deleted jbake example directory and the old biojs template directory

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

diff --git a/examples-jbake/templates/jvl_examples.ftl b/examples-jbake/templates/jvl_examples.ftl
deleted file mode 100644 (file)
index d0e40bf..0000000
--- a/examples-jbake/templates/jvl_examples.ftl
+++ /dev/null
@@ -1,104 +0,0 @@
-
-<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>
-<p>&nbsp;</p><div align="center">
-  <p align="center">
-    <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="${content.jvl},${content.jmol}" 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="${content.jvl},${content.jmol}" 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="${content.jvl},${content.jmol}" 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="${content.jvl},${content.jmol}" 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>
-  <p>
-    <h2>Linked amino acid and cDNA alignments for homologous proteins</h2>
-  </p>
-  <table width="90%">
-    <tr>
-      <td width="10%" valign="center"><@jvlitebutton appjar="${content.jvl},${content.jmol}" params={ "permissions":"all-permissions"
-                                                    , "file":"estrogenReceptorCdna.fa"
-                                                    , "file2":"estrogenReceptorProtein.fa"
-                                                    , "defaultColour":"Purine/Pyrimidine"
-                                                    , "showAnnotation":"false"
-                                                    , "windowHeight":"300"
-                                                    , "windowWidth":"800"
-                                                    , "showFullId":"false"} prots=true /></td>
-      <td valign="center">Displays a split window view of protein and its related cDNA</td>
-    </tr>
-  </table>
-</div>