utils/jalviewjs/site-resources/applets.html

   1 <!DOCTYPE html>
   2 <html>
   3 <head>
   4 <title>SwingJS test Jalview</title>
   5 <meta charset="utf-8" />
   6 <script src="swingjs/swingjs2.js"></script>
   7 <script src="swingjs/JalviewApplet.js"></script>
   8 <script>
   9 if (!self.SwingJS)alert('swingjs2.js was not found. It needs to be in swingjs folder in the same directory as ' + document.location.href)
  10 JalviewInfo = {
  11         code: null,
  12         main: "jalview.bin.Jalview",
  13         //core: "NONE",
  14         core:"_jalview",
  15         resourcePath: "examples",
  16         readyFunction: null,
  17         serverURL: 'https://chemapps.stolaf.edu/jmol/jsmol/php/jsmol.php',
  18         j2sPath: 'swingjs/j2s',
  19         console:'sysout',
  20         startButton:'Start Jalview',
  21         hideDesktop:true,
  22         embedInternalFrames:false,
  23         idPrefix:'%ID%',
  24         allowJavascript: true
  25 }
  26 </script>
  27 </head>
  28 <body>
  29 <!-- content template start
  30 JalviewApplet.js will add divs such as these:
  31 <div id="jalview0-desktop-div" style="width:0px;display:none"></div>
  32 <div id="jalview0-alignment-div" style="width:0px;display:none"></div>
  33  -->
  34 <p align="left">
  35 <h2>JalviewJS Button Examples</h2>
  36 Try out JalviewJS by pressing one of the buttons below.
  37 <a target="_blank" href="http://www.jalview.org/examples/applets.html">Original Java</a> (requires SeaMonkey browser)
  38 </p>
  39 <p>&nbsp;</p><div align="center">
  40   <p align="center">
  41     <h2>Ferredoxins, chloroplast precursor related UniRef50
  42       cluster</h2>
  43     <br /> (15 sequences x 150 residues)
  44   </p>
  45   <table width="90%">
  46     <tr>
  47       <td width="10%" valign="center">
  48       <applet
  49         code="jalview.bin.JalviewLite" width="140" height="35"
  50         archive="jalviewApplet.jar,JmolApplet-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.jar">
  51         <param name="permissions" value="sandbox"/>
  52         <param name="file" value="uniref50.fa"/>
  53         <param name="treeFile" value="ferredoxin.nw"/>
  54         <param name="userDefinedColour" value="C=yellow; R,K,H=FF5555; D,E=5555FF"/>
  55         <param name="sortByTree" value="True"/>
  56         <param name="showSequenceLogo" value="true"/>
  57         <param name="showGroupConsensus" value="true"/>
  58         <param name="showFullId" value="false"/>
  59         <param name="linkLabel_1" value="Uniprot"/>
  60         <param name="linkUrl_1" value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
  61         <param name="linkLabel_2" value="EMBL-EBI Search"/>
  62         <param name="linkUrl_2" value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"/>
  63         <param name="APPLICATION_URL" value="http://www.jalview.org/services/launchApp"/>
  64      </applet>
  65 </td>
  66       <td valign="center">User Defined Colours, loads an associated
  67         Newick format tree file which is used to sort the alignment, and
  68         group consensus and sequence logos are shown below the alignment.</td>
  69     </tr>
  70     <tr>
  71       <td width="10%" valign="center"><applet
  72    code="jalview.bin.JalviewLite" width="140" height="35"
  73    archive="jalviewApplet.jar,JmolApplet-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.jar">
  74 <param name="permissions" value="sandbox"/>
  75 <param name="file" value="uniref50.fa"/>
  76 <param name="features" value="exampleFeatures.txt"/>
  77 <param name="showFullId" value="false"/>
  78 <param name="windowHeight" value="500"/>
  79 <param name="windowWidth" value="650"/>
  80 <param name="showFeatureSettings" value="true"/>
  81 <param name="wrap" value="true"/>
  82 <param name="showAnnotation" value="false"/>
  83    <param name="linkLabel_1" value="Uniprot"/>
  84    <param name="linkUrl_1"
  85      value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
  86    <param name="linkLabel_2" value="EMBL-EBI Search"/>
  87    <param name="linkUrl_2"
  88      value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"/>
  89    <param name="APPLICATION_URL"
  90      value="http://www.jalview.org/services/launchApp"/>
  91 </applet>
  92 </td>
  93       <td valign="center">Displays a features file on the alignment</td>
  94     </tr>
  95     <tr>
  96       <td width="10%" valign="center"><applet
  97    code="jalview.bin.JalviewLite" width="140" height="35"
  98    archive="jalviewApplet.jar,JmolApplet-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.jar">
  99 <param name="permissions" value="sandbox"/>
 100 <param name="file" value="uniref50.fa"/>
 101 <param name="showFullId" value="false"/>
 102 <param name="windowHeight" value="500"/>
 103 <param name="windowWidth" value="650"/>
 104 <param name="wrap" value="true"/>
 105 <param name="debug" value="true"/>
 106 <param name="showAnnotation" value="false"/>
 107 <param name="defaultColour" value="Strand Propensity"/>
 108 <param name="PDBfile" value="1gaq.txt FER1_MAIZE"/>
 109    <param name="linkLabel_1" value="Uniprot"/>
 110    <param name="linkUrl_1"
 111      value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
