Changes in src/Parser/TremoloParser.cpp [765f16:3bdb6d]

File:

• src/Parser/TremoloParser.cpp (modified) (31 diffs)

src/Parser/TremoloParser.cpp

@@ -29 +29 @@
 #include "atom.hpp"
 #include "Bond/bond.hpp"
-#include "element.hpp"
+#include "Element/element.hpp"
 #include "molecule.hpp"
-#include "periodentafel.hpp"
+#include "Element/periodentafel.hpp"
 #include "Descriptors/AtomIdDescriptor.hpp"
 #include <map>
@@ -42 +42 @@
 using namespace std;
 
-// declare specialized static variables
-const std::string FormatParserTrait<tremolo>::name = "tremolo";
-const std::string FormatParserTrait<tremolo>::suffix = "data";
-const ParserTypes FormatParserTrait<tremolo>::type = tremolo;
-
 /**
  * Constructor.
  */
-FormatParser< tremolo >::FormatParser()  :
-  FormatParser_common(NULL)
-{
+TremoloParser::TremoloParser() {
   knownKeys["x"] = TremoloKey::x;
   knownKeys["u"] = TremoloKey::u;
@@ -94 +87 @@
  * Destructor.
  */
-FormatParser< tremolo >::~FormatParser() 
-{
-  std::cerr << "Clearing usedFields." << std::endl;
+TremoloParser::~TremoloParser() {
+        std::cerr << "Clearing usedFields." << std::endl;
   usedFields.clear();
   additionalAtomData.clear();
@@ -108 +100 @@
  * \param tremolo file
  */
-void FormatParser< tremolo >::load(istream* file) {
+void TremoloParser::load(istream* file) {
   string line;
   string::size_type location;
@@ -149 +141 @@
  * \param atoms atoms to store
  */
-void FormatParser< tremolo >::save(ostream* file, const std::vector<atom *> &AtomList) {
+void TremoloParser::save(ostream* file, const std::vector<atom *> &AtomList) {
   DoLog(0) && (Log() << Verbose(0) << "Saving changes to tremolo." << std::endl);
 
@@ -177 +169 @@
  * @param id of atom
  */
-void FormatParser< tremolo >::AtomInserted(atomId_t id)
+void TremoloParser::AtomInserted(atomId_t id)
 {
   std::map<int, TremoloAtomInfoContainer>::iterator iter = additionalAtomData.find(id);
   ASSERT(iter == additionalAtomData.end(),
-      "FormatParser< tremolo >::AtomInserted() - additionalAtomData already present for newly added atom "
+      "TremoloParser::AtomInserted() - additionalAtomData already present for newly added atom "
       +toString(id)+".");
   // don't add entry, as this gives a default resSeq of 0 not the molecule id
@@ -191 +183 @@
  * @param id of atom
  */
-void FormatParser< tremolo >::AtomRemoved(atomId_t id)
+void TremoloParser::AtomRemoved(atomId_t id)
 {
   std::map<int, TremoloAtomInfoContainer>::iterator iter = additionalAtomData.find(id);
   // as we do not insert AtomData on AtomInserted, we cannot be assured of its presence
 //  ASSERT(iter != additionalAtomData.end(),
-//      "FormatParser< tremolo >::AtomRemoved() - additionalAtomData is not present for atom "
+//      "TremoloParser::AtomRemoved() - additionalAtomData is not present for atom "
 //      +toString(id)+" to remove.");
   if (iter != additionalAtomData.end())
@@ -209 +201 @@
  *        but without the prexix "ATOMDATA"
  */
-void FormatParser< tremolo >::setFieldsForSave(std::string atomDataLine) {
+void TremoloParser::setFieldsForSave(std::string atomDataLine) {
   parseAtomDataKeysLine(atomDataLine, 0);
 }
@@ -220 +212 @@
  * \param reference to the atom of which information should be written
  */
-void FormatParser< tremolo >::saveLine(ostream* file, atom* currentAtom) {
-  //vector<string>::iterator it;
-  // TODO: Is unique for FormatParser< tremolo >::usedFields still required?
-  vector<string>::iterator it = unique(usedFields.begin(), usedFields.end()); // skips all duplicates in the vector
+void TremoloParser::saveLine(ostream* file, atom* currentAtom) {
+ /* vector<string>::iterator it;*/
+        vector<string>::iterator it = unique(usedFields.begin(), usedFields.end()); // skips all duplicates in the vector
 
