extensions/net.sf.basedb.reggie/trunk/resources/analysis/genotype_qc.jsp

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4642 28 Nov 17 nicklas 1 <%@ page
4642 28 Nov 17 nicklas 2   pageEncoding="UTF-8"
4642 28 Nov 17 nicklas 3   session="false"
4642 28 Nov 17 nicklas 4   import="net.sf.basedb.core.User"
4642 28 Nov 17 nicklas 5   import="net.sf.basedb.core.DbControl"
4642 28 Nov 17 nicklas 6   import="net.sf.basedb.core.SessionControl"
4642 28 Nov 17 nicklas 7   import="net.sf.basedb.core.Application"
4642 28 Nov 17 nicklas 8   import="net.sf.basedb.clients.web.Base"  
4642 28 Nov 17 nicklas 9   import="net.sf.basedb.clients.web.util.HTML"  
4642 28 Nov 17 nicklas 10   import="net.sf.basedb.clients.web.extensions.ExtensionsControl"
4642 28 Nov 17 nicklas 11 %>
4642 28 Nov 17 nicklas 12 <%@ taglib prefix="base" uri="/WEB-INF/base.tld" %>
4642 28 Nov 17 nicklas 13 <%@ taglib prefix="p" uri="/WEB-INF/path.tld" %>
4642 28 Nov 17 nicklas 14 <%
4642 28 Nov 17 nicklas 15 final SessionControl sc = Base.getExistingSessionControl(request, "net.sf.basedb.reggie", true);
4642 28 Nov 17 nicklas 16 final String ID = sc.getId();
4642 28 Nov 17 nicklas 17 final float scale = Base.getScale(sc);
4642 28 Nov 17 nicklas 18 final String home = ExtensionsControl.getHomeUrl("net.sf.basedb.reggie");
4642 28 Nov 17 nicklas 19 DbControl dc = null;
4642 28 Nov 17 nicklas 20 try
4642 28 Nov 17 nicklas 21 {
4642 28 Nov 17 nicklas 22   dc = sc.newDbControl();
4642 28 Nov 17 nicklas 23   final User user = User.getById(dc, sc.getLoggedInUserId());
4642 28 Nov 17 nicklas 24 %>
4642 28 Nov 17 nicklas 25 <base:page type="default" >
4642 28 Nov 17 nicklas 26 <base:head 
4642 28 Nov 17 nicklas 27   scripts="~../reggie-2.js,~genotype_qc.js" 
4642 28 Nov 17 nicklas 28   styles="path.css,~../css/reggie-2.css"
4646 14 Dec 17 nicklas 29 >
4646 14 Dec 17 nicklas 30 <style>
4728 04 Apr 18 nicklas 31 tbody.highlight
4646 14 Dec 17 nicklas 32 {
4646 14 Dec 17 nicklas 33   border-top-width: 1px;
4646 14 Dec 17 nicklas 34   border-top-style: dotted;
4646 14 Dec 17 nicklas 35 }
4646 14 Dec 17 nicklas 36
4646 14 Dec 17 nicklas 37 #compareTable
4646 14 Dec 17 nicklas 38 {
4646 14 Dec 17 nicklas 39   width: 100%; 
4646 14 Dec 17 nicklas 40   border-collapse: collapse;
4646 14 Dec 17 nicklas 41 }
4646 14 Dec 17 nicklas 42
4646 14 Dec 17 nicklas 43 #compareTable thead
4646 14 Dec 17 nicklas 44 {
4646 14 Dec 17 nicklas 45   border-bottom-width: 1px;
4646 14 Dec 17 nicklas 46   border-top-width: 0;
4646 14 Dec 17 nicklas 47 }
4646 14 Dec 17 nicklas 48
4646 14 Dec 17 nicklas 49 #compareTable td
4646 14 Dec 17 nicklas 50 {
4646 14 Dec 17 nicklas 51   text-align: center;
4646 14 Dec 17 nicklas 52   min-width: 4.5em;
4646 14 Dec 17 nicklas 53 }
4646 14 Dec 17 nicklas 54
4646 14 Dec 17 nicklas 55 #compareTable tbody td
4646 14 Dec 17 nicklas 56 {
4646 14 Dec 17 nicklas 57   padding-top: 1px;
4646 14 Dec 17 nicklas 58   padding-bottom: 1px;
