| Commit | Line | Data |
|---|
| 8e30e889 |
1 | <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> |
| 2 | <html xmlns="http://www.w3.org/1999/xhtml"> |
| 3 | <!-- |
| 4 | This file was generated by Devel::NYTProf version 4.06 |
| 5 | --> |
| 6 | <head> |
| 7 | <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> |
| 8 | <meta http-equiv="Content-Language" content="en-us" /> |
| 9 | <title>Profile of Bio/Phylo.pm</title> |
| 10 | <link rel="stylesheet" type="text/css" href="style.css" /> |
| 11 | <script type="text/javascript" src="js/jquery-min.js"></script> |
| 12 | |
| 13 | <script type="text/javascript" src="js/jquery-tablesorter-min.js"></script> |
| 14 | <link rel="stylesheet" type="text/css" href="js/style-tablesorter.css" /> |
| 15 | <script type="text/javascript"> |
| 16 | // when a column is first clicked on to sort it, use descending order |
| 17 | // XXX doesn't seem to work (and not just because the tablesorter formatSortingOrder() is broken) |
| 18 | $.tablesorter.defaults.sortInitialOrder = "desc"; |
| 19 | // add parser through the tablesorter addParser method |
| 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 | }); |
| 41 | </script> |
| 42 | </head> |
| 43 | |
| 44 | <body > |
| 45 | <div class="header" style="position: relative; overflow-x: hidden; overflow-y: hidden; z-index: 0; "> |
| 46 | <div class="header_back"> |
| 47 | <a href="index.html">← Index</a> |
| 48 | </div> |
| 49 | <div class="headerForeground" style="float: left"> |
| 50 | <span class="siteTitle">NYTProf Performance Profile</span> |
| 51 | <span class="siteSubtitle">  <span>« <span class="mode_btn mode_btn_selected">block view</span> • <span class="mode_btn"><a href="Bio-Phylo-pm-1138-line.html">line view</a></span> • <span class="mode_btn"><a href="Bio-Phylo-pm-1138-sub.html">sub view</a></span> »</span><br /> |
| 52 | For script/nytprof.pl |
| 53 | </span> |
| 54 | </div> |
| 55 | <div class="headerForeground" style="float: right; text-align: right"> |
| 56 | <span class="siteTitle"> </span> |
| 57 | <span class="siteSubtitle">Run on Thu May 31 16:29:39 2012<br />Reported on Thu May 31 16:37:00 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> |
| 60 | <div style="position: absolute; left: 0px; top: 2%; width: 100%; height: 99%; z-index: -1; background-color: rgb(16, 134, 253); "></div> |
| 61 | <div style="position: absolute; left: 0px; top: 4%; width: 100%; height: 97%; z-index: -1; background-color: rgb(16, 133, 252); "></div> |
| 62 | <div style="position: absolute; left: 0px; top: 6%; width: 100%; height: 95%; z-index: -1; background-color: rgb(15, 131, 250); "></div> |
| 63 | <div style="position: absolute; left: 0px; top: 8%; width: 100%; height: 93%; z-index: -1; background-color: rgb(15, 130, 249); "></div> |
| 64 | <div style="position: absolute; left: 0px; top: 10%; width: 100%; height: 91%; z-index: -1; background-color: rgb(15, 129, 248); "></div> |
| 65 | <div style="position: absolute; left: 0px; top: 12%; width: 100%; height: 89%; z-index: -1; background-color: rgb(14, 127, 246); "></div> |
| 66 | <div style="position: absolute; left: 0px; top: 14%; width: 100%; height: 87%; z-index: -1; background-color: rgb(14, 126, 245); "></div> |
| 67 | <div style="position: absolute; left: 0px; top: 16%; width: 100%; height: 85%; z-index: -1; background-color: rgb(14, 125, 244); "></div> |
| 68 | <div style="position: absolute; left: 0px; top: 18%; width: 100%; height: 83%; z-index: -1; background-color: rgb(13, 123, 242); "></div> |
| 69 | <div style="position: absolute; left: 0px; top: 20%; width: 100%; height: 81%; z-index: -1; background-color: rgb(13, 122, 241); "></div> |
| 70 | <div style="position: absolute; left: 0px; top: 22%; width: 100%; height: 79%; z-index: -1; background-color: rgb(13, 121, 240); "></div> |
| 71 | <div style="position: absolute; left: 0px; top: 24%; width: 100%; height: 77%; z-index: -1; background-color: rgb(12, 119, 238); "></div> |
| 72 | <div style="position: absolute; left: 0px; top: 26%; width: 100%; height: 75%; z-index: -1; background-color: rgb(12, 118, 237); "></div> |
| 73 | <div style="position: absolute; left: 0px; top: 28%; width: 100%; height: 73%; z-index: -1; background-color: rgb(12, 116, 235); "></div> |
| 74 | <div style="position: absolute; left: 0px; top: 30%; width: 100%; height: 71%; z-index: -1; background-color: rgb(11, 115, 234); "></div> |
| 75 | <div style="position: absolute; left: 0px; top: 32%; width: 100%; height: 69%; z-index: -1; background-color: rgb(11, 114, 233); "></div> |
| 76 | <div style="position: absolute; left: 0px; top: 34%; width: 100%; height: 67%; z-index: -1; background-color: rgb(11, 112, 231); "></div> |
| 77 | <div style="position: absolute; left: 0px; top: 36%; width: 100%; height: 65%; z-index: -1; background-color: rgb(10, 111, 230); "></div> |
| 78 | <div style="position: absolute; left: 0px; top: 38%; width: 100%; height: 63%; z-index: -1; background-color: rgb(10, 110, 229); "></div> |
| 79 | <div style="position: absolute; left: 0px; top: 40%; width: 100%; height: 61%; z-index: -1; background-color: rgb(10, 108, 227); "></div> |
| 80 | <div style="position: absolute; left: 0px; top: 42%; width: 100%; height: 59%; z-index: -1; background-color: rgb(9, 107, 226); "></div> |
| 81 | <div style="position: absolute; left: 0px; top: 44%; width: 100%; height: 57%; z-index: -1; background-color: rgb(9, 106, 225); "></div> |
| 82 | <div style="position: absolute; left: 0px; top: 46%; width: 100%; height: 55%; z-index: -1; background-color: rgb(9, 104, 223); "></div> |
| 83 | <div style="position: absolute; left: 0px; top: 48%; width: 100%; height: 53%; z-index: -1; background-color: rgb(8, 103, 222); "></div> |
| 84 | <div style="position: absolute; left: 0px; top: 50%; width: 100%; height: 51%; z-index: -1; background-color: rgb(8, 102, 221); "></div> |
| 85 | <div style="position: absolute; left: 0px; top: 52%; width: 100%; height: 49%; z-index: -1; background-color: rgb(8, 100, 219); "></div> |
| 86 | <div style="position: absolute; left: 0px; top: 54%; width: 100%; height: 47%; z-index: -1; background-color: rgb(7, 99, 218); "></div> |
| 87 | <div style="position: absolute; left: 0px; top: 56%; width: 100%; height: 45%; z-index: -1; background-color: rgb(7, 97, 216); "></div> |
| 88 | <div style="position: absolute; left: 0px; top: 58%; width: 100%; height: 43%; z-index: -1; background-color: rgb(7, 96, 215); "></div> |
| 89 | <div style="position: absolute; left: 0px; top: 60%; width: 100%; height: 41%; z-index: -1; background-color: rgb(6, 95, 214); "></div> |
| 90 | <div style="position: absolute; left: 0px; top: 62%; width: 100%; height: 39%; z-index: -1; background-color: rgb(6, 93, 212); "></div> |
| 91 | <div style="position: absolute; left: 0px; top: 64%; width: 100%; height: 37%; z-index: -1; background-color: rgb(6, 92, 211); "></div> |
| 92 | <div style="position: absolute; left: 0px; top: 66%; width: 100%; height: 35%; z-index: -1; background-color: rgb(5, 91, 210); "></div> |
| 93 | <div style="position: absolute; left: 0px; top: 68%; width: 100%; height: 33%; z-index: -1; background-color: rgb(5, 89, 208); "></div> |
| 94 | <div style="position: absolute; left: 0px; top: 70%; width: 100%; height: 31%; z-index: -1; background-color: rgb(5, 88, 207); "></div> |
| 95 | <div style="position: absolute; left: 0px; top: 72%; width: 100%; height: 29%; z-index: -1; background-color: rgb(4, 87, 206); "></div> |
| 96 | <div style="position: absolute; left: 0px; top: 74%; width: 100%; height: 27%; z-index: -1; background-color: rgb(4, 85, 204); "></div> |
| 97 | <div style="position: absolute; left: 0px; top: 76%; width: 100%; height: 25%; z-index: -1; background-color: rgb(4, 84, 203); "></div> |
| 98 | <div style="position: absolute; left: 0px; top: 78%; width: 100%; height: 23%; z-index: -1; background-color: rgb(3, 82, 201); "></div> |
| 99 | <div style="position: absolute; left: 0px; top: 80%; width: 100%; height: 21%; z-index: -1; background-color: rgb(3, 81, 200); "></div> |
| 100 | <div style="position: absolute; left: 0px; top: 82%; width: 100%; height: 19%; z-index: -1; background-color: rgb(3, 80, 199); "></div> |
| 101 | <div style="position: absolute; left: 0px; top: 84%; width: 100%; height: 17%; z-index: -1; background-color: rgb(2, 78, 197); "></div> |
| 102 | <div style="position: absolute; left: 0px; top: 86%; width: 100%; height: 15%; z-index: -1; background-color: rgb(2, 77, 196); "></div> |
| 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.pm">/Users/edenc/perl5/lib/perl5/Bio/Phylo.pm</a></td></tr> |
| 114 | <tr><td class="h">Statements</td><td align="left">Executed 45 statements in 3.50ms</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%">3.23ms</span></td><td class="c0"><span title="0.0%">3.54ms</span></td><td class="sub_name"><span style="display: none;">Bio::Phylo::::BEGIN@18</span>Bio::Phylo::<a href="Bio-Phylo-pm-1138-block.html#18">BEGIN@18</a></span></td></tr> |
| 130 | <tr><td class="c3">1</td><td class="c3">1</td><td class="c3">1</td><td class="c0"><span title="0.0%">1.79ms</span></td><td class="c0"><span title="0.0%">2.41ms</span></td><td class="sub_name"><span style="display: none;">Bio::Phylo::::BEGIN@14</span>Bio::Phylo::<a href="Bio-Phylo-pm-1138-block.html#14">BEGIN@14</a></span></td></tr> |
| 131 | <tr><td class="c3">1</td><td class="c3">1</td><td class="c3">1</td><td class="c0"><span title="0.0%">22µs</span></td><td class="c0"><span title="0.0%">54µs</span></td><td class="sub_name"><span style="display: none;">Bio::Phylo::::BEGIN@842</span>Bio::Phylo::<a href="Bio-Phylo-pm-1138-block.html#842">BEGIN@842</a></span></td></tr> |
| 132 | <tr><td class="c3">1</td><td class="c3">1</td><td class="c3">1</td><td class="c1"><span title="0.0%">13µs</span></td><td class="c3"><span title="0.0%">16µs</span></td><td class="sub_name"><span style="display: none;">Bio::Phylo::::BEGIN@2</span>Bio::Phylo::<a href="Bio-Phylo-pm-1138-block.html#2">BEGIN@2</a></span></td></tr> |
| 133 | <tr><td class="c3">1</td><td class="c3">1</td><td class="c3">1</td><td class="c1"><span title="0.0%">12µs</span></td><td class="c3"><span title="0.0%">14µs</span></td><td class="sub_name"><span style="display: none;">Bio::Phylo::::BEGIN@16</span>Bio::Phylo::<a href="Bio-Phylo-pm-1138-block.html#16">BEGIN@16</a></span></td></tr> |
| 134 | <tr><td class="c3">1</td><td class="c3">1</td><td class="c3">1</td><td class="c1"><span title="0.0%">12µs</span></td><td class="c1"><span title="0.0%">39µs</span></td><td class="sub_name"><span style="display: none;">Bio::Phylo::::BEGIN@867</span>Bio::Phylo::<a href="Bio-Phylo-pm-1138-block.html#867">BEGIN@867</a></span></td></tr> |
| 135 | <tr><td class="c3">1</td><td class="c3">1</td><td class="c3">1</td><td class="c1"><span title="0.0%">12µs</span></td><td class="c3"><span title="0.0%">16µs</span></td><td class="sub_name"><span style="display: none;">Bio::Phylo::::BEGIN@874</span>Bio::Phylo::<a href="Bio-Phylo-pm-1138-block.html#874">BEGIN@874</a></span></td></tr> |
| 136 | <tr><td class="c3">1</td><td class="c3">1</td><td class="c3">1</td><td class="c2"><span title="0.0%">11µs</span></td><td class="c3"><span title="0.0%">14µs</span></td><td class="sub_name"><span style="display: none;">Bio::Phylo::::BEGIN@15</span>Bio::Phylo::<a href="Bio-Phylo-pm-1138-block.html#15">BEGIN@15</a></span></td></tr> |
| 137 | <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%">38µs</span></td><td class="sub_name"><span style="display: none;">Bio::Phylo::::BEGIN@10</span>Bio::Phylo::<a href="Bio-Phylo-pm-1138-block.html#10">BEGIN@10</a></span></td></tr> |
| 138 | <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="c3"><span title="0.0%">19µs</span></td><td class="sub_name"><span style="display: none;">Bio::Phylo::::BEGIN@895</span>Bio::Phylo::<a href="Bio-Phylo-pm-1138-block.html#895">BEGIN@895</a></span></td></tr> |
| 139 | <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="c1"><span title="0.0%">36µs</span></td><td class="sub_name"><span style="display: none;">Bio::Phylo::::BEGIN@17</span>Bio::Phylo::<a href="Bio-Phylo-pm-1138-block.html#17">BEGIN@17</a></span></td></tr> |
| 140 | <tr><td class="c1">2</td><td class="c1">2</td><td class="c1">2</td><td class="c3"><span title="0.0%">8µs</span></td><td class="c3"><span title="0.0%">8µs</span></td><td class="sub_name"><span style="display: none;">Bio::Phylo::::import</span>Bio::Phylo::<a href="Bio-Phylo-pm-1138-block.html#34">import</a></span></td></tr> |
| 141 | <tr><td class="c3">1</td><td class="c3">1</td><td class="c3">1</td><td class="c3"><span title="0.0%">7µs</span></td><td class="c0"><span title="0.0%">4.68ms</span></td><td class="sub_name"><span style="display: none;">Bio::Phylo::::BEGIN@3</span>Bio::Phylo::<a href="Bio-Phylo-pm-1138-block.html#3">BEGIN@3</a></span></td></tr> |
| 142 | <tr><td class="c3">1</td><td class="c3">1</td><td class="c3">1</td><td class="c3"><span title="0.0%">7µs</span></td><td class="c3"><span title="0.0%">9µs</span></td><td class="sub_name"><span style="display: none;">Bio::Phylo::::BEGIN@897</span>Bio::Phylo::<a href="Bio-Phylo-pm-1138-block.html#897">BEGIN@897</a></span></td></tr> |
| 143 | <tr><td class="c3">1</td><td class="c3">1</td><td class="c3">1</td><td class="c3"><span title="0.0%">6µs</span></td><td class="c3"><span title="0.0%">6µs</span></td><td class="sub_name"><span style="display: none;">Bio::Phylo::::CORE:subst</span>Bio::Phylo::<a href="Bio-Phylo-pm-1138-block.html#Bio__Phylo__CORE_subst">CORE:subst</a> (opcode)</span></td></tr> |
| 144 | <tr><td class="c1">2</td><td class="c3">1</td><td class="c3">1</td><td class="c3"><span title="0.0%">5µs</span></td><td class="c3"><span title="0.0%">5µs</span></td><td class="sub_name"><span style="display: none;">Bio::Phylo::::CORE:substcont</span>Bio::Phylo::<a href="Bio-Phylo-pm-1138-block.html#Bio__Phylo__CORE_substcont">CORE:substcont</a> (opcode)</span></td></tr> |
| 145 | <tr><td class="c3">1</td><td class="c3">1</td><td class="c3">1</td><td class="c3"><span title="0.0%">3µs</span></td><td class="c3"><span title="0.0%">3µs</span></td><td class="sub_name"><span style="display: none;">Bio::Phylo::::get_logger</span>Bio::Phylo::<a href="Bio-Phylo-pm-1138-block.html#575">get_logger</a></span></td></tr> |
| 146 | <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::::CITATION</span>Bio::Phylo::<a href="Bio-Phylo-pm-1138-block.html#796">CITATION</a></span></td></tr> |
| 147 | <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::::DESTROY</span>Bio::Phylo::<a href="Bio-Phylo-pm-1138-block.html#845">DESTROY</a></span></td></tr> |
| 148 | <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::::VERBOSE</span>Bio::Phylo::<a href="Bio-Phylo-pm-1138-block.html#770">VERBOSE</a></span></td></tr> |
| 149 | <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::::VERSION</span>Bio::Phylo::<a href="Bio-Phylo-pm-1138-block.html#820">VERSION</a></span></td></tr> |
| 150 | <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::::_cleanup</span>Bio::Phylo::<a href="Bio-Phylo-pm-1138-block.html#906">_cleanup</a></span></td></tr> |
| 151 | <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::::_get_container</span>Bio::Phylo::<a href="Bio-Phylo-pm-1138-block.html#941">_get_container</a></span></td></tr> |
| 152 | <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::::_recurse_isa</span>Bio::Phylo::<a href="Bio-Phylo-pm-1138-block.html#888">_recurse_isa</a></span></td></tr> |
| 153 | <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::::_set_container</span>Bio::Phylo::<a href="Bio-Phylo-pm-1138-block.html#960">_set_container</a></span></td></tr> |
| 154 | <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::::clone</span>Bio::Phylo::<a href="Bio-Phylo-pm-1138-block.html#680">clone</a></span></td></tr> |
| 155 | <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::::get</span>Bio::Phylo::<a href="Bio-Phylo-pm-1138-block.html#598">get</a></span></td></tr> |
| 156 | <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::::get_desc</span>Bio::Phylo::<a href="Bio-Phylo-pm-1138-block.html#485">get_desc</a></span></td></tr> |
| 157 | <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::::get_generic</span>Bio::Phylo::<a href="Bio-Phylo-pm-1138-block.html#528">get_generic</a></span></td></tr> |
| 158 | <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::::get_guid</span>Bio::Phylo::<a href="Bio-Phylo-pm-1138-block.html#467">get_guid</a></span></td></tr> |
| 159 | <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::::get_internal_name</span>Bio::Phylo::<a href="Bio-Phylo-pm-1138-block.html#438">get_internal_name</a></span></td></tr> |
| 160 | <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::::get_nexus_name</span>Bio::Phylo::<a href="Bio-Phylo-pm-1138-block.html#407">get_nexus_name</a></span></td></tr> |
| 161 | <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::::get_obj_by_id</span>Bio::Phylo::<a href="Bio-Phylo-pm-1138-block.html#625">get_obj_by_id</a></span></td></tr> |
| 162 | <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::::get_score</span>Bio::Phylo::<a href="Bio-Phylo-pm-1138-block.html#503">get_score</a></span></td></tr> |
| 163 | <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::::new</span>Bio::Phylo::<a href="Bio-Phylo-pm-1138-block.html#144">new</a></span></td></tr> |
| 164 | <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::::set_desc</span>Bio::Phylo::<a href="Bio-Phylo-pm-1138-block.html#274">set_desc</a></span></td></tr> |
| 165 | <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::::set_generic</span>Bio::Phylo::<a href="Bio-Phylo-pm-1138-block.html#338">set_generic</a></span></td></tr> |
| 166 | <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::::set_guid</span>Bio::Phylo::<a href="Bio-Phylo-pm-1138-block.html#254">set_guid</a></span></td></tr> |
| 167 | <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::::set_score</span>Bio::Phylo::<a href="Bio-Phylo-pm-1138-block.html#295">set_score</a></span></td></tr> |
| 168 | <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::::to_string</span>Bio::Phylo::<a href="Bio-Phylo-pm-1138-block.html#644">to_string</a></span></td></tr> |
| 169 | </tbody></table> |
| 170 | Call graph for these subroutines as a |
| 171 | <a href="http://en.wikipedia.org/wiki/Graphviz">Graphviz</a> |
| 172 | <a href="Users-edenc-perl5-lib-perl5-Bio-Phylo-pm.dot">dot language file</a>. |
| 173 | |
| 174 | <table border="1" cellpadding="0"> |
| 175 | <thead> |
| 176 | <tr><th>Line</th> |
| 177 | <th><span title="Number of statements executed">State<br />ments</span></th> |
| 178 | <th><span title="Time spend executing statements on the line, |
| 179 | excluding time spent executing statements in any called subroutines">Time<br />on line</span></th> |
| 180 | <th><span title="Number of subroutines calls">Calls</span></th> |
| 181 | <th><span title="Time spent in subroutines called (inclusive)">Time<br />in subs</span></th> |
| 182 | <th class="left_indent_header">Code</th> |
| 183 | </tr> |
| 184 | |
| 185 | </thead> |
| 186 | <tbody> |
| 187 | <tr><td class="h"><a name="1"></a>1</td><td></td><td></td><td></td><td></td><td class="s">package Bio::Phylo;</td></tr> |
| 188 | <tr><td class="h"><a name="2"></a>2</td><td class="c3">2</td><td class="c3"><span title="Avg 12µs">23µs</span></td><td class="c3">2</td><td class="c3">19µs</td><td class="s"><div class="calls"><div class="calls_in"># spent 16µs (13+3) within Bio::Phylo::BEGIN@2 which was called: |
| 189 | # once (13µs+3µs) by Bio::Phylo::IO::BEGIN@4 at <a href="Bio-Phylo-pm-1138-block.html#2">line 2</a></div></div>use strict;<div class="calls"><div class="calls_out"># spent 16µs making 1 call to <a href="Bio-Phylo-pm-1138-block.html#2">Bio::Phylo::BEGIN@2</a> |
| 190 | # spent 3µs making 1 call to <a href="strict-pm-3-block.html#34">strict::import</a></div></div></td></tr> |
| 191 | <tr><td class="h"><a name="3"></a>3</td><td class="c3">2</td><td class="c3"><span title="Avg 17µs">33µs</span></td><td class="c3">2</td><td class="c0">9.35ms</td><td class="s"><div class="calls"><div class="calls_in"># spent 4.68ms (7µs+4.67) within Bio::Phylo::BEGIN@3 which was called: |
| 192 | # once (7µs+4.67ms) by Bio::Phylo::IO::BEGIN@4 at <a href="Bio-Phylo-pm-1138-block.html#3">line 3</a></div></div>use base 'Bio::Phylo::Identifiable';<div class="calls"><div class="calls_out"># spent 4.68ms making 1 call to <a href="Bio-Phylo-pm-1138-block.html#3">Bio::Phylo::BEGIN@3</a> |
