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20 | $.tablesorter.addParser({ |
21 | id: 'fmt_time', // name of this parser |
22 | is: function(s) { |
23 | return false; // return false so this parser is not auto detected |
24 | }, |
25 | format: function(orig) { // format data for normalization |
26 | // console.log(orig); |
27 | val = orig.replace(/ns/,''); |
28 | if (val != orig) { return val / (1000*1000*1000); } |
29 | val = orig.replace(/µs/,''); /* XXX use µ ? */ |
30 | if (val != orig) { return val / (1000*1000); } |
31 | var val = orig.replace(/ms/,''); |
32 | if (val != orig) { return val / (1000); } |
33 | var val = orig.replace(/s/,''); |
34 | if (val != orig) { return val; } |
35 | if (orig == '0') { return orig; } |
36 | console.log('no match for fmt_time of '.concat(orig)); |
37 | return orig; |
38 | }, |
39 | type: 'numeric' // set type, either numeric or text |
40 | }); |
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50 | <span class="siteTitle">NYTProf Performance Profile</span> |
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56 | <span class="siteTitle"> </span> |
57 | <span class="siteSubtitle">Run on Thu May 31 16:29:39 2012<br />Reported on Thu May 31 16:35:04 2012</span> |
58 | </div> |
59 | <div style="position: absolute; left: 0px; top: 0%; width: 100%; height: 101%; z-index: -1; background-color: rgb(17, 136, 255); "></div> |
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103 | <div style="position: absolute; left: 0px; top: 88%; width: 100%; height: 13%; z-index: -1; background-color: rgb(2, 76, 195); "></div> |
104 | <div style="position: absolute; left: 0px; top: 90%; width: 100%; height: 11%; z-index: -1; background-color: rgb(1, 74, 193); "></div> |
105 | <div style="position: absolute; left: 0px; top: 92%; width: 100%; height: 9%; z-index: -1; background-color: rgb(1, 73, 192); "></div> |
106 | <div style="position: absolute; left: 0px; top: 94%; width: 100%; height: 7%; z-index: -1; background-color: rgb(1, 72, 191); "></div> |
107 | <div style="position: absolute; left: 0px; top: 96%; width: 100%; height: 5%; z-index: -1; background-color: rgb(0, 70, 189); "></div> |
108 | <div style="position: absolute; left: 0px; top: 98%; width: 100%; height: 3%; z-index: -1; background-color: rgb(0, 69, 188); "></div> |
109 | <div style="position: absolute; left: 0px; top: 100%; width: 100%; height: 1%; z-index: -1; background-color: rgb(0, 68, 187); "></div> |
110 | </div> |
111 | |
112 | <div class="body_content"><br /> |
113 | <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> |
114 | <tr><td class="h">Statements</td><td align="left">Executed 15 statements in 747µs</td></tr></table> |
115 | |
116 | <table id="subs_table" border="1" cellpadding="0" class="tablesorter"> |
117 | <caption>Subroutines</caption> |
118 | <thead> |
119 | <tr> |
120 | <th>Calls</th> |
121 | <th><span title="Number of Places sub is called from">P</span></th> |
122 | <th><span title="Number of Files sub is called from">F</span></th> |
123 | <th>Exclusive<br />Time</th> |
124 | <th>Inclusive<br />Time</th> |
125 | <th>Subroutine</th> |
126 | </tr> |
127 | </thead> |
128 | <tbody> |
129 | <tr><td class="c3">1</td><td class="c3">1</td><td class="c3">1</td><td class="c0"><span title="0.0%">16µs</span></td><td class="c3"><span title="0.0%">18µs</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-sub.html#2">BEGIN@2</a></span></td></tr> |
130 | <tr><td class="c3">1</td><td class="c3">1</td><td class="c3">1</td><td class="c2"><span title="0.0%">9µs</span></td><td class="c3"><span title="0.0%">12µs</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-sub.html#4">BEGIN@4</a></span></td></tr> |
131 | <tr><td class="c3">1</td><td class="c3">1</td><td class="c3">1</td><td class="c3"><span title="0.0%">9µs</span></td><td class="c3"><span title="0.0%">24µs</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-sub.html#5">BEGIN@5</a></span></td></tr> |
132 | <tr><td class="c3">1</td><td class="c3">1</td><td class="c3">1</td><td class="c3"><span title="0.0%">9µs</span></td><td class="c1"><span title="0.0%">46µs</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-sub.html#3">BEGIN@3</a></span></td></tr> |
133 | <tr><td class="c3">1</td><td class="c3">1</td><td class="c3">1</td><td class="c3"><span title="0.0%">8µs</span></td><td class="c0"><span title="0.0%">358µs</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-sub.html#6">BEGIN@6</a></span></td></tr> |
134 | <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-sub.html#215">get_link</a></span></td></tr> |
135 | <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-sub.html#51">new</a></span></td></tr> |
136 | <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-sub.html#88">register</a></span></td></tr> |
137 | <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-sub.html#263">remove_link</a></span></td></tr> |
138 | <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-sub.html#171">set_link</a></span></td></tr> |
139 | <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-sub.html#124">unregister</a></span></td></tr> |
140 | </tbody></table> |
141 | Call graph for these subroutines as a |
142 | <a href="http://en.wikipedia.org/wiki/Graphviz">Graphviz</a> |
143 | <a href="Users-edenc-perl5-lib-perl5-Bio-Phylo-Mediators-TaxaMediator-pm.dot">dot language file</a>. |
144 | |
145 | <table border="1" cellpadding="0"> |
146 | <thead> |
147 | <tr><th>Line</th> |
148 | <th><span title="Number of statements executed">State<br />ments</span></th> |
149 | <th><span title="Time spend executing statements on the line, |
150 | excluding time spent executing statements in any called subroutines">Time<br />on line</span></th> |
151 | <th><span title="Number of subroutines calls">Calls</span></th> |
