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1 # $Id: RichSeqI.pm,v 1.8 2002/10/22 07:38:40 lapp Exp $
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2 #
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3 # BioPerl module for Bio::Seq::RichSeqI
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4 #
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5 # Cared for by Ewan Birney <birney@ebi.ac.uk>
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6 #
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7 # Copyright Ewan Birney
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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::Seq::RichSeqI - RichSeq interface, mainly for database orientated sequences
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16
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17 =head1 SYNOPSIS
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18
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19 @secondary = $richseq->get_secondary_accessions;
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20 $division = $richseq->division;
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21 $mol = $richseq->molecule;
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22 @dates = $richseq->get_dates;
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23 $seq_version = $richseq->seq_version;
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24 $pid = $richseq->pid;
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25 $keywords = $richseq->keywords;
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26
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27 =head1 DESCRIPTION
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28
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29 This interface extends the Bio::SeqI interface to give additional functionality
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30 to sequences with richer data sources, in particular from database sequences
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31 (EMBL, GenBank and Swissprot).
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32
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33 =head1 FEEDBACK
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34
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35 =head2 Mailing Lists
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36
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37 User feedback is an integral part of the evolution of this
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38 and other Bioperl modules. Send your comments and suggestions preferably
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39 to one of the Bioperl mailing lists.
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40 Your participation is much appreciated.
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41
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42 bioperl-l@bioperl.org - General discussion
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43 http://bio.perl.org/MailList.html - About the mailing lists
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44
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45 =head2 Reporting Bugs
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46
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47 Report bugs to the Bioperl bug tracking system to help us keep track
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48 the bugs and their resolution.
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49 Bug reports can be submitted via email or the web:
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50
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51 bioperl-bugs@bio.perl.org
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52 http://bugzilla.bioperl.org/
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53
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54 =head1 AUTHOR - Ewan Birney
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55
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56 Email birney@ebi.ac.uk
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57
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58 Describe contact details here
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59
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60 =head1 APPENDIX
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61
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62 The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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63
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64 =cut
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65
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66
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67 # Let the code begin...
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68
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69
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70 package Bio::Seq::RichSeqI;
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71 use vars qw(@ISA);
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72 use strict;
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73 use Bio::SeqI;
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74
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75 @ISA = ('Bio::SeqI');
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76
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77
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78 =head2 get_secondary_accessions
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79
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80 Title : get_secondary_accessions
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81 Usage :
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82 Function: Get the secondary accessions for a sequence.
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83 Example :
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84 Returns : an array of strings
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85 Args : none
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86
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87
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88 =cut
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89
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90 sub get_secondary_accessions{
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91 my ($self,@args) = @_;
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92
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93 $self->throw("hit get_secondary_accessions in interface definition - error");
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94
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95 }
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96
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97
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98 =head2 division
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99
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100 Title : division
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101 Usage :
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102 Function: Get (and set, depending on the implementation) the divison for
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103 a sequence.
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104
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105 Examples from GenBank are PLN (plants), PRI (primates), etc.
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106 Example :
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107 Returns : a string
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108 Args :
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109
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110
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111 =cut
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112
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113 sub division{
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114 my ($self,@args) = @_;
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115
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116 $self->throw("hit division in interface definition - error");
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117
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118 }
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119
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120
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121 =head2 molecule
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122
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123 Title : molecule
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124 Usage :
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125 Function: Get (and set, depending on the implementation) the molecule
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126 type for the sequence.
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127
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128 This is not necessarily the same as Bio::PrimarySeqI::alphabet(),
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129 because it is databank-specific.
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130 Example :
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131 Returns : a string
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132 Args :
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133
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134
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135 =cut
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136
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137 sub molecule{
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138 my ($self,@args) = @_;
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139
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140 $self->throw("hit molecule in interface definition - error");
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141 }
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142
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143 =head2 pid
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144
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145 Title : pid
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146 Usage :
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147 Function: Get (and set, depending on the implementation) the PID property
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148 for the sequence.
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149 Example :
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150 Returns : a string
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151 Args :
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152
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153
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154 =cut
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155
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156 sub pid {
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157 my ($self,@args) = @_;
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158
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159 $self->throw("hit pid in interface definition - error");
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160 }
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161
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162 =head2 get_dates
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163
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164 Title : get_dates
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165 Usage :
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166 Function: Get (and set, depending on the implementation) the dates the
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167 databank entry specified for the sequence
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168 Example :
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169 Returns : an array of strings
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170 Args :
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171
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172
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173 =cut
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174
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175 sub get_dates{
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176 my ($self,@args) = @_;
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177
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178 $self->throw("hit get_dates in interface definition - error");
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179
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180 }
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181
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182
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183 =head2 seq_version
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184
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185 Title : seq_version
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186 Usage :
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187 Function: Get (and set, depending on the implementation) the version string
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188 of the sequence.
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189 Example :
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190 Returns : a string
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191 Args :
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192
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193
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194 =cut
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195
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196 sub seq_version{
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197 my ($self,@args) = @_;
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198
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199 $self->throw("hit seq_version in interface definition - error");
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200
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201 }
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202
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203 =head2 keywords
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204
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205 Title : keywords
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206 Usage : $obj->keywords($newval)
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207 Function:
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208 Returns : value of keywords (a string)
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209 Args : newvalue (optional) (a string)
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210
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211
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212 =cut
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213
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214 sub keywords {
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215 my ($self) = @_;
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216 $self->throw("hit keywords in interface definition - error");
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217 }
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218
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219 1;
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