--- /dev/null
+ <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+ <html xmlns="http://www.w3.org/1999/xhtml">
+<!--
+This file was generated by Devel::NYTProf version 4.06
+-->
+<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/Analysis.pm</title>
+<link rel="stylesheet" type="text/css" href="style.css" />
+ <script type="text/javascript" src="js/jquery-min.js"></script>
+
+ <script type="text/javascript" src="js/jquery-tablesorter-min.js"></script>
+ <link rel="stylesheet" type="text/css" href="js/style-tablesorter.css" />
+ <script type="text/javascript">
+ // 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>
+</head>
+
+<body >
+<div class="header" style="position: relative; overflow-x: hidden; overflow-y: hidden; z-index: 0; ">
+<div class="header_back">
+ <a href="index.html">← Index</a>
+ </div>
+<div class="headerForeground" style="float: left">
+ <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-Analysis-pm-2080-line.html">line view</a></span> • <span class="mode_btn"><a href="lib-Text-Tradition-Analysis-pm-2080-sub.html">sub view</a></span> »</span><br />
+ For script/nytprof.pl
+ </span>
+</div>
+<div class="headerForeground" style="float: right; text-align: right">
+ <span class="siteTitle"> </span>
+ <span class="siteSubtitle">Run on Thu May 31 16:49:15 2012<br />Reported on Thu May 31 16:53:19 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>
+<div style="position: absolute; left: 0px; top: 8%; width: 100%; height: 93%; z-index: -1; background-color: rgb(15, 130, 249); "></div>
+<div style="position: absolute; left: 0px; top: 10%; width: 100%; height: 91%; z-index: -1; background-color: rgb(15, 129, 248); "></div>
+<div style="position: absolute; left: 0px; top: 12%; width: 100%; height: 89%; z-index: -1; background-color: rgb(14, 127, 246); "></div>
+<div style="position: absolute; left: 0px; top: 14%; width: 100%; height: 87%; z-index: -1; background-color: rgb(14, 126, 245); "></div>
+<div style="position: absolute; left: 0px; top: 16%; width: 100%; height: 85%; z-index: -1; background-color: rgb(14, 125, 244); "></div>
+<div style="position: absolute; left: 0px; top: 18%; width: 100%; height: 83%; z-index: -1; background-color: rgb(13, 123, 242); "></div>
+<div style="position: absolute; left: 0px; top: 20%; width: 100%; height: 81%; z-index: -1; background-color: rgb(13, 122, 241); "></div>
+<div style="position: absolute; left: 0px; top: 22%; width: 100%; height: 79%; z-index: -1; background-color: rgb(13, 121, 240); "></div>
+<div style="position: absolute; left: 0px; top: 24%; width: 100%; height: 77%; z-index: -1; background-color: rgb(12, 119, 238); "></div>
+<div style="position: absolute; left: 0px; top: 26%; width: 100%; height: 75%; z-index: -1; background-color: rgb(12, 118, 237); "></div>
+<div style="position: absolute; left: 0px; top: 28%; width: 100%; height: 73%; z-index: -1; background-color: rgb(12, 116, 235); "></div>
+<div style="position: absolute; left: 0px; top: 30%; width: 100%; height: 71%; z-index: -1; background-color: rgb(11, 115, 234); "></div>
+<div style="position: absolute; left: 0px; top: 32%; width: 100%; height: 69%; z-index: -1; background-color: rgb(11, 114, 233); "></div>
+<div style="position: absolute; left: 0px; top: 34%; width: 100%; height: 67%; z-index: -1; background-color: rgb(11, 112, 231); "></div>
+<div style="position: absolute; left: 0px; top: 36%; width: 100%; height: 65%; z-index: -1; background-color: rgb(10, 111, 230); "></div>
+<div style="position: absolute; left: 0px; top: 38%; width: 100%; height: 63%; z-index: -1; background-color: rgb(10, 110, 229); "></div>
+<div style="position: absolute; left: 0px; top: 40%; width: 100%; height: 61%; z-index: -1; background-color: rgb(10, 108, 227); "></div>
+<div style="position: absolute; left: 0px; top: 42%; width: 100%; height: 59%; z-index: -1; background-color: rgb(9, 107, 226); "></div>
+<div style="position: absolute; left: 0px; top: 44%; width: 100%; height: 57%; z-index: -1; background-color: rgb(9, 106, 225); "></div>
+<div style="position: absolute; left: 0px; top: 46%; width: 100%; height: 55%; z-index: -1; background-color: rgb(9, 104, 223); "></div>
+<div style="position: absolute; left: 0px; top: 48%; width: 100%; height: 53%; z-index: -1; background-color: rgb(8, 103, 222); "></div>
+<div style="position: absolute; left: 0px; top: 50%; width: 100%; height: 51%; z-index: -1; background-color: rgb(8, 102, 221); "></div>
+<div style="position: absolute; left: 0px; top: 52%; width: 100%; height: 49%; z-index: -1; background-color: rgb(8, 100, 219); "></div>
+<div style="position: absolute; left: 0px; top: 54%; width: 100%; height: 47%; z-index: -1; background-color: rgb(7, 99, 218); "></div>
+<div style="position: absolute; left: 0px; top: 56%; width: 100%; height: 45%; z-index: -1; background-color: rgb(7, 97, 216); "></div>
+<div style="position: absolute; left: 0px; top: 58%; width: 100%; height: 43%; z-index: -1; background-color: rgb(7, 96, 215); "></div>
+<div style="position: absolute; left: 0px; top: 60%; width: 100%; height: 41%; z-index: -1; background-color: rgb(6, 95, 214); "></div>
+<div style="position: absolute; left: 0px; top: 62%; width: 100%; height: 39%; z-index: -1; background-color: rgb(6, 93, 212); "></div>
+<div style="position: absolute; left: 0px; top: 64%; width: 100%; height: 37%; z-index: -1; background-color: rgb(6, 92, 211); "></div>
+<div style="position: absolute; left: 0px; top: 66%; width: 100%; height: 35%; z-index: -1; background-color: rgb(5, 91, 210); "></div>
+<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/Analysis.pm">/Users/edenc/share/src/stemmatology/stemmaweb/lib/Text/Tradition/Analysis.pm</a></td></tr>
+<tr><td class="h">Statements</td><td align="left">Executed 24 statements in 4.55ms</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%">6.67ms</span></td><td class="c0"><span title="0.0%">14.6ms</span></td><td class="sub_name"><span style="display: none;">Text::Tradition::Analysis::::BEGIN@10</span>Text::Tradition::Analysis::<a href="lib-Text-Tradition-Analysis-pm-2080-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="c0"><span title="0.0%">5.36ms</span></td><td class="c0"><span title="0.0%">5.91ms</span></td><td class="sub_name"><span style="display: none;">Text::Tradition::Analysis::::BEGIN@5</span>Text::Tradition::Analysis::<a href="lib-Text-Tradition-Analysis-pm-2080-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="c0"><span title="0.0%">55µs</span></td><td class="c2"><span title="0.0%">60µs</span></td><td class="sub_name"><span style="display: none;">Text::Tradition::Analysis::::BEGIN@3</span>Text::Tradition::Analysis::<a href="lib-Text-Tradition-Analysis-pm-2080-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="c3"><span title="0.0%">14µs</span></td><td class="c3"><span title="0.0%">18µs</span></td><td class="sub_name"><span style="display: none;">Text::Tradition::Analysis::::BEGIN@8</span>Text::Tradition::Analysis::<a href="lib-Text-Tradition-Analysis-pm-2080-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%">14µs</span></td><td class="c3"><span title="0.0%">55µs</span></td><td class="sub_name"><span style="display: none;">Text::Tradition::Analysis::::BEGIN@6</span>Text::Tradition::Analysis::<a href="lib-Text-Tradition-Analysis-pm-2080-block.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%">14µs</span></td><td class="c0"><span title="0.0%">140µs</span></td><td class="sub_name"><span style="display: none;">Text::Tradition::Analysis::::BEGIN@9</span>Text::Tradition::Analysis::<a href="lib-Text-Tradition-Analysis-pm-2080-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="c3"><span title="0.0%">13µs</span></td><td class="c3"><span title="0.0%">14µs</span></td><td class="sub_name"><span style="display: none;">Text::Tradition::Analysis::::BEGIN@11</span>Text::Tradition::Analysis::<a href="lib-Text-Tradition-Analysis-pm-2080-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="c3"><span title="0.0%">12µs</span></td><td class="c3"><span title="0.0%">23µs</span></td><td class="sub_name"><span style="display: none;">Text::Tradition::Analysis::::BEGIN@4</span>Text::Tradition::Analysis::<a href="lib-Text-Tradition-Analysis-pm-2080-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%">12µs</span></td><td class="c3"><span title="0.0%">22µs</span></td><td class="sub_name"><span style="display: none;">Text::Tradition::Analysis::::BEGIN@7</span>Text::Tradition::Analysis::<a href="lib-Text-Tradition-Analysis-pm-2080-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%">11µs</span></td><td class="c3"><span title="0.0%">12µs</span></td><td class="sub_name"><span style="display: none;">Text::Tradition::Analysis::::BEGIN@12</span>Text::Tradition::Analysis::<a href="lib-Text-Tradition-Analysis-pm-2080-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%">45µs</span></td><td class="sub_name"><span style="display: none;">Text::Tradition::Analysis::::BEGIN@14</span>Text::Tradition::Analysis::<a href="lib-Text-Tradition-Analysis-pm-2080-block.html#14">BEGIN@14</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::Analysis::::__ANON__[lib/Text/Tradition/Analysis.pm:284]</span>Text::Tradition::Analysis::<a href="lib-Text-Tradition-Analysis-pm-2080-block.html#284">__ANON__[lib/Text/Tradition/Analysis.pm:284]</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::Analysis::::_add_to_witlist</span>Text::Tradition::Analysis::<a href="lib-Text-Tradition-Analysis-pm-2080-block.html#310">_add_to_witlist</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::Analysis::::_desanitize_names</span>Text::Tradition::Analysis::<a href="lib-Text-Tradition-Analysis-pm-2080-block.html#516">_desanitize_names</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::Analysis::::_prune_group</span>Text::Tradition::Analysis::<a href="lib-Text-Tradition-Analysis-pm-2080-block.html#837">_prune_group</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::Analysis::::_prune_subtree</span>Text::Tradition::Analysis::<a href="lib-Text-Tradition-Analysis-pm-2080-block.html#855">_prune_subtree</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::Analysis::::_safe_wit_strings</span>Text::Tradition::Analysis::<a href="lib-Text-Tradition-Analysis-pm-2080-block.html#461">_safe_wit_strings</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::Analysis::::_safe_witstr</span>Text::Tradition::Analysis::<a href="lib-Text-Tradition-Analysis-pm-2080-block.html#509">_safe_witstr</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::Analysis::::_solve_variant_location</span>Text::Tradition::Analysis::<a href="lib-Text-Tradition-Analysis-pm-2080-block.html#667">_solve_variant_location</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::Analysis::::_symmdiff</span>Text::Tradition::Analysis::<a href="lib-Text-Tradition-Analysis-pm-2080-block.html#937">_symmdiff</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::Analysis::::_useful_variant</span>Text::Tradition::Analysis::<a href="lib-Text-Tradition-Analysis-pm-2080-block.html#888">_useful_variant</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::Analysis::::add_variant_wit</span>Text::Tradition::Analysis::<a href="lib-Text-Tradition-Analysis-pm-2080-block.html#878">add_variant_wit</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::Analysis::::analyze_location</span>Text::Tradition::Analysis::<a href="lib-Text-Tradition-Analysis-pm-2080-block.html#554">analyze_location</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::Analysis::::group_variants</span>Text::Tradition::Analysis::<a href="lib-Text-Tradition-Analysis-pm-2080-block.html#251">group_variants</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::Analysis::::perl_solver</span>Text::Tradition::Analysis::<a href="lib-Text-Tradition-Analysis-pm-2080-block.html#658">perl_solver</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::Analysis::::run_analysis</span>Text::Tradition::Analysis::<a href="lib-Text-Tradition-Analysis-pm-2080-block.html#137">run_analysis</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::Analysis::::solve_variants</span>Text::Tradition::Analysis::<a href="lib-Text-Tradition-Analysis-pm-2080-block.html#348">solve_variants</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::Analysis::::wit_stringify</span>Text::Tradition::Analysis::<a href="lib-Text-Tradition-Analysis-pm-2080-block.html#922">wit_stringify</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-Analysis-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::Analysis;</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="c3"><span title="Avg 21µs">41µs</span></td><td class="c3">2</td><td class="c3">66µs</td><td class="s"><div class="calls"><div class="calls_in"># spent 60µs (55+6) within Text::Tradition::Analysis::BEGIN@3 which was called:
+# once (55µs+6µs) by stemmaweb::Controller::Root::BEGIN@4 at <a href="lib-Text-Tradition-Analysis-pm-2080-block.html#3">line 3</a></div></div>use strict;<div class="calls"><div class="calls_out"># spent 60µs making 1 call to <a href="lib-Text-Tradition-Analysis-pm-2080-block.html#3">Text::Tradition::Analysis::BEGIN@3</a>
+# spent 6µs 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 18µs">35µs</span></td><td class="c3">2</td><td class="c3">33µs</td><td class="s"><div class="calls"><div class="calls_in"># spent 23µs (12+10) within Text::Tradition::Analysis::BEGIN@4 which was called:
+# once (12µs+10µs) by stemmaweb::Controller::Root::BEGIN@4 at <a href="lib-Text-Tradition-Analysis-pm-2080-block.html#4">line 4</a></div></div>use warnings;<div class="calls"><div class="calls_out"># spent 23µs making 1 call to <a href="lib-Text-Tradition-Analysis-pm-2080-block.html#4">Text::Tradition::Analysis::BEGIN@4</a>
+# spent 10µs 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="c0"><span title="Avg 131µs">262µs</span></td><td class="c3">2</td><td class="c0">6.08ms</td><td class="s"><div class="calls"><div class="calls_in"># spent 5.91ms (5.36+549µs) within Text::Tradition::Analysis::BEGIN@5 which was called:
+# once (5.36ms+549µs) by stemmaweb::Controller::Root::BEGIN@4 at <a href="lib-Text-Tradition-Analysis-pm-2080-block.html#5">line 5</a></div></div>use Benchmark;<div class="calls"><div class="calls_out"># spent 5.91ms making 1 call to <a href="lib-Text-Tradition-Analysis-pm-2080-block.html#5">Text::Tradition::Analysis::BEGIN@5</a>
+# spent 171µs making 1 call to <a href="Benchmark-pm-2081-block.html#460">Benchmark::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 21µs">42µs</span></td><td class="c3">2</td><td class="c2">97µs</td><td class="s"><div class="calls"><div class="calls_in"># spent 55µs (14+41) within Text::Tradition::Analysis::BEGIN@6 which was called:
+# once (14µs+41µs) by stemmaweb::Controller::Root::BEGIN@4 at <a href="lib-Text-Tradition-Analysis-pm-2080-block.html#6">line 6</a></div></div>use Encode qw/ encode_utf8 /;<div class="calls"><div class="calls_out"># spent 55µs making 1 call to <a href="lib-Text-Tradition-Analysis-pm-2080-block.html#6">Text::Tradition::Analysis::BEGIN@6</a>
+# spent 41µs 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="7"></a>7</td><td class="c3">2</td><td class="c3"><span title="Avg 18µs">35µs</span></td><td class="c3">2</td><td class="c3">31µs</td><td class="s"><div class="calls"><div class="calls_in"># spent 22µs (12+9) within Text::Tradition::Analysis::BEGIN@7 which was called:
+# once (12µs+9µs) by stemmaweb::Controller::Root::BEGIN@4 at <a href="lib-Text-Tradition-Analysis-pm-2080-block.html#7">line 7</a></div></div>use Exporter 'import';<div class="calls"><div class="calls_out"># spent 22µs making 1 call to <a href="lib-Text-Tradition-Analysis-pm-2080-block.html#7">Text::Tradition::Analysis::BEGIN@7</a>
+# spent 9µs 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 20µs">40µs</span></td><td class="c3">2</td><td class="c3">22µs</td><td class="s"><div class="calls"><div class="calls_in"># spent 18µs (14+4) within Text::Tradition::Analysis::BEGIN@8 which was called:
+# once (14µs+4µs) by stemmaweb::Controller::Root::BEGIN@4 at <a href="lib-Text-Tradition-Analysis-pm-2080-block.html#8">line 8</a></div></div>use Graph;<div class="calls"><div class="calls_out"># spent 18µs making 1 call to <a href="lib-Text-Tradition-Analysis-pm-2080-block.html#8">Text::Tradition::Analysis::BEGIN@8</a>
+# spent 4µs 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="9"></a>9</td><td class="c3">2</td><td class="c3"><span title="Avg 21µs">42µs</span></td><td class="c3">2</td><td class="c0">267µs</td><td class="s"><div class="calls"><div class="calls_in"># spent 140µs (14+127) within Text::Tradition::Analysis::BEGIN@9 which was called:
+# once (14µs+127µs) by stemmaweb::Controller::Root::BEGIN@4 at <a href="lib-Text-Tradition-Analysis-pm-2080-block.html#9">line 9</a></div></div>use JSON qw/ encode_json decode_json /;<div class="calls"><div class="calls_out"># spent 140µs making 1 call to <a href="lib-Text-Tradition-Analysis-pm-2080-block.html#9">Text::Tradition::Analysis::BEGIN@9</a>
+# spent 127µs making 1 call to <a href="JSON-pm-674-block.html#77">JSON::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 97µs">194µs</span></td><td class="c3">2</td><td class="c0">14.6ms</td><td class="s"><div class="calls"><div class="calls_in"># spent 14.6ms (6.67+7.90) within Text::Tradition::Analysis::BEGIN@10 which was called:
