| 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] -> String -> String
- showAlignmentBlock :: Int -> Int -> [ClustalAlignmentEntry] -> String -> String
- showAlignmentLine :: Int -> Int -> ClustalAlignmentEntry -> String
- data ClustalAlignmentEntry = ClustalAlignmentEntry {}
- data ClustalAlignmentSlice = ClustalAlignmentSlice {}
- data ClustalAlignmentEntrySlice = ClustalAlignmentEntrySlice {}
- data StructuralClustalAlignment = StructuralClustalAlignment {}
- data StructuralClustalAlignmentSlice = StructuralClustalAlignmentSlice {}
- 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
Constructors
| ClustalSummary | |
Instances
data PairwiseAlignmentSummary Source
Constructors
| PairwiseAlignmentSummary | |
Fields | |
data ClustalAlignment Source
Data structure for Clustal alignment format
Constructors
| ClustalAlignment | |
Fields | |
Instances
showAlignment :: Int -> Int -> Int -> [ClustalAlignmentEntry] -> String -> String Source
showAlignmentBlock :: Int -> Int -> [ClustalAlignmentEntry] -> String -> String Source
showAlignmentLine :: Int -> Int -> ClustalAlignmentEntry -> String Source
data ClustalAlignmentEntry Source
Constructors
| ClustalAlignmentEntry | |
Fields | |
data ClustalAlignmentSlice Source
Constructors
| ClustalAlignmentSlice | |
Fields | |
data ClustalAlignmentEntrySlice Source
Constructors
| ClustalAlignmentEntrySlice | |
Fields | |
data StructuralClustalAlignment Source
Data structure for structural Clustal alignment format
Constructors
| StructuralClustalAlignment | |
Fields | |
data StructuralClustalAlignmentSlice Source
Constructors
| StructuralClustalAlignmentSlice | |