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1 =head1 LICENSE
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2
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3 Copyright (c) 1999-2012 The European Bioinformatics Institute and
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4 Genome Research Limited. All rights reserved.
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5
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6 This software is distributed under a modified Apache license.
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7 For license details, please see
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8
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9 http://www.ensembl.org/info/about/code_licence.html
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10
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11 =head1 CONTACT
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12
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13 Please email comments or questions to the public Ensembl
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14 developers list at <dev@ensembl.org>.
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15
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16 Questions may also be sent to the Ensembl help desk at
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17 <helpdesk@ensembl.org>.
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18
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19 =cut
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20
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21 =head1 NAME
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22
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23 Bio::EnsEMBL::FeaturePair - Stores sequence Features which are
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24 themselves hits to other sequence features.
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25
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26 =head1 SYNOPSIS
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27
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28 my $feat = Bio::EnsEMBL::FeaturePair->new(
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29 -start => 132_231,
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30 -end => 132_321,
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31 -strand => -1,
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32 -slice => $slice,
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33 -hstart => 10,
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34 -hend => 100,
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35 -hstrand => 1,
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36 -score => 100,
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37 -percent_id => 92.0,
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38 -hseqname => 'ALUSX10.1',
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39 -analysis => $analysis
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40 );
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41
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42 my $hit_start = $feat->hstart();
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43 my $hit_end = $feat->hend();
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44 my $hit_strand = $feat->hstrand();
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45 my $analysis = $feat->analysis();
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46
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47 =head1 DESCRIPTION
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48
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49 A sequence feature object where the feature is itself a feature on
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50 another sequence - e.g. a blast hit where residues 1-40 of a protein
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51 sequence SW:HBA_HUMAN has hit to bases 100 - 220 on a genomic sequence
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52 HS120G22. The genomic sequence coordinates are represented by the
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53 start, end, strand attributes while the protein (hit) coordinates are
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54 represented by the hstart, hend, hstrand attributes.
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55
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56 $clone = $slice_adpator->fetch_by_region( 'clone', 'HS120G22' );
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57
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58 $fp = Bio::EnsEMBL::FeaturePair(
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59 -start => 100,
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60 -end => 220,
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61 -strand => 1,
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62 -slice => $clone,
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63 -hstart => 1,
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64 -hend => 40,
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65 -hstrand => 1,
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66 -percent_id => 92.0,
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67 -score => 100,
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68 -hseqname => 'SW:HBA_HUMAN',
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69 -species => 'Homo sapiens',
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70 -hspecies => 'Homo sapiens'
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71 );
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72
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73 =head1 METHODS
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74
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75 =cut
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76
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77 package Bio::EnsEMBL::FeaturePair;
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78
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79 use vars qw(@ISA);
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80 use strict;
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81
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82 use Bio::EnsEMBL::Feature;
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83 use Bio::EnsEMBL::Utils::Argument qw(rearrange);
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84 use Bio::EnsEMBL::Utils::Exception qw(throw deprecate warning);
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85
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86 @ISA = qw(Bio::EnsEMBL::Feature);
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87
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88
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89
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90 =head2 new
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91
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92 Arg [HSTART] : int - The start of the hit region (optional)
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93 Arg [HEND] : int - The end of the hit region (optional)
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94 Arg [HSTRAND] : (0,1,-1) - The strand of the hit region (optional)
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95 Arg [PERCENT_ID]: float - The precentage identity of the hit (optional)
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96 Arg [SCORE] : float - The score of the hit (optional)
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97 Arg [HSEQNAME] : string - The name of the hit sequence (optional)
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98 Arg [P_VALUE] : float - The pvalue or evalue (optional)
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99 Arg [SPECIES] : string - The species the query sequence is from (optional)
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100 Arg [HSPECIES] : string - The species the hit sequence is from (optional)
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101 Arg [COVERAGE] : string - The % of the query that this feature pair covers
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102 Arg [HCOVERAGE] : string - The % of the target this this feature pair covers
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103 Arg [...] : Named superclass constructor args (Bio::EnsEMBL::Feature)
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104 Example : $feat = Bio::EnsEMBL::FeaturePair->new(-start => 132_231,
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105 -end => 132_321,
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106 -strand => -1,
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107 -slice => $slice,
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108 -hstart => 10,
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109 -hend => 100,
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110 -hstrand => 1,
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111 -score => 100,
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112 -percent_id => 92.0,
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113 -hseqname => 'ALUSX10.1',
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114 -analysis => $analysis);
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115 Description: Creates a new Bio::EnsEMBL::FeaturePair object
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116 Returntype : Bio::EnsEMBL::FeaturePair
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117 Exceptions : throw if start > end
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118 throw if invalid strand is provided
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119 Caller : general
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120 Status : Stable
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121
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122 =cut
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123
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124 sub new {
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125 my $caller = shift;
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126
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127 my $class = ref($caller) || $caller;
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128
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129 my $self = $class->SUPER::new(@_);
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130
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131 my ($hstart,$hend,$hstrand,$percent_id,$score, $species, $hspecies,
