IndexFile Class Reference

#include <IndexFile.h>

Public Member Functions
	IndexFile (std::string _filename)
	~IndexFile ()
unsigned int	size ()
unsigned int	getNumElements ()
std::vector< unsigned int >	getAllElements ()
void	seek (off_t pos)
std::vector< unsigned int >	getNElements (off_t offset, size_t numElementsRange)
std::vector< unsigned int >	getNElements (size_t numElements)
std::vector< unsigned int >	getElements ()
bool	open ()
void	close ()

Detailed Description

Copyright (c) 2025 by The Board of Trustees of the University of Illinois. All rights reserved.

Definition at line 46 of file IndexFile.h.

Constructor & Destructor Documentation

IndexFile()

IndexFile::IndexFile ( std::string  _filename )

inline

Definition at line 54 of file IndexFile.h.

References NAMD_die(), and open().

                               : filename(_filename){
   version=0;
    open();
    if(fileStream.fail())
      NAMD_die("error in IndexFile::IndexFile");
  }

~IndexFile()

IndexFile::~IndexFile ( )

inline

Definition at line 61 of file IndexFile.h.

References close().

{close();}

Member Function Documentation

close()

void IndexFile::close ( )

inline

Definition at line 146 of file IndexFile.h.

Referenced by ~IndexFile().

{fileStream.close();}

getAllElements()

std::vector<unsigned int> IndexFile::getAllElements ( )

inline

Definition at line 64 of file IndexFile.h.

References NAMD_die().

Referenced by getElements(), and ParallelIOMgr::readInfoForParOutDcdSelection().

    {
      std::vector<unsigned int> index;
      index.resize(numElements);
      fileStream.read(reinterpret_cast<char*>(&index[0]), index.size()* sizeof(unsigned int));
      //      auto print = [] (const int &n){ std::cout << n << "\n";};
      //      std::for_each(index.begin(), index.end(), print);
      if(networkEndian)
          std::for_each(index.begin(), index.end(), [] (unsigned int &n) { n = ntohl(n);});
      if(fileStream.good())
        return index;
      else
        NAMD_die("error in IndexFile::getAllElements");
    }

getElements()

std::vector<unsigned int> IndexFile::getElements ( )

inline

Definition at line 99 of file IndexFile.h.

References getAllElements().

    {
      return getAllElements();
    }

getNElements() [1/2]

std::vector<unsigned int> IndexFile::getNElements ( off_t  offset, size_t  numElementsRange  )

inline

Definition at line 81 of file IndexFile.h.

References NAMD_die(), and seek().

Referenced by getNElements().

    {
      std::vector<unsigned int> index;
      index.resize(numElementsRange);
      seek(offset);
      fileStream.read(reinterpret_cast<char*>(&index[0]), index.size()* sizeof(unsigned int));
      if(networkEndian)
          std::for_each(index.begin(), index.end(), [] (unsigned int &n) { n = ntohl(n);});
      if(fileStream.good())
        return index;
      else
        NAMD_die("error in IndexFile::getNElements");
    }

getNElements() [2/2]

std::vector<unsigned int> IndexFile::getNElements ( size_t  numElements )

inline

Definition at line 95 of file IndexFile.h.

References getNElements().

                                                          {
    return getNElements(0, numElements);
  }

getNumElements()

unsigned int IndexFile::getNumElements ( )

inline

Definition at line 63 of file IndexFile.h.

{ return numElements;}

open()

bool IndexFile::open ( void  )

inline

Definition at line 104 of file IndexFile.h.

References NAMD_die().

Referenced by IndexFile().

  {
    fileStream.open(filename.c_str(), std::ios::in | std::ifstream::binary);
    // ifstream portable way to get file size
    fileStream.read(reinterpret_cast<char*>(&version), sizeof(unsigned short int));
    fileStream.seekg(0, fileStream.end);
    unsigned int lengthCheck = fileStream.tellg();
    unsigned int countedLength =0;
    fileStream.seekg(0, fileStream.beg);
    unsigned short beVersion=ntohs(version);
    if(version>=256)
      {
        if(ntohs(version)==1)
          {
            networkEndian = true;
            version = beVersion;

          }
      }
    switch (version) {
    case 0:
      numElements = lengthCheck/sizeof(unsigned int);
      break;
    case 1:
      fileStream.seekg(2, fileStream.beg); // need to seek past the version
      fileStream.read(reinterpret_cast<char*>(&numElements), sizeof(unsigned int));
      numElements = (networkEndian) ? ntohl(numElements) : numElements;     
      countedLength = (lengthCheck-sizeof(char)-sizeof(unsigned int))/sizeof(unsigned int);
      if(numElements!= countedLength)
        {
          std::string e="error in IndexFile::open mismatch in element count";
          e+=" file reports "+std::to_string(numElements)+ " counted  "+std::to_string(countedLength);
          NAMD_die(e.c_str());
        }
      break;
    default:
      NAMD_die("error in IndexFile::open unsupported version");
      break;
    }
    return(fileStream.is_open());
  }

seek()

void IndexFile::seek ( off_t  pos )

inline

Definition at line 79 of file IndexFile.h.

Referenced by getNElements().

{fileStream.seekg(pos);}

size()

unsigned int IndexFile::size ( )

inline

Definition at line 62 of file IndexFile.h.

{ return numElements;}

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The documentation for this class was generated from the following file:

• IndexFile.h