuery::AtomCommandLineQuery(string title, string _description) :
259 Dialog::AtomQuery(title, _description)
260{}
261
262CommandLineDialog::AtomCommandLineQuery::~AtomCommandLineQuery() {}
263
264bool CommandLineDialog::AtomCommandLineQuery::handle() {
265 int IdxOfAtom = -1;
266 if (CommandLineParser::getInstance().vm.count(getTitle())) {
267 IdxOfAtom = CommandLineParser::getInstance().vm[getTitle()].as<int>();
268 tmp = World::getInstance().getAtom(AtomById(IdxOfAtom));
269 return true;
270 } else {
271 DoeLog(1) && (eLog() << Verbose(1) << "CommandLineUI parsing error: Missing atom for " << getTitle() << "." << endl);
272 return false;
273 }
274}
275
276CommandLineDialog::AtomsCommandLineQuery::AtomsCommandLineQuery(string title, string _description) :
277 Dialog::AtomsQuery(title, _description)
278{}
279
280CommandLineDialog::AtomsCommandLineQuery::~AtomsCommandLineQuery() {}
281
282bool CommandLineDialog::AtomsCommandLineQuery::handle() {
283 std::vector<int> IdxOfAtom;
284 if (CommandLineParser::getInstance().vm.count(getTitle())) {
285 IdxOfAtom = CommandLineParser::getInstance().vm[getTitle()].as< std::vector<int> >();
286 for (std::vector<int>::iterator iter = IdxOfAtom.begin(); iter != IdxOfAtom.end(); ++iter) {
287 temp = World::getInstance().getAtom(AtomById(*iter));
288 if (temp)
289 tmp.push_back(temp);
290 }
291 return true;
292 } else {
293 DoeLog(1) && (eLog() << Verbose(1) << "CommandLineUI parsing error: Missing atoms for " << getTitle() << "." << endl);
294 return false;
295 }
296}
297
298CommandLineDialog::MoleculeCommandLineQuery::MoleculeCommandLineQuery(string title, string _description) :
299 Dialog::MoleculeQuery(title, _description)
300{}
301
302CommandLineDialog::MoleculeCommandLineQuery::~MoleculeCommandLineQuery() {}
303
304bool CommandLineDialog::MoleculeCommandLineQuery::handle() {
305 int IdxOfMol = -1;
306 if (CommandLineParser::getInstance().vm.count(getTitle())) {
307 IdxOfMol = CommandLineParser::getInstance().vm[getTitle()].as<int>();
308 tmp = World::getInstance().getMolecule(MoleculeById(IdxOfMol));
309 return true;
310 } else {
311 DoeLog(1) && (eLog() << Verbose(1) << "CommandLineUI parsing error: Missing molecule for " << getTitle() << "." << endl);
312 return false;
313 }
314}
315
316CommandLineDialog::MoleculesCommandLineQuery::MoleculesCommandLineQuery(string title, string _description) :
317 Dialog::MoleculesQuery(title, _description)
318{}
319
320CommandLineDialog::MoleculesCommandLineQuery::~MoleculesCommandLineQuery() {}
321
322bool CommandLineDialog::MoleculesCommandLineQuery::handle() {
323 std::vector<int> IdxOfMol;
324 if (CommandLineParser::getInstance().vm.count(getTitle())) {
325 IdxOfMol = CommandLineParser::getInstance().vm[getTitle()].as< std::vector<int> >();
326 for (std::vector<int>::iterator iter = IdxOfMol.begin(); iter != IdxOfMol.end(); ++iter) {
327 temp = World::getInstance().getMolecule(MoleculeById(*iter));
328 if (temp)
329 tmp.push_back(temp);
330 }
331 return true;
332 } else {
333 DoeLog(1) && (eLog() << Verbose(1) << "CommandLineUI parsing error: Missing molecules for " << getTitle() << "." << endl);
334 return false;
335 }
336}
337
338CommandLineDialog::VectorCommandLineQuery::VectorCommandLineQuery(string title, bool _check, string _description) :
339 Dialog::VectorQuery(title,_check, _description)
340{}
341
342CommandLineDialog::VectorCommandLineQuery::~VectorCommandLineQuery()
343{}
344
345bool CommandLineDialog::VectorCommandLineQuery::handle() {
346 VectorValue temp;
347 if (CommandLineParser::getInstance().vm.count(getTitle())) {
348 temp = CommandLineParser::getInstance().vm[getTitle()].as< VectorValue >();
349 tmp[0] = temp.x;
350 tmp[1] = temp.y;
351 tmp[2] = temp.z;
352 if ((check) && (!World::getInstance().getDomain().isInside(tmp))) {
353 DoeLog(1) && (eLog() << Verbose(1) << "Vector " << tmp << " would be outside of box domain." << endl);
354 return false;
355 }
356 return true;
357 } else {
358 DoeLog(1) && (eLog() << Verbose(1) << "CommandLineUI parsing error: Missing vector for " << getTitle() << "." << endl);
359 return false;
360 }
361}
362
363CommandLineDialog::VectorsCommandLineQuery::VectorsCommandLineQuery(string title, bool _check, string _description) :
364 Dialog::VectorsQuery(title,_check, _description)
365{}
366
367CommandLineDialog::VectorsCommandLineQuery::~VectorsCommandLineQuery()
368{}
369
370bool CommandLineDialog::VectorsCommandLineQuery::handle() {
