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