| 193 | # spent 4.67ms making 1 call to <a href="base-pm-22-block.html#58">base::import</a></div></div></td></tr> |
| 194 | <tr><td class="h"><a name="4"></a>4</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 195 | <tr><td class="h"><a name="5"></a>5</td><td></td><td></td><td></td><td></td><td class="s"># ABSTRACT: Phyloinformatic analysis using Perl</td></tr> |
| 196 | <tr><td class="h"><a name="6"></a>6</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 197 | <tr><td class="h"><a name="7"></a>7</td><td></td><td></td><td></td><td></td><td class="s"># Because we use a roll-your-own looks_like_number from</td></tr> |
| 198 | <tr><td class="h"><a name="8"></a>8</td><td></td><td></td><td></td><td></td><td class="s"># Bio::Phylo::Util::CONSTANT, here we don't have to worry</td></tr> |
| 199 | <tr><td class="h"><a name="9"></a>9</td><td></td><td></td><td></td><td></td><td class="s"># about older core S::U versions that don't have it...</td></tr> |
| 200 | <tr><td class="h"><a name="10"></a>10</td><td class="c3">2</td><td class="c3"><span title="Avg 14µs">28µs</span></td><td class="c3">2</td><td class="c0">68µs</td><td class="s"><div class="calls"><div class="calls_in"># spent 38µs (9+30) within Bio::Phylo::BEGIN@10 which was called: |
| 201 | # once (9µs+30µs) by Bio::Phylo::IO::BEGIN@4 at <a href="Bio-Phylo-pm-1138-block.html#10">line 10</a></div></div>use Scalar::Util qw'weaken blessed';<div class="calls"><div class="calls_out"># spent 38µs making 1 call to <a href="Bio-Phylo-pm-1138-block.html#10">Bio::Phylo::BEGIN@10</a> |
| 202 | # spent 30µs making 1 call to <a href="Exporter-pm-8-block.html#28">Exporter::import</a></div></div></td></tr> |
| 203 | <tr><td class="h"><a name="11"></a>11</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 204 | <tr><td class="h"><a name="12"></a>12</td><td></td><td></td><td></td><td></td><td class="s">#... instead, Bio::Phylo::Util::CONSTANT can worry about it</td></tr> |
| 205 | <tr><td class="h"><a name="13"></a>13</td><td></td><td></td><td></td><td></td><td class="s"># in one location, perhaps using the S::U version, or a drop-in</td></tr> |
| 206 | <tr><td class="h"><a name="14"></a>14</td><td class="c3">2</td><td class="c0"><span title="Avg 66µs">132µs</span></td><td class="c3">2</td><td class="c0">2.83ms</td><td class="s"><div class="calls"><div class="calls_in"># spent 2.41ms (1.79+621µs) within Bio::Phylo::BEGIN@14 which was called: |
| 207 | # once (1.79ms+621µs) by Bio::Phylo::IO::BEGIN@4 at <a href="Bio-Phylo-pm-1138-block.html#14">line 14</a></div></div>use Bio::Phylo::Util::CONSTANT '/looks_like/';<div class="calls"><div class="calls_out"># spent 2.41ms making 1 call to <a href="Bio-Phylo-pm-1138-block.html#14">Bio::Phylo::BEGIN@14</a> |
| 208 | # spent 414µs making 1 call to <a href="Exporter-pm-8-block.html#28">Exporter::import</a></div></div></td></tr> |
| 209 | <tr><td class="h"><a name="15"></a>15</td><td class="c3">2</td><td class="c3"><span title="Avg 14µs">27µs</span></td><td class="c3">2</td><td class="c3">18µs</td><td class="s"><div class="calls"><div class="calls_in"># spent 14µs (11+4) within Bio::Phylo::BEGIN@15 which was called: |
| 210 | # once (11µs+4µs) by Bio::Phylo::IO::BEGIN@4 at <a href="Bio-Phylo-pm-1138-block.html#15">line 15</a></div></div>use Bio::Phylo::Util::IDPool; # creates unique object IDs<div class="calls"><div class="calls_out"># spent 14µs making 1 call to <a href="Bio-Phylo-pm-1138-block.html#15">Bio::Phylo::BEGIN@15</a> |
| 211 | # spent 4µs making 1 call to <a href="UNIVERSAL-pm-738-block.html#16">UNIVERSAL::import</a></div></div></td></tr> |
| 212 | <tr><td class="h"><a name="16"></a>16</td><td class="c3">2</td><td class="c3"><span title="Avg 14µs">28µs</span></td><td class="c3">2</td><td class="c3">15µs</td><td class="s"><div class="calls"><div class="calls_in"># spent 14µs (12+1) within Bio::Phylo::BEGIN@16 which was called: |
| 213 | # once (12µs+1µs) by Bio::Phylo::IO::BEGIN@4 at <a href="Bio-Phylo-pm-1138-block.html#16">line 16</a></div></div>use Bio::Phylo::Identifiable; # for storing unique IDs inside an instance<div class="calls"><div class="calls_out"># spent 14µs making 1 call to <a href="Bio-Phylo-pm-1138-block.html#16">Bio::Phylo::BEGIN@16</a> |
| 214 | # spent 1µs making 1 call to <a href="UNIVERSAL-pm-738-block.html#16">UNIVERSAL::import</a></div></div></td></tr> |
| 215 | <tr><td class="h"><a name="17"></a>17</td><td class="c3">2</td><td class="c3"><span title="Avg 12µs">24µs</span></td><td class="c3">2</td><td class="c1">65µs</td><td class="s"><div class="calls"><div class="calls_in"># spent 36µs (8+28) within Bio::Phylo::BEGIN@17 which was called: |
| 216 | # once (8µs+28µs) by Bio::Phylo::IO::BEGIN@4 at <a href="Bio-Phylo-pm-1138-block.html#17">line 17</a></div></div>use Bio::Phylo::Util::Exceptions 'throw'; # defines exception classes and throws<div class="calls"><div class="calls_out"># spent 36µs making 1 call to <a href="Bio-Phylo-pm-1138-block.html#17">Bio::Phylo::BEGIN@17</a> |
| 217 | # spent 28µs making 1 call to <a href="Exporter-pm-8-block.html#28">Exporter::import</a></div></div></td></tr> |
| 218 | <tr><td class="h"><a name="18"></a>18</td><td class="c3">2</td><td class="c0"><span title="Avg 1.19ms">2.39ms</span></td><td class="c3">2</td><td class="c0">3.58ms</td><td class="s"><div class="calls"><div class="calls_in"># spent 3.54ms (3.23+314µs) within Bio::Phylo::BEGIN@18 which was called: |
| 219 | # once (3.23ms+314µs) by Bio::Phylo::IO::BEGIN@4 at <a href="Bio-Phylo-pm-1138-block.html#18">line 18</a></div></div>use Bio::Phylo::Util::Logger; # for logging, like log4perl/log4j<div class="calls"><div class="calls_out"># spent 3.54ms making 1 call to <a href="Bio-Phylo-pm-1138-block.html#18">Bio::Phylo::BEGIN@18</a> |
| 220 | # spent 34µs making 1 call to <a href="Exporter-pm-8-block.html#28">Exporter::import</a></div></div></td></tr> |
| 221 | <tr><td class="h"><a name="19"></a>19</td><td class="c3">1</td><td class="c3"><span title="Avg 4µs">4µs</span></td><td class="c3">1</td><td class="c3">13µs</td><td class="s">our ( $logger, $COMPAT ) = Bio::Phylo::Util::Logger->new;<div class="calls"><div class="calls_out"># spent 13µs making 1 call to <a href="Bio-Phylo-Util-Logger-pm-1164-block.html#77">Bio::Phylo::Util::Logger::new</a></div></div></td></tr> |
| 222 | <tr><td class="h"><a name="20"></a>20</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 223 | <tr><td class="h"><a name="21"></a>21</td><td></td><td></td><td></td><td></td><td class="s"># mediates one-to-many relationships between taxon and nodes,</td></tr> |
| 224 | <tr><td class="h"><a name="22"></a>22</td><td></td><td></td><td></td><td></td><td class="s"># taxon and sequences, taxa and forests, taxa and matrices.</td></tr> |
| 225 | <tr><td class="h"><a name="23"></a>23</td><td></td><td></td><td></td><td></td><td class="s"># Read up on the Mediator design pattern to learn how this works.</td></tr> |
| 226 | <tr><td class="h"><a name="24"></a>24</td><td class="c3">1</td><td class="c0"><span title="Avg 93µs">93µs</span></td><td></td><td></td><td class="s">require Bio::Phylo::Mediators::TaxaMediator;</td></tr> |
| 227 | <tr><td class="h"><a name="25"></a>25</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 228 | <tr><td class="h"><a name="26"></a>26</td><td></td><td></td><td></td><td></td><td class="s"># Include the revision number from subversion in $VERSION</td></tr> |
| 229 | <tr><td class="h"><a name="27"></a>27</td><td class="c3">1</td><td class="c3"><span title="Avg 700ns">700ns</span></td><td></td><td></td><td class="s">my $rev = '$Id: Phylo.pm 1660 2011-04-02 18:29:40Z rvos $';</td></tr> |
| 230 | <tr><td class="h"><a name="28"></a>28</td><td class="c3">1</td><td class="c3"><span title="Avg 28µs">28µs</span></td><td class="c1">3</td><td class="c3">12µs</td><td class="s">$rev =~ s/^[^\d]+(\d+)\b.*$/$1/;<div class="calls"><div class="calls_out"># spent 6µs making 1 call to <a href="Bio-Phylo-pm-1138-block.html#Bio__Phylo__CORE_subst">Bio::Phylo::CORE:subst</a> |
| 231 | # spent 5µs making 2 calls to <a href="Bio-Phylo-pm-1138-block.html#Bio__Phylo__CORE_substcont">Bio::Phylo::CORE:substcont</a>, avg 3µs/call</div></div></td></tr> |
| 232 | <tr><td class="h"><a name="29"></a>29</td><td class="c3">1</td><td class="c3"><span title="Avg 1µs">1µs</span></td><td></td><td></td><td class="s">our $VERSION = "0.48";</td></tr> |
| 233 | <tr><td class="h"><a name="30"></a>30</td><td class="c3">1</td><td class="c3"><span title="Avg 800ns">800ns</span></td><td></td><td></td><td class="s">$VERSION .= "_$rev";</td></tr> |
| 234 | <tr><td class="h"><a name="31"></a>31</td><td></td><td></td><td></td><td></td><td class="s">{</td></tr> |
| 235 | <tr><td class="h"><a name="32"></a>32</td><td class="c0">4</td><td class="c3"><span title="Avg 1µs">5µs</span></td><td></td><td></td><td class="s"> my $taxamediator = 'Bio::Phylo::Mediators::TaxaMediator';</td></tr> |
| 236 | <tr><td class="h"><a name="33"></a>33</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 237 | <tr><td class="h"><a name="34"></a>34</td><td></td><td></td><td></td><td></td><td class="s"><div class="calls"><div class="calls_in"># spent 8µs within Bio::Phylo::import which was called 2 times, avg 4µs/call: |
| 238 | # once (4µs+0s) by Bio::Phylo::IO::BEGIN@4 at <a href="Bio-Phylo-IO-pm-1136-block.html#4">line 4 of Bio/Phylo/IO.pm</a> |
| 239 | # once (3µs+0s) by Bio::Phylo::Mediators::TaxaMediator::BEGIN@4 at <a href="Bio-Phylo-Mediators-TaxaMediator-pm-1166-block.html#4">line 4 of Bio/Phylo/Mediators/TaxaMediator.pm</a></div></div> sub import {</td></tr> |
| 240 | <tr><td class="h"><a name="35"></a>35</td><td class="c0">6</td><td class="c3"><span title="Avg 2µs">12µs</span></td><td></td><td></td><td class="s"> my $class = shift;</td></tr> |
| 241 | <tr><td class="h"><a name="36"></a>36</td><td></td><td></td><td></td><td></td><td class="s"> if (@_) {</td></tr> |
| 242 | <tr><td class="h"><a name="37"></a>37</td><td></td><td></td><td></td><td></td><td class="s"> my %opt = looks_like_hash @_;</td></tr> |
| 243 | <tr><td class="h"><a name="38"></a>38</td><td></td><td></td><td></td><td></td><td class="s"> while ( my ( $key, $value ) = each %opt ) {</td></tr> |
| 244 | <tr><td class="h"><a name="39"></a>39</td><td></td><td></td><td></td><td></td><td class="s"> if ( $key =~ qr/^VERBOSE$/i ) {</td></tr> |
| 245 | <tr><td class="h"><a name="40"></a>40</td><td></td><td></td><td></td><td></td><td class="s"> $logger->VERBOSE( '-level' => $value, -class => $class );</td></tr> |
| 246 | <tr><td class="h"><a name="41"></a>41</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 247 | <tr><td class="h"><a name="42"></a>42</td><td></td><td></td><td></td><td></td><td class="s"> elsif ( $key =~ qr/^COMPAT$/i ) {</td></tr> |
| 248 | <tr><td class="h"><a name="43"></a>43</td><td></td><td></td><td></td><td></td><td class="s"> $COMPAT = ucfirst( lc($value) );</td></tr> |
| 249 | <tr><td class="h"><a name="44"></a>44</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 250 | <tr><td class="h"><a name="45"></a>45</td><td></td><td></td><td></td><td></td><td class="s"> else {</td></tr> |
| 251 | <tr><td class="h"><a name="46"></a>46</td><td></td><td></td><td></td><td></td><td class="s"> throw 'BadArgs' =></td></tr> |
| 252 | <tr><td class="h"><a name="47"></a>47</td><td></td><td></td><td></td><td></td><td class="s"> "'$key' is not a valid argument for import";</td></tr> |
| 253 | <tr><td class="h"><a name="48"></a>48</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 254 | <tr><td class="h"><a name="49"></a>49</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 255 | <tr><td class="h"><a name="50"></a>50</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 256 | <tr><td class="h"><a name="51"></a>51</td><td></td><td></td><td></td><td></td><td class="s"> return 1;</td></tr> |
| 257 | <tr><td class="h"><a name="52"></a>52</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 258 | <tr><td class="h"><a name="53"></a>53</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 259 | <tr><td class="h"><a name="54"></a>54</td><td></td><td></td><td></td><td></td><td class="s"> # the following hashes are used to hold state of inside-out objects. For</td></tr> |
| 260 | <tr><td class="h"><a name="55"></a>55</td><td></td><td></td><td></td><td></td><td class="s"> # example, $obj->set_name("name") is implemented as $name{ $obj->get_id }</td></tr> |
| 261 | <tr><td class="h"><a name="56"></a>56</td><td></td><td></td><td></td><td></td><td class="s"> # = $name. To avoid memory leaks (and subtle bugs, should a new object by</td></tr> |
| 262 | <tr><td class="h"><a name="57"></a>57</td><td></td><td></td><td></td><td></td><td class="s"> # the same id appear (though that shouldn't happen)), the hash slots</td></tr> |
| 263 | <tr><td class="h"><a name="58"></a>58</td><td></td><td></td><td></td><td></td><td class="s"> # occupied by $obj->get_id need to be reclaimed in the destructor. This</td></tr> |
| 264 | <tr><td class="h"><a name="59"></a>59</td><td></td><td></td><td></td><td></td><td class="s"> # is done by recursively calling the $obj->_cleanup methods in all of $obj's</td></tr> |
| 265 | <tr><td class="h"><a name="60"></a>60</td><td></td><td></td><td></td><td></td><td class="s"> # superclasses. To make that method easier to write, we create an array</td></tr> |
| 266 | <tr><td class="h"><a name="61"></a>61</td><td></td><td></td><td></td><td></td><td class="s"> # with the local inside-out hashes here, so that we can just iterate over</td></tr> |
| 267 | <tr><td class="h"><a name="62"></a>62</td><td></td><td></td><td></td><td></td><td class="s"> # them anonymously during destruction cleanup. Other classes do something</td></tr> |
| 268 | <tr><td class="h"><a name="63"></a>63</td><td></td><td></td><td></td><td></td><td class="s"> # like this as well.</td></tr> |
| 269 | <tr><td class="h"><a name="64"></a>64</td><td></td><td></td><td></td><td></td><td class="s"> my @fields = \(</td></tr> |
| 270 | <tr><td class="h"><a name="65"></a>65</td><td></td><td></td><td></td><td></td><td class="s"> my (</td></tr> |
| 271 | <tr><td class="h"><a name="66"></a>66</td><td></td><td></td><td></td><td></td><td class="s"> %guid,</td></tr> |
| 272 | <tr><td class="h"><a name="67"></a>67</td><td></td><td></td><td></td><td></td><td class="s"> %desc,</td></tr> |
| 273 | <tr><td class="h"><a name="68"></a>68</td><td></td><td></td><td></td><td></td><td class="s"> %score,</td></tr> |
| 274 | <tr><td class="h"><a name="69"></a>69</td><td></td><td></td><td></td><td></td><td class="s"> %generic,</td></tr> |
| 275 | <tr><td class="h"><a name="70"></a>70</td><td></td><td></td><td></td><td></td><td class="s"> %cache,</td></tr> |
| 276 | <tr><td class="h"><a name="71"></a>71</td><td></td><td></td><td></td><td></td><td class="s"> %container, # XXX weak reference</td></tr> |
| 277 | <tr><td class="h"><a name="72"></a>72</td><td></td><td></td><td></td><td></td><td class="s"> %objects # XXX weak reference</td></tr> |
| 278 | <tr><td class="h"><a name="73"></a>73</td><td></td><td></td><td></td><td></td><td class="s"> )</td></tr> |
| 279 | <tr><td class="h"><a name="74"></a>74</td><td></td><td></td><td></td><td></td><td class="s"> );</td></tr> |
| 280 | <tr><td class="h"><a name="75"></a>75</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 281 | <tr><td class="h"><a name="76"></a>76</td><td></td><td></td><td></td><td></td><td class="s">=head1 NAME</td></tr> |
| 282 | <tr><td class="h"><a name="77"></a>77</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 283 | <tr><td class="h"><a name="78"></a>78</td><td></td><td></td><td></td><td></td><td class="s">Bio::Phylo - Phylogenetic analysis using perl</td></tr> |
| 284 | <tr><td class="h"><a name="79"></a>79</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 285 | <tr><td class="h"><a name="80"></a>80</td><td></td><td></td><td></td><td></td><td class="s">=head1 SYNOPSIS</td></tr> |
| 286 | <tr><td class="h"><a name="81"></a>81</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 287 | <tr><td class="h"><a name="82"></a>82</td><td></td><td></td><td></td><td></td><td class="s"> # Actually, you would almost never use this module directly. This is </td></tr> |
| 288 | <tr><td class="h"><a name="83"></a>83</td><td></td><td></td><td></td><td></td><td class="s"> # the base class for other modules.</td></tr> |
| 289 | <tr><td class="h"><a name="84"></a>84</td><td></td><td></td><td></td><td></td><td class="s"> use Bio::Phylo;</td></tr> |
| 290 | <tr><td class="h"><a name="85"></a>85</td><td></td><td></td><td></td><td></td><td class="s"> </td></tr> |
| 291 | <tr><td class="h"><a name="86"></a>86</td><td></td><td></td><td></td><td></td><td class="s"> # sets global verbosity to 'error'</td></tr> |
| 292 | <tr><td class="h"><a name="87"></a>87</td><td></td><td></td><td></td><td></td><td class="s"> Bio::Phylo->VERBOSE( -level => Bio::Phylo::Util::Logger::ERROR );</td></tr> |
| 293 | <tr><td class="h"><a name="88"></a>88</td><td></td><td></td><td></td><td></td><td class="s"> </td></tr> |
| 294 | <tr><td class="h"><a name="89"></a>89</td><td></td><td></td><td></td><td></td><td class="s"> # sets verbosity for forest ojects to 'debug'</td></tr> |
| 295 | <tr><td class="h"><a name="90"></a>90</td><td></td><td></td><td></td><td></td><td class="s"> Bio::Phylo->VERBOSE( </td></tr> |
| 296 | <tr><td class="h"><a name="91"></a>91</td><td></td><td></td><td></td><td></td><td class="s"> -level => Bio::Phylo::Util::Logger::DEBUG, </td></tr> |
| 297 | <tr><td class="h"><a name="92"></a>92</td><td></td><td></td><td></td><td></td><td class="s"> -class => 'Bio::Phylo::Forest' </td></tr> |
| 298 | <tr><td class="h"><a name="93"></a>93</td><td></td><td></td><td></td><td></td><td class="s"> );</td></tr> |
| 299 | <tr><td class="h"><a name="94"></a>94</td><td></td><td></td><td></td><td></td><td class="s"> </td></tr> |
| 300 | <tr><td class="h"><a name="95"></a>95</td><td></td><td></td><td></td><td></td><td class="s"> # prints version, including SVN revision number</td></tr> |
| 301 | <tr><td class="h"><a name="96"></a>96</td><td></td><td></td><td></td><td></td><td class="s"> print Bio::Phylo->VERSION;</td></tr> |
| 302 | <tr><td class="h"><a name="97"></a>97</td><td></td><td></td><td></td><td></td><td class="s"> </td></tr> |
| 303 | <tr><td class="h"><a name="98"></a>98</td><td></td><td></td><td></td><td></td><td class="s"> # prints suggested citation</td></tr> |
| 304 | <tr><td class="h"><a name="99"></a>99</td><td></td><td></td><td></td><td></td><td class="s"> print Bio::Phylo->CITATION;</td></tr> |
| 305 | <tr><td class="h"><a name="100"></a>100</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 306 | <tr><td class="h"><a name="101"></a>101</td><td></td><td></td><td></td><td></td><td class="s">=head1 DESCRIPTION</td></tr> |
| 307 | <tr><td class="h"><a name="102"></a>102</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 308 | <tr><td class="h"><a name="103"></a>103</td><td></td><td></td><td></td><td></td><td class="s">This is the base class for the Bio::Phylo package for phylogenetic analysis using </td></tr> |
| 309 | <tr><td class="h"><a name="104"></a>104</td><td></td><td></td><td></td><td></td><td class="s">object-oriented perl5. In this file, methods are defined that are performed by other </td></tr> |
| 310 | <tr><td class="h"><a name="105"></a>105</td><td></td><td></td><td></td><td></td><td class="s">objects in the Bio::Phylo release that inherit from this base class (which you normally</td></tr> |
| 311 | <tr><td class="h"><a name="106"></a>106</td><td></td><td></td><td></td><td></td><td class="s">wouldn't use directly).</td></tr> |
| 312 | <tr><td class="h"><a name="107"></a>107</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 313 | <tr><td class="h"><a name="108"></a>108</td><td></td><td></td><td></td><td></td><td class="s">For general information on how to use Bio::Phylo, consult the manual</td></tr> |
| 314 | <tr><td class="h"><a name="109"></a>109</td><td></td><td></td><td></td><td></td><td class="s">(L<Bio::Phylo::Manual>).</td></tr> |
| 315 | <tr><td class="h"><a name="110"></a>110</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 316 | <tr><td class="h"><a name="111"></a>111</td><td></td><td></td><td></td><td></td><td class="s">If you come here because you are trying to debug a problem you run into in</td></tr> |
| 317 | <tr><td class="h"><a name="112"></a>112</td><td></td><td></td><td></td><td></td><td class="s">using Bio::Phylo, you may be interested in the "exceptions" system as discussed</td></tr> |
