Changes in / [9a8a6b:08d9df7]

Files:

• src/Actions/AtomAction/AddAction.cpp (modified) (3 diffs)
• src/Actions/AtomAction/AddAction.def (modified) (1 diff)
• src/Atom/atom.cpp (modified) (1 diff)
• src/molecule.cpp (modified) (1 diff)
• src/molecule.hpp (modified) (1 diff)
• tests/regression/Atoms/Add/post/test.pdb (modified) (1 diff)

src/Actions/AtomAction/AddAction.cpp

@@ -55 +55 @@
 #include "Action_impl_pre.hpp"
 /** =========== define the function ====================== */
-
-atom * getNewAtom(const AtomAddAction::AtomAddParameters &_params)
-{
-  atom * first = World::getInstance().createAtom();
-  first->setType(_params.elemental.get());
-  first->setPosition(_params.position.get());
-
-  return first;
-}
-
-std::vector<atomId_t> createAtoms(
-    const AtomAddAction::AtomAddParameters &_params,
-    std::vector<molecule *> &_molecules)
-{
-  std::vector<atomId_t> ids;
-  if (!_molecules.empty()) {
-    if (_molecules.size() == 1) {
-        atom *first = getNewAtom(_params);
-        molecule *mol = *_molecules.begin();
-        LOG(1, "Adding new atom with element " << first->getType()->getName()
-            << " at " << (first->getPosition()) << " to selected molecule "
-            << mol->getName()+".");
-        mol->AddAtom(first);
-      ids.push_back(first->getId());
-    }
-  } else {
-    atom *first = getNewAtom(_params);
-    molecule *mol = World::getInstance().createMolecule();
-    mol->setName("none");
-    mol->AddAtom(first);
-    LOG(1, "Adding new atom with element " << first->getType()->getName()
-        << " at " << (first->getPosition()) << " to new molecule.");
-    ids.push_back(first->getId());
-  }
-
-  return ids;
-}
-
 ActionState::ptr AtomAddAction::performCall() {
   // execute action
-  std::vector<molecule *> molecules = World::getInstance().getSelectedMolecules();
-  std::vector<atomId_t> ids = createAtoms(params, molecules);
-
-  if (molecules.size() > 1)
-     return Action::failure;
-  else
-    return ActionState::ptr(new AtomAddState(ids, params));
+  atom * first = World::getInstance().createAtom();
+  first->setType(params.elemental.get());
+  first->setPosition(params.position.get());
+  LOG(1, "Adding new atom with element " << first->getType()->getName() << " at " << (first->getPosition()) << ".");
+  // TODO: remove when all of World's atoms are stored.
+  std::vector<molecule *> molecules = World::getInstance().getAllMolecules();
+  if (!molecules.empty()) {
+    std::vector<molecule *>::iterator iter = molecules.begin();
+    (*iter)->AddAtom(first);
+  }
+  return ActionState::ptr(new AtomAddState(first->getId(), params));
 }
 
@@ -107 +73 @@
   AtomAddState *state = assert_cast<AtomAddState*>(_state.get());
 
-  for (std::vector<atomId_t>::const_iterator iter = state->ids.begin();
-      iter != state->ids.end(); ++iter) {
-    LOG(1, "Removing atom with id " << *iter << ".");
-    World::getInstance().destroyAtom(*iter);
-  }
+  LOG(1, "Removing atom with id " << state->id << ".");
+  World::getInstance().destroyAtom(state->id);
 
   return ActionState::ptr(_state);
@@ -119 +82 @@
   AtomAddState *state = assert_cast<AtomAddState*>(_state.get());
 
-  std::vector<molecule *> molecules = World::getInstance().getSelectedMolecules();
-  std::vector<atomId_t> newids = createAtoms(params, molecules);
+  atom * first = World::getInstance().createAtom();
+  first->setType(state->params.elemental.get());
+  first->setPosition(state->params.position.get());
+  LOG(1, "Re-adding new atom with element " << state->params.elemental.get()->getName() << " at " << state->params.position.get() << ".");
+  // TODO: remove when all of World's atoms are stored.
+  std::vector<molecule *> molecules = World::getInstance().getAllMolecules();
+  if (!molecules.empty()) {
+    std::vector<molecule *>::iterator iter = molecules.begin();
+    (*iter)->AddAtom(first);
+  }
+  if (first->getId() != state->id)
+    if (!first->changeId(state->id)) {
+      STATUS("Could not change atom id "+toString(first->getId())+"->"+toString(state->id)+".");
+      return Action::failure;
+    }
 
