C++ FileName::full方法代码示例

// DataIO_CCP4::WriteData()
int DataIO_CCP4::WriteData(FileName const& fname, DataSetList const& setList)
{
    // Open output file
    CpptrajFile outfile;
    if (outfile.OpenWrite(fname)) {
        mprinterr("Error: Could not open CCP4 output file '%s'.\n", fname.full());
        return 1;
    }
    // Warn about writing multiple sets
    if (setList.size() > 1)
        mprintf("Warning: %s: Writing multiple 3D sets in CCP4 format not supported.\n"
                "Warning:   Only writing first set.\n", fname.full());
    return WriteSet3D( setList.begin(), outfile );
}

/** Assuming lowest replica filename has been set, search for all other 
  * replica names assuming a naming scheme of '<PREFIX>.<EXT>[.<CEXT>]', 
  * where <EXT> is a numerical extension and <CEXT> is an optional 
  * compression extension. 
  * \return Found replica filenames, or an empty list on error. 
  */
File::NameArray File::SearchForReplicas(FileName const& fname, int debug) {
  NameArray replica_filenames;
  if (!File::Exists(fname)) {
    mprinterr("Error: '%s' does not correspond to a file.\n", fname.full());
    return replica_filenames;
  }
  RepName repName(fname, debug);
  if (repName.Error()) return replica_filenames;
  // Search for a replica number lower than this. Correct functioning
  // of the replica code requires the file specified by trajin be the
  // lowest # replica.
  if (File::Exists( repName.RepFilename( -1 ) )) {
    mprintf("Warning: Replica# found lower than file specified with trajin.\n"
            "Warning:   Found \"%s\"; 'trajin remdtraj' requires lowest # replica.\n",
            repName.RepFilename( -1 ).full());
  }
  // Add lowest replica filename, search for and add all replicas higher than it.
  replica_filenames.push_back( fname );
  int rep_offset = 0;
  bool search_for_files = true;
  FileName trajFilename;
  while (search_for_files) {
    ++rep_offset;
    trajFilename = repName.RepFilename( rep_offset );
    //mprintf("\t\tChecking for %s\n", trajFilename.full());
    if (File::Exists( trajFilename ))
      replica_filenames.push_back( trajFilename );
    else
      search_for_files = false;
  }
  return replica_filenames;
}

// TODO: Accept const ArgList so arguments are not reset?
CpptrajFile* DataFileList::AddCpptrajFile(FileName const& nameIn, 
                                          std::string const& descrip,
                                          CFtype typeIn, bool allowStdout)
{
  // If no filename and stdout not allowed, no output desired.
  if (nameIn.empty() && !allowStdout) return 0;
  FileName name;
  CpptrajFile* Current = 0;
  int currentIdx = -1;
  if (!nameIn.empty()) {
    name = nameIn;
    // Append ensemble number if set.
    if (ensembleNum_ != -1)
      name.Append( "." + integerToString(ensembleNum_) );
    // Check if filename in use by DataFile.
    DataFile* df = GetDataFile(name);
    if (df != 0) {
      mprinterr("Error: Text output file name '%s' already in use by data file '%s'.\n",
                nameIn.full(), df->DataFilename().full());
      return 0;
    }
    // Check if this filename already in use
    currentIdx = GetCpptrajFileIdx( name );
    if (currentIdx != -1) Current = cfList_[currentIdx];
  }
  // If no CpptrajFile associated with name, create new CpptrajFile
  if (Current==0) {
    switch (typeIn) {
      case TEXT: Current = new CpptrajFile(); break;
      case PDB:  Current = (CpptrajFile*)(new PDBfile()); break;
    }
    Current->SetDebug(debug_);
    // Set up file for writing. 
    //if (Current->SetupWrite( name, debug_ ))
    if (Current->OpenWrite( name ))
    {
      mprinterr("Error: Setting up text output file %s\n", name.full());
      delete Current;
      return 0;
    }
    cfList_.push_back( Current );
    cfData_.push_back( CFstruct(descrip, typeIn) );
  } else {
    // If Current type does not match typeIn do not allow.
    if (typeIn != cfData_[currentIdx].Type()) {
      mprinterr("Error: Cannot change type of text output for '%s'.\n", Current->Filename().full());
      return 0;
    }
    Current->SetDebug(debug_);
    // Update description
    if (!descrip.empty())
      cfData_[currentIdx].UpdateDescrip( descrip );
  }
  return Current;
}

