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1 # $Id: HMMERResult.pm,v 1.3 2002/10/22 07:45:18 lapp Exp $
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2 #
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3 # BioPerl module for Bio::Search::Result::HMMERResult
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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::Search::Result::HMMERResult - A Result object for HMMER results
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16
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17 =head1 SYNOPSIS
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18
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19 use Bio::Search::Result::HMMERResult;
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20 my $result = new Bio::Search::Result::HMMERResult
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21 ( -hmm_name => 'pfam',
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22 -sequence_file => 'roa1.pep',
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23 -hits => \@hits);
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24
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25 # generally we use Bio::SearchIO to build these objects
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26 use Bio::SearchIO;
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27 my $in = new Bio::SearchIO(-format => 'hmmer',
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28 -file => 'result.hmmer');
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29 while( my $result = $in->next_result ) {
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30 print $result->query_name, " ", $result->algorithm, " ", $result->num_hits(), " hits\n";
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31 }
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32
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33 =head1 DESCRIPTION
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34
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35 This is a specialization of L<Bio::Search::Result::GenericResult>.
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36 There are a few extra methods, specifically L<sequence_file>,
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37 L<hmm_name>, L<next_models>, and L<models>.
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38
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39 =head1 FEEDBACK
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40
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41 =head2 Mailing Lists
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42
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43 User feedback is an integral part of the evolution of this and other
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44 Bioperl modules. Send your comments and suggestions preferably to
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45 the Bioperl mailing list. Your participation is much appreciated.
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46
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47 bioperl-l@bioperl.org - General discussion
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48 http://bioperl.org/MailList.shtml - About the mailing lists
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49
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50 =head2 Reporting Bugs
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51
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52 Report bugs to the Bioperl bug tracking system to help us keep track
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53 of the bugs and their resolution. Bug reports can be submitted via
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54 email or the web:
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55
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56 bioperl-bugs@bioperl.org
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57 http://bugzilla.bioperl.org/
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58
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59 =head1 AUTHOR - Jason Stajich
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60
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61 Email jason@bioperl.org
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62
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63 Describe contact details here
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64
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65 =head1 CONTRIBUTORS
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66
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67 Additional contributors names and emails here
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68
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69 =head1 APPENDIX
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70
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71 The rest of the documentation details each of the object methods.
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72 Internal methods are usually preceded with a _
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73
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74 =cut
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75
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76
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77 # Let the code begin...
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78
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79
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80 package Bio::Search::Result::HMMERResult;
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81 use vars qw(@ISA);
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82 use strict;
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83
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84 use Bio::Search::Result::GenericResult;
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85
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86
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87 @ISA = qw(Bio::Search::Result::GenericResult );
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88
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89 =head2 new
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90
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91 Title : new
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92 Usage : my $obj = new Bio::Search::Result::HMMERResult();
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93 Function: Builds a new Bio::Search::Result::HMMERResult object
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94 Returns : Bio::Search::Result::HMMERResult
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95 Args : -hmm_name => string, name of hmm file
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96 -sequence_file => name of the sequence file
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97
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98 plus Bio::Search::Result::GenericResult parameters
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99
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100 -query_name => Name of query Sequence
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101 -query_accession => Query accession number (if available)
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102 -query_description => Description of query sequence
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103 -query_length => Length of query sequence
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104 -database_name => Name of database
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105 -database_letters => Number of residues in database
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106 -database_entries => Number of entries in database
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107 -parameters => hash ref of search parameters (key => value)
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108 -statistics => hash ref of search statistics (key => value)
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109 -algorithm => program name (blastx)
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110 -algorithm_version => version of the algorithm (2.1.2)
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111 -program_reference => literature reference string for this algorithm
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112
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113 =cut
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114
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115 sub new {
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116 my($class,@args) = @_;
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117 my $self = $class->SUPER::new(@args);
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118
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119 my ($hmm,$seqfile) = $self->_rearrange([qw(HMM_NAME SEQUENCE_FILE)],
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120 @args);
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121
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122 defined( $seqfile) && $self->sequence_file($seqfile);
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123 defined( $hmm) && $self->hmm_name($hmm);
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124
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125 return $self;
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126 }
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127
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128
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129 =head2 hmm_name
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130
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131 Title : hmm_name
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132 Usage : $obj->hmm_name($newval)
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133 Function: Get/Set the value of hmm_name
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134 Returns : value of hmm_name
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135 Args : newvalue (optional)
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136
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137
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138 =cut
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139
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140 sub hmm_name{
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141 my ($self,$value) = @_;
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142 if( defined $value) {
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143 $self->{'_hmm_name'} = $value;
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144 }
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145 return $self->{'_hmm_name'};
