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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CONTACT

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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