+# once (6.67ms+7.90ms) by stemmaweb::Controller::Root::BEGIN@4 at <a href="lib-Text-Tradition-Analysis-pm-2080-block.html#10">line 10</a></div></div>use LWP::UserAgent;<div class="calls"><div class="calls_out"># spent 14.6ms making 1 call to <a href="lib-Text-Tradition-Analysis-pm-2080-block.html#10">Text::Tradition::Analysis::BEGIN@10</a>
+# spent 4µs 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="11"></a>11</td><td class="c3">2</td><td class="c3"><span title="Avg 14µs">28µs</span></td><td class="c3">2</td><td class="c3">16µs</td><td class="s"><div class="calls"><div class="calls_in"># spent 14µs (13+1) within Text::Tradition::Analysis::BEGIN@11 which was called:
+# once (13µs+1µs) by stemmaweb::Controller::Root::BEGIN@4 at <a href="lib-Text-Tradition-Analysis-pm-2080-block.html#11">line 11</a></div></div>use Text::Tradition;<div class="calls"><div class="calls_out"># spent 14µs making 1 call to <a href="lib-Text-Tradition-Analysis-pm-2080-block.html#11">Text::Tradition::Analysis::BEGIN@11</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="12"></a>12</td><td class="c3">2</td><td class="c3"><span title="Avg 15µs">31µs</span></td><td class="c3">2</td><td class="c3">14µs</td><td class="s"><div class="calls"><div class="calls_in"># spent 12µs (11+1) within Text::Tradition::Analysis::BEGIN@12 which was called:
+# once (11µs+1µs) by stemmaweb::Controller::Root::BEGIN@4 at <a href="lib-Text-Tradition-Analysis-pm-2080-block.html#12">line 12</a></div></div>use Text::Tradition::Stemma;<div class="calls"><div class="calls_out"># spent 12µs making 1 call to <a href="lib-Text-Tradition-Analysis-pm-2080-block.html#12">Text::Tradition::Analysis::BEGIN@12</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="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 class="c3">2</td><td class="c0"><span title="Avg 1.89ms">3.78ms</span></td><td class="c3">2</td><td class="c3">82µs</td><td class="s"><div class="calls"><div class="calls_in"># spent 45µs (9+36) within Text::Tradition::Analysis::BEGIN@14 which was called:
+# once (9µs+36µs) by stemmaweb::Controller::Root::BEGIN@4 at <a href="lib-Text-Tradition-Analysis-pm-2080-block.html#14">line 14</a></div></div>use vars qw/ @EXPORT_OK /;<div class="calls"><div class="calls_out"># spent 45µs making 1 call to <a href="lib-Text-Tradition-Analysis-pm-2080-block.html#14">Text::Tradition::Analysis::BEGIN@14</a>
+# spent 36µs 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="15"></a>15</td><td class="c3">1</td><td class="c3"><span title="Avg 2µs">2µs</span></td><td></td><td></td><td class="s">@EXPORT_OK = qw/ run_analysis group_variants analyze_variant_location wit_stringify /;</td></tr>
+<tr><td class="h"><a name="16"></a>16</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="17"></a>17</td><td></td><td></td><td></td><td></td><td class="s">=head1 NAME</td></tr>
+<tr><td class="h"><a name="18"></a>18</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="19"></a>19</td><td></td><td></td><td></td><td></td><td class="s">Text::Tradition::Analysis - functions for stemma analysis of a tradition</td></tr>
+<tr><td class="h"><a name="20"></a>20</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="21"></a>21</td><td></td><td></td><td></td><td></td><td class="s">=head1 SYNOPSIS</td></tr>
+<tr><td class="h"><a name="22"></a>22</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="23"></a>23</td><td></td><td></td><td></td><td></td><td class="s"> use Text::Tradition;</td></tr>
+<tr><td class="h"><a name="24"></a>24</td><td></td><td></td><td></td><td></td><td class="s"> use Text::Tradition::Analysis qw/ run_analysis analyze_variant_location /;</td></tr>
+<tr><td class="h"><a name="25"></a>25</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="26"></a>26</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="27"></a>27</td><td></td><td></td><td></td><td></td><td class="s"> 'input' => 'TEI',</td></tr>
+<tr><td class="h"><a name="28"></a>28</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="29"></a>29</td><td></td><td></td><td></td><td></td><td class="s"> $t->add_stemma( 'dotfile' => $stemmafile );</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"> my $variant_data = run_analysis( $tradition );</td></tr>
+<tr><td class="h"><a name="32"></a>32</td><td></td><td></td><td></td><td></td><td class="s"> # Recalculate rank $n treating all orthographic variants as equivalent</td></tr>
+<tr><td class="h"><a name="33"></a>33</td><td></td><td></td><td></td><td></td><td class="s"> my $reanalyze = analyze_variant_location( $tradition, $n, 0, 'orthographic' );</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 DESCRIPTION</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">Text::Tradition is a library for representation and analysis of collated</td></tr>
+<tr><td class="h"><a name="38"></a>38</td><td></td><td></td><td></td><td></td><td class="s">texts, particularly medieval ones. The Collation is the central feature of</td></tr>
+<tr><td class="h"><a name="39"></a>39</td><td></td><td></td><td></td><td></td><td class="s">a Tradition, where the text, its sequence of readings, and its relationships</td></tr>
+<tr><td class="h"><a name="40"></a>40</td><td></td><td></td><td></td><td></td><td class="s">between readings are actually kept.</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">=head1 SUBROUTINES</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">=head2 run_analysis( $tradition, %opts )</td></tr>
+<tr><td class="h"><a name="45"></a>45</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="46"></a>46</td><td></td><td></td><td></td><td></td><td class="s">Runs the analysis described in analyze_variant_location on every location in the </td></tr>
+<tr><td class="h"><a name="47"></a>47</td><td></td><td></td><td></td><td></td><td class="s">collation of the given tradition, with the given options. These include:</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">=over 4</td></tr>
+<tr><td class="h"><a name="50"></a>50</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="51"></a>51</td><td></td><td></td><td></td><td></td><td class="s">=item * stemma_id - Specify which of the tradition's stemmata to use. Default</td></tr>
+<tr><td class="h"><a name="52"></a>52</td><td></td><td></td><td></td><td></td><td class="s">is 0 (i.e. the first).</td></tr>
+<tr><td class="h"><a name="53"></a>53</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="54"></a>54</td><td></td><td></td><td></td><td></td><td class="s">=item * ranks - Specify a list of location ranks to analyze; exclude the rest.</td></tr>
+<tr><td class="h"><a name="55"></a>55</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="56"></a>56</td><td></td><td></td><td></td><td></td><td class="s">=item * merge_types - Specify a list of relationship types, where related readings </td></tr>
+<tr><td class="h"><a name="57"></a>57</td><td></td><td></td><td></td><td></td><td class="s">should be treated as identical for the purposes of analysis.</td></tr>
+<tr><td class="h"><a name="58"></a>58</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="59"></a>59</td><td></td><td></td><td></td><td></td><td class="s">=item * exclude_type1 - Exclude those ranks whose groupings have only type-1 variants.</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">=back</td></tr>
+<tr><td class="h"><a name="62"></a>62</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="63"></a>63</td><td></td><td></td><td></td><td></td><td class="s">=begin testing</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">use Text::Tradition;</td></tr>
+<tr><td class="h"><a name="66"></a>66</td><td></td><td></td><td></td><td></td><td class="s">use Text::Tradition::Analysis qw/ run_analysis analyze_variant_location /;</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">my $datafile = 't/data/florilegium_tei_ps.xml';</td></tr>
+<tr><td class="h"><a name="69"></a>69</td><td></td><td></td><td></td><td></td><td class="s">my $tradition = Text::Tradition->new( 'input' => 'TEI',</td></tr>
+<tr><td class="h"><a name="70"></a>70</td><td></td><td></td><td></td><td></td><td class="s"> 'name' => 'test0',</td></tr>
+<tr><td class="h"><a name="71"></a>71</td><td></td><td></td><td></td><td></td><td class="s"> 'file' => $datafile );</td></tr>
+<tr><td class="h"><a name="72"></a>72</td><td></td><td></td><td></td><td></td><td class="s">my $s = $tradition->add_stemma( 'dotfile' => 't/data/florilegium.dot' );</td></tr>
+<tr><td class="h"><a name="73"></a>73</td><td></td><td></td><td></td><td></td><td class="s">is( ref( $s ), 'Text::Tradition::Stemma', "Added stemma to tradition" );</td></tr>
+<tr><td class="h"><a name="74"></a>74</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="75"></a>75</td><td></td><td></td><td></td><td></td><td class="s">my %expected_genealogical = (</td></tr>
+<tr><td class="h"><a name="76"></a>76</td><td></td><td></td><td></td><td></td><td class="s"> 1 => 0,</td></tr>
+<tr><td class="h"><a name="77"></a>77</td><td></td><td></td><td></td><td></td><td class="s"> 2 => 1,</td></tr>
+<tr><td class="h"><a name="78"></a>78</td><td></td><td></td><td></td><td></td><td class="s"> 3 => 0,</td></tr>
+<tr><td class="h"><a name="79"></a>79</td><td></td><td></td><td></td><td></td><td class="s"> 5 => 0,</td></tr>
+<tr><td class="h"><a name="80"></a>80</td><td></td><td></td><td></td><td></td><td class="s"> 7 => 0,</td></tr>
+<tr><td class="h"><a name="81"></a>81</td><td></td><td></td><td></td><td></td><td class="s"> 8 => 0,</td></tr>
+<tr><td class="h"><a name="82"></a>82</td><td></td><td></td><td></td><td></td><td class="s"> 10 => 0,</td></tr>
+<tr><td class="h"><a name="83"></a>83</td><td></td><td></td><td></td><td></td><td class="s"> 13 => 1,</td></tr>
+<tr><td class="h"><a name="84"></a>84</td><td></td><td></td><td></td><td></td><td class="s"> 33 => 0,</td></tr>
+<tr><td class="h"><a name="85"></a>85</td><td></td><td></td><td></td><td></td><td class="s"> 34 => 0,</td></tr>
+<tr><td class="h"><a name="86"></a>86</td><td></td><td></td><td></td><td></td><td class="s"> 37 => 0,</td></tr>
+<tr><td class="h"><a name="87"></a>87</td><td></td><td></td><td></td><td></td><td class="s"> 60 => 0,</td></tr>
+<tr><td class="h"><a name="88"></a>88</td><td></td><td></td><td></td><td></td><td class="s"> 81 => 1,</td></tr>
+<tr><td class="h"><a name="89"></a>89</td><td></td><td></td><td></td><td></td><td class="s"> 84 => 0,</td></tr>
+<tr><td class="h"><a name="90"></a>90</td><td></td><td></td><td></td><td></td><td class="s"> 87 => 0,</td></tr>
+<tr><td class="h"><a name="91"></a>91</td><td></td><td></td><td></td><td></td><td class="s"> 101 => 0,</td></tr>
+<tr><td class="h"><a name="92"></a>92</td><td></td><td></td><td></td><td></td><td class="s"> 102 => 0,</td></tr>
+<tr><td class="h"><a name="93"></a>93</td><td></td><td></td><td></td><td></td><td class="s"> 122 => 1,</td></tr>
+<tr><td class="h"><a name="94"></a>94</td><td></td><td></td><td></td><td></td><td class="s"> 157 => 0,</td></tr>
+<tr><td class="h"><a name="95"></a>95</td><td></td><td></td><td></td><td></td><td class="s"> 166 => 1,</td></tr>
+<tr><td class="h"><a name="96"></a>96</td><td></td><td></td><td></td><td></td><td class="s"> 169 => 1,</td></tr>
+<tr><td class="h"><a name="97"></a>97</td><td></td><td></td><td></td><td></td><td class="s"> 200 => 0,</td></tr>
+<tr><td class="h"><a name="98"></a>98</td><td></td><td></td><td></td><td></td><td class="s"> 216 => 1,</td></tr>
+<tr><td class="h"><a name="99"></a>99</td><td></td><td></td><td></td><td></td><td class="s"> 217 => 1,</td></tr>
+<tr><td class="h"><a name="100"></a>100</td><td></td><td></td><td></td><td></td><td class="s"> 219 => 1,</td></tr>
+<tr><td class="h"><a name="101"></a>101</td><td></td><td></td><td></td><td></td><td class="s"> 241 => 1,</td></tr>
+<tr><td class="h"><a name="102"></a>102</td><td></td><td></td><td></td><td></td><td class="s"> 242 => 1,</td></tr>
+<tr><td class="h"><a name="103"></a>103</td><td></td><td></td><td></td><td></td><td class="s"> 243 => 1,</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></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="106"></a>106</td><td></td><td></td><td></td><td></td><td class="s">my $data = run_analysis( $tradition );</td></tr>
+<tr><td class="h"><a name="107"></a>107</td><td></td><td></td><td></td><td></td><td class="s">my $c = $tradition->collation;</td></tr>
+<tr><td class="h"><a name="108"></a>108</td><td></td><td></td><td></td><td></td><td class="s">foreach my $row ( @{$data->{'variants'}} ) {</td></tr>
+<tr><td class="h"><a name="109"></a>109</td><td></td><td></td><td></td><td></td><td class="s"> # Account for rows that used to be "not useful"</td></tr>
+<tr><td class="h"><a name="110"></a>110</td><td></td><td></td><td></td><td></td><td class="s"> unless( exists $expected_genealogical{$row->{'id'}} ) {</td></tr>
+<tr><td class="h"><a name="111"></a>111</td><td></td><td></td><td></td><td></td><td class="s"> $expected_genealogical{$row->{'id'}} = 1;</td></tr>
+<tr><td class="h"><a name="112"></a>112</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr>
+<tr><td class="h"><a name="113"></a>113</td><td></td><td></td><td></td><td></td><td class="s"> my $gen_bool = $row->{'genealogical'} ? 1 : 0;</td></tr>
+<tr><td class="h"><a name="114"></a>114</td><td></td><td></td><td></td><td></td><td class="s"> is( $gen_bool, $expected_genealogical{$row->{'id'}}, </td></tr>
+<tr><td class="h"><a name="115"></a>115</td><td></td><td></td><td></td><td></td><td class="s"> "Got correct genealogical flag for row " . $row->{'id'} );</td></tr>
+<tr><td class="h"><a name="116"></a>116</td><td></td><td></td><td></td><td></td><td class="s"> # Check that we have the right row with the right groups</td></tr>
+<tr><td class="h"><a name="117"></a>117</td><td></td><td></td><td></td><td></td><td class="s"> my $rank = $row->{'id'};</td></tr>
+<tr><td class="h"><a name="118"></a>118</td><td></td><td></td><td></td><td></td><td class="s"> foreach my $rdghash ( @{$row->{'readings'}} ) {</td></tr>
+<tr><td class="h"><a name="119"></a>119</td><td></td><td></td><td></td><td></td><td class="s"> # Skip 'readings' that aren't really</td></tr>
+<tr><td class="h"><a name="120"></a>120</td><td></td><td></td><td></td><td></td><td class="s"> next unless $c->reading( $rdghash->{'readingid'} );</td></tr>
+<tr><td class="h"><a name="121"></a>121</td><td></td><td></td><td></td><td></td><td class="s"> # Check the rank</td></tr>
+<tr><td class="h"><a name="122"></a>122</td><td></td><td></td><td></td><td></td><td class="s"> is( $c->reading( $rdghash->{'readingid'} )->rank, $rank, </td></tr>
+<tr><td class="h"><a name="123"></a>123</td><td></td><td></td><td></td><td></td><td class="s"> "Got correct reading rank" );</td></tr>
+<tr><td class="h"><a name="124"></a>124</td><td></td><td></td><td></td><td></td><td class="s"> # Check the witnesses</td></tr>
+<tr><td class="h"><a name="125"></a>125</td><td></td><td></td><td></td><td></td><td class="s"> my @realwits = sort $c->reading_witnesses( $rdghash->{'readingid'} );</td></tr>
+<tr><td class="h"><a name="126"></a>126</td><td></td><td></td><td></td><td></td><td class="s"> my @sgrp = sort @{$rdghash->{'group'}};</td></tr>
+<tr><td class="h"><a name="127"></a>127</td><td></td><td></td><td></td><td></td><td class="s"> is_deeply( \@sgrp, \@realwits, "Reading analyzed with correct groups" );</td></tr>
+<tr><td class="h"><a name="128"></a>128</td><td></td><td></td><td></td><td></td><td class="s"> }</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">is( $data->{'variant_count'}, 58, "Got right total variant number" );</td></tr>
+<tr><td class="h"><a name="131"></a>131</td><td></td><td></td><td></td><td></td><td class="s"># TODO Make something meaningful of conflict count, maybe test other bits</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">=end testing</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">=cut</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">sub run_analysis {</td></tr>
+<tr><td class="h"><a name="138"></a>138</td><td></td><td></td><td></td><td></td><td class="s"> my( $tradition, %opts ) = @_;</td></tr>
+<tr><td class="h"><a name="139"></a>139</td><td></td><td></td><td></td><td></td><td class="s"> my $c = $tradition->collation;</td></tr>
+<tr><td class="h"><a name="140"></a>140</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="141"></a>141</td><td></td><td></td><td></td><td></td><td class="s"> my $stemma_id = $opts{'stemma_id'} || 0;</td></tr>
+<tr><td class="h"><a name="142"></a>142</td><td></td><td></td><td></td><td></td><td class="s"> my @ranks = ref( $opts{'ranks'} ) eq 'ARRAY' ? @{$opts{'ranks'}} : ();</td></tr>
+<tr><td class="h"><a name="143"></a>143</td><td></td><td></td><td></td><td></td><td class="s"> my @collapse = ref( $opts{'merge_types'} ) eq 'ARRAY' ? @{$opts{'merge_types'}} : ();</td></tr>
+<tr><td class="h"><a name="144"></a>144</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="145"></a>145</td><td></td><td></td><td></td><td></td><td class="s"> # Get the stemma </td></tr>
+<tr><td class="h"><a name="146"></a>146</td><td></td><td></td><td></td><td></td><td class="s"> my $stemma = $tradition->stemma( $stemma_id );</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"> # Figure out which witnesses we are working with - that is, the ones that</td></tr>
+<tr><td class="h"><a name="149"></a>149</td><td></td><td></td><td></td><td></td><td class="s"> # appear both in the stemma and in the tradition. All others are 'lacunose'</td></tr>
+<tr><td class="h"><a name="150"></a>150</td><td></td><td></td><td></td><td></td><td class="s"> # for our purposes.</td></tr>