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146 }
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147
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148
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149 =head2 sequence_file
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150
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151 Title : sequence_file
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152 Usage : $obj->sequence_file($newval)
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153 Function: Get/Set the value of sequence_file
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154 Returns : value of sequence_file
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155 Args : newvalue (optional)
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156
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157
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158 =cut
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159
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160 sub sequence_file{
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161 my ($self,$value) = @_;
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162 if( defined $value) {
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163 $self->{'_sequence_file'} = $value;
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164 }
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165 return $self->{'_sequence_file'};
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166
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167 }
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168
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169
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170 =head2 next_model
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171
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172 Title : next_model
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173 Usage : my $domain = $result->next_model
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174 Function: Returns the next domain - this
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175 is an alias for next_hit
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176 Returns : L<Bio::Search::Hit::HitI> object
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177 Args : none
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178
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179
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180 =cut
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181
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182 sub next_model{ shift->next_hit }
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183
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184 =head2 models
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185
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186 Title : models
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187 Usage : my @domains = $result->models;
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188 Function: Returns the list of HMM models seen - this
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189 is an alias for hits()
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190 Returns : Array of L<Bio::Search::Hit::HitI> objects
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191 Args : none
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192
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193
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194 =cut
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195
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196 sub models{ shift->hits }
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197
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198 =head2 Bio::Search::Result::GenericResult inherited methods
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199
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200 =cut
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201
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202 =head2 algorithm
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203
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204 Title : algorithm
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205 Usage : my $r_type = $hsp->algorithm
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206 Function: Obtain the name of the algorithm used to obtain the Result
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207 Returns : string (e.g., BLASTP)
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208 Args : [optional] scalar string to set value
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209
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210 =cut
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211
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212 =head2 algorithm_version
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213
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214 Title : algorithm_version
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215 Usage : my $r_version = $hsp->algorithm_version
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216 Function: Obtain the version of the algorithm used to obtain the Result
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217 Returns : string (e.g., 2.1.2)
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218 Args : [optional] scalar string to set algorithm version value
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219
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220 =cut
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221
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222 =head2 Bio::Search::Result::ResultI interface methods
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223
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224 Bio::Search::Result::ResultI implementation
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225
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226 =head2 next_hit
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227
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228 Title : next_hit
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229 Usage : while( $hit = $result->next_hit()) { ... }
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230 Function: Returns the next available Hit object, representing potential
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231 matches between the query and various entities from the database.
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232 Returns : a Bio::Search::Hit::HitI object or undef if there are no more.
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233 Args : none
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234
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235
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236 =cut
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237
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238 =head2 query_name
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239
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240 Title : query_name
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241 Usage : $id = $result->query_name();
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242 Function: Get the string identifier of the query used by the
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243 algorithm that performed the search.
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244 Returns : a string.
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245 Args : [optional] new string value for query name
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246
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247 =cut
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248
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249 =head2 query_accession
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250
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251 Title : query_accession
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252 Usage : $id = $result->query_accession();
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253 Function: Get the accession (if available) for the query sequence
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254 Returns : a string
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255 Args : [optional] new string value for accession
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256
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257 =cut
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258
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259 =head2 query_length
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260
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261 Title : query_length
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262 Usage : $id = $result->query_length();
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263 Function: Get the length of the query sequence
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264 used in the search.
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265 Returns : a number
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266 Args : [optional] new integer value for query length
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267
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268 =cut
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269
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270 =head2 query_description
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271
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272 Title : query_description
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273 Usage : $id = $result->query_description();
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274 Function: Get the description of the query sequence
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275 used in the search.
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276 Returns : a string
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277 Args : [optional] new string for the query description
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278
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279 =cut
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280
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281 =head2 database_name
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282
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283 Title : database_name
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284 Usage : $name = $result->database_name()
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285 Function: Used to obtain the name of the database that the query was searched
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286 against by the algorithm.
