LICENSE

Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute Copyright [2016-2024] EMBL-European Bioinformatics Institute

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

http://www.apache.org/licenses/LICENSE-2.0

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NAME

Bio::EnsEMBL::Map::Ditag

SYNOPSIS

my $feature = Bio::EnsEMBL::Map::Ditag->new(
  -dbID      => $tag_id,
  -name      => $name,
  -type      => $type,
  -tag_count => $tag_count,
  -sequence  => $sequence,
  -adaptor   => $dbAdaptor
);

DESCRIPTION

Represents an unmapped ditag object in the EnsEMBL database. Corresponds to original tag containing the full sequence. This can be a single piece of sequence like CAGE tags or a ditag with concatenated sequence from 5' and 3' end like GIS or GSC tags.

METHODS

new

Arg [1]    : (optional) int $dbID
Arg [2]    : (optional) string name
Arg [3]    : (optional) string type
Arg [4]    : (optional) int tag_count
Arg [5]    : (optional) string sequence
Arg [6]    : (optional) Bio::EnsEMBL::Map::DBSQL::DitagAdaptor $adaptor

Description: Creates a new ditag
Returntype : Bio::EnsEMBL::Map::Ditag
Exceptions : none
Caller     : general

name

Arg [1]    : (optional) string $type
Example    : $type = $ditag->name;
Description: Getter/Setter for the name of a ditag
Returntype : text
Caller     : general

dbID

Arg [1]    : (optional) int id
Example    : $ditag_id = $ditag->dbID;
Description: Getter/Setter for the dbID of a ditag
Returntype : int
Caller     : general

type

Arg [1]    : (optional) string $type
Example    : $type = $ditag->type;
Description: Getter/Setter for the type of a ditag
Returntype : text
Caller     : general

tag_count

Arg [1]    : (optional) string $tag_count
Example    : $type = $ditag->tag_count;
Description: Getter/Setter for the tag_count of a ditag
Returntype : int
Caller     : general

sequence

Arg [1]    : (optional) string $sequence
Example    : $sequence = $ditag->sequence;
Description: Getter/Setter for the sequence of a ditag
Returntype : text
Caller     : general

get_ditagFeatures

Arg        : none
Example    : @features = @{$ditag->get_ditagFeatures};
Description: Fetch ditag_features created from this ditag
Returntype : listref of Bio::EnsEMBL::Map::DitagFeature
Caller     : general