+<tr><td class="h"><a name="151"></a>151</td><td></td><td></td><td></td><td></td><td class="s"> my @lacunose = $stemma->hypotheticals;</td></tr>
+<tr><td class="h"><a name="152"></a>152</td><td></td><td></td><td></td><td></td><td class="s"> my @tradition_wits = map { $_->sigil } $tradition->witnesses;</td></tr>
+<tr><td class="h"><a name="153"></a>153</td><td></td><td></td><td></td><td></td><td class="s"> push( @lacunose, _symmdiff( [ $stemma->witnesses ], \@tradition_wits ) );</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"> # Find and mark 'common' ranks for exclusion, unless they were</td></tr>
+<tr><td class="h"><a name="156"></a>156</td><td></td><td></td><td></td><td></td><td class="s"> # explicitly specified.</td></tr>
+<tr><td class="h"><a name="157"></a>157</td><td></td><td></td><td></td><td></td><td class="s"> unless( @ranks ) {</td></tr>
+<tr><td class="h"><a name="158"></a>158</td><td></td><td></td><td></td><td></td><td class="s"> my %common_rank;</td></tr>
+<tr><td class="h"><a name="159"></a>159</td><td></td><td></td><td></td><td></td><td class="s"> foreach my $rdg ( $c->common_readings ) {</td></tr>
+<tr><td class="h"><a name="160"></a>160</td><td></td><td></td><td></td><td></td><td class="s"> $common_rank{$rdg->rank} = 1;</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"> @ranks = grep { !$common_rank{$_} } ( 1 .. $c->end->rank-1 );</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"> # Group the variants to send to the solver</td></tr>
+<tr><td class="h"><a name="166"></a>166</td><td></td><td></td><td></td><td></td><td class="s"> my @groups;</td></tr>
+<tr><td class="h"><a name="167"></a>167</td><td></td><td></td><td></td><td></td><td class="s"> my @use_ranks;</td></tr>
+<tr><td class="h"><a name="168"></a>168</td><td></td><td></td><td></td><td></td><td class="s"> my %lacunae;</td></tr>
+<tr><td class="h"><a name="169"></a>169</td><td></td><td></td><td></td><td></td><td class="s"> foreach my $rank ( @ranks ) {</td></tr>
+<tr><td class="h"><a name="170"></a>170</td><td></td><td></td><td></td><td></td><td class="s"> my $missing = [ @lacunose ];</td></tr>
+<tr><td class="h"><a name="171"></a>171</td><td></td><td></td><td></td><td></td><td class="s"> my $rankgroup = group_variants( $tradition, $rank, $missing, \@collapse );</td></tr>
+<tr><td class="h"><a name="172"></a>172</td><td></td><td></td><td></td><td></td><td class="s"> if( $opts{'exclude_type1'} ) {</td></tr>
+<tr><td class="h"><a name="173"></a>173</td><td></td><td></td><td></td><td></td><td class="s"> # Check to see whether this is a "useful" group.</td></tr>
+<tr><td class="h"><a name="174"></a>174</td><td></td><td></td><td></td><td></td><td class="s"> my( $rdgs, $grps ) = _useful_variant( $rankgroup, </td></tr>
+<tr><td class="h"><a name="175"></a>175</td><td></td><td></td><td></td><td></td><td class="s"> $stemma->graph, $c->ac_label );</td></tr>
+<tr><td class="h"><a name="176"></a>176</td><td></td><td></td><td></td><td></td><td class="s"> next unless @$rdgs;</td></tr>
+<tr><td class="h"><a name="177"></a>177</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr>
+<tr><td class="h"><a name="178"></a>178</td><td></td><td></td><td></td><td></td><td class="s"> push( @use_ranks, $rank );</td></tr>
+<tr><td class="h"><a name="179"></a>179</td><td></td><td></td><td></td><td></td><td class="s"> push( @groups, $rankgroup );</td></tr>
+<tr><td class="h"><a name="180"></a>180</td><td></td><td></td><td></td><td></td><td class="s"> $lacunae{$rank} = $missing;</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"> # Run the solver</td></tr>
+<tr><td class="h"><a name="183"></a>183</td><td></td><td></td><td></td><td></td><td class="s"> my $answer = solve_variants( $stemma, @groups );</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"> # Do further analysis on the answer</td></tr>
+<tr><td class="h"><a name="186"></a>186</td><td></td><td></td><td></td><td></td><td class="s"> my $conflict_count = 0;</td></tr>
+<tr><td class="h"><a name="187"></a>187</td><td></td><td></td><td></td><td></td><td class="s"> my $aclabel = $c->ac_label;</td></tr>
+<tr><td class="h"><a name="188"></a>188</td><td></td><td></td><td></td><td></td><td class="s"> foreach my $idx ( 0 .. $#use_ranks ) {</td></tr>
+<tr><td class="h"><a name="189"></a>189</td><td></td><td></td><td></td><td></td><td class="s"> my $location = $answer->{'variants'}->[$idx];</td></tr>
+<tr><td class="h"><a name="190"></a>190</td><td></td><td></td><td></td><td></td><td class="s"> # Add the rank back in</td></tr>
+<tr><td class="h"><a name="191"></a>191</td><td></td><td></td><td></td><td></td><td class="s"> $location->{'id'} = $use_ranks[$idx];</td></tr>
+<tr><td class="h"><a name="192"></a>192</td><td></td><td></td><td></td><td></td><td class="s"> # Note what our lacunae are</td></tr>
+<tr><td class="h"><a name="193"></a>193</td><td></td><td></td><td></td><td></td><td class="s"> my %lmiss;</td></tr>
+<tr><td class="h"><a name="194"></a>194</td><td></td><td></td><td></td><td></td><td class="s"> map { $lmiss{$_} = 1 } @{$lacunae{$use_ranks[$idx]}};</td></tr>
+<tr><td class="h"><a name="195"></a>195</td><td></td><td></td><td></td><td></td><td class="s"> # Run through the reading groups and add as 'lacunae' any redundant</td></tr>
+<tr><td class="h"><a name="196"></a>196</td><td></td><td></td><td></td><td></td><td class="s"> # a.c. witnesses (yes, we have to do this before the analysis, thus</td></tr>
+<tr><td class="h"><a name="197"></a>197</td><td></td><td></td><td></td><td></td><td class="s"> # identical loops before and after. Boo.)</td></tr>
+<tr><td class="h"><a name="198"></a>198</td><td></td><td></td><td></td><td></td><td class="s"> # TODO Consider making these callbacks to analyze_location</td></tr>
+<tr><td class="h"><a name="199"></a>199</td><td></td><td></td><td></td><td></td><td class="s"> foreach my $rdghash ( @{$location->{'readings'}} ) {</td></tr>
+<tr><td class="h"><a name="200"></a>200</td><td></td><td></td><td></td><td></td><td class="s"> my %rwits;</td></tr>
+<tr><td class="h"><a name="201"></a>201</td><td></td><td></td><td></td><td></td><td class="s"> map { $rwits{$_} = 1 } @{$rdghash->{'group'}};</td></tr>
+<tr><td class="h"><a name="202"></a>202</td><td></td><td></td><td></td><td></td><td class="s"> foreach my $rw ( keys %rwits ) {</td></tr>
+<tr><td class="h"><a name="203"></a>203</td><td></td><td></td><td></td><td></td><td class="s"> if( $rw =~ /^(.*)\Q$aclabel\E$/ ) {</td></tr>
+<tr><td class="h"><a name="204"></a>204</td><td></td><td></td><td></td><td></td><td class="s"> if( exists $rwits{$1} ) {</td></tr>
+<tr><td class="h"><a name="205"></a>205</td><td></td><td></td><td></td><td></td><td class="s"> $lmiss{$rw} = 1;</td></tr>
+<tr><td class="h"><a name="206"></a>206</td><td></td><td></td><td></td><td></td><td class="s"> delete $rwits{$rw};</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"> }</td></tr>
+<tr><td class="h"><a name="209"></a>209</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr>
+<tr><td class="h"><a name="210"></a>210</td><td></td><td></td><td></td><td></td><td class="s"> $rdghash->{'group'} = [ keys %rwits ];</td></tr>
+<tr><td class="h"><a name="211"></a>211</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr>
+<tr><td class="h"><a name="212"></a>212</td><td></td><td></td><td></td><td></td><td class="s"> $location->{'missing'} = [ keys %lmiss ];</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"> # Run the extra analysis we need.</td></tr>
+<tr><td class="h"><a name="215"></a>215</td><td></td><td></td><td></td><td></td><td class="s"> analyze_location( $tradition, $stemma->graph, $location );</td></tr>
+<tr><td class="h"><a name="216"></a>216</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="217"></a>217</td><td></td><td></td><td></td><td></td><td class="s"> # Do the final post-analysis tidying up of the data.</td></tr>
+<tr><td class="h"><a name="218"></a>218</td><td></td><td></td><td></td><td></td><td class="s"> foreach my $rdghash ( @{$location->{'readings'}} ) {</td></tr>
+<tr><td class="h"><a name="219"></a>219</td><td></td><td></td><td></td><td></td><td class="s"> $conflict_count++ </td></tr>
+<tr><td class="h"><a name="220"></a>220</td><td></td><td></td><td></td><td></td><td class="s"> if exists $rdghash->{'conflict'} && $rdghash->{'conflict'};</td></tr>
+<tr><td class="h"><a name="221"></a>221</td><td></td><td></td><td></td><td></td><td class="s"> # Add the reading text back in</td></tr>
+<tr><td class="h"><a name="222"></a>222</td><td></td><td></td><td></td><td></td><td class="s"> my $rdg = $c->reading( $rdghash->{'readingid'} );</td></tr>
+<tr><td class="h"><a name="223"></a>223</td><td></td><td></td><td></td><td></td><td class="s"> $rdghash->{'text'} = $rdg ? $rdg->text : $rdghash->{'readingid'};</td></tr>
+<tr><td class="h"><a name="224"></a>224</td><td></td><td></td><td></td><td></td><td class="s"> # Remove lacunose witnesses from this reading's list now that the</td></tr>
+<tr><td class="h"><a name="225"></a>225</td><td></td><td></td><td></td><td></td><td class="s"> # analysis is done </td></tr>
+<tr><td class="h"><a name="226"></a>226</td><td></td><td></td><td></td><td></td><td class="s"> my @realgroup;</td></tr>
+<tr><td class="h"><a name="227"></a>227</td><td></td><td></td><td></td><td></td><td class="s"> map { push( @realgroup, $_ ) unless $lmiss{$_} } @{$rdghash->{'group'}};</td></tr>
+<tr><td class="h"><a name="228"></a>228</td><td></td><td></td><td></td><td></td><td class="s"> $rdghash->{'group'} = \@realgroup;</td></tr>
+<tr><td class="h"><a name="229"></a>229</td><td></td><td></td><td></td><td></td><td class="s"> # TODO Record hypotheticals used to create group, if we end up</td></tr>
+<tr><td class="h"><a name="230"></a>230</td><td></td><td></td><td></td><td></td><td class="s"> # needing it</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"> $answer->{'conflict_count'} = $conflict_count;</td></tr>
+<tr><td class="h"><a name="234"></a>234</td><td></td><td></td><td></td><td></td><td class="s"> </td></tr>
+<tr><td class="h"><a name="235"></a>235</td><td></td><td></td><td></td><td></td><td class="s"> return $answer;</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"></td></tr>
+<tr><td class="h"><a name="238"></a>238</td><td></td><td></td><td></td><td></td><td class="s">=head2 group_variants( $tradition, $rank, $lacunose, @merge_relationship_types )</td></tr>
+<tr><td class="h"><a name="239"></a>239</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="240"></a>240</td><td></td><td></td><td></td><td></td><td class="s">Groups the variants at the given $rank of the collation, treating any</td></tr>
+<tr><td class="h"><a name="241"></a>241</td><td></td><td></td><td></td><td></td><td class="s">relationships in @merge_relationship_types as equivalent. $lacunose should</td></tr>
+<tr><td class="h"><a name="242"></a>242</td><td></td><td></td><td></td><td></td><td class="s">be a reference to an array, to which the sigla of lacunose witnesses at this </td></tr>
+<tr><td class="h"><a name="243"></a>243</td><td></td><td></td><td></td><td></td><td class="s">rank will be appended.</td></tr>
+<tr><td class="h"><a name="244"></a>244</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="245"></a>245</td><td></td><td></td><td></td><td></td><td class="s">Returns a hash $group_readings where $rdg is attested by the witnesses listed </td></tr>
+<tr><td class="h"><a name="246"></a>246</td><td></td><td></td><td></td><td></td><td class="s">in $group_readings->{$rdg}.</td></tr>
+<tr><td class="h"><a name="247"></a>247</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="248"></a>248</td><td></td><td></td><td></td><td></td><td class="s">=cut</td></tr>
+<tr><td class="h"><a name="249"></a>249</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="250"></a>250</td><td></td><td></td><td></td><td></td><td class="s"># Return group_readings, groups, lacunose</td></tr>
+<tr><td class="h"><a name="251"></a>251</td><td></td><td></td><td></td><td></td><td class="s">sub group_variants {</td></tr>
+<tr><td class="h"><a name="252"></a>252</td><td></td><td></td><td></td><td></td><td class="s"> my( $tradition, $rank, $lacunose, $collapse ) = @_;</td></tr>
+<tr><td class="h"><a name="253"></a>253</td><td></td><td></td><td></td><td></td><td class="s"> my $c = $tradition->collation;</td></tr>
+<tr><td class="h"><a name="254"></a>254</td><td></td><td></td><td></td><td></td><td class="s"> my $aclabel = $c->ac_label;</td></tr>
+<tr><td class="h"><a name="255"></a>255</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="256"></a>256</td><td></td><td></td><td></td><td></td><td class="s"> # Get the alignment table readings</td></tr>
+<tr><td class="h"><a name="257"></a>257</td><td></td><td></td><td></td><td></td><td class="s"> my %readings_at_rank;</td></tr>
+<tr><td class="h"><a name="258"></a>258</td><td></td><td></td><td></td><td></td><td class="s"> my %is_lacunose; # lookup table for $lacunose</td></tr>
+<tr><td class="h"><a name="259"></a>259</td><td></td><td></td><td></td><td></td><td class="s"> map { $is_lacunose{$_} = 1 } @$lacunose;</td></tr>
+<tr><td class="h"><a name="260"></a>260</td><td></td><td></td><td></td><td></td><td class="s"> my @gap_wits;</td></tr>
+<tr><td class="h"><a name="261"></a>261</td><td></td><td></td><td></td><td></td><td class="s"> foreach my $tablewit ( @{$c->alignment_table->{'alignment'}} ) {</td></tr>
+<tr><td class="h"><a name="262"></a>262</td><td></td><td></td><td></td><td></td><td class="s"> my $rdg = $tablewit->{'tokens'}->[$rank-1];</td></tr>
+<tr><td class="h"><a name="263"></a>263</td><td></td><td></td><td></td><td></td><td class="s"> my $wit = $tablewit->{'witness'};</td></tr>
+<tr><td class="h"><a name="264"></a>264</td><td></td><td></td><td></td><td></td><td class="s"> # Exclude the witness if it is "lacunose" which if we got here</td></tr>
+<tr><td class="h"><a name="265"></a>265</td><td></td><td></td><td></td><td></td><td class="s"> # means "not in the stemma".</td></tr>
+<tr><td class="h"><a name="266"></a>266</td><td></td><td></td><td></td><td></td><td class="s"> next if $is_lacunose{$wit};</td></tr>
+<tr><td class="h"><a name="267"></a>267</td><td></td><td></td><td></td><td></td><td class="s"> if( $rdg && $rdg->{'t'}->is_lacuna ) {</td></tr>
+<tr><td class="h"><a name="268"></a>268</td><td></td><td></td><td></td><td></td><td class="s"> _add_to_witlist( $wit, $lacunose, $aclabel );</td></tr>
+<tr><td class="h"><a name="269"></a>269</td><td></td><td></td><td></td><td></td><td class="s"> } elsif( $rdg ) {</td></tr>
+<tr><td class="h"><a name="270"></a>270</td><td></td><td></td><td></td><td></td><td class="s"> $readings_at_rank{$rdg->{'t'}->text} = $rdg->{'t'};</td></tr>
+<tr><td class="h"><a name="271"></a>271</td><td></td><td></td><td></td><td></td><td class="s"> } else {</td></tr>
+<tr><td class="h"><a name="272"></a>272</td><td></td><td></td><td></td><td></td><td class="s"> _add_to_witlist( $wit, \@gap_wits, $aclabel );</td></tr>
+<tr><td class="h"><a name="273"></a>273</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr>
+<tr><td class="h"><a name="274"></a>274</td><td></td><td></td><td></td><td></td><td class="s"> }</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"> # Group the readings, collapsing groups by relationship if needed</td></tr>
+<tr><td class="h"><a name="277"></a>277</td><td></td><td></td><td></td><td></td><td class="s"> my %grouped_readings;</td></tr>
+<tr><td class="h"><a name="278"></a>278</td><td></td><td></td><td></td><td></td><td class="s"> foreach my $rdg ( values %readings_at_rank ) {</td></tr>
+<tr><td class="h"><a name="279"></a>279</td><td></td><td></td><td></td><td></td><td class="s"> # Skip readings that have been collapsed into others.</td></tr>
+<tr><td class="h"><a name="280"></a>280</td><td></td><td></td><td></td><td></td><td class="s"> next if exists $grouped_readings{$rdg->id} && !$grouped_readings{$rdg->id};</td></tr>
+<tr><td class="h"><a name="281"></a>281</td><td></td><td></td><td></td><td></td><td class="s"> # Get the witness list, including from readings collapsed into this one.</td></tr>
+<tr><td class="h"><a name="282"></a>282</td><td></td><td></td><td></td><td></td><td class="s"> my @wits = $rdg->witnesses;</td></tr>
+<tr><td class="h"><a name="283"></a>283</td><td></td><td></td><td></td><td></td><td class="s"> if( $collapse ) {</td></tr>
+<tr><td class="h"><a name="284"></a>284</td><td></td><td></td><td></td><td></td><td class="s"> my $filter = sub { my $r = $_[0]; grep { $_ eq $r->type } @$collapse; };</td></tr>
+<tr><td class="h"><a name="285"></a>285</td><td></td><td></td><td></td><td></td><td class="s"> foreach my $other ( $rdg->related_readings( $filter ) ) {</td></tr>
+<tr><td class="h"><a name="286"></a>286</td><td></td><td></td><td></td><td></td><td class="s"> my @otherwits = $other->witnesses;</td></tr>
+<tr><td class="h"><a name="287"></a>287</td><td></td><td></td><td></td><td></td><td class="s"> push( @wits, @otherwits );</td></tr>
+<tr><td class="h"><a name="288"></a>288</td><td></td><td></td><td></td><td></td><td class="s"> $grouped_readings{$other->id} = 0;</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"> }</td></tr>
+<tr><td class="h"><a name="291"></a>291</td><td></td><td></td><td></td><td></td><td class="s"> # Filter the group to those witnesses in the stemma</td></tr>
+<tr><td class="h"><a name="292"></a>292</td><td></td><td></td><td></td><td></td><td class="s"> my @use_wits;</td></tr>
