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haddock documentation

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tpajenka
2014-04-11 20:23:12 +02:00
parent 3555ed5073
commit 45528934b7
6 changed files with 198 additions and 69 deletions
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147
src/Main.hs
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@@ -1,4 +1,4 @@
{-# LANGUAGE BangPatterns #-}
{-# LANGUAGE BangPatterns #-}
{-# LANGUAGE CPP #-}
{-# LANGUAGE DoAndIfThenElse #-}
{-# LANGUAGE OverlappingInstances #-}
@@ -14,8 +14,66 @@
-- Portability :
--
-- |
-- Program to find densely connected biclusters (DCB) in an undirected graph.
-- DCB are highly connected subgraphs whose nodes share similar attributes.
--
-- Each node of the source graph is linked with a table of attribute values
-- and for a certain number of attributes all nodes of a DCB must have
-- values within a specified range. Secondly, the density of the
-- subgraph must not exceed a threshold.
--
-----------------------------------------------------------------------------
-- /Using the program:/
--
-- >>> hgraph [<tokens>]... <adjacency> <attribute> <constraints>
--
-- The program expects 3 mandatory arguments for an input graph of size /n/:
--
-- (1) The plain text file that contains the adjacency matrix of the source
-- graph. The file must contain /n/ rows where each row consists of
-- exactly /n/ characters that are either @1@ if there exists an edge
-- between two nodes or @0@ otherwise.
-- The matrix must be symmetric.
--
-- (2) The plain text file that contains the attributes linked to the nodes.
-- It must consist of /n/ rows.
-- Each row consists of /a/ floating point numbers separated by tab
-- characters @\\t@ where /a/ is the number of attributes.
-- The /b/-th value in the /v/-th row is the attribute value of the /b/-th
-- attribute linked to the /v/-th node.
--
-- (3) The plain text file that contains the algorithm’s parameters. This file
-- contains 3 rows:
--
-- * The first row solely contains the minimum density for a DCB as floating
-- point number
--
-- * The second row solely contains the minimum number of matching
-- attributes for a DCB as an integer value.
--
-- * The third row contains the tolerances for each attribute as floating
-- point values separated by tab characters @\\t@ where the /b/-th value
-- is the tolerated range for the DCB’s node’s values of the /b/-th
-- attribute.
--
-- Rows are separated by newline characters @\\n@ and all floating point values
-- use dots as decimal separator.
--
-- You may prepend the mandatory parameters with certain tokens:
--
-- * @-h@ or @--help@ to display help (all following parameters are ignored)
--
-- * @-t@ or @--time@ to measure and display computation time
--
-- To enable multicore computation you need to append RTS options to the
-- program call as specified in the GHC manual.
--
-- <http://www.haskell.org/ghc/docs/latest/html/users_guide/using-smp.html#parallel-options>
--
-- Running on 4 threads:
--
-- >>> hgraph adjacency_matrix.adj attribute_matrix.attr properties.p +RTS -N4
--
----------------------------------------------------------------------------
module Main where
@@ -50,18 +108,19 @@ import System.Environment
import System.Exit (exitFailure, exitSuccess)
--import Test.QuickCheck.All (quickCheckAll)
data Params = Params { density :: Double
, matches :: Int
, range :: [Double]
-- | All secondary parameters that must be passed to the program packed into one data type.
data Params = Params { density :: Double -- ^ minimum density of a bicluster
, matches :: Int -- ^ required amount of matching attributes
, range :: [Double] -- ^ allowed divergence for each attribute
} deriving (Show,Eq)
instance NFData Params
-- | Parses a row of the adjacency matrix of a graph. The consistancy of line lengths is not tested
-- | Parses a row of the adjacency matrix of a graph. The consistency of line lengths is not tested
-- by this function! In case of a successfull parse a 'Left' ('Vector' a) is returned, otherwise a
-- 'Right ByteString' containing an error message.
-- 'Right' 'ByteString' containing an error message.
--
-- > 10101
-- > 01010
-- > 00100
@@ -69,6 +128,7 @@ instance NFData Params
-- > 10101
--
-- * Valid Values: @0@, @1@
--
-- * any invalid value raises an error
parseAdjMat :: (Num a, Unbox a) => ByteString -> Either (V.Vector a) ByteString
parseAdjMat input =
@@ -77,7 +137,7 @@ parseAdjMat input =
result = V.unfoldrN size parseAdjMat' input
in
if size == V.length result then Left result
else Right $ B.append (B.pack "(adjecency)cannot parse ") input
else Right $ B.append (B.pack "(adjacency)cannot parse ") input
where
--parseAdjMat' :: ByteString -> Maybe (a, ByteString)
parseAdjMat' input =
@@ -85,26 +145,30 @@ parseAdjMat input =
case c of
'0' -> Just (0, B.tail input)
'1' -> Just (1, B.tail input)
_ -> if isSpace c then parseAdjMat' (B.tail input)
else Nothing
_ -> Nothing
-- | Tests if a parse result is considered valid.
