From 7b047c0623c55b1a2644af552eb3d41a44f8e727 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Thu, 5 Mar 2015 14:36:18 +0000 Subject: [PATCH] JAL-1213 JAL-1395 add Jmol to JalviewLite classpath - need to find a way around this in the future --- examples-jbake/templates/jvl_embedded.ftl | 2 +- examples-jbake/templates/jvl_examples.ftl | 8 ++++---- examples-jbake/templates/jvl_formComplete.ftl | 2 +- examples-jbake/templates/jvl_javascriptLaunch.ftl | 2 +- examples-jbake/templates/jvl_linkedapplets_ng.ftl | 4 ++-- examples/applets.html | 8 ++++---- examples/embedded.html | 2 +- examples/embeddedWJmol.html | 2 +- examples/formComplete.html | 2 +- examples/javascriptLaunch.html | 2 +- examples/linkedapplets_ng.html | 4 ++-- 11 files changed, 19 insertions(+), 19 deletions(-) diff --git a/examples-jbake/templates/jvl_embedded.ftl b/examples-jbake/templates/jvl_embedded.ftl index b61c7a9..62d58b0 100644 --- a/examples-jbake/templates/jvl_embedded.ftl +++ b/examples-jbake/templates/jvl_embedded.ftl @@ -8,7 +8,7 @@
  • plantfdx.annotations - Jalview Alignment Annotations File
    • - <@jvlitebutton appjar="${content.jvl}" width=756 height=560 + <@jvlitebutton appjar="${content.jvl},${content.jmol}" width=756 height=560 params={ "file":"plantfdx.fa", "annotations":"plantfdx.annotations", diff --git a/examples-jbake/templates/jvl_examples.ftl b/examples-jbake/templates/jvl_examples.ftl index f2bf8b1..ec5c684 100644 --- a/examples-jbake/templates/jvl_examples.ftl +++ b/examples-jbake/templates/jvl_examples.ftl @@ -12,7 +12,7 @@ Try out JalviewLite by pressing one of the buttons below.
    - -
    - <@jvlitebutton appjar="${content.jvl}" params={ "permissions":"all-permissions" , "file":"uniref50.fa" + <@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" @@ -24,7 +24,7 @@ Try out JalviewLite by pressing one of the buttons below.
    group consensus and sequence logos are shown below the alignment.
    <@jvlitebutton appjar="${content.jvl}" params={ "permissions":"all-permissions", + <@jvlitebutton appjar="${content.jvl},${content.jmol}" params={ "permissions":"all-permissions", "file":"uniref50.fa" , "features":"exampleFeatures.txt" , "showFeatureSettings":"true" @@ -49,7 +49,7 @@ Try out JalviewLite by pressing one of the buttons below.
    FER1_MAIZE
    <@jvlitebutton appjar="${content.jvl}" params={ "permissions":"all-permissions" + <@jvlitebutton appjar="${content.jvl},${content.jmol}" params={ "permissions":"all-permissions" , "file":"jpred_msa.fasta" , "jnetfile":"jpred_msa.seq.concise" , "defaultColour":"Clustal" @@ -71,7 +71,7 @@ Try out JalviewLite by pressing one of the buttons below.

    -
    <@jvlitebutton appjar="${content.jvl}" params={ "permissions":"all-permissions" + <@jvlitebutton appjar="${content.jvl},${content.jmol}" params={ "permissions":"all-permissions" , "file":"RF00031_folded.stk" , "defaultColour":"Purine/Pyrimidine" , "showAnnotation":"true" diff --git a/examples-jbake/templates/jvl_formComplete.ftl b/examples-jbake/templates/jvl_formComplete.ftl index cab6cc3..ff82339 100644 --- a/examples-jbake/templates/jvl_formComplete.ftl +++ b/examples-jbake/templates/jvl_formComplete.ftl @@ -5,7 +5,7 @@ instance on the page.

    View the source in your browser to see how it has been done.
    View the full JalviewLite API documentation. + archive="${content.jvl},${content.jmol}" name="Jalview"> <#if content.permissions?exists> diff --git a/examples-jbake/templates/jvl_javascriptLaunch.ftl b/examples-jbake/templates/jvl_javascriptLaunch.ftl index 43ae6c2..a6ce80a 100644 --- a/examples-jbake/templates/jvl_javascriptLaunch.ftl +++ b/examples-jbake/templates/jvl_javascriptLaunch.ftl @@ -83,7 +83,7 @@ function startJalview(aligURL,title,alwvar) {
    +archive="${content.jvl},${content.jmol}" width="0" height="0"> <#if (content.permissions?exists)> diff --git a/examples-jbake/templates/jvl_linkedapplets_ng.ftl b/examples-jbake/templates/jvl_linkedapplets_ng.ftl index 1de2e58..6c0e6d5 100644 --- a/examples-jbake/templates/jvl_linkedapplets_ng.ftl +++ b/examples-jbake/templates/jvl_linkedapplets_ng.ftl @@ -24,7 +24,7 @@ +archive="jalviewApplet.jar,JmolApplet-12.2.4.jar" width="0" height="0"> diff --git a/examples/linkedapplets_ng.html b/examples/linkedapplets_ng.html index 9c88710..71f1540 100644 --- a/examples/linkedapplets_ng.html +++ b/examples/linkedapplets_ng.html @@ -201,7 +201,7 @@ var _gaq = _gaq || [];_gaq.push(["_setAccount", "UA-9060947-1"]);_gaq.push(["_tr