--- /dev/null
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+This file was generated by Devel::NYTProf version 4.06
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+<head>
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+ <meta http-equiv="Content-Language" content="en-us" />
+ <title>Profile of lib/Text/Tradition/Stemma.pm</title>
+<link rel="stylesheet" type="text/css" href="style.css" />
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+ // when a column is first clicked on to sort it, use descending order
+ // XXX doesn't seem to work (and not just because the tablesorter formatSortingOrder() is broken)
+ $.tablesorter.defaults.sortInitialOrder = "desc";
+ // add parser through the tablesorter addParser method
+ $.tablesorter.addParser({
+ id: 'fmt_time', // name of this parser
+ is: function(s) {
+ return false; // return false so this parser is not auto detected
+ },
+ format: function(orig) { // format data for normalization
+ // console.log(orig);
+ val = orig.replace(/ns/,'');
+ if (val != orig) { return val / (1000*1000*1000); }
+ val = orig.replace(/µs/,''); /* XXX use µ ? */
+ if (val != orig) { return val / (1000*1000); }
+ var val = orig.replace(/ms/,'');
+ if (val != orig) { return val / (1000); }
+ var val = orig.replace(/s/,'');
+ if (val != orig) { return val; }
+ if (orig == '0') { return orig; }
+ console.log('no match for fmt_time of '.concat(orig));
+ return orig;
+ },
+ type: 'numeric' // set type, either numeric or text
+ });
+ </script>
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+<div class="headerForeground" style="float: left">
+ <span class="siteTitle">NYTProf Performance Profile</span>
+ <span class="siteSubtitle">  <span>« <span class="mode_btn"><a href="lib-Text-Tradition-Stemma-pm-1135-block.html">block view</a></span> • <span class="mode_btn"><a href="lib-Text-Tradition-Stemma-pm-1135-line.html">line view</a></span> • <span class="mode_btn mode_btn_selected">sub view</span> »</span><br />
+ For script/nytprof.pl
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+ <span class="siteTitle"> </span>
+ <span class="siteSubtitle">Run on Thu May 31 16:49:15 2012<br />Reported on Thu May 31 16:50:49 2012</span>
+</div>
+<div style="position: absolute; left: 0px; top: 0%; width: 100%; height: 101%; z-index: -1; background-color: rgb(17, 136, 255); "></div>
+<div style="position: absolute; left: 0px; top: 2%; width: 100%; height: 99%; z-index: -1; background-color: rgb(16, 134, 253); "></div>
+<div style="position: absolute; left: 0px; top: 4%; width: 100%; height: 97%; z-index: -1; background-color: rgb(16, 133, 252); "></div>
+<div style="position: absolute; left: 0px; top: 6%; width: 100%; height: 95%; z-index: -1; background-color: rgb(15, 131, 250); "></div>
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+<div style="position: absolute; left: 0px; top: 68%; width: 100%; height: 33%; z-index: -1; background-color: rgb(5, 89, 208); "></div>
+<div style="position: absolute; left: 0px; top: 70%; width: 100%; height: 31%; z-index: -1; background-color: rgb(5, 88, 207); "></div>
+<div style="position: absolute; left: 0px; top: 72%; width: 100%; height: 29%; z-index: -1; background-color: rgb(4, 87, 206); "></div>
+<div style="position: absolute; left: 0px; top: 74%; width: 100%; height: 27%; z-index: -1; background-color: rgb(4, 85, 204); "></div>
+<div style="position: absolute; left: 0px; top: 76%; width: 100%; height: 25%; z-index: -1; background-color: rgb(4, 84, 203); "></div>
+<div style="position: absolute; left: 0px; top: 78%; width: 100%; height: 23%; z-index: -1; background-color: rgb(3, 82, 201); "></div>
+<div style="position: absolute; left: 0px; top: 80%; width: 100%; height: 21%; z-index: -1; background-color: rgb(3, 81, 200); "></div>
+<div style="position: absolute; left: 0px; top: 82%; width: 100%; height: 19%; z-index: -1; background-color: rgb(3, 80, 199); "></div>
+<div style="position: absolute; left: 0px; top: 84%; width: 100%; height: 17%; z-index: -1; background-color: rgb(2, 78, 197); "></div>
+<div style="position: absolute; left: 0px; top: 86%; width: 100%; height: 15%; z-index: -1; background-color: rgb(2, 77, 196); "></div>
+<div style="position: absolute; left: 0px; top: 88%; width: 100%; height: 13%; z-index: -1; background-color: rgb(2, 76, 195); "></div>
+<div style="position: absolute; left: 0px; top: 90%; width: 100%; height: 11%; z-index: -1; background-color: rgb(1, 74, 193); "></div>
+<div style="position: absolute; left: 0px; top: 92%; width: 100%; height: 9%; z-index: -1; background-color: rgb(1, 73, 192); "></div>
+<div style="position: absolute; left: 0px; top: 94%; width: 100%; height: 7%; z-index: -1; background-color: rgb(1, 72, 191); "></div>
+<div style="position: absolute; left: 0px; top: 96%; width: 100%; height: 5%; z-index: -1; background-color: rgb(0, 70, 189); "></div>
+<div style="position: absolute; left: 0px; top: 98%; width: 100%; height: 3%; z-index: -1; background-color: rgb(0, 69, 188); "></div>
+<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/Stemma.pm">/Users/edenc/share/src/stemmatology/stemmaweb/lib/Text/Tradition/Stemma.pm</a></td></tr>
+<tr><td class="h">Statements</td><td align="left">Executed 26 statements in 3.37ms</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%">5.52ms</span></td><td class="c0"><span title="0.0%">10.1ms</span></td><td class="sub_name"><span style="display: none;">Text::Tradition::Stemma::::BEGIN@7</span>Text::Tradition::Stemma::<a href="lib-Text-Tradition-Stemma-pm-1135-sub.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="c0"><span title="0.0%">2.45ms</span></td><td class="c0"><span title="0.0%">4.90ms</span></td><td class="sub_name"><span style="display: none;">Text::Tradition::Stemma::::BEGIN@10</span>Text::Tradition::Stemma::<a href="lib-Text-Tradition-Stemma-pm-1135-sub.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="c0"><span title="0.0%">1.63ms</span></td><td class="c0"><span title="0.0%">22.4ms</span></td><td class="sub_name"><span style="display: none;">Text::Tradition::Stemma::::BEGIN@3</span>Text::Tradition::Stemma::<a href="lib-Text-Tradition-Stemma-pm-1135-sub.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="c1"><span title="0.0%">26µs</span></td><td class="c3"><span title="0.0%">123µs</span></td><td class="sub_name"><span style="display: none;">Text::Tradition::Stemma::::BEGIN@5</span>Text::Tradition::Stemma::<a href="lib-Text-Tradition-Stemma-pm-1135-sub.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%">22µs</span></td><td class="c3"><span title="0.0%">26µs</span></td><td class="sub_name"><span style="display: none;">Text::Tradition::Stemma::::BEGIN@6</span>Text::Tradition::Stemma::<a href="lib-Text-Tradition-Stemma-pm-1135-sub.html#6">BEGIN@6</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%">20µs</span></td><td class="c3"><span title="0.0%">68µs</span></td><td class="sub_name"><span style="display: none;">Text::Tradition::Stemma::::BEGIN@4</span>Text::Tradition::Stemma::<a href="lib-Text-Tradition-Stemma-pm-1135-sub.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%">19µs</span></td><td class="c3"><span title="0.0%">199µs</span></td><td class="sub_name"><span style="display: none;">Text::Tradition::Stemma::::BEGIN@393</span>Text::Tradition::Stemma::<a href="lib-Text-Tradition-Stemma-pm-1135-sub.html#393">BEGIN@393</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%">18µs</span></td><td class="c0"><span title="0.0%">7.02ms</span></td><td class="sub_name"><span style="display: none;">Text::Tradition::Stemma::::BEGIN@12</span>Text::Tradition::Stemma::<a href="lib-Text-Tradition-Stemma-pm-1135-sub.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%">18µs</span></td><td class="c3"><span title="0.0%">20µs</span></td><td class="sub_name"><span style="display: none;">Text::Tradition::Stemma::::BEGIN@9</span>Text::Tradition::Stemma::<a href="lib-Text-Tradition-Stemma-pm-1135-sub.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="c3"><span title="0.0%">17µs</span></td><td class="c3"><span title="0.0%">72µs</span></td><td class="sub_name"><span style="display: none;">Text::Tradition::Stemma::::BEGIN@8</span>Text::Tradition::Stemma::<a href="lib-Text-Tradition-Stemma-pm-1135-sub.