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\chapter{Code Implementation}  \section{Smith-Waterman}  \subsection{Using the chord alphabet}  \item Chord data structures (alphabet), base 12 representation  \item Ignoring duration (future work)  \subsection{Bitwise representation of harmonies}  \item Cleverness with representing chords and harmonies as integers and allowing simple bitwise operations and bitmasks  \subsection{MIPS Implementation}  \item Used BU implementation, extreme speed results, but only for DNA and Protein sequences, the usual use case of Smith-Waterman  \item Optimized implementation for use with chord alphabet  \item Initialize distance matrix, extremely fast  \subsection{Speed considerations}  \item Initially implemented in Python, experience 100,000x speed-up  \subsection{Future considerations}  \item Fast SW extremely useful but also highly restrictive in its compactness and efficiency -- hard to modify  \item Adapt using local transpositions