152 | <th><span title="Time spent in subroutines called (inclusive)">Time<br />in subs</span></th> |
153 | <th class="left_indent_header">Code</th> |
154 | </tr> |
155 | |
156 | </thead> |
157 | <tbody> |
158 | <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> |
159 | <tr><td class="h"><a name="2"></a>2</td><td class="c3">2</td><td class="c3"><span title="Avg 13µs">26µs</span></td><td class="c3">2</td><td class="c3">21µs</td><td class="s"><div class="calls"><div class="calls_in"># spent 18µs (16+3) within Bio::Phylo::Mediators::TaxaMediator::BEGIN@2 which was called: |
160 | # once (16µs+3µs) by Bio::Phylo::IO::BEGIN@4 at <a href="Bio-Phylo-Mediators-TaxaMediator-pm-1166-sub.html#2">line 2</a></div></div>use strict;<div class="calls"><div class="calls_out"># spent 18µs making 1 call to <a href="Bio-Phylo-Mediators-TaxaMediator-pm-1166-sub.html#2">Bio::Phylo::Mediators::TaxaMediator::BEGIN@2</a> |
161 | # spent 3µs making 1 call to <a href="strict-pm-3-sub.html#34">strict::import</a></div></div></td></tr> |
162 | <tr><td class="h"><a name="3"></a>3</td><td class="c3">2</td><td class="c3"><span title="Avg 13µs">27µs</span></td><td class="c3">2</td><td class="c1">83µs</td><td class="s"><div class="calls"><div class="calls_in"># spent 46µs (9+37) within Bio::Phylo::Mediators::TaxaMediator::BEGIN@3 which was called: |
163 | # once (9µs+37µs) by Bio::Phylo::IO::BEGIN@4 at <a href="Bio-Phylo-Mediators-TaxaMediator-pm-1166-sub.html#3">line 3</a></div></div>use Scalar::Util qw'weaken';<div class="calls"><div class="calls_out"># spent 46µs making 1 call to <a href="Bio-Phylo-Mediators-TaxaMediator-pm-1166-sub.html#3">Bio::Phylo::Mediators::TaxaMediator::BEGIN@3</a> |
164 | # spent 37µs making 1 call to <a href="Exporter-pm-8-sub.html#28">Exporter::import</a></div></div></td></tr> |
165 | <tr><td class="h"><a name="4"></a>4</td><td class="c3">2</td><td class="c3"><span title="Avg 14µs">28µs</span></td><td class="c3">2</td><td class="c3">16µs</td><td class="s"><div class="calls"><div class="calls_in"># spent 12µs (9+3) within Bio::Phylo::Mediators::TaxaMediator::BEGIN@4 which was called: |
166 | # once (9µs+3µs) by Bio::Phylo::IO::BEGIN@4 at <a href="Bio-Phylo-Mediators-TaxaMediator-pm-1166-sub.html#4">line 4</a></div></div>use Bio::Phylo;<div class="calls"><div class="calls_out"># spent 12µs making 1 call to <a href="Bio-Phylo-Mediators-TaxaMediator-pm-1166-sub.html#4">Bio::Phylo::Mediators::TaxaMediator::BEGIN@4</a> |
167 | # spent 3µs making 1 call to <a href="Bio-Phylo-pm-1138-sub.html#34">Bio::Phylo::import</a></div></div></td></tr> |
168 | <tr><td class="h"><a name="5"></a>5</td><td class="c3">2</td><td class="c3"><span title="Avg 12µs">25µs</span></td><td class="c3">2</td><td class="c3">38µs</td><td class="s"><div class="calls"><div class="calls_in"># spent 24µs (9+15) within Bio::Phylo::Mediators::TaxaMediator::BEGIN@5 which was called: |
169 | # once (9µs+15µs) by Bio::Phylo::IO::BEGIN@4 at <a href="Bio-Phylo-Mediators-TaxaMediator-pm-1166-sub.html#5">line 5</a></div></div>use Bio::Phylo::Util::Exceptions;<div class="calls"><div class="calls_out"># spent 24µs making 1 call to <a href="Bio-Phylo-Mediators-TaxaMediator-pm-1166-sub.html#5">Bio::Phylo::Mediators::TaxaMediator::BEGIN@5</a> |
170 | # spent 15µs making 1 call to <a href="Exporter-pm-8-sub.html#28">Exporter::import</a></div></div></td></tr> |
171 | <tr><td class="h"><a name="6"></a>6</td><td class="c3">2</td><td class="c0"><span title="Avg 315µs">630µs</span></td><td class="c3">2</td><td class="c0">709µs</td><td class="s"><div class="calls"><div class="calls_in"># spent 358µs (8+351) within Bio::Phylo::Mediators::TaxaMediator::BEGIN@6 which was called: |
172 | # once (8µs+351µs) by Bio::Phylo::IO::BEGIN@4 at <a href="Bio-Phylo-Mediators-TaxaMediator-pm-1166-sub.html#6">line 6</a></div></div>use Bio::Phylo::Util::CONSTANT ':objecttypes';<div class="calls"><div class="calls_out"># spent 358µs making 1 call to <a href="Bio-Phylo-Mediators-TaxaMediator-pm-1166-sub.html#6">Bio::Phylo::Mediators::TaxaMediator::BEGIN@6</a> |
173 | # spent 351µs making 1 call to <a href="Exporter-pm-8-sub.html#28">Exporter::import</a></div></div></td></tr> |
174 | <tr><td class="h"><a name="7"></a>7</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
175 | <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> |
176 | <tr><td class="h"><a name="9"></a>9</td><td></td><td></td><td></td><td></td><td class="s">{</td></tr> |
177 | <tr><td class="h"><a name="10"></a>10</td><td class="c3">2</td><td class="c3"><span title="Avg 2µs">3µs</span></td><td class="c3">1</td><td class="c3">3µs</td><td class="s"> my $logger = Bio::Phylo::get_logger();<div class="calls"><div class="calls_out"> # spent 3µs making 1 call to <a href="Bio-Phylo-pm-1138-sub.html#575">Bio::Phylo::get_logger</a></div></div></td></tr> |
178 | <tr><td class="h"><a name="11"></a>11</td><td class="c3">1</td><td class="c3"><span title="Avg 100ns">100ns</span></td><td></td><td></td><td class="s"> my $self;</td></tr> |
179 | <tr><td class="h"><a name="12"></a>12</td><td class="c3">1</td><td class="c3"><span title="Avg 1µs">1µs</span></td><td></td><td></td><td class="s"> my ( @object, %id_by_type, %one_to_one, %one_to_many );</td></tr> |
180 | <tr><td class="h"><a name="13"></a>13</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
181 | <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> |
182 | <tr><td class="h"><a name="15"></a>15</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
183 | <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> |
184 | <tr><td class="h"><a name="17"></a>17</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
185 | <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> |
186 | <tr><td class="h"><a name="19"></a>19</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
187 | <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> |
