ifstream get parts of a formatted textfile

I am trying to extract to parts of unknown size from a database (textfile).
It is composed as follows
>Title\n                      //The '>' preceedes a section of the database and \n terminates this header
                                //That line thus contains the header or title for the following section
AACCCTAGCTAGCATCAGCACGACG\n
ACGACTAGCACTNACGGCGACCTCG\n
ACACGAGCTGCGCCATAGCAGCAGG\n
                               //Each line is terminated after some charackters with a linefeed '\n'
                               //Can be between some and some hundred thousands chaarackters.
                               //Only ACGNT however
>Next section\n
....
>Third section\n
...
>and so on for 100 MB\n
I would like to extract the header to a variable called scaffold
and the corresponding section of the database to a variable called code.
Boh are char*.
I use the following approach, but it only works for the first section thereafter it creates wierd
resutlts.
bool CDna2Protein::GetNextPart(const char * _filePath)
{
      if(!databasein.is_open())                         //Declared as class variable so I do not have
                                                                            //to keep opening and closing a file.
                                                                            //ifstream databasein;
            databasein.open(_filePath,ios_base::in);
      char          ch,
            test = '>';
      int pos = 0;
      char *line = new char[256];
      //Read in header for this part of the database
      databasein.getline(line,256,'\n');
      scaffold = new char[256];
      sprintf(scaffold,"%s",line);
      delete line;
      //Now get the current position in the file
      int before = databasein.tellg();
      before--; //Does seem to give the next position so account for that
      int after = 0;
      while(databasein.get(ch)) {
            if(ch == test) {    //test = '>';
                  databasein.putback(ch);
                           //I would like the next read starting with the charackter I just putback.
                  after = databasein.tellg();
                  after--;    //see above
                  break;
            }
      }
      int len = after-before;
                //Knowing the size of the database section create a buffer to hold it
      code = new char[len+1];
      databasein.seekg(before);
      databasein.get(code,len,test);   //test='>';
      databasein.seekg(after);
                //should hopefully end up at desired position within file
      code[len]='\0';

                //do some output for testing
      len = int(strlen(code));
      char *temp = new char[10];
      sprintf(temp,"%d",len);
      CString str = "Laenge von "+CString(scaffold)+": "+CString(temp);
      delete temp;
      StringToFile("c:\\gpfc++\\len.log",str);
      trim();
                //Need to figure out how to test for termination.
      return(true);
}
Besides the problem of getting wrong parts of the database posing for scaffold,
I also need to return false on reaching feof.
Thank you for any suggestions
Jens