Changeset 1259df


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:
f01769
Parents:
63fb7a
git-author:
Frederik Heber <heber@…> (06/01/15 08:56:36)
git-committer:
Frederik Heber <heber@…> (07/24/15 16:44:34)
Message:

Replaced World::getAllMolecules() wherever possible by const version.

Location:
src
Files:
22 edited

Legend:

Unmodified
Added
Removed

  • src/Actions/FillAction/FillVolumeAction.cpp

    r63fb7a r1259df  
    7878  }
    7979  molecule *filler = *(molecules.begin());
    80   for(molecule::const_iterator iter = filler->begin(); iter != filler->end(); ++iter)
     80  for(molecule::const_iterator iter = const_cast<const molecule *>(filler)->begin();
     81      iter != const_cast<const molecule *>(filler)->end();
     82      ++iter)
    8183    movedatoms.push_back( AtomicInfo(*(*iter)) );
    8284  LOG(1, "INFO: Chosen molecule has " << filler->size() << " atoms.");

  • src/Actions/FillAction/SuspendInMoleculeAction.cpp

    r63fb7a r1259df  
    141141  double clustervolume = 0.;
    142142  std::vector<double> GreatestDiameter(NDIM, 0.);
    143   for (std::vector<molecule *>::iterator iter = molecules.begin();
     143  for (std::vector<molecule *>::const_iterator iter = molecules.begin();
    144144      iter != molecules.end(); ++iter)
    145145  {

  • src/Actions/GraphAction/CreateAdjacencyAction.cpp

    r63fb7a r1259df  
    109109  // give info
    110110  size_t BondCount = 0;
    111   std::vector<molecule *> molecules = World::getInstance().getAllMolecules();
    112   for (std::vector<molecule *>::const_iterator iter = molecules.begin();
     111  std::vector<const molecule *> molecules = const_cast<const World &>(World::getInstance()).
     112      getAllMolecules();
     113  for (std::vector<const molecule *>::const_iterator iter = molecules.begin();
    113114      iter != molecules.end(); ++iter)
    114115    BondCount += (*iter)->getBondCount();

  • src/Actions/GraphAction/UpdateMoleculesAction.cpp

    r63fb7a r1259df  
    6767  LOG(0, "STATUS: Creating undo state.");
    6868  MolAtomList moleculelist;
    69   vector<molecule *> allmolecules = World::getInstance().getAllMolecules();
    70   for (vector<molecule *>::const_iterator moliter = allmolecules.begin(); moliter != allmolecules.end(); ++moliter) {
    71     std::vector<atomId_t> atomlist;
    72     atomlist.resize((*moliter)->size());
    73     for (molecule::const_iterator atomiter = (*moliter)->begin(); atomiter != (*moliter)->end(); ++atomiter) {
    74       atomlist.push_back((*atomiter)->getId());
     69  {
     70    vector<const molecule *> allmolecules = const_cast<const World &>(World::getInstance()).
     71        getAllMolecules();
     72    for (vector<const molecule *>::const_iterator moliter = allmolecules.begin(); moliter != allmolecules.end(); ++moliter) {
     73      std::vector<atomId_t> atomlist;
     74      atomlist.resize((*moliter)->size());
     75      for (molecule::const_iterator atomiter = (*moliter)->begin(); atomiter != (*moliter)->end(); ++atomiter) {
     76        atomlist.push_back((*atomiter)->getId());
     77      }
     78      moleculelist.insert( std::pair< moleculeId_t, std::vector<atomId_t> > ((*moliter)->getId(), atomlist));
    7579    }
    76     moleculelist.insert( std::pair< moleculeId_t, std::vector<atomId_t> > ((*moliter)->getId(), atomlist));
    7780  }
    7881  GraphUpdateMoleculesState *UndoState = new GraphUpdateMoleculesState(moleculelist, params);
    … …  
    8184  LOG(0, "STATUS: Removing all present molecules.");
    8285  MoleculeListClass *molecules = World::getInstance().getMolecules();
     86  vector<molecule *> allmolecules = World::getInstance().getAllMolecules();
    8387  for (vector<molecule *>::iterator MolRunner = allmolecules.begin(); MolRunner != allmolecules.end(); ++MolRunner) {
    8488    molecules->erase(*MolRunner);
    … …  
    9094  DFS();
    9195  DFS.UpdateMoleculeStructure();
    92   if (World::getInstance().numMolecules() == 0) {
     96  const size_t numMolecules =
     97      const_cast<const World &>(World::getInstance()).numMolecules();
     98  if (numMolecules == 0) {
    9399    //World::getInstance().destroyMolecule(mol);
    94100    STATUS("There are no molecules.");
    … …  
    96102  }
    97103
    98   LOG(1, "I scanned " << World::getInstance().numMolecules() << " molecules.");
     104  LOG(1, "I scanned " << numMolecules << " molecules.");
    99105
    100106  return ActionState::ptr(UndoState);

