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1 # $Id: Subset.pm,v 1.10 2012/05/10 14:19:20 mm14 Exp $
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2 #
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3 # Module to handle family members
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4 #
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5 # Cared for by Abel Ureta-Vidal <abel@ebi.ac.uk>
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6 #
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7 # Copyright Abel Ureta-Vidal
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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 Subset - 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 =head1 DESCRIPTION
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20
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21 =head1 CONTACT
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22
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23 Jessica Severin <jessica@ebi.ac.uk>
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24
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25 =head1 APPENDIX
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26
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27 The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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28
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29 =cut
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30
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31 package Bio::EnsEMBL::Compara::Subset;
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32
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33 use strict;
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34 use Bio::Species;
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35 use Bio::EnsEMBL::Utils::Exception;
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36 use Bio::EnsEMBL::Utils::Argument;
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37
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38 use Data::Dumper;
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39
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40 sub new {
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41 my ($class, @args) = @_;
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42 my $self = {};
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43
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44 bless $self,$class;
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45
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46 if (scalar @args) {
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47 #do this explicitly.
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48 my ($dbid, $description, $adaptor) = rearrange([qw(DBID NAME ADAPTOR)], @args);
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49
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50 $self->dbID($dbid) if($dbid);
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51 $self->description($description) if($description);
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52 $self->adaptor($adaptor) if($adaptor);
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53
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54 $self->{'_member_id_list'} = [];
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55 }
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56
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57 return $self;
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58 }
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59
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60 =head2 new_fast
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61
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62 Arg [1] : hash reference $hashref
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63 Example : none
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64 Description: This is an ultra fast constructor which requires knowledge of
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65 the objects internals to be used.
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66 Returntype :
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67 Exceptions : none
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68 Caller :
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69
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70 =cut
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71
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72 sub new_fast {
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73 my ($class, $hashref) = @_;
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74
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75 return bless $hashref, $class;
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76 }
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77
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78 =head2 adaptor
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79
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80 Title : adaptor
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81 Usage :
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82 Function: give the adaptor if known
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83 Example :
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84 Returns :
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85 Args :
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86
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87
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88 =cut
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89
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90 sub adaptor {
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91 my ($self, $value) = @_;
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92
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93 if (defined $value) {
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94 $self->{'_adaptor'} = $value;
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95 }
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96
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97 return $self->{'_adaptor'};
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98 }
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99
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100
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101 =head2 dbID
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102
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103 Arg [1] : int $dbID (optional)
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104 Example :
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105 Description:
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106 Returntype :
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107 Exceptions :
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108 Caller :
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109
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110 =cut
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111
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112 sub dbID {
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113 my $self = shift;
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114 $self->{'_dbID'} = shift if(@_);
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115 return $self->{'_dbID'};
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116 }
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117
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118 =head2 description
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119
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120 Arg [1] : string $description (optional)
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121 Example :
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122 Description:
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123 Returntype : string
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124 Exceptions :
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125 Caller :
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126
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127 =cut
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128
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129 sub description {
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130 my $self = shift;
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131 $self->{'_description'} = shift if(@_);
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132 return $self->{'_description'};
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133 }
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134
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135 =head2 dump_loc
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136
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137 Arg [1] : string $dump_loc (optional)
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138 Example :
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139 Description:
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140 Returntype : string
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141 Exceptions :
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142 Caller :
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143
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144 =cut
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145
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146 sub dump_loc {
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147 my $self = shift;
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148 $self->{'_dump_loc'} = shift if(@_);
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149 return $self->{'_dump_loc'};
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150 }
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151
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152 =head2 add_member_id
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153
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154 Arg [1] : $member_id
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155 Example : my $count = $subset->add_member_id($member_id);
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156 Description : Add a new member_id to the subset object and
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157 returns the number of member_ids already in the object
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158 Returntype : A scalar with the number of member_ids in the object
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159 Exceptions :
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160 Caller :
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161
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162 =cut
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163
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164 sub add_member_id {
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165 my $self = shift;
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166 my $count=0;
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167
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168 if(@_) {
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169 my $member_id = shift;
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170 $count = push @{$self->{'_member_id_list'}}, $member_id;
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171 #print("added $count element to list\n");
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172
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173 if(defined($self->adaptor)) {
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174 $self->adaptor->store_link($self, $member_id);
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175 }
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176 }
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177 return $count
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178 }
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179
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180
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181 =head2 add_member
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182
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183 Arg [1] : A Bio::EnsEMBL::Compara::Member
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184 Example : my $count = $subset->add_member($member);
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185 Description : Add a new Bio::EnsEMBL::Compara::Member to the subset object
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186 and returns the number of members already in the object.
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187 It also adds the member_id to the object.
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188 ReturnType : A scalar with the number of members in the object
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189 Exceptions :
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190 Caller :
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191
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192 =cut
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193
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194 sub add_member {
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195 my ($self, $member) = @_;
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196
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197 unless(defined($member) and $member->isa('Bio::EnsEMBL::Compara::Member')) {
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198 throw(
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199 "gene arg must be a [Bio::EnsEMBL::Compara::Member] ".
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200 "not a [$member]");
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201 }
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202
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203 return $self->add_member_id($member->dbID);
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204 }
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205
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206 sub member_id_list {
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207 my $self = shift;
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208
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209 return $self->{'_member_id_list'};
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210 }
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211
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212 sub count {
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213 my $self = shift;
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214
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215 return $#{$self->member_id_list()} + 1;
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216 }
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217
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218
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219 # FIXME There should be a function to print a FASTA file
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220 #sub output_to_fasta
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221
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222 1;
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