Changeset 8bc524 for molecuilder/src/molecule_graph.cpp

Timestamp:

Nov 3, 2009, 12:37:55 PM (16 years ago)

Author:

Frederik Heber <heber@…>

Children:

5f9f8b

Parents:

df0520

git-author:

Frederik Heber <heber@…> (11/03/09 08:41:45)

git-committer:

Frederik Heber <heber@…> (11/03/09 12:37:55)

Message:

Several memory bugfixes (thx valgrind).

• main() - shortened case switch after ParseCommandLineOptions()
• molecule::FragmentMolecule() - indentation around BondFragments fixed.
• LEAKFIX: main() - configuration was not destroyed in case switch.
• LEAKFIX: ~config() - BondGraph BG was not destroyed.
• LEAKFIX: ParseKeySetFile() - filename was not destroyed.
• LEAKFIX: molecule::FragmentMolecule() - BackEdgeStack (returned from DepthFirstSearchAnalysis()) was not destroyed.
• LEAKFIX: molecule::FragmentMolecule() - BondFragments was not destroyed.
• LEAKFIX: MemoryUsageObserver::~MemoryUsageObserver() -- frees all remaining unbfree'd memory
• BUGFIX: MoleculeListClass::OutputConfigForListOfFragments() - FragmentNumber was delete'd not Free'd
• BUGFIX: ParseCommandLineOptions() - Free() of ListOfLocalAtoms had FragmentCounter instead of i
• BUGFIX: ParseCommandLineOptions() had BackEdgeStack in case 'D' instead of LocalBackEdgeStack for the CycliCStructureAnalysis()
• BUGFIX: StackClass<T>::StackClass() did not initialize StackList to NULL (are pointers anyway).
• MolecularLeafWalker::FillBondStructureFromReference() - no more performs its actions recursively (just complicates things unnecessarily).
• ParseCommandLineOptions() and molecule::FragmentMolecule() adapted to MolecularLeafWalker::FillBondStructureFromReference() changes.
• DepthFirstSearchAnalysis_Init() now does all of the initialisation of DepthFirstSearchAnalysis() and get molecule instead of AtomCount and BondCount

Fixed Calloc:

• MemoryAllocatorTest::MallocTest() and MemoryAllocatorTest::CallocTest() perform test on array of 10 with writing to it (revealed Calloc() bug)
• LEAKFIX: MemoryAllocatorTest::tearDown() - instance was not free'd
• BUGFIX: Calloc() - calloc() is called with num and sizeof, not num and initial_value!
• FIX: Malloc() to Calloc(): CreateFatherLookupTable(), molecule::IsEqualToWithinThreshold(), molecule::ConstrainedPotential(), PrintPermutationMap(), FillDistanceList() (initialization not needed anymore due to Calloc(), molecule::MinimiseConstrainedPotential(), molecule::ParseOrderAtSiteFromFile(), StoreFragmentFromKeySet_Init() (initialization not needed anymore due to Calloc(), molecule::StoreFragmentFromKeySet(), molecule::PowerSetGenerator(), molecule::FragmentBOSSANOVA(), molecule::ScanForPeriodicCorrection(), molecule::CreateAdjacencyList(), InitializeBFSAccounting(), BreadthFirstSearchAdd_Init(), BuildInducedSubgraph_Init(), MoleculeListClass::AddHydrogenCorrection(), MoleculeLeafClass::FillListOfLocalAtoms(), MoleculeLeafClass::AssignKeySetsToFragment(), StackClass<T>::StackClass()

Signed-off-by: Frederik Heber <heber@…>

File:

• molecuilder/src/molecule_graph.cpp (modified) (10 diffs)

molecuilder/src/molecule_graph.cpp

@@ -126 +126 @@
 
     // create a list to map Tesselpoint::nr to atom *
-    AtomMap = Malloc<atom *> (AtomCount, "molecule::CreateAdjacencyList - **AtomCount");
+    AtomMap = Calloc<atom *> (AtomCount, "molecule::CreateAdjacencyList - **AtomCount");
     Walker = start;
     while (Walker->next != end) {
@@ -437 +437 @@
  * \param *out output stream for debugging
  * \param &DFS accounting structure to allocate
- * \param AtomCount number of nodes in graph
- * \param BondCount number of edges in graph
- */
-void DepthFirstSearchAnalysis_Init(ofstream *out, struct DFSAccounting &DFS, int AtomCount, int BondCount)
-{
-  DFS.AtomStack = new StackClass<atom *> (AtomCount);
+ * \param *mol molecule with AtomCount, BondCount and all atoms
+ */
+void DepthFirstSearchAnalysis_Init(ofstream *out, struct DFSAccounting &DFS, const molecule * const mol)
+{
+  DFS.AtomStack = new StackClass<atom *> (mol->AtomCount);
   DFS.CurrentGraphNr = 0;
   DFS.ComponentNumber = 0;
   DFS.BackStepping = false;
+  mol->ResetAllBondsToUnused();
+  mol->SetAtomValueToValue(-1, &atom::GraphNr);
+  mol->ActOnAllAtoms(&atom::InitComponentNr);
+  DFS.BackEdgeStack->ClearStack();
 }
 ;
@@ -456 +459 @@
 {
   delete (DFS.AtomStack);
+  // delete (DFS.BackEdgeStack); // DON'T free, see DepthFirstSearchAnalysis(), is returned as allocated
 }
 ;
@@ -479 +483 @@
 
