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1 # $Id: TranscriptI.pm,v 1.7 2002/10/22 07:38:41 lapp Exp $
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2 #
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3 # BioPerl module for Bio::SeqFeature::Gene::TranscriptI
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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::TranscriptI - Interface for a feature representing a
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16 transcript of exons, promoter(s), UTR, and a poly-adenylation site.
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17
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18 =head1 SYNOPSIS
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19
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20 #documentation 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 transcript.
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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::TranscriptI;
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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 promoters
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74
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75 Title : promoters()
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76 Usage : @proms = $transcript->promoters();
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77 Function: Get the promoter features of this transcript.
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78
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79 Note that OO-modeling of regulatory elements is not stable yet.
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80 This means that this method might change or even disappear in a
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81 future release. Be aware of this if you use it.
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82
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83 Returns : An array of Bio::SeqFeatureI implementing objects representing the
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84 promoter regions or sites.
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85 Args :
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86
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87 =cut
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88
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89 sub promoters {
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90 my ($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 exons
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95
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96 Title : exons()
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97 Usage : @exons = $transcript->exons();
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98 @inital = $transcript->exons('Initial');
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99 Function: Get the individual exons this transcript comprises of, or all exons
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100 of a specified type.
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101
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102 Refer to the documentation of the class that produced this
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103 transcript object for information about the possible types.
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104
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105 See Bio::SeqFeature::Gene::ExonI for properties of the
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106 returned objects.
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107
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108 Returns : An array of Bio::SeqFeature::Gene::ExonI implementing objects
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109 Args : An optional string specifying the type of the exon.
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110
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111 =cut
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112
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113 sub exons {
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114 my ($self, $type) = @_;
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115 $self->throw_not_implemented();
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116 }
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117
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118 =head2 introns
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119
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120 Title : introns()
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121 Usage : @introns = $transcript->introns();
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122 Function: Get all introns this transcript comprises of.
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123 Returns : An array of Bio::SeqFeatureI implementing objects representing the
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124 introns.
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125 Args :
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126
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127
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128 =cut
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129
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130 sub introns {
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131 my ($self) = @_;
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132 $self->throw_not_implemented();
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133 }
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134
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135 =head2 poly_A_site
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136
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137 Title : poly_A_site()
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138 Usage : $polyAsite = $transcript->poly_A_site();
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139 Function: Get the poly-adenylation site of this transcript.
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140 Returns : A Bio::SeqFeatureI implementing object.
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141 Args :
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142
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143
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144 =cut
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145
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146 sub poly_A_site {
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147 my ($self) = @_;
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148 $self->throw_not_implemented();
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149 }
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150
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151 =head2 utrs
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152
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153 Title : utrs()
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154 Usage : @utr_sites = $transcript->utrs();
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155 Function: Get the UTR regions this transcript comprises of.
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156
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157 See Bio::SeqFeature::Gene::ExonI for properties of the
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158 returned objects.
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159
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160 Returns : An array of Bio::SeqFeature::Gene::ExonI implementing objects
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161 Args :
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162
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163
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164 =cut
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165
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166 sub utrs {
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167 my ($self) = @_;
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168 $self->throw_not_implemented();
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169 }
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170
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171 =head2 mrna
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172
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173 Title : mrna()
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174 Usage : $mrna = $transcript->mrna();
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175 Function: Get the mRNA of the transcript as a sequence object.
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176
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177 Returns : A Bio::PrimarySeqI implementing object.
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178 Args :
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179
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180
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181 =cut
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182
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183 sub mrna {
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184 my ($self) = @_;
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185 $self->throw_not_implemented();
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186 }
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187
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188 =head2 cds
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189
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190 Title : cds()
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191 Usage : $cds = $transcript->cds();
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192 Function: Get the CDS (coding sequence) of the transcript as a sequence
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193 object.
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194
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195 Returns : A Bio::PrimarySeqI implementing object.
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196 Args :
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197
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198
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199 =cut
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200
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201 sub cds {
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202 my ($self) = @_;
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203 $self->throw_not_implemented();
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204 }
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205
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206 =head2 protein
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207
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208 Title : protein()
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209 Usage : $protein = $transcript->protein();
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210 Function: Get the protein encoded by the transcript as a sequence object.
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211
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212 Returns : A Bio::PrimarySeqI implementing object.
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213 Args :
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214
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215
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216 =cut
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217
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218 sub protein {
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219 my ($self) = @_;
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220 $self->throw_not_implemented();
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221 }
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222
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223 =head2 parent
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224
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225 Title : parent
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226 Usage : $obj->parent($newval)
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227 Function: get the parent gene of the transcript
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228 Returns : value of parent - a Bio::SeqFeature::Gene::GeneStructureI-compliant object
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229 Args : a Bio::SeqFeature::Gene::GeneStructureI-compliant object (optional)
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230
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231
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232 =cut
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233
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234 sub parent{
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235 my ($self,$value) = @_;
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236 if( defined $value) {
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237 if ($value->isa("Bio::SeqFeature::Gene::GeneStructureI")) {
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238 $self->{'parent'} = $value;
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239 } else {
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240 $self->throw("$value must be a Bio::SeqFeature::Gene::GeneStructureI")
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241 }
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242 }
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243 return $self->{'parent'};
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244 }
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245
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246
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247 1;
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