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2 xmlns:set="http://exslt.org/sets">
4 <xsl:output method="html"/>
5 <xsl:output encoding="utf-8"/>
6 <xsl:output doctype-system="http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"/>
7 <xsl:output doctype-public="-//W3C//DTD XHTML 1.0 Transitional//EN"/>
9 <xsl:template match="/">
13 <title>Cancer Summary: <xsl:value-of select="//individual/@name"/> <xsl:value-of select="//individual/@gender"/> <xsl:value-of select="//individual/@id"/></title>
15 <link rel="shortcut icon" href="/resources/report_resources/apipe_dashboard/images/gc_favicon.png" type="image/png" />
17 <link rel="stylesheet" href="/resources/report_resources/apipe_dashboard/css/master.css" type="text/css" media="screen" />
18 <link rel="stylesheet" href="/resources/report_resources/apipe_dashboard/css/tablesorter.css" type="text/css" media="screen" />
19 <script type="text/javascript" src="/resources/report_resources/jquery/jquery.js"></script>
20 <script type="text/javascript" src="/resources/report_resources/jquery/jquery.tablesorter.min.js"></script>
21 <script type="text/javascript">
22 $(document).ready(function() {
23 $("#tier_1_snps").tablesorter({
24 // sort on first column, ascending
28 $("#tier_1_insertions").tablesorter({
29 // sort on first column, ascending
33 $("#tier_1_deletions").tablesorter({
34 // sort on first column, ascending
39 <link rel="stylesheet" href="/resources/report_resources/cancer_card/css/zoom2.css" type="text/css" media="screen"></link>
40 <script type="text/javascript" src="/resources/report_resources/cancer_card/js/dom-drag.js"></script>
42 <script type="text/javascript" src="/resources/report_resources/cancer_card/js/HotSpot2.js"></script>
43 <script type="text/javascript">
44 addEvent(window, 'load', function() {
45 HotSpotController.init("zoomImage",300, '<xsl:value-of select="//individual/circos-images/@large"/>','ZTbutton'); });
47 function addEvent(obj, evType, fn) {
48 if (obj.addEventListener) {
49 obj.addEventListener(evType, fn, false);
51 } else if (obj.attachEvent) {
52 var r = obj.attachEvent("on" + evType, fn);
60 <script type="text/javascript">
61 $(document).ready(function() {
62 $("input[type=checkbox]").click(function() {
63 alert("Clicked: " + this.value);
68 <style type="text/css" media="screen">
69 table.info_table_group td {
74 padding: 0 10px 20px 10px;
78 border-bottom: 2px solid #CCC;
85 form.status_selector {
93 form.status_selector table {
98 form.status_selector table td.lbl {
104 form.status_selector table td.table_lbl {
113 <div class="container">
114 <div class="background">
115 <div class="page_header">
116 <table cellpadding="0" cellspacing="0" border="0">
119 <img src="/resources/report_resources/apipe_dashboard/images/gc_header_logo2.png" width="44" height="45" align="absmiddle" />
122 <h1><xsl:value-of select="//individual/@name"/> <xsl:value-of select="//individual/@gender"/> <xsl:value-of select="//individual/@id"/> Cancer Summary</h1>
127 <div class="page_padding">
128 <!-- <h2 class="page_title icon_instrument_data">Flow Cell <xsl:value-of select="//flow-cell/@id"/> Status</h2> -->
129 <table cellpadding="0" cellspacing="0" border="0" class="info_table_group">
132 <h3 class="group_header">Clinical Data</h3>
133 <table border="0" cellpadding="0" cellspacing="0">
136 <table border="0" cellpadding="0" cellspacing="0" class="info_table" width="100%">
141 <tr><td class="label">Name:</td><td class="value"><xsl:value-of select="//individual/@name"/></td></tr>
143 <td class="label">Gender:</td>
146 <xsl:when test="string(//individual/@gender)">
147 <xsl:value-of select="//individual/@gender"/>
155 <tr><td class="label">ID:</td><td class="value"><xsl:value-of select="//individual/@id"/></td></tr>
160 <table border="0" cellpadding="0" cellspacing="0" class="info_table" width="100%" style="float: left;">
166 <tr><td class="label">Year Diagnosed:</td><td class="value"><xsl:value-of select="//clinical-data/@diagnosis-year"/></td></tr>
167 <tr><td class="label">Diagnosed at Age:</td><td class="value"><xsl:value-of select="//clinical-data/@diagnosis-age"/></td></tr>
169 <xsl:when test="//clinical-data/@alive = '1'">
170 <tr><td class="label">Survived:</td><td class="value">Yes</td></tr>
173 <tr><td class="label">Survived:</td><td class="value">No</td></tr>
174 <tr><td class="label">Days Survived:</td><td class="value"><xsl:value-of select="//clinical-data/@days-survived"/></td></tr>
180 <table border="0" cellpadding="0" cellspacing="0" class="info_table" width="100%" style="float: left;">
186 <tr><td class="label">Treatment:</td><td class="value"><xsl:value-of select="//clinical-data/@treatment"/></td></tr>
