Changeset f10b0c for src/Actions/SelectionAction/Molecules

Timestamp:

Jun 11, 2012, 9:53:19 AM (13 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:

95f965

Parents:

b9c69d

git-author:

Michael Ankele <ankele@…> (04/24/12 13:55:16)

git-committer:

Frederik Heber <heber@…> (06/11/12 09:53:19)

Message:

disastrously big and ugly commit

• using new Parameter<T> classes:
  • Actions
  • Queries (all UIs)

• TODO:
  • actions crash cause Value is unset
  • no query<BoxVector>

Location:

src/Actions/SelectionAction/Molecules

Files:

• MoleculeByFormulaAction.cpp (modified) (3 diffs)
• MoleculeByIdAction.cpp (modified) (3 diffs)
• MoleculeByNameAction.cpp (modified) (3 diffs)
• MoleculeByOrderAction.cpp (modified) (1 diff)
• NotMoleculeByFormulaAction.cpp (modified) (3 diffs)
• NotMoleculeByIdAction.cpp (modified) (3 diffs)
• NotMoleculeByNameAction.cpp (modified) (3 diffs)
• NotMoleculeByOrderAction.cpp (modified) (1 diff)

src/Actions/SelectionAction/Molecules/MoleculeByFormulaAction.cpp

@@ -40 +40 @@
 /** =========== define the function ====================== */
 Action::state_ptr SelectionMoleculeByFormulaAction::performCall() {
-  LOG(1, "Selecting molecules with chemical formula " << params.formula << ":");
-//  std::vector<molecule *> matchingMolecules = World::getInstance().getAllMolecules(MoleculeByFormula(params.formula));
+  LOG(1, "Selecting molecules with chemical formula " << params.formula.get() << ":");
+//  std::vector<molecule *> matchingMolecules = World::getInstance().getAllMolecules(MoleculeByFormula(params.formula.get()));
   std::vector<molecule *> selectedMolecules =
-      World::getInstance().getAllMolecules(MoleculesBySelection() && MoleculeByFormula(params.formula));
+      World::getInstance().getAllMolecules(MoleculesBySelection() && MoleculeByFormula(params.formula.get()));
 //  BOOST_FOREACH(molecule *mol, matchingMolecules)
 //    LOG(1, "\t" << mol->getId() << ", " << mol->getName() << ".");
-  World::getInstance().selectAllMolecules(MoleculeByFormula(params.formula));
+  World::getInstance().selectAllMolecules(MoleculeByFormula(params.formula.get()));
   LOG(0, World::getInstance().countSelectedMolecules() << " molecules selected.");
   return Action::state_ptr(new SelectionMoleculeByFormulaState(selectedMolecules,params));
@@ -54 +54 @@
   SelectionMoleculeByFormulaState *state = assert_cast<SelectionMoleculeByFormulaState*>(_state.get());
 
-  World::getInstance().unselectAllMolecules(MoleculeByFormula(state->params.formula));
+  World::getInstance().unselectAllMolecules(MoleculeByFormula(state->params.formula.get()));
   BOOST_FOREACH( molecule *mol, state->selectedMolecules)
     World::getInstance().selectMolecule(mol);
@@ -64 +64 @@
   SelectionMoleculeByFormulaState *state = assert_cast<SelectionMoleculeByFormulaState*>(_state.get());
 
-  World::getInstance().selectAllMolecules(MoleculeByFormula(state->params.formula));
+  World::getInstance().selectAllMolecules(MoleculeByFormula(state->params.formula.get()));
 
   return Action::state_ptr(_state);

src/Actions/SelectionAction/Molecules/MoleculeByIdAction.cpp

@@ -38 +38 @@
 /** =========== define the function ====================== */
 Action::state_ptr SelectionMoleculeByIdAction::performCall() {
-  const molecule *mol = World::getInstance().getMolecule(MoleculeById(params.molindex));
+  const molecule *mol = World::getInstance().getMolecule(MoleculeById(params.molindex.get()));
   if (mol != NULL) {
     if (!World::getInstance().isSelected(mol)) {
       LOG(1, "Selecting molecule " << mol->name);
-      World::getInstance().selectAllMolecules(MoleculeById(params.molindex));
+      World::getInstance().selectAllMolecules(MoleculeById(params.molindex.get()));
       LOG(0, World::getInstance().countSelectedMolecules() << " molecules selected.");
       return Action::state_ptr(new SelectionMoleculeByIdState(params));
@@ -56 +56 @@
   SelectionMoleculeByIdState *state = assert_cast<SelectionMoleculeByIdState*>(_state.get());
 
