| Commit | Line | Data |
|---|
| 8e30e889 |
1 | <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> |
| 2 | <html xmlns="http://www.w3.org/1999/xhtml"> |
| 3 | <!-- |
| 4 | This file was generated by Devel::NYTProf version 4.06 |
| 5 | --> |
| 6 | <head> |
| 7 | <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> |
| 8 | <meta http-equiv="Content-Language" content="en-us" /> |
| 9 | <title>Profile of Bio/Phylo/IO.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"><a href="Bio-Phylo-IO-pm-1136-block.html">block view</a></span> • <span class="mode_btn mode_btn_selected">line view</span> • <span class="mode_btn"><a href="Bio-Phylo-IO-pm-1136-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 16:55:35 2012</span> |
| 58 | </div> |
| 59 | <div style="position: absolute; left: 0px; top: 0%; width: 100%; height: 101%; z-index: -1; background-color: rgb(17, 136, 255); "></div> |
| 60 | <div style="position: absolute; left: 0px; top: 2%; width: 100%; height: 99%; z-index: -1; background-color: rgb(16, 134, 253); "></div> |
| 61 | <div style="position: absolute; left: 0px; top: 4%; width: 100%; height: 97%; z-index: -1; background-color: rgb(16, 133, 252); "></div> |
| 62 | <div style="position: absolute; left: 0px; top: 6%; width: 100%; height: 95%; z-index: -1; background-color: rgb(15, 131, 250); "></div> |
| 63 | <div style="position: absolute; left: 0px; top: 8%; width: 100%; height: 93%; z-index: -1; background-color: rgb(15, 130, 249); "></div> |
| 64 | <div style="position: absolute; left: 0px; top: 10%; width: 100%; height: 91%; z-index: -1; background-color: rgb(15, 129, 248); "></div> |
| 65 | <div style="position: absolute; left: 0px; top: 12%; width: 100%; height: 89%; z-index: -1; background-color: rgb(14, 127, 246); "></div> |
| 66 | <div style="position: absolute; left: 0px; top: 14%; width: 100%; height: 87%; z-index: -1; background-color: rgb(14, 126, 245); "></div> |
| 67 | <div style="position: absolute; left: 0px; top: 16%; width: 100%; height: 85%; z-index: -1; background-color: rgb(14, 125, 244); "></div> |
| 68 | <div style="position: absolute; left: 0px; top: 18%; width: 100%; height: 83%; z-index: -1; background-color: rgb(13, 123, 242); "></div> |
| 69 | <div style="position: absolute; left: 0px; top: 20%; width: 100%; height: 81%; z-index: -1; background-color: rgb(13, 122, 241); "></div> |
| 70 | <div style="position: absolute; left: 0px; top: 22%; width: 100%; height: 79%; z-index: -1; background-color: rgb(13, 121, 240); "></div> |
| 71 | <div style="position: absolute; left: 0px; top: 24%; width: 100%; height: 77%; z-index: -1; background-color: rgb(12, 119, 238); "></div> |
| 72 | <div style="position: absolute; left: 0px; top: 26%; width: 100%; height: 75%; z-index: -1; background-color: rgb(12, 118, 237); "></div> |
| 73 | <div style="position: absolute; left: 0px; top: 28%; width: 100%; height: 73%; z-index: -1; background-color: rgb(12, 116, 235); "></div> |
| 74 | <div style="position: absolute; left: 0px; top: 30%; width: 100%; height: 71%; z-index: -1; background-color: rgb(11, 115, 234); "></div> |
| 75 | <div style="position: absolute; left: 0px; top: 32%; width: 100%; height: 69%; z-index: -1; background-color: rgb(11, 114, 233); "></div> |
| 76 | <div style="position: absolute; left: 0px; top: 34%; width: 100%; height: 67%; z-index: -1; background-color: rgb(11, 112, 231); "></div> |
| 77 | <div style="position: absolute; left: 0px; top: 36%; width: 100%; height: 65%; z-index: -1; background-color: rgb(10, 111, 230); "></div> |
| 78 | <div style="position: absolute; left: 0px; top: 38%; width: 100%; height: 63%; z-index: -1; background-color: rgb(10, 110, 229); "></div> |
| 79 | <div style="position: absolute; left: 0px; top: 40%; width: 100%; height: 61%; z-index: -1; background-color: rgb(10, 108, 227); "></div> |
| 80 | <div style="position: absolute; left: 0px; top: 42%; width: 100%; height: 59%; z-index: -1; background-color: rgb(9, 107, 226); "></div> |
| 81 | <div style="position: absolute; left: 0px; top: 44%; width: 100%; height: 57%; z-index: -1; background-color: rgb(9, 106, 225); "></div> |
| 82 | <div style="position: absolute; left: 0px; top: 46%; width: 100%; height: 55%; z-index: -1; background-color: rgb(9, 104, 223); "></div> |
| 83 | <div style="position: absolute; left: 0px; top: 48%; width: 100%; height: 53%; z-index: -1; background-color: rgb(8, 103, 222); "></div> |
| 84 | <div style="position: absolute; left: 0px; top: 50%; width: 100%; height: 51%; z-index: -1; background-color: rgb(8, 102, 221); "></div> |
| 85 | <div style="position: absolute; left: 0px; top: 52%; width: 100%; height: 49%; z-index: -1; background-color: rgb(8, 100, 219); "></div> |
| 86 | <div style="position: absolute; left: 0px; top: 54%; width: 100%; height: 47%; z-index: -1; background-color: rgb(7, 99, 218); "></div> |
| 87 | <div style="position: absolute; left: 0px; top: 56%; width: 100%; height: 45%; z-index: -1; background-color: rgb(7, 97, 216); "></div> |
| 88 | <div style="position: absolute; left: 0px; top: 58%; width: 100%; height: 43%; z-index: -1; background-color: rgb(7, 96, 215); "></div> |
| 89 | <div style="position: absolute; left: 0px; top: 60%; width: 100%; height: 41%; z-index: -1; background-color: rgb(6, 95, 214); "></div> |
| 90 | <div style="position: absolute; left: 0px; top: 62%; width: 100%; height: 39%; z-index: -1; background-color: rgb(6, 93, 212); "></div> |
| 91 | <div style="position: absolute; left: 0px; top: 64%; width: 100%; height: 37%; z-index: -1; background-color: rgb(6, 92, 211); "></div> |
| 92 | <div style="position: absolute; left: 0px; top: 66%; width: 100%; height: 35%; z-index: -1; background-color: rgb(5, 91, 210); "></div> |
| 93 | <div style="position: absolute; left: 0px; top: 68%; width: 100%; height: 33%; z-index: -1; background-color: rgb(5, 89, 208); "></div> |
| 94 | <div style="position: absolute; left: 0px; top: 70%; width: 100%; height: 31%; z-index: -1; background-color: rgb(5, 88, 207); "></div> |
| 95 | <div style="position: absolute; left: 0px; top: 72%; width: 100%; height: 29%; z-index: -1; background-color: rgb(4, 87, 206); "></div> |
| 96 | <div style="position: absolute; left: 0px; top: 74%; width: 100%; height: 27%; z-index: -1; background-color: rgb(4, 85, 204); "></div> |
| 97 | <div style="position: absolute; left: 0px; top: 76%; width: 100%; height: 25%; z-index: -1; background-color: rgb(4, 84, 203); "></div> |
| 98 | <div style="position: absolute; left: 0px; top: 78%; width: 100%; height: 23%; z-index: -1; background-color: rgb(3, 82, 201); "></div> |
| 99 | <div style="position: absolute; left: 0px; top: 80%; width: 100%; height: 21%; z-index: -1; background-color: rgb(3, 81, 200); "></div> |
| 100 | <div style="position: absolute; left: 0px; top: 82%; width: 100%; height: 19%; z-index: -1; background-color: rgb(3, 80, 199); "></div> |
| 101 | <div style="position: absolute; left: 0px; top: 84%; width: 100%; height: 17%; z-index: -1; background-color: rgb(2, 78, 197); "></div> |
| 102 | <div style="position: absolute; left: 0px; top: 86%; width: 100%; height: 15%; z-index: -1; background-color: rgb(2, 77, 196); "></div> |
| 103 | <div style="position: absolute; left: 0px; top: 88%; width: 100%; height: 13%; z-index: -1; background-color: rgb(2, 76, 195); "></div> |
| 104 | <div style="position: absolute; left: 0px; top: 90%; width: 100%; height: 11%; z-index: -1; background-color: rgb(1, 74, 193); "></div> |
| 105 | <div style="position: absolute; left: 0px; top: 92%; width: 100%; height: 9%; z-index: -1; background-color: rgb(1, 73, 192); "></div> |
| 106 | <div style="position: absolute; left: 0px; top: 94%; width: 100%; height: 7%; z-index: -1; background-color: rgb(1, 72, 191); "></div> |
| 107 | <div style="position: absolute; left: 0px; top: 96%; width: 100%; height: 5%; z-index: -1; background-color: rgb(0, 70, 189); "></div> |
| 108 | <div style="position: absolute; left: 0px; top: 98%; width: 100%; height: 3%; z-index: -1; background-color: rgb(0, 69, 188); "></div> |
| 109 | <div style="position: absolute; left: 0px; top: 100%; width: 100%; height: 1%; z-index: -1; background-color: rgb(0, 68, 187); "></div> |
| 110 | </div> |
| 111 | |
| 112 | <div class="body_content"><br /> |
| 113 | <table class="file_summary"><tr><td class="h">Filename</td><td align="left"><a href="file:///Users/edenc/perl5/lib/perl5/Bio/Phylo/IO.pm">/Users/edenc/perl5/lib/perl5/Bio/Phylo/IO.pm</a></td></tr> |
