haddock documentation
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README.txt
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28
README.txt
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@ -0,0 +1,28 @@
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How to build:
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$ cabal install --only-dependencies
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$ cabal configure
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$ cabal build
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Create documentation:
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$ cabal haddock --executables
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Build and create documentation with all hyperlinks
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$ cabal install --only-dependencies --enable-documentation
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$ cabal configure
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$ cabal build
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$ cabal haddock --executables
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Run:
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$ dist/build/hgraph/hgraph --help
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How to build (sandboxed, >=cabal 1.18, recommended):
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$ cabal sandbox init
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$ cabal install --only-dependencies
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$ cabal configure
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$ cabal build
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How to build (sandboxed, cabal-dev, deprecated):
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$ cabal-dev install --only-dependencies
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$ cabal-dev configure
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$ cabal-dev build
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@ -1,11 +1,11 @@
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{-# LANGUAGE FlexibleInstances #-}
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{-# LANGUAGE FlexibleInstances #-}
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{-# LANGUAGE OverlappingInstances #-}
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{-# LANGUAGE TypeOperators #-}
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{-# LANGUAGE TypeSynonymInstances #-}
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{-# LANGUAGE BangPatterns #-}
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-----------------------------------------------------------------------------
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--
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-- Module : DCB
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-- Module : DCB.DCB
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-- Copyright :
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-- License : AllRightsReserved
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--
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@ -13,10 +13,11 @@
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-- Stability :
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-- Portability :
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--
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-- |
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--DCB.DCB---------------------------------------------------------------------------
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-- | Computation of densely connected biclusters (DCB).
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--
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---------------------------------------------------------------------------
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module DCB.DCB (preprocess, maxDCB, step) where
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module DCB.DCB (preprocess, maxDCB, step, expand) where
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import Util
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import DCB.Structures
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import DCB.IO
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@ -74,11 +75,18 @@ instance (A.Shape sh, V.Unbox e) => NFData (Array A.U sh e) where
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{-# INLINE rnf #-}
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-- | Calculates all maximum DCB. A maximum DCB is a densely connected bicluster that cannot be
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-- expanded by any additional node without breaking the constraints.
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-- | Calculates all maximum DCB for the input seed graphs. A maximum DCB is a densely
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-- connected bicluster that cannot be expanded by any additional node without breaking
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-- the constraints.
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--
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-- This function does return the seed graphs themselves if they cannot be expanded.
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maxDCB :: [Graph] -> Adj -> Attr -> Density -> MaxDivergence -> Int -> [Graph]
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maxDCB :: [Graph] -- ^ seed graphs
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-> Adj -- ^ global adjacency matrix of all nodes
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-> Attr -- ^ global attribute matrix
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-> Density -- ^ required minimum graph’s density
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-> MaxDivergence -- ^ allowed divergence per attribute
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-> Int -- ^ required number of consistent attributes
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-> [Graph]
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maxDCB [] _ _ _ _ _ = []
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maxDCB gs adj attr dens maxDiv minHit =
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let next = L.map (expand adj attr dens maxDiv minHit) gs +|| (parBuffer 1000 rdeepseq)
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@ -90,20 +98,34 @@ maxDCB gs adj attr dens maxDiv minHit =
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-- append maximum solutions of prospective function calls and maximum solutions of this iteration
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-- | creates a step in iteration.
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-- Basically calls expand for every Graph left in our List of interesting Graphs
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-- and returns the expanded ones.
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step :: [Graph] -> Adj -> Attr -> Density -> MaxDivergence -> Int -> [Graph]
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-- | Yields all DCB that arise by adding one single node to any of the given seed graphs.
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--
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-- Basically calls 'expand' for every input graph and returns a list of the expanded ones.
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-- Each graph only contains once within the resulting list.
