From: tcofoegbu Date: Thu, 3 Sep 2015 16:07:42 +0000 (+0100) Subject: merge X-Git-Tag: Release_2_10_0~475^2 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=refs%2Fheads%2Ffeatures%2FJAL-857_dynamic-example-files;hp=4200d569e2d29da8594fcd3599493889b086db56;p=jalview.git merge --- diff --git a/examples-jbake/content/appletParameters.html b/examples-jbake/content/appletParameters.html index b936824..00817a8 100644 --- a/examples-jbake/content/appletParameters.html +++ b/examples-jbake/content/appletParameters.html @@ -334,7 +334,7 @@ the applet can be interacted with via its
  • RNA secondary structure annotation row
    • -
  • Jmol compatibility updated to Jmol 12.2.x series - download the JmolApplet here
    • +
  • Jmol compatibility updated to Jmol 12.2.x series - download the JmolApplet here
  • To use Jmol as the structure viewer for Jalview, you must include the jar file in the applet archive argument thus:
    archive="jalviewApplet.jar,Jmol-12.2.4.jar"
    diff --git a/examples-jbake/content/applets.html b/examples-jbake/content/applets.html index 011c10e..5049e30 100644 --- a/examples-jbake/content/applets.html +++ b/examples-jbake/content/applets.html @@ -1,7 +1,7 @@ title=JalviewLite Examples type=page jvl=jalviewApplet.jar -jmol=JmolApplet-12.2.4.jar +jmol=JmolApplet-14.2.14_2015.06.11.jar status=published level=0 class=jvl_examples.ftl diff --git a/examples-jbake/content/embedded.html b/examples-jbake/content/embedded.html index 3b6fc63..90a7fd0 100644 --- a/examples-jbake/content/embedded.html +++ b/examples-jbake/content/embedded.html @@ -1,7 +1,7 @@ title=Embedded Alignment type=page jvl=jalviewApplet.jar -jmol=JmolApplet-12.2.4.jar +jmol=JmolApplet-14.2.14_2015.06.11.jar class=jvl_embedded.ftl status=published level=2 diff --git a/examples-jbake/content/embeddedWJmol.html b/examples-jbake/content/embeddedWJmol.html index ecc5769..6e42245 100644 --- a/examples-jbake/content/embeddedWJmol.html +++ b/examples-jbake/content/embeddedWJmol.html @@ -1,7 +1,7 @@ title=Jalview and Jmol type=page jvl=jalviewApplet.jar -jmol=JmolApplet-12.2.4.jar +jmol=JmolApplet-14.2.14_2015.06.11.jar class=jvl_embeddedWJmol.ftl hclass=jvl_embeddedWJmol_hdr.ftl status=published diff --git a/examples-jbake/content/formComplete.html b/examples-jbake/content/formComplete.html index c2ee860..6a3f71e 100644 --- a/examples-jbake/content/formComplete.html +++ b/examples-jbake/content/formComplete.html @@ -1,7 +1,7 @@ title=Access from Javascript type=page jvl=jalviewApplet.jar -jmol=JmolApplet-12.2.4.jar +jmol=JmolApplet-14.2.14_2015.06.11.jar class=jvl_formComplete.ftl status=published level=2 diff --git a/examples-jbake/content/javascriptLaunch.html b/examples-jbake/content/javascriptLaunch.html index 6a0dc9b..1315ee9 100644 --- a/examples-jbake/content/javascriptLaunch.html +++ b/examples-jbake/content/javascriptLaunch.html @@ -1,7 +1,7 @@ title=Javascript Launch type=page jvl=jalviewApplet.jar -jmol=JmolApplet-12.2.4.jar +jmol=JmolApplet-14.2.14_2015.06.11.jar class=jvl_javascriptLaunch.ftl status=published level=2 diff --git a/examples-jbake/content/linkedapplets_ng.html b/examples-jbake/content/linkedapplets_ng.html index 310ffd6..f220c75 100644 --- a/examples-jbake/content/linkedapplets_ng.html +++ b/examples-jbake/content/linkedapplets_ng.html @@ -1,7 +1,7 @@ title=Linked JalviewLites type=page jvl=jalviewApplet.jar -jmol=JmolApplet-12.2.4.jar +jmol=JmolApplet-14.2.14_2015.06.11.jar class=jvl_linkedapplets_ng.ftl status=published level=1 diff --git a/examples-jbake/content/u_applets.html b/examples-jbake/content/u_applets.html index 149cafa..1a48358 100644 --- a/examples-jbake/content/u_applets.html +++ b/examples-jbake/content/u_applets.html @@ -1,7 +1,7 @@ title=JalviewLite Examples type=page jvl=u_jalviewApplet.jar -jmol=u_JmolApplet-12.2.4.jar +jmol=u_JmolApplet-14.2.14_2015.06.11.jar alteg=true status=published level=0 diff --git a/examples-jbake/content/u_embedded.html b/examples-jbake/content/u_embedded.html index 0b68657..d295406 100644 --- a/examples-jbake/content/u_embedded.html +++ b/examples-jbake/content/u_embedded.html @@ -1,7 +1,7 @@ title=Embedded Alignment type=page jvl=u_jalviewApplet.jar -jmol=u_JmolApplet-12.2.4.jar +jmol=u_JmolApplet-14.2.14_2015.06.11.jar alteg=true class=jvl_embedded.ftl status=published diff --git a/examples-jbake/content/u_embeddedWJmol.html b/examples-jbake/content/u_embeddedWJmol.html index af9fe88..0b54b60 100644 --- a/examples-jbake/content/u_embeddedWJmol.html +++ b/examples-jbake/content/u_embeddedWJmol.html @@ -1,7 +1,7 @@ title=Jalview and Jmol type=page jvl=u_jalviewApplet.jar -jmol=u_JmolApplet-12.2.4.jar +jmol=u_JmolApplet-14.2.14_2015.06.11.jar alteg=true class=jvl_embeddedWJmol.ftl hclass=jvl_embeddedWJmol_hdr.ftl diff --git a/examples-jbake/content/u_formComplete.html b/examples-jbake/content/u_formComplete.html index c4f5ba6..86700e2 100644 --- a/examples-jbake/content/u_formComplete.html +++ b/examples-jbake/content/u_formComplete.html @@ -1,7 +1,7 @@ title=Access from Javascript type=page jvl=u_jalviewApplet.jar -jmol=u_JmolApplet-12.2.4.jar +jmol=u_JmolApplet-14.2.14_2015.06.11.jar alteg=true class=jvl_formComplete.ftl status=published diff --git a/examples-jbake/content/u_javascriptLaunch.html b/examples-jbake/content/u_javascriptLaunch.html index 080cd3b..075b8ca 100644 --- a/examples-jbake/content/u_javascriptLaunch.html +++ b/examples-jbake/content/u_javascriptLaunch.html @@ -1,7 +1,7 @@ title=Javascript Launch type=page jvl=u_jalviewApplet.jar -jmol=u_JmolApplet-12.2.4.jar +jmol=u_JmolApplet-14.2.14_2015.06.11.jar alteg=true class=jvl_javascriptLaunch.ftl status=published diff --git a/examples-jbake/content/u_linkedapplets_ng.html b/examples-jbake/content/u_linkedapplets_ng.html index 43e1ef5..69003f9 100644 --- a/examples-jbake/content/u_linkedapplets_ng.html +++ b/examples-jbake/content/u_linkedapplets_ng.html @@ -1,7 +1,7 @@ title=Linked JalviewLites type=page jvl=u_jalviewApplet.jar -jmol=u_JmolApplet-12.2.4.jar +jmol=u_JmolApplet-14.2.14_2015.06.11.jar alteg=true class=jvl_linkedapplets_ng.ftl status=published diff --git a/examples/appletParameters.html b/examples/appletParameters.html index c880a84..a0f25d4 100644 --- a/examples/appletParameters.html +++ b/examples/appletParameters.html @@ -1,4 +1,3 @@ - - - Applet Parameters - - - - - - - - - - - - - - - - - - - - - - - -
    - - - -
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    JalviewLite Applet Parameter Documentation