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%">15µs</span></td><td class="c3"><span title="0.0%">257µs</span></td><td class="sub_name"><span style="display: none;">Text::Tradition::Stemma::::BEGIN@11</span>Text::Tradition::Stemma::<a href="lib-Text-Tradition-Stemma-pm-1135-sub.html#11">BEGIN@11</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::Stemma::::BUILD</span>Text::Tradition::Stemma::<a href="lib-Text-Tradition-Stemma-pm-1135-sub.html#111">BUILD</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::Stemma::::_by_vertex</span>Text::Tradition::Stemma::<a href="lib-Text-Tradition-Stemma-pm-1135-sub.html#277">_by_vertex</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::Stemma::::_dotquote</span>Text::Tradition::Stemma::<a href="lib-Text-Tradition-Stemma-pm-1135-sub.html#269">_dotquote</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::Stemma::::_graph_from_dot</span>Text::Tradition::Stemma::<a href="lib-Text-Tradition-Stemma-pm-1135-sub.html#119">_graph_from_dot</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::Stemma::::_make_dotline</span>Text::Tradition::Stemma::<a href="lib-Text-Tradition-Stemma-pm-1135-sub.html#259">_make_dotline</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::Stemma::::as_dot</span>Text::Tradition::Stemma::<a href="lib-Text-Tradition-Stemma-pm-1135-sub.html#156">as_dot</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::Stemma::::as_svg</span>Text::Tradition::Stemma::<a href="lib-Text-Tradition-Stemma-pm-1135-sub.html#336">as_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::Stemma::::editable</span>Text::Tradition::Stemma::<a href="lib-Text-Tradition-Stemma-pm-1135-sub.html#224">editable</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::Stemma::::extend_graph</span>Text::Tradition::Stemma::<a href="lib-Text-Tradition-Stemma-pm-1135-sub.html#290">extend_graph</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::Stemma::::hypotheticals</span>Text::Tradition::Stemma::<a href="lib-Text-Tradition-Stemma-pm-1135-sub.html#377">hypotheticals</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::Stemma::::throw</span>Text::Tradition::Stemma::<a href="lib-Text-Tradition-Stemma-pm-1135-sub.html#385">throw</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::Stemma::::witnesses</span>Text::Tradition::Stemma::<a href="lib-Text-Tradition-Stemma-pm-1135-sub.html#364">witnesses</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-Stemma-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::Stemma;</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="c0"><span title="Avg 98µs">197µs</span></td><td class="c3">2</td><td class="c0">22.4ms</td><td class="s"><div class="calls"><div class="calls_in"># spent 22.4ms (1.63+20.7) within Text::Tradition::Stemma::BEGIN@3 which was called:
+# once (1.63ms+20.7ms) by Text::Tradition::BEGIN@7 at <a href="lib-Text-Tradition-Stemma-pm-1135-sub.html#3">line 3</a></div></div>use Bio::Phylo::IO;<div class="calls"><div class="calls_out"># spent 22.4ms making 1 call to <a href="lib-Text-Tradition-Stemma-pm-1135-sub.html#3">Text::Tradition::Stemma::BEGIN@3</a>
+# spent 40µs making 1 call to <a href="Exporter-pm-8-sub.html#28">Exporter::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 25µs">51µs</span></td><td class="c3">2</td><td class="c3">117µs</td><td class="s"><div class="calls"><div class="calls_in"># spent 68µs (20+48) within Text::Tradition::Stemma::BEGIN@4 which was called:
+# once (20µs+48µs) by Text::Tradition::BEGIN@7 at <a href="lib-Text-Tradition-Stemma-pm-1135-sub.html#4">line 4</a></div></div>use Encode qw( decode_utf8 );<div class="calls"><div class="calls_out"># spent 68µs making 1 call to <a href="lib-Text-Tradition-Stemma-pm-1135-sub.html#4">Text::Tradition::Stemma::BEGIN@4</a>
+# spent 48µs making 1 call to <a href="Exporter-pm-8-sub.html#28">Exporter::import</a></div></div></td></tr>
+<tr><td class="h"><a name="5"></a>5</td><td class="c3">2</td><td class="c3"><span title="Avg 27µs">53µs</span></td><td class="c3">2</td><td class="c3">220µs</td><td class="s"><div class="calls"><div class="calls_in"># spent 123µs (26+97) within Text::Tradition::Stemma::BEGIN@5 which was called:
+# once (26µs+97µs) by Text::Tradition::BEGIN@7 at <a href="lib-Text-Tradition-Stemma-pm-1135-sub.html#5">line 5</a></div></div>use File::Temp;<div class="calls"><div class="calls_out"># spent 123µs making 1 call to <a href="lib-Text-Tradition-Stemma-pm-1135-sub.html#5">Text::Tradition::Stemma::BEGIN@5</a>
+# spent 97µs making 1 call to <a href="Exporter-pm-8-sub.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 24µs">47µs</span></td><td class="c3">2</td><td class="c3">30µs</td><td class="s"><div class="calls"><div class="calls_in"># spent 26µs (22+4) within Text::Tradition::Stemma::BEGIN@6 which was called:
+# once (22µs+4µs) by Text::Tradition::BEGIN@7 at <a href="lib-Text-Tradition-Stemma-pm-1135-sub.html#6">line 6</a></div></div>use Graph;<div class="calls"><div class="calls_out"># spent 26µs making 1 call to <a href="lib-Text-Tradition-Stemma-pm-1135-sub.html#6">Text::Tradition::Stemma::BEGIN@6</a>
+# spent 4µs making 1 call to <a href="UNIVERSAL-pm-738-sub.html#16">UNIVERSAL::import</a></div></div></td></tr>
+<tr><td class="h"><a name="7"></a>7</td><td class="c3">2</td><td class="c0"><span title="Avg 111µs">223µs</span></td><td class="c3">2</td><td class="c1">10.1ms</td><td class="s"><div class="calls"><div class="calls_in"># spent 10.1ms (5.52+4.56) within Text::Tradition::Stemma::BEGIN@7 which was called:
+# once (5.52ms+4.56ms) by Text::Tradition::BEGIN@7 at <a href="lib-Text-Tradition-Stemma-pm-1135-sub.html#7">line 7</a></div></div>use Graph::Reader::Dot;<div class="calls"><div class="calls_out"># spent 10.1ms making 1 call to <a href="lib-Text-Tradition-Stemma-pm-1135-sub.html#7">Text::Tradition::Stemma::BEGIN@7</a>
+# spent 4µs making 1 call to <a href="UNIVERSAL-pm-738-sub.html#16">UNIVERSAL::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 24µs">48µs</span></td><td class="c3">2</td><td class="c3">128µs</td><td class="s"><div class="calls"><div class="calls_in"># spent 72µs (17+56) within Text::Tradition::Stemma::BEGIN@8 which was called:
+# once (17µs+56µs) by Text::Tradition::BEGIN@7 at <a href="lib-Text-Tradition-Stemma-pm-1135-sub.html#8">line 8</a></div></div>use IPC::Run qw/ run binary /;<div class="calls"><div class="calls_out"># spent 72µs making 1 call to <a href="lib-Text-Tradition-Stemma-pm-1135-sub.html#8">Text::Tradition::Stemma::BEGIN@8</a>
+# spent 56µs making 1 call to <a href="Exporter-pm-8-sub.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="c3"><span title="Avg 24µs">48µs</span></td><td class="c3">2</td><td class="c3">22µs</td><td class="s"><div class="calls"><div class="calls_in"># spent 20µs (18+2) within Text::Tradition::Stemma::BEGIN@9 which was called:
+# once (18µs+2µs) by Text::Tradition::BEGIN@7 at <a href="lib-Text-Tradition-Stemma-pm-1135-sub.html#9">line 9</a></div></div>use Text::Tradition::Error;<div class="calls"><div class="calls_out"># spent 20µs making 1 call to <a href="lib-Text-Tradition-Stemma-pm-1135-sub.html#9">Text::Tradition::Stemma::BEGIN@9</a>
+# spent 2µs making 1 call to <a href="UNIVERSAL-pm-738-sub.html#16">UNIVERSAL::import</a></div></div></td></tr>
+<tr><td class="h"><a name="10"></a>10</td><td class="c3">2</td><td class="c0"><span title="Avg 85µs">169µs</span></td><td class="c3">2</td><td class="c3">4.98ms</td><td class="s"><div class="calls"><div class="calls_in"># spent 4.90ms (2.45+2.46) within Text::Tradition::Stemma::BEGIN@10 which was called:
+# once (2.45ms+2.46ms) by Text::Tradition::BEGIN@7 at <a href="lib-Text-Tradition-Stemma-pm-1135-sub.html#10">line 10</a></div></div>use Text::Tradition::StemmaUtil qw/ character_input phylip_pars parse_newick /;<div class="calls"><div class="calls_out"># spent 4.90ms making 1 call to <a href="lib-Text-Tradition-Stemma-pm-1135-sub.html#10">Text::Tradition::Stemma::BEGIN@10</a>
+# spent 76µs making 1 call to <a href="Exporter-pm-8-sub.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 24µs">47µs</span></td><td class="c3">2</td><td class="c3">500µs</td><td class="s"><div class="calls"><div class="calls_in"># spent 257µs (15+242) within Text::Tradition::Stemma::BEGIN@11 which was called:
