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1 # $Id: UpdateableSeqI.pm,v 1.4 2002/10/22 07:45:09 lapp Exp $
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2 #
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3 # BioPerl module for Bio::UpdateableSeqI
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4 #
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5 # Cared for by David Block <dblock@gene.pbi.nrc.ca>
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6 #
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7 # Copyright David Block
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8 #
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9 # You may distribute this module under the same terms as perl itself
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10
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11 # POD documentation - main docs before the code
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12
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13 =head1 NAME
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14
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15 Bio::UpdateableSeqI - Descendant of Bio::SeqI that allows updates
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16
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17 =head1 SYNOPSIS
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18
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19 See Bio::SeqI for most of the documentation.
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20 See the documentation of the methods for further details.
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21
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22 =head1 DESCRIPTION
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23
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24 Bio::UpdateableSeqI is an interface for Sequence objects which are
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25 expected to allow users to perform basic editing functions (update/delete)
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26 on their component SeqFeatures.
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27
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28 =head1 FEEDBACK
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29
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30 =head2 Mailing Lists
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31
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32 User feedback is an integral part of the evolution of this and other
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33 Bioperl modules. Send your comments and suggestions preferably to
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34 the Bioperl mailing list. Your participation is much appreciated.
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35
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36 bioperl-l@bioperl.org - General discussion
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37 http://bioperl.org/MailList.shtml - About the mailing lists
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38
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39 =head2 Reporting Bugs
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40
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41 Report bugs to the Bioperl bug tracking system to help us keep track
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42 of the bugs and their resolution. Bug reports can be submitted via
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43 email or the web:
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44
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45 bioperl-bugs@bioperl.org
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46 http://bugzilla.bioperl.org/
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47
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48 =head1 AUTHOR - David Block
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49
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50 Email dblock@gene.pbi.nrc.ca
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51
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52 =head1 CONTRIBUTORS
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53
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54 Ewan Birney forced me to this...
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55
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56 =head1 APPENDIX
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57
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58 The rest of the documentation details each of the object methods.
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59 Internal methods are usually preceded with a _
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60
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61 =cut
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62
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63
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64 # Let the code begin...
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65
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66
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67 package Bio::UpdateableSeqI;
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68 use vars qw(@ISA);
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69 use strict;
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70 use Carp;
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71
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72 # Object preamble - inherits from Bio::Root::Root
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73
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74 use Bio::SeqI;
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75
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76
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77 @ISA = qw(Bio::SeqI);
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78
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79
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80 =head2 delete_feature
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81
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82 Title : delete_feature
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83 Usage : my $orphanlist=$self->delete_feature($feature,$transcript,$gene);
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84 Function: deletes the specified $feature from the given transcript, if $transcript is sent and exists and $feature is a feature of $transcript,
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85 or from $gene if the $feature is a feature of $gene, or from $self if $transcript and $gene are not sent. Keeps track of the features
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86 of the $gene object that may be left as orphans and returns them as a listref.
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87 Example : I want to delete transcript 'abc' of gene 'def', with three exons, leaving only transcript 'ghi' with two exons.
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88 This will leave exons 1 and 3 part of 'ghi', but exon 2 will become an orphan.
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89 my $orphanlist=$seq->delete_feature($transcript{'abc'},undef,$gene{'def'});
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90 $orphanlist is a reference to a list containing $exon{'2'};
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91 Returns : a listref of orphaned features after the deletion of $feature (optional)
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92 Args : $feature - the feature to be deleted
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93 $transcript - the transcript containing the $feature, so that a $feature can be removed from only one transcript when there are multiple
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94 transcripts in a gene.
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95 $gene - the gene containing the $transcript and/or the $feature
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96
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97
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98 =cut
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99
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100 sub delete_feature{
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101 my ($self,$feature,$transcript,$gene) = @_;
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102
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103 $self->throw_not_implemented();
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104 }
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105
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106
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107 1;
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