source: extensions/net.sf.basedb.reggie/trunk/resources/flaggedalignment/search.jsp @ 4976

Last change on this file since 4976 was 4976, checked in by Nicklas Nordborg, 3 years ago

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

Added an indicator for re-processing that is enabled if there is no other alignment for the same specimen. Alignments from the same RNA (if a Qiacube filter is active) or library (if HET filter or libplate filter is active) are not counted as a separate alignment.

When the High HET filter is active there is also an indicator for DoNotUse that is active if there is another alignement without an "error" condition.

File size: 5.9 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: 15em;
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</style>
227</base:head>
228<base:body>
229
230  <p:path><p:pathelement 
231    title="Reggie" href="<%="../index.jsp?ID="+ID%>" 
232    /><p:pathelement title="Flagged alignment wizard" 
233    /></p:path>
234
235  <div class="content">
236
237  <form name="reggie" id="wizard" class="wizard">
238 
239  <div class="step" id="step-1">
240    <div class="step-no">1</div>
241    <div class="step-title" id="step-1-title">Flagged alignments</div>
242    <div class="step-content">
243
244      <table class="step-form">
245      <tr>
246        <td class="prompt">Filter</td>
247        <td>
248          <label><input type="radio" name="filter" id="noFilter" checked>No filter</label>
249          <label><input type="radio" name="filter" id="highHetFilter">High HET</label>
250          <select name="qiaCubeFilter" id="qiaCubeFilter">
251            <option value="">- QiaCube -</option>
252          </select>
253         
254          <select name="libPlateFilter" id="libPlateFilter">
255            <option value="">- LibPlate -</option>
256          </select>
257         
258          <select name="recentFilters" id="recentFilters" style="display: none;">
259            <option value="">- Recently used filters -</option>
260          </select>
261        </td>
262      </tr>
263      <tr>
264        <td class="prompt">Mode</td>
265        <td style="padding-top: 3px; padding-bottom: 6px;">
266          <label><input type="radio" name="mode" id="mode-genotype" checked value="genotype">Genotype analysis</label>
267          <label><input type="radio" name="mode" id="mode-reprocess" value="reprocess" disabled>Add comments and schedule re-processing</label>
268          <label><input type="radio" name="mode" id="mode-resolve" value="resolve" disabled>Resolve as <b>DoNotUse</b> or <b>OkToUse</b></label>
269        </td>
270      </tr>
271      </table>
272
273      <table id="itemTable" class="step-form" data-mode="genotype">
274      </table>
275    </div>
276  </div>
277 
278  <div id="wizard-status"></div>
279
280  <table class="navigation" id="navigation">
281  <tr>
282    <td><base:button id="gocancel" title="Cancel" /></td>
283    <td><base:button id="goreprocess" title="Register re-processing" image="<%=home+"/images/gonext.png"%>" /></td>
284    <td><base:button id="goresolve" title="Register resolutions" image="<%=home+"/images/gonext.png"%>" /></td>
285    <td id="gonext-message" class="message"></td>
286  </tr>
287  </table>
288 
289  </form>
290  </div>
291 
292</base:body>
293</base:page>
294<%
295}
296finally
297{
298  if (dc != null) dc.close();
299}
300%>
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