    @@ -165,9 +23,8 @@ var _gaq = _gaq || [];_gaq.push(["_setAccount", "UA-9060947-1"]);_gaq.push(["_tr The JalviewLite applet is configured through a series of applet parameters, which are described below. Once initialised, the applet can be interacted with via its -Javascript API. -

    Issues arising from tightening of Java Security default settings
    JalviewLite is provided as a signed applet with 'sandbox' permissions and wildcards that allow it to be run from any website. Unfortunately, earlier versions of Java are not compatible with these settings, so if you find that you cannot see any of the examples on the left, try the unsigned applet examples. -

    +Javascript API. +

    Issues arising from tightening of Java Security default settings
    JalviewLite is provided as a signed applet with 'sandbox' permissions and wildcards that allow it to be run from any website. Unfortunately, earlier versions of Java may not be compatible with these settings.

    For additional deployment notes, see below.

    Applet Parameters


    The applet takes the following initialisation parameters.

    @@ -487,7 +344,7 @@ the applet can be interacted with via its archive="jalviewApplet.jar, mydata.zip">
  • Use Jalview for input to a HTML form. For an example of how to - code this using Javascript, click here. + code this using Javascript, click here.
  • Embed Jalview into the web page, without the "Start Jalview" @@ -495,7 +352,7 @@ the applet can be interacted with via its <param name="embedded" value="true">
    • -

    **NEW FEATURES** in Jalview 2.8

    +

    **NEW FEATURES** in Jalview 2.8

    • Normalised sequence logo display
      • @@ -517,7 +374,7 @@ the applet can be interacted with via its
    • Javascript callbacks capabilities
      • oninit parameter and methods for registering javascript handlers for selections, mouseovers and linking to Jmol applets on the page.
      • To use javascript callbacks, ensure the applet tag includes the 'mayscript' attribute - either as a parameter (<param name="mayscript" value="true"/;gt;) or as a bare attribute in the applet html tag).
      • -
    • New jalviewLite java api methods for selecting, highlighting, scrolling and reordering sequences in an alignment view. +
    • New jalviewLite java api methods for selecting, highlighting, scrolling and reordering sequences in an alignment view.

    **NEW FEATURES** in Jalview 2.6

      @@ -599,30 +456,4 @@ the applet can be interacted with via its (All the usual Jalview File formats are valid, however each new line in an alignment file must be entered as a parameter)
    - - - - - - - - - - - diff --git a/examples/applets.html b/examples/applets.html old mode 100755 new mode 100644 index 0f49bbb..6ea7567 --- a/examples/applets.html +++ b/examples/applets.html @@ -1,4 +1,3 @@ - - - JalviewLite Examples - - - - - - - - - - - - - - - - - - - - - - - -
    - - - -
    - -
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    - Examples aren't working ?
    Try the unsigned applet demos -
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    Quick Links to jars for example:
    jalviewApplet.jar and JmolApplet.jar +

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    Quick Links to jars for example:
    jalviewApplet.jar and JmolApplet.jar

    @@ -177,7 +31,7 @@ var _gaq = _gaq || [];_gaq.push(["_setAccount", "UA-9060947-1"]);_gaq.push(["_tr

    JalviewLite Button Examples

    Try out JalviewLite by pressing one of the buttons below.
    - For more information on how to use the applet in your website, see the applet parameters and other documentation in the links to the left.

    + For more information on how to use the applet in your website, see the applet parameters and other documentation in the links to the left.

     

    Ferredoxins, chloroplast precursor related UniRef50 @@ -187,26 +41,23 @@ Try out JalviewLite by pressing one of the buttons below.

    - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + User Defined Colours, loads an associated Newick format tree file which is used to sort the alignment, and @@ -215,7 +66,7 @@ Try out JalviewLite by pressing one of the buttons below.
    + archive="jalviewApplet.jar,JmolApplet-14.2.14_2015.06.11.jar,java-json.jar,json_simple-1.1.jar"> @@ -240,7 +91,7 @@ Try out JalviewLite by pressing one of the buttons below.
    + archive="jalviewApplet.jar,JmolApplet-14.2.14_2015.06.11.jar,java-json.jar,json_simple-1.1.jar"> @@ -266,7 +117,7 @@ Try out JalviewLite by pressing one of the buttons below.
    + archive="jalviewApplet.jar,JmolApplet-14.2.14_2015.06.11.jar,java-json.jar,json_simple-1.1.jar"> @@ -297,7 +148,7 @@ Try out JalviewLite by pressing one of the buttons below.
    + archive="jalviewApplet.jar,JmolApplet-14.2.14_2015.06.11.jar,java-json.jar,json_simple-1.1.jar"> @@ -318,9 +169,10 @@ Try out JalviewLite by pressing one of the buttons below.

