Changes in src/Actions/FragmentationAction/SubgraphDissectionAction.cpp [d74077:952f38]

File:

• src/Actions/FragmentationAction/SubgraphDissectionAction.cpp (modified) (4 diffs)

src/Actions/FragmentationAction/SubgraphDissectionAction.cpp

@@ -10 +10 @@
 #include "Actions/FragmentationAction/SubgraphDissectionAction.hpp"
 #include "Actions/ActionRegistry.hpp"
+#include "atom.hpp"
+#include "config.hpp"
+#include "Helpers/Log.hpp"
+#include "molecule.hpp"
 #include "Descriptors/MoleculeDescriptor.hpp"
-
-#include "atom.hpp"
-#include "bond.hpp"
-#include "bondgraph.hpp"
-#include "config.hpp"
-#include "log.hpp"
-#include "molecule.hpp"
 #include "stackclass.hpp"
 #include "World.hpp"
@@ -28 +25 @@
 #include "UIElements/UIFactory.hpp"
 #include "UIElements/Dialog.hpp"
-#include "UIElements/ValueStorage.hpp"
+#include "Actions/ValueStorage.hpp"
 
 const char FragmentationSubgraphDissectionAction::NAME[] = "subgraph-dissect";
@@ -43 +40 @@
 };
 
-Dialog* FragmentationSubgraphDissectionAction::createDialog() {
-  Dialog *dialog = UIFactory::getInstance().makeDialog();
+Dialog* FragmentationSubgraphDissectionAction::fillDialog(Dialog *dialog) {
+  ASSERT(dialog,"No Dialog given when filling action dialog");
 
   dialog->queryEmpty(NAME, MapOfActions::getInstance().getDescription(NAME));
@@ -56 +53 @@
   // @TODO rather do the dissection afterwards
   MoleculeListClass *molecules = World::getInstance().getMolecules();
-  config * const configuration = World::getInstance().getConfig();
-
-  // 0a. remove all present molecules
-  vector<molecule *> allmolecules = World::getInstance().getAllMolecules();
-  for (vector<molecule *>::iterator MolRunner = allmolecules.begin(); MolRunner != allmolecules.end(); ++MolRunner) {
-    molecules->erase(*MolRunner);
-    World::getInstance().destroyMolecule(*MolRunner);
-  }
-
-  // 0b. remove all bonds and construct a molecule with all atoms
-  molecule *mol = World::getInstance().createMolecule();
-  vector <atom *> allatoms = World::getInstance().getAllAtoms();
-  for(vector<atom *>::iterator AtomRunner = allatoms.begin(); AtomRunner != allatoms.end(); ++AtomRunner) {
-    for(BondList::iterator BondRunner = (*AtomRunner)->ListOfBonds.begin(); !(*AtomRunner)->ListOfBonds.empty(); BondRunner = (*AtomRunner)->ListOfBonds.begin())
-      delete(*BondRunner);
-    mol->AddAtom(*AtomRunner);
-  }
-
-  // 1. create the bond structure of the single molecule
-  if (configuration->BG != NULL) {
-    if (!configuration->BG->ConstructBondGraph(mol)) {
-      World::getInstance().destroyMolecule(mol);
-      DoeLog(1) && (eLog()<< Verbose(1) << "There are no bonds." << endl);
-      return Action::failure;
-    }
-  } else {
-    DoeLog(1) && (eLog()<< Verbose(1) << "There is no BondGraph class present to create bonds." << endl);
-    return Action::failure;
-  }
-
-  // 2. scan for connected subgraphs
-  MoleculeLeafClass *Subgraphs = NULL;      // list of subgraphs from DFS analysis
-  class StackClass<bond *> *BackEdgeStack = NULL;
-  Subgraphs = mol->DepthFirstSearchAnalysis(BackEdgeStack);
-  delete(BackEdgeStack);
-  if ((Subgraphs == NULL) || (Subgraphs->next == NULL)) {
-    World::getInstance().destroyMolecule(mol);
-    DoeLog(1) && (eLog()<< Verbose(1) << "There are no atoms." << endl);
-    return Action::failure;
-  }
-
-  // 3. dissect (the following construct is needed to have the atoms not in the order of the DFS, but in
-  // the original one as parsed in)
-  // TODO: Optimize this, when molecules just contain pointer list of global atoms!
-
-  // 4a. create array of molecules to fill
-  const int MolCount = Subgraphs->next->Count();
-  char number[MAXSTRINGSIZE];
-  molecule **moleculelist = new molecule *[MolCount];
-  MoleculeLeafClass *MolecularWalker = Subgraphs;
-  for (int i=0;i<MolCount;i++) {
-    MolecularWalker = MolecularWalker->next;
-    moleculelist[i] = World::getInstance().createMolecule();
-    moleculelist[i]->ActiveFlag = true;
-    strncpy(moleculelist[i]->name, mol->name, MAXSTRINGSIZE);
-    if (MolCount > 1) {
-      sprintf(number, "-%d", i+1);
-      strncat(moleculelist[i]->name, number, MAXSTRINGSIZE - strlen(mol->name) - 1);
-    }
-    DoLog(1) && (Log() << Verbose(1) << "MolName is " << moleculelist[i]->name << ", id is " << moleculelist[i]->getId() << endl);
-    for (molecule::iterator iter = MolecularWalker->Leaf->begin(); iter != MolecularWalker->Leaf->end(); ++iter) {
-      DoLog(1) && (Log() << Verbose(1) << **iter << endl);
-    }
-    molecules->insert(moleculelist[i]);
-  }
-
-  // 4b. create and fill map of which atom is associated to which connected molecule (note, counting starts at 1)
-  int FragmentCounter = 0;
-  map<int, atom *> AtomToFragmentMap;
-  MolecularWalker = Subgraphs;
-  while (MolecularWalker->next != NULL) {
-    MolecularWalker = MolecularWalker->next;
-    for (molecule::iterator iter = MolecularWalker->Leaf->begin(); !MolecularWalker->Leaf->empty(); iter = MolecularWalker->Leaf->begin()) {
-      atom * Walker = *iter;
-      DoLog(1) && (Log() << Verbose(1) << "Re-linking " << Walker << "..." << endl);
-      MolecularWalker->Leaf->erase(iter);
-      moleculelist[FragmentCounter]->AddAtom(Walker);    // counting starts at 1
-    }
-    FragmentCounter++;
-  }
-  // TODO: When DepthFirstSearchAnalysis does not use AddCopyAtom() anymore, we don't need to delete all original atoms.
-  // 4d. destroy the original molecule
-  for (molecule::iterator AtomRunner = mol->begin(); !mol->empty(); AtomRunner = mol->begin())
-    World::getInstance().destroyAtom(*AtomRunner);
-  World::getInstance().destroyMolecule(mol);
-
-  // 4d. we don't need to redo bonds, as they are connected subgraphs and still maintain their ListOfBonds, but we have to remove them from first..last list
-  // TODO: check whether this is really not needed anymore
-  // 4e. free Leafs
-  MolecularWalker = Subgraphs;
-  while (MolecularWalker->next != NULL) {
-    MolecularWalker = MolecularWalker->next;
-    delete(MolecularWalker->previous);
-  }
-  delete(MolecularWalker);
-  delete[](moleculelist);
-  DoLog(1) && (Log() << Verbose(1) << "I scanned " << FragmentCounter << " molecules." << endl);
-
+  molecules->DissectMoleculeIntoConnectedSubgraphs(World::getInstance().getPeriode(), World::getInstance().getConfig());
   return Action::success;
 }