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+ // console.log(orig);
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+ if (val != orig) { return val / (1000*1000*1000); }
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+ var val = orig.replace(/ms/,'');
+ if (val != orig) { return val / (1000); }
+ var val = orig.replace(/s/,'');
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+ console.log('no match for fmt_time of '.concat(orig));
+ return orig;
+ },
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+ <span class="siteTitle">NYTProf Performance Profile</span>
+ <span class="siteSubtitle">  <span>« <span class="mode_btn mode_btn_selected">block view</span> • <span class="mode_btn"><a href="lib-Text-Tradition-StemmaUtil-pm-1171-line.html">line view</a></span> • <span class="mode_btn"><a href="lib-Text-Tradition-StemmaUtil-pm-1171-sub.html">sub view</a></span> »</span><br />
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+ <span class="siteSubtitle">Run on Thu May 31 16:49:15 2012<br />Reported on Thu May 31 16:52:42 2012</span>
+</div>
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+<div style="position: absolute; left: 0px; top: 100%; width: 100%; height: 1%; z-index: -1; background-color: rgb(0, 68, 187); "></div>
+</div>
+
+<div class="body_content"><br />
+<table class="file_summary"><tr><td class="h">Filename</td><td align="left"><a href="file:///Users/edenc/share/src/stemmatology/stemmaweb/lib/Text/Tradition/StemmaUtil.pm">/Users/edenc/share/src/stemmatology/stemmaweb/lib/Text/Tradition/StemmaUtil.pm</a></td></tr>
+<tr><td class="h">Statements</td><td align="left">Executed 28 statements in 2.51ms</td></tr></table>
+
+ <table id="subs_table" border="1" cellpadding="0" class="tablesorter">
+ <caption>Subroutines</caption>
+ <thead>
+ <tr>
+ <th>Calls</th>
+ <th><span title="Number of Places sub is called from">P</span></th>
+ <th><span title="Number of Files sub is called from">F</span></th>
+ <th>Exclusive<br />Time</th>
+ <th>Inclusive<br />Time</th>
+ <th>Subroutine</th>
+ </tr>
+ </thead>
+ <tbody>
+<tr><td class="c3">1</td><td class="c3">1</td><td class="c3">1</td><td class="c0"><span title="0.0%">1.48ms</span></td><td class="c0"><span title="0.0%">2.05ms</span></td><td class="sub_name"><span style="display: none;">Text::Tradition::StemmaUtil::::BEGIN@9</span>Text::Tradition::StemmaUtil::<a href="lib-Text-Tradition-StemmaUtil-pm-1171-block.html#9">BEGIN@9</a></span></td></tr>
+<tr><td class="c3">1</td><td class="c3">1</td><td class="c3">1</td><td class="c0"><span title="0.0%">37µs</span></td><td class="c1"><span title="0.0%">41µs</span></td><td class="sub_name"><span style="display: none;">Text::Tradition::StemmaUtil::::BEGIN@3</span>Text::Tradition::StemmaUtil::<a href="lib-Text-Tradition-StemmaUtil-pm-1171-block.html#3">BEGIN@3</a></span></td></tr>
+<tr><td class="c3">1</td><td class="c3">1</td><td class="c3">1</td><td class="c0"><span title="0.0%">13µs</span></td><td class="c0"><span title="0.0%">70µs</span></td><td class="sub_name"><span style="display: none;">Text::Tradition::StemmaUtil::::BEGIN@10</span>Text::Tradition::StemmaUtil::<a href="lib-Text-Tradition-StemmaUtil-pm-1171-block.html#10">BEGIN@10</a></span></td></tr>
+<tr><td class="c3">1</td><td class="c3">1</td><td class="c3">1</td><td class="c1"><span title="0.0%">12µs</span></td><td class="c3"><span title="0.0%">34µs</span></td><td class="sub_name"><span style="display: none;">Text::Tradition::StemmaUtil::::BEGIN@11</span>Text::Tradition::StemmaUtil::<a href="lib-Text-Tradition-StemmaUtil-pm-1171-block.html#11">BEGIN@11</a></span></td></tr>
+<tr><td class="c3">1</td><td class="c3">1</td><td class="c3">1</td><td class="c2"><span title="0.0%">11µs</span></td><td class="c3"><span title="0.0%">27µs</span></td><td class="sub_name"><span style="display: none;">Text::Tradition::StemmaUtil::::BEGIN@7</span>Text::Tradition::StemmaUtil::<a href="lib-Text-Tradition-StemmaUtil-pm-1171-block.html#7">BEGIN@7</a></span></td></tr>
+<tr><td class="c3">1</td><td class="c3">1</td><td class="c3">1</td><td class="c3"><span title="0.0%">10µs</span></td><td class="c3"><span title="0.0%">18µs</span></td><td class="sub_name"><span style="display: none;">Text::Tradition::StemmaUtil::::BEGIN@5</span>Text::Tradition::StemmaUtil::<a href="lib-Text-Tradition-StemmaUtil-pm-1171-block.html#5">BEGIN@5</a></span></td></tr>
+<tr><td class="c3">1</td><td class="c3">1</td><td class="c3">1</td><td class="c3"><span title="0.0%">10µs</span></td><td class="c3"><span title="0.0%">12µs</span></td><td class="sub_name"><span style="display: none;">Text::Tradition::StemmaUtil::::BEGIN@12</span>Text::Tradition::StemmaUtil::<a href="lib-Text-Tradition-StemmaUtil-pm-1171-block.html#12">BEGIN@12</a></span></td></tr>
+<tr><td class="c3">1</td><td class="c3">1</td><td class="c3">1</td><td class="c3"><span title="0.0%">9µs</span></td><td class="c3"><span title="0.0%">33µs</span></td><td class="sub_name"><span style="display: none;">Text::Tradition::StemmaUtil::::BEGIN@8</span>Text::Tradition::StemmaUtil::<a href="lib-Text-Tradition-StemmaUtil-pm-1171-block.html#8">BEGIN@8</a></span></td></tr>
+<tr><td class="c3">1</td><td class="c3">1</td><td class="c3">1</td><td class="c3"><span title="0.0%">9µs</span></td><td class="c3"><span title="0.0%">10µs</span></td><td class="sub_name"><span style="display: none;">Text::Tradition::StemmaUtil::::BEGIN@15</span>Text::Tradition::StemmaUtil::<a href="lib-Text-Tradition-StemmaUtil-pm-1171-block.html#15">BEGIN@15</a></span></td></tr>
