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- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
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- * This file is part of Jalview.
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- * Jalview is free software: you can redistribute it and/or
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- <li class="jvlite-nav-small"><a href="applets.html">JalviewLite Examples</a></li>
- <li ><a href="jalviewLiteJs.html">Javascript API</a></li>
- <li ><a href="appletParameters.html">Applet Parameters</a></li>
- <li ><a href="embedded.html">Embedded Alignment</a></li>
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- <li ><a href="linkedapplets_ng.html">Linked JalviewLite applets</a></li>
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-
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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#applets"> here</a> to view decorated page</b></div>
<!-- boiler plate link to alternate demopage -->
-
<div style="width: 100%">
-<div style="float:left;">
-</div><div style="border: 2px solid black; align: left; float:right;">
- Working on Snow Leopard or Java out of date ? Try <a href="u_applets.html">the unsigned applet demos</a>
+<div style="width:35%; align:left; float:right;">
+<div style="margin:8px; padding:10px; border: 2px solid black; align: left;">
+<p>Quick Links to jars for example:<br/><a href="jalviewApplet.jar">jalviewApplet.jar</a> and <a href="JmolApplet-14.2.14_2015.06.11.jar">JmolApplet.jar</a>
+</p></div>
</div>
</div>
<p align="left">
<h2>JalviewLite Button Examples</h2>
Try out JalviewLite by pressing one of the buttons below.<br/>
- For more information on how to use the applet in your website, see the <a href="appletParameters.html"><strong>applet parameters</strong></a> and other documentation in the links to the left.</p>
-<div align="center">
- <p>
+ For more information on how to use the applet in your website, see the <a href="javascript:doSubmit('appletParameters')"><strong>applet parameters</strong></a> and other documentation in the links to the left.</p>
+<p> </p><div align="center">
+ <p align="center">
<h2>Ferredoxins, chloroplast precursor related UniRef50
cluster</h2>
<br /> (15 sequences x 150 residues)
<table width="90%">
<tr>
<td width="10%" valign="center">
- <applet
- code="jalview.bin.JalviewLite" width="140" height="35"
- archive="jalviewApplet.jar">
-<param name="permissions" value="sandbox"/>
-<param name="file" value="uniref50.fa"/>
-<param name="treeFile" value="ferredoxin.nw"/>
-<param name="userDefinedColour" value="C=yellow; R,K,H=FF5555; D,E=5555FF"/>
-<param name="sortByTree" value="True"/>
-<param name="showSequenceLogo" value="true"/>
-<param name="showGroupConsensus" value="true"/>
-<param name="showFullId" value="false"/>
- <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>
+ <applet
+ code="jalview.bin.JalviewLite" width="140" height="35"
+ archive="jalviewApplet.jar,JmolApplet-14.2.14_2015.06.11.jar,java-json.jar,json_simple-1.1.jar">
+ <param name="permissions" value="sandbox"/>
+ <param name="file" value="uniref50.fa"/>
+ <param name="treeFile" value="ferredoxin.nw"/>
+ <param name="userDefinedColour" value="C=yellow; R,K,H=FF5555; D,E=5555FF"/>
+ <param name="sortByTree" value="True"/>
+ <param name="showSequenceLogo" value="true"/>
+ <param name="showGroupConsensus" value="true"/>
+ <param name="showFullId" value="false"/>
+ <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>
</td>
<td valign="center">User Defined Colours, loads an associated
Newick format tree file which is used to sort the alignment, and
<tr>
<td width="10%" valign="center"><applet
code="jalview.bin.JalviewLite" width="140" height="35"
- archive="jalviewApplet.jar">
+ archive="jalviewApplet.jar,JmolApplet-14.2.14_2015.06.11.jar,java-json.jar,json_simple-1.1.jar">
<param name="permissions" value="sandbox"/>
<param name="file" value="uniref50.fa"/>
