491 lines
23 KiB
XML
491 lines
23 KiB
XML
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<xsl:stylesheet xmlns:xsl="http://www.w3.org/1999/XSL/Transform" version="1.0"
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xmlns:set="http://exslt.org/sets">
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<xsl:output method="html"/>
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<xsl:output encoding="utf-8"/>
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<xsl:output doctype-system="http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"/>
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<xsl:output doctype-public="-//W3C//DTD XHTML 1.0 Transitional//EN"/>
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<xsl:template match="/">
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<html>
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<head>
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<title>Cancer Summary: <xsl:value-of select="//individual/@name"/> <xsl:value-of select="//individual/@gender"/> <xsl:value-of select="//individual/@id"/></title>
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<link rel="shortcut icon" href="/resources/report_resources/apipe_dashboard/images/gc_favicon.png" type="image/png" />
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<link rel="stylesheet" href="/resources/report_resources/apipe_dashboard/css/master.css" type="text/css" media="screen" />
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<link rel="stylesheet" href="/resources/report_resources/apipe_dashboard/css/tablesorter.css" type="text/css" media="screen" />
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<script type="text/javascript" src="/resources/report_resources/jquery/jquery.js"></script>
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<script type="text/javascript" src="/resources/report_resources/jquery/jquery.tablesorter.min.js"></script>
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<script type="text/javascript">
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$(document).ready(function() {
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$("#tier_1_snps").tablesorter({
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// sort on first column, ascending
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// sortList: [[0,0]]
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});
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$("#tier_1_insertions").tablesorter({
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// sort on first column, ascending
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//sortList: [[0,0]]
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});
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$("#tier_1_deletions").tablesorter({
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// sort on first column, ascending
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//sortList: [[0,0]]
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});
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});
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</script>
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<link rel="stylesheet" href="/resources/report_resources/cancer_card/css/zoom2.css" type="text/css" media="screen"></link>
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<script type="text/javascript" src="/resources/report_resources/cancer_card/js/dom-drag.js"></script>
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<script type="text/javascript" src="/resources/report_resources/cancer_card/js/HotSpot2.js"></script>
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<script type="text/javascript">
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addEvent(window, 'load', function() {
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HotSpotController.init("zoomImage",300, '<xsl:value-of select="//individual/circos-images/@large"/>','ZTbutton'); });
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function addEvent(obj, evType, fn) {
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if (obj.addEventListener) {
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obj.addEventListener(evType, fn, false);
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return true;
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} else if (obj.attachEvent) {
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var r = obj.attachEvent("on" + evType, fn);
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return r;
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} else {
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return false;
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}
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}
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</script>
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<script type="text/javascript">
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$(document).ready(function() {
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$("input[type=checkbox]").click(function() {
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alert("Clicked: " + this.value);
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});
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});
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</script>
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<style type="text/css" media="screen">
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table.info_table_group td {
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padding-right: 10px;
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}
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div.content_padding {
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padding: 0 10px 20px 10px;
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}
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h3.group_header {
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border-bottom: 2px solid #CCC;
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}
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div.circos_graph {
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float: left;
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width: 920px;
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}
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form.status_selector {
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margin: 0;
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padding: 0;
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float: right;
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font-size: 85%;
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font-weight: normal;
