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-              r42127c
+              r75363b
 #include "CodePatterns/MemDebug.hpp"
+#include <fstream>
+#include <iostream>
+#include <sstream>
+#include <string>
 #include "Graph.hpp"
 #include "CodePatterns/Log.hpp"
+#include "Helpers/defs.hpp"
+#include "Helpers/helpers.hpp"
 /** Constructor for class Graph.
 …
 };
+/** Parses the KeySet file and fills \a this 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
+ * \return true - parsing successfully, false - failure on parsing (FragmentList will be NULL)
+ */
+bool Graph::ParseKeySetFile(std::string &path)
+{
+  bool status = true;
+  std::ifstream InputFile;
+  std::stringstream line;
+  GraphTestPair testGraphInsert;
+  int NumberOfFragments = 0;
+  std::string filename;
+  // 1st pass: open file and read
+  LOG(1, "INFO: Parsing the KeySet file ... ");
+  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) && (CurrentSet.ScanBufferIntoKeySet(buffer))) {  // if at least one valid atom was added, write config
+        testGraphInsert = insert(GraphPair (CurrentSet,pair<int,double>(NumberOfFragments++,1)));  // store fragment number and current factor
+        if (!testGraphInsert.second) {
+          ELOG(0, "KeySet file must be corrupt as there are two equal key sets therein!");
+          performCriticalExit();
+        }
+      }
+    }
+    // 2. Free and done
+    InputFile.close();
+    InputFile.clear();
+    LOG(1, "INFO: ... done.");
+  } else {
+    ELOG(1, "File " << filename << " not found.");
+    status = false;
+  }
+  return status;
+};
+/** Stores key sets to file.
+ * \param &path path to file
+ * \return true - file written successfully, false - writing failed
+ */
+bool Graph::StoreKeySetFile(std::string &path)
+{
+  bool status =  true;
+  std::string line = path + KEYSETFILE;
+  std::ofstream output(line.c_str());
+  // open KeySet file
+  LOG(1, "INFO: Saving key sets of the total graph ... ");
+  if(output.good()) {
+    for(Graph::iterator runner = begin(); runner != end(); runner++) {
+      for (KeySet::iterator sprinter = (*runner).first.begin();sprinter != (*runner).first.end(); sprinter++) {
+        if (sprinter != (*runner).first.begin())
+          output << "\t";
+        output << *sprinter;
+      }
+      output << std::endl;
+    }
+    LOG(1, "INFO: done.");
+  } else {
+    ELOG(0, "Unable to open " << line << " for writing keysets!");
+    performCriticalExit();
+    status = false;
+  }
+  output.close();
+  output.clear();
+  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 *path path to file
+ * \return true - parsing successfully, false - failure on parsing
+ */
+bool Graph::ParseTEFactorsFile(char *path)
+{
+  bool status = true;
+  std::ifstream InputFile;
+  std::stringstream line;
+  GraphTestPair testGraphInsert;
+  int NumberOfFragments = 0;
+  double TEFactor;
+  char filename[MAXSTRINGSIZE];
+  // 2nd pass: open TEFactors file and read
+  LOG(1, "INFO: Parsing the TEFactors file ... ");
+  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 = begin();runner != end(); runner++) {
+      if (!InputFile.eof()) {
+        InputFile >> TEFactor;
+        (*runner).second.second = TEFactor;
+        LOG(2, "INFO: Setting " << ++NumberOfFragments << " fragment's TEFactor to " << (*runner).second.second << ".");
+      } else {
+        status = false;
+        break;
+      }
+    }
+    // 4. Free and done
+    InputFile.close();
+    LOG(1, "INFO: done.");
+  } else {
+    LOG(1, "INFO: File " << filename << " not found.");
+    status = false;
+  }
+  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 Graph::StoreTEFactorsFile(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);
+  LOG(1, "INFO: Saving TEFactors of the total graph ... ");
+  if(output != NULL) {
+    for(Graph::iterator runner = begin(); runner != end(); runner++)
+      output << (*runner).second.second << endl;
+    LOG(1, "INFO: done." << endl);
+  } else {
+    ELOG(2, "INFO: failed to open " << line << "." << endl);
+    status = false;
+  }
+  output.close();
+  return status;
+};
+/** For a given graph, sorts KeySets into a (index, keyset) map.
+ * \return ref to allocated map from index to keyset
+ */
+std::map<int,KeySet> * Graph::GraphToIndexedKeySet() const
+{
+  map<int,KeySet> *IndexKeySetList = new map<int,KeySet>;
+  for(const_iterator runner = begin(); runner != end(); runner++) {
+    IndexKeySetList->insert( pair<int,KeySet>(runner->second.first,runner->first) );
+  }
+  return IndexKeySetList;
+};

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Changeset 75363b for src/Fragmentation/Graph.cpp

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src/Fragmentation/Graph.cpp

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