| 114 | <tr><td class="h">Statements</td><td align="left">Executed 14 statements in 1.62ms</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%">5.80ms</span></td><td class="c0"><span title="0.0%">19.3ms</span></td><td class="sub_name"><span style="display: none;">Bio::Phylo::IO::::BEGIN@4</span>Bio::Phylo::IO::<a href="Bio-Phylo-IO-pm-1136-line.html#4">BEGIN@4</a></span></td></tr> |
| 130 | <tr><td class="c3">1</td><td class="c3">1</td><td class="c3">1</td><td class="c3"><span title="0.0%">28µs</span></td><td class="c3"><span title="0.0%">265µs</span></td><td class="sub_name"><span style="display: none;">Bio::Phylo::IO::::BEGIN@7</span>Bio::Phylo::IO::<a href="Bio-Phylo-IO-pm-1136-line.html#7">BEGIN@7</a></span></td></tr> |
| 131 | <tr><td class="c3">1</td><td class="c3">1</td><td class="c3">1</td><td class="c3"><span title="0.0%">27µs</span></td><td class="c3"><span title="0.0%">34µs</span></td><td class="sub_name"><span style="display: none;">Bio::Phylo::IO::::BEGIN@2</span>Bio::Phylo::IO::<a href="Bio-Phylo-IO-pm-1136-line.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%">17µs</span></td><td class="c3"><span title="0.0%">150µs</span></td><td class="sub_name"><span style="display: none;">Bio::Phylo::IO::::BEGIN@3</span>Bio::Phylo::IO::<a href="Bio-Phylo-IO-pm-1136-line.html#3">BEGIN@3</a></span></td></tr> |
| 133 | <tr><td class="c3">1</td><td class="c3">1</td><td class="c3">1</td><td class="c3"><span title="0.0%">16µs</span></td><td class="c3"><span title="0.0%">62µs</span></td><td class="sub_name"><span style="display: none;">Bio::Phylo::IO::::BEGIN@6</span>Bio::Phylo::IO::<a href="Bio-Phylo-IO-pm-1136-line.html#6">BEGIN@6</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%">16µs</span></td><td class="c0"><span title="0.0%">895µs</span></td><td class="sub_name"><span style="display: none;">Bio::Phylo::IO::::BEGIN@5</span>Bio::Phylo::IO::<a href="Bio-Phylo-IO-pm-1136-line.html#5">BEGIN@5</a></span></td></tr> |
| 135 | <tr><td class="c3">0</td><td class="c3">0</td><td class="c3">0</td><td class="c3"><span title="0.0%">0s</span></td><td class="c3"><span title="0.0%">0s</span></td><td class="sub_name"><span style="display: none;">Bio::Phylo::IO::::DESTROY</span>Bio::Phylo::IO::<a href="Bio-Phylo-IO-pm-1136-line.html#331">DESTROY</a></span></td></tr> |
| 136 | <tr><td class="c3">0</td><td class="c3">0</td><td class="c3">0</td><td class="c3"><span title="0.0%">0s</span></td><td class="c3"><span title="0.0%">0s</span></td><td class="sub_name"><span style="display: none;">Bio::Phylo::IO::::can_read</span>Bio::Phylo::IO::<a href="Bio-Phylo-IO-pm-1136-line.html#303">can_read</a></span></td></tr> |
| 137 | <tr><td class="c3">0</td><td class="c3">0</td><td class="c3">0</td><td class="c3"><span title="0.0%">0s</span></td><td class="c3"><span title="0.0%">0s</span></td><td class="sub_name"><span style="display: none;">Bio::Phylo::IO::::can_write</span>Bio::Phylo::IO::<a href="Bio-Phylo-IO-pm-1136-line.html#323">can_write</a></span></td></tr> |
| 138 | <tr><td class="c3">0</td><td class="c3">0</td><td class="c3">0</td><td class="c3"><span title="0.0%">0s</span></td><td class="c3"><span title="0.0%">0s</span></td><td class="sub_name"><span style="display: none;">Bio::Phylo::IO::::parse</span>Bio::Phylo::IO::<a href="Bio-Phylo-IO-pm-1136-line.html#155">parse</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::IO::::parse_matrix</span>Bio::Phylo::IO::<a href="Bio-Phylo-IO-pm-1136-line.html#211">parse_matrix</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::IO::::parse_tree</span>Bio::Phylo::IO::<a href="Bio-Phylo-IO-pm-1136-line.html#237">parse_tree</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::IO::::unparse</span>Bio::Phylo::IO::<a href="Bio-Phylo-IO-pm-1136-line.html#265">unparse</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-IO-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::IO;</td></tr> |
| 161 | <tr><td class="h"><a name="2"></a>2</td><td class="c3">2</td><td class="c3"><span title="Avg 25µs">49µs</span></td><td class="c3">2</td><td class="c3">41µs</td><td class="s"><div class="calls"><div class="calls_in"># spent 34µs (27+7) within Bio::Phylo::IO::BEGIN@2 which was called: |
| 162 | # once (27µs+7µs) by Text::Tradition::Stemma::BEGIN@3 at <a href="Bio-Phylo-IO-pm-1136-line.html#2">line 2</a></div></div>use strict;<div class="calls"><div class="calls_out"># spent 34µs making 1 call to <a href="Bio-Phylo-IO-pm-1136-line.html#2">Bio::Phylo::IO::BEGIN@2</a> |
| 163 | # spent 7µs making 1 call to <a href="strict-pm-3-line.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 24µs">48µs</span></td><td class="c3">2</td><td class="c3">282µs</td><td class="s"><div class="calls"><div class="calls_in"># spent 150µs (17+132) within Bio::Phylo::IO::BEGIN@3 which was called: |
| 165 | # once (17µs+132µs) by Text::Tradition::Stemma::BEGIN@3 at <a href="Bio-Phylo-IO-pm-1136-line.html#3">line 3</a></div></div>use base 'Exporter';<div class="calls"><div class="calls_out"># spent 150µs making 1 call to <a href="Bio-Phylo-IO-pm-1136-line.html#3">Bio::Phylo::IO::BEGIN@3</a> |
| 166 | # spent 133µs making 1 call to <a href="base-pm-22-line.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="c0"><span title="Avg 86µs">171µs</span></td><td class="c3">2</td><td class="c0">19.3ms</td><td class="s"><div class="calls"><div class="calls_in"># spent 19.3ms (5.80+13.5) within Bio::Phylo::IO::BEGIN@4 which was called: |
| 168 | # once (5.80ms+13.5ms) by Text::Tradition::Stemma::BEGIN@3 at <a href="Bio-Phylo-IO-pm-1136-line.html#4">line 4</a></div></div>use Bio::Phylo;<div class="calls"><div class="calls_out"># spent 19.3ms making 1 call to <a href="Bio-Phylo-IO-pm-1136-line.html#4">Bio::Phylo::IO::BEGIN@4</a> |
| 169 | # spent 6µs making 1 call to <a href="Bio-Phylo-pm-1138-line.html#34">Bio::Phylo::import</a></div></div></td></tr> |
| 170 | <tr><td class="h"><a name="5"></a>5</td><td class="c3">2</td><td class="c3"><span title="Avg 32µs">64µs</span></td><td class="c3">2</td><td class="c0">1.77ms</td><td class="s"><div class="calls"><div class="calls_in"># spent 895µs (16+879) within Bio::Phylo::IO::BEGIN@5 which was called: |
| 171 | # once (16µs+879µs) by Text::Tradition::Stemma::BEGIN@3 at <a href="Bio-Phylo-IO-pm-1136-line.html#5">line 5</a></div></div>use Bio::Phylo::Util::CONSTANT qw'/looks_like/ :objecttypes';<div class="calls"><div class="calls_out"># spent 895µs making 1 call to <a href="Bio-Phylo-IO-pm-1136-line.html#5">Bio::Phylo::IO::BEGIN@5</a> |
| 172 | # spent 879µs making 1 call to <a href="Exporter-pm-8-line.html#28">Exporter::import</a></div></div></td></tr> |
| 173 | <tr><td class="h"><a name="6"></a>6</td><td class="c3">2</td><td class="c3"><span title="Avg 22µs">43µs</span></td><td class="c3">2</td><td class="c3">108µs</td><td class="s"><div class="calls"><div class="calls_in"># spent 62µs (16+46) within Bio::Phylo::IO::BEGIN@6 which was called: |
| 174 | # once (16µs+46µs) by Text::Tradition::Stemma::BEGIN@3 at <a href="Bio-Phylo-IO-pm-1136-line.html#6">line 6</a></div></div>use Bio::Phylo::Util::Exceptions 'throw';<div class="calls"><div class="calls_out"># spent 62µs making 1 call to <a href="Bio-Phylo-IO-pm-1136-line.html#6">Bio::Phylo::IO::BEGIN@6</a> |
| 175 | # spent 46µs making 1 call to <a href="Exporter-pm-8-line.html#28">Exporter::import</a></div></div></td></tr> |
| 176 | <tr><td class="h"><a name="7"></a>7</td><td class="c3">2</td><td class="c0"><span title="Avg 617µs">1.23ms</span></td><td class="c3">2</td><td class="c3">502µs</td><td class="s"><div class="calls"><div class="calls_in"># spent 265µs (28+237) within Bio::Phylo::IO::BEGIN@7 which was called: |
| 177 | # once (28µs+237µs) by Text::Tradition::Stemma::BEGIN@3 at <a href="Bio-Phylo-IO-pm-1136-line.html#7">line 7</a></div></div>use IO::File;<div class="calls"><div class="calls_out"># spent 265µs making 1 call to <a href="Bio-Phylo-IO-pm-1136-line.html#7">Bio::Phylo::IO::BEGIN@7</a> |
| 178 | # spent 237µs making 1 call to <a href="Exporter-pm-8-line.html#28">Exporter::import</a></div></div></td></tr> |
| 179 | <tr><td class="h"><a name="8"></a>8</td><td class="c3">1</td><td class="c3"><span title="Avg 4µs">4µs</span></td><td></td><td></td><td class="s">our @EXPORT_OK = qw'parse unparse parse_matrix parse_tree';</td></tr> |
| 180 | <tr><td class="h"><a name="9"></a>9</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 181 | <tr><td class="h"><a name="10"></a>10</td><td></td><td></td><td></td><td></td><td class="s">=head1 NAME</td></tr> |
| 182 | <tr><td class="h"><a name="11"></a>11</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 183 | <tr><td class="h"><a name="12"></a>12</td><td></td><td></td><td></td><td></td><td class="s">Bio::Phylo::IO - Front end for parsers and serializers</td></tr> |
