C++ FileName::base方法代码示例

// =============================================================================
// ----- RepName Class ---------------------------------------------------------
// RepName CONSTRUCTOR
File::RepName::RepName(FileName const& fname, int debugIn) :
  extChar_('.')
{
  if (debugIn > 1)
    mprintf("\tREMDTRAJ: FileName=[%s]\n", fname.full());
  if ( fname.Ext().empty() ) {
    mprinterr("Error: Traj %s has no numerical extension, required for automatic\n"
              "Error:   detection of replica trajectories. Expected filename format is\n"
              "Error:   <Prefix>.<#> (with optional compression extension), examples:\n"
              "Error:   Rep.traj.nc.000,  remd.x.01.gz etc.\n", fname.base());
    return;
  }
  // Split off everything before replica extension
  size_t found = fname.Full().rfind( fname.Ext() );
  Prefix_.assign( fname.Full().substr(0, found) );
  ReplicaExt_.assign( fname.Ext() ); // This should be the numeric extension
  // Remove leading '.'
  if (ReplicaExt_[0] == '.') ReplicaExt_.erase(0,1);
  CompressExt_.assign( fname.Compress() );
  if (debugIn > 1) {
    mprintf("\tREMDTRAJ: Prefix=[%s], #Ext=[%s], CompressExt=[%s]\n",
            Prefix_.c_str(), ReplicaExt_.c_str(), CompressExt_.c_str());
  }
  // CHARMM replica numbers are format <name>_<num>
  if ( !validInteger(ReplicaExt_) ) {
    size_t uscore = fname.Full().rfind('_');
    if (uscore != std::string::npos) {
      Prefix_.assign( fname.Full().substr(0, uscore) );
      ReplicaExt_.assign( fname.Full().substr(uscore+1) );
      extChar_ = '_';
      if (debugIn > 0)
        mprintf("\tREMDTRAJ: CHARMM style replica names detected, prefix='%s' ext='%s'\n",
                Prefix_.c_str(), ReplicaExt_.c_str());
    }
  }
  // Check that the numerical extension is valid.
  if ( !validInteger(ReplicaExt_) ) {
    mprinterr("Error: Replica extension [%s] is not an integer.\n", ReplicaExt_.c_str());
    Prefix_.clear(); // Empty Prefix_ indicates error.
    return;
  }
  ExtWidth_ = (int)ReplicaExt_.size();
  if (debugIn > 1)
    mprintf("\tREMDTRAJ: Numerical Extension width=%i\n", ExtWidth_);
  // Store lowest replica number
  lowestRepnum_ = convertToInteger( ReplicaExt_ );
  // TODO: Do not allow negative replica numbers?
  if (debugIn > 1)
    mprintf("\tREMDTRAJ: index of first replica = %i\n", lowestRepnum_);
}

int DataIO_XVG::ReadData(FileName const& fname, 
                         DataSetList& datasetlist, std::string const& dsname)
{
  std::vector<std::string> Legends;
  BufferedLine infile;

  if (infile.OpenFileRead( fname )) return 1;
  const char* ptr = infile.Line();
  if (ptr == 0) return 1;
  // Skip any comments
  while (ptr != 0 && ptr[0] == '#')
    ptr = infile.Line();
  // Try to get set legends
  while (ptr != 0 && ptr[0] == '@') {
    ArgList line(ptr, " \t");
    if (line.Nargs() > 3 && line[1][0] == 's') {
      std::string legend = line.GetStringKey("legend");
      if (!legend.empty()) {
        // Spaces will cause issues with data set selection.
        for (std::string::iterator s = legend.begin(); s != legend.end(); ++s)
          if (*s == ' ') *s = '_';
        Legends.push_back( legend );
      }
    }
    ptr = infile.Line();
  }
  if (Legends.empty()) {
    mprinterr("Error: No set legends found in XVG file.\n");
    return 1;
  }
  if (ptr == 0) {
    mprinterr("Error: No data in XVG file.\n");
    return 1;
  }
  // Create 1 data set for each legend
  DataSetList::DataListType inputSets;
  for (unsigned int i = 0; i != Legends.size(); i++) {
    MetaData md( dsname, i );
    md.SetLegend( Legends[i] );
    DataSet_double* ds = new DataSet_double();
    if (ds == 0) return 1;
    ds->SetMeta( md );
    inputSets.push_back( ds );
  }
  mprintf("\t%s has %zu columns of data.\n", fname.base(), inputSets.size());
  // Should now be positioned at first line of data. Assume first column is time values.
  DataSetList::Darray Xvals;
  int expectedCols = (int)inputSets.size() + 1;
  while (ptr != 0) {
    int ncols = infile.TokenizeLine(" \t");
    if (ncols != expectedCols)
      mprinterr("Error: Line %i: %i columns != expected # cols %i\n", infile.LineNumber(),
                ncols, expectedCols);
    else {
      Xvals.push_back( atof( infile.NextToken() ) );
      for (unsigned int i = 0; i != inputSets.size(); i++)
        ((DataSet_double*)inputSets[i])->AddElement( atof( infile.NextToken() ) );
    }
    ptr = infile.Line();
  }
  infile.CloseFile();
  return (datasetlist.AddOrAppendSets( "", Xvals, inputSets ));
}

