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1 # $Id: FeatureGroup.pm,v 1.1.2.2 2003/09/17 09:19:21 allenday Exp $
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2 # BioPerl module for Bio::Expression::FeatureGroup
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3 #
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4 # Copyright Allen Day <allenday@ucla.edu>, Stanley Nelson <snelson@ucla.edu>
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5 # Human Genetics, UCLA Medical School, University of California, Los Angeles
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6
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7 # POD documentation - main docs before the code
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8
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9 =head1 NAME
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10
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11 Bio::Expression::FeatureGroup - a set of DNA/RNA features. ISA
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12 Bio::Expression::FeatureI
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13
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14 =head1 SYNOPSIS
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15
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16 #
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17
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18 =head1 DESCRIPTION
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19
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20 A set of DNA/RNA features.
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21
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22 =head1 FEEDBACK
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23
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24 =head2 Mailing Lists
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25
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26 User feedback is an integral part of the evolution of this and other
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27 Bioperl modules. Send your comments and suggestions preferably to one
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28 of the Bioperl mailing lists. Your participation is much appreciated.
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29
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30 bioperl-l@bioperl.org - General discussion
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31 http://bioperl.org/MailList.shtml - About the mailing lists
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32
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33 =head2 Reporting Bugs
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34
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35 Report bugs to the Bioperl bug tracking system to help us keep track
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36 the bugs and their resolution.
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37 Bug reports can be submitted via email or the web:
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38
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39 bioperl-bugs@bio.perl.org
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40 http://bugzilla.bioperl.org/
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41
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42 =head1 AUTHOR
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43
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44 Allen Day E<lt>allenday@ucla.eduE<gt>
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45
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46 =head1 APPENDIX
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47
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48 The rest of the documentation details each of the object
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49 methods. Internal methods are usually preceded with a _
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50
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51 =cut
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52
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53 # Let the code begin...
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54 package Bio::Expression::FeatureGroup;
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55
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56 use strict;
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57
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58 use base qw(Bio::Root::Root Bio::Expression::FeatureI);
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59 use vars qw($DEBUG);
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60
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61 =head2 new
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62
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63 Title : new
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64 Usage : $featuregroup = Bio::Expression::FeatureGroup->new(%args);
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65 Function: create a new featuregroup object
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66 Returns : a Bio::Expression::FeatureGroup object
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67 Args : an optional hash of parameters to be used in initialization:
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68 -id -- the featuregroup ID
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69 -type -- the featuregroup type
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70
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71 =cut
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72
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73 sub new {
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74 my($class,@args) = @_;
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75 my $self = bless {}, $class;
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76 $self->_initialize(@args);
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77 return $self;
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78 }
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79
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80 =head2 _initialize
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81
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82 Title : _initialize
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83 Usage : $featuregroup->_initialize(@args);
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84 Function: initialize the featuregroup object
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85 Returns : nothing
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86 Args : @args
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87
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88 =cut
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89
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90 sub _initialize{
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91 my ($self,@args) = @_;
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92 my %param = @args;
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93
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94 $self->type($param{-type});
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95 $self->id($param{-id} );
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96
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97 $self->SUPER::_initialize(@args);
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98 $DEBUG = 1 if( ! defined $DEBUG && $self->verbose > 0);
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99 }
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100
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101 =head2 type
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102
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103 Title : type
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104 Usage : $featuregroup->type($optional_arg);
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105 Function: get/set the type of the featuregroup
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106 Comments: this is probably going to be a string like
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107 "quality control", "mismatch blah blah", etc.
