Changeset d7cad1

Timestamp:

Jan 11, 2015, 4:42:43 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:

596cfa

Parents:

b6d92e

git-author:

Frederik Heber <heber@…> (12/12/14 08:28:30)

git-committer:

Frederik Heber <heber@…> (01/11/15 16:42:43)

Message:

Extended selection action for Molecule ids to multiple ids.

Files:

• src/Actions/SelectionAction/Atoms/NotAtomByIdAction.def (modified) (1 diff)
• src/Actions/SelectionAction/Molecules/MoleculeByIdAction.cpp (modified) (3 diffs)
• src/Actions/SelectionAction/Molecules/MoleculeByIdAction.def (modified) (2 diffs)
• src/Actions/SelectionAction/Molecules/NotMoleculeByIdAction.cpp (modified) (3 diffs)
• src/Actions/SelectionAction/Molecules/NotMoleculeByIdAction.def (modified) (2 diffs)
• src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) (2 diffs)
• src/UIElements/Views/Qt4/QtMoleculeList.cpp (modified) (1 diff)
• tests/regression/Selection/Molecules/MoleculeById/post/id2_4_missing.xyz (moved) (moved from tests/regression/Selection/Molecules/MoleculeById/post/id4_missing.xyz ) (2 diffs)
• tests/regression/Selection/Molecules/MoleculeById/post/water_id2_4.xyz (moved) (moved from tests/regression/Selection/Molecules/MoleculeById/post/water_id4.xyz ) (1 diff)
• tests/regression/Selection/Molecules/MoleculeById/testsuite-selection-select-molecule-by-id.at (modified) (3 diffs)
• tests/regression/Selection/Molecules/MoleculeById/testsuite-selection-unselect-molecule-by-id.at (modified) (3 diffs)

src/Actions/SelectionAction/Atoms/NotAtomByIdAction.def

@@ -26 +26 @@
 (STLVectorValidator< std::vector<atomId_t> >(AtomIdValidator()))
 
-
 #define statetypes (atomids_t)
 #define statereferences (undoatomids)

src/Actions/SelectionAction/Molecules/MoleculeByIdAction.cpp

@@ -53 +53 @@
 /** =========== define the function ====================== */
 ActionState::ptr SelectionMoleculeByIdAction::performCall() {
-  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.get()));
-      LOG(0, World::getInstance().countSelectedMolecules() << " molecules selected.");
-      return ActionState::ptr(new SelectionMoleculeByIdState(params));
+
+  enum Sucess {
+    NoStatus,
+    AllMoleculesUnselected,
+    MoleculesSelected,
+    MoleculeMissing
+  } status = NoStatus;
+
+  const molids_t molids = params.molids.get();
+  molids_t undomolids;
+  undomolids.reserve(molids.size());
+  for (molids_t::const_iterator iter = molids.begin(); iter != molids.end(); ++iter) {
+    const molecule *Walker = World::getInstance().getMolecule(MoleculeById(*iter));
+    if (Walker != NULL) {
+      if (!World::getInstance().isSelected(Walker)) {
+        LOG(1, "Selecting mol " << Walker->getName());
+        World::getInstance().selectMolecule(Walker);
+        undomolids.push_back(*iter);
+        if (status < MoleculeMissing)
+          status = MoleculesSelected;
+      } else {
+        if (status == NoStatus)
+          status = AllMoleculesUnselected;
+      }
     } else {
-      return Action::success;
+      status = MoleculeMissing;
     }
-  } else {
-    STATUS("Cannot find molecule by given index "+toString(params.molindex.get())+".");
-    return Action::failure;
   }
+  LOG(0, World::getInstance().countSelectedMolecules() << " mols selected.");
+
+  switch (status) {
+    case MoleculeMissing:
+      STATUS("Cannot find all mols with given ids.");
+      return Action::failure;
+      break;
+    case AllMoleculesUnselected:
+    case MoleculesSelected:
+      return ActionState::ptr(new SelectionMoleculeByIdState(undomolids, params));
+      break;
+    default:
+      STATUS("No mols have been selected.");
+      return Action::failure;
+      break;
+  }
+  return Action::failure;
 }
 
@@ -72 +103 @@
   SelectionMoleculeByIdState *state = assert_cast<SelectionMoleculeByIdState*>(_state.get());
 
-  World::getInstance().unselectAllMolecules(MoleculeById(state->params.molindex.get()));
+  for (molids_t::const_iterator iter = state->undomolids.begin();
+      iter != state->undomolids.end(); ++iter) {
+    const molecule *Walker = World::getInstance().getMolecule(MoleculeById(*iter));
+    World::getInstance().unselectMolecule(Walker);
+  }
 
   return ActionState::ptr(_state);
@@ -80 +115 @@
   SelectionMoleculeByIdState *state = assert_cast<SelectionMoleculeByIdState*>(_state.get());
 