-  World::getInstance().unselectAllMolecules(MoleculeById(state->params.molindex));
+  World::getInstance().unselectAllMolecules(MoleculeById(state->params.molindex.get()));
 
   return Action::state_ptr(_state);
@@ -64 +64 @@
   SelectionMoleculeByIdState *state = assert_cast<SelectionMoleculeByIdState*>(_state.get());
 
-  World::getInstance().selectAllMolecules(MoleculeById(state->params.molindex));
+  World::getInstance().selectAllMolecules(MoleculeById(state->params.molindex.get()));
 
   return Action::state_ptr(_state);

src/Actions/SelectionAction/Molecules/MoleculeByNameAction.cpp

@@ -40 +40 @@
 /** =========== define the function ====================== */
 Action::state_ptr SelectionMoleculeByNameAction::performCall() {
-  LOG(1, "Selecting all molecules called " << params.molname);
+  LOG(1, "Selecting all molecules called " << params.molname.get());
   std::vector<molecule *> selectedMolecules =
-      World::getInstance().getAllMolecules(MoleculesBySelection() && MoleculeByName(params.molname));
-  World::getInstance().selectAllMolecules(MoleculeByName(params.molname));
+      World::getInstance().getAllMolecules(MoleculesBySelection() && MoleculeByName(params.molname.get()));
+  World::getInstance().selectAllMolecules(MoleculeByName(params.molname.get()));
   LOG(0, World::getInstance().countSelectedMolecules() << " molecules selected.");
 
@@ -52 +52 @@
   SelectionMoleculeByNameState *state = assert_cast<SelectionMoleculeByNameState*>(_state.get());
 
-  World::getInstance().unselectAllMolecules(MoleculeByName(state->params.molname));
+  World::getInstance().unselectAllMolecules(MoleculeByName(state->params.molname.get()));
   BOOST_FOREACH( molecule *mol, state->selectedMolecules)
     World::getInstance().selectMolecule(mol);
@@ -62 +62 @@
   SelectionMoleculeByNameState *state = assert_cast<SelectionMoleculeByNameState*>(_state.get());
 
-  World::getInstance().selectAllMolecules(MoleculeByName(state->params.molname));
+  World::getInstance().selectAllMolecules(MoleculeByName(state->params.molname.get()));
 
   return Action::state_ptr(_state);

src/Actions/SelectionAction/Molecules/MoleculeByOrderAction.cpp

@@ -39 +39 @@
 
 Action::state_ptr SelectionMoleculeByOrderAction::performCall() {
-  molecule *mol = World::getInstance().getMolecule(MoleculeByOrder(params.molindex));
+  molecule *mol = World::getInstance().getMolecule(MoleculeByOrder(params.molindex.get()));
 
   if (mol != NULL) {

src/Actions/SelectionAction/Molecules/NotMoleculeByFormulaAction.cpp

@@ -40 +40 @@
 /** =========== define the function ====================== */
 Action::state_ptr SelectionNotMoleculeByFormulaAction::performCall() {
-  LOG(1, "Unselecting molecules with chemical formula " << params.formula << ":");
-  std::vector<molecule *> matchingMolecules = World::getInstance().getAllMolecules(MoleculeByFormula(params.formula));
+  LOG(1, "Unselecting molecules with chemical formula " << params.formula.get() << ":");
+  std::vector<molecule *> matchingMolecules = World::getInstance().getAllMolecules(MoleculeByFormula(params.formula.get()));
   std::vector<molecule *> unselectedMolecules = World::getInstance().getAllMolecules(!MoleculesBySelection());
-  World::getInstance().unselectAllMolecules(MoleculeByFormula(params.formula));
+  World::getInstance().unselectAllMolecules(MoleculeByFormula(params.formula.get()));
   LOG(0, World::getInstance().countSelectedMolecules() << " molecules remain selected.");
   return Action::state_ptr(new SelectionNotMoleculeByFormulaState(unselectedMolecules,params));
@@ -51 +51 @@
   SelectionNotMoleculeByFormulaState *state = assert_cast<SelectionNotMoleculeByFormulaState*>(_state.get());
 