/** Each rank searches for replica based on lowest replica number. */
int TrajIOarray::SearchForReplicas(FileName const& fname, Parallel::Comm const& ensComm,
                                   Parallel::Comm const& trajComm)
{
  RepName repName(fname, debug_);
  if (repName.Error()) return 1;
  // TODO check for lower replica number?
  FileName replicaFilename = repName.RepFilename( ensComm.Rank() );
  // Only traj comm masters actually check for files.
  if (trajComm.Master()) {
    if (!File::Exists( replicaFilename )) {
      File::ErrorMsg( replicaFilename.full() );
      rprinterr("Error: File '%s' not accessible.\n", replicaFilename.full());
      return 1;
    }
  }
  // At this point each rank has found its replica. Populate filename array.
  for (int offset = 0; offset < ensComm.Size(); ++offset)
    replica_filenames_.push_back( repName.RepFilename( offset ) );
  return 0;
}

bool File::Exists(FileName const& fn) {
  if (!fn.empty()) {
    FILE* infile = fopen(fn.full(), "rb");
    if (infile==0) {
      fileErrMsg_.assign( strerror(errno) );
      return false;
    }
    fclose(infile);
    return true;
  }
  return false;
}

// DataIO_OpenDx::ReadData()
int DataIO_OpenDx::ReadData(FileName const& fname, 
                            DataSetList& datasetlist, std::string const& dsname)
{
  // Add grid data set. Default to float for now.
  DataSet* ds = datasetlist.AddSet( DataSet::GRID_FLT, dsname, "GRID" );
  if (ds==0) return 1;
  if (LoadGrid(fname.full(), *ds)) {
    // Load failed. Erase grid data set.
    datasetlist.RemoveSet( ds );
    return 1;
  }
  return 0;
}

// ParmFile::ReadTopology()
int ParmFile::ReadTopology(Topology& Top, FileName const& fnameIn, 
                           ArgList const& argListIn, int debugIn) 
{
  if (fnameIn.empty()) {
    mprinterr("Error: No input topology name given.\n");
    return 1;
  }
  if (!File::Exists( fnameIn )) {
    mprinterr("Error: Topology '%s' does not exist.\n", fnameIn.full());
    return 1;
  }
  parmName_ = fnameIn;
  ArgList argIn = argListIn;
  ParmFormatType pfType;
  ParmIO* parmio = 0;
  Top.SetDebug( debugIn );
  // Only force bond search when 'bondsearch' is specified.
  bool bondsearch = false;
  if (argIn.Contains("bondsearch")) {
    Top.SetOffset( argIn.getKeyDouble("bondsearch", -1.0) );
    bondsearch = true;
  }
  // 'as' keyword specifies a format
  std::string as_arg = argIn.GetStringKey("as");
  if (!as_arg.empty()) {
    pfType = (ParmFormatType)FileTypes::GetFormatFromString( PF_KeyArray, as_arg, UNKNOWN_PARM );
    if (pfType == UNKNOWN_PARM) {
      mprinterr("Error: Topology format '%s' not recognized.\n", as_arg.c_str());
      return 1;
    }
    parmio = (ParmIO*)FileTypes::AllocIO( PF_AllocArray, pfType, false );
  } else
    parmio = DetectFormat( parmName_, pfType );
  if (parmio == 0) {
    mprinterr("Error: Could not determine format of topology '%s'\n", parmName_.full());
    return 1;
  }
  mprintf("\tReading '%s' as %s\n", parmName_.full(),
          FileTypes::FormatDescription(PF_AllocArray, pfType) );
  parmio->SetDebug( debugIn );
  if (parmio->processReadArgs(argIn)) return 1;
  int err = parmio->ReadParm( parmName_.Full(), Top);
  // Perform setup common to all parm files.
  if (err == 0) 
    err = Top.CommonSetup(bondsearch || parmio->NeedsBondSearch());
  else
    mprinterr("Error reading topology file '%s'\n", parmName_.full());
  delete parmio;
  if (err > 0) return 1;
  return 0;
}

// =============================================================================
// ----- 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_);
}

/** Add lowest replica file name and names from comma-separated list. */
int TrajIOarray::AddReplicasFromArgs(FileName const& name0,
                                     std::string const& commaNames)
{
  if (name0.empty()) return 1;
  if (!File::Exists( name0 )) {
    File::ErrorMsg( name0.full() );
    return 1;
  }
  replica_filenames_.push_back( name0 );
  ArgList remdtraj_list( commaNames, "," );
  for (ArgList::const_iterator fname = remdtraj_list.begin();
                               fname != remdtraj_list.end(); ++fname)
  {
    FileName trajFilename( *fname );
    if (!File::Exists( trajFilename )) {
      File::ErrorMsg( trajFilename.full() );
      return 1;
    }
    replica_filenames_.push_back( trajFilename );
  }
  return 0;
}

