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1 # $Id: Set.pm,v 1.13 2002/10/22 07:45:23 lapp Exp $
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2 #
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3 # BioPerl module for Bio::Tools::HMMER::Set
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4 #
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5 # Cared for by Ewan Birney <birney@sanger.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::Tools::HMMER::Set - Set of identical domains from HMMER matches
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16
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17 =head1 SYNOPSIS
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18
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19 # get a Set object probably from the results object
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20 print "Bits score over set ",$set->bits," evalue ",$set->evalue,"\n";
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21
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22 foreach $domain ( $set->each_Domain ) {
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23 print "Domain start ",$domain->start," end ",$domain->end,"\n";
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24 }
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25
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26 =head1 DESCRIPTION
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27
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28 Represents a set of HMMER domains hitting one sequence. HMMER reports two
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29 different scores, a per sequence total score (and evalue) and a per
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30 domain score and evalue. This object represents a collection of the same
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31 domain with the sequence bits score and evalue. (these attributes are also
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32 on the per domain scores, which you can get there).
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33
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34 =head1 FEEDBACK
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35
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36 =head2 Mailing Lists
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37
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38 User feedback is an integral part of the evolution of this and other
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39 Bioperl modules. Send your comments and suggestions preferably to one
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40 of the Bioperl mailing lists. Your participation is much appreciated.
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41
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42 bioperl-l@bioperl.org - General discussion
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43 http://www.bioperl.org/MailList.html - About the mailing lists
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44
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45 =head2 Reporting Bugs
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46
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47 Report bugs to the Bioperl bug tracking system to help us keep track
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48 the bugs and their resolution.
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49
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50 Bug reports can be submitted via email or the web:
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51
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52 bioperl-bugs@bioperl.org
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53 http://www.bugzilla.bioperl.org/
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54
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55 =head1 AUTHOR - Ewan Birney
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56
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57 Email birney@sanger.ac.uk
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58
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59 =head1 APPENDIX
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60
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61 The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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62
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63 =cut
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64
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65
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66 # Let the code begin...
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67
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68
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69 package Bio::Tools::HMMER::Set;
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70 use vars qw(@ISA);
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71 use strict;
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72
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73 use Bio::Root::Root;
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74 use Bio::Tools::HMMER::Domain;
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75
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76 @ISA = qw( Bio::Root::Root );
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77
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78 sub new {
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79 my($class,@args) = @_;
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80 my $self = $class->SUPER::new(@args);
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81 my ($name,$acc,$desc) = $self->_rearrange([qw(NAME ACCESSION DESC)],
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82 @args);
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83 $name && $self->name($name);
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84 $acc && $self->accession($acc);
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85 $desc && $self->desc($desc);
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86
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87
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88 $self->{'domains'} = [];
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89 $self->{'domainnames'} = {};
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90 return $self;
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91 }
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92
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93 =head2 add_Domain
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94
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95 Title : add_Domain
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96 Usage : $set->add_Domain($domain)
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97 Function: adds the domain to the list
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98 Returns : nothing
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99 Args : A Bio::Tools::HMMER::Domain object
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100
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101 =cut
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102
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103 sub add_Domain{
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104 my ($self,$domain) = @_;
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105
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106
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107 if( ! defined $domain || ! $domain->isa("Bio::Tools::HMMER::Domain") ) {
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108 $self->throw("[$domain] is not a Bio::Tools::HMMER::Domain. aborting");
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109 }
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110 return if $self->{'domainnames'}->{$domain->get_nse}++;
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111 push(@{$self->{'domains'}},$domain);
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112
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113 }
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114
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115 =head2 each_Domain
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116
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117 Title : each_Domain
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118 Usage : foreach $domain ( $set->each_Domain() )
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119 Function: returns an array of domain objects in this set
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120 Returns : array
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121 Args : none
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122
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123
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124 =cut
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125
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126 sub each_Domain{
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127 my ($self,@args) = @_;
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128
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129 return @{$self->{'domains'}};
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130 }
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131
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132 =head2 name
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133
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134 Title : name
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135 Usage : $obj->name($newval)
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136 Function:
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137 Example :
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138 Returns : value of name
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139 Args : newvalue (optional)
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140
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141
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142 =cut
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143
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144 sub name{
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145 my ($obj,$value) = @_;
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146 if( defined $value) {
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147 $obj->{'name'} = $value;
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148 }
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149 return $obj->{'name'};
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150
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151 }
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152
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153 =head2 desc
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154
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155 Title : desc
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156 Usage : $obj->desc($newval)
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157 Function:
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158 Example :
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159 Returns : value of desc
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160 Args : newvalue (optional)
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161
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162 =cut
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163
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164 sub desc{
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165 my ($self,$value) = @_;
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166 if( defined $value) {
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167 $self->{'desc'} = $value;
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168 }
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169 return $self->{'desc'};
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170
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171 }
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172
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173 =head2 accession
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174
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175 Title : accession
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176 Usage : $obj->accession($newval)
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177 Function:
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178 Example :
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179 Returns : value of accession
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180 Args : newvalue (optional)
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181
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182
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183 =cut
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184
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185 sub accession{
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186 my ($self,$value) = @_;
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187 if( defined $value) {
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188 $self->{'accession'} = $value;
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189 }
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190 return $self->{'accession'};
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191 }
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192
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193
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194 =head2 bits
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195
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196 Title : bits
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197 Usage : $obj->bits($newval)
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198 Function:
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199 Example :
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200 Returns : value of bits
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201 Args : newvalue (optional)
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202
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203
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204 =cut
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205
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206 sub bits{
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207 my ($obj,$value) = @_;
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208
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209 if( defined $value) {
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210 $obj->{'bits'} = $value;
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211 }
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212 return $obj->{'bits'};
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213
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214 }
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215
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216 =head2 evalue
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217
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218 Title : evalue
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219 Usage : $obj->evalue($newval)
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220 Function:
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221 Example :
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222 Returns : value of evalue
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223 Args : newvalue (optional)
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224
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225
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226 =cut
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227
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228 sub evalue{
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229 my ($obj,$value) = @_;
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230 if( defined $value) {
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231 $obj->{'evalue'} = $value;
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232 }
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233 return $obj->{'evalue'};
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234
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235 }
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236
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237
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238 sub addHMMUnit {
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239 my $self = shift;
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240 my $unit = shift;
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241
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242 $self->warn("Using old addHMMUnit call on Bio::Tools::HMMER::Set. Should replace with add_Domain");
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243 return $self->add_Domain($unit);
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244 }
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245
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246 sub eachHMMUnit {
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247 my $self = shift;
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248 $self->warn("Using old eachHMMUnit call on Bio::Tools::HMMER::Set. Should replace with each_Domain");
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249 return $self->each_Domain();
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250 }
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251
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252 1; # says use was ok
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253 __END__
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254
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