| Safe Haskell | None |
|---|---|
| Language | Haskell98 |
Bio.ClustalParser
Description
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 #
Parse Clustal alignment (.aln) from String
readClustalAlignment :: String -> IO (Either ParseError ClustalAlignment) #
Parse Clustal alignment (.aln) from filehandle
parseStructuralClustalAlignment :: String -> Either ParseError StructuralClustalAlignment #
Parse Clustal alignment (.aln) with secondary structure in dot-bracket notation from String (as produced by mlocarna)
readStructuralClustalAlignment :: String -> IO (Either ParseError StructuralClustalAlignment) #
Parse Clustal alignment (.aln) with secondary structure in dot-bracket notation from filehandle (as produced by mlocarna)
parseClustalSummary :: String -> Either ParseError ClustalSummary #
Parse Clustal summary (printed to STDOUT) from String
readClustalSummary :: String -> IO (Either ParseError ClustalSummary) #
Parse Clustal summary (printed to STDOUT) from file
data ClustalSummary #
Data type for clustal summary, containing information about the alignment process, usually printed to STDOUT
Constructors
| ClustalSummary | |
Instances
data ClustalAlignment #
Data structure for Clustal alignment format
Constructors
| ClustalAlignment | |
Fields | |
Instances
showAlignment :: Int -> Int -> Int -> [ClustalAlignmentEntry] -> Text -> String #
showAlignmentBlock :: Int -> Int -> [ClustalAlignmentEntry] -> Text -> String #
showAlignmentLine :: Int -> Int -> ClustalAlignmentEntry -> String #
data StructuralClustalAlignment #
Data structure for structural Clustal alignment format
Constructors
| StructuralClustalAlignment | |
Fields | |
Instances