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1 # $Id: GeneStructureI.pm,v 1.8 2002/10/22 07:38:41 lapp Exp $
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2 #
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3 # BioPerl module for Bio::SeqFeature::Gene::GeneStructureI
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4 #
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5 # Cared for by Hilmar Lapp <hlapp@gmx.net>
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6 #
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7 # Copyright Hilmar Lapp
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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::SeqFeature::Gene::GeneStructure - A feature representing an arbitrarily
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16 complex structure of a gene
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17
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18 =head1 SYNOPSIS
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19
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20 #documentaion needed
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21
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22 =head1 DESCRIPTION
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23
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24 A feature representing a gene structure.
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25
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26 =head1 FEEDBACK
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27
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28 =head2 Mailing Lists
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29
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30 User feedback is an integral part of the evolution of this
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31 and other Bioperl modules. Send your comments and suggestions preferably
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32 to one of the Bioperl mailing lists.
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33 Your participation is much appreciated.
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34
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35 bioperl-l@bioperl.org - General discussion
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36 http://bio.perl.org/MailList.html - About the mailing lists
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37
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38 =head2 Reporting Bugs
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39
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40 Report bugs to the Bioperl bug tracking system to help us keep track
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41 the bugs and their resolution.
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42 Bug reports can be submitted via email or the web:
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43
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44 bioperl-bugs@bio.perl.org
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45 http://bugzilla.bioperl.org/
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46
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47 =head1 AUTHOR - Hilmar Lapp
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48
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49 Email hlapp@gmx.net
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50
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51 Describe contact details here
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52
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53 =head1 APPENDIX
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54
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55 The rest of the documentation details each of the object methods.
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56 Internal methods are usually preceded with a _
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57
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58 =cut
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59
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60
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61 # Let the code begin...
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62
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63
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64 package Bio::SeqFeature::Gene::GeneStructureI;
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65 use vars qw(@ISA);
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66 use strict;
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67
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68 use Carp;
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69 use Bio::SeqFeatureI;
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70
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71 @ISA = qw(Bio::SeqFeatureI);
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72
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73 =head2 transcripts
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74
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75 Title : transcripts()
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76 Usage : @transcripts = $gene->transcripts();
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77 Function: Get the transcript features/sites of this gene structure.
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78
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79 See Bio::SeqFeature::Gene::TranscriptI for properties of the
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80 returned objects.
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81
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82 Returns : An array of Bio::SeqFeature::Gene::TranscriptI implementing objects
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83 representing the promoter regions or sites.
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84 Args :
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85
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86
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87 =cut
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88
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89 sub transcripts {
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90 my ($self) = @_;
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91 $self->throw_not_implemented();
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92 }
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93
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94 =head2 promoters
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95
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96 Title : promoters()
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97 Usage : @prom_sites = $gene->promoters();
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98 Function: Get the promoter features/sites of this gene structure.
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99
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100 Note that OO-modeling of regulatory elements is not stable yet.
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101 This means that this method might change or even disappear in a
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102 future release. Be aware of this if you use it.
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103
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104 Returns : An array of Bio::SeqFeatureI implementing objects representing the
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105 promoter regions or sites.
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106 Args :
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107
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108 =cut
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109
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110 sub promoters {
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111 my ($self) = @_;
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112 $self->throw_not_implemented();
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113 }
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114
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115 =head2 exons
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116
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117 Title : exons()
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118 Usage : @exons = $gene->exons();
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119 @inital = $gene->exons('Initial');
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120 Function: Get all exon features or all exons of specified type of this gene
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121 structure.
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122
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123 Refer to the documentation of the class that produced this gene
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124 structure object for information about the possible types.
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125
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126 See Bio::SeqFeature::Gene::ExonI for properties of the
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127 returned objects.
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128
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129 Returns : An array of Bio::SeqFeature::Gene::ExonI implementing objects
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130 representing the exon regions.
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131 Args : An optional string specifying the type of the exon.
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132
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133 =cut
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134
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135 sub exons {
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136 my ($self, $type) = @_;
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137 $self->throw_not_implemented();
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138 }
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139
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140 =head2 introns
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141
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142 Title : introns()
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143 Usage : @introns = $gene->introns();
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144 Function: Get all introns of this gene structure.
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145 Returns : An array of Bio::SeqFeatureI implementing objects representing the
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146 introns.
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147 Args :
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148
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149
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150 =cut
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151
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152 sub introns {
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153 my ($self) = @_;
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154 $self->throw_not_implemented();
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155 }
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156
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157 =head2 poly_A_sites
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158
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159 Title : poly_A_sites()
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160 Usage : @polyAsites = $gene->poly_A_sites();
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161 Function: Get the poly-adenylation features/sites of this gene structure.
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162 Returns : An array of Bio::SeqFeatureI implementing objects representing the
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163 poly-adenylation regions or sites.
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164 Args :
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165
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166
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167 =cut
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168
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169 sub poly_A_sites {
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170 my ($self) = @_;
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171 $self->throw_not_implemented();
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172 }
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173
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174 =head2 utrs
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175
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176 Title : utrs()
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177 Usage : @utr_sites = $gene->utrs();
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178 Function: Get the UTR features/sites of this gene structure.
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179
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180 See Bio::SeqFeature::Gene::ExonI for properties of the
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181 returned objects.
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182
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183 Returns : An array of Bio::SeqFeature::Gene::ExonI implementing objects
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184 representing the UTR regions or sites.
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185 Args :
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186
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187
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188 =cut
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189
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190 sub utrs {
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191 my ($self) = @_;
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192 $self->throw_not_implemented();
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193 }
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194
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195 1;
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