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-              r42127c
+              r75363b
 using namespace std;
-/** Scans a single line for number and puts them into \a KeySet.
- * \param *out output stream for debugging
- * \param *buffer buffer to scan
- * \param &CurrentSet filled KeySet on return
- * \return true - at least one valid atom id parsed, false - CurrentSet is empty
- */
-bool ScanBufferIntoKeySet(char *buffer, KeySet &CurrentSet)
+{
-  stringstream line;
-  int AtomNr;
-  int status = 0;
-  line.str(buffer);
-  while (!line.eof()) {
-    line >> AtomNr;
-    if (AtomNr >= 0) {
-      CurrentSet.insert(AtomNr);  // insert at end, hence in same order as in file!
-      status++;
-    } // else it's "-1" or else and thus must not be added
+  }
-  DoLog(1) && (Log() << Verbose(1) << "The scanned KeySet is ");
-  for(KeySet::iterator runner = CurrentSet.begin(); runner != CurrentSet.end(); runner++) {
-    DoLog(0) && (Log() << Verbose(0) << (*runner) << "\t");
+  }
-  DoLog(0) && (Log() << Verbose(0) << endl);
-  return (status != 0);
-};
-/** Parses the KeySet file and fills \a *FragmentList from the known molecule structure.
- * Does two-pass scanning:
- * -# Scans the keyset file and initialises a temporary graph
- * -# Scans TEFactors file and sets the TEFactor of each key set in the temporary graph accordingly
- * Finally, the temporary graph is inserted into the given \a FragmentList for return.
- * \param &path path to file
- * \param *FragmentList empty, filled on return
- * \return true - parsing successfully, false - failure on parsing (FragmentList will be NULL)
- */
-bool ParseKeySetFile(std::string &path, Graph *&FragmentList)
+{
-  bool status = true;
-  ifstream InputFile;
-  stringstream line;
-  GraphTestPair testGraphInsert;
-  int NumberOfFragments = 0;
-  string filename;
-  if (FragmentList == NULL) { // check list pointer
-    FragmentList = new Graph;
+  }
-  // 1st pass: open file and read
-  DoLog(1) && (Log() << Verbose(1) << "Parsing the KeySet file ... " << endl);
-  filename = path + KEYSETFILE;
-  InputFile.open(filename.c_str());
-  if (InputFile.good()) {
-    // each line represents a new fragment
-    char buffer[MAXSTRINGSIZE];
-    // 1. parse keysets and insert into temp. graph
-    while (!InputFile.eof()) {
-      InputFile.getline(buffer, MAXSTRINGSIZE);
-      KeySet CurrentSet;
-      if ((strlen(buffer) > 0) && (ScanBufferIntoKeySet(buffer, CurrentSet))) {  // if at least one valid atom was added, write config
-        testGraphInsert = FragmentList->insert(GraphPair (CurrentSet,pair<int,double>(NumberOfFragments++,1)));  // store fragment number and current factor
-        if (!testGraphInsert.second) {
-          DoeLog(0) && (eLog()<< Verbose(0) << "KeySet file must be corrupt as there are two equal key sets therein!" << endl);
-          performCriticalExit();
+        }
+      }
+    }
-    // 2. Free and done
-    InputFile.close();
-    InputFile.clear();
-    DoLog(1) && (Log() << Verbose(1) << "\t ... done." << endl);
-  } else {
-    DoLog(1) && (Log() << Verbose(1) << "\t ... File " << filename << " not found." << endl);
-    status = false;
+  }
-  return status;
-};
-/** Parses the TE factors file and fills \a *FragmentList from the known molecule structure.
- * -# Scans TEFactors file and sets the TEFactor of each key set in the temporary graph accordingly
- * \param *out output stream for debugging
- * \param *path path to file
- * \param *FragmentList graph whose nodes's TE factors are set on return
- * \return true - parsing successfully, false - failure on parsing
- */
-bool ParseTEFactorsFile(char *path, Graph *FragmentList)
+{
-  bool status = true;
-  ifstream InputFile;
-  stringstream line;
-  GraphTestPair testGraphInsert;
-  int NumberOfFragments = 0;
-  double TEFactor;
-  char filename[MAXSTRINGSIZE];
-  if (FragmentList == NULL) { // check list pointer
-    FragmentList = new Graph;
+  }
-  // 2nd pass: open TEFactors file and read