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108 Returns : the featuregroup type
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109 Args : a new value for the featuregroup type
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110
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111 =cut
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112
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113 sub type {
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114 my $self = shift;
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115 $self->{type} = shift if @_;
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116 return $self->{type};
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117 }
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118
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119 =head2 id
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120
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121 Title : id
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122 Usage : $featuregroup->id($optional_arg);
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123 Function: get/set the id of the featuregroup
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124 Returns : the featuregroup id
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125 Args : a new value for the featuregroup id
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126
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127 =cut
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128
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129 sub id {
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130 my $self = shift;
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131 $self->{id} = shift if @_;
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132 return $self->{id};
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133 }
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134
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135
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136 =head2 standard_deviation
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137
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138 Title : standard_deviation
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139 Usage : $featuregroup->standard_deviation($optional_arg);
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140 Function: get/set the standard deviation of the featuregroup value
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141 Returns : the featuregroup standard deviation
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142 Args : a new value for the featuregroup standard deviation
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143 Notes : this method does no calculation, it merely holds a value
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144
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145 =cut
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146
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147 sub standard_deviation {
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148 my $self = shift;
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149 $self->{standard_deviation} = shift if @_;
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150 return $self->{standard_deviation};
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151 }
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152
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153 =head2 quantitation
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154
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155 Title : quantitation
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156 Usage : $featuregroup->quantitation($optional_arg);
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157 Function: get/set the quantitation of the featuregroup
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158 Returns : the featuregroup's quantitated value
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159 Args : a new value for the featuregroup's quantitated value
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160 Notes : this method does no calculation, it merely holds a value
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161
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162 =cut
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163
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164 sub quantitation {
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165 my $self = shift;
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166 $self->{quantitation} = shift if @_;
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167 return $self->{quantitation};
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168 }
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169
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170 =head2 quantitation_units
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171
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172 Title : quantitation_units
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173 Usage : $featuregroup->quantitation_units($optional_arg);
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174 Function: get/set the quantitation units of the featuregroup
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175 Returns : the featuregroup's quantitated value units
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176 Args : a new value for the featuregroup's quantitated value units
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177
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178 =cut
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179
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180 sub quantitation_units {
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181 my $self = shift;
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182 $self->{quantitation_units} = shift if @_;
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183 return $self->{quantitation_units};
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184 }
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185
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186 =head2 presence
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187
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188 Title : presence
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189 Usage : $featuregroup->presence($optional_arg);
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190 Function: get/set the presence call of the featuregroup
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191 Returns : the featuregroup's presence call
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192 Args : a new value for the featuregroup's presence call
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193
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194 =cut
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195
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196 sub presence {
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197 my $self = shift;
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198 $self->{presence} = shift if @_;
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199 return $self->{presence};
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200 }
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201
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202 =head2 add_feature
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203
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204 Title : add_feature
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205 Usage : $feature_copy = $featuregroup->add_feature($feature);
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206 Function: add a feature to the featuregroup
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207 Returns : see this_feature()
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208 Args : a Bio::Expression::FeatureI compliant object
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209
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210 =cut
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211
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212 sub add_feature {
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213 my($self,@args) = @_;
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214 foreach my $feature (@args){
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215 $self->throw('Features must be Bio::Expression::FeatureI compliant') unless $feature->isa('Bio::Expression::FeatureI');
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216 push @{$self->{features}}, $feature;
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217 }
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218
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219 return $self->{features} ? $self->{features}->[-1] : undef;
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220 }
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221
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222 =head2 this_feature
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223
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224 Title : this_feature
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225 Usage : $feature = $featuregroup->this_feature
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226 Function: access the last feature added to the featuregroup
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227 Returns : the last feature added to the featuregroup
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228 Args : none
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229
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230 =cut
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231
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232 sub this_feature {
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233 my $self = shift;
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234 return $self->{features} ? $self->{features}->[-1] : undef;
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235 }
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236
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237 =head2 each_feature
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238
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239 Title : each_feature
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240 Usage : @features = $featuregroup->each_feature
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241 Function: returns a list of Bio::Expression::FeatureI compliant
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242 objects
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243 Returns : a list of objects
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244 Args : none
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245
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246 =cut
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247
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248 sub each_feature {
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249 my $self = shift;
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250 return @{$self->{features}} if defined($self->{features});
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251 return ();
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252 }
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253
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254 =head2 each_feature_quantitation
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255
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256 Title : each_feature_quantitation
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257 Usage : @featurequantitions = $featuregroup->each_feature_quantitation;
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258 Function: returns an list of quantitations of the features in the featuregroup
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259 Returns : a list of numeric values
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260 Args : none
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261
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262 =cut
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263
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264 sub each_feature_quantitation {
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265 my $self = shift;
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266 my @values = ();
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267 push @values, $_->value foreach $self->each_feature;
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268 return @values;
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269 }
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270
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271 =head2 is_qc
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272
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273 Title : is_qc
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274 Usage : $is_quality_control = $featuregroup->is_qc
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275 Function: get/set whether or not the featuregroup is used for quality control purposes
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276 Returns : a boolean (equivalent)
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277 Args : a new value
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278
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279 =cut
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280
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281 sub is_qc {
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282 my $self = shift;
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283 $self->{is_qc} = shift if defined @_;
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284 return $self->{is_qc};
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285 }
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286
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287 1;
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