| 318 | <tr><td class="h"><a name="113"></a>113</td><td></td><td></td><td></td><td></td><td class="s">in L<Bio::Phylo::Util::Exceptions>. In addition, you may find the logging system</td></tr> |
| 319 | <tr><td class="h"><a name="114"></a>114</td><td></td><td></td><td></td><td></td><td class="s">in L<Bio::Phylo::Util::Logger> of use to localize problems.</td></tr> |
| 320 | <tr><td class="h"><a name="115"></a>115</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 321 | <tr><td class="h"><a name="116"></a>116</td><td></td><td></td><td></td><td></td><td class="s">=head1 METHODS</td></tr> |
| 322 | <tr><td class="h"><a name="117"></a>117</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 323 | <tr><td class="h"><a name="118"></a>118</td><td></td><td></td><td></td><td></td><td class="s">=head2 CONSTRUCTOR</td></tr> |
| 324 | <tr><td class="h"><a name="119"></a>119</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 325 | <tr><td class="h"><a name="120"></a>120</td><td></td><td></td><td></td><td></td><td class="s">=over</td></tr> |
| 326 | <tr><td class="h"><a name="121"></a>121</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 327 | <tr><td class="h"><a name="122"></a>122</td><td></td><td></td><td></td><td></td><td class="s">=item new()</td></tr> |
| 328 | <tr><td class="h"><a name="123"></a>123</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 329 | <tr><td class="h"><a name="124"></a>124</td><td></td><td></td><td></td><td></td><td class="s">The Bio::Phylo root constructor is rarely used directly. Rather, many other </td></tr> |
| 330 | <tr><td class="h"><a name="125"></a>125</td><td></td><td></td><td></td><td></td><td class="s">objects in Bio::Phylo internally go up the inheritance tree to this constructor. </td></tr> |
| 331 | <tr><td class="h"><a name="126"></a>126</td><td></td><td></td><td></td><td></td><td class="s">The arguments shown here can therefore also be passed to any of the child </td></tr> |
| 332 | <tr><td class="h"><a name="127"></a>127</td><td></td><td></td><td></td><td></td><td class="s">classes' constructors, which will pass them on up the inheritance tree. Generally, </td></tr> |
| 333 | <tr><td class="h"><a name="128"></a>128</td><td></td><td></td><td></td><td></td><td class="s">constructors in Bio::Phylo subclasses can process as arguments all methods that </td></tr> |
| 334 | <tr><td class="h"><a name="129"></a>129</td><td></td><td></td><td></td><td></td><td class="s">have set_* in their names. The arguments are named for the methods, but "set_" </td></tr> |
| 335 | <tr><td class="h"><a name="130"></a>130</td><td></td><td></td><td></td><td></td><td class="s">has been replaced with a dash "-", e.g. the method "set_name" becomes the </td></tr> |
| 336 | <tr><td class="h"><a name="131"></a>131</td><td></td><td></td><td></td><td></td><td class="s">argument "-name" in the constructor.</td></tr> |
| 337 | <tr><td class="h"><a name="132"></a>132</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 338 | <tr><td class="h"><a name="133"></a>133</td><td></td><td></td><td></td><td></td><td class="s"> Type : Constructor</td></tr> |
| 339 | <tr><td class="h"><a name="134"></a>134</td><td></td><td></td><td></td><td></td><td class="s"> Title : new</td></tr> |
| 340 | <tr><td class="h"><a name="135"></a>135</td><td></td><td></td><td></td><td></td><td class="s"> Usage : my $phylo = Bio::Phylo->new;</td></tr> |
| 341 | <tr><td class="h"><a name="136"></a>136</td><td></td><td></td><td></td><td></td><td class="s"> Function: Instantiates Bio::Phylo object</td></tr> |
| 342 | <tr><td class="h"><a name="137"></a>137</td><td></td><td></td><td></td><td></td><td class="s"> Returns : a Bio::Phylo object </td></tr> |
| 343 | <tr><td class="h"><a name="138"></a>138</td><td></td><td></td><td></td><td></td><td class="s"> Args : Optional, any number of setters. For example,</td></tr> |
| 344 | <tr><td class="h"><a name="139"></a>139</td><td></td><td></td><td></td><td></td><td class="s"> Bio::Phylo->new( -name => $name )</td></tr> |
| 345 | <tr><td class="h"><a name="140"></a>140</td><td></td><td></td><td></td><td></td><td class="s"> will call set_name( $name ) internally</td></tr> |
| 346 | <tr><td class="h"><a name="141"></a>141</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 347 | <tr><td class="h"><a name="142"></a>142</td><td></td><td></td><td></td><td></td><td class="s">=cut</td></tr> |
| 348 | <tr><td class="h"><a name="143"></a>143</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 349 | <tr><td class="h"><a name="144"></a>144</td><td></td><td></td><td></td><td></td><td class="s"> sub new {</td></tr> |
| 350 | <tr><td class="h"><a name="145"></a>145</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 351 | <tr><td class="h"><a name="146"></a>146</td><td></td><td></td><td></td><td></td><td class="s"> # $class could be a child class, called from $class->SUPER::new(@_)</td></tr> |
| 352 | <tr><td class="h"><a name="147"></a>147</td><td></td><td></td><td></td><td></td><td class="s"> # or an object, e.g. $node->new(%args) in which case we create a new</td></tr> |
| 353 | <tr><td class="h"><a name="148"></a>148</td><td></td><td></td><td></td><td></td><td class="s"> # object that's bless into the same class as the invocant. No, that's</td></tr> |
| 354 | <tr><td class="h"><a name="149"></a>149</td><td></td><td></td><td></td><td></td><td class="s"> # not the same thing as a clone.</td></tr> |
| 355 | <tr><td class="h"><a name="150"></a>150</td><td></td><td></td><td></td><td></td><td class="s"> my $class = shift;</td></tr> |
| 356 | <tr><td class="h"><a name="151"></a>151</td><td></td><td></td><td></td><td></td><td class="s"> if ( my $reference = ref $class ) {</td></tr> |
| 357 | <tr><td class="h"><a name="152"></a>152</td><td></td><td></td><td></td><td></td><td class="s"> $class = $reference;</td></tr> |
| 358 | <tr><td class="h"><a name="153"></a>153</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 359 | <tr><td class="h"><a name="154"></a>154</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 360 | <tr><td class="h"><a name="155"></a>155</td><td></td><td></td><td></td><td></td><td class="s"> # happens only and exactly once because this</td></tr> |
| 361 | <tr><td class="h"><a name="156"></a>156</td><td></td><td></td><td></td><td></td><td class="s"> # root class is visited from every constructor</td></tr> |
| 362 | <tr><td class="h"><a name="157"></a>157</td><td></td><td></td><td></td><td></td><td class="s"> my $self = $class->SUPER::new();</td></tr> |
| 363 | <tr><td class="h"><a name="158"></a>158</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 364 | <tr><td class="h"><a name="159"></a>159</td><td></td><td></td><td></td><td></td><td class="s"> # register for get_obj_by_id</td></tr> |
| 365 | <tr><td class="h"><a name="160"></a>160</td><td></td><td></td><td></td><td></td><td class="s"> my $id = $self->get_id;</td></tr> |
| 366 | <tr><td class="h"><a name="161"></a>161</td><td></td><td></td><td></td><td></td><td class="s"> $objects{$id} = $self;</td></tr> |
| 367 | <tr><td class="h"><a name="162"></a>162</td><td></td><td></td><td></td><td></td><td class="s"> weaken( $objects{$id} );</td></tr> |
| 368 | <tr><td class="h"><a name="163"></a>163</td><td></td><td></td><td></td><td></td><td class="s"> </td></tr> |
| 369 | <tr><td class="h"><a name="164"></a>164</td><td></td><td></td><td></td><td></td><td class="s"> # notify user</td></tr> |
| 370 | <tr><td class="h"><a name="165"></a>165</td><td></td><td></td><td></td><td></td><td class="s"> $logger->info("constructor called for '$class' - $id");</td></tr> |
| 371 | <tr><td class="h"><a name="166"></a>166</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 372 | <tr><td class="h"><a name="167"></a>167</td><td></td><td></td><td></td><td></td><td class="s"> # processing arguments</td></tr> |
| 373 | <tr><td class="h"><a name="168"></a>168</td><td></td><td></td><td></td><td></td><td class="s"> if ( @_ and @_ = looks_like_hash @_ ) {</td></tr> |
| 374 | <tr><td class="h"><a name="169"></a>169</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 375 | <tr><td class="h"><a name="170"></a>170</td><td></td><td></td><td></td><td></td><td class="s"> # process all arguments</td></tr> |
| 376 | <tr><td class="h"><a name="171"></a>171</td><td></td><td></td><td></td><td></td><td class="s"> ARG: while (@_) {</td></tr> |
| 377 | <tr><td class="h"><a name="172"></a>172</td><td></td><td></td><td></td><td></td><td class="s"> my $key = shift @_;</td></tr> |
| 378 | <tr><td class="h"><a name="173"></a>173</td><td></td><td></td><td></td><td></td><td class="s"> my $value = shift @_;</td></tr> |
| 379 | <tr><td class="h"><a name="174"></a>174</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 380 | <tr><td class="h"><a name="175"></a>175</td><td></td><td></td><td></td><td></td><td class="s"> # this is a bioperl arg, meant to set</td></tr> |
| 381 | <tr><td class="h"><a name="176"></a>176</td><td></td><td></td><td></td><td></td><td class="s"> # verbosity at a per class basis. In</td></tr> |
| 382 | <tr><td class="h"><a name="177"></a>177</td><td></td><td></td><td></td><td></td><td class="s"> # bioperl, the $verbose argument is</td></tr> |
| 383 | <tr><td class="h"><a name="178"></a>178</td><td></td><td></td><td></td><td></td><td class="s"> # subsequently carried around in that</td></tr> |
| 384 | <tr><td class="h"><a name="179"></a>179</td><td></td><td></td><td></td><td></td><td class="s"> # class, here we delegate that to the</td></tr> |
| 385 | <tr><td class="h"><a name="180"></a>180</td><td></td><td></td><td></td><td></td><td class="s"> # logger, which has roughly the same</td></tr> |
| 386 | <tr><td class="h"><a name="181"></a>181</td><td></td><td></td><td></td><td></td><td class="s"> # effect.</td></tr> |
| 387 | <tr><td class="h"><a name="182"></a>182</td><td></td><td></td><td></td><td></td><td class="s"> if ( $key eq '-verbose' ) {</td></tr> |
| 388 | <tr><td class="h"><a name="183"></a>183</td><td></td><td></td><td></td><td></td><td class="s"> $logger->VERBOSE(</td></tr> |
| 389 | <tr><td class="h"><a name="184"></a>184</td><td></td><td></td><td></td><td></td><td class="s"> '-level' => $value,</td></tr> |
| 390 | <tr><td class="h"><a name="185"></a>185</td><td></td><td></td><td></td><td></td><td class="s"> '-class' => $class,</td></tr> |
| 391 | <tr><td class="h"><a name="186"></a>186</td><td></td><td></td><td></td><td></td><td class="s"> );</td></tr> |
| 392 | <tr><td class="h"><a name="187"></a>187</td><td></td><td></td><td></td><td></td><td class="s"> next ARG;</td></tr> |
| 393 | <tr><td class="h"><a name="188"></a>188</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 394 | <tr><td class="h"><a name="189"></a>189</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 395 | <tr><td class="h"><a name="190"></a>190</td><td></td><td></td><td></td><td></td><td class="s"> # notify user</td></tr> |
| 396 | <tr><td class="h"><a name="191"></a>191</td><td></td><td></td><td></td><td></td><td class="s"> $logger->debug(</td></tr> |
| 397 | <tr><td class="h"><a name="192"></a>192</td><td></td><td></td><td></td><td></td><td class="s"> "processing constructor arg '${key}' => '${value}'");</td></tr> |
| 398 | <tr><td class="h"><a name="193"></a>193</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 399 | <tr><td class="h"><a name="194"></a>194</td><td></td><td></td><td></td><td></td><td class="s"> # don't access data structures directly, call mutators</td></tr> |
| 400 | <tr><td class="h"><a name="195"></a>195</td><td></td><td></td><td></td><td></td><td class="s"> # in child classes or __PACKAGE__</td></tr> |
| 401 | <tr><td class="h"><a name="196"></a>196</td><td></td><td></td><td></td><td></td><td class="s"> my $mutator = $key;</td></tr> |
| 402 | <tr><td class="h"><a name="197"></a>197</td><td></td><td></td><td></td><td></td><td class="s"> $mutator =~ s/^-/set_/;</td></tr> |
| 403 | <tr><td class="h"><a name="198"></a>198</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 404 | <tr><td class="h"><a name="199"></a>199</td><td></td><td></td><td></td><td></td><td class="s"> # backward compat fixes:</td></tr> |
| 405 | <tr><td class="h"><a name="200"></a>200</td><td></td><td></td><td></td><td></td><td class="s"> $mutator =~ s/^set_pos$/set_position/;</td></tr> |
| 406 | <tr><td class="h"><a name="201"></a>201</td><td></td><td></td><td></td><td></td><td class="s"> $mutator =~ s/^set_matrix$/set_raw/;</td></tr> |
| 407 | <tr><td class="h"><a name="202"></a>202</td><td></td><td></td><td></td><td></td><td class="s"> eval { $self->$mutator($value); };</td></tr> |
| 408 | <tr><td class="h"><a name="203"></a>203</td><td></td><td></td><td></td><td></td><td class="s"> if ($@) {</td></tr> |
| 409 | <tr><td class="h"><a name="204"></a>204</td><td></td><td></td><td></td><td></td><td class="s"> if ( blessed $@ and $@->can('rethrow') ) {</td></tr> |
| 410 | <tr><td class="h"><a name="205"></a>205</td><td></td><td></td><td></td><td></td><td class="s"> $@->rethrow;</td></tr> |
| 411 | <tr><td class="h"><a name="206"></a>206</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 412 | <tr><td class="h"><a name="207"></a>207</td><td></td><td></td><td></td><td></td><td class="s"> elsif ( not ref($@)</td></tr> |
| 413 | <tr><td class="h"><a name="208"></a>208</td><td></td><td></td><td></td><td></td><td class="s"> and $@ =~ /^Can't locate object method / )</td></tr> |
| 414 | <tr><td class="h"><a name="209"></a>209</td><td></td><td></td><td></td><td></td><td class="s"> {</td></tr> |
| 415 | <tr><td class="h"><a name="210"></a>210</td><td></td><td></td><td></td><td></td><td class="s"> throw 'BadArgs' =></td></tr> |
| 416 | <tr><td class="h"><a name="211"></a>211</td><td></td><td></td><td></td><td></td><td class="s">"The named argument '${key}' cannot be passed to the constructor of ${class}";</td></tr> |
| 417 | <tr><td class="h"><a name="212"></a>212</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 418 | <tr><td class="h"><a name="213"></a>213</td><td></td><td></td><td></td><td></td><td class="s"> else {</td></tr> |
| 419 | <tr><td class="h"><a name="214"></a>214</td><td></td><td></td><td></td><td></td><td class="s"> throw 'Generic' => $@;</td></tr> |
| 420 | <tr><td class="h"><a name="215"></a>215</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 421 | <tr><td class="h"><a name="216"></a>216</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 422 | <tr><td class="h"><a name="217"></a>217</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 423 | <tr><td class="h"><a name="218"></a>218</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 424 | <tr><td class="h"><a name="219"></a>219</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 425 | <tr><td class="h"><a name="220"></a>220</td><td></td><td></td><td></td><td></td><td class="s"> # register with mediator</td></tr> |
| 426 | <tr><td class="h"><a name="221"></a>221</td><td></td><td></td><td></td><td></td><td class="s"> # TODO this is irrelevant for some child classes,</td></tr> |
| 427 | <tr><td class="h"><a name="222"></a>222</td><td></td><td></td><td></td><td></td><td class="s"> # so should be re-factored into somewhere nearer the</td></tr> |
| 428 | <tr><td class="h"><a name="223"></a>223</td><td></td><td></td><td></td><td></td><td class="s"> # tips of the inheritance tree. The hack where we</td></tr> |
| 429 | <tr><td class="h"><a name="224"></a>224</td><td></td><td></td><td></td><td></td><td class="s"> # skip over direct instances of Writable is so that</td></tr> |
| 430 | <tr><td class="h"><a name="225"></a>225</td><td></td><td></td><td></td><td></td><td class="s"> # we don't register things like <format> and <matrix> tags</td></tr> |
| 431 | <tr><td class="h"><a name="226"></a>226</td><td></td><td></td><td></td><td></td><td class="s"> if ( ref $self ne 'Bio::Phylo::NeXML::Writable' ) {</td></tr> |
| 432 | <tr><td class="h"><a name="227"></a>227</td><td></td><td></td><td></td><td></td><td class="s"> $taxamediator->register($self);</td></tr> |
| 433 | <tr><td class="h"><a name="228"></a>228</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 434 | <tr><td class="h"><a name="229"></a>229</td><td></td><td></td><td></td><td></td><td class="s"> return $self;</td></tr> |
| 435 | <tr><td class="h"><a name="230"></a>230</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 436 | <tr><td class="h"><a name="231"></a>231</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 437 | <tr><td class="h"><a name="232"></a>232</td><td></td><td></td><td></td><td></td><td class="s">=back</td></tr> |
| 438 | <tr><td class="h"><a name="233"></a>233</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 439 | <tr><td class="h"><a name="234"></a>234</td><td></td><td></td><td></td><td></td><td class="s">=head2 MUTATORS</td></tr> |
| 440 | <tr><td class="h"><a name="235"></a>235</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 441 | <tr><td class="h"><a name="236"></a>236</td><td></td><td></td><td></td><td></td><td class="s">=over</td></tr> |
| 442 | <tr><td class="h"><a name="237"></a>237</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 443 | <tr><td class="h"><a name="238"></a>238</td><td></td><td></td><td></td><td></td><td class="s">=item set_guid()</td></tr> |
| 444 | <tr><td class="h"><a name="239"></a>239</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 445 | <tr><td class="h"><a name="240"></a>240</td><td></td><td></td><td></td><td></td><td class="s">Sets invocant GUID.</td></tr> |
| 446 | <tr><td class="h"><a name="241"></a>241</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 447 | <tr><td class="h"><a name="242"></a>242</td><td></td><td></td><td></td><td></td><td class="s"> Type : Mutator</td></tr> |
| 448 | <tr><td class="h"><a name="243"></a>243</td><td></td><td></td><td></td><td></td><td class="s"> Title : set_guid</td></tr> |
| 449 | <tr><td class="h"><a name="244"></a>244</td><td></td><td></td><td></td><td></td><td class="s"> Usage : $obj->set_guid($guid);</td></tr> |
| 450 | <tr><td class="h"><a name="245"></a>245</td><td></td><td></td><td></td><td></td><td class="s"> Function: Assigns an object's GUID.</td></tr> |
| 451 | <tr><td class="h"><a name="246"></a>246</td><td></td><td></td><td></td><td></td><td class="s"> Returns : Modified object.</td></tr> |
| 452 | <tr><td class="h"><a name="247"></a>247</td><td></td><td></td><td></td><td></td><td class="s"> Args : A scalar</td></tr> |
| 453 | <tr><td class="h"><a name="248"></a>248</td><td></td><td></td><td></td><td></td><td class="s"> Notes : This field can be used for storing an identifier that is</td></tr> |
| 454 | <tr><td class="h"><a name="249"></a>249</td><td></td><td></td><td></td><td></td><td class="s"> unambiguous within a given content. For example, an LSID,</td></tr> |
| 455 | <tr><td class="h"><a name="250"></a>250</td><td></td><td></td><td></td><td></td><td class="s"> a genbank accession number, etc.</td></tr> |
| 456 | <tr><td class="h"><a name="251"></a>251</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 457 | <tr><td class="h"><a name="252"></a>252</td><td></td><td></td><td></td><td></td><td class="s">=cut</td></tr> |
| 458 | <tr><td class="h"><a name="253"></a>253</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 459 | <tr><td class="h"><a name="254"></a>254</td><td></td><td></td><td></td><td></td><td class="s"> sub set_guid {</td></tr> |
| 460 | <tr><td class="h"><a name="255"></a>255</td><td></td><td></td><td></td><td></td><td class="s"> my ( $self, $guid ) = @_;</td></tr> |
| 461 | <tr><td class="h"><a name="256"></a>256</td><td></td><td></td><td></td><td></td><td class="s"> $guid{ $self->get_id } = $guid;</td></tr> |
| 462 | <tr><td class="h"><a name="257"></a>257</td><td></td><td></td><td></td><td></td><td class="s"> return $self;</td></tr> |
| 463 | <tr><td class="h"><a name="258"></a>258</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 464 | <tr><td class="h"><a name="259"></a>259</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 465 | <tr><td class="h"><a name="260"></a>260</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 466 | <tr><td class="h"><a name="261"></a>261</td><td></td><td></td><td></td><td></td><td class="s">=item set_desc()</td></tr> |
| 467 | <tr><td class="h"><a name="262"></a>262</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 468 | <tr><td class="h"><a name="263"></a>263</td><td></td><td></td><td></td><td></td><td class="s">Sets invocant description.</td></tr> |
