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+ <span class="siteSubtitle">Run on Thu May 31 16:49:15 2012<br />Reported on Thu May 31 16:52:41 2012</span>
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+</div>
+
+<div class="body_content"><br />
+<table class="file_summary"><tr><td class="h">Filename</td><td align="left"><a href="file:///Users/edenc/perl5/lib/perl5/Bio/Phylo/Mediators/TaxaMediator.pm">/Users/edenc/perl5/lib/perl5/Bio/Phylo/Mediators/TaxaMediator.pm</a></td></tr>
+<tr><td class="h">Statements</td><td align="left">Executed 15 statements in 1.48ms</td></tr></table>
+
+ <table id="subs_table" border="1" cellpadding="0" class="tablesorter">
+ <caption>Subroutines</caption>
+ <thead>
+ <tr>
+ <th>Calls</th>
+ <th><span title="Number of Places sub is called from">P</span></th>
+ <th><span title="Number of Files sub is called from">F</span></th>
+ <th>Exclusive<br />Time</th>
+ <th>Inclusive<br />Time</th>
+ <th>Subroutine</th>
+ </tr>
+ </thead>
+ <tbody>
+<tr><td class="c3">1</td><td class="c3">1</td><td class="c3">1</td><td class="c0"><span title="0.0%">33µs</span></td><td class="c3"><span title="0.0%">39µs</span></td><td class="sub_name"><span style="display: none;">Bio::Phylo::Mediators::TaxaMediator::::BEGIN@2</span>Bio::Phylo::Mediators::TaxaMediator::<a href="Bio-Phylo-Mediators-TaxaMediator-pm-1166-block.html#2">BEGIN@2</a></span></td></tr>
+<tr><td class="c3">1</td><td class="c3">1</td><td class="c3">1</td><td class="c0"><span title="0.0%">30µs</span></td><td class="c3"><span title="0.0%">35µs</span></td><td class="sub_name"><span style="display: none;">Bio::Phylo::Mediators::TaxaMediator::::BEGIN@4</span>Bio::Phylo::Mediators::TaxaMediator::<a href="Bio-Phylo-Mediators-TaxaMediator-pm-1166-block.html#4">BEGIN@4</a></span></td></tr>
+<tr><td class="c3">1</td><td class="c3">1</td><td class="c3">1</td><td class="c3"><span title="0.0%">18µs</span></td><td class="c3"><span title="0.0%">52µs</span></td><td class="sub_name"><span style="display: none;">Bio::Phylo::Mediators::TaxaMediator::::BEGIN@5</span>Bio::Phylo::Mediators::TaxaMediator::<a href="Bio-Phylo-Mediators-TaxaMediator-pm-1166-block.html#5">BEGIN@5</a></span></td></tr>
+<tr><td class="c3">1</td><td class="c3">1</td><td class="c3">1</td><td class="c3"><span title="0.0%">16µs</span></td><td class="c1"><span title="0.0%">84µs</span></td><td class="sub_name"><span style="display: none;">Bio::Phylo::Mediators::TaxaMediator::::BEGIN@3</span>Bio::Phylo::Mediators::TaxaMediator::<a href="Bio-Phylo-Mediators-TaxaMediator-pm-1166-block.html#3">BEGIN@3</a></span></td></tr>
+<tr><td class="c3">1</td><td class="c3">1</td><td class="c3">1</td><td class="c3"><span title="0.0%">14µs</span></td><td class="c0"><span title="0.0%">640µs</span></td><td class="sub_name"><span style="display: none;">Bio::Phylo::Mediators::TaxaMediator::::BEGIN@6</span>Bio::Phylo::Mediators::TaxaMediator::<a href="Bio-Phylo-Mediators-TaxaMediator-pm-1166-block.html#6">BEGIN@6</a></span></td></tr>
+<tr><td class="c3">0</td><td class="c3">0</td><td class="c3">0</td><td class="c3"><span title="0.0%">0s</span></td><td class="c3"><span title="0.0%">0s</span></td><td class="sub_name"><span style="display: none;">Bio::Phylo::Mediators::TaxaMediator::::get_link</span>Bio::Phylo::Mediators::TaxaMediator::<a href="Bio-Phylo-Mediators-TaxaMediator-pm-1166-block.html#215">get_link</a></span></td></tr>
+<tr><td class="c3">0</td><td class="c3">0</td><td class="c3">0</td><td class="c3"><span title="0.0%">0s</span></td><td class="c3"><span title="0.0%">0s</span></td><td class="sub_name"><span style="display: none;">Bio::Phylo::Mediators::TaxaMediator::::new</span>Bio::Phylo::Mediators::TaxaMediator::<a href="Bio-Phylo-Mediators-TaxaMediator-pm-1166-block.html#51">new</a></span></td></tr>
+<tr><td class="c3">0</td><td class="c3">0</td><td class="c3">0</td><td class="c3"><span title="0.0%">0s</span></td><td class="c3"><span title="0.0%">0s</span></td><td class="sub_name"><span style="display: none;">Bio::Phylo::Mediators::TaxaMediator::::register</span>Bio::Phylo::Mediators::TaxaMediator::<a href="Bio-Phylo-Mediators-TaxaMediator-pm-1166-block.html#88">register</a></span></td></tr>
+<tr><td class="c3">0</td><td class="c3">0</td><td class="c3">0</td><td class="c3"><span title="0.0%">0s</span></td><td class="c3"><span title="0.0%">0s</span></td><td class="sub_name"><span style="display: none;">Bio::Phylo::Mediators::TaxaMediator::::remove_link</span>Bio::Phylo::Mediators::TaxaMediator::<a href="Bio-Phylo-Mediators-TaxaMediator-pm-1166-block.html#263">remove_link</a></span></td></tr>
+<tr><td class="c3">0</td><td class="c3">0</td><td class="c3">0</td><td class="c3"><span title="0.0%">0s</span></td><td class="c3"><span title="0.0%">0s</span></td><td class="sub_name"><span style="display: none;">Bio::Phylo::Mediators::TaxaMediator::::set_link</span>Bio::Phylo::Mediators::TaxaMediator::<a href="Bio-Phylo-Mediators-TaxaMediator-pm-1166-block.html#171">set_link</a></span></td></tr>
+<tr><td class="c3">0</td><td class="c3">0</td><td class="c3">0</td><td class="c3"><span title="0.0%">0s</span></td><td class="c3"><span title="0.0%">0s</span></td><td class="sub_name"><span style="display: none;">Bio::Phylo::Mediators::TaxaMediator::::unregister</span>Bio::Phylo::Mediators::TaxaMediator::<a href="Bio-Phylo-Mediators-TaxaMediator-pm-1166-block.html#124">unregister</a></span></td></tr>
+</tbody></table>
+ Call graph for these subroutines as a
+ <a href="http://en.wikipedia.org/wiki/Graphviz">Graphviz</a>
+ <a href="Users-edenc-perl5-lib-perl5-Bio-Phylo-Mediators-TaxaMediator-pm.dot">dot language file</a>.