// Parm_CIF::ReadParm()
int Parm_CIF::ReadParm(FileName const& fname, Topology &TopIn) {
  CIFfile infile;
  CIFfile::DataBlock::data_it line;

  if (infile.Read( fname, debug_ )) return 1;
  CIFfile::DataBlock const& block = infile.GetDataBlock("_atom_site");
  if (block.empty()) {
    mprinterr("Error: CIF data block '_atom_site' not found.\n");
    return 1;
  }
  // Does this CIF contain multiple models?
  int Nmodels = 0;
  int model_col = block.ColumnIndex("pdbx_PDB_model_num");
  if (model_col != -1) {
    line = block.end();
    --line;
    Nmodels = convertToInteger( (*line)[model_col] );
    if (Nmodels > 1)
      mprintf("Warning: CIF '%s' contains %i models. Using first model for topology.\n", 
              fname.full(), Nmodels);
  }
  // Get essential columns
  int COL[NENTRY];
  for (int i = 0; i < (int)NENTRY; i++) {
    COL[i] = block.ColumnIndex(Entries[i]);
    if (COL[i] == -1) {
      mprinterr("Error: In CIF file '%s' could not find entry '%s' in block '%s'\n",
                fname.full(), Entries[i], block.Header().c_str());
      return 1;
    }
    if (debug_>0) mprintf("DEBUG: '%s' column = %i\n", Entries[i], COL[i]);
  }
  // Get optional columns
  int occ_col = block.ColumnIndex("occupancy");
  int bfac_col = block.ColumnIndex("B_iso_or_equiv");
  int icode_col = block.ColumnIndex("pdbx_PDB_ins_code");
  int altloc_col = block.ColumnIndex("label_alt_id");
  std::vector<AtomExtra> extra;

  // Loop over all atom sites
  int current_res = 0;
  double XYZ[3];
  double occupancy = 1.0;
  double bfactor = 0.0;
  char altloc = ' ';
  char icode;
  icode = ' ';
  Frame Coords;
  for (line = block.begin(); line != block.end(); ++line) {
    // If more than 1 model check if we are done.
    if (Nmodels > 1) {
      if ( convertToInteger( (*line)[model_col] ) > 1 )
        break;
    }
    if (occ_col != -1) occupancy = convertToDouble( (*line)[ occ_col ] );
    if (bfac_col != -1) bfactor = convertToDouble( (*line)[ bfac_col ] );
    if (altloc_col != -1) altloc = (*line)[ altloc_col ][0];
    // '.' altloc means blank?
    if (altloc == '.') altloc = ' ';
    extra.push_back( AtomExtra(occupancy, bfactor, altloc) );
    if (icode_col != -1) {
      icode = (*line)[ icode_col ][0];
      // '?' icode means blank
      if (icode == '?') icode = ' ';
    }
    XYZ[0] = convertToDouble( (*line)[ COL[X] ] );
    XYZ[1] = convertToDouble( (*line)[ COL[Y] ] );
    XYZ[2] = convertToDouble( (*line)[ COL[Z] ] );
    NameType currentResName( (*line)[ COL[RNAME] ] );
    // It seems that in some CIF files, there doesnt have to be a residue
    // number. Check if residue name has changed.
    if ( (*line)[ COL[RNUM] ][0] == '.' ) {
      Topology::res_iterator lastResidue = TopIn.ResEnd();
      --lastResidue;
      if ( currentResName != (*lastResidue).Name() )
        current_res = TopIn.Nres() + 1;
    } else
      current_res = convertToInteger( (*line)[ COL[RNUM] ] );
    TopIn.AddTopAtom( Atom((*line)[ COL[ANAME] ], "  "),
                      Residue(currentResName, current_res, icode,
                              (*line)[ COL[CHAINID] ][0]) );
    Coords.AddXYZ( XYZ );
  }
  if (TopIn.SetExtraAtomInfo( 0, extra )) return 1;
  // Search for bonds // FIXME nobondsearch?
  BondSearch( TopIn, Coords, Offset_, debug_ );
  // Get title. 
  CIFfile::DataBlock const& entryblock = infile.GetDataBlock("_entry");
  std::string ciftitle;
  if (!entryblock.empty())
    ciftitle = entryblock.Data("id");
  TopIn.SetParmName( ciftitle, infile.CIFname() );
  // Get unit cell parameters if present.
  CIFfile::DataBlock const& cellblock = infile.GetDataBlock("_cell");
  if (!cellblock.empty()) {
    double cif_box[6];
    cif_box[0] = convertToDouble( cellblock.Data("length_a") );
    cif_box[1] = convertToDouble( cellblock.Data("length_b") );
    cif_box[2] = convertToDouble( cellblock.Data("length_c") );
//.........这里部分代码省略.........