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}
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form.status_selector table {
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margin: 0;
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padding: 0;
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}
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form.status_selector table td.lbl {
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padding-right: 10px;
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padding-left: 5px;
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}
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form.status_selector table td.table_lbl {
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font-weight: bold;
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padding-right: 8px;
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padding-left: 3px;
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}
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</style>
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</head>
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<body>
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<div class="container">
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<div class="background">
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<div class="page_header">
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<table cellpadding="0" cellspacing="0" border="0">
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<tr>
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<td>
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<img src="/resources/report_resources/apipe_dashboard/images/gc_header_logo2.png" width="44" height="45" align="absmiddle" />
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</td>
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<td>
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<h1><xsl:value-of select="//individual/@name"/> <xsl:value-of select="//individual/@gender"/> <xsl:value-of select="//individual/@id"/> Cancer Summary</h1>
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</td>
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</tr>
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</table>
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</div>
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<div class="page_padding">
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<!-- <h2 class="page_title icon_instrument_data">Flow Cell <xsl:value-of select="//flow-cell/@id"/> Status</h2> -->
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<table cellpadding="0" cellspacing="0" border="0" class="info_table_group">
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<tr>
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<td>
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<h3 class="group_header">Clinical Data</h3>
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<table border="0" cellpadding="0" cellspacing="0">
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<tr>
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<td>
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<table border="0" cellpadding="0" cellspacing="0" class="info_table" width="100%">
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<colgroup>
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<col/>
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<col width="100%"/>
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</colgroup>
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<tr><td class="label">Name:</td><td class="value"><xsl:value-of select="//individual/@name"/></td></tr>
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<tr>
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<td class="label">Gender:</td>
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<td class="value">
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<xsl:choose>
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<xsl:when test="string(//individual/@gender)">
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<xsl:value-of select="//individual/@gender"/>
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</xsl:when>
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<xsl:otherwise>
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Not Provided
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</xsl:otherwise>
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</xsl:choose>
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</td>
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</tr>
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<tr><td class="label">ID:</td><td class="value"><xsl:value-of select="//individual/@id"/></td></tr>
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</table>
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</td>
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<td>
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<table border="0" cellpadding="0" cellspacing="0" class="info_table" width="100%" style="float: left;">
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<colgroup>
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<col/>
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<col width="100%"/>
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</colgroup>
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<tr><td class="label">Year Diagnosed:</td><td class="value"><xsl:value-of select="//clinical-data/@diagnosis-year"/></td></tr>
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<tr><td class="label">Diagnosed at Age:</td><td class="value"><xsl:value-of select="//clinical-data/@diagnosis-age"/></td></tr>
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<xsl:choose>
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<xsl:when test="//clinical-data/@alive = '1'">
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<tr><td class="label">Survived:</td><td class="value">Yes</td></tr>
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</xsl:when>
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<xsl:otherwise>
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<tr><td class="label">Survived:</td><td class="value">No</td></tr>
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<tr><td class="label">Days Survived:</td><td class="value"><xsl:value-of select="//clinical-data/@days-survived"/></td></tr>
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</xsl:otherwise>
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</xsl:choose>
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</table>
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</td>
