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Alignment Free
Alignments
assignSource (Gaps)
bandedChainAlignment
clearClipping (Gaps)
clearGaps (Gaps)
col
cols
countGaps (Gaps)
gapValue
getProjectedPosition
getScore (LocalAlignmentEnumerator)
globalAlignment
globalAlignmentScore
globalMsaAlignment
heaviestCommonSubsequence
heaviestIncreasingSubsequence
host (ConsensusScoreSequenceEntry)
insertGap
insertGaps
integrateAlign
isGap (Gaps)
isReversed
length (Gaps)
localAlignment
longestCommonSubsequence
longestIncreasingSubsequence
matchRefinement
nextLocalAlignment
position (ConsensusScoreSequenceEntry)
removeGap
removeGaps
row
rows
scoreGap
scoreGapExtend
scoreGapOpen
scoreMatch
scoreMismatch
sequenceEntryForScore (Score)
setScoreGap
setScoreGapExtend
setScoreGapOpen
setScoreMatch
setScoreMismatch
setSource (Gaps)
setStrings
toSourcePosition
toViewPosition
unclippedLength (Gaps)
value (ConsensusScoreSequenceEntry)
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