+
+ <table border="1" cellpadding="0">
+ <thead>
+ <tr><th>Line</th>
+ <th><span title="Number of statements executed">State<br />ments</span></th>
+ <th><span title="Time spend executing statements on the line,
+ excluding time spent executing statements in any called subroutines">Time<br />on line</span></th>
+ <th><span title="Number of subroutines calls">Calls</span></th>
+ <th><span title="Time spent in subroutines called (inclusive)">Time<br />in subs</span></th>
+ <th class="left_indent_header">Code</th>
+ </tr>
+
+ </thead>
+ <tbody>
+ <tr><td class="h"><a name="1"></a>1</td><td></td><td></td><td></td><td></td><td class="s">package Bio::Phylo::Mediators::TaxaMediator;</td></tr>
+<tr><td class="h"><a name="2"></a>2</td><td class="c3">2</td><td class="c3"><span title="Avg 27µs">53µs</span></td><td class="c3">2</td><td class="c3">46µs</td><td class="s"><div class="calls"><div class="calls_in"># spent 39µs (33+7) within Bio::Phylo::Mediators::TaxaMediator::BEGIN@2 which was called:
+# once (33µs+7µs) by Bio::Phylo::IO::BEGIN@4 at <a href="Bio-Phylo-Mediators-TaxaMediator-pm-1166-block.html#2">line 2</a></div></div>use strict;<div class="calls"><div class="calls_out"># spent 39µs making 1 call to <a href="Bio-Phylo-Mediators-TaxaMediator-pm-1166-block.html#2">Bio::Phylo::Mediators::TaxaMediator::BEGIN@2</a>
+# spent 7µs making 1 call to <a href="strict-pm-3-block.html#34">strict::import</a></div></div></td></tr>
+<tr><td class="h"><a name="3"></a>3</td><td class="c3">2</td><td class="c3"><span title="Avg 28µs">56µs</span></td><td class="c3">2</td><td class="c1">152µs</td><td class="s"><div class="calls"><div class="calls_in"># spent 84µs (16+68) within Bio::Phylo::Mediators::TaxaMediator::BEGIN@3 which was called:
+# once (16µs+68µs) by Bio::Phylo::IO::BEGIN@4 at <a href="Bio-Phylo-Mediators-TaxaMediator-pm-1166-block.html#3">line 3</a></div></div>use Scalar::Util qw'weaken';<div class="calls"><div class="calls_out"># spent 84µs making 1 call to <a href="Bio-Phylo-Mediators-TaxaMediator-pm-1166-block.html#3">Bio::Phylo::Mediators::TaxaMediator::BEGIN@3</a>
+# spent 68µs making 1 call to <a href="Exporter-pm-8-block.html#28">Exporter::import</a></div></div></td></tr>
+<tr><td class="h"><a name="4"></a>4</td><td class="c3">2</td><td class="c1"><span title="Avg 32µs">64µs</span></td><td class="c3">2</td><td class="c3">40µs</td><td class="s"><div class="calls"><div class="calls_in"># spent 35µs (30+5) within Bio::Phylo::Mediators::TaxaMediator::BEGIN@4 which was called:
+# once (30µs+5µs) by Bio::Phylo::IO::BEGIN@4 at <a href="Bio-Phylo-Mediators-TaxaMediator-pm-1166-block.html#4">line 4</a></div></div>use Bio::Phylo;<div class="calls"><div class="calls_out"># spent 35µs making 1 call to <a href="Bio-Phylo-Mediators-TaxaMediator-pm-1166-block.html#4">Bio::Phylo::Mediators::TaxaMediator::BEGIN@4</a>
+# spent 5µs making 1 call to <a href="Bio-Phylo-pm-1138-block.html#34">Bio::Phylo::import</a></div></div></td></tr>
+<tr><td class="h"><a name="5"></a>5</td><td class="c3">2</td><td class="c2"><span title="Avg 30µs">60µs</span></td><td class="c3">2</td><td class="c3">87µs</td><td class="s"><div class="calls"><div class="calls_in"># spent 52µs (18+35) within Bio::Phylo::Mediators::TaxaMediator::BEGIN@5 which was called:
+# once (18µs+35µs) by Bio::Phylo::IO::BEGIN@4 at <a href="Bio-Phylo-Mediators-TaxaMediator-pm-1166-block.html#5">line 5</a></div></div>use Bio::Phylo::Util::Exceptions;<div class="calls"><div class="calls_out"># spent 52µs making 1 call to <a href="Bio-Phylo-Mediators-TaxaMediator-pm-1166-block.html#5">Bio::Phylo::Mediators::TaxaMediator::BEGIN@5</a>
+# spent 35µs making 1 call to <a href="Exporter-pm-8-block.html#28">Exporter::import</a></div></div></td></tr>
+<tr><td class="h"><a name="6"></a>6</td><td class="c3">2</td><td class="c0"><span title="Avg 615µs">1.23ms</span></td><td class="c3">2</td><td class="c0">1.27ms</td><td class="s"><div class="calls"><div class="calls_in"># spent 640µs (14+626) within Bio::Phylo::Mediators::TaxaMediator::BEGIN@6 which was called:
+# once (14µs+626µs) by Bio::Phylo::IO::BEGIN@4 at <a href="Bio-Phylo-Mediators-TaxaMediator-pm-1166-block.html#6">line 6</a></div></div>use Bio::Phylo::Util::CONSTANT ':objecttypes';<div class="calls"><div class="calls_out"># spent 640µs making 1 call to <a href="Bio-Phylo-Mediators-TaxaMediator-pm-1166-block.html#6">Bio::Phylo::Mediators::TaxaMediator::BEGIN@6</a>
+# spent 626µs making 1 call to <a href="Exporter-pm-8-block.html#28">Exporter::import</a></div></div></td></tr>
+<tr><td class="h"><a name="7"></a>7</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="8"></a>8</td><td></td><td></td><td></td><td></td><td class="s"># XXX this class only has weak references</td></tr>
+<tr><td class="h"><a name="9"></a>9</td><td></td><td></td><td></td><td></td><td class="s">{</td></tr>
+<tr><td class="h"><a name="10"></a>10</td><td class="c0">4</td><td class="c3"><span title="Avg 2µs">9µs</span></td><td class="c3">1</td><td class="c3">6µs</td><td class="s"> my $logger = Bio::Phylo::get_logger();<div class="calls"><div class="calls_out"> # spent 6µs making 1 call to <a href="Bio-Phylo-pm-1138-block.html#575">Bio::Phylo::get_logger</a></div></div></td></tr>
+<tr><td class="h"><a name="11"></a>11</td><td></td><td></td><td></td><td></td><td class="s"> my $self;</td></tr>
+<tr><td class="h"><a name="12"></a>12</td><td></td><td></td><td></td><td></td><td class="s"> my ( @object, %id_by_type, %one_to_one, %one_to_many );</td></tr>
+<tr><td class="h"><a name="13"></a>13</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="14"></a>14</td><td></td><td></td><td></td><td></td><td class="s">=head1 NAME</td></tr>
+<tr><td class="h"><a name="15"></a>15</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="16"></a>16</td><td></td><td></td><td></td><td></td><td class="s">Bio::Phylo::Mediators::TaxaMediator - Mediator for links between taxa and other objects</td></tr>