    -
    + + archive="jalviewApplet.jar,JmolApplet-14.2.14_2015.06.11.jar,java-json.jar,json_simple-1.1.jar"> @@ -339,30 +191,3 @@ Try out JalviewLite by pressing one of the buttons below.
    		Displays a split window view of protein and its related cDNA
    - - - - - - - - - - - - diff --git a/examples/embedded.html b/examples/embedded.html index ce17f7d..5891225 100644 --- a/examples/embedded.html +++ b/examples/embedded.html @@ -1,4 +1,3 @@ - - - Embedded Alignment - - - - - - - - - - - - - - - - - - - - - - - -
    - - - -
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    -
    - Examples aren't working ?
    Try the unsigned applet demos -
    -
    -

    Quick Links to jars for example:
    jalviewApplet.jar and JmolApplet.jar +

    +

    Quick Links to jars for example:
    jalviewApplet.jar and JmolApplet.jar

    @@ -185,7 +40,7 @@ var _gaq = _gaq || [];_gaq.push(["_setAccount", "UA-9060947-1"]);_gaq.push(["_tr + archive="jalviewApplet.jar,JmolApplet-14.2.14_2015.06.11.jar"> @@ -203,28 +58,3 @@ var _gaq = _gaq || [];_gaq.push(["_setAccount", "UA-9060947-1"]);_gaq.push(["_tr

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    - Examples aren't working ?
    Try the unsigned applet demos -
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    Quick Links to jars for example:
    jalviewApplet.jar and JmolApplet.jar +

    +

    Quick Links to jars for example:
    jalviewApplet.jar and JmolApplet.jar

    @@ -266,37 +278,71 @@ function genHref()

    Structure and Alignment

    This demo shows how JalviewLite and Jmol can be integrated with the JalviewLite javascript library.

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    - - - -
    -
    -
    - Examples aren't working ?
    Try the unsigned applet demos -
    -
    -

    Quick Links to jars for example:
    jalviewApplet.jar and JmolApplet.jar +

    +

    Quick Links to jars for example:
    jalviewApplet.jar and JmolApplet.jar

    -

    JalviewLite API Demo

    +

    JalviewLite API Demo

    Using the Javascript API to fill out forms using data from JalviewLite
    Click the Javascript buttons below to interact with the Applet instance on the page.

    View the source in your browser to see how it has been done.
    -View the full JalviewLite API documentation. +View the full JalviewLite API documentation. + archive="jalviewApplet.jar,JmolApplet-14.2.14_2015.06.11.jar" name="Jalview"> @@ -224,28 +79,3 @@ View the source in your browser to see how it has been done.
    - - - - - - - - - - diff --git a/examples/includes/footer_jv.html b/examples/includes/footer_jv.html new file mode 100644 index 0000000..3459fe6 --- /dev/null +++ b/examples/includes/footer_jv.html @@ -0,0 +1,50 @@ + + + +
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    + + + + diff --git a/examples/jalviewLiteJs.html b/examples/jalviewLiteJs.html index c72e801..f91efa3 100644 --- a/examples/jalviewLiteJs.html +++ b/examples/jalviewLiteJs.html @@ -1,4 +1,3 @@ - - - Javascript API - - - - - - - - - - - - - - - - - - - - - - - -
    - - - -
    - - - -

    The jalviewLite applet's application programming interface (API) includes two components. A JalviewLite Javascript Library and the public methods on the JalviewLite applet. +

    The jalviewLite applet's application programming interface (API) includes two components. A JalviewLite Javascript Library and the public methods on the JalviewLite applet.

