Changes in / [0ac85c3:27e464]

Location:

src

Files:

• Atom/AtomicInfo.cpp (modified) (1 diff)
• Atom/atom.cpp (modified) (5 diffs)
• Atom/atom.hpp (modified) (4 diffs)
• Atom/atom_observable.cpp (modified) (1 diff)
• Atom/atom_observable.hpp (modified) (1 diff)
• Fragmentation/Exporters/HydrogenPool.cpp (modified) (1 diff)
• Fragmentation/Exporters/SaturatedFragment.cpp (modified) (2 diffs)
• Graph/BuildInducedSubgraph.cpp (modified) (2 diffs)
• Parser/PdbParser.cpp (modified) (1 diff)
• UIElements/Makefile.am (modified) (5 diffs)
• UIElements/Qt4/QtMainWindow.cpp (modified) (3 diffs)
• UIElements/Views/Qt4/MoleculeList/QtMoleculeItem.cpp (added)
• UIElements/Views/Qt4/MoleculeList/QtMoleculeItem.hpp (added)
• UIElements/Views/Qt4/MoleculeList/QtMoleculeItemFactory.cpp (added)
• UIElements/Views/Qt4/MoleculeList/QtMoleculeItemFactory.hpp (added)
• UIElements/Views/Qt4/MoleculeList/QtMoleculeList.cpp (added)
• UIElements/Views/Qt4/MoleculeList/QtMoleculeList.hpp (added)
• UIElements/Views/Qt4/MoleculeList/QtMoleculeListView.cpp (added)
• UIElements/Views/Qt4/MoleculeList/QtMoleculeListView.hpp (added)
• UIElements/Views/Qt4/MoleculeList/SpecificItems/QtMoleculeItem_atomcount.hpp (added)
• UIElements/Views/Qt4/MoleculeList/SpecificItems/QtMoleculeItem_formula.hpp (added)
• UIElements/Views/Qt4/MoleculeList/SpecificItems/QtMoleculeItem_name.hpp (added)
• UIElements/Views/Qt4/MoleculeList/SpecificItems/QtMoleculeItem_occurrence.hpp (added)
• UIElements/Views/Qt4/MoleculeList/SpecificItems/QtMoleculeItem_visibility.hpp (added)
• UIElements/Views/Qt4/QtMoleculeList.cpp (deleted)
• UIElements/Views/Qt4/QtMoleculeList.hpp (deleted)
• builder.cpp (modified) (1 diff)
• molecule.cpp (modified) (5 diffs)
• molecule.hpp (modified) (1 diff)
• moleculelist.cpp (modified) (1 diff)

src/Atom/AtomicInfo.cpp

@@ -88 +88 @@
   bool status = true;
   if (_atom.getId() != Id)
-    status = _atom.changeId(Id);
+    status &= _atom.changeId(Id);
 
   // set its father
-  atom * const _father = World::getInstance().getAtom(AtomById(FatherId));
-  if (_father == NULL)
-    _atom.father = &_atom;
-  else
-    _atom.father = _father;
+  if (status) {
+    atom * const _father = World::getInstance().getAtom(AtomById(FatherId));
+    if ((_father == NULL) || (Id == FatherId)) {
+      _atom.father = &_atom;
+      // don't sign on
+    } else {
+      _atom.father = _father;
+      _father->signOn(&_atom);
+    }
 
-  // setting molecule
-  molecule * const _mol = World::getInstance().getMolecule(MoleculeById(MolId));
-  if (_mol != NULL)
-    _atom.setMolecule(_mol); // this is ok, mol is const within AtomicInfo, but not outside (atoms need to register)
-  _atom.changeNr(Nr);
+    // setting molecule
+    molecule * const _mol = World::getInstance().getMolecule(MoleculeById(MolId));
+    if (_mol != NULL)
+      _atom.setMolecule(_mol); // this is ok, mol is const within AtomicInfo, but not outside (atoms need to register)
+    _atom.changeNr(Nr);
+  }
 
   return status;

src/Atom/atom.cpp

@@ -58 +58 @@
   mol(0)
 {
-  // sign on to global atom change tracker
+  // note AtomObserver about inserted atom
   AtomObserver::getInstance().AtomInserted(this);
 }
@@ -69 +69 @@
     mol(0)
 {
-  // sign on to global atom change tracker
+  // sign on to father atom to be notified when it is removed
+  father->signOn(this);
+
+  // note AtomObserver about inserted atom
   AtomObserver::getInstance().AtomInserted(this);
 };
@@ -84 +87 @@
 atom::~atom()
 {
+  // sign off from possible father
+  if ((father != this) && (father != NULL))
+    father->signOff(this);
+
   removeFromMolecule();
-  // sign off from global atom change tracker
+  // note AtomObserver about removed atom
   AtomObserver::getInstance().AtomRemoved(this);
 }
@@ -125 +132 @@
     return father->GetTrueFather();
   }
-};
+}
+
+void atom::setFather(atom * const _father)
+{
+  // sign off from old father
+  if ((father != this) && (father != NULL))
+    father->signOff(this);
+
+  father = _father;
+  father->signOn(this);
+}
 
