Changeset 63fb7a for src


Ignore:
Timestamp:
Jul 24, 2015, 4:44:34 PM (10 years ago)
Author:
Frederik Heber <heber@…>
Branches:
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
Children:
1259df
Parents:
795c0f
git-author:
Frederik Heber <heber@…> (06/01/15 08:48:35)
git-committer:
Frederik Heber <heber@…> (07/24/15 16:44:34)
Message:

Replaced getMolecule() by const access version where possible.

  • so far this is done done via const_casting the World.
Location:
src
Files:
16 edited

Legend:

Unmodified
Added
Removed

  • src/Actions/MoleculeAction/StretchBondAction.cpp

    r795c0f r63fb7a  
    6161    return Action::failure;
    6262  }
    63   const molecule *mol = atoms[0]->getMolecule();
     63  molecule *mol = World::getInstance().
     64      getMolecule(MoleculeById(atoms[0]->getMolecule()->getId()));
    6465  if (mol != atoms[1]->getMolecule()) {
    6566    STATUS("The two selected atoms must belong to the same molecule.");
    … …  
    101102  const Vector NegativeShift = -state->shift * state->bondplane.getNormal();
    102103  Box &domain = World::getInstance().getDomain();
    103   for (molecule::iterator iter = state->mol->begin();
    104       iter != state->mol->end(); ++iter) {
     104  molecule *mol = World::getInstance().
     105      getMolecule(MoleculeById(state->mol->getId()));
     106  for (molecule::iterator iter = mol->begin();
     107      iter != mol->end(); ++iter) {
    105108    const Vector &position = (*iter)->getPosition();
    106109    // for each atom determine on which side of plane it is and shift accordingly
    … …  
    122125  const Vector NegativeShift = -state->shift * state->bondplane.getNormal();
    123126  Box &domain = World::getInstance().getDomain();
    124   for (molecule::iterator iter = state->mol->begin();
    125       iter != state->mol->end(); ++iter) {
     127  molecule *mol = World::getInstance().
     128      getMolecule(MoleculeById(state->mol->getId()));
     129  for (molecule::iterator iter = mol->begin();
     130      iter != mol->end(); ++iter) {
    126131    const Vector &position = (*iter)->getPosition();
    127132    // for each atom determine on which side of plane it is and shift accordingly

  • src/Actions/SelectionAction/Molecules/MoleculeByIdAction.cpp

    r795c0f r63fb7a  
    6565  undomolids.reserve(molids.size());
    6666  for (molids_t::const_iterator iter = molids.begin(); iter != molids.end(); ++iter) {
    67     const molecule *Walker = World::getInstance().getMolecule(MoleculeById(*iter));
     67    const molecule *Walker = const_cast<const World &>(World::getInstance()).
     68        getMolecule(MoleculeById(*iter));
    6869    if (Walker != NULL) {
    6970      if (!World::getInstance().isSelected(Walker)) {
    … …  
    105106  for (molids_t::const_iterator iter = state->undomolids.begin();
    106107      iter != state->undomolids.end(); ++iter) {
    107     const molecule *Walker = World::getInstance().getMolecule(MoleculeById(*iter));
     108    const molecule *Walker = const_cast<const World &>(World::getInstance()).
     109        getMolecule(MoleculeById(*iter));
    108110    World::getInstance().unselectMolecule(Walker);
    109111  }
    … …  
    117119  for (molids_t::const_iterator iter = state->undomolids.begin();
    118120      iter != state->undomolids.end(); ++iter) {
    119     const molecule *Walker = World::getInstance().getMolecule(MoleculeById(*iter));
     121    const molecule *Walker = const_cast<const World &>(World::getInstance()).
     122        getMolecule(MoleculeById(*iter));
    120123    World::getInstance().selectMolecule(Walker);
    121124  }

  • src/Actions/SelectionAction/Molecules/MoleculeByOrderAction.cpp

    r795c0f r63fb7a  
    5454
    5555ActionState::ptr SelectionMoleculeByOrderAction::performCall() {
    56   molecule *mol = World::getInstance().getMolecule(MoleculeByOrder(params.molindex.get()));
     56  const molecule *mol = const_cast<const World &>(World::getInstance()).
     57      getMolecule(MoleculeByOrder(params.molindex.get()));
    5758
    5859  if (mol != NULL) {

