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1 # $Id: Range.pm,v 1.17 2002/10/22 07:38:24 lapp Exp $
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2 #
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3 # BioPerl module for Bio::Range
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4 #
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5 # Cared for by Heikki Lehvaslaiho <heikki@ebi.ac.uk>
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6 #
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7 # Copywright Matthew Pocock
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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
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14 =head1 NAME
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15
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16 Bio::Range - Pure perl RangeI implementation
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17
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18 =head1 SYNOPSIS
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19
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20 $range = new Bio::Range(-start=>10, -end=>30, -strand=>+1);
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21 $r2 = new Bio::Range(-start=>15, -end=>200, -strand=>+1);
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22
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23 print join(', ', $range->union($r2), "\n";
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24 print join(', ', $range->intersection($r2), "\n";
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25
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26 print $range->overlaps($r2), "\n";
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27 print $range->contains($r2), "\n";
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28
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29 =head1 DESCRIPTION
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30
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31 This provides a pure perl implementation of the BioPerl range
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32 interface.
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33
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34 Ranges are modeled as having (start, end, length, strand). They use
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35 Bio-coordinates - all points E<gt>= start and E<lt>= end are within the
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36 range. End is always greater-than or equal-to start, and length is
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37 greather than or equal to 1. The behaviour of a range is undefined if
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38 ranges with negative numbers or zero are used.
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39
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40 So, in summary:
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41
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42 length = end - start + 1
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43 end >= start
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44 strand = (-1 | 0 | +1)
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45
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46 =head1 FEEDBACK
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47
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48 =head2 Mailing Lists
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49
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50 User feedback is an integral part of the evolution of this and other
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51 Bioperl modules. Send your comments and suggestions preferably to one
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52 of the Bioperl mailing lists. Your participation is much appreciated.
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53
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54 bioperl-l@bioperl.org - General discussion
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55 http://bio.perl.org/MailList.html - About the mailing lists
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56
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57 =head2 Reporting Bugs
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58
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59 Report bugs to the Bioperl bug tracking system to help us keep track
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60 the bugs and their resolution. Bug reports can be submitted via email
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61 or the web:
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62
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63 bioperl-bugs@bio.perl.org
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64 http://bugzilla.bioperl.org/
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65
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66 =head1 AUTHOR - Heikki Lehvaslaiho
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67
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68 Email heikki@ebi.ac.uk
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69
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70 =head1 APPENDIX
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71
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72 The rest of the documentation details each of the object
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73 methods. Internal methods are usually preceded with a _
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74
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75 =cut
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76
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77 package Bio::Range;
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78
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79 use strict;
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80 use Carp;
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81 use integer;
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82 use Bio::RangeI;
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83 use Bio::Root::Root;
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84
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85 use vars qw(@ISA);
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86
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87 @ISA = qw(Bio::Root::Root Bio::RangeI);
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88
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89 =head1 Constructors
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90
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91 =head2 new
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92
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93 Title : new
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94 Usage : $range = Bio::Range->new(-start => 100, -end=> 200, -strand = +1);
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95 Function: generates a new Bio::Range
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96 Returns : a new range
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97 Args : two of (-start, -end, '-length') - the third is calculated
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98 : -strand (defaults to 0)
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99
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100 =cut
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101
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102 sub new {
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103 my ($caller, @args) = @_;
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104 my $self = $caller->SUPER::new(@args);
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105 my ($strand, $start, $end, $length) =
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106 $self->_rearrange([qw(STRAND
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107 START
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108 END
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109 LENGTH
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110 )],@args);
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111 $self->strand($strand || 0);
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112
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113 if(defined $start ) {
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114 $self->start($start);
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115 if(defined $end) {
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116 $self->end($end);
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117 } elsif(defined $length) {
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118 $self->end($self->start()+ $length - 1);
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119 }
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120 } elsif(defined $end && defined $length ) {
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121 $self->end($end);
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122 $self->start($self->end() - $length + 1);
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123 }
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124 return $self;
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125 }
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126
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127 =head1 Member variable access
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128
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129 These methods let you get at and set the member variables
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130
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131 =head2 start
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132
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133 Title : start
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134 Function : return or set the start co-ordinate
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135 Example : $s = $range->start(); $range->start(7);
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136 Returns : the value of the start co-ordinate
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137 Args : optionally, the new start co-ordinate
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138 Overrides: Bio::RangeI::start
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139
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140 =cut
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141
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142 sub start {
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143 my ($self,$value) = @_;
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144 if( defined $value) {
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145 $self->throw("'$value' is not an integer.\n")
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146 unless $value =~ /^[-+]?\d+$/;
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147 $self->{'start'} = $value;
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148 }
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149 return $self->{'start'};
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150 }
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151
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152 =head2 end
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153
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154 Title : end
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155 Function : return or set the end co-ordinate
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156 Example : $e = $range->end(); $range->end(2000);
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157 Returns : the value of the end co-ordinate
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158 Args : optionally, the new end co-ordinate
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159 Overrides: Bio::RangeI::end
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160
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161 =cut
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162
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163 sub end {
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164
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165 my ($self,$value) = @_;
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166 if( defined $value) {
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167 $self->throw("'$value' is not an integer.\n")
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168 unless $value =~ /^[-+]?\d+$/;
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169 $self->{'end'} = $value;
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170 }
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171 return $self->{'end'};
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172 }
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173
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174 =head2 strand
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175
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176 Title : strand
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177 Function : return or set the strandidness
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178 Example : $st = $range->strand(); $range->strand(-1);
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179 Returns : the value of the strandedness (-1, 0 or 1)
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180 Args : optionaly, the new strand - (-1, 0, 1) or (-, ., +).