<param name="features" value="exampleFeatures.txt"/>
<tr>
<td width="10%" valign="center"><applet
code="jalview.bin.JalviewLite" width="140" height="35"
- archive="jalviewApplet.jar,JmolApplet-12.2.4.jar">
+ archive="jalviewApplet.jar,JmolApplet-14.2.14_2015.06.11.jar,java-json.jar,json_simple-1.1.jar">
<param name="permissions" value="sandbox"/>
<param name="file" value="uniref50.fa"/>
<param name="showFullId" value="false"/>
<param name="windowHeight" value="500"/>
<param name="windowWidth" value="650"/>
<param name="wrap" value="true"/>
+<param name="debug" value="true"/>
<param name="showAnnotation" value="false"/>
<param name="defaultColour" value="Strand Propensity"/>
+<param name="PDBfile" value="1gaq.txt FER1_MAIZE"/>
<param name="linkLabel_1" value="Uniprot"/>
<param name="linkUrl_1"
value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
<tr>
<td width="10%" valign="center"><applet
code="jalview.bin.JalviewLite" width="140" height="35"
- archive="jalviewApplet.jar">
+ archive="jalviewApplet.jar,JmolApplet-14.2.14_2015.06.11.jar,java-json.jar,json_simple-1.1.jar">
<param name="permissions" value="sandbox"/>
<param name="file" value="jpred_msa.fasta"/>
+<param name="jnetfile" value="jpred_msa.seq.concise"/>
<param name="showFullId" value="false"/>
<param name="windowHeight" value="515"/>
<param name="windowWidth" value="650"/>
<tr>
<td width="10%" valign="center"><applet
code="jalview.bin.JalviewLite" width="140" height="35"
- archive="jalviewApplet.jar">
+ archive="jalviewApplet.jar,JmolApplet-14.2.14_2015.06.11.jar,java-json.jar,json_simple-1.1.jar">
<param name="permissions" value="sandbox"/>
<param name="file" value="RF00031_folded.stk"/>
<param name="showFullId" value="false"/>
secondary structure annotation</td>
</tr>
</table>
-</div>
-<!-- content template end -->
-
-
-
-</div> <!-- end content div -->
-
-</div> <!-- content -->
-</div> <!-- pagewrap -->
-<div id ="footer">
-<div id="innerFooter">
-<div id="copyright"><p>Published under <a href="http://creativecommons.org/licenses/by-sa/3.0/">CC-SA 3.0</a></p></div>
-<div id="cite">
-<p>
-If you use Jalview in your work, please cite this publication:
-</p>
-<br />
-<p>
-Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)
-"Jalview Version 2 - a multiple sequence alignment editor and analysis workbench"
-Bioinformatics 25 (9) 1189-1191 <a href="http://dx.doi.org/10.1093/bioinformatics/btp033">doi: 10.1093/bioinformatics/btp033</a>
-</p>
-</div>
-</div>
-</div>
-</body>
-</html>
+ <p>
+ <h2>Linked Protein and cDNA alignments for a family of Steroid Receptors</h2>
+ </p>
+ <table width="90%">
+ <tr>
+ <td width="10%" valign="center">
+<applet
+ code="jalview.bin.JalviewLite" width="140" height="35"
+ archive="jalviewApplet.jar,JmolApplet-14.2.14_2015.06.11.jar,java-json.jar,json_simple-1.1.jar">
+<param name="permissions" value="sandbox"/>
+<param name="file2" value="estrogenReceptorCdna_frag.fa"/>
+<param name="file" value="estrogenReceptorProtein_frag.fa"/>
+<param name="enableSplitFrame" value="true"/>
+<param name="scaleProteinAsCdna" value="true"/>
+<param name="showFullId" value="false"/>
+<param name="windowHeight" value="300"/>
+<param name="windowWidth" value="800"/>
+<param name="showAnnotation" value="true"/>
+<param name="showSequenceLogo" value="true"/>
+<param name="defaultColour" value="Purine/Pyrimidine"/>
+ <param name="APPLICATION_URL"
+ value="http://www.jalview.org/services/launchApp"/>
+</applet>
+</td>
+ <td valign="center">Displays a split window view showing aligned protein
+ and a reconstructed cDNA alignment.<br />Proteins were aligned with <a
+ href="http://www.drive5.com/muscle">Muscle</a> (version 3.8.31,
+ via the Jalvew Desktop).<br />Data retrieved from Uniprot and
+ ENA, after Thornton, Need and Crews, <a
+ href="http://dx.doi.org/10.1126/science.1086185">Science 19
+ September 2003: 301 (5640), 1714-1717</a>
+ </td>
+ </tr>
+ </table>
git://source.jalview.org / jalview.git / blobdiff