| 184 | <tr><td class="h"><a name="13"></a>13</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 185 | <tr><td class="h"><a name="14"></a>14</td><td></td><td></td><td></td><td></td><td class="s">=head1 SYNOPSIS</td></tr> |
| 186 | <tr><td class="h"><a name="15"></a>15</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 187 | <tr><td class="h"><a name="16"></a>16</td><td></td><td></td><td></td><td></td><td class="s"> use Bio::Phylo::IO qw(parse unparse);</td></tr> |
| 188 | <tr><td class="h"><a name="17"></a>17</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 189 | <tr><td class="h"><a name="18"></a>18</td><td></td><td></td><td></td><td></td><td class="s"> # returns an unblessed array reference of block objects,</td></tr> |
| 190 | <tr><td class="h"><a name="19"></a>19</td><td></td><td></td><td></td><td></td><td class="s"> # i.e. taxa, matrix or forest objects</td></tr> |
| 191 | <tr><td class="h"><a name="20"></a>20</td><td></td><td></td><td></td><td></td><td class="s"> my $blocks = parse(</td></tr> |
| 192 | <tr><td class="h"><a name="21"></a>21</td><td></td><td></td><td></td><td></td><td class="s"> '-file' => $file,</td></tr> |
| 193 | <tr><td class="h"><a name="22"></a>22</td><td></td><td></td><td></td><td></td><td class="s"> '-format' => 'nexus',</td></tr> |
| 194 | <tr><td class="h"><a name="23"></a>23</td><td></td><td></td><td></td><td></td><td class="s"> '-encoding' => ':encoding(UTF-8)', # optional, default is system-dependent</td></tr> |
| 195 | <tr><td class="h"><a name="24"></a>24</td><td></td><td></td><td></td><td></td><td class="s"> );</td></tr> |
| 196 | <tr><td class="h"><a name="25"></a>25</td><td></td><td></td><td></td><td></td><td class="s"> </td></tr> |
| 197 | <tr><td class="h"><a name="26"></a>26</td><td></td><td></td><td></td><td></td><td class="s"> for my $block ( @{ $blocks } ) {</td></tr> |
| 198 | <tr><td class="h"><a name="27"></a>27</td><td></td><td></td><td></td><td></td><td class="s"> if ( $block->isa('Bio::Phylo::Taxa') ) {</td></tr> |
| 199 | <tr><td class="h"><a name="28"></a>28</td><td></td><td></td><td></td><td></td><td class="s"> my $taxa = $block;</td></tr> |
| 200 | <tr><td class="h"><a name="29"></a>29</td><td></td><td></td><td></td><td></td><td class="s"> # do something with the taxa</td></tr> |
| 201 | <tr><td class="h"><a name="30"></a>30</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 202 | <tr><td class="h"><a name="31"></a>31</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 203 | <tr><td class="h"><a name="32"></a>32</td><td></td><td></td><td></td><td></td><td class="s"> </td></tr> |
| 204 | <tr><td class="h"><a name="33"></a>33</td><td></td><td></td><td></td><td></td><td class="s"> # returns a Bio::Phylo::Project object</td></tr> |
| 205 | <tr><td class="h"><a name="34"></a>34</td><td></td><td></td><td></td><td></td><td class="s"> my $project = parse(</td></tr> |
| 206 | <tr><td class="h"><a name="35"></a>35</td><td></td><td></td><td></td><td></td><td class="s"> '-file' => $file,</td></tr> |
| 207 | <tr><td class="h"><a name="36"></a>36</td><td></td><td></td><td></td><td></td><td class="s"> '-format' => 'nexus',</td></tr> |
| 208 | <tr><td class="h"><a name="37"></a>37</td><td></td><td></td><td></td><td></td><td class="s"> '-as_project' => 1</td></tr> |
| 209 | <tr><td class="h"><a name="38"></a>38</td><td></td><td></td><td></td><td></td><td class="s"> )</td></tr> |
| 210 | <tr><td class="h"><a name="39"></a>39</td><td></td><td></td><td></td><td></td><td class="s"> my ($taxa) = @{ $project->get_taxa };</td></tr> |
| 211 | <tr><td class="h"><a name="40"></a>40</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 212 | <tr><td class="h"><a name="41"></a>41</td><td></td><td></td><td></td><td></td><td class="s"> # parsing a tree from a newick string</td></tr> |
| 213 | <tr><td class="h"><a name="42"></a>42</td><td></td><td></td><td></td><td></td><td class="s"> my $tree_string = '(((A,B),C),D);';</td></tr> |
| 214 | <tr><td class="h"><a name="43"></a>43</td><td></td><td></td><td></td><td></td><td class="s"> my $tree = Bio::Phylo::IO->parse(</td></tr> |
| 215 | <tr><td class="h"><a name="44"></a>44</td><td></td><td></td><td></td><td></td><td class="s"> '-string' => $tree_string,</td></tr> |
| 216 | <tr><td class="h"><a name="45"></a>45</td><td></td><td></td><td></td><td></td><td class="s"> '-format' => 'newick',</td></tr> |
| 217 | <tr><td class="h"><a name="46"></a>46</td><td></td><td></td><td></td><td></td><td class="s"> )->first;</td></tr> |
| 218 | <tr><td class="h"><a name="47"></a>47</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 219 | <tr><td class="h"><a name="48"></a>48</td><td></td><td></td><td></td><td></td><td class="s"> # note: newick parsers return </td></tr> |
| 220 | <tr><td class="h"><a name="49"></a>49</td><td></td><td></td><td></td><td></td><td class="s"> # 'Bio::Phylo::Forest'! Call </td></tr> |
| 221 | <tr><td class="h"><a name="50"></a>50</td><td></td><td></td><td></td><td></td><td class="s"> # ->first to retrieve the first </td></tr> |
| 222 | <tr><td class="h"><a name="51"></a>51</td><td></td><td></td><td></td><td></td><td class="s"> # tree of the forest.</td></tr> |
| 223 | <tr><td class="h"><a name="52"></a>52</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 224 | <tr><td class="h"><a name="53"></a>53</td><td></td><td></td><td></td><td></td><td class="s"> # prints 'Bio::Phylo::Forest::Tree'</td></tr> |
| 225 | <tr><td class="h"><a name="54"></a>54</td><td></td><td></td><td></td><td></td><td class="s"> print ref $tree, "\n";</td></tr> |
| 226 | <tr><td class="h"><a name="55"></a>55</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 227 | <tr><td class="h"><a name="56"></a>56</td><td></td><td></td><td></td><td></td><td class="s"> # parsing a table</td></tr> |
| 228 | <tr><td class="h"><a name="57"></a>57</td><td></td><td></td><td></td><td></td><td class="s"> my $table_string = qq(A,1,2|B,1,2|C,2,2|D,2,1);</td></tr> |
| 229 | <tr><td class="h"><a name="58"></a>58</td><td></td><td></td><td></td><td></td><td class="s"> my $matrix = Bio::Phylo::IO->parse(</td></tr> |
| 230 | <tr><td class="h"><a name="59"></a>59</td><td></td><td></td><td></td><td></td><td class="s"> '-string' => $table_string,</td></tr> |
| 231 | <tr><td class="h"><a name="60"></a>60</td><td></td><td></td><td></td><td></td><td class="s"> '-format' => 'table',</td></tr> |
| 232 | <tr><td class="h"><a name="61"></a>61</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 233 | <tr><td class="h"><a name="62"></a>62</td><td></td><td></td><td></td><td></td><td class="s"> # Data type, see Bio::Phylo::Parsers::Table</td></tr> |
| 234 | <tr><td class="h"><a name="63"></a>63</td><td></td><td></td><td></td><td></td><td class="s"> '-type' => 'STANDARD',</td></tr> |
| 235 | <tr><td class="h"><a name="64"></a>64</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 236 | <tr><td class="h"><a name="65"></a>65</td><td></td><td></td><td></td><td></td><td class="s"> # field separator </td></tr> |
| 237 | <tr><td class="h"><a name="66"></a>66</td><td></td><td></td><td></td><td></td><td class="s"> '-fieldsep' => ',',</td></tr> |
| 238 | <tr><td class="h"><a name="67"></a>67</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 239 | <tr><td class="h"><a name="68"></a>68</td><td></td><td></td><td></td><td></td><td class="s"> # line separator</td></tr> |
| 240 | <tr><td class="h"><a name="69"></a>69</td><td></td><td></td><td></td><td></td><td class="s"> '-linesep' => '|' </td></tr> |
| 241 | <tr><td class="h"><a name="70"></a>70</td><td></td><td></td><td></td><td></td><td class="s"> );</td></tr> |
| 242 | <tr><td class="h"><a name="71"></a>71</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 243 | <tr><td class="h"><a name="72"></a>72</td><td></td><td></td><td></td><td></td><td class="s"> # prints 'Bio::Phylo::Matrices::Matrix'</td></tr> |
| 244 | <tr><td class="h"><a name="73"></a>73</td><td></td><td></td><td></td><td></td><td class="s"> print ref $matrix, "\n"; </td></tr> |
| 245 | <tr><td class="h"><a name="74"></a>74</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 246 | <tr><td class="h"><a name="75"></a>75</td><td></td><td></td><td></td><td></td><td class="s"> # parsing a list of taxa</td></tr> |
| 247 | <tr><td class="h"><a name="76"></a>76</td><td></td><td></td><td></td><td></td><td class="s"> my $taxa_string = 'A:B:C:D';</td></tr> |
| 248 | <tr><td class="h"><a name="77"></a>77</td><td></td><td></td><td></td><td></td><td class="s"> my $taxa = Bio::Phylo::IO->parse(</td></tr> |
