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1 # $Id: ztr.pm,v 1.8 2002/10/22 07:38:42 lapp Exp $
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2 # BioPerl module for Bio::SeqIO::ztr
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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::ztr - ztr 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 ztr 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::ztr;
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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 => $self->verbose(), -type => 'Bio::Seq::SeqWithQuality'));
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83 }
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84
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85 my ($compression) = $self->_rearrange([qw[COMPRESSION]], @args);
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86 $compression = 2 unless defined $compression;
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87 $self->compression($compression);
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88
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89 unless ($READ_AVAIL) {
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90 Bio::Root::Root->throw( -class => 'Bio::Root::SystemException',
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91 -text => "Bio::SeqIO::staden::read is not available; make sure the bioperl-ext package has been installed successfully!"
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92 );
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93 }
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94 }
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95
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96 =head2 next_seq
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97
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98 Title : next_seq
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99 Usage : $seq = $stream->next_seq()
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100 Function: returns the next sequence in the stream
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101 Returns : Bio::SeqWithQuality object
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102 Args : NONE
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103
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104 =cut
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105
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106 sub next_seq {
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107
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108 my ($self) = @_;
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109
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110 my ($seq, $id, $desc, $qual) = $self->read_trace($self->_fh, 'ztr');
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111
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112 # create the seq object
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113 $seq = $self->sequence_factory->create(-seq => $seq,
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114 -id => $id,
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115 -primary_id => $id,
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116 -desc => $desc,
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117 -alphabet => 'DNA',
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118 -qual => $qual
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119 );
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120 return $seq;
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121 }
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122
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123 =head2 write_seq
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124
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125 Title : write_seq
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126 Usage : $stream->write_seq(@seq)
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127 Function: writes the $seq object into the stream
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128 Returns : 1 for success and 0 for error
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129 Args : Bio::Seq object
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130
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131
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132 =cut
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133
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134 sub write_seq {
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135 my ($self,@seq) = @_;
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136
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137 my $fh = $self->_fh;
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138 foreach my $seq (@seq) {
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139 $self->write_trace($fh, $seq, 'ztr' . $self->compression);
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140 }
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141
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142 $self->flush if $self->_flush_on_write && defined $self->_fh;
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143 return 1;
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144 }
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145
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146 =head2 compression
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147
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148 Title : compression
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149 Usage : $stream->compression(3);
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150 Function: determines the level of ZTR compression
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151 Returns : the current (or newly set) value.
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152 Args : 1, 2 or 3 - any other (defined) value will cause the compression
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153 to be reset to the default of 2.
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154
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155
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156 =cut
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157
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158 sub compression {
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159
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160 my ($self, $val) = @_;
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161
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162 if (defined $val) {
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163 if ($val =~ m/^1|2|3$/o) {
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164 $self->{_compression} = $val;
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165 } else {
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166 $self->{_compression} = 2;
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167 }
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168 }
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169
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170 return $self->{_compression};
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171 }
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172
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173 1;
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