Take low-level Event
s
and turn them high-level data
structures.
- data Stockholm = Stockholm [Ann FileAnnotation] [Ann (ColumnAnnotation InFile)] [StockholmSeq]
- data StockholmSeq = StSeq !SeqLabel !SeqData [Ann SequenceAnnotation] [Ann (ColumnAnnotation InSeq)]
- data Ann d = Ann {
- feature :: !d
- text :: !ByteString
- data FileAnnotation
- data SequenceAnnotation
- data ColumnAnnotation a
- data InFile
- data InSeq
- parseDoc :: Resource m => Conduit Event m Stockholm
- renderDoc :: Resource m => Conduit Stockholm m Event
Data types
An Stockholm 1.0 formatted file represented in memory.
data StockholmSeq Source
A sequence in Stockholm 1.0 format.
A generic annotation.
Ann | |
|
data FileAnnotation Source
Possible file annotations.
AC | Accession number: Accession number in form PFxxxxx.version or PBxxxxxx. |
ID | Identification: One word name for family. |
DE | Definition: Short description of family. |
AU | Author: Authors of the entry. |
SE | Source of seed: The source suggesting the seed members belong to one family. |
GA | Gathering method: Search threshold to build the full alignment. |
TC | Trusted Cutoff: Lowest sequence score and domain score of match in the full alignment. |
NC | Noise Cutoff: Highest sequence score and domain score of match not in full alignment. |
TP | Type: Type of family (presently Family, Domain, Motif or Repeat). |
SQ | Sequence: Number of sequences in alignment. |
AM | Alignment Method: The order ls and fs hits are aligned to the model to build the full align. |
DC | Database Comment: Comment about database reference. |
DR | Database Reference: Reference to external database. |
RC | Reference Comment: Comment about literature reference. |
RN | Reference Number: Reference Number. |
RM | Reference Medline: Eight digit medline UI number. |
RT | Reference Title: Reference Title. |
RA | Reference Author: Reference Author |
RL | Reference Location: Journal location. |
PI | Previous identifier: Record of all previous ID lines. |
KW | Keywords: Keywords. |
CC | Comment: Comments. |
NE | Pfam accession: Indicates a nested domain. |
NL | Location: Location of nested domains - sequence ID, start and end of insert. |
F_Other !ByteString | Other file annotation. |
data SequenceAnnotation Source
Possible sequence annotations.
data ColumnAnnotation a Source