#include <stdlib.h>
#include <string.h>
#include <iostream.h>
#include <fstream.h>
#include <stdio.h>
#include "../Utils/hash.h"
#include "seq_stream.h"

/********************************************************************
 *  Init()                                                          *
 *    Initializes an instance of Stream.                            *
 *                                                                  *
 *  Input:  const Config &cfg   Configuration information           *
 *          const int intern    internal stream identifier          *
 *          const int extern    external stream identifier          *
 *  Output: none                                                    *
 *******************************************************************/


void Stream::Init(const Config &cfg, 
		  const int intern_id, const int extern_id) {
  // initialize all the arrays
  current_seq.Allocate(cfg.seq_len);
  current_seq.Set(-1);  // initialize the array to be empty
  num_in_seq = -1;
  num_pairs_read = 0;
  num_anoms = 0;
  num_seqs_fnd = 0;
  int_sid = intern_id;
  ext_sid = extern_id;
  max_hdist = 0;
  seq_hdist = 0;
  lf.Allocate(cfg.lf_size);
  lf.Set(0);
  seq_lfc = 0;
  max_lfc = 0;
  ready = 0;
  seq_len = cfg.seq_len;
}

/*********************************************************************
 * Append()                                                          *
 *   This function puts the integer given into the current_seq array *
 *   as the last element.  It flags ready according to whether       *
 *   current_seq is full.  Updates num_in_seq, ready, current_seq,   *
 *   num_seqs_fnd, and num_pairs_read.                               *
 *                                                                   *
 *  Input:  const int new_value  The next value to be put into the   *
 *                          current_seq array                        *
 *  Output: none                                                     *
 ********************************************************************/

void Stream::Append(const int new_value)
{
  // missing system call - zero the current sequence 
  if (new_value == -1) {    
    num_in_seq = -1;
    ready = 0;
  } 
  else {
    num_pairs_read++;
    if (num_in_seq < seq_len - 1) {  // window not yet full
      num_in_seq++; 
      current_seq[num_in_seq] = new_value;  
      if (num_in_seq == seq_len - 1) {
	ready = 1;
        ++num_seqs_fnd;
      }
    } 

    else { 
      // Roll over current_seq array
      for (int k = 0; k < num_in_seq; k++) {
	current_seq[k] = current_seq[k + 1];
      }
      current_seq[num_in_seq] = new_value;  
      ++num_seqs_fnd;
    }
  }
}

/********************************************************************
 * AddToDB()                                                        *
 *                                                                  *
 *    Adds current_seq to the database if it isn't already there;   *
 *    Returns 0 if it is already there, 1 if it is new.  Updates    * 
 *    normal and db_size.                                           * 
 *                                                                  *
 * Input: SeqForest &normal  Forest of normal sequences             *
 *        int &db_size       Number of unique sequences in the      *
 *                           database                               *
 *        const int total_pairs_read  Number of pairs read from the *
 *                           entire input stream                    *
 *        const Config &cfg  Configuration Information              *
 * Output: 0 if sequence isn't new, 1 if it is                      *
 ********************************************************************/


int Stream::AddToDB(SeqForest &normal, int &db_size, const int
		    total_pairs_read, const Config &cfg) const 
{
  int is_new;

  // If there is not a tree with the same root as this sequence has,
  // make a new tree with that root and flag trees_found
  if (!normal.trees_found[current_seq[0]]) {
    normal.trees[current_seq[0]].SetRoot(current_seq[0]); 
    normal.trees_found[current_seq[0]] = 1;
  } 
  // Try to add the sequence.  If it's already there, is_new will be
  // set to 0, otherwise it will be set to 1.
  is_new = normal.trees[current_seq[0]].InsertSeq(current_seq, 0,
						    seq_len-1);  
  db_size += is_new;
  if ((is_new && cfg.verbose) || cfg.very_verbose) {
    ReportNewSeq(cfg, total_pairs_read, db_size);
  } 
  if (is_new) 
    return 1;
  else 
    return 0;
} 


