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1 # $Id: SequenceStreamI.pm,v 1.3 2002/10/22 07:45:14 lapp Exp $
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2 #
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3 # BioPerl module for Bio::Factory::SequenceStreamI
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4 #
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5 # Cared for by Jason Stajich <jason@bioperl.org>
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6 #
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7 # Copyright Jason Stajich
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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 # POD documentation - main docs before the code
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12
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13 =head1 NAME
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14
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15 Bio::Factory::SequenceStreamI - Interface describing the basics of a Sequence Stream.
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16
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17 =head1 SYNOPSIS
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18
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19 # get a SequenceStreamI object somehow like with SeqIO
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20 use Bio::SeqIO;
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21 my $in = new Bio::SeqIO(-file => '< fastafile');
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22 while( my $seq = $in->next_seq ) {
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23 }
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24
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25 =head1 DESCRIPTION
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26
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27 This interface is for describing objects which produces
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28 Bio::PrimarySeqI objects or processes Bio::PrimarySeqI objects to a
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29 data stream.
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30
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31 =head1 FEEDBACK
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32
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33 =head2 Mailing Lists
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34
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35 User feedback is an integral part of the evolution of this and other
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36 Bioperl modules. Send your comments and suggestions preferably to
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37 the Bioperl mailing list. Your participation is much appreciated.
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38
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39 bioperl-l@bioperl.org - General discussion
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40 http://bioperl.org/MailList.shtml - About the mailing lists
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41
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42 =head2 Reporting Bugs
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43
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44 Report bugs to the Bioperl bug tracking system to help us keep track
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45 of the bugs and their resolution. Bug reports can be submitted via
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46 email or the web:
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47
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48 bioperl-bugs@bioperl.org
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49 http://bugzilla.bioperl.org/
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50
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51 =head1 AUTHOR - Jason Stajich
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52
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53 Email jason@bioperl.org
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54
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55 Describe contact details here
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56
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57 =head1 CONTRIBUTORS
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58
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59 Additional contributors names and emails here
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60
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61 =head1 APPENDIX
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62
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63 The rest of the documentation details each of the object methods.
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64 Internal methods are usually preceded with a _
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65
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66 =cut
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67
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68
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69 # Let the code begin...
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70
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71
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72 package Bio::Factory::SequenceStreamI;
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73 use vars qw(@ISA);
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74 use strict;
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75 use Bio::Root::RootI;
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76
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77 @ISA= qw(Bio::Root::RootI);
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78
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79 =head2 next_seq
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80
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81 Title : next_seq
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82 Usage : $seq = stream->next_seq
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83 Function: Reads the next sequence object from the stream and returns it.
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84
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85 Certain driver modules may encounter entries in the stream that
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86 are either misformatted or that use syntax not yet understood
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87 by the driver. If such an incident is recoverable, e.g., by
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88 dismissing a feature of a feature table or some other non-mandatory
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89 part of an entry, the driver will issue a warning. In the case
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90 of a non-recoverable situation an exception will be thrown.
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91 Do not assume that you can resume parsing the same stream after
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92 catching the exception. Note that you can always turn recoverable
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93 errors into exceptions by calling $stream->verbose(2).
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94 Returns : a Bio::Seq sequence object
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95 Args : none
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96
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97 See L<Bio::Root::RootI>
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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 shift->throw_not_implemented();
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103 }
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104
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105 =head2 write_seq
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106
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107 Title : write_seq
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108 Usage : $stream->write_seq($seq)
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109 Function: writes the $seq object into the stream
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110 Returns : 1 for success and 0 for error
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111 Args : Bio::Seq object
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112
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113 =cut
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114
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115 sub write_seq {
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116 shift->throw_not_implemented();
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117 }
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118
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119 =head2 sequence_factory
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120
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121 Title : sequence_factory
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122 Usage : $seqio->sequence_factory($seqfactory)
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123 Function: Get the Bio::Factory::SequenceFactoryI
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124 Returns : Bio::Factory::SequenceFactoryI
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125 Args : none
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126
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127
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128 =cut
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129
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130 sub sequence_factory{
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131 shift->throw_not_implemented();
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132 }
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133
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134 1;
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