188 | <tr><td class="h"><a name="21"></a>21</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
189 | <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> |
190 | <tr><td class="h"><a name="23"></a>23</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
191 | <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> |
192 | <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> |
193 | <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> |
194 | <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> |
195 | <tr><td class="h"><a name="28"></a>28</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
196 | <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> |
197 | <tr><td class="h"><a name="30"></a>30</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
198 | <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> |
199 | <tr><td class="h"><a name="32"></a>32</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
200 | <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> |
201 | <tr><td class="h"><a name="34"></a>34</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
202 | <tr><td class="h"><a name="35"></a>35</td><td></td><td></td><td></td><td></td><td class="s">=over</td></tr> |
203 | <tr><td class="h"><a name="36"></a>36</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
204 | <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> |
205 | <tr><td class="h"><a name="38"></a>38</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
206 | <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> |
207 | <tr><td class="h"><a name="40"></a>40</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
208 | <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> |
209 | <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> |
210 | <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> |
211 | <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> |
212 | <tr><td class="h"><a name="45"></a>45</td><td></td><td></td><td></td><td></td><td class="s"> object.</td></tr> |
213 | <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> |
214 | <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> |
215 | <tr><td class="h"><a name="48"></a>48</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
216 | <tr><td class="h"><a name="49"></a>49</td><td></td><td></td><td></td><td></td><td class="s">=cut</td></tr> |
217 | <tr><td class="h"><a name="50"></a>50</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
218 | <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> |
219 | <tr><td class="h"><a name="52"></a>52</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
220 | <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> |
221 | <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> |
222 | <tr><td class="h"><a name="55"></a>55</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
223 | <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> |
224 | <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> |
225 | <tr><td class="h"><a name="58"></a>58</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
226 | <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> |
227 | <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> |
228 | <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> |
229 | <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> |
230 | <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> |
231 | <tr><td class="h"><a name="64"></a>64</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
232 | <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> |
233 | <tr><td class="h"><a name="66"></a>66</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
234 | <tr><td class="h"><a name="67"></a>67</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
235 | <tr><td class="h"><a name="68"></a>68</td><td></td><td></td><td></td><td></td><td class="s">=back</td></tr> |
236 | <tr><td class="h"><a name="69"></a>69</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
237 | <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> |
238 | <tr><td class="h"><a name="71"></a>71</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
239 | <tr><td class="h"><a name="72"></a>72</td><td></td><td></td><td></td><td></td><td class="s">=over</td></tr> |
240 | <tr><td class="h"><a name="73"></a>73</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
241 | <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> |
242 | <tr><td class="h"><a name="75"></a>75</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
243 | <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> |
244 | <tr><td class="h"><a name="77"></a>77</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
245 | <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> |
246 | <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> |
247 | <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> |
248 | <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> |
249 | <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> |
250 | <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> |
251 | <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> |
252 | <tr><td class="h"><a name="85"></a>85</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
253 | <tr><td class="h"><a name="86"></a>86</td><td></td><td></td><td></td><td></td><td class="s">=cut</td></tr> |
254 | <tr><td class="h"><a name="87"></a>87</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
255 | <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> |
256 | <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> |
257 | <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> |
258 | <tr><td class="h"><a name="91"></a>91</td><td></td><td></td><td></td><td></td><td class="s"> </td></tr> |
259 | <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> |