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132 $p_value, $hseqname, $f1,$f2, $coverage, $hcoverage, $group_id,$level_id, $external_db_id, $extra_data, $external_db_name, $external_display_db_name) =
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133 rearrange(['HSTART','HEND','HSTRAND','PERCENT_ID','SCORE','SPECIES',
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134 'HSPECIES', 'P_VALUE', 'HSEQNAME', 'FEATURE1','FEATURE2',
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135 'COVERAGE', 'HCOVERAGE', 'GROUP_ID','LEVEL_ID', 'EXTERNAL_DB_ID', 'EXTRA_DATA', 'DBNAME', 'DB_DISPLAY_NAME'], @_);
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136
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137 if(defined($hstart) && defined($hend) && ($hend < $hstart)) {
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138 throw('HSTART must be less than or equal to HEND');
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139 }
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140
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141 if(defined($hstrand) && $hstrand != 1 && $hstrand != -1 && $hstrand != 0) {
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142 throw('HSTRAND must be one of (0,1,-1)');
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143 }
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144
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145 $self->{'hstart'} = $hstart;
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146 $self->{'hend'} = $hend;
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147 $self->{'hstrand'} = $hstrand;
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148 $self->{'score'} = $score;
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149 $self->{'percent_id'} = $percent_id;
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150 $self->{'species'} = $species;
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151 $self->{'hspecies'} = $hspecies;
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152 $self->{'hseqname'} = $hseqname;
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153 $self->{'coverage'} = $coverage;
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154 $self->{'hcoverage'} = $hcoverage;
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155 $self->{'p_value'} = $p_value;
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156 $self->{'group_id'} = $group_id;
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157 $self->{'level_id'} = $level_id;
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158 $self->{'external_db_id'} = $external_db_id;
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159 $self->{'extra_data'} = $extra_data;
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160 $self->{'dbname'} = $external_db_name;
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161 $self->{'db_display_name'} = $external_display_db_name;
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162
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163 #
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164 # Feature1 and Feature2 arg handling for backwards compatibility
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165 #
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166 if($f1) {
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167 deprecate("Using FEATURE1 arg to construct FeaturePairs" .
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168 " is deprecated.\nUse the args START,END,STRAND,SLICE instead");
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169
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170 #eval because we are not exactly sure what f1 arg will look like
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171 eval {
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172 $self->{'start'} = $f1->start();
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173 $self->{'end'} = $f1->end();
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174 $self->{'strand'} = $f1->strand();
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175 $self->{'slice'} = $f1->contig();
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176 $self->{'analysis'} = $f1->analysis() if($f1->analysis());
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177 };
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178 }
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179
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180 if($f2) {
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181 deprecate("Using FEATURE2 arg to construct FeaturePairs is deprecated" .
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182 "\nUse the args HSTART,HEND,HSTRAND,HSEQNAME instead");
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183
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184 #eval because we are not exactly sure what f2 arg will look like
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185 eval {
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186 $self->{'hseqname'} = $f2->seqname();
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187 $self->{'hstart'} = $f2->start();
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188 $self->{'hend'} = $f2->end();
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189 $self->{'hstrand'} = $f2->strand();
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190 $self->{'analysis'} = $f2->analysis() if($f2->analysis());
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191 };
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192 }
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193
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194 return $self;
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195 }
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196
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197
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198
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199 =head2 hseqname
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200
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201 Arg [1] : string $hseqname (optional)
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202 Example : $hseqname = $fp->hseqname();
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203 Description: Getter/Setter for the name of the hit sequence
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204 Returntype : string
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205 Exceptions : none
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206 Caller : general
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207 Status : Stable
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208
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209 =cut
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210
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211 sub hseqname {
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212 my $self = shift;
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213 $self->{'hseqname'} = shift if(@_);
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214 return $self->{hseqname};
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215 }
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216
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217
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218
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219 =head2 hstart
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220
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221 Arg [1] : string $hstart (optional)
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222 Example : $hstart = $fp->hstart();
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223 Description: Getter/Setter for the start coordinate on the hit sequence
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224 Returntype : int
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225 Exceptions : none
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226 Caller : general
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227 Status : Stable
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228
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229 =cut
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230
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231 sub hstart{
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232 my $self = shift;
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233 $self->{'hstart'} = shift if(@_);
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234 return $self->{'hstart'};
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235 }
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236
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237
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238 =head2 hend
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239
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240 Arg [1] : string $hend (optional)
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241 Example : $hend = $fp->hend();
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242 Description: Getter/Setter for the end coordinate on the hit sequence
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243 Returntype : int
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244 Exceptions : none
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245 Caller : general
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246 Status : Stable
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247
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248 =cut
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249
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250 sub hend{
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251 my $self = shift;
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252 $self->{'hend'} = shift if(@_);
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253 return $self->{'hend'};
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254 }
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255
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256
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257
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258 =head2 hstrand
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259
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260 Arg [1] : int $hstrand (optional)
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261 Example : $hstrand = $fp->hstrand
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262 Description: Getter/Setter for the orientation of the hit on the hit sequence