//.........这里部分代码省略.........
    // The default maskstr is the Oxygen atom of the solvent
    summaryfile_ = actionArgs.GetStringKey("summary");
    // Divide site size by 2 to make it half the edge length (or radius)
    site_size_ = actionArgs.getKeyDouble("site_size", 2.5) / 2.0;
    sphere_ = actionArgs.hasKey("sphere");
    // If it's a sphere, square the radius to compare with
    if (sphere_)
      site_size_ *= site_size_;
    datafile_ = actionArgs.GetStringKey("out");
    std::string ds_name = actionArgs.GetStringKey("name");
    if (ds_name.empty())
      ds_name = myDSL_.GenerateDefaultName("SPAM");

    // Parse through the peaks file and extract the peaks
    CpptrajFile peakfile;
    if (peakfile.OpenRead(filename)) {
      mprinterr("SPAM: Error: Could not open %s for reading!\n", filename.full());
      return Action::ERR;
    }
    std::string line = peakfile.GetLine();
    int npeaks = 0;
    while (!line.empty()) {
      if (sscanf(line.c_str(), "%d", &npeaks) != 1) {
        line = peakfile.GetLine();
        continue;
      }
      line = peakfile.GetLine();
      break;
    }
    while (!line.empty()) {
      double x, y, z, dens;
      if (sscanf(line.c_str(), "C %lg %lg %lg %lg", &x, &y, &z, &dens) != 4) {
        line = peakfile.GetLine();
        continue;
      }
      line = peakfile.GetLine();
      peaks_.push_back(Vec3(x, y, z));
    }
    peakfile.CloseFile();
    // Check that our initial number of peaks matches our parsed peaks. Warn
    // otherwise
    if (npeaks != (int)peaks_.size())
      mprinterr("SPAM: Warning: %s claims to have %d peaks, but really has %d!\n",
                filename.full(), npeaks, peaks_.size());
    // Now add all of the data sets
    MetaData md(ds_name);
    for (int i = 0; i < (int)peaks_.size(); i++) {
      md.SetAspect( integerToString(i+1) ); // TODO: Should this be Idx?
      if (myDSL_.AddSet(DataSet::DOUBLE, md) == 0) return Action::ERR;
      // Add a new list of integers to keep track of omitted frames
      std::vector<int> vec;
      peakFrameData_.push_back(vec);
    }
  }

  // Print info now
  if (purewater_) {
    mprintf("SPAM: Calculating bulk value for pure solvent\n");
    if (!datafile_.empty())
      mprintf("SPAM: Printing solvent energies to %s\n", datafile_.c_str());
    mprintf("SPAM: Using a %.2f Angstrom non-bonded cutoff with shifted EEL.\n",
            sqrt(cut2_));
    if (reorder_)
      mprintf("SPAM: Warning: Re-ordering makes no sense for pure solvent.\n");
    if (!summaryfile_.empty())
      mprintf("SPAM: Printing solvent SPAM summary to %s\n", summaryfile_.c_str());
  }else {
    mprintf("SPAM: Solvent [%s] density peaks taken from %s.\n",
            solvname_.c_str(), filename.base());
    mprintf("SPAM: %d density peaks will be analyzed from %s.\n",
            peaks_.size(), filename.base());
    mprintf("SPAM: Occupation information printed to %s.\n", infofile_->Filename().full());
    mprintf("SPAM: Sites are ");
    if (sphere_)
      mprintf("spheres with diameter %.3lf\n", site_size_);
    else
      mprintf("boxes with edge length %.3lf\n", site_size_);
    if (reorder_) {
      mprintf("SPAM: Re-ordering trajectory so each site always has ");
      mprintf("the same water molecule.\n");
    }
    if (summaryfile_.empty() && datafile_.empty()) {
      if (!reorder_) {
        mprinterr("SPAM: Error: Not re-ordering trajectory or calculating energies. ");
        mprinterr("Nothing to do!\n");
        return Action::ERR;
      }
      mprintf("SPAM: Not calculating any SPAM energies\n");
    }else {
      mprintf("SPAM: Using a non-bonded cutoff of %.2lf Ang. with a EEL shifting function.\n",
              sqrt(cut2_));
      mprintf("SPAM: Bulk solvent SPAM energy taken as %.3lf kcal/mol\n", bulk_);
    }
  }
  mprintf("#Citation: Cui, G.; Swails, J.M.; Manas, E.S.; \"SPAM: A Simple Approach\n"
          "#          for Profiling Bound Water Molecules\"\n"
          "#          J. Chem. Theory Comput., 2013, 9 (12), pp 5539–5549.\n");

  return Action::OK;
}