+# once (15µs+242µs) by Text::Tradition::BEGIN@7 at <a href="lib-Text-Tradition-Stemma-pm-1135-sub.html#11">line 11</a></div></div>use XML::LibXML;<div class="calls"><div class="calls_out"># spent 257µs making 1 call to <a href="lib-Text-Tradition-Stemma-pm-1135-sub.html#11">Text::Tradition::Stemma::BEGIN@11</a>
+# spent 242µs making 1 call to <a href="XML-LibXML-pm-1093-sub.html#182">XML::LibXML::import</a></div></div></td></tr>
+<tr><td class="h"><a name="12"></a>12</td><td class="c3">2</td><td class="c0"><span title="Avg 1.18ms">2.35ms</span></td><td class="c3">2</td><td class="c0">14.0ms</td><td class="s"><div class="calls"><div class="calls_in"># spent 7.02ms (18µs+7.00) within Text::Tradition::Stemma::BEGIN@12 which was called:
+# once (18µs+7.00ms) by Text::Tradition::BEGIN@7 at <a href="lib-Text-Tradition-Stemma-pm-1135-sub.html#12">line 12</a></div></div>use Moose;<div class="calls"><div class="calls_out"># spent 7.02ms making 1 call to <a href="lib-Text-Tradition-Stemma-pm-1135-sub.html#12">Text::Tradition::Stemma::BEGIN@12</a>
+# spent 7.00ms making 1 call to <a href="Moose-Exporter-pm-82-sub.html#402">Moose::Exporter::__ANON__[Moose/Exporter.pm:492]</a></div></div></td></tr>
+<tr><td class="h"><a name="13"></a>13</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="14"></a>14</td><td></td><td></td><td></td><td></td><td class="s">=head1 NAME</td></tr>
+<tr><td class="h"><a name="15"></a>15</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="16"></a>16</td><td></td><td></td><td></td><td></td><td class="s">Text::Tradition::Stemma - a representation of a I<stemma codicum> for a Text::Tradition</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 SYNOPSIS</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"> use Text::Tradition;</td></tr>
+<tr><td class="h"><a name="21"></a>21</td><td></td><td></td><td></td><td></td><td class="s"> my $t = Text::Tradition->new( </td></tr>
+<tr><td class="h"><a name="22"></a>22</td><td></td><td></td><td></td><td></td><td class="s"> 'name' => 'this is a text',</td></tr>
+<tr><td class="h"><a name="23"></a>23</td><td></td><td></td><td></td><td></td><td class="s"> 'input' => 'TEI',</td></tr>
+<tr><td class="h"><a name="24"></a>24</td><td></td><td></td><td></td><td></td><td class="s"> 'file' => '/path/to/tei_parallel_seg_file.xml' );</td></tr>
+<tr><td class="h"><a name="25"></a>25</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="26"></a>26</td><td></td><td></td><td></td><td></td><td class="s"> my $s = $tradition->add_stemma( dotfile => '/path/to/stemma.dot' );</td></tr>
+<tr><td class="h"><a name="27"></a>27</td><td></td><td></td><td></td><td></td><td class="s"> </td></tr>
+<tr><td class="h"><a name="28"></a>28</td><td></td><td></td><td></td><td></td><td class="s">=head1 DESCRIPTION</td></tr>
+<tr><td class="h"><a name="29"></a>29</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="30"></a>30</td><td></td><td></td><td></td><td></td><td class="s">Text::Tradition is a library for representation and analysis of collated</td></tr>
+<tr><td class="h"><a name="31"></a>31</td><td></td><td></td><td></td><td></td><td class="s">texts, particularly medieval ones. The Stemma is a representation of the</td></tr>
+<tr><td class="h"><a name="32"></a>32</td><td></td><td></td><td></td><td></td><td class="s">copying relationships between the witnesses in a Tradition, modelled with</td></tr>
+<tr><td class="h"><a name="33"></a>33</td><td></td><td></td><td></td><td></td><td class="s">a connected rooted directed acyclic graph (CRDAG).</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">=head1 DOT SYNTAX</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">The easiest way to define a stemma is to use a special form of the 'dot' </td></tr>
+<tr><td class="h"><a name="38"></a>38</td><td></td><td></td><td></td><td></td><td class="s">syntax of GraphViz. </td></tr>
+<tr><td class="h"><a name="39"></a>39</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="40"></a>40</td><td></td><td></td><td></td><td></td><td class="s">Each stemma opens with the line</td></tr>
+<tr><td class="h"><a name="41"></a>41</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="42"></a>42</td><td></td><td></td><td></td><td></td><td class="s"> digraph Stemma {</td></tr>
+<tr><td class="h"><a name="43"></a>43</td><td></td><td></td><td></td><td></td><td class="s"> </td></tr>
+<tr><td class="h"><a name="44"></a>44</td><td></td><td></td><td></td><td></td><td class="s">and continues with a list of all manuscript witnesses in the stemma, whether</td></tr>
+<tr><td class="h"><a name="45"></a>45</td><td></td><td></td><td></td><td></td><td class="s">extant witnesses or missing archetypes or hyparchetypes. Each of these is</td></tr>
+<tr><td class="h"><a name="46"></a>46</td><td></td><td></td><td></td><td></td><td class="s">listed by its sigil on its own line, e.g.:</td></tr>
+<tr><td class="h"><a name="47"></a>47</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="48"></a>48</td><td></td><td></td><td></td><td></td><td class="s"> alpha [ class=hypothetical ]</td></tr>
+<tr><td class="h"><a name="49"></a>49</td><td></td><td></td><td></td><td></td><td class="s"> 1 [ class=hypothetical,label=* ]</td></tr>
+<tr><td class="h"><a name="50"></a>50</td><td></td><td></td><td></td><td></td><td class="s"> Ms4 [ class=extant ]</td></tr>
+<tr><td class="h"><a name="51"></a>51</td><td></td><td></td><td></td><td></td><td class="s"> </td></tr>
+<tr><td class="h"><a name="52"></a>52</td><td></td><td></td><td></td><td></td><td class="s">Extant witnesses are listed with class=extant; missing or postulated witnesses</td></tr>
+<tr><td class="h"><a name="53"></a>53</td><td></td><td></td><td></td><td></td><td class="s">are listed with class=hypothetical. Anonymous hyparchetypes must be given a </td></tr>
+<tr><td class="h"><a name="54"></a>54</td><td></td><td></td><td></td><td></td><td class="s">unique name or number, but can be represented as anonymous with the addition </td></tr>
+<tr><td class="h"><a name="55"></a>55</td><td></td><td></td><td></td><td></td><td class="s">of 'label=*' to their lines. Greek letters or other special characters may be</td></tr>
+<tr><td class="h"><a name="56"></a>56</td><td></td><td></td><td></td><td></td><td class="s">used as names, but they must always be wrapped in double quotes.</td></tr>
+<tr><td class="h"><a name="57"></a>57</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="58"></a>58</td><td></td><td></td><td></td><td></td><td class="s">Links between manuscripts are then listed with arrow notation, as below. These </td></tr>
+<tr><td class="h"><a name="59"></a>59</td><td></td><td></td><td></td><td></td><td class="s">lines show the direction of copying, one step at a time, for the entire stemma.</td></tr>
+<tr><td class="h"><a name="60"></a>60</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="61"></a>61</td><td></td><td></td><td></td><td></td><td class="s"> alpha -> 1</td></tr>
+<tr><td class="h"><a name="62"></a>62</td><td></td><td></td><td></td><td></td><td class="s"> 1 -> Ms4</td></tr>
+<tr><td class="h"><a name="63"></a>63</td><td></td><td></td><td></td><td></td><td class="s"> </td></tr>
+<tr><td class="h"><a name="64"></a>64</td><td></td><td></td><td></td><td></td><td class="s">The final line in the definition should be the closing brace:</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"> }</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">Thus for a set of extant manuscripts A, B, and C, where A and B were copied </td></tr>
+<tr><td class="h"><a name="69"></a>69</td><td></td><td></td><td></td><td></td><td class="s">from the archetype O and C was copied from B, the definition would be:</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"> digraph Stemma {</td></tr>
+<tr><td class="h"><a name="72"></a>72</td><td></td><td></td><td></td><td></td><td class="s"> O [ class=hypothetical]</td></tr>
+<tr><td class="h"><a name="73"></a>73</td><td></td><td></td><td></td><td></td><td class="s"> A [ class=extant ]</td></tr>
