Method nextWithName

src/rnabloom/io/FastaReader.java:106–152

()

    }

    @Override
    public synchronized String[] nextWithName() 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");
        }
        
        String name = null;
        Matcher m = RECORD_NAME_COMMENT_PATTERN.matcher(header);
        if (m.matches()) {
            name = m.group(1);
            if (removeNameSuffix) {
                Matcher m2 = RECORD_NAME_PATTERN.matcher(name);
                if (m2.matches()) {
                    name = m2.group(1);
                }
            }
        }
        else {
            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 new String[]{name, builder.toString()};
    }
    
    public synchronized void nextWithName(FastaRecord fr) throws FileFormatException {
        if (!itr.hasNext()) {