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\r <td valign="top" width="587" bgcolor="#F2F2FF"><!-- InstanceBeginEditable name="Contents" -->
- <p>Jalview comes in two distinct flavours.<br>
- <br>
- The main application allows connection to multiple web services provided
- at the University of Dundee as well as a host of additional useful features
- such as printing, making images from your alignment and annotating your
- alignment. You need to download and install this software.</p>
- <p>The applet version runs in web browsers and is a useful interactive
- display for precalculated alignments, features and annotations files.
- It does not have the full functionality of the main application, such
- as making images, saving files, running web service jobs due to security
- restrictions imposed on applets.</p>
- <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
- of Jalview, which runs within your web browser. </p>
- <H4 align="center"> Ferredoxins, chloroplast precursor related UniRef50
- cluster<br>
- (15 sequences x 150 residues)</H4>
- <div align="center"> </div>
- <div align="center">
- <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="uniref50.fa">
- <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="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>
- </tr>
- </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="uniref50.fa">
- <param name="features" value="exampleFeatures.txt">
- <param name="showFeatureSettings" value="true">
- <param name="wrap" value="true">
- <param name="showAnnotation" value="false">
- <param name="windowHeight" value="500">
- <param name="windowWidth" value="650">
- <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 features file on the alignment</td>
- </tr>
- </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,JmolApplet-12.1.13.jar">
- <param name="file" value="uniref50.fa">
- <param name="defaultColour" value="Strand Propensity">
- <param name="wrap" value="true">
- <param name="showAnnotation" value="false">
- <param name="windowHeight" value="500">
- <param name="windowWidth" value="650">
- <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">
- <param name="PDBfile" value="1gaq.txt FER1_MAIZE">
- </applet> </td>
- <td width="165">Associates PDB file 1GAQ with sequence FER1_MAIZE</td>
- </tr>
- </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>
- <!-- InstanceEndEditable --></td>\r </tr>\r </table>\r</div>\r</body>\r<!-- InstanceEnd --></html>\r
\ No newline at end of file
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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>
+<!-- content template start -->
+
+<p align="left">
+<h2>JalviewLite Button Examples</h2>
+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
+ cluster</h2>
+ <br /> (15 sequences x 150 residues)
+ </p>
+ <table width="90%">
+ <tr>
+ <td width="10%" valign="center">
+ <applet
+ code="jalview.bin.JalviewLite" width="140" height="35"
+ 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"/>
+ <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
+ group consensus and sequence logos are shown below the alignment.</td>
+ </tr>
+ <tr>
+ <td width="10%" valign="center"><applet
+ code="jalview.bin.JalviewLite" width="140" height="35"
+ 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"/>
+<param name="showFullId" value="false"/>
+<param name="windowHeight" value="500"/>
+<param name="windowWidth" value="650"/>
+<param name="showFeatureSettings" value="true"/>
+<param name="wrap" value="true"/>
+<param name="showAnnotation" 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">Displays a features file on the alignment</td>
+ </tr>
+ <tr>
+ <td width="10%" valign="center"><applet
+ code="jalview.bin.JalviewLite" width="140" height="35"
+ 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"/>
+ <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">Associates PDB file 1GAQ with sequence
+ FER1_MAIZE</td>
+ </tr>
+ <tr>
+ <td width="10%" valign="center"><applet
+ code="jalview.bin.JalviewLite" width="140" height="35"
+ 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"/>
+<param name="showFullId" value="false"/>
+<param name="windowHeight" value="515"/>
+<param name="windowWidth" value="650"/>
+<param name="showAnnotation" value="true"/>
+<param name="defaultColour" value="Clustal"/>
+ <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="middle">Displays a Multiple Sequence Alignment
+ Based JPred Prediction for a Sequence</td>
+ </tr>
+ </table>
+ <p>
+ <h2>RF00031 RFAM Alignment with per sequence secondary
+ structure</h2>
+ </p>
+ <table width="90%">
+ <tr>
+ <td width="10%" valign="center"><applet
+ code="jalview.bin.JalviewLite" width="140" height="35"
+ archive="jalviewApplet.jar,JmolApplet-14.6.4_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"/>
+<param name="windowHeight" value="515"/>
+<param name="windowWidth" value="650"/>
+<param name="showAnnotation" 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 an RFAM RNA fold family with
+ secondary structure annotation</td>
+ </tr>
+ </table>
+ <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-14.6.4_2016.10.26.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="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 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>
+ </tr>
+ </table>
git://source.jalview.org / jalview.git / blobdiff