Bio/FeatureHolderI.pm

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