260 | <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> |
261 | <tr><td class="h"><a name="94"></a>94</td><td></td><td></td><td></td><td></td><td class="s"> </td></tr> |
262 | <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> |
263 | <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> |
264 | <tr><td class="h"><a name="97"></a>97</td><td></td><td></td><td></td><td></td><td class="s"> </td></tr> |
265 | <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> |
266 | <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> |
267 | <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> |
268 | <tr><td class="h"><a name="101"></a>101</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
269 | <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> |
270 | <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> |
271 | <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> |
272 | <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> |
273 | <tr><td class="h"><a name="106"></a>106</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
274 | <tr><td class="h"><a name="107"></a>107</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
275 | <tr><td class="h"><a name="108"></a>108</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
276 | <tr><td class="h"><a name="109"></a>109</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
277 | <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> |
278 | <tr><td class="h"><a name="111"></a>111</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
279 | <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> |
280 | <tr><td class="h"><a name="113"></a>113</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
281 | <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> |
282 | <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> |
283 | <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> |
284 | <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> |
285 | <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> |
286 | <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> |
287 | <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> |
288 | <tr><td class="h"><a name="121"></a>121</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
289 | <tr><td class="h"><a name="122"></a>122</td><td></td><td></td><td></td><td></td><td class="s">=cut</td></tr> |
290 | <tr><td class="h"><a name="123"></a>123</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
291 | <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> |
292 | <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> |
293 | <tr><td class="h"><a name="126"></a>126</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
294 | <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> |
295 | <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> |
296 | <tr><td class="h"><a name="129"></a>129</td><td></td><td></td><td></td><td></td><td class="s"> </td></tr> |
297 | <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> |
298 | <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> |
299 | <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> |
300 | <tr><td class="h"><a name="133"></a>133</td><td></td><td></td><td></td><td></td><td class="s"> } </td></tr> |
301 | <tr><td class="h"><a name="134"></a>134</td><td></td><td></td><td></td><td></td><td class="s"> </td></tr> |
302 | <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> |
303 | <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> |
304 | <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> |
305 | <tr><td class="h"><a name="138"></a>138</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
306 | <tr><td class="h"><a name="139"></a>139</td><td></td><td></td><td></td><td></td><td class="s"> </td></tr> |
307 | <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> |
308 | <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> |
309 | <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> |
310 | <tr><td class="h"><a name="143"></a>143</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
311 | <tr><td class="h"><a name="144"></a>144</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
312 | <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> |
313 | <tr><td class="h"><a name="146"></a>146</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
314 | <tr><td class="h"><a name="147"></a>147</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
315 | <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> |
316 | <tr><td class="h"><a name="149"></a>149</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
317 | <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> |
318 | <tr><td class="h"><a name="151"></a>151</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
319 | <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> |
320 | <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> |
321 | <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> |
322 | <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> |
323 | <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> |
324 | <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> |
325 | <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> |
326 | <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> |
327 | <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> |
328 | <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> |
329 | <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> |
330 | <tr><td class="h"><a name="163"></a>163</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
331 | <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> |
332 | <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> |
333 | <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> |
