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1 # $Id: pln.pm,v 1.7 2002/10/22 07:38:42 lapp Exp $
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2 # BioPerl module for Bio::SeqIO::pln
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3 #
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4 # Cared for by Aaron Mackey <amackey@virginia.edu>
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5 #
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6 # Copyright Aaron Mackey
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7 #
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8 # You may distribute this module under the same terms as perl itself
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9
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10 # POD documentation - main docs before the code
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11
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12 =head1 NAME
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13
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14 Bio::SeqIO::pln - pln trace sequence input/output stream
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15
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16 =head1 SYNOPSIS
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17
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18 Do not use this module directly. Use it via the Bio::SeqIO class.
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19
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20 =head1 DESCRIPTION
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21
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22 This object can transform Bio::Seq objects to and from pln trace
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23 files.
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24
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25 =head1 FEEDBACK
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26
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27 =head2 Mailing Lists
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28
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29 User feedback is an integral part of the evolution of this and other
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30 Bioperl modules. Send your comments and suggestions preferably to one
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31 of the Bioperl mailing lists. Your participation is much appreciated.
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32
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33 bioperl-l@bioperl.org - General discussion
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34 http://bioperl.org/MailList.shtml - About the mailing lists
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35
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36 =head2 Reporting Bugs
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37
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38 Report bugs to the Bioperl bug tracking system to help us keep track
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39 the bugs and their resolution.
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40 Bug reports can be submitted via email or the web:
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41
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42 bioperl-bugs@bio.perl.org
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43 http://bugzilla.bioperl.org/
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44
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45 =head1 AUTHORS - Aaron Mackey
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46
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47 Email: amackey@virginia.edu
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48
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49 =head1 APPENDIX
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50
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51 The rest of the documentation details each of the object
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52 methods. Internal methods are usually preceded with a _
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53
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54 =cut
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55
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56 # Let the code begin...
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57
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58 package Bio::SeqIO::pln;
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59 use vars qw(@ISA $READ_AVAIL);
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60 use strict;
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61 # Object preamble - inherits from Bio::Root::Object
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62
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63 use Bio::SeqIO;
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64 use Bio::Seq::SeqFactory;
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65
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66 push @ISA, qw( Bio::SeqIO );
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67
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68 sub BEGIN {
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69 eval { require Bio::SeqIO::staden::read; };
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70 if ($@) {
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71 $READ_AVAIL = 0;
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72 } else {
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73 push @ISA, "Bio::SeqIO::staden::read";
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74 $READ_AVAIL = 1;
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75 }
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76 }
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77
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78 sub _initialize {
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79 my($self,@args) = @_;
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80 $self->SUPER::_initialize(@args);
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81 if( ! defined $self->sequence_factory ) {
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82 $self->sequence_factory(new Bio::Seq::SeqFactory(-verbose => $self->verbose(), -type => 'Bio::Seq'));
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83 }
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84 unless ($READ_AVAIL) {
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85 Bio::Root::Root->throw( -class => 'Bio::Root::SystemException',
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86 -text => "Bio::SeqIO::staden::read is not available; make sure the bioperl-ext package has been installed successfully!"
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87 );
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88 }
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89 }
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90
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91 =head2 next_seq
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92
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93 Title : next_seq
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94 Usage : $seq = $stream->next_seq()
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95 Function: returns the next sequence in the stream
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96 Returns : Bio::SeqWithQuality object
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97 Args : NONE
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98
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99 =cut
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100
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101 sub next_seq {
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102
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103 my ($self) = @_;
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104
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105 my ($seq, $id, $desc, $qual) = $self->read_trace($self->_fh, 'pln');
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106
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107 # create the seq object
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108 $seq = $self->sequence_factory->create(-seq => $seq,
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109 -id => $id,
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110 -primary_id => $id,
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111 -desc => $desc,
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112 -alphabet => 'DNA',
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113 -qual => $qual
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114 );
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115 return $seq;
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116 }
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117
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118 =head2 write_seq
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119
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120 Title : write_seq
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121 Usage : $stream->write_seq(@seq)
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122 Function: writes the $seq object into the stream
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123 Returns : 1 for success and 0 for error
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124 Args : Bio::Seq object
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125
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126
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127 =cut
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128
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129 sub write_seq {
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130 my ($self,@seq) = @_;
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131
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132 my $fh = $self->_fh;
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133 foreach my $seq (@seq) {
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134 $self->write_trace($fh, $seq, 'pln');
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135 }
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136
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137 $self->flush if $self->_flush_on_write && defined $self->_fh;
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138 return 1;
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139 }
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140
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141 1;
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