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1 # $Id: Fuzzy.pm,v 1.24 2002/12/01 00:05:20 jason Exp $
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2 #
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3 # BioPerl module for Bio::Location::Fuzzy
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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::Fuzzy - Implementation of a Location on a Sequence
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14 which has unclear start and/or end locations
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15
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16 =head1 SYNOPSIS
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17
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18 use Bio::Location::Fuzzy;
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19 my $fuzzylocation = new Bio::Location::Fuzzy(-start => '<30',
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20 -end => 90,
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21 -location_type => '.');
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22
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23 print "location string is ", $fuzzylocation->to_FTstring(), "\n";
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24 print "location is of the type ", $fuzzylocation->location_type, "\n";
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25
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26 =head1 DESCRIPTION
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27
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28 This module contains the necessary methods for representing a
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29 Fuzzy Location, one that does not have clear start and/or end points.
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30 This will initially serve to handle features from Genbank/EMBL feature
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31 tables that are written as 1^100 meaning between bases 1 and 100 or
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32 E<lt>100..300 meaning it starts somewhere before 100. Advanced
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33 implementations of this interface may be able to handle the necessary
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34 logic of overlaps/intersection/contains/union. It was constructed to
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35 handle fuzzy locations that can be represented in Genbank/EMBL.
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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 package Bio::Location::Fuzzy;
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69 use vars qw(@ISA );
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70 use strict;
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71
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72 use Bio::Location::FuzzyLocationI;
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73 use Bio::Location::Atomic;
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74
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75 @ISA = qw(Bio::Location::Atomic Bio::Location::FuzzyLocationI );
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76
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77 BEGIN {
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78 use vars qw( %FUZZYCODES %FUZZYPOINTENCODE %FUZZYRANGEENCODE
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79 @LOCATIONCODESBSANE );
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80
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81 @LOCATIONCODESBSANE = (undef, 'EXACT', 'WITHIN', 'BETWEEN',
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82 'BEFORE', 'AFTER');
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83
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84 %FUZZYCODES = ( 'EXACT' => '..', # Position is 'exact
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85 # Exact position is unknown, but is within the range specified, ((1.2)..100)
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86 'WITHIN' => '.',
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87 # 1^2
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88 'BETWEEN' => '^',
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89 # <100
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90 'BEFORE' => '<',
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91 # >10
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92 'AFTER' => '>');
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93
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94 # The following regular expressions map to fuzzy location types. Every
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95 # expression must match the complete encoded point string, and must
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96 # contain two groups identifying min and max. Empty matches are automatic.
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97 # converted to undef, except for 'EXACT', for which max is set to equal
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98 # min.
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99 %FUZZYPOINTENCODE = (
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100 '\>(\d+)(.{0})' => 'AFTER',
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101 '\<(.{0})(\d+)' => 'BEFORE',
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102 '(\d+)' => 'EXACT',
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103 '(\d+)(.{0})\>' => 'AFTER',
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104 '(.{0})(\d+)\<' => 'BEFORE',
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105 '(\d+)\.(\d+)' => 'WITHIN',
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106 '(\d+)\^(\d+)' => 'BETWEEN',
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107 );
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108
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109 %FUZZYRANGEENCODE = ( '\.' => 'WITHIN',
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110 '\.\.' => 'EXACT',
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111 '\^' => 'BETWEEN' );
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112
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113 }
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114
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115 =head2 new
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116
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117 Title : new
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118 Usage : my $fuzzyloc = new Bio::Location::Fuzzy( @args);
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119 Function:
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120 Returns :
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121 Args : -start => value for start (initialize by superclass)