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263 Returntype : 0,1,-1
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264 Exceptions : thrown
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265 Caller : general
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266 Status : Stable
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267
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268 =cut
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269
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270 sub hstrand{
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271 my $self = shift;
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272
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273 if(@_) {
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274 my $hstrand = shift;
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275 if(defined($hstrand) && $hstrand != 1 && $hstrand != 0 && $hstrand != -1) {
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276 throw('hstrand must be one of (-1,0,1)');
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277 }
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278 $self->{'hstrand'} = $hstrand;
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279 }
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280
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281 return $self->{'hstrand'};
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282 }
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283
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284 =head2 hslice
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285
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286 Arg [1] : (optional) Bio::EnsEMBL::Slice $slice
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287 Example : $hseqname = $featurepair->hslice()->seq_region_name();
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288 Description: Getter/Setter for the Slice that is associated with this
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289 hit feature. The slice represents the underlying sequence that this
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290 feature is on. Note that this method call is analagous to the
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291 old SeqFeature methods contig(), entire_seq(), attach_seq(),
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292 etc.
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293 Returntype : Bio::EnsEMBL::Slice
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294 Exceptions : thrown if an invalid argument is passed
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295 Caller : general
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296 Status : Stable
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297
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298 =cut
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299
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300 sub hslice {
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301 my $self = shift;
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302
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303 if(@_) {
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304 my $sl = shift;
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305 if(defined($sl) && (!ref($sl) || !($sl->isa('Bio::EnsEMBL::Slice') ) )) {
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306 throw('slice argument must be a Bio::EnsEMBL::Slice');
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307 }
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308
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309 $self->{'hslice'} = $sl;
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310 }
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311
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312 return $self->{'hslice'};
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313 }
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314
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315 =head2 hseq_region_name
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316
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317 Arg [1] : none
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318 Example : print $feature->hseq_region_name();
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319 Description: Gets the name of the hseq_region which this feature is on.
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320 Returns undef if this Feature is not on a hslice.
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321 Returntype : string or undef
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322 Exceptions : none
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323 Caller : general
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324 Status : Stable
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325
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326 =cut
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327
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328 sub hseq_region_name {
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329 my $self = shift;
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330 my $slice = $self->{'hslice'};
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331
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332 return ($slice) ? $slice->seq_region_name() : undef;
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333 }
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334
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335
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336 =head2 hseq_region_strand
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337
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338 Arg [1] : none
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339 Example : print $feature->hseq_region_strand();
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340 Description: Returns the strand of the hseq_region which this feature is on
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341 (i.e. feature_strand * slice_strand)
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342 Returns undef if this Feature is not on a hslice.
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343 Returntype : 1,0,-1 or undef
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344 Exceptions : none
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345 Caller : general
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346 Status : Stable
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347
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348 =cut
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349
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350
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351 sub hseq_region_strand {
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352 my $self = shift;
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353 my $slice = $self->{'hslice'};
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354
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355 return ($slice) ? $slice->strand() * $self->{'hstrand'} : undef;
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356 }
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357
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358 =head2 hseq_region_start
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359
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360 Arg [1] : none
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361 Example : print $feature->hseq_region_start();
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362 Description: Convenience method which returns the absolute start of this
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363 feature on the hseq_region, as opposed to the relative (hslice)
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364 position.
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365
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366 Returns undef if this feature is not on a hslice.
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367 Returntype : int or undef
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368 Exceptions : none
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369 Caller : general
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370 Status : Stable
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371
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372 =cut
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373
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374 sub hseq_region_start {
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375 my $self = shift;
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376 my $slice = $self->{'hslice'};
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377
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378 return undef if(!$slice);
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379
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380 if($slice->strand == 1) {
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381 return undef if(!defined($self->{'hstart'}));
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382 return $slice->start() + $self->{'hstart'} - 1;
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383 } else {
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384 return undef if(!defined($self->{'hend'}));
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385 return $slice->end() - $self->{'hend'} + 1;
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386 }
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387 }
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388
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389
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390 =head2 hseq_region_end
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391
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392 Arg [1] : none
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393 Example : print $feature->hseq_region_end();
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394 Description: Convenience method which returns the absolute end of this
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395 feature on the hseq_region, as opposed to the relative (hslice)
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396 position.
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397
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398 Returns undef if this feature is not on a hslice.