/*********************************************************************
 *  CompareSeq()                                                     *
 *    Compares the current sequence in this stream to the database,  *
 *    in the manner indicated by the configuration file.  Reports    *
 *    on anomalies if told to by the configuration file.  Updates    *
 *    num_anoms, seq_hdist, max_hdist, seq_lfc, and max_lfc.         *
 *                                                                   *
 *    Input:  const Config &cfg: Information from configuration file *
 *            const SeqForest &normal: DB of normal sequences        *
 *            const int total_pairs_read: Number of pairs read from  *
 *                                  all of the streams               *
 *    Output: none                                                   *
 ********************************************************************/

void Stream::CompareSeq(const Config &cfg, const SeqForest &normal,
			const int total_pairs_read) 
{
  int is_anom;     // flag to indicate whether current_seq is an anomaly 

  is_anom = ComputeMisses(normal);
  if ((is_anom) && (cfg.compute_hdist)) {
    ComputeHDist(normal);
  }
  if (cfg.lf_size > 1) {
    ComputeLF(is_anom, cfg.lf_size);
  }
  // if we're in verbose mode and either current_seq is an anomaly or
  // its locality frame contains an anomaly, report it
  if ((cfg.very_verbose) || (cfg.verbose && (is_anom || seq_lfc))) {
    ReportSeq(cfg, total_pairs_read, is_anom);
  }
}

/*********************************************************************
 *  ComputeMisses()                                                  *
 *    Compares the current sequence to the database sequences.  If   *
 *    there is an exact match, we return 0.  Otherwise we return 1.  *
 *    Updates num_anoms and seq_hdist.                               *
 *                                                                   *
 *    Input:  const SeqForest &normal:  DB of normal sequences       *
 *    Output: 0 if there is an exact match                           *
 *            1 if the sequence is anomalous                         *
 ********************************************************************/


int Stream::ComputeMisses(const SeqForest &normal)
{
  if (normal.IsSeqInForest(current_seq, seq_len)) {
    seq_hdist = 0;
    return(0);
  }

  // We have an anomaly
  ++num_anoms;
  return(1);
} 

/*********************************************************************
 *  ComputeHDist()                                                   *
 *    Compares the current sequence in this stream to each sequence  *
 *    in the database in turn, adding up the number of mismatches    *
 *    between the two sequences.  The smallest difference between    *
 *    the current sequence and the database sequences is the minimum *
 *    Hamming distance for the current sequence.  If this minimum    *
 *    Hamming distance is greater than the largest minimum Hamming   *
 *    distance encountered so far, then the variable max_hdist is    *
 *    updated.  Updates seq_hdist and max_hdist.                     *
 *                                                                   *
 *    Input:  const SeqForest &normal: DB of normal sequences        *
 *                                                                   *
 *    Output: none                                                   *
 ********************************************************************/

void Stream::ComputeHDist(const SeqForest &normal)
{
  int misses_on_this_seq;    // the number of mismatches between
                             // current_seq and the sequence we're
			     // comparing it with at the moment
  seq_hdist = seq_len;       // start with seq_hdist as high as
			     // possible  

  // We compare current_seq with each sequence in our database tree
  for (int i = 0; i < normal.trees.Size(); i++) { 
    // Have we seen any sequences starting with element i?  If not, we
    // can go on to consider sequences starting with element i+1.
    if (normal.trees_found[i]) { 
      misses_on_this_seq =
	normal.trees[i].ComputeHDistForTree(current_seq, 0,
					    seq_len-1);  
      if (misses_on_this_seq < seq_hdist) {
	seq_hdist = misses_on_this_seq;
      }
    }
  }  

  if (seq_hdist > max_hdist) {
    max_hdist = seq_hdist;
  }
} 


/*********************************************************************
 *  ComputeLF()                                                      *
 *    Computes the number of misses in current_seq's locality frame. *
 *    Updates lf, seq_lfc and max_lfc.                               *
 *                                                                   *
 *    Input:  const int is_anom   Flag to indicate whether           *
 *                          current_seq is an anomaly                *
 *            const int lf_size   Size of locality frame             *
 *    Output: none                                                   *
 ********************************************************************/


void Stream::ComputeLF(const int is_anom, const int lf_size)
{
  // When num_seqs_fnd is less than lf_size, the locality frame
  // array is not full
  if (num_seqs_fnd <= lf_size) {
     lf[num_seqs_fnd-1] = is_anom;
     seq_lfc += is_anom;
  }
  else {
    // We're about to remove the first element of lf; since seq_lfc is
    // the sum of the elements of lf, we should subtract lf[0] from
    // seq_lfc to remove it from the sum.
    seq_lfc -= lf[0];
    // Now we add is_anom and seq_lfc is the sum of the new locality
    // frame.
    seq_lfc += is_anom;