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<td>
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<table border="0" cellpadding="0" cellspacing="0" class="info_table" width="100%" style="float: left;">
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<colgroup>
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<col/>
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<col width="100%"/>
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</colgroup>
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<tr><td class="label">Treatment:</td><td class="value"><xsl:value-of select="//clinical-data/@treatment"/></td></tr>
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<tr><td class="label">Outcome:</td><td class="value"><xsl:value-of select="//clinical-data/@outcome"/></td></tr>
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<tr><td class="label">AMP:</td><td class="value"><xsl:value-of select="//clinical-data/@amp"/></td></tr>
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</table>
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</td>
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</tr>
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</table>
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</td>
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<td>
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<h3 class="group_header">Sequencing Stats</h3>
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<table border="0" cellpadding="0" cellspacing="0" class="info_table" width="100%">
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<colgroup>
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<col/>
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<col width="100%"/>
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</colgroup>
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<tr><td class="label">Normal Coverage:</td><td class="value"><xsl:value-of select="//samples/sample/models/model/@normal-haploid-coverage"/>X</td></tr>
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<tr><td class="label">Tumor Coverage:</td><td class="value"><xsl:value-of select="//samples/sample/models/model/@tumor-haploid-coverage"/>X</td></tr>
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</table>
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</td>
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</tr>
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</table>
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<hr style="margin-bottom: 0;"/>
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<h2 class="report_section" style="margin-bottom: 0; margin-top: 0">Circos Graph   <a id="ZTbutton" href="javascript: void(0);" style="font-size: 85%; font-weight: normal;">[toggle zoom]</a></h2>
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<p id="ZTthumbnail">
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<img>
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<xsl:attribute name="id">zoomImage</xsl:attribute>
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<xsl:attribute name="src"><xsl:value-of select="//individual/circos-images/@small"/></xsl:attribute>
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<xsl:attribute name="width">920</xsl:attribute>
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<xsl:attribute name="height">920</xsl:attribute>
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</img>
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</p>
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<h2 class="report_section" style="margin-bottom: 0">Tier 1 SNPs
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<!-- <form class="status_selector">
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<input type="hidden" name="table" value="tier_1_snps"/>
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<table cellpadding="0" cellspacing="0">
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<tr>
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<td class="table_lbl">Show:</td>
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<xsl:for-each select="set:distinct(//variants/snps/snp/@validation-status)">
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<td class="cb">
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<input type="checkbox"><xsl:attribute name="value"><xsl:value-of select="."/></xsl:attribute></input>
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</td>
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<td class="lbl">
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<xsl:value-of select="."/>
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</td>
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</xsl:for-each>
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</tr>
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</table>
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</form>
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-->
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</h2>
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<table id="tier_1_snps" class="list tablesorter" width="100%" cellspacing="0" cellpadding="0" border="0" style="margin-top: 0;">
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<xsl:choose>
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<xsl:when test="count(//variants/snps/snp) > 0">
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<thead>
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<tr>
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<th>validation status</th>
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<th>chromosome</th>
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<th class="last">start</th>
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<th class="last">reference</th>
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<th class="last">variant</th>
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<th class="last">gene</th>
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<th class="last">amino acid change</th>
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<th class="last">trv type</th>
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</tr>
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</thead>
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<tbody>
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<xsl:for-each select="//variants/snps/snp">
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<xsl:sort select="@validation-status" data-type="text" order="ascending"/>
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<xsl:sort select="@chromosome" data-type="number" order="ascending"/>