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

    r63fb7a r1259df  
    5656ActionState::ptr SelectionMoleculeByFormulaAction::performCall() {
    5757  LOG(1, "Selecting molecules with chemical formula " << params.formula.get() << ":");
    58 //  std::vector<molecule *> matchingMolecules = World::getInstance().getAllMolecules(MoleculeByFormula(params.formula.get()));
    59   std::vector<molecule *> selectedMolecules =
    60       World::getInstance().getAllMolecules(MoleculesBySelection() && MoleculeByFormula(params.formula.get()));
     58  std::vector<const molecule *> selectedMolecules =
     59      const_cast<const World &>(World::getInstance()).
     60      getAllMolecules(MoleculesBySelection() && MoleculeByFormula(params.formula.get()));
    6161//  BOOST_FOREACH(molecule *mol, matchingMolecules)
    6262//    LOG(1, "\t" << mol->getId() << ", " << mol->getName() << ".");
    … …  
    7070
    7171  World::getInstance().unselectAllMolecules(MoleculeByFormula(state->params.formula.get()));
    72   BOOST_FOREACH( molecule *mol, state->selectedMolecules)
     72  BOOST_FOREACH( const molecule *mol, state->selectedMolecules)
    7373    World::getInstance().selectMolecule(mol);
    7474

  • src/Actions/SelectionAction/Molecules/MoleculeByFormulaAction.def

    r63fb7a r1259df  
    2222(FormulaValidator())
    2323
    24 #define statetypes (std::vector<molecule*>)
     24#define statetypes (std::vector<const molecule*>)
    2525#define statereferences (selectedMolecules)
    2626

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

    r63fb7a r1259df  
    5656ActionState::ptr SelectionMoleculeByNameAction::performCall() {
    5757  LOG(1, "Selecting all molecules called " << params.molname.get());
    58   std::vector<molecule *> selectedMolecules =
    59       World::getInstance().getAllMolecules(MoleculesBySelection() && MoleculeByName(params.molname.get()));
     58  std::vector<const molecule *> selectedMolecules =
     59      const_cast<const World &>(World::getInstance()).
     60      getAllMolecules(MoleculesBySelection() && MoleculeByName(params.molname.get()));
    6061  World::getInstance().selectAllMolecules(MoleculeByName(params.molname.get()));
    6162  LOG(0, World::getInstance().countSelectedMolecules() << " molecules selected.");
    … …  
    6869
    6970  World::getInstance().unselectAllMolecules(MoleculeByName(state->params.molname.get()));
    70   BOOST_FOREACH( molecule *mol, state->selectedMolecules)
     71  BOOST_FOREACH( const molecule *mol, state->selectedMolecules)
    7172    World::getInstance().selectMolecule(mol);
    7273

  • src/Actions/SelectionAction/Molecules/MoleculeByNameAction.def

    r63fb7a r1259df  
    2424(DummyValidator< std::string >())
    2525
    26 #define statetypes (std::vector<molecule *>)
     26#define statetypes (std::vector<const molecule *>)
    2727#define statereferences (selectedMolecules)
    2828