+<tr><td class="h"><a name="17"></a>17</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="18"></a>18</td><td></td><td></td><td></td><td></td><td class="s">=head1 SYNOPSIS</td></tr>
+<tr><td class="h"><a name="19"></a>19</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="20"></a>20</td><td></td><td></td><td></td><td></td><td class="s"> # no direct usage</td></tr>
+<tr><td class="h"><a name="21"></a>21</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="22"></a>22</td><td></td><td></td><td></td><td></td><td class="s">=head1 DESCRIPTION</td></tr>
+<tr><td class="h"><a name="23"></a>23</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="24"></a>24</td><td></td><td></td><td></td><td></td><td class="s">This module manages links between taxon objects and other objects linked to </td></tr>
+<tr><td class="h"><a name="25"></a>25</td><td></td><td></td><td></td><td></td><td class="s">them. It is an implementation of the Mediator design pattern (e.g. see </td></tr>
+<tr><td class="h"><a name="26"></a>26</td><td></td><td></td><td></td><td></td><td class="s">L<http://www.atug.com/andypatterns/RM.htm>,</td></tr>
+<tr><td class="h"><a name="27"></a>27</td><td></td><td></td><td></td><td></td><td class="s">L<http://home.earthlink.net/~huston2/dp/mediator.html>).</td></tr>
+<tr><td class="h"><a name="28"></a>28</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="29"></a>29</td><td></td><td></td><td></td><td></td><td class="s">Methods defined in this module are meant only for internal usage by Bio::Phylo.</td></tr>
+<tr><td class="h"><a name="30"></a>30</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="31"></a>31</td><td></td><td></td><td></td><td></td><td class="s">=head1 METHODS</td></tr>
+<tr><td class="h"><a name="32"></a>32</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="33"></a>33</td><td></td><td></td><td></td><td></td><td class="s">=head2 CONSTRUCTOR</td></tr>
+<tr><td class="h"><a name="34"></a>34</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="35"></a>35</td><td></td><td></td><td></td><td></td><td class="s">=over</td></tr>
+<tr><td class="h"><a name="36"></a>36</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="37"></a>37</td><td></td><td></td><td></td><td></td><td class="s">=item new()</td></tr>
+<tr><td class="h"><a name="38"></a>38</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="39"></a>39</td><td></td><td></td><td></td><td></td><td class="s">TaxaMediator constructor.</td></tr>
+<tr><td class="h"><a name="40"></a>40</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="41"></a>41</td><td></td><td></td><td></td><td></td><td class="s"> Type : Constructor</td></tr>
+<tr><td class="h"><a name="42"></a>42</td><td></td><td></td><td></td><td></td><td class="s"> Title : new</td></tr>
+<tr><td class="h"><a name="43"></a>43</td><td></td><td></td><td></td><td></td><td class="s"> Usage : my $mediator = Bio::Phylo::Taxa::TaxaMediator->new;</td></tr>
+<tr><td class="h"><a name="44"></a>44</td><td></td><td></td><td></td><td></td><td class="s"> Function: Instantiates a Bio::Phylo::Taxa::TaxaMediator</td></tr>
+<tr><td class="h"><a name="45"></a>45</td><td></td><td></td><td></td><td></td><td class="s"> object.</td></tr>
+<tr><td class="h"><a name="46"></a>46</td><td></td><td></td><td></td><td></td><td class="s"> Returns : A Bio::Phylo::Taxa::TaxaMediator object (singleton).</td></tr>
+<tr><td class="h"><a name="47"></a>47</td><td></td><td></td><td></td><td></td><td class="s"> Args : None.</td></tr>
+<tr><td class="h"><a name="48"></a>48</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="49"></a>49</td><td></td><td></td><td></td><td></td><td class="s">=cut</td></tr>
+<tr><td class="h"><a name="50"></a>50</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="51"></a>51</td><td></td><td></td><td></td><td></td><td class="s"> sub new {</td></tr>
+<tr><td class="h"><a name="52"></a>52</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="53"></a>53</td><td></td><td></td><td></td><td></td><td class="s"> # could be child class</td></tr>
+<tr><td class="h"><a name="54"></a>54</td><td></td><td></td><td></td><td></td><td class="s"> my $class = shift;</td></tr>
+<tr><td class="h"><a name="55"></a>55</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="56"></a>56</td><td></td><td></td><td></td><td></td><td class="s"> # notify user</td></tr>
+<tr><td class="h"><a name="57"></a>57</td><td></td><td></td><td></td><td></td><td class="s"> $logger->info("constructor called for '$class'");</td></tr>
+<tr><td class="h"><a name="58"></a>58</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="59"></a>59</td><td></td><td></td><td></td><td></td><td class="s"> # singleton class</td></tr>
+<tr><td class="h"><a name="60"></a>60</td><td></td><td></td><td></td><td></td><td class="s"> if ( not $self ) {</td></tr>
+<tr><td class="h"><a name="61"></a>61</td><td></td><td></td><td></td><td></td><td class="s"> $logger->debug("first time instantiation of singleton");</td></tr>
+<tr><td class="h"><a name="62"></a>62</td><td></td><td></td><td></td><td></td><td class="s"> $self = \$class;</td></tr>
+<tr><td class="h"><a name="63"></a>63</td><td></td><td></td><td></td><td></td><td class="s"> bless $self, $class;</td></tr>
+<tr><td class="h"><a name="64"></a>64</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr>
+<tr><td class="h"><a name="65"></a>65</td><td></td><td></td><td></td><td></td><td class="s"> return $self;</td></tr>
+<tr><td class="h"><a name="66"></a>66</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr>
+<tr><td class="h"><a name="67"></a>67</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="68"></a>68</td><td></td><td></td><td></td><td></td><td class="s">=back</td></tr>
