xsact-1.6: Cluster EST sequences Source code Contents Index

Pairs

Synopsis

data Match = Match !Suffix !Suffix data SMPair = SMPair !Dir !EST !EST !Int [Block] class Pair a n | a -> n where score :: a -> Int ests :: a -> (n, n) pairs :: Bool -> [Match] -> [SMPair] matches :: [[Suffix]] -> [Match] sort_pure :: [Match] -> [Match] sort_io :: [EST] -> String -> [Match] -> IO [Match] mpairs :: Bool -> [Match] -> [(Maybe MPair, Maybe MPair)] elim_bs :: SMPair -> SMPair psort :: [SMPair] -> [SMPair] collect :: Bool -> [Match] -> [([Match], [Match])] blocks :: ([Match], [Match]) -> (Maybe MPair, Maybe MPair) showmatch :: Match -> String direction :: SMPair -> Bool prefixes :: Int -> [[Gene]] merge_suffix_lists :: [EST] -> Int -> String -> IO [Match] show_header :: SMPair -> String show_regs :: SMPair -> String

Documentation

data Match Source

Constructors Match !Suffix !Suffix Instances Show Match Pair Match EST

data SMPair Source

Constructors SMPair !Dir !EST !EST !Int [Block] Instances Show SMPair Pair SMPair EST

class Pair a n | a -> n where Source

Methods score :: a -> Int Source ests :: a -> (n, n) Source Instances Pair SMPair EST Pair SMPair EST Pair MPair EST Pair MPair EST Pair Match EST Pair Match EST

pairs :: Bool -> [Match] -> [SMPair] Source

Construct scored pairs from {tt Match}es.

matches :: [[Suffix]] -> [Match] Source

sort_pure :: [Match] -> [Match] Source

sort_io :: [EST] -> String -> [Match] -> IO [Match] Source

mpairs :: Bool -> [Match] -> [(Maybe MPair, Maybe MPair)] Source

elim_bs :: SMPair -> SMPair Source

psort :: [SMPair] -> [SMPair] Source

sort pairs by score

collect :: Bool -> [Match] -> [([Match], [Match])] Source

blocks :: ([Match], [Match]) -> (Maybe MPair, Maybe MPair) Source

showmatch :: Match -> String Source

direction :: SMPair -> Bool Source

prefixes :: Int -> [[Gene]] Source

calculate prefixes (also used in Xsact)

merge_suffix_lists :: [EST] -> Int -> String -> IO [Match] Source

show_header :: SMPair -> String Source

show_regs :: SMPair -> String Source

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