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287 Returns : a scalar string
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288 Args : [optional] new string for the db name
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289
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290 =cut
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291
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292 =head2 database_letters
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293
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294 Title : database_letters
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295 Usage : $size = $result->database_letters()
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296 Function: Used to obtain the size of database that was searched against.
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297 Returns : a scalar integer (units specific to algorithm, but probably the
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298 total number of residues in the database, if available) or undef if
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299 the information was not available to the Processor object.
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300 Args : [optional] new scalar integer for number of letters in db
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301
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302
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303 =cut
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304
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305 =head2 database_entries
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306
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307 Title : database_entries
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308 Usage : $num_entries = $result->database_entries()
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309 Function: Used to obtain the number of entries contained in the database.
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310 Returns : a scalar integer representing the number of entities in the database
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311 or undef if the information was not available.
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312 Args : [optional] new integer for the number of sequence entries in the db
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313
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314
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315 =cut
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316
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317 =head2 get_parameter
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318
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319 Title : get_parameter
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320 Usage : my $gap_ext = $report->get_parameter('gapext')
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321 Function: Returns the value for a specific parameter used
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322 when running this report
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323 Returns : string
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324 Args : name of parameter (string)
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325
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326 =cut
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327
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328 =head2 available_parameters
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329
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330 Title : available_parameters
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331 Usage : my @params = $report->available_paramters
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332 Function: Returns the names of the available parameters
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333 Returns : Return list of available parameters used for this report
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334 Args : none
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335
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336 =cut
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337
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338 =head2 get_statistic
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339
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340 Title : get_statistic
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341 Usage : my $gap_ext = $report->get_statistic('kappa')
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342 Function: Returns the value for a specific statistic available
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343 from this report
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344 Returns : string
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345 Args : name of statistic (string)
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346
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347 =cut
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348
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349 =head2 available_statistics
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350
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351 Title : available_statistics
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352 Usage : my @statnames = $report->available_statistics
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353 Function: Returns the names of the available statistics
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354 Returns : Return list of available statistics used for this report
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355 Args : none
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356
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357 =cut
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358
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359 =head2 Bio::Search::Result::GenericResult specific methods
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360
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361 =cut
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362
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363 =head2 add_hit
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364
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365 Title : add_hit
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366 Usage : $report->add_hit($hit)
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367 Function: Adds a HitI to the stored list of hits
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368 Returns : Number of HitI currently stored
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369 Args : Bio::Search::Hit::HitI
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370
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371 =cut
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372
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373 =head2 rewind
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374
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375 Title : rewind
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376 Usage : $result->rewind;
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377 Function: Allow one to reset the Hit iteration to the beginning
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378 Since this is an in-memory implementation
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379 Returns : none
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380 Args : none
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381
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382 =cut
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383
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384 sub rewind{
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385 my ($self) = @_;
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386 $self->{'_hitindex'} = 0;
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387 }
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388
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389
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390 =head2 add_parameter
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391
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392 Title : add_parameter
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393 Usage : $report->add_parameter('gapext', 11);
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394 Function: Adds a parameter
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395 Returns : none
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396 Args : key - key value name for this parama
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397 value - value for this parameter
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398
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399 =cut
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400
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401 =head2 add_statistic
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402
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403 Title : add_statistic
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404 Usage : $report->add_statistic('lambda', 2.3);
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405 Function: Adds a parameter
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406 Returns : none
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407 Args : key - key value name for this parama
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408 value - value for this parameter
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409
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410 =cut
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411
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412 =head2 num_hits
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413
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414 Title : num_hits
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415 Usage : my $hitcount= $result->num_hits
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416 Function: returns the number of hits for this query result
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417 Returns : integer
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418 Args : none
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419
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420
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421 =cut
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422
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423 =head2 hits
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424
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425 Title : hits
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426 Usage : my @hits = $result->hits
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427 Function: Returns the available hits for this Result
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428 Returns : Array of L<Bio::Search::Hit::HitI> objects
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429 Args : none
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430
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431
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432 =cut
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433
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434 =head2 program_reference
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435
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436 Title : program_reference
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437 Usage : $obj->program_reference($newval)
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438 Function:
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439 Returns : value of the literature reference for the algorithm
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440 Args : newvalue (optional)
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441
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442
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443 =cut
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444
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445 1;
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