-  World::getInstance().selectAllMolecules(MoleculeById(state->params.molindex.get()));
+  for (molids_t::const_iterator iter = state->undomolids.begin();
+      iter != state->undomolids.end(); ++iter) {
+    const molecule *Walker = World::getInstance().getMolecule(MoleculeById(*iter));
+    World::getInstance().selectMolecule(Walker);
+  }
 
   return ActionState::ptr(_state);

src/Actions/SelectionAction/Molecules/MoleculeByIdAction.def

@@ -7 +7 @@
 
 // all includes and forward declarations necessary for non-integral types below
+#include <vector>
 #include "types.hpp"
 
+typedef std::vector<moleculeId_t> molids_t;
+
+#include "Parameters/Validators/STLVectorValidator.hpp"
 #include "Parameters/Validators/Specific/MoleculeIdValidator.hpp"
 
@@ -14 +18 @@
 // ValueStorage by the token "Z" -> first column: int, Z, "Z"
 // "undefine" if no parameters are required, use (NOPARAM_DEFAULT) for each (undefined) default value
-#define paramtypes (moleculeId_t)
+#define paramtypes (molids_t)
 #define paramtokens ("select-molecule-by-id")
-#define paramdescriptions ("molecule index")
+#define paramdescriptions ("molecule indices to select")
 #undef paramdefaults
-#define paramreferences (molindex)
+#define paramreferences (molids)
 #define paramvalids \
-(MoleculeIdValidator())
+(STLVectorValidator< std::vector<moleculeId_t> >(MoleculeIdValidator()))
 
-#undef statetypes
-#undef statereferences
+#define statetypes (molids_t)
+#define statereferences (undomolids)
 
 // some defines for all the names, you may use ACTION, STATE and PARAMS

src/Actions/SelectionAction/Molecules/NotMoleculeByIdAction.cpp

@@ -53 +53 @@
 /** =========== define the function ====================== */
 ActionState::ptr SelectionNotMoleculeByIdAction::performCall() {
-  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.get()));
-      LOG(0, World::getInstance().countSelectedMolecules() << " molecules remain selected.");
-      return ActionState::ptr(new SelectionNotMoleculeByIdState(params));
+  enum Sucess {
+    NoStatus,
+    AllMoleculesSelected,
+    MoleculesUnselected,
+    MoleculeMissing
+  } status = NoStatus;
+
+  const molids_t molids = params.molids.get();
+  molids_t undomolids;
+  undomolids.reserve(molids.size());
+  for (molids_t::const_iterator iter = molids.begin(); iter != molids.end(); ++iter) {
+    const molecule *Walker = World::getInstance().getMolecule(MoleculeById(*iter));
+    if (Walker != NULL) {
+      if (World::getInstance().isSelected(Walker)) {
+        LOG(1, "Unselecting mol " << Walker->getName());
+        World::getInstance().unselectMolecule(Walker);
+        undomolids.push_back(*iter);
+        if (status < MoleculeMissing)
+          status = MoleculesUnselected;
+      } else {
+        if (status == NoStatus)
+          status = AllMoleculesSelected;
+      }
     } else {
-      return Action::success;
+      status = MoleculeMissing;
     }
-  } else {
-    STATUS("Cannot find molecule by given index "+toString(params.molindex.get())+".");
-    return Action::failure;
   }
+  LOG(0, World::getInstance().countSelectedMolecules() << " mols remain selected.");
+
+  switch (status) {
+    case MoleculeMissing:
+      STATUS("Cannot find all mols by given ids.");
+      return Action::failure;
+      break;
+    case AllMoleculesSelected:
+    case MoleculesUnselected:
+      return ActionState::ptr(new SelectionNotMoleculeByIdState(undomolids, params));
+      break;
+    default:
+      STATUS("No mols have been selected.");
+      return Action::failure;
+      break;
+  }
+  return Action::failure;
 }
 
@@ -72 +102 @@
   SelectionNotMoleculeByIdState *state = assert_cast<SelectionNotMoleculeByIdState*>(_state.get());
 
-  World::getInstance().selectAllMolecules(MoleculeById(state->params.molindex.get()));
+  for (molids_t::const_iterator iter = state->undomolids.begin();
+      iter != state->undomolids.end(); ++iter) {
+    const molecule *Walker = World::getInstance().getMolecule(MoleculeById(*iter));
+    World::getInstance().selectMolecule(Walker);
+  }
 
   return ActionState::ptr(_state);
@@ -80 +114 @@
   SelectionNotMoleculeByIdState *state = assert_cast<SelectionNotMoleculeByIdState*>(_state.get());
 