-- | Tests if a parse result @(a, 'ByteString')@ is considered valid where @a@ is the parsed object
-- and the 'ByteString' is the remaining string that could not be parsed.
testParse :: Maybe (a, ByteString) -> Maybe a
testParse Nothing = Nothing
testParse (Just (a, rem)) = if emptyLine rem then Just a else Nothing
-- | Parses a row of the attribute matrix of a graph. The consistancy of line lengths is not tested
-- by this function! In case of a successfull parse a 'Left [a]' is returned, otherwise a
-- 'Right ByteString' containing an error message.
-- | Parses a row of the attribute matrix of a graph. The consistency of line lengths is not tested
-- by this function! In case of a successfull parse a @'Left' [a]@ is returned, otherwise a
-- @'Right' 'ByteString'@ containing the error message.
--
-- > 1 2.3
-- > -1 2.1
-- > 4 2.7
-- > 2.2 -3e-4
-- > 3 2.3
--
-- * Valid: Doubles divided by specified delimter
-- * Valid: 'Double's divided by specified delimter
--
-- * any invalid value raises an error
parseAttr :: Char -> ByteString -> Either [Double] ByteString
parseAttr :: Char -- ^ delimiter
-> ByteString -- ^ text to parse
-> Either [Double] ByteString
parseAttr delim input = parseAttr' (B.split delim input)
where parseAttr' :: [ByteString] -> Either [Double] ByteString
parseAttr' (row:rem) =
@@ -116,10 +180,18 @@ parseAttr delim input = parseAttr' (B.split delim input)
parseAttr' [] = Left []
-- | Parses parameter file.
-- First line: Density (Double)
-- Second line: requied matches (Int)
-- Third line is the tolerance for each attribute (Double values)
parseParams :: Char -> [ByteString] -> Either Params ByteString
--
-- * First line: 'Density'
--
-- * Second line: requied matches ('Int')
--
-- * Third line is the tolerance for each attribute ('Double' values), see 'parseAttr'
--
-- In case of an error during the parsing a @'Right' 'ByteString'@ containing the error
-- message is returned instead of a @'Left' 'Params'@
parseParams :: Char -- ^delimiter
-> [ByteString] -- ^ text to parse
-> Either Params ByteString
parseParams delim input
| length input /= 3 = Right $ B.pack ("(params)amount of lines does not match (expected 3, got "
++ show (length input) ++ ")")
@@ -134,7 +206,7 @@ parseParams delim input
_ -> Right $ B.append (B.pack "(param - density)cannot parse ") (head input)
-- | checks if a given Text is empty (Empty String, whitespaces)
-- | Checks if a given text is empty (empty string, whitespaces).
emptyLine :: ByteString -> Bool
emptyLine a
| B.null a = True
@@ -171,21 +243,21 @@ doCalculation adj attr p =
doAll' gs a b c d e = gs ++ doAll' (step gs a b c d e) a b c d e
--}
-- | gets the length of the 'Left a'.
-- | Gets the length of the @'Left' [a]@.
--
-- @0@ if Left a empty or no valid constructor.
-- @0@ if @[a]@ in @Left [a]@ is empty or it is a 'Right' value.
getLength :: Either [a] b -> Int
getLength (Left a) = length a
getLength (Right _) = 0
-- | gets the length of the Left ('Vector a').
-- | Gets the length of the @'Left' ('Vector' v)@.
--
-- @0@ if Left a empty or no valid constructor.
-- @0@ if @a@ in 'Left a' is empty or it is a 'Right' value.
getLengthV :: (Unbox a) => Either (V.Vector a) b -> Int
getLengthV (Left a) = V.length a
getLengthV (Right _) = 0
-- | prints the Help and exits
-- | Prints the help and exits.
showHelp :: IO ()
showHelp = do
putStrLn $ "Usage: hgraph [<tokens>]... <adjacency> <attribute> <constraints>\n"++
@@ -209,7 +281,7 @@ showHelp = do
"\n"
exitSuccess
-- | checks if the submitted Text is empty. If not it will be printed out and the program aborts
-- | Checks if the submitted text is empty. If not it will be printed out and the program aborts.
checkError :: ByteString -> IO ()
checkError a
| emptyLine a = return ()
@@ -221,7 +293,7 @@ checkError a
-- changed to return () to disable Debug.
debug a = return () --putStrLn a
-- | Removes one trailing carriage return character @\\r@ if existant.
-- | Removes one trailing carriage return character @\\r@ if existent.
removeCarriageReturn :: ByteString -> ByteString
removeCarriageReturn input =
if B.last input == '\r' then B.init input
@@ -237,11 +309,12 @@ removeCarriageReturn input =
-- invalid tokens) that parameter and all following parameters are
-- believed to be file paths.
--
-- 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"])
-- 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])
processTokens [] = (False, False, [])
-- single token with prefix "--"
@@ -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