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step :: [Graph]
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-> Adj -- ^ global adjacency matrix of all nodes
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-> Attr -- ^ global attribute matrix
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-> Density -- ^ required minimum graph’s density
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-> MaxDivergence -- ^ allowed divergence per attribute
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-> Int -- ^ required number of consistent attributes
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-> [Graph]
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step gs@((ind,_,_):_) a b c d e = traceEvent ("step from " P.++ show (A.extent ind) ) $
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filterLayer $ concat $ map (expand a b c d e ) gs
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+|| (parBuffer 1000 rdeepseq)
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-- TODO: remove @((ind,_,_):_) for exhaustive pattern
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-- TODO: remove @((ind,_,_):_) for exhaustive pattern, ind only needed for traceEvent
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-- | calculates all possible additions to one Graph, yielding a list of valid expansions
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-- i.e. constraint a == Just Constraints for all returned Graphs
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expand :: Adj -> Attr -> Density -> MaxDivergence -> Int -> Graph -> [Graph]
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-- | Calculates all possible additions to one Graph, yielding a list of valid DCB
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-- that fulfill all DCB constraints.
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--
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expand :: Adj -- ^ global adjacency matrix of all nodes
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-> Attr -- ^ global attribute matrix
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-> Density -- ^ required minimum graph’s density
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-> MaxDivergence -- ^ allowed divergence per attribute
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-> Int -- ^ required number of consistent attributes
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-> Graph -- ^ graph to expand
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-> [Graph]
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expand adj attr d div req g@(ind,_,_) = --trace ("expanding graph "P.++ B.unpack (outputGraph [g]))
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mapMaybe (addPoint adj attr d div req g)
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(V.toList $ V.findIndices (==True) $ A.toUnboxed $ addablePoints adj g)
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@ -231,7 +253,7 @@ addPoint :: Adj -- ^ global adjacency matrix of all nodes
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-> Attr -- ^ global attribute matrix
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-> Density -- ^ required minimum graph’s density
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-> MaxDivergence -- ^ allowed divergence per attribute
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-> Int -- ^ equired number of consistent attributes
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-> Int -- ^ required number of consistent attributes
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-> Graph -- ^ base graph
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-> Int -- ^ node to extend base graph by
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-> Maybe Graph
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@ -1,5 +1,7 @@
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{-# LANGUAGE OverlappingInstances #-}
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{-# LANGUAGE OverlappingInstances #-}
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{-# LANGUAGE TypeSynonymInstances #-}
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-- | Functions to transform graphs and DCBs into text.
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module DCB.IO where
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import Control.Parallel.Strategies
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@ -15,14 +17,14 @@ import Util
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-- | creates a default-formatted output with \",\" in between elements
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-- and \"\\n\" in between dimensions
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-- | creates a default-formatted output with @,@ in between elements
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-- and @\\n@ in between dimensions
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--
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-- calls '_outputArray' with preset properties
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outputArray :: (Unbox a, Show a) => Array U DIM2 a -> B.ByteString
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outputArray a = _outputArray a "\t" "\n"
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-- | creates a formatted output from a DIM2 repa-Array
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-- | creates a formatted output from a 'DIM2' repa-'Data.Array.Repa.Array'
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--
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-- * First String is the between-element-separator
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--
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@ -40,8 +42,8 @@ _outputArray a itt lt = B.concat $
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| sj-1 == j = show (a!(ix2 i j)) -- no "," for last one..
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| otherwise = show (a!(ix2 i j)) ++ itt ++ (_outputArray'' shape i (j+1) a itt)
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-- | creates a default-formatted output with \",\" in between elements
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-- and \"\\n\" in between dimensions
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-- | creates a default-formatted output with @,@ in between elements
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-- and @\\n@ in between dimensions
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--
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-- calls '_outputArray' with preset properties
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outputGraph :: [Graph] -> B.ByteString
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@ -54,7 +56,7 @@ outputGraph gs = B.concat $ L.map (flipto3 _outputGraph "," "\n") (L.sort gs)
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--
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-- * Second String is the between-dimensions-separator
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--
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-- Example Output with \",\" and \"\\n\":
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-- Example Output with @,@ and @\\n@:
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--
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-- > Density:
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-- > 0.7619047619047619
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@ -1,6 +1,8 @@
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{-# LANGUAGE FlexibleInstances #-}
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{-# LANGUAGE FlexibleInstances #-}
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{-# LANGUAGE OverlappingInstances #-}
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{-# LANGUAGE TypeSynonymInstances #-}
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-- | Data structures used for DCB computation.