 /** Sets father to itself or its father in case of copying a molecule.
@@ -325 +342 @@
   return atom1->getType()->getAtomicNumber() < atom2->getType()->getAtomicNumber();
 }
+/*
+void atom::update(Observable *publisher)
+{}
+
+void atom::recieveNotification(Observable *publisher, Notification_ptr notification)
+{
+  ASSERT(0, "atom::recieveNotification() - we are not signed on to any notifications.");
+}
+*/
+void atom::subjectKilled(Observable *publisher)
+{
+  // as publisher has been half-deallocated (Observable is one of the base classes, hence
+  // becomes destroyed latest), we cannot senibly cast it anymore.
+  // Hence, we simply have to check here whether it is NOT one of the other instances
+  // we are signed on to.
+  father = this;
+  // no need to sign off
+}

src/Atom/atom.hpp

@@ -25 +25 @@
 #include "atom_bondedparticle.hpp"
 #include "atom_graphnode.hpp"
+#include "atom_observable.hpp"
 #include "atom_particleinfo.hpp"
 #include "Atom/TesselPoint.hpp"
 #include "types.hpp"
 
+#include "CodePatterns/Observer/Observer.hpp"
 #include "CodePatterns/enumeration.hpp"
 
@@ -44 +46 @@
  * Class incorporates position, type
  */
-class atom : public GraphNode, public BondedParticle, public TesselPoint {
+class atom :
+            public GraphNode,
+            public BondedParticle,
+            public TesselPoint
+{
   friend atom* NewAtom(atomId_t);
   friend void  DeleteAtom(atom*);
+
+  atom *father;   //!< In many-body bond order fragmentations points to originating atom
+  int *sort;      //!< sort criteria
+
 public:
-    atom *father;   //!< In many-body bond order fragmentations points to originating atom
-    int *sort;      //!< sort criteria
 
   /** Clones this atom.
@@ -130 +138 @@
    */
   const atom *GetTrueFather() const;
+
+  /** Const getter for the atoms father.
+   *
+   * \return father of this atom
+   */
+  atom * const getFather() const
+  { return father; }
+
+  /** Sets the father for this atom.
+   *
+   * \param _father ptr to father atom
+   */
+  void setFather(atom * const _father);
 
   /** Compares the indices of \a this atom with a given \a ptr.
@@ -228 +249 @@
     void unsetMolecule();
 
+//    virtual void update(Observable *publisher);
+//    virtual void recieveNotification(Observable *publisher, Notification_ptr notification);
+    virtual void subjectKilled(Observable *publisher);
 
   private:

src/Atom/atom_observable.cpp

@@ -55 +55 @@
 AtomObservable::~AtomObservable()
 {}
+
+void AtomObservable::subjectKilled(Observable *publisher)
+{}

src/Atom/atom_observable.hpp

@@ -41 +41 @@
   AtomObservable();
   virtual ~AtomObservable();
+
+protected:
+
+  virtual void subjectKilled(Observable *publisher);
 };
 

src/Fragmentation/Exporters/HydrogenPool.cpp

@@ -68 +68 @@
   ++HydrogenCount;
 
-  // give warning if pool has more than thereshold
+  // give warning if pool has more than threshold
   if (HydrogenCount >= WARNINGTHRESHOLD) {
     ELOG(2, "HydrogenPool contains more hydrogen atoms than limit.");

src/Fragmentation/Exporters/SaturatedFragment.cpp

@@ -311 +311 @@
   _atom->setFixedIon(true);
   // if we replace hydrogen, we mark it as our father, otherwise we are just an added hydrogen with no father
-  _atom->father = _father;
+  _atom->setFather(_father);
   SaturationHydrogens.insert(_atom->getId());
 
@@ -387 +387 @@
   _atom->setFixedIon(replacement->getFixedIon());
   // if we replace hydrogen, we mark it as our father, otherwise we are just an added hydrogen with no father
-  _atom->father = replacement;
+  _atom->setFather(replacement);
   SaturationHydrogens.insert(_atom->getId());
   return _atom;