-  World::getInstance().unselectAllMolecules(MoleculeById(state->params.molindex.get()));
+  for (molids_t::const_iterator iter = state->undomolids.begin();
+      iter != state->undomolids.end(); ++iter) {
+    const molecule *Walker = World::getInstance().getMolecule(MoleculeById(*iter));
+    World::getInstance().unselectMolecule(Walker);
+  }
 
   return ActionState::ptr(_state);

src/Actions/SelectionAction/Molecules/NotMoleculeByIdAction.def

@@ -7 +7 @@
 
 // all includes and forward declarations necessary for non-integral types below
+#include <vector>
 #include "types.hpp"
 
+typedef std::vector<moleculeId_t> molids_t;
+
+#include "Parameters/Validators/STLVectorValidator.hpp"
 #include "Parameters/Validators/Specific/MoleculeIdValidator.hpp"
 
@@ -14 +18 @@
 // ValueStorage by the token "Z" -> first column: int, Z, "Z"
 // "undefine" if no parameters are required, use (NOPARAM_DEFAULT) for each (undefined) default value
-#define paramtypes (moleculeId_t)
+#define paramtypes (molids_t)
 #define paramtokens ("unselect-molecule-by-id")
-#define paramdescriptions ("molecule index")
+#define paramdescriptions ("molecule indices to unselect")
 #undef paramdefaults
-#define paramreferences (molindex)
+#define paramreferences (molids)
 #define paramvalids \
-(MoleculeIdValidator())
+(STLVectorValidator< std::vector<moleculeId_t> >(MoleculeIdValidator()))
 
-#undef statetypes
-#undef statereferences
+#define statetypes (molids_t)
+#define statereferences (undomolids)
 
 // some defines for all the names, you may use ACTION, STATE and PARAMS

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

@@ -150 +150 @@
      const molecule *mol = Walker->getMolecule();
      ASSERT(mol, "Atom without molecule has been clicked.");
+     molids_t ids(1, mol->getId());
      if (!World::getInstance().isSelected(mol))
-       SelectionMoleculeById(mol->getId());
+       SelectionMoleculeById(ids);
      else
-       SelectionNotMoleculeById(mol->getId());
+       SelectionNotMoleculeById(ids);
    }
    emit clicked(no);
@@ -163 +164 @@
    const molecule *mol= World::getInstance().getMolecule(MoleculeById(no));
    ASSERT(mol, "Atom without molecule has been clicked.");
+   molids_t ids(1, mol->getId());
    if (!World::getInstance().isSelected(mol))
-     SelectionMoleculeById(mol->getId());
+     SelectionMoleculeById(ids);
    else
-     SelectionNotMoleculeById(mol->getId());
+     SelectionNotMoleculeById(ids);
    emit clicked(no);
 }

src/UIElements/Views/Qt4/QtMoleculeList.cpp

@@ -268 +268 @@
   // Select all molecules which belong to newly selected rows.
   QModelIndex index;
-  QModelIndexList items = selected.indexes();
-  foreach (index, items)
-    if (index.column() == 0){
-      int mol_id = model()->data(index, Qt::UserRole).toInt();
-      if (mol_id < 0)
-        continue;
-      //std::cout << "select molecule" << std::endl;
-      MoleCuilder::SelectionMoleculeById(mol_id);
-    }
+  {
+    QModelIndexList items = selected.indexes();
+    molids_t ids;
+    ids.reserve(items.size());
+    foreach (index, items)
+      if (index.column() == 0){
+        int mol_id = model()->data(index, Qt::UserRole).toInt();
+        if (mol_id < 0)
+          continue;
+        ids.push_back(mol_id);
+        //std::cout << "select molecule" << std::endl;
+      }
+    MoleCuilder::SelectionMoleculeById(ids);
+  }
 
   // Unselect all molecules which belong to newly unselected rows.
-  items = deselected.indexes();
-  foreach (index, items)
-    if (index.column() == 0){
-      int mol_id = model()->data(index, Qt::UserRole).toInt();
-      if (mol_id < 0)
-        continue;
-      //std::cout << "unselect molecule" << std::endl;
-      MoleCuilder::SelectionNotMoleculeById(mol_id);
-    }
+  {
+    QModelIndexList items = deselected.indexes();
+    molids_t ids;
+    ids.reserve(items.size());
+    foreach (index, items)
+      if (index.column() == 0){
+        int mol_id = model()->data(index, Qt::UserRole).toInt();
+        if (mol_id < 0)
+          continue;
+        //std::cout << "unselect molecule" << std::endl;
+        ids.push_back(mol_id);
+      }
+    MoleCuilder::SelectionNotMoleculeById(ids);
+  }
 
   selecting = false;

tests/regression/Selection/Molecules/MoleculeById/post/id2_4_missing.xyz

@@ -1 @@
-1026
+1023
         Created by molecuilder for select-molecule-by-id test
 O       0       0       0.504284
@@ -7 +7 @@
 H       0.758602        0       3.86571
 H       0.758602        0       2.85714
-O       0       0       6.21857
-H       0.758602        0       6.72285
-H       0.758602        0       5.71429
 O       0       0       9.07571
 H       0.758602        0       9.58

tests/regression/Selection/Molecules/MoleculeById/post/water_id2_4.xyz

@@ -1 @@
-3
+6
         Created by molecuilder for select-molecule-by-id test
+O       0       0       6.21857
+H       0.758602        0       6.72285
+H       0.758602        0       5.71429
 O       0       0       11.9329
 H       0.758602        0       12.4371

tests/regression/Selection/Molecules/MoleculeById/testsuite-selection-select-molecule-by-id.at

