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1 # $Id: HMMERHit.pm,v 1.3 2002/10/22 07:45:17 lapp Exp $
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2 #
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3 # BioPerl module for Bio::Search::Hit::HMMERHit
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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::Hit::HMMERHit - A Hit module for HMMER hits
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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::Hit::HMMERHit;
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20 my $hit = new Bio::Search::Hit::HMMERHit;
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21 # use it in the same way as Bio::Search::Hit::GenericHit
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22
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23 =head1 DESCRIPTION
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24
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25 This is a specialization of L<Bio::Search::Hit::GenericHit>. There
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26 are a few news methods L<next_domain> and L<domains>. Note that
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27 L<bits> and L<iteration> make no sense for this object and will
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28 return 0.
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29
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30 =head1 FEEDBACK
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31
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32 =head2 Mailing Lists
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33
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34 User feedback is an integral part of the evolution of this and other
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35 Bioperl modules. Send your comments and suggestions preferably to
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36 the Bioperl mailing list. Your participation is much appreciated.
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37
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38 bioperl-l@bioperl.org - General discussion
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39 http://bioperl.org/MailList.shtml - About the mailing lists
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40
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41 =head2 Reporting Bugs
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42
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43 Report bugs to the Bioperl bug tracking system to help us keep track
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44 of the bugs and their resolution. Bug reports can be submitted via
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45 email or the web:
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46
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47 bioperl-bugs@bioperl.org
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48 http://bugzilla.bioperl.org/
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49
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50 =head1 AUTHOR - Jason Stajich
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51
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52 Email jason@bioperl.org
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53
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54 Describe contact details here
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55
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56 =head1 CONTRIBUTORS
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57
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58 Additional contributors names and emails here
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59
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60 =head1 APPENDIX
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61
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62 The rest of the documentation details each of the object methods.
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63 Internal methods are usually preceded with a _
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64
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65 =cut
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66
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67
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68 # Let the code begin...
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69
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70
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71 package Bio::Search::Hit::HMMERHit;
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72 use vars qw(@ISA);
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73 use strict;
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74
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75 use Bio::Search::Hit::GenericHit;
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76
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77 @ISA = qw(Bio::Search::Hit::GenericHit );
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78
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79 =head2 new
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80
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81 Title : new
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82 Usage : my $obj = new Bio::Search::Hit::HMMERHit();
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83 Function: Builds a new Bio::Search::Hit::HMMERHit object
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84 Returns : Bio::Search::Hit::HMMERHit
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85 Args :
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86
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87 Plus the Bio::Search::Hit::GenericHit inherited params
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88 -name => Name of Hit (required)
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89 -description => Description (optional)
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90 -accession => Accession number (optional)
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91 -length => Length of the Hit (optional)
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92 -score => Raw Score for the Hit (optional)
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93 -significance => Significance value for the Hit (optional)
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94 -algorithm => Algorithm used (BLASTP, FASTX, etc...)
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95 -hsps => Array ref of HSPs for this Hit.
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96
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97
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98 =cut
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99
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100
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101 =head2 next_domain
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102
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103 Title : next_domain
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104 Usage : my $domain = $hit->next_domain();
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105 Function: An alias for L<next_hsp()>, this will return the next HSP
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106 Returns : L<Bio::Search::HSP::HSPI> object
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107 Args : none
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108
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109
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110 =cut
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111
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112 sub next_domain{ shift->next_hsp }
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113
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114 =head2 domains
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115
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116 Title : domains
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117 Usage : my @domains = $hit->domains();
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118 Function: An alias for L<hsps()>, this will return the full list of hsps
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119 Returns : array of L<Bio::Search::HSP::HSPI> objects
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120 Args : none
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121
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122
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123 =cut
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124
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125 sub domains{ shift->hsps() }
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126
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127
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128 =head2 inherited Bio::Search::Hit::GenericHit methods
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129
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130 =cut
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131
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132 =head2 add_hsp
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133
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134 Title : add_hsp
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135 Usage : $hit->add_hsp($hsp)
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136 Function: Add a HSP to the collection of HSPs for a Hit
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137 Returns : number of HSPs in the Hit
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138 Args : Bio::Search::HSP::HSPI object
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139
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140
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141 =cut
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142
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143 =head2 Bio::Search::Hit::HitI methods
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144
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145 =cut
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146
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147 =head2 name
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148
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149 Title : name
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150 Usage : $hit_name = $hit->name();
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151 Function: returns the name of the Hit sequence
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152 Returns : a scalar string
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153 Args : [optional] scalar string to set the name
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154
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155 =cut
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156
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157 =head2 accession
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158
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159 Title : accession
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160 Usage : $acc = $hit->accession();
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161 Function: Retrieve the accession (if available) for the hit
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162 Returns : a scalar string (empty string if not set)
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163 Args : none
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164
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165 =cut
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166
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167 =head2 description
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168
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169 Title : description
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170 Usage : $desc = $hit->description();
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171 Function: Retrieve the description for the hit
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172 Returns : a scalar string
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173 Args : [optional] scalar string to set the descrition
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174
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175 =cut
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176
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177 =head2 length
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178
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179 Title : length
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180 Usage : my $len = $hit->length
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181 Function: Returns the length of the hit
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182 Returns : integer
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183 Args : [optional] integer to set the length
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184
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185 =cut
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186
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187 =head2 algorithm
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188
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189 Title : algorithm
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190 Usage : $alg = $hit->algorithm();
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191 Function: Gets the algorithm specification that was used to obtain the hit
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192 For BLAST, the algorithm denotes what type of sequence was aligned
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193 against what (BLASTN: dna-dna, BLASTP prt-prt, BLASTX translated
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194 dna-prt, TBLASTN prt-translated dna, TBLASTX translated
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195 dna-translated dna).