334 | <tr><td class="h"><a name="167"></a>167</td><td></td><td></td><td></td><td></td><td class="s"> );</td></tr> |
335 | <tr><td class="h"><a name="168"></a>168</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
336 | <tr><td class="h"><a name="169"></a>169</td><td></td><td></td><td></td><td></td><td class="s">=cut</td></tr> |
337 | <tr><td class="h"><a name="170"></a>170</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
338 | <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> |
339 | <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> |
340 | <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> |
341 | <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> |
342 | <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> |
343 | <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> |
344 | <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> |
345 | <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> |
346 | <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> |
347 | <tr><td class="h"><a name="180"></a>180</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
348 | <tr><td class="h"><a name="181"></a>181</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
349 | <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> |
350 | <tr><td class="h"><a name="183"></a>183</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
351 | <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> |
352 | <tr><td class="h"><a name="185"></a>185</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
353 | <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> |
354 | <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> |
355 | <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> |
356 | <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> |
357 | <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> |
358 | <tr><td class="h"><a name="191"></a>191</td><td></td><td></td><td></td><td></td><td class="s"> );</td></tr> |
359 | <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> |
360 | <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> |
361 | <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> |
362 | <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> |
363 | <tr><td class="h"><a name="196"></a>196</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
364 | <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> |
365 | <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> |
366 | <tr><td class="h"><a name="199"></a>199</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
367 | <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> |
368 | <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> |
369 | <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> |
370 | <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> |
371 | <tr><td class="h"><a name="204"></a>204</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
372 | <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> |
373 | <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> |
374 | <tr><td class="h"><a name="207"></a>207</td><td></td><td></td><td></td><td></td><td class="s"> );</td></tr> |
375 | <tr><td class="h"><a name="208"></a>208</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
376 | <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> |
377 | <tr><td class="h"><a name="210"></a>210</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
378 | <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> |
379 | <tr><td class="h"><a name="212"></a>212</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
380 | <tr><td class="h"><a name="213"></a>213</td><td></td><td></td><td></td><td></td><td class="s">=cut</td></tr> |
381 | <tr><td class="h"><a name="214"></a>214</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
382 | <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> |
383 | <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> |
384 | <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> |
385 | <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> |
386 | <tr><td class="h"><a name="219"></a>219</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
387 | <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> |
388 | <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> |
389 | <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> |
390 | <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> |
391 | <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> |
392 | <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> |
393 | <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> |
394 | <tr><td class="h"><a name="227"></a>227</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
395 | <tr><td class="h"><a name="228"></a>228</td><td></td><td></td><td></td><td></td><td class="s"> </td></tr> |
396 | <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> |
397 | <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> |
398 | <tr><td class="h"><a name="231"></a>231</td><td></td><td></td><td></td><td></td><td class="s"> else {</td></tr> |
399 | <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> |
400 | <tr><td class="h"><a name="233"></a>233</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
401 | <tr><td class="h"><a name="234"></a>234</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
402 | <tr><td class="h"><a name="235"></a>235</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
403 | <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> |
404 | <tr><td class="h"><a name="237"></a>237</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
405 | <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> |
406 | <tr><td class="h"><a name="239"></a>239</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
407 | <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> |
