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1 # $Id: ClusterI.pm,v 1.3 2002/10/25 01:29:37 lapp Exp $
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2 #
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3 # BioPerl module for Bio::ClusterI
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4 #
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5 # Cared for by Shawn Hoon <shawnh@fugu-sg.org>
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6 #
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7 # Copyright Shawn Hoon
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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::ClusterI - Cluster Interface
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16
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17 =head1 SYNOPSIS
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18
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19 # see the implementations of this interface for details but
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20 # basically
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21
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22 my $cluster= $cluster->new(-description=>"POLYUBIQUITIN",
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23 -members =>[$seq1,$seq2]);
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24 my @members = $cluster->get_members();
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25 my @sub_members = $cluster->get_members(-species=>"homo sapiens");
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26
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27
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28
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29 =head1 DESCRIPTION
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30
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31 This interface is the basic structure for a cluster of bioperl objects.
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32 In this case it is up to the implementer to check arguments
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33 and initialize whatever new object the implementing class is designed for.
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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 # Let the code begin...
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73
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74 package Bio::ClusterI;
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75 use vars qw(@ISA);
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76 use strict;
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77
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78 use Bio::Root::RootI;
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79
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80 @ISA = qw(Bio::Root::RootI);
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81
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82 =head1 Implementation Specific Functions
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83
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84 These functions are the ones that a specific implementation must
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85 define.
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86
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87 =head2 new
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88
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89 We dont mandate but encourage implementors to support at least the
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90 following named parameters upon object initialization.
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91
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92 Argument Description
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93 -------- -----------
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94 -display_id the display ID or name for the cluster
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95 -description the consensus description or name of the cluster
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96 -members the array of objects belonging to the family
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97
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98 =cut
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99
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100 =head2 display_id
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101
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102 Title : display_id
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103 Usage :
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104 Function: Get the display name or identifier for the cluster
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105 Returns : a string
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106 Args :
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107
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108 =cut
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109
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110 sub display_id{
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111 shift->throw_not_implemented();
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112 }
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113
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114
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115 =head2 description
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116
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117 Title : description
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118 Usage : Bio::ClusterI->description("POLYUBIQUITIN")
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119 Function: get/set for the consensus description of the cluster
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120 Returns : the description string
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121 Args : Optional the description string
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122
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123 =cut
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124
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125 sub description{
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126 shift->throw_not_implemented();
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127 }
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128
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129 =head2 size
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130
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131 Title : size
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132 Usage : Bio::ClusterI->size();
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133 Function: get/set for the size of the family,
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134 calculated from the number of members
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135 Returns : the size of the family
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136 Args :
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137
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138 =cut
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139
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140 sub size {
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141 shift->throw_not_implemented();
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142 }
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143
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144 =head2 cluster_score
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145
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146 Title : cluster_score
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147 Usage : $cluster ->cluster_score(100);
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148 Function: get/set for cluster_score which
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149 represent the score in which the clustering
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150 algorithm assigns to this cluster.
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151 Returns : a number
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152
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153 =cut
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154
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155 sub cluster_score{
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156 shift->throw_not_implemented();
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157 }
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158
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159 =head2 get_members
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160
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161 Title : get_members
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162 Usage : Bio::ClusterI->get_members(($seq1, $seq2));
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163 Function: retrieve the members of the family by some criteria, for
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164 example :
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165 $cluster->get_members(-species => 'homo sapiens');
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166
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167 Will return all members if no criteria are provided.
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168
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169 Returns : the array of members
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170 Args :
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171
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172 =cut
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173
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174 sub get_members {
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175 shift->throw_not_implemented();
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176 }
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177
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178 1;
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