| 249 | <tr><td class="h"><a name="78"></a>78</td><td></td><td></td><td></td><td></td><td class="s"> '-string' => $taxa_string,</td></tr> |
| 250 | <tr><td class="h"><a name="79"></a>79</td><td></td><td></td><td></td><td></td><td class="s"> '-format' => 'taxlist',</td></tr> |
| 251 | <tr><td class="h"><a name="80"></a>80</td><td></td><td></td><td></td><td></td><td class="s"> '-fieldsep' => ':'</td></tr> |
| 252 | <tr><td class="h"><a name="81"></a>81</td><td></td><td></td><td></td><td></td><td class="s"> );</td></tr> |
| 253 | <tr><td class="h"><a name="82"></a>82</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 254 | <tr><td class="h"><a name="83"></a>83</td><td></td><td></td><td></td><td></td><td class="s"> # prints 'Bio::Phylo::Taxa'</td></tr> |
| 255 | <tr><td class="h"><a name="84"></a>84</td><td></td><td></td><td></td><td></td><td class="s"> print ref $taxa, "\n";</td></tr> |
| 256 | <tr><td class="h"><a name="85"></a>85</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 257 | <tr><td class="h"><a name="86"></a>86</td><td></td><td></td><td></td><td></td><td class="s"> # matches taxon names in tree to $taxa object</td></tr> |
| 258 | <tr><td class="h"><a name="87"></a>87</td><td></td><td></td><td></td><td></td><td class="s"> $tree->cross_reference($taxa); </td></tr> |
| 259 | <tr><td class="h"><a name="88"></a>88</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 260 | <tr><td class="h"><a name="89"></a>89</td><td></td><td></td><td></td><td></td><td class="s"> # likewise for matrix </td></tr> |
| 261 | <tr><td class="h"><a name="90"></a>90</td><td></td><td></td><td></td><td></td><td class="s"> $matrix->cross_reference($taxa);</td></tr> |
| 262 | <tr><td class="h"><a name="91"></a>91</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 263 | <tr><td class="h"><a name="92"></a>92</td><td></td><td></td><td></td><td></td><td class="s"> print unparse(</td></tr> |
| 264 | <tr><td class="h"><a name="93"></a>93</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 265 | <tr><td class="h"><a name="94"></a>94</td><td></td><td></td><td></td><td></td><td class="s"> # pass the tree object, </td></tr> |
| 266 | <tr><td class="h"><a name="95"></a>95</td><td></td><td></td><td></td><td></td><td class="s"> # crossreferenced to taxa, which</td></tr> |
| 267 | <tr><td class="h"><a name="96"></a>96</td><td></td><td></td><td></td><td></td><td class="s"> # are crossreferenced to the matrix</td></tr> |
| 268 | <tr><td class="h"><a name="97"></a>97</td><td></td><td></td><td></td><td></td><td class="s"> '-phylo' => $tree, </td></tr> |
| 269 | <tr><td class="h"><a name="98"></a>98</td><td></td><td></td><td></td><td></td><td class="s"> '-format' => 'pagel'</td></tr> |
| 270 | <tr><td class="h"><a name="99"></a>99</td><td></td><td></td><td></td><td></td><td class="s"> );</td></tr> |
| 271 | <tr><td class="h"><a name="100"></a>100</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 272 | <tr><td class="h"><a name="101"></a>101</td><td></td><td></td><td></td><td></td><td class="s"> # prints a pagel data file:</td></tr> |
| 273 | <tr><td class="h"><a name="102"></a>102</td><td></td><td></td><td></td><td></td><td class="s"> #4 2</td></tr> |
| 274 | <tr><td class="h"><a name="103"></a>103</td><td></td><td></td><td></td><td></td><td class="s"> #A,n1,0.000000,1,2</td></tr> |
| 275 | <tr><td class="h"><a name="104"></a>104</td><td></td><td></td><td></td><td></td><td class="s"> #B,n1,0.000000,1,2</td></tr> |
| 276 | <tr><td class="h"><a name="105"></a>105</td><td></td><td></td><td></td><td></td><td class="s"> #n1,n2,0.000000</td></tr> |
| 277 | <tr><td class="h"><a name="106"></a>106</td><td></td><td></td><td></td><td></td><td class="s"> #C,n2,0.000000,2,2</td></tr> |
| 278 | <tr><td class="h"><a name="107"></a>107</td><td></td><td></td><td></td><td></td><td class="s"> #n2,n3,0.000000</td></tr> |
| 279 | <tr><td class="h"><a name="108"></a>108</td><td></td><td></td><td></td><td></td><td class="s"> #D,n3,0.000000,2,1</td></tr> |
| 280 | <tr><td class="h"><a name="109"></a>109</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 281 | <tr><td class="h"><a name="110"></a>110</td><td></td><td></td><td></td><td></td><td class="s">=head1 DESCRIPTION</td></tr> |
| 282 | <tr><td class="h"><a name="111"></a>111</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 283 | <tr><td class="h"><a name="112"></a>112</td><td></td><td></td><td></td><td></td><td class="s">The IO module is the front end for parsing and serializing phylogenetic</td></tr> |
| 284 | <tr><td class="h"><a name="113"></a>113</td><td></td><td></td><td></td><td></td><td class="s">data objects. It is a non-OO module that optionally exports the 'parse' and</td></tr> |
| 285 | <tr><td class="h"><a name="114"></a>114</td><td></td><td></td><td></td><td></td><td class="s">'unparse' subroutines into the caller's namespace, using the</td></tr> |
| 286 | <tr><td class="h"><a name="115"></a>115</td><td></td><td></td><td></td><td></td><td class="s">C<< use Bio::Phylo::IO qw(parse unparse); >> directive. Alternatively, you can</td></tr> |
| 287 | <tr><td class="h"><a name="116"></a>116</td><td></td><td></td><td></td><td></td><td class="s">call the subroutines as class methods. The C<< parse >> and</td></tr> |
| 288 | <tr><td class="h"><a name="117"></a>117</td><td></td><td></td><td></td><td></td><td class="s">C<< unparse >> subroutines load and dispatch the appropriate sub-modules at</td></tr> |
| 289 | <tr><td class="h"><a name="118"></a>118</td><td></td><td></td><td></td><td></td><td class="s">runtime, depending on the '-format' argument.</td></tr> |
| 290 | <tr><td class="h"><a name="119"></a>119</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 291 | <tr><td class="h"><a name="120"></a>120</td><td></td><td></td><td></td><td></td><td class="s">=head2 CLASS METHODS</td></tr> |
| 292 | <tr><td class="h"><a name="121"></a>121</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 293 | <tr><td class="h"><a name="122"></a>122</td><td></td><td></td><td></td><td></td><td class="s">=over</td></tr> |
| 294 | <tr><td class="h"><a name="123"></a>123</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 295 | <tr><td class="h"><a name="124"></a>124</td><td></td><td></td><td></td><td></td><td class="s">=item parse()</td></tr> |
| 296 | <tr><td class="h"><a name="125"></a>125</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 297 | <tr><td class="h"><a name="126"></a>126</td><td></td><td></td><td></td><td></td><td class="s">Parses a file or string.</td></tr> |
| 298 | <tr><td class="h"><a name="127"></a>127</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 299 | <tr><td class="h"><a name="128"></a>128</td><td></td><td></td><td></td><td></td><td class="s"> Type : Class method</td></tr> |
| 300 | <tr><td class="h"><a name="129"></a>129</td><td></td><td></td><td></td><td></td><td class="s"> Title : parse</td></tr> |
| 301 | <tr><td class="h"><a name="130"></a>130</td><td></td><td></td><td></td><td></td><td class="s"> Usage : my $obj = Bio::Phylo::IO->parse(%options);</td></tr> |
| 302 | <tr><td class="h"><a name="131"></a>131</td><td></td><td></td><td></td><td></td><td class="s"> Function: Creates (file) handle, </td></tr> |
| 303 | <tr><td class="h"><a name="132"></a>132</td><td></td><td></td><td></td><td></td><td class="s"> instantiates appropriate parser.</td></tr> |
| 304 | <tr><td class="h"><a name="133"></a>133</td><td></td><td></td><td></td><td></td><td class="s"> Returns : A Bio::Phylo::* object</td></tr> |
| 305 | <tr><td class="h"><a name="134"></a>134</td><td></td><td></td><td></td><td></td><td class="s"> Args : -file => (path),</td></tr> |
| 306 | <tr><td class="h"><a name="135"></a>135</td><td></td><td></td><td></td><td></td><td class="s"> or</td></tr> |
| 307 | <tr><td class="h"><a name="136"></a>136</td><td></td><td></td><td></td><td></td><td class="s"> -string => (scalar),</td></tr> |
| 308 | <tr><td class="h"><a name="137"></a>137</td><td></td><td></td><td></td><td></td><td class="s"> -format => (description format),</td></tr> |
| 309 | <tr><td class="h"><a name="138"></a>138</td><td></td><td></td><td></td><td></td><td class="s"> -(other) => (parser specific options)</td></tr> |
| 310 | <tr><td class="h"><a name="139"></a>139</td><td></td><td></td><td></td><td></td><td class="s"> Comments: The parse method makes assumptions about </td></tr> |
| 311 | <tr><td class="h"><a name="140"></a>140</td><td></td><td></td><td></td><td></td><td class="s"> the capabilities of Bio::Phylo::Parsers::* </td></tr> |
