Bio/SeqIO/game/gameHandler.pm

   1 # $Id:
   2 #
   3 # BioPerl module for Bio::SeqIO::game::gameHandler
   4 #
   5 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   6 #
   7 # Cared for by Sheldon McKay <mckays@cshl.edu>
   8 #
   9 # You may distribute this module under the same terms as perl itself
  10 #
  11
  12 # POD documentation - main docs before the code
  13
  14 =head1 NAME
  15
  16 Bio::SeqIO::game::gameHandler -- PerlSAX handler for game-XML
  17
  18 =head1 SYNOPSIS
  19
  20 This modules is not used directly
  21
  22 =head1 DESCRIPTION
  23
  24 Bio::SeqIO::game::gameHandler is the top-level XML handler invoked by PerlSAX
  25
  26 =head1 FEEDBACK
  27
  28 =head2 Mailing Lists
  29
  30 User feedback is an integral part of the evolution of this
  31 and other Bioperl modules. Send your comments and suggestions preferably
  32 to one of the Bioperl mailing lists.
  33
  34 Your participation is much appreciated.
  35
  36   bioperl-l@bioperl.org                  - General discussion
  37   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  38
  39 =head2 Support
  40
  41 Please direct usage questions or support issues to the mailing list:
  42
  43 I<bioperl-l@bioperl.org>
  44
  45 rather than to the module maintainer directly. Many experienced and
  46 reponsive experts will be able look at the problem and quickly
  47 address it. Please include a thorough description of the problem
  48 with code and data examples if at all possible.
  49
  50 =head2 Reporting Bugs
  51
  52 Report bugs to the Bioperl bug tracking system to help us keep track
  53 of the bugs and their resolution. Bug reports can be submitted via the
  54 web:
  55
  56   https://github.com/bioperl/bioperl-live/issues
  57
  58 =head1 AUTHOR - Sheldon McKay
  59
  60 Email mckays@cshl.edu
  61
  62 =head1 APPENDIX
  63
  64 The rest of the documentation details each of the object
  65 methods. Internal methods are usually preceded with a _
  66
  67 =cut
  68
  69 package Bio::SeqIO::game::gameHandler;
  70
  71 use Bio::SeqIO::game::seqHandler;
  72 use strict;
  73 use vars qw {};
  74
  75 use base qw(Bio::SeqIO::game::gameSubs);
  76
  77 =head2 start_document
  78
  79  Title   : start_document
  80  Function: begin parsing the document
  81
  82 =cut
  83
  84 sub start_document {
  85     my ($self, $document) = @_;
  86
  87     $self->SUPER::start_document($document);
  88
  89     $self->{sequences}    = {};
  90     $self->{annotations}  = {};
  91     $self->{computations} = {};
  92     $self->{map_position} = {};
  93     $self->{focus}        = {};
  94 }
  95
  96 =head2 end_document
  97
  98  Title   : end_document
  99  Function: finish parsing the document
 100
 101 =cut
 102
 103 sub end_document {
 104     my ($self, $document) = @_;
 105
 106     $self->SUPER::end_document($document);
 107
 108     return $self;
 109 }
 110
 111 =head2 load
 112
 113  Title   : load
 114  Usage   : $seqs = $handler->load
 115  Function: start parsing
 116  Returns : a ref to a list of sequence objects
 117  Args    : an optional flag to suppress <computation_analysis> elements (not used yet)
 118
 119 =cut
 120
 121 sub load {
 122     my $self = shift;
 123     my $suppress_comps = shift;
 124     my @seqs = ();
 125
 126     for ( 1..$self->{game} ) {
 127         my $seq  = $self->{sequences}->{$_}
 128           or $self->throw("No sequences defined");
 129         my $ann  = $self->{annotations}->{$_};
 130         my $comp = $self->{computations}->{$_};
 131         my $map  = $self->{map_position}->{$_};
 132         my $foc  = $self->{focus}->{$_}
 133           or $self->throw("No main sequence defined");
 134         my $src  = $self->{has_source};
 135
 136         my $bio = Bio::SeqIO::game::seqHandler->new( $seq, $ann, $comp, $map, $src );
 137         push @seqs, $bio->convert;
 138     }
 139
 140     \@seqs;
 141 }
 142
 143 =head2 s_game
 144
 145  Title   : s_game
 146  Function: begin parsing game element
 147
 148 =cut
 149
 150 sub s_game {
 151     my ($self, $e) = @_;
 152     my $el = $self->curr_element;
 153     $self->{game}++;
 154
 155     my $version = $el->{Attributes}->{version};
 156
 157     unless ( defined $version ) {
 158         $self->complain("No GAME-xml version specified -- guessing v1.2\n");
 159         $version = 1.2;
 160     }
 161     if ( defined($version) && $version == 1.2) {
 162         $self->{origin_offset} = 1;
 163     } else {
 164         $self->{origin_offset} = 0;
 165     }
 166
 167     if (defined($version) && ($version != 1.2)) {
 168         $self->complain("GAME version $version is not supported\n",
 169                         "I'll try anyway but I may fail!\n");
 170     }
 171
 172 }
 173
 174 =head2 e_game
 175
 176  Title   : e_game
 177  Function: process the game element
 178
 179 =cut
 180
 181 sub e_game {
 182     my ($self, $el) = @_;
 183     $self->flush( $el );
 184 }
 185
 186 =head2 e_seq
 187
 188  Title   : e_seq
 189  Function: process the sequence element
 190
 191 =cut
 192
 193 sub e_seq {
 194     my ($self, $e) = @_;
 195     my $el = $self->curr_element();
 196     $self->{sequences}->{$self->{game}} ||= [];
 197     my $seqs = $self->{sequences}->{$self->{game}};
 198
 199     if ( defined $el->{Attributes}->{focus} ) {
 200         $self->{focus}->{$self->{game}} = $el;
 201     }
 202     push @{$seqs}, $el;
 203
 204     $self->flush;
 205 }
 206
 207 =head2 e_map_position
 208
 209  Title   : e_map_position
 210  Function: process the map_position element
 211
 212 =cut
 213
 214 sub e_map_position {
 215     my ($self, $e) = @_;
 216     my $el = $self->curr_element;
 217     $self->{map_position}->{$self->{game}} = $el;
 218 }
 219
 220 =head2 e_annotation
 221
 222  Title   : e_annotation
 223  Function: process the annotation
 224
 225 =cut
 226
 227 sub e_annotation {
 228     my ($self, $e) = shift;
 229     my $el = $self->curr_element;
 230     $self->{annotations}->{$self->{game}} ||= [];
 231     my $anns = $self->{annotations}->{$self->{game}};
 232     push @{$anns}, $el;
 233 }
 234
 235 1;