371 std::vector<VectorValue> temporary;
372 if (CommandLineParser::getInstance().vm.count(getTitle())) {
373 temporary = CommandLineParser::getInstance().vm[getTitle()].as< std::vector<VectorValue> >();
374 for(std::vector<VectorValue>::iterator iter = temporary.begin(); iter != temporary.end(); ++iter) {
375 temp[0] = (*iter).x;
376 temp[1] = (*iter).y;
377 temp[2] = (*iter).z;
378 if ((!check) || (World::getInstance().getDomain().isInside(temp)))
379 tmp.push_back(temp);
380 else
381 DoeLog(1) && (eLog() << Verbose(1) << "Vector " << temp << " would be outside of box domain." << endl);
382 }
383 return true;
384 } else {
385 DoeLog(1) && (eLog() << Verbose(1) << "CommandLineUI parsing error: Missing vectors for " << getTitle() << "." << endl);
386 return false;
387 }
388}
389
390CommandLineDialog::BoxCommandLineQuery::BoxCommandLineQuery(string title, string _description) :
391 Dialog::BoxQuery(title, _description)
392{}
393
394CommandLineDialog::BoxCommandLineQuery::~BoxCommandLineQuery()
395{}
396
397bool CommandLineDialog::BoxCommandLineQuery::handle() {
398 BoxValue temp;
399 if (CommandLineParser::getInstance().vm.count(getTitle())) {
400 temp = CommandLineParser::getInstance().vm[getTitle()].as< BoxValue >();
401 Matrix M;
402 M.set(0,0, temp.xx);
403 M.set(0,1, temp.yx);
404 M.set(0,2, temp.zx);
405 M.set(1,0, temp.yx);
406 M.set(1,1, temp.yy);
407 M.set(1,2, temp.zy);
408 M.set(2,0, temp.zx);
409 M.set(2,1, temp.zy);
410 M.set(2,2, temp.zz);
411 tmp.setM(M);
412 return true;
413 } else {
414 DoeLog(1) && (eLog() << Verbose(1) << "CommandLineUI parsing error: Missing symmetric box matrix for " << getTitle() << "." << endl);
415 return false;
416 }
417}
418
419CommandLineDialog::ElementCommandLineQuery::ElementCommandLineQuery(string title, string _description) :
420 Dialog::ElementQuery(title, _description)
421{}
422
423CommandLineDialog::ElementCommandLineQuery::~ElementCommandLineQuery()
424{}
425
426bool CommandLineDialog::ElementCommandLineQuery::handle() {
427 // TODO: vector of ints and removing first is not correctly implemented yet. How to remove from a vector?
428 periodentafel *periode = World::getInstance().getPeriode();
429 if (CommandLineParser::getInstance().vm.count(getTitle())) {
430 int Z = CommandLineParser::getInstance().vm[getTitle()].as< int >();
431 tmp = periode->FindElement(Z);
432 ASSERT(tmp != NULL, "Invalid element specified in ElementCommandLineQuery");
433 return true;
434 } else {
435 DoeLog(1) && (eLog() << Verbose(1) << "CommandLineUI parsing error: Missing element for " << getTitle() << "." << endl);
436 return false;
437 }
438}
439
440CommandLineDialog::ElementsCommandLineQuery::ElementsCommandLineQuery(string title, string _description) :
441 Dialog::ElementsQuery(title, _description)
442{}
443
444CommandLineDialog::ElementsCommandLineQuery::~ElementsCommandLineQuery()
445{}
446
447bool CommandLineDialog::ElementsCommandLineQuery::handle() {
448 // TODO: vector of ints and removing first is not correctly implemented yet. How to remove from a vector?
449 periodentafel *periode = World::getInstance().getPeriode();
450 if (CommandLineParser::getInstance().vm.count(getTitle())) {
451 vector<int> AllElements = CommandLineParser::getInstance().vm[getTitle()].as< vector<int> >();
452 for (vector<int>::iterator ZRunner = AllElements.begin(); ZRunner != AllElements.end(); ++ZRunner) {
453 temp = periode->FindElement(*ZRunner);
454 ASSERT(temp != NULL, "Invalid element specified in ElementCommandLineQuery");
455 tmp.push_back(temp);
456 }
457 return true;
458 } else {
459 DoeLog(1) && (eLog() << Verbose(1) << "CommandLineUI parsing error: Missing elements for " << getTitle() << "." << endl);
460 return false;
461 }
462}
463
464CommandLineDialog::FileCommandLineQuery::FileCommandLineQuery(string title, string _description) :
465 Dialog::FileQuery(title, _description)
466{}
467
468CommandLineDialog::FileCommandLineQuery::~FileCommandLineQuery() {}
469
470bool CommandLineDialog::FileCommandLineQuery::handle() {
471 if (CommandLineParser::getInstance().vm.count(getTitle())) {
472 tmp = CommandLineParser::getInstance().vm[getTitle()].as< boost::filesystem::path >();
473 return true;
474 } else {
475 DoeLog(1) && (eLog() << Verbose(1) << "CommandLineUI parsing error: Missing string for " << getTitle() << "." << endl);
476 return false;
477 }
478}
479
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