-  World::getInstance().selectAllMolecules(MoleculeByFormula(state->params.formula));
+  World::getInstance().selectAllMolecules(MoleculeByFormula(state->params.formula.get()));
   BOOST_FOREACH( molecule *mol, state->unselectedMolecules)
     World::getInstance().unselectMolecule(mol);
@@ -61 +61 @@
   SelectionNotMoleculeByFormulaState *state = assert_cast<SelectionNotMoleculeByFormulaState*>(_state.get());
 
-  World::getInstance().unselectAllMolecules(MoleculeByFormula(state->params.formula));
+  World::getInstance().unselectAllMolecules(MoleculeByFormula(state->params.formula.get()));
 
   return Action::state_ptr(_state);

src/Actions/SelectionAction/Molecules/NotMoleculeByIdAction.cpp

@@ -38 +38 @@
 /** =========== define the function ====================== */
 Action::state_ptr SelectionNotMoleculeByIdAction::performCall() {
-  const molecule *mol = World::getInstance().getMolecule(MoleculeById(params.molindex));
+  const molecule *mol = World::getInstance().getMolecule(MoleculeById(params.molindex.get()));
   if (mol != NULL) {
     if (World::getInstance().isSelected(mol)) {
       LOG(1, "Unselecting molecule " << mol->name);
-      World::getInstance().unselectAllMolecules(MoleculeById(params.molindex));
+      World::getInstance().unselectAllMolecules(MoleculeById(params.molindex.get()));
       LOG(0, World::getInstance().countSelectedMolecules() << " molecules remain selected.");
       return Action::state_ptr(new SelectionNotMoleculeByIdState(params));
@@ -56 +56 @@
   SelectionNotMoleculeByIdState *state = assert_cast<SelectionNotMoleculeByIdState*>(_state.get());
 
-  World::getInstance().selectAllMolecules(MoleculeById(state->params.molindex));
+  World::getInstance().selectAllMolecules(MoleculeById(state->params.molindex.get()));
 
   return Action::state_ptr(_state);
@@ -64 +64 @@
   SelectionNotMoleculeByIdState *state = assert_cast<SelectionNotMoleculeByIdState*>(_state.get());
 
-  World::getInstance().unselectAllMolecules(MoleculeById(state->params.molindex));
+  World::getInstance().unselectAllMolecules(MoleculeById(state->params.molindex.get()));
 
   return Action::state_ptr(_state);

src/Actions/SelectionAction/Molecules/NotMoleculeByNameAction.cpp

@@ -40 +40 @@
 /** =========== define the function ====================== */
 Action::state_ptr SelectionNotMoleculeByNameAction::performCall() {
-  LOG(1, "Unselecting all molecule called " << params.molname);
+  LOG(1, "Unselecting all molecule called " << params.molname.get());
   std::vector<molecule *> unselectedMolecules =
-      World::getInstance().getAllMolecules((!MoleculesBySelection()) && MoleculeByName(params.molname));
-  World::getInstance().unselectAllMolecules(MoleculeByName(params.molname));
+      World::getInstance().getAllMolecules((!MoleculesBySelection()) && MoleculeByName(params.molname.get()));
+  World::getInstance().unselectAllMolecules(MoleculeByName(params.molname.get()));
   LOG(0, World::getInstance().countSelectedMolecules() << " molecules remain selected.");
 
@@ -52 +52 @@
   SelectionNotMoleculeByNameState *state = assert_cast<SelectionNotMoleculeByNameState*>(_state.get());
 
-  World::getInstance().selectAllMolecules(MoleculeByName(state->params.molname));
+  World::getInstance().selectAllMolecules(MoleculeByName(state->params.molname.get()));
   BOOST_FOREACH( molecule *mol, state->unselectedMolecules)
     World::getInstance().unselectMolecule(mol);
@@ -62 +62 @@
   SelectionNotMoleculeByNameState *state = assert_cast<SelectionNotMoleculeByNameState*>(_state.get());
 
-  World::getInstance().unselectAllMolecules(MoleculeByName(state->params.molname));
+  World::getInstance().unselectAllMolecules(MoleculeByName(state->params.molname.get()));
 
   return Action::state_ptr(_state);

src/Actions/SelectionAction/Molecules/NotMoleculeByOrderAction.cpp

@@ -39 +39 @@
 
 Action::state_ptr SelectionNotMoleculeByOrderAction::performCall() {
-  molecule *mol = World::getInstance().getMolecule(MoleculeByOrder(params.molindex));
+  molecule *mol = World::getInstance().getMolecule(MoleculeByOrder(params.molindex.get()));
 
   if (mol != NULL) {