-  if (newids.size() != state->ids.size()) {
-    STATUS("Could not recreate all atoms after undo.");
-    for (std::vector<atomId_t>::const_iterator iter = newids.begin(); iter != newids.end();++iter)
-      World::getInstance().destroyAtom(*iter);
-    return Action::failure;
-  }
-
-  std::vector<atomId_t>::const_iterator newiter = newids.begin();
-  std::vector<atomId_t>::const_iterator olditer = state->ids.begin();
-  bool status=true;
-  for (; newiter != newids.end(); ++newiter, ++olditer) {
-    atom * first = World::getInstance().getAtom(AtomById(*newiter));
-    ASSERT( first != NULL,
-        "AtomAddAction::performRedo() - re-created atom not present?");
-    if (first->getId() != *olditer)
-      if (!first->changeId(*olditer)) {
-        STATUS("Could not change atom id "+toString(first->getId())+"->"+toString(*olditer)+".");
-        // remove all created atoms
-        for (std::vector<atomId_t>::const_iterator iter = state->ids.begin(); iter != olditer;++iter)
-          World::getInstance().destroyAtom(*iter);
-        olditer = state->ids.end();
-        for (std::vector<atomId_t>::const_iterator iter = newiter; iter != newids.end();++iter)
-          World::getInstance().destroyAtom(*iter);
-        status = false;
-        break;
-      }
-  }
-  ASSERT( olditer == state->ids.end(),
-      "AtomAddAction::performRedo() - after all unequal amount of ids in new and old?");
-
-  if (!status) {
-    return Action::failure;
-  } else
-    return ActionState::ptr(_state);
+  return ActionState::ptr(_state);
 }
 

src/Actions/AtomAction/AddAction.def

@@ -27 +27 @@
 (BoxVectorValidator())
 
-#define statetypes (std::vector<atomId_t>)
-#define statereferences (ids)
+#define statetypes (const atomId_t)
+#define statereferences (id)
 
 // some defines for all the names, you may use ACTION, STATE and PARAMS

src/Atom/atom.cpp

@@ -264 +264 @@
   // first we move ourselves in the world
   // the world lets us know if that succeeded
-  atomId_t oldid = id;
   if(world->changeAtomId(id,newId,this)){
     OBSERVE;
     id = newId;
-    if (mol != NULL)
-      mol->changeAtomId(oldid, newId);
     NOTIFY(IndexChanged);
     return true;

src/molecule.cpp

@@ -168 +168 @@
     return false;
   }
-}
-
-bool molecule::changeAtomId(int oldId, int newId)
-{
-  OBSERVE;
-  if ((!atomIds.contains( oldId )) || (atomIds.contains( newId )))
-    return false;
-  atomIds.erase( oldId );
-  atomIds.insert( newId );
-  return true;
 }
 

src/molecule.hpp

@@ -237 +237 @@
    */
   bool changeAtomNr(int oldNr, int newNr, atom* target=0);
-
-  friend bool atom::changeId(atomId_t newId);
-  /**
-   * used when changing an ParticleInfo::Id.
-   * Note that this number is global (and the molecule uses it to know which atoms belong to it)
-   *
-   * @param oldId old Id
-   * @param newId new Id to set
-   * @return indicates wether the change could be done or not.
-   */
-  bool changeAtomId(int oldId, int newId);
 
   /** Updates the internal lookup fro local to global indices.

tests/regression/Atoms/Add/post/test.pdb

@@ -1 +1 @@
 REMARK created by molecuilder on Wed Feb  2 18:06:07 2011
-ATOM      1 H01 0non 01         10.000  10.000  10.000  0.00  0.00           H 0
+ATOM      1 H01 0-   00         10.000  10.000  10.000  0.00  0.00           H 0
 END