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122 -end => value for end (initialize by superclass)
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123 -strand => value for strand (initialize by superclass)
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124 -location_type => either ('EXACT', 'WITHIN', 'BETWEEN') OR
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125 ( 1,2,3)
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126 -start_ext=> extension for start - defaults to 0,
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127 -start_fuz= fuzzy code for start can be
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128 ( 'EXACT', 'WITHIN', 'BETWEEN', 'BEFORE', 'AFTER') OR
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129 a value 1 - 5 corresponding to index+1 above
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130 -end_ext=> extension for end - defaults to 0,
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131 -end_fuz= fuzzy code for end can be
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132 ( 'EXACT', 'WITHIN', 'BETWEEN', 'BEFORE', 'AFTER') OR
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133 a value 1 - 5 corresponding to index+1 above
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134
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135 =cut
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136
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137 sub new {
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138 my ($class, @args) = @_;
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139 my $self = $class->SUPER::new(@args);
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140 my ($location_type, $start_ext, $start_fuz, $end_ext, $end_fuz) =
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141 $self->_rearrange([ qw(LOCATION_TYPE START_EXT START_FUZ
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142 END_EXT END_FUZ )
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143 ], @args);
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144
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145 $location_type && $self->location_type($location_type);
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146 $start_ext && $self->max_start($self->min_start + $start_ext);
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147 $end_ext && $self->max_end($self->min_end + $end_ext);
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148 $start_fuz && $self->start_pos_type($start_fuz);
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149 $end_fuz && $self->end_pos_type($end_fuz);
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150
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151 return $self;
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152 }
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153
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154 =head2 location_type
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155
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156 Title : location_type
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157 Usage : my $location_type = $location->location_type();
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158 Function: Get location type encoded as text
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159 Returns : string ('EXACT', 'WITHIN', 'BETWEEN')
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160 Args : none
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161
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162 =cut
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163
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164 sub location_type {
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165 my ($self,$value) = @_;
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166 if( defined $value || ! defined $self->{'_location_type'} ) {
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167 $value = 'EXACT' unless defined $value;
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168 if(! defined $FUZZYCODES{$value}) {
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169 $value = uc($value);
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170 if( $value =~ /\.\./ ) {
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171 $value = 'EXACT';
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172 } elsif( $value =~ /^\.$/ ) {
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173 $value = 'WITHIN';
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174 } elsif( $value =~ /\^/ ) {
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175 $value = 'BETWEEN';
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176
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177
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178 $self->throw("Use Bio::Location::Simple for IN-BETWEEN locations [". $self->start. "] and [". $self->end. "]")
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179 if defined $self->start && defined $self->end && ($self->end - 1 == $self->start);
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180
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181
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182 } elsif( $value ne 'EXACT' && $value ne 'WITHIN' &&
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183 $value ne 'BETWEEN' ) {
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184 $self->throw("Did not specify a valid location type");
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185 }
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186 }
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187 $self->{'_location_type'} = $value;
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188 }
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189 return $self->{'_location_type'};
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190 }
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191
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192 =head1 LocationI methods
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193
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194 =head2 length
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195
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196 Title : length
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197 Usage : $length = $fuzzy_loc->length();
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198 Function: Get the length of this location.
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199
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200 Note that the length of a fuzzy location will always depend
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201 on the currently active interpretation of start and end. The
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202 result will therefore vary for different CoordinatePolicy objects.