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399 Returntype : int or undef
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400 Exceptions : none
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401 Caller : general
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402 Status : Stable
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403
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404 =cut
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405
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406 sub hseq_region_end {
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407 my $self = shift;
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408 my $slice = $self->{'hslice'};
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409
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410 return undef if(!$slice);
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411
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412 if($slice->strand == 1) {
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413 return undef if(!defined($self->{'hend'}));
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414 return $slice->start() + $self->{'hend'} - 1;
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415 } else {
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416 return undef if(!defined($self->{'hstart'}));
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417 return $slice->end() - $self->{'hstart'} + 1;
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418 }
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419 }
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420
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421 =head2 score
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422
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423 Arg [1] : float $score (optional)
|
|
|
424 Example : $score = $fp->score();
|
|
|
425 Description: Getter/Setter for the score of this feature pair
|
|
|
426 Returntype : float
|
|
|
427 Exceptions : none
|
|
|
428 Caller : general
|
|
|
429 Status : Stable
|
|
|
430
|
|
|
431 =cut
|
|
|
432
|
|
|
433 sub score{
|
|
|
434 my $self = shift;
|
|
|
435 $self->{'score'} = shift if(@_);
|
|
|
436 return $self->{'score'};
|
|
|
437 }
|
|
|
438
|
|
|
439
|
|
|
440
|
|
|
441 =head2 percent_id
|
|
|
442
|
|
|
443 Arg [1] : float $percent_id (optional)
|
|
|
444 Example : $percent_id = $fp->percent_id();
|
|
|
445 Description: Getter/Setter for the percentage identity of this feature pair
|
|
|
446 Returntype : float
|
|
|
447 Exceptions : none
|
|
|
448 Caller : general
|
|
|
449 Status : Stable
|
|
|
450
|
|
|
451 =cut
|
|
|
452
|
|
|
453 sub percent_id {
|
|
|
454 my $self = shift;
|
|
|
455 $self->{'percent_id'} = shift if(@_);
|
|
|
456 return $self->{'percent_id'};
|
|
|
457 }
|
|
|
458
|
|
|
459
|
|
|
460
|
|
|
461 =head2 species
|
|
|
462
|
|
|
463 Arg [1] : string $genus_species_name (optional)
|
|
|
464 e.g. Homo_sapiens or Mus_musculus
|
|
|
465 Example : $species = $fp->species();
|
|
|
466 Description: get/set on the species of feature1
|
|
|
467 Returntype : string
|
|
|
468 Execeptions: none
|
|
|
469 Caller : general
|
|
|
470 Status : Stable
|
|
|
471
|
|
|
472 =cut
|
|
|
473
|
|
|
474 sub species{
|
|
|
475 my $self = shift;
|
|
|
476 $self->{'species'} = shift if(@_);
|
|
|
477 return $self->{'species'};
|
|
|
478 }
|
|
|
479
|
|
|
480
|
|
|
481 =head2 hspecies
|
|
|
482
|
|
|
483 Arg [1] : string $genus_species_name (optional)
|
|
|
484 e.g. Homo_sapiens or Mus_musculus
|
|
|
485 Example : $hspecies = $fp->hspecies
|
|
|
486 Description: get/set on the species of feature2
|
|
|
487 Returntype : string
|
|
|
488 Execeptions: none
|
|
|
489 Caller : general
|
|
|
490 Status : Stable
|
|
|
491
|
|
|
492 =cut
|
|
|
493
|
|
|
494 sub hspecies{
