<!-- boiler plate link to alternate demopage -->
<div style="width: 100%">
-<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>
-
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<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="javascript:doSubmit('appletParameters')"><strong>applet parameters</strong></a> and other documentation in the links to the left.</p>
+Try out JalviewLite by pressing one of the buttons below.
+ <a href="view-source:http://www.jalview.org/builds/develop/examples/applets.html" target="_blank">View the source for the examples below here</a> (If the link doesn't work on your browser try going to <a href="http://www.jalview.org/builds/develop/examples/applets.html">this page</a> and viewing the page source manually).<br/>
+ For more information on how to use the applet in your website, see the <a href="javascript:doSubmit('appletDeployment')"><strong>applet deployment,</strong></a> <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
<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">
+ 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="uniref50.fa"/>
<param name="treeFile" value="ferredoxin.nw"/>
<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">
+ 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="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-14.2.14_2015.06.11.jar,java-json.jar,json_simple-1.1.jar">
+ 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="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"/>
<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">
+ 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="jpred_msa.fasta"/>
<param name="jnetfile" value="jpred_msa.seq.concise"/>
</applet>
</td>
<td valign="middle">Displays a Multiple Sequence Alignment
- Based JNet Prediction for a Sequence</td>
+ Based JPred Prediction for a Sequence</td>
</tr>
</table>
<p>
<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">
+ 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="RF00031_folded.stk"/>
<param name="showFullId" value="false"/>
<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">
+ 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="estrogenReceptorCdna.fa"/>
-<param name="file2" value="estrogenReceptorProtein.fa"/>
+<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="windowWidth" value="800"/>
<param name="showAnnotation" value="true"/>
<param name="showSequenceLogo" value="true"/>
-<param name="defaultColour" value="Purine/Pyrimidine"/>
+<param name="defaultColourNuc" value="Purine/Pyrimidine"/>
+<param name="defaultColourProt" value="Clustal"/>
<param name="APPLICATION_URL"
value="http://www.jalview.org/services/launchApp"/>
</applet>
</td>
- <td valign="center">Displays a split window view of protein
- and its related cDNA.<br />Data retrieved from Uniprot and ENA,
- after Thornton, Need and Crews, <a
+ <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 Jalview 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>
git://source.jalview.org / jalview.git / blobdiff