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203
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204 Returns : an integer
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205 Args : none
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206
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207 =cut
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208
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209 #sub length {
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210 # my($self) = @_;
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211 # return $self->SUPER::length() if( !$self->start || !$self->end);
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212 # $self->warn('Length is not valid for a FuzzyLocation');
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213 # return 0;
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214 #}
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215
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216 =head2 start
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217
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218 Title : start
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219 Usage : $start = $fuzzy->start();
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220 Function: get/set start of this range, handling fuzzy_starts
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221 Returns : a positive integer representing the start of the location
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222 Args : start location on set (can be fuzzy point string)
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223
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224 =cut
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225
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226 sub start {
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227 my($self,$value) = @_;
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228 if( defined $value ) {
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229 my ($encode,$min,$max) = $self->_fuzzypointdecode($value);
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230 $self->start_pos_type($encode);
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231 $self->min_start($min);
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232 $self->max_start($max);
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233 }
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234
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235 $self->throw("Use Bio::Location::Simple for IN-BETWEEN locations [". $self->SUPER::start. "] and [". $self->SUPER::end. "]")
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236 if $self->location_type eq 'BETWEEN' && defined $self->SUPER::end && ($self->SUPER::end - 1 == $self->SUPER::start);
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237
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238 return $self->SUPER::start();
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239 }
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240
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241 =head2 end
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242
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243 Title : end
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244 Usage : $end = $fuzzy->end();
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245 Function: get/set end of this range, handling fuzzy_ends
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246 Returns : a positive integer representing the end of the range
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247 Args : end location on set (can be fuzzy string)
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248
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249 =cut
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250
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251 sub end {
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252 my($self,$value) = @_;
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253 if( defined $value ) {
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254 my ($encode,$min,$max) = $self->_fuzzypointdecode($value);
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255 $self->end_pos_type($encode);
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256 $self->min_end($min);
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257 $self->max_end($max);
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258 }
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259
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260 $self->throw("Use Bio::Location::Simple for IN-BETWEEN locations [". $self->SUPER::start. "] and [". $self->SUPER::end. "]")
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261 if $self->location_type eq 'BETWEEN' && defined $self->SUPER::start && ($self->SUPER::end - 1 == $self->SUPER::start);
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262
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263 return $self->SUPER::end();
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264 }
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265
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266 =head2 min_start
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267
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268 Title : min_start
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269 Usage : $min_start = $fuzzy->min_start();
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270 Function: get/set the minimum starting point
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271 Returns : the minimum starting point from the contained sublocations
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272 Args : integer or undef on set
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273
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274 =cut
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275
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276 sub min_start {
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277 my ($self,@args) = @_;
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278
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279 if(@args) {
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280 $self->{'_min_start'} = $args[0]; # the value may be undef!
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281 }
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282 return $self->{'_min_start'};
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283 }
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284
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285 =head2 max_start
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286
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287 Title : max_start
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288 Usage : my $maxstart = $location->max_start();
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289 Function: Get/set maximum starting location of feature startpoint
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290 Returns : integer or undef if no maximum starting point.
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291 Args : integer or undef on set
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292
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293 =cut
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294
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295 sub max_start {
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296 my ($self,@args) = @_;
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297
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298 if(@args) {
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299 $self->{'_max_start'} = $args[0]; # the value may be undef!
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300 }
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301 return $self->{'_max_start'};
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302 }
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303
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304 =head2 start_pos_type
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305
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306 Title : start_pos_type
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307 Usage : my $start_pos_type = $location->start_pos_type();
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308 Function: Get/set start position type.
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309 Returns : type of position coded as text
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310 ('BEFORE', 'AFTER', 'EXACT','WITHIN', 'BETWEEN')
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311 Args : a string on set
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312
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313 =cut
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314
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315 sub start_pos_type {
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316 my ($self,$value) = @_;
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317 if(defined $value && $value =~ /^\d+$/ ) {
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318 if( $value == 0 ) { $value = 'EXACT'; }
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319 else {
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320 my $v = $LOCATIONCODESBSANE[$value];
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321 if( ! defined $v ) {
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322 $self->warn("Provided value $value which I don't understand, reverting to 'EXACT'");
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323 $v = 'EXACT';
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324 }
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325 $value = $v;
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326 }
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327 }
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328 if(defined($value)) {
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329 $self->{'_start_pos_type'} = $value;
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330 }
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331 return $self->{'_start_pos_type'};
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332 }
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333
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334 =head2 min_end
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335
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336 Title : min_end
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337 Usage : my $minend = $location->min_end();
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338 Function: Get/set minimum ending location of feature endpoint
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339 Returns : integer or undef if no minimum ending point.
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340 Args : integer or undef on set
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341
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342 =cut
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343
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344 sub min_end {
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345 my ($self,@args) = @_;
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346
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347 if(@args) {
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348 $self->{'_min_end'} = $args[0]; # the value may be undef!