+<tr><td class="h"><a name="293"></a>293</td><td></td><td></td><td></td><td></td><td class="s"> foreach my $wit ( @wits ) {</td></tr>
+<tr><td class="h"><a name="294"></a>294</td><td></td><td></td><td></td><td></td><td class="s"> next if $is_lacunose{$wit};</td></tr>
+<tr><td class="h"><a name="295"></a>295</td><td></td><td></td><td></td><td></td><td class="s"> push( @use_wits, $wit );</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"> $grouped_readings{$rdg->id} = \@use_wits; </td></tr>
+<tr><td class="h"><a name="298"></a>298</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr>
+<tr><td class="h"><a name="299"></a>299</td><td></td><td></td><td></td><td></td><td class="s"> $grouped_readings{'(omitted)'} = \@gap_wits if @gap_wits;</td></tr>
+<tr><td class="h"><a name="300"></a>300</td><td></td><td></td><td></td><td></td><td class="s"> # Get rid of our collapsed readings</td></tr>
+<tr><td class="h"><a name="301"></a>301</td><td></td><td></td><td></td><td></td><td class="s"> map { delete $grouped_readings{$_} unless $grouped_readings{$_} } </td></tr>
+<tr><td class="h"><a name="302"></a>302</td><td></td><td></td><td></td><td></td><td class="s"> keys %grouped_readings </td></tr>
+<tr><td class="h"><a name="303"></a>303</td><td></td><td></td><td></td><td></td><td class="s"> if $collapse;</td></tr>
+<tr><td class="h"><a name="304"></a>304</td><td></td><td></td><td></td><td></td><td class="s"> </td></tr>
+<tr><td class="h"><a name="305"></a>305</td><td></td><td></td><td></td><td></td><td class="s"> # Return the result</td></tr>
+<tr><td class="h"><a name="306"></a>306</td><td></td><td></td><td></td><td></td><td class="s"> return \%grouped_readings;</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"></td></tr>
+<tr><td class="h"><a name="309"></a>309</td><td></td><td></td><td></td><td></td><td class="s"># Helper function to ensure that X and X a.c. never appear in the same list.</td></tr>
+<tr><td class="h"><a name="310"></a>310</td><td></td><td></td><td></td><td></td><td class="s">sub _add_to_witlist {</td></tr>
+<tr><td class="h"><a name="311"></a>311</td><td></td><td></td><td></td><td></td><td class="s"> my( $wit, $list, $acstr ) = @_;</td></tr>
+<tr><td class="h"><a name="312"></a>312</td><td></td><td></td><td></td><td></td><td class="s"> my %inlist;</td></tr>
+<tr><td class="h"><a name="313"></a>313</td><td></td><td></td><td></td><td></td><td class="s"> my $idx = 0;</td></tr>
+<tr><td class="h"><a name="314"></a>314</td><td></td><td></td><td></td><td></td><td class="s"> map { $inlist{$_} = $idx++ } @$list;</td></tr>
+<tr><td class="h"><a name="315"></a>315</td><td></td><td></td><td></td><td></td><td class="s"> if( $wit =~ /^(.*)\Q$acstr\E$/ ) {</td></tr>
+<tr><td class="h"><a name="316"></a>316</td><td></td><td></td><td></td><td></td><td class="s"> my $acwit = $1;</td></tr>
+<tr><td class="h"><a name="317"></a>317</td><td></td><td></td><td></td><td></td><td class="s"> unless( exists $inlist{$acwit} ) {</td></tr>
+<tr><td class="h"><a name="318"></a>318</td><td></td><td></td><td></td><td></td><td class="s"> push( @$list, $acwit.$acstr );</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"> } else {</td></tr>
+<tr><td class="h"><a name="321"></a>321</td><td></td><td></td><td></td><td></td><td class="s"> if( exists( $inlist{$wit.$acstr} ) ) {</td></tr>
+<tr><td class="h"><a name="322"></a>322</td><td></td><td></td><td></td><td></td><td class="s"> # Replace the a.c. version with the main witness</td></tr>
+<tr><td class="h"><a name="323"></a>323</td><td></td><td></td><td></td><td></td><td class="s"> my $i = $inlist{$wit.$acstr};</td></tr>
+<tr><td class="h"><a name="324"></a>324</td><td></td><td></td><td></td><td></td><td class="s"> $list->[$i] = $wit;</td></tr>
+<tr><td class="h"><a name="325"></a>325</td><td></td><td></td><td></td><td></td><td class="s"> } else {</td></tr>
+<tr><td class="h"><a name="326"></a>326</td><td></td><td></td><td></td><td></td><td class="s"> push( @$list, $wit );</td></tr>
+<tr><td class="h"><a name="327"></a>327</td><td></td><td></td><td></td><td></td><td class="s"> }</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"></td></tr>
+<tr><td class="h"><a name="331"></a>331</td><td></td><td></td><td></td><td></td><td class="s">=head2 solve_variants( $graph, @groups ) </td></tr>
+<tr><td class="h"><a name="332"></a>332</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="333"></a>333</td><td></td><td></td><td></td><td></td><td class="s">Sends the set of groups to the external graph solver service and returns</td></tr>
+<tr><td class="h"><a name="334"></a>334</td><td></td><td></td><td></td><td></td><td class="s">a cleaned-up answer, adding the rank IDs back where they belong.</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">The JSON has the form </td></tr>
+<tr><td class="h"><a name="337"></a>337</td><td></td><td></td><td></td><td></td><td class="s"> { "graph": [ stemmagraph DOT string without newlines ],</td></tr>
+<tr><td class="h"><a name="338"></a>338</td><td></td><td></td><td></td><td></td><td class="s"> "groupings": [ array of arrays of groups, one per rank ] }</td></tr>
+<tr><td class="h"><a name="339"></a>339</td><td></td><td></td><td></td><td></td><td class="s"> </td></tr>
+<tr><td class="h"><a name="340"></a>340</td><td></td><td></td><td></td><td></td><td class="s">The answer has the form </td></tr>
+<tr><td class="h"><a name="341"></a>341</td><td></td><td></td><td></td><td></td><td class="s"> { "variants" => [ array of variant location structures ],</td></tr>
+<tr><td class="h"><a name="342"></a>342</td><td></td><td></td><td></td><td></td><td class="s"> "variant_count" => total,</td></tr>
+<tr><td class="h"><a name="343"></a>343</td><td></td><td></td><td></td><td></td><td class="s"> "conflict_count" => number of conflicts detected,</td></tr>
+<tr><td class="h"><a name="344"></a>344</td><td></td><td></td><td></td><td></td><td class="s"> "genealogical_count" => number of solutions found }</td></tr>
+<tr><td class="h"><a name="345"></a>345</td><td></td><td></td><td></td><td></td><td class="s"> </td></tr>
+<tr><td class="h"><a name="346"></a>346</td><td></td><td></td><td></td><td></td><td class="s">=cut</td></tr>
+<tr><td class="h"><a name="347"></a>347</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="348"></a>348</td><td></td><td></td><td></td><td></td><td class="s">sub solve_variants {</td></tr>
+<tr><td class="h"><a name="349"></a>349</td><td></td><td></td><td></td><td></td><td class="s"> my( $stemma, @groups ) = @_;</td></tr>
+<tr><td class="h"><a name="350"></a>350</td><td></td><td></td><td></td><td></td><td class="s"> my $aclabel = $stemma->collation->ac_label;</td></tr>
+<tr><td class="h"><a name="351"></a>351</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="352"></a>352</td><td></td><td></td><td></td><td></td><td class="s"> # Filter the groups down to distinct groups, and work out what graph</td></tr>
+<tr><td class="h"><a name="353"></a>353</td><td></td><td></td><td></td><td></td><td class="s"> # should be used in the calculation of each group. We want to send each</td></tr>
+<tr><td class="h"><a name="354"></a>354</td><td></td><td></td><td></td><td></td><td class="s"> # distinct problem to the solver only once.</td></tr>
+<tr><td class="h"><a name="355"></a>355</td><td></td><td></td><td></td><td></td><td class="s"> # We need a whole bunch of lookup tables for this.</td></tr>
+<tr><td class="h"><a name="356"></a>356</td><td></td><td></td><td></td><td></td><td class="s"> my $index_groupkeys = {}; # Save the order of readings</td></tr>
+<tr><td class="h"><a name="357"></a>357</td><td></td><td></td><td></td><td></td><td class="s"> my $group_indices = {}; # Save the indices that have a given grouping</td></tr>
+<tr><td class="h"><a name="358"></a>358</td><td></td><td></td><td></td><td></td><td class="s"> my $graph_problems = {}; # Save the groupings for the given graph</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"> foreach my $idx ( 0..$#groups ) {</td></tr>
+<tr><td class="h"><a name="361"></a>361</td><td></td><td></td><td></td><td></td><td class="s"> my $ghash = $groups[$idx];</td></tr>
+<tr><td class="h"><a name="362"></a>362</td><td></td><td></td><td></td><td></td><td class="s"> my @grouping;</td></tr>
+<tr><td class="h"><a name="363"></a>363</td><td></td><td></td><td></td><td></td><td class="s"> # Sort the groupings from big to little, and scan for a.c. witnesses</td></tr>
+<tr><td class="h"><a name="364"></a>364</td><td></td><td></td><td></td><td></td><td class="s"> # that would need an extended graph.</td></tr>
+<tr><td class="h"><a name="365"></a>365</td><td></td><td></td><td></td><td></td><td class="s"> my @acwits; # note which AC witnesses crop up at this rank</td></tr>
+<tr><td class="h"><a name="366"></a>366</td><td></td><td></td><td></td><td></td><td class="s"> my @idxkeys = sort { scalar @{$ghash->{$b}} <=> scalar @{$ghash->{$a}} }</td></tr>
+<tr><td class="h"><a name="367"></a>367</td><td></td><td></td><td></td><td></td><td class="s"> keys %$ghash;</td></tr>
+<tr><td class="h"><a name="368"></a>368</td><td></td><td></td><td></td><td></td><td class="s"> foreach my $rdg ( @idxkeys ) {</td></tr>
+<tr><td class="h"><a name="369"></a>369</td><td></td><td></td><td></td><td></td><td class="s"> my @sg = sort @{$ghash->{$rdg}};</td></tr>
+<tr><td class="h"><a name="370"></a>370</td><td></td><td></td><td></td><td></td><td class="s"> push( @acwits, grep { $_ =~ /\Q$aclabel\E$/ } @sg );</td></tr>
+<tr><td class="h"><a name="371"></a>371</td><td></td><td></td><td></td><td></td><td class="s"> push( @grouping, \@sg );</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"> # Save the reading order</td></tr>
+<tr><td class="h"><a name="374"></a>374</td><td></td><td></td><td></td><td></td><td class="s"> $index_groupkeys->{$idx} = \@idxkeys;</td></tr>
+<tr><td class="h"><a name="375"></a>375</td><td></td><td></td><td></td><td></td><td class="s"> </td></tr>
+<tr><td class="h"><a name="376"></a>376</td><td></td><td></td><td></td><td></td><td class="s"> # Now associate the distinct group with this index</td></tr>
+<tr><td class="h"><a name="377"></a>377</td><td></td><td></td><td></td><td></td><td class="s"> my $gstr = wit_stringify( \@grouping );</td></tr>
+<tr><td class="h"><a name="378"></a>378</td><td></td><td></td><td></td><td></td><td class="s"> push( @{$group_indices->{$gstr}}, $idx );</td></tr>
+<tr><td class="h"><a name="379"></a>379</td><td></td><td></td><td></td><td></td><td class="s"> </td></tr>
+<tr><td class="h"><a name="380"></a>380</td><td></td><td></td><td></td><td></td><td class="s"> # Finally, add the group to the list to be calculated for this graph.</td></tr>
+<tr><td class="h"><a name="381"></a>381</td><td></td><td></td><td></td><td></td><td class="s"> map { s/\Q$aclabel\E$// } @acwits;</td></tr>
+<tr><td class="h"><a name="382"></a>382</td><td></td><td></td><td></td><td></td><td class="s"> my $graph = $stemma->extend_graph( \@acwits );</td></tr>
+<tr><td class="h"><a name="383"></a>383</td><td></td><td></td><td></td><td></td><td class="s"> unless( exists $graph_problems->{"$graph"} ) {</td></tr>
+<tr><td class="h"><a name="384"></a>384</td><td></td><td></td><td></td><td></td><td class="s"> $graph_problems->{"$graph"} = { 'object' => $graph, 'groups' => [] };</td></tr>
+<tr><td class="h"><a name="385"></a>385</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr>
+<tr><td class="h"><a name="386"></a>386</td><td></td><td></td><td></td><td></td><td class="s"> push( @{$graph_problems->{"$graph"}->{'groups'}}, \@grouping );</td></tr>
+<tr><td class="h"><a name="387"></a>387</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr>
+<tr><td class="h"><a name="388"></a>388</td><td></td><td></td><td></td><td></td><td class="s"> </td></tr>
+<tr><td class="h"><a name="389"></a>389</td><td></td><td></td><td></td><td></td><td class="s"> ## For each distinct graph, send its groups to the solver.</td></tr>
+<tr><td class="h"><a name="390"></a>390</td><td></td><td></td><td></td><td></td><td class="s"> $DB::single = 1;</td></tr>
+<tr><td class="h"><a name="391"></a>391</td><td></td><td></td><td></td><td></td><td class="s"> my $solver_url = 'http://byzantini.st/cgi-bin/graphcalc.cgi';</td></tr>
+<tr><td class="h"><a name="392"></a>392</td><td></td><td></td><td></td><td></td><td class="s"> my $ua = LWP::UserAgent->new();</td></tr>
+<tr><td class="h"><a name="393"></a>393</td><td></td><td></td><td></td><td></td><td class="s"> ## Witness map is a HACK to get around limitations in node names from IDP</td></tr>
+<tr><td class="h"><a name="394"></a>394</td><td></td><td></td><td></td><td></td><td class="s"> my $witness_map = {};</td></tr>
+<tr><td class="h"><a name="395"></a>395</td><td></td><td></td><td></td><td></td><td class="s"> ## Variables to store answers as they come back</td></tr>
+<tr><td class="h"><a name="396"></a>396</td><td></td><td></td><td></td><td></td><td class="s"> my $variants = [ ( undef ) x ( scalar keys %$index_groupkeys ) ];</td></tr>
+<tr><td class="h"><a name="397"></a>397</td><td></td><td></td><td></td><td></td><td class="s"> my $genealogical = 0;</td></tr>
+<tr><td class="h"><a name="398"></a>398</td><td></td><td></td><td></td><td></td><td class="s"> foreach my $graphkey ( keys %$graph_problems ) {</td></tr>
+<tr><td class="h"><a name="399"></a>399</td><td></td><td></td><td></td><td></td><td class="s"> my $graph = $graph_problems->{$graphkey}->{'object'};</td></tr>
+<tr><td class="h"><a name="400"></a>400</td><td></td><td></td><td></td><td></td><td class="s"> my $groupings = $graph_problems->{$graphkey}->{'groups'};</td></tr>
+<tr><td class="h"><a name="401"></a>401</td><td></td><td></td><td></td><td></td><td class="s"> my $json = encode_json( _safe_wit_strings( $graph, $stemma->collation,</td></tr>
+<tr><td class="h"><a name="402"></a>402</td><td></td><td></td><td></td><td></td><td class="s"> $groupings, $witness_map ) );</td></tr>
+<tr><td class="h"><a name="403"></a>403</td><td></td><td></td><td></td><td></td><td class="s"> # Send it off and get the result</td></tr>
+<tr><td class="h"><a name="404"></a>404</td><td></td><td></td><td></td><td></td><td class="s"> my $resp = $ua->post( $solver_url, 'Content-Type' => 'application/json', </td></tr>
+<tr><td class="h"><a name="405"></a>405</td><td></td><td></td><td></td><td></td><td class="s"> 'Content' => $json ); </td></tr>
+<tr><td class="h"><a name="406"></a>406</td><td></td><td></td><td></td><td></td><td class="s"> my $answer;</td></tr>
+<tr><td class="h"><a name="407"></a>407</td><td></td><td></td><td></td><td></td><td class="s"> my $used_idp;</td></tr>
+<tr><td class="h"><a name="408"></a>408</td><td></td><td></td><td></td><td></td><td class="s"> if( $resp->is_success ) {</td></tr>
+<tr><td class="h"><a name="409"></a>409</td><td></td><td></td><td></td><td></td><td class="s"> $answer = _desanitize_names( decode_json( $resp->content ), $witness_map );</td></tr>
+<tr><td class="h"><a name="410"></a>410</td><td></td><td></td><td></td><td></td><td class="s"> $used_idp = 1;</td></tr>
+<tr><td class="h"><a name="411"></a>411</td><td></td><td></td><td></td><td></td><td class="s"> } else {</td></tr>
+<tr><td class="h"><a name="412"></a>412</td><td></td><td></td><td></td><td></td><td class="s"> # Fall back to the old method.</td></tr>
+<tr><td class="h"><a name="413"></a>413</td><td></td><td></td><td></td><td></td><td class="s"> warn "IDP solver returned " . $resp->status_line . " / " . $resp->content</td></tr>
+<tr><td class="h"><a name="414"></a>414</td><td></td><td></td><td></td><td></td><td class="s"> . "; falling back to perl method";</td></tr>
+<tr><td class="h"><a name="415"></a>415</td><td></td><td></td><td></td><td></td><td class="s"> $answer = perl_solver( $graph, @$groupings );</td></tr>
+<tr><td class="h"><a name="416"></a>416</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr>
+<tr><td class="h"><a name="417"></a>417</td><td></td><td></td><td></td><td></td><td class="s"> ## The answer is the evaluated groupings, plus a boolean for whether</td></tr>
+<tr><td class="h"><a name="418"></a>418</td><td></td><td></td><td></td><td></td><td class="s"> ## they were genealogical. Reconstruct our original groups.</td></tr>
+<tr><td class="h"><a name="419"></a>419</td><td></td><td></td><td></td><td></td><td class="s"> foreach my $gidx ( 0 .. $#{$groupings} ) {</td></tr>
+<tr><td class="h"><a name="420"></a>420</td><td></td><td></td><td></td><td></td><td class="s"> my( $calc_groups, $result ) = @{$answer->[$gidx]};</td></tr>
+<tr><td class="h"><a name="421"></a>421</td><td></td><td></td><td></td><td></td><td class="s"> if( $result ) {</td></tr>
+<tr><td class="h"><a name="422"></a>422</td><td></td><td></td><td></td><td></td><td class="s"> $genealogical++;</td></tr>
+<tr><td class="h"><a name="423"></a>423</td><td></td><td></td><td></td><td></td><td class="s"> # Prune the calculated groups, in case the IDP solver failed to.</td></tr>
+<tr><td class="h"><a name="424"></a>424</td><td></td><td></td><td></td><td></td><td class="s"> if( $used_idp ) {</td></tr>
+<tr><td class="h"><a name="425"></a>425</td><td></td><td></td><td></td><td></td><td class="s"> my @pruned_groups;</td></tr>
+<tr><td class="h"><a name="426"></a>426</td><td></td><td></td><td></td><td></td><td class="s"> foreach my $cg ( @$calc_groups ) {</td></tr>
+<tr><td class="h"><a name="427"></a>427</td><td></td><td></td><td></td><td></td><td class="s"> # This is a little wasteful but the path of least</td></tr>