+<tr><td class="h"><a name="74"></a>74</td><td></td><td></td><td></td><td></td><td class="s"> B [ class=extant ]</td></tr>
+<tr><td class="h"><a name="75"></a>75</td><td></td><td></td><td></td><td></td><td class="s"> C [ class=extant ]</td></tr>
+<tr><td class="h"><a name="76"></a>76</td><td></td><td></td><td></td><td></td><td class="s"> O -> A</td></tr>
+<tr><td class="h"><a name="77"></a>77</td><td></td><td></td><td></td><td></td><td class="s"> O -> B</td></tr>
+<tr><td class="h"><a name="78"></a>78</td><td></td><td></td><td></td><td></td><td class="s"> B -> C</td></tr>
+<tr><td class="h"><a name="79"></a>79</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr>
+<tr><td class="h"><a name="80"></a>80</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="81"></a>81</td><td></td><td></td><td></td><td></td><td class="s">=head1 CONSTRUCTOR</td></tr>
+<tr><td class="h"><a name="82"></a>82</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="83"></a>83</td><td></td><td></td><td></td><td></td><td class="s">=head2 new</td></tr>
+<tr><td class="h"><a name="84"></a>84</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="85"></a>85</td><td></td><td></td><td></td><td></td><td class="s">The constructor. This should generally be called from Text::Tradition, but</td></tr>
+<tr><td class="h"><a name="86"></a>86</td><td></td><td></td><td></td><td></td><td class="s">if called directly it takes the following options:</td></tr>
+<tr><td class="h"><a name="87"></a>87</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="88"></a>88</td><td></td><td></td><td></td><td></td><td class="s">=over</td></tr>
+<tr><td class="h"><a name="89"></a>89</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="90"></a>90</td><td></td><td></td><td></td><td></td><td class="s">=item * collation - The collation with which the stemma is associated.</td></tr>
+<tr><td class="h"><a name="91"></a>91</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="92"></a>92</td><td></td><td></td><td></td><td></td><td class="s">=item * dot - A filehandle open to a DOT representation of the stemma graph.</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">=back</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">=cut</td></tr>
+<tr><td class="h"><a name="97"></a>97</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="98"></a>98</td><td class="c3">1</td><td class="c3"><span title="Avg 4µs">4µs</span></td><td class="c3">1</td><td class="c3">3.57ms</td><td class="s">has collation => (<div class="calls"><div class="calls_out"># spent 3.57ms making 1 call to <a href="Moose-pm-62-sub.html#70">Moose::has</a></div></div></td></tr>
+<tr><td class="h"><a name="99"></a>99</td><td></td><td></td><td></td><td></td><td class="s"> is => 'ro',</td></tr>
+<tr><td class="h"><a name="100"></a>100</td><td></td><td></td><td></td><td></td><td class="s"> isa => 'Text::Tradition::Collation',</td></tr>
+<tr><td class="h"><a name="101"></a>101</td><td></td><td></td><td></td><td></td><td class="s"> required => 1,</td></tr>
+<tr><td class="h"><a name="102"></a>102</td><td></td><td></td><td></td><td></td><td class="s"> weak_ref => 1,</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"></td></tr>
+<tr><td class="h"><a name="105"></a>105</td><td class="c3">1</td><td class="c3"><span title="Avg 4µs">4µs</span></td><td class="c3">1</td><td class="c3">3.88ms</td><td class="s">has graph => (<div class="calls"><div class="calls_out"># spent 3.88ms making 1 call to <a href="Moose-pm-62-sub.html#70">Moose::has</a></div></div></td></tr>
+<tr><td class="h"><a name="106"></a>106</td><td></td><td></td><td></td><td></td><td class="s"> is => 'rw',</td></tr>
+<tr><td class="h"><a name="107"></a>107</td><td></td><td></td><td></td><td></td><td class="s"> isa => 'Graph',</td></tr>
+<tr><td class="h"><a name="108"></a>108</td><td></td><td></td><td></td><td></td><td class="s"> predicate => 'has_graph',</td></tr>
+<tr><td class="h"><a name="109"></a>109</td><td></td><td></td><td></td><td></td><td class="s"> );</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">sub BUILD {</td></tr>
+<tr><td class="h"><a name="112"></a>112</td><td></td><td></td><td></td><td></td><td class="s"> my( $self, $args ) = @_;</td></tr>
+<tr><td class="h"><a name="113"></a>113</td><td></td><td></td><td></td><td></td><td class="s"> # If we have been handed a dotfile, initialize it into a graph.</td></tr>
+<tr><td class="h"><a name="114"></a>114</td><td></td><td></td><td></td><td></td><td class="s"> if( exists $args->{'dot'} ) {</td></tr>
+<tr><td class="h"><a name="115"></a>115</td><td></td><td></td><td></td><td></td><td class="s"> $self->_graph_from_dot( $args->{'dot'} );</td></tr>
+<tr><td class="h"><a name="116"></a>116</td><td></td><td></td><td></td><td></td><td class="s"> }</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"></td></tr>
+<tr><td class="h"><a name="119"></a>119</td><td></td><td></td><td></td><td></td><td class="s">sub _graph_from_dot {</td></tr>
+<tr><td class="h"><a name="120"></a>120</td><td></td><td></td><td></td><td></td><td class="s"> my( $self, $dotfh ) = @_;</td></tr>
+<tr><td class="h"><a name="121"></a>121</td><td></td><td></td><td></td><td></td><td class="s"> my $reader = Graph::Reader::Dot->new();</td></tr>
+<tr><td class="h"><a name="122"></a>122</td><td></td><td></td><td></td><td></td><td class="s"> my $graph = $reader->read_graph( $dotfh );</td></tr>
+<tr><td class="h"><a name="123"></a>123</td><td></td><td></td><td></td><td></td><td class="s"> if( $graph ) {</td></tr>
+<tr><td class="h"><a name="124"></a>124</td><td></td><td></td><td></td><td></td><td class="s"> $self->graph( $graph );</td></tr>
+<tr><td class="h"><a name="125"></a>125</td><td></td><td></td><td></td><td></td><td class="s"> # Go through the nodes and set any non-hypothetical node to extant.</td></tr>
+<tr><td class="h"><a name="126"></a>126</td><td></td><td></td><td></td><td></td><td class="s"> foreach my $v ( $self->graph->vertices ) {</td></tr>
+<tr><td class="h"><a name="127"></a>127</td><td></td><td></td><td></td><td></td><td class="s"> $self->graph->set_vertex_attribute( $v, 'class', 'extant' )</td></tr>
+<tr><td class="h"><a name="128"></a>128</td><td></td><td></td><td></td><td></td><td class="s"> unless $self->graph->has_vertex_attribute( $v, 'class' );</td></tr>
+<tr><td class="h"><a name="129"></a>129</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr>
+<tr><td class="h"><a name="130"></a>130</td><td></td><td></td><td></td><td></td><td class="s"> } else {</td></tr>
+<tr><td class="h"><a name="131"></a>131</td><td></td><td></td><td></td><td></td><td class="s"> throw( "Failed to parse dot in $dotfh" );</td></tr>
+<tr><td class="h"><a name="132"></a>132</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr>
+<tr><td class="h"><a name="133"></a>133</td><td></td><td></td><td></td><td></td><td class="s">}</td></tr>
+<tr><td class="h"><a name="134"></a>134</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="135"></a>135</td><td></td><td></td><td></td><td></td><td class="s">=head1 METHODS</td></tr>
+<tr><td class="h"><a name="136"></a>136</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="137"></a>137</td><td></td><td></td><td></td><td></td><td class="s">=head2 as_dot( \%options )</td></tr>
+<tr><td class="h"><a name="138"></a>138</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="139"></a>139</td><td></td><td></td><td></td><td></td><td class="s">Returns a normal dot representation of the stemma layout, suitable for rendering</td></tr>
+<tr><td class="h"><a name="140"></a>140</td><td></td><td></td><td></td><td></td><td class="s">with GraphViz. Options include:</td></tr>
+<tr><td class="h"><a name="141"></a>141</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="142"></a>142</td><td></td><td></td><td></td><td></td><td class="s">=over</td></tr>
+<tr><td class="h"><a name="143"></a>143</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="144"></a>144</td><td></td><td></td><td></td><td></td><td class="s">=item * graph - A hashref of global graph options.</td></tr>
+<tr><td class="h"><a name="145"></a>145</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="146"></a>146</td><td></td><td></td><td></td><td></td><td class="s">=item * node - A hashref of global node options.</td></tr>