| 469 | <tr><td class="h"><a name="264"></a>264</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 470 | <tr><td class="h"><a name="265"></a>265</td><td></td><td></td><td></td><td></td><td class="s"> Type : Mutator</td></tr> |
| 471 | <tr><td class="h"><a name="266"></a>266</td><td></td><td></td><td></td><td></td><td class="s"> Title : set_desc</td></tr> |
| 472 | <tr><td class="h"><a name="267"></a>267</td><td></td><td></td><td></td><td></td><td class="s"> Usage : $obj->set_desc($desc);</td></tr> |
| 473 | <tr><td class="h"><a name="268"></a>268</td><td></td><td></td><td></td><td></td><td class="s"> Function: Assigns an object's description.</td></tr> |
| 474 | <tr><td class="h"><a name="269"></a>269</td><td></td><td></td><td></td><td></td><td class="s"> Returns : Modified object.</td></tr> |
| 475 | <tr><td class="h"><a name="270"></a>270</td><td></td><td></td><td></td><td></td><td class="s"> Args : Argument must be a string.</td></tr> |
| 476 | <tr><td class="h"><a name="271"></a>271</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 477 | <tr><td class="h"><a name="272"></a>272</td><td></td><td></td><td></td><td></td><td class="s">=cut</td></tr> |
| 478 | <tr><td class="h"><a name="273"></a>273</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 479 | <tr><td class="h"><a name="274"></a>274</td><td></td><td></td><td></td><td></td><td class="s"> sub set_desc {</td></tr> |
| 480 | <tr><td class="h"><a name="275"></a>275</td><td></td><td></td><td></td><td></td><td class="s"> my ( $self, $desc ) = @_;</td></tr> |
| 481 | <tr><td class="h"><a name="276"></a>276</td><td></td><td></td><td></td><td></td><td class="s"> $desc{ $self->get_id } = $desc;</td></tr> |
| 482 | <tr><td class="h"><a name="277"></a>277</td><td></td><td></td><td></td><td></td><td class="s"> return $self;</td></tr> |
| 483 | <tr><td class="h"><a name="278"></a>278</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 484 | <tr><td class="h"><a name="279"></a>279</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 485 | <tr><td class="h"><a name="280"></a>280</td><td></td><td></td><td></td><td></td><td class="s">=item set_score()</td></tr> |
| 486 | <tr><td class="h"><a name="281"></a>281</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 487 | <tr><td class="h"><a name="282"></a>282</td><td></td><td></td><td></td><td></td><td class="s">Sets invocant score.</td></tr> |
| 488 | <tr><td class="h"><a name="283"></a>283</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 489 | <tr><td class="h"><a name="284"></a>284</td><td></td><td></td><td></td><td></td><td class="s"> Type : Mutator</td></tr> |
| 490 | <tr><td class="h"><a name="285"></a>285</td><td></td><td></td><td></td><td></td><td class="s"> Title : set_score</td></tr> |
| 491 | <tr><td class="h"><a name="286"></a>286</td><td></td><td></td><td></td><td></td><td class="s"> Usage : $obj->set_score($score);</td></tr> |
| 492 | <tr><td class="h"><a name="287"></a>287</td><td></td><td></td><td></td><td></td><td class="s"> Function: Assigns an object's numerical score.</td></tr> |
| 493 | <tr><td class="h"><a name="288"></a>288</td><td></td><td></td><td></td><td></td><td class="s"> Returns : Modified object.</td></tr> |
| 494 | <tr><td class="h"><a name="289"></a>289</td><td></td><td></td><td></td><td></td><td class="s"> Args : Argument must be any of</td></tr> |
| 495 | <tr><td class="h"><a name="290"></a>290</td><td></td><td></td><td></td><td></td><td class="s"> perl's number formats, or undefined</td></tr> |
| 496 | <tr><td class="h"><a name="291"></a>291</td><td></td><td></td><td></td><td></td><td class="s"> to reset score.</td></tr> |
| 497 | <tr><td class="h"><a name="292"></a>292</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 498 | <tr><td class="h"><a name="293"></a>293</td><td></td><td></td><td></td><td></td><td class="s">=cut</td></tr> |
| 499 | <tr><td class="h"><a name="294"></a>294</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 500 | <tr><td class="h"><a name="295"></a>295</td><td></td><td></td><td></td><td></td><td class="s"> sub set_score {</td></tr> |
| 501 | <tr><td class="h"><a name="296"></a>296</td><td></td><td></td><td></td><td></td><td class="s"> my ( $self, $score ) = @_;</td></tr> |
| 502 | <tr><td class="h"><a name="297"></a>297</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 503 | <tr><td class="h"><a name="298"></a>298</td><td></td><td></td><td></td><td></td><td class="s"> # $score must be a number (or undefined)</td></tr> |
| 504 | <tr><td class="h"><a name="299"></a>299</td><td></td><td></td><td></td><td></td><td class="s"> if ( defined $score ) {</td></tr> |
| 505 | <tr><td class="h"><a name="300"></a>300</td><td></td><td></td><td></td><td></td><td class="s"> if ( !looks_like_number($score) ) {</td></tr> |
| 506 | <tr><td class="h"><a name="301"></a>301</td><td></td><td></td><td></td><td></td><td class="s"> throw 'BadNumber' => "score \"$score\" is a bad number";</td></tr> |
| 507 | <tr><td class="h"><a name="302"></a>302</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 508 | <tr><td class="h"><a name="303"></a>303</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 509 | <tr><td class="h"><a name="304"></a>304</td><td></td><td></td><td></td><td></td><td class="s"> # notify user</td></tr> |
| 510 | <tr><td class="h"><a name="305"></a>305</td><td></td><td></td><td></td><td></td><td class="s"> $logger->info("setting score '$score'");</td></tr> |
| 511 | <tr><td class="h"><a name="306"></a>306</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 512 | <tr><td class="h"><a name="307"></a>307</td><td></td><td></td><td></td><td></td><td class="s"> else {</td></tr> |
| 513 | <tr><td class="h"><a name="308"></a>308</td><td></td><td></td><td></td><td></td><td class="s"> $logger->info("unsetting score");</td></tr> |
| 514 | <tr><td class="h"><a name="309"></a>309</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 515 | <tr><td class="h"><a name="310"></a>310</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 516 | <tr><td class="h"><a name="311"></a>311</td><td></td><td></td><td></td><td></td><td class="s"> # this resets the score if $score was undefined</td></tr> |
| 517 | <tr><td class="h"><a name="312"></a>312</td><td></td><td></td><td></td><td></td><td class="s"> $score{ $self->get_id } = $score;</td></tr> |
| 518 | <tr><td class="h"><a name="313"></a>313</td><td></td><td></td><td></td><td></td><td class="s"> return $self;</td></tr> |
| 519 | <tr><td class="h"><a name="314"></a>314</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 520 | <tr><td class="h"><a name="315"></a>315</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 521 | <tr><td class="h"><a name="316"></a>316</td><td></td><td></td><td></td><td></td><td class="s">=item set_generic()</td></tr> |
| 522 | <tr><td class="h"><a name="317"></a>317</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 523 | <tr><td class="h"><a name="318"></a>318</td><td></td><td></td><td></td><td></td><td class="s">Sets generic key/value pair(s).</td></tr> |
| 524 | <tr><td class="h"><a name="319"></a>319</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 525 | <tr><td class="h"><a name="320"></a>320</td><td></td><td></td><td></td><td></td><td class="s"> Type : Mutator</td></tr> |
| 526 | <tr><td class="h"><a name="321"></a>321</td><td></td><td></td><td></td><td></td><td class="s"> Title : set_generic</td></tr> |
| 527 | <tr><td class="h"><a name="322"></a>322</td><td></td><td></td><td></td><td></td><td class="s"> Usage : $obj->set_generic( %generic );</td></tr> |
| 528 | <tr><td class="h"><a name="323"></a>323</td><td></td><td></td><td></td><td></td><td class="s"> Function: Assigns generic key/value pairs to the invocant.</td></tr> |
| 529 | <tr><td class="h"><a name="324"></a>324</td><td></td><td></td><td></td><td></td><td class="s"> Returns : Modified object.</td></tr> |
| 530 | <tr><td class="h"><a name="325"></a>325</td><td></td><td></td><td></td><td></td><td class="s"> Args : Valid arguments constitute:</td></tr> |
| 531 | <tr><td class="h"><a name="326"></a>326</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 532 | <tr><td class="h"><a name="327"></a>327</td><td></td><td></td><td></td><td></td><td class="s"> * key/value pairs, for example:</td></tr> |
| 533 | <tr><td class="h"><a name="328"></a>328</td><td></td><td></td><td></td><td></td><td class="s"> $obj->set_generic( '-lnl' => 0.87565 );</td></tr> |
| 534 | <tr><td class="h"><a name="329"></a>329</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 535 | <tr><td class="h"><a name="330"></a>330</td><td></td><td></td><td></td><td></td><td class="s"> * or a hash ref, for example:</td></tr> |
| 536 | <tr><td class="h"><a name="331"></a>331</td><td></td><td></td><td></td><td></td><td class="s"> $obj->set_generic( { '-lnl' => 0.87565 } );</td></tr> |
| 537 | <tr><td class="h"><a name="332"></a>332</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 538 | <tr><td class="h"><a name="333"></a>333</td><td></td><td></td><td></td><td></td><td class="s"> * or nothing, to reset the stored hash, e.g.</td></tr> |
| 539 | <tr><td class="h"><a name="334"></a>334</td><td></td><td></td><td></td><td></td><td class="s"> $obj->set_generic( );</td></tr> |
| 540 | <tr><td class="h"><a name="335"></a>335</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 541 | <tr><td class="h"><a name="336"></a>336</td><td></td><td></td><td></td><td></td><td class="s">=cut</td></tr> |
| 542 | <tr><td class="h"><a name="337"></a>337</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 543 | <tr><td class="h"><a name="338"></a>338</td><td></td><td></td><td></td><td></td><td class="s"> sub set_generic {</td></tr> |
| 544 | <tr><td class="h"><a name="339"></a>339</td><td></td><td></td><td></td><td></td><td class="s"> my $self = shift;</td></tr> |
| 545 | <tr><td class="h"><a name="340"></a>340</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 546 | <tr><td class="h"><a name="341"></a>341</td><td></td><td></td><td></td><td></td><td class="s"> # retrieve id just once, don't call $self->get_id in loops, inefficient</td></tr> |
| 547 | <tr><td class="h"><a name="342"></a>342</td><td></td><td></td><td></td><td></td><td class="s"> my $id = $self->get_id;</td></tr> |
| 548 | <tr><td class="h"><a name="343"></a>343</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 549 | <tr><td class="h"><a name="344"></a>344</td><td></td><td></td><td></td><td></td><td class="s"> # this initializes the hash if it didn't exist yet, or resets it if no args</td></tr> |
| 550 | <tr><td class="h"><a name="345"></a>345</td><td></td><td></td><td></td><td></td><td class="s"> if ( !defined $generic{$id} || !@_ ) {</td></tr> |
| 551 | <tr><td class="h"><a name="346"></a>346</td><td></td><td></td><td></td><td></td><td class="s"> $generic{$id} = {};</td></tr> |
| 552 | <tr><td class="h"><a name="347"></a>347</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 553 | <tr><td class="h"><a name="348"></a>348</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 554 | <tr><td class="h"><a name="349"></a>349</td><td></td><td></td><td></td><td></td><td class="s"> # have args</td></tr> |
| 555 | <tr><td class="h"><a name="350"></a>350</td><td></td><td></td><td></td><td></td><td class="s"> if (@_) {</td></tr> |
| 556 | <tr><td class="h"><a name="351"></a>351</td><td></td><td></td><td></td><td></td><td class="s"> my %args;</td></tr> |
| 557 | <tr><td class="h"><a name="352"></a>352</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 558 | <tr><td class="h"><a name="353"></a>353</td><td></td><td></td><td></td><td></td><td class="s"> # have a single arg, a hash ref</td></tr> |
| 559 | <tr><td class="h"><a name="354"></a>354</td><td></td><td></td><td></td><td></td><td class="s"> if ( scalar @_ == 1 && looks_like_instance( $_[0], 'HASH' ) ) {</td></tr> |
| 560 | <tr><td class="h"><a name="355"></a>355</td><td></td><td></td><td></td><td></td><td class="s"> %args = %{ $_[0] };</td></tr> |
| 561 | <tr><td class="h"><a name="356"></a>356</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 562 | <tr><td class="h"><a name="357"></a>357</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 563 | <tr><td class="h"><a name="358"></a>358</td><td></td><td></td><td></td><td></td><td class="s"> # multiple args, hopefully even size key/value pairs</td></tr> |
| 564 | <tr><td class="h"><a name="359"></a>359</td><td></td><td></td><td></td><td></td><td class="s"> else {</td></tr> |
| 565 | <tr><td class="h"><a name="360"></a>360</td><td></td><td></td><td></td><td></td><td class="s"> %args = looks_like_hash @_;</td></tr> |
| 566 | <tr><td class="h"><a name="361"></a>361</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 567 | <tr><td class="h"><a name="362"></a>362</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 568 | <tr><td class="h"><a name="363"></a>363</td><td></td><td></td><td></td><td></td><td class="s"> # notify user</td></tr> |
| 569 | <tr><td class="h"><a name="364"></a>364</td><td></td><td></td><td></td><td></td><td class="s"> $logger->info("setting generic key/value pairs %{args}");</td></tr> |
| 570 | <tr><td class="h"><a name="365"></a>365</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 571 | <tr><td class="h"><a name="366"></a>366</td><td></td><td></td><td></td><td></td><td class="s"> # fill up the hash</td></tr> |
| 572 | <tr><td class="h"><a name="367"></a>367</td><td></td><td></td><td></td><td></td><td class="s"> foreach my $key ( keys %args ) {</td></tr> |
| 573 | <tr><td class="h"><a name="368"></a>368</td><td></td><td></td><td></td><td></td><td class="s"> $generic{$id}->{$key} = $args{$key};</td></tr> |
| 574 | <tr><td class="h"><a name="369"></a>369</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 575 | <tr><td class="h"><a name="370"></a>370</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 576 | <tr><td class="h"><a name="371"></a>371</td><td></td><td></td><td></td><td></td><td class="s"> return $self;</td></tr> |
| 577 | <tr><td class="h"><a name="372"></a>372</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 578 | <tr><td class="h"><a name="373"></a>373</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 579 | <tr><td class="h"><a name="374"></a>374</td><td></td><td></td><td></td><td></td><td class="s">=back</td></tr> |
| 580 | <tr><td class="h"><a name="375"></a>375</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 581 | <tr><td class="h"><a name="376"></a>376</td><td></td><td></td><td></td><td></td><td class="s">=head2 ACCESSORS</td></tr> |
| 582 | <tr><td class="h"><a name="377"></a>377</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 583 | <tr><td class="h"><a name="378"></a>378</td><td></td><td></td><td></td><td></td><td class="s">=over</td></tr> |
| 584 | <tr><td class="h"><a name="379"></a>379</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 585 | <tr><td class="h"><a name="380"></a>380</td><td></td><td></td><td></td><td></td><td class="s">=item get_nexus_name()</td></tr> |
| 586 | <tr><td class="h"><a name="381"></a>381</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 587 | <tr><td class="h"><a name="382"></a>382</td><td></td><td></td><td></td><td></td><td class="s">Gets invocant's name, modified to be safely used in nexus files. This means that:</td></tr> |
| 588 | <tr><td class="h"><a name="383"></a>383</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 589 | <tr><td class="h"><a name="384"></a>384</td><td></td><td></td><td></td><td></td><td class="s">=item * </td></tr> |
| 590 | <tr><td class="h"><a name="385"></a>385</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 591 | <tr><td class="h"><a name="386"></a>386</td><td></td><td></td><td></td><td></td><td class="s">names with spaces in them that aren't 'single quoted' have their spaces replaced</td></tr> |
| 592 | <tr><td class="h"><a name="387"></a>387</td><td></td><td></td><td></td><td></td><td class="s">with underscores</td></tr> |
| 593 | <tr><td class="h"><a name="388"></a>388</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 594 | <tr><td class="h"><a name="389"></a>389</td><td></td><td></td><td></td><td></td><td class="s">=item * </td></tr> |
| 595 | <tr><td class="h"><a name="390"></a>390</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 596 | <tr><td class="h"><a name="391"></a>391</td><td></td><td></td><td></td><td></td><td class="s">names with any of the following characters in them are single quoted: </td></tr> |
| 597 | <tr><td class="h"><a name="392"></a>392</td><td></td><td></td><td></td><td></td><td class="s"> -^*(){}[]+=;:"\<>/,</td></tr> |
| 598 | <tr><td class="h"><a name="393"></a>393</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 599 | <tr><td class="h"><a name="394"></a>394</td><td></td><td></td><td></td><td></td><td class="s">=item * </td></tr> |
| 600 | <tr><td class="h"><a name="395"></a>395</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 601 | <tr><td class="h"><a name="396"></a>396</td><td></td><td></td><td></td><td></td><td class="s">names with single quotes inside them (i.e. not around them) are "double quoted"</td></tr> |
| 602 | <tr><td class="h"><a name="397"></a>397</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 603 | <tr><td class="h"><a name="398"></a>398</td><td></td><td></td><td></td><td></td><td class="s"> Type : Accessor</td></tr> |
| 604 | <tr><td class="h"><a name="399"></a>399</td><td></td><td></td><td></td><td></td><td class="s"> Title : get_nexus_name</td></tr> |
| 605 | <tr><td class="h"><a name="400"></a>400</td><td></td><td></td><td></td><td></td><td class="s"> Usage : my $name = $obj->get_nexus_name;</td></tr> |
| 606 | <tr><td class="h"><a name="401"></a>401</td><td></td><td></td><td></td><td></td><td class="s"> Function: Returns the object's name.</td></tr> |
| 607 | <tr><td class="h"><a name="402"></a>402</td><td></td><td></td><td></td><td></td><td class="s"> Returns : A string</td></tr> |
| 608 | <tr><td class="h"><a name="403"></a>403</td><td></td><td></td><td></td><td></td><td class="s"> Args : None</td></tr> |
| 609 | <tr><td class="h"><a name="404"></a>404</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 610 | <tr><td class="h"><a name="405"></a>405</td><td></td><td></td><td></td><td></td><td class="s">=cut</td></tr> |
| 611 | <tr><td class="h"><a name="406"></a>406</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 612 | <tr><td class="h"><a name="407"></a>407</td><td></td><td></td><td></td><td></td><td class="s"> sub get_nexus_name {</td></tr> |
| 613 | <tr><td class="h"><a name="408"></a>408</td><td></td><td></td><td></td><td></td><td class="s"> my $self = shift;</td></tr> |
| 614 | <tr><td class="h"><a name="409"></a>409</td><td></td><td></td><td></td><td></td><td class="s"> my $name = $self->get_internal_name;</td></tr> |
| 615 | <tr><td class="h"><a name="410"></a>410</td><td></td><td></td><td></td><td></td><td class="s"> if ( $name =~ /\s/ && $name !~ /^'.+'$/ ) {</td></tr> |
| 616 | <tr><td class="h"><a name="411"></a>411</td><td></td><td></td><td></td><td></td><td class="s"> $name =~ s/\s/_/g;</td></tr> |
| 617 | <tr><td class="h"><a name="412"></a>412</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 618 | <tr><td class="h"><a name="413"></a>413</td><td></td><td></td><td></td><td></td><td class="s"> if ( $name =~ /(?:\-|\^|\*|\(|\)|{|}|\[|\]|\+|=|;|:|"|\\|<|>|\/|,)/</td></tr> |
| 619 | <tr><td class="h"><a name="414"></a>414</td><td></td><td></td><td></td><td></td><td class="s"> && $name !~ /^'.+'$/ )</td></tr> |
| 620 | <tr><td class="h"><a name="415"></a>415</td><td></td><td></td><td></td><td></td><td class="s"> {</td></tr> |
| 621 | <tr><td class="h"><a name="416"></a>416</td><td></td><td></td><td></td><td></td><td class="s"> $name = "'${name}'";</td></tr> |
| 622 | <tr><td class="h"><a name="417"></a>417</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 623 | <tr><td class="h"><a name="418"></a>418</td><td></td><td></td><td></td><td></td><td class="s"> if ( $name =~ /'/ && $name !~ /^".+"$/ && $name !~ /^'.+'$/ ) {</td></tr> |
| 624 | <tr><td class="h"><a name="419"></a>419</td><td></td><td></td><td></td><td></td><td class="s"> $name = "\"${name}\"";</td></tr> |
| 625 | <tr><td class="h"><a name="420"></a>420</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 626 | <tr><td class="h"><a name="421"></a>421</td><td></td><td></td><td></td><td></td><td class="s"> return $name;</td></tr> |
