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1 # $Id: AlleleNode.pm,v 1.4 2002/10/22 07:45:24 lapp Exp $
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2 #
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3 # BioPerl module for Bio::Tree::AlleleNode
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4 #
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5 # Cared for by Jason Stajich <jason@bioperl.org>
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6 #
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7 # Copyright Jason Stajich
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8 #
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9 # You may distribute this module under the same terms as perl itself
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10
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11 # POD documentation - main docs before the code
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12
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13 =head1 NAME
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14
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15 Bio::Tree::AlleleNode - DESCRIPTION of Object
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16
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17 =head1 SYNOPSIS
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18
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19 Give standard usage here
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20
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21 =head1 DESCRIPTION
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22
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23 Describe the object here
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24
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25 =head1 FEEDBACK
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26
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27 =head2 Mailing Lists
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28
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29 User feedback is an integral part of the evolution of this and other
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30 Bioperl modules. Send your comments and suggestions preferably to
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31 the Bioperl mailing list. Your participation is much appreciated.
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32
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33 bioperl-l@bioperl.org - General discussion
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34 http://bioperl.org/MailList.shtml - About the mailing lists
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35
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36 =head2 Reporting Bugs
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37
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38 Report bugs to the Bioperl bug tracking system to help us keep track
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39 of the bugs and their resolution. Bug reports can be submitted via
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40 email or the web:
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41
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42 bioperl-bugs@bioperl.org
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43 http://bugzilla.bioperl.org/
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44
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45 =head1 AUTHOR - Jason Stajich
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46
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47 Email jason@bioperl.org
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48
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49 Describe contact details here
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50
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51 =head1 CONTRIBUTORS
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52
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53 Additional contributors names and emails here
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54
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55 =head1 APPENDIX
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56
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57 The rest of the documentation details each of the object methods.
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58 Internal methods are usually preceded with a _
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59
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60 =cut
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61
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62
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63 # Let the code begin...
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64
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65
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66 package Bio::Tree::AlleleNode;
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67 use vars qw(@ISA);
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68 use strict;
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69
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70 use Bio::Tree::Node;
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71
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72 @ISA = qw(Bio::Tree::Node );
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73
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74 =head2 new
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75
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76 Title : new
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77 Usage : my $obj = new Bio::Tree::AlleleNode();
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78 Function: Builds a new Bio::Tree::AlleleNode object
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79 Returns : Bio::Tree::AlleleNode
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80 Args :
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81
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82
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83 =cut
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84
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85 sub new {
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86 my($class,@args) = @_;
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87
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88 my $self = $class->SUPER::new(@args);
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89
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90 my ($alleles) = $self->_rearrange([qw(ALLELES)], @args);
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91 $self->{'_data'} = {};
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92 if( defined $alleles ) {
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93 if( ref($alleles) !~ /HASH/i ) {
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94 $self->warn("Must specify a valid HASH reference for the -alleles value...Ignoring initializing input");
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95
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96 } else {
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97 foreach my $mkr ( keys %{$alleles} ) {
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98 $self->add_alleles($mkr,@{$alleles->{$mkr}});
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99 }
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100 }
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101 }
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102 return $self;
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103 }
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104
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105 =head2 add_alleles
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106
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107 Title : add_alleles
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108 Usage : $node->add_alleles($mkr,@alleles);
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109 Function: Adds allele(s) for $mkr, @alleles can be a single or
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110 multiple alleles. If the same marker is added more than one, the
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111 previous value will be overwritten with a warning.
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112 Returns : none
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113 Args : $marker => marker name
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114 @alleles => alleles for the marker
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115
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116
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117 =cut
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118
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119 sub add_alleles{
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120 my ($self,$marker,@alleles) = @_;
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121 if( ! defined $marker || $marker eq '' ) {
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122 $self->warn("must specify a valid marker name for add_alleles");
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123 return;
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124 }
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125 if( $self->{'_data'}->{$marker} ) {
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126 $self->warn("Overwriting value of $marker");
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127 }
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128 $self->{'_data'}->{$marker} = []; # reset the array ref
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129 foreach my $a ( sort @alleles ) {
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130 next if ! defined $a; # skip undef alleles
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131 push @{$self->{'_data'}->{$marker}},$a;
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132 }
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133 }
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134
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135 =head2 get_alleles
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136
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137 Title : get_alleles
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138 Usage : my @alleles = $node->get_alleles($marker);
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139 Function: Return the alleles for a marker $marker
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140 Returns : Array of Alleles for a marker or empty array
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141 Args : $marker name
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142
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143 =cut
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144
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145 sub get_alleles{
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146 my ($self,$marker) = @_;
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147 if( defined $self->{'_data'}->{$marker} ) {
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148 return @{$self->{'_data'}->{$marker}};
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149 }
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150 return ();
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151 }
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152
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153 =head2 get_marker_names
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154
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155 Title : get_marker_names
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156 Usage : my @names =$node->get_marker_names();
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157 Function: Return the names of the markers that have been added to this node
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158 Returns : List of Marker Names
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159 Args : none
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160
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161 =cut
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162
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163 sub get_marker_names{
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164 my ($self) = @_;
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165 return keys %{$self->{'_data'}};
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166 }
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167
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168 =head2 purge_markers
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169
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170 Title : purge_markers
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171 Usage : $node->purge_markers;
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172 Function: Reset the markers and alleles
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173 Returns : none
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174 Args : none
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175
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176
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177 =cut
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178
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179 sub purge_markers{
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180 my ($self) = @_;
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181 $self->{'_data'} = {};
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182 return;
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183 }
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184
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185
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186 1;
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