+<tr><td class="c3">1</td><td class="c3">1</td><td class="c3">1</td><td class="c3"><span title="0.0%">8µs</span></td><td class="c2"><span title="0.0%">38µs</span></td><td class="sub_name"><span style="display: none;">Text::Tradition::StemmaUtil::::BEGIN@14</span>Text::Tradition::StemmaUtil::<a href="lib-Text-Tradition-StemmaUtil-pm-1171-block.html#14">BEGIN@14</a></span></td></tr>
+<tr><td class="c3">1</td><td class="c3">1</td><td class="c3">1</td><td class="c3"><span title="0.0%">8µs</span></td><td class="c3"><span title="0.0%">9µs</span></td><td class="sub_name"><span style="display: none;">Text::Tradition::StemmaUtil::::BEGIN@13</span>Text::Tradition::StemmaUtil::<a href="lib-Text-Tradition-StemmaUtil-pm-1171-block.html#13">BEGIN@13</a></span></td></tr>
+<tr><td class="c3">1</td><td class="c3">1</td><td class="c3">1</td><td class="c3"><span title="0.0%">8µs</span></td><td class="c3"><span title="0.0%">15µs</span></td><td class="sub_name"><span style="display: none;">Text::Tradition::StemmaUtil::::BEGIN@4</span>Text::Tradition::StemmaUtil::<a href="lib-Text-Tradition-StemmaUtil-pm-1171-block.html#4">BEGIN@4</a></span></td></tr>
+<tr><td class="c3">1</td><td class="c3">1</td><td class="c3">1</td><td class="c3"><span title="0.0%">7µs</span></td><td class="c3"><span title="0.0%">29µs</span></td><td class="sub_name"><span style="display: none;">Text::Tradition::StemmaUtil::::BEGIN@6</span>Text::Tradition::StemmaUtil::<a href="lib-Text-Tradition-StemmaUtil-pm-1171-block.html#6">BEGIN@6</a></span></td></tr>
+<tr><td class="c3">0</td><td class="c3">0</td><td class="c3">0</td><td class="c3"><span title="0.0%">0s</span></td><td class="c3"><span title="0.0%">0s</span></td><td class="sub_name"><span style="display: none;">Text::Tradition::StemmaUtil::::_add_tree_children</span>Text::Tradition::StemmaUtil::<a href="lib-Text-Tradition-StemmaUtil-pm-1171-block.html#243">_add_tree_children</a></span></td></tr>
+<tr><td class="c3">0</td><td class="c3">0</td><td class="c3">0</td><td class="c3"><span title="0.0%">0s</span></td><td class="c3"><span title="0.0%">0s</span></td><td class="sub_name"><span style="display: none;">Text::Tradition::StemmaUtil::::_convert_characters</span>Text::Tradition::StemmaUtil::<a href="lib-Text-Tradition-StemmaUtil-pm-1171-block.html#79">_convert_characters</a></span></td></tr>
+<tr><td class="c3">0</td><td class="c3">0</td><td class="c3">0</td><td class="c3"><span title="0.0%">0s</span></td><td class="c3"><span title="0.0%">0s</span></td><td class="sub_name"><span style="display: none;">Text::Tradition::StemmaUtil::::_graph_from_bio</span>Text::Tradition::StemmaUtil::<a href="lib-Text-Tradition-StemmaUtil-pm-1171-block.html#228">_graph_from_bio</a></span></td></tr>
+<tr><td class="c3">0</td><td class="c3">0</td><td class="c3">0</td><td class="c3"><span title="0.0%">0s</span></td><td class="c3"><span title="0.0%">0s</span></td><td class="sub_name"><span style="display: none;">Text::Tradition::StemmaUtil::::_make_character_matrix</span>Text::Tradition::StemmaUtil::<a href="lib-Text-Tradition-StemmaUtil-pm-1171-block.html#50">_make_character_matrix</a></span></td></tr>
+<tr><td class="c3">0</td><td class="c3">0</td><td class="c3">0</td><td class="c3"><span title="0.0%">0s</span></td><td class="c3"><span title="0.0%">0s</span></td><td class="sub_name"><span style="display: none;">Text::Tradition::StemmaUtil::::_normalize_witname</span>Text::Tradition::StemmaUtil::<a href="lib-Text-Tradition-StemmaUtil-pm-1171-block.html#71">_normalize_witname</a></span></td></tr>
+<tr><td class="c3">0</td><td class="c3">0</td><td class="c3">0</td><td class="c3"><span title="0.0%">0s</span></td><td class="c3"><span title="0.0%">0s</span></td><td class="sub_name"><span style="display: none;">Text::Tradition::StemmaUtil::::character_input</span>Text::Tradition::StemmaUtil::<a href="lib-Text-Tradition-StemmaUtil-pm-1171-block.html#37">character_input</a></span></td></tr>
+<tr><td class="c3">0</td><td class="c3">0</td><td class="c3">0</td><td class="c3"><span title="0.0%">0s</span></td><td class="c3"><span title="0.0%">0s</span></td><td class="sub_name"><span style="display: none;">Text::Tradition::StemmaUtil::::newick_to_svg</span>Text::Tradition::StemmaUtil::<a href="lib-Text-Tradition-StemmaUtil-pm-1171-block.html#213">newick_to_svg</a></span></td></tr>
+<tr><td class="c3">0</td><td class="c3">0</td><td class="c3">0</td><td class="c3"><span title="0.0%">0s</span></td><td class="c3"><span title="0.0%">0s</span></td><td class="sub_name"><span style="display: none;">Text::Tradition::StemmaUtil::::parse_newick</span>Text::Tradition::StemmaUtil::<a href="lib-Text-Tradition-StemmaUtil-pm-1171-block.html#191">parse_newick</a></span></td></tr>
+<tr><td class="c3">0</td><td class="c3">0</td><td class="c3">0</td><td class="c3"><span title="0.0%">0s</span></td><td class="c3"><span title="0.0%">0s</span></td><td class="sub_name"><span style="display: none;">Text::Tradition::StemmaUtil::::phylip_pars</span>Text::Tradition::StemmaUtil::<a href="lib-Text-Tradition-StemmaUtil-pm-1171-block.html#118">phylip_pars</a></span></td></tr>
+<tr><td class="c3">0</td><td class="c3">0</td><td class="c3">0</td><td class="c3"><span title="0.0%">0s</span></td><td class="c3"><span title="0.0%">0s</span></td><td class="sub_name"><span style="display: none;">Text::Tradition::StemmaUtil::::throw</span>Text::Tradition::StemmaUtil::<a href="lib-Text-Tradition-StemmaUtil-pm-1171-block.html#253">throw</a></span></td></tr>
+</tbody></table>
+ Call graph for these subroutines as a
+ <a href="http://en.wikipedia.org/wiki/Graphviz">Graphviz</a>
+ <a href="Users-edenc-share-src-stemmatology-stemmaweb-lib-Text-Tradition-StemmaUtil-pm.dot">dot language file</a>.
