JAL-1541 added Jsoup to the InstallAnywhere config
[jalview.git] / examples-jbake / templates / jvl_examples.ftl
1
2 <p align="left">
3 <h2>JalviewLite Button Examples</h2>
4 Try out JalviewLite by pressing one of the buttons below.<br/>
5  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>
6 <p>&nbsp;</p><div align="center">
7   <p align="center">
8     <h2>Ferredoxins, chloroplast precursor related UniRef50
9       cluster</h2>
10     <br /> (15 sequences x 150 residues)
11   </p>
12   <table width="90%">
13     <tr>
14       <td width="10%" valign="center">
15         <@jvlitebutton appjar="${content.jvl}" params={ "permissions":"all-permissions" , "file":"uniref50.fa"
16                        , "treeFile":"ferredoxin.nw"
17                        , "userDefinedColour":"C=yellow; R,K,H=FF5555; D,E=5555FF"
18                        , "showFullId":"false"
19                        , "sortByTree":"True"
20                        , "showSequenceLogo":"true"
21                        , "showGroupConsensus":"true"} prots=true /></td>
22       <td valign="center">User Defined Colours, loads an associated
23         Newick format tree file which is used to sort the alignment, and
24         group consensus and sequence logos are shown below the alignment.</td>
25     </tr>
26     <tr>
27       <td width="10%" valign="center"><@jvlitebutton appjar="${content.jvl}" params={ "permissions":"all-permissions",
28        "file":"uniref50.fa"
29                                                      , "features":"exampleFeatures.txt"
30                                                      , "showFeatureSettings":"true"
31                                                      , "wrap":"true"
32                                                      , "showAnnotation":"false"
33                                                      , "windowHeight":"500"
34                                                      , "windowWidth":"650"
35                                                      , "showFullId":"false"}/></td>
36       <td valign="center">Displays a features file on the alignment</td>
37     </tr>
38     <tr>
39       <td width="10%" valign="center"><@jvlitebutton appjar="${content.jvl},${content.jmol}" params={ "permissions":"all-permissions"
40                                                      , "file":"uniref50.fa"
41                                                      , "defaultColour":"Strand Propensity"
42                                                      , "wrap":"true"
43                                                      , "showAnnotation":"false"
44                                                      , "windowHeight":"500"
45                                                      , "windowWidth":"650"
46                                                      , "showFullId":"false"
47                                                      , "PDBfile":"1gaq.txt FER1_MAIZE"} /></td>
48       <td valign="center">Associates PDB file 1GAQ with sequence
49         FER1_MAIZE</td>
50     </tr>
51     <tr>
52       <td width="10%" valign="center"><@jvlitebutton appjar="${content.jvl}" params={ "permissions":"all-permissions"
53                                                        , "file":"jpred_msa.fasta"
54                                                        , "jnetfile":"jpred_msa.seq.concise"
55                                                        , "defaultColour":"Clustal"
56                                                        , "showAnnotation":"true"
57                                                        , "windowHeight":"515"
58                                                        , "windowWidth":"650"
59                                                        , "showConservation":"false"
60                                                        , "showQuality":"false"
61                                                        , "showConsensus":"false"
62                                                        , "showFullId":"false"} />
63                                                        </td>
64       <td valign="middle">Displays a Multiple Sequence Alignment
65         Based JNet Prediction for a Sequence</td>
66     </tr>
67   </table>
68   <p>
69     <h2>RF00031 RFAM Alignment with per sequence secondary
70       structure</h2>
71   </p>
72   <table width="90%">
73     <tr>
74       <td width="10%" valign="center"><@jvlitebutton appjar="${content.jvl}" params={ "permissions":"all-permissions"
75                                                      , "file":"RF00031_folded.stk"
76                                                      , "defaultColour":"Purine/Pyrimidine"
77                                                      , "showAnnotation":"true"
78                                                      , "windowHeight":"515"
79                                                      , "windowWidth":"650"
80                                                      , "showConservation":"false"
81                                                      , "showQuality":"false"
82                                                      , "showConsensus":"true"
83                                                      , "showFullId":"false"} prots=false /></td>
84       <td valign="center">Displays an RFAM RNA fold family with
85         secondary structure annotation</td>
86     </tr>
87   </table>
88 </div>