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349 }
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350 return $self->{'_min_end'};
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351 }
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352
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353 =head2 max_end
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354
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355 Title : max_end
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356 Usage : my $maxend = $location->max_end();
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357 Function: Get/set maximum ending location of feature endpoint
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358 Returns : integer or undef if no maximum ending point.
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359 Args : integer or undef on set
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360
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361 =cut
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362
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363 sub max_end {
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364 my ($self,@args) = @_;
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365
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366 if(@args) {
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367 $self->{'_max_end'} = $args[0]; # the value may be undef!
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368 }
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369 return $self->{'_max_end'};
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370 }
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371
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372 =head2 end_pos_type
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373
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374 Title : end_pos_type
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375 Usage : my $end_pos_type = $location->end_pos_type();
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376 Function: Get/set end position type.
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377 Returns : type of position coded as text
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378 ('BEFORE', 'AFTER', 'EXACT','WITHIN', 'BETWEEN')
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379 Args : a string on set
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380
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381 =cut
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382
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383 sub end_pos_type {
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384 my ($self,$value) = @_;
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385 if( defined $value && $value =~ /^\d+$/ ) {
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386 if( $value == 0 ) { $value = 'EXACT'; }
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387 else {
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388 my $v = $LOCATIONCODESBSANE[$value];
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389 if( ! defined $v ) {
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390 $self->warn("Provided value $value which I don't understand, reverting to 'EXACT'");
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391 $v = 'EXACT';
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392 }
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393 $value = $v;
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394 }
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395 }
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396
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397 if(defined($value)) {
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398 $self->{'_end_pos_type'} = $value;
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399 }
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400 return $self->{'_end_pos_type'};
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401 }
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402
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403 =head2 seq_id
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404
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405 Title : seq_id
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406 Usage : my $seqid = $location->seq_id();
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407 Function: Get/Set seq_id that location refers to
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408 Returns : seq_id
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409 Args : [optional] seq_id value to set
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410
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411 =cut
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412
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413 =head2 coordinate_policy
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414
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415 Title : coordinate_policy
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416 Usage : $policy = $location->coordinate_policy();
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417 $location->coordinate_policy($mypolicy); # set may not be possible
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418 Function: Get the coordinate computing policy employed by this object.
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419
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420 See Bio::Location::CoordinatePolicyI for documentation about
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421 the policy object and its use.
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422
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423 The interface *does not* require implementing classes to accept
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424 setting of a different policy. The implementation provided here
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425 does, however, allow to do so.
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426
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427 Implementors of this interface are expected to initialize every
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428 new instance with a CoordinatePolicyI object. The implementation
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429 provided here will return a default policy object if none has
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430 been set yet. To change this default policy object call this
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431 method as a class method with an appropriate argument. Note that
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432 in this case only subsequently created Location objects will be
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433 affected.
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434
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435 Returns : A Bio::Location::CoordinatePolicyI implementing object.
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436 Args : On set, a Bio::Location::CoordinatePolicyI implementing object.
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437
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438 =cut
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439
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440 =head2 to_FTstring
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441
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442 Title : to_FTstring
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443 Usage : my $locstr = $location->to_FTstring()
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444 Function: Get/Set seq_id that location refers to
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445 Returns : seq_id
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446 Args : [optional] seq_id value to set
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447
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448 =cut
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449
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450 sub to_FTstring {
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451 my ($self) = @_;
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452 my (%vals) = ( 'start' => $self->start,
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453 'min_start' => $self->min_start,
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454 'max_start' => $self->max_start,
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455 'start_code' => $self->start_pos_type,
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456 'end' => $self->end,
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457 'min_end' => $self->min_end,
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458 'max_end' => $self->max_end,
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459 'end_code' => $self->end_pos_type );
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460
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461 my (%strs) = ( 'start' => '',
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462 'end' => '');
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463 my ($delimiter) = $FUZZYCODES{$self->location_type};
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464 # I'm lazy, lets do this in a loop since behaviour will be the same for
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465 # start and end
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466 foreach my $point ( qw(start end) ) {
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467 if( $vals{$point."_code"} ne 'EXACT' ) {
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468
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469 if( (!defined $vals{"min_$point"} ||
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470 !defined $vals{"max_$point"})
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471 && ( $vals{$point."_code"} eq 'WITHIN' ||
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472 $vals{$point."_code"} eq 'BETWEEN')
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473 ) {
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474 $vals{"min_$point"} = '' unless defined $vals{"min_$point"};
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475 $vals{"max_$point"} = '' unless defined $vals{"max_$point"};
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476
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477 $self->warn("Fuzzy codes for start are in a strange state, (".
