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1 # $Id: BaseSeqProcessor.pm,v 1.2 2002/11/02 21:04:19 lapp Exp $
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2 #
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3 # BioPerl module for Bio::Seq::BaseSeqProcessor
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4 #
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5 # Cared for by Hilmar Lapp <hlapp at gmx.net>
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6 #
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7 # Copyright Hilmar Lapp
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8 #
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9 # You may distribute this module under the same terms as perl itself
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10
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11 #
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12 # (c) Hilmar Lapp, hlapp at gmx.net, 2002.
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13 # (c) GNF, Genomics Institute of the Novartis Research Foundation, 2002.
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14 #
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15 # You may distribute this module under the same terms as perl itself.
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16 # Refer to the Perl Artistic License (see the license accompanying this
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17 # software package, or see http://www.perl.com/language/misc/Artistic.html)
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18 # for the terms under which you may use, modify, and redistribute this module.
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19 #
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20 # THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED
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21 # WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF
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22 # MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
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23 #
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24
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25 # POD documentation - main docs before the code
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26
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27 =head1 NAME
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28
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29 Bio::Seq::BaseSeqProcessor - Base implementation for a SequenceProcessor
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30
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31 =head1 SYNOPSIS
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32
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33 # you need to derive your own processor from this one
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34
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35 =head1 DESCRIPTION
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36
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37 This provides just a basic framework for implementations of
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38 L<Bio::Factory::SequenceProcessorI>.
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39
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40 Essentially what it does is support a parameter to new() to set
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41 sequence factory and source stream, and a next_seq() implementation
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42 that will use a queue to be filled by a class overriding
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43 process_seq().
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44
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45 =head1 FEEDBACK
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46
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47 =head2 Mailing Lists
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48
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49 User feedback is an integral part of the evolution of this and other
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50 Bioperl modules. Send your comments and suggestions preferably to
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51 the Bioperl mailing list. Your participation is much appreciated.
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52
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53 bioperl-l@bioperl.org - General discussion
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54 http://bioperl.org/MailList.shtml - About the mailing lists
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55
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56 =head2 Reporting Bugs
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57
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58 Report bugs to the Bioperl bug tracking system to help us keep track
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59 of the bugs and their resolution. Bug reports can be submitted via
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60 email or the web:
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61
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62 bioperl-bugs@bioperl.org
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63 http://bioperl.org/bioperl-bugs/
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64
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65 =head1 AUTHOR - Hilmar Lapp
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66
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67 Email hlapp at gmx.net
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68
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69 Describe contact details here
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70
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71 =head1 CONTRIBUTORS
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72
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73 Additional contributors names and emails here
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74
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75 =head1 APPENDIX
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76
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77 The rest of the documentation details each of the object methods.
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78 Internal methods are usually preceded with a _
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79
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80 =cut
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81
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82
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83 # Let the code begin...
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84
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85
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86 package Bio::Seq::BaseSeqProcessor;
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87 use vars qw(@ISA);
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88 use strict;
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89
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90 # Object preamble - inherits from Bio::Root::Root
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91
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92 use Bio::Root::Root;
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93 use Bio::Factory::SequenceProcessorI;
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94
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95 @ISA = qw(Bio::Root::Root Bio::Factory::SequenceProcessorI);
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96
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97 =head2 new
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98
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99 Title : new
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100 Usage : my $obj = new Bio::Seq::BaseSeqProcessor();
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101 Function: Builds a new Bio::Seq::BaseSeqProcessor object
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102 Returns : an instance of Bio::Seq::BaseSeqProcessor
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103 Args : Named parameters. Currently supported are
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104 -seqfactory the Bio::Factory::SequenceFactoryI object to use
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105 -source_stream the Bio::Factory::SequenceStreamI object to
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106 which we are chained
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107
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108
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109 =cut
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110
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111 sub new {
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112 my($class,@args) = @_;
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113
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114 my $self = $class->SUPER::new(@args);
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115
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116 my ($stream,$fact) =
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117 $self->_rearrange([qw(SOURCE_STREAM SEQFACTORY)], @args);
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118
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119 $self->{'_queue'} = [];
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120 $self->sequence_factory($fact) if $fact;
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121 $self->source_stream($stream) if $stream;
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122
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123 return $self;
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124 }
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125
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126 =head1 L<Bio::Factory::SequenceProcessorI> methods
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127
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128 =cut
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129
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130 =head2 source_stream
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131
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132 Title : source_stream
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133 Usage : $obj->source_stream($newval)
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134 Function: Get/set the source sequence stream for this sequence
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135 processor.