// DataIO_Mdout::ReadData()
int DataIO_Mdout::ReadData(FileName const& fname,
                            DataSetList& datasetlist, std::string const& dsname)
{
  mprintf("\tReading from mdout file: %s\n", fname.full());
  BufferedLine buffer;
  if (buffer.OpenFileRead( fname )) return 1;
  const char* ptr = buffer.Line();
  if (ptr == 0) {
    mprinterr("Error: Nothing in MDOUT file: %s\n", fname.full());
    return 1;
  }
  // ----- PARSE THE INPUT SECTION ----- 
  int imin = -1;           // imin for this file
  const char* Trigger = 0; // Trigger for storing energies, must be 8 chars long.
  int frame = 0;           // Frame counter for this file
  double dt = 1.0;         // Timestep for this file (MD)
  double t0 = 0.0;         // Initial time for this file (MD)
  int ntpr = 1;            // Value of ntpr
  int irest = 0;           // Value of irest
  while ( ptr != 0 && strncmp(ptr, "   2.  CONTROL  DATA", 20) != 0 )
    ptr = buffer.Line();
  if (ptr == 0) return EOF_ERROR();
  // Determine whether this is dynamics or minimization, get dt
  ptr = buffer.Line(); // Dashes 
  ptr = buffer.Line(); // Blank 
  ptr = buffer.Line(); // title line
  while ( strncmp(ptr, "   3.  ATOMIC", 13) != 0 ) 
  {
    ArgList mdin_args( ptr, " ,=" ); // Remove commas, equal signs
    // Scan for stuff we want
    //mprintf("DEBUG:\tInput[%i] %s", mdin_args.Nargs(), mdin_args.ArgLine());
    for (int col=0; col < mdin_args.Nargs(); col += 2) {
      int col1 = col + 1;
      if (mdin_args[col] == "imin") {
        imin = convertToInteger( mdin_args[ col1 ] );
        if (debug_ > 0) mprintf("\t\tMDIN: imin is %i\n", imin);
        // Set a trigger for printing. For imin5 this is the word minimization.
        // For imin0 or imin1 this is NSTEP.
        if      (imin==0) Trigger = " NSTEP =";
        else if (imin==1) Trigger = "   NSTEP";
        else if (imin==5) Trigger = "minimiza";
        // Since imin0 and imin1 first trigger has no data, set frame 1 lower.
        if (imin==1 || imin==0) frame = -1;
      } else if (mdin_args[col] == "dt") {
        dt = convertToDouble( mdin_args[ col1 ] );
        if (debug_ > 0) mprintf("\t\tMDIN: dt is %f\n", dt);
      } else if (mdin_args[col] == "t") {
        t0 = convertToDouble( mdin_args[ col1 ] );
        if (debug_ > 0) mprintf("\t\tMDIN: t is %f\n", t0);
      } else if (mdin_args[col] == "ntpr") {
        ntpr = convertToInteger( mdin_args[ col1 ] );
        if (debug_ > 0) mprintf("\t\tMDIN: ntpr is %i\n", ntpr);
      } else if (mdin_args[col] == "irest") {
        irest = convertToInteger( mdin_args[ col1 ] );
        if (debug_ > 0) mprintf("\t\tMDIN: irest is %i\n", irest);
      }
    }
    ptr = buffer.Line();
    if (ptr == 0) return EOF_ERROR();
  }
  if (Trigger == 0) {
    mprinterr("Error: Could not determine whether MDOUT is md, min, or post-process.\n");
    return 1;
  }
  // ----- PARSE THE ATOMIC ... SECTION -----
  while ( ptr != 0 && strncmp(ptr, "   4.  RESULTS", 14) != 0 )
  {
    ptr = buffer.Line();
    // If run is a restart, set the initial time value.
    if (irest == 1) {
      if (strncmp(ptr, " begin time", 11) == 0) {
        sscanf(ptr, " begin time read from input coords = %lf", &t0);
        if (debug_ > 0) mprintf("\t\tMD restart initial time= %f\n", t0);
      }
    }
  }
  if (ptr == 0) return EOF_ERROR();
  // ----- PARSE THE RESULTS SECTION -----
  bool finalE = false;
  int nstep;
  int minStep = 0; // For imin=1 only
  if (irest == 0)
    nstep = 0;
  else
    nstep = ntpr;
  double Energy[N_FIELDTYPES];
  std::fill( Energy, Energy+N_FIELDTYPES, 0.0 );
  std::vector<bool> EnergyExists(N_FIELDTYPES, false);
  DataSetList::Darray TimeVals;
  DataSetList::DataListType inputSets(N_FIELDTYPES, 0);
  Sarray Name(2);
  double time = 0.0;
  while (ptr != 0) {
    // Check for end of imin 0 or 1 run; do not record Average and Stdevs
    if ( (imin == 1 && (strncmp(ptr, "                    FINAL", 25) == 0 ||
                        strncmp(ptr, "   5.  TIMINGS",            14) == 0   )) ||
         (imin == 0 && strncmp(ptr, "      A V", 9) == 0))
      finalE = true;
    // Check for '| TI region  2' to prevent reading duplicate energies
//.........这里部分代码省略.........