|
|
|
495 my $self = shift;
|
|
|
496 $self->{'hspecies'} = shift if(@_);
|
|
|
497 return $self->{'hspecies'};
|
|
|
498 }
|
|
|
499
|
|
|
500
|
|
|
501 =head2 coverage
|
|
|
502
|
|
|
503 Arg [1] : number (percentage) $coverage (optional)
|
|
|
504 Example : $cov = $fp->coverage();
|
|
|
505 Description: Getter/Setter for the % of the query covered by the feature
|
|
|
506 Returntype : string
|
|
|
507 Exceptions : none
|
|
|
508 Caller : general
|
|
|
509 Status : Stable
|
|
|
510
|
|
|
511 =cut
|
|
|
512
|
|
|
513 sub coverage {
|
|
|
514 my $self = shift;
|
|
|
515 $self->{'coverage'} = shift if(@_);
|
|
|
516 return $self->{'coverage'};
|
|
|
517 }
|
|
|
518
|
|
|
519
|
|
|
520 =head2 hcoverage
|
|
|
521
|
|
|
522 Arg [1] : number (percentage) $hcoverage (optional)
|
|
|
523 Example : $hcov = $fp->hcoverage();
|
|
|
524 Description: Getter/Setter for the % of the target covered by the feature
|
|
|
525 Returntype : string
|
|
|
526 Exceptions : none
|
|
|
527 Caller : general
|
|
|
528 Status : Stable
|
|
|
529
|
|
|
530 =cut
|
|
|
531
|
|
|
532 sub hcoverage {
|
|
|
533 my $self = shift;
|
|
|
534 $self->{'hcoverage'} = shift if(@_);
|
|
|
535 return $self->{'hcoverage'};
|
|
|
536 }
|
|
|
537
|
|
|
538 =head2 external_db_id
|
|
|
539
|
|
|
540 Arg [1] : int $external_db_id (optional)
|
|
|
541 Example : $ex_db = $fp->external_db_id();
|
|
|
542 Description: Getter/Setter for the external_db_id taregt source database feature
|
|
|
543 Returntype : string
|
|
|
544 Exceptions : none
|
|
|
545 Caller : general
|
|
|
546 Status : At Risk
|
|
|
547
|
|
|
548 =cut
|
|
|
549
|
|
|
550 sub external_db_id {
|
|
|
551 my $self = shift;
|
|
|
552 $self->{'external_db_id'} = shift if(@_);
|
|
|
553 return $self->{'external_db_id'};
|
|
|
554 }
|
|
|
555
|
|
|
556
|
|
|
557 =head2 db_name
|
|
|
558
|
|
|
559 Arg [1] : string $external_db_name (optional)
|
|
|
560 Example : $ex_db_name = $fp->dbname();
|
|
|
561 Description: Getter/Setter for the external_db_name attribute, name of external database
|
|
|
562 Returntype : string
|
|
|
563 Exceptions : none
|
|
|
564 Caller : general
|
|
|
565 Status : At Risk
|
|
|
566
|
|
|
567 =cut
|
|
|
568
|
|
|
569 sub db_name {
|
|
|
570 my $self = shift;
|
|
|
571 $self->{'dbname'} = shift if(@_);
|
|
|
572 return $self->{'dbname'};
|
|
|
573 }
|
|
|
574
|
|
|
575 =head2 db_display_name
|
|
|
576
|
|
|
577 Arg [1] : string $db_display_name (optional)
|
|
|
578 Example : $ex_db_display_name = $fp->db_display_name();
|
|
|
579 Description: Getter/Setter for the db_display_name attribute
|
|
|
580 The preferred display name for the external database.
|
|
|
581 Returntype : string
|
|
|
582 Exceptions : none
|
|
|
583 Caller : general
|
|
|
584 Status : At Risk
|
|
|
585
|
|
|
586 =cut
|
|
|
587
|
|
|
588 sub db_display_name {
|
|
|
589 my $self = shift;
|
|
|
590 $self->{'db_display_name'} = shift if(@_);
|
|
|
591 return $self->{'db_display_name'};
|
|
|
592 }
|
|
|
593
|
|
|
594
|
|
|
595
|
|
|
596 =head2 p_value
|
|
|
597
|
|
|
598 Arg [1] : float $p_value (optional)
|
|
|
599 Example : $eval = $fp->p_value
|
|
|
600 Description: Getter Setter for the evalue / pvalue of this feature
|
|
|
601 Returntype : float
|
|
|
602 Exceptions : none
|
|
|
603 Caller : general
|
|
|
604 Status : Stable
|
|
|
605
|
|
|
606 =cut
|
|
|
607
|
|
|
608 sub p_value{
|
|
|
609 my $self = shift;
|
|
|
610 $self->{'p_value'} = shift if(@_);
|
|
|
611 return $self->{'p_value'};
|
|
|
612 }
|
|
|
613
|
|
|
614
|
|
|
615
|
|
|
616 =head2 display_id
|
|
|
617
|
|
|
618 Arg [1] : none
|
|
|
619 Example : print $fp->display_id();
|
|
|
620 Description: This method returns a string that is considered to be
|
|
|
621 the 'display' identifier. For feature pairs this is the
|
|
|
622 hseqname if it is available otherwise it is an empty string.
