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JAL-3210 Barebones gradle/buildship/eclipse. See README
[jalview.git] / examples / applets.html
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-<!--
- * 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>&nbsp;</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>