+<tr><td class="h"><a name="69"></a>69</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="70"></a>70</td><td></td><td></td><td></td><td></td><td class="s">=head2 METHODS</td></tr>
+<tr><td class="h"><a name="71"></a>71</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="72"></a>72</td><td></td><td></td><td></td><td></td><td class="s">=over</td></tr>
+<tr><td class="h"><a name="73"></a>73</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="74"></a>74</td><td></td><td></td><td></td><td></td><td class="s">=item register()</td></tr>
+<tr><td class="h"><a name="75"></a>75</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="76"></a>76</td><td></td><td></td><td></td><td></td><td class="s">Stores argument in invocant's cache.</td></tr>
+<tr><td class="h"><a name="77"></a>77</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="78"></a>78</td><td></td><td></td><td></td><td></td><td class="s"> Type : Method</td></tr>
+<tr><td class="h"><a name="79"></a>79</td><td></td><td></td><td></td><td></td><td class="s"> Title : register</td></tr>
+<tr><td class="h"><a name="80"></a>80</td><td></td><td></td><td></td><td></td><td class="s"> Usage : $mediator->register( $obj );</td></tr>
+<tr><td class="h"><a name="81"></a>81</td><td></td><td></td><td></td><td></td><td class="s"> Function: Stores an object in mediator's cache, if relevant</td></tr>
+<tr><td class="h"><a name="82"></a>82</td><td></td><td></td><td></td><td></td><td class="s"> Returns : $self</td></tr>
+<tr><td class="h"><a name="83"></a>83</td><td></td><td></td><td></td><td></td><td class="s"> Args : An object, $obj</td></tr>
+<tr><td class="h"><a name="84"></a>84</td><td></td><td></td><td></td><td></td><td class="s"> Comments: This method is called every time an object is instantiated.</td></tr>
+<tr><td class="h"><a name="85"></a>85</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="86"></a>86</td><td></td><td></td><td></td><td></td><td class="s">=cut</td></tr>
+<tr><td class="h"><a name="87"></a>87</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="88"></a>88</td><td></td><td></td><td></td><td></td><td class="s"> sub register {</td></tr>
+<tr><td class="h"><a name="89"></a>89</td><td></td><td></td><td></td><td></td><td class="s"> my ( $self, $obj ) = @_;</td></tr>
+<tr><td class="h"><a name="90"></a>90</td><td></td><td></td><td></td><td></td><td class="s"> my $id = $obj->get_id;</td></tr>
+<tr><td class="h"><a name="91"></a>91</td><td></td><td></td><td></td><td></td><td class="s"> </td></tr>
+<tr><td class="h"><a name="92"></a>92</td><td></td><td></td><td></td><td></td><td class="s"> if ( ref $obj && $obj->can('_type') ) {</td></tr>
+<tr><td class="h"><a name="93"></a>93</td><td></td><td></td><td></td><td></td><td class="s"> my $type = $obj->_type;</td></tr>
+<tr><td class="h"><a name="94"></a>94</td><td></td><td></td><td></td><td></td><td class="s"> </td></tr>
+<tr><td class="h"><a name="95"></a>95</td><td></td><td></td><td></td><td></td><td class="s"> # node, forest, matrix, datum, taxon, taxa</td></tr>
+<tr><td class="h"><a name="96"></a>96</td><td></td><td></td><td></td><td></td><td class="s"> if ( $type == _NODE_ || $type == _TAXON_ || $type == _DATUM_ || $type == _TAXA_ || $type == _FOREST_ || $type == _MATRIX_ ) {</td></tr>
+<tr><td class="h"><a name="97"></a>97</td><td></td><td></td><td></td><td></td><td class="s"> </td></tr>
+<tr><td class="h"><a name="98"></a>98</td><td></td><td></td><td></td><td></td><td class="s"> # index by type</td></tr>
+<tr><td class="h"><a name="99"></a>99</td><td></td><td></td><td></td><td></td><td class="s"> $id_by_type{$type} = {} unless $id_by_type{$type};</td></tr>
+<tr><td class="h"><a name="100"></a>100</td><td></td><td></td><td></td><td></td><td class="s"> $id_by_type{$type}->{$id} = 1;</td></tr>
+<tr><td class="h"><a name="101"></a>101</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="102"></a>102</td><td></td><td></td><td></td><td></td><td class="s"> # store in object cache</td></tr>
+<tr><td class="h"><a name="103"></a>103</td><td></td><td></td><td></td><td></td><td class="s"> $object[$id] = $obj;</td></tr>
+<tr><td class="h"><a name="104"></a>104</td><td></td><td></td><td></td><td></td><td class="s"> weaken $object[$id];</td></tr>
+<tr><td class="h"><a name="105"></a>105</td><td></td><td></td><td></td><td></td><td class="s"> return $self;</td></tr>
+<tr><td class="h"><a name="106"></a>106</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr>
+<tr><td class="h"><a name="107"></a>107</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr>
+<tr><td class="h"><a name="108"></a>108</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr>
+<tr><td class="h"><a name="109"></a>109</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="110"></a>110</td><td></td><td></td><td></td><td></td><td class="s">=item unregister()</td></tr>
+<tr><td class="h"><a name="111"></a>111</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="112"></a>112</td><td></td><td></td><td></td><td></td><td class="s">Removes argument from invocant's cache.</td></tr>
+<tr><td class="h"><a name="113"></a>113</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="114"></a>114</td><td></td><td></td><td></td><td></td><td class="s"> Type : Method</td></tr>
+<tr><td class="h"><a name="115"></a>115</td><td></td><td></td><td></td><td></td><td class="s"> Title : unregister</td></tr>
+<tr><td class="h"><a name="116"></a>116</td><td></td><td></td><td></td><td></td><td class="s"> Usage : $mediator->unregister( $obj );</td></tr>
+<tr><td class="h"><a name="117"></a>117</td><td></td><td></td><td></td><td></td><td class="s"> Function: Cleans up mediator's cache of $obj and $obj's relations</td></tr>
+<tr><td class="h"><a name="118"></a>118</td><td></td><td></td><td></td><td></td><td class="s"> Returns : $self</td></tr>