   TremoloKey::atomDataKey currentField;
@@ -317 +308 @@
  * \param reference to the atom of which to take the neighbor information
  */
-void FormatParser< tremolo >::writeNeighbors(ostream* file, int numberOfNeighbors, atom* currentAtom) {
+void TremoloParser::writeNeighbors(ostream* file, int numberOfNeighbors, atom* currentAtom) {
   const BondList& ListOfBonds = currentAtom->getListOfBonds();
   // sort bonded indices
@@ -340 +331 @@
  * \param with which offset the keys begin within the line
  */
-void FormatParser< tremolo >::parseAtomDataKeysLine(string line, int offset) {
+void TremoloParser::parseAtomDataKeysLine(string line, int offset) {
   string keyword;
   stringstream lineStream;
@@ -362 +353 @@
  *  \a atomdata_string.
  *
- *  We just call \sa  FormatParser< tremolo >::parseAtomDataKeysLine() which is left
+ *  We just call \sa TremoloParser::parseAtomDataKeysLine() which is left
  *  private.,
  *
  * @param atomdata_string line to parse with space-separated values
  */
-void FormatParser< tremolo >::setAtomData(const std::string &atomdata_string)
+void TremoloParser::setAtomData(const std::string &atomdata_string)
 {
   parseAtomDataKeysLine(atomdata_string, 0);
@@ -380 +371 @@
  * \param *newmol molecule to add atom to
  */
-void FormatParser< tremolo >::readAtomDataLine(string line, molecule *newmol = NULL) {
+void TremoloParser::readAtomDataLine(string line, molecule *newmol = NULL) {
   vector<string>::iterator it;
   stringstream lineStream;
@@ -398 +389 @@
   tokenizer tokens(line, whitespacesep);
   ASSERT(tokens.begin() != tokens.end(),
-      "FormatParser< tremolo >::readAtomDataLine - empty string, need at least ' '!");
+      "TremoloParser::readAtomDataLine - empty string, need at least ' '!");
   tokenizer::iterator tok_iter = tokens.begin();
   // then associate each token to each file
@@ -410 +401 @@
         // for the moment, assume there are always three dimensions
         for (int i=0;i<NDIM;i++) {
-          ASSERT(tok_iter != tokens.end(), "FormatParser< tremolo >::readAtomDataLine() - no value for x["+toString(i)+"]!");
+          ASSERT(tok_iter != tokens.end(), "TremoloParser::readAtomDataLine() - no value for x["+toString(i)+"]!");
           DoLog(4) && (Log() << Verbose(4) << "INFO: Parsing key " << keyName << " with next token " << *tok_iter << std::endl);
           newAtom->set(i, toDouble(*tok_iter));
@@ -419 +410 @@
         // for the moment, assume there are always three dimensions
         for (int i=0;i<NDIM;i++) {
-          ASSERT(tok_iter != tokens.end(), "FormatParser< tremolo >::readAtomDataLine() - no value for u["+toString(i)+"]!");
+          ASSERT(tok_iter != tokens.end(), "TremoloParser::readAtomDataLine() - no value for u["+toString(i)+"]!");
           DoLog(4) && (Log() << Verbose(4) << "INFO: Parsing key " << keyName << " with next token " << *tok_iter << std::endl);
           tempVector[i] = toDouble(*tok_iter);
@@ -428 +419 @@
       case TremoloKey::type :
       {
-        ASSERT(tok_iter != tokens.end(), "FormatParser< tremolo >::readAtomDataLine() - no value for "+keyName+"!");
+        ASSERT(tok_iter != tokens.end(), "TremoloParser::readAtomDataLine() - no value for "+keyName+"!");
         DoLog(4) && (Log() << Verbose(4) << "INFO: Parsing key " << keyName << " with next token " << *tok_iter << std::endl);
         std::string element(knownTypes[(*tok_iter)]);
@@ -440 +431 @@
       }
       case TremoloKey::Id :
-        ASSERT(tok_iter != tokens.end(), "FormatParser< tremolo >::readAtomDataLine() - no value for "+keyName+"!");
+        ASSERT(tok_iter != tokens.end(), "TremoloParser::readAtomDataLine() - no value for "+keyName+"!");
         DoLog(4) && (Log() << Verbose(4) << "INFO: Parsing key " << keyName << " with next token " << *tok_iter << std::endl);
         atomIdMap[toInt(*tok_iter)] = newAtom->getId();
@@ -447 +438 @@
       case TremoloKey::neighbors :
         for (int i=0;i<atoi(it->substr(it->find("=") + 1, 1).c_str());i++) {
-          ASSERT(tok_iter != tokens.end(), "FormatParser< tremolo >::readAtomDataLine() - no value for "+keyName+"!");
