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| 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/Util/Logger.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-Util-Logger-pm-1164-line.html">line view</a></span> • <span class="mode_btn"><a href="Bio-Phylo-Util-Logger-pm-1164-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 16:49:15 2012<br />Reported on Thu May 31 16:52:40 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> |
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| 80 | <div style="position: absolute; left: 0px; top: 42%; width: 100%; height: 59%; z-index: -1; background-color: rgb(9, 107, 226); "></div> |
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| 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> |
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| 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/Util/Logger.pm">/Users/edenc/perl5/lib/perl5/Bio/Phylo/Util/Logger.pm</a></td></tr> |
| 114 | <tr><td class="h">Statements</td><td align="left">Executed 38 statements in 2.33ms</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%">43µs</span></td><td class="c3"><span title="0.0%">43µs</span></td><td class="sub_name"><span style="display: none;">Bio::Phylo::Util::Logger::::new</span>Bio::Phylo::Util::Logger::<a href="Bio-Phylo-Util-Logger-pm-1164-block.html#77">new</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%">31µs</span></td><td class="c1"><span title="0.0%">56µs</span></td><td class="sub_name"><span style="display: none;">Bio::Phylo::Util::Logger::::BEGIN@13</span>Bio::Phylo::Util::Logger::<a href="Bio-Phylo-Util-Logger-pm-1164-block.html#13">BEGIN@13</a></span></td></tr> |
| 131 | <tr><td class="c3">1</td><td class="c3">1</td><td class="c3">1</td><td class="c1"><span title="0.0%">28µs</span></td><td class="c3"><span title="0.0%">35µs</span></td><td class="sub_name"><span style="display: none;">Bio::Phylo::Util::Logger::::BEGIN@2</span>Bio::Phylo::Util::Logger::<a href="Bio-Phylo-Util-Logger-pm-1164-block.html#2">BEGIN@2</a></span></td></tr> |
| 132 | <tr><td class="c3">1</td><td class="c3">1</td><td class="c3">1</td><td class="c3"><span title="0.0%">20µs</span></td><td class="c3"><span title="0.0%">23µs</span></td><td class="sub_name"><span style="display: none;">Bio::Phylo::Util::Logger::::BEGIN@4</span>Bio::Phylo::Util::Logger::<a href="Bio-Phylo-Util-Logger-pm-1164-block.html#4">BEGIN@4</a></span></td></tr> |
| 133 | <tr><td class="c3">1</td><td class="c3">1</td><td class="c3">1</td><td class="c3"><span title="0.0%">19µs</span></td><td class="c3"><span title="0.0%">41µs</span></td><td class="sub_name"><span style="display: none;">Bio::Phylo::Util::Logger::::BEGIN@9</span>Bio::Phylo::Util::Logger::<a href="Bio-Phylo-Util-Logger-pm-1164-block.html#9">BEGIN@9</a></span></td></tr> |
| 134 | <tr><td class="c3">1</td><td class="c3">1</td><td class="c3">1</td><td class="c3"><span title="0.0%">14µs</span></td><td class="c2"><span title="0.0%">55µs</span></td><td class="sub_name"><span style="display: none;">Bio::Phylo::Util::Logger::::BEGIN@8</span>Bio::Phylo::Util::Logger::<a href="Bio-Phylo-Util-Logger-pm-1164-block.html#8">BEGIN@8</a></span></td></tr> |
| 135 | <tr><td class="c3">1</td><td class="c3">1</td><td class="c3">1</td><td class="c3"><span title="0.0%">14µs</span></td><td class="c0"><span title="0.0%">147µs</span></td><td class="sub_name"><span style="display: none;">Bio::Phylo::Util::Logger::::BEGIN@3</span>Bio::Phylo::Util::Logger::<a href="Bio-Phylo-Util-Logger-pm-1164-block.html#3">BEGIN@3</a></span></td></tr> |
| 136 | <tr><td class="c3">1</td><td class="c3">1</td><td class="c3">1</td><td class="c3"><span title="0.0%">14µs</span></td><td class="c0"><span title="0.0%">87µs</span></td><td class="sub_name"><span style="display: none;">Bio::Phylo::Util::Logger::::BEGIN@7</span>Bio::Phylo::Util::Logger::<a href="Bio-Phylo-Util-Logger-pm-1164-block.html#7">BEGIN@7</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%">5µs</span></td><td class="c3"><span title="0.0%">5µs</span></td><td class="sub_name"><span style="display: none;">Bio::Phylo::Util::Logger::::CORE:subst</span>Bio::Phylo::Util::Logger::<a href="Bio-Phylo-Util-Logger-pm-1164-block.html#Bio__Phylo__Util__Logger__CORE_subst">CORE:subst</a> (opcode)</span></td></tr> |
| 138 | <tr><td class="c3">0</td><td class="c3">0</td><td class="c3">0</td><td class="c3"><span title="0.0%">0s</span></td><td class="c3"><span title="0.0%">0s</span></td><td class="sub_name"><span style="display: none;">Bio::Phylo::Util::Logger::::DESTROY</span>Bio::Phylo::Util::Logger::<a href="Bio-Phylo-Util-Logger-pm-1164-block.html#154">DESTROY</a></span></td></tr> |
| 139 | <tr><td class="c3">0</td><td class="c3">0</td><td class="c3">0</td><td class="c3"><span title="0.0%">0s</span></td><td class="c3"><span title="0.0%">0s</span></td><td class="sub_name"><span style="display: none;">Bio::Phylo::Util::Logger::::PREFIX</span>Bio::Phylo::Util::Logger::<a href="Bio-Phylo-Util-Logger-pm-1164-block.html#106">PREFIX</a></span></td></tr> |
| 140 | <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::Util::Logger::::VERBOSE</span>Bio::Phylo::Util::Logger::<a href="Bio-Phylo-Util-Logger-pm-1164-block.html#112">VERBOSE</a></span></td></tr> |
| 141 | <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::Util::Logger::::set_listeners</span>Bio::Phylo::Util::Logger::<a href="Bio-Phylo-Util-Logger-pm-1164-block.html#93">set_listeners</a></span></td></tr> |
| 142 | </tbody></table> |
| 143 | Call graph for these subroutines as a |
| 144 | <a href="http://en.wikipedia.org/wiki/Graphviz">Graphviz</a> |
| 145 | <a href="Users-edenc-perl5-lib-perl5-Bio-Phylo-Util-Logger-pm.dot">dot language file</a>. |
| 146 | |
| 147 | <table border="1" cellpadding="0"> |
| 148 | <thead> |
| 149 | <tr><th>Line</th> |
| 150 | <th><span title="Number of statements executed">State<br />ments</span></th> |
| 151 | <th><span title="Time spend executing statements on the line, |
| 152 | excluding time spent executing statements in any called subroutines">Time<br />on line</span></th> |
| 153 | <th><span title="Number of subroutines calls">Calls</span></th> |
| 154 | <th><span title="Time spent in subroutines called (inclusive)">Time<br />in subs</span></th> |
| 155 | <th class="left_indent_header">Code</th> |
| 156 | </tr> |
| 157 | |
| 158 | </thead> |
| 159 | <tbody> |
| 160 | <tr><td class="h"><a name="1"></a>1</td><td></td><td></td><td></td><td></td><td class="s">package Bio::Phylo::Util::Logger;</td></tr> |
| 161 | <tr><td class="h"><a name="2"></a>2</td><td class="c3">2</td><td class="c3"><span title="Avg 23µs">46µs</span></td><td class="c3">2</td><td class="c3">42µs</td><td class="s"><div class="calls"><div class="calls_in"># spent 35µs (28+7) within Bio::Phylo::Util::Logger::BEGIN@2 which was called: |
| 162 | # once (28µs+7µs) by Bio::Phylo::BEGIN@18 at <a href="Bio-Phylo-Util-Logger-pm-1164-block.html#2">line 2</a></div></div>use strict;<div class="calls"><div class="calls_out"># spent 35µs making 1 call to <a href="Bio-Phylo-Util-Logger-pm-1164-block.html#2">Bio::Phylo::Util::Logger::BEGIN@2</a> |
| 163 | # spent 7µs making 1 call to <a href="strict-pm-3-block.html#34">strict::import</a></div></div></td></tr> |
| 164 | <tr><td class="h"><a name="3"></a>3</td><td class="c3">2</td><td class="c3"><span title="Avg 22µs">44µs</span></td><td class="c3">2</td><td class="c0">280µs</td><td class="s"><div class="calls"><div class="calls_in"># spent 147µs (14+133) within Bio::Phylo::Util::Logger::BEGIN@3 which was called: |
| 165 | # once (14µs+133µs) by Bio::Phylo::BEGIN@18 at <a href="Bio-Phylo-Util-Logger-pm-1164-block.html#3">line 3</a></div></div>use base 'Exporter';<div class="calls"><div class="calls_out"># spent 147µs making 1 call to <a href="Bio-Phylo-Util-Logger-pm-1164-block.html#3">Bio::Phylo::Util::Logger::BEGIN@3</a> |
| 166 | # spent 133µs making 1 call to <a href="base-pm-22-block.html#58">base::import</a></div></div></td></tr> |
| 167 | <tr><td class="h"><a name="4"></a>4</td><td class="c3">2</td><td class="c3"><span title="Avg 28µs">55µs</span></td><td class="c3">2</td><td class="c3">25µs</td><td class="s"><div class="calls"><div class="calls_in"># spent 23µs (20+3) within Bio::Phylo::Util::Logger::BEGIN@4 which was called: |
| 168 | # once (20µs+3µs) by Bio::Phylo::BEGIN@18 at <a href="Bio-Phylo-Util-Logger-pm-1164-block.html#4">line 4</a></div></div>use File::Spec;<div class="calls"><div class="calls_out"># spent 23µs making 1 call to <a href="Bio-Phylo-Util-Logger-pm-1164-block.html#4">Bio::Phylo::Util::Logger::BEGIN@4</a> |
| 169 | # spent 3µs making 1 call to <a href="UNIVERSAL-pm-738-block.html#16">UNIVERSAL::import</a></div></div></td></tr> |
| 170 | <tr><td class="h"><a name="5"></a>5</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 171 | <tr><td class="h"><a name="6"></a>6</td><td></td><td></td><td></td><td></td><td class="s">#use Filter::Simple;</td></tr> |
| 172 | <tr><td class="h"><a name="7"></a>7</td><td class="c3">2</td><td class="c3"><span title="Avg 26µs">51µs</span></td><td class="c3">2</td><td class="c0">160µs</td><td class="s"><div class="calls"><div class="calls_in"># spent 87µs (14+73) within Bio::Phylo::Util::Logger::BEGIN@7 which was called: |
| 173 | # once (14µs+73µs) by Bio::Phylo::BEGIN@18 at <a href="Bio-Phylo-Util-Logger-pm-1164-block.html#7">line 7</a></div></div>use Bio::Phylo::Util::CONSTANT qw'looks_like_hash looks_like_instance';<div class="calls"><div class="calls_out"># spent 87µs making 1 call to <a href="Bio-Phylo-Util-Logger-pm-1164-block.html#7">Bio::Phylo::Util::Logger::BEGIN@7</a> |
| 174 | # spent 73µs making 1 call to <a href="Exporter-pm-8-block.html#28">Exporter::import</a></div></div></td></tr> |
| 175 | <tr><td class="h"><a name="8"></a>8</td><td class="c3">2</td><td class="c3"><span title="Avg 22µs">44µs</span></td><td class="c3">2</td><td class="c1">96µs</td><td class="s"><div class="calls"><div class="calls_in"># spent 55µs (14+41) within Bio::Phylo::Util::Logger::BEGIN@8 which was called: |
| 176 | # once (14µs+41µs) by Bio::Phylo::BEGIN@18 at <a href="Bio-Phylo-Util-Logger-pm-1164-block.html#8">line 8</a></div></div>use Bio::Phylo::Util::Exceptions 'throw';<div class="calls"><div class="calls_out"># spent 55µs making 1 call to <a href="Bio-Phylo-Util-Logger-pm-1164-block.html#8">Bio::Phylo::Util::Logger::BEGIN@8</a> |