+
+ <table border="1" cellpadding="0">
+ <thead>
+ <tr><th>Line</th>
+ <th><span title="Number of statements executed">State<br />ments</span></th>
+ <th><span title="Time spend executing statements on the line,
+ excluding time spent executing statements in any called subroutines">Time<br />on line</span></th>
+ <th><span title="Number of subroutines calls">Calls</span></th>
+ <th><span title="Time spent in subroutines called (inclusive)">Time<br />in subs</span></th>
+ <th class="left_indent_header">Code</th>
+ </tr>
+
+ </thead>
+ <tbody>
+ <tr><td class="h"><a name="1"></a>1</td><td></td><td></td><td></td><td></td><td class="s">package Text::Tradition::StemmaUtil;</td></tr>
+<tr><td class="h"><a name="2"></a>2</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="3"></a>3</td><td class="c3">2</td><td class="c1"><span title="Avg 14µs">28µs</span></td><td class="c3">2</td><td class="c3">46µs</td><td class="s"><div class="calls"><div class="calls_in"># spent 41µs (37+5) within Text::Tradition::StemmaUtil::BEGIN@3 which was called:
+# once (37µs+5µs) by Text::Tradition::Stemma::BEGIN@10 at <a href="lib-Text-Tradition-StemmaUtil-pm-1171-block.html#3">line 3</a></div></div>use strict;<div class="calls"><div class="calls_out"># spent 41µs making 1 call to <a href="lib-Text-Tradition-StemmaUtil-pm-1171-block.html#3">Text::Tradition::StemmaUtil::BEGIN@3</a>
+# spent 4µs making 1 call to <a href="strict-pm-3-block.html#34">strict::import</a></div></div></td></tr>
+<tr><td class="h"><a name="4"></a>4</td><td class="c3">2</td><td class="c3"><span title="Avg 12µs">25µs</span></td><td class="c3">2</td><td class="c3">22µs</td><td class="s"><div class="calls"><div class="calls_in"># spent 15µs (8+7) within Text::Tradition::StemmaUtil::BEGIN@4 which was called:
+# once (8µs+7µs) by Text::Tradition::Stemma::BEGIN@10 at <a href="lib-Text-Tradition-StemmaUtil-pm-1171-block.html#4">line 4</a></div></div>use warnings;<div class="calls"><div class="calls_out"># spent 15µs making 1 call to <a href="lib-Text-Tradition-StemmaUtil-pm-1171-block.html#4">Text::Tradition::StemmaUtil::BEGIN@4</a>
+# spent 7µs making 1 call to <a href="warnings-pm-2-block.html#386">warnings::import</a></div></div></td></tr>
+<tr><td class="h"><a name="5"></a>5</td><td class="c3">2</td><td class="c2"><span title="Avg 13µs">26µs</span></td><td class="c3">2</td><td class="c3">25µs</td><td class="s"><div class="calls"><div class="calls_in"># spent 18µs (10+7) within Text::Tradition::StemmaUtil::BEGIN@5 which was called:
+# once (10µs+7µs) by Text::Tradition::Stemma::BEGIN@10 at <a href="lib-Text-Tradition-StemmaUtil-pm-1171-block.html#5">line 5</a></div></div>use Exporter 'import';<div class="calls"><div class="calls_out"># spent 18µs making 1 call to <a href="lib-Text-Tradition-StemmaUtil-pm-1171-block.html#5">Text::Tradition::StemmaUtil::BEGIN@5</a>
+# spent 7µs making 1 call to <a href="Exporter-pm-8-block.html#28">Exporter::import</a></div></div></td></tr>
+<tr><td class="h"><a name="6"></a>6</td><td class="c3">2</td><td class="c3"><span title="Avg 12µs">25µs</span></td><td class="c3">2</td><td class="c3">51µs</td><td class="s"><div class="calls"><div class="calls_in"># spent 29µs (7+22) within Text::Tradition::StemmaUtil::BEGIN@6 which was called:
+# once (7µs+22µs) by Text::Tradition::Stemma::BEGIN@10 at <a href="lib-Text-Tradition-StemmaUtil-pm-1171-block.html#6">line 6</a></div></div>use vars qw/ @EXPORT_OK /;<div class="calls"><div class="calls_out"># spent 29µs making 1 call to <a href="lib-Text-Tradition-StemmaUtil-pm-1171-block.html#6">Text::Tradition::StemmaUtil::BEGIN@6</a>
+# spent 22µs making 1 call to <a href="vars-pm-6-block.html#10">vars::import</a></div></div></td></tr>
+<tr><td class="h"><a name="7"></a>7</td><td class="c3">2</td><td class="c1"><span title="Avg 14µs">27µs</span></td><td class="c3">2</td><td class="c3">43µs</td><td class="s"><div class="calls"><div class="calls_in"># spent 27µs (11+16) within Text::Tradition::StemmaUtil::BEGIN@7 which was called:
+# once (11µs+16µs) by Text::Tradition::Stemma::BEGIN@10 at <a href="lib-Text-Tradition-StemmaUtil-pm-1171-block.html#7">line 7</a></div></div>use Bio::Phylo::IO;<div class="calls"><div class="calls_out"># spent 27µs making 1 call to <a href="lib-Text-Tradition-StemmaUtil-pm-1171-block.html#7">Text::Tradition::StemmaUtil::BEGIN@7</a>
+# spent 16µs making 1 call to <a href="Exporter-pm-8-block.html#28">Exporter::import</a></div></div></td></tr>
+<tr><td class="h"><a name="8"></a>8</td><td class="c3">2</td><td class="c3"><span title="Avg 12µs">24µs</span></td><td class="c3">2</td><td class="c3">56µs</td><td class="s"><div class="calls"><div class="calls_in"># spent 33µs (9+23) within Text::Tradition::StemmaUtil::BEGIN@8 which was called:
+# once (9µs+23µs) by Text::Tradition::Stemma::BEGIN@10 at <a href="lib-Text-Tradition-StemmaUtil-pm-1171-block.html#8">line 8</a></div></div>use Encode qw( decode_utf8 );<div class="calls"><div class="calls_out"># spent 33µs making 1 call to <a href="lib-Text-Tradition-StemmaUtil-pm-1171-block.html#8">Text::Tradition::StemmaUtil::BEGIN@8</a>
+# spent 23µs making 1 call to <a href="Exporter-pm-8-block.html#28">Exporter::import</a></div></div></td></tr>
+<tr><td class="h"><a name="9"></a>9</td><td class="c3">2</td><td class="c0"><span title="Avg 62µs">125µs</span></td><td class="c3">2</td><td class="c0">2.14ms</td><td class="s"><div class="calls"><div class="calls_in"># spent 2.05ms (1.48+565µs) within Text::Tradition::StemmaUtil::BEGIN@9 which was called:
+# once (1.48ms+565µs) by Text::Tradition::Stemma::BEGIN@10 at <a href="lib-Text-Tradition-StemmaUtil-pm-1171-block.html#9">line 9</a></div></div>use File::chdir;<div class="calls"><div class="calls_out"># spent 2.05ms making 1 call to <a href="lib-Text-Tradition-StemmaUtil-pm-1171-block.html#9">Text::Tradition::StemmaUtil::BEGIN@9</a>
+# spent 92µs making 1 call to <a href="Exporter-pm-8-block.html#28">Exporter::import</a></div></div></td></tr>
+<tr><td class="h"><a name="10"></a>10</td><td class="c3">2</td><td class="c1"><span title="Avg 14µs">27µs</span></td><td class="c3">2</td><td class="c0">128µs</td><td class="s"><div class="calls"><div class="calls_in"># spent 70µs (13+58) within Text::Tradition::StemmaUtil::BEGIN@10 which was called:
+# once (13µs+58µs) by Text::Tradition::Stemma::BEGIN@10 at <a href="lib-Text-Tradition-StemmaUtil-pm-1171-block.html#10">line 10</a></div></div>use File::Temp;<div class="calls"><div class="calls_out"># spent 70µs making 1 call to <a href="lib-Text-Tradition-StemmaUtil-pm-1171-block.html#10">Text::Tradition::StemmaUtil::BEGIN@10</a>
+# spent 58µs making 1 call to <a href="Exporter-pm-8-block.html#28">Exporter::import</a></div></div></td></tr>
+<tr><td class="h"><a name="11"></a>11</td><td class="c3">2</td><td class="c3"><span title="Avg 13µs">26µs</span></td><td class="c3">2</td><td class="c3">57µs</td><td class="s"><div class="calls"><div class="calls_in"># spent 34µs (12+22) within Text::Tradition::StemmaUtil::BEGIN@11 which was called:
+# once (12µs+22µs) by Text::Tradition::Stemma::BEGIN@10 at <a href="lib-Text-Tradition-StemmaUtil-pm-1171-block.html#11">line 11</a></div></div>use File::Which;<div class="calls"><div class="calls_out"># spent 34µs making 1 call to <a href="lib-Text-Tradition-StemmaUtil-pm-1171-block.html#11">Text::Tradition::StemmaUtil::BEGIN@11</a>
+# spent 22µs making 1 call to <a href="Exporter-pm-8-block.html#28">Exporter::import</a></div></div></td></tr>
+<tr><td class="h"><a name="12"></a>12</td><td class="c3">2</td><td class="c3"><span title="Avg 12µs">23µs</span></td><td class="c3">2</td><td class="c3">14µs</td><td class="s"><div class="calls"><div class="calls_in"># spent 12µs (10+2) within Text::Tradition::StemmaUtil::BEGIN@12 which was called:
+# once (10µs+2µs) by Text::Tradition::Stemma::BEGIN@10 at <a href="lib-Text-Tradition-StemmaUtil-pm-1171-block.html#12">line 12</a></div></div>use Graph;<div class="calls"><div class="calls_out"># spent 12µs making 1 call to <a href="lib-Text-Tradition-StemmaUtil-pm-1171-block.html#12">Text::Tradition::StemmaUtil::BEGIN@12</a>
+# spent 2µs making 1 call to <a href="UNIVERSAL-pm-738-block.html#16">UNIVERSAL::import</a></div></div></td></tr>
+<tr><td class="h"><a name="13"></a>13</td><td class="c3">2</td><td class="c3"><span title="Avg 13µs">25µs</span></td><td class="c3">2</td><td class="c3">10µs</td><td class="s"><div class="calls"><div class="calls_in"># spent 9µs (8+1) within Text::Tradition::StemmaUtil::BEGIN@13 which was called:
+# once (8µs+1µs) by Text::Tradition::Stemma::BEGIN@10 at <a href="lib-Text-Tradition-StemmaUtil-pm-1171-block.html#13">line 13</a></div></div>use Graph::Reader::Dot;<div class="calls"><div class="calls_out"># spent 9µs making 1 call to <a href="lib-Text-Tradition-StemmaUtil-pm-1171-block.html#13">Text::Tradition::StemmaUtil::BEGIN@13</a>
+# spent 1µs making 1 call to <a href="UNIVERSAL-pm-738-block.html#16">UNIVERSAL::import</a></div></div></td></tr>
+<tr><td class="h"><a name="14"></a>14</td><td class="c3">2</td><td class="c3"><span title="Avg 12µs">24µs</span></td><td class="c3">2</td><td class="c1">68µs</td><td class="s"><div class="calls"><div class="calls_in"># spent 38µs (8+30) within Text::Tradition::StemmaUtil::BEGIN@14 which was called:
+# once (8µs+30µs) by Text::Tradition::Stemma::BEGIN@10 at <a href="lib-Text-Tradition-StemmaUtil-pm-1171-block.html#14">line 14</a></div></div>use IPC::Run qw/ run binary /;<div class="calls"><div class="calls_out"># spent 38µs making 1 call to <a href="lib-Text-Tradition-StemmaUtil-pm-1171-block.html#14">Text::Tradition::StemmaUtil::BEGIN@14</a>
+# spent 30µs making 1 call to <a href="Exporter-pm-8-block.html#28">Exporter::import</a></div></div></td></tr>
+<tr><td class="h"><a name="15"></a>15</td><td class="c3">2</td><td class="c0"><span title="Avg 1.05ms">2.09ms</span></td><td class="c3">2</td><td class="c3">12µs</td><td class="s"><div class="calls"><div class="calls_in"># spent 10µs (9+1) within Text::Tradition::StemmaUtil::BEGIN@15 which was called:
+# once (9µs+1µs) by Text::Tradition::Stemma::BEGIN@10 at <a href="lib-Text-Tradition-StemmaUtil-pm-1171-block.html#15">line 15</a></div></div>use Text::Tradition::Error;<div class="calls"><div class="calls_out"># spent 10µs making 1 call to <a href="lib-Text-Tradition-StemmaUtil-pm-1171-block.html#15">Text::Tradition::StemmaUtil::BEGIN@15</a>
+# spent 1µs making 1 call to <a href="UNIVERSAL-pm-738-block.html#16">UNIVERSAL::import</a></div></div></td></tr>
+<tr><td class="h"><a name="16"></a>16</td><td class="c3">1</td><td class="c3"><span title="Avg 3µs">3µs</span></td><td></td><td></td><td class="s">@EXPORT_OK = qw/ character_input phylip_pars parse_newick newick_to_svg /;</td></tr>
+<tr><td class="h"><a name="17"></a>17</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="18"></a>18</td><td></td><td></td><td></td><td></td><td class="s">=head1 NAME</td></tr>
+<tr><td class="h"><a name="19"></a>19</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="20"></a>20</td><td></td><td></td><td></td><td></td><td class="s">Text::Tradition::StemmaUtil - standalone utilities for distance tree calculations</td></tr>
+<tr><td class="h"><a name="21"></a>21</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="22"></a>22</td><td></td><td></td><td></td><td></td><td class="s">=head1 DESCRIPTION</td></tr>
+<tr><td class="h"><a name="23"></a>23</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="24"></a>24</td><td></td><td></td><td></td><td></td><td class="s">This package contains a set of utilities for running phylogenetic analysis on</td></tr>
+<tr><td class="h"><a name="25"></a>25</td><td></td><td></td><td></td><td></td><td class="s">text collations.</td></tr>
+<tr><td class="h"><a name="26"></a>26</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="27"></a>27</td><td></td><td></td><td></td><td></td><td class="s">=head1 SUBROUTINES</td></tr>
+<tr><td class="h"><a name="28"></a>28</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="29"></a>29</td><td></td><td></td><td></td><td></td><td class="s">=head2 character_input( $alignment_table )</td></tr>
+<tr><td class="h"><a name="30"></a>30</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="31"></a>31</td><td></td><td></td><td></td><td></td><td class="s">Returns a character matrix string suitable for Phylip programs, which </td></tr>
+<tr><td class="h"><a name="32"></a>32</td><td></td><td></td><td></td><td></td><td class="s">corresponds to the given alignment table. See Text::Tradition::Collation </td></tr>
+<tr><td class="h"><a name="33"></a>33</td><td></td><td></td><td></td><td></td><td class="s">for a description of the alignment table format.</td></tr>
+<tr><td class="h"><a name="34"></a>34</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="35"></a>35</td><td></td><td></td><td></td><td></td><td class="s">=cut</td></tr>
+<tr><td class="h"><a name="36"></a>36</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="37"></a>37</td><td></td><td></td><td></td><td></td><td class="s">sub character_input {</td></tr>
+<tr><td class="h"><a name="38"></a>38</td><td></td><td></td><td></td><td></td><td class="s"> my $table = shift;</td></tr>
+<tr><td class="h"><a name="39"></a>39</td><td></td><td></td><td></td><td></td><td class="s"> my $character_matrix = _make_character_matrix( $table );</td></tr>
+<tr><td class="h"><a name="40"></a>40</td><td></td><td></td><td></td><td></td><td class="s"> my $input = '';</td></tr>
+<tr><td class="h"><a name="41"></a>41</td><td></td><td></td><td></td><td></td><td class="s"> my $rows = scalar @{$character_matrix};</td></tr>
+<tr><td class="h"><a name="42"></a>42</td><td></td><td></td><td></td><td></td><td class="s"> my $columns = scalar @{$character_matrix->[0]} - 1;</td></tr>
+<tr><td class="h"><a name="43"></a>43</td><td></td><td></td><td></td><td></td><td class="s"> $input .= "\t$rows\t$columns\n";</td></tr>
+<tr><td class="h"><a name="44"></a>44</td><td></td><td></td><td></td><td></td><td class="s"> foreach my $row ( @{$character_matrix} ) {</td></tr>
+<tr><td class="h"><a name="45"></a>45</td><td></td><td></td><td></td><td></td><td class="s"> $input .= join( '', @$row ) . "\n";</td></tr>
+<tr><td class="h"><a name="46"></a>46</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr>
+<tr><td class="h"><a name="47"></a>47</td><td></td><td></td><td></td><td></td><td class="s"> return $input;</td></tr>
