source: extensions/net.sf.basedb.reggie/trunk/resources/flaggedalignment/search.jsp @ 4982

Last change on this file since 4982 was 4982, checked in by Nicklas Nordborg, 3 years ago

References #1054: Even more functionality in the Flagged alignment wizard

Added PreNormalizedRNA as an option for the DoNotUse annotation. The options is of course only available if the alignment has a pre-normalied RNA item in the parent chain.

A minor complication is present when filtering on a QiaCube. It is possible that alignments from both a pre-normalized and a regular RNA exists and that there is a mixup that only affects the pre-normalized RNA. But the "Resolve" options are grouped by QiaCube positions so there is only one set of options for the two alignments. If the PreNormalizedRNA option is selected, only the pre-normalized RNA is marked as DoNotUse and we rely on the auto-unflag option to fix the regular RNA as if the Ok checkbox had been selected.

File size: 6.2 KB
Line 
1<%@ page
2  pageEncoding="UTF-8"
3  session="false"
4  import="net.sf.basedb.core.User"
5  import="net.sf.basedb.core.DbControl"
6  import="net.sf.basedb.core.SessionControl"
7  import="net.sf.basedb.core.Application"
8  import="net.sf.basedb.util.formatter.DateFormatter"
9  import="net.sf.basedb.util.formatter.Formatter"
10  import="net.sf.basedb.clients.web.Base" 
11  import="net.sf.basedb.clients.web.extensions.ExtensionsControl"
12  import="java.util.Date"
13%>
14<%@ taglib prefix="base" uri="/WEB-INF/base.tld" %>
15<%@ taglib prefix="tbl" uri="/WEB-INF/table.tld" %>
16<%@ taglib prefix="p" uri="/WEB-INF/path.tld" %>
17<%
18final SessionControl sc = Base.getExistingSessionControl(request, "net.sf.basedb.reggie", true);
19final String ID = sc.getId();
20final float scale = Base.getScale(sc);
21final String home = ExtensionsControl.getHomeUrl("net.sf.basedb.reggie");
22DbControl dc = null;
23try
24{
25  dc = sc.newDbControl();
26  final User user = User.getById(dc, sc.getLoggedInUserId());
27%>
28<base:page type="default" title="Flagged alignments wizard">
29<base:head 
30  scripts="~../reggie-2.js,~search.js" 
31  styles="path.css,toolbar.css,~../css/reggie-2.css"
32  >
33<style>
34#itemTable
35{
36  width: 100%;
37  border-collapse: collapse;
38}
39
40#itemTable thead
41{
42  border-bottom-width: 1px;
43  border-top-width: 1px;
44}
45
46#itemTable thead th
47{
48  padding: 2px;
49  text-align: left;
50}
51
52tbody.highlight
53{
54  border-top-width: 1px;
55  border-top-style: dotted;
56}
57
58tr.dotted-above
59{
60  border-top-width: 1px;
61  border-top-style: dotted;
62}
63
64
65#itemTable .highlight.evenrow
66{
67  border-top-color: transparent;
68}
69
70#itemTable tbody td
71{
72  padding: 2px;
73  text-align: left;
74  vertical-align: middle;
75}
76
77.colormatched
78{
79  background-color: #ffff00;
80  outline: 1px solid #a8a800;
81  margin: -1px;
82  padding: 1px;
83}
84
85.colormatched-2
86{
87  background-color: #a8ffff;
88  outline: 1px solid #66a8a8;
89  margin: -1px;
90  padding: 1px;
91}
92
93.text-col
94{}
95
96.text-col img
97{
98  float: right;
99  margin-left: 2px;
100}
101
102#itemTable .icon-col
103{
104  text-align: right;
105}
106
107#itemTable .num-col
108{
109  text-align: center;
110}
111
112#itemTable .flag-col
113{
114  text-align: center;
115}
116
117#itemTable .comment-col input
118{
119  width: calc(100% - 12px);
120}
121
122#itemTable .text-col img.case-summary
123{
124  float: left;
125  margin-right: 2px;
126  margin-left: 0;
127}
128
129.bg-messages
130{
131  background-color: #f0f0f0;
132}
133
134.highlight:hover .bg-messages
135{
136  background-color: #e0e0e0;
137  /* transistions copied from BASE to make it match */
138  transition: all 0.3s ease 0.1s;
139  -moz-transition: all 0.3s ease 0.1s;
140  -webkit-transition: all 0.3s ease 0.1s;
141}
142
143.ignored-mismatch
144{
145  text-decoration-line: line-through;
146}
147
148.commonpart
149{
150  color: #666666;
151  font-style: italic;
152}
153
154.diffpart
155{
156  font-weight: bold;
157}
158
159.mode-genotype, .mode-reprocess, .mode-resolve
160{
161  display:none;
162}
163
