Merge branch 'JAL-957_jbake' into Release_2_8_Branch

[jalview.git] / examples-jbake / templates / jvl_examples.ftl

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+
+<p align="left">
+<h2>JalviewLite Button Examples</h2>
+Try out JalviewLite by pressing one of the buttons below.<br/>
+ For more information on how to use the applet in your website, see the <a href="appletParameters.html"><strong>applet parameters</strong></a> and other documentation in the links to the left.</p>
+<div align="center">
+  <p>
+    <h2>Ferredoxins, chloroplast precursor related UniRef50
+      cluster</h2>
+    <br /> (15 sequences x 150 residues)
+  </p>
+  <table width="90%">
+    <tr>
+      <td width="10%" valign="center">
+       <@jvlitebutton appjar="${content.jvl}" params={ "permissions":"all-permissions" , "file":"uniref50.fa"
+                      , "treeFile":"ferredoxin.nw"
+                      , "userDefinedColour":"C=yellow; R,K,H=FF5555; D,E=5555FF"
+                      , "showFullId":"false"
+                      , "sortByTree":"True"
+                      , "showSequenceLogo":"true"
+                      , "showGroupConsensus":"true"} prots=true /></td>
+      <td valign="center">User Defined Colours, loads an associated
+       Newick format tree file which is used to sort the alignment, and
+       group consensus and sequence logos are shown below the alignment.</td>
+    </tr>
+    <tr>
+      <td width="10%" valign="center"><@jvlitebutton appjar="${content.jvl}" params={ "permissions":"all-permissions",
+       "file":"uniref50.fa"
+                                                    , "features":"exampleFeatures.txt"
+                                                    , "showFeatureSettings":"true"
+                                                    , "wrap":"true"
+                                                    , "showAnnotation":"false"
+                                                    , "windowHeight":"500"
+                                                    , "windowWidth":"650"
+                                                    , "showFullId":"false"}/></td>
+      <td valign="center">Displays a features file on the alignment</td>
+    </tr>
+    <tr>
+      <td width="10%" valign="center"><@jvlitebutton appjar="${content.jvl},${content.jmol}" params={ "permissions":"all-permissions"
+                                                    , "file":"uniref50.fa"
+                                                    , "defaultColour":"Strand Propensity"
+                                                    , "wrap":"true"
+                                                    , "showAnnotation":"false"
+                                                    , "windowHeight":"500"
+                                                    , "windowWidth":"650"
+                                                    , "showFullId":"false"
+                                                    , "PDBfile":"1gaq.txt FER1_MAIZE"} /></td>
+      <td valign="center">Associates PDB file 1GAQ with sequence
+       FER1_MAIZE</td>
+    </tr>
+    <tr>
+      <td width="10%" valign="center"><@jvlitebutton appjar="${content.jvl}" params={ "permissions":"all-permissions"
+                                                      , "file":"jpred_msa.fasta"
+                                                      , "jnetfile":"jpred_msa.seq.concise"
+                                                      , "defaultColour":"Clustal"
+                                                      , "showAnnotation":"true"
+                                                      , "windowHeight":"515"
+                                                      , "windowWidth":"650"
+                                                      , "showConservation":"false"
+                                                      , "showQuality":"false"
+                                                      , "showConsensus":"false"
+                                                      , "showFullId":"false"} />
+                                                      </td>
+      <td valign="middle">Displays a Multiple Sequence Alignment
+       Based JNet Prediction for a Sequence</td>
+    </tr>
+  </table>
+  <p>
+    <h2>RF00031 RFAM Alignment with per sequence secondary
+      structure</h2>
+  </p>
+  <table width="90%">
+    <tr>
+      <td width="10%" valign="center"><@jvlitebutton appjar="${content.jvl}" params={ "permissions":"all-permissions"
+                                                    , "file":"RF00031_folded.stk"
+                                                    , "defaultColour":"Purine/Pyrimidine"
+                                                    , "showAnnotation":"true"
+                                                    , "windowHeight":"515"
+                                                    , "windowWidth":"650"
+                                                    , "showConservation":"false"
+                                                    , "showQuality":"false"
+                                                    , "showConsensus":"true"
+                                                    , "showFullId":"false"} prots=false /></td>
+      <td valign="center">Displays an RFAM RNA fold family with
+       secondary structure annotation</td>
+    </tr>
+  </table>
+</div>