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<tr>
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<td class="validation_status"><xsl:value-of select="@validation-status"/></td>
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<td><xsl:value-of select="@chromosome"/></td>
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<td class="last">
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<xsl:variable name="start" select="@start"/><xsl:value-of select="format-number($start, '#,##0')"/>
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</td>
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<td class="last"><xsl:value-of select="@reference-allele"/></td>
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<td class="last"><xsl:value-of select="@variant-allele"/></td>
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<td class="last"><xsl:value-of select="@gene"/></td>
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<td class="last"><xsl:value-of select="@amino-acid-change"/></td>
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<td class="last"><xsl:value-of select="@trv-type"/></td>
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</tr>
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</xsl:for-each>
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</tbody>
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</xsl:when>
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<xsl:otherwise>
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<tr><td><span class="note">None found.</span></td></tr>
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</xsl:otherwise>
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</xsl:choose>
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</table>
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<h2 class="report_section" style="margin-bottom: 0">Tier 1 Insertions</h2>
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<table id="tier_1_insertions" class="list tablesorter" width="100%" cellspacing="0" cellpadding="0" border="0" style="margin-top: 0;">
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<xsl:choose>
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<xsl:when test="count(//variants/insertions/insertion) > 0">
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<thead>
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<tr>
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<th>validation status</th>
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<th>chromosome</th>
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<th class="last">start</th>
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<th class="last">stop</th>
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<th class="last">variant</th>
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<th class="last">gene</th>
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<th class="last">amino acid change</th>
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<th class="last">trv type</th>
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</tr>
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</thead>
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<tbody>
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<xsl:for-each select="//variants/insertions/insertion">
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<xsl:sort select="@validation-status" data-type="text" order="ascending"/>
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<xsl:sort select="@chromosome" data-type="number" order="ascending"/>
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<tr>
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<td class="validation_status"><xsl:value-of select="@validation-status"/></td>
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<td><xsl:value-of select="@chromosome"/></td>
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<td class="last">
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<xsl:variable name="start" select="@start"/><xsl:value-of select="format-number($start, '#,##0')"/>
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</td>
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<td class="last">
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<xsl:variable name="stop" select="@stop"/><xsl:value-of select="format-number($stop, '#,##0')"/>
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</td>
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<td class="last"><xsl:value-of select="@variant-allele"/></td>
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<td class="last"><xsl:value-of select="@gene"/></td>
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<td class="last"><xsl:value-of select="@amino-acid-change"/></td>
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<td class="last"><xsl:value-of select="@trv-type"/></td>
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</tr>
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</xsl:for-each>
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</tbody>
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</xsl:when>
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<xsl:otherwise>
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<tr><td><span class="note">None found.</span></td></tr>
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</xsl:otherwise>
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</xsl:choose>
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</table>
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<h2 class="report_section" style="margin-bottom: 0">Tier 1 Deletions</h2>
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<table id="tier_1_deletions" class="list tablesorter" width="100%" cellspacing="0" cellpadding="0" border="0" style="margin-top: 0;">
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<xsl:choose>
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<xsl:when test="count(//variants/deletions/deletion) > 0">
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<thead>
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<tr>
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<th>validation status</th>
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<th>chromosome</th>
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<th class="last">start</th>
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<th class="last">stop</th>
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<th class="last">reference</th>
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<th class="last">gene</th>
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<th class="last">amino acid change</th>
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<th class="last">trv type</th>
