BiobaseXNA 0.9.1.0 → 0.9.1.1

raw patch · 2 files changed

+57/−1 lines, 2 files

Files

• Biobase/Primary/Bounds.hs +55/−0
• BiobaseXNA.cabal +2/−1

@@ -0,0 +1,55 @@++-- | A special class of bounds for RNA/pair encodings that are used to index+-- into tables. We typically encode more in the alphabets than we want to use+-- to index, so in order to keep things simple, we have specialized bounds.++module Biobase.Primary.Bounds where++{-++-- | 'minNormal' and 'maxNormal' encode for, say, ACGU; while 'minExtended' and+-- 'maxExtended' would allow 'N' as well. See Biobase.RNA and+-- Biobase.RNA.ViennaPair for instances.++class Bounded a => Bounds a where+  minNormal :: a+  maxNormal :: a+  minExtended :: a+  maxExtended :: a++++-- * Instances for tuples of size 2-6++instance (Bounds a, Bounds b) => Bounds (a,b) where+  minNormal = (minNormal, minNormal)+  maxNormal = (maxNormal, maxNormal)+  minExtended = (minExtended, minExtended)+  maxExtended = (maxExtended, maxExtended)++instance (Bounds a, Bounds b, Bounds c) => Bounds (a,b,c) where+  minNormal = (minNormal, minNormal, minNormal)+  maxNormal = (maxNormal, maxNormal, maxNormal)+  minExtended = (minExtended, minExtended, minExtended)+  maxExtended = (maxExtended, maxExtended, maxExtended)++instance (Bounds a, Bounds b, Bounds c, Bounds d) => Bounds (a,b,c,d) where+  minNormal = (minNormal, minNormal, minNormal, minNormal)+  maxNormal = (maxNormal, maxNormal, maxNormal, maxNormal)+  minExtended = (minExtended, minExtended, minExtended, minExtended)+  maxExtended = (maxExtended, maxExtended, maxExtended, maxExtended)++instance (Bounds a, Bounds b, Bounds c, Bounds d, Bounds e) => Bounds (a,b,c,d,e) where+  minNormal = (minNormal, minNormal, minNormal, minNormal, minNormal)+  maxNormal = (maxNormal, maxNormal, maxNormal, maxNormal, maxNormal)+  minExtended = (minExtended, minExtended, minExtended, minExtended, minExtended)+  maxExtended = (maxExtended, maxExtended, maxExtended, maxExtended, maxExtended)++instance (Bounds a, Bounds b, Bounds c, Bounds d, Bounds e, Bounds f) => Bounds (a,b,c,d,e,f) where+  minNormal = (minNormal, minNormal, minNormal, minNormal, minNormal, minNormal)+  maxNormal = (maxNormal, maxNormal, maxNormal, maxNormal, maxNormal, maxNormal)+  minExtended = (minExtended, minExtended, minExtended, minExtended, minExtended, minExtended)+  maxExtended = (maxExtended, maxExtended, maxExtended, maxExtended, maxExtended, maxExtended)++-}+

@@ -1,5 +1,5 @@ name:           BiobaseXNA-version:        0.9.1.0+version:        0.9.1.1 author:         Christian Hoener zu Siederdissen maintainer:     choener@bioinf.uni-leipzig.de homepage:       http://www.bioinf.uni-leipzig.de/~choener/@@ -64,6 +64,7 @@   exposed-modules:     Biobase.Primary     Biobase.Primary.AA+    Biobase.Primary.Bounds     Biobase.Primary.Hashed     Biobase.Primary.IUPAC     Biobase.Primary.Letter