| 177 | # spent 41µs making 1 call to <a href="Exporter-pm-8-block.html#28">Exporter::import</a></div></div></td></tr> |
| 178 | <tr><td class="h"><a name="9"></a>9</td><td class="c3">2</td><td class="c0"><span title="Avg 138µs">276µs</span></td><td class="c3">2</td><td class="c3">63µs</td><td class="s"><div class="calls"><div class="calls_in"># spent 41µs (19+22) within Bio::Phylo::Util::Logger::BEGIN@9 which was called: |
| 179 | # once (19µs+22µs) by Bio::Phylo::BEGIN@18 at <a href="Bio-Phylo-Util-Logger-pm-1164-block.html#9">line 9</a></div></div>use Config;<div class="calls"><div class="calls_out"># spent 41µs making 1 call to <a href="Bio-Phylo-Util-Logger-pm-1164-block.html#9">Bio::Phylo::Util::Logger::BEGIN@9</a> |
| 180 | # spent 22µs making 1 call to <a href="Config-pm-47-block.html#38">Config::import</a></div></div></td></tr> |
| 181 | <tr><td class="h"><a name="10"></a>10</td><td class="c3">1</td><td class="c3"><span title="Avg 500ns">500ns</span></td><td></td><td></td><td class="s">our ( $volume, $class_dir, $file, $VERBOSE, $AUTOLOAD, $TRACEBACK, @EXPORT_OK,</td></tr> |
| 182 | <tr><td class="h"><a name="11"></a>11</td><td></td><td></td><td></td><td></td><td class="s"> %EXPORT_TAGS );</td></tr> |
| 183 | <tr><td class="h"><a name="12"></a>12</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 184 | <tr><td class="h"><a name="13"></a>13</td><td></td><td></td><td></td><td></td><td class="s"><div class="calls"><div class="calls_in"># spent 56µs (31+25) within Bio::Phylo::Util::Logger::BEGIN@13 which was called: |
| 185 | # once (31µs+25µs) by Bio::Phylo::BEGIN@18 at <a href="Bio-Phylo-Util-Logger-pm-1164-block.html#36">line 36</a></div></div>BEGIN {</td></tr> |
| 186 | <tr><td class="h"><a name="14"></a>14</td><td class="c0">6</td><td class="c3"><span title="Avg 5µs">31µs</span></td><td></td><td></td><td class="s"> @EXPORT_OK = qw(DEBUG INFO WARN ERROR FATAL);</td></tr> |
| 187 | <tr><td class="h"><a name="15"></a>15</td><td></td><td></td><td></td><td></td><td class="s"> %EXPORT_TAGS = ( 'levels' => [@EXPORT_OK] );</td></tr> |
| 188 | <tr><td class="h"><a name="16"></a>16</td><td></td><td></td><td></td><td></td><td class="s"> my $class_file = __FILE__;</td></tr> |
| 189 | <tr><td class="h"><a name="17"></a>17</td><td></td><td></td><td class="c3">1</td><td class="c3">20µs</td><td class="s"> ( $volume, $class_dir, $file ) = File::Spec->splitpath($class_file);<div class="calls"><div class="calls_out"> # spent 20µs making 1 call to <a href="File-Spec-Unix-pm-17-block.html#258">File::Spec::Unix::splitpath</a></div></div></td></tr> |
| 190 | <tr><td class="h"><a name="18"></a>18</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 191 | <tr><td class="h"><a name="19"></a>19</td><td></td><td></td><td></td><td></td><td class="s"> # By default, the logger formats its messages to show where the logging</td></tr> |
| 192 | <tr><td class="h"><a name="20"></a>20</td><td></td><td></td><td></td><td></td><td class="s"> # method (i.e. debug, info, warn, error or fatal) was called, (e.g in</td></tr> |
| 193 | <tr><td class="h"><a name="21"></a>21</td><td></td><td></td><td></td><td></td><td class="s"> # the synopsis the $logger->info method was called in Bio/Phylo.pm on</td></tr> |
| 194 | <tr><td class="h"><a name="22"></a>22</td><td></td><td></td><td></td><td></td><td class="s"> # line 280). However, in some cases you may want to have the message be</td></tr> |
| 195 | <tr><td class="h"><a name="23"></a>23</td><td></td><td></td><td></td><td></td><td class="s"> # formatted to originate earlier in the call stack. An example of</td></tr> |
| 196 | <tr><td class="h"><a name="24"></a>24</td><td></td><td></td><td></td><td></td><td class="s"> # this is in Bio::Phylo::Util::Exceptions, which calls $logger->error</td></tr> |
| 197 | <tr><td class="h"><a name="25"></a>25</td><td></td><td></td><td></td><td></td><td class="s"> # automatically every time an exception is thrown. This behaviour would</td></tr> |
| 198 | <tr><td class="h"><a name="26"></a>26</td><td></td><td></td><td></td><td></td><td class="s"> # not be very useful if the resulting message is shown to originate from</td></tr> |
| 199 | <tr><td class="h"><a name="27"></a>27</td><td></td><td></td><td></td><td></td><td class="s"> # within the "throw" method - so instead it seems to originate from</td></tr> |
| 200 | <tr><td class="h"><a name="28"></a>28</td><td></td><td></td><td></td><td></td><td class="s"> # where the exception was thrown, i.e. one frame up in the call stack.</td></tr> |
| 201 | <tr><td class="h"><a name="29"></a>29</td><td></td><td></td><td></td><td></td><td class="s"> # This behaviour can be achieved by changing the value of the</td></tr> |
| 202 | <tr><td class="h"><a name="30"></a>30</td><td></td><td></td><td></td><td></td><td class="s"> # $Bio::Phylo::Util::Logger::TRACEBACK variable. For each increment in</td></tr> |
| 203 | <tr><td class="h"><a name="31"></a>31</td><td></td><td></td><td></td><td></td><td class="s"> # that variable, the logger moves one frame up in the call stack.</td></tr> |
| 204 | <tr><td class="h"><a name="32"></a>32</td><td></td><td></td><td></td><td></td><td class="s"> $TRACEBACK = 0;</td></tr> |
| 205 | <tr><td class="h"><a name="33"></a>33</td><td></td><td></td><td class="c3">1</td><td class="c3">5µs</td><td class="s"> $class_dir =~ s/Bio.Phylo.Util.?$//;<div class="calls"><div class="calls_out"> # spent 5µs making 1 call to <a href="Bio-Phylo-Util-Logger-pm-1164-block.html#Bio__Phylo__Util__Logger__CORE_subst">Bio::Phylo::Util::Logger::CORE:subst</a></div></div></td></tr> |
| 206 | <tr><td class="h"><a name="34"></a>34</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 207 | <tr><td class="h"><a name="35"></a>35</td><td></td><td></td><td></td><td></td><td class="s"># printf STDERR "[ %s starting, will use PREFIX=%s where applicable ]\n", __PACKAGE__, $class_dir;</td></tr> |
| 208 | <tr><td class="h"><a name="36"></a>36</td><td class="c3">1</td><td class="c0"><span title="Avg 765µs">765µs</span></td><td class="c3">1</td><td class="c3">56µs</td><td class="s">}<div class="calls"><div class="calls_out"># spent 56µs making 1 call to <a href="Bio-Phylo-Util-Logger-pm-1164-block.html#13">Bio::Phylo::Util::Logger::BEGIN@13</a></div></div></td></tr> |
| 209 | <tr><td class="h"><a name="37"></a>37</td><td></td><td></td><td></td><td></td><td class="s">{</td></tr> |
| 210 | <tr><td class="h"><a name="38"></a>38</td><td class="c0">7</td><td class="c3"><span title="Avg 443ns">3µs</span></td><td></td><td></td><td class="s"> my $self;</td></tr> |
| 211 | <tr><td class="h"><a name="39"></a>39</td><td></td><td></td><td></td><td></td><td class="s"> my %VERBOSE;</td></tr> |
| 212 | <tr><td class="h"><a name="40"></a>40</td><td></td><td></td><td></td><td></td><td class="s"> my @listeners;</td></tr> |
| 213 | <tr><td class="h"><a name="41"></a>41</td><td></td><td></td><td></td><td></td><td class="s"> my ( $fatal, $error, $warn, $info, $debug ) = ( 0 .. 4 );</td></tr> |
| 214 | <tr><td class="h"><a name="42"></a>42</td><td></td><td></td><td></td><td></td><td class="s"> $VERBOSE = $warn;</td></tr> |
| 215 | <tr><td class="h"><a name="43"></a>43</td><td></td><td></td><td></td><td></td><td class="s"> for my $method (qw(fatal error warn info debug)) {</td></tr> |
| 216 | <tr><td class="h"><a name="44"></a>44</td><td class="c0">5</td><td class="c0"><span title="Avg 188µs">942µs</span></td><td></td><td></td><td class="s"> eval <<"CODE_TEMPLATE";<div class="calls"><div class="calls_out"> # spent 0s executing statements in <a href="(eval 756)[Bio-Phylo-Util-Logger-pm-44]-2620-line.html">string eval</a></div></div></td></tr> |
| 217 | <tr><td class="h"><a name="45"></a>45</td><td></td><td></td><td></td><td></td><td class="s"> sub $method {</td></tr> |
| 218 | <tr><td class="h"><a name="46"></a>46</td><td></td><td></td><td></td><td></td><td class="s"> my ( \$self, \$msg ) = \@_;</td></tr> |
| 219 | <tr><td class="h"><a name="47"></a>47</td><td></td><td></td><td></td><td></td><td class="s"> my ( \$package, \$file1up, \$line1up, \$subroutine ) = caller( \$TRACEBACK + 1 );</td></tr> |
| 220 | <tr><td class="h"><a name="48"></a>48</td><td></td><td></td><td></td><td></td><td class="s"> my ( \$pack0up, \$filename, \$line, \$sub0up ) = caller( \$TRACEBACK + 0 );</td></tr> |
| 221 | <tr><td class="h"><a name="49"></a>49</td><td></td><td></td><td></td><td></td><td class="s"> my \$verbosity;</td></tr> |
| 222 | <tr><td class="h"><a name="50"></a>50</td><td></td><td></td><td></td><td></td><td class="s"> if ( exists \$VERBOSE{\$subroutine} ) {</td></tr> |
| 223 | <tr><td class="h"><a name="51"></a>51</td><td></td><td></td><td></td><td></td><td class="s"> \$verbosity = \$VERBOSE{\$subroutine};</td></tr> |
| 224 | <tr><td class="h"><a name="52"></a>52</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 225 | <tr><td class="h"><a name="53"></a>53</td><td></td><td></td><td></td><td></td><td class="s"> elsif ( exists \$VERBOSE{\$pack0up} ) {</td></tr> |
| 226 | <tr><td class="h"><a name="54"></a>54</td><td></td><td></td><td></td><td></td><td class="s"> \$verbosity = \$VERBOSE{\$pack0up};</td></tr> |
| 227 | <tr><td class="h"><a name="55"></a>55</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 228 | <tr><td class="h"><a name="56"></a>56</td><td></td><td></td><td></td><td></td><td class="s"> else {</td></tr> |
| 229 | <tr><td class="h"><a name="57"></a>57</td><td></td><td></td><td></td><td></td><td class="s"> \$verbosity = \$VERBOSE;</td></tr> |
| 230 | <tr><td class="h"><a name="58"></a>58</td><td></td><td></td><td></td><td></td><td class="s"> } </td></tr> |
| 231 | <tr><td class="h"><a name="59"></a>59</td><td></td><td></td><td></td><td></td><td class="s"> if ( \$verbosity >= \$${method} ) { </td></tr> |
| 232 | <tr><td class="h"><a name="60"></a>60</td><td></td><td></td><td></td><td></td><td class="s"> my \$log_string;</td></tr> |
| 233 | <tr><td class="h"><a name="61"></a>61</td><td></td><td></td><td></td><td></td><td class="s"> if ( substr(\$filename,0,length(\$class_dir)) eq \$class_dir ) {</td></tr> |
| 234 | <tr><td class="h"><a name="62"></a>62</td><td></td><td></td><td></td><td></td><td class="s"> \$log_string = sprintf( "%s %s [\\\$PREFIX/%s, %s] - %s\\n",</td></tr> |
| 235 | <tr><td class="h"><a name="63"></a>63</td><td></td><td></td><td></td><td></td><td class="s"> uc("$method"), \$subroutine, substr(\$filename,length(\$class_dir)), \$line, \$msg );</td></tr> |