+<tr><td class="h"><a name="147"></a>147</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="148"></a>148</td><td></td><td></td><td></td><td></td><td class="s">=item * edge - A hashref of global edge options.</td></tr>
+<tr><td class="h"><a name="149"></a>149</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="150"></a>150</td><td></td><td></td><td></td><td></td><td class="s">=back</td></tr>
+<tr><td class="h"><a name="151"></a>151</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="152"></a>152</td><td></td><td></td><td></td><td></td><td class="s">See the GraphViz documentation for the list of available options.</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">=cut</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">sub as_dot {</td></tr>
+<tr><td class="h"><a name="157"></a>157</td><td></td><td></td><td></td><td></td><td class="s"> my( $self, $opts ) = @_;</td></tr>
+<tr><td class="h"><a name="158"></a>158</td><td></td><td></td><td></td><td></td><td class="s"> </td></tr>
+<tr><td class="h"><a name="159"></a>159</td><td></td><td></td><td></td><td></td><td class="s"> ## See if we are including any a.c. witnesses in this graph.</td></tr>
+<tr><td class="h"><a name="160"></a>160</td><td></td><td></td><td></td><td></td><td class="s"> my $graph = $self->graph;</td></tr>
+<tr><td class="h"><a name="161"></a>161</td><td></td><td></td><td></td><td></td><td class="s"> if( exists $opts->{'layerwits'} ) {</td></tr>
+<tr><td class="h"><a name="162"></a>162</td><td></td><td></td><td></td><td></td><td class="s"> $graph = $self->extend_graph( $opts->{'layerwits'} );</td></tr>
+<tr><td class="h"><a name="163"></a>163</td><td></td><td></td><td></td><td></td><td class="s"> }</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"> # Get default and specified options</td></tr>
+<tr><td class="h"><a name="166"></a>166</td><td></td><td></td><td></td><td></td><td class="s"> my %graphopts = (</td></tr>
+<tr><td class="h"><a name="167"></a>167</td><td></td><td></td><td></td><td></td><td class="s"> # 'ratio' => 1,</td></tr>
+<tr><td class="h"><a name="168"></a>168</td><td></td><td></td><td></td><td></td><td class="s"> );</td></tr>
+<tr><td class="h"><a name="169"></a>169</td><td></td><td></td><td></td><td></td><td class="s"> my %nodeopts = (</td></tr>
+<tr><td class="h"><a name="170"></a>170</td><td></td><td></td><td></td><td></td><td class="s"> 'fontsize' => 11,</td></tr>
+<tr><td class="h"><a name="171"></a>171</td><td></td><td></td><td></td><td></td><td class="s"> 'style' => 'filled',</td></tr>
+<tr><td class="h"><a name="172"></a>172</td><td></td><td></td><td></td><td></td><td class="s"> 'fillcolor' => 'white',</td></tr>
+<tr><td class="h"><a name="173"></a>173</td><td></td><td></td><td></td><td></td><td class="s"> 'color' => 'white',</td></tr>
+<tr><td class="h"><a name="174"></a>174</td><td></td><td></td><td></td><td></td><td class="s"> 'shape' => 'ellipse', # Shape for the extant nodes</td></tr>
+<tr><td class="h"><a name="175"></a>175</td><td></td><td></td><td></td><td></td><td class="s"> );</td></tr>
+<tr><td class="h"><a name="176"></a>176</td><td></td><td></td><td></td><td></td><td class="s"> my %edgeopts = (</td></tr>
+<tr><td class="h"><a name="177"></a>177</td><td></td><td></td><td></td><td></td><td class="s"> 'arrowhead' => 'none',</td></tr>
+<tr><td class="h"><a name="178"></a>178</td><td></td><td></td><td></td><td></td><td class="s"> );</td></tr>
+<tr><td class="h"><a name="179"></a>179</td><td></td><td></td><td></td><td></td><td class="s"> @graphopts{ keys %{$opts->{'graph'}} } = values %{$opts->{'graph'}} </td></tr>
+<tr><td class="h"><a name="180"></a>180</td><td></td><td></td><td></td><td></td><td class="s"> if $opts->{'graph'};</td></tr>
+<tr><td class="h"><a name="181"></a>181</td><td></td><td></td><td></td><td></td><td class="s"> @nodeopts{ keys %{$opts->{'node'}} } = values %{$opts->{'node'}} </td></tr>
+<tr><td class="h"><a name="182"></a>182</td><td></td><td></td><td></td><td></td><td class="s"> if $opts->{'node'};</td></tr>
+<tr><td class="h"><a name="183"></a>183</td><td></td><td></td><td></td><td></td><td class="s"> @edgeopts{ keys %{$opts->{'edge'}} } = values %{$opts->{'edge'}} </td></tr>
+<tr><td class="h"><a name="184"></a>184</td><td></td><td></td><td></td><td></td><td class="s"> if $opts->{'edge'};</td></tr>
+<tr><td class="h"><a name="185"></a>185</td><td></td><td></td><td></td><td></td><td class="s"> </td></tr>
+<tr><td class="h"><a name="186"></a>186</td><td></td><td></td><td></td><td></td><td class="s"> my @dotlines;</td></tr>
+<tr><td class="h"><a name="187"></a>187</td><td></td><td></td><td></td><td></td><td class="s"> push( @dotlines, 'digraph stemma {' );</td></tr>
+<tr><td class="h"><a name="188"></a>188</td><td></td><td></td><td></td><td></td><td class="s"> ## Print out the global attributes</td></tr>
+<tr><td class="h"><a name="189"></a>189</td><td></td><td></td><td></td><td></td><td class="s"> push( @dotlines, _make_dotline( 'graph', %graphopts ) ) if keys %graphopts;</td></tr>
+<tr><td class="h"><a name="190"></a>190</td><td></td><td></td><td></td><td></td><td class="s"> push( @dotlines, _make_dotline( 'edge', %edgeopts ) ) if keys %edgeopts;</td></tr>
+<tr><td class="h"><a name="191"></a>191</td><td></td><td></td><td></td><td></td><td class="s"> push( @dotlines, _make_dotline( 'node', %nodeopts ) ) if keys %nodeopts;</td></tr>
+<tr><td class="h"><a name="192"></a>192</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="193"></a>193</td><td></td><td></td><td></td><td></td><td class="s"> # Add each of the nodes.</td></tr>
+<tr><td class="h"><a name="194"></a>194</td><td></td><td></td><td></td><td></td><td class="s"> foreach my $n ( $graph->vertices ) {</td></tr>
+<tr><td class="h"><a name="195"></a>195</td><td></td><td></td><td></td><td></td><td class="s"> if( $graph->has_vertex_attribute( $n, 'label' ) ) {</td></tr>
+<tr><td class="h"><a name="196"></a>196</td><td></td><td></td><td></td><td></td><td class="s"> my $ltext = $graph->get_vertex_attribute( $n, 'label' );</td></tr>
+<tr><td class="h"><a name="197"></a>197</td><td></td><td></td><td></td><td></td><td class="s"> push( @dotlines, _make_dotline( $n, 'label' => $ltext ) );</td></tr>
+<tr><td class="h"><a name="198"></a>198</td><td></td><td></td><td></td><td></td><td class="s"> } else {</td></tr>
+<tr><td class="h"><a name="199"></a>199</td><td></td><td></td><td></td><td></td><td class="s"> # Use the default display settings.</td></tr>
+<tr><td class="h"><a name="200"></a>200</td><td></td><td></td><td></td><td></td><td class="s"> $n = _dotquote( $n );</td></tr>
+<tr><td class="h"><a name="201"></a>201</td><td></td><td></td><td></td><td></td><td class="s"> push( @dotlines, " $n;" );</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"> }</td></tr>
+<tr><td class="h"><a name="204"></a>204</td><td></td><td></td><td></td><td></td><td class="s"> # Add each of our edges.</td></tr>
+<tr><td class="h"><a name="205"></a>205</td><td></td><td></td><td></td><td></td><td class="s"> foreach my $e ( $graph->edges ) {</td></tr>
+<tr><td class="h"><a name="206"></a>206</td><td></td><td></td><td></td><td></td><td class="s"> my( $from, $to ) = map { _dotquote( $_ ) } @$e;</td></tr>
+<tr><td class="h"><a name="207"></a>207</td><td></td><td></td><td></td><td></td><td class="s"> push( @dotlines, " $from -> $to;" );</td></tr>
+<tr><td class="h"><a name="208"></a>208</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr>
+<tr><td class="h"><a name="209"></a>209</td><td></td><td></td><td></td><td></td><td class="s"> push( @dotlines, '}' );</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"> return join( "\n", @dotlines );</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"></td></tr>
+<tr><td class="h"><a name="214"></a>214</td><td></td><td></td><td></td><td></td><td class="s">=head2 editable( $opts )</td></tr>
+<tr><td class="h"><a name="215"></a>215</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="216"></a>216</td><td></td><td></td><td></td><td></td><td class="s">Returns a version of the graph rendered in our definition format. The</td></tr>