-  DoLog(1) && (Log() << Verbose(1) << "Parsing the TEFactors file ... " << endl);
-  sprintf(filename, "%s/%s%s", path, FRAGMENTPREFIX, TEFACTORSFILE);
-  InputFile.open(filename);
-  if (InputFile != NULL) {
-    // 3. add found TEFactors to each keyset
-    NumberOfFragments = 0;
-    for(Graph::iterator runner = FragmentList->begin();runner != FragmentList->end(); runner++) {
-      if (!InputFile.eof()) {
-        InputFile >> TEFactor;
-        (*runner).second.second = TEFactor;
-        DoLog(2) && (Log() << Verbose(2) << "Setting " << ++NumberOfFragments << " fragment's TEFactor to " << (*runner).second.second << "." << endl);
-      } else {
-        status = false;
-        break;
+      }
+    }
-    // 4. Free and done
-    InputFile.close();
-    DoLog(1) && (Log() << Verbose(1) << "done." << endl);
-  } else {
-    DoLog(1) && (Log() << Verbose(1) << "File " << filename << " not found." << endl);
-    status = false;
+  }
-  return status;
-};
-/** Stores key sets to file.
- * \param KeySetList Graph with Keysets
- * \param &path path to file
- * \return true - file written successfully, false - writing failed
- */
-bool StoreKeySetFile(Graph &KeySetList, std::string &path)
+{
-  bool status =  true;
-  string line = path + KEYSETFILE;
-  ofstream output(line.c_str());
-  // open KeySet file
-  DoLog(1) && (Log() << Verbose(1) << "Saving key sets of the total graph ... ");
-  if(output.good()) {
-    for(Graph::iterator runner = KeySetList.begin(); runner != KeySetList.end(); runner++) {
-      for (KeySet::iterator sprinter = (*runner).first.begin();sprinter != (*runner).first.end(); sprinter++) {
-        if (sprinter != (*runner).first.begin())
-          output << "\t";
-        output << *sprinter;
+      }
-      output << endl;
+    }
-    DoLog(0) && (Log() << Verbose(0) << "done." << endl);
-  } else {
-    DoeLog(0) && (eLog()<< Verbose(0) << "Unable to open " << line << " for writing keysets!" << endl);
-    performCriticalExit();
-    status = false;
+  }
-  output.close();
-  output.clear();
-  return status;
-};
-/** Stores TEFactors to file.
- * \param *out output stream for debugging
- * \param KeySetList Graph with factors
- * \param *path path to file
- * \return true - file written successfully, false - writing failed
- */
-bool StoreTEFactorsFile(Graph &KeySetList, char *path)
+{
-  ofstream output;
-  bool status =  true;
-  string line;
-  // open TEFactors file
-  line = path;
-  line.append("/");
-  line += FRAGMENTPREFIX;
-  line += TEFACTORSFILE;
-  output.open(line.c_str(), ios::out);
-  DoLog(1) && (Log() << Verbose(1) << "Saving TEFactors of the total graph ... ");
-  if(output != NULL) {
-    for(Graph::iterator runner = KeySetList.begin(); runner != KeySetList.end(); runner++)
-      output << (*runner).second.second << endl;
-    DoLog(1) && (Log() << Verbose(1) << "done." << endl);
-  } else {
-    DoLog(1) && (Log() << Verbose(1) << "failed to open " << line << "." << endl);
-    status = false;
+  }
-  output.close();
-  return status;
-};
-/** For a given graph, sorts KeySets into a (index, keyset) map.
- * \param *GlobalKeySetList list of keysets with global ids (valid in "this" molecule) needed for adaptive increase
- * \return map from index to keyset
- */
-std::map<int,KeySet> * GraphToIndexedKeySet(Graph *GlobalKeySetList)
+{
-  map<int,KeySet> *IndexKeySetList = new map<int,KeySet>;
-  for(Graph::iterator runner = GlobalKeySetList->begin(); runner != GlobalKeySetList->end(); runner++) {
-    IndexKeySetList->insert( pair<int,KeySet>(runner->second.first,runner->first) );
+  }
-  return IndexKeySetList;
-};
 /** Inserts a (\a No, \a value) pair into the list, overwriting present one.

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Changeset 75363b for src/Fragmentation/fragmentation_helpers.cpp

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src/Fragmentation/fragmentation_helpers.cpp

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