Changeset 765f16 for src/Parser/TremoloParser.cpp

Timestamp:

Oct 14, 2011, 3:15:30 PM (14 years ago)

Author:

Frederik Heber <heber@…>

Branches:

Action_Thermostats, Add_AtomRandomPerturbation, Add_FitFragmentPartialChargesAction, Add_RotateAroundBondAction, Add_SelectAtomByNameAction, Added_ParseSaveFragmentResults, AddingActions_SaveParseParticleParameters, Adding_Graph_to_ChangeBondActions, Adding_MD_integration_tests, Adding_ParticleName_to_Atom, Adding_StructOpt_integration_tests, AtomFragments, Automaking_mpqc_open, AutomationFragmentation_failures, Candidate_v1.5.4, Candidate_v1.6.0, Candidate_v1.6.1, ChangeBugEmailaddress, ChangingTestPorts, ChemicalSpaceEvaluator, CombiningParticlePotentialParsing, Combining_Subpackages, Debian_Package_split, Debian_package_split_molecuildergui_only, Disabling_MemDebug, Docu_Python_wait, EmpiricalPotential_contain_HomologyGraph, EmpiricalPotential_contain_HomologyGraph_documentation, Enable_parallel_make_install, Enhance_userguide, Enhanced_StructuralOptimization, Enhanced_StructuralOptimization_continued, Example_ManyWaysToTranslateAtom, Exclude_Hydrogens_annealWithBondGraph, FitPartialCharges_GlobalError, Fix_BoundInBox_CenterInBox_MoleculeActions, Fix_ChargeSampling_PBC, Fix_ChronosMutex, Fix_FitPartialCharges, Fix_FitPotential_needs_atomicnumbers, Fix_ForceAnnealing, Fix_IndependentFragmentGrids, Fix_ParseParticles, Fix_ParseParticles_split_forward_backward_Actions, Fix_PopActions, Fix_QtFragmentList_sorted_selection, Fix_Restrictedkeyset_FragmentMolecule, Fix_StatusMsg, Fix_StepWorldTime_single_argument, Fix_Verbose_Codepatterns, Fix_fitting_potentials, Fixes, ForceAnnealing_goodresults, ForceAnnealing_oldresults, ForceAnnealing_tocheck, ForceAnnealing_with_BondGraph, ForceAnnealing_with_BondGraph_continued, ForceAnnealing_with_BondGraph_continued_betteresults, ForceAnnealing_with_BondGraph_contraction-expansion, FragmentAction_writes_AtomFragments, FragmentMolecule_checks_bonddegrees, GeometryObjects, Gui_Fixes, Gui_displays_atomic_force_velocity, ImplicitCharges, IndependentFragmentGrids, IndependentFragmentGrids_IndividualZeroInstances, IndependentFragmentGrids_IntegrationTest, IndependentFragmentGrids_Sole_NN_Calculation, JobMarket_RobustOnKillsSegFaults, JobMarket_StableWorkerPool, JobMarket_unresolvable_hostname_fix, MoreRobust_FragmentAutomation, ODR_violation_mpqc_open, PartialCharges_OrthogonalSummation, PdbParser_setsAtomName, PythonUI_with_named_parameters, QtGui_reactivate_TimeChanged_changes, Recreated_GuiChecks, Rewrite_FitPartialCharges, RotateToPrincipalAxisSystem_UndoRedo, SaturateAtoms_findBestMatching, SaturateAtoms_singleDegree, StoppableMakroAction, Subpackage_CodePatterns, Subpackage_JobMarket, Subpackage_LinearAlgebra, Subpackage_levmar, Subpackage_mpqc_open, Subpackage_vmg, Switchable_LogView, ThirdParty_MPQC_rebuilt_buildsystem, TrajectoryDependenant_MaxOrder, TremoloParser_IncreasedPrecision, TremoloParser_MultipleTimesteps, TremoloParser_setsAtomName, Ubuntu_1604_changes, stable

Children:

d3d6c6

Parents:

9a6b76e

git-author:

Frederik Heber <heber@…> (09/27/11 19:04:36)

git-committer:

Frederik Heber <heber@…> (10/14/11 15:15:30)

Message:

Huge Refactoring of FormatParserStorage and all FormatParser's.

FormatParser:

• FormatParser is now a template, specialized by enum ParserTypes.
• new struct FormatParserTrait is as well a template of same type, containing parser-specific information in static entities.
• all FormatParsers are now specializations of this FormatParser.
• all Parsers can be accessed in a unified manner, given in the new class FormatParserInterface.
• common functions are placed in FormatParser_common.hpp as one cannot partially specialize a function class.
• some boost preprocessor magic is used in ParserTypes and FormatParserTraits to define the template specialization or to create the ParserTypes enumeration.

FormatParserStorage:

• We construct all lookup tables and alikes via boost preprocessor magic from a list of all available parser (enums).
• we use the templated getParser() and addParser() functions to serve parsers to the outside. Instances are as usual created only once.

Tests:

• tests only had to be changed because of the "renaming" of the Parsers.

File:

• src/Parser/TremoloParser.cpp (modified) (30 diffs)

src/Parser/TremoloParser.cpp

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