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1 # $Id: CytoMap.pm,v 1.2 2002/10/22 07:45:15 lapp Exp $
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2 #
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3 # BioPerl module for Bio::Map::CytoMap
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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::Map::CytoMap - A Bio::MapI compliant map implementation handling cytogenic bands
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16
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17 =head1 SYNOPSIS
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18
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19 use Bio::Map::CytoMap;
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20 my $map = new Bio::Map::CytoMap(-name => 'human1',
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21 -species => $human);
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22 foreach my $marker ( @markers ) { # get a list of markers somewhere
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23 $map->add_element($marker);
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24 }
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25
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26 =head1 DESCRIPTION
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27
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28 This is the simple implementation of cytogenetic maps based on
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29 L<Bio::Map::MapI>. It handles the essential storage of name, species,
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30 type, and units as well as in memory representation of the elements of
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31 a map.
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32
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33 For CytoMaps type is hard coded to be 'cytogeneticmap' and
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34 units are set to '' but can be set to something else.
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35
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36 =head1 FEEDBACK
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37
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38 =head2 Mailing Lists
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39
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40 User feedback is an integral part of the evolution of this and other
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41 Bioperl modules. Send your comments and suggestions preferably to
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42 the Bioperl mailing list. Your participation is much appreciated.
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43
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44 bioperl-l@bioperl.org - General discussion
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45 http://bioperl.org/MailList.shtml - About the mailing lists
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46
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47 =head2 Reporting Bugs
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48
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49 Report bugs to the Bioperl bug tracking system to help us keep track
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50 of the bugs and their resolution. Bug reports can be submitted via
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51 email or the web:
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52
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53 bioperl-bugs@bioperl.org
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54 http://bugzilla.bioperl.org/
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55
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56 =head1 AUTHOR - Heikki Lehvaslaiho
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57
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58 Email heikki@ebi.ac.uk
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59
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60 =head1 CONTRIBUTORS
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61
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62 Jason Stajich jason@bioperl.org
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63 Lincoln Stein lstein@cshl.org
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64
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65 =head1 APPENDIX
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66
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67 The rest of the documentation details each of the object methods.
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68 Internal methods are usually preceded with a _
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69
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70 =cut
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71
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72
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73 # Let the code begin...
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74
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75
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76 package Bio::Map::CytoMap;
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77 use vars qw(@ISA $MAPCOUNT);
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78 use strict;
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79
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80 # Object preamble - inherits from Bio::Root::Root
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81
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82 use Bio::Root::Root;
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83 use Bio::Map::SimpleMap;
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84
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85 @ISA = qw(Bio::Root::Root Bio::Map::SimpleMap);
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86 BEGIN { $MAPCOUNT = 1; }
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87
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88 =head2 Modified methods
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89
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90 All methods present in L<Bio::Map::SimpleMap> are implemted by this
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91 class. Most of the methods are inherited from SimpleMap. The following
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92 methods have been modified to refelect the needs of cytogenetic maps.
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93
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94 =head2 new
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95
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96 Title : new
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97 Usage : my $obj = new Bio::Map::CytoMap();
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98 Function: Builds a new Bio::Map::CytoMap object
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99 Returns : Bio::Map::CytoMap
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100 Args : -name => name of map (string)
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101 -species => species for this map (Bio::Species) [optional]
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102 -elements=> elements to initialize with
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103 (arrayref of Bio::Map::MappableI objects) [optional]
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104
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105 -uid => Unique Id
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106 =cut
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107
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108 sub new {
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109 my($class,@args) = @_;
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110
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111 my $self = $class->SUPER::new(@args);
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112
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113 $self->{'_elements'} = [];
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114 $self->{'_name'} = '';
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115 $self->{'_species'} = '';
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116 $self->{'_units'} = '';
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117 $self->{'_type'} = 'cyto';
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118 $self->{'_uid'} = $MAPCOUNT++;
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119 my ($name, $type,$species, $units,
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120 $elements,$uid) = $self->_rearrange([qw(NAME TYPE
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121 SPECIES UNITS
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122 ELEMENTS UID)], @args);
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123 defined $name && $self->name($name);
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124 defined $species && $self->species($species);
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125 defined $units && $self->units($units);
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126 defined $type && $self->type($type);
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127 defined $uid && $self->unique_id($uid);
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128
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129 if( $elements && ref($elements) =~ /array/ ) {
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130 foreach my $item ( @$elements ) {
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131 $self->add_element($item);
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132 }
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133 }
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134 return $self;
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135 }
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136
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137 =head2 type
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138
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139 Title : type
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140 Usage : my $type = $map->type
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141 Function: Get hard-coded Map type
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142 Returns : String coding map type
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143 Args :
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144
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145 =cut
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146
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147 sub type {
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148 my ($self) = @_;
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149 return $self->{'_type'};
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150 }
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151
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152
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153 =head2 length
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154
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155 Title : length
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156 Usage : my $length = $map->length();
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157 Function: Retrieves the length of the map,
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158 Returns : undef since length is not calculatable for
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159 cytogenetic maps
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160 Args : none
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161
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162 =cut
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163
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164 sub length{
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165 my ($self,@args) = @_;
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166 return undef;
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167 }
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168
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169 =head2 Methods inherited from L<Bio::Map::SimpleMap>
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170
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171 =cut
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172
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173 =head2 species
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174
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175 Title : species
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176 Usage : my $species = $map->species;
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177 Function: Get/Set Species for a map
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178 Returns : Bio::Species object or string
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179 Args : (optional) Bio::Species or string
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180
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181 =cut
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182
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183 =head2 units
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184
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185 Title : units
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186 Usage : $map->units('cM');
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187 Function: Get/Set units for a map
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188 Returns : units for a map
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189 Args : units for a map (string)
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190
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191 =cut
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192
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193 =head2 name
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194
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195 Title : name
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196 Usage : my $name = $map->name
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197 Function: Get/Set Map name
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198 Returns : Map name
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199 Args : (optional) string
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200
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201 =cut
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202
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203 =head2 unique_id
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204
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205 Title : unique_id
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206 Usage : my $id = $map->unique_id;
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207 Function: Get/Set the unique ID for this map
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208 Returns : a unique identifier
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209 Args : [optional] new identifier to set
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210
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211 =cut
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212
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213 =head2 each_element
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214
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215 Title : each_element
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216 Usage : my @elements = $map->each_element;
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217 Function: Retrieves all the elements in a map
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218 unordered
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219 Returns : Array of Bio::Map::MappableI objects
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220 Args : none
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221
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222
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223 =cut
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224
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225 =head2 New methods
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226
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227 =cut
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228
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229
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230 1;
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