/**
 ** Copyright (c) 2007-2010 Illumina, Inc.
 **
 ** This software is covered by the "Illumina Genome Analyzer Software
 ** License Agreement" and the "Illumina Source Code License Agreement",
 ** and certain third party copyright/licenses, and any user of this
 ** source file is bound by the terms therein (see accompanying files
 ** Illumina_Genome_Analyzer_Software_License_Agreement.pdf and
 ** Illumina_Source_Code_License_Agreement.pdf and third party
 ** copyright/license notices).
 **
 ** This file is part of the Consensus Assessment of Sequence And VAriation
 ** (CASAVA) software package.
 **
 ** \file variance/indelReadsStats.cpp
 **
 ** \brief
 **
 ** 
 **
 ** \author
 **/

#include "variance/indelReadsStats.h"

/* ----- ----- ----- ----- ----- -----
 *
 * ----- Auxillary funcitons     -----
 *
 * ----- ----- ----- ----- ----- ----- */


/* ----- ----- ----- ----- ----- -----
 *
 * ----- Manipulation Functions  -----
 *
 * ----- ----- ----- ----- ----- ----- */

void IndelReadsStats::load(string file) {
  // Clear all previous data
  this->machineNames.clear();
  this->runNums.clear();
  this->laneNums.clear();
  this->meanInsSize.clear();
  this->sdInsSize.clear();
  this->keys.clear();

  ifstream fileStream;
  fileStream.open(file.c_str(), ios_base::in);

  string line;
  while(! fileStream.eof()) {
    getline(fileStream, line);
    if (line.substr(0, 1).compare("#") == 0 ||
	line.length() == 0) {
      continue;
    }

    vector<string> data;
    Export::tsvToArray(line, data, '\t');

    //this->machineNames.push_back(data[STAT_MACHINE_NAME_IDX]);
    //this->runNums.push_back(atoi(data[STAT_RUN_NUM_IDX].c_str()));
    //this->laneNums.push_back(atoi(data[STAT_LANE_NUM_IDX].c_str()));
    //this->meanInsSize.push_back(atof(data[STAT_INS_SIZE_MEAN_IDX].c_str()));
    //this->sdInsSize.push_back(atof(data[STAT_INS_SIZE_SD_IDX].c_str()));

    // Get key string
    stringstream skey;
    skey << data[STAT_MACHINE_NAME_IDX] << ":"
	 << data[STAT_RUN_NUM_IDX] << ":"
	 << data[STAT_LANE_NUM_IDX];
    string key = skey.str();

    // Make sure key does not already exist
    //if (this->meanInsSize.find(key)->compare(map::end)) {
    //} else {
    // We should throw some kind of an error or warning...
    //}

    // Simply just write over previous value for now...

    // Assign key value pairs
    this->machineNames[key] = data[STAT_MACHINE_NAME_IDX];
    this->runNums[key]      = atoi(data[STAT_RUN_NUM_IDX].c_str());
    this->laneNums[key]     = atoi(data[STAT_LANE_NUM_IDX].c_str());
    this->meanInsSize[key]  = atof(data[STAT_INS_SIZE_MEAN_IDX].c_str());
    this->sdInsSize[key]    = atof(data[STAT_INS_SIZE_SD_IDX].c_str());

    // Add key to keys vector
    this->keys.push_back(key);
  }
  fileStream.close();
}

/* ----- ----- ----- ----- -----
 *
 * ----- Access Functions  -----
 *
 * ----- ----- ----- ----- -----  */

double IndelReadsStats::getMeanInsSize(string m, int r, int l) {
  stringstream skey;
  skey << m << ":" << r << ":" << l;
  string key = skey.str();

  // Return -1 if key not found
  /*
  if (this->meanInsSize.find(key) == map::end) {
    return(-1);
  }
  */

  return(this->meanInsSize[key]);

  /*
  int len = this->machineNames.size();
  for (int idx = 0; idx < len; idx++) {
    if (this->machineNames[idx].compare(m) == 0 &&
	this->runNums[idx] == r &&
	this->laneNums[idx] == l) {
      return(this->meanInsSize[idx]);
    }
  }
  cerr << "[Warning]: Unable to find mean index for: "
       << m << ", " << r << ", " << l << endl;
  return(-1);
  */
}

double IndelReadsStats::getSdInsSize(string m, int r, int l) {
  stringstream skey;
  skey << m << ":" << r << ":" << l;
  string key = skey.str();

  // Return -1 if key not found
  /*
  if (this->sdInsSize.find(key) == map::end) {
    return(-1);
  }
  */

  return(this->sdInsSize[key]);

  /*
  int len = this->machineNames.size();
  for (int idx = 0; idx < len; idx++) {
    if (this->machineNames[idx].compare(m) == 0 &&
	this->runNums[idx] == r &&
	this->laneNums[idx] == l) {
      return(this->sdInsSize[idx]);
    }
  }
  cerr << "[Warning]: Unable to find mean index for: "
       << m << ", " << r << ", " << l << endl;
  return(-1);
  */
}

string IndelReadsStats::toString() {
  stringstream con;

  const unsigned int numKeys = this->keys.size();
  for (unsigned int ii = 0; ii < numKeys; ii++) {
    string key = keys[ii];
    con << machineNames[key] << "\t" << runNums[key] << "\t"
	<< laneNums[key] << "\t" << meanInsSize[key] << "\t"
	<< sdInsSize[key] << "\n";
  }

  return(con.str());
}

/* ----- ----- ----- ----- -----
 *
 * ----- Test Functions -- -----
 *
 * ----- ----- ----- ----- -----  */

/*
int main( int numArgs, char* args [] )
{
  return(0);
}
*/

// END OF FILE