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

    r63fb7a r1259df  
    5656ActionState::ptr SelectionNotMoleculeByFormulaAction::performCall() {
    5757  LOG(1, "Unselecting molecules with chemical formula " << params.formula.get() << ":");
    58   std::vector<molecule *> matchingMolecules = World::getInstance().getAllMolecules(MoleculeByFormula(params.formula.get()));
    59   std::vector<molecule *> unselectedMolecules = World::getInstance().getAllMolecules(!MoleculesBySelection());
     58  std::vector<const molecule *> matchingMolecules =
     59      const_cast<const World &>(World::getInstance()).
     60      getAllMolecules(MoleculeByFormula(params.formula.get()));
     61  std::vector<const molecule *> unselectedMolecules =
     62      const_cast<const World &>(World::getInstance()).
     63      getAllMolecules(!MoleculesBySelection());
    6064  World::getInstance().unselectAllMolecules(MoleculeByFormula(params.formula.get()));
    6165  LOG(0, World::getInstance().countSelectedMolecules() << " molecules remain selected.");
    … …  
    6771
    6872  World::getInstance().selectAllMolecules(MoleculeByFormula(state->params.formula.get()));
    69   BOOST_FOREACH( molecule *mol, state->unselectedMolecules)
     73  BOOST_FOREACH( const molecule *mol, state->unselectedMolecules)
    7074    World::getInstance().unselectMolecule(mol);
    7175

  • src/Actions/SelectionAction/Molecules/NotMoleculeByFormulaAction.def

    r63fb7a r1259df  
    2222(FormulaValidator())
    2323
    24 #define statetypes (std::vector<molecule*>)
     24#define statetypes (std::vector<const molecule*>)
    2525#define statereferences (unselectedMolecules)
    2626

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

    r63fb7a r1259df  
    5656ActionState::ptr SelectionNotMoleculeByNameAction::performCall() {
    5757  LOG(1, "Unselecting all molecule called " << params.molname.get());
    58   std::vector<molecule *> unselectedMolecules =
    59       World::getInstance().getAllMolecules((!MoleculesBySelection()) && MoleculeByName(params.molname.get()));
     58  std::vector<const molecule *> unselectedMolecules =
     59      const_cast<const World &>(World::getInstance()).
     60        getAllMolecules((!MoleculesBySelection()) && MoleculeByName(params.molname.get()));
    6061  World::getInstance().unselectAllMolecules(MoleculeByName(params.molname.get()));
    6162  LOG(0, World::getInstance().countSelectedMolecules() << " molecules remain selected.");
    … …  
    6869
    6970  World::getInstance().selectAllMolecules(MoleculeByName(state->params.molname.get()));
    70   BOOST_FOREACH( molecule *mol, state->unselectedMolecules)
     71  BOOST_FOREACH( const molecule *mol, state->unselectedMolecules)
    7172    World::getInstance().unselectMolecule(mol);
    7273

  • src/Actions/SelectionAction/Molecules/NotMoleculeByNameAction.def

    r63fb7a r1259df  
    2222(DummyValidator< std::string >())
    2323
    24 #define statetypes (std::vector<molecule *>)
     24#define statetypes (std::vector<const molecule *>)
    2525#define statereferences (unselectedMolecules)
    2626

  • src/Actions/WorldAction/BoundInBoxAction.cpp

    r63fb7a r1259df  
    5656  // create undo state
    5757  std::vector< boost::shared_ptr<Vector> > OldPositions;
    58   std::vector<molecule*> AllMolecules = World::getInstance().getAllMolecules();
    59   for (vector<molecule*>::iterator MolRunner = AllMolecules.begin();
    60       MolRunner != AllMolecules.end();
    61       ++MolRunner) {
    62     for(molecule::const_iterator AtomRunner = (*MolRunner)->begin();
    63         AtomRunner != (*MolRunner)->end();
    64         ++AtomRunner) {
    65       OldPositions.push_back(
    66           boost::shared_ptr<Vector>(new Vector(
    67               (*AtomRunner)->getPosition()
    68               ))
    69           );
     58  {
     59    std::vector<const molecule*> AllMolecules = const_cast<const World &>(World::getInstance()).
     60        getAllMolecules();
     61    for (vector<const molecule*>::iterator MolRunner = AllMolecules.begin();
     62        MolRunner != AllMolecules.end();
     63        ++MolRunner) {
     64      for(molecule::const_iterator AtomRunner = (*MolRunner)->begin();
     65          AtomRunner != (*MolRunner)->end();
     66          ++AtomRunner) {
     67        OldPositions.push_back(
     68            boost::shared_ptr<Vector>(new Vector(
     69                (*AtomRunner)->getPosition()
     70                ))
     71            );
     72      }
    7073    }
    7174  }
    … …  
    7376
    7477  // center
     78  std::vector<molecule*> AllMolecules = World::getInstance().getAllMolecules();
    7579  for (std::vector<molecule*>::iterator MolRunner = AllMolecules.begin(); MolRunner != AllMolecules.end(); ++MolRunner) {
    7680    (*MolRunner)->BoundInBox();

