Safe Haskell | None |
---|---|
Language | Haskell98 |
Parse Clustal output For more information on Clustal tools consult: http://www.clustal.org/
- parseClustalAlignment :: String -> Either ParseError ClustalAlignment
- readClustalAlignment :: String -> IO (Either ParseError ClustalAlignment)
- parseStructuralClustalAlignment :: String -> Either ParseError StructuralClustalAlignment
- readStructuralClustalAlignment :: String -> IO (Either ParseError StructuralClustalAlignment)
- parseClustalSummary :: String -> Either ParseError ClustalSummary
- readClustalSummary :: String -> IO (Either ParseError ClustalSummary)
- data ClustalSummary = ClustalSummary {}
- data SequenceParameters = SequenceParameters {}
- data PairwiseAlignmentSummary = PairwiseAlignmentSummary {}
- data GroupSummary = GroupSummary {}
- data ClustalAlignment = ClustalAlignment {}
- showAlignment :: Int -> Int -> Int -> [ClustalAlignmentEntry] -> Text -> String
- showAlignmentBlock :: Int -> Int -> [ClustalAlignmentEntry] -> Text -> String
- showAlignmentLine :: Int -> Int -> ClustalAlignmentEntry -> String
- data ClustalAlignmentEntry = ClustalAlignmentEntry {}
- data ClustalAlignmentSlice = ClustalAlignmentSlice {}
- data ClustalAlignmentEntrySlice = ClustalAlignmentEntrySlice {}
- data StructuralClustalAlignment = StructuralClustalAlignment {}
- data StructuralClustalAlignmentEntrySlice = StructuralClustalAlignmentEntrySlice {}
Documentation
parseClustalAlignment :: String -> Either ParseError ClustalAlignment Source #
Parse Clustal alignment (.aln) from String
readClustalAlignment :: String -> IO (Either ParseError ClustalAlignment) Source #
Parse Clustal alignment (.aln) from filehandle
parseStructuralClustalAlignment :: String -> Either ParseError StructuralClustalAlignment Source #
Parse Clustal alignment (.aln) with secondary structure in dot-bracket notation from String (as produced by mlocarna)
readStructuralClustalAlignment :: String -> IO (Either ParseError StructuralClustalAlignment) Source #
Parse Clustal alignment (.aln) with secondary structure in dot-bracket notation from filehandle (as produced by mlocarna)
parseClustalSummary :: String -> Either ParseError ClustalSummary Source #
Parse Clustal summary (printed to STDOUT) from String
readClustalSummary :: String -> IO (Either ParseError ClustalSummary) Source #
Parse Clustal summary (printed to STDOUT) from file
data ClustalSummary Source #
Data type for clustal summary, containing information about the alignment process, usually printed to STDOUT
data ClustalAlignment Source #
Data structure for Clustal alignment format
showAlignment :: Int -> Int -> Int -> [ClustalAlignmentEntry] -> Text -> String Source #
showAlignmentBlock :: Int -> Int -> [ClustalAlignmentEntry] -> Text -> String Source #
showAlignmentLine :: Int -> Int -> ClustalAlignmentEntry -> String Source #
data ClustalAlignmentEntry Source #
data ClustalAlignmentSlice Source #
data StructuralClustalAlignment Source #
Data structure for structural Clustal alignment format