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196 Returns : a scalar string
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197 Args : [optional] scalar string to set the algorithm
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198
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199 =cut
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200
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201 =head2 raw_score
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202
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203 Title : raw_score
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204 Usage : $score = $hit->raw_score();
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205 Function: Gets the "raw score" generated by the algorithm. What
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206 this score is exactly will vary from algorithm to algorithm,
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207 returning undef if unavailable.
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208 Returns : a scalar value
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209 Args : [optional] scalar value to set the raw score
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210
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211 =cut
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212
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213 =head2 significance
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214
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215 Title : significance
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216 Usage : $significance = $hit->significance();
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217 Function: Used to obtain the E or P value of a hit, i.e. the probability that
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218 this particular hit was obtained purely by random chance. If
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219 information is not available (nor calculatable from other
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220 information sources), return undef.
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221 Returns : a scalar value or undef if unavailable
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222 Args : [optional] scalar value to set the significance
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223
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224 =cut
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225
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226 =head2 bits
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227
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228 Usage : $hit_object->bits();
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229 Purpose : Gets the bit score of the best HSP for the current hit.
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230 Example : $bits = $hit_object->bits();
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231 Returns : Integer or undef if bit score is not set
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232 Argument : n/a
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233
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234 See Also : L<score()|score>
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235
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236 =cut
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237
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238 sub bits { return 0 }
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239
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240 =head2 next_hsp
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241
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242 Title : next_hsp
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243 Usage : while( $hsp = $obj->next_hsp()) { ... }
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244 Function : Returns the next available High Scoring Pair
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245 Example :
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246 Returns : Bio::Search::HSP::HSPI object or null if finished
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247 Args : none
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248
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249 =cut
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250
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251 =head2 hsps
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252
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253 Usage : $hit_object->hsps();
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254 Purpose : Get a list containing all HSP objects.
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255 : Get the numbers of HSPs for the current hit.
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256 Example : @hsps = $hit_object->hsps();
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257 : $num = $hit_object->hsps(); # alternatively, use num_hsps()
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258 Returns : Array context : list of Bio::Search::HSP::BlastHSP.pm objects.
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259 : Scalar context: integer (number of HSPs).
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260 : (Equivalent to num_hsps()).
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261 Argument : n/a. Relies on wantarray
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262 Throws : Exception if the HSPs have not been collected.
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263
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264 See Also : L<hsp()|hsp>, L<num_hsps()|num_hsps>
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265
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266 =cut
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267
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268 =head2 num_hsps
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269
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270 Usage : $hit_object->num_hsps();
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271 Purpose : Get the number of HSPs for the present Blast hit.
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272 Example : $nhsps = $hit_object->num_hsps();
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273 Returns : Integer
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274 Argument : n/a
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275 Throws : Exception if the HSPs have not been collected.
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276
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277 See Also : L<hsps()|hsps>
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278
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279 =cut
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280
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281 =head2 rewind
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282
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283 Title : rewind
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284 Usage : $hit->rewind;
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285 Function: Allow one to reset the HSP iteration to the beginning
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286 Since this is an in-memory implementation
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287 Returns : none
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288 Args : none
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289
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290 =cut
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291
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292 =head2 iteration
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293
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294 Title : iteration
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295 Usage : $obj->iteration($newval)
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296 Function: PSI-BLAST iteration
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297 Returns : value of iteration
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298 Args : newvalue (optional)
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299
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300
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301 =cut
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302
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303
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304 sub iteration { return 0 }
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305
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306 1;
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