Changeset 4e855e for src/parser.cpp

Timestamp:

Feb 4, 2011, 6:56:38 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:

febef3

Parents:

fd3788

git-author:

Frederik Heber <heber@…> (02/04/11 18:54:12)

git-committer:

Frederik Heber <heber@…> (02/04/11 18:56:38)

Message:

BondGraph::LoadBondLengthTable() now accepts istream instead of const char *.

• This has been quite a lot of work because the matrix parsing is involved.
• Hence, the fix is not really clean, this should get fixed as soon as we deal with the BondGraph implementation.
• This fixes ticket #130.

File:

• src/parser.cpp (modified) (14 diffs)

src/parser.cpp

@@ -22 +22 @@
 
 #include <cstring>
+#include <iomanip>
 
 #include "Helpers/helpers.hpp"
@@ -158 +159 @@
  *    -# allocate matrix
  *    -# loop over found column and row counts and parse in each entry
- * \param *name directory with files
+ * \param &input input stream
  * \param skiplines number of inital lines to skip
  * \param skiplines number of inital columns to skip
@@ -164 +165 @@
  * \return parsing successful
  */
-bool MatrixContainer::ParseMatrix(const char *name, int skiplines, int skipcolumns, int MatrixNr)
-{
-  ifstream input;
+bool MatrixContainer::ParseMatrix(std::istream &input, int skiplines, int skipcolumns, int MatrixNr)
+{
   stringstream line;
   string token;
   char filename[1023];
 