| 236 | <tr><td class="h"><a name="64"></a>64</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 237 | <tr><td class="h"><a name="65"></a>65</td><td></td><td></td><td></td><td></td><td class="s"> else {</td></tr> |
| 238 | <tr><td class="h"><a name="66"></a>66</td><td></td><td></td><td></td><td></td><td class="s"> \$log_string = sprintf( "%s %s [%s, %s] - %s\\n",</td></tr> |
| 239 | <tr><td class="h"><a name="67"></a>67</td><td></td><td></td><td></td><td></td><td class="s"> uc("$method"), \$subroutine, \$filename, \$line, \$msg ); </td></tr> |
| 240 | <tr><td class="h"><a name="68"></a>68</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 241 | <tr><td class="h"><a name="69"></a>69</td><td></td><td></td><td></td><td></td><td class="s"> print STDERR \$log_string;</td></tr> |
| 242 | <tr><td class="h"><a name="70"></a>70</td><td></td><td></td><td></td><td></td><td class="s"> \$_->( \$log_string, uc("$method"), \$subroutine, \$filename, \$line, \$msg ) for \@listeners;</td></tr> |
| 243 | <tr><td class="h"><a name="71"></a>71</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 244 | <tr><td class="h"><a name="72"></a>72</td><td></td><td></td><td></td><td></td><td class="s"> return \$self; </td></tr> |
| 245 | <tr><td class="h"><a name="73"></a>73</td><td></td><td></td><td></td><td></td><td class="s"> } </td></tr> |
| 246 | <tr><td class="h"><a name="74"></a>74</td><td></td><td></td><td></td><td></td><td class="s">CODE_TEMPLATE</td></tr> |
| 247 | <tr><td class="h"><a name="75"></a>75</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 248 | <tr><td class="h"><a name="76"></a>76</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 249 | <tr><td class="h"><a name="77"></a>77</td><td></td><td></td><td></td><td></td><td class="s"><div class="calls"><div class="calls_in"># spent 43µs within Bio::Phylo::Util::Logger::new which was called: |
| 250 | # once (43µs+0s) by Bio::Phylo::IO::BEGIN@4 at <a href="Bio-Phylo-pm-1138-block.html#19">line 19 of Bio/Phylo.pm</a></div></div> sub new {</td></tr> |
| 251 | <tr><td class="h"><a name="78"></a>78</td><td class="c0">4</td><td class="c3"><span title="Avg 9µs">34µs</span></td><td></td><td></td><td class="s"> my $package = shift;</td></tr> |
| 252 | <tr><td class="h"><a name="79"></a>79</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 253 | <tr><td class="h"><a name="80"></a>80</td><td></td><td></td><td></td><td></td><td class="s"> # singleton object</td></tr> |
| 254 | <tr><td class="h"><a name="81"></a>81</td><td class="c3">2</td><td class="c3"><span title="Avg 8µs">16µs</span></td><td></td><td></td><td class="s"> if ( not $self ) {</td></tr> |
| 255 | <tr><td class="h"><a name="82"></a>82</td><td></td><td></td><td></td><td></td><td class="s"> $self = \$package;</td></tr> |
| 256 | <tr><td class="h"><a name="83"></a>83</td><td></td><td></td><td></td><td></td><td class="s"> bless $self, $package;</td></tr> |
| 257 | <tr><td class="h"><a name="84"></a>84</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 258 | <tr><td class="h"><a name="85"></a>85</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 259 | <tr><td class="h"><a name="86"></a>86</td><td></td><td></td><td></td><td></td><td class="s"> # process args</td></tr> |
| 260 | <tr><td class="h"><a name="87"></a>87</td><td></td><td></td><td></td><td></td><td class="s"> $self->VERBOSE(@_) if @_;</td></tr> |
| 261 | <tr><td class="h"><a name="88"></a>88</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 262 | <tr><td class="h"><a name="89"></a>89</td><td></td><td></td><td></td><td></td><td class="s"> # done</td></tr> |
| 263 | <tr><td class="h"><a name="90"></a>90</td><td></td><td></td><td></td><td></td><td class="s"> return $self;</td></tr> |
| 264 | <tr><td class="h"><a name="91"></a>91</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 265 | <tr><td class="h"><a name="92"></a>92</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 266 | <tr><td class="h"><a name="93"></a>93</td><td></td><td></td><td></td><td></td><td class="s"> sub set_listeners {</td></tr> |
| 267 | <tr><td class="h"><a name="94"></a>94</td><td></td><td></td><td></td><td></td><td class="s"> my ( $self, @args ) = @_;</td></tr> |
| 268 | <tr><td class="h"><a name="95"></a>95</td><td></td><td></td><td></td><td></td><td class="s"> for my $arg (@args) {</td></tr> |
| 269 | <tr><td class="h"><a name="96"></a>96</td><td></td><td></td><td></td><td></td><td class="s"> if ( looks_like_instance $arg, 'CODE' ) {</td></tr> |
| 270 | <tr><td class="h"><a name="97"></a>97</td><td></td><td></td><td></td><td></td><td class="s"> push @listeners, $arg;</td></tr> |
| 271 | <tr><td class="h"><a name="98"></a>98</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 272 | <tr><td class="h"><a name="99"></a>99</td><td></td><td></td><td></td><td></td><td class="s"> else {</td></tr> |
| 273 | <tr><td class="h"><a name="100"></a>100</td><td></td><td></td><td></td><td></td><td class="s"> throw 'BadArgs' => "$arg not a CODE reference";</td></tr> |
| 274 | <tr><td class="h"><a name="101"></a>101</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 275 | <tr><td class="h"><a name="102"></a>102</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 276 | <tr><td class="h"><a name="103"></a>103</td><td></td><td></td><td></td><td></td><td class="s"> return $self;</td></tr> |
| 277 | <tr><td class="h"><a name="104"></a>104</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 278 | <tr><td class="h"><a name="105"></a>105</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 279 | <tr><td class="h"><a name="106"></a>106</td><td></td><td></td><td></td><td></td><td class="s"> sub PREFIX {</td></tr> |
| 280 | <tr><td class="h"><a name="107"></a>107</td><td></td><td></td><td></td><td></td><td class="s"> my ( $self, $prefix ) = @_;</td></tr> |
| 281 | <tr><td class="h"><a name="108"></a>108</td><td></td><td></td><td></td><td></td><td class="s"> $class_dir = $prefix if $prefix;</td></tr> |
| 282 | <tr><td class="h"><a name="109"></a>109</td><td></td><td></td><td></td><td></td><td class="s"> return $class_dir;</td></tr> |
| 283 | <tr><td class="h"><a name="110"></a>110</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 284 | <tr><td class="h"><a name="111"></a>111</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 285 | <tr><td class="h"><a name="112"></a>112</td><td></td><td></td><td></td><td></td><td class="s"> sub VERBOSE {</td></tr> |
| 286 | <tr><td class="h"><a name="113"></a>113</td><td></td><td></td><td></td><td></td><td class="s"> my $self = shift;</td></tr> |
| 287 | <tr><td class="h"><a name="114"></a>114</td><td></td><td></td><td></td><td></td><td class="s"> if (@_) {</td></tr> |
| 288 | <tr><td class="h"><a name="115"></a>115</td><td></td><td></td><td></td><td></td><td class="s"> my %opt = looks_like_hash @_;</td></tr> |
| 289 | <tr><td class="h"><a name="116"></a>116</td><td></td><td></td><td></td><td></td><td class="s"> if ( defined $opt{'-level'} ) {</td></tr> |
| 290 | <tr><td class="h"><a name="117"></a>117</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 291 | <tr><td class="h"><a name="118"></a>118</td><td></td><td></td><td></td><td></td><td class="s"> # check validity</td></tr> |
| 292 | <tr><td class="h"><a name="119"></a>119</td><td></td><td></td><td></td><td></td><td class="s"> if ( $opt{'-level'} > $debug xor $opt{'-level'} < $fatal ) {</td></tr> |
| 293 | <tr><td class="h"><a name="120"></a>120</td><td></td><td></td><td></td><td></td><td class="s"> throw 'OutOfBounds' =></td></tr> |
| 294 | <tr><td class="h"><a name="121"></a>121</td><td></td><td></td><td></td><td></td><td class="s">"'-level' can be between $fatal and $debug, not $opt{'-level'}";</td></tr> |
| 295 | <tr><td class="h"><a name="122"></a>122</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 296 | <tr><td class="h"><a name="123"></a>123</td><td></td><td></td><td></td><td></td><td class="s"> if ( $opt{'-class'} ) {</td></tr> |
| 297 | <tr><td class="h"><a name="124"></a>124</td><td></td><td></td><td></td><td></td><td class="s"> $VERBOSE{ $opt{'-class'} } = $opt{'-level'};</td></tr> |
| 298 | <tr><td class="h"><a name="125"></a>125</td><td></td><td></td><td></td><td></td><td class="s"> $self->info(</td></tr> |
| 299 | <tr><td class="h"><a name="126"></a>126</td><td></td><td></td><td></td><td></td><td class="s">"Changed verbosity for class $opt{'-class'} to $opt{'-level'}"</td></tr> |
| 300 | <tr><td class="h"><a name="127"></a>127</td><td></td><td></td><td></td><td></td><td class="s"> );</td></tr> |
| 301 | <tr><td class="h"><a name="128"></a>128</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 302 | <tr><td class="h"><a name="129"></a>129</td><td></td><td></td><td></td><td></td><td class="s"> elsif ( $opt{'-method'} ) {</td></tr> |
| 303 | <tr><td class="h"><a name="130"></a>130</td><td></td><td></td><td></td><td></td><td class="s"> if ( ref $opt{'-method'} eq 'ARRAY' ) {</td></tr> |
| 304 | <tr><td class="h"><a name="131"></a>131</td><td></td><td></td><td></td><td></td><td class="s"> for my $method ( @{ $opt{'-method'} } ) {</td></tr> |
| 305 | <tr><td class="h"><a name="132"></a>132</td><td></td><td></td><td></td><td></td><td class="s"> $VERBOSE{$method} = $opt{'-level'};</td></tr> |
| 306 | <tr><td class="h"><a name="133"></a>133</td><td></td><td></td><td></td><td></td><td class="s"> $self->info(</td></tr> |
| 307 | <tr><td class="h"><a name="134"></a>134</td><td></td><td></td><td></td><td></td><td class="s"> "Changed verbosity for method $method to $opt{'-level'}"</td></tr> |
| 308 | <tr><td class="h"><a name="135"></a>135</td><td></td><td></td><td></td><td></td><td class="s"> ); </td></tr> |
| 309 | <tr><td class="h"><a name="136"></a>136</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 310 | <tr><td class="h"><a name="137"></a>137</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 311 | <tr><td class="h"><a name="138"></a>138</td><td></td><td></td><td></td><td></td><td class="s"> else {</td></tr> |
| 312 | <tr><td class="h"><a name="139"></a>139</td><td></td><td></td><td></td><td></td><td class="s"> $VERBOSE{ $opt{'-method'} } = $opt{'-level'};</td></tr> |
| 313 | <tr><td class="h"><a name="140"></a>140</td><td></td><td></td><td></td><td></td><td class="s"> $self->info(</td></tr> |
| 314 | <tr><td class="h"><a name="141"></a>141</td><td></td><td></td><td></td><td></td><td class="s"> "Changed verbosity for method $opt{'-method'} to $opt{'-level'}"</td></tr> |
