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1 # $Id: SplitLocationI.pm,v 1.14 2002/12/01 00:05:20 jason Exp $
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2 #
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3 # BioPerl module for Bio::Location::SplitLocationI
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4 # Cared for by Jason Stajich <jason@bioperl.org>
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5 #
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6 # Copyright Jason Stajich
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7 #
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8 # You may distribute this module under the same terms as perl itself
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9 # POD documentation - main docs before the code
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10
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11 =head1 NAME
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12
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13 Bio::SplitLocationI - Abstract interface of a Location on a Sequence
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14 which has multiple locations (start/end points)
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15
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16 =head1 SYNOPSIS
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17
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18 # get a SplitLocationI somehow
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19 print $splitlocation->start, "..", $splitlocation->end, "\n";
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20 my @sublocs = $splitlocation->sub_Location();
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21
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22 my $count = 1;
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23 # print the start/end points of the sub locations
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24 foreach my $location ( sort { $a->start <=> $b->start }
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25 @sublocs ) {
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26 printf "sub feature %d [%d..%d]\n", $location->start,$location->end;
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27 $count++;
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28 }
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29
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30 =head1 DESCRIPTION
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31
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32 This interface encapsulates the necessary methods for representing the
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33 location of a sequence feature that has more that just a single
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34 start/end pair. Some examples of this are the annotated exons in a
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35 gene or the annotated CDS in a sequence file.
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36
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37 =head1 FEEDBACK
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38
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39 User feedback is an integral part of the evolution of this and other
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40 Bioperl modules. Send your comments and suggestions preferably to one
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41 of the Bioperl mailing lists. Your participation is much appreciated.
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42
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43 bioperl-l@bioperl.org - General discussion
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44 http://bio.perl.org/MailList.html - About the mailing lists
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45
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46 =head2 Reporting Bugs
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47
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48 Report bugs to the Bioperl bug tracking system to help us keep track
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49 the bugs and their resolution. Bug reports can be submitted via email
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50 or the web:
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51
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52 bioperl-bugs@bio.perl.org
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53 http://bugzilla.bioperl.org/
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54
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55 =head1 AUTHOR - Jason Stajich
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56
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57 Email jason@bioperl.org
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58
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59 =head1 APPENDIX
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60
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61 The rest of the documentation details each of the object
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62 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 # Let the code begin...
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67
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68
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69 package Bio::Location::SplitLocationI;
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70 use vars qw(@ISA);
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71 use strict;
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72
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73 use Bio::LocationI;
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74 use Carp;
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75
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76 @ISA = qw(Bio::LocationI);
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77
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78
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79 =head2 sub_Location
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80
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81 Title : sub_Location
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82 Usage : @locations = $feat->sub_Location();
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83 Function: Returns an array of LocationI objects
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84 Returns : An array
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85 Args : none
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86
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87 =cut
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88
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89 sub sub_Location {
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90 my ($self,@args) = @_;
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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 splittype
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95
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96 Title : splittype
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97 Usage : $splittype = $fuzzy->splittype();
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98 Function: get/set the split splittype
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99 Returns : the splittype of split feature (join, order)
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100 Args : splittype to set
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101
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102 =cut
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103
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104 sub splittype {
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105 my($self) = @_;
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106 $self->throw_not_implemented();
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107 }
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108
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109
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110 =head2 is_single_sequence
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111
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112 Title : is_single_sequence
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113 Usage : if($splitloc->is_single_sequence()) {
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114 print "Location object $splitloc is split ".
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115 "but only across a single sequence\n";
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116 }
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117 Function: Determine whether this location is split across a single or
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118 multiple sequences.
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119 Returns : TRUE if all sublocations lie on the same sequence as the root
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120 location (feature), and FALSE otherwise.
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121 Args : none
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122
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123 =cut
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124
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125 sub is_single_sequence {
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126 my ($self) = @_;
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127 $self->throw_not_implemented();
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128 }
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129
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130 =head1 Bio::LocationI methods
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131
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132 Bio::LocationI inherited methods follow
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133
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134 =head2 min_start
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135
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136 Title : min_start
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137 Usage : my $minstart = $location->min_start();
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138 Function: Get minimum starting location of feature startpoint
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139 Returns : integer or undef if no maximum starting point.
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140 Args : none
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141
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142 =cut
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143
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144 =head2 max_start
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145
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146 Title : max_start
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147 Usage : my $maxstart = $location->max_start();
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148 Function: Get maximum starting location of feature startpoint
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149 Returns : integer or undef if no maximum starting point.
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150 Args : none
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151
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152 =cut
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153
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154 =head2 start_pos_type
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155
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156 Title : start_pos_type
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157 Usage : my $start_pos_type = $location->start_pos_type();
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158 Function: Get start position type (ie <,>, ^)
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159 Returns : type of position coded as text
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160 ('BEFORE', 'AFTER', 'EXACT','WITHIN', 'BETWEEN')
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161 Args : none
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162
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163 =cut
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164
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165 =head2 min_end
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166
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167 Title : min_end
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168 Usage : my $minend = $location->min_end();
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169 Function: Get minimum ending location of feature endpoint
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170 Returns : integer or undef if no minimum ending point.
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171 Args : none
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172
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173 =cut
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174
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175 =head2 max_end
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176
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177 Title : max_end
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178 Usage : my $maxend = $location->max_end();
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179 Function: Get maximum ending location of feature endpoint
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180 Returns : integer or undef if no maximum ending point.
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181 Args : none
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182
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183 =cut
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184
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185 =head2 end_pos_type
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186
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187 Title : end_pos_type
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188 Usage : my $end_pos_type = $location->end_pos_type();
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189 Function: Get end position type (ie <,>, ^)
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190 Returns : type of position coded as text
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191 ('BEFORE', 'AFTER', 'EXACT','WITHIN', 'BETWEEN')
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192 Args : none
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193
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194 =cut
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195
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196 =head2 seq_id
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197
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198 Title : seq_id
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199 Usage : my $seqid = $location->seq_id();
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200 Function: Get/Set seq_id that location refers to
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201 Returns : seq_id
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202 Args : [optional] seq_id value to set
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203
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204 =cut
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205
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206 =head2 coordinate_policy
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207
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208 Title : coordinate_policy
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209 Usage : $policy = $location->coordinate_policy();
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210 $location->coordinate_policy($mypolicy); # set may not be possible
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211 Function: Get the coordinate computing policy employed by this object.
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212
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213 See Bio::Location::CoordinatePolicyI for documentation about
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214 the policy object and its use.
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215
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216 The interface *does not* require implementing classes to accept
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217 setting of a different policy. The implementation provided here
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218 does, however, allow to do so.
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219
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220 Implementors of this interface are expected to initialize every
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221 new instance with a CoordinatePolicyI object. The implementation
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222 provided here will return a default policy object if none has
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223 been set yet. To change this default policy object call this
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224 method as a class method with an appropriate argument. Note that
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225 in this case only subsequently created Location objects will be
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226 affected.
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227
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228 Returns : A Bio::Location::CoordinatePolicyI implementing object.
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229 Args : On set, a Bio::Location::CoordinatePolicyI implementing object.
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230
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231 =cut
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232
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233 =head2 to_FTstring
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234
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235 Title : to_FTstring
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236 Usage : my $locstr = $location->to_FTstring()
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237 Function: returns the FeatureTable string of this location
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238 Returns : string
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239 Args : none
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240
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241 =cut
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242
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243 1;
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244
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