examples-jbake/templates/jvl_examples.ftl

   1
   2 <p align="left">
   3   Try out JalviewLite by pressing one of the buttons below. For more information on how to use the applet in your website, see the <a
   4                                                                                                                                       href="appletParameters.html"><strong>applet parameters</strong></a> and other documentation in the links to the left.</p>
   5 <div align="center">
   6   <p>
   7     <h2>Ferredoxins, chloroplast precursor related UniRef50
   8       cluster</h2>
   9     <br /> (15 sequences x 150 residues)
  10   </p>
  11   <table width="90%">
  12     <tr>
  13       <td width="10%" valign="center">
  14         <@jvlitebutton appjar="${content.jvl}" params={ "permissions":"all-permissions" , "file":"uniref50.fa"
  15                        , "treeFile":"ferredoxin.nw"
  16                        , "userDefinedColour":"C=yellow; R,K,H=FF5555; D,E=5555FF"
  17                        , "showFullId":"false"
  18                        , "sortByTree":"True"
  19                        , "showSequenceLogo":"true"
  20                        , "showGroupConsensus":"true"} prots=true /></td>
  21       <td valign="center">User Defined Colours, loads an associated
  22         Newick format tree file which is used to sort the alignment, and
  23         group consensus and sequence logos are shown below the alignment.</td>
  24     </tr>
  25     <tr>
  26       <td width="10%" valign="center"><@jvlitebutton appjar="${content.jvl}" params={ "permissions":"all-permissions",
  27        "file":"uniref50.fa"
  28                                                      , "features":"exampleFeatures.txt"
  29                                                      , "showFeatureSettings":"true"
  30                                                      , "wrap":"true"
  31                                                      , "showAnnotation":"false"
  32                                                      , "windowHeight":"500"
  33                                                      , "windowWidth":"650"
  34                                                      , "showFullId":"false"}/></td>
  35       <td valign="center">Displays a features file on the alignment</td>
  36     </tr>
  37     <tr>
  38       <td width="10%" valign="center"><@jvlitebutton appjar="${content.jvl},${content.jmol}" params={ "permissions":"all-permissions"
  39                                                      , "file":"uniref50.fa"
  40                                                      , "defaultColour":"Strand Propensity"
  41                                                      , "wrap":"true"
  42                                                      , "showAnnotation":"false"
  43                                                      , "windowHeight":"500"
  44                                                      , "windowWidth":"650"
  45                                                      , "showFullId":"false"
  46                                                      , "PDBfile":"1gaq.txt FER1_MAIZE"} /></td>
  47       <td valign="center">Associates PDB file 1GAQ with sequence
  48         FER1_MAIZE</td>
  49     </tr>
  50     <tr>
  51       <td width="10%" valign="center"><@jvlitebutton appjar="${content.jvl}" params={ "permissions":"all-permissions"
  52                                                        , "file":"jpred_msa.fasta"
  53                                                        , "jnetfile":"jpred_msa.seq.concise"
  54                                                        , "defaultColour":"Clustal"
  55                                                        , "showAnnotation":"true"
  56                                                        , "windowHeight":"515"
  57                                                        , "windowWidth":"650"
  58                                                        , "showConservation":"false"
  59                                                        , "showQuality":"false"
  60                                                        , "showConsensus":"false"
  61                                                        , "showFullId":"false"} />
  62                                                        </td>
  63       <td valign="middle">Displays a Multiple Sequence Alignment
  64         Based JNet Prediction for a Sequence</td>
  65     </tr>
  66   </table>
  67   <p>
  68     <h2>RF00031 RFAM Alignment with per sequence secondary
  69       structure</h2>
  70   </p>
  71   <table width="90%">
  72     <tr>
  73       <td width="10%" valign="center"><@jvlitebutton appjar="${content.jvl}" params={ "permissions":"all-permissions"
  74                                                      , "file":"RF00031_folded.stk"
  75                                                      , "defaultColour":"Purine/Pyrimidine"
  76                                                      , "showAnnotation":"true"
  77                                                      , "windowHeight":"515"
  78                                                      , "windowWidth":"650"
  79                                                      , "showConservation":"false"
  80                                                      , "showQuality":"false"
  81                                                      , "showConsensus":"true"
  82                                                      , "showFullId":"false"} prots=false /></td>
  83       <td valign="center">Displays an RFAM RNA fold family with
  84         secondary structure annotation</td>
  85     </tr>
  86   </table>