4646 14 Dec 17 nicklas 59 }
4646 14 Dec 17 nicklas 60
4646 14 Dec 17 nicklas 61 #compareTable .italic
4646 14 Dec 17 nicklas 62 {
4646 14 Dec 17 nicklas 63   font-style: italic;
4646 14 Dec 17 nicklas 64 }
4646 14 Dec 17 nicklas 65
4646 14 Dec 17 nicklas 66 #compareTable .icon-col
4646 14 Dec 17 nicklas 67 {
4646 14 Dec 17 nicklas 68   width: 20px;
4646 14 Dec 17 nicklas 69   max-width: 20px;
4646 14 Dec 17 nicklas 70   min-width: 0;
4646 14 Dec 17 nicklas 71 }
4646 14 Dec 17 nicklas 72
4728 04 Apr 18 nicklas 73 #compareTable .text-col
4646 14 Dec 17 nicklas 74 {
4646 14 Dec 17 nicklas 75   text-align: left;
4728 04 Apr 18 nicklas 76   padding-left: 2px;
4646 14 Dec 17 nicklas 77 }
4646 14 Dec 17 nicklas 78
4728 04 Apr 18 nicklas 79 .text-col img
4678 12 Feb 18 nicklas 80 {
4728 04 Apr 18 nicklas 81   float: right;
4678 12 Feb 18 nicklas 82 }
4678 12 Feb 18 nicklas 83
4728 04 Apr 18 nicklas 84 .comment input
4648 15 Dec 17 nicklas 85 {
4728 04 Apr 18 nicklas 86   width: 95%;
4728 04 Apr 18 nicklas 87   min-width: 20em;
4648 15 Dec 17 nicklas 88 }
4728 04 Apr 18 nicklas 89
4728 04 Apr 18 nicklas 90 .commonpart
4648 15 Dec 17 nicklas 91 {
4728 04 Apr 18 nicklas 92   color: #666666;
4728 04 Apr 18 nicklas 93   font-style: italic;
4648 15 Dec 17 nicklas 94 }
4648 15 Dec 17 nicklas 95
4728 04 Apr 18 nicklas 96 .diffpart
4646 14 Dec 17 nicklas 97 {
4728 04 Apr 18 nicklas 98   font-weight: bold;
4646 14 Dec 17 nicklas 99 }
4728 04 Apr 18 nicklas 100
4646 14 Dec 17 nicklas 101 </style>
4646 14 Dec 17 nicklas 102 </base:head>
4642 28 Nov 17 nicklas 103 <base:body>
4642 28 Nov 17 nicklas 104
4642 28 Nov 17 nicklas 105   <p:path><p:pathelement 
4642 28 Nov 17 nicklas 106     title="Reggie" href="<%="../index.jsp?ID="+ID%>" 
7217 30 May 23 nicklas 107     /><p:pathelement title="Genotype quality control (RNAseq)" 
4642 28 Nov 17 nicklas 108     /></p:path>
4642 28 Nov 17 nicklas 109
4642 28 Nov 17 nicklas 110   <div class="content">
4642 28 Nov 17 nicklas 111   <form name="reggie" id="wizard" class="wizard">
4642 28 Nov 17 nicklas 112
4642 28 Nov 17 nicklas 113   <div class="step auto-hide" id="step-1">
4642 28 Nov 17 nicklas 114     <div class="step-no">1</div>
4642 28 Nov 17 nicklas 115     <div class="step-title">Select aligned sequences</div>
4642 28 Nov 17 nicklas 116     <div class="step-content">
4642 28 Nov 17 nicklas 117     
4642 28 Nov 17 nicklas 118       <table class="step-form">
4646 14 Dec 17 nicklas 119       <tr>
4646 14 Dec 17 nicklas 120         <td class="prompt">Already checked</td>
4646 14 Dec 17 nicklas 121         <td class="input" id="alreadyChecked"></td>
4646 14 Dec 17 nicklas 122         <td class="status" id="alreadyChecked.status"></td>
4646 14 Dec 17 nicklas 123         <td class="help"><span id="alreadyChecked.message" class="message"></span>
7202 25 May 23 nicklas 124           Existing tumor and normal items that has already been checked.