+<tr><td class="h"><a name="428"></a>428</td><td></td><td></td><td></td><td></td><td class="s"> # resistance. Send both the stemma, which knows what</td></tr>
+<tr><td class="h"><a name="429"></a>429</td><td></td><td></td><td></td><td></td><td class="s"> # its hypotheticals are, and the actual graph used.</td></tr>
+<tr><td class="h"><a name="430"></a>430</td><td></td><td></td><td></td><td></td><td class="s"> my @pg = _prune_group( $cg, $stemma, $graph );</td></tr>
+<tr><td class="h"><a name="431"></a>431</td><td></td><td></td><td></td><td></td><td class="s"> push( @pruned_groups, \@pg );</td></tr>
+<tr><td class="h"><a name="432"></a>432</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr>
+<tr><td class="h"><a name="433"></a>433</td><td></td><td></td><td></td><td></td><td class="s"> $calc_groups = \@pruned_groups;</td></tr>
+<tr><td class="h"><a name="434"></a>434</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr>
+<tr><td class="h"><a name="435"></a>435</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr>
+<tr><td class="h"><a name="436"></a>436</td><td></td><td></td><td></td><td></td><td class="s"> # Retrieve the key for the original group that went to the solver</td></tr>
+<tr><td class="h"><a name="437"></a>437</td><td></td><td></td><td></td><td></td><td class="s"> my $input_group = wit_stringify( $groupings->[$gidx] );</td></tr>
+<tr><td class="h"><a name="438"></a>438</td><td></td><td></td><td></td><td></td><td class="s"> foreach my $oidx ( @{$group_indices->{$input_group}} ) {</td></tr>
+<tr><td class="h"><a name="439"></a>439</td><td></td><td></td><td></td><td></td><td class="s"> my @readings = @{$index_groupkeys->{$oidx}};</td></tr>
+<tr><td class="h"><a name="440"></a>440</td><td></td><td></td><td></td><td></td><td class="s"> my $vstruct = {</td></tr>
+<tr><td class="h"><a name="441"></a>441</td><td></td><td></td><td></td><td></td><td class="s"> 'genealogical' => $result,</td></tr>
+<tr><td class="h"><a name="442"></a>442</td><td></td><td></td><td></td><td></td><td class="s"> 'readings' => [],</td></tr>
+<tr><td class="h"><a name="443"></a>443</td><td></td><td></td><td></td><td></td><td class="s"> };</td></tr>
+<tr><td class="h"><a name="444"></a>444</td><td></td><td></td><td></td><td></td><td class="s"> foreach my $ridx ( 0 .. $#readings ) {</td></tr>
+<tr><td class="h"><a name="445"></a>445</td><td></td><td></td><td></td><td></td><td class="s"> push( @{$vstruct->{'readings'}},</td></tr>
+<tr><td class="h"><a name="446"></a>446</td><td></td><td></td><td></td><td></td><td class="s"> { 'readingid' => $readings[$ridx],</td></tr>
+<tr><td class="h"><a name="447"></a>447</td><td></td><td></td><td></td><td></td><td class="s"> 'group' => $calc_groups->[$ridx] } );</td></tr>
+<tr><td class="h"><a name="448"></a>448</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr>
+<tr><td class="h"><a name="449"></a>449</td><td></td><td></td><td></td><td></td><td class="s"> $variants->[$oidx] = $vstruct;</td></tr>
+<tr><td class="h"><a name="450"></a>450</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr>
+<tr><td class="h"><a name="451"></a>451</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr>
+<tr><td class="h"><a name="452"></a>452</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr>
+<tr><td class="h"><a name="453"></a>453</td><td></td><td></td><td></td><td></td><td class="s"> </td></tr>
+<tr><td class="h"><a name="454"></a>454</td><td></td><td></td><td></td><td></td><td class="s"> return { 'variants' => $variants, </td></tr>
+<tr><td class="h"><a name="455"></a>455</td><td></td><td></td><td></td><td></td><td class="s"> 'variant_count' => scalar @$variants,</td></tr>
+<tr><td class="h"><a name="456"></a>456</td><td></td><td></td><td></td><td></td><td class="s"> 'genealogical_count' => $genealogical };</td></tr>
+<tr><td class="h"><a name="457"></a>457</td><td></td><td></td><td></td><td></td><td class="s">}</td></tr>
+<tr><td class="h"><a name="458"></a>458</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="459"></a>459</td><td></td><td></td><td></td><td></td><td class="s">#### HACKERY to cope with IDP's limited idea of what a node name looks like ###</td></tr>
+<tr><td class="h"><a name="460"></a>460</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="461"></a>461</td><td></td><td></td><td></td><td></td><td class="s">sub _safe_wit_strings {</td></tr>
+<tr><td class="h"><a name="462"></a>462</td><td></td><td></td><td></td><td></td><td class="s"> my( $graph, $c, $groupings, $witness_map ) = @_;</td></tr>
+<tr><td class="h"><a name="463"></a>463</td><td></td><td></td><td></td><td></td><td class="s"> # Parse the graph we were given into a stemma.</td></tr>
+<tr><td class="h"><a name="464"></a>464</td><td></td><td></td><td></td><td></td><td class="s"> my $safegraph = Graph->new();</td></tr>
+<tr><td class="h"><a name="465"></a>465</td><td></td><td></td><td></td><td></td><td class="s"> # Convert the graph to a safe representation and store the conversion.</td></tr>
+<tr><td class="h"><a name="466"></a>466</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="467"></a>467</td><td></td><td></td><td></td><td></td><td class="s"> my $sn = _safe_witstr( $n );</td></tr>
+<tr><td class="h"><a name="468"></a>468</td><td></td><td></td><td></td><td></td><td class="s"> if( exists $witness_map->{$sn} ) {</td></tr>
+<tr><td class="h"><a name="469"></a>469</td><td></td><td></td><td></td><td></td><td class="s"> warn "Ambiguous stringification $sn for $n and " . $witness_map->{$sn}</td></tr>
+<tr><td class="h"><a name="470"></a>470</td><td></td><td></td><td></td><td></td><td class="s"> if $witness_map->{$sn} ne $n;</td></tr>
+<tr><td class="h"><a name="471"></a>471</td><td></td><td></td><td></td><td></td><td class="s"> } else {</td></tr>
+<tr><td class="h"><a name="472"></a>472</td><td></td><td></td><td></td><td></td><td class="s"> $witness_map->{$sn} = $n;</td></tr>
+<tr><td class="h"><a name="473"></a>473</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr>
+<tr><td class="h"><a name="474"></a>474</td><td></td><td></td><td></td><td></td><td class="s"> $safegraph->add_vertex( $sn );</td></tr>
+<tr><td class="h"><a name="475"></a>475</td><td></td><td></td><td></td><td></td><td class="s"> $safegraph->set_vertex_attributes( $sn, </td></tr>
+<tr><td class="h"><a name="476"></a>476</td><td></td><td></td><td></td><td></td><td class="s"> $graph->get_vertex_attributes( $n ) );</td></tr>
+<tr><td class="h"><a name="477"></a>477</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr>
+<tr><td class="h"><a name="478"></a>478</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="479"></a>479</td><td></td><td></td><td></td><td></td><td class="s"> my @safe_e = ( _safe_witstr( $e->[0] ), _safe_witstr( $e->[1] ) );</td></tr>
+<tr><td class="h"><a name="480"></a>480</td><td></td><td></td><td></td><td></td><td class="s"> $safegraph->add_edge( @safe_e );</td></tr>
+<tr><td class="h"><a name="481"></a>481</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr>
+<tr><td class="h"><a name="482"></a>482</td><td></td><td></td><td></td><td></td><td class="s"> my $safe_stemma = Text::Tradition::Stemma->new( </td></tr>
+<tr><td class="h"><a name="483"></a>483</td><td></td><td></td><td></td><td></td><td class="s"> 'collation' => $c, 'graph' => $safegraph );</td></tr>
+<tr><td class="h"><a name="484"></a>484</td><td></td><td></td><td></td><td></td><td class="s"> </td></tr>
+<tr><td class="h"><a name="485"></a>485</td><td></td><td></td><td></td><td></td><td class="s"> # Now convert the witness groupings to a safe representation.</td></tr>
+<tr><td class="h"><a name="486"></a>486</td><td></td><td></td><td></td><td></td><td class="s"> my $safe_groupings = [];</td></tr>
+<tr><td class="h"><a name="487"></a>487</td><td></td><td></td><td></td><td></td><td class="s"> foreach my $grouping ( @$groupings ) {</td></tr>
+<tr><td class="h"><a name="488"></a>488</td><td></td><td></td><td></td><td></td><td class="s"> my $safe_grouping = [];</td></tr>
+<tr><td class="h"><a name="489"></a>489</td><td></td><td></td><td></td><td></td><td class="s"> foreach my $group ( @$grouping ) {</td></tr>
+<tr><td class="h"><a name="490"></a>490</td><td></td><td></td><td></td><td></td><td class="s"> my $safe_group = [];</td></tr>
+<tr><td class="h"><a name="491"></a>491</td><td></td><td></td><td></td><td></td><td class="s"> foreach my $n ( @$group ) {</td></tr>
+<tr><td class="h"><a name="492"></a>492</td><td></td><td></td><td></td><td></td><td class="s"> my $sn = _safe_witstr( $n );</td></tr>
+<tr><td class="h"><a name="493"></a>493</td><td></td><td></td><td></td><td></td><td class="s"> warn "Ambiguous stringification $sn for $n and " . $witness_map->{$sn}</td></tr>
+<tr><td class="h"><a name="494"></a>494</td><td></td><td></td><td></td><td></td><td class="s"> if exists $witness_map->{$sn} && $witness_map->{$sn} ne $n;</td></tr>
+<tr><td class="h"><a name="495"></a>495</td><td></td><td></td><td></td><td></td><td class="s"> $witness_map->{$sn} = $n;</td></tr>
+<tr><td class="h"><a name="496"></a>496</td><td></td><td></td><td></td><td></td><td class="s"> push( @$safe_group, $sn );</td></tr>
+<tr><td class="h"><a name="497"></a>497</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr>
+<tr><td class="h"><a name="498"></a>498</td><td></td><td></td><td></td><td></td><td class="s"> push( @$safe_grouping, $safe_group );</td></tr>
+<tr><td class="h"><a name="499"></a>499</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr>
+<tr><td class="h"><a name="500"></a>500</td><td></td><td></td><td></td><td></td><td class="s"> push( @$safe_groupings, $safe_grouping );</td></tr>
+<tr><td class="h"><a name="501"></a>501</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr>
+<tr><td class="h"><a name="502"></a>502</td><td></td><td></td><td></td><td></td><td class="s"> </td></tr>
+<tr><td class="h"><a name="503"></a>503</td><td></td><td></td><td></td><td></td><td class="s"> # Return it all in the struct we expect. We have stored the reductions</td></tr>
+<tr><td class="h"><a name="504"></a>504</td><td></td><td></td><td></td><td></td><td class="s"> # in the $witness_map that we were passed.</td></tr>
+<tr><td class="h"><a name="505"></a>505</td><td></td><td></td><td></td><td></td><td class="s"> return { 'graph' => $safe_stemma->editable( { 'linesep' => ' ' } ), </td></tr>
+<tr><td class="h"><a name="506"></a>506</td><td></td><td></td><td></td><td></td><td class="s"> 'groupings' => $safe_groupings };</td></tr>
+<tr><td class="h"><a name="507"></a>507</td><td></td><td></td><td></td><td></td><td class="s">}</td></tr>
+<tr><td class="h"><a name="508"></a>508</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="509"></a>509</td><td></td><td></td><td></td><td></td><td class="s">sub _safe_witstr {</td></tr>
+<tr><td class="h"><a name="510"></a>510</td><td></td><td></td><td></td><td></td><td class="s"> my $witstr = shift;</td></tr>
+<tr><td class="h"><a name="511"></a>511</td><td></td><td></td><td></td><td></td><td class="s"> $witstr =~ s/\s+/_/g;</td></tr>
+<tr><td class="h"><a name="512"></a>512</td><td></td><td></td><td></td><td></td><td class="s"> $witstr =~ s/[^\w\d-]//g;</td></tr>
+<tr><td class="h"><a name="513"></a>513</td><td></td><td></td><td></td><td></td><td class="s"> return $witstr;</td></tr>
+<tr><td class="h"><a name="514"></a>514</td><td></td><td></td><td></td><td></td><td class="s">}</td></tr>
+<tr><td class="h"><a name="515"></a>515</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="516"></a>516</td><td></td><td></td><td></td><td></td><td class="s">sub _desanitize_names {</td></tr>
+<tr><td class="h"><a name="517"></a>517</td><td></td><td></td><td></td><td></td><td class="s"> my( $jsonstruct, $witness_map ) = @_;</td></tr>
+<tr><td class="h"><a name="518"></a>518</td><td></td><td></td><td></td><td></td><td class="s"> my $result = [];</td></tr>
+<tr><td class="h"><a name="519"></a>519</td><td></td><td></td><td></td><td></td><td class="s"> foreach my $grouping ( @$jsonstruct ) {</td></tr>
+<tr><td class="h"><a name="520"></a>520</td><td></td><td></td><td></td><td></td><td class="s"> my $real_grouping = [];</td></tr>
+<tr><td class="h"><a name="521"></a>521</td><td></td><td></td><td></td><td></td><td class="s"> foreach my $element ( @$grouping ) {</td></tr>
+<tr><td class="h"><a name="522"></a>522</td><td></td><td></td><td></td><td></td><td class="s"> if( ref( $element ) eq 'ARRAY' ) {</td></tr>
+<tr><td class="h"><a name="523"></a>523</td><td></td><td></td><td></td><td></td><td class="s"> # it's the groupset.</td></tr>
+<tr><td class="h"><a name="524"></a>524</td><td></td><td></td><td></td><td></td><td class="s"> my $real_groupset = [];</td></tr>
+<tr><td class="h"><a name="525"></a>525</td><td></td><td></td><td></td><td></td><td class="s"> foreach my $group ( @$element ) {</td></tr>
+<tr><td class="h"><a name="526"></a>526</td><td></td><td></td><td></td><td></td><td class="s"> my $real_group = [];</td></tr>
+<tr><td class="h"><a name="527"></a>527</td><td></td><td></td><td></td><td></td><td class="s"> foreach my $n ( @$group ) {</td></tr>
+<tr><td class="h"><a name="528"></a>528</td><td></td><td></td><td></td><td></td><td class="s"> my $rn = $witness_map->{$n};</td></tr>
+<tr><td class="h"><a name="529"></a>529</td><td></td><td></td><td></td><td></td><td class="s"> push( @$real_group, $rn );</td></tr>
+<tr><td class="h"><a name="530"></a>530</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr>
+<tr><td class="h"><a name="531"></a>531</td><td></td><td></td><td></td><td></td><td class="s"> push( @$real_groupset, $real_group );</td></tr>
+<tr><td class="h"><a name="532"></a>532</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr>
+<tr><td class="h"><a name="533"></a>533</td><td></td><td></td><td></td><td></td><td class="s"> push( @$real_grouping, $real_groupset );</td></tr>
+<tr><td class="h"><a name="534"></a>534</td><td></td><td></td><td></td><td></td><td class="s"> } else {</td></tr>
+<tr><td class="h"><a name="535"></a>535</td><td></td><td></td><td></td><td></td><td class="s"> # It is the boolean, not actually a group.</td></tr>
+<tr><td class="h"><a name="536"></a>536</td><td></td><td></td><td></td><td></td><td class="s"> push( @$real_grouping, $element );</td></tr>
+<tr><td class="h"><a name="537"></a>537</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr>
+<tr><td class="h"><a name="538"></a>538</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr>
+<tr><td class="h"><a name="539"></a>539</td><td></td><td></td><td></td><td></td><td class="s"> push( @$result, $real_grouping );</td></tr>
+<tr><td class="h"><a name="540"></a>540</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr>
+<tr><td class="h"><a name="541"></a>541</td><td></td><td></td><td></td><td></td><td class="s"> return $result;</td></tr>
+<tr><td class="h"><a name="542"></a>542</td><td></td><td></td><td></td><td></td><td class="s">}</td></tr>
+<tr><td class="h"><a name="543"></a>543</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="544"></a>544</td><td></td><td></td><td></td><td></td><td class="s">### END HACKERY ###</td></tr>
+<tr><td class="h"><a name="545"></a>545</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="546"></a>546</td><td></td><td></td><td></td><td></td><td class="s">=head2 analyze_location ( $tradition, $graph, $location_hash )</td></tr>
+<tr><td class="h"><a name="547"></a>547</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="548"></a>548</td><td></td><td></td><td></td><td></td><td class="s">Given the tradition, its stemma graph, and the solution from the graph solver,</td></tr>
+<tr><td class="h"><a name="549"></a>549</td><td></td><td></td><td></td><td></td><td class="s">work out the rest of the information we want. For each reading we need missing, </td></tr>
+<tr><td class="h"><a name="550"></a>550</td><td></td><td></td><td></td><td></td><td class="s">conflict, reading_parents, independent_occurrence, followed, not_followed, and follow_unknown. Alters the location_hash in place.</td></tr>
+<tr><td class="h"><a name="551"></a>551</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="552"></a>552</td><td></td><td></td><td></td><td></td><td class="s">=cut</td></tr>
+<tr><td class="h"><a name="553"></a>553</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="554"></a>554</td><td></td><td></td><td></td><td></td><td class="s">sub analyze_location {</td></tr>
+<tr><td class="h"><a name="555"></a>555</td><td></td><td></td><td></td><td></td><td class="s"> my ( $tradition, $graph, $variant_row ) = @_;</td></tr>
+<tr><td class="h"><a name="556"></a>556</td><td></td><td></td><td></td><td></td><td class="s"> </td></tr>
+<tr><td class="h"><a name="557"></a>557</td><td></td><td></td><td></td><td></td><td class="s"> # Make a hash of all known node memberships, and make the subgraphs.</td></tr>
+<tr><td class="h"><a name="558"></a>558</td><td></td><td></td><td></td><td></td><td class="s"> my $contig = {};</td></tr>
+<tr><td class="h"><a name="559"></a>559</td><td></td><td></td><td></td><td></td><td class="s"> my $reading_roots = {};</td></tr>
+<tr><td class="h"><a name="560"></a>560</td><td></td><td></td><td></td><td></td><td class="s"> my $subgraph = {};</td></tr>
+<tr><td class="h"><a name="561"></a>561</td><td></td><td></td><td></td><td></td><td class="s"> foreach my $rdghash ( @{$variant_row->{'readings'}} ) {</td></tr>
+<tr><td class="h"><a name="562"></a>562</td><td></td><td></td><td></td><td></td><td class="s"> my $rid = $rdghash->{'readingid'};</td></tr>
