NAME
Bio::DOOP::SequenceFeature - Object for the sequence features
DESCRIPTION
This object give access for the sequence features ( motif, repeat, cpg
and tss annotaion ). This object also contain some web based code
for visualize the feature in picture.
AUTHOR
Tibor Nagy, Godollo, Hungary
METHODS
new
$seqfeat = Bio::DOOP::SequenceFeature->new($db,"112");
You can create the object with new. The arguments is the following:
$db is a Bio::DOOP::DBSQL object, the second argument is a
SequenceFeature primary id.
get_id
Return the primary id of the features. Use for MySQL queryes
get_score
Return the score of the feature. I do not know too much about it.
get_start
Return the start position of the feature.
get_end
Return the end position of the feature
get_png_topleft
Return the picture position of the feature. Used by a web code
get_png_topright
Return the picture position of the feature. Used by a web code
get_png_bottomleft
Return the picture position of the feature. Used by a web code
get_png_bottomright
Return the picture position of the feature. Used by a web code
get_seq
Return the sequence of the feature.
get_type
Return the type of the feature. (con, ssr, tfbs, rep, cpg, tss)
get_motifid
Return the motif primary id, if the feature type is con. Else it is NULL
get_tfbsid
Return the tfbs primary id, if the feature type is tfbs. Else it is NULL
get_cpgid
Return the cpg primary id, if the feature type is cpg. Else it is NULL
get_repeatid
Return the repeat primary id, if the feature type is rep. Else it is NULL
get_ssrid
Return the ssr primary id, if the feature type is ssr. Else it is NULL
get_tssid
Return the tss primary id, if the feature type is tss. Else it is NULL
get_seqid
Return the sequence primary id that is contain this feature
get_motif
$motif = $seqfeat->get_motif;
Return the motif object associated to the feature.
If the feature type is not con this value is NULL