| 627 | <tr><td class="h"><a name="422"></a>422</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 628 | <tr><td class="h"><a name="423"></a>423</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 629 | <tr><td class="h"><a name="424"></a>424</td><td></td><td></td><td></td><td></td><td class="s">=item get_internal_name()</td></tr> |
| 630 | <tr><td class="h"><a name="425"></a>425</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 631 | <tr><td class="h"><a name="426"></a>426</td><td></td><td></td><td></td><td></td><td class="s">Gets invocant's 'fallback' name (possibly autogenerated).</td></tr> |
| 632 | <tr><td class="h"><a name="427"></a>427</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 633 | <tr><td class="h"><a name="428"></a>428</td><td></td><td></td><td></td><td></td><td class="s"> Type : Accessor</td></tr> |
| 634 | <tr><td class="h"><a name="429"></a>429</td><td></td><td></td><td></td><td></td><td class="s"> Title : get_internal_name</td></tr> |
| 635 | <tr><td class="h"><a name="430"></a>430</td><td></td><td></td><td></td><td></td><td class="s"> Usage : my $name = $obj->get_internal_name;</td></tr> |
| 636 | <tr><td class="h"><a name="431"></a>431</td><td></td><td></td><td></td><td></td><td class="s"> Function: Returns the object's name (if none was set, the name</td></tr> |
| 637 | <tr><td class="h"><a name="432"></a>432</td><td></td><td></td><td></td><td></td><td class="s"> is a combination of the $obj's class and its UID).</td></tr> |
| 638 | <tr><td class="h"><a name="433"></a>433</td><td></td><td></td><td></td><td></td><td class="s"> Returns : A string</td></tr> |
| 639 | <tr><td class="h"><a name="434"></a>434</td><td></td><td></td><td></td><td></td><td class="s"> Args : None</td></tr> |
| 640 | <tr><td class="h"><a name="435"></a>435</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 641 | <tr><td class="h"><a name="436"></a>436</td><td></td><td></td><td></td><td></td><td class="s">=cut</td></tr> |
| 642 | <tr><td class="h"><a name="437"></a>437</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 643 | <tr><td class="h"><a name="438"></a>438</td><td></td><td></td><td></td><td></td><td class="s"> sub get_internal_name {</td></tr> |
| 644 | <tr><td class="h"><a name="439"></a>439</td><td></td><td></td><td></td><td></td><td class="s"> my $self = shift;</td></tr> |
| 645 | <tr><td class="h"><a name="440"></a>440</td><td></td><td></td><td></td><td></td><td class="s"> if ( my $name = $self->get_name ) {</td></tr> |
| 646 | <tr><td class="h"><a name="441"></a>441</td><td></td><td></td><td></td><td></td><td class="s"> return $name;</td></tr> |
| 647 | <tr><td class="h"><a name="442"></a>442</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 648 | <tr><td class="h"><a name="443"></a>443</td><td></td><td></td><td></td><td></td><td class="s"> else {</td></tr> |
| 649 | <tr><td class="h"><a name="444"></a>444</td><td></td><td></td><td></td><td></td><td class="s"> my $internal_name = ref $self;</td></tr> |
| 650 | <tr><td class="h"><a name="445"></a>445</td><td></td><td></td><td></td><td></td><td class="s"> $internal_name =~ s/.*:://;</td></tr> |
| 651 | <tr><td class="h"><a name="446"></a>446</td><td></td><td></td><td></td><td></td><td class="s"> $internal_name .= $self->get_id;</td></tr> |
| 652 | <tr><td class="h"><a name="447"></a>447</td><td></td><td></td><td></td><td></td><td class="s"> return $internal_name;</td></tr> |
| 653 | <tr><td class="h"><a name="448"></a>448</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 654 | <tr><td class="h"><a name="449"></a>449</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 655 | <tr><td class="h"><a name="450"></a>450</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 656 | <tr><td class="h"><a name="451"></a>451</td><td></td><td></td><td></td><td></td><td class="s">=item get_guid()</td></tr> |
| 657 | <tr><td class="h"><a name="452"></a>452</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 658 | <tr><td class="h"><a name="453"></a>453</td><td></td><td></td><td></td><td></td><td class="s">Gets invocant GUID.</td></tr> |
| 659 | <tr><td class="h"><a name="454"></a>454</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 660 | <tr><td class="h"><a name="455"></a>455</td><td></td><td></td><td></td><td></td><td class="s"> Type : Accessor</td></tr> |
| 661 | <tr><td class="h"><a name="456"></a>456</td><td></td><td></td><td></td><td></td><td class="s"> Title : get_guid</td></tr> |
| 662 | <tr><td class="h"><a name="457"></a>457</td><td></td><td></td><td></td><td></td><td class="s"> Usage : my $guid = $obj->get_guid;</td></tr> |
| 663 | <tr><td class="h"><a name="458"></a>458</td><td></td><td></td><td></td><td></td><td class="s"> Function: Assigns an object's GUID.</td></tr> |
| 664 | <tr><td class="h"><a name="459"></a>459</td><td></td><td></td><td></td><td></td><td class="s"> Returns : Scalar.</td></tr> |
| 665 | <tr><td class="h"><a name="460"></a>460</td><td></td><td></td><td></td><td></td><td class="s"> Args : None</td></tr> |
| 666 | <tr><td class="h"><a name="461"></a>461</td><td></td><td></td><td></td><td></td><td class="s"> Notes : This field can be used for storing an identifier that is</td></tr> |
| 667 | <tr><td class="h"><a name="462"></a>462</td><td></td><td></td><td></td><td></td><td class="s"> unambiguous within a given content. For example, an LSID,</td></tr> |
| 668 | <tr><td class="h"><a name="463"></a>463</td><td></td><td></td><td></td><td></td><td class="s"> a genbank accession number, etc.</td></tr> |
| 669 | <tr><td class="h"><a name="464"></a>464</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 670 | <tr><td class="h"><a name="465"></a>465</td><td></td><td></td><td></td><td></td><td class="s">=cut</td></tr> |
| 671 | <tr><td class="h"><a name="466"></a>466</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 672 | <tr><td class="h"><a name="467"></a>467</td><td></td><td></td><td></td><td></td><td class="s"> sub get_guid {</td></tr> |
| 673 | <tr><td class="h"><a name="468"></a>468</td><td></td><td></td><td></td><td></td><td class="s"> my $self = shift;</td></tr> |
| 674 | <tr><td class="h"><a name="469"></a>469</td><td></td><td></td><td></td><td></td><td class="s"> return $guid{ $self->get_id };</td></tr> |
| 675 | <tr><td class="h"><a name="470"></a>470</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 676 | <tr><td class="h"><a name="471"></a>471</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 677 | <tr><td class="h"><a name="472"></a>472</td><td></td><td></td><td></td><td></td><td class="s">=item get_desc()</td></tr> |
| 678 | <tr><td class="h"><a name="473"></a>473</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 679 | <tr><td class="h"><a name="474"></a>474</td><td></td><td></td><td></td><td></td><td class="s">Gets invocant description.</td></tr> |
| 680 | <tr><td class="h"><a name="475"></a>475</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 681 | <tr><td class="h"><a name="476"></a>476</td><td></td><td></td><td></td><td></td><td class="s"> Type : Accessor</td></tr> |
| 682 | <tr><td class="h"><a name="477"></a>477</td><td></td><td></td><td></td><td></td><td class="s"> Title : get_desc</td></tr> |
| 683 | <tr><td class="h"><a name="478"></a>478</td><td></td><td></td><td></td><td></td><td class="s"> Usage : my $desc = $obj->get_desc;</td></tr> |
| 684 | <tr><td class="h"><a name="479"></a>479</td><td></td><td></td><td></td><td></td><td class="s"> Function: Returns the object's description (if any).</td></tr> |
| 685 | <tr><td class="h"><a name="480"></a>480</td><td></td><td></td><td></td><td></td><td class="s"> Returns : A string</td></tr> |
| 686 | <tr><td class="h"><a name="481"></a>481</td><td></td><td></td><td></td><td></td><td class="s"> Args : None</td></tr> |
| 687 | <tr><td class="h"><a name="482"></a>482</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 688 | <tr><td class="h"><a name="483"></a>483</td><td></td><td></td><td></td><td></td><td class="s">=cut</td></tr> |
| 689 | <tr><td class="h"><a name="484"></a>484</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 690 | <tr><td class="h"><a name="485"></a>485</td><td></td><td></td><td></td><td></td><td class="s"> sub get_desc {</td></tr> |
| 691 | <tr><td class="h"><a name="486"></a>486</td><td></td><td></td><td></td><td></td><td class="s"> my $self = shift;</td></tr> |
| 692 | <tr><td class="h"><a name="487"></a>487</td><td></td><td></td><td></td><td></td><td class="s"> return $desc{ $self->get_id };</td></tr> |
| 693 | <tr><td class="h"><a name="488"></a>488</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 694 | <tr><td class="h"><a name="489"></a>489</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 695 | <tr><td class="h"><a name="490"></a>490</td><td></td><td></td><td></td><td></td><td class="s">=item get_score()</td></tr> |
| 696 | <tr><td class="h"><a name="491"></a>491</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 697 | <tr><td class="h"><a name="492"></a>492</td><td></td><td></td><td></td><td></td><td class="s">Gets invocant's score.</td></tr> |
| 698 | <tr><td class="h"><a name="493"></a>493</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 699 | <tr><td class="h"><a name="494"></a>494</td><td></td><td></td><td></td><td></td><td class="s"> Type : Accessor</td></tr> |
| 700 | <tr><td class="h"><a name="495"></a>495</td><td></td><td></td><td></td><td></td><td class="s"> Title : get_score</td></tr> |
| 701 | <tr><td class="h"><a name="496"></a>496</td><td></td><td></td><td></td><td></td><td class="s"> Usage : my $score = $obj->get_score;</td></tr> |
| 702 | <tr><td class="h"><a name="497"></a>497</td><td></td><td></td><td></td><td></td><td class="s"> Function: Returns the object's numerical score (if any).</td></tr> |
| 703 | <tr><td class="h"><a name="498"></a>498</td><td></td><td></td><td></td><td></td><td class="s"> Returns : A number</td></tr> |
| 704 | <tr><td class="h"><a name="499"></a>499</td><td></td><td></td><td></td><td></td><td class="s"> Args : None</td></tr> |
| 705 | <tr><td class="h"><a name="500"></a>500</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 706 | <tr><td class="h"><a name="501"></a>501</td><td></td><td></td><td></td><td></td><td class="s">=cut</td></tr> |
| 707 | <tr><td class="h"><a name="502"></a>502</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 708 | <tr><td class="h"><a name="503"></a>503</td><td></td><td></td><td></td><td></td><td class="s"> sub get_score {</td></tr> |
| 709 | <tr><td class="h"><a name="504"></a>504</td><td></td><td></td><td></td><td></td><td class="s"> my $self = shift;</td></tr> |
| 710 | <tr><td class="h"><a name="505"></a>505</td><td></td><td></td><td></td><td></td><td class="s"> $logger->debug("getting score");</td></tr> |
| 711 | <tr><td class="h"><a name="506"></a>506</td><td></td><td></td><td></td><td></td><td class="s"> return $score{ $self->get_id };</td></tr> |
| 712 | <tr><td class="h"><a name="507"></a>507</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 713 | <tr><td class="h"><a name="508"></a>508</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 714 | <tr><td class="h"><a name="509"></a>509</td><td></td><td></td><td></td><td></td><td class="s">=item get_generic()</td></tr> |
| 715 | <tr><td class="h"><a name="510"></a>510</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 716 | <tr><td class="h"><a name="511"></a>511</td><td></td><td></td><td></td><td></td><td class="s">Gets generic hashref or hash value(s).</td></tr> |
| 717 | <tr><td class="h"><a name="512"></a>512</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 718 | <tr><td class="h"><a name="513"></a>513</td><td></td><td></td><td></td><td></td><td class="s"> Type : Accessor</td></tr> |
| 719 | <tr><td class="h"><a name="514"></a>514</td><td></td><td></td><td></td><td></td><td class="s"> Title : get_generic</td></tr> |
| 720 | <tr><td class="h"><a name="515"></a>515</td><td></td><td></td><td></td><td></td><td class="s"> Usage : my $value = $obj->get_generic($key);</td></tr> |
| 721 | <tr><td class="h"><a name="516"></a>516</td><td></td><td></td><td></td><td></td><td class="s"> or</td></tr> |
| 722 | <tr><td class="h"><a name="517"></a>517</td><td></td><td></td><td></td><td></td><td class="s"> my %hash = %{ $obj->get_generic() };</td></tr> |
| 723 | <tr><td class="h"><a name="518"></a>518</td><td></td><td></td><td></td><td></td><td class="s"> Function: Returns the object's generic data. If an</td></tr> |
| 724 | <tr><td class="h"><a name="519"></a>519</td><td></td><td></td><td></td><td></td><td class="s"> argument is used, it is considered a key</td></tr> |
| 725 | <tr><td class="h"><a name="520"></a>520</td><td></td><td></td><td></td><td></td><td class="s"> for which the associated value is returned.</td></tr> |
| 726 | <tr><td class="h"><a name="521"></a>521</td><td></td><td></td><td></td><td></td><td class="s"> Without arguments, a reference to the whole</td></tr> |
| 727 | <tr><td class="h"><a name="522"></a>522</td><td></td><td></td><td></td><td></td><td class="s"> hash is returned.</td></tr> |
| 728 | <tr><td class="h"><a name="523"></a>523</td><td></td><td></td><td></td><td></td><td class="s"> Returns : A value or an array reference of values</td></tr> |
| 729 | <tr><td class="h"><a name="524"></a>524</td><td></td><td></td><td></td><td></td><td class="s"> Args : A key (string) or an array reference of keys</td></tr> |
| 730 | <tr><td class="h"><a name="525"></a>525</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 731 | <tr><td class="h"><a name="526"></a>526</td><td></td><td></td><td></td><td></td><td class="s">=cut</td></tr> |
| 732 | <tr><td class="h"><a name="527"></a>527</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 733 | <tr><td class="h"><a name="528"></a>528</td><td></td><td></td><td></td><td></td><td class="s"> sub get_generic {</td></tr> |
| 734 | <tr><td class="h"><a name="529"></a>529</td><td></td><td></td><td></td><td></td><td class="s"> my ( $self, $key ) = @_;</td></tr> |
| 735 | <tr><td class="h"><a name="530"></a>530</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 736 | <tr><td class="h"><a name="531"></a>531</td><td></td><td></td><td></td><td></td><td class="s"> # retrieve just once</td></tr> |
| 737 | <tr><td class="h"><a name="532"></a>532</td><td></td><td></td><td></td><td></td><td class="s"> my $id = $self->get_id;</td></tr> |
| 738 | <tr><td class="h"><a name="533"></a>533</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 739 | <tr><td class="h"><a name="534"></a>534</td><td></td><td></td><td></td><td></td><td class="s"> # might not even have a generic hash yet, make one on-the-fly</td></tr> |
| 740 | <tr><td class="h"><a name="535"></a>535</td><td></td><td></td><td></td><td></td><td class="s"> if ( not defined $generic{$id} ) {</td></tr> |
| 741 | <tr><td class="h"><a name="536"></a>536</td><td></td><td></td><td></td><td></td><td class="s"> $generic{$id} = {};</td></tr> |
| 742 | <tr><td class="h"><a name="537"></a>537</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 743 | <tr><td class="h"><a name="538"></a>538</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 744 | <tr><td class="h"><a name="539"></a>539</td><td></td><td></td><td></td><td></td><td class="s"> # have an argument</td></tr> |
| 745 | <tr><td class="h"><a name="540"></a>540</td><td></td><td></td><td></td><td></td><td class="s"> if ( defined $key ) {</td></tr> |
| 746 | <tr><td class="h"><a name="541"></a>541</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 747 | <tr><td class="h"><a name="542"></a>542</td><td></td><td></td><td></td><td></td><td class="s"> if ( ref($key) eq 'ARRAY' ) {</td></tr> |
| 748 | <tr><td class="h"><a name="543"></a>543</td><td></td><td></td><td></td><td></td><td class="s"> my @result = @generic{@$key};</td></tr> |
| 749 | <tr><td class="h"><a name="544"></a>544</td><td></td><td></td><td></td><td></td><td class="s"> return \@result;</td></tr> |
| 750 | <tr><td class="h"><a name="545"></a>545</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 751 | <tr><td class="h"><a name="546"></a>546</td><td></td><td></td><td></td><td></td><td class="s"> else {</td></tr> |
| 752 | <tr><td class="h"><a name="547"></a>547</td><td></td><td></td><td></td><td></td><td class="s"> # notify user</td></tr> |
| 753 | <tr><td class="h"><a name="548"></a>548</td><td></td><td></td><td></td><td></td><td class="s"> $logger->debug("getting value for key '$key'");</td></tr> |
| 754 | <tr><td class="h"><a name="549"></a>549</td><td></td><td></td><td></td><td></td><td class="s"> return $generic{$id}->{$key};</td></tr> |
| 755 | <tr><td class="h"><a name="550"></a>550</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 756 | <tr><td class="h"><a name="551"></a>551</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 757 | <tr><td class="h"><a name="552"></a>552</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 758 | <tr><td class="h"><a name="553"></a>553</td><td></td><td></td><td></td><td></td><td class="s"> # no argument, wants whole hash</td></tr> |
| 759 | <tr><td class="h"><a name="554"></a>554</td><td></td><td></td><td></td><td></td><td class="s"> else {</td></tr> |
| 760 | <tr><td class="h"><a name="555"></a>555</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 761 | <tr><td class="h"><a name="556"></a>556</td><td></td><td></td><td></td><td></td><td class="s"> # notify user</td></tr> |
| 762 | <tr><td class="h"><a name="557"></a>557</td><td></td><td></td><td></td><td></td><td class="s"> $logger->debug("retrieving generic hash");</td></tr> |
| 763 | <tr><td class="h"><a name="558"></a>558</td><td></td><td></td><td></td><td></td><td class="s"> return $generic{$id};</td></tr> |
| 764 | <tr><td class="h"><a name="559"></a>559</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 765 | <tr><td class="h"><a name="560"></a>560</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 766 | <tr><td class="h"><a name="561"></a>561</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 767 | <tr><td class="h"><a name="562"></a>562</td><td></td><td></td><td></td><td></td><td class="s">=item get_logger()</td></tr> |
| 768 | <tr><td class="h"><a name="563"></a>563</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 769 | <tr><td class="h"><a name="564"></a>564</td><td></td><td></td><td></td><td></td><td class="s">Gets a logger object.</td></tr> |
| 770 | <tr><td class="h"><a name="565"></a>565</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 771 | <tr><td class="h"><a name="566"></a>566</td><td></td><td></td><td></td><td></td><td class="s"> Type : Accessor</td></tr> |
| 772 | <tr><td class="h"><a name="567"></a>567</td><td></td><td></td><td></td><td></td><td class="s"> Title : get_logger</td></tr> |
| 773 | <tr><td class="h"><a name="568"></a>568</td><td></td><td></td><td></td><td></td><td class="s"> Usage : my $logger = $obj->get_logger;</td></tr> |
| 774 | <tr><td class="h"><a name="569"></a>569</td><td></td><td></td><td></td><td></td><td class="s"> Function: Returns a Bio::Phylo::Util::Logger object</td></tr> |
| 775 | <tr><td class="h"><a name="570"></a>570</td><td></td><td></td><td></td><td></td><td class="s"> Returns : Bio::Phylo::Util::Logger</td></tr> |
| 776 | <tr><td class="h"><a name="571"></a>571</td><td></td><td></td><td></td><td></td><td class="s"> Args : None</td></tr> |
| 777 | <tr><td class="h"><a name="572"></a>572</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 778 | <tr><td class="h"><a name="573"></a>573</td><td></td><td></td><td></td><td></td><td class="s">=cut</td></tr> |
| 779 | <tr><td class="h"><a name="574"></a>574</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 780 | <tr><td class="h"><a name="575"></a>575</td><td class="c3">1</td><td class="c3"><span title="Avg 7µs">7µs</span></td><td></td><td></td><td class="s"><div class="calls"><div class="calls_in"># spent 3µs within Bio::Phylo::get_logger which was called: |
| 781 | # once (3µs+0s) by Bio::Phylo::IO::BEGIN@4 at <a href="Bio-Phylo-Mediators-TaxaMediator-pm-1166-block.html#10">line 10 of Bio/Phylo/Mediators/TaxaMediator.pm</a></div></div> sub get_logger { $logger }</td></tr> |
| 782 | <tr><td class="h"><a name="576"></a>576</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 783 | <tr><td class="h"><a name="577"></a>577</td><td></td><td></td><td></td><td></td><td class="s">=back</td></tr> |
| 784 | <tr><td class="h"><a name="578"></a>578</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 785 | <tr><td class="h"><a name="579"></a>579</td><td></td><td></td><td></td><td></td><td class="s">=head2 PACKAGE METHODS</td></tr> |
