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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::Utils::Argument - Utility functions for argument handling
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24
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25 =head1 SYNOPSIS
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26
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27 use Bio::EnsEMBL::Utils::Argument qw(rearrange)
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28
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29 package Feature;
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30
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31 sub new {
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32 my $class = shift;
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33 my ( $start, $end, $strand ) =
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34 rearrange( [ 'START', 'END', 'STRAND' ], @_ );
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35
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36 return
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37 bless( { 'start' => $start, 'end' => $end, 'strand' => $strand },
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38 $class );
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39 }
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40
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41 =head1 DESCRIPTION
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42
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43 This is derived from the Bio::Root module in BioPerl. The _rearrange
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44 object method taken from BioPerl has been renamed rearrange and is now
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45 a static class method. This method was originally written by Lincoln
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46 Stein, and has since been refactored several times by various people (as
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47 described below).
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48
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49 It is recommended that this package be used instead of inheriting
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50 unnecessarily from the Bio::EnsEMBL::Root or Bio::Root object.
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51
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52 =head1 METHODS
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53
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54 =cut
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55
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56 package Bio::EnsEMBL::Utils::Argument;
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57
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58 use strict;
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59 use warnings;
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60
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61 use Exporter;
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62
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63 use vars qw(@ISA @EXPORT);
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64
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65 @ISA = qw(Exporter);
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66 @EXPORT = qw(rearrange);
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67
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68
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69
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70 =head2 rearrange
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71
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72 Usage : rearrange( array_ref, list_of_arguments)
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73 Purpose : Rearranges named parameters to requested order.
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74 Example : use Bio::EnsEMBL::Utils::Argument qw(rearrange);
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75 : rearrange([qw(SEQUENCE ID DESC)],@param);
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76 : Where @param = (-sequence => $s,
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77 : -id => $i,
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78 : -desc => $d);
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79 Returns : @params - an array of parameters in the requested order.
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80 : The above example would return ($s, $i, $d)
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81 Argument : $order : a reference to an array which describes the desired
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82 : order of the named parameters.
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83 : @param : an array of parameters, either as a list (in
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84 : which case the function simply returns the list),
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85 : or as an associative array with hyphenated tags
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86 : (in which case the function sorts the values
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87 : according to @{$order} and returns that new array.)
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88 : The tags can be upper, lower, or mixed case
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89 : but they must start with a hyphen (at least the
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90 : first one should be hyphenated.)
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91 Source : This function was taken from CGI.pm, written by Dr. Lincoln
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92 : Stein, and adapted for use in Bio::Seq by Richard Resnick and
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93 : then adapted for use in Bio::Root::Object.pm by Steve A. Chervitz.
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94 : This has since been adapted as an exported static method in this
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95 class Bio::EnsEMBL::Utils::Argument
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96 Comments : (SAC)
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97 : This method may not be appropriate for method calls that are
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98 : within in an inner loop if efficiency is a concern.
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99 :
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100 : Parameters can be specified using any of these formats:
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101 : @param = (-name=>'me', -color=>'blue');
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102 : @param = (-NAME=>'me', -COLOR=>'blue');
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103 : @param = (-Name=>'me', -Color=>'blue');
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104 : A leading hyphenated argument is used by this function to
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105 : indicate that named parameters are being used.
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106 : Therefore, a ('me', 'blue') list will be returned as-is.
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107 :
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108 : Note that Perl will confuse unquoted, hyphenated tags as
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109 : function calls if there is a function of the same name
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110 : in the current namespace:
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111 : -name => 'foo' is interpreted as -&name => 'foo'
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112 :
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113 : For ultimate safety, put single quotes around the tag:
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114 : ('-name'=>'me', '-color' =>'blue');
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115 : This can be a bit cumbersome and I find not as readable
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116 : as using all uppercase, which is also fairly safe:
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117 : (-NAME=>'me', -COLOR =>'blue');
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118 :
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119 : Personal note (SAC): I have found all uppercase tags to
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120 : be more managable: it involves less single-quoting,
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121 : the code is more readable, and there are no method naming
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122 : conlicts.
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123 : Regardless of the style, it greatly helps to line
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124 : the parameters up vertically for long/complex lists.
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125
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126 =cut
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127
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128
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129 sub rearrange {
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130 my $order = shift;
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131
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132 if ( $order eq "Bio::EnsEMBL::Utils::Argument" ) {
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133 # skip object if one provided
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134 $order = shift;
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135 }
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136
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137 # If we've got parameters, we need to check to see whether
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138 # they are named or simply listed. If they are listed, we
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139 # can just return them.
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140 unless ( @_ && $_[0] && substr( $_[0], 0, 1 ) eq '-' ) {
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141 return @_;
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142 }
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143
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144 # Push undef onto the end if % 2 != 0 to stop warnings
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145 push @_,undef unless $#_ %2;
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146 my %param;
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147 while( @_ ) {
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148 #deletes all dashes & uppercases at the same time
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149 (my $key = shift) =~ tr/a-z\055/A-Z/d;
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150 $param{$key} = shift;
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151 }
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152
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153 # What we intend to do is loop through the @{$order} variable,
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154 # and for each value, we use that as a key into our associative
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155 # array, pushing the value at that key onto our return array.
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156 return map { $param{uc($_)} } @$order;
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157 }
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158
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159 1;
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160
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161
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