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

#include "nlsr_sm.hpp"

namespace nlsr
{

    using namespace std;

    void
    SequencingManager::splittSequenceNo(uint64_t seqNo)
    {
        combinedSeqNo=seqNo;
        adjLsaSeq = (combinedSeqNo & 0xFFFFF);
        corLsaSeq = ((combinedSeqNo >> 20) & 0xFFFFF);
        nameLsaSeq = ((combinedSeqNo >> 40) & 0xFFFFF);
    }

    void
    SequencingManager::combineSequenceNo()
    {
        combinedSeqNo=0;
        combinedSeqNo = combinedSeqNo | adjLsaSeq;
        combinedSeqNo = combinedSeqNo | (corLsaSeq<<20);
        combinedSeqNo = combinedSeqNo | (nameLsaSeq<<40);
    }

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

    void
    SequencingManager::initiateSeqNoFromFile()
    {
        cout<<"Seq File Name: "<< seqFileNameWithPath<<endl;
        std::ifstream inputFile(seqFileNameWithPath.c_str(),ios::binary);
        if ( inputFile.good() )
        {
            inputFile>>combinedSeqNo;
            splittSequenceNo(combinedSeqNo);
            adjLsaSeq+=10;
            corLsaSeq+=10;
            nameLsaSeq+=10;
            combineSequenceNo();
            inputFile.close();
        }
        else
        {
            splittSequenceNo(0);
        }
    }

    void
    SequencingManager::setSeqFileName(string filePath)
    {
        seqFileNameWithPath=filePath;
        if( seqFileNameWithPath.empty() )
        {
            seqFileNameWithPath=getUserHomeDirectory();
        }
        seqFileNameWithPath=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