    // roll over the array
    for (int i = 0; i < lf_size-1; i++) {
      lf[i] = lf[i+1];
    }
    lf[lf_size-1] = is_anom;
  }
  if (seq_lfc > max_lfc) {
    max_lfc = seq_lfc;
  }
}

/*********************************************************************
 *  ReportSeq()                                                      *
 *    This function reports data about a sequence.  Specifically, it *
 *    can report the external stream id, a number indicating where   *
 *    the first element of the current sequence occurs in the input, *
 *    a number indicating how many pairs from this particular data   *
 *    stream have been read prior to the first element of the        *
 *    sequence, the minimum Hamming distance for the current         *
 *    sequence, the locality frame count, the locality frame count,  *
 *    and whether this particular sequence is itself an anomaly (it  *
 *    could be that some other sequence in its locality frame is     *
 *    anomalous).  The configuration file determines which of those  *
 *    possible data are reported and in what format. Updates no      *
 *    values.                                                        *
 *                                                                   *
 *    Input:  const Config &cfg  Configuration information           *
 *            const int total_pairs_read  Total number of pairs read *
 *                               from the input stream from any data *
 *                               stream, not just this one           *
 *            const int is_anom  flag for whether the current        *
 *                               sequence is itself an anomaly       * 
 *    Output: none                                                   *
 ********************************************************************/

void Stream::ReportSeq(const Config &cfg, const int total_pairs_read,
		       const int is_anom)   const
{
  for (int i = 0; i < cfg.num_fvars; i++) {
    switch (cfg.write_val[i]) {
    case 'a':
      printf(cfg.fmt_str[i], is_anom); break;
    case 'c':
      if (cfg.lf_size > 1) {
	printf(cfg.fmt_str[i], seq_lfc); 
      }
      break;
    case 'h':
      if (cfg.compute_hdist) {
	printf(cfg.fmt_str[i], seq_hdist); 
      }
      break;
    case 'i': 
      printf(cfg.fmt_str[i], num_pairs_read); break;
    case 'p':
      printf(cfg.fmt_str[i], total_pairs_read); break;
    case 's': 
      printf(cfg.fmt_str[i], ext_sid); break;
    }
  }
  printf(cfg.fmt_str[cfg.num_fvars]);
}


/*********************************************************************
 *  ReportNewSeq()                                                   *
 *    This function reports on sequences which have been newly added *
 *    to the database.  It can report the external stream            *
 *    identifier, where the first element of the sequence occurs     *
 *    both within the whole input stream and within its own data     *
 *    stream, and the number of unique sequences in the database     *
 *    after this sequence has been added.  The configuration file    *
 *    determines which of those possible data are reported and in    *
 *    what format.  Updates no values.                               * 
 *                                                                   *
 *    Input:  const Config &cfg  Configuration information           *
 *            const int total_pairs_read  Total number of pairs read *
 *                               from the input stream from any data *
 *                               stream, not just this one           *
 *            const int db_size  Number of unique sequences          *
 *                               in the database                     *
 *    Output: none                                                   *
 ********************************************************************/

void Stream::ReportNewSeq(const Config &cfg, const int total_pairs_read,
			  const int db_size) const
{
  for (int i = 0; i < cfg.num_fvars; i++) {
    switch (cfg.write_val[i]) {
    case 'd':
      printf(cfg.fmt_str[i], db_size); break;
    case 'i': 
      printf(cfg.fmt_str[i], num_pairs_read); break;
    case 'p':
      printf(cfg.fmt_str[i], total_pairs_read); break;
    case 's': 
      printf(cfg.fmt_str[i], ext_sid); break;
    }
  }
  printf(cfg.fmt_str[cfg.num_fvars]);
}