public static void uniprotParse(String filename, String [] accessions, String [] sequences) throws IOException {

    Scanner lineScanner = new Scanner(new File(filename));     
    int n =  0;
    boolean foundAC = false;    // True when AC line is encountered
    boolean foundSQ = false;    // True when SQ line is encountered
    String sequence="";         // accumulates the sequence
    String accession = "";      // stores the primary accession
    while(lineScanner.hasNextLine( )){
        String line = lineScanner.nextLine();
        if (line.startsWith("//")){
                accessions[n] = accession;
                sequences[n] = sequence;
                foundAC = false;
                foundSQ = false;
                sequence = "";
                n++;
        }
        else if (foundSQ){
                sequence += line.replace(" ", "");
        }
        else if (line.startsWith("AC")){
                if (foundAC) continue;
                foundAC = true;
                accession = line.substring(5, line.length()-1).split(";")[0];
        }
        else if (line.startsWith("SQ")){
                foundSQ = true;
        }
    }
    lineScanner.close();
}