BiobaseInfernal 0.7.0.1 → 0.7.1.0
raw patch · 2 files changed
+10/−5 lines, 2 filesdep +repadep ~BiobaseXNAdep ~PrimitiveArrayPVP: major bump suggested
API removals or changes: PVP suggests a major version bump
Dependencies added: repa
Dependency ranges changed: BiobaseXNA, PrimitiveArray
API changes (from Hackage documentation)
- Biobase.SElab.CM: accession :: Lens CM CM (Accession Rfam) (Accession Rfam)
+ Biobase.SElab.CM: accession :: Lens' CM (Accession Rfam)
- Biobase.SElab.CM: emits :: Lens State State Emits Emits
+ Biobase.SElab.CM: emits :: Lens' State Emits
- Biobase.SElab.CM: gathering :: Lens CM CM BitScore BitScore
+ Biobase.SElab.CM: gathering :: Lens' CM BitScore
- Biobase.SElab.CM: hmm :: Lens CM CM (Maybe HMM3) (Maybe HMM3)
+ Biobase.SElab.CM: hmm :: Lens' CM (Maybe HMM3)
- Biobase.SElab.CM: localBegin :: Lens CM CM (Map StateID BitScore) (Map StateID BitScore)
+ Biobase.SElab.CM: localBegin :: Lens' CM (Map StateID BitScore)
- Biobase.SElab.CM: localEnd :: Lens CM CM (Map StateID BitScore) (Map StateID BitScore)
+ Biobase.SElab.CM: localEnd :: Lens' CM (Map StateID BitScore)
- Biobase.SElab.CM: name :: Lens CM CM (Identification Rfam) (Identification Rfam)
+ Biobase.SElab.CM: name :: Lens' CM (Identification Rfam)
- Biobase.SElab.CM: nodeID :: Lens State State NodeID NodeID
+ Biobase.SElab.CM: nodeID :: Lens' State NodeID
- Biobase.SElab.CM: nodeType :: Lens State State NodeType NodeType
+ Biobase.SElab.CM: nodeType :: Lens' State NodeType
- Biobase.SElab.CM: nodes :: Lens CM CM (Map NodeID (NodeType, [StateID])) (Map NodeID (NodeType, [StateID]))
+ Biobase.SElab.CM: nodes :: Lens' CM (Map NodeID (NodeType, [StateID]))
- Biobase.SElab.CM: noiseCutoff :: Lens CM CM (Maybe BitScore) (Maybe BitScore)
+ Biobase.SElab.CM: noiseCutoff :: Lens' CM (Maybe BitScore)
- Biobase.SElab.CM: nullModel :: Lens CM CM (Vector BitScore) (Vector BitScore)
+ Biobase.SElab.CM: nullModel :: Lens' CM (Vector BitScore)
- Biobase.SElab.CM: pair :: Traversal Emits Emits [(Char, Char, BitScore)] [(Char, Char, BitScore)]
+ Biobase.SElab.CM: pair :: Traversal' Emits [(Char, Char, BitScore)]
- Biobase.SElab.CM: single :: Traversal Emits Emits [(Char, BitScore)] [(Char, BitScore)]
+ Biobase.SElab.CM: single :: Traversal' Emits [(Char, BitScore)]
- Biobase.SElab.CM: stateID :: Lens State State StateID StateID
+ Biobase.SElab.CM: stateID :: Lens' State StateID
- Biobase.SElab.CM: stateType :: Lens State State StateType StateType
+ Biobase.SElab.CM: stateType :: Lens' State StateType
- Biobase.SElab.CM: states :: Lens CM CM (Map StateID State) (Map StateID State)
+ Biobase.SElab.CM: states :: Lens' CM (Map StateID State)
- Biobase.SElab.CM: transitions :: Lens State State [(StateID, BitScore)] [(StateID, BitScore)]
+ Biobase.SElab.CM: transitions :: Lens' State [(StateID, BitScore)]
- Biobase.SElab.CM: trustedCutoff :: Lens CM CM BitScore BitScore
+ Biobase.SElab.CM: trustedCutoff :: Lens' CM BitScore
- Biobase.SElab.CM: unsorted :: Lens CM CM (Map ByteString ByteString) (Map ByteString ByteString)
+ Biobase.SElab.CM: unsorted :: Lens' CM (Map ByteString ByteString)
- Biobase.SElab.CM: version :: Lens CM CM CMVersion CMVersion
+ Biobase.SElab.CM: version :: Lens' CM CMVersion
- Biobase.SElab.HMM: acc :: Lens HMM3 HMM3 (Maybe (Accession HMM)) (Maybe (Accession HMM))
+ Biobase.SElab.HMM: acc :: Lens' HMM3 (Maybe (Accession HMM))
- Biobase.SElab.HMM: alignMap :: Lens HMM3 HMM3 Bool Bool
+ Biobase.SElab.HMM: alignMap :: Lens' HMM3 Bool
- Biobase.SElab.HMM: alph :: Lens HMM3 HMM3 Alphabet Alphabet
+ Biobase.SElab.HMM: alph :: Lens' HMM3 Alphabet
- Biobase.SElab.HMM: compo :: Lens HMM3 HMM3 [NegLogProb] [NegLogProb]
+ Biobase.SElab.HMM: compo :: Lens' HMM3 [NegLogProb]
- Biobase.SElab.HMM: cs :: Lens HMM3 HMM3 Bool Bool
+ Biobase.SElab.HMM: cs :: Lens' HMM3 Bool
- Biobase.SElab.HMM: date :: Lens HMM3 HMM3 ByteString ByteString
+ Biobase.SElab.HMM: date :: Lens' HMM3 ByteString