| 786 | <tr><td class="h"><a name="580"></a>580</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 787 | <tr><td class="h"><a name="581"></a>581</td><td></td><td></td><td></td><td></td><td class="s">=over</td></tr> |
| 788 | <tr><td class="h"><a name="582"></a>582</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 789 | <tr><td class="h"><a name="583"></a>583</td><td></td><td></td><td></td><td></td><td class="s">=item get()</td></tr> |
| 790 | <tr><td class="h"><a name="584"></a>584</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 791 | <tr><td class="h"><a name="585"></a>585</td><td></td><td></td><td></td><td></td><td class="s">Attempts to execute argument string as method on invocant.</td></tr> |
| 792 | <tr><td class="h"><a name="586"></a>586</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 793 | <tr><td class="h"><a name="587"></a>587</td><td></td><td></td><td></td><td></td><td class="s"> Type : Accessor</td></tr> |
| 794 | <tr><td class="h"><a name="588"></a>588</td><td></td><td></td><td></td><td></td><td class="s"> Title : get</td></tr> |
| 795 | <tr><td class="h"><a name="589"></a>589</td><td></td><td></td><td></td><td></td><td class="s"> Usage : my $treename = $tree->get('get_name');</td></tr> |
| 796 | <tr><td class="h"><a name="590"></a>590</td><td></td><td></td><td></td><td></td><td class="s"> Function: Alternative syntax for safely accessing</td></tr> |
| 797 | <tr><td class="h"><a name="591"></a>591</td><td></td><td></td><td></td><td></td><td class="s"> any of the object data; useful for</td></tr> |
| 798 | <tr><td class="h"><a name="592"></a>592</td><td></td><td></td><td></td><td></td><td class="s"> interpolating runtime $vars.</td></tr> |
| 799 | <tr><td class="h"><a name="593"></a>593</td><td></td><td></td><td></td><td></td><td class="s"> Returns : (context dependent)</td></tr> |
| 800 | <tr><td class="h"><a name="594"></a>594</td><td></td><td></td><td></td><td></td><td class="s"> Args : a SCALAR variable, e.g. $var = 'get_name';</td></tr> |
| 801 | <tr><td class="h"><a name="595"></a>595</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 802 | <tr><td class="h"><a name="596"></a>596</td><td></td><td></td><td></td><td></td><td class="s">=cut</td></tr> |
| 803 | <tr><td class="h"><a name="597"></a>597</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 804 | <tr><td class="h"><a name="598"></a>598</td><td></td><td></td><td></td><td></td><td class="s"> sub get {</td></tr> |
| 805 | <tr><td class="h"><a name="599"></a>599</td><td></td><td></td><td></td><td></td><td class="s"> my ( $self, $var ) = @_;</td></tr> |
| 806 | <tr><td class="h"><a name="600"></a>600</td><td></td><td></td><td></td><td></td><td class="s"> if ( $self->can($var) ) {</td></tr> |
| 807 | <tr><td class="h"><a name="601"></a>601</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 808 | <tr><td class="h"><a name="602"></a>602</td><td></td><td></td><td></td><td></td><td class="s"> # notify user</td></tr> |
| 809 | <tr><td class="h"><a name="603"></a>603</td><td></td><td></td><td></td><td></td><td class="s"> $logger->debug("retrieving return value for method '$var'");</td></tr> |
| 810 | <tr><td class="h"><a name="604"></a>604</td><td></td><td></td><td></td><td></td><td class="s"> return $self->$var;</td></tr> |
| 811 | <tr><td class="h"><a name="605"></a>605</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 812 | <tr><td class="h"><a name="606"></a>606</td><td></td><td></td><td></td><td></td><td class="s"> else {</td></tr> |
| 813 | <tr><td class="h"><a name="607"></a>607</td><td></td><td></td><td></td><td></td><td class="s"> my $ref = ref $self;</td></tr> |
| 814 | <tr><td class="h"><a name="608"></a>608</td><td></td><td></td><td></td><td></td><td class="s"> throw 'UnknownMethod' => "sorry, a '$ref' can't '$var'";</td></tr> |
| 815 | <tr><td class="h"><a name="609"></a>609</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 816 | <tr><td class="h"><a name="610"></a>610</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 817 | <tr><td class="h"><a name="611"></a>611</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 818 | <tr><td class="h"><a name="612"></a>612</td><td></td><td></td><td></td><td></td><td class="s">=item get_obj_by_id()</td></tr> |
| 819 | <tr><td class="h"><a name="613"></a>613</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 820 | <tr><td class="h"><a name="614"></a>614</td><td></td><td></td><td></td><td></td><td class="s">Attempts to fetch an in-memory object by its UID</td></tr> |
| 821 | <tr><td class="h"><a name="615"></a>615</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 822 | <tr><td class="h"><a name="616"></a>616</td><td></td><td></td><td></td><td></td><td class="s"> Type : Accessor</td></tr> |
| 823 | <tr><td class="h"><a name="617"></a>617</td><td></td><td></td><td></td><td></td><td class="s"> Title : get_obj_by_id</td></tr> |
| 824 | <tr><td class="h"><a name="618"></a>618</td><td></td><td></td><td></td><td></td><td class="s"> Usage : my $obj = Bio::Phylo->get_obj_by_id($uid);</td></tr> |
| 825 | <tr><td class="h"><a name="619"></a>619</td><td></td><td></td><td></td><td></td><td class="s"> Function: Fetches an object from the IDPool cache</td></tr> |
| 826 | <tr><td class="h"><a name="620"></a>620</td><td></td><td></td><td></td><td></td><td class="s"> Returns : A Bio::Phylo object </td></tr> |
| 827 | <tr><td class="h"><a name="621"></a>621</td><td></td><td></td><td></td><td></td><td class="s"> Args : A unique id</td></tr> |
| 828 | <tr><td class="h"><a name="622"></a>622</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 829 | <tr><td class="h"><a name="623"></a>623</td><td></td><td></td><td></td><td></td><td class="s">=cut</td></tr> |
| 830 | <tr><td class="h"><a name="624"></a>624</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 831 | <tr><td class="h"><a name="625"></a>625</td><td></td><td></td><td></td><td></td><td class="s"> sub get_obj_by_id {</td></tr> |
| 832 | <tr><td class="h"><a name="626"></a>626</td><td></td><td></td><td></td><td></td><td class="s"> my ( $class, $id ) = @_;</td></tr> |
| 833 | <tr><td class="h"><a name="627"></a>627</td><td></td><td></td><td></td><td></td><td class="s"> return $objects{$id};</td></tr> |
| 834 | <tr><td class="h"><a name="628"></a>628</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 835 | <tr><td class="h"><a name="629"></a>629</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 836 | <tr><td class="h"><a name="630"></a>630</td><td></td><td></td><td></td><td></td><td class="s">=item to_string()</td></tr> |
| 837 | <tr><td class="h"><a name="631"></a>631</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 838 | <tr><td class="h"><a name="632"></a>632</td><td></td><td></td><td></td><td></td><td class="s">Serializes object to general purpose string</td></tr> |
| 839 | <tr><td class="h"><a name="633"></a>633</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 840 | <tr><td class="h"><a name="634"></a>634</td><td></td><td></td><td></td><td></td><td class="s"> Type : Serializer</td></tr> |
| 841 | <tr><td class="h"><a name="635"></a>635</td><td></td><td></td><td></td><td></td><td class="s"> Title : to_string()</td></tr> |
| 842 | <tr><td class="h"><a name="636"></a>636</td><td></td><td></td><td></td><td></td><td class="s"> Usage : print $obj->to_string();</td></tr> |
| 843 | <tr><td class="h"><a name="637"></a>637</td><td></td><td></td><td></td><td></td><td class="s"> Function: Serializes object to general purpose string</td></tr> |
| 844 | <tr><td class="h"><a name="638"></a>638</td><td></td><td></td><td></td><td></td><td class="s"> Returns : String </td></tr> |
| 845 | <tr><td class="h"><a name="639"></a>639</td><td></td><td></td><td></td><td></td><td class="s"> Args : None</td></tr> |
| 846 | <tr><td class="h"><a name="640"></a>640</td><td></td><td></td><td></td><td></td><td class="s"> Comments: This is YAML</td></tr> |
| 847 | <tr><td class="h"><a name="641"></a>641</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 848 | <tr><td class="h"><a name="642"></a>642</td><td></td><td></td><td></td><td></td><td class="s">=cut</td></tr> |
| 849 | <tr><td class="h"><a name="643"></a>643</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 850 | <tr><td class="h"><a name="644"></a>644</td><td></td><td></td><td></td><td></td><td class="s"> sub to_string {</td></tr> |
| 851 | <tr><td class="h"><a name="645"></a>645</td><td></td><td></td><td></td><td></td><td class="s"> my $self = shift;</td></tr> |
| 852 | <tr><td class="h"><a name="646"></a>646</td><td></td><td></td><td></td><td></td><td class="s"> my $class = ref $self;</td></tr> |
| 853 | <tr><td class="h"><a name="647"></a>647</td><td></td><td></td><td></td><td></td><td class="s"> my $id = $self->get_id;</td></tr> |
| 854 | <tr><td class="h"><a name="648"></a>648</td><td></td><td></td><td></td><td></td><td class="s"> my $internal_name = $self->get_internal_name;</td></tr> |
| 855 | <tr><td class="h"><a name="649"></a>649</td><td></td><td></td><td></td><td></td><td class="s"> my $name = $self->get_name;</td></tr> |
| 856 | <tr><td class="h"><a name="650"></a>650</td><td></td><td></td><td></td><td></td><td class="s"> my $score = $self->get_score;</td></tr> |
| 857 | <tr><td class="h"><a name="651"></a>651</td><td></td><td></td><td></td><td></td><td class="s"> my $desc = $self->get_desc;</td></tr> |
| 858 | <tr><td class="h"><a name="652"></a>652</td><td></td><td></td><td></td><td></td><td class="s"> return <<"SERIALIZED_OBJECT";</td></tr> |
| 859 | <tr><td class="h"><a name="653"></a>653</td><td></td><td></td><td></td><td></td><td class="s">class: $class</td></tr> |
| 860 | <tr><td class="h"><a name="654"></a>654</td><td></td><td></td><td></td><td></td><td class="s">id: $id</td></tr> |
| 861 | <tr><td class="h"><a name="655"></a>655</td><td></td><td></td><td></td><td></td><td class="s">internal_name: $internal_name</td></tr> |
| 862 | <tr><td class="h"><a name="656"></a>656</td><td></td><td></td><td></td><td></td><td class="s">name: $name</td></tr> |
| 863 | <tr><td class="h"><a name="657"></a>657</td><td></td><td></td><td></td><td></td><td class="s">score: $score</td></tr> |
| 864 | <tr><td class="h"><a name="658"></a>658</td><td></td><td></td><td></td><td></td><td class="s">desc: $desc</td></tr> |
| 865 | <tr><td class="h"><a name="659"></a>659</td><td></td><td></td><td></td><td></td><td class="s">SERIALIZED_OBJECT</td></tr> |
| 866 | <tr><td class="h"><a name="660"></a>660</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 867 | <tr><td class="h"><a name="661"></a>661</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 868 | <tr><td class="h"><a name="662"></a>662</td><td></td><td></td><td></td><td></td><td class="s">=item clone()</td></tr> |
| 869 | <tr><td class="h"><a name="663"></a>663</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 870 | <tr><td class="h"><a name="664"></a>664</td><td></td><td></td><td></td><td></td><td class="s">Clones invocant.</td></tr> |
| 871 | <tr><td class="h"><a name="665"></a>665</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 872 | <tr><td class="h"><a name="666"></a>666</td><td></td><td></td><td></td><td></td><td class="s"> Type : Utility method</td></tr> |
| 873 | <tr><td class="h"><a name="667"></a>667</td><td></td><td></td><td></td><td></td><td class="s"> Title : clone</td></tr> |
| 874 | <tr><td class="h"><a name="668"></a>668</td><td></td><td></td><td></td><td></td><td class="s"> Usage : my $clone = $object->clone;</td></tr> |
| 875 | <tr><td class="h"><a name="669"></a>669</td><td></td><td></td><td></td><td></td><td class="s"> Function: Creates a copy of the invocant object.</td></tr> |
| 876 | <tr><td class="h"><a name="670"></a>670</td><td></td><td></td><td></td><td></td><td class="s"> Returns : A copy of the invocant.</td></tr> |
| 877 | <tr><td class="h"><a name="671"></a>671</td><td></td><td></td><td></td><td></td><td class="s"> Args : None.</td></tr> |
| 878 | <tr><td class="h"><a name="672"></a>672</td><td></td><td></td><td></td><td></td><td class="s"> Comments: Cloning is currently experimental, use with caution.</td></tr> |
| 879 | <tr><td class="h"><a name="673"></a>673</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 880 | <tr><td class="h"><a name="674"></a>674</td><td></td><td></td><td></td><td></td><td class="s">=cut</td></tr> |
| 881 | <tr><td class="h"><a name="675"></a>675</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 882 | <tr><td class="h"><a name="676"></a>676</td><td></td><td></td><td></td><td></td><td class="s"> # TODO this needs overrides in a number of subclasses,</td></tr> |
| 883 | <tr><td class="h"><a name="677"></a>677</td><td></td><td></td><td></td><td></td><td class="s"> # in particular in Bio::Phylo::Taxa and Bio::Phylo::Taxa::Taxon</td></tr> |
| 884 | <tr><td class="h"><a name="678"></a>678</td><td></td><td></td><td></td><td></td><td class="s"> # classes because of the asymmetry between set_forest/get_forests,</td></tr> |
| 885 | <tr><td class="h"><a name="679"></a>679</td><td></td><td></td><td></td><td></td><td class="s"> # set_node/get_nodes etc.</td></tr> |
| 886 | <tr><td class="h"><a name="680"></a>680</td><td></td><td></td><td></td><td></td><td class="s"> sub clone {</td></tr> |
| 887 | <tr><td class="h"><a name="681"></a>681</td><td></td><td></td><td></td><td></td><td class="s"> my ( $self, %subs ) = @_;</td></tr> |
| 888 | <tr><td class="h"><a name="682"></a>682</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 889 | <tr><td class="h"><a name="683"></a>683</td><td></td><td></td><td></td><td></td><td class="s"> # may not work yet! warn user</td></tr> |
| 890 | <tr><td class="h"><a name="684"></a>684</td><td></td><td></td><td></td><td></td><td class="s"> $logger->info("cloning is experimental, use with caution");</td></tr> |
| 891 | <tr><td class="h"><a name="685"></a>685</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 892 | <tr><td class="h"><a name="686"></a>686</td><td></td><td></td><td></td><td></td><td class="s"> # get inheritance tree</td></tr> |
| 893 | <tr><td class="h"><a name="687"></a>687</td><td></td><td></td><td></td><td></td><td class="s"> my ( $class, $isa, $seen ) = ( ref($self), [], {} );</td></tr> |
| 894 | <tr><td class="h"><a name="688"></a>688</td><td></td><td></td><td></td><td></td><td class="s"> _recurse_isa( $class, $isa, $seen );</td></tr> |
| 895 | <tr><td class="h"><a name="689"></a>689</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 896 | <tr><td class="h"><a name="690"></a>690</td><td></td><td></td><td></td><td></td><td class="s"> # walk symbol table, get symmetrical set_foo/get_foo pairs</td></tr> |
| 897 | <tr><td class="h"><a name="691"></a>691</td><td></td><td></td><td></td><td></td><td class="s"> my %methods;</td></tr> |
| 898 | <tr><td class="h"><a name="692"></a>692</td><td></td><td></td><td></td><td></td><td class="s"> for my $package ( $class, @{$isa} ) {</td></tr> |
| 899 | <tr><td class="h"><a name="693"></a>693</td><td></td><td></td><td></td><td></td><td class="s"> my %symtable;</td></tr> |
| 900 | <tr><td class="h"><a name="694"></a>694</td><td></td><td></td><td></td><td></td><td class="s"> eval "\%symtable = \%${package}::";</td></tr> |
| 901 | <tr><td class="h"><a name="695"></a>695</td><td></td><td></td><td></td><td></td><td class="s"> SETTER: for my $setter ( keys %symtable ) {</td></tr> |
| 902 | <tr><td class="h"><a name="696"></a>696</td><td></td><td></td><td></td><td></td><td class="s"> next SETTER if $setter !~ m/^set_/;</td></tr> |
| 903 | <tr><td class="h"><a name="697"></a>697</td><td></td><td></td><td></td><td></td><td class="s"> my $getter = $setter;</td></tr> |
| 904 | <tr><td class="h"><a name="698"></a>698</td><td></td><td></td><td></td><td></td><td class="s"> $getter =~ s/^s/g/;</td></tr> |
| 905 | <tr><td class="h"><a name="699"></a>699</td><td></td><td></td><td></td><td></td><td class="s"> next SETTER if not exists $symtable{$getter};</td></tr> |
| 906 | <tr><td class="h"><a name="700"></a>700</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 907 | <tr><td class="h"><a name="701"></a>701</td><td></td><td></td><td></td><td></td><td class="s"> # have a symmetrical set_foo/get_foo pair, check</td></tr> |
| 908 | <tr><td class="h"><a name="702"></a>702</td><td></td><td></td><td></td><td></td><td class="s"> # if they're code (not variables, for example)</td></tr> |
| 909 | <tr><td class="h"><a name="703"></a>703</td><td></td><td></td><td></td><td></td><td class="s"> my $get_ref = $class->can($getter);</td></tr> |
| 910 | <tr><td class="h"><a name="704"></a>704</td><td></td><td></td><td></td><td></td><td class="s"> my $set_ref = $class->can($setter);</td></tr> |
| 911 | <tr><td class="h"><a name="705"></a>705</td><td></td><td></td><td></td><td></td><td class="s"> if ( looks_like_instance( $get_ref, 'CODE' )</td></tr> |
| 912 | <tr><td class="h"><a name="706"></a>706</td><td></td><td></td><td></td><td></td><td class="s"> and looks_like_instance( $set_ref, 'CODE' ) )</td></tr> |
| 913 | <tr><td class="h"><a name="707"></a>707</td><td></td><td></td><td></td><td></td><td class="s"> {</td></tr> |
| 914 | <tr><td class="h"><a name="708"></a>708</td><td></td><td></td><td></td><td></td><td class="s"> $methods{$getter} = $setter;</td></tr> |
| 915 | <tr><td class="h"><a name="709"></a>709</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 916 | <tr><td class="h"><a name="710"></a>710</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 917 | <tr><td class="h"><a name="711"></a>711</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 918 | <tr><td class="h"><a name="712"></a>712</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 919 | <tr><td class="h"><a name="713"></a>713</td><td></td><td></td><td></td><td></td><td class="s"> # instantiate the clone</td></tr> |
| 920 | <tr><td class="h"><a name="714"></a>714</td><td></td><td></td><td></td><td></td><td class="s"> my @new;</td></tr> |
| 921 | <tr><td class="h"><a name="715"></a>715</td><td></td><td></td><td></td><td></td><td class="s"> if ( $subs{'new'} ) {</td></tr> |
| 922 | <tr><td class="h"><a name="716"></a>716</td><td></td><td></td><td></td><td></td><td class="s"> @new = @{ $subs{'new'} };</td></tr> |
| 923 | <tr><td class="h"><a name="717"></a>717</td><td></td><td></td><td></td><td></td><td class="s"> delete $subs{'new'};</td></tr> |
| 924 | <tr><td class="h"><a name="718"></a>718</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 925 | <tr><td class="h"><a name="719"></a>719</td><td></td><td></td><td></td><td></td><td class="s"> my $clone = $class->new(@new);</td></tr> |
| 926 | <tr><td class="h"><a name="720"></a>720</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 927 | <tr><td class="h"><a name="721"></a>721</td><td></td><td></td><td></td><td></td><td class="s"> # populate the clone</td></tr> |
| 928 | <tr><td class="h"><a name="722"></a>722</td><td></td><td></td><td></td><td></td><td class="s"> for my $getter ( keys %methods ) {</td></tr> |
| 929 | <tr><td class="h"><a name="723"></a>723</td><td></td><td></td><td></td><td></td><td class="s"> my $setter = $methods{$getter};</td></tr> |
| 930 | <tr><td class="h"><a name="724"></a>724</td><td></td><td></td><td></td><td></td><td class="s"> if ( exists $subs{$setter} ) {</td></tr> |
| 931 | <tr><td class="h"><a name="725"></a>725</td><td></td><td></td><td></td><td></td><td class="s"> $logger->info("method $setter for $clone overridden");</td></tr> |
| 932 | <tr><td class="h"><a name="726"></a>726</td><td></td><td></td><td></td><td></td><td class="s"> if ( looks_like_instance( $subs{$setter}, 'CODE' ) ) {</td></tr> |
| 933 | <tr><td class="h"><a name="727"></a>727</td><td></td><td></td><td></td><td></td><td class="s"> $subs{$setter}->( $self, $clone );</td></tr> |
| 934 | <tr><td class="h"><a name="728"></a>728</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 935 | <tr><td class="h"><a name="729"></a>729</td><td></td><td></td><td></td><td></td><td class="s"> delete $subs{$setter};</td></tr> |
| 936 | <tr><td class="h"><a name="730"></a>730</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 937 | <tr><td class="h"><a name="731"></a>731</td><td></td><td></td><td></td><td></td><td class="s"> else {</td></tr> |
| 938 | <tr><td class="h"><a name="732"></a>732</td><td></td><td></td><td></td><td></td><td class="s"> eval {</td></tr> |