src/Graph/BuildInducedSubgraph.cpp

@@ -63 +63 @@
   LOG(3, "Filling Parent List.");
   for (molecule::iterator iter = Son->begin(); iter != Son->end(); ++iter) {
-    ParentList[(*iter)->father] = (*iter);
+    ParentList[(*iter)->getFather()] = (*iter);
     // Outputting List for debugging
-    LOG(4, "INFO: ParentList[] of " << (*iter)->father << " is " << *ParentList[(*iter)->father] << ".");
+    LOG(4, "INFO: ParentList[] of " << (*iter)->getFather() << " is " << *ParentList[(*iter)->getFather()] << ".");
   }
 }
@@ -77 +77 @@
   for (molecule::iterator iter = Father->begin(); iter != Father->end(); ++iter) {
     if (ParentList.count(*iter)) {
-      if (ParentList[(*iter)]->father != (*iter)) {
+      if (ParentList[(*iter)]->getFather() != (*iter)) {
         status = false;
       } else {

src/Parser/PdbParser.cpp

@@ -360 +360 @@
 {
   if (additionalAtomData.find(_atom->getId()) != additionalAtomData.end()) {
-  } else if (additionalAtomData.find(_atom->father->getId()) != additionalAtomData.end()) {
+  } else if (additionalAtomData.find(_atom->getFather()->getId()) != additionalAtomData.end()) {
     // use info from direct father
-    additionalAtomData[_atom->getId()] = additionalAtomData[_atom->father->getId()];
+    additionalAtomData[_atom->getId()] = additionalAtomData[_atom->getFather()->getId()];
   } else if (additionalAtomData.find(_atom->GetTrueFather()->getId()) != additionalAtomData.end()) {
     // use info from topmost father

src/UIElements/Makefile.am

@@ -167 +167 @@
   UIElements/Qt4/QtDialog.cpp \
   UIElements/Qt4/QtUIFactory.cpp \
+  UIElements/Views/Qt4/MoleculeList/QtMoleculeItem.cpp \
+  UIElements/Views/Qt4/MoleculeList/QtMoleculeItemFactory.cpp \
+  UIElements/Views/Qt4/MoleculeList/QtMoleculeList.cpp \
+  UIElements/Views/Qt4/MoleculeList/QtMoleculeListView.cpp \
   UIElements/Menu/Qt4/QtMenuPipe.cpp \
   UIElements/Views/Qt4/QtElementList.cpp \
@@ -173 +177 @@
   UIElements/Views/Qt4/QtInfoBox.cpp \
   UIElements/Views/Qt4/QtLogBox.cpp \
-  UIElements/Views/Qt4/QtMoleculeList.cpp \
   UIElements/Views/Qt4/QtShapeController.cpp \
   UIElements/Views/Qt4/QtShapeList.cpp \
@@ -195 +198 @@
   UIElements/Menu/Qt4/QMenu_tooltip.hpp \
   UIElements/Menu/Qt4/QtMenuPipe.hpp \
-  UIElements/Views/Qt4/QDebugStream.hpp \
+  UIElements/Views/Qt4/MoleculeList/QtMoleculeList.hpp \
+  UIElements/Views/Qt4/MoleculeList/QtMoleculeListView.hpp \
   UIElements/Views/Qt4/QtElementList.hpp \
   UIElements/Views/Qt4/QtFragmentList.hpp \
@@ -201 +205 @@
   UIElements/Views/Qt4/QtInfoBox.hpp \
   UIElements/Views/Qt4/QtLogBox.hpp \
-  UIElements/Views/Qt4/QtMoleculeList.hpp \
   UIElements/Views/Qt4/QtShapeController.hpp \
   UIElements/Views/Qt4/QtShapeList.hpp \
@@ -224 +227 @@
   UIElements/Menu/Qt4/QtMenu.hpp \
   UIElements/Qt4/Query/QtQueryList.hpp \
-  UIElements/Qt4/QtUIFactory.hpp
+  UIElements/Qt4/QtUIFactory.hpp \
+  UIElements/Views/Qt4/MoleculeList/QtMoleculeItem.hpp \
+  UIElements/Views/Qt4/MoleculeList/QtMoleculeItemFactory.hpp \
+  UIElements/Views/Qt4/MoleculeList/SpecificItems/QtMoleculeItem_atomcount.hpp \
+  UIElements/Views/Qt4/MoleculeList/SpecificItems/QtMoleculeItem_formula.hpp \
+  UIElements/Views/Qt4/MoleculeList/SpecificItems/QtMoleculeItem_name.hpp \
+  UIElements/Views/Qt4/MoleculeList/SpecificItems/QtMoleculeItem_occurrence.hpp \
+  UIElements/Views/Qt4/MoleculeList/SpecificItems/QtMoleculeItem_visibility.hpp \
+  UIElements/Views/Qt4/QDebugStream.hpp
 
 lib_LTLIBRARIES += libMolecuilderUI.la

src/UIElements/Qt4/QtMainWindow.cpp

@@ -53 +53 @@
 
 #include "Menu/Qt4/QtMenu.hpp"
-#include "Views/Qt4/QtMoleculeList.hpp"
+#include "Views/Qt4/MoleculeList/QtMoleculeList.hpp"
+#include "Views/Qt4/MoleculeList/QtMoleculeListView.hpp"
 #include "Views/Qt4/QtElementList.hpp"
 #include "Views/Qt4/QtFragmentList.hpp"
@@ -95 +96 @@
   QVBoxLayout *layout = new QVBoxLayout(layoutwidget);
 
