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1 # $Id: SeqI.pm,v 1.25 2002/12/05 13:46:30 heikki Exp $
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2 #
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3 # BioPerl module for Bio::SeqI
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4 #
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5 # Cared for by Ewan Birney <birney@ebi.ac.uk>
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6 #
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7 # Copyright Ewan Birney
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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::SeqI [Developers] - Abstract Interface of Sequence (with features)
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16
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17 =head1 SYNOPSIS
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18
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19 # Bio::SeqI is the interface class for sequences.
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20
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21 # If you are a newcomer to bioperl, you should
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22 # start with Bio::Seq documentation. This
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23 # documentation is mainly for developers using
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24 # Bioperl.
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25
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26 # Bio::SeqI implements Bio::PrimarySeqI
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27 $seq = $seqobj->seq(); # actual sequence as a string
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28 $seqstr = $seqobj->subseq(10,50);
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29
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30 # Bio::SeqI has annotationcollections
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31
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32 $ann = $seqobj->annotation(); # annotation object
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33
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34 # Bio::SeqI has sequence features
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35 # features must implement Bio::SeqFeatureI
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36
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37 @features = $seqobj->get_SeqFeatures(); # just top level
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38 @features = $seqobj->get_all_SeqFeatures(); # descend into sub features
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39
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40
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41
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42 =head1 DESCRIPTION
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43
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44 Bio::SeqI is the abstract interface of annotated Sequences. These
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45 methods are those which you can be guarenteed to get for any Bio::SeqI
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46 - for most users of the package the documentation (and methods) in
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47 this class are not at useful - this is a developers only class which
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48 defines what methods have to be implmented by other Perl objects to
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49 comply to the Bio::SeqI interface. Go "perldoc Bio::Seq" or "man
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50 Bio::Seq" for more information.
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51
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52
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53 There aren't many here, because too many complicated functions here
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54 prevent implementations which are just wrappers around a database or
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55 similar delayed mechanisms.
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56
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57 Most of the clever stuff happens inside the SeqFeatureI system.
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58
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59 A good reference implementation is Bio::Seq which is a pure perl
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60 implementation of this class with alot of extra pieces for extra
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61 manipulation. However, if you want to be able to use any sequence
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62 object in your analysis, if you can do it just using these methods,
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63 then you know you will be future proof and compatible with other
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64 implementations of Seq.
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65
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66 =head1 FEEDBACK
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67
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68 =head2 Mailing Lists
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69
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70 User feedback is an integral part of the evolution of this and other
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71 Bioperl modules. Send your comments and suggestions preferably to one
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72 of the Bioperl mailing lists. Your participation is much appreciated.
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73
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74 bioperl-l@bioperl.org - General discussion
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75 http://bio.perl.org/MailList.html - About the mailing lists
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76
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77 =head2 Reporting Bugs
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78
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79 Report bugs to the Bioperl bug tracking system to help us keep track
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80 the bugs and their resolution. Bug reports can be submitted via email
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81 or the web:
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82
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83 bioperl-bugs@bio.perl.org
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84 http://bugzilla.bioperl.org/
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85
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86 =head1 AUTHOR - Ewan Birney
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87
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88 Email birney@sanger.ac.uk
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89
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90
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91 =head1 APPENDIX
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92
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93 The rest of the documentation details each of the object
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94 methods. Internal methods are usually preceded with a _
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95
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96 =cut
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97
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98 #'
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99 # Let the code begin...
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100
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101
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102 package Bio::SeqI;
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103 use strict;
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104
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105 use vars qw(@ISA);
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106 use Bio::PrimarySeqI;
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107 use Bio::AnnotatableI;
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108 use Bio::FeatureHolderI;
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109
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110 # Object preamble - inheriets from Bio::PrimarySeqI
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111
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112 @ISA = qw(Bio::PrimarySeqI Bio::AnnotatableI Bio::FeatureHolderI);
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113
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114 =head2 get_SeqFeatures
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115
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116 Title : get_SeqFeatures
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117 Usage : my @feats = $seq->get_SeqFeatures();
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118 Function: retrieve just the toplevel sequence features attached to this seq
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119 Returns : array of Bio::SeqFeatureI objects
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120 Args : none
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121
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122 This method comes through extension of Bio::FeatureHolderI. See
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123 L<Bio::FeatureHolderI> and L<Bio::SeqFeatureI> for more information.
