lib/Bio/FeatureHolderI.pm

   1 #
   2 # BioPerl module for Bio::FeatureHolderI
   3 #
   4 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   5 #
   6 # Cared for by Hilmar Lapp <hlapp at gmx.net>
   7 #
   8 # Copyright Hilmar Lapp
   9 #
  10 # You may distribute this module under the same terms as perl itself
  11
  12 # POD documentation - main docs before the code
  13
  14 =head1 NAME
  15
  16 Bio::FeatureHolderI - the base interface an object with features must implement
  17
  18 =head1 SYNOPSIS
  19
  20     use Bio::SeqIO;
  21     # get a feature-holding object somehow: for example, Bio::SeqI objects
  22     # have features
  23     my $seqio = Bio::SeqIO->new(-fh => \*STDIN, -format => 'genbank');
  24     while (my $seq = $seqio->next_seq()) {
  25         # $seq is-a Bio::FeatureHolderI, hence:
  26         my @feas = $seq->get_SeqFeatures();
  27         # each element is-a Bio::SeqFeatureI
  28         foreach my $fea (@feas) {
  29             # do something with the feature objects
  30         }
  31     }
  32
  33 =head1 DESCRIPTION
  34
  35 This is the base interface that all feature-holding objects must
  36 implement.
  37
  38 Popular feature-holders are for instance L<Bio::Seq> objects. Since
  39 L<Bio::SeqFeatureI> defines a sub_SeqFeature() method, most
  40 Bio::SeqFeatureI implementations like L<Bio::SeqFeature::Generic> will
  41 implement the feature holder interface as well.
  42
  43 =head1 FEEDBACK
  44
  45 =head2 Mailing Lists
  46
  47 User feedback is an integral part of the evolution of this and other
  48 Bioperl modules. Send your comments and suggestions preferably to
  49 the Bioperl mailing list.  Your participation is much appreciated.
  50
  51   bioperl-l@bioperl.org                  - General discussion
  52   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  53
  54 =head2 Support
  55
  56 Please direct usage questions or support issues to the mailing list:
  57
  58 I<bioperl-l@bioperl.org>
  59
  60 rather than to the module maintainer directly. Many experienced and
  61 reponsive experts will be able look at the problem and quickly
  62 address it. Please include a thorough description of the problem
  63 with code and data examples if at all possible.
  64
  65 =head2 Reporting Bugs
  66
  67 Report bugs to the Bioperl bug tracking system to help us keep track
  68 of the bugs and their resolution. Bug reports can be submitted via the
  69 web:
  70
  71   https://github.com/bioperl/bioperl-live/issues
  72
  73 =head1 AUTHOR - Hilmar Lapp
  74
  75 Email hlapp at gmx.net
  76
  77 =head1 CONTRIBUTORS
  78
  79 Steffen Grossmann [SG], grossman-at-molgen.mpg.de
  80 Mark A. Jensen, maj -at- fortinbras -dot- us
  81
  82 =head1 APPENDIX
  83
  84 The rest of the documentation details each of the object methods.
  85 Internal methods are usually preceded with a _
  86
  87 =cut
  88
  89
  90 # Let the code begin...
  91
  92
  93
  94 package Bio::FeatureHolderI;
  95 use strict;
  96 use Carp;
  97
  98 use base qw(Bio::Root::RootI);
  99
 100 =head2 get_SeqFeatures()
 101
 102  Usage   : @feats = $obj->get_SeqFeatures()
 103  Function: Get the feature objects held by this feature holder.
 104  Example :
 105  Returns : an array of Bio::SeqFeatureI implementing objects
 106            if tag specified, return features having that tag
 107  Args    : [optional] scalar string (feature tag)
 108
 109 =cut
 110
 111 sub get_SeqFeatures {
 112   shift->throw_not_implemented();
 113 }
 114
 115 =head2 add_SeqFeature()
 116
 117  Usage   : $feat->add_SeqFeature($subfeat);
 118            $feat->add_SeqFeature($subfeat,'EXPAND')
 119  Function: Add a SeqFeature into the subSeqFeature array.
 120            with no 'EXPAND' qualifer, subfeat will be tested
 121            as to whether it lies inside the parent, and throw
 122            an exception if not.
 123
 124            If EXPAND is used and the object implements Bio::RangeI
 125            (which is not guaranteed), the parent''s start/end/strand
 126            will be extended so that the new subFeature can be accomodated.
