Method List
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#alignment SmithWaterman
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#alignment Alignment
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#alignmentI Alignment
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#alignmentJ Alignment
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#alignment_count Alignment
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#alignment_local SmithWaterman
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#alignments Matcher
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#aside Alignment
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#endI Alignment
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#endJ Alignment
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#init_from_hash Alignment
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#initialize Matcher
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#initialize Alignment
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#input_sequence Matcher
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#limit Matcher
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#number_of_blank Alignment
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#reserve_target_sequence Matcher
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#reversed Alignment
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#scan Matcher
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#score Alignment
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#score_a Alignment
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#source Alignment
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#startI Alignment
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#startJ Alignment
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#to_h Alignment
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#to_s Alignment