| 312 | <tr><td class="h"><a name="141"></a>141</td><td></td><td></td><td></td><td></td><td class="s"> modules: i) their names match those of the</td></tr> |
| 313 | <tr><td class="h"><a name="142"></a>142</td><td></td><td></td><td></td><td></td><td class="s"> -format => (blah) arguments, insofar that </td></tr> |
| 314 | <tr><td class="h"><a name="143"></a>143</td><td></td><td></td><td></td><td></td><td class="s"> ucfirst(blah) . '.pm' is an existing module; </td></tr> |
| 315 | <tr><td class="h"><a name="144"></a>144</td><td></td><td></td><td></td><td></td><td class="s"> ii) the modules implement a _from_handle, </td></tr> |
| 316 | <tr><td class="h"><a name="145"></a>145</td><td></td><td></td><td></td><td></td><td class="s"> or a _from_string method. Exceptions are </td></tr> |
| 317 | <tr><td class="h"><a name="146"></a>146</td><td></td><td></td><td></td><td></td><td class="s"> thrown if either assumption is violated. </td></tr> |
| 318 | <tr><td class="h"><a name="147"></a>147</td><td></td><td></td><td></td><td></td><td class="s"> </td></tr> |
| 319 | <tr><td class="h"><a name="148"></a>148</td><td></td><td></td><td></td><td></td><td class="s"> If @ARGV contains even key/value pairs such</td></tr> |
| 320 | <tr><td class="h"><a name="149"></a>149</td><td></td><td></td><td></td><td></td><td class="s"> as "format newick file <filename>" (note: no</td></tr> |
| 321 | <tr><td class="h"><a name="150"></a>150</td><td></td><td></td><td></td><td></td><td class="s"> dashes) these will be prepended to @_, for</td></tr> |
| 322 | <tr><td class="h"><a name="151"></a>151</td><td></td><td></td><td></td><td></td><td class="s"> one-liners. </td></tr> |
| 323 | <tr><td class="h"><a name="152"></a>152</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 324 | <tr><td class="h"><a name="153"></a>153</td><td></td><td></td><td></td><td></td><td class="s">=cut</td></tr> |
| 325 | <tr><td class="h"><a name="154"></a>154</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 326 | <tr><td class="h"><a name="155"></a>155</td><td></td><td></td><td></td><td></td><td class="s">sub parse {</td></tr> |
| 327 | <tr><td class="h"><a name="156"></a>156</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 328 | <tr><td class="h"><a name="157"></a>157</td><td></td><td></td><td></td><td></td><td class="s"> # first argument could be the package name or an object reference</td></tr> |
| 329 | <tr><td class="h"><a name="158"></a>158</td><td></td><td></td><td></td><td></td><td class="s"> # if called as Bio::Phylo::IO->parse or as $io->parse, respectively</td></tr> |
| 330 | <tr><td class="h"><a name="159"></a>159</td><td></td><td></td><td></td><td></td><td class="s"> shift if $_[0] and $_[0] eq __PACKAGE__ or ref $_[0] eq __PACKAGE__;</td></tr> |
| 331 | <tr><td class="h"><a name="160"></a>160</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 332 | <tr><td class="h"><a name="161"></a>161</td><td></td><td></td><td></td><td></td><td class="s"> # arguments were provided on the command line, in @ARGV</td></tr> |
| 333 | <tr><td class="h"><a name="162"></a>162</td><td></td><td></td><td></td><td></td><td class="s"> if (@ARGV) {</td></tr> |
| 334 | <tr><td class="h"><a name="163"></a>163</td><td></td><td></td><td></td><td></td><td class="s"> my $i = 0;</td></tr> |
| 335 | <tr><td class="h"><a name="164"></a>164</td><td></td><td></td><td></td><td></td><td class="s"> while ( $i < @ARGV ) {</td></tr> |
| 336 | <tr><td class="h"><a name="165"></a>165</td><td></td><td></td><td></td><td></td><td class="s"> my ( $key, $value ) = ( $ARGV[$i], $ARGV[ $i + 1 ] );</td></tr> |
| 337 | <tr><td class="h"><a name="166"></a>166</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 338 | <tr><td class="h"><a name="167"></a>167</td><td></td><td></td><td></td><td></td><td class="s"> # shell words have no -dash prefix, so we</td></tr> |
| 339 | <tr><td class="h"><a name="168"></a>168</td><td></td><td></td><td></td><td></td><td class="s"> # add it here</td></tr> |
| 340 | <tr><td class="h"><a name="169"></a>169</td><td></td><td></td><td></td><td></td><td class="s"> $key = "-$key" if $key !~ /^-/;</td></tr> |
| 341 | <tr><td class="h"><a name="170"></a>170</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 342 | <tr><td class="h"><a name="171"></a>171</td><td></td><td></td><td></td><td></td><td class="s"> # we put @ARGV key/value pairs at the</td></tr> |
| 343 | <tr><td class="h"><a name="172"></a>172</td><td></td><td></td><td></td><td></td><td class="s"> # front of the @_ array</td></tr> |
| 344 | <tr><td class="h"><a name="173"></a>173</td><td></td><td></td><td></td><td></td><td class="s"> unshift @_, $key, $value;</td></tr> |
| 345 | <tr><td class="h"><a name="174"></a>174</td><td></td><td></td><td></td><td></td><td class="s"> $i += 2;</td></tr> |
| 346 | <tr><td class="h"><a name="175"></a>175</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 347 | <tr><td class="h"><a name="176"></a>176</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 348 | <tr><td class="h"><a name="177"></a>177</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 349 | <tr><td class="h"><a name="178"></a>178</td><td></td><td></td><td></td><td></td><td class="s"> # turn merged @ARGV and @_ arguments into a hash</td></tr> |
| 350 | <tr><td class="h"><a name="179"></a>179</td><td></td><td></td><td></td><td></td><td class="s"> my %opts = looks_like_hash @_;</td></tr> |
| 351 | <tr><td class="h"><a name="180"></a>180</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 352 | <tr><td class="h"><a name="181"></a>181</td><td></td><td></td><td></td><td></td><td class="s"> # there must be at least one of these args as a data source</td></tr> |
| 353 | <tr><td class="h"><a name="182"></a>182</td><td></td><td></td><td></td><td></td><td class="s"> my @sources = qw(-file -string -handle -url);</td></tr> |
| 354 | <tr><td class="h"><a name="183"></a>183</td><td></td><td></td><td></td><td></td><td class="s"> my ($source) = grep { defined $_ } @opts{@sources};</td></tr> |
| 355 | <tr><td class="h"><a name="184"></a>184</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 356 | <tr><td class="h"><a name="185"></a>185</td><td></td><td></td><td></td><td></td><td class="s"> # check provided arguments</td></tr> |
| 357 | <tr><td class="h"><a name="186"></a>186</td><td></td><td></td><td></td><td></td><td class="s"> throw 'OddHash' => 'Odd number of elements in hash assignment' if !@_;</td></tr> |
| 358 | <tr><td class="h"><a name="187"></a>187</td><td></td><td></td><td></td><td></td><td class="s"> throw 'BadArgs' => 'No format specified' unless $opts{'-format'};</td></tr> |
| 359 | <tr><td class="h"><a name="188"></a>188</td><td></td><td></td><td></td><td></td><td class="s"> throw 'BadArgs' => 'No parseable data source specified' unless $source;</td></tr> |
| 360 | <tr><td class="h"><a name="189"></a>189</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 361 | <tr><td class="h"><a name="190"></a>190</td><td></td><td></td><td></td><td></td><td class="s"> # instantiate parser subclass and process data</td></tr> |
| 362 | <tr><td class="h"><a name="191"></a>191</td><td></td><td></td><td></td><td></td><td class="s"> my $lib = 'Bio::Phylo::Parsers::' . ucfirst $opts{'-format'};</td></tr> |
| 363 | <tr><td class="h"><a name="192"></a>192</td><td></td><td></td><td></td><td></td><td class="s"> return looks_like_class($lib)->_new(@_)->_process;</td></tr> |
| 364 | <tr><td class="h"><a name="193"></a>193</td><td></td><td></td><td></td><td></td><td class="s">}</td></tr> |
| 365 | <tr><td class="h"><a name="194"></a>194</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 366 | <tr><td class="h"><a name="195"></a>195</td><td></td><td></td><td></td><td></td><td class="s">=item parse_matrix()</td></tr> |
| 367 | <tr><td class="h"><a name="196"></a>196</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 368 | <tr><td class="h"><a name="197"></a>197</td><td></td><td></td><td></td><td></td><td class="s">Parses a file or string.</td></tr> |
| 369 | <tr><td class="h"><a name="198"></a>198</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 370 | <tr><td class="h"><a name="199"></a>199</td><td></td><td></td><td></td><td></td><td class="s"> Type : Class method</td></tr> |
| 371 | <tr><td class="h"><a name="200"></a>200</td><td></td><td></td><td></td><td></td><td class="s"> Title : parse_matrix</td></tr> |
| 372 | <tr><td class="h"><a name="201"></a>201</td><td></td><td></td><td></td><td></td><td class="s"> Usage : my $matrix = Bio::Phylo::IO->parse_matrix(%options);</td></tr> |