187 <tr><td class="label">Outcome:</td><td class="value"><xsl:value-of select="//clinical-data/@outcome"/></td></tr>
188 <tr><td class="label">AMP:</td><td class="value"><xsl:value-of select="//clinical-data/@amp"/></td></tr>
196 <h3 class="group_header">Sequencing Stats</h3>
197 <table border="0" cellpadding="0" cellspacing="0" class="info_table" width="100%">
202 <tr><td class="label">Normal Coverage:</td><td class="value"><xsl:value-of select="//samples/sample/models/model/@normal-haploid-coverage"/>X</td></tr>
203 <tr><td class="label">Tumor Coverage:</td><td class="value"><xsl:value-of select="//samples/sample/models/model/@tumor-haploid-coverage"/>X</td></tr>
208 <hr style="margin-bottom: 0;"/>
209 <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>
212 <xsl:attribute name="id">zoomImage</xsl:attribute>
213 <xsl:attribute name="src"><xsl:value-of select="//individual/circos-images/@small"/></xsl:attribute>
214 <xsl:attribute name="width">920</xsl:attribute>
215 <xsl:attribute name="height">920</xsl:attribute>
218 <h2 class="report_section" style="margin-bottom: 0">Tier 1 SNPs
219 <!-- <form class="status_selector">
220 <input type="hidden" name="table" value="tier_1_snps"/>
221 <table cellpadding="0" cellspacing="0">
223 <td class="table_lbl">Show:</td>
224 <xsl:for-each select="set:distinct(//variants/snps/snp/@validation-status)">
226 <input type="checkbox"><xsl:attribute name="value"><xsl:value-of select="."/></xsl:attribute></input>
229 <xsl:value-of select="."/>
238 <table id="tier_1_snps" class="list tablesorter" width="100%" cellspacing="0" cellpadding="0" border="0" style="margin-top: 0;">
240 <xsl:when test="count(//variants/snps/snp) > 0">
244 <th>validation status</th>
246 <th class="last">start</th>
247 <th class="last">reference</th>
248 <th class="last">variant</th>
249 <th class="last">gene</th>
250 <th class="last">amino acid change</th>
251 <th class="last">trv type</th>
255 <xsl:for-each select="//variants/snps/snp">
256 <xsl:sort select="@validation-status" data-type="text" order="ascending"/>
257 <xsl:sort select="@chromosome" data-type="number" order="ascending"/>
259 <td class="validation_status"><xsl:value-of select="@validation-status"/></td>
260 <td><xsl:value-of select="@chromosome"/></td>
262 <xsl:variable name="start" select="@start"/><xsl:value-of select="format-number($start, '#,##0')"/>
264 <td class="last"><xsl:value-of select="@reference-allele"/></td>
265 <td class="last"><xsl:value-of select="@variant-allele"/></td>
266 <td class="last"><xsl:value-of select="@gene"/></td>
267 <td class="last"><xsl:value-of select="@amino-acid-change"/></td>
268 <td class="last"><xsl:value-of select="@trv-type"/></td>
274 <tr><td><span class="note">None found.</span></td></tr>
279 <h2 class="report_section" style="margin-bottom: 0">Tier 1 Insertions</h2>
280 <table id="tier_1_insertions" class="list tablesorter" width="100%" cellspacing="0" cellpadding="0" border="0" style="margin-top: 0;">
282 <xsl:when test="count(//variants/insertions/insertion) > 0">
285 <th>validation status</th>
287 <th class="last">start</th>
288 <th class="last">stop</th>
289 <th class="last">variant</th>
290 <th class="last">gene</th>
291 <th class="last">amino acid change</th>
292 <th class="last">trv type</th>
296 <xsl:for-each select="//variants/insertions/insertion">
297 <xsl:sort select="@validation-status" data-type="text" order="ascending"/>
298 <xsl:sort select="@chromosome" data-type="number" order="ascending"/>
300 <td class="validation_status"><xsl:value-of select="@validation-status"/></td>
301 <td><xsl:value-of select="@chromosome"/></td>
303 <xsl:variable name="start" select="@start"/><xsl:value-of select="format-number($start, '#,##0')"/>
306 <xsl:variable name="stop" select="@stop"/><xsl:value-of select="format-number($stop, '#,##0')"/>
308 <td class="last"><xsl:value-of select="@variant-allele"/></td>
309 <td class="last"><xsl:value-of select="@gene"/></td>
310 <td class="last"><xsl:value-of select="@amino-acid-change"/></td>
311 <td class="last"><xsl:value-of select="@trv-type"/></td>
317 <tr><td><span class="note">None found.</span></td></tr>
322 <h2 class="report_section" style="margin-bottom: 0">Tier 1 Deletions</h2>
323 <table id="tier_1_deletions" class="list tablesorter" width="100%" cellspacing="0" cellpadding="0" border="0" style="margin-top: 0;">
325 <xsl:when test="count(//variants/deletions/deletion) > 0">
328 <th>validation status</th>
330 <th class="last">start</th>
331 <th class="last">stop</th>
332 <th class="last">reference</th>
333 <th class="last">gene</th>
334 <th class="last">amino acid change</th>
335 <th class="last">trv type</th>
339 <xsl:for-each select="//variants/deletions/deletion">