 127  Example :
 128  Returns : nothing
 129  Args    : a Bio::SeqFeatureI object
 130
 131 =cut
 132
 133 sub add_SeqFeature {
 134   shift->throw_not_implemented();
 135 }
 136
 137
 138 =head2 remove_SeqFeatures()
 139
 140  Usage   : $obj->remove_SeqFeatures
 141  Function: Removes all sub SeqFeatures.  If you want to remove only a subset,
 142            remove that subset from the returned array, and add back the rest.
 143  Returns : The array of Bio::SeqFeatureI implementing sub-features that was
 144            deleted from this feature.
 145  Args    : none
 146
 147 =cut
 148
 149 sub remove_SeqFeatures {
 150   shift->throw_not_implemented();
 151 }
 152
 153 =head2 feature_count
 154
 155  Title   : feature_count
 156  Usage   : $obj->feature_count()
 157  Function: Return the number of SeqFeatures attached to a feature holder.
 158
 159            This is before flattening a possible sub-feature tree.
 160
 161            We provide a default implementation here that just counts
 162            the number of objects returned by get_SeqFeatures().
 163            Implementors may want to override this with a more
 164            efficient implementation.
 165
 166  Returns : integer representing the number of SeqFeatures
 167  Args    : None
 168
 169 At some day we may want to expand this method to allow for a feature
 170 filter to be passed in.
 171
 172 Our default implementation allows for any number of additional
 173 arguments and will pass them on to get_SeqFeatures(). I.e., in order to
 174 support filter arguments, just support them in get_SeqFeatures().
 175
 176 =cut
 177
 178 sub feature_count {
 179     return scalar(shift->get_SeqFeatures(@_));
 180 }
 181
 182 =head2 get_all_SeqFeatures
 183
 184  Title   : get_all_SeqFeatures
 185  Usage   :
 186  Function: Get the flattened tree of feature objects held by this
 187            feature holder. The difference to get_SeqFeatures is that
 188            the entire tree of sub-features will be flattened out.
 189
 190            We provide a default implementation here, so implementors
 191            don''t necessarily need to implement this method.
 192
 193  Example :
 194  Returns : an array of Bio::SeqFeatureI implementing objects
 195  Args    : none
 196
 197 At some day we may want to expand this method to allow for a feature
 198 filter to be passed in.
 199
 200 Our default implementation allows for any number of additional
 201 arguments and will pass them on to any invocation of
 202 get_SeqFeatures(), wherever a component of the tree implements
 203 FeatureHolderI. I.e., in order to support filter arguments, just
 204 support them in get_SeqFeatures().
 205
 206 =cut
 207
 208 sub get_all_SeqFeatures{
 209     my $self = shift;
 210     my @flatarr;
 211
 212     foreach my $feat ( $self->get_SeqFeatures(@_) ){
 213         push(@flatarr,$feat);
 214         &_add_flattened_SeqFeatures(\@flatarr,$feat,@_);
 215     }
 216
 217     # needed to deal with subfeatures which appear more than once in the hierarchy [SG]
 218     my %seen = ();
 219     my @uniq_flatarr = ();
 220     foreach my $feat (@flatarr) {
 221         push(@uniq_flatarr, $feat) unless $seen{$feat}++;
 222     }
 223     return @uniq_flatarr;
 224 }
 225
 226 sub _add_flattened_SeqFeatures {
 227     my ($arrayref,$feat,@args) = @_;
 228     my @subs = ();
 229
 230     if($feat->isa("Bio::FeatureHolderI")) {
 231         @subs = $feat->get_SeqFeatures(@args);
 232     } elsif($feat->isa("Bio::SeqFeatureI")) {
 233         @subs = $feat->sub_SeqFeature();
 234     } else {
 235         confess ref($feat)." is neither a FeatureHolderI nor a SeqFeatureI. ".
 236             "Don't know how to flatten.";
 237     }
 238     foreach my $sub (@subs) {
 239         push(@$arrayref,$sub);
 240         &_add_flattened_SeqFeatures($arrayref,$sub);
 241     }
 242
 243 }
 244
 245 sub set_ParentIDs_from_hierarchy(){
 246     # DEPRECATED - use IDHandler
 247     my $self = shift;
 248     require "Bio/SeqFeature/Tools/IDHandler.pm";
 249     Bio::SeqFeature::Tools::IDHandler->new->set_ParentIDs_from_hierarchy($self);
 250 }
 251
 252 sub create_hierarchy_from_ParentIDs(){
 253     # DEPRECATED - use IDHandler
 254     my $self = shift;
 255     require "Bio/SeqFeature/Tools/IDHandler.pm";
 256     Bio::SeqFeature::Tools::IDHandler->new->create_hierarchy_from_ParentIDs($self);
 257 }
 258
 259
 260
 261 1;