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1 # $Id: WABAHSP.pm,v 1.5 2002/10/22 07:45:17 lapp Exp $
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2 #
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3 # BioPerl module for Bio::Search::HSP::WABAHSP
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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::HSP::WABAHSP - HSP object suitable for describing WABA alignments
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16
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17 =head1 SYNOPSIS
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18
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19 # use this object as you would a GenericHSP
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20 # a few other methods have been added including state
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21
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22 =head1 DESCRIPTION
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23
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24 This object implements a few of the extra methods such as
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25 hmmstate_string which returns the HMM state representation for the
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26 WABA alignment. We also must implement a method to calculate
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27 homology_string since it is not returned by the algorithm in the
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28 machine readable format.
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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 # Let the code begin...
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68
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69
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70 package Bio::Search::HSP::WABAHSP;
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71 use vars qw(@ISA);
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72 use strict;
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73 use Bio::Root::RootI;
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74 use Bio::Search::HSP::GenericHSP;
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75
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76 @ISA = qw(Bio::Search::HSP::GenericHSP );
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77
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78 =head2 new
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79
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80 Title : new
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81 Usage : my $obj = new Bio::Search::HSP::WABAHSP();
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82 Function: Builds a new Bio::Search::HSP::WABAHSP object
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83 Returns : Bio::Search::HSP::WABAHSP
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84 Args : -hmmstate_seq => the string representing the state output from WABA
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85
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86 =cut
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87
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88 sub new {
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89 my($class,@args) = @_;
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90
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91 # gotta do some preprocessing before we send the arguments to the superclass
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92 my ($len,$qs,$hs) = Bio::Root::RootI->_rearrange([qw(HSP_LENGTH
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93 QUERY_SEQ
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94 HIT_SEQ)],@args);
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95 if( $len != length($qs) ) {
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96 Bio::Root::RootI->warn("HSP_LENGTH must equal length of query_seq string, using value from QUERY_SEQ\n");
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97 $len = length($qs);
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98 }
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99 my( $homol_seq,$gapct,$identical) = ('',0,0);
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100
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101 for(my $i=0;$i<$len;$i++) {
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102 my $q = substr($qs,$i,1);
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103 my $h = substr($hs,$i,1);
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104 if( $q eq '-' || $h eq '-' ) {
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105 $homol_seq .= ' ';
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106 $gapct ++;
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107 } elsif( $q eq $h ) {
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108 $homol_seq .= '|';
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109 $identical++;
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110 } else {
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111 $homol_seq .= ' ';
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112 }
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113 }
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114 my $self = $class->SUPER::new('-conserved' => $identical,
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115 '-identical' => $identical,
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116 '-gaps' => $gapct,
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117 '-homology_seq' => $homol_seq,
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118 @args);
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119
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120 my ($hmmst) = $self->_rearrange([qw(HMMSTATE_SEQ)],@args);
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121 defined $hmmst && $self->hmmstate_string($hmmst);
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122
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123 $self->add_tag_value('Target' , join(" ","Sequence:".$self->hit->seq_id,
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124 $self->hit->start, $self->hit->end));
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125
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126 return $self;
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127 }
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128
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129 =head2 hmmstate_string
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130
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131 Title : hmmstate_string
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132 Usage : my $hmmseq = $wabahsp->hmmstate_string();
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133 Function: Get/Set the WABA HMM stateseq
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134 Returns : string
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135 Args : [optional] string
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136
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137
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138 =cut
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139
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140 sub hmmstate_string{
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141 my ($self,$val) = @_;
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142 if( defined $val ) {
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143 $self->{'_hmmstate_string'} = $val;
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144 }
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145 return $self->{'_hmmstate_string'};
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146 }
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147
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148 =head2 homolgy_string
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149
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150 Title : homolgy_string
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151 Usage : my $homology_str = $hsp->homology_string();
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152 Function: Homology string must be calculated for a WABA HSP so we can do
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153 so here and cache the result so it is only done once
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154 Returns : string
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155 Args : none
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156
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157
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158 =cut
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159
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160 sub homolgy_string{
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161 my ($self) = @_;
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162 return '';
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163 }
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164
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165
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166 1;
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