| 939 | <tr><td class="h"><a name="733"></a>733</td><td></td><td></td><td></td><td></td><td class="s"> $logger->info("copying $getter => $setter");</td></tr> |
| 940 | <tr><td class="h"><a name="734"></a>734</td><td></td><td></td><td></td><td></td><td class="s"> my $value = $self->$getter;</td></tr> |
| 941 | <tr><td class="h"><a name="735"></a>735</td><td></td><td></td><td></td><td></td><td class="s"> if ( defined $value ) {</td></tr> |
| 942 | <tr><td class="h"><a name="736"></a>736</td><td></td><td></td><td></td><td></td><td class="s"> $clone->$setter($value);</td></tr> |
| 943 | <tr><td class="h"><a name="737"></a>737</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 944 | <tr><td class="h"><a name="738"></a>738</td><td></td><td></td><td></td><td></td><td class="s"> };</td></tr> |
| 945 | <tr><td class="h"><a name="739"></a>739</td><td></td><td></td><td></td><td></td><td class="s"> if ($@) {</td></tr> |
| 946 | <tr><td class="h"><a name="740"></a>740</td><td></td><td></td><td></td><td></td><td class="s"> $logger->warn("failed copy of $getter => $setter: \n$@");</td></tr> |
| 947 | <tr><td class="h"><a name="741"></a>741</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 948 | <tr><td class="h"><a name="742"></a>742</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 949 | <tr><td class="h"><a name="743"></a>743</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 950 | <tr><td class="h"><a name="744"></a>744</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 951 | <tr><td class="h"><a name="745"></a>745</td><td></td><td></td><td></td><td></td><td class="s"> # execute additional code refs</td></tr> |
| 952 | <tr><td class="h"><a name="746"></a>746</td><td></td><td></td><td></td><td></td><td class="s"> $_->( $self, $clone )</td></tr> |
| 953 | <tr><td class="h"><a name="747"></a>747</td><td></td><td></td><td></td><td></td><td class="s"> for ( grep { looks_like_instance( $_, 'CODE' ) } values %subs );</td></tr> |
| 954 | <tr><td class="h"><a name="748"></a>748</td><td></td><td></td><td></td><td></td><td class="s"> return $clone;</td></tr> |
| 955 | <tr><td class="h"><a name="749"></a>749</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 956 | <tr><td class="h"><a name="750"></a>750</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 957 | <tr><td class="h"><a name="751"></a>751</td><td></td><td></td><td></td><td></td><td class="s">=item VERBOSE()</td></tr> |
| 958 | <tr><td class="h"><a name="752"></a>752</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 959 | <tr><td class="h"><a name="753"></a>753</td><td></td><td></td><td></td><td></td><td class="s">Getter and setter for the verbosity level. Refer to L<Bio::Phylo::Util::Logger> for more</td></tr> |
| 960 | <tr><td class="h"><a name="754"></a>754</td><td></td><td></td><td></td><td></td><td class="s">info on available verbosity levels.</td></tr> |
| 961 | <tr><td class="h"><a name="755"></a>755</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 962 | <tr><td class="h"><a name="756"></a>756</td><td></td><td></td><td></td><td></td><td class="s"> Type : Accessor</td></tr> |
| 963 | <tr><td class="h"><a name="757"></a>757</td><td></td><td></td><td></td><td></td><td class="s"> Title : VERBOSE()</td></tr> |
| 964 | <tr><td class="h"><a name="758"></a>758</td><td></td><td></td><td></td><td></td><td class="s"> Usage : Bio::Phylo->VERBOSE( -level => $level )</td></tr> |
| 965 | <tr><td class="h"><a name="759"></a>759</td><td></td><td></td><td></td><td></td><td class="s"> Function: Sets/gets verbose level</td></tr> |
| 966 | <tr><td class="h"><a name="760"></a>760</td><td></td><td></td><td></td><td></td><td class="s"> Returns : Verbose level</td></tr> |
| 967 | <tr><td class="h"><a name="761"></a>761</td><td></td><td></td><td></td><td></td><td class="s"> Args : -level => $level</td></tr> |
| 968 | <tr><td class="h"><a name="762"></a>762</td><td></td><td></td><td></td><td></td><td class="s"> Comments:</td></tr> |
| 969 | <tr><td class="h"><a name="763"></a>763</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 970 | <tr><td class="h"><a name="764"></a>764</td><td></td><td></td><td></td><td></td><td class="s">=cut</td></tr> |
| 971 | <tr><td class="h"><a name="765"></a>765</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 972 | <tr><td class="h"><a name="766"></a>766</td><td></td><td></td><td></td><td></td><td class="s"> # Verbosity is mostly handled by the logger, actually. This method</td></tr> |
| 973 | <tr><td class="h"><a name="767"></a>767</td><td></td><td></td><td></td><td></td><td class="s"> # is just here for backward compatibility (and ease of use).</td></tr> |
| 974 | <tr><td class="h"><a name="768"></a>768</td><td></td><td></td><td></td><td></td><td class="s"> # TODO have a facility to turn log levels (warn/error/fatal) into</td></tr> |
| 975 | <tr><td class="h"><a name="769"></a>769</td><td></td><td></td><td></td><td></td><td class="s"> # throws</td></tr> |
| 976 | <tr><td class="h"><a name="770"></a>770</td><td></td><td></td><td></td><td></td><td class="s"> sub VERBOSE {</td></tr> |
| 977 | <tr><td class="h"><a name="771"></a>771</td><td></td><td></td><td></td><td></td><td class="s"> my $class = shift;</td></tr> |
| 978 | <tr><td class="h"><a name="772"></a>772</td><td></td><td></td><td></td><td></td><td class="s"> if (@_) {</td></tr> |
| 979 | <tr><td class="h"><a name="773"></a>773</td><td></td><td></td><td></td><td></td><td class="s"> my %opt = looks_like_hash @_;</td></tr> |
| 980 | <tr><td class="h"><a name="774"></a>774</td><td></td><td></td><td></td><td></td><td class="s"> $logger->VERBOSE(%opt);</td></tr> |
| 981 | <tr><td class="h"><a name="775"></a>775</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 982 | <tr><td class="h"><a name="776"></a>776</td><td></td><td></td><td></td><td></td><td class="s"> # notify user</td></tr> |
| 983 | <tr><td class="h"><a name="777"></a>777</td><td></td><td></td><td></td><td></td><td class="s"> $logger->info("Changed verbosity level to '$opt{-level}'");</td></tr> |
| 984 | <tr><td class="h"><a name="778"></a>778</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 985 | <tr><td class="h"><a name="779"></a>779</td><td></td><td></td><td></td><td></td><td class="s"> return $Bio::Phylo::Util::Logger::VERBOSE;</td></tr> |
| 986 | <tr><td class="h"><a name="780"></a>780</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 987 | <tr><td class="h"><a name="781"></a>781</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 988 | <tr><td class="h"><a name="782"></a>782</td><td></td><td></td><td></td><td></td><td class="s">=item CITATION()</td></tr> |
| 989 | <tr><td class="h"><a name="783"></a>783</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 990 | <tr><td class="h"><a name="784"></a>784</td><td></td><td></td><td></td><td></td><td class="s">Returns suggested citation.</td></tr> |
| 991 | <tr><td class="h"><a name="785"></a>785</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 992 | <tr><td class="h"><a name="786"></a>786</td><td></td><td></td><td></td><td></td><td class="s"> Type : Accessor</td></tr> |
| 993 | <tr><td class="h"><a name="787"></a>787</td><td></td><td></td><td></td><td></td><td class="s"> Title : CITATION</td></tr> |
| 994 | <tr><td class="h"><a name="788"></a>788</td><td></td><td></td><td></td><td></td><td class="s"> Usage : $phylo->CITATION;</td></tr> |
| 995 | <tr><td class="h"><a name="789"></a>789</td><td></td><td></td><td></td><td></td><td class="s"> Function: Returns suggested citation.</td></tr> |
| 996 | <tr><td class="h"><a name="790"></a>790</td><td></td><td></td><td></td><td></td><td class="s"> Returns : Returns suggested citation.</td></tr> |
| 997 | <tr><td class="h"><a name="791"></a>791</td><td></td><td></td><td></td><td></td><td class="s"> Args : None</td></tr> |
| 998 | <tr><td class="h"><a name="792"></a>792</td><td></td><td></td><td></td><td></td><td class="s"> Comments:</td></tr> |
| 999 | <tr><td class="h"><a name="793"></a>793</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 1000 | <tr><td class="h"><a name="794"></a>794</td><td></td><td></td><td></td><td></td><td class="s">=cut</td></tr> |
| 1001 | <tr><td class="h"><a name="795"></a>795</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 1002 | <tr><td class="h"><a name="796"></a>796</td><td></td><td></td><td></td><td></td><td class="s"> sub CITATION {</td></tr> |
| 1003 | <tr><td class="h"><a name="797"></a>797</td><td></td><td></td><td></td><td></td><td class="s"> return <<'CITATION';</td></tr> |
| 1004 | <tr><td class="h"><a name="798"></a>798</td><td></td><td></td><td></td><td></td><td class="s">Rutger A Vos, Jason Caravas, Klaas Hartmann, Mark A Jensen and Chase Miller, 2011.</td></tr> |
| 1005 | <tr><td class="h"><a name="799"></a>799</td><td></td><td></td><td></td><td></td><td class="s">Bio::Phylo - phyloinformatic analysis using Perl. BMC Bioinformatics 12:63.</td></tr> |
| 1006 | <tr><td class="h"><a name="800"></a>800</td><td></td><td></td><td></td><td></td><td class="s">doi:10.1186/1471-2105-12-63</td></tr> |
| 1007 | <tr><td class="h"><a name="801"></a>801</td><td></td><td></td><td></td><td></td><td class="s">CITATION</td></tr> |
| 1008 | <tr><td class="h"><a name="802"></a>802</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 1009 | <tr><td class="h"><a name="803"></a>803</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 1010 | <tr><td class="h"><a name="804"></a>804</td><td></td><td></td><td></td><td></td><td class="s">=item VERSION()</td></tr> |
| 1011 | <tr><td class="h"><a name="805"></a>805</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 1012 | <tr><td class="h"><a name="806"></a>806</td><td></td><td></td><td></td><td></td><td class="s">Gets version number (including revision number).</td></tr> |
| 1013 | <tr><td class="h"><a name="807"></a>807</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 1014 | <tr><td class="h"><a name="808"></a>808</td><td></td><td></td><td></td><td></td><td class="s"> Type : Accessor</td></tr> |
| 1015 | <tr><td class="h"><a name="809"></a>809</td><td></td><td></td><td></td><td></td><td class="s"> Title : VERSION</td></tr> |
| 1016 | <tr><td class="h"><a name="810"></a>810</td><td></td><td></td><td></td><td></td><td class="s"> Usage : $phylo->VERSION;</td></tr> |
| 1017 | <tr><td class="h"><a name="811"></a>811</td><td></td><td></td><td></td><td></td><td class="s"> Function: Returns version number</td></tr> |
| 1018 | <tr><td class="h"><a name="812"></a>812</td><td></td><td></td><td></td><td></td><td class="s"> (including SVN revision number).</td></tr> |
| 1019 | <tr><td class="h"><a name="813"></a>813</td><td></td><td></td><td></td><td></td><td class="s"> Alias :</td></tr> |
| 1020 | <tr><td class="h"><a name="814"></a>814</td><td></td><td></td><td></td><td></td><td class="s"> Returns : SCALAR</td></tr> |
| 1021 | <tr><td class="h"><a name="815"></a>815</td><td></td><td></td><td></td><td></td><td class="s"> Args : NONE</td></tr> |
| 1022 | <tr><td class="h"><a name="816"></a>816</td><td></td><td></td><td></td><td></td><td class="s"> Comments:</td></tr> |
| 1023 | <tr><td class="h"><a name="817"></a>817</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 1024 | <tr><td class="h"><a name="818"></a>818</td><td></td><td></td><td></td><td></td><td class="s">=cut</td></tr> |
| 1025 | <tr><td class="h"><a name="819"></a>819</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 1026 | <tr><td class="h"><a name="820"></a>820</td><td></td><td></td><td></td><td></td><td class="s"> sub VERSION { $VERSION }</td></tr> |
| 1027 | <tr><td class="h"><a name="821"></a>821</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 1028 | <tr><td class="h"><a name="822"></a>822</td><td></td><td></td><td></td><td></td><td class="s">=begin comment</td></tr> |
| 1029 | <tr><td class="h"><a name="823"></a>823</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 1030 | <tr><td class="h"><a name="824"></a>824</td><td></td><td></td><td></td><td></td><td class="s">Invocant destructor.</td></tr> |
| 1031 | <tr><td class="h"><a name="825"></a>825</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 1032 | <tr><td class="h"><a name="826"></a>826</td><td></td><td></td><td></td><td></td><td class="s"> Type : Destructor</td></tr> |
| 1033 | <tr><td class="h"><a name="827"></a>827</td><td></td><td></td><td></td><td></td><td class="s"> Title : DESTROY</td></tr> |
| 1034 | <tr><td class="h"><a name="828"></a>828</td><td></td><td></td><td></td><td></td><td class="s"> Usage : $phylo->DESTROY</td></tr> |
| 1035 | <tr><td class="h"><a name="829"></a>829</td><td></td><td></td><td></td><td></td><td class="s"> Function: Destroys Phylo object</td></tr> |
| 1036 | <tr><td class="h"><a name="830"></a>830</td><td></td><td></td><td></td><td></td><td class="s"> Alias :</td></tr> |
| 1037 | <tr><td class="h"><a name="831"></a>831</td><td></td><td></td><td></td><td></td><td class="s"> Returns : TRUE</td></tr> |
| 1038 | <tr><td class="h"><a name="832"></a>832</td><td></td><td></td><td></td><td></td><td class="s"> Args : none</td></tr> |
| 1039 | <tr><td class="h"><a name="833"></a>833</td><td></td><td></td><td></td><td></td><td class="s"> Comments: You don't really need this,</td></tr> |
| 1040 | <tr><td class="h"><a name="834"></a>834</td><td></td><td></td><td></td><td></td><td class="s"> it is called automatically when</td></tr> |
| 1041 | <tr><td class="h"><a name="835"></a>835</td><td></td><td></td><td></td><td></td><td class="s"> the object goes out of scope.</td></tr> |
| 1042 | <tr><td class="h"><a name="836"></a>836</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 1043 | <tr><td class="h"><a name="837"></a>837</td><td></td><td></td><td></td><td></td><td class="s">=end comment</td></tr> |
| 1044 | <tr><td class="h"><a name="838"></a>838</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 1045 | <tr><td class="h"><a name="839"></a>839</td><td></td><td></td><td></td><td></td><td class="s">=cut</td></tr> |
| 1046 | <tr><td class="h"><a name="840"></a>840</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 1047 | <tr><td class="h"><a name="841"></a>841</td><td></td><td></td><td></td><td></td><td class="s"> {</td></tr> |
| 1048 | <tr><td class="h"><a name="842"></a>842</td><td class="c3">2</td><td class="c0"><span title="Avg 66µs">132µs</span></td><td class="c3">2</td><td class="c0">85µs</td><td class="s"><div class="calls"><div class="calls_in"># spent 54µs (22+31) within Bio::Phylo::BEGIN@842 which was called: |
| 1049 | # once (22µs+31µs) by Bio::Phylo::IO::BEGIN@4 at <a href="Bio-Phylo-pm-1138-block.html#842">line 842</a></div></div> no warnings 'recursion';<div class="calls"><div class="calls_out"> # spent 54µs making 1 call to <a href="Bio-Phylo-pm-1138-block.html#842">Bio::Phylo::BEGIN@842</a> |
| 1050 | # spent 31µs making 1 call to <a href="warnings-pm-2-block.html#401">warnings::unimport</a></div></div></td></tr> |
| 1051 | <tr><td class="h"><a name="843"></a>843</td><td class="c3">1</td><td class="c3"><span title="Avg 500ns">500ns</span></td><td></td><td></td><td class="s"> my %isa_for_class;</td></tr> |
| 1052 | <tr><td class="h"><a name="844"></a>844</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 1053 | <tr><td class="h"><a name="845"></a>845</td><td></td><td></td><td></td><td></td><td class="s"> sub DESTROY {</td></tr> |
| 1054 | <tr><td class="h"><a name="846"></a>846</td><td></td><td></td><td></td><td></td><td class="s"> my $self = shift;</td></tr> |
| 1055 | <tr><td class="h"><a name="847"></a>847</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 1056 | <tr><td class="h"><a name="848"></a>848</td><td></td><td></td><td></td><td></td><td class="s"> # delete from get_obj_by_id</td></tr> |
| 1057 | <tr><td class="h"><a name="849"></a>849</td><td></td><td></td><td></td><td></td><td class="s"> my $id;</td></tr> |
| 1058 | <tr><td class="h"><a name="850"></a>850</td><td></td><td></td><td></td><td></td><td class="s"> if ( defined( $id = $self->get_id ) ) {</td></tr> |
| 1059 | <tr><td class="h"><a name="851"></a>851</td><td></td><td></td><td></td><td></td><td class="s"> delete $objects{$id};</td></tr> |
| 1060 | <tr><td class="h"><a name="852"></a>852</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 1061 | <tr><td class="h"><a name="853"></a>853</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 1062 | <tr><td class="h"><a name="854"></a>854</td><td></td><td></td><td></td><td></td><td class="s"> # build full @ISA from child to here</td></tr> |
| 1063 | <tr><td class="h"><a name="855"></a>855</td><td></td><td></td><td></td><td></td><td class="s"> my $class = ref $self;</td></tr> |
| 1064 | <tr><td class="h"><a name="856"></a>856</td><td></td><td></td><td></td><td></td><td class="s"> my $isa;</td></tr> |
| 1065 | <tr><td class="h"><a name="857"></a>857</td><td></td><td></td><td></td><td></td><td class="s"> unless ( $isa = $isa_for_class{$class} ) {</td></tr> |
| 1066 | <tr><td class="h"><a name="858"></a>858</td><td></td><td></td><td></td><td></td><td class="s"> $isa = [];</td></tr> |
| 1067 | <tr><td class="h"><a name="859"></a>859</td><td></td><td></td><td></td><td></td><td class="s"> my $seen = {};</td></tr> |
| 1068 | <tr><td class="h"><a name="860"></a>860</td><td></td><td></td><td></td><td></td><td class="s"> _recurse_isa( $class, $isa, $seen );</td></tr> |
| 1069 | <tr><td class="h"><a name="861"></a>861</td><td></td><td></td><td></td><td></td><td class="s"> $isa_for_class{$class} = $isa;</td></tr> |
| 1070 | <tr><td class="h"><a name="862"></a>862</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 1071 | <tr><td class="h"><a name="863"></a>863</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 1072 | <tr><td class="h"><a name="864"></a>864</td><td></td><td></td><td></td><td></td><td class="s"> # call *all* _cleanup methods, wouldn't work if simply SUPER::_cleanup</td></tr> |
| 1073 | <tr><td class="h"><a name="865"></a>865</td><td></td><td></td><td></td><td></td><td class="s"> # given multiple inheritance</td></tr> |
| 1074 | <tr><td class="h"><a name="866"></a>866</td><td></td><td></td><td></td><td></td><td class="s"> {</td></tr> |
| 1075 | <tr><td class="h"><a name="867"></a>867</td><td class="c3">2</td><td class="c0"><span title="Avg 41µs">82µs</span></td><td class="c3">2</td><td class="c1">66µs</td><td class="s"><div class="calls"><div class="calls_in"># spent 39µs (12+27) within Bio::Phylo::BEGIN@867 which was called: |
| 1076 | # once (12µs+27µs) by Bio::Phylo::IO::BEGIN@4 at <a href="Bio-Phylo-pm-1138-block.html#867">line 867</a></div></div> no strict 'refs';<div class="calls"><div class="calls_out"> # spent 39µs making 1 call to <a href="Bio-Phylo-pm-1138-block.html#867">Bio::Phylo::BEGIN@867</a> |
| 1077 | # spent 27µs making 1 call to <a href="strict-pm-3-block.html#39">strict::unimport</a></div></div></td></tr> |
| 1078 | <tr><td class="h"><a name="868"></a>868</td><td></td><td></td><td></td><td></td><td class="s"> for my $SUPER ( @{$isa} ) {</td></tr> |
| 1079 | <tr><td class="h"><a name="869"></a>869</td><td></td><td></td><td></td><td></td><td class="s"> if ( $SUPER->can('_cleanup') ) {</td></tr> |
| 1080 | <tr><td class="h"><a name="870"></a>870</td><td></td><td></td><td></td><td></td><td class="s"> my $cleanup = "${SUPER}::_cleanup";</td></tr> |
| 1081 | <tr><td class="h"><a name="871"></a>871</td><td></td><td></td><td></td><td></td><td class="s"> $self->$cleanup;</td></tr> |
| 1082 | <tr><td class="h"><a name="872"></a>872</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 1083 | <tr><td class="h"><a name="873"></a>873</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 1084 | <tr><td class="h"><a name="874"></a>874</td><td class="c3">2</td><td class="c0"><span title="Avg 57µs">114µs</span></td><td class="c3">2</td><td class="c3">21µs</td><td class="s"><div class="calls"><div class="calls_in"># spent 16µs (12+5) within Bio::Phylo::BEGIN@874 which was called: |
| 1085 | # once (12µs+5µs) by Bio::Phylo::IO::BEGIN@4 at <a href="Bio-Phylo-pm-1138-block.html#874">line 874</a></div></div> use strict;<div class="calls"><div class="calls_out"> # spent 16µs making 1 call to <a href="Bio-Phylo-pm-1138-block.html#874">Bio::Phylo::BEGIN@874</a> |
| 1086 | # spent 4µs making 1 call to <a href="strict-pm-3-block.html#34">strict::import</a></div></div></td></tr> |
| 1087 | <tr><td class="h"><a name="875"></a>875</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 1088 | <tr><td class="h"><a name="876"></a>876</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 1089 | <tr><td class="h"><a name="877"></a>877</td><td></td><td></td><td></td><td></td><td class="s"> #$logger->debug("done cleaning up '$self'"); # XXX</td></tr> |