+<tr><td class="h"><a name="563"></a>563</td><td></td><td></td><td></td><td></td><td class="s"> map { $contig->{$_} = $rid } @{$rdghash->{'group'}};</td></tr>
+<tr><td class="h"><a name="564"></a>564</td><td></td><td></td><td></td><td></td><td class="s"> </td></tr>
+<tr><td class="h"><a name="565"></a>565</td><td></td><td></td><td></td><td></td><td class="s"> # Make the subgraph.</td></tr>
+<tr><td class="h"><a name="566"></a>566</td><td></td><td></td><td></td><td></td><td class="s"> my $part = $graph->copy;</td></tr>
+<tr><td class="h"><a name="567"></a>567</td><td></td><td></td><td></td><td></td><td class="s"> my %these_vertices;</td></tr>
+<tr><td class="h"><a name="568"></a>568</td><td></td><td></td><td></td><td></td><td class="s"> map { $these_vertices{$_} = 1 } @{$rdghash->{'group'}};</td></tr>
+<tr><td class="h"><a name="569"></a>569</td><td></td><td></td><td></td><td></td><td class="s"> $part->delete_vertices( grep { !$these_vertices{$_} } $part->vertices );</td></tr>
+<tr><td class="h"><a name="570"></a>570</td><td></td><td></td><td></td><td></td><td class="s"> $subgraph->{$rid} = $part;</td></tr>
+<tr><td class="h"><a name="571"></a>571</td><td></td><td></td><td></td><td></td><td class="s"> # Get the reading roots.</td></tr>
+<tr><td class="h"><a name="572"></a>572</td><td></td><td></td><td></td><td></td><td class="s"> map { $reading_roots->{$_} = $rid } $part->predecessorless_vertices;</td></tr>
+<tr><td class="h"><a name="573"></a>573</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr>
+<tr><td class="h"><a name="574"></a>574</td><td></td><td></td><td></td><td></td><td class="s"> </td></tr>
+<tr><td class="h"><a name="575"></a>575</td><td></td><td></td><td></td><td></td><td class="s"> # Now that we have all the node group memberships, calculate followed/</td></tr>
+<tr><td class="h"><a name="576"></a>576</td><td></td><td></td><td></td><td></td><td class="s"> # non-followed/unknown values for each reading. Also figure out the</td></tr>
+<tr><td class="h"><a name="577"></a>577</td><td></td><td></td><td></td><td></td><td class="s"> # reading's evident parent(s).</td></tr>
+<tr><td class="h"><a name="578"></a>578</td><td></td><td></td><td></td><td></td><td class="s"> foreach my $rdghash ( @{$variant_row->{'readings'}} ) {</td></tr>
+<tr><td class="h"><a name="579"></a>579</td><td></td><td></td><td></td><td></td><td class="s"> # Group string key - TODO do we need this?</td></tr>
+<tr><td class="h"><a name="580"></a>580</td><td></td><td></td><td></td><td></td><td class="s"> my $gst = wit_stringify( $rdghash->{'group'} );</td></tr>
+<tr><td class="h"><a name="581"></a>581</td><td></td><td></td><td></td><td></td><td class="s"> my $rid = $rdghash->{'readingid'};</td></tr>
+<tr><td class="h"><a name="582"></a>582</td><td></td><td></td><td></td><td></td><td class="s"> # Get the subgraph</td></tr>
+<tr><td class="h"><a name="583"></a>583</td><td></td><td></td><td></td><td></td><td class="s"> my $part = $subgraph->{$rid};</td></tr>
+<tr><td class="h"><a name="584"></a>584</td><td></td><td></td><td></td><td></td><td class="s"> </td></tr>
+<tr><td class="h"><a name="585"></a>585</td><td></td><td></td><td></td><td></td><td class="s"> # Start figuring things out. </td></tr>
+<tr><td class="h"><a name="586"></a>586</td><td></td><td></td><td></td><td></td><td class="s"> my @roots = $part->predecessorless_vertices;</td></tr>
+<tr><td class="h"><a name="587"></a>587</td><td></td><td></td><td></td><td></td><td class="s"> $rdghash->{'independent_occurrence'} = scalar @roots;</td></tr>
+<tr><td class="h"><a name="588"></a>588</td><td></td><td></td><td></td><td></td><td class="s"> $rdghash->{'followed'} = scalar( $part->vertices ) - scalar( @roots );</td></tr>
+<tr><td class="h"><a name="589"></a>589</td><td></td><td></td><td></td><td></td><td class="s"> # Find the parent readings, if any, of this reading.</td></tr>
+<tr><td class="h"><a name="590"></a>590</td><td></td><td></td><td></td><td></td><td class="s"> my %rdgparents;</td></tr>
+<tr><td class="h"><a name="591"></a>591</td><td></td><td></td><td></td><td></td><td class="s"> foreach my $wit ( @roots ) {</td></tr>
+<tr><td class="h"><a name="592"></a>592</td><td></td><td></td><td></td><td></td><td class="s"> # Look in the main stemma to find this witness's extant or known-reading</td></tr>
+<tr><td class="h"><a name="593"></a>593</td><td></td><td></td><td></td><td></td><td class="s"> # immediate ancestor(s), and look up the reading that each ancestor olds.</td></tr>
+<tr><td class="h"><a name="594"></a>594</td><td></td><td></td><td></td><td></td><td class="s"> my @check = $graph->predecessors( $wit );</td></tr>
+<tr><td class="h"><a name="595"></a>595</td><td></td><td></td><td></td><td></td><td class="s"> while( @check ) {</td></tr>
+<tr><td class="h"><a name="596"></a>596</td><td></td><td></td><td></td><td></td><td class="s"> my @next;</td></tr>
+<tr><td class="h"><a name="597"></a>597</td><td></td><td></td><td></td><td></td><td class="s"> foreach my $wparent( @check ) {</td></tr>
+<tr><td class="h"><a name="598"></a>598</td><td></td><td></td><td></td><td></td><td class="s"> my $preading = $contig->{$wparent};</td></tr>
+<tr><td class="h"><a name="599"></a>599</td><td></td><td></td><td></td><td></td><td class="s"> if( $preading ) {</td></tr>
+<tr><td class="h"><a name="600"></a>600</td><td></td><td></td><td></td><td></td><td class="s"> $rdgparents{$preading} = 1;</td></tr>
+<tr><td class="h"><a name="601"></a>601</td><td></td><td></td><td></td><td></td><td class="s"> } else {</td></tr>
+<tr><td class="h"><a name="602"></a>602</td><td></td><td></td><td></td><td></td><td class="s"> push( @next, $graph->predecessors( $wparent ) );</td></tr>
+<tr><td class="h"><a name="603"></a>603</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr>
+<tr><td class="h"><a name="604"></a>604</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr>
+<tr><td class="h"><a name="605"></a>605</td><td></td><td></td><td></td><td></td><td class="s"> @check = @next;</td></tr>
+<tr><td class="h"><a name="606"></a>606</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr>
+<tr><td class="h"><a name="607"></a>607</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr>
+<tr><td class="h"><a name="608"></a>608</td><td></td><td></td><td></td><td></td><td class="s"> $rdghash->{'reading_parents'} = [ keys %rdgparents ];</td></tr>
+<tr><td class="h"><a name="609"></a>609</td><td></td><td></td><td></td><td></td><td class="s"> </td></tr>
+<tr><td class="h"><a name="610"></a>610</td><td></td><td></td><td></td><td></td><td class="s"> # Find the number of times this reading was altered, and the number of</td></tr>
+<tr><td class="h"><a name="611"></a>611</td><td></td><td></td><td></td><td></td><td class="s"> # times we're not sure.</td></tr>
+<tr><td class="h"><a name="612"></a>612</td><td></td><td></td><td></td><td></td><td class="s"> my( %nofollow, %unknownfollow );</td></tr>
+<tr><td class="h"><a name="613"></a>613</td><td></td><td></td><td></td><td></td><td class="s"> foreach my $wit ( $part->vertices ) {</td></tr>
+<tr><td class="h"><a name="614"></a>614</td><td></td><td></td><td></td><td></td><td class="s"> foreach my $wchild ( $graph->successors( $wit ) ) {</td></tr>
+<tr><td class="h"><a name="615"></a>615</td><td></td><td></td><td></td><td></td><td class="s"> next if $part->has_vertex( $wchild );</td></tr>
+<tr><td class="h"><a name="616"></a>616</td><td></td><td></td><td></td><td></td><td class="s"> if( $reading_roots->{$wchild} && $contig->{$wchild} ) {</td></tr>
+<tr><td class="h"><a name="617"></a>617</td><td></td><td></td><td></td><td></td><td class="s"> # It definitely changed here.</td></tr>
+<tr><td class="h"><a name="618"></a>618</td><td></td><td></td><td></td><td></td><td class="s"> $nofollow{$wchild} = 1;</td></tr>
+<tr><td class="h"><a name="619"></a>619</td><td></td><td></td><td></td><td></td><td class="s"> } elsif( !($contig->{$wchild}) ) {</td></tr>
+<tr><td class="h"><a name="620"></a>620</td><td></td><td></td><td></td><td></td><td class="s"> # The child is a hypothetical node not definitely in</td></tr>
+<tr><td class="h"><a name="621"></a>621</td><td></td><td></td><td></td><td></td><td class="s"> # any group. Answer is unknown.</td></tr>
+<tr><td class="h"><a name="622"></a>622</td><td></td><td></td><td></td><td></td><td class="s"> $unknownfollow{$wchild} = 1;</td></tr>
+<tr><td class="h"><a name="623"></a>623</td><td></td><td></td><td></td><td></td><td class="s"> } # else it's a non-root node in a known group, and therefore</td></tr>
+<tr><td class="h"><a name="624"></a>624</td><td></td><td></td><td></td><td></td><td class="s"> # is presumed to have its reading from its group, not this link.</td></tr>
+<tr><td class="h"><a name="625"></a>625</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr>
+<tr><td class="h"><a name="626"></a>626</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr>
+<tr><td class="h"><a name="627"></a>627</td><td></td><td></td><td></td><td></td><td class="s"> $rdghash->{'not_followed'} = keys %nofollow;</td></tr>
+<tr><td class="h"><a name="628"></a>628</td><td></td><td></td><td></td><td></td><td class="s"> $rdghash->{'follow_unknown'} = keys %unknownfollow;</td></tr>
+<tr><td class="h"><a name="629"></a>629</td><td></td><td></td><td></td><td></td><td class="s"> </td></tr>
+<tr><td class="h"><a name="630"></a>630</td><td></td><td></td><td></td><td></td><td class="s"> # Now say whether this reading represents a conflict.</td></tr>
+<tr><td class="h"><a name="631"></a>631</td><td></td><td></td><td></td><td></td><td class="s"> unless( $variant_row->{'genealogical'} ) {</td></tr>
+<tr><td class="h"><a name="632"></a>632</td><td></td><td></td><td></td><td></td><td class="s"> $rdghash->{'conflict'} = @roots != 1;</td></tr>
+<tr><td class="h"><a name="633"></a>633</td><td></td><td></td><td></td><td></td><td class="s"> } </td></tr>
+<tr><td class="h"><a name="634"></a>634</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr>
+<tr><td class="h"><a name="635"></a>635</td><td></td><td></td><td></td><td></td><td class="s">}</td></tr>
+<tr><td class="h"><a name="636"></a>636</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="637"></a>637</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="638"></a>638</td><td></td><td></td><td></td><td></td><td class="s">=head2 perl_solver( $tradition, $rank, $stemma_id, @merge_relationship_types )</td></tr>
+<tr><td class="h"><a name="639"></a>639</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="640"></a>640</td><td></td><td></td><td></td><td></td><td class="s">** NOTE ** This method should hopefully not be called - it is not guaranteed </td></tr>
+<tr><td class="h"><a name="641"></a>641</td><td></td><td></td><td></td><td></td><td class="s">to be correct. Serves as a backup for the real solver.</td></tr>
+<tr><td class="h"><a name="642"></a>642</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="643"></a>643</td><td></td><td></td><td></td><td></td><td class="s">Runs an analysis of the given tradition, at the location given in $rank, </td></tr>
+<tr><td class="h"><a name="644"></a>644</td><td></td><td></td><td></td><td></td><td class="s">against the graph of the stemma specified in $stemma_id. The argument </td></tr>
+<tr><td class="h"><a name="645"></a>645</td><td></td><td></td><td></td><td></td><td class="s">@merge_relationship_types is an optional list of relationship types for</td></tr>
+<tr><td class="h"><a name="646"></a>646</td><td></td><td></td><td></td><td></td><td class="s">which readings so related should be treated as equivalent.</td></tr>
+<tr><td class="h"><a name="647"></a>647</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="648"></a>648</td><td></td><td></td><td></td><td></td><td class="s">Returns a nested array data structure as follows:</td></tr>
+<tr><td class="h"><a name="649"></a>649</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="650"></a>650</td><td></td><td></td><td></td><td></td><td class="s"> [ [ group_list, is_genealogical ], [ group_list, is_genealogical ] ... ]</td></tr>
+<tr><td class="h"><a name="651"></a>651</td><td></td><td></td><td></td><td></td><td class="s"> </td></tr>
+<tr><td class="h"><a name="652"></a>652</td><td></td><td></td><td></td><td></td><td class="s">where the group list is the array of arrays passed in for each element of @groups,</td></tr>
+<tr><td class="h"><a name="653"></a>653</td><td></td><td></td><td></td><td></td><td class="s">possibly with the addition of hypothetical readings.</td></tr>
+<tr><td class="h"><a name="654"></a>654</td><td></td><td></td><td></td><td></td><td class="s"> </td></tr>
+<tr><td class="h"><a name="655"></a>655</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="656"></a>656</td><td></td><td></td><td></td><td></td><td class="s">=cut</td></tr>
+<tr><td class="h"><a name="657"></a>657</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="658"></a>658</td><td></td><td></td><td></td><td></td><td class="s">sub perl_solver {</td></tr>
+<tr><td class="h"><a name="659"></a>659</td><td></td><td></td><td></td><td></td><td class="s"> my( $graph, @groups ) = @_;</td></tr>
+<tr><td class="h"><a name="660"></a>660</td><td></td><td></td><td></td><td></td><td class="s"> my @answer;</td></tr>
+<tr><td class="h"><a name="661"></a>661</td><td></td><td></td><td></td><td></td><td class="s"> foreach my $g ( @groups ) {</td></tr>
+<tr><td class="h"><a name="662"></a>662</td><td></td><td></td><td></td><td></td><td class="s"> push( @answer, _solve_variant_location( $graph, $g ) );</td></tr>
+<tr><td class="h"><a name="663"></a>663</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr>
+<tr><td class="h"><a name="664"></a>664</td><td></td><td></td><td></td><td></td><td class="s"> return \@answer;</td></tr>
+<tr><td class="h"><a name="665"></a>665</td><td></td><td></td><td></td><td></td><td class="s">}</td></tr>
+<tr><td class="h"><a name="666"></a>666</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="667"></a>667</td><td></td><td></td><td></td><td></td><td class="s">sub _solve_variant_location {</td></tr>
+<tr><td class="h"><a name="668"></a>668</td><td></td><td></td><td></td><td></td><td class="s"> my( $graph, $groups ) = @_;</td></tr>
+<tr><td class="h"><a name="669"></a>669</td><td></td><td></td><td></td><td></td><td class="s"> # Now do the work. </td></tr>
+<tr><td class="h"><a name="670"></a>670</td><td></td><td></td><td></td><td></td><td class="s"> my $contig = {};</td></tr>
+<tr><td class="h"><a name="671"></a>671</td><td></td><td></td><td></td><td></td><td class="s"> my $subgraph = {};</td></tr>
+<tr><td class="h"><a name="672"></a>672</td><td></td><td></td><td></td><td></td><td class="s"> my $is_conflicted;</td></tr>
+<tr><td class="h"><a name="673"></a>673</td><td></td><td></td><td></td><td></td><td class="s"> my $conflict = {};</td></tr>
+<tr><td class="h"><a name="674"></a>674</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="675"></a>675</td><td></td><td></td><td></td><td></td><td class="s"> # Mark each ms as in its own group, first.</td></tr>
+<tr><td class="h"><a name="676"></a>676</td><td></td><td></td><td></td><td></td><td class="s"> foreach my $g ( @$groups ) {</td></tr>
+<tr><td class="h"><a name="677"></a>677</td><td></td><td></td><td></td><td></td><td class="s"> my $gst = wit_stringify( $g );</td></tr>
+<tr><td class="h"><a name="678"></a>678</td><td></td><td></td><td></td><td></td><td class="s"> map { $contig->{$_} = $gst } @$g;</td></tr>
+<tr><td class="h"><a name="679"></a>679</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr>
+<tr><td class="h"><a name="680"></a>680</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="681"></a>681</td><td></td><td></td><td></td><td></td><td class="s"> # Now for each unmarked node in the graph, initialize an array</td></tr>
+<tr><td class="h"><a name="682"></a>682</td><td></td><td></td><td></td><td></td><td class="s"> # for possible group memberships. We will use this later to</td></tr>
+<tr><td class="h"><a name="683"></a>683</td><td></td><td></td><td></td><td></td><td class="s"> # resolve potential conflicts.</td></tr>
+<tr><td class="h"><a name="684"></a>684</td><td></td><td></td><td></td><td></td><td class="s"> map { $contig->{$_} = [] unless $contig->{$_} } $graph->vertices;</td></tr>
+<tr><td class="h"><a name="685"></a>685</td><td></td><td></td><td></td><td></td><td class="s"> foreach my $g ( sort { scalar @$b <=> scalar @$a } @$groups ) {</td></tr>
+<tr><td class="h"><a name="686"></a>686</td><td></td><td></td><td></td><td></td><td class="s"> my $gst = wit_stringify( $g ); # This is the group name</td></tr>
+<tr><td class="h"><a name="687"></a>687</td><td></td><td></td><td></td><td></td><td class="s"> # Copy the graph, and delete all non-members from the new graph.</td></tr>
+<tr><td class="h"><a name="688"></a>688</td><td></td><td></td><td></td><td></td><td class="s"> my $part = $graph->copy;</td></tr>
+<tr><td class="h"><a name="689"></a>689</td><td></td><td></td><td></td><td></td><td class="s"> my @group_roots;</td></tr>
+<tr><td class="h"><a name="690"></a>690</td><td></td><td></td><td></td><td></td><td class="s"> $part->delete_vertices( </td></tr>
+<tr><td class="h"><a name="691"></a>691</td><td></td><td></td><td></td><td></td><td class="s"> grep { !ref( $contig->{$_} ) && $contig->{$_} ne $gst } $graph->vertices );</td></tr>
+<tr><td class="h"><a name="692"></a>692</td><td></td><td></td><td></td><td></td><td class="s"> </td></tr>