+<tr><td class="h"><a name="217"></a>217</td><td></td><td></td><td></td><td></td><td class="s">output separates statements with a newline; set $opts->{'linesep'} to the </td></tr>
+<tr><td class="h"><a name="218"></a>218</td><td></td><td></td><td></td><td></td><td class="s">empty string or to a space if the result is to be sent via JSON.</td></tr>
+<tr><td class="h"><a name="219"></a>219</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="220"></a>220</td><td></td><td></td><td></td><td></td><td class="s">Any layer witnesses to be included should be passed via $opts->{'layerwits'}.</td></tr>
+<tr><td class="h"><a name="221"></a>221</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="222"></a>222</td><td></td><td></td><td></td><td></td><td class="s">=cut</td></tr>
+<tr><td class="h"><a name="223"></a>223</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="224"></a>224</td><td></td><td></td><td></td><td></td><td class="s">sub editable {</td></tr>
+<tr><td class="h"><a name="225"></a>225</td><td></td><td></td><td></td><td></td><td class="s"> my( $self, $opts ) = @_;</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"> ## See if we are including any a.c. witnesses in this graph.</td></tr>
+<tr><td class="h"><a name="228"></a>228</td><td></td><td></td><td></td><td></td><td class="s"> my $graph = $self->graph;</td></tr>
+<tr><td class="h"><a name="229"></a>229</td><td></td><td></td><td></td><td></td><td class="s"> if( exists $opts->{'layerwits'} ) {</td></tr>
+<tr><td class="h"><a name="230"></a>230</td><td></td><td></td><td></td><td></td><td class="s"> $graph = $self->extend_graph( $opts->{'layerwits'} );</td></tr>
+<tr><td class="h"><a name="231"></a>231</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr>
+<tr><td class="h"><a name="232"></a>232</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="233"></a>233</td><td></td><td></td><td></td><td></td><td class="s"> # Create the graph</td></tr>
+<tr><td class="h"><a name="234"></a>234</td><td></td><td></td><td></td><td></td><td class="s"> my $join = ( $opts && exists $opts->{'linesep'} ) ? $opts->{'linesep'} : "\n";</td></tr>
+<tr><td class="h"><a name="235"></a>235</td><td></td><td></td><td></td><td></td><td class="s"> my @dotlines;</td></tr>
+<tr><td class="h"><a name="236"></a>236</td><td></td><td></td><td></td><td></td><td class="s"> push( @dotlines, 'digraph stemma {' );</td></tr>
+<tr><td class="h"><a name="237"></a>237</td><td></td><td></td><td></td><td></td><td class="s"> my @real; # A cheap sort</td></tr>
+<tr><td class="h"><a name="238"></a>238</td><td></td><td></td><td></td><td></td><td class="s"> foreach my $n ( sort $self->graph->vertices ) {</td></tr>
+<tr><td class="h"><a name="239"></a>239</td><td></td><td></td><td></td><td></td><td class="s"> my $c = $self->graph->get_vertex_attribute( $n, 'class' );</td></tr>
+<tr><td class="h"><a name="240"></a>240</td><td></td><td></td><td></td><td></td><td class="s"> $c = 'extant' unless $c;</td></tr>
+<tr><td class="h"><a name="241"></a>241</td><td></td><td></td><td></td><td></td><td class="s"> if( $c eq 'extant' ) {</td></tr>
+<tr><td class="h"><a name="242"></a>242</td><td></td><td></td><td></td><td></td><td class="s"> push( @real, $n );</td></tr>
+<tr><td class="h"><a name="243"></a>243</td><td></td><td></td><td></td><td></td><td class="s"> } else {</td></tr>
+<tr><td class="h"><a name="244"></a>244</td><td></td><td></td><td></td><td></td><td class="s"> push( @dotlines, _make_dotline( $n, 'class' => $c ) );</td></tr>
+<tr><td class="h"><a name="245"></a>245</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr>
+<tr><td class="h"><a name="246"></a>246</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr>
+<tr><td class="h"><a name="247"></a>247</td><td></td><td></td><td></td><td></td><td class="s"> # Now do the real ones</td></tr>
+<tr><td class="h"><a name="248"></a>248</td><td></td><td></td><td></td><td></td><td class="s"> foreach my $n ( @real ) {</td></tr>
+<tr><td class="h"><a name="249"></a>249</td><td></td><td></td><td></td><td></td><td class="s"> push( @dotlines, _make_dotline( $n, 'class' => 'extant' ) );</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"> foreach my $e ( sort _by_vertex $self->graph->edges ) {</td></tr>
+<tr><td class="h"><a name="252"></a>252</td><td></td><td></td><td></td><td></td><td class="s"> my( $from, $to ) = map { _dotquote( $_ ) } @$e;</td></tr>
+<tr><td class="h"><a name="253"></a>253</td><td></td><td></td><td></td><td></td><td class="s"> push( @dotlines, " $from -> $to;" );</td></tr>
+<tr><td class="h"><a name="254"></a>254</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr>
+<tr><td class="h"><a name="255"></a>255</td><td></td><td></td><td></td><td></td><td class="s"> push( @dotlines, '}' );</td></tr>
+<tr><td class="h"><a name="256"></a>256</td><td></td><td></td><td></td><td></td><td class="s"> return join( $join, @dotlines );</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">sub _make_dotline {</td></tr>
+<tr><td class="h"><a name="260"></a>260</td><td></td><td></td><td></td><td></td><td class="s"> my( $obj, %attr ) = @_;</td></tr>
+<tr><td class="h"><a name="261"></a>261</td><td></td><td></td><td></td><td></td><td class="s"> my @pairs;</td></tr>
+<tr><td class="h"><a name="262"></a>262</td><td></td><td></td><td></td><td></td><td class="s"> foreach my $k ( keys %attr ) {</td></tr>
+<tr><td class="h"><a name="263"></a>263</td><td></td><td></td><td></td><td></td><td class="s"> my $v = _dotquote( $attr{$k} );</td></tr>
+<tr><td class="h"><a name="264"></a>264</td><td></td><td></td><td></td><td></td><td class="s"> push( @pairs, "$k=$v" );</td></tr>
+<tr><td class="h"><a name="265"></a>265</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr>
+<tr><td class="h"><a name="266"></a>266</td><td></td><td></td><td></td><td></td><td class="s"> return sprintf( " %s [ %s ];", _dotquote( $obj ), join( ', ', @pairs ) );</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"> </td></tr>
+<tr><td class="h"><a name="269"></a>269</td><td></td><td></td><td></td><td></td><td class="s">sub _dotquote {</td></tr>
+<tr><td class="h"><a name="270"></a>270</td><td></td><td></td><td></td><td></td><td class="s"> my( $str ) = @_;</td></tr>
+<tr><td class="h"><a name="271"></a>271</td><td></td><td></td><td></td><td></td><td class="s"> return $str if $str =~ /^[A-Za-z0-9]+$/;</td></tr>
+<tr><td class="h"><a name="272"></a>272</td><td></td><td></td><td></td><td></td><td class="s"> $str =~ s/\"/\\\"/g;</td></tr>
+<tr><td class="h"><a name="273"></a>273</td><td></td><td></td><td></td><td></td><td class="s"> $str = '"' . $str . '"';</td></tr>
+<tr><td class="h"><a name="274"></a>274</td><td></td><td></td><td></td><td></td><td class="s"> return $str;</td></tr>
+<tr><td class="h"><a name="275"></a>275</td><td></td><td></td><td></td><td></td><td class="s">}</td></tr>
+<tr><td class="h"><a name="276"></a>276</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="277"></a>277</td><td></td><td></td><td></td><td></td><td class="s">sub _by_vertex {</td></tr>
+<tr><td class="h"><a name="278"></a>278</td><td></td><td></td><td></td><td></td><td class="s"> return $a->[0].$a->[1] cmp $b->[0].$b->[1];</td></tr>
+<tr><td class="h"><a name="279"></a>279</td><td></td><td></td><td></td><td></td><td class="s">}</td></tr>
+<tr><td class="h"><a name="280"></a>280</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="281"></a>281</td><td></td><td></td><td></td><td></td><td class="s">=head2 extend_graph( $layered_witnesses )</td></tr>
+<tr><td class="h"><a name="282"></a>282</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="283"></a>283</td><td></td><td></td><td></td><td></td><td class="s">Returns a graph which is the original stemma with witness layers added for the</td></tr>
+<tr><td class="h"><a name="284"></a>284</td><td></td><td></td><td></td><td></td><td class="s">list in @$layered_witnesses. A layered (a.c.) witness is added as a parent</td></tr>
+<tr><td class="h"><a name="285"></a>285</td><td></td><td></td><td></td><td></td><td class="s">of its main version, and additionally shares all other parents and children with</td></tr>
+<tr><td class="h"><a name="286"></a>286</td><td></td><td></td><td></td><td></td><td class="s">that version.</td></tr>