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module DCB.Structures where
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import Data.Array.Repa as A hiding ((++))
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@ -19,7 +21,7 @@ type Attr = Matrix A.U Double
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-- | Adjacency-Matrix
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type Adj = Matrix A.U Int8
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-- | Matrix storing the extent of a 'Graph'’s constraints fulfillment.
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-- | 'Matrix' storing the extent of a 'Graph'’s constraints fulfillment.
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-- It stores the minimum (zeroth column) and maximum (first column) value of all
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-- the 'Graph'’s nodes per attribute.
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-- The 'Vector' stores values of @1@ if the bounds are within the allowed range
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137
src/Main.hs
137
src/Main.hs
@ -1,4 +1,4 @@
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{-# LANGUAGE BangPatterns #-}
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{-# LANGUAGE BangPatterns #-}
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{-# LANGUAGE CPP #-}
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{-# LANGUAGE DoAndIfThenElse #-}
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{-# LANGUAGE OverlappingInstances #-}
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@ -14,8 +14,66 @@
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-- Portability :
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--
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-- |
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-- Program to find densely connected biclusters (DCB) in an undirected graph.
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-- DCB are highly connected subgraphs whose nodes share similar attributes.
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--
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-----------------------------------------------------------------------------
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-- Each node of the source graph is linked with a table of attribute values
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-- and for a certain number of attributes all nodes of a DCB must have
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-- values within a specified range. Secondly, the density of the
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-- subgraph must not exceed a threshold.
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--
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-- /Using the program:/
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--
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-- >>> hgraph [<tokens>]... <adjacency> <attribute> <constraints>
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--
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-- The program expects 3 mandatory arguments for an input graph of size /n/:
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--
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-- (1) The plain text file that contains the adjacency matrix of the source
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-- graph. The file must contain /n/ rows where each row consists of
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-- exactly /n/ characters that are either @1@ if there exists an edge
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-- between two nodes or @0@ otherwise.
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-- The matrix must be symmetric.
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--
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-- (2) The plain text file that contains the attributes linked to the nodes.
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-- It must consist of /n/ rows.
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-- Each row consists of /a/ floating point numbers separated by tab
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-- characters @\\t@ where /a/ is the number of attributes.
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-- The /b/-th value in the /v/-th row is the attribute value of the /b/-th
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-- attribute linked to the /v/-th node.
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--
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-- (3) The plain text file that contains the algorithm’s parameters. This file
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-- contains 3 rows:
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--
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-- * The first row solely contains the minimum density for a DCB as floating
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-- point number
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--
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-- * The second row solely contains the minimum number of matching
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-- attributes for a DCB as an integer value.
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--
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-- * The third row contains the tolerances for each attribute as floating
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-- point values separated by tab characters @\\t@ where the /b/-th value
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-- is the tolerated range for the DCB’s node’s values of the /b/-th
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-- attribute.
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--
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-- Rows are separated by newline characters @\\n@ and all floating point values
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-- use dots as decimal separator.
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--
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-- You may prepend the mandatory parameters with certain tokens:
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--
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-- * @-h@ or @--help@ to display help (all following parameters are ignored)
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--
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-- * @-t@ or @--time@ to measure and display computation time
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--
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-- To enable multicore computation you need to append RTS options to the
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-- program call as specified in the GHC manual.
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--
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-- <http://www.haskell.org/ghc/docs/latest/html/users_guide/using-smp.html#parallel-options>
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--
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-- Running on 4 threads:
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--
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-- >>> hgraph adjacency_matrix.adj attribute_matrix.attr properties.p +RTS -N4
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--
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----------------------------------------------------------------------------
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module Main where
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@ -50,18 +108,19 @@ import System.Environment
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import System.Exit (exitFailure, exitSuccess)
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--import Test.QuickCheck.All (quickCheckAll)
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data Params = Params { density :: Double
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, matches :: Int
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, range :: [Double]
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-- | All secondary parameters that must be passed to the program packed into one data type.