| 315 | <tr><td class="h"><a name="142"></a>142</td><td></td><td></td><td></td><td></td><td class="s"> );</td></tr> |
| 316 | <tr><td class="h"><a name="143"></a>143</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 317 | <tr><td class="h"><a name="144"></a>144</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 318 | <tr><td class="h"><a name="145"></a>145</td><td></td><td></td><td></td><td></td><td class="s"> else {</td></tr> |
| 319 | <tr><td class="h"><a name="146"></a>146</td><td></td><td></td><td></td><td></td><td class="s"> $VERBOSE = $opt{'-level'};</td></tr> |
| 320 | <tr><td class="h"><a name="147"></a>147</td><td></td><td></td><td></td><td></td><td class="s"> $self->info("Changed global verbosity to $VERBOSE");</td></tr> |
| 321 | <tr><td class="h"><a name="148"></a>148</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 322 | <tr><td class="h"><a name="149"></a>149</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 323 | <tr><td class="h"><a name="150"></a>150</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 324 | <tr><td class="h"><a name="151"></a>151</td><td></td><td></td><td></td><td></td><td class="s"> return $VERBOSE;</td></tr> |
| 325 | <tr><td class="h"><a name="152"></a>152</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 326 | <tr><td class="h"><a name="153"></a>153</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 327 | <tr><td class="h"><a name="154"></a>154</td><td></td><td></td><td></td><td></td><td class="s"> sub DESTROY {</td></tr> |
| 328 | <tr><td class="h"><a name="155"></a>155</td><td></td><td></td><td></td><td></td><td class="s"> } # empty destructor so we don't go up inheritance tree at the end</td></tr> |
| 329 | <tr><td class="h"><a name="156"></a>156</td><td></td><td></td><td></td><td></td><td class="s"> # log levels</td></tr> |
| 330 | <tr><td class="h"><a name="157"></a>157</td><td></td><td></td><td></td><td></td><td class="s"> sub FATAL () { 0 }</td></tr> |
| 331 | <tr><td class="h"><a name="158"></a>158</td><td></td><td></td><td></td><td></td><td class="s"> sub ERROR () { 1 }</td></tr> |
| 332 | <tr><td class="h"><a name="159"></a>159</td><td></td><td></td><td></td><td></td><td class="s"> sub WARN () { 2 }</td></tr> |
| 333 | <tr><td class="h"><a name="160"></a>160</td><td></td><td></td><td></td><td></td><td class="s"> sub INFO () { 3 }</td></tr> |
| 334 | <tr><td class="h"><a name="161"></a>161</td><td></td><td></td><td></td><td></td><td class="s"> sub DEBUG () { 4 }</td></tr> |
| 335 | <tr><td class="h"><a name="162"></a>162</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 336 | <tr><td class="h"><a name="163"></a>163</td><td></td><td></td><td></td><td></td><td class="s"> # source filtering to get rid of all logger calls.</td></tr> |
| 337 | <tr><td class="h"><a name="164"></a>164</td><td></td><td></td><td></td><td></td><td class="s"> # This doesn't seem to improve performance by much</td></tr> |
| 338 | <tr><td class="h"><a name="165"></a>165</td><td></td><td></td><td></td><td></td><td class="s"> # and the regexes might not work if there are</td></tr> |
| 339 | <tr><td class="h"><a name="166"></a>166</td><td></td><td></td><td></td><td></td><td class="s"> # parentheses inside the logging string so this is</td></tr> |
| 340 | <tr><td class="h"><a name="167"></a>167</td><td></td><td></td><td></td><td></td><td class="s"> # highly experimental. Also, it requires modules</td></tr> |
| 341 | <tr><td class="h"><a name="168"></a>168</td><td></td><td></td><td></td><td></td><td class="s"> # to "use" Bio::Phylo::Util::Logger explicitly instead</td></tr> |
| 342 | <tr><td class="h"><a name="169"></a>169</td><td></td><td></td><td></td><td></td><td class="s"> # of calling get_logger up the inheritance tree. All</td></tr> |
| 343 | <tr><td class="h"><a name="170"></a>170</td><td></td><td></td><td></td><td></td><td class="s"> # in all this is pretty useless and buggy at this point</td></tr> |
| 344 | <tr><td class="h"><a name="171"></a>171</td><td></td><td></td><td></td><td></td><td class="s"> # so let's just comment this out.</td></tr> |
| 345 | <tr><td class="h"><a name="172"></a>172</td><td></td><td></td><td></td><td></td><td class="s"> # FILTER {</td></tr> |
| 346 | <tr><td class="h"><a name="173"></a>173</td><td></td><td></td><td></td><td></td><td class="s"> # my $debug_regex = '$logger->debug(';</td></tr> |
| 347 | <tr><td class="h"><a name="174"></a>174</td><td></td><td></td><td></td><td></td><td class="s"> # my $info_regex = '$logger->info(';</td></tr> |
| 348 | <tr><td class="h"><a name="175"></a>175</td><td></td><td></td><td></td><td></td><td class="s"> # my $warn_regex = '$logger->warn(';</td></tr> |
| 349 | <tr><td class="h"><a name="176"></a>176</td><td></td><td></td><td></td><td></td><td class="s"> # my $error_regex = '$logger->error(';</td></tr> |
| 350 | <tr><td class="h"><a name="177"></a>177</td><td></td><td></td><td></td><td></td><td class="s"> # my $fatal_regex = '$logger->fatal(';</td></tr> |
| 351 | <tr><td class="h"><a name="178"></a>178</td><td></td><td></td><td></td><td></td><td class="s"> #</td></tr> |
| 352 | <tr><td class="h"><a name="179"></a>179</td><td></td><td></td><td></td><td></td><td class="s"> # s/\Q$debug_regex\E[^\)]+?\);//g unless $ENV{'BIO_PHYLO_LOGGING'};</td></tr> |
| 353 | <tr><td class="h"><a name="180"></a>180</td><td></td><td></td><td></td><td></td><td class="s"> # s/\Q$info_regex\E[^\)]+?\);//g unless $ENV{'BIO_PHYLO_LOGGING'};</td></tr> |
| 354 | <tr><td class="h"><a name="181"></a>181</td><td></td><td></td><td></td><td></td><td class="s"> # s/\Q$warn_regex\E[^\)]+?\);//g unless $ENV{'BIO_PHYLO_LOGGING'};</td></tr> |
| 355 | <tr><td class="h"><a name="182"></a>182</td><td></td><td></td><td></td><td></td><td class="s"> # s/\Q$error_regex\E[^\)]+?\);//g unless $ENV{'BIO_PHYLO_LOGGING'};</td></tr> |
| 356 | <tr><td class="h"><a name="183"></a>183</td><td></td><td></td><td></td><td></td><td class="s"> # s/\Q$fatal_regex\E[^\)]+?\);//g unless $ENV{'BIO_PHYLO_LOGGING'};</td></tr> |
| 357 | <tr><td class="h"><a name="184"></a>184</td><td></td><td></td><td></td><td></td><td class="s"> #</td></tr> |
| 358 | <tr><td class="h"><a name="185"></a>185</td><td></td><td></td><td></td><td></td><td class="s"> # };</td></tr> |
| 359 | <tr><td class="h"><a name="186"></a>186</td><td></td><td></td><td></td><td></td><td class="s">}</td></tr> |
| 360 | <tr><td class="h"><a name="187"></a>187</td><td class="c3">1</td><td class="c3"><span title="Avg 16µs">16µs</span></td><td></td><td></td><td class="s">1;</td></tr> |
| 361 | <tr><td class="h"><a name="188"></a>188</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 362 | <tr><td class="h"><a name="189"></a>189</td><td></td><td></td><td></td><td></td><td class="s">=head1 NAME</td></tr> |
| 363 | <tr><td class="h"><a name="190"></a>190</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 364 | <tr><td class="h"><a name="191"></a>191</td><td></td><td></td><td></td><td></td><td class="s">Bio::Phylo::Util::Logger - Logger of internal messages of several severity</td></tr> |
| 365 | <tr><td class="h"><a name="192"></a>192</td><td></td><td></td><td></td><td></td><td class="s">levels </td></tr> |
| 366 | <tr><td class="h"><a name="193"></a>193</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 367 | <tr><td class="h"><a name="194"></a>194</td><td></td><td></td><td></td><td></td><td class="s">=head1 SYNOPSIS</td></tr> |
| 368 | <tr><td class="h"><a name="195"></a>195</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 369 | <tr><td class="h"><a name="196"></a>196</td><td></td><td></td><td></td><td></td><td class="s"> use strict;</td></tr> |
| 370 | <tr><td class="h"><a name="197"></a>197</td><td></td><td></td><td></td><td></td><td class="s"> use Bio::Phylo::Util::Logger ':levels'; # import level constants</td></tr> |
| 371 | <tr><td class="h"><a name="198"></a>198</td><td></td><td></td><td></td><td></td><td class="s"> use Bio::Phylo::IO 'parse';</td></tr> |
| 372 | <tr><td class="h"><a name="199"></a>199</td><td></td><td></td><td></td><td></td><td class="s"> use Bio::Phylo::Factory; </td></tr> |
| 373 | <tr><td class="h"><a name="200"></a>200</td><td></td><td></td><td></td><td></td><td class="s"> </td></tr> |
| 374 | <tr><td class="h"><a name="201"></a>201</td><td></td><td></td><td></td><td></td><td class="s"> # Set the verbosity level of the tree class.</td></tr> |
| 375 | <tr><td class="h"><a name="202"></a>202</td><td></td><td></td><td></td><td></td><td class="s"> # "DEBUG" is the most verbose level. All log messages</td></tr> |
| 376 | <tr><td class="h"><a name="203"></a>203</td><td></td><td></td><td></td><td></td><td class="s"> # emanating from the tree class will be </td></tr> |
| 377 | <tr><td class="h"><a name="204"></a>204</td><td></td><td></td><td></td><td></td><td class="s"> # transmitted. For this to work the level constants</td></tr> |
| 378 | <tr><td class="h"><a name="205"></a>205</td><td></td><td></td><td></td><td></td><td class="s"> # have to have been imported!</td></tr> |
| 379 | <tr><td class="h"><a name="206"></a>206</td><td></td><td></td><td></td><td></td><td class="s"> use Bio::Phylo::Forest::Tree 'verbose' => DEBUG; # note: DEBUG is not quoted!</td></tr> |
| 380 | <tr><td class="h"><a name="207"></a>207</td><td></td><td></td><td></td><td></td><td class="s"> </td></tr> |
| 381 | <tr><td class="h"><a name="208"></a>208</td><td></td><td></td><td></td><td></td><td class="s"> # Create a file handle for logger to write to.</td></tr> |
| 382 | <tr><td class="h"><a name="209"></a>209</td><td></td><td></td><td></td><td></td><td class="s"> # This is not necessary, by default the logger</td></tr> |
| 383 | <tr><td class="h"><a name="210"></a>210</td><td></td><td></td><td></td><td></td><td class="s"> # writes to STDERR, but sometimes you will want</td></tr> |
| 384 | <tr><td class="h"><a name="211"></a>211</td><td></td><td></td><td></td><td></td><td class="s"> # to write to a file, as per this example.</td></tr> |
| 385 | <tr><td class="h"><a name="212"></a>212</td><td></td><td></td><td></td><td></td><td class="s"> open my $fh, '>', 'parsing.log' or die $!;</td></tr> |
| 386 | <tr><td class="h"><a name="213"></a>213</td><td></td><td></td><td></td><td></td><td class="s"> </td></tr> |
| 387 | <tr><td class="h"><a name="214"></a>214</td><td></td><td></td><td></td><td></td><td class="s"> # Create a logger object.</td></tr> |
