update documentation a bit. Add in docs (saying not to use) for publi…

…c function that was only used for testing. Also make note of the fact that new_seq is currently bugged

include/digest/digester.hpp

@@ -198,6 +198,7 @@ template <BadCharPolicy P> class Digester {
 	/**
 	 * @brief replaces the current sequence with the new one. It's like starting
 	 * over with a completely new seqeunce
+	 * <b> Currently is bugged. Don't use </b>
 	 *
 	 * @param seq const char pointer to new sequence to be hashed
 	 * @param len length of the new sequence
@@ -222,6 +223,7 @@ template <BadCharPolicy P> class Digester {
 	/**
 	 * @brief replaces the current sequence with the new one. It's like starting
 	 * over with a completely new sequence
+	 * <b> Currently is bugged. Don't use </b>
 	 *
 	 * @param seq const std string reference to the new sequence to be hashed
 	 * @param start position in new sequence to start from

include/digest/window_minimizer.hpp

@@ -138,9 +138,19 @@ template <BadCharPolicy P, class T> class WindowMin : public Digester<P> {
 	unsigned get_large_wind_kmer_am() { return large_window; }
 
 	// function is mainly to help with tests
+	/**
+	 * @brief gets the size of the internal rmq data structure being used. Mainly used to help with tests (so you probably shouldn't use it).
+	 * 
+	 * @return size_t, the size of the internal rmq data structure object
+	 */
 	size_t get_ds_size() { return ds_size; }
 
 	// function is mainly to help with tests
+	/**
+	 * @brief checks if we have generated the first minimizer. Mainly used to help with tests (so you probably shouldn't use it).
+	 * 
+	 * @return bool, if we have already obtained a minimizer
+	 */
 	bool get_is_minimized() { return is_minimized; }
 
   protected: