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1 =head1 NAME
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2
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3 Bio::DB::GFF::Segment -- Simple DNA segment object
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4
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5 =head1 SYNOPSIS
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6
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7 See L<Bio::DB::GFF>.
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8
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9 =head1 DESCRIPTION
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10
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11 Bio::DB::GFF::Segment provides the basic representation of a range of
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12 DNA contained in a GFF database. It is the base class from which the
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13 Bio::DB::GFF::RelSegment and Bio::DB::GFF::Feature classes are
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14 derived.
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15
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16 Generally, you will not create or manipulate Bio::DB::GFF::Segment
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17 objects directly, but use those that are returned by the Bio::DB::GFF
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18 module.
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19
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20 =cut
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21
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22 package Bio::DB::GFF::Segment;
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23
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24 use strict;
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25 use Bio::Root::Root;
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26 use Bio::Annotation::Collection;
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27 use Bio::RangeI;
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28 use Bio::Das::SegmentI;
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29 use Bio::SeqI;
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30
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31 use vars qw(@ISA);
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32 @ISA = qw(Bio::Root::Root Bio::RangeI Bio::SeqI Bio::Das::SegmentI);
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33
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34 use overload
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35 '""' => 'asString',
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36 eq => 'equals',
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37 fallback => 1;
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38
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39 =head1 API
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40
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41 The remainder of this document describes the API for
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42 Bio::DB::GFF::Segment.
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43
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44 =cut
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45
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46 =head2 new
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47
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48 Title : new
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49 Usage : $s = Bio::DB::GFF::Segment->new(@args)
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50 Function: create a new segment
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51 Returns : a new Bio::DB::GFF::Segment object
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52 Args : see below
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53 Status : Public
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54
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55 This method creates a new Bio::DB::GFF::Segment object. Generally
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56 this is called automatically by the Bio::DB::GFF module and
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57 derivatives.
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58
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59 There are five positional arguments:
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60
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61 $factory a Bio::DB::GFF::Adaptor to use for database access
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62 $sourceseq ID of the source sequence
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63 $sourceclass class of the source sequence
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64 $start start of the desired segment relative to source sequence
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65 $stop stop of the desired segment relative to source sequence
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66
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67 =cut
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68
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69 sub new {
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70 my $class = shift;
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71 my ($factory,$segclass,$segname,$start,$stop) = @_;
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72 $segclass = $segname->class if ref($segname) && $segname->can('class');
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73 $segclass ||= 'Sequence';
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74
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75 $factory or $class->throw("->new(): provide a factory argument");
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76 $class = ref $class if ref $class;
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77 return bless { factory => $factory,
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78 sourceseq => $segname,
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79 class => $segclass,
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80 start => $start,
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81 stop => $stop,
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82 strand => 0,
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83 },$class;
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84 }
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85
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86 # read-only accessors
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87
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88 =head2 factory
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89
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90 Title : factory
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91 Usage : $s->factory
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92 Function: get the factory object
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93 Returns : a Bio::DB::GFF::Adaptor
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94 Args : none
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95 Status : Public
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96
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97 This is a read-only accessor for the Bio::DB::GFF::Adaptor object used
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98 to create the segment.
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99
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100 =cut
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101
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102 sub factory { shift->{factory} }
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103
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104 # start, stop, length
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105
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106 =head2 start
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107
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108 Title : start
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109 Usage : $s->start
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110 Function: start of segment
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111 Returns : integer
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112 Args : none
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113 Status : Public
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114
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115 This is a read-only accessor for the start of the segment.
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116
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117 =cut
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118
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119 sub start { shift->{start} }
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120
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121 =head2 end
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122
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123 Title : end
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124 Usage : $s->end
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125 Function: end of segment
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126 Returns : integer
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127 Args : none
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128 Status : Public
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129
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130 This is a read-only accessor for the end of the segment.
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131
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132 =cut
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133
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134 sub end { shift->{stop} }
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135
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136 =head2 stop
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137
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138 Title : stop
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139 Usage : $s->stop
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140 Function: stop of segment
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141 Returns : integer
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142 Args : none
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143 Status : Public
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144
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145 This is an alias for end(), provided for AcePerl compatibility.
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146
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147 =cut
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148
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149 *stop = \&end;
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150
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151 =head2 length
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152
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153 Title : length
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154 Usage : $s->length
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155 Function: length of segment
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156 Returns : integer
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157 Args : none
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158 Status : Public
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159
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160 Returns the length of the segment. Always a positive number.
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161
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162 =cut
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163
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164 sub length { abs($_[0]->{start} - $_[0]->{stop})+1 }
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165
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166
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167 =head2 strand
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168
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169 Title : strand
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170 Usage : $s->strand
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171 Function: strand of segment
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172 Returns : +1,0,-1
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173 Args : none
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174 Status : Public
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175
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176 Returns the strand on which the segment resides, either +1, 0 or -1.
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177
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178 =cut
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179
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180 sub strand {
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181 my $self = shift;
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182 0;
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183 }
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184
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185 =head2 low
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186
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187 Title : low
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188 Usage : $s->low
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189 Function: return lower coordinate
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190 Returns : lower coordinate
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191 Args : none
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192 Status : Public
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193
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194 Returns the lower coordinate, either start or end.
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195
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196 =cut
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197
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198 sub low {
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199 my $self = shift;
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200 my ($start,$stop) = ($self->start,$self->stop);
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201 return $start < $stop ? $start : $stop;
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202 }
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203 *abs_low = \&low;
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204
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205 =head2 high
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206
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207 Title : high
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208 Usage : $s->high
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209 Function: return higher coordinate
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210 Returns : higher coordinate
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211 Args : none
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212 Status : Public
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213
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214 Returns the higher coordinate, either start or end.
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215
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216 =cut
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217
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218 sub high {
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219 my $self = shift;
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220 my ($start,$stop) = ($self->start,$self->stop);
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221 return $start > $stop ? $start : $stop;
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222 }
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223 *abs_high = \&high;
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224
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225 =head2 sourceseq
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226
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227 Title : sourceseq
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228 Usage : $s->sourceseq
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229 Function: get the segment source
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230 Returns : a string
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231 Args : none
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232 Status : Public
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233
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234 Returns the name of the source sequence for this segment.
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235
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236 =cut
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237
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238 sub sourceseq { shift->{sourceseq} }
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239
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240 =head2 class
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241
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242 Title : class
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243 Usage : $s->class([$newclass])
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244 Function: get the source sequence class
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245 Returns : a string
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246 Args : new class (optional)
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247 Status : Public
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248
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249 Gets or sets the class for the source sequence for this segment.
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250
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251 =cut
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252
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253 sub class {
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254 my $self = shift;
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255 my $d = $self->{class};
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256 $self->{class} = shift if @_;
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257 $d;
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258 }
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259
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260 =head2 subseq
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261
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262 Title : subseq
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263 Usage : $s->subseq($start,$stop)
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264 Function: generate a subsequence
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265 Returns : a Bio::DB::GFF::Segment object
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266 Args : start and end of subsequence
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267 Status : Public
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268
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269 This method generates a new segment from the start and end positions
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270 given in the arguments. If stop E<lt> start, then the strand is reversed.
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271
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272 =cut
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273
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274 sub subseq {
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275 my $self = shift;
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276 my ($newstart,$newstop) = @_;
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277 my ($refseq,$start,$stop,$class) = ($self->{sourceseq},
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278 $self->{start},$self->{stop},
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279 $self->class);
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280
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281 # We deliberately force subseq to return objects of type RelSegment
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282 # Otherwise, when we get a subsequence from a Feature object,
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283 # its method and source go along for the ride, which is incorrect.
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284 my $new = $self->new_from_segment($self);
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285 if ($start <= $stop) {
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286 @{$new}{qw(start stop)} = ($start + $newstart - 1, $start + $newstop - 1);
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287 } else {
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288 @{$new}{qw(start stop)} = ($start - ($newstart - 1), $start - ($newstop - 1)),
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289
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290 }
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291
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292 $new;
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293 }
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294
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295 =head2 seq
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296
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297 Title : seq
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298 Usage : $s->seq
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299 Function: get the sequence string for this segment
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300 Returns : a string
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301 Args : none
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302 Status : Public
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303
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304 Returns the sequence for this segment as a simple string. (-) strand
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305 segments are automatically reverse complemented
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306
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307 This method is also called dna() and protein() for backward
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308 compatibility with AceDB.
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309
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310 =cut
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311
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312 sub seq {
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313 my $self = shift;
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314 my ($ref,$class,$start,$stop,$strand)
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315 = @{$self}{qw(sourceseq class start stop strand)};
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316 # ($start,$stop) = ($stop,$start) if $strand eq '-';
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317 $self->factory->dna($ref,$start,$stop,$class);
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318 }
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319
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320 *protein = *dna = \&seq;
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321
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322
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323 =head2 primary_seq
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324
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325 Title : primary_seq
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326 Usage : $s->primary_seq
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327 Function: returns a Bio::PrimarySeqI compatible object
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328 Returns : a Bio::PrimarySeqI object
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329 Args : none
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330 Status : Public
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331
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332 This is for compatibility with BioPerl's separation of SeqI
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333 from PrimarySeqI. It just returns itself.
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334
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335 =cut
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336
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337 #'
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338
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339 sub primary_seq { shift }
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340
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341 =head2 type
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342
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343 Title : type
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344 Usage : $s->type
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345 Function: return the string "feature"
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346 Returns : the string "feature"
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347 Args : none
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348 Status : Public
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349
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350 This is for future sequence ontology-compatibility and
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351 represents the default type of a feature on the genome
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352
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353 =cut
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354
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355 sub type { "feature" }
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356
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357 =head2 equals
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358
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359 Title : equals
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360 Usage : $s->equals($d)
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361 Function: segment equality
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362 Returns : true, if two segments are equal
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363 Args : another segment
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364 Status : Public
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365
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366 Returns true if the two segments have the same source sequence, start and stop.
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367
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368 =cut
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369
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370 sub equals {
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371 my $self = shift;
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372 my $peer = shift;
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373 return unless defined $peer;
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374 return $self->asString eq $peer unless ref($peer) && $peer->isa('Bio::DB::GFF::Segment');
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375 return $self->{start} eq $peer->{start}
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376 && $self->{stop} eq $peer->{stop}
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377 && $self->{sourceseq} eq $peer->{sourceseq};
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378 }
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379
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380 =head2 asString
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381
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382 Title : asString
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383 Usage : $s->asString
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384 Function: human-readable string for segment
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385 Returns : a string
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386 Args : none
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387 Status : Public
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388
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389 Returns a human-readable string representing this sequence. Format
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390 is:
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391
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392 sourceseq/start,stop
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393
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394 =cut
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395
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396 sub asString {
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397 my $self = shift;
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398 my $label = $self->refseq;
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399 my $start = $self->start;
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400 my $stop = $self->stop;
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401 return "$label:$start,$stop";
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402 }
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403
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404 =head2 clone
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405
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406 Title : clone
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407 Usage : $copy = $s->clone
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408 Function: make a copy of this segment
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409 Returns : a Bio::DB::GFF::Segment object
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410 Args : none
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411 Status : Public
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412
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413 This method creates a copy of the segment and returns it.
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414
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415 =cut
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416
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417 # deep copy of the thing
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418 sub clone {
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419 my $self = shift;
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420 my %h = %$self;
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421 return bless \%h,ref($self);
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422 }
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423
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424 =head2 error
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425
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426 Title : error
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427 Usage : $error = $s->error([$new_error])
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428 Function: get or set the last error
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429 Returns : a string
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430 Args : an error message (optional)
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431 Status : Public
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432
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433 In case of a fault, this method can be used to obtain the last error
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434 message. Internally it is called to set the error message.
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435
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436 =cut
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437
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438 sub error {
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439 my $self = shift;
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440 my $g = $self->{error};
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441 $self->{error} = shift if @_;
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442 $g;
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443 }
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444
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445 =head1 Relative Addressing Methods
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446
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447 The following methods are provided for compatibility with
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448 Bio::DB::GFF::RelSegment, which provides relative addressing
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449 functions.
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450
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451 =head2 abs_start
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452
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453 Title : abs_start
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454 Usage : $s->abs_start
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455 Function: the absolute start of the segment
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456 Returns : an integer
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457 Args : none
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458 Status : Public
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459
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460 This is an alias to start(), and provided for API compatibility with
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461 Bio::DB::GFF::RelSegment.
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462
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463 =cut
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464
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465 *abs_start = \&start;
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466
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467 =head2 abs_end
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468
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469 Title : abs_end
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470 Usage : $s->abs_end
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471 Function: the absolute stop of the segment
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472 Returns : an integer
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473 Args : none
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474 Status : Public
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475
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476 This is an alias to stop(), and provided for API compatibility with
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477 Bio::DB::GFF::RelSegment.
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478
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479 =cut
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480
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481 *abs_stop = \&stop;
|
|
|
482 *abs_end = \&stop;
|
|
|
483
|
|
|
484 =head2 abs_strand
|
|
|
485
|
|
|
486 Title : abs_strand
|
|
|
487 Usage : $s->abs_strand
|
|
|
488 Function: the absolute strand of the segment
|
|
|
489 Returns : +1,0,-1
|
|
|
490 Args : none
|
|
|
491 Status : Public
|
|
|
492
|
|
|
493 This is an alias to strand(), and provided for API compatibility with
|
|
|
494 Bio::DB::GFF::RelSegment.
|
|
|
495
|
|
|
496 =cut
|
|
|
497
|
|
|
498 sub abs_strand {
|
|
|
499 my $self = shift;
|
|
|
500 return $self->abs_end <=> $self->abs_start;
|
|
|
501 }
|
|
|
502
|
|
|
503 =head2 abs_ref
|
|
|
504
|
|
|
505 Title : abs_ref
|
|
|
506 Usage : $s->abs_ref
|
|
|
507 Function: the reference sequence for this segment
|
|
|
508 Returns : a string
|
|
|
509 Args : none
|
|
|
510 Status : Public
|
|
|
511
|
|
|
512 This is an alias to sourceseq(), and is here to provide API
|
|
|
513 compatibility with Bio::DB::GFF::RelSegment.
|
|
|
514
|
|
|
515 =cut
|
|
|
516
|
|
|
517 *abs_ref = \&sourceseq;
|
|
|
518
|
|
|
519 =head2 refseq
|
|
|
520
|
|
|
521 Title : refseq
|
|
|
522 Usage : $s->refseq
|
|
|
523 Function: get or set the reference sequence
|
|
|
524 Returns : a string
|
|
|
525 Args : none
|
|
|
526 Status : Public
|
|
|
527
|
|
|
528 Examine or change the reference sequence. This is an alias to
|
|
|
529 sourceseq(), provided here for API compatibility with
|
|
|
530 Bio::DB::GFF::RelSegment.
|
|
|
531
|
|
|
532 =cut
|
|
|
533
|
|
|
534 *refseq = \&sourceseq;
|
|
|
535
|
|
|
536 =head2 ref
|
|
|
537
|
|
|
538 Title : ref
|
|
|
539 Usage : $s->refseq
|
|
|
540 Function: get or set the reference sequence
|
|
|
541 Returns : a string
|
|
|
542 Args : none
|
|
|
543 Status : Public
|
|
|
544
|
|
|
545 An alias for refseq()
|
|
|
546
|
|
|
547 =cut
|
|
|
548
|
|
|
549 sub ref { shift->refseq(@_) }
|
|
|
550
|
|
|
551 =head2 seq_id
|
|
|
552
|
|
|
553 Title : seq_id
|
|
|
554 Usage : $ref = $s->seq_id
|
|
|
555 Function: get the reference sequence in a LocationI-compatible way
|
|
|
556 Returns : a string
|
|
|
557 Args : none
|
|
|
558 Status : Public
|
|
|
559
|
|
|
560 An alias for refseq() but only allows reading.
|
|
|
561
|
|
|
562 =cut
|
|
|
563
|
|
|
564 sub seq_id { shift->refseq }
|
|
|
565
|
|
|
566 =head2 truncated
|
|
|
567
|
|
|
568 Title : truncated
|
|
|
569 Usage : $truncated = $s->truncated
|
|
|
570 Function: Flag indicating that the segment was truncated during creation
|
|
|
571 Returns : A boolean flag
|
|
|
572 Args : none
|
|
|
573 Status : Public
|
|
|
574
|
|
|
575 This indicates that the sequence was truncated during creation. The
|
|
|
576 returned flag is undef if no truncation occured. If truncation did
|
|
|
577 occur, the flag is actually an array ref in which the first element is
|
|
|
578 true if truncation occurred on the left, and the second element
|
|
|
579 occurred if truncation occurred on the right.
|
|
|
580
|
|
|
581 =cut
|
|
|
582
|
|
|
583 sub truncated {
|
|
|
584 my $self = shift;
|
|
|
585 my $hash = $self->{truncated} or return;
|
|
|
586 CORE::ref($hash) eq 'HASH' or return [1,1]; # paranoia -- not that this would ever happen ;-)
|
|
|
587 return [$hash->{start},$hash->{stop}];
|
|
|
588 }
|
|
|
589
|
|
|
590 =head2 Bio::RangeI Methods
|
|
|
591
|
|
|
592 The following Bio::RangeI methods are supported:
|
|
|
593
|
|
|
594 overlaps(), contains(), equals(),intersection(),union(),overlap_extent()
|
|
|
595
|
|
|
596 =cut
|
|
|
597
|
|
|
598 sub overlaps {
|
|
|
599 my $self = shift;
|
|
|
600 my($other,$so) = @_;
|
|
|
601 if ($other->isa('Bio::DB::GFF::RelSegment')) {
|
|
|
602 return if $self->abs_ref ne $other->abs_ref;
|
|
|
603 }
|
|
|
604 $self->SUPER::overlaps(@_);
|
|
|
605 }
|
|
|
606
|
|
|
607 sub contains {
|
|
|
608 my $self = shift;
|
|
|
609 my($other,$so) = @_;
|
|
|
610 if ($other->isa('Bio::DB::GFF::RelSegment')) {
|
|
|
611 return if $self->abs_ref ne $other->abs_ref;
|
|
|
612 }
|
|
|
613 $self->SUPER::contains(@_);
|
|
|
614 }
|
|
|
615 #sub equals {
|
|
|
616 # my $self = shift;
|
|
|
617 # my($other,$so) = @_;
|
|
|
618 # if ($other->isa('Bio::DB::GFF::RelSegment')) {
|
|
|
619 # return if $self->abs_ref ne $other->abs_ref;
|
|
|
620 # }
|
|
|
621 # $self->SUPER::equals(@_);
|
|
|
622 #}
|
|
|
623 sub intersection {
|
|
|
624 my $self = shift;
|
|
|
625 my($other,$so) = @_;
|
|
|
626 if ($other->isa('Bio::DB::GFF::RelSegment')) {
|
|
|
627 return if $self->abs_ref ne $other->abs_ref;
|
|
|
628 }
|
|
|
629 $self->SUPER::intersection(@_);
|
|
|
630 }
|
|
|
631 sub union {
|
|
|
632 my $self = shift;
|
|
|
633 my($other) = @_;
|
|
|
634 if ($other->isa('Bio::DB::GFF::RelSegment')) {
|
|
|
635 return if $self->abs_ref ne $other->abs_ref;
|
|
|
636 }
|
|
|
637 $self->SUPER::union(@_);
|
|
|
638 }
|
|
|
639
|
|
|
640 sub overlap_extent {
|
|
|
641 my $self = shift;
|
|
|
642 my($other) = @_;
|
|
|
643 if ($other->isa('Bio::DB::GFF::RelSegment')) {
|
|
|
644 return if $self->abs_ref ne $other->abs_ref;
|
|
|
645 }
|
|
|
646 $self->SUPER::overlap_extent(@_);
|
|
|
647 }
|
|
|
648
|
|
|
649
|
|
|
650 =head2 Bio::SeqI implementation
|
|
|
651
|
|
|
652 =cut
|
|
|
653
|
|
|
654 =head2 primary_id
|
|
|
655
|
|
|
656 Title : primary_id
|
|
|
657 Usage : $unique_implementation_key = $obj->primary_id;
|
|
|
658 Function: Returns the unique id for this object in this
|
|
|
659 implementation. This allows implementations to manage their
|
|
|
660 own object ids in a way the implementaiton can control
|
|
|
661 clients can expect one id to map to one object.
|
|
|
662
|
|
|
663 For sequences with no accession number, this method should
|
|
|
664 return a stringified memory location.
|
|
|
665
|
|
|
666 Returns : A string
|
|
|
667 Args : None
|
|
|
668 Status : Virtual
|
|
|
669
|
|
|
670
|
|
|
671 =cut
|
|
|
672
|
|
|
673 sub primary_id {
|
|
|
674 my ($obj,$value) = @_;
|
|
|
675
|
|
|
676 if( defined $value) {
|
|
|
677 $obj->{'primary_id'} = $value;
|
|
|
678 }
|
|
|
679 if( ! exists $obj->{'primary_id'} ) {
|
|
|
680 return "$obj";
|
|
|
681 }
|
|
|
682 return $obj->{'primary_id'};
|
|
|
683 }
|
|
|
684
|
|
|
685
|
|
|
686 =head2 display_name
|
|
|
687
|
|
|
688 Title : display_name
|
|
|
689 Usage : $id = $obj->display_name or $obj->display_name($newid);
|
|
|
690 Function: Gets or sets the display id, also known as the common name of
|
|
|
691 the Seq object.
|
|
|
692
|
|
|
693 The semantics of this is that it is the most likely string
|
|
|
694 to be used as an identifier of the sequence, and likely to
|
|
|
695 have "human" readability. The id is equivalent to the LOCUS
|
|
|
696 field of the GenBank/EMBL databanks and the ID field of the
|
|
|
697 Swissprot/sptrembl database. In fasta format, the >(\S+) is
|
|
|
698 presumed to be the id, though some people overload the id
|
|
|
699 to embed other information. Bioperl does not use any
|
|
|
700 embedded information in the ID field, and people are
|
|
|
701 encouraged to use other mechanisms (accession field for
|
|
|
702 example, or extending the sequence object) to solve this.
|
|
|
703
|
|
|
704 Notice that $seq->id() maps to this function, mainly for
|
|
|
705 legacy/convenience issues.
|
|
|
706 Returns : A string
|
|
|
707 Args : None or a new id
|
|
|
708
|
|
|
709 Note, this used to be called display_id(), and this name is preserved for
|
|
|
710 backward compatibility. The default is to return the seq_id().
|
|
|
711
|
|
|
712 =cut
|
|
|
713
|
|
|
714 sub display_name { shift->seq_id }
|
|
|
715 *display_id = \&display_name;
|
|
|
716
|
|
|
717 =head2 accession_number
|
|
|
718
|
|
|
719 Title : accession_number
|
|
|
720 Usage : $unique_biological_key = $obj->accession_number;
|
|
|
721 Function: Returns the unique biological id for a sequence, commonly
|
|
|
722 called the accession_number. For sequences from established
|
|
|
723 databases, the implementors should try to use the correct
|
|
|
724 accession number. Notice that primary_id() provides the
|
|
|
725 unique id for the implemetation, allowing multiple objects
|
|
|
726 to have the same accession number in a particular implementation.
|
|
|
727
|
|
|
728 For sequences with no accession number, this method should return
|
|
|
729 "unknown".
|
|
|
730 Returns : A string
|
|
|
731 Args : None
|
|
|
732
|
|
|
733
|
|
|
734 =cut
|
|
|
735
|
|
|
736 sub accession_number {
|
|
|
737 return 'unknown';
|
|
|
738 }
|
|
|
739
|
|
|
740 =head2 alphabet
|
|
|
741
|
|
|
742 Title : alphabet
|
|
|
743 Usage : if( $obj->alphabet eq 'dna' ) { /Do Something/ }
|
|
|
744 Function: Returns the type of sequence being one of
|
|
|
745 'dna', 'rna' or 'protein'. This is case sensitive.
|
|
|
746
|
|
|
747 This is not called <type> because this would cause
|
|
|
748 upgrade problems from the 0.5 and earlier Seq objects.
|
|
|
749
|
|
|
750 Returns : a string either 'dna','rna','protein'. NB - the object must
|
|
|
751 make a call of the type - if there is no type specified it
|
|
|
752 has to guess.
|
|
|
753 Args : none
|
|
|
754 Status : Virtual
|
|
|
755
|
|
|
756
|
|
|
757 =cut
|
|
|
758
|
|
|
759 sub alphabet{
|
|
|
760 return 'dna'; # no way this will be anything other than dna!
|
|
|
761 }
|
|
|
762
|
|
|
763 =head2 desc
|
|
|
764
|
|
|
765 Title : desc
|
|
|
766 Usage : $seqobj->desc($string) or $seqobj->desc()
|
|
|
767 Function: Sets or gets the description of the sequence
|
|
|
768 Example :
|
|
|
769 Returns : The description
|
|
|
770 Args : The description or none
|
|
|
771
|
|
|
772
|
|
|
773 =cut
|
|
|
774
|
|
|
775 sub desc { shift->asString }
|
|
|
776
|
|
|
777 =head2 species
|
|
|
778
|
|
|
779 Title : species
|
|
|
780 Usage : $species = $seq->species() or $seq->species($species)
|
|
|
781 Function: Gets or sets the species
|
|
|
782 Example :
|
|
|
783 Returns : Bio::Species object
|
|
|
784 Args : None or Bio::Species object
|
|
|
785
|
|
|
786 See L<Bio::Species> for more information
|
|
|
787
|
|
|
788 =cut
|
|
|
789
|
|
|
790 sub species {
|
|
|
791 my ($self, $species) = @_;
|
|
|
792 if ($species) {
|
|
|
793 $self->{'species'} = $species;
|
|
|
794 } else {
|
|
|
795 return $self->{'species'};
|
|
|
796 }
|
|
|
797 }
|
|
|
798
|
|
|
799 =head2 annotation
|
|
|
800
|
|
|
801 Title : annotation
|
|
|
802 Usage : $ann = $seq->annotation or $seq->annotation($annotation)
|
|
|
803 Function: Gets or sets the annotation
|
|
|
804 Example :
|
|
|
805 Returns : Bio::Annotation object
|
|
|
806 Args : None or Bio::Annotation object
|
|
|
807
|
|
|
808 See L<Bio::Annotation> for more information
|
|
|
809
|
|
|
810 =cut
|
|
|
811
|
|
|
812 sub annotation {
|
|
|
813 my ($obj,$value) = @_;
|
|
|
814 if( defined $value || ! defined $obj->{'annotation'} ) {
|
|
|
815 $value = new Bio::Annotation::Collection() unless defined $value;
|
|
|
816 $obj->{'annotation'} = $value;
|
|
|
817 }
|
|
|
818 return $obj->{'annotation'};
|
|
|
819
|
|
|
820 }
|
|
|
821
|
|
|
822 =head2 is_circular
|
|
|
823
|
|
|
824 Title : is_circular
|
|
|
825 Usage : if( $obj->is_circular) { /Do Something/ }
|
|
|
826 Function: Returns true if the molecule is circular
|
|
|
827 Returns : Boolean value
|
|
|
828 Args : none
|
|
|
829
|
|
|
830 =cut
|
|
|
831
|
|
|
832 sub is_circular{
|
|
|
833 return 0;
|
|
|
834 }
|
|
|
835
|
|
|
836
|
|
|
837 1;
|
|
|
838 __END__
|
|
|
839
|
|
|
840 =head1 BUGS
|
|
|
841
|
|
|
842 Report them please.
|
|
|
843
|
|
|
844 =head1 SEE ALSO
|
|
|
845
|
|
|
846 L<bioperl>
|
|
|
847
|
|
|
848 =head1 AUTHOR
|
|
|
849
|
|
|
850 Lincoln Stein E<lt>lstein@cshl.orgE<gt>.
|
|
|
851
|
|
|
852 Copyright (c) 2001 Cold Spring Harbor Laboratory.
|
|
|
853
|
|
|
854 This library is free software; you can redistribute it and/or modify
|
|
|
855 it under the same terms as Perl itself.
|
|
|
856
|
|
|
857 =head1 CONTRIBUTORS
|
|
|
858
|
|
|
859 Jason Stajich E<lt>jason@bioperl.orgE<gt>.
|
|
|
860
|
|
|
861 =cut
|
|
|
862
|
