examples/applets.html

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  21 <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>
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  24 <div style="width: 100%">
  25 <div style="width:35%; align:left; float:right;">
  26 <div style="margin:8px; padding:10px; border: 2px solid black; align: left;">
  27 <p>Quick Links to jars for example:<br/><a href="jalviewApplet.jar">jalviewApplet.jar</a> and <a href="JmolApplet-14.2.14_2015.06.11.jar">JmolApplet.jar</a>
  28 </p></div>
  29 </div>
  30 </div>
  31
  32 <!-- content template start -->
  33
  34 <p align="left">
  35 <h2>JalviewLite Button Examples</h2>
  36 Try out JalviewLite by pressing one of the buttons below.<br/>
  37  For more information on how to use the applet in your website, see the <a href="javascript:doSubmit('appletParameters')"><strong>applet parameters</strong></a> and other documentation in the links to the left.</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-14.2.14_2015.06.11.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-14.2.14_2015.06.11.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-14.2.14_2015.06.11.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-14.2.14_2015.06.11.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 JNet 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-14.2.14_2015.06.11.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-14.2.14_2015.06.11.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="defaultColour" value="Purine/Pyrimidine"/>
 191    <param name="APPLICATION_URL"
 192      value="http://www.jalview.org/services/launchApp"/>
 193 </applet>
 194 </td>
 195       <td valign="center">Displays a split window view showing aligned protein
 196         and a reconstructed cDNA alignment.<br />Proteins were aligned with <a
 197         href="http://www.drive5.com/muscle">Muscle</a> (version 3.8.31,
 198         via the Jalvew Desktop).<br />Data retrieved from Uniprot and
 199         ENA, after Thornton, Need and Crews, <a
 200         href="http://dx.doi.org/10.1126/science.1086185">Science 19
 201           September 2003: 301 (5640), 1714-1717</a>
 202       </td>
 203     </tr>
 204   </table>