|
|
|
623 Returntype : string
|
|
|
624 Exceptions : none
|
|
|
625 Caller : web drawing code
|
|
|
626 Status : Stable
|
|
|
627
|
|
|
628 =cut
|
|
|
629
|
|
|
630 sub display_id {
|
|
|
631 my $self = shift;
|
|
|
632 return $self->{'hseqname'} || '';
|
|
|
633 }
|
|
|
634
|
|
|
635
|
|
|
636 =head2 identical_matches
|
|
|
637
|
|
|
638 Arg [1] : int $identical_matches (optional)
|
|
|
639 Example :
|
|
|
640 Description: get/set on the number of identical matches
|
|
|
641 Returntype : int
|
|
|
642 Execeptions: none
|
|
|
643 Caller : general
|
|
|
644 Status : Stable
|
|
|
645
|
|
|
646 =cut
|
|
|
647
|
|
|
648 sub identical_matches{
|
|
|
649 my ($self,$arg) = @_;
|
|
|
650
|
|
|
651 if (defined($arg)) {
|
|
|
652 return $self->{'_identical_matches'} = $arg;
|
|
|
653 }
|
|
|
654 return $self->{'_identical_matches'};
|
|
|
655 }
|
|
|
656
|
|
|
657 =head2 positive_matches
|
|
|
658
|
|
|
659 Arg [1] : int $positive_matches (optional)
|
|
|
660 Example :
|
|
|
661 Description: get/set on the number of positive matches
|
|
|
662 Returntype : int
|
|
|
663 Execeptions: none
|
|
|
664 Caller : general
|
|
|
665 Status : Stable
|
|
|
666
|
|
|
667 =cut
|
|
|
668
|
|
|
669 sub positive_matches{
|
|
|
670 my ($self,$arg) = @_;
|
|
|
671
|
|
|
672 if (defined($arg)) {
|
|
|
673 return $self->{'_positive_matches'} = $arg;
|
|
|
674 }
|
|
|
675 return $self->{'_positive_matches'};
|
|
|
676 }
|
|
|
677
|
|
|
678 =head2 group_id
|
|
|
679
|
|
|
680 Arg [1] : int $group_id
|
|
|
681 Example : none
|
|
|
682 Description: get/set for attribute group_id
|
|
|
683 Returntype : int
|
|
|
684 Exceptions : none
|
|
|
685 Caller : general
|
|
|
686 Status : Stable
|
|
|
687
|
|
|
688 =cut
|
|
|
689
|
|
|
690 sub group_id {
|
|
|
691 my ($self, $arg) = @_;
|
|
|
692
|
|
|
693 if ( defined $arg ) {
|
|
|
694 $self->{'group_id'} = $arg ;
|
|
|
695 }
|
|
|
696 return $self->{'group_id'};
|
|
|
697 }
|
|
|
698
|
|
|
699 =head2 level_id
|
|
|
700
|
|
|
701 Arg [1] : int $level_id
|
|
|
702 Example : none
|
|
|
703 Description: get/set for attribute level_id
|
|
|
704 Returntype : int
|
|
|
705 Exceptions : none
|
|
|
706 Caller : general
|
|
|
707 Status : Stable
|
|
|
708
|
|
|
709 =cut
|
|
|
710
|
|
|
711 sub level_id {
|
|
|
712 my ($self, $arg) = @_;
|
|
|
713
|
|
|
714 if ( defined $arg ) {
|
|
|
715 $self->{'level_id'} = $arg ;
|
|
|
716 }
|
|
|
717 return $self->{'level_id'};
|
|
|
718 }
|
|
|
719
|
|
|
720
|
|
|
721
|
|
|
722
|
|
|
723
|
|
|
724
|
|
|
725 =head1 DEPRECATED METHODS
|
|
|
726
|
|
|
727 =cut
|
|
|
728
|
|
|
729
|
|
|
730 =head2 feature1
|
|
|
731
|
|
|
732 Description: DEPRECATED use start(), end(), strand(), slice(), etc.
|
|
|
733 methods instead
|
|
|
734
|
|
|
735 =cut
|
|
|
736
|
|
|
737 sub feature1 {
|
|
|
738 my ($self,$arg) = @_;
|
|
|
739
|
|
|
740 deprecate('Use start(), end(), strand(), slice(), etc. methods instead.');
|
|
|
741
|
|
|
742 if($arg) {
|
|
|
743 $self->start($arg->start());
|
|
|
744 $self->end($arg->end());
|
|
|
745 $self->strand($arg->strand());
|
|
|
746 $self->score($arg->score());
|
|
|
747 $self->percent_id($arg->percent_id());
|
|
|
748 $self->analysis($arg->analysis);
|
|
|
749 if($arg->contig){
|
|
|
750 $self->slice($arg->contig);
|
|
|
751 }
|
|
|
752 }
|
|
|
753
|
|
|
754 return $self;