+<tr><td class="h"><a name="119"></a>119</td><td></td><td></td><td></td><td></td><td class="s"> Args : An object, $obj</td></tr>
+<tr><td class="h"><a name="120"></a>120</td><td></td><td></td><td></td><td></td><td class="s"> Comments: This method is called every time an object is destroyed.</td></tr>
+<tr><td class="h"><a name="121"></a>121</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="122"></a>122</td><td></td><td></td><td></td><td></td><td class="s">=cut</td></tr>
+<tr><td class="h"><a name="123"></a>123</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="124"></a>124</td><td></td><td></td><td></td><td></td><td class="s"> sub unregister {</td></tr>
+<tr><td class="h"><a name="125"></a>125</td><td></td><td></td><td></td><td></td><td class="s"> my ( $self, $obj ) = @_;</td></tr>
+<tr><td class="h"><a name="126"></a>126</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="127"></a>127</td><td></td><td></td><td></td><td></td><td class="s"> my $id = $obj->get_id;</td></tr>
+<tr><td class="h"><a name="128"></a>128</td><td></td><td></td><td></td><td></td><td class="s"> if ( defined $id ) {</td></tr>
+<tr><td class="h"><a name="129"></a>129</td><td></td><td></td><td></td><td></td><td class="s"> </td></tr>
+<tr><td class="h"><a name="130"></a>130</td><td></td><td></td><td></td><td></td><td class="s"> # remove from object cache</td></tr>
+<tr><td class="h"><a name="131"></a>131</td><td></td><td></td><td></td><td></td><td class="s"> if ( exists $object[$id] ) {</td></tr>
+<tr><td class="h"><a name="132"></a>132</td><td></td><td></td><td></td><td></td><td class="s"> delete $object[$id];</td></tr>
+<tr><td class="h"><a name="133"></a>133</td><td></td><td></td><td></td><td></td><td class="s"> } </td></tr>
+<tr><td class="h"><a name="134"></a>134</td><td></td><td></td><td></td><td></td><td class="s"> </td></tr>
+<tr><td class="h"><a name="135"></a>135</td><td></td><td></td><td></td><td></td><td class="s"> # remove from one-to-one mapping</td></tr>
+<tr><td class="h"><a name="136"></a>136</td><td></td><td></td><td></td><td></td><td class="s"> if ( exists $one_to_one{$id} ) {</td></tr>
+<tr><td class="h"><a name="137"></a>137</td><td></td><td></td><td></td><td></td><td class="s"> delete $one_to_one{$id};</td></tr>
+<tr><td class="h"><a name="138"></a>138</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr>
+<tr><td class="h"><a name="139"></a>139</td><td></td><td></td><td></td><td></td><td class="s"> </td></tr>
+<tr><td class="h"><a name="140"></a>140</td><td></td><td></td><td></td><td></td><td class="s"> # remove from one-to-many mapping</td></tr>
+<tr><td class="h"><a name="141"></a>141</td><td></td><td></td><td></td><td></td><td class="s"> if ( exists $one_to_many{$id} ) {</td></tr>
+<tr><td class="h"><a name="142"></a>142</td><td></td><td></td><td></td><td></td><td class="s"> delete $one_to_many{$id}; </td></tr>
+<tr><td class="h"><a name="143"></a>143</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr>
+<tr><td class="h"><a name="144"></a>144</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr>
+<tr><td class="h"><a name="145"></a>145</td><td></td><td></td><td></td><td></td><td class="s"> return $self;</td></tr>
+<tr><td class="h"><a name="146"></a>146</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr>
+<tr><td class="h"><a name="147"></a>147</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="148"></a>148</td><td></td><td></td><td></td><td></td><td class="s">=item set_link()</td></tr>
+<tr><td class="h"><a name="149"></a>149</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="150"></a>150</td><td></td><td></td><td></td><td></td><td class="s">Creates link between objects.</td></tr>
+<tr><td class="h"><a name="151"></a>151</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="152"></a>152</td><td></td><td></td><td></td><td></td><td class="s"> Type : Method</td></tr>
+<tr><td class="h"><a name="153"></a>153</td><td></td><td></td><td></td><td></td><td class="s"> Title : set_link</td></tr>
+<tr><td class="h"><a name="154"></a>154</td><td></td><td></td><td></td><td></td><td class="s"> Usage : $mediator->set_link( -one => $obj1, -many => $obj2 );</td></tr>
+<tr><td class="h"><a name="155"></a>155</td><td></td><td></td><td></td><td></td><td class="s"> Function: Creates link between objects</td></tr>
+<tr><td class="h"><a name="156"></a>156</td><td></td><td></td><td></td><td></td><td class="s"> Returns : $self</td></tr>
+<tr><td class="h"><a name="157"></a>157</td><td></td><td></td><td></td><td></td><td class="s"> Args : -one => $obj1 (source of a one-to-many relationship)</td></tr>
+<tr><td class="h"><a name="158"></a>158</td><td></td><td></td><td></td><td></td><td class="s"> -many => $obj2 (target of a one-to-many relationship)</td></tr>
+<tr><td class="h"><a name="159"></a>159</td><td></td><td></td><td></td><td></td><td class="s"> Comments: This method is called from within, for example, set_taxa</td></tr>
+<tr><td class="h"><a name="160"></a>160</td><td></td><td></td><td></td><td></td><td class="s"> method calls. A call like $taxa->set_matrix( $matrix ),</td></tr>
+<tr><td class="h"><a name="161"></a>161</td><td></td><td></td><td></td><td></td><td class="s"> and likewise a call like $matrix->set_taxa( $taxa ), are </td></tr>
+<tr><td class="h"><a name="162"></a>162</td><td></td><td></td><td></td><td></td><td class="s"> both internally rerouted to:</td></tr>
+<tr><td class="h"><a name="163"></a>163</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="164"></a>164</td><td></td><td></td><td></td><td></td><td class="s"> $mediator->set_link( </td></tr>
+<tr><td class="h"><a name="165"></a>165</td><td></td><td></td><td></td><td></td><td class="s"> -one => $taxa, </td></tr>
+<tr><td class="h"><a name="166"></a>166</td><td></td><td></td><td></td><td></td><td class="s"> -many => $matrix </td></tr>