   *out << Verbose(0) << "Begin of DepthFirstSearchAnalysis" << endl;
-  DepthFirstSearchAnalysis_Init(out, DFS, AtomCount, BondCount);
+  DepthFirstSearchAnalysis_Init(out, DFS, this);
+
   DFS.Root = start->next;
-
-  ResetAllBondsToUnused();
-  SetAtomValueToValue(-1, &atom::GraphNr);
-  ActOnAllAtoms(&atom::InitComponentNr);
-  DFS.BackEdgeStack->ClearStack();
   while (DFS.Root != end) { // if there any atoms at all
-    // (1) mark all edges unused, empty stack, set atom->GraphNr = 0 for all
+    // (1) mark all edges unused, empty stack, set atom->GraphNr = -1 for all
     DFS.AtomStack->ClearStack();
 
@@ -602 +602 @@
 {
   BFS.AtomCount = AtomCount;
-  BFS.PredecessorList = Malloc<atom*> (AtomCount, "molecule::BreadthFirstSearchAdd_Init: **PredecessorList");
+  BFS.PredecessorList = Calloc<atom*> (AtomCount, "molecule::BreadthFirstSearchAdd_Init: **PredecessorList");
   BFS.ShortestPathList = Malloc<int> (AtomCount, "molecule::BreadthFirstSearchAdd_Init: *ShortestPathList");
-  BFS.ColorList = Malloc<enum Shading> (AtomCount, "molecule::BreadthFirstSearchAdd_Init: *ColorList");
+  BFS.ColorList = Calloc<enum Shading> (AtomCount, "molecule::BreadthFirstSearchAdd_Init: *ColorList");
   BFS.BFSStack = new StackClass<atom *> (AtomCount);
 
-  for (int i = AtomCount; i--;) {
-    BFS.PredecessorList[i] = NULL;
+  for (int i = AtomCount; i--;)
     BFS.ShortestPathList[i] = -1;
-    BFS.ColorList[i] = white;
-  }
 };
 
@@ -1002 +999 @@
 
   // allocate storage structure
-  CurrentBonds = Malloc<int> (8, "molecule::CheckAdjacencyFileAgainstMolecule - CurrentBonds"); // contains parsed bonds of current atom
+  CurrentBonds = Calloc<int> (8, "molecule::CheckAdjacencyFileAgainstMolecule - CurrentBonds"); // contains parsed bonds of current atom
   return true;
 }
@@ -1137 +1134 @@
   BFS.AtomCount = AtomCount;
   BFS.BondOrder = BondOrder;
-  BFS.PredecessorList = Malloc<atom*> (AtomCount, "molecule::BreadthFirstSearchAdd_Init: **PredecessorList");
-  BFS.ShortestPathList = Malloc<int> (AtomCount, "molecule::BreadthFirstSearchAdd_Init: *ShortestPathList");
+  BFS.PredecessorList = Calloc<atom*> (AtomCount, "molecule::BreadthFirstSearchAdd_Init: **PredecessorList");
+  BFS.ShortestPathList = Calloc<int> (AtomCount, "molecule::BreadthFirstSearchAdd_Init: *ShortestPathList");
   BFS.ColorList = Malloc<enum Shading> (AtomCount, "molecule::BreadthFirstSearchAdd_Init: *ColorList");
   BFS.BFSStack = new StackClass<atom *> (AtomCount);
@@ -1148 +1145 @@
   // initialise each vertex as white with no predecessor, empty queue, color Root lightgray
   for (int i = AtomCount; i--;) {
-    BFS.PredecessorList[i] = NULL;
     BFS.ShortestPathList[i] = -1;
     if ((AddedAtomList != NULL) && (AddedAtomList[i] != NULL)) // mark already present atoms (i.e. Root and maybe others) as visited
@@ -1155 +1151 @@
       BFS.ColorList[i] = white;
   }
-  BFS.ShortestPathList[Root->nr] = 0;
+  //BFS.ShortestPathList[Root->nr] = 0; //is set due to Calloc()
 }
 ;
@@ -1302 +1298 @@
 {
   // reset parent list
-  ParentList = Malloc<atom*> (AtomCount, "molecule::BuildInducedSubgraph_Init: **ParentList");
+  ParentList = Calloc<atom*> (AtomCount, "molecule::BuildInducedSubgraph_Init: **ParentList");
   *out << Verbose(3) << "Resetting ParentList." << endl;
-  for (int i = AtomCount; i--;)
-    ParentList[i] = NULL;
 }
 ;