- Biobase.SElab.HMM: description :: Lens HMM3 HMM3 (Maybe ByteString) (Maybe ByteString)
+ Biobase.SElab.HMM: description :: Lens' HMM3 (Maybe ByteString)
- Biobase.SElab.HMM: idd :: Lens HMM3 HMM3 (Identification HMM) (Identification HMM)
+ Biobase.SElab.HMM: idd :: Lens' HMM3 (Identification HMM)
- Biobase.SElab.HMM: insertE :: Lens Node Node [NegLogProb] [NegLogProb]
+ Biobase.SElab.HMM: insertE :: Lens' Node [NegLogProb]
- Biobase.SElab.HMM: leng :: Lens HMM3 HMM3 Int Int
+ Biobase.SElab.HMM: leng :: Lens' HMM3 Int
- Biobase.SElab.HMM: matchE :: Lens Node Node [NegLogProb] [NegLogProb]
+ Biobase.SElab.HMM: matchE :: Lens' Node [NegLogProb]
- Biobase.SElab.HMM: nid :: Lens Node Node Int Int
+ Biobase.SElab.HMM: nid :: Lens' Node Int
- Biobase.SElab.HMM: nodes :: Lens HMM3 HMM3 [Node] [Node]
+ Biobase.SElab.HMM: nodes :: Lens' HMM3 [Node]
- Biobase.SElab.HMM: rf :: Lens HMM3 HMM3 Bool Bool
+ Biobase.SElab.HMM: rf :: Lens' HMM3 Bool
- Biobase.SElab.HMM: symAlph :: Lens HMM3 HMM3 [ByteString] [ByteString]
+ Biobase.SElab.HMM: symAlph :: Lens' HMM3 [ByteString]
- Biobase.SElab.HMM: trans :: Lens Node Node [NegLogProb] [NegLogProb]
+ Biobase.SElab.HMM: trans :: Lens' Node [NegLogProb]
- Biobase.SElab.HMM: transHeaders :: Lens HMM3 HMM3 [ByteString] [ByteString]
+ Biobase.SElab.HMM: transHeaders :: Lens' HMM3 [ByteString]
- Biobase.SElab.HMM: version :: Lens HMM3 HMM3 (ByteString, ByteString) (ByteString, ByteString)
+ Biobase.SElab.HMM: version :: Lens' HMM3 (ByteString, ByteString)
- Biobase.SElab.RfamNames: modelAC :: Lens ModelNames ModelNames (Accession Rfam) (Accession Rfam)
+ Biobase.SElab.RfamNames: modelAC :: Lens' ModelNames (Accession Rfam)
- Biobase.SElab.RfamNames: modelID :: Lens ModelNames ModelNames (Identification Rfam) (Identification Rfam)
+ Biobase.SElab.RfamNames: modelID :: Lens' ModelNames (Identification Rfam)
- Biobase.SElab.RfamNames: speciesAC :: Lens ModelNames ModelNames (Maybe (Accession Species)) (Maybe (Accession Species))
+ Biobase.SElab.RfamNames: speciesAC :: Lens' ModelNames (Maybe (Accession Species))
- Biobase.SElab.RfamNames: speciesID :: Lens ModelNames ModelNames (Maybe (Identification Species)) (Maybe (Identification Species))
+ Biobase.SElab.RfamNames: speciesID :: Lens' ModelNames (Maybe (Identification Species))
- Biobase.SElab.Taxonomy: accession :: Lens Taxonomy Taxonomy (Accession Species) (Accession Species)
+ Biobase.SElab.Taxonomy: accession :: Lens' Taxonomy (Accession Species)
- Biobase.SElab.Taxonomy: classification :: Lens Taxonomy Taxonomy [Classification] [Classification]
+ Biobase.SElab.Taxonomy: classification :: Lens' Taxonomy [Classification]
- Biobase.SElab.Taxonomy: name :: Lens Taxonomy Taxonomy (Identification Species) (Identification Species)
+ Biobase.SElab.Taxonomy: name :: Lens' Taxonomy (Identification Species)
Files
- Biobase/SElab/CM.hs +2/−2
- BiobaseInfernal.cabal +8/−3
Biobase/SElab/CM.hs view
@@ -25,11 +25,11 @@ import Prelude as P import Data.List (genericLength) -import "PrimitiveArray" Data.Array.Repa.Index+import Data.Array.Repa.Index import Data.Array.Repa.Index as R import Data.Array.Repa.Shape as R-import Data.ExtShape as R+import Data.Array.Repa.ExtShape as R import Biobase.SElab.Types import qualified Biobase.SElab.HMM as HMM
BiobaseInfernal.cabal view
@@ -1,5 +1,5 @@ name: BiobaseInfernal-version: 0.7.0.1+version: 0.7.1.0 author: Christian Hoener zu Siederdissen maintainer: choener@tbi.univie.ac.at homepage: http://www.tbi.univie.ac.at/~choener/@@ -26,6 +26,10 @@ . . .+ Changes in 0.7.1.0+ .+ * bumped dependencies, compatible to newest BiobaseXNA, PrimitiveArray+ . Changes in 0.7.0.0 . * work-in-progress release (some features missing)@@ -53,11 +57,12 @@ either-unwrap == 1.1 , lens == 3.* , primitive >= 0.5 ,+ repa == 3.2.* , transformers == 0.3.* , tuple == 0.2.* , vector >= 0.10 ,- BiobaseXNA == 0.6.3.* ,- PrimitiveArray >= 0.4.0.1+ BiobaseXNA == 0.7.* ,+ PrimitiveArray == 0.5.* exposed-modules: -- Biobase.Infernal