  • src/Actions/SelectionAction/Molecules/NotMoleculeByIdAction.cpp

    r795c0f r63fb7a  
    6464  undomolids.reserve(molids.size());
    6565  for (molids_t::const_iterator iter = molids.begin(); iter != molids.end(); ++iter) {
    66     const molecule *Walker = World::getInstance().getMolecule(MoleculeById(*iter));
     66    const molecule *Walker = const_cast<const World &>(World::getInstance()).
     67        getMolecule(MoleculeById(*iter));
    6768    if (Walker != NULL) {
    6869      if (World::getInstance().isSelected(Walker)) {
    … …  
    104105  for (molids_t::const_iterator iter = state->undomolids.begin();
    105106      iter != state->undomolids.end(); ++iter) {
    106     const molecule *Walker = World::getInstance().getMolecule(MoleculeById(*iter));
     107    const molecule *Walker = const_cast<const World &>(World::getInstance()).
     108        getMolecule(MoleculeById(*iter));
    107109    World::getInstance().selectMolecule(Walker);
    108110  }
    … …  
    116118  for (molids_t::const_iterator iter = state->undomolids.begin();
    117119      iter != state->undomolids.end(); ++iter) {
    118     const molecule *Walker = World::getInstance().getMolecule(MoleculeById(*iter));
     120    const molecule *Walker = const_cast<const World &>(World::getInstance()).
     121        getMolecule(MoleculeById(*iter));
    119122    World::getInstance().unselectMolecule(Walker);
    120123  }

  • src/Actions/SelectionAction/Molecules/NotMoleculeByOrderAction.cpp

    r795c0f r63fb7a  
    5454
    5555ActionState::ptr SelectionNotMoleculeByOrderAction::performCall() {
    56   molecule *mol = World::getInstance().getMolecule(MoleculeByOrder(params.molindex.get()));
     56  const molecule *mol = const_cast<const World &>(World::getInstance()).
     57      getMolecule(MoleculeByOrder(params.molindex.get()));
    5758
    5859  if (mol != NULL) {

