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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.util.formatter.WellCoordinateFormatter" |
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import="net.sf.basedb.clients.web.Base" |
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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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<%@ taglib prefix="tbl" uri="/WEB-INF/table.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,~create_manual_pool.js,~pools.js" |
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styles="path.css,toolbar.css,~../css/reggie-2.css" |
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> |
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<style> |
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|
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#pool-table |
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{ |
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width: 100%; |
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} |
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|
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#pool-name |
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{ |
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font-size: 125%; |
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} |
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|
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#pool-table th, #pool-table td |
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{ |
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text-align: left; |
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padding: 2px 0.5em 2px 0.5em; |
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} |
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|
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#lib-table table |
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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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#lib-table thead, #lib-table tbody |
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{ |
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border-bottom-width: 1px; |
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} |
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|
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#lib-table th, #lib-table td |
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{ |
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text-align: left; |
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padding: 2px 0.5em 2px 0.5em; |
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border-right-width: 1px; |
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} |
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|
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#lib-table tbody#lib-table-rows tr |
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{ |
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border-bottom-width: 1px; |
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border-bottom-style: dotted; |
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} |
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|
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#lib-table tbody#lib-table-rows tr.excluded |
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{ |
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font-style: italic; |
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color: #666666; |
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} |
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|
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#lib-table .check |
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{ |
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width: 25px; |
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text-align: center; |
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border-left: 0; |
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} |
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|
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#lib-table .name |
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{ |
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width: 12em; |
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} |
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|
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#lib-table .barcode |
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{ |
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width: 6em; |
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} |
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|
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#lib-table .plate |
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{ |
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width: 12em; |
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} |
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|
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#lib-table .remain |
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{ |
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width: 4em; |
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text-align: center; |
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} |
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|
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#lib-table .adapter |
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{ |
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width: 4em; |
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text-align: center; |
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} |
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|
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|
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#lib-table .molarity |
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{ |
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width: 4em; |
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text-align: center; |
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} |
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|
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#lib-table .volume |
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{ |
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width: 4em; |
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text-align: center; |
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} |
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|
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#lib-table .eb |
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{ |
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width: 4em; |
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text-align: center; |
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} |
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|
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#lib-table .status |
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{ |
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width: 20px; |
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max-width: 20px; |
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background-position: 50% 50%; |
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background-repeat: no-repeat; |
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border-right: 0; |
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} |
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|
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td.volume, span.volume |