+<tr><td class="h"><a name="48"></a>48</td><td></td><td></td><td></td><td></td><td class="s">}</td></tr>
+<tr><td class="h"><a name="49"></a>49</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="50"></a>50</td><td></td><td></td><td></td><td></td><td class="s">sub _make_character_matrix {</td></tr>
+<tr><td class="h"><a name="51"></a>51</td><td></td><td></td><td></td><td></td><td class="s"> my( $table ) = @_;</td></tr>
+<tr><td class="h"><a name="52"></a>52</td><td></td><td></td><td></td><td></td><td class="s"> # Push the names of the witnesses to initialize the rows of the matrix.</td></tr>
+<tr><td class="h"><a name="53"></a>53</td><td></td><td></td><td></td><td></td><td class="s"> my @matrix = map { [ _normalize_witname( $_->{'witness'} ) ] } </td></tr>
+<tr><td class="h"><a name="54"></a>54</td><td></td><td></td><td></td><td></td><td class="s"> @{$table->{'alignment'}};</td></tr>
+<tr><td class="h"><a name="55"></a>55</td><td></td><td></td><td></td><td></td><td class="s"> foreach my $token_index ( 0 .. $table->{'length'} - 1) {</td></tr>
+<tr><td class="h"><a name="56"></a>56</td><td></td><td></td><td></td><td></td><td class="s"> # First implementation: make dumb alignment table, caring about</td></tr>
+<tr><td class="h"><a name="57"></a>57</td><td></td><td></td><td></td><td></td><td class="s"> # nothing except which reading is in which position.</td></tr>
+<tr><td class="h"><a name="58"></a>58</td><td></td><td></td><td></td><td></td><td class="s"> my @pos_readings = map { $_->{'tokens'}->[$token_index] }</td></tr>
+<tr><td class="h"><a name="59"></a>59</td><td></td><td></td><td></td><td></td><td class="s"> @{$table->{'alignment'}};</td></tr>
+<tr><td class="h"><a name="60"></a>60</td><td></td><td></td><td></td><td></td><td class="s"> my @pos_text = map { $_ ? $_->{'t'} : $_ } @pos_readings;</td></tr>
+<tr><td class="h"><a name="61"></a>61</td><td></td><td></td><td></td><td></td><td class="s"> my @chars = _convert_characters( \@pos_text );</td></tr>
+<tr><td class="h"><a name="62"></a>62</td><td></td><td></td><td></td><td></td><td class="s"> foreach my $idx ( 0 .. $#matrix ) {</td></tr>
+<tr><td class="h"><a name="63"></a>63</td><td></td><td></td><td></td><td></td><td class="s"> push( @{$matrix[$idx]}, $chars[$idx] );</td></tr>
+<tr><td class="h"><a name="64"></a>64</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr>
+<tr><td class="h"><a name="65"></a>65</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr>
+<tr><td class="h"><a name="66"></a>66</td><td></td><td></td><td></td><td></td><td class="s"> return \@matrix;</td></tr>
+<tr><td class="h"><a name="67"></a>67</td><td></td><td></td><td></td><td></td><td class="s">} </td></tr>
+<tr><td class="h"><a name="68"></a>68</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="69"></a>69</td><td></td><td></td><td></td><td></td><td class="s"># Helper function to make the witness name something legal for pars</td></tr>
+<tr><td class="h"><a name="70"></a>70</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="71"></a>71</td><td></td><td></td><td></td><td></td><td class="s">sub _normalize_witname {</td></tr>
+<tr><td class="h"><a name="72"></a>72</td><td></td><td></td><td></td><td></td><td class="s"> my( $witname ) = @_;</td></tr>
+<tr><td class="h"><a name="73"></a>73</td><td></td><td></td><td></td><td></td><td class="s"> $witname =~ s/\s+/ /g;</td></tr>
+<tr><td class="h"><a name="74"></a>74</td><td></td><td></td><td></td><td></td><td class="s"> $witname =~ s/[\[\]\(\)\:;,]//g;</td></tr>
+<tr><td class="h"><a name="75"></a>75</td><td></td><td></td><td></td><td></td><td class="s"> $witname = substr( $witname, 0, 10 );</td></tr>
+<tr><td class="h"><a name="76"></a>76</td><td></td><td></td><td></td><td></td><td class="s"> return sprintf( "%-10s", $witname );</td></tr>
+<tr><td class="h"><a name="77"></a>77</td><td></td><td></td><td></td><td></td><td class="s">}</td></tr>
+<tr><td class="h"><a name="78"></a>78</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="79"></a>79</td><td></td><td></td><td></td><td></td><td class="s">sub _convert_characters {</td></tr>
+<tr><td class="h"><a name="80"></a>80</td><td></td><td></td><td></td><td></td><td class="s"> my $row = shift;</td></tr>
+<tr><td class="h"><a name="81"></a>81</td><td></td><td></td><td></td><td></td><td class="s"> # This is a simple algorithm that treats every reading as different.</td></tr>
+<tr><td class="h"><a name="82"></a>82</td><td></td><td></td><td></td><td></td><td class="s"> # Eventually we will want to be able to specify how relationships</td></tr>
+<tr><td class="h"><a name="83"></a>83</td><td></td><td></td><td></td><td></td><td class="s"> # affect the character matrix.</td></tr>
+<tr><td class="h"><a name="84"></a>84</td><td></td><td></td><td></td><td></td><td class="s"> my %unique = ( '__UNDEF__' => 'X',</td></tr>
+<tr><td class="h"><a name="85"></a>85</td><td></td><td></td><td></td><td></td><td class="s"> '#LACUNA#' => '?',</td></tr>
+<tr><td class="h"><a name="86"></a>86</td><td></td><td></td><td></td><td></td><td class="s"> );</td></tr>
+<tr><td class="h"><a name="87"></a>87</td><td></td><td></td><td></td><td></td><td class="s"> my %count;</td></tr>
+<tr><td class="h"><a name="88"></a>88</td><td></td><td></td><td></td><td></td><td class="s"> my $ctr = 0;</td></tr>
+<tr><td class="h"><a name="89"></a>89</td><td></td><td></td><td></td><td></td><td class="s"> foreach my $word ( @$row ) {</td></tr>
+<tr><td class="h"><a name="90"></a>90</td><td></td><td></td><td></td><td></td><td class="s"> if( $word && !exists $unique{$word} ) {</td></tr>
+<tr><td class="h"><a name="91"></a>91</td><td></td><td></td><td></td><td></td><td class="s"> $unique{$word} = chr( 65 + $ctr );</td></tr>
+<tr><td class="h"><a name="92"></a>92</td><td></td><td></td><td></td><td></td><td class="s"> $ctr++;</td></tr>
+<tr><td class="h"><a name="93"></a>93</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr>
+<tr><td class="h"><a name="94"></a>94</td><td></td><td></td><td></td><td></td><td class="s"> $count{$word}++ if $word;</td></tr>
+<tr><td class="h"><a name="95"></a>95</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr>
+<tr><td class="h"><a name="96"></a>96</td><td></td><td></td><td></td><td></td><td class="s"> # Try to keep variants under 8 by lacunizing any singletons.</td></tr>
+<tr><td class="h"><a name="97"></a>97</td><td></td><td></td><td></td><td></td><td class="s"> if( scalar( keys %unique ) > 8 ) {</td></tr>
+<tr><td class="h"><a name="98"></a>98</td><td></td><td></td><td></td><td></td><td class="s"> foreach my $word ( keys %count ) {</td></tr>
+<tr><td class="h"><a name="99"></a>99</td><td></td><td></td><td></td><td></td><td class="s"> if( $count{$word} == 1 ) {</td></tr>
+<tr><td class="h"><a name="100"></a>100</td><td></td><td></td><td></td><td></td><td class="s"> $unique{$word} = '?';</td></tr>
+<tr><td class="h"><a name="101"></a>101</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr>
+<tr><td class="h"><a name="102"></a>102</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr>
+<tr><td class="h"><a name="103"></a>103</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr>