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478 join(",", ($vals{"min_$point"},
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479 $vals{"max_$point"},
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480 $vals{$point."_code"})). ")");
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481 return '';
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482 }
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483 if( defined $vals{$point."_code"} &&
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484 ($vals{$point."_code"} eq 'BEFORE' ||
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485 $vals{$point."_code"} eq 'AFTER')
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486 ) {
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487 $strs{$point} .= $FUZZYCODES{$vals{$point."_code"}};
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488 }
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489 if( defined $vals{"min_$point"} ) {
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490 $strs{$point} .= $vals{"min_$point"};
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491 }
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492 if( defined $vals{$point."_code"} &&
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493 ($vals{$point."_code"} eq 'WITHIN' ||
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494 $vals{$point."_code"} eq 'BETWEEN')
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495 ) {
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496 $strs{$point} .= $FUZZYCODES{$vals{$point."_code"}};
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497 }
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498 if( defined $vals{"max_$point"} ) {
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499 $strs{$point} .= $vals{"max_$point"};
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500 }
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501 if(($vals{$point."_code"} eq 'WITHIN') ||
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502 ($vals{$point."_code"} eq 'BETWEEN')) {
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503 $strs{$point} = "(".$strs{$point}.")";
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504 }
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505 } else {
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506 $strs{$point} = $vals{$point};
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507 }
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508
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509 }
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510 my $str = $strs{'start'} . $delimiter . $strs{'end'};
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511 if($self->is_remote() && $self->seq_id()) {
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512 $str = $self->seq_id() . ":" . $str;
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513 }
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514 if( $self->strand == -1 ) {
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515 $str = "complement(" . $str . ")";
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516 } elsif($self->location_type() eq "WITHIN") {
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517 $str = "(".$str.")";
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518 }
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519 return $str;
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520 }
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521
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522 =head2 _fuzzypointdecode
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523
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524 Title : _fuzzypointdecode
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525 Usage : ($type,$min,$max) = $self->_fuzzypointdecode('<5');
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526 Function: Decode a fuzzy string.
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527 Returns : A 3-element array consisting of the type of location, the
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528 minimum integer, and the maximum integer describing the range
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529 of coordinates this start or endpoint refers to. Minimum or
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530 maximum coordinate may be undefined.
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531 : Returns empty array on fail.
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532 Args : fuzzypoint string
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533
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534 =cut
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535
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536 sub _fuzzypointdecode {
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537 my ($self, $string) = @_;
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538 return () if( !defined $string);
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539 # strip off leading and trailing space
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540 $string =~ s/^\s*(\S+)\s*/$1/;
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541 foreach my $pattern ( keys %FUZZYPOINTENCODE ) {
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542 if( $string =~ /^$pattern$/ ) {
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543 my ($min,$max) = ($1,$2);
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544 if($FUZZYPOINTENCODE{$pattern} eq 'EXACT') {
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545 $max = $min;
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546 } else {
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547 $max = undef if(length($max) == 0);
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548 $min = undef if(length($min) == 0);
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549 }
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550 return ($FUZZYPOINTENCODE{$pattern},$min,$max);
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551 }
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552 }
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553 if( $self->verbose >= 1 ) {
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554 $self->warn("could not find a valid fuzzy encoding for $string");
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555 }
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556 return ();
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557 }
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558
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559 1;
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560
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