- Fix build problem caused by the recent textproc/hs-tagsoup update

- Port PORTREVISION
- Tidy up pkg-descr

Reported by:	LambdaBSD-exp
Approved by:	jacula (maintainer)

science/hs-bio/Makefile

@@ -7,6 +7,7 @@
 
 PORTNAME=	bio
 PORTVERSION=	0.4
+PORTREVISION=	1
 CATEGORIES=	science haskell
 
 MAINTAINER=	jacula@gmail.com

science/hs-bio/files/patch-Bio__Alignment__BlastXML.hs

@@ -0,0 +1,61 @@
+--- ./Bio/Alignment/BlastXML.hs.orig	2009-06-16 12:30:17.000000000 +0200
++++ ./Bio/Alignment/BlastXML.hs	2010-05-20 12:08:16.000000000 +0200
+@@ -20,6 +20,8 @@
+ import Control.Parallel
+ import Data.List (isPrefixOf)
+ 
++type STag = Tag String
++
+ -- | Parse BLAST results in XML format
+ readXML :: FilePath -> IO [BlastResult]
+ readXML fp = do 
+@@ -38,7 +40,7 @@
+                   in  rest `par` first : if null rest then [] else breaks p rest
+ breaks _ []     = []
+ 
+-getFrom :: [Tag] -> String -> String
++getFrom :: [STag] -> String -> String
+ getFrom list tag = let xs = sections (isTagOpenName tag) list 
+                    in if null xs || null (head xs) || (null . drop 1 . head) xs 
+                       then error ("Couldn't find tag '"++show tag++"' in\n"++showSome list)
+@@ -47,11 +49,11 @@
+                              x -> error ("Unexpeced tag: "++ show x)
+ 
+ -- Use pattern match since 'length' is strict, defeating the purpose.
+-showSome :: [Tag] -> String
++showSome :: [STag] -> String
+ showSome a@(_:_:_:_:_:_:_) = (init . show . take 5 $ a)++" ... ]"
+ showSome a                 = show a
+ 
+-xml2br :: [Tag] -> [[Tag]] -> BlastResult
++xml2br :: [STag] -> [[STag]] -> BlastResult
+ xml2br h is = BlastResult { blastprogram = get "BlastOutput_program"
+                           , blastversion = bv
+                           , blastdate = bd 
+@@ -64,7 +66,7 @@
+     where (bv,bd) = B.break (=='[') $ get "BlastOutput_version"
+           get = B.pack . getFrom h
+ 
+-iter2rec :: [[Tag]] -> BlastRecord
++iter2rec :: [[STag]] -> BlastRecord
+ iter2rec (i:hs) = BlastRecord 
+               { query = B.pack $ get "Iteration_query-def"
+               , qlength = read $ get "Iteration_query-len"
+@@ -73,7 +75,7 @@
+     where get = getFrom i
+ iter2rec [] = error "iter2rec: got empty list of sections!"
+ 
+-hit2hit :: [Tag] -> BlastHit
++hit2hit :: [STag] -> BlastHit
+ hit2hit hs = BlastHit 
+              { subject = B.pack $ get "Hit_def"
+              , slength = read $ get "Hit_len"
+@@ -82,7 +84,7 @@
+     where get = getFrom hs
+ 
+ 
+-hsp2match :: [Tag] -> BlastMatch
++hsp2match :: [STag] -> BlastMatch
+ hsp2match ms = BlastMatch
+                { bits   = read $ get "Hsp_bit-score"
+                , e_val  = read $ get "Hsp_evalue"

science/hs-bio/pkg-descr

@@ -1,5 +1,6 @@
-This is a collection of Haskell data structures and algorithms useful for
-building bioinformatics-related tools and utilities.
+This is a collection of Haskell data structures and algorithms useful
+for building bioinformatics-related tools and utilities.
+
 Current list of features includes: a Sequence data type supporting
 protein and nucleotide sequences and conversion between them.