+<tr><td class="h"><a name="104"></a>104</td><td></td><td></td><td></td><td></td><td class="s"> my %u = reverse %unique;</td></tr>
+<tr><td class="h"><a name="105"></a>105</td><td></td><td></td><td></td><td></td><td class="s"> if( scalar( keys %u ) > 8 ) {</td></tr>
+<tr><td class="h"><a name="106"></a>106</td><td></td><td></td><td></td><td></td><td class="s"> warn "Have more than 8 variants on this location; phylip will break";</td></tr>
+<tr><td class="h"><a name="107"></a>107</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr>
+<tr><td class="h"><a name="108"></a>108</td><td></td><td></td><td></td><td></td><td class="s"> my @chars = map { $_ ? $unique{$_} : $unique{'__UNDEF__' } } @$row;</td></tr>
+<tr><td class="h"><a name="109"></a>109</td><td></td><td></td><td></td><td></td><td class="s"> return @chars;</td></tr>
+<tr><td class="h"><a name="110"></a>110</td><td></td><td></td><td></td><td></td><td class="s">}</td></tr>
+<tr><td class="h"><a name="111"></a>111</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="112"></a>112</td><td></td><td></td><td></td><td></td><td class="s">=head2 phylip_pars( $character_matrix )</td></tr>
+<tr><td class="h"><a name="113"></a>113</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="114"></a>114</td><td></td><td></td><td></td><td></td><td class="s">Runs Phylip Pars on the given character matrix. Returns results in Newick format.</td></tr>
+<tr><td class="h"><a name="115"></a>115</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="116"></a>116</td><td></td><td></td><td></td><td></td><td class="s">=cut</td></tr>
+<tr><td class="h"><a name="117"></a>117</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="118"></a>118</td><td></td><td></td><td></td><td></td><td class="s">sub phylip_pars {</td></tr>
+<tr><td class="h"><a name="119"></a>119</td><td></td><td></td><td></td><td></td><td class="s"> my( $charmatrix ) = @_;</td></tr>
+<tr><td class="h"><a name="120"></a>120</td><td></td><td></td><td></td><td></td><td class="s"> # Set up a temporary directory for all the default Phylip files.</td></tr>
+<tr><td class="h"><a name="121"></a>121</td><td></td><td></td><td></td><td></td><td class="s"> my $phylip_dir = File::Temp->newdir();</td></tr>
+<tr><td class="h"><a name="122"></a>122</td><td></td><td></td><td></td><td></td><td class="s"> # $phylip_dir->unlink_on_destroy(0);</td></tr>
+<tr><td class="h"><a name="123"></a>123</td><td></td><td></td><td></td><td></td><td class="s"> # We need an infile, and we need a command input file.</td></tr>
+<tr><td class="h"><a name="124"></a>124</td><td></td><td></td><td></td><td></td><td class="s"> open( MATRIX, ">$phylip_dir/infile" ) or die "Could not write $phylip_dir/infile";</td></tr>
+<tr><td class="h"><a name="125"></a>125</td><td></td><td></td><td></td><td></td><td class="s"> print MATRIX $charmatrix;</td></tr>
+<tr><td class="h"><a name="126"></a>126</td><td></td><td></td><td></td><td></td><td class="s"> close MATRIX;</td></tr>
+<tr><td class="h"><a name="127"></a>127</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="128"></a>128</td><td></td><td></td><td></td><td></td><td class="s"> open( CMD, ">$phylip_dir/cmdfile" ) or die "Could not write $phylip_dir/cmdfile";</td></tr>
+<tr><td class="h"><a name="129"></a>129</td><td></td><td></td><td></td><td></td><td class="s"> ## TODO any configuration parameters we want to set here</td></tr>
+<tr><td class="h"><a name="130"></a>130</td><td></td><td></td><td></td><td></td><td class="s"># U Search for best tree? Yes</td></tr>
+<tr><td class="h"><a name="131"></a>131</td><td></td><td></td><td></td><td></td><td class="s"># S Search option? More thorough search</td></tr>
+<tr><td class="h"><a name="132"></a>132</td><td></td><td></td><td></td><td></td><td class="s"># V Number of trees to save? 100</td></tr>
+<tr><td class="h"><a name="133"></a>133</td><td></td><td></td><td></td><td></td><td class="s"># J Randomize input order of species? No. Use input order</td></tr>
+<tr><td class="h"><a name="134"></a>134</td><td></td><td></td><td></td><td></td><td class="s"># O Outgroup root? No, use as outgroup species 1</td></tr>
+<tr><td class="h"><a name="135"></a>135</td><td></td><td></td><td></td><td></td><td class="s"># T Use Threshold parsimony? No, use ordinary parsimony</td></tr>
+<tr><td class="h"><a name="136"></a>136</td><td></td><td></td><td></td><td></td><td class="s"># W Sites weighted? No</td></tr>
+<tr><td class="h"><a name="137"></a>137</td><td></td><td></td><td></td><td></td><td class="s"># M Analyze multiple data sets? No</td></tr>
+<tr><td class="h"><a name="138"></a>138</td><td></td><td></td><td></td><td></td><td class="s"># I Input species interleaved? Yes</td></tr>
+<tr><td class="h"><a name="139"></a>139</td><td></td><td></td><td></td><td></td><td class="s"># 0 Terminal type (IBM PC, ANSI, none)? ANSI</td></tr>
+<tr><td class="h"><a name="140"></a>140</td><td></td><td></td><td></td><td></td><td class="s"># 1 Print out the data at start of run No</td></tr>
+<tr><td class="h"><a name="141"></a>141</td><td></td><td></td><td></td><td></td><td class="s"># 2 Print indications of progress of run Yes</td></tr>
+<tr><td class="h"><a name="142"></a>142</td><td></td><td></td><td></td><td></td><td class="s"># 3 Print out tree Yes</td></tr>
+<tr><td class="h"><a name="143"></a>143</td><td></td><td></td><td></td><td></td><td class="s"># 4 Print out steps in each site No</td></tr>
+<tr><td class="h"><a name="144"></a>144</td><td></td><td></td><td></td><td></td><td class="s"># 5 Print character at all nodes of tree No</td></tr>
+<tr><td class="h"><a name="145"></a>145</td><td></td><td></td><td></td><td></td><td class="s"># 6 Write out trees onto tree file? Yes</td></tr>
+<tr><td class="h"><a name="146"></a>146</td><td></td><td></td><td></td><td></td><td class="s"> print CMD "Y\n";</td></tr>
+<tr><td class="h"><a name="147"></a>147</td><td></td><td></td><td></td><td></td><td class="s"> close CMD;</td></tr>
+<tr><td class="h"><a name="148"></a>148</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="149"></a>149</td><td></td><td></td><td></td><td></td><td class="s"> # And then we run the program.</td></tr>
+<tr><td class="h"><a name="150"></a>150</td><td></td><td></td><td></td><td></td><td class="s"> my $program = File::Which::which( 'pars' );</td></tr>
+<tr><td class="h"><a name="151"></a>151</td><td></td><td></td><td></td><td></td><td class="s"> unless( -x $program ) {</td></tr>
+<tr><td class="h"><a name="152"></a>152</td><td></td><td></td><td></td><td></td><td class="s"> throw( "Phylip pars not found in path" );</td></tr>
+<tr><td class="h"><a name="153"></a>153</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr>
+<tr><td class="h"><a name="154"></a>154</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="155"></a>155</td><td></td><td></td><td></td><td></td><td class="s"> {</td></tr>
+<tr><td class="h"><a name="156"></a>156</td><td></td><td></td><td></td><td></td><td class="s"> # We need to run it in our temporary directory where we have created</td></tr>
+<tr><td class="h"><a name="157"></a>157</td><td></td><td></td><td></td><td></td><td class="s"> # all the expected files.</td></tr>