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data Params = Params { density :: Double -- ^ minimum density of a bicluster
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, matches :: Int -- ^ required amount of matching attributes
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, range :: [Double] -- ^ allowed divergence for each attribute
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} deriving (Show,Eq)
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instance NFData Params
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-- | Parses a row of the adjacency matrix of a graph. The consistancy of line lengths is not tested
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-- | Parses a row of the adjacency matrix of a graph. The consistency of line lengths is not tested
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-- by this function! In case of a successfull parse a 'Left' ('Vector' a) is returned, otherwise a
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-- 'Right ByteString' containing an error message.
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-- 'Right' 'ByteString' containing an error message.
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--
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-- > 10101
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-- > 01010
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-- > 00100
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@ -69,6 +128,7 @@ instance NFData Params
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-- > 10101
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--
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-- * Valid Values: @0@, @1@
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--
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-- * any invalid value raises an error
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parseAdjMat :: (Num a, Unbox a) => ByteString -> Either (V.Vector a) ByteString
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parseAdjMat input =
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@ -77,7 +137,7 @@ parseAdjMat input =
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result = V.unfoldrN size parseAdjMat' input
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in
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if size == V.length result then Left result
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else Right $ B.append (B.pack "(adjecency)cannot parse ") input
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else Right $ B.append (B.pack "(adjacency)cannot parse ") input
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where
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--parseAdjMat' :: ByteString -> Maybe (a, ByteString)
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parseAdjMat' input =
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@ -85,26 +145,30 @@ parseAdjMat input =
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case c of
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'0' -> Just (0, B.tail input)
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'1' -> Just (1, B.tail input)
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_ -> if isSpace c then parseAdjMat' (B.tail input)
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else Nothing
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_ -> Nothing
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-- | Tests if a parse result is considered valid.
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-- | Tests if a parse result @(a, 'ByteString')@ is considered valid where @a@ is the parsed object
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-- and the 'ByteString' is the remaining string that could not be parsed.
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testParse :: Maybe (a, ByteString) -> Maybe a
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testParse Nothing = Nothing
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testParse (Just (a, rem)) = if emptyLine rem then Just a else Nothing
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-- | Parses a row of the attribute matrix of a graph. The consistancy of line lengths is not tested
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-- by this function! In case of a successfull parse a 'Left [a]' is returned, otherwise a
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-- 'Right ByteString' containing an error message.
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-- | Parses a row of the attribute matrix of a graph. The consistency of line lengths is not tested
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-- by this function! In case of a successfull parse a @'Left' [a]@ is returned, otherwise a
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-- @'Right' 'ByteString'@ containing the error message.
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--
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-- > 1 2.3
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-- > -1 2.1
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-- > 4 2.7
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-- > 2.2 -3e-4
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-- > 3 2.3
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--
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-- * Valid: Doubles divided by specified delimter
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-- * Valid: 'Double's divided by specified delimter
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--
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-- * any invalid value raises an error
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parseAttr :: Char -> ByteString -> Either [Double] ByteString
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parseAttr :: Char -- ^ delimiter
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-> ByteString -- ^ text to parse
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-> Either [Double] ByteString
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parseAttr delim input = parseAttr' (B.split delim input)
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where parseAttr' :: [ByteString] -> Either [Double] ByteString
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parseAttr' (row:rem) =
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@ -116,10 +180,18 @@ parseAttr delim input = parseAttr' (B.split delim input)
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parseAttr' [] = Left []
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-- | Parses parameter file.
