#include <iostream>
#include <fstream>
#include <string>
#include <map>

/**
 * You need string.h for strtok and strcpy.  MANDATORY!
 * Not having the right headers can cause a CRASH!
 */
#include <string.h>

using namespace std;

int main()
{
   ifstream inFILE("infile.fasta");
   /* You're not using this */
   //int inGuard = 1;               //using a guard variable

   /**
    * If you put it inside the loop, it goes out of scope every loop.
    * That's good when you want that, and bad when you don't.
    * Since you want the value to stay the same every loop, you don't.
    */
   string entryID;

   map <string, string>FastaSeq;   //Declare a map to hold each sequence entry

   while (inFILE.good()) {
      string line;        //declare string for each line
      /* moved above */
      //string entryID, sequence;    //declare two strings for key and value for map
      char *sPtr;        //Declare char pointer sPtr for tokens
      getline(inFILE, line);    //Read the whole line

      //Initialize char pointer sArray for conversion of the string to char*    
      char *sArray = new char[line.length() + 1];
      strcpy(sArray, line.c_str());

      if (sArray[0] == '>') {
         sPtr = strtok(sArray, " ");    //Using space as delimiter get the first token.
         /**
          * If your program crashes, odds are you won't see anything printed to cout.
          * use cerr for debugging instead, it prints instantly instead of being held for later.
          *
          * Use cerr for errors/debugging, cout for data output.
          */
         //cout << sPtr << " ";       //Print the first token only
         cerr << endl << sPtr << " ";
         entryID = sPtr;             //assign the first token as key for the map
         continue;
     } else  {
         sPtr = strtok(sArray, " ");    //Get all the tokens with " " as delimiter.

         /**
          * Always, always, always check your pointers!
          * Never assume strtok must have worked.
          * This is what broke your last 3 programs.
          */
         //FastaSeq[entryID] += sPtr;   // assign first part of sequence to map

         /**
          * The loop checks for NULL, so inside, sPtr is safe to use.
          */
         while (sPtr != NULL) {          //For all tokens
//            cout << sPtr;
            cerr << sPtr;
            FastaSeq[entryID] += sPtr;   // assign more token to sequence
            sPtr = strtok(NULL, " ");
         }
      }

      delete [] sArray;      /* NOT OPTIONAL! */
   }

   cerr << endl << endl;
   inFILE.close();

   //print the map
   map <string, string>::const_iterator seq_itr;

   /**
    * You made an iterator but didn't point it to anything.
    * This is bad for the same reason an unchecked pointer to
    * nothing is bad.
    *
    * Imagine a loop like for(x=0; x != 10; x++) but it's not an int,
    * instead you use z.begin() and z.end().  ++ still works.
    */
   seq_itr=FastaSeq.begin();

//   if (seq_itr != FastaSeq.end()){
   while(seq_itr != FastaSeq.end()) {
      cout << seq_itr->first << " ";

      /**
       * ???  Not sure what you're trying to do here.
       * You can't print an iterator, just its contents (first, second)
       */
      // cout << seq_itr << seq_itr->second << endl;
      cout << seq_itr->second << endl;

      /**
       * You can call ++ on an iterator, it's effectively i=i.next();
       */
      seq_itr++;
   }

    return 0;
}