bio-0.5: A bioinformatics library

Bio.GFF3.FeatureHierSequences

Documentation

data FeatureHierSequences Source

Instances

features :: FeatureHierSequences -> Set FeatureSource

sequences :: FeatureHierSequences -> [Sequence a]Source

fromLists :: (Error e, MonadError e m) => [Feature] -> [Sequence a] -> m FeatureHierSequencesSource

parse :: (Error e, MonadError e m) => ByteString -> m FeatureHierSequencesSource

lookupId :: (Error e, MonadError e m) => FeatureHierSequences -> SeqName -> m FeatureSource

parents :: FeatureHierSequences -> Feature -> [Feature]Source

children :: FeatureHierSequences -> Feature -> [Feature]Source

seqData :: (Error e, MonadError e m) => FeatureHierSequences -> SeqLoc -> m SeqDataSource

getSequence :: (Error e, MonadError e m) => FeatureHierSequences -> SeqName -> m SeqDataSource

featureSequence :: (Error e, MonadError e m) => FeatureHierSequences -> Feature -> m (Sequence a)Source

runGFF :: FilePath -> ErrorT String (Reader FeatureHierSequences) a -> ErrorT String IO aSource

runGFFIO :: FilePath -> ErrorT String (ReaderT FeatureHierSequences IO) a -> ErrorT String IO aSource

asksGFF :: (Error e, MonadError e m, MonadReader FeatureHierSequences m) => (FeatureHierSequences -> a -> m b) -> a -> m bSource