  • src/Actions/WorldAction/CenterInBoxAction.cpp

    r63fb7a r1259df  
    6868  oa << matrix;
    6969  std::vector< boost::shared_ptr<Vector> > OldPositions;
    70   std::vector<molecule*> AllMolecules = World::getInstance().getAllMolecules();
    71   for (std::vector<molecule*>::iterator MolRunner = AllMolecules.begin();
    72       MolRunner != AllMolecules.end();
    73       ++MolRunner) {
    74     for(molecule::const_iterator AtomRunner = (*MolRunner)->begin();
    75         AtomRunner != (*MolRunner)->end();
    76         ++AtomRunner) {
    77       OldPositions.push_back(
    78           boost::shared_ptr<Vector>(new Vector(
    79               (*AtomRunner)->getPosition()
    80               ))
    81           );
     70  {
     71    std::vector<const molecule*> AllMolecules = const_cast<const World &>(World::getInstance()).
     72        getAllMolecules();
     73    for (std::vector<const molecule*>::iterator MolRunner = AllMolecules.begin();
     74        MolRunner != AllMolecules.end();
     75        ++MolRunner) {
     76      for(molecule::const_iterator AtomRunner = (*MolRunner)->begin();
     77          AtomRunner != (*MolRunner)->end();
     78          ++AtomRunner) {
     79        OldPositions.push_back(
     80            boost::shared_ptr<Vector>(new Vector(
     81                (*AtomRunner)->getPosition()
     82                ))
     83            );
     84      }
    8285    }
    8386  }
    … …  
    8790
    8891  // center atoms
     92  std::vector<molecule*> AllMolecules = World::getInstance().getAllMolecules();
    8993  for (std::vector<molecule*>::iterator MolRunner = AllMolecules.begin(); MolRunner != AllMolecules.end(); ++MolRunner) {
    9094    (*MolRunner)->CenterInBox();

  • src/Actions/WorldAction/RepeatBoxAction.cpp

    r63fb7a r1259df  
    6363void repeatMoleculesinDomain(
    6464    std::vector< unsigned int > Repeater,
    65     const std::vector<molecule *> &AllMolecules)
     65    const std::vector<const molecule *> &AllMolecules)
    6666{
    6767  LOG(0, "STATUS: Repeating box " << Repeater << " times for (x,y,z) axis.");
    … …  
    8585
    8686  // add molecules in each repeated domain part
    87   molecule *newmol = NULL;
    8887  std::vector<Vector> vectors;
    8988  MoleculeListClass *molecules = World::getInstance().getMolecules();
    … …  
    9695        if ((n[0] == 0) && (n[1] == 0) && (n[2] == 0))
    9796          continue;
    98         for (vector<molecule *>::const_iterator MolRunner = AllMolecules.begin(); MolRunner != AllMolecules.end(); ++MolRunner) {
    99           molecule * const mol = *MolRunner;
     97        for (vector<const molecule *>::const_iterator MolRunner = AllMolecules.begin(); MolRunner != AllMolecules.end(); ++MolRunner) {
     98          const molecule * const mol = *MolRunner;
    10099          LOG(2, "DEBUG: Current mol is " << mol->name << "." << endl);
    101           newmol = mol->CopyMolecule();
     100          molecule * const newmol = mol->CopyMolecule();
    102101          // TODO: remove this when World does not have MoleculeListClass anymore.
    103102          molecules->insert(newmol);
    … …  
    114113
    115114ActionState::ptr WorldRepeatBoxAction::performCall() {
    116   std::vector<molecule *> AllMolecules;
    117115  DoLog(0) && (Log() << Verbose(0) << "Using all molecules." << endl);
    118   AllMolecules = World::getInstance().getAllMolecules();
     116  std::vector<const molecule *> AllMolecules =
     117      const_cast<const World &>(World::getInstance()).getAllMolecules();
    119118
    120119  // prepare undo state
    121120  RealSpaceMatrix olddomain = World::getInstance().getDomain().getM();
    122   std::set<molecule *> oldmolecules;
    123   for(std::vector<molecule *>::const_iterator iter = AllMolecules.begin();
     121  std::set<const molecule *> oldmolecules;
     122  for(std::vector<const molecule *>::const_iterator iter = AllMolecules.begin();
    124123      iter != AllMolecules.end();
    125124      ++iter)
    … …  
    160159  WorldRepeatBoxState *state = assert_cast<WorldRepeatBoxState*>(_state.get());
    161160
    162   std::vector<molecule *> originalmolecules;
    163   for(std::set<molecule *>::const_iterator iter = state->oldmolecules.begin();
     161  std::vector<const molecule *> originalmolecules;
     162  for(std::set<const molecule *>::const_iterator iter = state->oldmolecules.begin();
    164163      iter != state->oldmolecules.end();
    165164      ++iter)