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-- First line: Density (Double)
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-- Second line: requied matches (Int)
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-- Third line is the tolerance for each attribute (Double values)
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parseParams :: Char -> [ByteString] -> Either Params ByteString
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--
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-- * First line: 'Density'
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--
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-- * Second line: requied matches ('Int')
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--
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-- * Third line is the tolerance for each attribute ('Double' values), see 'parseAttr'
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--
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-- In case of an error during the parsing a @'Right' 'ByteString'@ containing the error
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-- message is returned instead of a @'Left' 'Params'@
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parseParams :: Char -- ^delimiter
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-> [ByteString] -- ^ text to parse
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-> Either Params ByteString
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parseParams delim input
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| length input /= 3 = Right $ B.pack ("(params)amount of lines does not match (expected 3, got "
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++ show (length input) ++ ")")
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@ -134,7 +206,7 @@ parseParams delim input
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_ -> Right $ B.append (B.pack "(param - density)cannot parse ") (head input)
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-- | checks if a given Text is empty (Empty String, whitespaces)
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-- | Checks if a given text is empty (empty string, whitespaces).
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emptyLine :: ByteString -> Bool
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emptyLine a
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| B.null a = True
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@ -171,21 +243,21 @@ doCalculation adj attr p =
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doAll' gs a b c d e = gs ++ doAll' (step gs a b c d e) a b c d e
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--}
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-- | gets the length of the 'Left a'.
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-- | Gets the length of the @'Left' [a]@.
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--
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-- @0@ if Left a empty or no valid constructor.
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-- @0@ if @[a]@ in @Left [a]@ is empty or it is a 'Right' value.
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getLength :: Either [a] b -> Int
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getLength (Left a) = length a
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getLength (Right _) = 0
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-- | gets the length of the Left ('Vector a').
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-- | Gets the length of the @'Left' ('Vector' v)@.
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--
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-- @0@ if Left a empty or no valid constructor.
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-- @0@ if @a@ in 'Left a' is empty or it is a 'Right' value.
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getLengthV :: (Unbox a) => Either (V.Vector a) b -> Int
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getLengthV (Left a) = V.length a
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getLengthV (Right _) = 0
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-- | prints the Help and exits
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-- | Prints the help and exits.
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showHelp :: IO ()
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showHelp = do
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putStrLn $ "Usage: hgraph [<tokens>]... <adjacency> <attribute> <constraints>\n"++
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@ -209,7 +281,7 @@ showHelp = do
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"\n"
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exitSuccess
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-- | checks if the submitted Text is empty. If not it will be printed out and the program aborts
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-- | Checks if the submitted text is empty. If not it will be printed out and the program aborts.
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checkError :: ByteString -> IO ()
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checkError a
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| emptyLine a = return ()
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@ -221,7 +293,7 @@ checkError a
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-- changed to return () to disable Debug.
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debug a = return () --putStrLn a
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-- | Removes one trailing carriage return character @\\r@ if existant.
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-- | Removes one trailing carriage return character @\\r@ if existent.
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removeCarriageReturn :: ByteString -> ByteString
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removeCarriageReturn input =
|
||||
if B.last input == '\r' then B.init input
|
||||
@ -240,6 +312,7 @@ removeCarriageReturn input =
|
||||
-- The returned tupel contains the existance of the /time/ token,
|
||||
-- existance of the /help/ token and all remaining file paths in that
|
||||
-- order.
|
||||
--
|
||||
-- >>> processTokens ["--time", "-t", "foo.txt"] == (True, False, ["foo.txt"])
|
||||
-- >>> processTokens ["-tx", "--help"] == (False, False, ["-tx", "--help"])
|
||||
processTokens :: [String] -> (Bool, Bool, [FilePath])
|
||||
@ -310,20 +383,20 @@ main = do
|
||||
if adjLines /= attrLines then
|
||||
checkError $ B.pack $ "Adjacency Matrix size "++ show adjLines ++
|
||||
" differs from Attribute Matrix " ++ show attrLines ++
|
||||
".\n"
|
||||
"."
|
||||
else return ()
|
||||
|
||||
if adjLines /= adjNum then
|
||||
checkError $ B.pack $ "Adjacency Matrix is not square.\n" ++
|
||||
"Read format is " ++ show adjLines ++
|
||||
"x" ++ show adjNum ++ ".\n"
|
||||
"x" ++ show adjNum ++ "."