-  input.open(name, ios::in);
   //Log() << Verbose(1) << "Opening " << name << " ... "  << input << endl;
-  if (input == NULL) {
-    DoeLog(1) && (eLog()<< Verbose(1) << endl << "MatrixContainer::ParseMatrix: Unable to open " << name << ", is the directory correct?" << endl);
+  if (input.bad()) {
+    DoeLog(1) && (eLog()<< Verbose(1) << endl << "MatrixContainer::ParseMatrix: Unable to parse istream." << endl);
     //performCriticalExit();
     return false;
@@ -190 +189 @@
   for(int k=skipcolumns;k--;)
     line >> Header[MatrixNr];
-  //Log() << Verbose(0) << line.str() << endl;
+  Log() << Verbose(0) << line.str() << endl;
   ColumnCounter[MatrixNr]=0;
   while ( getline(line,token, '\t') ) {
@@ -196 +195 @@
       ColumnCounter[MatrixNr]++;
   }
-  //Log() << Verbose(0) << line.str() << endl;
-  //Log() << Verbose(1) << "ColumnCounter[" << MatrixNr << "]: " << ColumnCounter[MatrixNr] << "." << endl;
+  Log() << Verbose(0) << line.str() << endl;
+  Log() << Verbose(1) << "ColumnCounter[" << MatrixNr << "]: " << ColumnCounter[MatrixNr] << "." << endl;
   if (ColumnCounter[MatrixNr] == 0) {
-    DoeLog(0) && (eLog()<< Verbose(0) << "ColumnCounter[" << MatrixNr << "]: " << ColumnCounter[MatrixNr] << " from file " << name << ", this is probably an error!" << endl);
+    DoeLog(0) && (eLog()<< Verbose(0) << "ColumnCounter[" << MatrixNr << "]: " << ColumnCounter[MatrixNr] << " from ostream." << endl);
     performCriticalExit();
   }
@@ -207 +206 @@
   while (!input.eof()) {
     input.getline(filename, 1023);
-    //Log() << Verbose(0) << "Comparing: " << strncmp(filename,"MeanForce",9) << endl;
+    Log() << Verbose(0) << "Comparing: " << strncmp(filename,"MeanForce",9) << endl;
     RowCounter[MatrixNr]++; // then line was not last MeanForce
     if (strncmp(filename,"MeanForce", 9) == 0) {
@@ -213 +212 @@
     }
   }
-  //Log() << Verbose(1) << "RowCounter[" << MatrixNr << "]: " << RowCounter[MatrixNr] << " from file " << name << "." << endl;
+  Log() << Verbose(1) << "RowCounter[" << MatrixNr << "]: " << RowCounter[MatrixNr] << " from input stream." << endl;
   if (RowCounter[MatrixNr] == 0) {
-    DoeLog(0) && (eLog()<< Verbose(0) << "RowCounter[" << MatrixNr << "]: " << RowCounter[MatrixNr] << " from file " << name << ", this is probably an error!" << endl);
+    DoeLog(0) && (eLog()<< Verbose(0) << "RowCounter[" << MatrixNr << "]: " << RowCounter[MatrixNr] << " from input stream." << endl);
     performCriticalExit();
   }
@@ -233 +232 @@
       input.getline(Header[MatrixNr], 1023);    // skip header
     line.str(Header[MatrixNr]);
+    Log() << Verbose(0) << "Header: " << line.str() << endl;
     for(int k=skipcolumns;k--;)  // skip columns in header too
       line >> filename;
@@ -245 +245 @@
       input.getline(filename, 1023);
       stringstream lines(filename);
-      //Log() << Verbose(2) << "Matrix at level " << j << ":";// << filename << endl;
+      Log() << Verbose(2) << "Matrix at level " << j << ":";// << filename << endl;
       for(int k=skipcolumns;k--;)
         lines >> filename;
       for(int k=0;(k<ColumnCounter[MatrixNr]) && (!lines.eof());k++) {
         lines >> Matrix[MatrixNr][j][k];
-        //Log() << Verbose(1) << " " << setprecision(2) << Matrix[MatrixNr][j][k] << endl;
+        Log() << Verbose(1) << " " << setprecision(2) << Matrix[MatrixNr][j][k] << endl;
       }
       if (Matrix[MatrixNr][ RowCounter[MatrixNr] ] != NULL)
@@ -261 +261 @@
     DoeLog(1) && (eLog()<< Verbose(1) << "Matrix nr. " << MatrixNr << " has column and row count of (" << ColumnCounter[MatrixNr] << "," << RowCounter[MatrixNr] << "), could not allocate nor parse!" << endl); 
   }
-  input.close();
   return true;
 };
@@ -327 +326 @@
     file.str(" ");
     file << name << FRAGMENTPREFIX << FragmentNumber << prefix << suffix;
-    if (!ParseMatrix(file.str().c_str(), skiplines, skipcolumns, i))
+    std::ifstream input(file.str().c_str());
+    if (!ParseMatrix(input, skiplines, skipcolumns, i)) {
+      input.close();
       return false;
+    }
+    input.close();
     delete[](FragmentNumber);
   }
@@ -628 +631 @@
     strncat(filename, prefix, 1023-strlen(filename));
     strncat(filename, suffix.c_str(), 1023-strlen(filename));
-    ParseMatrix(filename, skiplines, skipcolumns, MatrixCounter);
+    std::ifstream input(filename);
+    ParseMatrix(input, skiplines, skipcolumns, MatrixCounter);
+    input.close();
   }
   return status;
@@ -764 +769 @@
     strncat(filename, prefix, 1023-strlen(filename));
     strncat(filename, suffix.c_str(), 1023-strlen(filename));
-    ParseMatrix(filename, skiplines, skipcolumns, MatrixCounter);
+    std::ifstream input(filename);
+    ParseMatrix(input, skiplines, skipcolumns, MatrixCounter);
+    input.close();
   }
  
@@ -992 +999 @@
     strncat(filename, prefix, 1023-strlen(filename));
     strncat(filename, suffix.c_str(), 1023-strlen(filename));
-    ParseMatrix(filename, skiplines, skipcolumns, MatrixCounter);
+    std::ifstream input(filename);
+    ParseMatrix(input, skiplines, skipcolumns, MatrixCounter);
+    input.close();
   }