164table[data-mode=genotype] .mode-genotype
165{
166  display: table-cell;
167}
168
169table[data-mode=reprocess] .mode-reprocess
170{
171  display: table-cell;
172}
173
174table[data-mode=resolve] .mode-resolve
175{
176  display: table-cell;
177}
178
179table[data-mode=reprocess] thead.mode-reprocess
180{
181  display: table-header-group;
182  border: 0;
183}
184
185table[data-mode=resolve] thead.mode-resolve
186{
187  display: table-header-group;
188  border: 0;
189}
190
191td.mode-reprocess
192{
193  background-color: #FFFFF0;
194}
195
196.mode-reprocess-header
197{
198  background-color: #FFFFF0;
199  border-width: 1px;
200  font-size: 120%;
201}
202
203.recommend-reprocess .mode-reprocess select
204{
205  border-right-width: 8px;
206  border-right-color: #2288AA;
207}
208
209td.mode-resolve
210{
211  background-color: #FFFFF0;
212}
213
214.mode-resolve-header
215{
216  background-color: #FFFFF0;
217  border-width: 1px;
218  font-size: 120%;
219}
220
221.recommend-donotuse .mode-resolve select
222{
223  border-right-width: 8px;
224  border-right-color: #2288AA;
225}
226
227select.donotuse-options
228{
229    width: calc(100% - 10px);
230}
231
232span.donotuse
233{
234  font-style: italic;
235  color: #666666;
236}
237
238option.donotuse
239{
240  color: #999999;
241}
242
243.reprocess-warning .reprocess-wrapper:after
244{
245  content: url('../images/warning.png');
246  vertical-align: bottom;
247  padding: 2px;
248}
249</style>
250</base:head>
251<base:body>
252
253  <p:path><p:pathelement 
254    title="Reggie" href="<%="../index.jsp?ID="+ID%>" 
255    /><p:pathelement title="Flagged alignment wizard" 
256    /></p:path>
257
258  <div class="content">
259
260  <form name="reggie" id="wizard" class="wizard">
261 
262  <div class="step" id="step-1">
263    <div class="step-no">1</div>
264    <div class="step-title" id="step-1-title">Flagged alignments</div>
265    <div class="step-content">
266
267      <table class="step-form">
268      <tr>
269        <td class="prompt">Filter</td>
270        <td>
271          <label><input type="radio" name="filter" id="noFilter" checked>No filter</label>
272          <label><input type="radio" name="filter" id="highHetFilter">High HET</label>
273          <select name="qiaCubeFilter" id="qiaCubeFilter">
274            <option value="">- QiaCube -</option>
275          </select>
276         
277          <select name="libPlateFilter" id="libPlateFilter">
278            <option value="">- LibPlate -</option>
279          </select>
280         
281          <select name="recentFilters" id="recentFilters" style="display: none;">
282            <option value="">- Recently used filters -</option>
283          </select>
284        </td>
285      </tr>
286      <tr>
287        <td class="prompt">Mode</td>
288        <td style="padding-top: 3px; padding-bottom: 6px;">
289          <label><input type="radio" name="mode" id="mode-genotype" checked value="genotype">Genotype analysis</label>
290          <label><input type="radio" name="mode" id="mode-reprocess" value="reprocess" disabled>Add comments and schedule re-processing</label>
291          <label><input type="radio" name="mode" id="mode-resolve" value="resolve" disabled>Resolve as <b>DoNotUse</b> or <b>OkToUse</b></label>
292        </td>
293      </tr>
294      </table>
295
296      <table id="itemTable" class="step-form" data-mode="genotype">
297      </table>
298    </div>
299  </div>
300 
301  <div id="wizard-status"></div>
302
303  <table class="navigation" id="navigation">
304  <tr>
305    <td><base:button id="gocancel" title="Cancel" /></td>
306    <td><base:button id="goreprocess" title="Register re-processing" image="<%=home+"/images/gonext.png"%>" /></td>
307    <td><base:button id="goresolve" title="Register resolutions" image="<%=home+"/images/gonext.png"%>" /></td>
308    <td id="gonext-message" class="message"></td>
309  </tr>
310  </table>
311 
312  </form>
313  </div>
314 
315</base:body>
316</base:page>
317<%
318}
319finally
320{
321  if (dc != null) dc.close();
322}
323%>
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