+<tr><td class="h"><a name="287"></a>287</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="288"></a>288</td><td></td><td></td><td></td><td></td><td class="s">=cut</td></tr>
+<tr><td class="h"><a name="289"></a>289</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="290"></a>290</td><td></td><td></td><td></td><td></td><td class="s">sub extend_graph {</td></tr>
+<tr><td class="h"><a name="291"></a>291</td><td></td><td></td><td></td><td></td><td class="s"> my( $self, $layerwits ) = @_;</td></tr>
+<tr><td class="h"><a name="292"></a>292</td><td></td><td></td><td></td><td></td><td class="s"> # For each 'layered' witness in the layerwits array, add it to the graph</td></tr>
+<tr><td class="h"><a name="293"></a>293</td><td></td><td></td><td></td><td></td><td class="s"> # as an ancestor of the 'main' witness, and otherwise with the same parent/</td></tr>
+<tr><td class="h"><a name="294"></a>294</td><td></td><td></td><td></td><td></td><td class="s"> # child links as its main analogue.</td></tr>
+<tr><td class="h"><a name="295"></a>295</td><td></td><td></td><td></td><td></td><td class="s"> # TOOD Handle case where B is copied from A but corrected from C</td></tr>
+<tr><td class="h"><a name="296"></a>296</td><td></td><td></td><td></td><td></td><td class="s"> </td></tr>
+<tr><td class="h"><a name="297"></a>297</td><td></td><td></td><td></td><td></td><td class="s"> # Iterate through, adding a.c. witnesses</td></tr>
+<tr><td class="h"><a name="298"></a>298</td><td></td><td></td><td></td><td></td><td class="s"> my $actag = $self->collation->ac_label;</td></tr>
+<tr><td class="h"><a name="299"></a>299</td><td></td><td></td><td></td><td></td><td class="s"> my $graph = $self->graph->copy;</td></tr>
+<tr><td class="h"><a name="300"></a>300</td><td></td><td></td><td></td><td></td><td class="s"> foreach my $lw ( @$layerwits ) {</td></tr>
+<tr><td class="h"><a name="301"></a>301</td><td></td><td></td><td></td><td></td><td class="s"> # Add the layered witness and set it with the same attributes as</td></tr>
+<tr><td class="h"><a name="302"></a>302</td><td></td><td></td><td></td><td></td><td class="s"> # its 'main' analogue</td></tr>
+<tr><td class="h"><a name="303"></a>303</td><td></td><td></td><td></td><td></td><td class="s"> my $lwac = $lw . $self->collation->ac_label;</td></tr>
+<tr><td class="h"><a name="304"></a>304</td><td></td><td></td><td></td><td></td><td class="s"> $graph->add_vertex( $lwac );</td></tr>
+<tr><td class="h"><a name="305"></a>305</td><td></td><td></td><td></td><td></td><td class="s"> $graph->set_vertex_attributes( $lwac,</td></tr>
+<tr><td class="h"><a name="306"></a>306</td><td></td><td></td><td></td><td></td><td class="s"> $graph->get_vertex_attributes( $lw ) );</td></tr>
+<tr><td class="h"><a name="307"></a>307</td><td></td><td></td><td></td><td></td><td class="s"> </td></tr>
+<tr><td class="h"><a name="308"></a>308</td><td></td><td></td><td></td><td></td><td class="s"> # Set it as ancestor to the main witness</td></tr>
+<tr><td class="h"><a name="309"></a>309</td><td></td><td></td><td></td><td></td><td class="s"> $graph->add_edge( $lwac, $lw );</td></tr>
+<tr><td class="h"><a name="310"></a>310</td><td></td><td></td><td></td><td></td><td class="s"> </td></tr>
+<tr><td class="h"><a name="311"></a>311</td><td></td><td></td><td></td><td></td><td class="s"> # Give it the same ancestors and descendants as the main witness has,</td></tr>
+<tr><td class="h"><a name="312"></a>312</td><td></td><td></td><td></td><td></td><td class="s"> # bearing in mind that those ancestors and descendants might also just</td></tr>
+<tr><td class="h"><a name="313"></a>313</td><td></td><td></td><td></td><td></td><td class="s"> # have had a layered witness defined.</td></tr>
+<tr><td class="h"><a name="314"></a>314</td><td></td><td></td><td></td><td></td><td class="s"> foreach my $v ( $graph->predecessors( $lw ) ) {</td></tr>
+<tr><td class="h"><a name="315"></a>315</td><td></td><td></td><td></td><td></td><td class="s"> next if $v eq $lwac; # Don't add a loop</td></tr>
+<tr><td class="h"><a name="316"></a>316</td><td></td><td></td><td></td><td></td><td class="s"> $graph->add_edge( $v, $lwac );</td></tr>
+<tr><td class="h"><a name="317"></a>317</td><td></td><td></td><td></td><td></td><td class="s"> $graph->add_edge( $v.$self->collation->ac_label, $lwac )</td></tr>
+<tr><td class="h"><a name="318"></a>318</td><td></td><td></td><td></td><td></td><td class="s"> if $graph->has_vertex( $v.$self->collation->ac_label );</td></tr>
+<tr><td class="h"><a name="319"></a>319</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr>
+<tr><td class="h"><a name="320"></a>320</td><td></td><td></td><td></td><td></td><td class="s"> foreach my $v ( $graph->successors( $lw ) ) {</td></tr>
+<tr><td class="h"><a name="321"></a>321</td><td></td><td></td><td></td><td></td><td class="s"> next if $v eq $lwac; # but this shouldn't occur</td></tr>
+<tr><td class="h"><a name="322"></a>322</td><td></td><td></td><td></td><td></td><td class="s"> $graph->add_edge( $lwac, $v );</td></tr>
+<tr><td class="h"><a name="323"></a>323</td><td></td><td></td><td></td><td></td><td class="s"> $graph->add_edge( $lwac, $v.$self->collation->ac_label )</td></tr>
+<tr><td class="h"><a name="324"></a>324</td><td></td><td></td><td></td><td></td><td class="s"> if $graph->has_vertex( $v.$self->collation->ac_label );</td></tr>
+<tr><td class="h"><a name="325"></a>325</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr>
+<tr><td class="h"><a name="326"></a>326</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr>
+<tr><td class="h"><a name="327"></a>327</td><td></td><td></td><td></td><td></td><td class="s"> return $graph;</td></tr>
+<tr><td class="h"><a name="328"></a>328</td><td></td><td></td><td></td><td></td><td class="s">}</td></tr>
+<tr><td class="h"><a name="329"></a>329</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="330"></a>330</td><td></td><td></td><td></td><td></td><td class="s">=head2 as_svg</td></tr>
+<tr><td class="h"><a name="331"></a>331</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="332"></a>332</td><td></td><td></td><td></td><td></td><td class="s">Returns an SVG representation of the graph, calling as_dot first.</td></tr>
+<tr><td class="h"><a name="333"></a>333</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="334"></a>334</td><td></td><td></td><td></td><td></td><td class="s">=cut</td></tr>
+<tr><td class="h"><a name="335"></a>335</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="336"></a>336</td><td></td><td></td><td></td><td></td><td class="s">sub as_svg {</td></tr>
+<tr><td class="h"><a name="337"></a>337</td><td></td><td></td><td></td><td></td><td class="s"> my( $self, $opts ) = @_;</td></tr>
+<tr><td class="h"><a name="338"></a>338</td><td></td><td></td><td></td><td></td><td class="s"> my $dot = $self->as_dot( $opts );</td></tr>
+<tr><td class="h"><a name="339"></a>339</td><td></td><td></td><td></td><td></td><td class="s"> my @cmd = qw/dot -Tsvg/;</td></tr>
+<tr><td class="h"><a name="340"></a>340</td><td></td><td></td><td></td><td></td><td class="s"> my $svg;</td></tr>
+<tr><td class="h"><a name="341"></a>341</td><td></td><td></td><td></td><td></td><td class="s"> my $dotfile = File::Temp->new();</td></tr>
+<tr><td class="h"><a name="342"></a>342</td><td></td><td></td><td></td><td></td><td class="s"> ## TODO REMOVE</td></tr>
+<tr><td class="h"><a name="343"></a>343</td><td></td><td></td><td></td><td></td><td class="s"> # $dotfile->unlink_on_destroy(0);</td></tr>
+<tr><td class="h"><a name="344"></a>344</td><td></td><td></td><td></td><td></td><td class="s"> binmode $dotfile, ':utf8';</td></tr>
+<tr><td class="h"><a name="345"></a>345</td><td></td><td></td><td></td><td></td><td class="s"> print $dotfile $dot;</td></tr>
+<tr><td class="h"><a name="346"></a>346</td><td></td><td></td><td></td><td></td><td class="s"> push( @cmd, $dotfile->filename );</td></tr>
+<tr><td class="h"><a name="347"></a>347</td><td></td><td></td><td></td><td></td><td class="s"> run( \@cmd, ">", binary(), \$svg );</td></tr>
+<tr><td class="h"><a name="348"></a>348</td><td></td><td></td><td></td><td></td><td class="s"> # HACK: Parse the SVG and change the dimensions.</td></tr>
