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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  27
  28 <p align="left">
  29 <h2>JalviewLite Button Examples</h2>
  30 Try out JalviewLite by pressing one of the buttons below.
  31   <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/>
  32  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>
  33 <p>&nbsp;</p><div align="center">
  34   <p align="center">
  35     <h2>Ferredoxins, chloroplast precursor related UniRef50
  36       cluster</h2>
  37     <br /> (15 sequences x 150 residues)
  38   </p>
  39   <table width="90%">
  40     <tr>
  41       <td width="10%" valign="center">
  42       <applet
  43         code="jalview.bin.JalviewLite" width="140" height="35"
  44         archive="jalviewApplet.jar,JmolApplet-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.jar">
  45         <param name="permissions" value="sandbox"/>
  46         <param name="file" value="uniref50.fa"/>
  47         <param name="treeFile" value="ferredoxin.nw"/>
  48         <param name="userDefinedColour" value="C=yellow; R,K,H=FF5555; D,E=5555FF"/>
  49         <param name="sortByTree" value="True"/>
  50         <param name="showSequenceLogo" value="true"/>
  51         <param name="showGroupConsensus" value="true"/>
  52         <param name="showFullId" value="false"/>
  53         <param name="linkLabel_1" value="Uniprot"/>
  54         <param name="linkUrl_1" value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
  55         <param name="linkLabel_2" value="EMBL-EBI Search"/>
  56         <param name="linkUrl_2" value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"/>
  57         <param name="APPLICATION_URL" value="http://www.jalview.org/services/launchApp"/>
  58      </applet>
  59 </td>
  60       <td valign="center">User Defined Colours, loads an associated
  61         Newick format tree file which is used to sort the alignment, and
  62         group consensus and sequence logos are shown below the alignment.</td>
  63     </tr>
  64     <tr>
  65       <td width="10%" valign="center"><applet
  66    code="jalview.bin.JalviewLite" width="140" height="35"
  67    archive="jalviewApplet.jar,JmolApplet-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.jar">
  68 <param name="permissions" value="sandbox"/>
  69 <param name="file" value="uniref50.fa"/>
  70 <param name="features" value="exampleFeatures.txt"/>
  71 <param name="showFullId" value="false"/>
  72 <param name="windowHeight" value="500"/>
  73 <param name="windowWidth" value="650"/>
  74 <param name="showFeatureSettings" value="true"/>
  75 <param name="wrap" value="true"/>
  76 <param name="showAnnotation" value="false"/>
  77    <param name="linkLabel_1" value="Uniprot"/>
  78    <param name="linkUrl_1"
  79      value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
  80    <param name="linkLabel_2" value="EMBL-EBI Search"/>
  81    <param name="linkUrl_2"
  82      value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"/>
  83    <param name="APPLICATION_URL"
  84      value="http://www.jalview.org/services/launchApp"/>
  85 </applet>
  86 </td>
  87       <td valign="center">Displays a features file on the alignment</td>
  88     </tr>
  89     <tr>
  90       <td width="10%" valign="center"><applet
  91    code="jalview.bin.JalviewLite" width="140" height="35"
  92    archive="jalviewApplet.jar,JmolApplet-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.jar">
  93 <param name="permissions" value="sandbox"/>
  94 <param name="file" value="uniref50.fa"/>
  95 <param name="showFullId" value="false"/>
  96 <param name="windowHeight" value="500"/>
  97 <param name="windowWidth" value="650"/>
  98 <param name="wrap" value="true"/>
  99 <param name="debug" value="true"/>
 100 <param name="showAnnotation" value="false"/>
 101 <param name="defaultColour" value="Strand Propensity"/>
 102 <param name="PDBfile" value="1gaq.txt FER1_MAIZE"/>
 103    <param name="linkLabel_1" value="Uniprot"/>
 104    <param name="linkUrl_1"
 105      value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
 106    <param name="linkLabel_2" value="EMBL-EBI Search"/>
 107    <param name="linkUrl_2"
 108      value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"/>