 112    <param name="linkLabel_2" value="EMBL-EBI Search"/>
 113    <param name="linkUrl_2"
 114      value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"/>
 115    <param name="APPLICATION_URL"
 116      value="http://www.jalview.org/services/launchApp"/>
 117 </applet>
 118 </td>
 119       <td valign="center">Associates PDB file 1GAQ with sequence
 120         FER1_MAIZE</td>
 121     </tr>
 122     <tr>
 123       <td width="10%" valign="center"><applet
 124    code="jalview.bin.JalviewLite" width="140" height="35"
 125    archive="jalviewApplet.jar,JmolApplet-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.jar">
 126 <param name="permissions" value="sandbox"/>
 127 <param name="file" value="jpred_msa.fasta"/>
 128 <param name="jnetfile" value="jpred_msa.seq.concise"/>
 129 <param name="showFullId" value="false"/>
 130 <param name="windowHeight" value="515"/>
 131 <param name="windowWidth" value="650"/>
 132 <param name="showAnnotation" value="true"/>
 133 <param name="defaultColour" value="Clustal"/>
 134    <param name="linkLabel_1" value="Uniprot"/>
 135    <param name="linkUrl_1"
 136      value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
 137    <param name="linkLabel_2" value="EMBL-EBI Search"/>
 138    <param name="linkUrl_2"
 139      value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"/>
 140    <param name="APPLICATION_URL"
 141      value="http://www.jalview.org/services/launchApp"/>
 142 </applet>
 143                                                        </td>
 144       <td valign="middle">Displays a Multiple Sequence Alignment
 145         Based JPred Prediction for a Sequence</td>
 146     </tr>
 147   </table>
 148   <p>
 149     <h2>RF00031 RFAM Alignment with per sequence secondary
 150       structure</h2>
 151   </p>
 152   <table width="90%">
 153     <tr>
 154       <td width="10%" valign="center"><applet
 155    code="jalview.bin.JalviewLite" width="140" height="35"
 156    archive="jalviewApplet.jar,JmolApplet-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.jar">
 157 <param name="permissions" value="sandbox"/>
 158 <param name="file" value="RF00031_folded.stk"/>
 159 <param name="showFullId" value="false"/>
 160 <param name="windowHeight" value="515"/>
 161 <param name="windowWidth" value="650"/>
 162 <param name="showAnnotation" value="true"/>
 163 <param name="defaultColour" value="Purine/Pyrimidine"/>
 164    <param name="APPLICATION_URL"
 165      value="http://www.jalview.org/services/launchApp"/>
 166 </applet>
 167 </td>
 168       <td valign="center">Displays an RFAM RNA fold family with
 169         secondary structure annotation</td>
 170     </tr>
 171   </table>
 172   <p>
 173     <h2>Linked Protein and cDNA alignments for a family of Steroid Receptors</h2>
 174   </p>
 175   <table width="90%">
 176     <tr>
 177       <td width="10%" valign="center">
 178 <applet
 179    code="jalview.bin.JalviewLite" width="140" height="35"
 180    archive="jalviewApplet.jar,JmolApplet-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.jar">
 181 <param name="permissions" value="sandbox"/>
 182 <param name="file2" value="estrogenReceptorCdna_frag.fa"/>
 183 <param name="file" value="estrogenReceptorProtein_frag.fa"/>
 184 <param name="enableSplitFrame" value="true"/>
 185 <param name="scaleProteinAsCdna" value="true"/>
 186 <param name="showFullId" value="false"/>
 187 <param name="windowHeight" value="300"/>
 188 <param name="windowWidth" value="800"/>
 189 <param name="showAnnotation" value="true"/>
 190 <param name="showSequenceLogo" value="true"/>
 191 <param name="defaultColourNuc" value="Purine/Pyrimidine"/>
 192 <param name="defaultColourProt" value="Clustal"/>
 193    <param name="APPLICATION_URL"
 194      value="http://www.jalview.org/services/launchApp"/>
 195 </applet>
 196 </td>
 197       <td valign="center">Displays a split window view showing aligned protein
 198         and a reconstructed cDNA alignment.<br />Proteins were aligned with <a
 199         href="http://www.drive5.com/muscle">Muscle</a> (version 3.8.31,
 200         via the Jalview Desktop).<br />Data retrieved from Uniprot and
 201         ENA, after Thornton, Need and Crews, <a
 202         href="http://dx.doi.org/10.1126/science.1086185">Science 19
 203           September 2003: 301 (5640), 1714-1717</a>
 204       </td>
 205     </tr>
 206   </table>
 207 </div>
 208 <div id="sysout" style="width:500px;height:300px;background:yellow;overflow:auto"></div>
 209
 210 </body>
 211 </html>
 212 <!--
 213  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
 214  * Copyright (C) $$Year-Rel$$ The Jalview Authors
 215  *
 216  * This file is part of Jalview.
 217  *
 218  * Jalview is free software: you can redistribute it and/or
 219  * modify it under the terms of the GNU General Public License
 220  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
 221  *
 222  * Jalview is distributed in the hope that it will be useful, but
 223  * WITHOUT ANY WARRANTY; without even the implied warranty
 224  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
 225  * PURPOSE.  See the GNU General Public License for more details.
 226  *
 227  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
 228  * The Jalview Authors are detailed in the 'AUTHORS' file.
 229 -->
 230