  • src/Descriptors/unittests/MoleculeDescriptorUnitTest.cpp

    r795c0f r63fb7a  
    111111void MoleculeDescriptorTest::MoleculeIdTest(){
    112112  // test Molecules from boundaries and middle of the set
    113   molecule* testMolecule;
    114   testMolecule = World::getInstance().getMolecule(MoleculeById(moleculeIds[0]));
     113  const molecule* testMolecule;
     114  testMolecule = const_cast<const World &>(World::getInstance()).
     115      getMolecule(MoleculeById(moleculeIds[0]));
    115116  CPPUNIT_ASSERT(testMolecule);
    116117  CPPUNIT_ASSERT_EQUAL( moleculeIds[0], testMolecule->getId());
    117   testMolecule = World::getInstance().getMolecule(MoleculeById(moleculeIds[MOLECULE_COUNT/2]));
     118  testMolecule = const_cast<const World &>(World::getInstance()).
     119      getMolecule(MoleculeById(moleculeIds[MOLECULE_COUNT/2]));
    118120  CPPUNIT_ASSERT(testMolecule);
    119121  CPPUNIT_ASSERT_EQUAL( moleculeIds[MOLECULE_COUNT/2], testMolecule->getId());
    120   testMolecule = World::getInstance().getMolecule(MoleculeById(moleculeIds[MOLECULE_COUNT-1]));
     122  testMolecule = const_cast<const World &>(World::getInstance()).
     123      getMolecule(MoleculeById(moleculeIds[MOLECULE_COUNT-1]));
    121124  CPPUNIT_ASSERT(testMolecule);
    122125  CPPUNIT_ASSERT_EQUAL( moleculeIds[MOLECULE_COUNT-1], testMolecule->getId());
    … …  
    132135  }
    133136  // test from outside of set
    134   testMolecule = World::getInstance().getMolecule(MoleculeById(outsideId));
     137  testMolecule = const_cast<const World &>(World::getInstance()).
     138      getMolecule(MoleculeById(outsideId));
    135139  CPPUNIT_ASSERT(!testMolecule);
    136140}
    … …  
    189193void MoleculeDescriptorTest::MoleculeNameTest()
    190194{
    191   molecule* testMolecule;
     195  const molecule* testMolecule;
    192196
    193197  // name each molecule
    … …  
    197201  // retrieve each
    198202  for(int i=1;i<=MOLECULE_COUNT;++i) {
    199     testMolecule = World::getInstance().getMolecule(MoleculeByName(toString(i)));
     203    testMolecule = const_cast<const World &>(World::getInstance()).
     204        getMolecule(MoleculeByName(toString(i)));
    200205    CPPUNIT_ASSERT_EQUAL( moleculeIds[i-1], testMolecule->getId());
    201206  }
    202207
    203208  // check for non-present name
    204   testMolecule = World::getInstance().getMolecule(MoleculeByName("not present"));
     209  testMolecule = const_cast<const World &>(World::getInstance()).
     210      getMolecule(MoleculeByName("not present"));
    205211  CPPUNIT_ASSERT(!testMolecule);
    206212}
    … …  
    209215void MoleculeDescriptorTest::MoleculeOrderTest()
    210216{
    211   molecule* testMolecule;
     217  const molecule* testMolecule;
    212218
    213219  // test in normal order: 1, 2, ...
    214220  for(int i=1;i<=MOLECULE_COUNT;++i){
    215     testMolecule = World::getInstance().getMolecule(MoleculeByOrder(i));
     221    testMolecule = const_cast<const World &>(World::getInstance()).
     222        getMolecule(MoleculeByOrder(i));
    216223    CPPUNIT_ASSERT_EQUAL( moleculeIds[i-1], testMolecule->getId());
    217224  }
    … …  
    219226  // test in reverse order: -1, -2, ...
    220227  for(int i=1; i<= MOLECULE_COUNT;++i){
    221     testMolecule = World::getInstance().getMolecule(MoleculeByOrder(-i));
     228    testMolecule = const_cast<const World &>(World::getInstance()).
     229        getMolecule(MoleculeByOrder(-i));
    222230    CPPUNIT_ASSERT_EQUAL( moleculeIds[(int)MOLECULE_COUNT-i], testMolecule->getId());
    223231  }
    224232
    225233  // test from outside of set
    226   testMolecule = World::getInstance().getMolecule(MoleculeByOrder(MOLECULE_COUNT+1));
    227   CPPUNIT_ASSERT(!testMolecule);
    228   testMolecule = World::getInstance().getMolecule(MoleculeByOrder(-MOLECULE_COUNT-1));
    229   CPPUNIT_ASSERT(!testMolecule);
    230 }
     234  testMolecule = const_cast<const World &>(World::getInstance()).
     235      getMolecule(MoleculeByOrder(MOLECULE_COUNT+1));
     236  CPPUNIT_ASSERT(!testMolecule);
     237  testMolecule = const_cast<const World &>(World::getInstance()).
     238      getMolecule(MoleculeByOrder(-MOLECULE_COUNT-1));
     239  CPPUNIT_ASSERT(!testMolecule);
     240}

  • src/Parameters/StreamOperators.hpp

    r795c0f r63fb7a  
    127127  ConvertTo<unsigned int> converter;
    128128  const moleculeId_t temp_value = converter(line);
    129   const molecule *mol = World::getInstance().getMolecule(MoleculeById(temp_value));
     129  const molecule *mol = const_cast<const World &>(World::getInstance()).
     130      getMolecule(MoleculeById(temp_value));
    130131  ASSERT( mol != NULL,
    131132      "operator>>(std::istream& ist, const molecule* & m) - invalid molecule id "
    … …  
    162163      iter != tok.end(); ++iter) {
    163164    const moleculeId_t temp_value = converter(*iter);
    164     const molecule *mol = World::getInstance().getMolecule(MoleculeById(temp_value));
     165    const molecule *mol = const_cast<const World &>(World::getInstance()).
     166        getMolecule(MoleculeById(temp_value));
    165167    ASSERT( mol != NULL,
    166168        "operator>>(std::istream& ist, std::vector<const molecule*> & m) - invalid molecule id "

  • src/Parameters/Validators/Specific/MoleculeIdValidator.cpp

    r795c0f r63fb7a  
    4343bool MoleculeIdValidator::isValid(const moleculeId_t & _value) const
    4444{
    45   return (World::getInstance().getMolecule(MoleculeById(_value)) != NULL);
     45  return (const_cast<const World &>(World::getInstance()).getMolecule(MoleculeById(_value)) != NULL);
    4646}
    4747