+<tr><td class="h"><a name="349"></a>349</td><td></td><td></td><td></td><td></td><td class="s"> # Get rid of width and height attributes to allow scaling.</td></tr>
+<tr><td class="h"><a name="350"></a>350</td><td></td><td></td><td></td><td></td><td class="s"> my $parser = XML::LibXML->new();</td></tr>
+<tr><td class="h"><a name="351"></a>351</td><td></td><td></td><td></td><td></td><td class="s"> my $svgdoc = $parser->parse_string( decode_utf8( $svg ) );</td></tr>
+<tr><td class="h"><a name="352"></a>352</td><td></td><td></td><td></td><td></td><td class="s"> $svgdoc->documentElement->removeAttribute('width');</td></tr>
+<tr><td class="h"><a name="353"></a>353</td><td></td><td></td><td></td><td></td><td class="s"> $svgdoc->documentElement->removeAttribute('height');</td></tr>
+<tr><td class="h"><a name="354"></a>354</td><td></td><td></td><td></td><td></td><td class="s"> # Return the result</td></tr>
+<tr><td class="h"><a name="355"></a>355</td><td></td><td></td><td></td><td></td><td class="s"> return decode_utf8( $svgdoc->toString );</td></tr>
+<tr><td class="h"><a name="356"></a>356</td><td></td><td></td><td></td><td></td><td class="s">}</td></tr>
+<tr><td class="h"><a name="357"></a>357</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="358"></a>358</td><td></td><td></td><td></td><td></td><td class="s">=head2 witnesses</td></tr>
+<tr><td class="h"><a name="359"></a>359</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="360"></a>360</td><td></td><td></td><td></td><td></td><td class="s">Returns a list of the extant witnesses represented in the stemma.</td></tr>
+<tr><td class="h"><a name="361"></a>361</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="362"></a>362</td><td></td><td></td><td></td><td></td><td class="s">=cut</td></tr>
+<tr><td class="h"><a name="363"></a>363</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="364"></a>364</td><td></td><td></td><td></td><td></td><td class="s">sub witnesses {</td></tr>
+<tr><td class="h"><a name="365"></a>365</td><td></td><td></td><td></td><td></td><td class="s"> my $self = shift;</td></tr>
+<tr><td class="h"><a name="366"></a>366</td><td></td><td></td><td></td><td></td><td class="s"> my @wits = grep { $self->graph->get_vertex_attribute( $_, 'class' ) eq 'extant' }</td></tr>
+<tr><td class="h"><a name="367"></a>367</td><td></td><td></td><td></td><td></td><td class="s"> $self->graph->vertices;</td></tr>
+<tr><td class="h"><a name="368"></a>368</td><td></td><td></td><td></td><td></td><td class="s"> return @wits;</td></tr>
+<tr><td class="h"><a name="369"></a>369</td><td></td><td></td><td></td><td></td><td class="s">}</td></tr>
+<tr><td class="h"><a name="370"></a>370</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="371"></a>371</td><td></td><td></td><td></td><td></td><td class="s">=head2 hypotheticals</td></tr>
+<tr><td class="h"><a name="372"></a>372</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="373"></a>373</td><td></td><td></td><td></td><td></td><td class="s">Returns a list of the hypothetical witnesses represented in the stemma.</td></tr>
+<tr><td class="h"><a name="374"></a>374</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="375"></a>375</td><td></td><td></td><td></td><td></td><td class="s">=cut</td></tr>
+<tr><td class="h"><a name="376"></a>376</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="377"></a>377</td><td></td><td></td><td></td><td></td><td class="s">sub hypotheticals {</td></tr>
+<tr><td class="h"><a name="378"></a>378</td><td></td><td></td><td></td><td></td><td class="s"> my $self = shift;</td></tr>
+<tr><td class="h"><a name="379"></a>379</td><td></td><td></td><td></td><td></td><td class="s"> my @wits = grep </td></tr>
+<tr><td class="h"><a name="380"></a>380</td><td></td><td></td><td></td><td></td><td class="s"> { $self->graph->get_vertex_attribute( $_, 'class' ) eq 'hypothetical' }</td></tr>
+<tr><td class="h"><a name="381"></a>381</td><td></td><td></td><td></td><td></td><td class="s"> $self->graph->vertices;</td></tr>
+<tr><td class="h"><a name="382"></a>382</td><td></td><td></td><td></td><td></td><td class="s"> return @wits;</td></tr>
+<tr><td class="h"><a name="383"></a>383</td><td></td><td></td><td></td><td></td><td class="s">}</td></tr>
+<tr><td class="h"><a name="384"></a>384</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="385"></a>385</td><td></td><td></td><td></td><td></td><td class="s">sub throw {</td></tr>
+<tr><td class="h"><a name="386"></a>386</td><td></td><td></td><td></td><td></td><td class="s"> Text::Tradition::Error->throw( </td></tr>
+<tr><td class="h"><a name="387"></a>387</td><td></td><td></td><td></td><td></td><td class="s"> 'ident' => 'Stemma error',</td></tr>
+<tr><td class="h"><a name="388"></a>388</td><td></td><td></td><td></td><td></td><td class="s"> 'message' => $_[0],</td></tr>
+<tr><td class="h"><a name="389"></a>389</td><td></td><td></td><td></td><td></td><td class="s"> );</td></tr>
+<tr><td class="h"><a name="390"></a>390</td><td></td><td></td><td></td><td></td><td class="s">}</td></tr>
+<tr><td class="h"><a name="391"></a>391</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="392"></a>392</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="393"></a>393</td><td class="c3">2</td><td class="c1"><span title="Avg 40µs">80µs</span></td><td class="c3">2</td><td class="c3">380µs</td><td class="s"><div class="calls"><div class="calls_in"># spent 199µs (19+180) within Text::Tradition::Stemma::BEGIN@393 which was called:
+# once (19µs+180µs) by Text::Tradition::BEGIN@7 at <a href="lib-Text-Tradition-Stemma-pm-1135-sub.html#393">line 393</a></div></div>no Moose;<div class="calls"><div class="calls_out"># spent 199µs making 1 call to <a href="lib-Text-Tradition-Stemma-pm-1135-sub.html#393">Text::Tradition::Stemma::BEGIN@393</a>
+# spent 180µs making 1 call to <a href="Moose-Exporter-pm-82-sub.html#670">Moose::Exporter::__ANON__[Moose/Exporter.pm:678]</a></div></div></td></tr>
+<tr><td class="h"><a name="394"></a>394</td><td class="c3">1</td><td class="c3"><span title="Avg 5µs">5µs</span></td><td class="c3">2</td><td class="c2">6.10ms</td><td class="s">__PACKAGE__->meta->make_immutable;<div class="calls"><div class="calls_out"># spent 6.09ms making 1 call to <a href="Class-MOP-Class-pm-103-sub.html#1280">Class::MOP::Class::make_immutable</a>
+# spent 17µs making 1 call to <a href="Class-MOP-Package-pm-122-sub.html#221">Text::Tradition::Stemma::meta</a></div></div></td></tr>
+<tr><td class="h"><a name="395"></a>395</td><td></td><td></td><td></td><td></td><td class="s"> </td></tr>
+<tr><td class="h"><a name="396"></a>396</td><td class="c3">1</td><td class="c3"><span title="Avg 41µs">41µs</span></td><td></td><td></td><td class="s">1;</td></tr>
+<tr><td class="h"><a name="397"></a>397</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="398"></a>398</td><td></td><td></td><td></td><td></td><td class="s">=head1 LICENSE</td></tr>
+<tr><td class="h"><a name="399"></a>399</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="400"></a>400</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="401"></a>401</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="402"></a>402</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="403"></a>403</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="404"></a>404</td><td></td><td></td><td></td><td></td><td class="s">=head1 AUTHOR</td></tr>
+<tr><td class="h"><a name="405"></a>405</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="406"></a>406</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() {
+
+ $("#subs_table").tablesorter({
+ sortList: [[3,1]],
+ headers: {
+ 3: { sorter: 'fmt_time' },
+ 4: { sorter: 'fmt_time' }
+ }
+ });
+
+ } ); </script>
+
+ <div class="footer">Report produced by the
+ <a href="http://search.cpan.org/dist/Devel-NYTProf/">NYTProf 4.06</a>
+ Perl profiler, developed by
+ <a href="http://www.linkedin.com/in/timbunce">Tim Bunce</a> and
+ <a href="http://code.nytimes.com">Adam Kaplan</a>.
+ </div>
+ <br /><br /><br /><br /><br /><br /><br /><br /><br /><br />
+ </body></html>
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projects / scpubgit/stemmatology.git / blobdiff