|
|
|
755 }
|
|
|
756
|
|
|
757 =head2 feature2
|
|
|
758
|
|
|
759 Description: DEPRECATED use hstart(), hend(), hstrand() etc.
|
|
|
760 methods instead
|
|
|
761
|
|
|
762 =cut
|
|
|
763
|
|
|
764 sub feature2 {
|
|
|
765 my ($self,$arg) = @_;
|
|
|
766
|
|
|
767 deprecate('Use hstart(),hend(),hstrand(),hseqname() methods instead.');
|
|
|
768
|
|
|
769 if (defined($arg)) {
|
|
|
770 $self->hstart($arg->start());
|
|
|
771 $self->hend($arg->end());
|
|
|
772 $self->hstrand($arg->strand());
|
|
|
773 $self->hseqname($arg->seqname());
|
|
|
774 return $arg;
|
|
|
775 }
|
|
|
776
|
|
|
777 return new Bio::EnsEMBL::Feature(
|
|
|
778 -START => $self->hstart(),
|
|
|
779 -END => $self->hend(),
|
|
|
780 -STRAND => $self->hstrand(),
|
|
|
781 -SCORE => $self->score(),
|
|
|
782 -PERCENT_ID => $self->percent_id(),
|
|
|
783 -ANALYSIS => $self->analysis,
|
|
|
784 -SEQNAME => $self->hseqname());
|
|
|
785 }
|
|
|
786
|
|
|
787
|
|
|
788
|
|
|
789
|
|
|
790 =head2 invert
|
|
|
791
|
|
|
792 Arg [1] : (optional) Bio::EnsEMBL::Slice $newslice
|
|
|
793 Example : $feature->invert();
|
|
|
794 Description: This method is used to swap the hit and query sides of this
|
|
|
795 feature in place. A new slice may optionally provided which
|
|
|
796 this feature will be placed on. If no slice is provided the
|
|
|
797 feature slice will be set to undef.
|
|
|
798 Returntype : none
|
|
|
799 Exceptions : none
|
|
|
800 Caller : pipeline (BlastMiniGenewise)
|
|
|
801
|
|
|
802 =cut
|
|
|
803
|
|
|
804 sub invert {
|
|
|
805 my ($self,$slice) = @_;
|
|
|
806
|
|
|
807 if (! defined $slice && defined $self->hslice) {
|
|
|
808 $slice = $self->hslice;
|
|
|
809 }
|
|
|
810
|
|
|
811 my $hstart = $self->{'hstart'};
|
|
|
812 my $hend = $self->{'hend'};
|
|
|
813 my $hstrand = $self->{'hstrand'};
|
|
|
814 my $hspecies = $self->{'hspecies'};
|
|
|
815 my $hseqname = $self->{'hseqname'};
|
|
|
816
|
|
|
817 my $start = $self->{'start'};
|
|
|
818 my $end = $self->{'end'};
|
|
|
819 my $strand = $self->{'strand'};
|
|
|
820 my $species = $self->{'species'};
|
|
|
821 my $seqname = $self->seqname();
|
|
|
822
|
|
|
823 $self->{'start'} = $hstart;
|
|
|
824 $self->{'end'} = $hend;
|
|
|
825 $self->{'strand'} = $hstrand;
|
|
|
826 $self->{'species'} = $hspecies;
|
|
|
827 $self->{'seqname'} = $hseqname if(defined($hseqname));
|
|
|
828
|
|
|
829 $self->{'hstart'} = $start;
|
|
|
830 $self->{'hend'} = $end;
|
|
|
831 $self->{'hstrand'} = $strand;
|
|
|
832 $self->{'hseqname'} = $seqname;
|
|
|
833 $self->{'hspecies'} = $species;
|
|
|
834
|
|
|
835 $self->{'hslice'} = $self->slice;
|
|
|
836 $self->{'slice'} = $slice;
|
|
|
837 }
|
|
|
838
|
|
|
839
|
|
|
840
|
|
|
841 =head2 validate
|
|
|
842
|
|
|
843 Description: DEPRECATED do not use
|
|
|
844
|
|
|
845 =cut
|
|
|
846
|
|
|
847 sub validate {
|
|
|
848 my ($self) = @_;
|
|
|
849
|
|
|
850 deprecate('This method does nothing and should not be used.');
|
|
|
851 }
|
|
|
852
|
|
|
853 =head2 validate_prot_feature
|
|
|
854
|
|
|
855 Description: DEPRECATED do not use
|
|
|
856
|
|
|
857 =cut
|
|
|
858
|
|
|
859 sub validate_prot_feature{
|
|
|
860 my ($self) = @_;
|
|
|
861
|
|
|
862 deprecate('This method does nothing and should not be used.');
|
|
|
863 }
|
|
|
864
|
|
|
865
|
|
|
866 =head2 set_featurepair_fields
|
|
|
867
|
|
|
868 Description: DEPRECATED do not use
|
|
|
869
|
|
|
870 =cut
|
|
|
871
|
|
|
872 sub set_featurepair_fields {
|
|
|
873 my ($self, $start, $end, $strand, $score, $seqname, $hstart, $hend,
|
|
|
874 $hstrand, $hseqname, $analysis, $e_value, $perc_id,
|
|
|
875 $phase, $end_phase) = @_;
|
|
|
876
|
|
|
877 deprecate("Use individual Getter/Setters or Constructor arguments " .