  • src/UIElements/CommandLineUI/Query/MoleculesCommandLineQuery.cpp

    r795c0f r63fb7a  
    6161    }
    6262    for (std::vector<int>::iterator iter = IdxOfMol.begin(); iter != IdxOfMol.end(); ++iter) {
    63       const molecule *temp_element = World::getInstance().getMolecule(MoleculeById(*iter));
     63      const molecule *temp_element = const_cast<const World &>(World::getInstance()).
     64          getMolecule(MoleculeById(*iter));
    6465      if (temp_element)
    6566        temp.push_back(temp_element);

  • src/UIElements/Views/Qt4/MoleculeList/QtMoleculeItem.cpp

    r795c0f r63fb7a  
    7171void QtMoleculeItem::signOnToMolecule()
    7272{
    73   const molecule *mol = World::getInstance().getMolecule(MoleculeById(molid));
     73  const molecule * const mol = const_cast<const World &>(World::getInstance()).
     74      getMolecule(MoleculeById(molid));
    7475  if (mol != NULL) {
    7576    if (!IsSignedOn)
    … …  
    8384void QtMoleculeItem::signOffFromMolecule()
    8485{
    85   const molecule *mol = World::getInstance().getMolecule(MoleculeById(molid));
     86  const molecule * const mol = const_cast<const World &>(World::getInstance()).
     87      getMolecule(MoleculeById(molid));
    8688  if (mol != NULL) {
    8789    if (IsSignedOn)
    … …  
    140142const molecule * const QtMoleculeItem::getMolecule() const
    141143{
    142   const molecule * mol = World::getInstance().getMolecule(MoleculeById(molid));
     144  const molecule * const mol = const_cast<const World &>(World::getInstance()).getMolecule(MoleculeById(molid));
    143145  ASSERT (mol != NULL,
    144146      "QtMoleculeItem::getMolecule() - mol with "+toString(molid)+" is gone.");

  • src/UIElements/Views/Qt4/MoleculeList/QtMoleculeList.cpp

    r795c0f r63fb7a  
    578578            QtMoleculeItemFactory::NAME));
    579579    const moleculeId_t molid = ItemToMoleculeId(_item);
    580     const molecule *mol = World::getInstance().getMolecule(MoleculeById(molid));
     580    const molecule *mol = const_cast<const World &>(World::getInstance()).
     581        getMolecule(MoleculeById(molid));
    581582    if (std::binary_search(
    582583            toBeRemovedItems_copy.begin(), toBeRemovedItems_copy.end(),
    … …  
    624625//    LOG(1, "Adding molecule " << (*moliter)->getName());
    625626    // check that World knows the molecule still
    626     const molecule * const mol =
    627         World::getInstance().getMolecule(MoleculeById((*moliter)->getId()));
     627    const molecule * const mol = const_cast<const World &>(World::getInstance()).
     628        getMolecule(MoleculeById((*moliter)->getId()));
    628629    if ((mol != NULL) && (mol == *moliter)) {
    629630      addMolecule(mol);

  • src/UIElements/Views/Qt4/MoleculeList/SpecificItems/QtMoleculeItem_atomcount.hpp

    r795c0f r63fb7a  
    4444  void internal_updateState()
    4545  {
    46     const molecule * mol = World::getInstance().getMolecule(MoleculeById(molid));
     46    const molecule * mol = const_cast<const World &>(World::getInstance()).
     47        getMolecule(MoleculeById(molid));
    4748    if (mol != NULL)
    4849      setText(QString::number(mol->getAtomCount()));

  • src/UIElements/Views/Qt4/MoleculeList/SpecificItems/QtMoleculeItem_formula.hpp

    r795c0f r63fb7a  
    4747  void internal_updateState()
    4848  {
    49     const molecule * mol = World::getInstance().getMolecule(MoleculeById(molid));
     49    const molecule * mol = const_cast<const World &>(World::getInstance()).
     50        getMolecule(MoleculeById(molid));
    5051    if (mol != NULL)
    5152      setText(QString(mol->getFormula().toString().c_str()));

  • src/UIElements/Views/Qt4/MoleculeList/SpecificItems/QtMoleculeItem_name.hpp

    r795c0f r63fb7a  
    4444  void internal_updateState()
    4545  {
    46     const molecule * mol = World::getInstance().getMolecule(MoleculeById(molid));
     46    const molecule * mol = const_cast<const World &>(World::getInstance()).
     47        getMolecule(MoleculeById(molid));
    4748    if (mol != NULL)
    4849      setText(QString(mol->getName().c_str()));