340 <xsl:sort select="@validation-status" data-type="text" order="ascending"/>
341 <xsl:sort select="@chromosome" data-type="number" order="ascending"/>
343 <td class="validation_status"><xsl:value-of select="@validation-status"/></td>
344 <td><xsl:value-of select="@chromosome"/></td>
346 <xsl:variable name="start" select="@start"/><xsl:value-of select="format-number($start, '#,##0')"/>
349 <xsl:variable name="stop" select="@stop"/><xsl:value-of select="format-number($stop, '#,##0')"/>
351 <td class="last"><xsl:value-of select="@reference-allele"/></td>
352 <td class="last"><xsl:value-of select="@gene"/></td>
353 <td class="last"><xsl:value-of select="@amino-acid-change"/></td>
354 <td class="last"><xsl:value-of select="@trv-type"/></td>
360 <tr><td><span class="note">None found.</span></td></tr>
365 <h2 class="report_section" style="margin-bottom: 0;">Structural Variations (translocations)</h2>
366 <table id="sv_translocations" class="list" width="100%" cellspacing="0" cellpadding="0" border="0" style="margin-top: 0;">
368 <xsl:when test="count(//structural-variants/translocations/translocation) > 0">
371 <th>validation status</th>
372 <th class="last">chromosome</th>
373 <th class="last">position</th>
375 <th class="last">chromosome</th>
376 <th class="last">position</th>
380 <xsl:for-each select="//structural-variants/translocations/translocation">
381 <xsl:sort select="@validation-status" data-type="text" order="ascending"/>
382 <xsl:sort select="start/@chromosome" data-type="number" order="ascending"/>
384 <td class="validation_status"><xsl:value-of select="@validation-status"/></td>
385 <td class="last"><xsl:value-of select="start/@chromosome"/></td>
387 <xsl:variable name="start_position" select="start/@position"/><xsl:value-of select="format-number($start_position, '#,##0')"/>
390 <td class="last"><span style="font-size: 100%; font-weight: bold;">→</span></td>
392 <td class="last"><xsl:value-of select="stop/@chromosome"/></td>
394 <xsl:variable name="stop_position" select="stop/@position"/><xsl:value-of select="format-number($stop_position, '#,##0')"/>
401 <tr><td><span class="note">None found.</span></td></tr>
406 <h2 class="report_section" style="margin-bottom: 0;">Structural Variations (insertions)</h2>
407 <table id="sv_insertions" class="list" width="100%" cellspacing="0" cellpadding="0" border="0" style="margin-top: 0;">
410 <xsl:when test="count(//structural-variants/insertions/insertion) > 0">
413 <th>validation status</th>
414 <th class="last">chromosome</th>
415 <th class="last">start</th>
416 <th class="last">stop</th>
417 <th class="last">size</th>
420 <xsl:for-each select="//structural-variants/insertions/insertion">
421 <xsl:sort select="@validation-status" data-type="number" order="ascending"/>
422 <xsl:sort select="start/@chromosome" data-type="number" order="ascending"/>
424 <td class="validation_status"><xsl:value-of select="@validation-status"/></td>
425 <td class="last"><xsl:value-of select="start/@chromosome"/></td>
427 <xsl:variable name="start_position" select="start/@position"/><xsl:value-of select="format-number($start_position, '#,##0')"/>
430 <xsl:variable name="stop_position" select="stop/@position"/><xsl:value-of select="format-number($stop_position, '#,##0')"/>
432 <xsl:variable name="size" select="@size"/><xsl:value-of select="format-number($size, '#,##0')"/>
438 <tr><td><span class="note">None found.</span></td></tr>
444 <h2 class="report_section" style="margin-bottom: 0;">Structural Variations (deletions)</h2>
445 <table id="sv_deletions" class="list" width="100%" cellspacing="0" cellpadding="0" border="0" style="margin-top: 0;">
447 <xsl:when test="count(//structural-variants/deletions/deletion) > 0">
450 <th>validation status</th>
451 <th class="last">chromosome</th>
452 <th class="last">start</th>
453 <th class="last">stop</th>
454 <th class="last">size</th>
458 <xsl:for-each select="//structural-variants/deletions/deletion">
459 <xsl:sort select="@validation-status" data-type="number" order="ascending"/>
460 <xsl:sort select="start/@chromosome" data-type="number" order="ascending"/>
462 <td class="validation_status"><xsl:value-of select="@validation-status"/></td>
463 <td class="last"><xsl:value-of select="start/@chromosome"/></td>
465 <xsl:variable name="start_position" select="start/@position"/><xsl:value-of select="format-number($start_position, '#,##0')"/>
468 <xsl:variable name="stop_position" select="stop/@position"/><xsl:value-of select="format-number($stop_position, '#,##0')"/>
471 <xsl:variable name="size" select="@size"/><xsl:value-of select="format-number($size, '#,##0')"/>
478 <tr><td><span class="note">None found.</span></td></tr>