+<tr><td class="h"><a name="167"></a>167</td><td></td><td></td><td></td><td></td><td class="s"> );</td></tr>
+<tr><td class="h"><a name="168"></a>168</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="169"></a>169</td><td></td><td></td><td></td><td></td><td class="s">=cut</td></tr>
+<tr><td class="h"><a name="170"></a>170</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="171"></a>171</td><td></td><td></td><td></td><td></td><td class="s"> sub set_link {</td></tr>
+<tr><td class="h"><a name="172"></a>172</td><td></td><td></td><td></td><td></td><td class="s"> my $self = shift;</td></tr>
+<tr><td class="h"><a name="173"></a>173</td><td></td><td></td><td></td><td></td><td class="s"> my %opt = @_;</td></tr>
+<tr><td class="h"><a name="174"></a>174</td><td></td><td></td><td></td><td></td><td class="s"> my ( $one, $many ) = ( $opt{'-one'}, $opt{'-many'} );</td></tr>
+<tr><td class="h"><a name="175"></a>175</td><td></td><td></td><td></td><td></td><td class="s"> my ( $one_id, $many_id ) = ( $one->get_id, $many->get_id );</td></tr>
+<tr><td class="h"><a name="176"></a>176</td><td></td><td></td><td></td><td></td><td class="s"> $one_to_one{$many_id} = $one_id;</td></tr>
+<tr><td class="h"><a name="177"></a>177</td><td></td><td></td><td></td><td></td><td class="s"> $one_to_many{$one_id} = {} unless $one_to_many{$one_id};</td></tr>
+<tr><td class="h"><a name="178"></a>178</td><td></td><td></td><td></td><td></td><td class="s"> $one_to_many{$one_id}->{$many_id} = $many->_type;</td></tr>
+<tr><td class="h"><a name="179"></a>179</td><td></td><td></td><td></td><td></td><td class="s"> return $self;</td></tr>
+<tr><td class="h"><a name="180"></a>180</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr>
+<tr><td class="h"><a name="181"></a>181</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="182"></a>182</td><td></td><td></td><td></td><td></td><td class="s">=item get_link()</td></tr>
+<tr><td class="h"><a name="183"></a>183</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="184"></a>184</td><td></td><td></td><td></td><td></td><td class="s">Retrieves link between objects.</td></tr>
+<tr><td class="h"><a name="185"></a>185</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="186"></a>186</td><td></td><td></td><td></td><td></td><td class="s"> Type : Method</td></tr>
+<tr><td class="h"><a name="187"></a>187</td><td></td><td></td><td></td><td></td><td class="s"> Title : get_link</td></tr>
+<tr><td class="h"><a name="188"></a>188</td><td></td><td></td><td></td><td></td><td class="s"> Usage : $mediator->get_link( </td></tr>
+<tr><td class="h"><a name="189"></a>189</td><td></td><td></td><td></td><td></td><td class="s"> -source => $obj, </td></tr>
+<tr><td class="h"><a name="190"></a>190</td><td></td><td></td><td></td><td></td><td class="s"> -type => _CONSTANT_,</td></tr>
+<tr><td class="h"><a name="191"></a>191</td><td></td><td></td><td></td><td></td><td class="s"> );</td></tr>
+<tr><td class="h"><a name="192"></a>192</td><td></td><td></td><td></td><td></td><td class="s"> Function: Retrieves link between objects</td></tr>
+<tr><td class="h"><a name="193"></a>193</td><td></td><td></td><td></td><td></td><td class="s"> Returns : Linked object</td></tr>
+<tr><td class="h"><a name="194"></a>194</td><td></td><td></td><td></td><td></td><td class="s"> Args : -source => $obj (required, the source of the link)</td></tr>
+<tr><td class="h"><a name="195"></a>195</td><td></td><td></td><td></td><td></td><td class="s"> -type => a constant from Bio::Phylo::Util::CONSTANT</td></tr>
+<tr><td class="h"><a name="196"></a>196</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="197"></a>197</td><td></td><td></td><td></td><td></td><td class="s"> (-type is optional, used to filter returned results in </td></tr>
+<tr><td class="h"><a name="198"></a>198</td><td></td><td></td><td></td><td></td><td class="s"> one-to-many query).</td></tr>
+<tr><td class="h"><a name="199"></a>199</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="200"></a>200</td><td></td><td></td><td></td><td></td><td class="s"> Comments: This method is called from within, for example, get_taxa</td></tr>
+<tr><td class="h"><a name="201"></a>201</td><td></td><td></td><td></td><td></td><td class="s"> method calls. A call like $matrix->get_taxa()</td></tr>
+<tr><td class="h"><a name="202"></a>202</td><td></td><td></td><td></td><td></td><td class="s"> and likewise a call like $forest->get_taxa(), are </td></tr>
+<tr><td class="h"><a name="203"></a>203</td><td></td><td></td><td></td><td></td><td class="s"> both internally rerouted to:</td></tr>
+<tr><td class="h"><a name="204"></a>204</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="205"></a>205</td><td></td><td></td><td></td><td></td><td class="s"> $mediator->get_link( </td></tr>
+<tr><td class="h"><a name="206"></a>206</td><td></td><td></td><td></td><td></td><td class="s"> -source => $self # e.g. $matrix or $forest </td></tr>
+<tr><td class="h"><a name="207"></a>207</td><td></td><td></td><td></td><td></td><td class="s"> );</td></tr>
+<tr><td class="h"><a name="208"></a>208</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="209"></a>209</td><td></td><td></td><td></td><td></td><td class="s"> A call like $taxa->get_matrices() is rerouted to:</td></tr>
+<tr><td class="h"><a name="210"></a>210</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="211"></a>211</td><td></td><td></td><td></td><td></td><td class="s"> $mediator->get_link( -source => $taxa, -type => _MATRIX_ );</td></tr>
+<tr><td class="h"><a name="212"></a>212</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="213"></a>213</td><td></td><td></td><td></td><td></td><td class="s">=cut</td></tr>
+<tr><td class="h"><a name="214"></a>214</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="215"></a>215</td><td></td><td></td><td></td><td></td><td class="s"> sub get_link {</td></tr>
