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1 # $Id: FeatureHolderI.pm,v 1.2 2002/11/19 07:04:22 lapp Exp $
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2 #
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3 # BioPerl module for Bio::FeatureHolderI
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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 # 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::FeatureHolderI - the base interface an object with features must implement
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16
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17 =head1 SYNOPSIS
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18
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19 use Bio::SeqIO;
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20 # get a feature-holding object somehow: for example, Bio::SeqI objects
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21 # have features
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22 my $seqio = Bio::SeqIO->new(-fh => \*STDIN, -format => 'genbank);
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23 while (my $seq = $seqio->next_seq()) {
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24 # $seq is-a Bio::FeatureHolderI, hence:
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25 my @feas = $seq->get_SeqFeatures();
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26 # each element is-a Bio::SeqFeatureI
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27 foreach my $fea (@feas) {
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28 # do something with the feature objects
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29 }
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30 }
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31
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32 =head1 DESCRIPTION
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33
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34 This is the base interface that all feature-holding objects must
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35 implement.
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36
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37 Popular feature-holders are for instance L<Bio::Seq> objects. Since
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38 L<Bio::SeqFeatureI> defines a sub_SeqFeature() method, most
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39 Bio::SeqFeatureI implementations like L<Bio::SeqFeature::Generic> will
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40 implement the feature holder interface as well.
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41
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42 =head1 FEEDBACK
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43
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44 =head2 Mailing Lists
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45
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46 User feedback is an integral part of the evolution of this and other
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47 Bioperl modules. Send your comments and suggestions preferably to
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48 the Bioperl mailing list. Your participation is much appreciated.
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49
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50 bioperl-l@bioperl.org - General discussion
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51 http://bioperl.org/MailList.shtml - About the mailing lists
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52
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53 =head2 Reporting Bugs
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54
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55 Report bugs to the Bioperl bug tracking system to help us keep track
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56 of the bugs and their resolution. Bug reports can be submitted via
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57 email or the web:
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58
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59 bioperl-bugs@bioperl.org
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60 http://bioperl.org/bioperl-bugs/
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61
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62 =head1 AUTHOR - Hilmar Lapp
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63
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64 Email hlapp at gmx.net
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65
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66 Describe contact details here
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67
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68 =head1 CONTRIBUTORS
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69
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70 Additional contributors names and emails here
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71
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72 =head1 APPENDIX
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73
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74 The rest of the documentation details each of the object methods.
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75 Internal methods are usually preceded with a _
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76
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77 =cut
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78
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79
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80 # Let the code begin...
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81
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82
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83 package Bio::FeatureHolderI;
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84 use vars qw(@ISA);
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85 use strict;
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86 use Carp;
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87 use Bio::Root::RootI;
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88
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89 @ISA = qw( Bio::Root::RootI );
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90
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91 =head2 get_SeqFeatures
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92
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93 Title : get_SeqFeatures
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94 Usage :
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95 Function: Get the feature objects held by this feature holder.
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96 Example :
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97 Returns : an array of Bio::SeqFeatureI implementing objects
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98 Args : none
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99
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100 At some day we may want to expand this method to allow for a feature
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101 filter to be passed in.
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102
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103 =cut
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104
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105 sub get_SeqFeatures{
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106 shift->throw_not_implemented();
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107 }
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108
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109 =head2 feature_count
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110
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111 Title : feature_count
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112 Usage : $obj->feature_count()
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113 Function: Return the number of SeqFeatures attached to a feature holder.
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114
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115 This is before flattening a possible sub-feature tree.
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116
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117 We provide a default implementation here that just counts
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118 the number of objects returned by get_SeqFeatures().
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119 Implementors may want to override this with a more
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120 efficient implementation.
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121
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122 Returns : integer representing the number of SeqFeatures
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123 Args : None
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124
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125 At some day we may want to expand this method to allow for a feature
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126 filter to be passed in.
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127
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128 Our default implementation allows for any number of additional
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129 arguments and will pass them on to get_SeqFeatures(). I.e., in order to
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130 support filter arguments, just support them in get_SeqFeatures().
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131
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132 =cut
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133
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134 sub feature_count {
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135 return scalar(shift->get_SeqFeatures(@_));
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136 }
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137
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138 =head2 get_all_SeqFeatures
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139
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140 Title : get_all_SeqFeatures
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141 Usage :
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142 Function: Get the flattened tree of feature objects held by this
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143 feature holder. The difference to get_SeqFeatures is that
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144 the entire tree of sub-features will be flattened out.
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145
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146 We provide a default implementation here, so implementors
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147 don''t necessarily need to implement this method.
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148
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149 Example :
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150 Returns : an array of Bio::SeqFeatureI implementing objects
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151 Args : none
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152
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153 At some day we may want to expand this method to allow for a feature
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154 filter to be passed in.
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155
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156 Our default implementation allows for any number of additional
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157 arguments and will pass them on to any invocation of
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158 get_SeqFeatures(), wherever a component of the tree implements
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159 FeatureHolderI. I.e., in order to support filter arguments, just
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160 support them in get_SeqFeatures().
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161
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162 =cut
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163
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164 sub get_all_SeqFeatures{
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165 my $self = shift;
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166 my @flatarr;
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167
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168 foreach my $feat ( $self->get_SeqFeatures(@_) ){
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169 push(@flatarr,$feat);
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170 &_add_flattened_SeqFeatures(\@flatarr,$feat,@_);
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171 }
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172 return @flatarr;
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173 }
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174
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175 sub _add_flattened_SeqFeatures {
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176 my ($arrayref,$feat,@args) = @_;
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177 my @subs = ();
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178
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179 if($feat->isa("Bio::FeatureHolderI")) {
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180 @subs = $feat->get_SeqFeatures(@args);
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181 } elsif($feat->isa("Bio::SeqFeatureI")) {
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182 @subs = $feat->sub_SeqFeature();
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183 } else {
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184 confess ref($feat)." is neither a FeatureHolderI nor a SeqFeatureI. ".
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185 "Don't know how to flatten.";
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186 }
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187 foreach my $sub (@subs) {
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188 push(@$arrayref,$sub);
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189 &_add_flattened_SeqFeatures($arrayref,$sub);
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190 }
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191
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192 }
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193
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194 1;
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