+<tr><td class="h"><a name="693"></a>693</td><td></td><td></td><td></td><td></td><td class="s"> # Now look to see if our group is connected.</td></tr>
+<tr><td class="h"><a name="694"></a>694</td><td></td><td></td><td></td><td></td><td class="s"> if( @$g > 1 ) {</td></tr>
+<tr><td class="h"><a name="695"></a>695</td><td></td><td></td><td></td><td></td><td class="s"> # We have to take directionality into account.</td></tr>
+<tr><td class="h"><a name="696"></a>696</td><td></td><td></td><td></td><td></td><td class="s"> # How many root nodes do we have?</td></tr>
+<tr><td class="h"><a name="697"></a>697</td><td></td><td></td><td></td><td></td><td class="s"> my @roots = grep { ref( $contig->{$_} ) || $contig->{$_} eq $gst } </td></tr>
+<tr><td class="h"><a name="698"></a>698</td><td></td><td></td><td></td><td></td><td class="s"> $part->predecessorless_vertices;</td></tr>
+<tr><td class="h"><a name="699"></a>699</td><td></td><td></td><td></td><td></td><td class="s"> # Assuming that @$g > 1, find the first root node that has at</td></tr>
+<tr><td class="h"><a name="700"></a>700</td><td></td><td></td><td></td><td></td><td class="s"> # least one successor belonging to our group. If this reading</td></tr>
+<tr><td class="h"><a name="701"></a>701</td><td></td><td></td><td></td><td></td><td class="s"> # is genealogical, there should be only one, but we will check</td></tr>
+<tr><td class="h"><a name="702"></a>702</td><td></td><td></td><td></td><td></td><td class="s"> # that implicitly later.</td></tr>
+<tr><td class="h"><a name="703"></a>703</td><td></td><td></td><td></td><td></td><td class="s"> foreach my $root ( @roots ) {</td></tr>
+<tr><td class="h"><a name="704"></a>704</td><td></td><td></td><td></td><td></td><td class="s"> # Prune the tree to get rid of extraneous hypotheticals.</td></tr>
+<tr><td class="h"><a name="705"></a>705</td><td></td><td></td><td></td><td></td><td class="s"> $root = _prune_subtree( $part, $root, $contig );</td></tr>
+<tr><td class="h"><a name="706"></a>706</td><td></td><td></td><td></td><td></td><td class="s"> next unless $root;</td></tr>
+<tr><td class="h"><a name="707"></a>707</td><td></td><td></td><td></td><td></td><td class="s"> # Save this root for our group.</td></tr>
+<tr><td class="h"><a name="708"></a>708</td><td></td><td></td><td></td><td></td><td class="s"> push( @group_roots, $root );</td></tr>
+<tr><td class="h"><a name="709"></a>709</td><td></td><td></td><td></td><td></td><td class="s"> # Get all the successor nodes of our root.</td></tr>
+<tr><td class="h"><a name="710"></a>710</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr>
+<tr><td class="h"><a name="711"></a>711</td><td></td><td></td><td></td><td></td><td class="s"> } else {</td></tr>
+<tr><td class="h"><a name="712"></a>712</td><td></td><td></td><td></td><td></td><td class="s"> # Dispense with the trivial case of one reading.</td></tr>
+<tr><td class="h"><a name="713"></a>713</td><td></td><td></td><td></td><td></td><td class="s"> my $wit = $g->[0];</td></tr>
+<tr><td class="h"><a name="714"></a>714</td><td></td><td></td><td></td><td></td><td class="s"> @group_roots = ( $wit );</td></tr>
+<tr><td class="h"><a name="715"></a>715</td><td></td><td></td><td></td><td></td><td class="s"> foreach my $v ( $part->vertices ) {</td></tr>
+<tr><td class="h"><a name="716"></a>716</td><td></td><td></td><td></td><td></td><td class="s"> $part->delete_vertex( $v ) unless $v eq $wit;</td></tr>
+<tr><td class="h"><a name="717"></a>717</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr>
+<tr><td class="h"><a name="718"></a>718</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr>
+<tr><td class="h"><a name="719"></a>719</td><td></td><td></td><td></td><td></td><td class="s"> </td></tr>
+<tr><td class="h"><a name="720"></a>720</td><td></td><td></td><td></td><td></td><td class="s"> if( @group_roots > 1 ) {</td></tr>
+<tr><td class="h"><a name="721"></a>721</td><td></td><td></td><td></td><td></td><td class="s"> $conflict->{$gst} = 1;</td></tr>
+<tr><td class="h"><a name="722"></a>722</td><td></td><td></td><td></td><td></td><td class="s"> $is_conflicted = 1;</td></tr>
+<tr><td class="h"><a name="723"></a>723</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr>
+<tr><td class="h"><a name="724"></a>724</td><td></td><td></td><td></td><td></td><td class="s"> # Paint the 'hypotheticals' with our group.</td></tr>
+<tr><td class="h"><a name="725"></a>725</td><td></td><td></td><td></td><td></td><td class="s"> foreach my $wit ( $part->vertices ) {</td></tr>
+<tr><td class="h"><a name="726"></a>726</td><td></td><td></td><td></td><td></td><td class="s"> if( ref( $contig->{$wit} ) ) {</td></tr>
+<tr><td class="h"><a name="727"></a>727</td><td></td><td></td><td></td><td></td><td class="s"> push( @{$contig->{$wit}}, $gst );</td></tr>
+<tr><td class="h"><a name="728"></a>728</td><td></td><td></td><td></td><td></td><td class="s"> } elsif( $contig->{$wit} ne $gst ) {</td></tr>
+<tr><td class="h"><a name="729"></a>729</td><td></td><td></td><td></td><td></td><td class="s"> warn "How did we get here?";</td></tr>
+<tr><td class="h"><a name="730"></a>730</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr>
+<tr><td class="h"><a name="731"></a>731</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr>
+<tr><td class="h"><a name="732"></a>732</td><td></td><td></td><td></td><td></td><td class="s"> </td></tr>
+<tr><td class="h"><a name="733"></a>733</td><td></td><td></td><td></td><td></td><td class="s"> </td></tr>
+<tr><td class="h"><a name="734"></a>734</td><td></td><td></td><td></td><td></td><td class="s"> # Save the relevant subgraph.</td></tr>
+<tr><td class="h"><a name="735"></a>735</td><td></td><td></td><td></td><td></td><td class="s"> $subgraph->{$gst} = $part;</td></tr>
+<tr><td class="h"><a name="736"></a>736</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr>
+<tr><td class="h"><a name="737"></a>737</td><td></td><td></td><td></td><td></td><td class="s"> </td></tr>
+<tr><td class="h"><a name="738"></a>738</td><td></td><td></td><td></td><td></td><td class="s"> # For each of our hypothetical readings, flatten its 'contig' array if</td></tr>
+<tr><td class="h"><a name="739"></a>739</td><td></td><td></td><td></td><td></td><td class="s"> # the array contains zero or one group. If we have any unflattened arrays,</td></tr>
+<tr><td class="h"><a name="740"></a>740</td><td></td><td></td><td></td><td></td><td class="s"> # we may need to run the resolution process. If the reading is already known</td></tr>
+<tr><td class="h"><a name="741"></a>741</td><td></td><td></td><td></td><td></td><td class="s"> # to have a conflict, flatten the 'contig' array to nothing; we won't resolve</td></tr>
+<tr><td class="h"><a name="742"></a>742</td><td></td><td></td><td></td><td></td><td class="s"> # it.</td></tr>
+<tr><td class="h"><a name="743"></a>743</td><td></td><td></td><td></td><td></td><td class="s"> my @resolve;</td></tr>
+<tr><td class="h"><a name="744"></a>744</td><td></td><td></td><td></td><td></td><td class="s"> foreach my $wit ( keys %$contig ) {</td></tr>
+<tr><td class="h"><a name="745"></a>745</td><td></td><td></td><td></td><td></td><td class="s"> next unless ref( $contig->{$wit} );</td></tr>
+<tr><td class="h"><a name="746"></a>746</td><td></td><td></td><td></td><td></td><td class="s"> if( @{$contig->{$wit}} > 1 ) {</td></tr>
+<tr><td class="h"><a name="747"></a>747</td><td></td><td></td><td></td><td></td><td class="s"> if( $is_conflicted ) {</td></tr>
+<tr><td class="h"><a name="748"></a>748</td><td></td><td></td><td></td><td></td><td class="s"> $contig->{$wit} = ''; # We aren't going to decide.</td></tr>
+<tr><td class="h"><a name="749"></a>749</td><td></td><td></td><td></td><td></td><td class="s"> } else {</td></tr>
+<tr><td class="h"><a name="750"></a>750</td><td></td><td></td><td></td><td></td><td class="s"> push( @resolve, $wit ); </td></tr>
+<tr><td class="h"><a name="751"></a>751</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr>
+<tr><td class="h"><a name="752"></a>752</td><td></td><td></td><td></td><td></td><td class="s"> } else {</td></tr>
+<tr><td class="h"><a name="753"></a>753</td><td></td><td></td><td></td><td></td><td class="s"> my $gst = pop @{$contig->{$wit}};</td></tr>
+<tr><td class="h"><a name="754"></a>754</td><td></td><td></td><td></td><td></td><td class="s"> $contig->{$wit} = $gst || '';</td></tr>
+<tr><td class="h"><a name="755"></a>755</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr>
+<tr><td class="h"><a name="756"></a>756</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr>
+<tr><td class="h"><a name="757"></a>757</td><td></td><td></td><td></td><td></td><td class="s"> </td></tr>
+<tr><td class="h"><a name="758"></a>758</td><td></td><td></td><td></td><td></td><td class="s"> if( @resolve ) {</td></tr>
+<tr><td class="h"><a name="759"></a>759</td><td></td><td></td><td></td><td></td><td class="s"> my $still_contig = {};</td></tr>
+<tr><td class="h"><a name="760"></a>760</td><td></td><td></td><td></td><td></td><td class="s"> foreach my $h ( @resolve ) {</td></tr>
+<tr><td class="h"><a name="761"></a>761</td><td></td><td></td><td></td><td></td><td class="s"> # For each of the hypothetical readings with more than one possibility,</td></tr>
+<tr><td class="h"><a name="762"></a>762</td><td></td><td></td><td></td><td></td><td class="s"> # try deleting it from each of its member subgraphs in turn, and see</td></tr>
+<tr><td class="h"><a name="763"></a>763</td><td></td><td></td><td></td><td></td><td class="s"> # if that breaks the contiguous grouping.</td></tr>
+<tr><td class="h"><a name="764"></a>764</td><td></td><td></td><td></td><td></td><td class="s"> # TODO This can still break in a corner case where group A can use </td></tr>
+<tr><td class="h"><a name="765"></a>765</td><td></td><td></td><td></td><td></td><td class="s"> # either vertex 1 or 2, and group B can use either vertex 2 or 1.</td></tr>
+<tr><td class="h"><a name="766"></a>766</td><td></td><td></td><td></td><td></td><td class="s"> # Revisit this if necessary; it could get brute-force nasty.</td></tr>
+<tr><td class="h"><a name="767"></a>767</td><td></td><td></td><td></td><td></td><td class="s"> foreach my $gst ( @{$contig->{$h}} ) {</td></tr>
+<tr><td class="h"><a name="768"></a>768</td><td></td><td></td><td></td><td></td><td class="s"> my $gpart = $subgraph->{$gst}->copy();</td></tr>
+<tr><td class="h"><a name="769"></a>769</td><td></td><td></td><td></td><td></td><td class="s"> # If we have come this far, there is only one root and everything</td></tr>
+<tr><td class="h"><a name="770"></a>770</td><td></td><td></td><td></td><td></td><td class="s"> # is reachable from it.</td></tr>
+<tr><td class="h"><a name="771"></a>771</td><td></td><td></td><td></td><td></td><td class="s"> my( $root ) = $gpart->predecessorless_vertices; </td></tr>
+<tr><td class="h"><a name="772"></a>772</td><td></td><td></td><td></td><td></td><td class="s"> my $reachable = {};</td></tr>
+<tr><td class="h"><a name="773"></a>773</td><td></td><td></td><td></td><td></td><td class="s"> map { $reachable->{$_} = 1 } $gpart->vertices;</td></tr>
+<tr><td class="h"><a name="774"></a>774</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="775"></a>775</td><td></td><td></td><td></td><td></td><td class="s"> # Try deleting the hypothetical node. </td></tr>
+<tr><td class="h"><a name="776"></a>776</td><td></td><td></td><td></td><td></td><td class="s"> $gpart->delete_vertex( $h );</td></tr>
+<tr><td class="h"><a name="777"></a>777</td><td></td><td></td><td></td><td></td><td class="s"> if( $h eq $root ) {</td></tr>
+<tr><td class="h"><a name="778"></a>778</td><td></td><td></td><td></td><td></td><td class="s"> # See if we still have a single root.</td></tr>
+<tr><td class="h"><a name="779"></a>779</td><td></td><td></td><td></td><td></td><td class="s"> my @roots = $gpart->predecessorless_vertices;</td></tr>
+<tr><td class="h"><a name="780"></a>780</td><td></td><td></td><td></td><td></td><td class="s"> warn "This shouldn't have happened" unless @roots;</td></tr>
+<tr><td class="h"><a name="781"></a>781</td><td></td><td></td><td></td><td></td><td class="s"> if( @roots > 1 ) {</td></tr>
+<tr><td class="h"><a name="782"></a>782</td><td></td><td></td><td></td><td></td><td class="s"> # $h is needed by this group.</td></tr>
+<tr><td class="h"><a name="783"></a>783</td><td></td><td></td><td></td><td></td><td class="s"> if( exists( $still_contig->{$h} ) ) {</td></tr>
+<tr><td class="h"><a name="784"></a>784</td><td></td><td></td><td></td><td></td><td class="s"> # Conflict!</td></tr>
+<tr><td class="h"><a name="785"></a>785</td><td></td><td></td><td></td><td></td><td class="s"> $conflict->{$gst} = 1;</td></tr>
+<tr><td class="h"><a name="786"></a>786</td><td></td><td></td><td></td><td></td><td class="s"> $still_contig->{$h} = '';</td></tr>
+<tr><td class="h"><a name="787"></a>787</td><td></td><td></td><td></td><td></td><td class="s"> } else {</td></tr>
+<tr><td class="h"><a name="788"></a>788</td><td></td><td></td><td></td><td></td><td class="s"> $still_contig->{$h} = $gst;</td></tr>
+<tr><td class="h"><a name="789"></a>789</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr>
+<tr><td class="h"><a name="790"></a>790</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr>
+<tr><td class="h"><a name="791"></a>791</td><td></td><td></td><td></td><td></td><td class="s"> } else {</td></tr>
+<tr><td class="h"><a name="792"></a>792</td><td></td><td></td><td></td><td></td><td class="s"> # $h is somewhere in the middle. See if everything</td></tr>
+<tr><td class="h"><a name="793"></a>793</td><td></td><td></td><td></td><td></td><td class="s"> # else can still be reached from the root.</td></tr>
+<tr><td class="h"><a name="794"></a>794</td><td></td><td></td><td></td><td></td><td class="s"> my %still_reachable = ( $root => 1 );</td></tr>
+<tr><td class="h"><a name="795"></a>795</td><td></td><td></td><td></td><td></td><td class="s"> map { $still_reachable{$_} = 1 }</td></tr>
+<tr><td class="h"><a name="796"></a>796</td><td></td><td></td><td></td><td></td><td class="s"> $gpart->all_successors( $root );</td></tr>
+<tr><td class="h"><a name="797"></a>797</td><td></td><td></td><td></td><td></td><td class="s"> foreach my $v ( keys %$reachable ) {</td></tr>
+<tr><td class="h"><a name="798"></a>798</td><td></td><td></td><td></td><td></td><td class="s"> next if $v eq $h;</td></tr>
+<tr><td class="h"><a name="799"></a>799</td><td></td><td></td><td></td><td></td><td class="s"> if( !$still_reachable{$v}</td></tr>
+<tr><td class="h"><a name="800"></a>800</td><td></td><td></td><td></td><td></td><td class="s"> && ( $contig->{$v} eq $gst </td></tr>
+<tr><td class="h"><a name="801"></a>801</td><td></td><td></td><td></td><td></td><td class="s"> || ( exists $still_contig->{$v} </td></tr>
+<tr><td class="h"><a name="802"></a>802</td><td></td><td></td><td></td><td></td><td class="s"> && $still_contig->{$v} eq $gst ) ) ) {</td></tr>
+<tr><td class="h"><a name="803"></a>803</td><td></td><td></td><td></td><td></td><td class="s"> # We need $h.</td></tr>
+<tr><td class="h"><a name="804"></a>804</td><td></td><td></td><td></td><td></td><td class="s"> if( exists $still_contig->{$h} ) {</td></tr>
+<tr><td class="h"><a name="805"></a>805</td><td></td><td></td><td></td><td></td><td class="s"> # Conflict!</td></tr>
+<tr><td class="h"><a name="806"></a>806</td><td></td><td></td><td></td><td></td><td class="s"> $conflict->{$gst} = 1;</td></tr>
+<tr><td class="h"><a name="807"></a>807</td><td></td><td></td><td></td><td></td><td class="s"> $still_contig->{$h} = '';</td></tr>
+<tr><td class="h"><a name="808"></a>808</td><td></td><td></td><td></td><td></td><td class="s"> } else {</td></tr>
+<tr><td class="h"><a name="809"></a>809</td><td></td><td></td><td></td><td></td><td class="s"> $still_contig->{$h} = $gst;</td></tr>
+<tr><td class="h"><a name="810"></a>810</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr>
+<tr><td class="h"><a name="811"></a>811</td><td></td><td></td><td></td><td></td><td class="s"> last;</td></tr>
+<tr><td class="h"><a name="812"></a>812</td><td></td><td></td><td></td><td></td><td class="s"> } # else we don't need $h in this group.</td></tr>
+<tr><td class="h"><a name="813"></a>813</td><td></td><td></td><td></td><td></td><td class="s"> } # end foreach $v</td></tr>
+<tr><td class="h"><a name="814"></a>814</td><td></td><td></td><td></td><td></td><td class="s"> } # endif $h eq $root</td></tr>
+<tr><td class="h"><a name="815"></a>815</td><td></td><td></td><td></td><td></td><td class="s"> } # end foreach $gst</td></tr>
+<tr><td class="h"><a name="816"></a>816</td><td></td><td></td><td></td><td></td><td class="s"> } # end foreach $h</td></tr>
+<tr><td class="h"><a name="817"></a>817</td><td></td><td></td><td></td><td></td><td class="s"> </td></tr>
+<tr><td class="h"><a name="818"></a>818</td><td></td><td></td><td></td><td></td><td class="s"> # Now we have some hypothetical vertices in $still_contig that are the </td></tr>
+<tr><td class="h"><a name="819"></a>819</td><td></td><td></td><td></td><td></td><td class="s"> # "real" group memberships. Replace these in $contig.</td></tr>
+<tr><td class="h"><a name="820"></a>820</td><td></td><td></td><td></td><td></td><td class="s"> foreach my $v ( keys %$contig ) {</td></tr>
+<tr><td class="h"><a name="821"></a>821</td><td></td><td></td><td></td><td></td><td class="s"> next unless ref $contig->{$v};</td></tr>