| 373 | <tr><td class="h"><a name="202"></a>202</td><td></td><td></td><td></td><td></td><td class="s"> Function: Creates (file) handle, </td></tr> |
| 374 | <tr><td class="h"><a name="203"></a>203</td><td></td><td></td><td></td><td></td><td class="s"> instantiates appropriate parser.</td></tr> |
| 375 | <tr><td class="h"><a name="204"></a>204</td><td></td><td></td><td></td><td></td><td class="s"> Returns : A Bio::Phylo::Matrices::Matrix object</td></tr> |
| 376 | <tr><td class="h"><a name="205"></a>205</td><td></td><td></td><td></td><td></td><td class="s"> Args : Same as parse()</td></tr> |
| 377 | <tr><td class="h"><a name="206"></a>206</td><td></td><td></td><td></td><td></td><td class="s"> Comments: This method is syntactical sugar to get the first matrix</td></tr> |
| 378 | <tr><td class="h"><a name="207"></a>207</td><td></td><td></td><td></td><td></td><td class="s"> out of a file/handle/string</td></tr> |
| 379 | <tr><td class="h"><a name="208"></a>208</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 380 | <tr><td class="h"><a name="209"></a>209</td><td></td><td></td><td></td><td></td><td class="s">=cut</td></tr> |
| 381 | <tr><td class="h"><a name="210"></a>210</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 382 | <tr><td class="h"><a name="211"></a>211</td><td></td><td></td><td></td><td></td><td class="s">sub parse_matrix {</td></tr> |
| 383 | <tr><td class="h"><a name="212"></a>212</td><td></td><td></td><td></td><td></td><td class="s"> my ($matrix) = @{</td></tr> |
| 384 | <tr><td class="h"><a name="213"></a>213</td><td></td><td></td><td></td><td></td><td class="s"> parse(</td></tr> |
| 385 | <tr><td class="h"><a name="214"></a>214</td><td></td><td></td><td></td><td></td><td class="s"> @_,</td></tr> |
| 386 | <tr><td class="h"><a name="215"></a>215</td><td></td><td></td><td></td><td></td><td class="s"> '-as_project' => 1,</td></tr> |
| 387 | <tr><td class="h"><a name="216"></a>216</td><td></td><td></td><td></td><td></td><td class="s"> )->get_items(_MATRIX_)</td></tr> |
| 388 | <tr><td class="h"><a name="217"></a>217</td><td></td><td></td><td></td><td></td><td class="s"> };</td></tr> |
| 389 | <tr><td class="h"><a name="218"></a>218</td><td></td><td></td><td></td><td></td><td class="s"> return $matrix;</td></tr> |
| 390 | <tr><td class="h"><a name="219"></a>219</td><td></td><td></td><td></td><td></td><td class="s">}</td></tr> |
| 391 | <tr><td class="h"><a name="220"></a>220</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 392 | <tr><td class="h"><a name="221"></a>221</td><td></td><td></td><td></td><td></td><td class="s">=item parse_tree()</td></tr> |
| 393 | <tr><td class="h"><a name="222"></a>222</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 394 | <tr><td class="h"><a name="223"></a>223</td><td></td><td></td><td></td><td></td><td class="s">Parses a file or string.</td></tr> |
| 395 | <tr><td class="h"><a name="224"></a>224</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 396 | <tr><td class="h"><a name="225"></a>225</td><td></td><td></td><td></td><td></td><td class="s"> Type : Class method</td></tr> |
| 397 | <tr><td class="h"><a name="226"></a>226</td><td></td><td></td><td></td><td></td><td class="s"> Title : parse_tree</td></tr> |
| 398 | <tr><td class="h"><a name="227"></a>227</td><td></td><td></td><td></td><td></td><td class="s"> Usage : my $tree = Bio::Phylo::IO->parse_tree(%options);</td></tr> |
| 399 | <tr><td class="h"><a name="228"></a>228</td><td></td><td></td><td></td><td></td><td class="s"> Function: Creates (file) handle, </td></tr> |
| 400 | <tr><td class="h"><a name="229"></a>229</td><td></td><td></td><td></td><td></td><td class="s"> instantiates appropriate parser.</td></tr> |
| 401 | <tr><td class="h"><a name="230"></a>230</td><td></td><td></td><td></td><td></td><td class="s"> Returns : A Bio::Phylo::Forest::Tree object</td></tr> |
| 402 | <tr><td class="h"><a name="231"></a>231</td><td></td><td></td><td></td><td></td><td class="s"> Args : Same as parse()</td></tr> |
| 403 | <tr><td class="h"><a name="232"></a>232</td><td></td><td></td><td></td><td></td><td class="s"> Comments: This method is syntactical sugar to get the first tree</td></tr> |
| 404 | <tr><td class="h"><a name="233"></a>233</td><td></td><td></td><td></td><td></td><td class="s"> out of a file/handle/string</td></tr> |
| 405 | <tr><td class="h"><a name="234"></a>234</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 406 | <tr><td class="h"><a name="235"></a>235</td><td></td><td></td><td></td><td></td><td class="s">=cut</td></tr> |
| 407 | <tr><td class="h"><a name="236"></a>236</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 408 | <tr><td class="h"><a name="237"></a>237</td><td></td><td></td><td></td><td></td><td class="s">sub parse_tree {</td></tr> |
| 409 | <tr><td class="h"><a name="238"></a>238</td><td></td><td></td><td></td><td></td><td class="s"> my ($tree) = @{</td></tr> |
| 410 | <tr><td class="h"><a name="239"></a>239</td><td></td><td></td><td></td><td></td><td class="s"> parse(</td></tr> |
| 411 | <tr><td class="h"><a name="240"></a>240</td><td></td><td></td><td></td><td></td><td class="s"> @_,</td></tr> |
| 412 | <tr><td class="h"><a name="241"></a>241</td><td></td><td></td><td></td><td></td><td class="s"> '-as_project' => 1,</td></tr> |
| 413 | <tr><td class="h"><a name="242"></a>242</td><td></td><td></td><td></td><td></td><td class="s"> )->get_items(_TREE_)</td></tr> |
| 414 | <tr><td class="h"><a name="243"></a>243</td><td></td><td></td><td></td><td></td><td class="s"> };</td></tr> |
| 415 | <tr><td class="h"><a name="244"></a>244</td><td></td><td></td><td></td><td></td><td class="s"> return $tree;</td></tr> |
| 416 | <tr><td class="h"><a name="245"></a>245</td><td></td><td></td><td></td><td></td><td class="s">}</td></tr> |
| 417 | <tr><td class="h"><a name="246"></a>246</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 418 | <tr><td class="h"><a name="247"></a>247</td><td></td><td></td><td></td><td></td><td class="s">=item unparse()</td></tr> |
| 419 | <tr><td class="h"><a name="248"></a>248</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 420 | <tr><td class="h"><a name="249"></a>249</td><td></td><td></td><td></td><td></td><td class="s">Unparses object(s) to a string.</td></tr> |
| 421 | <tr><td class="h"><a name="250"></a>250</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 422 | <tr><td class="h"><a name="251"></a>251</td><td></td><td></td><td></td><td></td><td class="s"> Type : Class method</td></tr> |
| 423 | <tr><td class="h"><a name="252"></a>252</td><td></td><td></td><td></td><td></td><td class="s"> Title : unparse</td></tr> |
| 424 | <tr><td class="h"><a name="253"></a>253</td><td></td><td></td><td></td><td></td><td class="s"> Usage : my $string = Bio::Phylo::IO->unparse(</td></tr> |
| 425 | <tr><td class="h"><a name="254"></a>254</td><td></td><td></td><td></td><td></td><td class="s"> %options</td></tr> |
| 426 | <tr><td class="h"><a name="255"></a>255</td><td></td><td></td><td></td><td></td><td class="s"> );</td></tr> |
| 427 | <tr><td class="h"><a name="256"></a>256</td><td></td><td></td><td></td><td></td><td class="s"> Function: Turns Bio::Phylo object into a </td></tr> |
| 428 | <tr><td class="h"><a name="257"></a>257</td><td></td><td></td><td></td><td></td><td class="s"> string according to specified format.</td></tr> |
| 429 | <tr><td class="h"><a name="258"></a>258</td><td></td><td></td><td></td><td></td><td class="s"> Returns : SCALAR</td></tr> |
| 430 | <tr><td class="h"><a name="259"></a>259</td><td></td><td></td><td></td><td></td><td class="s"> Args : -phylo => (Bio::Phylo object),</td></tr> |
| 431 | <tr><td class="h"><a name="260"></a>260</td><td></td><td></td><td></td><td></td><td class="s"> -format => (description format),</td></tr> |
| 432 | <tr><td class="h"><a name="261"></a>261</td><td></td><td></td><td></td><td></td><td class="s"> -(other) => (parser specific options)</td></tr> |
| 433 | <tr><td class="h"><a name="262"></a>262</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 434 | <tr><td class="h"><a name="263"></a>263</td><td></td><td></td><td></td><td></td><td class="s">=cut</td></tr> |
| 435 | <tr><td class="h"><a name="264"></a>264</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 436 | <tr><td class="h"><a name="265"></a>265</td><td></td><td></td><td></td><td></td><td class="s">sub unparse {</td></tr> |
| 437 | <tr><td class="h"><a name="266"></a>266</td><td></td><td></td><td></td><td></td><td class="s"> if ( $_[0] and $_[0] eq __PACKAGE__ or ref $_[0] eq __PACKAGE__ ) {</td></tr> |
