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<%@ page |
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pageEncoding="UTF-8" |
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session="false" |
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import="net.sf.basedb.core.User" |
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import="net.sf.basedb.core.DbControl" |
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import="net.sf.basedb.core.SessionControl" |
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import="net.sf.basedb.core.Application" |
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import="net.sf.basedb.clients.web.Base" |
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import="net.sf.basedb.clients.web.util.HTML" |
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import="net.sf.basedb.clients.web.extensions.ExtensionsControl" |
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%> |
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<%@ taglib prefix="base" uri="/WEB-INF/base.tld" %> |
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<%@ taglib prefix="p" uri="/WEB-INF/path.tld" %> |
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<% |
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final SessionControl sc = Base.getExistingSessionControl(request, "net.sf.basedb.reggie", true); |
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final String ID = sc.getId(); |
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final float scale = Base.getScale(sc); |
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final String home = ExtensionsControl.getHomeUrl("net.sf.basedb.reggie"); |
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DbControl dc = null; |
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try |
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{ |
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dc = sc.newDbControl(); |
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final User user = User.getById(dc, sc.getLoggedInUserId()); |
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%> |
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<base:page type="default" > |
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<base:head |
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scripts="~../reggie-2.js,~genotype_standalone_check.js" |
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styles="path.css,~../css/reggie-2.css" |
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> |
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<style> |
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tbody.highlight |
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{ |
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border-top-width: 1px; |
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border-top-style: dotted; |
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} |
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|
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#compareTable |
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{ |
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width: 100%; |
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border-collapse: collapse; |
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} |
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|
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#compareTable thead |
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{ |
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border-bottom-width: 1px; |
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border-top-width: 0; |
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} |
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|
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#compareTable td |
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{ |
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text-align: center; |
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min-width: 4.5em; |
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} |
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|
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#compareTable tbody td |
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{ |
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padding-top: 1px; |
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padding-bottom: 1px; |
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} |
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|
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#compareTable .italic |
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{ |
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font-style: italic; |
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} |
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|
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#compareTable .icon-col |
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{ |
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width: 20px; |
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max-width: 20px; |
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min-width: 0; |
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} |
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|
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#compareTable .text-col |
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{ |
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text-align: left; |
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padding-left: 2px; |
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} |
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|
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.text-col img |
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{ |
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float: right; |
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} |
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|
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.comment input |
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{ |
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width: 95%; |
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min-width: 20em; |
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} |
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|
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.commonpart |
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{ |
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color: #666666; |
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font-style: italic; |
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} |
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|
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.diffpart |
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{ |
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font-weight: bold; |
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} |
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|
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</style> |
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</base:head> |
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<base:body> |
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|
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<p:path><p:pathelement |
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title="Reggie" href="<%="../index.jsp?ID="+ID%>" |
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/><p:pathelement title="Genotype check standalone VCF files" |
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/></p:path> |
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|
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<div class="content"> |
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<form name="reggie" id="wizard" class="wizard"> |
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|
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<div class="step auto-hide" id="step-1"> |
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<div class="step-no">1</div> |
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<div class="step-title">Select VCF files</div> |
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<div class="step-content"> |
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|
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<table class="step-form"> |
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<tr> |
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<td class="prompt">Existing items</td> |
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<td class="input" id="alreadyChecked"></td> |
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<td class="status" id="alreadyChecked.status"></td> |
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<td class="help"><span id="alreadyChecked.message" class="message"></span> |
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Existing tumor and normal items with genotype information. |
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</td> |
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</tr> |
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<tr class="align-top"> |
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<td class="prompt">VCF files</td> |
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<td class="input"> |
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<select class="required" multiple size="20" |
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name="files" id="files"></select> |
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|
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<base:buttongroup style="margin-top: 0.5em;"> |
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<base:button title="Browse…" id="btnBrowse" /> |
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</base:buttongroup> |
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</td> |
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<td class="status" id="files.status"></td> |
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<td class="help"><span id="files.message" class="message"></span> |
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Select one or more VCF files that should be checked. The VCF |
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files need to have data for the same SNP:s that are used |
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in the genotype QC system. |
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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> |
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|
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<div class="step auto-hide" id="step-2"> |
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<div class="step-no">2</div> |
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<div class="step-title" id="step-2-title">Genotype comparison results</div> |
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<div class="step-content"> |
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<div id="comparisons"></div> |
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</div> |
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</div> |
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|
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<div id="wizard-status"></div> |
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<div id="wizard-progress"></div> |
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|
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<table class="navigation" id="navigation"> |
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<tr> |
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<td><base:button id="gocancel" title="Cancel" /></td> |
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<td><base:button id="gonext" title="Next" image="<%=home+"/images/gonext.png"%>" /></td> |
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<td><base:button id="goregister" title="Register" image="<%=home+"/images/import.png"%>" /></td> |
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<td><base:button id="gorestart" title="Restart" image="<%=home+"/images/goback.png"%>" /></td> |
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<td id="gonext-message" class="message"></td> |
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</tr> |
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</table> |
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|
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</form> |
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</div> |
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|
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</base:body> |
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</base:page> |
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<% |
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} |
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finally |
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{ |
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if (dc != null) dc.close(); |
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} |
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%> |