408 | <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> |
409 | <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> |
410 | <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> |
411 | <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> |
412 | <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> |
413 | <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> |
414 | <tr><td class="h"><a name="247"></a>247</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
415 | <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> |
416 | <tr><td class="h"><a name="249"></a>249</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
417 | <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> |
418 | <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> |
419 | <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> |
420 | <tr><td class="h"><a name="253"></a>253</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
421 | <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> |
422 | <tr><td class="h"><a name="255"></a>255</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
423 | <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> |
424 | <tr><td class="h"><a name="257"></a>257</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
425 | <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> |
426 | <tr><td class="h"><a name="259"></a>259</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
427 | <tr><td class="h"><a name="260"></a>260</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
428 | <tr><td class="h"><a name="261"></a>261</td><td></td><td></td><td></td><td></td><td class="s">=cut</td></tr> |
429 | <tr><td class="h"><a name="262"></a>262</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
430 | <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> |
431 | <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> |
432 | <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> |
433 | <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> |
434 | <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> |
435 | <tr><td class="h"><a name="268"></a>268</td><td></td><td></td><td></td><td></td><td class="s"> my $one_id;</td></tr> |
436 | <tr><td class="h"><a name="269"></a>269</td><td></td><td></td><td></td><td></td><td class="s"> if ($one) {</td></tr> |
437 | <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> |
438 | <tr><td class="h"><a name="271"></a>271</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
439 | <tr><td class="h"><a name="272"></a>272</td><td></td><td></td><td></td><td></td><td class="s"> else {</td></tr> |
440 | <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> |
441 | <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> |
442 | <tr><td class="h"><a name="275"></a>275</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
443 | <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> |
444 | <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> |
445 | <tr><td class="h"><a name="278"></a>278</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
446 | <tr><td class="h"><a name="279"></a>279</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
447 | <tr><td class="h"><a name="280"></a>280</td><td></td><td></td><td></td><td></td><td class="s">=back</td></tr> |
448 | <tr><td class="h"><a name="281"></a>281</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
449 | <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> |
450 | <tr><td class="h"><a name="283"></a>283</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
451 | <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> |
452 | <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> |
453 | <tr><td class="h"><a name="286"></a>286</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
454 | <tr><td class="h"><a name="287"></a>287</td><td></td><td></td><td></td><td></td><td class="s">=over</td></tr> |
455 | <tr><td class="h"><a name="288"></a>288</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
456 | <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> |
457 | <tr><td class="h"><a name="290"></a>290</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
458 | <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> |
459 | <tr><td class="h"><a name="292"></a>292</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
460 | <tr><td class="h"><a name="293"></a>293</td><td></td><td></td><td></td><td></td><td class="s">=back</td></tr> |
461 | <tr><td class="h"><a name="294"></a>294</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
462 | <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> |
463 | <tr><td class="h"><a name="296"></a>296</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
464 | <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> |
465 | <tr><td class="h"><a name="298"></a>298</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
466 | <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> |
467 | <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> |
468 | <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> |
469 | <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> |
470 | <tr><td class="h"><a name="303"></a>303</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
471 | <tr><td class="h"><a name="304"></a>304</td><td></td><td></td><td></td><td></td><td class="s">=cut</td></tr> |
472 | <tr><td class="h"><a name="305"></a>305</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
473 | <tr><td class="h"><a name="306"></a>306</td><td></td><td></td><td></td><td></td><td class="s">}</td></tr> |
474 | <tr><td class="h"><a name="307"></a>307</td><td class="c3">1</td><td class="c3"><span title="Avg 7µs">7µs</span></td><td></td><td></td><td class="s">1;</td></tr> |
475 | </tbody></table></div> |
476 | |
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