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124
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125 =cut
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126
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127 =head2 get_all_SeqFeatures
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128
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129 Title : get_all_SeqFeatures
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130 Usage : @features = $annseq->get_all_SeqFeatures()
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131 Function: returns all SeqFeatures, included sub SeqFeatures
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132 Returns : an array of Bio::SeqFeatureI objects
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133 Args : none
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134
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135 This method comes through extension of Bio::FeatureHolderI. See
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136 L<Bio::FeatureHolderI> and L<Bio::SeqFeatureI> for more information.
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137
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138 =cut
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139
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140 =head2 feature_count
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141
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142 Title : feature_count
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143 Usage : $seq->feature_count()
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144 Function: Return the number of SeqFeatures attached to a sequence
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145 Returns : integer representing the number of SeqFeatures
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146 Args : none
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147
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148 This method comes through extension of Bio::FeatureHolderI. See
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149 L<Bio::FeatureHolderI> for more information.
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150
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151 =cut
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152
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153 =head2 seq
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154
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155 Title : seq
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156 Usage : my $string = $seq->seq();
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157 Function: Retrieves the sequence string for the sequence object
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158 Returns : string
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159 Args : none
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160
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161
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162 =cut
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163
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164 sub seq{
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165 my ($self) = @_;
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166 $self->throw_not_implemented();
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167 }
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168
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169 =head2 write_GFF
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170
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171 Title : write_GFF
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172 Usage : $seq->write_GFF(\*FILEHANDLE);
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173 Function: Convience method to write out all the sequence features
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174 in GFF format to the provided filehandle (STDOUT by default)
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175 Returns : none
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176 Args : [optional] filehandle to write to (default is STDOUT)
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177
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178
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179 =cut
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180
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181 sub write_GFF{
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182 my ($self,$fh) = @_;
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183
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184 $fh || do { $fh = \*STDOUT; };
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185
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186 foreach my $sf ( $self->get_all_SeqFeatures() ) {
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187 print $fh $sf->gff_string, "\n";
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188 }
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189
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190 }
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191
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192 =head2 annotation
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193
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194 Title : annotation
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195 Usage : $obj->annotation($seq_obj)
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196 Function: retrieve the attached annotation object
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197 Returns : Bio::AnnotationCollectionI or none;
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198
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199 See L<Bio::AnnotationCollectionI> and L<Bio::Annotation::Collection>
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200 for more information. This method comes through extension from
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201 L<Bio::AnnotatableI>.
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202
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203 =cut
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204
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205 =head2 species
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206
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207 Title : species
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208 Usage :
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209 Function: Gets or sets the species
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210 Example : $species = $self->species();
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211 Returns : Bio::Species object
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212 Args : Bio::Species object or none;
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213
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214 See L<Bio::Species> for more information
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215
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216 =cut
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217
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218 sub species {
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219 my ($self) = @_;
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220 $self->throw_not_implemented();
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221 }
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222
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223 =head2 primary_seq
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224
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225 Title : primary_seq
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226 Usage : $obj->primary_seq($newval)
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227 Function: Retrieve the underlying Bio::PrimarySeqI object if available.
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228 This is in the event one has a sequence with lots of features
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229 but want to be able to narrow the object to just one with
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230 the basics of a sequence (no features or annotations).
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231 Returns : Bio::PrimarySeqI
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232 Args : Bio::PrimarySeqI or none;
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233
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234 See L<Bio::PrimarySeqI> for more information
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235
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236 =cut
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237
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238 sub primary_seq {
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239 my ($self) = @_;
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240 $self->throw_not_implemented;
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241 }
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242
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243 1;
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