| 1090 | <tr><td class="h"><a name="878"></a>878</td><td></td><td></td><td></td><td></td><td class="s"> # cleanup from mediator</td></tr> |
| 1091 | <tr><td class="h"><a name="879"></a>879</td><td></td><td></td><td></td><td></td><td class="s"> $taxamediator->unregister($self);</td></tr> |
| 1092 | <tr><td class="h"><a name="880"></a>880</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 1093 | <tr><td class="h"><a name="881"></a>881</td><td></td><td></td><td></td><td></td><td class="s"> # done cleaning up, id can be reclaimed</td></tr> |
| 1094 | <tr><td class="h"><a name="882"></a>882</td><td></td><td></td><td></td><td></td><td class="s"> Bio::Phylo::Util::IDPool->_reclaim($self);</td></tr> |
| 1095 | <tr><td class="h"><a name="883"></a>883</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 1096 | <tr><td class="h"><a name="884"></a>884</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 1097 | <tr><td class="h"><a name="885"></a>885</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 1098 | <tr><td class="h"><a name="886"></a>886</td><td></td><td></td><td></td><td></td><td class="s"> # starting from $class, push all superclasses (+$class) into @$isa,</td></tr> |
| 1099 | <tr><td class="h"><a name="887"></a>887</td><td></td><td></td><td></td><td></td><td class="s"> # %$seen is just a helper to avoid getting stuck in cycles</td></tr> |
| 1100 | <tr><td class="h"><a name="888"></a>888</td><td></td><td></td><td></td><td></td><td class="s"> sub _recurse_isa {</td></tr> |
| 1101 | <tr><td class="h"><a name="889"></a>889</td><td></td><td></td><td></td><td></td><td class="s"> my ( $class, $isa, $seen ) = @_;</td></tr> |
| 1102 | <tr><td class="h"><a name="890"></a>890</td><td></td><td></td><td></td><td></td><td class="s"> if ( not $seen->{$class} ) {</td></tr> |
| 1103 | <tr><td class="h"><a name="891"></a>891</td><td></td><td></td><td></td><td></td><td class="s"> $seen->{$class} = 1;</td></tr> |
| 1104 | <tr><td class="h"><a name="892"></a>892</td><td></td><td></td><td></td><td></td><td class="s"> push @{$isa}, $class;</td></tr> |
| 1105 | <tr><td class="h"><a name="893"></a>893</td><td></td><td></td><td></td><td></td><td class="s"> my @isa;</td></tr> |
| 1106 | <tr><td class="h"><a name="894"></a>894</td><td></td><td></td><td></td><td></td><td class="s"> {</td></tr> |
| 1107 | <tr><td class="h"><a name="895"></a>895</td><td class="c3">2</td><td class="c3"><span title="Avg 17µs">34µs</span></td><td class="c3">2</td><td class="c3">30µs</td><td class="s"><div class="calls"><div class="calls_in"># spent 19µs (8+11) within Bio::Phylo::BEGIN@895 which was called: |
| 1108 | # once (8µs+11µs) by Bio::Phylo::IO::BEGIN@4 at <a href="Bio-Phylo-pm-1138-block.html#895">line 895</a></div></div> no strict 'refs';<div class="calls"><div class="calls_out"> # spent 19µs making 1 call to <a href="Bio-Phylo-pm-1138-block.html#895">Bio::Phylo::BEGIN@895</a> |
| 1109 | # spent 11µs making 1 call to <a href="strict-pm-3-block.html#39">strict::unimport</a></div></div></td></tr> |
| 1110 | <tr><td class="h"><a name="896"></a>896</td><td></td><td></td><td></td><td></td><td class="s"> @isa = @{"${class}::ISA"};</td></tr> |
| 1111 | <tr><td class="h"><a name="897"></a>897</td><td class="c3">2</td><td class="c0"><span title="Avg 137µs">275µs</span></td><td class="c3">2</td><td class="c3">11µs</td><td class="s"><div class="calls"><div class="calls_in"># spent 9µs (7+2) within Bio::Phylo::BEGIN@897 which was called: |
| 1112 | # once (7µs+2µs) by Bio::Phylo::IO::BEGIN@4 at <a href="Bio-Phylo-pm-1138-block.html#897">line 897</a></div></div> use strict;<div class="calls"><div class="calls_out"> # spent 9µs making 1 call to <a href="Bio-Phylo-pm-1138-block.html#897">Bio::Phylo::BEGIN@897</a> |
| 1113 | # spent 2µs making 1 call to <a href="strict-pm-3-block.html#34">strict::import</a></div></div></td></tr> |
| 1114 | <tr><td class="h"><a name="898"></a>898</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 1115 | <tr><td class="h"><a name="899"></a>899</td><td></td><td></td><td></td><td></td><td class="s"> _recurse_isa( $_, $isa, $seen ) for @isa;</td></tr> |
| 1116 | <tr><td class="h"><a name="900"></a>900</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 1117 | <tr><td class="h"><a name="901"></a>901</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 1118 | <tr><td class="h"><a name="902"></a>902</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 1119 | <tr><td class="h"><a name="903"></a>903</td><td></td><td></td><td></td><td></td><td class="s"> # child classes probably should have a method like this,</td></tr> |
| 1120 | <tr><td class="h"><a name="904"></a>904</td><td></td><td></td><td></td><td></td><td class="s"> # if their objects hold internal state anyway (b/c they'll</td></tr> |
| 1121 | <tr><td class="h"><a name="905"></a>905</td><td></td><td></td><td></td><td></td><td class="s"> # be inside-out objects).</td></tr> |
| 1122 | <tr><td class="h"><a name="906"></a>906</td><td></td><td></td><td></td><td></td><td class="s"> sub _cleanup {</td></tr> |
| 1123 | <tr><td class="h"><a name="907"></a>907</td><td></td><td></td><td></td><td></td><td class="s"> my $self = shift;</td></tr> |
| 1124 | <tr><td class="h"><a name="908"></a>908</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 1125 | <tr><td class="h"><a name="909"></a>909</td><td></td><td></td><td></td><td></td><td class="s"> #$logger->debug("cleaning up '$self'"); # XXX</td></tr> |
| 1126 | <tr><td class="h"><a name="910"></a>910</td><td></td><td></td><td></td><td></td><td class="s"> my $id = $self->get_id;</td></tr> |
| 1127 | <tr><td class="h"><a name="911"></a>911</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 1128 | <tr><td class="h"><a name="912"></a>912</td><td></td><td></td><td></td><td></td><td class="s"> # cleanup local fields</td></tr> |
| 1129 | <tr><td class="h"><a name="913"></a>913</td><td></td><td></td><td></td><td></td><td class="s"> if ( defined $id ) {</td></tr> |
| 1130 | <tr><td class="h"><a name="914"></a>914</td><td></td><td></td><td></td><td></td><td class="s"> for my $field (@fields) {</td></tr> |
| 1131 | <tr><td class="h"><a name="915"></a>915</td><td></td><td></td><td></td><td></td><td class="s"> delete $field->{$id};</td></tr> |
| 1132 | <tr><td class="h"><a name="916"></a>916</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 1133 | <tr><td class="h"><a name="917"></a>917</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 1134 | <tr><td class="h"><a name="918"></a>918</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 1135 | <tr><td class="h"><a name="919"></a>919</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 1136 | <tr><td class="h"><a name="920"></a>920</td><td></td><td></td><td></td><td></td><td class="s">=begin comment</td></tr> |
| 1137 | <tr><td class="h"><a name="921"></a>921</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 1138 | <tr><td class="h"><a name="922"></a>922</td><td></td><td></td><td></td><td></td><td class="s"> Type : Internal method</td></tr> |
| 1139 | <tr><td class="h"><a name="923"></a>923</td><td></td><td></td><td></td><td></td><td class="s"> Title : _get_container</td></tr> |
| 1140 | <tr><td class="h"><a name="924"></a>924</td><td></td><td></td><td></td><td></td><td class="s"> Usage : $phylo->_get_container;</td></tr> |
| 1141 | <tr><td class="h"><a name="925"></a>925</td><td></td><td></td><td></td><td></td><td class="s"> Function: Retrieves the object that contains the invocant (e.g. for a node,</td></tr> |
| 1142 | <tr><td class="h"><a name="926"></a>926</td><td></td><td></td><td></td><td></td><td class="s"> returns the tree it is in).</td></tr> |
| 1143 | <tr><td class="h"><a name="927"></a>927</td><td></td><td></td><td></td><td></td><td class="s"> Returns : Bio::Phylo::* object</td></tr> |
| 1144 | <tr><td class="h"><a name="928"></a>928</td><td></td><td></td><td></td><td></td><td class="s"> Args : None</td></tr> |
| 1145 | <tr><td class="h"><a name="929"></a>929</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 1146 | <tr><td class="h"><a name="930"></a>930</td><td></td><td></td><td></td><td></td><td class="s">=end comment</td></tr> |
| 1147 | <tr><td class="h"><a name="931"></a>931</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 1148 | <tr><td class="h"><a name="932"></a>932</td><td></td><td></td><td></td><td></td><td class="s">=cut</td></tr> |
| 1149 | <tr><td class="h"><a name="933"></a>933</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 1150 | <tr><td class="h"><a name="934"></a>934</td><td></td><td></td><td></td><td></td><td class="s"> # this is the converse of $listable->get_entities, i.e.</td></tr> |
| 1151 | <tr><td class="h"><a name="935"></a>935</td><td></td><td></td><td></td><td></td><td class="s"> # every entity in a listable object holds a reference</td></tr> |
| 1152 | <tr><td class="h"><a name="936"></a>936</td><td></td><td></td><td></td><td></td><td class="s"> # to its container. We actually use this surprisingly</td></tr> |
| 1153 | <tr><td class="h"><a name="937"></a>937</td><td></td><td></td><td></td><td></td><td class="s"> # rarely, and because I read somewhere (heh) it's bad</td></tr> |
| 1154 | <tr><td class="h"><a name="938"></a>938</td><td></td><td></td><td></td><td></td><td class="s"> # to have the objects of a has-a relationship fiddle with</td></tr> |
| 1155 | <tr><td class="h"><a name="939"></a>939</td><td></td><td></td><td></td><td></td><td class="s"> # their container we hide this method from abuse. Then</td></tr> |
| 1156 | <tr><td class="h"><a name="940"></a>940</td><td></td><td></td><td></td><td></td><td class="s"> # again, sometimes it's handy ;-)</td></tr> |
| 1157 | <tr><td class="h"><a name="941"></a>941</td><td></td><td></td><td></td><td></td><td class="s"> sub _get_container {</td></tr> |
| 1158 | <tr><td class="h"><a name="942"></a>942</td><td></td><td></td><td></td><td></td><td class="s"> my $self = shift;</td></tr> |
| 1159 | <tr><td class="h"><a name="943"></a>943</td><td></td><td></td><td></td><td></td><td class="s"> return $container{ $self->get_id };</td></tr> |
| 1160 | <tr><td class="h"><a name="944"></a>944</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 1161 | <tr><td class="h"><a name="945"></a>945</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 1162 | <tr><td class="h"><a name="946"></a>946</td><td></td><td></td><td></td><td></td><td class="s">=begin comment</td></tr> |
| 1163 | <tr><td class="h"><a name="947"></a>947</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 1164 | <tr><td class="h"><a name="948"></a>948</td><td></td><td></td><td></td><td></td><td class="s"> Type : Internal method</td></tr> |
| 1165 | <tr><td class="h"><a name="949"></a>949</td><td></td><td></td><td></td><td></td><td class="s"> Title : _set_container</td></tr> |
| 1166 | <tr><td class="h"><a name="950"></a>950</td><td></td><td></td><td></td><td></td><td class="s"> Usage : $phylo->_set_container($obj);</td></tr> |
| 1167 | <tr><td class="h"><a name="951"></a>951</td><td></td><td></td><td></td><td></td><td class="s"> Function: Creates a reference from the invocant to the object that contains</td></tr> |
| 1168 | <tr><td class="h"><a name="952"></a>952</td><td></td><td></td><td></td><td></td><td class="s"> it (e.g. for a node, creates a reference to the tree it is in).</td></tr> |
| 1169 | <tr><td class="h"><a name="953"></a>953</td><td></td><td></td><td></td><td></td><td class="s"> Returns : Bio::Phylo::* object</td></tr> |
| 1170 | <tr><td class="h"><a name="954"></a>954</td><td></td><td></td><td></td><td></td><td class="s"> Args : A Bio::Phylo::Listable object</td></tr> |
| 1171 | <tr><td class="h"><a name="955"></a>955</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 1172 | <tr><td class="h"><a name="956"></a>956</td><td></td><td></td><td></td><td></td><td class="s">=end comment</td></tr> |
| 1173 | <tr><td class="h"><a name="957"></a>957</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 1174 | <tr><td class="h"><a name="958"></a>958</td><td></td><td></td><td></td><td></td><td class="s">=cut</td></tr> |
| 1175 | <tr><td class="h"><a name="959"></a>959</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 1176 | <tr><td class="h"><a name="960"></a>960</td><td></td><td></td><td></td><td></td><td class="s"> sub _set_container {</td></tr> |
| 1177 | <tr><td class="h"><a name="961"></a>961</td><td></td><td></td><td></td><td></td><td class="s"> my ( $self, $container ) = @_;</td></tr> |
| 1178 | <tr><td class="h"><a name="962"></a>962</td><td></td><td></td><td></td><td></td><td class="s"> my $id = $self->get_id;</td></tr> |
| 1179 | <tr><td class="h"><a name="963"></a>963</td><td></td><td></td><td></td><td></td><td class="s"> if ( blessed $container ) {</td></tr> |
| 1180 | <tr><td class="h"><a name="964"></a>964</td><td></td><td></td><td></td><td></td><td class="s"> if ( $container->can('can_contain') ) {</td></tr> |
| 1181 | <tr><td class="h"><a name="965"></a>965</td><td></td><td></td><td></td><td></td><td class="s"> if ( $container->can_contain($self) ) {</td></tr> |
| 1182 | <tr><td class="h"><a name="966"></a>966</td><td></td><td></td><td></td><td></td><td class="s"> if ( $container->contains($self) ) {</td></tr> |
| 1183 | <tr><td class="h"><a name="967"></a>967</td><td></td><td></td><td></td><td></td><td class="s"> $container{$id} = $container;</td></tr> |
| 1184 | <tr><td class="h"><a name="968"></a>968</td><td></td><td></td><td></td><td></td><td class="s"> weaken( $container{$id} );</td></tr> |
| 1185 | <tr><td class="h"><a name="969"></a>969</td><td></td><td></td><td></td><td></td><td class="s"> return $self;</td></tr> |
| 1186 | <tr><td class="h"><a name="970"></a>970</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 1187 | <tr><td class="h"><a name="971"></a>971</td><td></td><td></td><td></td><td></td><td class="s"> else {</td></tr> |
| 1188 | <tr><td class="h"><a name="972"></a>972</td><td></td><td></td><td></td><td></td><td class="s"> throw 'ObjectMismatch' => "'$self' not in '$container'";</td></tr> |
| 1189 | <tr><td class="h"><a name="973"></a>973</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 1190 | <tr><td class="h"><a name="974"></a>974</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 1191 | <tr><td class="h"><a name="975"></a>975</td><td></td><td></td><td></td><td></td><td class="s"> else {</td></tr> |
| 1192 | <tr><td class="h"><a name="976"></a>976</td><td></td><td></td><td></td><td></td><td class="s"> throw 'ObjectMismatch' =></td></tr> |
| 1193 | <tr><td class="h"><a name="977"></a>977</td><td></td><td></td><td></td><td></td><td class="s"> "'$container' cannot contain '$self'";</td></tr> |
| 1194 | <tr><td class="h"><a name="978"></a>978</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 1195 | <tr><td class="h"><a name="979"></a>979</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 1196 | <tr><td class="h"><a name="980"></a>980</td><td></td><td></td><td></td><td></td><td class="s"> else {</td></tr> |
| 1197 | <tr><td class="h"><a name="981"></a>981</td><td></td><td></td><td></td><td></td><td class="s"> throw 'ObjectMismatch' => "Invalid objects";</td></tr> |
| 1198 | <tr><td class="h"><a name="982"></a>982</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 1199 | <tr><td class="h"><a name="983"></a>983</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 1200 | <tr><td class="h"><a name="984"></a>984</td><td></td><td></td><td></td><td></td><td class="s"> else {</td></tr> |
| 1201 | <tr><td class="h"><a name="985"></a>985</td><td></td><td></td><td></td><td></td><td class="s"> throw 'BadArgs' => "Argument not an object";</td></tr> |
| 1202 | <tr><td class="h"><a name="986"></a>986</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 1203 | <tr><td class="h"><a name="987"></a>987</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 1204 | <tr><td class="h"><a name="988"></a>988</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 1205 | <tr><td class="h"><a name="989"></a>989</td><td></td><td></td><td></td><td></td><td class="s">=back</td></tr> |
| 1206 | <tr><td class="h"><a name="990"></a>990</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 1207 | <tr><td class="h"><a name="991"></a>991</td><td></td><td></td><td></td><td></td><td class="s">=head1 SEE ALSO</td></tr> |
| 1208 | <tr><td class="h"><a name="992"></a>992</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 1209 | <tr><td class="h"><a name="993"></a>993</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> |
| 1210 | <tr><td class="h"><a name="994"></a>994</td><td></td><td></td><td></td><td></td><td class="s">for any user or developer questions and discussions.</td></tr> |
| 1211 | <tr><td class="h"><a name="995"></a>995</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 1212 | <tr><td class="h"><a name="996"></a>996</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> |
| 1213 | <tr><td class="h"><a name="997"></a>997</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 1214 | <tr><td class="h"><a name="998"></a>998</td><td></td><td></td><td></td><td></td><td class="s">=head1 CITATION</td></tr> |
| 1215 | <tr><td class="h"><a name="999"></a>999</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 1216 | <tr><td class="h"><a name="1000"></a>1000</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> |
| 1217 | <tr><td class="h"><a name="1001"></a>1001</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 1218 | <tr><td class="h"><a name="1002"></a>1002</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> |
| 1219 | <tr><td class="h"><a name="1003"></a>1003</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> |
| 1220 | <tr><td class="h"><a name="1004"></a>1004</td><td></td><td></td><td></td><td></td><td class="s">I<BMC Bioinformatics> B<12>:63.</td></tr> |
| 1221 | <tr><td class="h"><a name="1005"></a>1005</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> |
| 1222 | <tr><td class="h"><a name="1006"></a>1006</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 1223 | <tr><td class="h"><a name="1007"></a>1007</td><td></td><td></td><td></td><td></td><td class="s">=cut</td></tr> |
| 1224 | <tr><td class="h"><a name="1008"></a>1008</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 1225 | <tr><td class="h"><a name="1009"></a>1009</td><td></td><td></td><td></td><td></td><td class="s">}</td></tr> |
| 1226 | <tr><td class="h"><a name="1010"></a>1010</td><td class="c3">1</td><td class="c3"><span title="Avg 23µs">23µs</span></td><td></td><td></td><td class="s">1;</td></tr> |
| 1227 | <tr><td class="s"><a name=""></a> </td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 1228 | <tr><td class="h"><a name="Bio__Phylo__CORE_subst"></a></td><td></td><td></td><td></td><td></td><td class="s"><div class="calls"><div class="calls_in"># spent 6µs within Bio::Phylo::CORE:subst which was called: |
| 1229 | # once (6µs+0s) by Bio::Phylo::IO::BEGIN@4 at <a href="Bio-Phylo-pm-1138-block.html#28">line 28</a></div></div>sub Bio::Phylo::CORE:subst; # opcode<br /> </td></tr> |
| 1230 | <tr><td class="h"><a name="Bio__Phylo__CORE_substcont"></a></td><td></td><td></td><td></td><td></td><td class="s"><div class="calls"><div class="calls_in"># spent 5µs within Bio::Phylo::CORE:substcont which was called 2 times, avg 3µs/call: |
| 1231 | # 2 times (5µs+0s) by Bio::Phylo::IO::BEGIN@4 at <a href="Bio-Phylo-pm-1138-block.html#28">line 28</a>, avg 3µs/call</div></div>sub Bio::Phylo::CORE:substcont; # opcode<br /> </td></tr> |
| 1232 | </tbody></table></div> |
| 1233 | |
| 1234 | <script type="text/javascript"> $(document).ready(function() { |
| 1235 | |
| 1236 | $("#subs_table").tablesorter({ |
| 1237 | sortList: [[3,1]], |
| 1238 | headers: { |
| 1239 | 3: { sorter: 'fmt_time' }, |
| 1240 | 4: { sorter: 'fmt_time' } |
| 1241 | } |
| 1242 | }); |
| 1243 | |
| 1244 | } ); </script> |
| 1245 | |
| 1246 | <div class="footer">Report produced by the |
| 1247 | <a href="http://search.cpan.org/dist/Devel-NYTProf/">NYTProf 4.06</a> |
| 1248 | Perl profiler, developed by |
| 1249 | <a href="http://www.linkedin.com/in/timbunce">Tim Bunce</a> and |
| 1250 | <a href="http://code.nytimes.com">Adam Kaplan</a>. |
| 1251 | </div> |
| 1252 | <br /><br /><br /><br /><br /><br /><br /><br /><br /><br /> |
| 1253 | </body></html> |
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