|
||||
else return ()
|
||||
|
||||
-- it is accaptable if the parameters file contains more attributes than the attribute matrix
|
||||
if attrParams < attrNum then
|
||||
checkError $ B.pack $ "Attribute Matrix format does not match Parameter.\n" ++
|
||||
"Attribute Matrix has " ++ show attrNum ++ " attributes.\n" ++
|
||||
"Parameters implicate" ++ show attrParams ++ " attributes.\n"
|
||||
"Parameters implicate " ++ show attrParams ++ " attributes."
|
||||
else return ()
|
||||
|
||||
----- EXTRACT MATRICES
|
||||
|
14
src/Util.hs
14
src/Util.hs
@ -1,8 +1,8 @@
|
||||
-- | A collection of utility functions for working with functions, lists and strings.
|
||||
module Util where
|
||||
|
||||
import Control.Parallel.Strategies
|
||||
import qualified Data.Map as Map
|
||||
import qualified Data.Set as Set
|
||||
|
||||
-- | Move first argument to first place (for style uniformity)
|
||||
flip1 :: (a -> b) -> (a -> b)
|
||||
@ -83,6 +83,8 @@ infixl 1 +||
|
||||
(+||) :: a -> Strategy a -> a
|
||||
a +|| b = a `using` b
|
||||
|
||||
-- | The function 'appendS' appends the string representation of the third element
|
||||
-- to the second element followed by the first element as separator string.
|
||||
appendS :: (Show a) => String -> String -> a -> String
|
||||
appendS sep a b = (a ++ show b) ++ sep
|
||||
|
||||
@ -106,8 +108,8 @@ remDupsBy f (l:ls) = l:(remDups' l ls)
|
||||
|
||||
-- When removing duplicates, the first function assigns the input to a bucket,
|
||||
-- the second function checks whether it is already in the bucket (linear search).
|
||||
-- | /O(n^2)/ Removes duplicate elements from a list. Performs better than
|
||||
-- 'Prelude.nub' by exploiting features of the 'Ord' class.
|
||||
-- | /O(n^2)./ Removes duplicate elements from a list. Performs better than
|
||||
-- 'Data.List.nub' by exploiting features of the 'Ord' class.
|
||||
ordNubBy :: (Ord b) => (a -> b) -> (a -> a -> Bool) -> [a] -> [a]
|
||||
ordNubBy p f l = go Map.empty l
|
||||
where
|
||||
@ -124,14 +126,14 @@ ordNubBy p f l = go Map.empty l
|
||||
elem_by eq y (x:xs) = y `eq` x || elem_by eq y xs
|
||||
|
||||
|
||||
-- | Returns weather a string only contains whitespace or not.
|
||||
-- | Returns whether a string only contains whitespace characters or not.
|
||||
isWhitespace :: String -> Bool
|
||||
isWhitespace "" = True
|
||||
isWhitespace (a:as) = (a `elem` " \r\n\t") && isWhitespace as
|
||||
|
||||
-- | Tests whether an 'Either' type is 'Left'.
|
||||
isLeft :: Either a b -> Bool
|
||||
isLeft a = case a of Left _ -> True; _ -> False
|
||||
isLeft a = either (\e -> True) (\e -> False) a
|
||||
|
||||
-- | Tests whether an 'Either' type is 'Right'.
|
||||
isRight :: Either a b -> Bool
|
||||
@ -139,7 +141,7 @@ isRight = not . isLeft
|
||||
|
||||
-- | The 'part' function takes a predicate and a list of tuples and returns
|
||||
-- the pair of lists of left elements which do and right elements which do not satisfy the
|
||||
-- predicate, respectively; i.e.,
|
||||
-- predicate, respectively; i. e.,
|
||||
--
|
||||
-- > part (\a b -> elem a b) [(1, [1, 3]), (2, [3, 4]), (0, [0, 5])] == ([1, 0], [[3, 4]])
|
||||
part :: (a -> b -> Bool) -> [(a, b)] -> ([a], [b])
|
||||
|
Loading…
Reference in New Issue
Block a user