|
||
|
|
</tr>
|
||
|
|
</thead>
|
||
|
|
<tbody>
|
||
|
|
<xsl:for-each select="//variants/deletions/deletion">
|
||
|
|
<xsl:sort select="@validation-status" data-type="text" order="ascending"/>
|
||
|
|
<xsl:sort select="@chromosome" data-type="number" order="ascending"/>
|
||
|
|
<tr>
|
||
|
|
<td class="validation_status"><xsl:value-of select="@validation-status"/></td>
|
||
|
|
<td><xsl:value-of select="@chromosome"/></td>
|
||
|
|
<td class="last">
|
||
|
|
<xsl:variable name="start" select="@start"/><xsl:value-of select="format-number($start, '#,##0')"/>
|
||
|
|
</td>
|
||
|
|
<td class="last">
|
||
|
|
<xsl:variable name="stop" select="@stop"/><xsl:value-of select="format-number($stop, '#,##0')"/>
|
||
|
|
</td>
|
||
|
|
<td class="last"><xsl:value-of select="@reference-allele"/></td>
|
||
|
|
<td class="last"><xsl:value-of select="@gene"/></td>
|
||
|
|
<td class="last"><xsl:value-of select="@amino-acid-change"/></td>
|
||
|
|
<td class="last"><xsl:value-of select="@trv-type"/></td>
|
||
|
|
</tr>
|
||
|
|
</xsl:for-each>
|
||
|
|
</tbody>
|
||
|
|
</xsl:when>
|
||
|
|
<xsl:otherwise>
|
||
|
|
<tr><td><span class="note">None found.</span></td></tr>
|
||
|
|
</xsl:otherwise>
|
||
|
|
</xsl:choose>
|
||
|
|
</table>
|
||
|
|
|
||
|
|
<h2 class="report_section" style="margin-bottom: 0;">Structural Variations (translocations)</h2>
|
||
|
|
<table id="sv_translocations" class="list" width="100%" cellspacing="0" cellpadding="0" border="0" style="margin-top: 0;">
|
||
|
|
<xsl:choose>
|
||
|
|
<xsl:when test="count(//structural-variants/translocations/translocation) > 0">
|
||
|
|
<thead>
|
||
|
|
<tr>
|
||
|
|
<th>validation status</th>
|
||
|
|
<th class="last">chromosome</th>
|
||
|
|
<th class="last">position</th>
|
||
|
|
<th> </th>
|
||
|
|
<th class="last">chromosome</th>
|
||
|
|
<th class="last">position</th>
|
||
|
|
</tr>
|
||
|
|
</thead>
|
||
|
|
<tbody>
|
||
|
|
<xsl:for-each select="//structural-variants/translocations/translocation">
|
||
|
|
<xsl:sort select="@validation-status" data-type="text" order="ascending"/>
|
||
|
|
<xsl:sort select="start/@chromosome" data-type="number" order="ascending"/>
|
||
|
|
<tr>
|
||
|
|
<td class="validation_status"><xsl:value-of select="@validation-status"/></td>
|
||
|
|
<td class="last"><xsl:value-of select="start/@chromosome"/></td>
|
||
|
|
<td class="last">
|
||
|
|
<xsl:variable name="start_position" select="start/@position"/><xsl:value-of select="format-number($start_position, '#,##0')"/>
|
||
|
|
</td>
|
||
|
|
|
||
|
|
<td class="last"><span style="font-size: 100%; font-weight: bold;">→</span></td>
|
||
|
|
|
||
|
|
<td class="last"><xsl:value-of select="stop/@chromosome"/></td>
|
||
|
|
<td class="last">
|
||
|
|
<xsl:variable name="stop_position" select="stop/@position"/><xsl:value-of select="format-number($stop_position, '#,##0')"/>
|
||
|
|
</td>
|
||
|
|
</tr>
|
||
|
|
</xsl:for-each>
|
||
|
|
</tbody>
|
||
|
|
</xsl:when>
|
||
|
|
<xsl:otherwise>
|
||
|
|
<tr><td><span class="note">None found.</span></td></tr>
|
||
|
|
</xsl:otherwise>
|
||
|
|
</xsl:choose>
|
||
|
|
</table>
|
||
|
|
|
||
|
|
<h2 class="report_section" style="margin-bottom: 0;">Structural Variations (insertions)</h2>
|
||
|
|
<table id="sv_insertions" class="list" width="100%" cellspacing="0" cellpadding="0" border="0" style="margin-top: 0;">
|
||
|
|
<tbody>
|
||
|
|
<xsl:choose>
|
||
|
|
<xsl:when test="count(//structural-variants/insertions/insertion) > 0">
|
||
|
|
<thead>
|
||
|
|
<tr>
|
||
|
|
<th>validation status</th>
|
||
|
|
<th class="last">chromosome</th>
|
||
|
|
<th class="last">start</th>
|
||
|
|
<th class="last">stop</th>
|
||
|
|
<th class="last">size</th>
|
||
|
|
</tr>
|
||
|
|
</thead>
|
||
|
|
<xsl:for-each select="//structural-variants/insertions/insertion">
|
||
|
|
<xsl:sort select="@validation-status" data-type="number" order="ascending"/>
|
||
|
|
<xsl:sort select="start/@chromosome" data-type="number" order="ascending"/>
|
||
|
|
<tr>
|
||
|
|
<td class="validation_status"><xsl:value-of select="@validation-status"/></td>
|
||
|
|
<td class="last"><xsl:value-of select="start/@chromosome"/></td>
|
||
|
|
<td class="last">
|
||
|
|
<xsl:variable name="start_position" select="start/@position"/><xsl:value-of select="format-number($start_position, '#,##0')"/>
|
||
|
|
</td>
|
||
|
|
<td class="last">
|
||
|
|
<xsl:variable name="stop_position" select="stop/@position"/><xsl:value-of select="format-number($stop_position, '#,##0')"/>
|
||
|
|
</td>
|
||
|
|
<xsl:variable name="size" select="@size"/><xsl:value-of select="format-number($size, '#,##0')"/>
|
||
|
|
|
||
|
|
</tr>
|
||
|
|
</xsl:for-each>
|
||
|
|
</xsl:when>
|
||
|
|
<xsl:otherwise>
|
||
|
|
<tr><td><span class="note">None found.</span></td></tr>
|
||
|
|
</xsl:otherwise>
|
||
|
|
</xsl:choose>
|
||
|
|
</tbody>
|
||
|
|
</table>
|
||
|
|
|
||
|
|
<h2 class="report_section" style="margin-bottom: 0;">Structural Variations (deletions)</h2>
|
||
|
|
<table id="sv_deletions" class="list" width="100%" cellspacing="0" cellpadding="0" border="0" style="margin-top: 0;">
|
||
|
|
<xsl:choose>
|
||
|
|
<xsl:when test="count(//structural-variants/deletions/deletion) > 0">
|
||
|
|
<thead>
|
||
|
|
<tr>
|
||
|
|
<th>validation status</th>
|
||
|
|
<th class="last">chromosome</th>
|
||
|
|
<th class="last">start</th>
|
||
|
|
<th class="last">stop</th>
|
||
|
|
<th class="last">size</th>
|
||
|
|
</tr>
|
||
|
|
</thead>
|
||
|
|
<tbody>
|
||
|
|
<xsl:for-each select="//structural-variants/deletions/deletion">
|
||
|
|
<xsl:sort select="@validation-status" data-type="number" order="ascending"/>
|
||
|
|
<xsl:sort select="start/@chromosome" data-type="number" order="ascending"/>
|
||
|
|
<tr>
|
||
|
|
<td class="validation_status"><xsl:value-of select="@validation-status"/></td>
|
||
|
|
<td class="last"><xsl:value-of select="start/@chromosome"/></td>
|
||
|
|
<td class="last">
|
||
|
|
<xsl:variable name="start_position" select="start/@position"/><xsl:value-of select="format-number($start_position, '#,##0')"/>
|
||
|
|
</td>
|
||
|
|
<td class="last">
|
||
|
|
<xsl:variable name="stop_position" select="stop/@position"/><xsl:value-of select="format-number($stop_position, '#,##0')"/>
|
||
|
|
</td>
|
||
|
|
<td class="last">
|
||
|
|
<xsl:variable name="size" select="@size"/><xsl:value-of select="format-number($size, '#,##0')"/>
|
||
|
|
</td>
|
||
|
|
</tr>
|
||
|
|
</xsl:for-each>
|
||
|
|
</tbody>
|
||
|
|
</xsl:when>
|
||
|
|
<xsl:otherwise>
|
||
|
|
<tr><td><span class="note">None found.</span></td></tr>
|
||
|
|
</xsl:otherwise>
|
||
|
|
</xsl:choose>
|
||
|
|
</table>
|
||
|
|
</div>
|
||
|
|
</div>
|
||
|
|
</div>
|
||
|
|
</body>
|
||
|
|
</html>
|
||
|
|
|
||
|
|
</xsl:template>
|
||
|
|
|
||
|
|
</xsl:stylesheet>
|