1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
|
<!--
* Jalview - A Sequence Alignment Editor and Viewer (2.11.4.1)
* Copyright (C) 2024 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<div id="view_decorated" name="view_decorated" style="margin:8px; padding:10px; border: 2px solid red; text-align:center; display:none;"><b>Click <a href="index.html#embedded"> here</a> to view decorated page</b></div>
<!-- boiler plate link to alternate demopage -->
<div style="width: 100%">
<div style="width:35%; align:left; float:right;">
</div>
</div>
<!-- content template start -->
<h2>Embedded viewing of Alignments</h2>
<p>The alignment below was generated from the following files:
<ul>
<li><a href="plantfdx.fa">plantfdx.fa</a> - Alignment file in
FASTA format</li>
<li><a href="plantfdx.features">plantfdx.features</a> - Jalview
Format Sequence Features file</li>
<li><a href="plantfdx.annotations">plantfdx.annotations</a> -
Jalview Alignment Annotations File</li>
</ul>
<a href="view-source:http://www.jalview.org/builds/develop/examples/embedded.html" target="_blank">View the source code for this example here</a> (If the link doesn't work on your browser try going to <a href="http://www.jalview.org/builds/develop/examples/embedded.html">this page</a> and viewing the page source manually).<p>
<applet
code="jalview.bin.JalviewLite" width="756" height="560"
archive="jalviewApplet.jar,JmolApplet-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.jar">
<param name="permissions" value="sandbox"/>
<param name="file" value="plantfdx.fa"/>
<param name="features" value="plantfdx.features"/>
<param name="userDefinedColour" value="C=yellow; R,K,H=FF5555; D,E=5555FF"/>
<param name="showFullId" value="false"/>
<param name="embedded" value="true"/>
<param name="linkLabel_1" value="Uniprot"/>
<param name="linkUrl_1"
value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
<param name="linkLabel_2" value="EMBL-EBI Search"/>
<param name="linkUrl_2"
value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"/>
<param name="APPLICATION_URL"
value="http://www.jalview.org/services/launchApp"/>
</applet>
</p>
<!-- content template end -->
|