  • src/Actions/WorldAction/RepeatBoxAction.def

    r63fb7a r1259df  
    2828(STLVectorValidator< std::vector< unsigned int > >(NDIM, NDIM))
    2929
    30 #define statetypes (RealSpaceMatrix)(std::set< molecule *>)
     30#define statetypes (RealSpaceMatrix)(std::set< const molecule *>)
    3131#define statereferences (olddomain)(oldmolecules)
    3232

  • src/Descriptors/unittests/MoleculeDescriptorUnitTest.cpp

    r63fb7a r1259df  
    7070
    7171// some helper functions
    72 static bool hasAllMolecules(std::vector<molecule*> molecules,moleculeId_t ids[MOLECULE_COUNT], std::set<moleculeId_t> excluded = std::set<moleculeId_t>()){
     72static bool hasAllMolecules(
     73    std::vector<const molecule*> &molecules,
     74    moleculeId_t ids[MOLECULE_COUNT],
     75    std::set<moleculeId_t> excluded = std::set<moleculeId_t>())
     76{
    7377  for(int i=0;i<MOLECULE_COUNT;++i){
    7478    moleculeId_t id = ids[i];
    7579    if(!excluded.count(id)){
    76       std::vector<molecule*>::iterator iter;
     80      std::vector<const molecule*>::const_iterator iter;
    7781      bool res=false;
    7882      for(iter=molecules.begin();iter!=molecules.end();++iter){
    … …  
    8892}
    8993
    90 static bool hasNoDuplicateMolecules(std::vector<molecule*> molecules){
     94static bool hasNoDuplicateMolecules(std::vector<const molecule*> &molecules){
    9195  std::set<moleculeId_t> found;
    92   std::vector<molecule*>::iterator iter;
     96  std::vector<const molecule*>::const_iterator iter;
    9397  for(iter=molecules.begin();iter!=molecules.end();++iter){
    9498    int id = (*iter)->getId();
    … …  
    102106
    103107void MoleculeDescriptorTest::MoleculeBaseSetsTest(){
    104   std::vector<molecule*> allMolecules = World::getInstance().getAllMolecules(AllMolecules());
     108  std::vector<const molecule*> allMolecules =
     109      const_cast<const World &>(World::getInstance()).getAllMolecules(AllMolecules());
    105110  CPPUNIT_ASSERT_EQUAL( true , hasAllMolecules(allMolecules,moleculeIds));
    106111  CPPUNIT_ASSERT_EQUAL( true , hasNoDuplicateMolecules(allMolecules));
    107112
    108   std::vector<molecule*> noMolecules = World::getInstance().getAllMolecules(NoMolecules());
     113  std::vector<const molecule*> noMolecules =
     114      const_cast<const World &>(World::getInstance()).getAllMolecules(NoMolecules());
    109115  CPPUNIT_ASSERT_EQUAL( true , noMolecules.empty());
    110116}
    … …  
    142148  // test some elementary set operations
    143149  {
    144     std::vector<molecule*> testMolecules = World::getInstance().getAllMolecules(AllMolecules()||NoMolecules());
     150    std::vector<const molecule*> testMolecules =
     151        const_cast<const World &>(World::getInstance()).getAllMolecules(AllMolecules()||NoMolecules());
    145152    CPPUNIT_ASSERT_EQUAL( true , hasAllMolecules(testMolecules,moleculeIds));
    146153    CPPUNIT_ASSERT_EQUAL( true , hasNoDuplicateMolecules(testMolecules));
    … …  
    148155
    149156  {
    150     std::vector<molecule*> testMolecules = World::getInstance().getAllMolecules(NoMolecules()||AllMolecules());
     157    std::vector<const molecule*> testMolecules =
     158        const_cast<const World &>(World::getInstance()).getAllMolecules(NoMolecules()||AllMolecules());
    151159    CPPUNIT_ASSERT_EQUAL( true , hasAllMolecules(testMolecules,moleculeIds));
    152160    CPPUNIT_ASSERT_EQUAL( true , hasNoDuplicateMolecules(testMolecules));
    … …  
    154162
    155163  {