+<tr><td class="h"><a name="216"></a>216</td><td></td><td></td><td></td><td></td><td class="s"> my $self = shift;</td></tr>
+<tr><td class="h"><a name="217"></a>217</td><td></td><td></td><td></td><td></td><td class="s"> my %opt = @_;</td></tr>
+<tr><td class="h"><a name="218"></a>218</td><td></td><td></td><td></td><td></td><td class="s"> my $id = $opt{'-source'}->get_id;</td></tr>
+<tr><td class="h"><a name="219"></a>219</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="220"></a>220</td><td></td><td></td><td></td><td></td><td class="s"> # have to get many objects,</td></tr>
+<tr><td class="h"><a name="221"></a>221</td><td></td><td></td><td></td><td></td><td class="s"> # i.e. source was a taxon/taxa</td></tr>
+<tr><td class="h"><a name="222"></a>222</td><td></td><td></td><td></td><td></td><td class="s"> if ( defined $opt{'-type'} ) { </td></tr>
+<tr><td class="h"><a name="223"></a>223</td><td></td><td></td><td></td><td></td><td class="s"> my $type = $opt{'-type'};</td></tr>
+<tr><td class="h"><a name="224"></a>224</td><td></td><td></td><td></td><td></td><td class="s"> my @ids = grep { $one_to_many{$id}->{$_} == $type } keys %{ $one_to_many{$id} };</td></tr>
+<tr><td class="h"><a name="225"></a>225</td><td></td><td></td><td></td><td></td><td class="s"> my @result = @object[@ids];</td></tr>
+<tr><td class="h"><a name="226"></a>226</td><td></td><td></td><td></td><td></td><td class="s"> return \@result;</td></tr>
+<tr><td class="h"><a name="227"></a>227</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr>
+<tr><td class="h"><a name="228"></a>228</td><td></td><td></td><td></td><td></td><td class="s"> </td></tr>
+<tr><td class="h"><a name="229"></a>229</td><td></td><td></td><td></td><td></td><td class="s"> # have to get one object, i.e. source</td></tr>
+<tr><td class="h"><a name="230"></a>230</td><td></td><td></td><td></td><td></td><td class="s"> # was something that links to taxon/taxa</td></tr>
+<tr><td class="h"><a name="231"></a>231</td><td></td><td></td><td></td><td></td><td class="s"> else {</td></tr>
+<tr><td class="h"><a name="232"></a>232</td><td></td><td></td><td></td><td></td><td class="s"> return exists $one_to_one{$id} ? $object[$one_to_one{$id}] : undef;</td></tr>
+<tr><td class="h"><a name="233"></a>233</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr>
+<tr><td class="h"><a name="234"></a>234</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr>
+<tr><td class="h"><a name="235"></a>235</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="236"></a>236</td><td></td><td></td><td></td><td></td><td class="s">=item remove_link()</td></tr>
+<tr><td class="h"><a name="237"></a>237</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="238"></a>238</td><td></td><td></td><td></td><td></td><td class="s">Removes link between objects.</td></tr>
+<tr><td class="h"><a name="239"></a>239</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="240"></a>240</td><td></td><td></td><td></td><td></td><td class="s"> Type : Method</td></tr>
+<tr><td class="h"><a name="241"></a>241</td><td></td><td></td><td></td><td></td><td class="s"> Title : remove_link</td></tr>
+<tr><td class="h"><a name="242"></a>242</td><td></td><td></td><td></td><td></td><td class="s"> Usage : $mediator->remove_link( -one => $obj1, -many => $obj2 );</td></tr>
+<tr><td class="h"><a name="243"></a>243</td><td></td><td></td><td></td><td></td><td class="s"> Function: Removes link between objects</td></tr>
+<tr><td class="h"><a name="244"></a>244</td><td></td><td></td><td></td><td></td><td class="s"> Returns : $self</td></tr>
+<tr><td class="h"><a name="245"></a>245</td><td></td><td></td><td></td><td></td><td class="s"> Args : -one => $obj1 (source of a one-to-many relationship)</td></tr>
+<tr><td class="h"><a name="246"></a>246</td><td></td><td></td><td></td><td></td><td class="s"> -many => $obj2 (target of a one-to-many relationship)</td></tr>
+<tr><td class="h"><a name="247"></a>247</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="248"></a>248</td><td></td><td></td><td></td><td></td><td class="s"> (-many argument is optional)</td></tr>
+<tr><td class="h"><a name="249"></a>249</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="250"></a>250</td><td></td><td></td><td></td><td></td><td class="s"> Comments: This method is called from within, for example, </td></tr>
+<tr><td class="h"><a name="251"></a>251</td><td></td><td></td><td></td><td></td><td class="s"> unset_taxa method calls. A call like $matrix->unset_taxa() </td></tr>
+<tr><td class="h"><a name="252"></a>252</td><td></td><td></td><td></td><td></td><td class="s"> is rerouted to:</td></tr>
+<tr><td class="h"><a name="253"></a>253</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="254"></a>254</td><td></td><td></td><td></td><td></td><td class="s"> $mediator->remove_link( -many => $matrix );</td></tr>
+<tr><td class="h"><a name="255"></a>255</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="256"></a>256</td><td></td><td></td><td></td><td></td><td class="s"> A call like $taxa->unset_matrix( $matrix ); is rerouted to:</td></tr>
+<tr><td class="h"><a name="257"></a>257</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="258"></a>258</td><td></td><td></td><td></td><td></td><td class="s"> $mediator->remove_link( -one => $taxa, -many => $matrix );</td></tr>
+<tr><td class="h"><a name="259"></a>259</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="260"></a>260</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="261"></a>261</td><td></td><td></td><td></td><td></td><td class="s">=cut</td></tr>
+<tr><td class="h"><a name="262"></a>262</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="263"></a>263</td><td></td><td></td><td></td><td></td><td class="s"> sub remove_link {</td></tr>
