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1 =head1 LICENSE
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2
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3 Copyright (c) 1999-2012 The European Bioinformatics Institute and
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4 Genome Research Limited. All rights reserved.
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5
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6 This software is distributed under a modified Apache license.
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7 For license details, please see
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8
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9 http://www.ensembl.org/info/about/code_licence.html
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10
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11 =head1 CONTACT
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12
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13 Please email comments or questions to the public Ensembl
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14 developers list at <dev@ensembl.org>.
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15
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16 Questions may also be sent to the Ensembl help desk at
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17 <helpdesk@ensembl.org>.
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18
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19 =cut
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20
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21 =head1 NAME
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22
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23 Bio::EnsEMBL::IdMapping::Entry - object representing a ScoredMappingMatrix entry
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24
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25 =head1 SYNOPSIS
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26
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27 =head1 DESCRIPTION
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28
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29 This object represents a ScoredMappingMatrix entry. It is defined by a
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30 pair of a source and target object's internal Id and a score for this
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31 mapping.
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32
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33 =head1 METHODS
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34
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35 new
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36 new_fast
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37 source
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38 target
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39 score
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40 to_string
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41
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42 =cut
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43
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44 package Bio::EnsEMBL::IdMapping::Entry;
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45
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46 use strict;
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47 use warnings;
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48 no warnings 'uninitialized';
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49
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50 use Bio::EnsEMBL::Utils::Exception qw(throw warning);
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51
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52
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53 =head2 new
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54
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55 Example : my $entry = Bio::EnsEMBL::IdMapping::Entry->new();
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56 Description : Constructor. This is a no-argument constructor, so you need to
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57 populate the object manually. Rarely used since in most cases
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58 new_fast() is preferred.
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59 Return type : a Bio::EnsEMBL::IdMapping::Entry object
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60 Exceptions : none
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61 Caller : general
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62 Status : At Risk
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63 : under development
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64
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65 =cut
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66
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67 sub new {
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68 my $caller = shift;
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69 my $class = ref($caller) || $caller;
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70
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71 my $self = [];
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72 bless ($self, $class);
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73
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74 return $self;
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75 }
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76
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77
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78 =head2 new_fast
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79
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80 Arg[1] : Arrayref $array_ref - the arrayref to bless into the Entry
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81 object
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82 Example : my $entry = Bio::EnsEMBL::IdMapping::Entry->new_fast([
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83 $source_gene->id, $target_gene->id, 0.9]);
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84 Description : Fast constructor.
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85 Return type : a Bio::EnsEMBL::IdMapping::Entry object
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86 Exceptions : none
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87 Caller : general
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88 Status : At Risk
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89 : under development
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90
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91 =cut
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92
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93 sub new_fast {
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94 my $class = shift;
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95 my $array_ref = shift;
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96 return bless $array_ref, $class;
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97 }
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98
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99
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100 =head2 source
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101
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102 Arg[1] : (optional) Int - source object's internal Id
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103 Description : Getter/setter for source object's internal Id.
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104 Return type : Int
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105 Exceptions : none
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106 Caller : general
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107 Status : At Risk
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108 : under development
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109
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110 =cut
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111
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112 sub source {
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113 my $self = shift;
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114 $self->[0] = shift if (@_);
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115 return $self->[0];
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116 }
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117
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118
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119 =head2 target
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120
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121 Arg[1] : (optional) Int - target object's internal Id
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122 Description : Getter/setter for target object's internal Id.
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123 Return type : Int
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124 Exceptions : none
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125 Caller : general
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126 Status : At Risk
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127 : under development
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128
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129 =cut
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130
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131 sub target {
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132 my $self = shift;
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133 $self->[1] = shift if (@_);
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134 return $self->[1];
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135 }
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136
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137
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138 =head2 score
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139
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140 Arg[1] : (optional) Float - a score
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141 Description : Getter/setter for score for the mapping between source and
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142 target object.
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143 Return type : Float
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144 Exceptions : none
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145 Caller : general
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146 Status : At Risk
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147 : under development
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148
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149 =cut
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150
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151 sub score {
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152 my $self = shift;
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153 $self->[2] = shift if (@_);
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154 return $self->[2];
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155 }
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156
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157
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158 =head2 to_string
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159
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160 Example : print LOG $entry->to_string, "\n";
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161 Description : Returns a string representation of the Entry object. Useful for
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162 debugging and logging.
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163 Return type : String
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164 Exceptions : none
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165 Caller : general
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166 Status : At Risk
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167 : under development
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168
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169 =cut
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170
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171 sub to_string {
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172 my $self = shift;
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173 return sprintf('%-10s%-10s%-5.6f', $self->source, $self->target, $self->score);
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174 }
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175
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176
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177 1;
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178
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