Matrix

Documentation

removeChar :: Bool -> Maybe [AA] -> AAMap -> AAMap

Filter gaps out of the map. If no gaps are wanted, remove the entire position

getClusterFrequencyMap :: Seq FastaSequence -> ClusterFrequencyMap

Get the frequencies of amino acid pairs for each position in a cluster

getBlockMap :: Bool -> Maybe [AA] -> [ClusterFrequencyMap] -> BlockMap

Get the frequency matrix from a list of frequency maps from clusters. We no longer care about positions after this.

joinBlockMaps :: [BlockMap] -> FrequencyMap

Join together all frequency maps into a single frequency map.

getBlosum :: FrequencyMap -> Blosum

Get the blosum matrix of each AA entry