/** Free the given temporary file name. */
void FreeTempName(FileName const& temp) {
  TempFileNames_.remove( temp );
  if (Exists(temp)) remove(temp.full());
}

// DataIO_OpenDx::WriteData()
int DataIO_OpenDx::WriteData(FileName const& fname, DataSetList const& setList)
{
  // Open output file
  CpptrajFile outfile;
  if (outfile.OpenWrite(fname)) {
    mprinterr("Error: Could not open OpenDX output file.\n");
    return 1;
  }
  // Warn about writing multiple sets
  if (setList.size() > 1)
    mprintf("Warning: %s: Writing multiple 3D sets in OpenDX format may result in unexpected behavior\n", fname.full());
  int err = 0;
  for (DataSetList::const_iterator set = setList.begin(); set != setList.end(); ++set)
    err += WriteSet3D( *(*set), outfile );
  return err;
}

// Action_Spam::init()
Action::RetType Action_Spam::Init(ArgList& actionArgs, TopologyList* PFL, DataSetList* DSL, DataFileList* DFL, int debugIn)
{
  // Always use imaged distances
  InitImaging(true);
  // This is needed everywhere in this function scope
  FileName filename;

  // See if we're doing pure water. If so, we don't need a peak file
  purewater_ = actionArgs.hasKey("purewater");

  if (purewater_) {
    // We still need the cutoff
    double cut = actionArgs.getKeyDouble("cut", 12.0);
    cut2_ = cut * cut;
    doublecut_ = 2 * cut;
    onecut2_ = 1 / cut2_;
    // See if we write to a data file
    datafile_ = actionArgs.GetStringKey("out");
    // Generate the data set name, and hold onto the master data set list
    std::string ds_name = actionArgs.GetStringKey("name");
    if (ds_name.empty())
      ds_name = myDSL_.GenerateDefaultName("SPAM");
    // We only have one data set averaging over every water. Add it here
    myDSL_.AddSet(DataSet::DOUBLE, ds_name, NULL);
    solvname_ = actionArgs.GetStringKey("solv");
    if (solvname_.empty())
      solvname_ = std::string("WAT");
  }else {
    // Get the file name with the peaks defined in it
    filename.SetFileName( actionArgs.GetStringNext() );

    if (filename.empty() || !File::Exists(filename)) {
      mprinterr("Spam: Error: Peak file [%s] does not exist!\n", filename.full());
      return Action::ERR;
    }

    // Get the remaining optional arguments
    solvname_ = actionArgs.GetStringKey("solv");
    if (solvname_.empty())
      solvname_ = std::string("WAT");
    reorder_ = actionArgs.hasKey("reorder");
    bulk_ = actionArgs.getKeyDouble("bulk", 0.0);
    double cut = actionArgs.getKeyDouble("cut", 12.0);
    cut2_ = cut * cut;
    doublecut_ = 2 * cut;
    onecut2_ = 1 / cut2_;
    std::string infoname = actionArgs.GetStringKey("info");
    if (infoname.empty())
      infoname = std::string("spam.info");
    infofile_ = DFL->AddCpptrajFile(infoname, "SPAM info");
    if (infofile_ == 0) return Action::ERR;
    // 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?
//.........这里部分代码省略.........