 109    <param name="APPLICATION_URL"
 110      value="http://www.jalview.org/services/launchApp"/>
 111 </applet>
 112 </td>
 113       <td valign="center">Associates PDB file 1GAQ with sequence
 114         FER1_MAIZE</td>
 115     </tr>
 116     <tr>
 117       <td width="10%" valign="center"><applet
 118    code="jalview.bin.JalviewLite" width="140" height="35"
 119    archive="jalviewApplet.jar,JmolApplet-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.jar">
 120 <param name="permissions" value="sandbox"/>
 121 <param name="file" value="jpred_msa.fasta"/>
 122 <param name="jnetfile" value="jpred_msa.seq.concise"/>
 123 <param name="showFullId" value="false"/>
 124 <param name="windowHeight" value="515"/>
 125 <param name="windowWidth" value="650"/>
 126 <param name="showAnnotation" value="true"/>
 127 <param name="defaultColour" value="Clustal"/>
 128    <param name="linkLabel_1" value="Uniprot"/>
 129    <param name="linkUrl_1"
 130      value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
 131    <param name="linkLabel_2" value="EMBL-EBI Search"/>
 132    <param name="linkUrl_2"
 133      value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"/>
 134    <param name="APPLICATION_URL"
 135      value="http://www.jalview.org/services/launchApp"/>
 136 </applet>
 137                                                        </td>
 138       <td valign="middle">Displays a Multiple Sequence Alignment
 139         Based JPred Prediction for a Sequence</td>
 140     </tr>
 141   </table>
 142   <p>
 143     <h2>RF00031 RFAM Alignment with per sequence secondary
 144       structure</h2>
 145   </p>
 146   <table width="90%">
 147     <tr>
 148       <td width="10%" valign="center"><applet
 149    code="jalview.bin.JalviewLite" width="140" height="35"
 150    archive="jalviewApplet.jar,JmolApplet-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.jar">
 151 <param name="permissions" value="sandbox"/>
 152 <param name="file" value="RF00031_folded.stk"/>
 153 <param name="showFullId" value="false"/>
 154 <param name="windowHeight" value="515"/>
 155 <param name="windowWidth" value="650"/>
 156 <param name="showAnnotation" value="true"/>
 157 <param name="defaultColour" value="Purine/Pyrimidine"/>
 158    <param name="APPLICATION_URL"
 159      value="http://www.jalview.org/services/launchApp"/>
 160 </applet>
 161 </td>
 162       <td valign="center">Displays an RFAM RNA fold family with
 163         secondary structure annotation</td>
 164     </tr>
 165   </table>
 166   <p>
 167     <h2>Linked Protein and cDNA alignments for a family of Steroid Receptors</h2>
 168   </p>
 169   <table width="90%">
 170     <tr>
 171       <td width="10%" valign="center">
 172 <applet
 173    code="jalview.bin.JalviewLite" width="140" height="35"
 174    archive="jalviewApplet.jar,JmolApplet-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.jar">
 175 <param name="permissions" value="sandbox"/>
 176 <param name="file2" value="estrogenReceptorCdna_frag.fa"/>
 177 <param name="file" value="estrogenReceptorProtein_frag.fa"/>
 178 <param name="enableSplitFrame" value="true"/>
 179 <param name="scaleProteinAsCdna" value="true"/>
 180 <param name="showFullId" value="false"/>
 181 <param name="windowHeight" value="300"/>
 182 <param name="windowWidth" value="800"/>
 183 <param name="showAnnotation" value="true"/>
 184 <param name="showSequenceLogo" value="true"/>
 185 <param name="defaultColourNuc" value="Purine/Pyrimidine"/>
 186 <param name="defaultColourProt" value="Clustal"/>
 187    <param name="APPLICATION_URL"
 188      value="http://www.jalview.org/services/launchApp"/>
 189 </applet>
 190 </td>
 191       <td valign="center">Displays a split window view showing aligned protein
 192         and a reconstructed cDNA alignment.<br />Proteins were aligned with <a
 193         href="http://www.drive5.com/muscle">Muscle</a> (version 3.8.31,
 194         via the Jalview Desktop).<br />Data retrieved from Uniprot and
 195         ENA, after Thornton, Need and Crews, <a
 196         href="http://dx.doi.org/10.1126/science.1086185">Science 19
 197           September 2003: 301 (5640), 1714-1717</a>
 198       </td>
 199     </tr>
 200   </table>