public List<AcidSequence> parseChunk() {
		ArrayList<AcidSequence> list = new ArrayList<AcidSequence>();
		
		// Begin with an initial sequence
		// TODO: assumes file is not empty
		AcidSequence sequence = new AcidSequence();
		// While the file is not finished and we have not reached the 
		// total number of sequences per chunk...
		while (scanner.hasNextLine() && list.size() < chunkSize) {
			// Get a line from the FASTA file...
			String line = scanner.nextLine();
			
			// If the line begins with a '>'...
			if (!line.isEmpty() && line.charAt(0) == '>') {
				// then it is the start of a new Sequence
				// and should be used as the description.
				sequence = new AcidSequence(line.substring(1));
			}
			// If the line is empty, then we have reached
			// the end of a sequence...
			else if (line.isEmpty() || 
					 line.charAt(0) == '\n' ||
					 !scanner.hasNextLine()) {
				// so add it to the list.
				list.add(sequence);
			}
			// Otherwise, the line must be part of the current
			// sequence's data...
			else {
				// so append it to the data of the current Sequence.
				sequence.appendSequence(line);
			}
		}
		return list;
	}