-  moleculeList = new QtMoleculeList(worldTab);
+  QtMoleculeListView *moleculeListView = new QtMoleculeListView(worldTab);
+  moleculeList = new QtMoleculeList;
+  moleculeListView->setModel(moleculeList);
+
   elementList = new QtElementList(worldTab);
   homologyList = new QtHomologyList(worldTab);
@@ -129 +133 @@
   layout->addWidget(worldTab);
   splitter2->addWidget(layoutwidget);
-  worldTab->addTab(moleculeList, "Molecules");
+  worldTab->addTab(moleculeListView, "Molecules");
   worldTab->addTab(elementList, "All Elements");
   worldTab->addTab(fragmentList, "All Fragments");

src/builder.cpp

@@ -39 +39 @@
 #include "UIElements/UIFactory.hpp"
 
+#ifdef LOG_OBSERVER
+#include "CodePatterns/Observer/ObserverLog.hpp"
+#endif
+
 /********************************************** Main routine **************************************/
 
 int main(int argc, char **argv)
 {
+#ifdef LOG_OBSERVER
+  ObserverLog::getInstance().enableLogging();
+#endif
+
   initGeneral();
 

src/molecule.cpp

@@ -35 +35 @@
 #include "CodePatterns/MemDebug.hpp"
 
-#include <cstring>
+#include <algorithm>
 #include <boost/bind.hpp>
 #include <boost/foreach.hpp>
+#include <cstring>
 
 #include <gsl/gsl_inline.h>
@@ -102 +103 @@
 molecule::~molecule()
 {
+  // inform all UI elements about imminent removal before anything is lost
+  {
+    OBSERVE;
+    NOTIFY(AboutToBeRemoved);
+  }
   CleanupMolecule();
 };
@@ -648 +654 @@
 void removeAtomsinMolecule(molecule *&_mol)
 {
+  // copy list of atoms from molecule as it will be changed
+  std::vector<atom *> atoms;
+  atoms.resize(_mol->getAtomCount(), NULL);
+  std::copy(_mol->begin(), _mol->end(), atoms.begin());
   // remove each atom from world
-  for(molecule::iterator AtomRunner = _mol->begin(); !_mol->empty(); AtomRunner = _mol->begin())
+  for(std::vector<atom *>::iterator AtomRunner = atoms.begin();
+      AtomRunner != atoms.end(); ++AtomRunner)
     World::getInstance().destroyAtom(*AtomRunner);
   // make sure that pointer os not usable
@@ -934 +945 @@
     output << "Map is ";
     for (molecule::const_iterator iter = begin(); iter != end(); ++iter) {
-      if ((*iter)->father == NULL) {
+      if ((*iter)->getFather() == NULL) {
         AtomicMap[(*iter)->getNr()] = -2;
       } else {
@@ -940 +951 @@
       //for (int i=0;i<AtomCount;i++) { // search atom
         //for (int j=0;j<OtherMolecule->getAtomCount();j++) {
-          //LOG(4, "Comparing father " << (*iter)->father << " with the other one " << (*runner)->father << ".");
-          if ((*iter)->father == (*runner))
+          //LOG(4, "Comparing father " << (*iter)->getFather() << " with the other one " << (*runner)->getFather() << ".");
+          if ((*iter)->getFather() == (*runner))
             AtomicMap[(*iter)->getNr()] = (*runner)->getNr();
         }

src/molecule.hpp

@@ -113 +113 @@
     AtomMoved,
     MoleculeNameChanged,
+    AboutToBeRemoved,
     NotificationType_MAX
   };

src/moleculelist.cpp

@@ -409 +409 @@
     for (molecule::const_iterator iter = (*ListRunner)->begin(); iter != (*ListRunner)->end(); ++iter) {
       //LOG(1, "(*iter): " << *(*iter) << " with first bond " << *((*iter)->getListOfBonds().begin()) << ".");
-      if (((*iter)->getType()->getAtomicNumber() == 1) && (((*iter)->father == NULL)
-          || ((*iter)->father->getType()->getAtomicNumber() != 1))) { // if it's a hydrogen
+      if (((*iter)->getType()->getAtomicNumber() == 1) && (((*iter)->getFather() == NULL)
+          || ((*iter)->getFather()->getType()->getAtomicNumber() != 1))) { // if it's a hydrogen
         for (molecule::const_iterator runner = (*ListRunner)->begin(); runner != (*ListRunner)->end(); ++runner) {
           //LOG(2, "Runner: " << *(*runner) << " with first bond " << *((*iter)->getListOfBonds().begin()) << ".");