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Class Summary | |
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AlignerHelper | Static utility to construct alignment routines from a common library of methods. |
AlignerHelper.Cut | Defines a 'cut' row for divide-and-conquer alignment in which a new anchor is found. |
AnchoredPairwiseSequenceAligner<S extends Sequence<C>,C extends Compound> | This algorithm uses a divide-and-conquer approach to find optimal pairwise global sequence alignments (from the
first until the last Compound of each Sequence ) with the restriction that any alignment produced
will connect the query sequence to the target sequence at the anchors. |
GuanUberbacher<S extends Sequence<C>,C extends Compound> | Guan and Uberbacher defined an algorithm for pairwise global sequence alignments (from the first until the last
Compound of each Sequence ). |
Enum Summary | |
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AlignerHelper.Last | Defines a traceback pointer for the three edit operations: substitution (match/replacement of a query compound with a target compound), deletion (removal of a query compound leaving a gap in the target sequence), and insertion (addition of a target compound opening a gap in the query sequence). |
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