    156     std::vector<molecule*> testMolecules = World::getInstance().getAllMolecules(NoMolecules()&&AllMolecules());
     164    std::vector<const molecule*> testMolecules =
     165        const_cast<const World &>(World::getInstance()).getAllMolecules(NoMolecules()&&AllMolecules());
    157166    CPPUNIT_ASSERT_EQUAL( true , testMolecules.empty());
    158167  }
    159168
    160169  {
    161     std::vector<molecule*> testMolecules = World::getInstance().getAllMolecules(AllMolecules()&&NoMolecules());
     170    std::vector<const molecule*> testMolecules =
     171        const_cast<const World &>(World::getInstance()).getAllMolecules(AllMolecules()&&NoMolecules());
    162172    CPPUNIT_ASSERT_EQUAL( true , testMolecules.empty());
    163173  }
    164174
    165175  {
    166     std::vector<molecule*> testMolecules = World::getInstance().getAllMolecules(!AllMolecules());
     176    std::vector<const molecule*> testMolecules =
     177        const_cast<const World &>(World::getInstance()).getAllMolecules(!AllMolecules());
    167178    CPPUNIT_ASSERT_EQUAL( true , testMolecules.empty());
    168179  }
    169180
    170181  {
    171     std::vector<molecule*> testMolecules = World::getInstance().getAllMolecules(!NoMolecules());
     182    std::vector<const molecule*> testMolecules =
     183        const_cast<const World &>(World::getInstance()).getAllMolecules(!NoMolecules());
    172184    CPPUNIT_ASSERT_EQUAL( true , hasAllMolecules(testMolecules,moleculeIds));
    173185    CPPUNIT_ASSERT_EQUAL( true , hasNoDuplicateMolecules(testMolecules));
    … …  
    176188  // exclude and include some molecules
    177189  {
    178     std::vector<molecule*> testMolecules = World::getInstance().getAllMolecules(AllMolecules()&&(!MoleculeById(moleculeIds[MOLECULE_COUNT/2])));
     190    std::vector<const molecule*> testMolecules =
     191        const_cast<const World &>(World::getInstance()).getAllMolecules(AllMolecules()&&(!MoleculeById(moleculeIds[MOLECULE_COUNT/2])));
    179192    std::set<moleculeId_t> excluded;
    180193    excluded.insert(moleculeIds[MOLECULE_COUNT/2]);
    … …  
    185198
    186199  {
    187     std::vector<molecule*> testMolecules = World::getInstance().getAllMolecules(NoMolecules()||(MoleculeById(moleculeIds[MOLECULE_COUNT/2])));
     200    std::vector<const molecule*> testMolecules =
     201        const_cast<const World &>(World::getInstance()).getAllMolecules(NoMolecules()||(MoleculeById(moleculeIds[MOLECULE_COUNT/2])));
    188202    CPPUNIT_ASSERT_EQUAL( (size_t)1, testMolecules.size());
    189203    CPPUNIT_ASSERT_EQUAL( moleculeIds[MOLECULE_COUNT/2], testMolecules[0]->getId());

  • src/Parameters/Specifics/Value_molecule.cpp

    r63fb7a r1259df  
    3737#include "Value_molecule.hpp"
    3838
     39#include "Descriptors/MoleculeNameDescriptor.hpp"
     40
    3941#include "molecule.hpp"
    4042#include "World.hpp"
    … …  
    4345{
    4446  const molecule * _mol = NULL;
    45   const vector<molecule *> molecules = World::getInstance().getAllMolecules();
    46   for (vector<molecule *>::const_iterator moliter = molecules.begin();
    47       moliter != molecules.end(); ++moliter) {
    48     if ((*moliter)->getName() == _name) {
    49       _mol = *moliter;
    50       break;
    51     }
    52   }
     47  const vector<const molecule *> molecules = const_cast<const World &>(World::getInstance()).
     48      getAllMolecules(MoleculeByName(_name));
     49  _mol = *molecules.begin();
    5350  return _mol;
    5451}