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181 Overrides: Bio::RangeI::Strand
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182
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183 =cut
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184
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185 sub strand {
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186 my $self = shift;
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187 if(@_) {
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188 my $val = shift;
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189 $val =~ tr/+/1/;
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190 $val =~ tr/-/-1/;
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191 $val =~ tr/./0/;
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192 if($val == -1 || $val == 0 || $val == 1 ) {
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193 $self->{'strand'} = $val;
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194 }
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195 }
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196 return $self->{'strand'};
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197 }
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198
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199 =head2 length
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200
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201 Title : length
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202 Function : returns the length of this range
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203 Example : $length = $range->length();
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204 Returns : the length of this range, equal to end - start + 1
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205 Args : if you attempt to set the length, and exeption will be thrown
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206 Overrides: Bio::RangeI::Length
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207
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208 =cut
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209
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210 sub length {
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211 my $self = shift;
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212 if(@_) {
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213 confess ref($self), "->length() is read-only";
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214 }
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215 return $self->end() - $self->start() + 1;
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216 }
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217
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218 =head2 toString
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219
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220 Title : toString
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221 Function: stringifies this range
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222 Example : print $range->toString(), "\n";
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223 Returns : a string representation of this range
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224
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225 =cut
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226
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227 sub toString {
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228 my $self = shift;
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229 return "(${\$self->start}, ${\$self->end}) strand=${\$self->strand}";
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230 }
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231
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232 =head1 Boolean Methods
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233
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234 These methods return true or false.
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235
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236 $range->overlaps($otherRange) && print "Ranges overlap\n";
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237
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238 =head2 overlaps
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239
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240 Title : overlaps
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241 Usage : if($r1->overlaps($r2)) { do stuff }
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242 Function : tests if $r2 overlaps $r1
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243 Args : a range to test for overlap with
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244 Returns : true if the ranges overlap, false otherwise
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245 Inherited: Bio::RangeI
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246
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247 =head2 contains
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248
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249 Title : contains
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250 Usage : if($r1->contains($r2) { do stuff }
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251 Function : tests wether $r1 totaly contains $r2
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252 Args : a range to test for being contained
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253 Returns : true if the argument is totaly contained within this range
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254 Inherited: Bio::RangeI
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255
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256 =head2 equals
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257
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258 Title : equals
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259 Usage : if($r1->equals($r2))
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260 Function : test whether $r1 has the same start, end, length as $r2
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261 Args : a range to test for equality
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262 Returns : true if they are describing the same range
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263 Inherited: Bio::RangeI
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264
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265 =head1 Geometrical methods
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266
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267 These methods do things to the geometry of ranges, and return
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268 triplets (start, end, strand) from which new ranges could be built.
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269
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270 =head2 intersection
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271
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272 Title : intersection
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273 Usage : ($start, $stop, $strand) = $r1->intersection($r2)
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274 Function : gives the range that is contained by both ranges
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275 Args : a range to compare this one to
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276 Returns : nothing if they do not overlap, or the range that they do overlap
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277 Inherited: Bio::RangeI::intersection
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278
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279 =cut
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280
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281 =head2 union
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282
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283 Title : union
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284 Usage : ($start, $stop, $strand) = $r1->union($r2);
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285 : ($start, $stop, $strand) = Bio::Range->union(@ranges);
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286 Function : finds the minimal range that contains all of the ranges
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287 Args : a range or list of ranges to find the union of
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288 Returns : the range containing all of the ranges
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289 Inherited: Bio::RangeI::union
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290
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291 =cut
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292
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293 1;
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