src/sequencing-manager.cpp

#include <string>
#include <iostream>
#include <fstream>
#include <pwd.h>
#include <cstdlib>
#include <unistd.h>

#include "sequencing-manager.hpp"
#include "logger.hpp"

namespace nlsr {

INIT_LOGGER("SequencingManager");

using namespace std;

void
SequencingManager::splittSequenceNo(uint64_t seqNo)
{
  m_combinedSeqNo = seqNo;
  m_adjLsaSeq = (m_combinedSeqNo & 0xFFFFF);
  m_corLsaSeq = ((m_combinedSeqNo >> 20) & 0xFFFFF);
  m_nameLsaSeq = ((m_combinedSeqNo >> 40) & 0xFFFFF);
}

void
SequencingManager::combineSequenceNo()
{
  m_combinedSeqNo = 0;
  m_combinedSeqNo = m_combinedSeqNo | m_adjLsaSeq;
  m_combinedSeqNo = m_combinedSeqNo | (m_corLsaSeq << 20);
  m_combinedSeqNo = m_combinedSeqNo | (m_nameLsaSeq << 40);
}

void
SequencingManager::writeSeqNoToFile()
{
  std::ofstream outputFile(m_seqFileNameWithPath.c_str(), ios::binary);
  outputFile << m_combinedSeqNo;
  outputFile.close();
}

void
SequencingManager::initiateSeqNoFromFile()
{
  cout << "Seq File Name: " << m_seqFileNameWithPath << endl;
  std::ifstream inputFile(m_seqFileNameWithPath.c_str(), ios::binary);
  if (inputFile.good()) {
    inputFile >> m_combinedSeqNo;
    splittSequenceNo(m_combinedSeqNo);
    m_adjLsaSeq += 10;
    m_corLsaSeq += 10;
    m_nameLsaSeq += 10;
    combineSequenceNo();
    inputFile.close();
  }
  else {
    splittSequenceNo(0);
  }
}

void
SequencingManager::setSeqFileName(string filePath)
{
  m_seqFileNameWithPath = filePath;
  if (m_seqFileNameWithPath.empty()) {
    m_seqFileNameWithPath = getUserHomeDirectory();
  }
  m_seqFileNameWithPath = m_seqFileNameWithPath + "/nlsrSeqNo.txt";
}

string
SequencingManager::getUserHomeDirectory()
{
  string homeDirPath(getpwuid(getuid())->pw_dir);
  if (homeDirPath.empty()) {
    homeDirPath = getenv("HOME");
  }
  return homeDirPath;
}

ostream&
operator<<(ostream& os, const SequencingManager& sm)
{
  std::cout << "----SequencingManager----" << std::endl;
  std::cout << "Adj LSA seq no: " << sm.getAdjLsaSeq() << endl;
  std::cout << "Cor LSA Seq no: " << sm.getCorLsaSeq() << endl;
  std::cout << "Name LSA Seq no: " << sm.getNameLsaSeq() << endl;
  std::cout << "Combined LSDB Seq no: " << sm.getCombinedSeqNo() << endl;
  return os;
}

}//namespace nlsr