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2 #
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3 # $Id: SeqI.pm,v 1.7 2002/10/22 07:38:29 lapp Exp $
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4 #
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5 # BioPerl module for Bio::DB::SeqI.pm
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6 #
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7 # Cared for by Ewan Birney <birney@ebi.ac.uk>
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8 #
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9 # Copyright Ewan Birney
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10 #
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11 # You may distribute this module under the same terms as perl itself
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12
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13 # POD documentation - main docs before the code
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14
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15 =head1 NAME
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16
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17 Bio::DB::SeqI - Abstract Interface for Sequence databases
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18
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19 =head1 SYNOPSIS
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20
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21 # get a Bio::DB::SeqI somehow
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22
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23 $seq = $seqdb->get_Seq_by_id('some-id');
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24 $seq = $seqdb->get_Seq_by_acc('some-accession-number');
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25
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26 @ids = $seqdb->get_all_ids();
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27 $stream = $seqdb->get_PrimarySeq_stream();
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28 while((my $seq = $stream->next_seq()) {
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29 # $seq is a PrimarySeqI compliant object
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30 }
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31
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32
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33 =head1 DESCRIPTION
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34
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35 Abstract interface for a sequence database
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36
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37 =head1 FEEDBACK
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38
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39 =head2 Mailing Lists
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40
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41 User feedback is an integral part of the evolution of this and other
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42 Bioperl modules. Send your comments and suggestions preferably to one
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43 of the Bioperl mailing lists. Your participation is much appreciated.
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44
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45 bioperl-l@bioperl.org - General discussion
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46 http://bioperl.org/MailList.shtml - About the mailing lists
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47
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48 =head2 Reporting Bugs
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49
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50 Report bugs to the Bioperl bug tracking system to help us keep track
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51 the bugs and their resolution.
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52 Bug reports can be submitted via email or the web:
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53
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54 bioperl-bugs@bio.perl.org
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55 http://bugzilla.bioperl.org/
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56
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57 =head1 AUTHOR - Ewan Birney
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58
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59 Email birney@ebi.ac.uk
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60
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61 Describe contact details here
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62
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63 =head1 APPENDIX
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64
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65 The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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66
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67 =cut
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68
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69
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70 # Let the code begin...
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71
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72
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73 package Bio::DB::SeqI;
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74 use vars qw(@ISA);
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75 use strict;
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76
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77 # Object preamble - inherits from Bio::Root::Object
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78
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79 use Bio::DB::RandomAccessI;
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80 @ISA = qw(Bio::DB::RandomAccessI);
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81
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82 =head1 Methods inherieted from Bio::DB::RandomAccessI
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83
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84 =head2 get_Seq_by_id
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85
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86 Title : get_Seq_by_id
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87 Usage : $seq = $db->get_Seq_by_id('ROA1_HUMAN')
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88 Function: Gets a Bio::Seq object by its name
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89 Returns : a Bio::Seq object
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90 Args : the id (as a string) of a sequence
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91 Throws : "id does not exist" exception
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92
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93
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94 =cut
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95
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96 =head2 get_Seq_by_acc
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97
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98 Title : get_Seq_by_acc
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99 Usage : $seq = $db->get_Seq_by_acc('X77802');
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100 Function: Gets a Bio::Seq object by accession number
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101 Returns : A Bio::Seq object
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102 Args : accession number (as a string)
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103 Throws : "acc does not exist" exception
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104
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105
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106 =cut
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107
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108 =head1 Methods [that were] specific for Bio::DB::SeqI
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109
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110 =head2 get_PrimarySeq_stream
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111
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112 Title : get_PrimarySeq_stream
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113 Usage : $stream = get_PrimarySeq_stream
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114 Function: Makes a Bio::SeqIO compliant object
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115 which provides a single method, next_seq
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116 Returns : Bio::SeqIO
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117 Args : none
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118
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119 =cut
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120
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121 sub get_PrimarySeq_stream{
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122 my ($self,@args) = @_;
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123
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124 $self->throw("Object did not provide a PrimarySeq stream object");
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125 }
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126
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127 =head2 get_all_primary_ids
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128
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129 Title : get_all_ids
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130 Usage : @ids = $seqdb->get_all_primary_ids()
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131 Function: gives an array of all the primary_ids of the
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132 sequence objects in the database. These
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133 maybe ids (display style) or accession numbers
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134 or something else completely different - they
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135 *are not* meaningful outside of this database
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136 implementation.
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137 Example :
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138 Returns : an array of strings
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139 Args : none
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140
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141
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142 =cut
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143
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144 sub get_all_primary_ids{
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145 my ($self,@args) = @_;
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146 $self->throw("Object did not provide a get_all_ids method");
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147 }
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148
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149
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150 =head2 get_Seq_by_primary_id
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151
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152 Title : get_Seq_by_primary_id
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153 Usage : $seq = $db->get_Seq_by_primary_id($primary_id_string);
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154 Function: Gets a Bio::Seq object by the primary id. The primary
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155 id in these cases has to come from $db->get_all_primary_ids.
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156 There is no other way to get (or guess) the primary_ids
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157 in a database.
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158
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159 The other possibility is to get Bio::PrimarySeqI objects
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160 via the get_PrimarySeq_stream and the primary_id field
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161 on these objects are specified as the ids to use here.
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162 Returns : A Bio::Seq object
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163 Args : accession number (as a string)
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164 Throws : "acc does not exist" exception
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165
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166
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167 =cut
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168
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169 sub get_Seq_by_primary_id {
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170 my ($self,@args) = @_;
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171
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172 $self->throw("Abstract database call of get_Seq_by_primary_id. Your database has not implemented this method!");
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173
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174 }
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175
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176 1;
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177
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178
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179
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