| 438 | <tr><td class="h"><a name="267"></a>267</td><td></td><td></td><td></td><td></td><td class="s"> shift;</td></tr> |
| 439 | <tr><td class="h"><a name="268"></a>268</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 440 | <tr><td class="h"><a name="269"></a>269</td><td></td><td></td><td></td><td></td><td class="s"> my %opts;</td></tr> |
| 441 | <tr><td class="h"><a name="270"></a>270</td><td></td><td></td><td></td><td></td><td class="s"> if ( !@_ || scalar @_ % 2 ) {</td></tr> |
| 442 | <tr><td class="h"><a name="271"></a>271</td><td></td><td></td><td></td><td></td><td class="s"> throw 'OddHash' => 'Odd number of elements in hash assignment';</td></tr> |
| 443 | <tr><td class="h"><a name="272"></a>272</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 444 | <tr><td class="h"><a name="273"></a>273</td><td></td><td></td><td></td><td></td><td class="s"> %opts = looks_like_hash @_;</td></tr> |
| 445 | <tr><td class="h"><a name="274"></a>274</td><td></td><td></td><td></td><td></td><td class="s"> if ( !$opts{-format} ) {</td></tr> |
| 446 | <tr><td class="h"><a name="275"></a>275</td><td></td><td></td><td></td><td></td><td class="s"> throw 'BadFormat' => 'no format specified.';</td></tr> |
| 447 | <tr><td class="h"><a name="276"></a>276</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 448 | <tr><td class="h"><a name="277"></a>277</td><td></td><td></td><td></td><td></td><td class="s"> if ( !$opts{-phylo} ) {</td></tr> |
| 449 | <tr><td class="h"><a name="278"></a>278</td><td></td><td></td><td></td><td></td><td class="s"> throw 'BadArgs' => 'no object to unparse specified.';</td></tr> |
| 450 | <tr><td class="h"><a name="279"></a>279</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 451 | <tr><td class="h"><a name="280"></a>280</td><td></td><td></td><td></td><td></td><td class="s"> my $lib = 'Bio::Phylo::Unparsers::' . ucfirst $opts{-format};</td></tr> |
| 452 | <tr><td class="h"><a name="281"></a>281</td><td></td><td></td><td></td><td></td><td class="s"> my $unparser = looks_like_class($lib)->_new(%opts);</td></tr> |
| 453 | <tr><td class="h"><a name="282"></a>282</td><td></td><td></td><td></td><td></td><td class="s"> if ( $unparser->can('_to_string') ) {</td></tr> |
| 454 | <tr><td class="h"><a name="283"></a>283</td><td></td><td></td><td></td><td></td><td class="s"> return $unparser->_to_string;</td></tr> |
| 455 | <tr><td class="h"><a name="284"></a>284</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 456 | <tr><td class="h"><a name="285"></a>285</td><td></td><td></td><td></td><td></td><td class="s"> else {</td></tr> |
| 457 | <tr><td class="h"><a name="286"></a>286</td><td></td><td></td><td></td><td></td><td class="s"> throw 'ObjectMismatch' => 'the unparser can\'t convert to strings.';</td></tr> |
| 458 | <tr><td class="h"><a name="287"></a>287</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr> |
| 459 | <tr><td class="h"><a name="288"></a>288</td><td></td><td></td><td></td><td></td><td class="s">}</td></tr> |
| 460 | <tr><td class="h"><a name="289"></a>289</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 461 | <tr><td class="h"><a name="290"></a>290</td><td></td><td></td><td></td><td></td><td class="s">=item can_read()</td></tr> |
| 462 | <tr><td class="h"><a name="291"></a>291</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 463 | <tr><td class="h"><a name="292"></a>292</td><td></td><td></td><td></td><td></td><td class="s">Tests whether L<Bio::Phylo::IO> can read provided syntax format.</td></tr> |
| 464 | <tr><td class="h"><a name="293"></a>293</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 465 | <tr><td class="h"><a name="294"></a>294</td><td></td><td></td><td></td><td></td><td class="s"> Type : Class method</td></tr> |
| 466 | <tr><td class="h"><a name="295"></a>295</td><td></td><td></td><td></td><td></td><td class="s"> Title : can_read</td></tr> |
| 467 | <tr><td class="h"><a name="296"></a>296</td><td></td><td></td><td></td><td></td><td class="s"> Usage : &do_something if Bio::Phylo::IO->can_read('foo');</td></tr> |
| 468 | <tr><td class="h"><a name="297"></a>297</td><td></td><td></td><td></td><td></td><td class="s"> Function: Tests whether Bio::Phylo::IO can read provided syntax format.</td></tr> |
| 469 | <tr><td class="h"><a name="298"></a>298</td><td></td><td></td><td></td><td></td><td class="s"> Returns : Boolean</td></tr> |
| 470 | <tr><td class="h"><a name="299"></a>299</td><td></td><td></td><td></td><td></td><td class="s"> Args : A syntax format name, like "nexml"</td></tr> |
| 471 | <tr><td class="h"><a name="300"></a>300</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 472 | <tr><td class="h"><a name="301"></a>301</td><td></td><td></td><td></td><td></td><td class="s">=cut</td></tr> |
| 473 | <tr><td class="h"><a name="302"></a>302</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 474 | <tr><td class="h"><a name="303"></a>303</td><td></td><td></td><td></td><td></td><td class="s">sub can_read {</td></tr> |
| 475 | <tr><td class="h"><a name="304"></a>304</td><td></td><td></td><td></td><td></td><td class="s"> my ( $self, $format ) = @_;</td></tr> |
| 476 | <tr><td class="h"><a name="305"></a>305</td><td></td><td></td><td></td><td></td><td class="s"> my $package = 'Bio::Phylo::Parsers::' . ucfirst($format);</td></tr> |
| 477 | <tr><td class="h"><a name="306"></a>306</td><td></td><td></td><td></td><td></td><td class="s"> eval { looks_like_class $package };</td></tr> |
| 478 | <tr><td class="h"><a name="307"></a>307</td><td></td><td></td><td></td><td></td><td class="s"> return ! $@;</td></tr> |
| 479 | <tr><td class="h"><a name="308"></a>308</td><td></td><td></td><td></td><td></td><td class="s">}</td></tr> |
| 480 | <tr><td class="h"><a name="309"></a>309</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 481 | <tr><td class="h"><a name="310"></a>310</td><td></td><td></td><td></td><td></td><td class="s">=item can_write()</td></tr> |
| 482 | <tr><td class="h"><a name="311"></a>311</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 483 | <tr><td class="h"><a name="312"></a>312</td><td></td><td></td><td></td><td></td><td class="s">Tests whether L<Bio::Phylo::IO> can write provided syntax format.</td></tr> |
| 484 | <tr><td class="h"><a name="313"></a>313</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 485 | <tr><td class="h"><a name="314"></a>314</td><td></td><td></td><td></td><td></td><td class="s"> Type : Class method</td></tr> |
| 486 | <tr><td class="h"><a name="315"></a>315</td><td></td><td></td><td></td><td></td><td class="s"> Title : can_write</td></tr> |
| 487 | <tr><td class="h"><a name="316"></a>316</td><td></td><td></td><td></td><td></td><td class="s"> Usage : &do_something if Bio::Phylo::IO->can_write('foo');</td></tr> |
| 488 | <tr><td class="h"><a name="317"></a>317</td><td></td><td></td><td></td><td></td><td class="s"> Function: Tests whether Bio::Phylo::IO can write provided syntax format.</td></tr> |
| 489 | <tr><td class="h"><a name="318"></a>318</td><td></td><td></td><td></td><td></td><td class="s"> Returns : Boolean</td></tr> |
| 490 | <tr><td class="h"><a name="319"></a>319</td><td></td><td></td><td></td><td></td><td class="s"> Args : A syntax format name, like "nexml"</td></tr> |
| 491 | <tr><td class="h"><a name="320"></a>320</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 492 | <tr><td class="h"><a name="321"></a>321</td><td></td><td></td><td></td><td></td><td class="s">=cut</td></tr> |
| 493 | <tr><td class="h"><a name="322"></a>322</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 494 | <tr><td class="h"><a name="323"></a>323</td><td></td><td></td><td></td><td></td><td class="s">sub can_write {</td></tr> |
| 495 | <tr><td class="h"><a name="324"></a>324</td><td></td><td></td><td></td><td></td><td class="s"> my ( $self, $format ) = @_;</td></tr> |
| 496 | <tr><td class="h"><a name="325"></a>325</td><td></td><td></td><td></td><td></td><td class="s"> my $package = 'Bio::Phylo::Unparsers::' . ucfirst($format);</td></tr> |
| 497 | <tr><td class="h"><a name="326"></a>326</td><td></td><td></td><td></td><td></td><td class="s"> eval { looks_like_class $package };</td></tr> |
| 498 | <tr><td class="h"><a name="327"></a>327</td><td></td><td></td><td></td><td></td><td class="s"> return ! $@; </td></tr> |
| 499 | <tr><td class="h"><a name="328"></a>328</td><td></td><td></td><td></td><td></td><td class="s">}</td></tr> |
| 500 | <tr><td class="h"><a name="329"></a>329</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 501 | <tr><td class="h"><a name="330"></a>330</td><td></td><td></td><td></td><td></td><td class="s"># this just to prevent from calling __PACKAGE__->SUPER::DESTROY</td></tr> |