4646 14 Dec 17 nicklas 125         </td>
4646 14 Dec 17 nicklas 126       </tr>
4642 28 Nov 17 nicklas 127       <tr class="align-top">
4642 28 Nov 17 nicklas 128         <td class="prompt">Aligned sequences</td>
4642 28 Nov 17 nicklas 129         <td class="input">
4642 28 Nov 17 nicklas 130           <select class="required yellow-label-support" multiple size="30"
4642 28 Nov 17 nicklas 131             name="alignedSequences" id="alignedSequences"></select>
4642 28 Nov 17 nicklas 132             
4642 28 Nov 17 nicklas 133           <base:buttongroup style="margin-top: 0.5em;">
4642 28 Nov 17 nicklas 134             <base:button title="Select manually&hellip;" id="btnSelectAlignedSequences" />
4642 28 Nov 17 nicklas 135           </base:buttongroup>
4642 28 Nov 17 nicklas 136         </td>
4642 28 Nov 17 nicklas 137         <td class="status" id="alignedSequences.status"></td>
4642 28 Nov 17 nicklas 138         <td class="help"><span id="alignedSequences.message" class="message"></span>
4642 28 Nov 17 nicklas 139           Select the sequences that should be checked. The list contains aligned sequences 
4642 28 Nov 17 nicklas 140           that has not yet been checked.
4642 28 Nov 17 nicklas 141         </td>
4642 28 Nov 17 nicklas 142       </tr>
4642 28 Nov 17 nicklas 143       </table>
4642 28 Nov 17 nicklas 144     </div>
4642 28 Nov 17 nicklas 145   </div>
4646 14 Dec 17 nicklas 146
4648 15 Dec 17 nicklas 147   <div class="step auto-hide" id="step-2">
4646 14 Dec 17 nicklas 148     <div class="step-no">2</div>
4646 14 Dec 17 nicklas 149     <div class="step-title" id="step-2-title">Genotype comparison results</div>
4646 14 Dec 17 nicklas 150     <div class="step-content">
4646 14 Dec 17 nicklas 151       <div id="comparisons"></div>
4646 14 Dec 17 nicklas 152     </div>
4646 14 Dec 17 nicklas 153   </div>
4646 14 Dec 17 nicklas 154   
4646 14 Dec 17 nicklas 155   
4642 28 Nov 17 nicklas 156     <div id="wizard-status"></div>
4646 14 Dec 17 nicklas 157     <div id="wizard-progress"></div>
4642 28 Nov 17 nicklas 158   
4642 28 Nov 17 nicklas 159     <table class="navigation" id="navigation">
4642 28 Nov 17 nicklas 160     <tr>
4642 28 Nov 17 nicklas 161       <td><base:button id="gocancel" title="Cancel" /></td>
4642 28 Nov 17 nicklas 162       <td><base:button id="gonext" title="Next" image="<%=home+"/images/gonext.png"%>" /></td>
4642 28 Nov 17 nicklas 163       <td><base:button id="goregister" title="Register" image="<%=home+"/images/import.png"%>"  /></td>
4642 28 Nov 17 nicklas 164       <td><base:button id="gorestart" title="Restart" image="<%=home+"/images/goback.png"%>" /></td>
4642 28 Nov 17 nicklas 165       <td id="gonext-message" class="message"></td>
4642 28 Nov 17 nicklas 166     </tr>
4642 28 Nov 17 nicklas 167     </table>
4642 28 Nov 17 nicklas 168   
4642 28 Nov 17 nicklas 169   </form>
4642 28 Nov 17 nicklas 170   </div>
4642 28 Nov 17 nicklas 171   
4642 28 Nov 17 nicklas 172 </base:body>
4642 28 Nov 17 nicklas 173 </base:page>
4642 28 Nov 17 nicklas 174 <%
4642 28 Nov 17 nicklas 175 }
4642 28 Nov 17 nicklas 176 finally
4642 28 Nov 17 nicklas 177 {
4642 28 Nov 17 nicklas 178   if (dc != null) dc.close();
4642 28 Nov 17 nicklas 179 }
4642 28 Nov 17 nicklas 180 %>

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