public Vector read(String filename){

    

        Vector sequence_list = new Vector();

        pos = 0; char tmp;

        data = loadfile(filename);

        tmp = getNextToken(); // ">"

        

        do{     

        String sequence = "";    

        String organName = "";

        //read header name

        do{

            organName+= tmp;

            tmp = getNextToken();

        }while(tmp != '\n');       

        //read in sequence

        do{

            tmp = getNextToken();

            if(tmp!='\n' && tmp!='#' && tmp!='>')

                sequence += tmp;    

        }while(tmp!='#' && tmp!='>');

        

        Fasta fasta = new Fasta(organName,sequence);

        sequence_list.add(fasta); 

       

        }while(tmp != '#');    

        return sequence_list;

    }