Method next

src/rnabloom/io/FastaReader.java:70–104

()

    private String header = null;
    
    @Override
    public synchronized String next() throws FileFormatException {
        if (!itr.hasNext()) {
            return null;
        }
        
        if (header == null) {
            header = itr.next().trim();
        }
        
        if (header.isEmpty()) {
            return null; //throw new FileFormatException("Empty FASTA header");
        }
        else if (header.charAt(0) != '>') {
            throw new FileFormatException("Incorrect FASTA header format");
        }
        
        StringBuilder builder = new StringBuilder();
        while (itr.hasNext()) {
            String line = itr.next().trim();
            if (line.isEmpty()) {
                header = null;
                break;
            }
            else if (line.charAt(0) == '>') {
                header = line;
                break;
            }
            else {
                builder.append(line);
            }
        }
        
        return builder.toString();
    }

    @Override
    public synchronized String[] nextWithName() throws FileFormatException {