| 388 | <tr><td class="h"><a name="215"></a>215</td><td></td><td></td><td></td><td></td><td class="s"> my $fac = Bio::Phylo::Factory->new;</td></tr> |
| 389 | <tr><td class="h"><a name="216"></a>216</td><td></td><td></td><td></td><td></td><td class="s"> my $logger = $fac->create_logger;</td></tr> |
| 390 | <tr><td class="h"><a name="217"></a>217</td><td></td><td></td><td></td><td></td><td class="s"> </td></tr> |
| 391 | <tr><td class="h"><a name="218"></a>218</td><td></td><td></td><td></td><td></td><td class="s"> # Set the verbosity level of the set_name</td></tr> |
| 392 | <tr><td class="h"><a name="219"></a>219</td><td></td><td></td><td></td><td></td><td class="s"> # method in the base class. Messages coming</td></tr> |
| 393 | <tr><td class="h"><a name="220"></a>220</td><td></td><td></td><td></td><td></td><td class="s"> # from this method will be transmitted.</td></tr> |
| 394 | <tr><td class="h"><a name="221"></a>221</td><td></td><td></td><td></td><td></td><td class="s"> $logger->VERBOSE( </td></tr> |
| 395 | <tr><td class="h"><a name="222"></a>222</td><td></td><td></td><td></td><td></td><td class="s"> '-level' => DEBUG, # note, not quoted, this is a constant!</td></tr> |
| 396 | <tr><td class="h"><a name="223"></a>223</td><td></td><td></td><td></td><td></td><td class="s"> '-method' => 'Bio::Phylo::set_name', # quoted, otherwise bareword error!</td></tr> |
| 397 | <tr><td class="h"><a name="224"></a>224</td><td></td><td></td><td></td><td></td><td class="s"> );</td></tr> |
| 398 | <tr><td class="h"><a name="225"></a>225</td><td></td><td></td><td></td><td></td><td class="s"> </td></tr> |
| 399 | <tr><td class="h"><a name="226"></a>226</td><td></td><td></td><td></td><td></td><td class="s"> # 'Listeners' are subroutine references that</td></tr> |
| 400 | <tr><td class="h"><a name="227"></a>227</td><td></td><td></td><td></td><td></td><td class="s"> # are executed when a message is transmitted.</td></tr> |
| 401 | <tr><td class="h"><a name="228"></a>228</td><td></td><td></td><td></td><td></td><td class="s"> # The first argument passed to these subroutines</td></tr> |
| 402 | <tr><td class="h"><a name="229"></a>229</td><td></td><td></td><td></td><td></td><td class="s"> # is the log message. This particular listener</td></tr> |
| 403 | <tr><td class="h"><a name="230"></a>230</td><td></td><td></td><td></td><td></td><td class="s"> # will write the message to the 'parsing.log'</td></tr> |
| 404 | <tr><td class="h"><a name="231"></a>231</td><td></td><td></td><td></td><td></td><td class="s"> # file, if the $fh file handle is still open.</td></tr> |
| 405 | <tr><td class="h"><a name="232"></a>232</td><td></td><td></td><td></td><td></td><td class="s"> $logger->set_listeners(</td></tr> |
| 406 | <tr><td class="h"><a name="233"></a>233</td><td></td><td></td><td></td><td></td><td class="s"> sub {</td></tr> |
| 407 | <tr><td class="h"><a name="234"></a>234</td><td></td><td></td><td></td><td></td><td class="s"> my ($msg) = @_;</td></tr> |
| 408 | <tr><td class="h"><a name="235"></a>235</td><td></td><td></td><td></td><td></td><td class="s"> if ( $fh->opened ) {</td></tr> |
| 409 | <tr><td class="h"><a name="236"></a>236</td><td></td><td></td><td></td><td></td><td class="s"> print $fh $msg;</td></tr> |
| 410 | <tr><td class="h"><a name="237"></a>237</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 411 | <tr><td class="h"><a name="238"></a>238</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 412 | <tr><td class="h"><a name="239"></a>239</td><td></td><td></td><td></td><td></td><td class="s"> );</td></tr> |
| 413 | <tr><td class="h"><a name="240"></a>240</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 414 | <tr><td class="h"><a name="241"></a>241</td><td></td><td></td><td></td><td></td><td class="s"> # Now parse a tree, and see what is logged.</td></tr> |
| 415 | <tr><td class="h"><a name="242"></a>242</td><td></td><td></td><td></td><td></td><td class="s"> my $tree = parse( </td></tr> |
| 416 | <tr><td class="h"><a name="243"></a>243</td><td></td><td></td><td></td><td></td><td class="s"> '-format' => 'newick', </td></tr> |
| 417 | <tr><td class="h"><a name="244"></a>244</td><td></td><td></td><td></td><td></td><td class="s"> '-string' => do { local $/; <DATA> },</td></tr> |
| 418 | <tr><td class="h"><a name="245"></a>245</td><td></td><td></td><td></td><td></td><td class="s"> )->first;</td></tr> |
| 419 | <tr><td class="h"><a name="246"></a>246</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 420 | <tr><td class="h"><a name="247"></a>247</td><td></td><td></td><td></td><td></td><td class="s"> # Cleanly close the log handle.</td></tr> |
| 421 | <tr><td class="h"><a name="248"></a>248</td><td></td><td></td><td></td><td></td><td class="s"> close $fh;</td></tr> |
| 422 | <tr><td class="h"><a name="249"></a>249</td><td></td><td></td><td></td><td></td><td class="s"> </td></tr> |
| 423 | <tr><td class="h"><a name="250"></a>250</td><td></td><td></td><td></td><td></td><td class="s"> __DATA__</td></tr> |
| 424 | <tr><td class="h"><a name="251"></a>251</td><td></td><td></td><td></td><td></td><td class="s"> ((((A,B),C),D),E);</td></tr> |
| 425 | <tr><td class="h"><a name="252"></a>252</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 426 | <tr><td class="h"><a name="253"></a>253</td><td></td><td></td><td></td><td></td><td class="s">The example above will write something like the following to the log file:</td></tr> |
| 427 | <tr><td class="h"><a name="254"></a>254</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 428 | <tr><td class="h"><a name="255"></a>255</td><td></td><td></td><td></td><td></td><td class="s"> INFO Bio::Phylo::Forest::Tree::new [$PREFIX/Bio/Phylo/Forest/Tree.pm, 99] - constructor called for 'Bio::Phylo::Forest::Tree'</td></tr> |
| 429 | <tr><td class="h"><a name="256"></a>256</td><td></td><td></td><td></td><td></td><td class="s"> INFO Bio::Phylo::set_name [$PREFIX/Bio/Phylo.pm, 281] - setting name 'A'</td></tr> |
| 430 | <tr><td class="h"><a name="257"></a>257</td><td></td><td></td><td></td><td></td><td class="s"> INFO Bio::Phylo::set_name [$PREFIX/Bio/Phylo.pm, 281] - setting name 'B'</td></tr> |
| 431 | <tr><td class="h"><a name="258"></a>258</td><td></td><td></td><td></td><td></td><td class="s"> INFO Bio::Phylo::set_name [$PREFIX/Bio/Phylo.pm, 281] - setting name 'C'</td></tr> |
| 432 | <tr><td class="h"><a name="259"></a>259</td><td></td><td></td><td></td><td></td><td class="s"> INFO Bio::Phylo::set_name [$PREFIX/Bio/Phylo.pm, 281] - setting name 'D'</td></tr> |
| 433 | <tr><td class="h"><a name="260"></a>260</td><td></td><td></td><td></td><td></td><td class="s"> INFO Bio::Phylo::set_name [$PREFIX/Bio/Phylo.pm, 281] - setting name 'E'</td></tr> |
| 434 | <tr><td class="h"><a name="261"></a>261</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 435 | <tr><td class="h"><a name="262"></a>262</td><td></td><td></td><td></td><td></td><td class="s">=head1 DESCRIPTION</td></tr> |
| 436 | <tr><td class="h"><a name="263"></a>263</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 437 | <tr><td class="h"><a name="264"></a>264</td><td></td><td></td><td></td><td></td><td class="s">This class defines a logger, a utility object for logging messages.</td></tr> |
| 438 | <tr><td class="h"><a name="265"></a>265</td><td></td><td></td><td></td><td></td><td class="s">The other objects in Bio::Phylo use this logger to give detailed feedback</td></tr> |
| 439 | <tr><td class="h"><a name="266"></a>266</td><td></td><td></td><td></td><td></td><td class="s">about what they are doing at per-class, per-method, user-configurable log levels</td></tr> |
| 440 | <tr><td class="h"><a name="267"></a>267</td><td></td><td></td><td></td><td></td><td class="s">(DEBUG, INFO, WARN, ERROR and FATAL). These log levels are constants that are</td></tr> |
| 441 | <tr><td class="h"><a name="268"></a>268</td><td></td><td></td><td></td><td></td><td class="s">optionally exported by this class by passing the ':levels' argument to your</td></tr> |
| 442 | <tr><td class="h"><a name="269"></a>269</td><td></td><td></td><td></td><td></td><td class="s">'use' statement, like so:</td></tr> |
| 443 | <tr><td class="h"><a name="270"></a>270</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 444 | <tr><td class="h"><a name="271"></a>271</td><td></td><td></td><td></td><td></td><td class="s"> use Bio::Phylo::Util::Logger ':levels';</td></tr> |
| 445 | <tr><td class="h"><a name="272"></a>272</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 446 | <tr><td class="h"><a name="273"></a>273</td><td></td><td></td><td></td><td></td><td class="s">If for some reason you don't want this behaviour (i.e. because there is</td></tr> |
| 447 | <tr><td class="h"><a name="274"></a>274</td><td></td><td></td><td></td><td></td><td class="s">something else by these same names in your namespace) you must use the fully</td></tr> |
| 448 | <tr><td class="h"><a name="275"></a>275</td><td></td><td></td><td></td><td></td><td class="s">qualified names for these levels, i.e. Bio::Phylo::Util::Logger::DEBUG and</td></tr> |
| 449 | <tr><td class="h"><a name="276"></a>276</td><td></td><td></td><td></td><td></td><td class="s">so on.</td></tr> |
| 450 | <tr><td class="h"><a name="277"></a>277</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 451 | <tr><td class="h"><a name="278"></a>278</td><td></td><td></td><td></td><td></td><td class="s">The least verbose is level FATAL, in which case only 'fatal' messages are shown. </td></tr> |
| 452 | <tr><td class="h"><a name="279"></a>279</td><td></td><td></td><td></td><td></td><td class="s">The most verbose level, DEBUG, shows debugging messages, including from internal </td></tr> |
| 453 | <tr><td class="h"><a name="280"></a>280</td><td></td><td></td><td></td><td></td><td class="s">methods (i.e. ones that start with underscores, and special 'ALLCAPS' perl </td></tr> |
| 454 | <tr><td class="h"><a name="281"></a>281</td><td></td><td></td><td></td><td></td><td class="s">methods like DESTROY or TIEARRAY). For example, to monitor what the root class </td></tr> |
| 455 | <tr><td class="h"><a name="282"></a>282</td><td></td><td></td><td></td><td></td><td class="s">is doing, you would say:</td></tr> |
| 456 | <tr><td class="h"><a name="283"></a>283</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 457 | <tr><td class="h"><a name="284"></a>284</td><td></td><td></td><td></td><td></td><td class="s"> $logger->( -class => 'Bio::Phylo', -level => DEBUG )</td></tr> |
