<p align="left">For more information on how to use the applet in your
website, see <a href="appletParameters.html"><strong>full list of applet
parameters.</strong></a></p>
- <p> Pressing one of the buttons below will load up a cut down version
+ <p> Pressing one of the buttons below will load up JalviewLite, a cut down version
of Jalview, which runs within your web browser. </p>
<H4 align="center"> Ferredoxins, chloroplast precursor related UniRef50
cluster<br>
<td width="100"> <applet code="jalview.bin.JalviewLite"
width="140" height="35"
archive="jalviewApplet.jar">
- <param name="file" value="uniref50.fa">
- <param name="treeFile" value="ferredoxin.nw">
+ <param name="file" value="uniref50.fa">
\r <param name="treeFile" value="ferredoxin.nw">
<param name="userDefinedColour" value="C=yellow; R,K,H=FF5555; D,E=5555FF">
<param name="showFullId" value="false">
- <param name="RGB" value="F2F2FF">
- <param name="linkLabel_1" value="SRS">
+ <param name="RGB" value="F2F2FF">
\r <param name="sortByTree" value="True">
\r <param name="showSequenceLogo" value="true">
\r <param name="showGroupConsensus" value="true">
\r <param name="linkLabel_1" value="SRS">
<param name="linkUrl_1" value="http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[uniprot-all:$SEQUENCE_ID$]+-vn+2">
<param name="linkLabel_2" value="Uniprot">
<param name="linkUrl_2" value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">
<param name="APPLICATION_URL" value="http://www.jalview.org/services/launchApp">
</applet></td>
<td width="165">User Defined Colours, loads an associated Newick
- format tree file</td>
+ format tree file which is used to sort the alignment, and group consensus and sequence logos are shown below the alignment.</td>
</tr>
</table></td>
</tr>
</table></td>
</tr>
</table>
- <p> </p>
+ <p> </p>
<table width="300" border="1" cellspacing="0" cellpadding="0">
<tr>
<td><table width="300" border="0" cellspacing="0" cellpadding="0">
<tr>
<td width="100"> <applet code="jalview.bin.JalviewLite"
width="140" height="35"
- archive="jalviewApplet.jar,JmolApplet-12.1.13.jar">
- <param name="file" value="uniref50.fa">
- <param name="defaultColour" value="Strand Propensity">
+ archive="jalviewApplet.jar,JmolApplet-12.2.4.jar">
+ <param name="file" value="uniref50.fa">
\r <!-- <param name="debug" value="true">
+ -->
\r <param name="defaultColour" value="Strand Propensity">
<param name="wrap" value="true">
<param name="showAnnotation" value="false">
<param name="windowHeight" value="500">
</table></td>
</tr>
</table>
- <p> </p>
- <table width="300" border="1" cellspacing="0" cellpadding="0">
- <tr>
- <td><table width="300" border="0" cellspacing="0" cellpadding="0">
- <tr>
- <td width="100"> <applet code="jalview.bin.JalviewLite"
- width="140" height="35"
- archive="jalviewApplet.jar">
- <param name="file" value="jpred_msa.fasta">
- <param name="jnetfile" value="jpred_msa.seq.concise">
- <param name="defaultColour" value="Clustal">
- <param name="showAnnotation" value="true">
- <param name="windowHeight" value="515">
- <param name="windowWidth" value="650">
- <param name="showConservation" value="false">
- <param name="showQuality" value="false">
- <param name="showConsensus" value="false">
- <param name="showFullId" value="false">
- <param name="RGB" value="F2F2FF">
- <param name="linkLabel_1" value="SRS">
- <param name="linkUrl_1" value="http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[uniprot-all:$SEQUENCE_ID$]+-vn+2">
- <param name="linkLabel_2" value="Uniprot">
- <param name="linkUrl_2" value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">
- <param name="APPLICATION_URL" value="http://www.jalview.org/services/launchApp">
- </applet> </td>
- <td width="165">Displays a Multiple Sequence Alignment Based
- JNet Prediction for a Sequence</td>
- </tr>
- </table></td>
- </tr>
- </table>
- </div>
+ <p> </p>
\r <table width="300" border="1" cellspacing="0" cellpadding="0">
\r <tr>
\r <td><table width="300" border="0" cellspacing="0"
\r cellpadding="0">
\r <tr>
\r <td width="100"><applet code="jalview.bin.JalviewLite"
\r width="140" height="35" archive="jalviewApplet.jar">
\r <param name="file" value="jpred_msa.fasta">
\r <param name="jnetfile" value="jpred_msa.seq.concise">
\r <param name="defaultColour" value="Clustal">
\r <param name="showAnnotation" value="true">
\r <param name="windowHeight" value="515">
\r <param name="windowWidth" value="650">
\r <param name="showConservation" value="false">
\r <param name="showQuality" value="false">
\r <param name="showConsensus" value="false">
\r <param name="showFullId" value="false">
\r <param name="RGB" value="F2F2FF">
\r <param name="linkLabel_1" value="SRS">
\r <param name="linkUrl_1"
\r value="http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[uniprot-all:$SEQUENCE_ID$]+-vn+2">
\r <param name="linkLabel_2" value="Uniprot">
\r <param name="linkUrl_2"
\r value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">
\r <param name="APPLICATION_URL"
\r value="http://www.jalview.org/services/launchApp">
\r </applet></td>
\r <td width="165">Displays a Multiple Sequence Alignment
\r Based JNet Prediction for a Sequence</td>
\r </tr>
\r </table></td>
\r </tr>
\r </table>
\r <p> </p>
\r <table width="300" border="1" cellspacing="0" cellpadding="0">
\r <tr>
\r <td><table width="300" border="0" cellspacing="0" cellpadding="0">
\r <tr>
\r <td width="100"> <applet code="jalview.bin.JalviewLite"
\r width="140" height="35"
\r archive="jalviewApplet.jar">
\r <param name="file" value="RF00031_folded.stk">
\r <param name="defaultColour" value="Purine/Pyrimidine">
\r <param name="showAnnotation" value="true">
\r <param name="windowHeight" value="515">
\r <param name="windowWidth" value="650">
\r <param name="showConservation" value="false">
\r <param name="showQuality" value="false">
\r <param name="showConsensus" value="true">
\r <param name="showFullId" value="false">
\r <param name="RGB" value="F2F2FF">
\r <param name="APPLICATION_URL" value="http://www.jalview.org/services/launchApp">
\r </applet> </td>
\r <td width="165">Displays an RFAM RNA fold family with secondary structure annotation</td>
\r </tr>
\r </table></td>
\r </tr>
\r </table>
\r </div>
\r <p> </p>
\r <p>For more JalviewLite examples, follow the links below.
\r <ul>
\r <li><a href="embedded.html">JalviewLite embedded in the web page</a></li>
\r <li><a href="formComplete.html">use Javascript to control and get data from JalviewLite</a></li>
\r <li><a href="linkedapplets_ng.html">use Javascript to make two jalviewLite instances talk to each other</a></li>
\r <li><a href="embeddedWJmol.html">configure JalviewLite to talk to a Jmol applet on the page.</a></li>
\r </ul>
<!-- InstanceEndEditable --></td>\r </tr>\r </table>\r</div>\r</body>\r<!-- InstanceEnd --></html>\r
\ No newline at end of file
git://source.jalview.org / jalview.git / blobdiff