  • src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp

    r795c0f r63fb7a  
    6969static QGLSceneNode *createMoleculeMesh(const moleculeId_t molid, QObject *parent)
    7070{
    71   const molecule *molref = World::getInstance().getMolecule(MoleculeById(molid));
     71  const molecule *molref = const_cast<const World &>(World::getInstance()).
     72      getMolecule(MoleculeById(molid));
    7273  if (molref == NULL) {
    7374    ELOG(1, "Could not createMoleculeMesh, molecule with id " << molid << " already gone.");
    … …  
    156157{
    157158  // sign on as observer (obtain non-const instance before)
    158   const molecule *_molecule = World::getInstance().getMolecule(MoleculeById(moleculeid));
     159  const molecule *_molecule = const_cast<const World &>(World::getInstance()).
     160      getMolecule(MoleculeById(moleculeid));
    159161  if (_molecule != NULL) {
    160162    _molecule->signOn(this, molecule::AtomInserted);
    … …  
    194196{
    195197  // sign on as observer (obtain non-const instance before)
    196   const molecule *_molecule = World::getInstance().getMolecule(MoleculeById(moleculeid));
     198  const molecule *_molecule = const_cast<const World &>(World::getInstance()).
     199      getMolecule(MoleculeById(moleculeid));
    197200  if (_molecule != NULL) {
    198201    _molecule->signOn(this, molecule::AtomInserted);
    … …  
    225228{
    226229  if (isSignedOn) {
    227     const molecule *_molecule = World::getInstance().getMolecule(MoleculeById(moleculeid));
     230    const molecule *_molecule = const_cast<const World &>(World::getInstance()).
     231        getMolecule(MoleculeById(moleculeid));
    228232    if (_molecule != NULL) {
    229233      _molecule->signOff(this, molecule::AtomInserted);
    … …  
    247251void GLMoleculeObject_molecule::init()
    248252{
    249   const molecule *_molecule = World::getInstance().getMolecule(MoleculeById(moleculeid));
     253  const molecule * const _molecule = const_cast<const World &>(World::getInstance()).
     254      getMolecule(MoleculeById(moleculeid));
    250255  if (_molecule == NULL) {
    251256    ELOG(1, "GLMoleculeObject_molecule cannot init, molecule with "
    … …  
    320325void GLMoleculeObject_molecule::reinit()
    321326{
    322   const molecule *_molecule = World::getInstance().getMolecule(MoleculeById(moleculeid));
     327  const molecule * const _molecule = const_cast<const World &>(World::getInstance()).
     328      getMolecule(MoleculeById(moleculeid));
    323329  if (_molecule == NULL) {
    324330    ELOG(1, "GLMoleculeObject_molecule cannot reinit, molecule with "
    … …  
    348354{
    349355  isBoundingBoxUptodate = true;
    350   const molecule *_molecule = World::getInstance().getMolecule(MoleculeById(moleculeid));
     356  const molecule * const _molecule = const_cast<const World &>(World::getInstance()).
     357      getMolecule(MoleculeById(moleculeid));
    351358  if (_molecule == NULL) {
    352359    ELOG(1, "GLMoleculeObject_molecule cannot updateBoundingBox, molecule with "
    … …  
    375382void GLMoleculeObject_molecule::recieveNotification(Observable *publisher, Notification_ptr notification)
    376383{
    377   const molecule *_molecule = World::getInstance().getMolecule(MoleculeById(moleculeid));
     384  const molecule * const _molecule = const_cast<const World &>(World::getInstance()).
     385      getMolecule(MoleculeById(moleculeid));
    378386  if (publisher == dynamic_cast<const Observable*>(_molecule)){
    379387    // notofication from atom

  • src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp

    r795c0f r63fb7a  
    162162{
    163163   LOG(3, "INFO: GLMoleculeObject_molecule - mol " << no << " has been clicked.");
    164    const molecule *mol= World::getInstance().getMolecule(MoleculeById(no));
     164   const molecule * const mol= const_cast<const World &>(World::getInstance()).
     165       getMolecule(MoleculeById(no));
    165166   ASSERT(mol, "Atom without molecule has been clicked.");
    166167   molids_t ids(1, mol->getId());
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