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136
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137 Example :
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138 Returns : A Bio::Factory::SequenceStreamI compliant object
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139 Args : on set, new value (a Bio::Factory::SequenceStreamI compliant
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140 object)
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141
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142
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143 =cut
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144
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145 sub source_stream{
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146 my $self = shift;
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147
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148 if(@_) {
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149 my $stream = shift;
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150 my $fact = $stream->sequence_factory();
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151 $self->sequence_factory($fact)
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152 unless $self->sequence_factory() || (! $fact);
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153 return $self->{'source_stream'} = $stream;
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154 }
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155 return $self->{'source_stream'};
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156 }
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157
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158 =head1 L<Bio::Factory::SequenceStreamI> methods
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159
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160 =cut
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161
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162 =head2 next_seq
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163
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164 Title : next_seq
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165 Usage : $seq = stream->next_seq
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166 Function: Reads the next sequence object from the stream and returns it.
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167
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168 This implementation will obtain objects from the source
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169 stream as necessary and pass them to process_seq() for
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170 processing. This method will return the objects one at a
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171 time that process_seq() returns.
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172
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173 Returns : a Bio::Seq sequence object
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174 Args : none
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175
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176 See L<Bio::Factory::SequenceStreamI::next_seq>
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177
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178 =cut
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179
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180 sub next_seq{
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181 my $self = shift;
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182 my $seq;
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183
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184 # if the queue is empty, fetch next from source and process it
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185 if(@{$self->{'_queue'}} == 0) {
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186 my @seqs = ();
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187 while($seq = $self->source_stream->next_seq()) {
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188 @seqs = $self->process_seq($seq);
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189 # we may get zero seqs returned
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190 last if @seqs;
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191 }
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192 push(@{$self->{'_queue'}}, @seqs) if @seqs;
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193 }
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194 # take next from the queue of seqs
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195 $seq = shift(@{$self->{'_queue'}});
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196 return $seq;
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197 }
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198
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199 =head2 write_seq
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200
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201 Title : write_seq
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202 Usage : $stream->write_seq($seq)
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203 Function: writes the $seq object into the stream
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204
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205 This implementation passes the sequences to the source
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206 stream unaltered. You need to override this in order to
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207 have sequence objects altered before output.
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208
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209 Returns : 1 for success and 0 for error
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210 Args : Bio::Seq object
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211
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212 =cut
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213
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214 sub write_seq{
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215 return shift->source_stream->write_seq(@_);
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216 }
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217
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218 =head2 sequence_factory
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219
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220 Title : sequence_factory
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221 Usage : $seqio->sequence_factory($seqfactory)
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222 Function: Get the Bio::Factory::SequenceFactoryI
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223 Returns : Bio::Factory::SequenceFactoryI
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224 Args : none
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225
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226
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227 =cut
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228
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229 sub sequence_factory{
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230 my $self = shift;
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231
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232 return $self->{'sequence_factory'} = shift if @_;
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233 return $self->{'sequence_factory'};
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234 }
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235
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236 =head2 object_factory
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237
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238 Title : object_factory
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239 Usage : $obj->object_factory($newval)
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240 Function: This is an alias to sequence_factory with a more generic name.
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241 Example :
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242 Returns : a L<Bio::Factory::ObjectFactoryI> compliant object
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243 Args : on set, new value (a L<Bio::Factory::ObjectFactoryI>
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244 compliant object or undef, optional)
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245
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246
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247 =cut
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248
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249 sub object_factory{
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250 return shift->sequence_factory(@_);
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251 }
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252
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253 =head2 close
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254
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255 Title : close
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256 Usage :
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257 Function: Closes the stream. We override this here in order to cascade
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258 to the source stream.
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259 Example :
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260 Returns :
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261 Args : none
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262
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263
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264 =cut
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265
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266 sub close{
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267 my $self = shift;
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268 return $self->source_stream() ? $self->source_stream->close(@_) : 1;
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269 }
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270
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271 =head1 To be overridden by a derived class
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272
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273 =cut
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274
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275 =head2 process_seq
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276
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277 Title : process_seq
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278 Usage :
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279 Function: This is the method that is supposed to do the actual
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280 processing. It needs to be overridden to do what you want
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281 it to do.
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282
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283 Generally, you do not have to override or implement any other
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284 method to derive your own sequence processor.
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285
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286 The implementation provided here just returns the unaltered
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287 input sequence and hence is not very useful other than
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288 serving as a neutral default processor.
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289
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290 Example :
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291 Returns : An array of zero or more Bio::PrimarySeqI (or derived
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292 interface) compliant object as the result of processing the
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293 input sequence.
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294 Args : A Bio::PrimarySeqI (or derived interface) compliant object
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295 to be processed.
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296
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297
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298 =cut
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299
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300 sub process_seq{
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301 my ($self,$seq) = @_;
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302
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303 return ($seq);
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304 }
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305
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306 1;
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