+<tr><td class="h"><a name="158"></a>158</td><td></td><td></td><td></td><td></td><td class="s"> local $CWD = $phylip_dir;</td></tr>
+<tr><td class="h"><a name="159"></a>159</td><td></td><td></td><td></td><td></td><td class="s"> my @cmd = ( $program );</td></tr>
+<tr><td class="h"><a name="160"></a>160</td><td></td><td></td><td></td><td></td><td class="s"> run \@cmd, '<', 'cmdfile', '>', '/dev/null';</td></tr>
+<tr><td class="h"><a name="161"></a>161</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr>
+<tr><td class="h"><a name="162"></a>162</td><td></td><td></td><td></td><td></td><td class="s"> # Now our output should be in 'outfile' and our tree in 'outtree',</td></tr>
+<tr><td class="h"><a name="163"></a>163</td><td></td><td></td><td></td><td></td><td class="s"> # both in the temp directory.</td></tr>
+<tr><td class="h"><a name="164"></a>164</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="165"></a>165</td><td></td><td></td><td></td><td></td><td class="s"> my @outtree;</td></tr>
+<tr><td class="h"><a name="166"></a>166</td><td></td><td></td><td></td><td></td><td class="s"> if( -f "$phylip_dir/outtree" ) {</td></tr>
+<tr><td class="h"><a name="167"></a>167</td><td></td><td></td><td></td><td></td><td class="s"> open( TREE, "$phylip_dir/outtree" ) or die "Could not open outtree for read";</td></tr>
+<tr><td class="h"><a name="168"></a>168</td><td></td><td></td><td></td><td></td><td class="s"> @outtree = <TREE>;</td></tr>
+<tr><td class="h"><a name="169"></a>169</td><td></td><td></td><td></td><td></td><td class="s"> close TREE;</td></tr>
+<tr><td class="h"><a name="170"></a>170</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr>
+<tr><td class="h"><a name="171"></a>171</td><td></td><td></td><td></td><td></td><td class="s"> return join( '', @outtree ) if @outtree;</td></tr>
+<tr><td class="h"><a name="172"></a>172</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="173"></a>173</td><td></td><td></td><td></td><td></td><td class="s"> # If we got this far, we are about to throw an error.</td></tr>
+<tr><td class="h"><a name="174"></a>174</td><td></td><td></td><td></td><td></td><td class="s"> my @error;</td></tr>
+<tr><td class="h"><a name="175"></a>175</td><td></td><td></td><td></td><td></td><td class="s"> if( -f "$phylip_dir/outfile" ) {</td></tr>
+<tr><td class="h"><a name="176"></a>176</td><td></td><td></td><td></td><td></td><td class="s"> open( OUTPUT, "$phylip_dir/outfile" ) or die "Could not open output for read";</td></tr>
+<tr><td class="h"><a name="177"></a>177</td><td></td><td></td><td></td><td></td><td class="s"> @error = <OUTPUT>;</td></tr>
+<tr><td class="h"><a name="178"></a>178</td><td></td><td></td><td></td><td></td><td class="s"> close OUTPUT;</td></tr>
+<tr><td class="h"><a name="179"></a>179</td><td></td><td></td><td></td><td></td><td class="s"> } else {</td></tr>
+<tr><td class="h"><a name="180"></a>180</td><td></td><td></td><td></td><td></td><td class="s"> push( @error, "Neither outtree nor output file was produced!" );</td></tr>
+<tr><td class="h"><a name="181"></a>181</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr>
+<tr><td class="h"><a name="182"></a>182</td><td></td><td></td><td></td><td></td><td class="s"> throw( join( '', @error ) );</td></tr>
+<tr><td class="h"><a name="183"></a>183</td><td></td><td></td><td></td><td></td><td class="s">}</td></tr>
+<tr><td class="h"><a name="184"></a>184</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="185"></a>185</td><td></td><td></td><td></td><td></td><td class="s">=head2 parse_newick( $newick_string )</td></tr>
+<tr><td class="h"><a name="186"></a>186</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="187"></a>187</td><td></td><td></td><td></td><td></td><td class="s">Parses the given Newick tree(s) into one or more undirected Graph objects.</td></tr>
+<tr><td class="h"><a name="188"></a>188</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="189"></a>189</td><td></td><td></td><td></td><td></td><td class="s">=cut</td></tr>
+<tr><td class="h"><a name="190"></a>190</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="191"></a>191</td><td></td><td></td><td></td><td></td><td class="s">sub parse_newick {</td></tr>
+<tr><td class="h"><a name="192"></a>192</td><td></td><td></td><td></td><td></td><td class="s"> my $newick = shift;</td></tr>
+<tr><td class="h"><a name="193"></a>193</td><td></td><td></td><td></td><td></td><td class="s"> my @trees;</td></tr>
+<tr><td class="h"><a name="194"></a>194</td><td></td><td></td><td></td><td></td><td class="s"> # Parse the result into a tree</td></tr>
+<tr><td class="h"><a name="195"></a>195</td><td></td><td></td><td></td><td></td><td class="s"> my $forest = Bio::Phylo::IO->parse( </td></tr>
+<tr><td class="h"><a name="196"></a>196</td><td></td><td></td><td></td><td></td><td class="s"> -format => 'newick',</td></tr>
+<tr><td class="h"><a name="197"></a>197</td><td></td><td></td><td></td><td></td><td class="s"> -string => $newick,</td></tr>
+<tr><td class="h"><a name="198"></a>198</td><td></td><td></td><td></td><td></td><td class="s"> );</td></tr>
+<tr><td class="h"><a name="199"></a>199</td><td></td><td></td><td></td><td></td><td class="s"> # Turn the tree into a graph, starting with the root node</td></tr>
+<tr><td class="h"><a name="200"></a>200</td><td></td><td></td><td></td><td></td><td class="s"> foreach my $tree ( @{$forest->get_entities} ) {</td></tr>
+<tr><td class="h"><a name="201"></a>201</td><td></td><td></td><td></td><td></td><td class="s"> push( @trees, _graph_from_bio( $tree ) );</td></tr>
+<tr><td class="h"><a name="202"></a>202</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr>
+<tr><td class="h"><a name="203"></a>203</td><td></td><td></td><td></td><td></td><td class="s"> return \@trees;</td></tr>
+<tr><td class="h"><a name="204"></a>204</td><td></td><td></td><td></td><td></td><td class="s">}</td></tr>
+<tr><td class="h"><a name="205"></a>205</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="206"></a>206</td><td></td><td></td><td></td><td></td><td class="s">=head2 newick_to_svg( $newick_string )</td></tr>
+<tr><td class="h"><a name="207"></a>207</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="208"></a>208</td><td></td><td></td><td></td><td></td><td class="s">Uses the FigTree utility (if installed) to transform the given Newick tree(s)</td></tr>
+<tr><td class="h"><a name="209"></a>209</td><td></td><td></td><td></td><td></td><td class="s">into a graph visualization.</td></tr>
+<tr><td class="h"><a name="210"></a>210</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="211"></a>211</td><td></td><td></td><td></td><td></td><td class="s">=cut</td></tr>
+<tr><td class="h"><a name="212"></a>212</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="213"></a>213</td><td></td><td></td><td></td><td></td><td class="s">sub newick_to_svg {</td></tr>
+<tr><td class="h"><a name="214"></a>214</td><td></td><td></td><td></td><td></td><td class="s"> my $newick = shift;</td></tr>
+<tr><td class="h"><a name="215"></a>215</td><td></td><td></td><td></td><td></td><td class="s"> my $program = File::Which::which( 'figtree' );</td></tr>
+<tr><td class="h"><a name="216"></a>216</td><td></td><td></td><td></td><td></td><td class="s"> unless( -x $program ) {</td></tr>