| 502 | <tr><td class="h"><a name="331"></a>331</td><td></td><td></td><td></td><td></td><td class="s">sub DESTROY {</td></tr> |
| 503 | <tr><td class="h"><a name="332"></a>332</td><td></td><td></td><td></td><td></td><td class="s"> return 1;</td></tr> |
| 504 | <tr><td class="h"><a name="333"></a>333</td><td></td><td></td><td></td><td></td><td class="s">}</td></tr> |
| 505 | <tr><td class="h"><a name="334"></a>334</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 506 | <tr><td class="h"><a name="335"></a>335</td><td></td><td></td><td></td><td></td><td class="s">=back</td></tr> |
| 507 | <tr><td class="h"><a name="336"></a>336</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 508 | <tr><td class="h"><a name="337"></a>337</td><td></td><td></td><td></td><td></td><td class="s">=head1 SEE ALSO</td></tr> |
| 509 | <tr><td class="h"><a name="338"></a>338</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 510 | <tr><td class="h"><a name="339"></a>339</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> |
| 511 | <tr><td class="h"><a name="340"></a>340</td><td></td><td></td><td></td><td></td><td class="s">for any user or developer questions and discussions.</td></tr> |
| 512 | <tr><td class="h"><a name="341"></a>341</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 513 | <tr><td class="h"><a name="342"></a>342</td><td></td><td></td><td></td><td></td><td class="s">=over</td></tr> |
| 514 | <tr><td class="h"><a name="343"></a>343</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 515 | <tr><td class="h"><a name="344"></a>344</td><td></td><td></td><td></td><td></td><td class="s">=item L<Bio::Phylo::Parsers::Fasta></td></tr> |
| 516 | <tr><td class="h"><a name="345"></a>345</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 517 | <tr><td class="h"><a name="346"></a>346</td><td></td><td></td><td></td><td></td><td class="s">=item L<Bio::Phylo::Parsers::Newick></td></tr> |
| 518 | <tr><td class="h"><a name="347"></a>347</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 519 | <tr><td class="h"><a name="348"></a>348</td><td></td><td></td><td></td><td></td><td class="s">=item L<Bio::Phylo::Parsers::Nexml></td></tr> |
| 520 | <tr><td class="h"><a name="349"></a>349</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 521 | <tr><td class="h"><a name="350"></a>350</td><td></td><td></td><td></td><td></td><td class="s">=item L<Bio::Phylo::Parsers::Nexus></td></tr> |
| 522 | <tr><td class="h"><a name="351"></a>351</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 523 | <tr><td class="h"><a name="352"></a>352</td><td></td><td></td><td></td><td></td><td class="s">=item L<Bio::Phylo::Parsers::Phylip></td></tr> |
| 524 | <tr><td class="h"><a name="353"></a>353</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 525 | <tr><td class="h"><a name="354"></a>354</td><td></td><td></td><td></td><td></td><td class="s">=item L<Bio::Phylo::Parsers::Phyloxml></td></tr> |
| 526 | <tr><td class="h"><a name="355"></a>355</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 527 | <tr><td class="h"><a name="356"></a>356</td><td></td><td></td><td></td><td></td><td class="s">=item L<Bio::Phylo::Parsers::Table></td></tr> |
| 528 | <tr><td class="h"><a name="357"></a>357</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 529 | <tr><td class="h"><a name="358"></a>358</td><td></td><td></td><td></td><td></td><td class="s">=item L<Bio::Phylo::Parsers::Taxlist></td></tr> |
| 530 | <tr><td class="h"><a name="359"></a>359</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 531 | <tr><td class="h"><a name="360"></a>360</td><td></td><td></td><td></td><td></td><td class="s">=item L<Bio::Phylo::Parsers::Tolweb></td></tr> |
| 532 | <tr><td class="h"><a name="361"></a>361</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 533 | <tr><td class="h"><a name="362"></a>362</td><td></td><td></td><td></td><td></td><td class="s">=item L<Bio::Phylo::Unparsers::Mrp></td></tr> |
| 534 | <tr><td class="h"><a name="363"></a>363</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 535 | <tr><td class="h"><a name="364"></a>364</td><td></td><td></td><td></td><td></td><td class="s">=item L<Bio::Phylo::Unparsers::Newick></td></tr> |
| 536 | <tr><td class="h"><a name="365"></a>365</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 537 | <tr><td class="h"><a name="366"></a>366</td><td></td><td></td><td></td><td></td><td class="s">=item L<Bio::Phylo::Unparsers::Nexml></td></tr> |
| 538 | <tr><td class="h"><a name="367"></a>367</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 539 | <tr><td class="h"><a name="368"></a>368</td><td></td><td></td><td></td><td></td><td class="s">=item L<Bio::Phylo::Unparsers::Nexus></td></tr> |
| 540 | <tr><td class="h"><a name="369"></a>369</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 541 | <tr><td class="h"><a name="370"></a>370</td><td></td><td></td><td></td><td></td><td class="s">=item L<Bio::Phylo::Unparsers::Pagel></td></tr> |
| 542 | <tr><td class="h"><a name="371"></a>371</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 543 | <tr><td class="h"><a name="372"></a>372</td><td></td><td></td><td></td><td></td><td class="s">=item L<Bio::Phylo::Unparsers::Phylip></td></tr> |
| 544 | <tr><td class="h"><a name="373"></a>373</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 545 | <tr><td class="h"><a name="374"></a>374</td><td></td><td></td><td></td><td></td><td class="s">=item L<Bio::Phylo::Unparsers::Phyloxml></td></tr> |
| 546 | <tr><td class="h"><a name="375"></a>375</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 547 | <tr><td class="h"><a name="376"></a>376</td><td></td><td></td><td></td><td></td><td class="s">=item L<Bio::Phylo::Manual></td></tr> |
| 548 | <tr><td class="h"><a name="377"></a>377</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 549 | <tr><td class="h"><a name="378"></a>378</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> |
| 550 | <tr><td class="h"><a name="379"></a>379</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 551 | <tr><td class="h"><a name="380"></a>380</td><td></td><td></td><td></td><td></td><td class="s">=back</td></tr> |
| 552 | <tr><td class="h"><a name="381"></a>381</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 553 | <tr><td class="h"><a name="382"></a>382</td><td></td><td></td><td></td><td></td><td class="s">=head1 CITATION</td></tr> |
| 554 | <tr><td class="h"><a name="383"></a>383</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 555 | <tr><td class="h"><a name="384"></a>384</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> |
| 556 | <tr><td class="h"><a name="385"></a>385</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 557 | <tr><td class="h"><a name="386"></a>386</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> |
| 558 | <tr><td class="h"><a name="387"></a>387</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> |
| 559 | <tr><td class="h"><a name="388"></a>388</td><td></td><td></td><td></td><td></td><td class="s">I<BMC Bioinformatics> B<12>:63.</td></tr> |
| 560 | <tr><td class="h"><a name="389"></a>389</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> |
| 561 | <tr><td class="h"><a name="390"></a>390</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 562 | <tr><td class="h"><a name="391"></a>391</td><td></td><td></td><td></td><td></td><td class="s">=cut</td></tr> |
| 563 | <tr><td class="h"><a name="392"></a>392</td><td></td><td></td><td></td><td></td><td class="s"></td></tr> |
| 564 | <tr><td class="h"><a name="393"></a>393</td><td class="c3">1</td><td class="c3"><span title="Avg 10µs">10µs</span></td><td></td><td></td><td class="s">1;</td></tr> |
| 565 | </tbody></table></div> |
| 566 | |
| 567 | <script type="text/javascript"> $(document).ready(function() { |
| 568 | |
| 569 | $("#subs_table").tablesorter({ |
| 570 | sortList: [[3,1]], |
| 571 | headers: { |
| 572 | 3: { sorter: 'fmt_time' }, |
| 573 | 4: { sorter: 'fmt_time' } |
| 574 | } |
| 575 | }); |
| 576 | |
| 577 | } ); </script> |
| 578 | |
| 579 | <div class="footer">Report produced by the |
| 580 | <a href="http://search.cpan.org/dist/Devel-NYTProf/">NYTProf 4.06</a> |
| 581 | Perl profiler, developed by |
| 582 | <a href="http://www.linkedin.com/in/timbunce">Tim Bunce</a> and |
| 583 | <a href="http://code.nytimes.com">Adam Kaplan</a>. |
| 584 | </div> |
| 585 | <br /><br /><br /><br /><br /><br /><br /><br /><br /><br /> |
| 586 | </body></html> |
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