+<tr><td class="h"><a name="264"></a>264</td><td></td><td></td><td></td><td></td><td class="s"> my $self = shift;</td></tr>
+<tr><td class="h"><a name="265"></a>265</td><td></td><td></td><td></td><td></td><td class="s"> my %opt = @_;</td></tr>
+<tr><td class="h"><a name="266"></a>266</td><td></td><td></td><td></td><td></td><td class="s"> my ( $one, $many ) = ( $opt{'-one'}, $opt{'-many'} );</td></tr>
+<tr><td class="h"><a name="267"></a>267</td><td></td><td></td><td></td><td></td><td class="s"> my $many_id = $many->get_id;</td></tr>
+<tr><td class="h"><a name="268"></a>268</td><td></td><td></td><td></td><td></td><td class="s"> my $one_id;</td></tr>
+<tr><td class="h"><a name="269"></a>269</td><td></td><td></td><td></td><td></td><td class="s"> if ($one) {</td></tr>
+<tr><td class="h"><a name="270"></a>270</td><td></td><td></td><td></td><td></td><td class="s"> $one_id = $one->get_id; </td></tr>
+<tr><td class="h"><a name="271"></a>271</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr>
+<tr><td class="h"><a name="272"></a>272</td><td></td><td></td><td></td><td></td><td class="s"> else {</td></tr>
+<tr><td class="h"><a name="273"></a>273</td><td></td><td></td><td></td><td></td><td class="s"> my $target = $self->get_link( '-source' => $many );</td></tr>
+<tr><td class="h"><a name="274"></a>274</td><td></td><td></td><td></td><td></td><td class="s"> $one_id = $target->get_id if $target;</td></tr>
+<tr><td class="h"><a name="275"></a>275</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr>
+<tr><td class="h"><a name="276"></a>276</td><td></td><td></td><td></td><td></td><td class="s"> delete $one_to_many{$one_id}->{$many_id} if $one_to_many{$one_id}; </td></tr>
+<tr><td class="h"><a name="277"></a>277</td><td></td><td></td><td></td><td></td><td class="s"> delete $one_to_one{$many_id};</td></tr>
+<tr><td class="h"><a name="278"></a>278</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr>
+<tr><td class="h"><a name="279"></a>279</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="280"></a>280</td><td></td><td></td><td></td><td></td><td class="s">=back</td></tr>
+<tr><td class="h"><a name="281"></a>281</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="282"></a>282</td><td></td><td></td><td></td><td></td><td class="s">=head1 SEE ALSO</td></tr>
+<tr><td class="h"><a name="283"></a>283</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="284"></a>284</td><td></td><td></td><td></td><td></td><td class="s">There is a mailing list at L<https://groups.google.com/forum/#!forum/bio-phylo> </td></tr>
+<tr><td class="h"><a name="285"></a>285</td><td></td><td></td><td></td><td></td><td class="s">for any user or developer questions and discussions.</td></tr>
+<tr><td class="h"><a name="286"></a>286</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="287"></a>287</td><td></td><td></td><td></td><td></td><td class="s">=over</td></tr>
+<tr><td class="h"><a name="288"></a>288</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="289"></a>289</td><td></td><td></td><td></td><td></td><td class="s">=item L<Bio::Phylo::Manual></td></tr>
+<tr><td class="h"><a name="290"></a>290</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="291"></a>291</td><td></td><td></td><td></td><td></td><td class="s">Also see the manual: L<Bio::Phylo::Manual> and L<http://rutgervos.blogspot.com>.</td></tr>
+<tr><td class="h"><a name="292"></a>292</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="293"></a>293</td><td></td><td></td><td></td><td></td><td class="s">=back</td></tr>
+<tr><td class="h"><a name="294"></a>294</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="295"></a>295</td><td></td><td></td><td></td><td></td><td class="s">=head1 CITATION</td></tr>
+<tr><td class="h"><a name="296"></a>296</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="297"></a>297</td><td></td><td></td><td></td><td></td><td class="s">If you use Bio::Phylo in published research, please cite it:</td></tr>
+<tr><td class="h"><a name="298"></a>298</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="299"></a>299</td><td></td><td></td><td></td><td></td><td class="s">B<Rutger A Vos>, B<Jason Caravas>, B<Klaas Hartmann>, B<Mark A Jensen></td></tr>
+<tr><td class="h"><a name="300"></a>300</td><td></td><td></td><td></td><td></td><td class="s">and B<Chase Miller>, 2011. Bio::Phylo - phyloinformatic analysis using Perl.</td></tr>
+<tr><td class="h"><a name="301"></a>301</td><td></td><td></td><td></td><td></td><td class="s">I<BMC Bioinformatics> B<12>:63.</td></tr>
+<tr><td class="h"><a name="302"></a>302</td><td></td><td></td><td></td><td></td><td class="s">L<http://dx.doi.org/10.1186/1471-2105-12-63></td></tr>
+<tr><td class="h"><a name="303"></a>303</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="304"></a>304</td><td></td><td></td><td></td><td></td><td class="s">=cut</td></tr>
+<tr><td class="h"><a name="305"></a>305</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="306"></a>306</td><td></td><td></td><td></td><td></td><td class="s">}</td></tr>
+<tr><td class="h"><a name="307"></a>307</td><td class="c3">1</td><td class="c3"><span title="Avg 11µs">11µs</span></td><td></td><td></td><td class="s">1;</td></tr>
+</tbody></table></div>
+
+ <script type="text/javascript"> $(document).ready(function() {
+
+ $("#subs_table").tablesorter({
+ sortList: [[3,1]],
+ headers: {
+ 3: { sorter: 'fmt_time' },
+ 4: { sorter: 'fmt_time' }
+ }
+ });
+
+ } ); </script>
+
+ <div class="footer">Report produced by the
+ <a href="http://search.cpan.org/dist/Devel-NYTProf/">NYTProf 4.06</a>
+ Perl profiler, developed by
+ <a href="http://www.linkedin.com/in/timbunce">Tim Bunce</a> and
+ <a href="http://code.nytimes.com">Adam Kaplan</a>.
+ </div>
+ <br /><br /><br /><br /><br /><br /><br /><br /><br /><br />
+ </body></html>
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