-<!DOCTYPE html>
-<html>
-<head>
-<title>SwingJS test Jalview</title>
-<meta charset="utf-8" />
-<script src="swingjs/swingjs2.js"></script>
-<script src="swingjs/JalviewApplet.js"></script>
-<script>
-if (!self.SwingJS)alert('swingjs2.js was not found. It needs to be in swingjs folder in the same directory as ' + document.location.href)
-JalviewInfo = {
- code: null,
- main: "jalview.bin.Jalview",
- //core: "NONE",
- core:"_jalview",
- resourcePath: "examples",
- readyFunction: null,
- serverURL: 'https://chemapps.stolaf.edu/jmol/jsmol/php/jsmol.php',
- j2sPath: 'swingjs/j2s',
- console:'sysout',
- startButton:'Start Jalview',
- hideDesktop:true,
- embedInternalFrames:false,
- idPrefix:'%ID%',
- allowJavascript: true
-}
-</script>
-</head>
-<body>
-<!-- content template start
-JalviewApplet.js will add divs such as these:
-<div id="jalview0-desktop-div" style="width:0px;display:none"></div>
-<div id="jalview0-alignment-div" style="width:0px;display:none"></div>
- -->
-<p align="left">
-<h2>JalviewJS Button Examples</h2>
-Try out JalviewJS by pressing one of the buttons below.
-<a target="_blank" href="http://www.jalview.org/examples/applets.html">Original Java</a> (requires SeaMonkey browser)
-</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>
-</div>
-<div id="sysout" style="width:500px;height:300px;background:yellow;overflow:auto"></div>
-
-</body>
-</html>
-<!--
- * 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.
--->
-