+<tr><td class="h"><a name="822"></a>822</td><td></td><td></td><td></td><td></td><td class="s"> $contig->{$v} = $still_contig->{$v};</td></tr>
+<tr><td class="h"><a name="823"></a>823</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr>
+<tr><td class="h"><a name="824"></a>824</td><td></td><td></td><td></td><td></td><td class="s"> } # end if @resolve</td></tr>
+<tr><td class="h"><a name="825"></a>825</td><td></td><td></td><td></td><td></td><td class="s"> </td></tr>
+<tr><td class="h"><a name="826"></a>826</td><td></td><td></td><td></td><td></td><td class="s"> my $is_genealogical = keys %$conflict ? JSON::false : JSON::true;</td></tr>
+<tr><td class="h"><a name="827"></a>827</td><td></td><td></td><td></td><td></td><td class="s"> my $variant_row = [ [], $is_genealogical ];</td></tr>
+<tr><td class="h"><a name="828"></a>828</td><td></td><td></td><td></td><td></td><td class="s"> # Fill in the groupings from $contig.</td></tr>
+<tr><td class="h"><a name="829"></a>829</td><td></td><td></td><td></td><td></td><td class="s"> foreach my $g ( @$groups ) {</td></tr>
+<tr><td class="h"><a name="830"></a>830</td><td></td><td></td><td></td><td></td><td class="s"> my $gst = wit_stringify( $g );</td></tr>
+<tr><td class="h"><a name="831"></a>831</td><td></td><td></td><td></td><td></td><td class="s"> my @realgroup = grep { $contig->{$_} eq $gst } keys %$contig;</td></tr>
+<tr><td class="h"><a name="832"></a>832</td><td></td><td></td><td></td><td></td><td class="s"> push( @{$variant_row->[0]}, \@realgroup );</td></tr>
+<tr><td class="h"><a name="833"></a>833</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr>
+<tr><td class="h"><a name="834"></a>834</td><td></td><td></td><td></td><td></td><td class="s"> return $variant_row;</td></tr>
+<tr><td class="h"><a name="835"></a>835</td><td></td><td></td><td></td><td></td><td class="s">}</td></tr>
+<tr><td class="h"><a name="836"></a>836</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="837"></a>837</td><td></td><td></td><td></td><td></td><td class="s">sub _prune_group {</td></tr>
+<tr><td class="h"><a name="838"></a>838</td><td></td><td></td><td></td><td></td><td class="s"> my( $group, $stemma, $graph ) = @_;</td></tr>
+<tr><td class="h"><a name="839"></a>839</td><td></td><td></td><td></td><td></td><td class="s"> # Get these into a form prune_subtree will recognize. Make a "contighash"</td></tr>
+<tr><td class="h"><a name="840"></a>840</td><td></td><td></td><td></td><td></td><td class="s"> my $hypohash = {};</td></tr>
+<tr><td class="h"><a name="841"></a>841</td><td></td><td></td><td></td><td></td><td class="s"> map { $hypohash->{$_} = 1 } @$group;</td></tr>
+<tr><td class="h"><a name="842"></a>842</td><td></td><td></td><td></td><td></td><td class="s"> # ...with reference values for hypotheticals.</td></tr>
+<tr><td class="h"><a name="843"></a>843</td><td></td><td></td><td></td><td></td><td class="s"> map { $hypohash->{$_} = [] } $stemma->hypotheticals;</td></tr>
+<tr><td class="h"><a name="844"></a>844</td><td></td><td></td><td></td><td></td><td class="s"> # Make our subgraph</td></tr>
+<tr><td class="h"><a name="845"></a>845</td><td></td><td></td><td></td><td></td><td class="s"> my $subgraph = $graph->copy;</td></tr>
+<tr><td class="h"><a name="846"></a>846</td><td></td><td></td><td></td><td></td><td class="s"> map { $subgraph->delete_vertex( $_ ) unless exists $hypohash->{$_} }</td></tr>
+<tr><td class="h"><a name="847"></a>847</td><td></td><td></td><td></td><td></td><td class="s"> $subgraph->vertices;</td></tr>
+<tr><td class="h"><a name="848"></a>848</td><td></td><td></td><td></td><td></td><td class="s"> # ...and find the root.</td></tr>
+<tr><td class="h"><a name="849"></a>849</td><td></td><td></td><td></td><td></td><td class="s"> my( $root ) = $subgraph->predecessorless_vertices;</td></tr>
+<tr><td class="h"><a name="850"></a>850</td><td></td><td></td><td></td><td></td><td class="s"> # Now prune and return the remaining vertices.</td></tr>
+<tr><td class="h"><a name="851"></a>851</td><td></td><td></td><td></td><td></td><td class="s"> _prune_subtree( $subgraph, $root, $hypohash );</td></tr>
+<tr><td class="h"><a name="852"></a>852</td><td></td><td></td><td></td><td></td><td class="s"> return $subgraph->vertices;</td></tr>
+<tr><td class="h"><a name="853"></a>853</td><td></td><td></td><td></td><td></td><td class="s">}</td></tr>
+<tr><td class="h"><a name="854"></a>854</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="855"></a>855</td><td></td><td></td><td></td><td></td><td class="s">sub _prune_subtree {</td></tr>
+<tr><td class="h"><a name="856"></a>856</td><td></td><td></td><td></td><td></td><td class="s"> my( $tree, $root, $contighash ) = @_;</td></tr>
+<tr><td class="h"><a name="857"></a>857</td><td></td><td></td><td></td><td></td><td class="s"> # First, delete hypothetical leaves / orphans until there are none left.</td></tr>
+<tr><td class="h"><a name="858"></a>858</td><td></td><td></td><td></td><td></td><td class="s"> my @orphan_hypotheticals = grep { ref( $contighash->{$_} ) } </td></tr>
+<tr><td class="h"><a name="859"></a>859</td><td></td><td></td><td></td><td></td><td class="s"> $tree->successorless_vertices;</td></tr>
+<tr><td class="h"><a name="860"></a>860</td><td></td><td></td><td></td><td></td><td class="s"> while( @orphan_hypotheticals ) {</td></tr>
+<tr><td class="h"><a name="861"></a>861</td><td></td><td></td><td></td><td></td><td class="s"> $tree->delete_vertices( @orphan_hypotheticals );</td></tr>
+<tr><td class="h"><a name="862"></a>862</td><td></td><td></td><td></td><td></td><td class="s"> @orphan_hypotheticals = grep { ref( $contighash->{$_} ) } </td></tr>
+<tr><td class="h"><a name="863"></a>863</td><td></td><td></td><td></td><td></td><td class="s"> $tree->successorless_vertices;</td></tr>
+<tr><td class="h"><a name="864"></a>864</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr>
+<tr><td class="h"><a name="865"></a>865</td><td></td><td></td><td></td><td></td><td class="s"> # Then delete a hypothetical root with only one successor, moving the</td></tr>
+<tr><td class="h"><a name="866"></a>866</td><td></td><td></td><td></td><td></td><td class="s"> # root to the first child that has no other predecessors.</td></tr>
+<tr><td class="h"><a name="867"></a>867</td><td></td><td></td><td></td><td></td><td class="s"> while( $tree->successors( $root ) == 1 && ref $contighash->{$root} ) {</td></tr>
+<tr><td class="h"><a name="868"></a>868</td><td></td><td></td><td></td><td></td><td class="s"> my @nextroot = $tree->successors( $root );</td></tr>
+<tr><td class="h"><a name="869"></a>869</td><td></td><td></td><td></td><td></td><td class="s"> $tree->delete_vertex( $root );</td></tr>
+<tr><td class="h"><a name="870"></a>870</td><td></td><td></td><td></td><td></td><td class="s"> ( $root ) = grep { $tree->is_predecessorless_vertex( $_ ) } @nextroot;</td></tr>
+<tr><td class="h"><a name="871"></a>871</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr>
+<tr><td class="h"><a name="872"></a>872</td><td></td><td></td><td></td><td></td><td class="s"> # The tree has been modified in place, but we need to know the new root.</td></tr>
+<tr><td class="h"><a name="873"></a>873</td><td></td><td></td><td></td><td></td><td class="s"> $root = undef unless $root && $tree->has_vertex( $root );</td></tr>
+<tr><td class="h"><a name="874"></a>874</td><td></td><td></td><td></td><td></td><td class="s"> return $root;</td></tr>
+<tr><td class="h"><a name="875"></a>875</td><td></td><td></td><td></td><td></td><td class="s">}</td></tr>
+<tr><td class="h"><a name="876"></a>876</td><td></td><td></td><td></td><td></td><td class="s"># Add the variant, subject to a.c. representation logic.</td></tr>
+<tr><td class="h"><a name="877"></a>877</td><td></td><td></td><td></td><td></td><td class="s"># This assumes that we will see the 'main' version before the a.c. version.</td></tr>
+<tr><td class="h"><a name="878"></a>878</td><td></td><td></td><td></td><td></td><td class="s">sub add_variant_wit {</td></tr>
+<tr><td class="h"><a name="879"></a>879</td><td></td><td></td><td></td><td></td><td class="s"> my( $arr, $wit, $acstr ) = @_;</td></tr>
+<tr><td class="h"><a name="880"></a>880</td><td></td><td></td><td></td><td></td><td class="s"> my $skip;</td></tr>
+<tr><td class="h"><a name="881"></a>881</td><td></td><td></td><td></td><td></td><td class="s"> if( $wit =~ /^(.*)\Q$acstr\E$/ ) {</td></tr>
+<tr><td class="h"><a name="882"></a>882</td><td></td><td></td><td></td><td></td><td class="s"> my $real = $1;</td></tr>
+<tr><td class="h"><a name="883"></a>883</td><td></td><td></td><td></td><td></td><td class="s"> $skip = grep { $_ =~ /^\Q$real\E$/ } @$arr;</td></tr>
+<tr><td class="h"><a name="884"></a>884</td><td></td><td></td><td></td><td></td><td class="s"> } </td></tr>
+<tr><td class="h"><a name="885"></a>885</td><td></td><td></td><td></td><td></td><td class="s"> push( @$arr, $wit ) unless $skip;</td></tr>
+<tr><td class="h"><a name="886"></a>886</td><td></td><td></td><td></td><td></td><td class="s">}</td></tr>
+<tr><td class="h"><a name="887"></a>887</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="888"></a>888</td><td></td><td></td><td></td><td></td><td class="s">sub _useful_variant {</td></tr>
+<tr><td class="h"><a name="889"></a>889</td><td></td><td></td><td></td><td></td><td class="s"> my( $group_readings, $graph, $acstr ) = @_;</td></tr>
+<tr><td class="h"><a name="890"></a>890</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="891"></a>891</td><td></td><td></td><td></td><td></td><td class="s"> # TODO Decide what to do with AC witnesses</td></tr>
+<tr><td class="h"><a name="892"></a>892</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="893"></a>893</td><td></td><td></td><td></td><td></td><td class="s"> # Sort by group size and return</td></tr>
+<tr><td class="h"><a name="894"></a>894</td><td></td><td></td><td></td><td></td><td class="s"> my $is_useful = 0;</td></tr>
+<tr><td class="h"><a name="895"></a>895</td><td></td><td></td><td></td><td></td><td class="s"> my( @readings, @groups ); # The sorted groups for our answer.</td></tr>
+<tr><td class="h"><a name="896"></a>896</td><td></td><td></td><td></td><td></td><td class="s"> foreach my $rdg ( sort { @{$group_readings->{$b}} <=> @{$group_readings->{$a}} } </td></tr>
+<tr><td class="h"><a name="897"></a>897</td><td></td><td></td><td></td><td></td><td class="s"> keys %$group_readings ) {</td></tr>
+<tr><td class="h"><a name="898"></a>898</td><td></td><td></td><td></td><td></td><td class="s"> push( @readings, $rdg );</td></tr>
+<tr><td class="h"><a name="899"></a>899</td><td></td><td></td><td></td><td></td><td class="s"> push( @groups, $group_readings->{$rdg} );</td></tr>
+<tr><td class="h"><a name="900"></a>900</td><td></td><td></td><td></td><td></td><td class="s"> if( @{$group_readings->{$rdg}} > 1 ) {</td></tr>
+<tr><td class="h"><a name="901"></a>901</td><td></td><td></td><td></td><td></td><td class="s"> $is_useful++;</td></tr>
+<tr><td class="h"><a name="902"></a>902</td><td></td><td></td><td></td><td></td><td class="s"> } else {</td></tr>
+<tr><td class="h"><a name="903"></a>903</td><td></td><td></td><td></td><td></td><td class="s"> my( $wit ) = @{$group_readings->{$rdg}};</td></tr>
+<tr><td class="h"><a name="904"></a>904</td><td></td><td></td><td></td><td></td><td class="s"> $wit =~ s/^(.*)\Q$acstr\E$/$1/;</td></tr>
+<tr><td class="h"><a name="905"></a>905</td><td></td><td></td><td></td><td></td><td class="s"> $is_useful++ unless( $graph->is_sink_vertex( $wit ) );</td></tr>
+<tr><td class="h"><a name="906"></a>906</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr>
+<tr><td class="h"><a name="907"></a>907</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr>
+<tr><td class="h"><a name="908"></a>908</td><td></td><td></td><td></td><td></td><td class="s"> if( $is_useful > 1 ) {</td></tr>
+<tr><td class="h"><a name="909"></a>909</td><td></td><td></td><td></td><td></td><td class="s"> return( \@readings, \@groups );</td></tr>
+<tr><td class="h"><a name="910"></a>910</td><td></td><td></td><td></td><td></td><td class="s"> } else {</td></tr>
+<tr><td class="h"><a name="911"></a>911</td><td></td><td></td><td></td><td></td><td class="s"> return( [], [] );</td></tr>
+<tr><td class="h"><a name="912"></a>912</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr>
+<tr><td class="h"><a name="913"></a>913</td><td></td><td></td><td></td><td></td><td class="s">}</td></tr>
+<tr><td class="h"><a name="914"></a>914</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="915"></a>915</td><td></td><td></td><td></td><td></td><td class="s">=head2 wit_stringify( $groups )</td></tr>
+<tr><td class="h"><a name="916"></a>916</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="917"></a>917</td><td></td><td></td><td></td><td></td><td class="s">Takes an array of witness groupings and produces a string like</td></tr>
+<tr><td class="h"><a name="918"></a>918</td><td></td><td></td><td></td><td></td><td class="s">['A','B'] / ['C','D','E'] / ['F']</td></tr>
+<tr><td class="h"><a name="919"></a>919</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="920"></a>920</td><td></td><td></td><td></td><td></td><td class="s">=cut</td></tr>
+<tr><td class="h"><a name="921"></a>921</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="922"></a>922</td><td></td><td></td><td></td><td></td><td class="s">sub wit_stringify {</td></tr>
+<tr><td class="h"><a name="923"></a>923</td><td></td><td></td><td></td><td></td><td class="s"> my $groups = shift;</td></tr>
+<tr><td class="h"><a name="924"></a>924</td><td></td><td></td><td></td><td></td><td class="s"> my @gst;</td></tr>
+<tr><td class="h"><a name="925"></a>925</td><td></td><td></td><td></td><td></td><td class="s"> # If we were passed an array of witnesses instead of an array of </td></tr>
+<tr><td class="h"><a name="926"></a>926</td><td></td><td></td><td></td><td></td><td class="s"> # groupings, then "group" the witnesses first.</td></tr>
+<tr><td class="h"><a name="927"></a>927</td><td></td><td></td><td></td><td></td><td class="s"> unless( ref( $groups->[0] ) ) {</td></tr>
+<tr><td class="h"><a name="928"></a>928</td><td></td><td></td><td></td><td></td><td class="s"> my $mkgrp = [ $groups ];</td></tr>
+<tr><td class="h"><a name="929"></a>929</td><td></td><td></td><td></td><td></td><td class="s"> $groups = $mkgrp;</td></tr>
+<tr><td class="h"><a name="930"></a>930</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr>
+<tr><td class="h"><a name="931"></a>931</td><td></td><td></td><td></td><td></td><td class="s"> foreach my $g ( @$groups ) {</td></tr>
+<tr><td class="h"><a name="932"></a>932</td><td></td><td></td><td></td><td></td><td class="s"> push( @gst, '[' . join( ',', map { "'$_'" } @$g ) . ']' );</td></tr>
+<tr><td class="h"><a name="933"></a>933</td><td></td><td></td><td></td><td></td><td class="s"> }</td></tr>
+<tr><td class="h"><a name="934"></a>934</td><td></td><td></td><td></td><td></td><td class="s"> return join( ' / ', @gst );</td></tr>
+<tr><td class="h"><a name="935"></a>935</td><td></td><td></td><td></td><td></td><td class="s">}</td></tr>
+<tr><td class="h"><a name="936"></a>936</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="937"></a>937</td><td></td><td></td><td></td><td></td><td class="s">sub _symmdiff {</td></tr>
+<tr><td class="h"><a name="938"></a>938</td><td></td><td></td><td></td><td></td><td class="s"> my( $lista, $listb ) = @_;</td></tr>
+<tr><td class="h"><a name="939"></a>939</td><td></td><td></td><td></td><td></td><td class="s"> my %union;</td></tr>
+<tr><td class="h"><a name="940"></a>940</td><td></td><td></td><td></td><td></td><td class="s"> my %scalars;</td></tr>
+<tr><td class="h"><a name="941"></a>941</td><td></td><td></td><td></td><td></td><td class="s"> map { $union{$_} = 1; $scalars{$_} = $_ } @$lista;</td></tr>
+<tr><td class="h"><a name="942"></a>942</td><td></td><td></td><td></td><td></td><td class="s"> map { $union{$_} += 1; $scalars{$_} = $_ } @$listb;</td></tr>
+<tr><td class="h"><a name="943"></a>943</td><td></td><td></td><td></td><td></td><td class="s"> my @set = grep { $union{$_} == 1 } keys %union;</td></tr>
+<tr><td class="h"><a name="944"></a>944</td><td></td><td></td><td></td><td></td><td class="s"> return map { $scalars{$_} } @set;</td></tr>
+<tr><td class="h"><a name="945"></a>945</td><td></td><td></td><td></td><td></td><td class="s">}</td></tr>
+<tr><td class="h"><a name="946"></a>946</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="947"></a>947</td><td class="c3">1</td><td class="c3"><span title="Avg 8µs">8µs</span></td><td></td><td></td><td class="s">1;</td></tr>
+<tr><td class="h"><a name="948"></a>948</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="949"></a>949</td><td></td><td></td><td></td><td></td><td class="s">=head1 LICENSE</td></tr>
+<tr><td class="h"><a name="950"></a>950</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="951"></a>951</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="952"></a>952</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="953"></a>953</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="954"></a>954</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="955"></a>955</td><td></td><td></td><td></td><td></td><td class="s">=head1 AUTHOR</td></tr>
+<tr><td class="h"><a name="956"></a>956</td><td></td><td></td><td></td><td></td><td class="s"></td></tr>
+<tr><td class="h"><a name="957"></a>957</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>
\ No newline at end of file
projects / scpubgit/stemmatology.git / blobdiff