|
|
|
878 " instead.\nThere is no advantage to using this method.");
|
|
|
879
|
|
|
880 throw('interface fault') if (@_ < 12 or @_ > 15);
|
|
|
881
|
|
|
882 $self->start($start);
|
|
|
883 $self->end($end);
|
|
|
884 $self->strand($strand);
|
|
|
885 $self->score($score);
|
|
|
886 $self->seqname($seqname);
|
|
|
887 $self->hstart($hstart);
|
|
|
888 $self->hend($hend);
|
|
|
889 $self->hstrand($hstrand);
|
|
|
890 $self->hseqname($hseqname);
|
|
|
891 $self->analysis($analysis);
|
|
|
892 $self->p_value ($e_value) if (defined $e_value);
|
|
|
893 $self->percent_id ($perc_id) if (defined $perc_id);
|
|
|
894 $self->phase ($phase) if (defined $phase);
|
|
|
895 $self->end_phase ($end_phase) if (defined $end_phase);
|
|
|
896 }
|
|
|
897
|
|
|
898
|
|
|
899 =head2 gffstring
|
|
|
900
|
|
|
901 Description: DEPRECATED do not use
|
|
|
902
|
|
|
903 =cut
|
|
|
904
|
|
|
905 sub gffstring {
|
|
|
906 my ($self) = @_;
|
|
|
907
|
|
|
908 deprecate('Do not use');
|
|
|
909
|
|
|
910 my $str .= (defined $self->slice) ? $self->slice->name()."\t": "\t";
|
|
|
911 $str .= "\t"; #source tag
|
|
|
912 $str .= "\t"; #primary tag
|
|
|
913 $str .= (defined $self->start) ? $self->start."\t" : "\t";
|
|
|
914 $str .= (defined $self->end) ? $self->end."\t" : "\t";
|
|
|
915 $str .= (defined $self->score) ? $self->score."\t" : "\t";
|
|
|
916 $str .= (defined $self->strand) ? $self->strand."\t" : ".\t";
|
|
|
917 $str .= ".\t"; #phase
|
|
|
918 $str .= ".\t"; #end phase
|
|
|
919
|
|
|
920 my $hstrand = "+";
|
|
|
921
|
|
|
922 if (($self->hstrand)&&($self->hstrand == -1)) {
|
|
|
923 $hstrand = "-";
|
|
|
924 }
|
|
|
925
|
|
|
926 #Append a few FeaturePair specific things
|
|
|
927 $str .= (defined $self->hseqname) ? $self->hseqname."\t" : "\t";
|
|
|
928 $str .= (defined $self->hstart) ? $self->hstart."\t" : "\t";
|
|
|
929 $str .= (defined $self->hend) ? $self->hend."\t" : "\t";
|
|
|
930 $str .= (defined $self->hstrand) ? $hstrand."\t" : "\t";
|
|
|
931 $str .= (defined $self->hphase) ? $self->hphase."\t" : ".\t";
|
|
|
932
|
|
|
933 return $str;
|
|
|
934 }
|
|
|
935
|
|
|
936
|
|
|
937
|
|
|
938
|
|
|
939 =head2 hphase
|
|
|
940
|
|
|
941 Description: DEPRECATED do not use
|
|
|
942
|
|
|
943 =cut
|
|
|
944
|
|
|
945 sub hphase {
|
|
|
946 my ($self, $value) = @_;
|
|
|
947
|
|
|
948 deprecate('This method does nothing useful.');
|
|
|
949
|
|
|
950 if (defined($value)) {
|
|
|
951 $self->{_hphase} = $value;
|
|
|
952 }
|
|
|
953
|
|
|
954 return $self->{_hphase};
|
|
|
955 }
|
|
|
956
|
|
|
957
|
|
|
958 =head2 hend_phase
|
|
|
959
|
|
|
960 Description: DEPRECATED do not use
|
|
|
961
|
|
|
962 =cut
|
|
|
963
|
|
|
964 sub hend_phase {
|
|
|
965 my ($self, $value) = @_;
|
|
|
966
|
|
|
967 deprecate('This method does nothing useful.');
|
|
|
968
|
|
|
969 if (defined($value)) {
|
|
|
970 $self->{_hend_phase} = $value;
|
|
|
971 }
|
|
|
972 return $self->{_hend_phase};
|
|
|
973 }
|
|
|
974
|
|
|
975 sub extra_data {
|
|
|
976 my $self = shift;
|
|
|
977 $self->{'extra_data'} = shift if(@_);
|
|
|
978 return $self->{'extra_data'};
|
|
|
979 }
|
|
|
980
|
|
|
981 sub type {
|
|
|
982 my $self = shift;
|
|
|
983 $self->{'extra_data'}->{'type'} = shift if(@_);
|
|
|
984 if (exists $self->{'extra_data'}) {
|
|
|
985 return $self->{'extra_data'}->{'type'};
|
|
|
986 }
|
|
|
987 return;
|
|
|
988 }
|
|
|
989
|
|
|
990 1;
|