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{ |
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color: #C80000; |
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} |
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|
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td.eb, span.eb |
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{ |
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color: #0000C8; |
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} |
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|
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#lib-table td.remarks |
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{ |
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font-style: italic; |
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} |
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|
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#lib-table .warning .status |
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{ |
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background-image: url('../images/warning.png'); |
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} |
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|
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#lib-table .lib-error .status |
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{ |
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background-image: url('../images/error.png'); |
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padding-left: 25px; |
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color: #C80000; |
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} |
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|
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#lib-table .lib-error .remarks |
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{ |
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color: #C80000; |
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} |
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|
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.wizard.flash-error #lib-table .lib-error .status |
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{ |
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animation: enlarge 1s infinite; |
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} |
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|
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.wizard.flash-error #lib-table .lib-error |
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{ |
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animation: flash 1s infinite; |
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} |
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|
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|
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#lib-table-pool-summary td |
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{ |
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font-weight: bold; |
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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="Create manual pool" |
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/></p:path> |
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|
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<div class="content" id="content"> |
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|
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<form name="reggie" id="wizard" class="wizard"> |
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<input type="hidden" name="poolName"> |
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|
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<div class="step" id="step-1"> |
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<div class="step-no">1</div> |
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<div class="step-title">Select pool options and libraries</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">Target molarity</td> |
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<td class="input"> |
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<select name="target_molarity" id="target_molarity" style="width: 4em;"> |
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<option value="1">1.0 |
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<option value="2" selected>2.0 |
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</select> |
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nM |
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</td> |
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<td class="status" id="target_molarity.status"></td> |
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<td class="help"></td> |
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</tr> |
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<tr> |
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<td class="prompt">Average volume / lib</td> |
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<td class="input"> |
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<input type="text" class="text" name="target_volume" id="target_volume" |
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value="5" style="width: 4em;"> µl (2--20) |
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</td> |
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<td class="status" id="target_volume.status"></td> |
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<td class="help" rowspan="2"> |
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<span id="target_volume.message" class="message"></span> |
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Select a target volume when mixing each lib to 2nM before pooling. |
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Use the <b>Dynamic</b> strategy to prioritize final pool molarity by mixing |
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different volume for each library. Use the <b>Fixed</b> strategy to mix all |
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libraries to the given volume. |
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</td> |
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</tr> |
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<tr> |
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<td class="prompt">Mixing strategy</td> |
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<td class="input"> |
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<label><input type="radio" name="mixing_strategy" id="mixing_strategy_dynamic" value="dynamic" checked |
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>Dynamic</label> |
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<label><input type="radio" name="mixing_strategy" id="mixing_strategy_fixed" value="fixed" |
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>Fixed</label> |
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</td> |
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<td class="status" id="mixing_strategy.status"></td> |
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</tr> |
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</table> |
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|
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<tbl:toolbar subclass="topborder bottomborder bg-filled-50"> |
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<tbl:button |
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id="btnSelectLibraries" |
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title="Select libraries…" |
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image="<%=home+"/images/new.png"%>" |
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tooltip="Select libraries to include in the pool" |
