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1 # $Id: MapperI.pm,v 1.5 2002/11/08 09:28:24 heikki Exp $
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2 #
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3 # bioperl module for Bio::Coordinate::MapperI
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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 # Copyright Heikki Lehvaslaiho
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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::Coordinate::MapperI - Interface describing coordinate mappers
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16
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17 =head1 SYNOPSIS
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18
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19 # not to be used directly
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20
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21 =head1 DESCRIPTION
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22
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23 MapperI defines methods for classes capable for mapping locations
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24 between coordinate systems.
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25
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26 =head1 FEEDBACK
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27
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28 =head2 Mailing Lists
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29
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30 User feedback is an integral part of the evolution of this and other
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31 Bioperl modules. Send your comments and suggestions preferably to the
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32 Bioperl mailing lists Your participation is much appreciated.
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33
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34 bioperl-l@bioperl.org - General discussion
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35 http://bio.perl.org/MailList.html - About the mailing lists
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36
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37 =head2 Reporting Bugs
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38
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39 report bugs to the Bioperl bug tracking system to help us keep track
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40 the bugs and their resolution. Bug reports can be submitted via
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41 email or the web:
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42
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43 bioperl-bugs@bio.perl.org
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44 http://bugzilla.bioperl.org/
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45
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46 =head1 AUTHOR - Heikki Lehvaslaiho
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47
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48 Email: heikki@ebi.ac.uk
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49 Address:
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50
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51 EMBL Outstation, European Bioinformatics Institute
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52 Wellcome Trust Genome Campus, Hinxton
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53 Cambs. CB10 1SD, United Kingdom
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54
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55 =head1 CONTRIBUTORS
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56
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57 Additional contributors names and emails here
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58
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59 =head1 APPENDIX
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60
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61 The rest of the documentation details each of the object
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62 methods. Internal methods are usually preceded with a _
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63
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64 =cut
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65
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66
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67 # Let the code begin...
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68
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69 package Bio::Coordinate::MapperI;
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70 use vars qw(@ISA );
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71 use strict;
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72
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73 # Object preamble - inherits from Bio::Root::RootI
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74 use Bio::Root::RootI;
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75
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76 @ISA = qw(Bio::Root::RootI);
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77
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78
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79
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80 =head2 in
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81
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82 Title : in
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83 Usage : $obj->in('peptide');
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84 Function: Set and read the input coordinate system.
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85 Example :
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86 Returns : value of input system
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87 Args : new value (optional), Bio::LocationI
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88
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89 =cut
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90
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91 sub in {
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92 my ($self,$value) = @_;
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93
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94 $self->throw_not_implemented();
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95
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96 }
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97
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98
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99 =head2 out
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100
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101 Title : out
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102 Usage : $obj->out('peptide');
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103 Function: Set and read the output coordinate system.
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104 Example :
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105 Returns : value of output system
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106 Args : new value (optional), Bio::LocationI
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107
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108 =cut
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109
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110 sub out {
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111 my ($self,$value) = @_;
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112
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113 $self->throw_not_implemented();
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114 }
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115
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116 =head2 swap
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117
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118 Title : swap
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119 Usage : $obj->swap;
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120 Function: Swap the direction of mapping: input <-> output)
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121 Example :
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122 Returns : 1
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123 Args :
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124
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125 =cut
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126
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127 sub swap {
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128 my ($self) = @_;
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129
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130 $self->throw_not_implemented();
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131
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132 }
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133
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134 =head2 test
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135
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136 Title : test
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137 Usage : $obj->test;
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138 Function: test that both components are of same length
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139 Example :
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140 Returns : ( 1 | undef )
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141 Args :
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142
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143 =cut
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144
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145 sub test {
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146 my ($self) = @_;
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147
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148 $self->throw_not_implemented();
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149 }
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150
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151
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152 =head2 map
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153
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154 Title : map
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155 Usage : $newpos = $obj->map($loc);
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156 Function: Map the location from the input coordinate system
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157 to a new value in the output coordinate system.
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158 Example :
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159 Returns : new value in the output coordiante system
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160 Args : Bio::LocationI
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161
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162 =cut
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163
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164 sub map {
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165 my ($self,$value) = @_;
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166
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167 $self->throw_not_implemented();
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168
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169 }
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170
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171 =head2 return_match
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172
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173 Title : return_match
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174 Usage : $obj->return_match(1);
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175 Function: A flag to turn on the simplified mode of
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176 returning only one joined Match object or undef
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177 Example :
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178 Returns : boolean
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179 Args : boolean (optional)
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180
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181 =cut
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182
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183 sub return_match {
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184 my ($self,$value) = @_;
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185 if( defined $value) {
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186 $value ? ( $self->{'_return_match'} = 1 ) :
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187 ( $self->{'_return_match'} = 0 );
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188 }
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189 return $self->{'_return_match'} || 0 ;
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190 }
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191
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192 1;
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193
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