| 458 | <tr><td class="h"><a name="285"></a>285</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 459 | <tr><td class="h"><a name="286"></a>286</td><td></td><td></td><td></td><td></td><td class="s">To define global verbosity you can omit the -class argument. To set verbosity</td></tr> |
| 460 | <tr><td class="h"><a name="287"></a>287</td><td></td><td></td><td></td><td></td><td class="s">at a more granular level, you can use the -method argument, which takes a </td></tr> |
| 461 | <tr><td class="h"><a name="288"></a>288</td><td></td><td></td><td></td><td></td><td class="s">fully qualified method name such as 'Bio::Phylo::set_name', such that messages</td></tr> |
| 462 | <tr><td class="h"><a name="289"></a>289</td><td></td><td></td><td></td><td></td><td class="s">originating from within that method's body get a different verbosity level.</td></tr> |
| 463 | <tr><td class="h"><a name="290"></a>290</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 464 | <tr><td class="h"><a name="291"></a>291</td><td></td><td></td><td></td><td></td><td class="s">=head1 METHODS</td></tr> |
| 465 | <tr><td class="h"><a name="292"></a>292</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 466 | <tr><td class="h"><a name="293"></a>293</td><td></td><td></td><td></td><td></td><td class="s">=head2 CONSTRUCTOR</td></tr> |
| 467 | <tr><td class="h"><a name="294"></a>294</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 468 | <tr><td class="h"><a name="295"></a>295</td><td></td><td></td><td></td><td></td><td class="s">=over</td></tr> |
| 469 | <tr><td class="h"><a name="296"></a>296</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 470 | <tr><td class="h"><a name="297"></a>297</td><td></td><td></td><td></td><td></td><td class="s">=item new()</td></tr> |
| 471 | <tr><td class="h"><a name="298"></a>298</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 472 | <tr><td class="h"><a name="299"></a>299</td><td></td><td></td><td></td><td></td><td class="s">Constructor for Logger.</td></tr> |
| 473 | <tr><td class="h"><a name="300"></a>300</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 474 | <tr><td class="h"><a name="301"></a>301</td><td></td><td></td><td></td><td></td><td class="s"> Type : Constructor</td></tr> |
| 475 | <tr><td class="h"><a name="302"></a>302</td><td></td><td></td><td></td><td></td><td class="s"> Title : new</td></tr> |
| 476 | <tr><td class="h"><a name="303"></a>303</td><td></td><td></td><td></td><td></td><td class="s"> Usage : my $logger = Bio::Phylo::Util::Logger->new;</td></tr> |
| 477 | <tr><td class="h"><a name="304"></a>304</td><td></td><td></td><td></td><td></td><td class="s"> Function: Instantiates a logger</td></tr> |
| 478 | <tr><td class="h"><a name="305"></a>305</td><td></td><td></td><td></td><td></td><td class="s"> Returns : a Bio::Phylo::Util::Logger object</td></tr> |
| 479 | <tr><td class="h"><a name="306"></a>306</td><td></td><td></td><td></td><td></td><td class="s"> Args : -verbose => Bio::Phylo::Util::Logger::INFO (DEBUG/INFO/WARN/ERROR/FATAL)</td></tr> |
| 480 | <tr><td class="h"><a name="307"></a>307</td><td></td><td></td><td></td><td></td><td class="s"> -package => a package for which to set verbosity (optional) </td></tr> |
| 481 | <tr><td class="h"><a name="308"></a>308</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 482 | <tr><td class="h"><a name="309"></a>309</td><td></td><td></td><td></td><td></td><td class="s">=back</td></tr> |
| 483 | <tr><td class="h"><a name="310"></a>310</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 484 | <tr><td class="h"><a name="311"></a>311</td><td></td><td></td><td></td><td></td><td class="s">=head2 VERBOSITY LEVELS</td></tr> |
| 485 | <tr><td class="h"><a name="312"></a>312</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 486 | <tr><td class="h"><a name="313"></a>313</td><td></td><td></td><td></td><td></td><td class="s">=over</td></tr> |
| 487 | <tr><td class="h"><a name="314"></a>314</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 488 | <tr><td class="h"><a name="315"></a>315</td><td></td><td></td><td></td><td></td><td class="s">=item FATAL</td></tr> |
| 489 | <tr><td class="h"><a name="316"></a>316</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 490 | <tr><td class="h"><a name="317"></a>317</td><td></td><td></td><td></td><td></td><td class="s">Rarely happens, usually an exception is thrown instead.</td></tr> |
| 491 | <tr><td class="h"><a name="318"></a>318</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 492 | <tr><td class="h"><a name="319"></a>319</td><td></td><td></td><td></td><td></td><td class="s">=item ERROR</td></tr> |
| 493 | <tr><td class="h"><a name="320"></a>320</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 494 | <tr><td class="h"><a name="321"></a>321</td><td></td><td></td><td></td><td></td><td class="s">If this happens, something is seriously wrong that needs to be addressed.</td></tr> |
| 495 | <tr><td class="h"><a name="322"></a>322</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 496 | <tr><td class="h"><a name="323"></a>323</td><td></td><td></td><td></td><td></td><td class="s">=item WARN</td></tr> |
| 497 | <tr><td class="h"><a name="324"></a>324</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 498 | <tr><td class="h"><a name="325"></a>325</td><td></td><td></td><td></td><td></td><td class="s">If this happens, something is seriously wrong that needs to be addressed.</td></tr> |
| 499 | <tr><td class="h"><a name="326"></a>326</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 500 | <tr><td class="h"><a name="327"></a>327</td><td></td><td></td><td></td><td></td><td class="s">=item INFO</td></tr> |
| 501 | <tr><td class="h"><a name="328"></a>328</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 502 | <tr><td class="h"><a name="329"></a>329</td><td></td><td></td><td></td><td></td><td class="s">If something weird is happening, turn up verbosity to this level as it might</td></tr> |
| 503 | <tr><td class="h"><a name="330"></a>330</td><td></td><td></td><td></td><td></td><td class="s">explain some of the assumptions the code is making.</td></tr> |
| 504 | <tr><td class="h"><a name="331"></a>331</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 505 | <tr><td class="h"><a name="332"></a>332</td><td></td><td></td><td></td><td></td><td class="s">=item DEBUG</td></tr> |
| 506 | <tr><td class="h"><a name="333"></a>333</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 507 | <tr><td class="h"><a name="334"></a>334</td><td></td><td></td><td></td><td></td><td class="s">This is very verbose, probably only useful if you write core Bio::Phylo code.</td></tr> |
| 508 | <tr><td class="h"><a name="335"></a>335</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 509 | <tr><td class="h"><a name="336"></a>336</td><td></td><td></td><td></td><td></td><td class="s">=back</td></tr> |
| 510 | <tr><td class="h"><a name="337"></a>337</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 511 | <tr><td class="h"><a name="338"></a>338</td><td></td><td></td><td></td><td></td><td class="s">=head2 LOGGING METHODS</td></tr> |
| 512 | <tr><td class="h"><a name="339"></a>339</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 513 | <tr><td class="h"><a name="340"></a>340</td><td></td><td></td><td></td><td></td><td class="s">=over</td></tr> |
| 514 | <tr><td class="h"><a name="341"></a>341</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 515 | <tr><td class="h"><a name="342"></a>342</td><td></td><td></td><td></td><td></td><td class="s">=item log()</td></tr> |
| 516 | <tr><td class="h"><a name="343"></a>343</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 517 | <tr><td class="h"><a name="344"></a>344</td><td></td><td></td><td></td><td></td><td class="s">Prints argument debugging message, depending on verbosity.</td></tr> |
| 518 | <tr><td class="h"><a name="345"></a>345</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 519 | <tr><td class="h"><a name="346"></a>346</td><td></td><td></td><td></td><td></td><td class="s"> Type : logging method</td></tr> |
| 520 | <tr><td class="h"><a name="347"></a>347</td><td></td><td></td><td></td><td></td><td class="s"> Title : log</td></tr> |
| 521 | <tr><td class="h"><a name="348"></a>348</td><td></td><td></td><td></td><td></td><td class="s"> Usage : $logger->log( "WARN", "warning message" );</td></tr> |
| 522 | <tr><td class="h"><a name="349"></a>349</td><td></td><td></td><td></td><td></td><td class="s"> Function: prints logging message, depending on verbosity</td></tr> |
| 523 | <tr><td class="h"><a name="350"></a>350</td><td></td><td></td><td></td><td></td><td class="s"> Returns : invocant</td></tr> |
| 524 | <tr><td class="h"><a name="351"></a>351</td><td></td><td></td><td></td><td></td><td class="s"> Args : message log level, logging message</td></tr> |
| 525 | <tr><td class="h"><a name="352"></a>352</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 526 | <tr><td class="h"><a name="353"></a>353</td><td></td><td></td><td></td><td></td><td class="s">=item debug()</td></tr> |
| 527 | <tr><td class="h"><a name="354"></a>354</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 528 | <tr><td class="h"><a name="355"></a>355</td><td></td><td></td><td></td><td></td><td class="s">Prints argument debugging message, depending on verbosity.</td></tr> |
| 529 | <tr><td class="h"><a name="356"></a>356</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 530 | <tr><td class="h"><a name="357"></a>357</td><td></td><td></td><td></td><td></td><td class="s"> Type : logging method</td></tr> |
| 531 | <tr><td class="h"><a name="358"></a>358</td><td></td><td></td><td></td><td></td><td class="s"> Title : debug</td></tr> |
| 532 | <tr><td class="h"><a name="359"></a>359</td><td></td><td></td><td></td><td></td><td class="s"> Usage : $logger->debug( "debugging message" );</td></tr> |
| 533 | <tr><td class="h"><a name="360"></a>360</td><td></td><td></td><td></td><td></td><td class="s"> Function: prints debugging message, depending on verbosity</td></tr> |
| 534 | <tr><td class="h"><a name="361"></a>361</td><td></td><td></td><td></td><td></td><td class="s"> Returns : invocant</td></tr> |
| 535 | <tr><td class="h"><a name="362"></a>362</td><td></td><td></td><td></td><td></td><td class="s"> Args : logging message</td></tr> |
| 536 | <tr><td class="h"><a name="363"></a>363</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 537 | <tr><td class="h"><a name="364"></a>364</td><td></td><td></td><td></td><td></td><td class="s">=item info()</td></tr> |