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/> |
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<tbl:button |
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id="btnRemove" |
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title="Remove" |
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image="<%=home+"/images/delete.png"%>" |
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tooltip="Remove the selected libraries from the pool" |
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/> |
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<tbl:button |
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id="btnTargetVolume" |
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title="Separate mix volume…" |
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image="<%=home+"/images/specimen.png"%>" |
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tooltip="Set volume to use in the pool for separately mixed libraries (dynamic mixing only)" |
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/> |
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<tbl:button |
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id="btnComment" |
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title="Comments…" |
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image="<%=home+"/images/comment.png"%>" |
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tooltip="Add a comment to the selected libraries" |
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/> |
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</tbl:toolbar> |
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|
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<div id="pool-table" class="bottomborder"> |
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<table> |
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<tr> |
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<th id="pool-name" style="width: 25%;"></th> |
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<td style="border-left: 1px solid #A0A0A0;" rowspan="2"> |
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nicklas |
279 |
<textarea name="poolComments" id="poolComments" style="width: 100%; height: 3.5em;"></textarea> |
2805 |
15 Oct 14 |
nicklas |
280 |
</td> |
2137 |
13 Nov 13 |
nicklas |
281 |
</tr> |
2137 |
13 Nov 13 |
nicklas |
282 |
<tr> |
2137 |
13 Nov 13 |
nicklas |
283 |
<td style="width: 25%;" id="pool-summary">0 libs • 0.00nM • 0.0µl</td> |
2137 |
13 Nov 13 |
nicklas |
284 |
</tr> |
2137 |
13 Nov 13 |
nicklas |
285 |
</table> |
2137 |
13 Nov 13 |
nicklas |
286 |
</div> |
2137 |
13 Nov 13 |
nicklas |
287 |
|
2137 |
13 Nov 13 |
nicklas |
288 |
<div id="lib-table" style="display: none;"> |
2151 |
26 Nov 13 |
nicklas |
289 |
<div style="margin: 1em;" class="messagecontainer note"> |
2151 |
26 Nov 13 |
nicklas |
290 |
<base:icon image="info.png"/> |
2151 |
26 Nov 13 |
nicklas |
291 |
<b>Separate mix:</b> <span id="num_separate_mix"></span>, |
2151 |
26 Nov 13 |
nicklas |
292 |
<b>Low quantity:</b> <span id="num_low_quantity"></span>, |
2151 |
26 Nov 13 |
nicklas |
293 |
<b>Excluded:</b> <span id="num_excluded"></span> |
2151 |
26 Nov 13 |
nicklas |
294 |
</div> |
2151 |
26 Nov 13 |
nicklas |
295 |
<table class="bottomborder topborder"> |
3026 |
11 Dec 14 |
nicklas |
296 |
<thead class="bg-filled-100"> |
2137 |
13 Nov 13 |
nicklas |
297 |
<tr> |
2137 |
13 Nov 13 |
nicklas |
298 |
<th class="check"></th> |
2137 |
13 Nov 13 |
nicklas |
299 |
<th class="name"></th> |
2137 |
13 Nov 13 |
nicklas |
300 |
<th class="barcode"></th> |
2137 |
13 Nov 13 |
nicklas |
301 |
<th class="plate"></th> |
2454 |
23 May 14 |
nicklas |
302 |
<th class="remain">Remain</th> |
2454 |
23 May 14 |
nicklas |
303 |
<th class="adapter">Adapter</th> |
2137 |
13 Nov 13 |
nicklas |
304 |
<th class="molarity">DNA</th> |
2137 |
13 Nov 13 |
nicklas |
305 |
<th class="volume">Volume</th> |
2137 |
13 Nov 13 |
nicklas |
306 |
<th class="eb">EB</th> |
2805 |
15 Oct 14 |
nicklas |
307 |
<th class="remarks" colspan="2"></th> |
2137 |
13 Nov 13 |
nicklas |
308 |
</tr> |
2137 |
13 Nov 13 |
nicklas |
309 |
<tr> |
2805 |
15 Oct 14 |
nicklas |
310 |
<th class="check"><base:icon image="check_uncheck.png" tooltip="Check/uncheck all" id="checkAll" /></th> |
2137 |
13 Nov 13 |
nicklas |
311 |
<th class="name">Library</th> |
2137 |
13 Nov 13 |
nicklas |
312 |
<th class="barcode">Barcode</th> |
2137 |
13 Nov 13 |
nicklas |
313 |
<th class="plate">Work plate</th> |
2137 |
13 Nov 13 |
nicklas |
314 |
<th class="molarity">(µl)</th> |
2454 |
23 May 14 |
nicklas |
315 |
<th class="adapter">(%)</th> |
2137 |
13 Nov 13 |
nicklas |
316 |
<th class="molarity">(nM)</th> |
2137 |
13 Nov 13 |
nicklas |
317 |
<th class="volume">(µl)</th> |
2137 |
13 Nov 13 |
nicklas |
318 |
<th class="eb">(µl)</th> |
2805 |
15 Oct 14 |
nicklas |
319 |
<th class="remarks" colspan="2">Remarks</th> |
2137 |
13 Nov 13 |
nicklas |
320 |
</tr> |
2137 |
13 Nov 13 |
nicklas |
321 |
</thead> |
2137 |
13 Nov 13 |
nicklas |
322 |
<tbody id="lib-table-rows"></tbody> |
2137 |
13 Nov 13 |
nicklas |
323 |
<tbody style="border-bottom: 0;"> |
2137 |
13 Nov 13 |
nicklas |
324 |
<tr id="lib-table-pool-summary"> |
3026 |
11 Dec 14 |
nicklas |
325 |
<td colspan="8" class="bg-filled-100" style="text-align: right; border-left: 0;">EB volume to add</td> |
2137 |
13 Nov 13 |
nicklas |
326 |
<td class="eb" id="pool.eb"></td> |
3026 |
11 Dec 14 |
nicklas |
327 |
<td class="remarks bg-filled-100" id="pool.remarks" colspan="2"></td> |
2137 |
13 Nov 13 |
nicklas |
328 |
</tr> |
2137 |
13 Nov 13 |
nicklas |
329 |
</tbody> |
2137 |
13 Nov 13 |
nicklas |
330 |
</table> |
2137 |
13 Nov 13 |
nicklas |
331 |
<div style="margin: 1em; font-style: italic;"> |
2140 |
18 Nov 13 |
nicklas |
332 |
* Low quantity = The remaining quantity of this library too low to mix to target molarity for the pool. |
2137 |
13 Nov 13 |
nicklas |
333 |
</div> |
2137 |
13 Nov 13 |
nicklas |
334 |
</div> |
2137 |
13 Nov 13 |
nicklas |
335 |
|
2137 |
13 Nov 13 |
nicklas |
336 |
<div id="not-selected" class="messagecontainer note">No libraries have been selected</div> |
2805 |
15 Oct 14 |
nicklas |
337 |
</div> |
2137 |
13 Nov 13 |
nicklas |
338 |
</div> |
2137 |
13 Nov 13 |
nicklas |
339 |
|
2805 |
15 Oct 14 |
nicklas |
340 |
<div id="wizard-status"></div> |
2137 |
13 Nov 13 |
nicklas |
341 |
|
2805 |
15 Oct 14 |
nicklas |
342 |
<table class="navigation" id="navigation"> |
2805 |
15 Oct 14 |
nicklas |
343 |
<tr> |
2805 |
15 Oct 14 |
nicklas |
344 |
<td><base:button id="gocancel" title="Cancel" /></td> |
2805 |
15 Oct 14 |
nicklas |
345 |
<td><base:button id="gonext" title="Next" image="<%=home+"/images/gonext.png"%>" /></td> |
2805 |
15 Oct 14 |
nicklas |
346 |
<td><base:button id="goregister" title="Register" image="<%=home+"/images/import.png"%>" /></td> |
2805 |
15 Oct 14 |
nicklas |
347 |
<td><base:button id="gorestart" title="Restart" image="<%=home+"/images/goback.png"%>" /></td> |
2805 |
15 Oct 14 |
nicklas |
348 |
<td id="gonext-message" class="message"></td> |
2805 |
15 Oct 14 |
nicklas |
349 |
</tr> |
2137 |
13 Nov 13 |
nicklas |
350 |
</table> |
2137 |
13 Nov 13 |
nicklas |
351 |
|
2137 |
13 Nov 13 |
nicklas |
352 |
</form> |
2137 |
13 Nov 13 |
nicklas |
353 |
</div> |
2137 |
13 Nov 13 |
nicklas |
354 |
|
2137 |
13 Nov 13 |
nicklas |
355 |
</base:body> |
2137 |
13 Nov 13 |
nicklas |
356 |
</base:page> |
2137 |
13 Nov 13 |
nicklas |
357 |
<% |
2137 |
13 Nov 13 |
nicklas |
358 |
} |
2137 |
13 Nov 13 |
nicklas |
359 |
finally |
2137 |
13 Nov 13 |
nicklas |
360 |
{ |
2137 |
13 Nov 13 |
nicklas |
361 |
if (dc != null) dc.close(); |
2137 |
13 Nov 13 |
nicklas |
362 |
} |
2137 |
13 Nov 13 |
nicklas |
363 |
%> |