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1 # $Id: CollectionI.pm,v 1.2 2002/10/22 07:45:20 lapp Exp $
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2 #
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3 # BioPerl module for Bio::SeqFeature::CollectionI
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4 #
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5 # Cared for by Jason Stajich <jason@bioperl.org>
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6 #
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7 # Copyright Jason Stajich
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8 #
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9 # You may distribute this module under the same terms as perl itself
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10
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11 # POD documentation - main docs before the code
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12
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13 =head1 NAME
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14
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15 Bio::SeqFeature::CollectionI - An interface for a collection of SeqFeatureI objects.
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16
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17 =head1 SYNOPSIS
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18
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19
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20 # get a Bio::SeqFeature::CollectionI somehow
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21 # perhaps a Bio::SeqFeature::Collection
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22
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23
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24 use Bio::SeqFeature::Collection;
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25 my $collection = new Bio::SeqFeature::Collection;
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26 $collection->add_features(\@featurelist);
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27
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28
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29 $collection->features(-attributes =>
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30 [ { 'location' => new Bio::Location::Simple
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31 (-start=> 1, -end => 300) ,
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32 'overlaps' }]);
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33
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34 =head1 DESCRIPTION
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35
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36 This interface describes the basic methods needed for a collection of Sequence Features.
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37
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38 =head1 FEEDBACK
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39
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40 =head2 Mailing Lists
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41
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42 User feedback is an integral part of the evolution of this and other
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43 Bioperl modules. Send your comments and suggestions preferably to
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44 the Bioperl mailing list. Your participation is much appreciated.
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45
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46 bioperl-l@bioperl.org - General discussion
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47 http://bioperl.org/MailList.shtml - About the mailing lists
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48
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49 =head2 Reporting Bugs
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50
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51 Report bugs to the Bioperl bug tracking system to help us keep track
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52 of the bugs and their resolution. Bug reports can be submitted via
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53 email or the web:
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54
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55 bioperl-bugs@bioperl.org
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56 http://bugzilla.bioperl.org/
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57
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58 =head1 AUTHOR - Jason Stajich
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59
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60 Email jason@bioperl.org
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61
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62 Describe contact details here
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63
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64 =head1 CONTRIBUTORS
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65
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66 Additional contributors names and emails here
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67
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68 =head1 APPENDIX
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69
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70 The rest of the documentation details each of the object methods.
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71 Internal methods are usually preceded with a _
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72
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73 =cut
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74
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75
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76 # Let the code begin...
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77
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78
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79 package Bio::SeqFeature::CollectionI;
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80 use vars qw(@ISA);
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81 use strict;
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82 use Carp;
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83 use Bio::Root::RootI;
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84
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85 @ISA = qw( Bio::Root::RootI );
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86
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87
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88 =head2 add_features
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89
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90 Title : add_features
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91 Usage : $collection->add_features(\@features);
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92 Function:
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93 Returns : number of features added
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94 Args : arrayref of Bio::SeqFeatureI objects to index
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95
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96 =cut
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97
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98 sub add_features{
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99 shift->throw_not_implemented();
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100 }
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101
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102
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103 =head2 features
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104
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105 Title : features
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106 Usage : my @f = $collection->features(@args);
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107 Returns : a list of Bio::SeqFeatureI objects
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108 Args : see below
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109 Status : public
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110
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111 This routine will retrieve features associated with this collection
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112 object. It can be used to return all features, or a subset based on
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113 their type, location, or attributes.
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114
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115 -types List of feature types to return. Argument is an array
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116 of Bio::Das::FeatureTypeI objects or a set of strings
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117 that can be converted into FeatureTypeI objects.
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118
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119 -callback A callback to invoke on each feature. The subroutine
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120 will be passed to each Bio::SeqFeatureI object in turn.
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121
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122 -attributes A hash reference containing attributes to match.
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123
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124 The -attributes argument is a hashref containing one or more attributes
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125 to match against:
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126
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127 -attributes => { Gene => 'abc-1',
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128 Note => 'confirmed' }
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129
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130 Attribute matching is simple exact string matching, and multiple
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131 attributes are ANDed together. See L<Bio::DB::ConstraintsI> for a
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132 more sophisticated take on this.
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133
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134 If one provides a callback, it will be invoked on each feature in
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135 turn. If the callback returns a false value, iteration will be
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136 interrupted. When a callback is provided, the method returns undef.
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137
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138 =cut
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139
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140 sub features{
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141 shift->throw_not_implemented();
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142 }
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143
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144 1;
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