AnnotPair.pir

#
# AnnotPair : a pair of start/stop lines in a masterfile.
#

- PerlClass PirObject::AnnotPair
- InheritsFrom  PirObject
- FieldsTable

# Field name            Struct          Type            Comments
#---------------------- --------------- --------------- -----------------------
type                    single          string          Usually G (Gene)
genename                single          string          Name of gene
startpos                single          int4            Position of the START line
endpos                  single          int4            Position of the END line
direction               single          string          "==>" or "<==" or "*==>" or "<==*"
startline               single          string          Whole START line
endline                 single          string          Whole END line
startmulticomment       array           string          Multiline comment associated with START line
endmulticomment         array           string          Multiline comment associated with END line
startlinenumber         single          int4            Optional line number in masterfile.
endlinenumber           single          int4            Optional line number in masterfile.
introntype              single          string          Only for introns, type as identified by RNAWeasel
globaltype              single          string          Only for introns, global type as identified by RNAWeasel when more than 1 intron.


# These fields are used internally by MFannot; they do not correspond to features
# of a masterfile.
splicescore             single          int4            A score calculate for splice site
phase                   single          int4            Phase of intron 0 if intron split a tri-nt else 1 or 2
score                   single          string          Score or evalue for RNA identified by RNASpinner (evalue) or HMMweasel (score)
lengthofref             single          int4            The length of homologous gene.
lengthofthis            single          int4            The length of the protein.
firstmissingexon        single          int4            Boolean 1 if the first exon was suspected to be not here else 0.
posiffusion             single          int4            Indicate if it's the first or the second gene of fusion
namefusiongene          single          string          Name of gene fusioned with.
idbyblast               single          int4            1 if annotation is make from blast result.
idbyexo                 single          int4            1 if annotation is make from exonerate result.
idbyHMM                 single          int4            1 if annotation is make from HMMweasel result.
idbyRNA                 single          int4            1 if annotation is make from RNAweasel result.
isIntronic              single          int4            1 if gene is an intronic gene.
RNAcomment              single          string          comment given by RNAfinder
altexons                array           <AnnotPair>     list of AP alternatif exon only for G.
exoscore                single          int4            raw score defined by exonerate
possStart               array           string          List of possible start.
isFusioned              single          int4            0 no fusion, 1 fusion.
origine                 single          string          Define origine of gene pt|pt_cyano|mt|mt_alpha
IdORF                   single          string          A string in order to identified ORF.
HMMlen                  single          int4            Lenght of HMMmodel.
isDup                   single          int4            Indication for possible duplication
HMMmatch                single          string          Indicate match of HMMmodel
containStruc            single          int4            1 if contain particular structure (e.g: dpo or rpo) else 0

- EndFieldsTable

- Methods

our $RCS_VERSION='$Id: AnnotPair.pir,v 1.17 2011/08/20 20:31:39 nbeck Exp $';
our ($VERSION) = ($RCS_VERSION =~ m#,v ([\w\.]+)#);

# Nothing to see here. Move along.