| 538 | <tr><td class="h"><a name="365"></a>365</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 539 | <tr><td class="h"><a name="366"></a>366</td><td></td><td></td><td></td><td></td><td class="s">Prints argument informational message, depending on verbosity.</td></tr> |
| 540 | <tr><td class="h"><a name="367"></a>367</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 541 | <tr><td class="h"><a name="368"></a>368</td><td></td><td></td><td></td><td></td><td class="s"> Type : logging method</td></tr> |
| 542 | <tr><td class="h"><a name="369"></a>369</td><td></td><td></td><td></td><td></td><td class="s"> Title : info</td></tr> |
| 543 | <tr><td class="h"><a name="370"></a>370</td><td></td><td></td><td></td><td></td><td class="s"> Usage : $logger->info( "info message" );</td></tr> |
| 544 | <tr><td class="h"><a name="371"></a>371</td><td></td><td></td><td></td><td></td><td class="s"> Function: prints info message, depending on verbosity</td></tr> |
| 545 | <tr><td class="h"><a name="372"></a>372</td><td></td><td></td><td></td><td></td><td class="s"> Returns : invocant</td></tr> |
| 546 | <tr><td class="h"><a name="373"></a>373</td><td></td><td></td><td></td><td></td><td class="s"> Args : logging message</td></tr> |
| 547 | <tr><td class="h"><a name="374"></a>374</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 548 | <tr><td class="h"><a name="375"></a>375</td><td></td><td></td><td></td><td></td><td class="s">=item warn()</td></tr> |
| 549 | <tr><td class="h"><a name="376"></a>376</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 550 | <tr><td class="h"><a name="377"></a>377</td><td></td><td></td><td></td><td></td><td class="s">Prints argument warning message, depending on verbosity.</td></tr> |
| 551 | <tr><td class="h"><a name="378"></a>378</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 552 | <tr><td class="h"><a name="379"></a>379</td><td></td><td></td><td></td><td></td><td class="s"> Type : logging method</td></tr> |
| 553 | <tr><td class="h"><a name="380"></a>380</td><td></td><td></td><td></td><td></td><td class="s"> Title : warn</td></tr> |
| 554 | <tr><td class="h"><a name="381"></a>381</td><td></td><td></td><td></td><td></td><td class="s"> Usage : $logger->warn( "warning message" );</td></tr> |
| 555 | <tr><td class="h"><a name="382"></a>382</td><td></td><td></td><td></td><td></td><td class="s"> Function: prints warning message, depending on verbosity</td></tr> |
| 556 | <tr><td class="h"><a name="383"></a>383</td><td></td><td></td><td></td><td></td><td class="s"> Returns : invocant</td></tr> |
| 557 | <tr><td class="h"><a name="384"></a>384</td><td></td><td></td><td></td><td></td><td class="s"> Args : logging message</td></tr> |
| 558 | <tr><td class="h"><a name="385"></a>385</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 559 | <tr><td class="h"><a name="386"></a>386</td><td></td><td></td><td></td><td></td><td class="s">=item error()</td></tr> |
| 560 | <tr><td class="h"><a name="387"></a>387</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 561 | <tr><td class="h"><a name="388"></a>388</td><td></td><td></td><td></td><td></td><td class="s">Prints argument error message, depending on verbosity.</td></tr> |
| 562 | <tr><td class="h"><a name="389"></a>389</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 563 | <tr><td class="h"><a name="390"></a>390</td><td></td><td></td><td></td><td></td><td class="s"> Type : logging method</td></tr> |
| 564 | <tr><td class="h"><a name="391"></a>391</td><td></td><td></td><td></td><td></td><td class="s"> Title : error</td></tr> |
| 565 | <tr><td class="h"><a name="392"></a>392</td><td></td><td></td><td></td><td></td><td class="s"> Usage : $logger->error( "error message" );</td></tr> |
| 566 | <tr><td class="h"><a name="393"></a>393</td><td></td><td></td><td></td><td></td><td class="s"> Function: prints error message, depending on verbosity</td></tr> |
| 567 | <tr><td class="h"><a name="394"></a>394</td><td></td><td></td><td></td><td></td><td class="s"> Returns : invocant</td></tr> |
| 568 | <tr><td class="h"><a name="395"></a>395</td><td></td><td></td><td></td><td></td><td class="s"> Args : logging message</td></tr> |
| 569 | <tr><td class="h"><a name="396"></a>396</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 570 | <tr><td class="h"><a name="397"></a>397</td><td></td><td></td><td></td><td></td><td class="s">=item fatal()</td></tr> |
| 571 | <tr><td class="h"><a name="398"></a>398</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 572 | <tr><td class="h"><a name="399"></a>399</td><td></td><td></td><td></td><td></td><td class="s">Prints argument fatal message, depending on verbosity.</td></tr> |
| 573 | <tr><td class="h"><a name="400"></a>400</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 574 | <tr><td class="h"><a name="401"></a>401</td><td></td><td></td><td></td><td></td><td class="s"> Type : logging method</td></tr> |
| 575 | <tr><td class="h"><a name="402"></a>402</td><td></td><td></td><td></td><td></td><td class="s"> Title : fatal</td></tr> |
| 576 | <tr><td class="h"><a name="403"></a>403</td><td></td><td></td><td></td><td></td><td class="s"> Usage : $logger->fatal( "fatal message" );</td></tr> |
| 577 | <tr><td class="h"><a name="404"></a>404</td><td></td><td></td><td></td><td></td><td class="s"> Function: prints fatal message, depending on verbosity</td></tr> |
| 578 | <tr><td class="h"><a name="405"></a>405</td><td></td><td></td><td></td><td></td><td class="s"> Returns : invocant</td></tr> |
| 579 | <tr><td class="h"><a name="406"></a>406</td><td></td><td></td><td></td><td></td><td class="s"> Args : logging message</td></tr> |
| 580 | <tr><td class="h"><a name="407"></a>407</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 581 | <tr><td class="h"><a name="408"></a>408</td><td></td><td></td><td></td><td></td><td class="s">=item set_listeners()</td></tr> |
| 582 | <tr><td class="h"><a name="409"></a>409</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 583 | <tr><td class="h"><a name="410"></a>410</td><td></td><td></td><td></td><td></td><td class="s">Adds listeners to send log messages to.</td></tr> |
| 584 | <tr><td class="h"><a name="411"></a>411</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 585 | <tr><td class="h"><a name="412"></a>412</td><td></td><td></td><td></td><td></td><td class="s"> Type : Mutator</td></tr> |
| 586 | <tr><td class="h"><a name="413"></a>413</td><td></td><td></td><td></td><td></td><td class="s"> Title : set_listeners()</td></tr> |
| 587 | <tr><td class="h"><a name="414"></a>414</td><td></td><td></td><td></td><td></td><td class="s"> Usage : $logger->set_listeners( sub { warn shift } )</td></tr> |
| 588 | <tr><td class="h"><a name="415"></a>415</td><td></td><td></td><td></td><td></td><td class="s"> Function: Sets additional listeners to log to (e.g. a file)</td></tr> |
| 589 | <tr><td class="h"><a name="416"></a>416</td><td></td><td></td><td></td><td></td><td class="s"> Returns : invocant</td></tr> |
| 590 | <tr><td class="h"><a name="417"></a>417</td><td></td><td></td><td></td><td></td><td class="s"> Args : One or more code references</td></tr> |
| 591 | <tr><td class="h"><a name="418"></a>418</td><td></td><td></td><td></td><td></td><td class="s"> Comments: On execution of the listeners, the @_ arguments are:</td></tr> |
| 592 | <tr><td class="h"><a name="419"></a>419</td><td></td><td></td><td></td><td></td><td class="s"> $log_string, # the formatted log string</td></tr> |
| 593 | <tr><td class="h"><a name="420"></a>420</td><td></td><td></td><td></td><td></td><td class="s"> $level, # log level, i.e DEBUG, INFO, WARN, ERROR or FATAL</td></tr> |
| 594 | <tr><td class="h"><a name="421"></a>421</td><td></td><td></td><td></td><td></td><td class="s"> $subroutine, # the calling subroutine</td></tr> |
| 595 | <tr><td class="h"><a name="422"></a>422</td><td></td><td></td><td></td><td></td><td class="s"> $filename, # filename where log method was called</td></tr> |
| 596 | <tr><td class="h"><a name="423"></a>423</td><td></td><td></td><td></td><td></td><td class="s"> $line, # line where log method was called</td></tr> |
| 597 | <tr><td class="h"><a name="424"></a>424</td><td></td><td></td><td></td><td></td><td class="s"> $msg # the unformatted message</td></tr> |
| 598 | <tr><td class="h"><a name="425"></a>425</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 599 | <tr><td class="h"><a name="426"></a>426</td><td></td><td></td><td></td><td></td><td class="s">=item PREFIX()</td></tr> |
| 600 | <tr><td class="h"><a name="427"></a>427</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 601 | <tr><td class="h"><a name="428"></a>428</td><td></td><td></td><td></td><td></td><td class="s">Getter and setter of path prefix to strip from source file paths in messages.</td></tr> |
| 602 | <tr><td class="h"><a name="429"></a>429</td><td></td><td></td><td></td><td></td><td class="s">By default, messages will have a field such as C<[$PREFIX/Bio/Phylo.pm, 280]>,</td></tr> |
| 603 | <tr><td class="h"><a name="430"></a>430</td><td></td><td></td><td></td><td></td><td class="s">which indicates the message was sent from line 280 in file Bio/Phylo.pm inside</td></tr> |
| 604 | <tr><td class="h"><a name="431"></a>431</td><td></td><td></td><td></td><td></td><td class="s">path $PREFIX. This is done so that your log won't be cluttered with </td></tr> |
| 605 | <tr><td class="h"><a name="432"></a>432</td><td></td><td></td><td></td><td></td><td class="s">unnecessarily long paths. To find out what C<$PREFIX> is set to, call the </td></tr> |
| 606 | <tr><td class="h"><a name="433"></a>433</td><td></td><td></td><td></td><td></td><td class="s">PREFIX() method on the logger, and to change it provide a path argument </td></tr> |
| 607 | <tr><td class="h"><a name="434"></a>434</td><td></td><td></td><td></td><td></td><td class="s">relative to which the paths to source files will be constructed.</td></tr> |
| 608 | <tr><td class="h"><a name="435"></a>435</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 609 | <tr><td class="h"><a name="436"></a>436</td><td></td><td></td><td></td><td></td><td class="s"> Type : Mutator/Accessor</td></tr> |
| 610 | <tr><td class="h"><a name="437"></a>437</td><td></td><td></td><td></td><td></td><td class="s"> Title : PREFIX()</td></tr> |
| 611 | <tr><td class="h"><a name="438"></a>438</td><td></td><td></td><td></td><td></td><td class="s"> Usage : $logger->PREFIX( '/path/to/bio/phylo' )</td></tr> |