  • src/UIElements/Qt4/Query/MoleculeQtQuery.cpp

    r63fb7a r1259df  
    5555  inputBox = new QComboBox();
    5656  // add all molecules to the combo box
    57   vector<molecule*> molecules = World::getInstance().getAllMolecules();
    58   for(vector<molecule*>::iterator iter  = molecules.begin();
     57  vector<const molecule*> molecules =
     58      const_cast<const World &>(World::getInstance()).getAllMolecules();
     59  for(vector<const molecule*>::const_iterator iter  = molecules.begin();
    5960      iter != molecules.end();
    6061      ++iter) {

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

    r63fb7a r1259df  
    273273  changing = true;
    274274
    275   const std::vector<molecule*> &molecules = World::getInstance().getAllMolecules();
     275  const std::vector<const molecule*> &molecules =
     276      const_cast<const World &>(World::getInstance()).getAllMolecules();
    276277
    277278  clear();
    … …  
    288289  toBeSetVisibilityItems.clear();
    289290
    290   for (std::vector<molecule*>::const_iterator iter = molecules.begin();
     291  for (std::vector<const molecule*>::const_iterator iter = molecules.begin();
    291292      iter != molecules.end();
    292293      iter++)

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

    r63fb7a r1259df  
    106106      if ((index.column() == 0) && (selectionModel()->isSelected(index))) {
    107107        const moleculeId_t mol_id = moleculelist->IndexToMoleculeId(index);
    108         const molecule * const mol = World::getInstance().getMolecule(MoleculeById(mol_id));
     108        const molecule * const mol = const_cast<const World &>(World::getInstance()).
     109            getMolecule(MoleculeById(mol_id));
    109110        // check for invalid molecule
    110111        if (mol_id < 0)
    … …  
    129130      if ((index.column() == 0) && (!selectionModel()->isSelected(index))) {
    130131        const moleculeId_t mol_id = moleculelist->IndexToMoleculeId(index);
    131         const molecule * const mol = World::getInstance().getMolecule(MoleculeById(mol_id));
     132        const molecule * const mol = const_cast<const World &>(World::getInstance()).
     133            getMolecule(MoleculeById(mol_id));
    132134        // check for invalid molecule
    133135        if (mol_id < 0)

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

    r63fb7a r1259df  
    107107void GLWorldScene::init()
    108108{
    109   const std::vector<molecule *> &molecules = World::getInstance().getAllMolecules();
    110 
    111   for (std::vector<molecule*>::const_iterator moliter = molecules.begin();
     109  const std::vector<const molecule *> &molecules =
     110      const_cast<const World &>(World::getInstance()).getAllMolecules();
     111
     112  for (std::vector<const molecule*>::const_iterator moliter = molecules.begin();
    112113      moliter != molecules.end();
    113114      moliter++) {
    … …  
    125126void GLWorldScene::update()
    126127{
    127   const std::vector<molecule *> &molecules = World::getInstance().getAllMolecules();
    128 
    129   for (std::vector<molecule*>::const_iterator moliter = molecules.begin();
     128  const std::vector<const molecule *> &molecules =
     129      const_cast<const World &>(World::getInstance()).getAllMolecules();
     130
     131  for (std::vector<const molecule*>::const_iterator moliter = molecules.begin();
    130132      moliter != molecules.end();
    131133      moliter++) {
    … …  
    243245  LOG(3, "INFO: GLWorldScene: Received signal selectionChanged.");
    244246
    245   const std::vector<molecule*> &molecules = World::getInstance().getAllMolecules();
     247  const std::vector<const molecule*> &molecules =
     248      const_cast<const World &>(World::getInstance()).getAllMolecules();
    246249
    247250  if (molecules.size() > 0) {
    248     for (std::vector<molecule*>::const_iterator Runner = molecules.begin();
     251    for (std::vector<const molecule*>::const_iterator Runner = molecules.begin();
    249252        Runner != molecules.end();
    250253        Runner++) {
    251254
    252255      // molecule selected but not in scene?
    253       const bool isSelected = World::getInstance().isSelected(*Runner);
     256      const bool isSelected =
     257          const_cast<const World &>(World::getInstance()).isSelected(*Runner);
    254258      if (isSelected){
    255259        MoleculeNodeMap::iterator iter = MoleculesinSceneMap.find((*Runner)->getId());
Note: See TracChangeset for help on using the changeset viewer.