+          ASSERT(tok_iter != tokens.end(), "TremoloParser::readAtomDataLine() - no value for "+keyName+"!");
           DoLog(4) && (Log() << Verbose(4) << "INFO: Parsing key " << keyName << " with next token " << *tok_iter << std::endl);
           lineStream << *tok_iter << "\t";
@@ -456 +447 @@
         break;
       default :
-        ASSERT(tok_iter != tokens.end(), "FormatParser< tremolo >::readAtomDataLine() - no value for "+keyName+"!");
+        ASSERT(tok_iter != tokens.end(), "TremoloParser::readAtomDataLine() - no value for "+keyName+"!");
         DoLog(4) && (Log() << Verbose(4) << "INFO: Parsing key " << keyName << " with next token " << *tok_iter << std::endl);
         atomInfo->set(currentField, *tok_iter);
@@ -476 +467 @@
  * \param atomid world id of the atom the information belongs to
  */
-void FormatParser< tremolo >::readNeighbors(stringstream* line, int numberOfNeighbors, int atomId) {
+void TremoloParser::readNeighbors(stringstream* line, int numberOfNeighbors, int atomId) {
   int neighborId = 0;
   for (int i = 0; i < numberOfNeighbors; i++) {
@@ -498 +489 @@
  * \return true if the field name is used
  */
-bool FormatParser< tremolo >::isUsedField(string fieldName) {
+bool TremoloParser::isUsedField(string fieldName) {
   bool fieldNameExists = false;
   for (vector<string>::iterator usedField = usedFields.begin(); usedField != usedFields.end(); usedField++) {
@@ -514 +505 @@
  * Id found in the parsed file.
  */
-void FormatParser< tremolo >::processNeighborInformation() {
+void TremoloParser::processNeighborInformation() {
   if (!isUsedField("neighbors")) {
     return;
@@ -547 +538 @@
  * \return input string with modified atom IDs
  */
-std::string FormatParser< tremolo >::adaptIdDependentDataString(string data) {
+string TremoloParser::adaptIdDependentDataString(string data) {
   // there might be no IDs
   if (data == "-") {
@@ -572 +563 @@
  * as they might differ from the originally read IDs.
  */
-void FormatParser< tremolo >::adaptImprData() {
+void TremoloParser::adaptImprData() {
   if (!isUsedField("imprData")) {
     return;
@@ -588 +579 @@
  * as they might differ from the originally read IDs.
  */
-void FormatParser< tremolo >::adaptTorsion() {
+void TremoloParser::adaptTorsion() {
   if (!isUsedField("torsion")) {
     return;
@@ -603 +594 @@
  *
  */
-void FormatParser< tremolo >::createKnownTypesByIdentity()
+void TremoloParser::createKnownTypesByIdentity()
 {
   // remove old mapping
@@ -620 +611 @@
  * @param file input stream of .potentials file
  */
-void FormatParser< tremolo >::parseKnownTypes(std::istream &file)
+void TremoloParser::parseKnownTypes(std::istream &file)
 {
   const periodentafel *periode = World::getInstance().getPeriode();
@@ -641 +632 @@
       tokenizer tokens(line, tokensep);
       ASSERT(tokens.begin() != tokens.end(),
-          "FormatParser< tremolo >::parseKnownTypes() - line with 'particle:' but no particles separated by comma.");
+          "TremoloParser::parseKnownTypes() - line with 'particle:' but no particles separated by comma.");
       // look for particle_type
       std::string particle_type("NULL");
@@ -652 +643 @@
           tokenizer token((*tok_iter), equalitysep);
           ASSERT(token.begin() != token.end(),
-                    "FormatParser< tremolo >::parseKnownTypes() - could not split particle_type by equality sign");
+                    "TremoloParser::parseKnownTypes() - could not split particle_type by equality sign");
           tokenizer::iterator particle_iter = token.begin();
           particle_iter++;
@@ -661 +652 @@
           tokenizer token((*tok_iter), equalitysep);
           ASSERT(token.begin() != token.end(),
-                    "FormatParser< tremolo >::parseKnownTypes() - could not split particle_type by equality sign");
+                    "TremoloParser::parseKnownTypes() - could not split particle_type by equality sign");
           tokenizer::iterator element_iter = token.begin();
           element_iter++;