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1 # $Id: FuzzyLocationI.pm,v 1.17 2002/12/01 00:05:20 jason Exp $
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2 #
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3 # BioPerl module for Bio::Location::FuzzyLocationI
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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::Location::FuzzyLocationI - Abstract interface of a Location on a Sequence
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14 which has unclear start/end location
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15
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16 =head1 SYNOPSIS
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17
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18 # Get a FuzzyLocationI object somehow
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19 print "Fuzzy FT location string is ", $location->to_FTstring();
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20 print "location is of the type ", $location->loc_type, "\n";
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21
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22 =head1 DESCRIPTION
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23
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24 This interface encapsulates the necessary methods for representing a
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25 Fuzzy Location, one that does not have clear start and/or end points.
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26 This will initially serve to handle features from Genbank/EMBL feature
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27 tables that are written as 1^100 meaning between bases 1 and 100 or
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28 E<lt>100..300 meaning it starts somewhere before 100. Advanced
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29 implementations of this interface may be able to handle the necessary
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30 logic of overlaps/intersection/contains/union. It was constructed to
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31 handle fuzzy locations that can be represented in Genbank/EMBL.
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32
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33 =head1 FEEDBACK
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34
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35 User feedback is an integral part of the evolution of this and other
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36 Bioperl modules. Send your comments and suggestions preferably to one
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37 of the Bioperl mailing lists. Your participation is much appreciated.
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38
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39 bioperl-l@bioperl.org - General discussion
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40 http://bio.perl.org/MailList.html - About the mailing lists
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41
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42 =head2 Reporting Bugs
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43
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44 Report bugs to the Bioperl bug tracking system to help us keep track
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45 the bugs and their resolution. Bug reports can be submitted via email
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46 or the web:
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47
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48 bioperl-bugs@bio.perl.org
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49 http://bugzilla.bioperl.org/
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50
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51 =head1 AUTHOR - Jason Stajich
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52
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53 Email jason@bioperl.org
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54
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55 =head1 APPENDIX
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56
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57 The rest of the documentation details each of the object
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58 methods. Internal methods are usually preceded with a _
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59
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60 =cut
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61
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62 # Let the code begin...
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63
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64
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65 package Bio::Location::FuzzyLocationI;
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66 use vars qw(@ISA);
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67 use strict;
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68
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69 use Bio::LocationI;
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70 use Carp;
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71
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72 @ISA = qw(Bio::LocationI);
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73
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74 =head1 LocationI methods
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75
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76 =head2 location_type
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77
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78 Title : loc_type
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79 Usage : my $location_type = $location->location_type();
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80 Function: Get location type encoded as text
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81 Returns : string ('EXACT', 'WITHIN', 'BETWEEN')
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82 Args : none
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83
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84 =cut
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85
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86 sub location_type {
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87 my ($self) = @_;
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88 $self->throw_not_implemented();
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89 }
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90
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91 =head1 Bio::LocationI methods
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92
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93 Bio::LocationI methods follow
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94
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95 =head2 min_start
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96
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97 Title : min_start
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98 Usage : my $minstart = $location->min_start();
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99 Function: Get minimum starting location of feature startpoint
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100 Returns : integer or undef if no maximum starting point.
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101 Args : none
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102
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103 =cut
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104
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105 =head2 max_start
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106
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107 Title : max_start
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108 Usage : my $maxstart = $location->max_start();
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109 Function: Get maximum starting location of feature startpoint
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110 Returns : integer or undef if no maximum starting point.
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111 Args : none
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112
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113 =cut
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114
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115 =head2 start_pos_type
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116
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117 Title : start_pos_type
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118 Usage : my $start_pos_type = $location->start_pos_type();
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119 Function: Get start position type (ie <,>, ^)
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120 Returns : type of position coded as text
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121 ('BEFORE', 'AFTER', 'EXACT','WITHIN', 'BETWEEN')
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122 Args : none
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123
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124 =cut
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125
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126 =head2 min_end
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127
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128 Title : min_end
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129 Usage : my $minend = $location->min_end();
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130 Function: Get minimum ending location of feature endpoint
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131 Returns : integer or undef if no minimum ending point.
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132 Args : none
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133
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134 =cut
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135
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136 =head2 max_end
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137
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138 Title : max_end
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139 Usage : my $maxend = $location->max_end();
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140 Function: Get maximum ending location of feature endpoint
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141 Returns : integer or undef if no maximum ending point.
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142 Args : none
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143
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144 =cut
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145
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146 =head2 end_pos_type
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147
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148 Title : end_pos_type
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149 Usage : my $end_pos_type = $location->end_pos_type();
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150 Function: Get end position type (ie <,>, ^)
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151 Returns : type of position coded as text
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152 ('BEFORE', 'AFTER', 'EXACT','WITHIN', 'BETWEEN')
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153 Args : none
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154
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155 =cut
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156
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157 =head2 seq_id
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158
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159 Title : seq_id
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160 Usage : my $seqid = $location->seq_id();
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161 Function: Get/Set seq_id that location refers to
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162 Returns : seq_id
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163 Args : [optional] seq_id value to set
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164
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165 =cut
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166
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167 =head2 coordinate_policy
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168
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169 Title : coordinate_policy
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170 Usage : $policy = $location->coordinate_policy();
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171 $location->coordinate_policy($mypolicy); # set may not be possible
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172 Function: Get the coordinate computing policy employed by this object.
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173
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174 See Bio::Location::CoordinatePolicyI for documentation about
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175 the policy object and its use.
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176
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177 The interface *does not* require implementing classes to accept
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178 setting of a different policy. The implementation provided here
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179 does, however, allow to do so.
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180
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181 Implementors of this interface are expected to initialize every
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182 new instance with a CoordinatePolicyI object. The implementation
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183 provided here will return a default policy object if none has
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184 been set yet. To change this default policy object call this
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185 method as a class method with an appropriate argument. Note that
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186 in this case only subsequently created Location objects will be
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187 affected.
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188
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189 Returns : A Bio::Location::CoordinatePolicyI implementing object.
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190 Args : On set, a Bio::Location::CoordinatePolicyI implementing object.
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191
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192 =cut
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193
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194 =head2 to_FTstring
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195
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196 Title : to_FTstring
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197 Usage : my $locstr = $location->to_FTstring()
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198 Function: returns the FeatureTable string of this location
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199 Returns : string
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200 Args : none
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201
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202 =cut
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203
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204 1;
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