@@ -25 +25 @@
 srcfile=box.xyz
 testfile=test.xyz
-targetfile=water_id4.xyz
+targetfile=water_id2_4.xyz
 AT_CHECK([cp -n ${regressionpath}/pre/$srcfile $testfile], 0)
-AT_CHECK([../../molecuilder -i $testfile -I --select-molecule-by-id 4 -s $targetfile], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder -i $testfile -I --select-molecule-by-id 2 4 -s $targetfile], 0, [stdout], [stderr])
 AT_CHECK([diff -I '.*Created by molecuilder.*' $targetfile ${regressionpath}/post/$targetfile], 0, [ignore], [ignore])
 
@@ -41 +41 @@
 targetfile=empty.xyz
 AT_CHECK([cp -n ${regressionpath}/pre/$srcfile $testfile], 0)
-AT_CHECK([../../molecuilder -i $testfile -I --select-molecule-by-id 4 --undo -s $targetfile], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder -i $testfile -I --select-molecule-by-id 2 4 --undo -s $targetfile], 0, [stdout], [stderr])
 AT_CHECK([diff -I '.*Created by molecuilder.*' $targetfile ${regressionpath}/post/$targetfile], 0, [ignore], [ignore])
 
@@ -53 +53 @@
 srcfile=box.xyz
 testfile=test.xyz
-targetfile=water_id4.xyz
+targetfile=water_id2_4.xyz
 AT_CHECK([cp -n ${regressionpath}/pre/$srcfile $testfile], 0)
-AT_CHECK([../../molecuilder -i $testfile -I --select-molecule-by-id 4 --undo --redo -s $targetfile], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder -i $testfile -I --select-molecule-by-id 2 4 --undo --redo -s $targetfile], 0, [stdout], [stderr])
 AT_CHECK([diff -I '.*Created by molecuilder.*' $targetfile ${regressionpath}/post/$targetfile], 0, [ignore], [ignore])
 

tests/regression/Selection/Molecules/MoleculeById/testsuite-selection-unselect-molecule-by-id.at

@@ -25 +25 @@
 srcfile=box.xyz
 testfile=test.xyz
-targetfile=id4_missing.xyz
+targetfile=id2_4_missing.xyz
 AT_CHECK([cp -n ${regressionpath}/pre/$srcfile $testfile], 0)
-AT_CHECK([../../molecuilder -i $testfile -I --select-all-molecules --unselect-molecule-by-id 4 -s $targetfile], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder -i $testfile -I --select-all-molecules --unselect-molecule-by-id 2 4 -s $targetfile], 0, [stdout], [stderr])
 AT_CHECK([diff -I '.*Created by molecuilder.*' $targetfile ${regressionpath}/post/$targetfile], 0, [ignore], [ignore])
 
@@ -41 +41 @@
 targetfile=box.xyz
 AT_CHECK([cp -n ${regressionpath}/pre/$srcfile $testfile], 0)
-AT_CHECK([../../molecuilder -i $testfile -I --select-all-molecules --unselect-molecule-by-id 4 --undo -s $targetfile], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder -i $testfile -I --select-all-molecules --unselect-molecule-by-id 2 4 --undo -s $targetfile], 0, [stdout], [stderr])
 AT_CHECK([diff -I '.*Created by molecuilder.*' $targetfile ${regressionpath}/post/$targetfile], 0, [ignore], [ignore])
 
@@ -53 +53 @@
 srcfile=box.xyz
 testfile=test.xyz
-targetfile=id4_missing.xyz
+targetfile=id2_4_missing.xyz
 AT_CHECK([cp -n ${regressionpath}/pre/$srcfile $testfile], 0)
-AT_CHECK([../../molecuilder -i $testfile -I --select-all-molecules --unselect-molecule-by-id 4 --undo --redo -s $targetfile], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder -i $testfile -I --select-all-molecules --unselect-molecule-by-id 2 4 --undo --redo -s $targetfile], 0, [stdout], [stderr])
 AT_CHECK([diff -I '.*Created by molecuilder.*' $targetfile ${regressionpath}/post/$targetfile], 0, [ignore], [ignore])