| 612 | <tr><td class="h"><a name="439"></a>439</td><td></td><td></td><td></td><td></td><td class="s"> Function: Sets/gets $PREFIX</td></tr> |
| 613 | <tr><td class="h"><a name="440"></a>440</td><td></td><td></td><td></td><td></td><td class="s"> Returns : Verbose level</td></tr> |
| 614 | <tr><td class="h"><a name="441"></a>441</td><td></td><td></td><td></td><td></td><td class="s"> Args : Optional: a path</td></tr> |
| 615 | <tr><td class="h"><a name="442"></a>442</td><td></td><td></td><td></td><td></td><td class="s"> Comments:</td></tr> |
| 616 | <tr><td class="h"><a name="443"></a>443</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 617 | <tr><td class="h"><a name="444"></a>444</td><td></td><td></td><td></td><td></td><td class="s">=item VERBOSE()</td></tr> |
| 618 | <tr><td class="h"><a name="445"></a>445</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 619 | <tr><td class="h"><a name="446"></a>446</td><td></td><td></td><td></td><td></td><td class="s">Setter for the verbose level. This comes in five levels: </td></tr> |
| 620 | <tr><td class="h"><a name="447"></a>447</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 621 | <tr><td class="h"><a name="448"></a>448</td><td></td><td></td><td></td><td></td><td class="s"> FATAL = only fatal messages (though, when something fatal happens, you'll most </td></tr> |
| 622 | <tr><td class="h"><a name="449"></a>449</td><td></td><td></td><td></td><td></td><td class="s"> likely get an exception object), </td></tr> |
| 623 | <tr><td class="h"><a name="450"></a>450</td><td></td><td></td><td></td><td></td><td class="s"> </td></tr> |
| 624 | <tr><td class="h"><a name="451"></a>451</td><td></td><td></td><td></td><td></td><td class="s"> ERROR = errors (hopefully recoverable), </td></tr> |
| 625 | <tr><td class="h"><a name="452"></a>452</td><td></td><td></td><td></td><td></td><td class="s"> </td></tr> |
| 626 | <tr><td class="h"><a name="453"></a>453</td><td></td><td></td><td></td><td></td><td class="s"> WARN = warnings (recoverable), </td></tr> |
| 627 | <tr><td class="h"><a name="454"></a>454</td><td></td><td></td><td></td><td></td><td class="s"> </td></tr> |
| 628 | <tr><td class="h"><a name="455"></a>455</td><td></td><td></td><td></td><td></td><td class="s"> INFO = info (useful diagnostics), </td></tr> |
| 629 | <tr><td class="h"><a name="456"></a>456</td><td></td><td></td><td></td><td></td><td class="s"> </td></tr> |
| 630 | <tr><td class="h"><a name="457"></a>457</td><td></td><td></td><td></td><td></td><td class="s"> DEBUG = debug (almost every method call)</td></tr> |
| 631 | <tr><td class="h"><a name="458"></a>458</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 632 | <tr><td class="h"><a name="459"></a>459</td><td></td><td></td><td></td><td></td><td class="s">Without additional arguments, i.e. by just calling VERBOSE( -level => $level ),</td></tr> |
| 633 | <tr><td class="h"><a name="460"></a>460</td><td></td><td></td><td></td><td></td><td class="s">you set the global verbosity level. By default this is 2. By increasing this</td></tr> |
| 634 | <tr><td class="h"><a name="461"></a>461</td><td></td><td></td><td></td><td></td><td class="s">level, the number of messages quickly becomes too great to make sense out of.</td></tr> |
| 635 | <tr><td class="h"><a name="462"></a>462</td><td></td><td></td><td></td><td></td><td class="s">To focus on a particular class, you can add the -class => 'Some::Class' </td></tr> |
| 636 | <tr><td class="h"><a name="463"></a>463</td><td></td><td></td><td></td><td></td><td class="s">(where 'Some::Class' stands for any of the class names in the Bio::Phylo </td></tr> |
| 637 | <tr><td class="h"><a name="464"></a>464</td><td></td><td></td><td></td><td></td><td class="s">release) argument, which means that messages originating from that class will </td></tr> |
| 638 | <tr><td class="h"><a name="465"></a>465</td><td></td><td></td><td></td><td></td><td class="s">have a different (presumably higher) verbosity level than the global level. </td></tr> |
| 639 | <tr><td class="h"><a name="466"></a>466</td><td></td><td></td><td></td><td></td><td class="s">By adding the -method => 'Fully::Qualified::method_name' (say, </td></tr> |
| 640 | <tr><td class="h"><a name="467"></a>467</td><td></td><td></td><td></td><td></td><td class="s">'Bio::Phylo::set_name'), you can change the verbosity of a specific method. When</td></tr> |
| 641 | <tr><td class="h"><a name="468"></a>468</td><td></td><td></td><td></td><td></td><td class="s">evaluating whether or not to transmit a message, the method-specific verbosity</td></tr> |
| 642 | <tr><td class="h"><a name="469"></a>469</td><td></td><td></td><td></td><td></td><td class="s">level takes precedence over the class-specific level, which takes precedence</td></tr> |
| 643 | <tr><td class="h"><a name="470"></a>470</td><td></td><td></td><td></td><td></td><td class="s">over the global level.</td></tr> |
| 644 | <tr><td class="h"><a name="471"></a>471</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 645 | <tr><td class="h"><a name="472"></a>472</td><td></td><td></td><td></td><td></td><td class="s"> Type : Mutator</td></tr> |
| 646 | <tr><td class="h"><a name="473"></a>473</td><td></td><td></td><td></td><td></td><td class="s"> Title : VERBOSE()</td></tr> |
| 647 | <tr><td class="h"><a name="474"></a>474</td><td></td><td></td><td></td><td></td><td class="s"> Usage : $logger->VERBOSE( -level => $level )</td></tr> |
| 648 | <tr><td class="h"><a name="475"></a>475</td><td></td><td></td><td></td><td></td><td class="s"> Function: Sets/gets verbose level</td></tr> |
| 649 | <tr><td class="h"><a name="476"></a>476</td><td></td><td></td><td></td><td></td><td class="s"> Returns : Verbose level</td></tr> |
| 650 | <tr><td class="h"><a name="477"></a>477</td><td></td><td></td><td></td><td></td><td class="s"> Args : -level => 4 # or lower</td></tr> |
| 651 | <tr><td class="h"><a name="478"></a>478</td><td></td><td></td><td></td><td></td><td class="s"> </td></tr> |
| 652 | <tr><td class="h"><a name="479"></a>479</td><td></td><td></td><td></td><td></td><td class="s"> # optional, or any other class </td></tr> |
| 653 | <tr><td class="h"><a name="480"></a>480</td><td></td><td></td><td></td><td></td><td class="s"> -class => 'Bio::Phylo' </td></tr> |
| 654 | <tr><td class="h"><a name="481"></a>481</td><td></td><td></td><td></td><td></td><td class="s"> </td></tr> |
| 655 | <tr><td class="h"><a name="482"></a>482</td><td></td><td></td><td></td><td></td><td class="s"> # optional, fully qualified method name</td></tr> |
| 656 | <tr><td class="h"><a name="483"></a>483</td><td></td><td></td><td></td><td></td><td class="s"> -method' => 'Bio::Phylo::set_name' </td></tr> |
| 657 | <tr><td class="h"><a name="484"></a>484</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 658 | <tr><td class="h"><a name="485"></a>485</td><td></td><td></td><td></td><td></td><td class="s">=back</td></tr> |
| 659 | <tr><td class="h"><a name="486"></a>486</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 660 | <tr><td class="h"><a name="487"></a>487</td><td></td><td></td><td></td><td></td><td class="s">=head1 SEE ALSO</td></tr> |
| 661 | <tr><td class="h"><a name="488"></a>488</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 662 | <tr><td class="h"><a name="489"></a>489</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> |
| 663 | <tr><td class="h"><a name="490"></a>490</td><td></td><td></td><td></td><td></td><td class="s">for any user or developer questions and discussions.</td></tr> |
| 664 | <tr><td class="h"><a name="491"></a>491</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 665 | <tr><td class="h"><a name="492"></a>492</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> |
| 666 | <tr><td class="h"><a name="493"></a>493</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 667 | <tr><td class="h"><a name="494"></a>494</td><td></td><td></td><td></td><td></td><td class="s">=head1 CITATION</td></tr> |
| 668 | <tr><td class="h"><a name="495"></a>495</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 669 | <tr><td class="h"><a name="496"></a>496</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> |
| 670 | <tr><td class="h"><a name="497"></a>497</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 671 | <tr><td class="h"><a name="498"></a>498</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> |
| 672 | <tr><td class="h"><a name="499"></a>499</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> |
| 673 | <tr><td class="h"><a name="500"></a>500</td><td></td><td></td><td></td><td></td><td class="s">I<BMC Bioinformatics> B<12>:63.</td></tr> |
| 674 | <tr><td class="h"><a name="501"></a>501</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> |
| 675 | <tr><td class="h"><a name="502"></a>502</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 676 | <tr><td class="h"><a name="- -"></a>- -</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 677 | <tr><td class="h"><a name="505"></a>505</td><td></td><td></td><td></td><td></td><td class="s">=cut</td></tr> |
| 678 | <tr><td class="s"><a name=""></a> </td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 679 | <tr><td class="h"><a name="Bio__Phylo__Util__Logger__CORE_subst"></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::Util::Logger::CORE:subst which was called: |
| 680 | # once (5µs+0s) by Bio::Phylo::Util::Logger::BEGIN@13 at <a href="Bio-Phylo-Util-Logger-pm-1164-block.html#33">line 33</a></div></div>sub Bio::Phylo::Util::Logger::CORE:subst; # opcode<br /> </td></tr> |
| 681 | </tbody></table></div> |
| 682 | |
| 683 | <script type="text/javascript"> $(document).ready(function() { |
| 684 | |
| 685 | $("#subs_table").tablesorter({ |
| 686 | sortList: [[3,1]], |
| 687 | headers: { |
| 688 | 3: { sorter: 'fmt_time' }, |
| 689 | 4: { sorter: 'fmt_time' } |
| 690 | } |
| 691 | }); |
| 692 | |
| 693 | } ); </script> |
| 694 | |
| 695 | <div class="footer">Report produced by the |
| 696 | <a href="http://search.cpan.org/dist/Devel-NYTProf/">NYTProf 4.06</a> |
| 697 | Perl profiler, developed by |
| 698 | <a href="http://www.linkedin.com/in/timbunce">Tim Bunce</a> and |
| 699 | <a href="http://code.nytimes.com">Adam Kaplan</a>. |
| 700 | </div> |
| 701 | <br /><br /><br /><br /><br /><br /><br /><br /><br /><br /> |
| 702 | </body></html> |
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