+<tr><td class="h"><a name="217"></a>217</td><td></td><td></td><td></td><td></td><td class="s"> throw( "FigTree commandline utility not found in path" );</td></tr>
+<tr><td class="h"><a name="218"></a>218</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr>
+<tr><td class="h"><a name="219"></a>219</td><td></td><td></td><td></td><td></td><td class="s"> my $svg;</td></tr>
+<tr><td class="h"><a name="220"></a>220</td><td></td><td></td><td></td><td></td><td class="s"> my $nfile = File::Temp->new();</td></tr>
+<tr><td class="h"><a name="221"></a>221</td><td></td><td></td><td></td><td></td><td class="s"> print $nfile $newick;</td></tr>
+<tr><td class="h"><a name="222"></a>222</td><td></td><td></td><td></td><td></td><td class="s"> close $nfile;</td></tr>
+<tr><td class="h"><a name="223"></a>223</td><td></td><td></td><td></td><td></td><td class="s"> my @cmd = ( $program, '-graphic', 'SVG', $nfile );</td></tr>
+<tr><td class="h"><a name="224"></a>224</td><td></td><td></td><td></td><td></td><td class="s"> run( \@cmd, ">", binary(), \$svg );</td></tr>
+<tr><td class="h"><a name="225"></a>225</td><td></td><td></td><td></td><td></td><td class="s"> return decode_utf8( $svg );</td></tr>
+<tr><td class="h"><a name="226"></a>226</td><td></td><td></td><td></td><td></td><td class="s">}</td></tr>
+<tr><td class="h"><a name="227"></a>227</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="228"></a>228</td><td></td><td></td><td></td><td></td><td class="s">sub _graph_from_bio {</td></tr>
+<tr><td class="h"><a name="229"></a>229</td><td></td><td></td><td></td><td></td><td class="s"> my $tree = shift;</td></tr>
+<tr><td class="h"><a name="230"></a>230</td><td></td><td></td><td></td><td></td><td class="s"> my $graph = Graph->new( 'undirected' => 1 );</td></tr>
+<tr><td class="h"><a name="231"></a>231</td><td></td><td></td><td></td><td></td><td class="s"> # Give all the intermediate anonymous nodes a name.</td></tr>
+<tr><td class="h"><a name="232"></a>232</td><td></td><td></td><td></td><td></td><td class="s"> my $i = 0;</td></tr>
+<tr><td class="h"><a name="233"></a>233</td><td></td><td></td><td></td><td></td><td class="s"> foreach my $n ( @{$tree->get_entities} ) {</td></tr>
+<tr><td class="h"><a name="234"></a>234</td><td></td><td></td><td></td><td></td><td class="s"> next if $n->get_name;</td></tr>
+<tr><td class="h"><a name="235"></a>235</td><td></td><td></td><td></td><td></td><td class="s"> $n->set_name( $i++ );</td></tr>
+<tr><td class="h"><a name="236"></a>236</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr>
+<tr><td class="h"><a name="237"></a>237</td><td></td><td></td><td></td><td></td><td class="s"> my $root = $tree->get_root->get_name;</td></tr>
+<tr><td class="h"><a name="238"></a>238</td><td></td><td></td><td></td><td></td><td class="s"> $graph->add_vertex( $root );</td></tr>
+<tr><td class="h"><a name="239"></a>239</td><td></td><td></td><td></td><td></td><td class="s"> _add_tree_children( $graph, $root, $tree->get_root->get_children() );</td></tr>
+<tr><td class="h"><a name="240"></a>240</td><td></td><td></td><td></td><td></td><td class="s"> return $graph;</td></tr>
+<tr><td class="h"><a name="241"></a>241</td><td></td><td></td><td></td><td></td><td class="s">}</td></tr>
+<tr><td class="h"><a name="242"></a>242</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="243"></a>243</td><td></td><td></td><td></td><td></td><td class="s">sub _add_tree_children {</td></tr>
+<tr><td class="h"><a name="244"></a>244</td><td></td><td></td><td></td><td></td><td class="s"> my( $graph, $parent, $tree_children ) = @_;</td></tr>
+<tr><td class="h"><a name="245"></a>245</td><td></td><td></td><td></td><td></td><td class="s"> foreach my $c ( @$tree_children ) {</td></tr>
+<tr><td class="h"><a name="246"></a>246</td><td></td><td></td><td></td><td></td><td class="s"> my $child = $c->get_name;</td></tr>
+<tr><td class="h"><a name="247"></a>247</td><td></td><td></td><td></td><td></td><td class="s"> $graph->add_vertex( $child );</td></tr>
+<tr><td class="h"><a name="248"></a>248</td><td></td><td></td><td></td><td></td><td class="s"> $graph->add_path( $parent, $child );</td></tr>
+<tr><td class="h"><a name="249"></a>249</td><td></td><td></td><td></td><td></td><td class="s"> _add_tree_children( $graph, $child, $c->get_children() );</td></tr>
+<tr><td class="h"><a name="250"></a>250</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr>
+<tr><td class="h"><a name="251"></a>251</td><td></td><td></td><td></td><td></td><td class="s">}</td></tr>
+<tr><td class="h"><a name="252"></a>252</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="253"></a>253</td><td></td><td></td><td></td><td></td><td class="s">sub throw {</td></tr>
+<tr><td class="h"><a name="254"></a>254</td><td></td><td></td><td></td><td></td><td class="s"> Text::Tradition::Error->throw( </td></tr>
+<tr><td class="h"><a name="255"></a>255</td><td></td><td></td><td></td><td></td><td class="s"> 'ident' => 'StemmaUtil error',</td></tr>
+<tr><td class="h"><a name="256"></a>256</td><td></td><td></td><td></td><td></td><td class="s"> 'message' => $_[0],</td></tr>
+<tr><td class="h"><a name="257"></a>257</td><td></td><td></td><td></td><td></td><td class="s"> );</td></tr>
+<tr><td class="h"><a name="258"></a>258</td><td></td><td></td><td></td><td></td><td class="s">}</td></tr>
+<tr><td class="h"><a name="259"></a>259</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="260"></a>260</td><td class="c3">1</td><td class="c3"><span title="Avg 6µs">6µs</span></td><td></td><td></td><td class="s">1;</td></tr>
+<tr><td class="h"><a name="261"></a>261</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="262"></a>262</td><td></td><td></td><td></td><td></td><td class="s">=head1 LICENSE</td></tr>
+<tr><td class="h"><a name="263"></a>263</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="264"></a>264</td><td></td><td></td><td></td><td></td><td class="s">This package is free software and is provided "as is" without express</td></tr>
+<tr><td class="h"><a name="265"></a>265</td><td></td><td></td><td></td><td></td><td class="s">or implied warranty. You can redistribute it and/or modify it under</td></tr>
+<tr><td class="h"><a name="266"></a>266</td><td></td><td></td><td></td><td></td><td class="s">the same terms as Perl itself.</td></tr>
+<tr><td class="h"><a name="267"></a>267</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="268"></a>268</td><td></td><td></td><td></td><td></td><td class="s">=head1 AUTHOR</td></tr>
+<tr><td class="h"><a name="269"></a>269</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="270"></a>270</td><td></td><td></td><td></td><td></td><td class="s">Tara L Andrews E<lt>aurum@cpan.orgE<gt></td></tr>
+</tbody></table></div>
+
+ <script type="text/javascript"> $(document).ready(function() {
+
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+ sortList: [[3,1]],
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+ 3: { sorter: 'fmt_time' },
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+
+ <div class="footer">Report produced by the
+ <a href="http://search.cpan.org/dist/Devel-NYTProf/">NYTProf 4.06</a>
+ Perl profiler, developed by
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