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1 #
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2 # BioPerl module for Bio::Cluster::FamilyI
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3 #
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4 # Cared for by Shawn Hoon <shawnh@fugu-sg.org>
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5 #
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6 # Copyright Shawn Hoon
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7 #
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8 # You may distribute this module under the same terms as perl itself
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9
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10 # POD documentation - main docs before the code
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11
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12 =head1 NAME
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13
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14 Bio::Cluster::FamilyI - Family Interface
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15
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16 =head1 SYNOPSIS
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17
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18 # see the implementations of this interface for details but
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19 # basically
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20
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21 my $cluster= $cluster->new(-description=>"POLYUBIQUITIN",
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22 -members =>[$seq1,$seq2]);
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23 my @members = $cluster->get_members();
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24 my @sub_members = $cluster->get_members(-species=>"homo sapiens");
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25
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26
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27
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28 =head1 DESCRIPTION
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29
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30 This interface if for a Family object representing a family of
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31 biological objects. A generic implementation for this may be
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32 found a Bio::Cluster::Family.
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33
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34
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35 =head1 FEEDBACK
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36
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37 =head2 Mailing Lists
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38
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39 User feedback is an integral part of the evolution of this and other
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40 Bioperl modules. Send your comments and suggestions preferably to
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41 the Bioperl mailing list. Your participation is much appreciated.
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42
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43 bioperl-l@bioperl.org - General discussion
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44 http://bioperl.org/MailList.shtml - About the mailing lists
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45
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46 =head2 Reporting Bugs
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47
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48 Report bugs to the Bioperl bug tracking system to help us keep track
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49 of the bugs and their resolution. Bug reports can be submitted via
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50 email or the web:
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51
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52 bioperl-bugs@bioperl.org
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53 http://bugzilla.bioperl.org/
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54
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55 =head1 AUTHOR - Shawn Hoon
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56
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57 Email shawnh@fugu-sg.org
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58
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59
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60 =head1 CONTRIBUTORS
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61
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62 Additional contributors names and emails here
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63
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64 =head1 APPENDIX
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65
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66 The rest of the documentation details each of the object methods.
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67 Internal methods are usually preceded with a _
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68
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69 =cut
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70
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71
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72 package Bio::Cluster::FamilyI;
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73 use vars qw(@ISA);
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74 use strict;
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75
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76 use Bio::ClusterI;
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77
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78 @ISA = qw(Bio::ClusterI);
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79
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80 =head2 new
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81
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82 We dont mandate but encourage implementors to support at least the
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83 following named parameters upon object initialization.
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84
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85 Arguments Description
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86 --------- -----------
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87 -family_id the name of the family
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88 -description the consensus description of the family
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89 -annotation_score the confidence by which the consensus description is
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90 representative of the family
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91 -members the members belonging to the family
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92 -alignment the multiple alignment of the members
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93
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94 =cut
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95
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96
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97 =head2 family_id
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98
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99 Title : family_id
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100 Usage : Bio::Cluster::FamilyI->family_id("znfp");
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101 Function: get/set for the family id
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102 Returns : the family id
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103 Args : the family id
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104
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105 =cut
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106
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107 sub family_id{
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108 shift->throw_not_implemented();
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109 }
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110
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111 =head2 family_score
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112
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113 Title : family_score
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114 Usage : Bio::Cluster::FamilyI->family_score(95);
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115 Function: get/set for the score of algorithm used to generate
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116 the family if present
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117 Returns : the score
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118 Args : the score
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119
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120 =cut
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121
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122 sub family_score {
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123 shift->throw_not_implemented();
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124 }
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125
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126
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127 =head1 Methods inherited from L<Bio::ClusterI>
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128
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129 =cut
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130
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131 =head2 display_id
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132
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133 Title : display_id
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134 Usage :
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135 Function: Get the display name or identifier for the cluster
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136 Returns : a string
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137 Args :
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138
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139 =cut
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140
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141 =head2 get_members
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142
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143 Title : get_members
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144 Usage : Bio::Cluster::FamilyI->get_members();
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145 Function: get the members of the family
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146 Returns : the array of members
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147 Args : the array of members
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148
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149 =cut
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150
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151 =head2 description
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152
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153 Title : description
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154 Usage : Bio::Cluster::FamilyI->description("Zinc Finger Protein");
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155 Function: get/set for the description of the family
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156 Returns : the description
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157 Args : the description
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158
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159 =cut
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160
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161
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162 =head2 size
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163
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164 Title : size
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165 Usage : Bio::Cluster::FamilyI->size();
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166 Function: get/set for the description of the family
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167 Returns : size
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168 Args :
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169
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170 =cut
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171
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172 =head2 cluster_score
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173
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174 Title : cluster_score
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175 Usage : $cluster ->cluster_score(100);
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176 Function: get/set for cluster_score which
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177 represent the score in which the clustering
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178 algorithm assigns to this cluster.
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179 Returns : a number
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180
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181 =cut
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182
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183 1;
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