    Notes

      @@ -411,30 +267,4 @@ public static String getVersion() public static boolean debug - - - - - -
    - -
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    - - - + \ No newline at end of file diff --git a/examples/javascript/jalview.js b/examples/javascript/jalview.js index dfe8c26..fa38582 100644 --- a/examples/javascript/jalview.js +++ b/examples/javascript/jalview.js @@ -17,6 +17,14 @@ * The Jalview Authors are detailed in the 'AUTHORS' file. */ + + + + + + + + // default console to report messages var _console = document.getElementById("stdout"); var _jvapps = new Array(); @@ -338,3 +346,37 @@ function _jmolMessagecallback(jmid, statmess) { } } + + + function lJvApp() { + setTimeout(function() { + //alert("in lJvApp"); + var jvapp = document.getElementById("jvapp"); + var jvfollower = document.getElementById("jvfollower"); + //console.log(">>>>>>>> lJvApp" + jvapp); + linkJvJmol(jvapp); + }, 200); + setConsole(document.getElementById("stdout")); + }; + + function lJvFollow() { + setTimeout(function() { + //alert("in lJvFollow"); + var jvapp = document.getElementById("jvapp"); + var jvfollower = document.getElementById("jvfollower"); + console.log(">>>>>>> lJvFollow" + jvfollower); + linkJvJmol(jvfollower); + }, 200); + }; + + function lJvA() { + setTimeout(function() { + //alert("lJvA"); + jvfollower = document.getElementById("jvA"); + setConsole(document.getElementById("stdout")); + //sep = jvfollower.getSeparator(); + //jvapp.setSeparator(""+jvapp.getSeparator()); + linkJvJmol(jvfollower, "jmolView", modeltofiles); + }, 100); + }; + diff --git a/examples/javascript/jvcontroller.js b/examples/javascript/jvcontroller.js new file mode 100644 index 0000000..885b2fa --- /dev/null +++ b/examples/javascript/jvcontroller.js @@ -0,0 +1,130 @@ +/** + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors + * + * This file is part of Jalview. + * + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. + * + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * PURPOSE. See the GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ + + + + var currentPage = "applets"; + + function createAppletTag(code, name, archive, width, height, params){ + var app = document.createElement('applet'); + app.code= code; + app.width = width; + app.height = height; + app.archive = archive; + + var arrayLength = params.length; + for (var i = 0; i < arrayLength; i++) { + //console.log('name : '+ params[i][0] + ' code : '+ params[i][1]); + var param = document.createElement('param'); + param.name = params[i][0]; + param.value = params[i][1]; + app.appendChild(param); + } + return app; + } + + function readCookie(name) { + var nameEQ = name + "="; + var ca = document.cookie.split(';'); + for(var i=0;i < ca.length;i++) { + var c = ca[i]; + while (c.charAt(0)==' ') c = c.substring(1,c.length); + if (c.indexOf(nameEQ) == 0) return c.substring(nameEQ.length,c.length); + } + return null; + } + + function setOrUpdateCookie(name, value, days) { + var expires; + if (days) { + var date = new Date(); + date.setTime(date.getTime() + (days * 24 * 60 * 60 * 1000)); + expires = "; expires=" + date.toGMTString(); + } + else { + expires = ""; + } + document.cookie = name + "=" + value + expires + "; path=/"; + } + + $(function(){ + var url = window.location.href; + var end = url.length; + var start = url.lastIndexOf("#"); + var newPage = url.substring(start + 1, end); + var page = ((start === -1) ? currentPage : newPage); + //alert("page:" + page); + if(page === "embeddedWJmol"){ + // do nothing embeddedWJmol page already include + + $('#header').load("includes/header_jv.html"); + //$('#content').load(page + ".html"); + $('#nav').load("includes/nav_jv.html"); + $('#footer').load("includes/footer_jv.html"); + $('#'+ currentPage).addClass('active-trail active'); + }else{ + $('#header').load("includes/header_jv.html"); + $('#content').load(page + ".html"); + $('#nav').load("includes/nav_jv.html"); + $('#footer').load("includes/footer_jv.html"); + $('#'+ currentPage).addClass('active-trail active'); + } + }); + + +function doSubmit(target){ + var currentPage = target+'.html'; + //alert("page:" + target); + if(target == "embeddedWJmol"){ + //loadJMolPage(); + window.location.href = 'embeddedWJmol.html#' + target; + $('#content').load(currentPage); + }else{ + window.location.href = 'index.html#' + target; + $('#content').load(currentPage); + } + updateLinks(target); +} + + + +function updateLinks(target) { + var ul = document.getElementById("menu"); + var items = ul.getElementsByTagName("li"); + for (var i = 0; i < items.length; ++i) { + removeClass(items[i], "active-trail active"); + } + $('#'+ target).addClass('active-trail active'); +} + +function hasClass(ele,cls) { + return !!ele.className.match(new RegExp('(\\s|^)'+cls+'(\\s|$)')); +} + +function addClass(ele,cls) { + if (!hasClass(ele,cls)) ele.className += " "+cls; +} + +function removeClass(ele,cls) { + if (hasClass(ele,cls)) { + var reg = new RegExp('(\\s|^)'+cls+'(\\s|$)'); + ele.className=ele.className.replace(reg,' '); + } +} + diff --git a/examples/javascriptLaunch.html b/examples/javascriptLaunch.html index 24e4516..c6668ce 100644 --- a/examples/javascriptLaunch.html +++ b/examples/javascriptLaunch.html @@ -1,4 +1,3 @@ - - - Javascript Launch - - - - - - - - - - - - - - - - - - - - - - - -
    - - - -
    - -
    -
    - Examples aren't working ?
    Try the unsigned applet demos -
    -
    -

    Quick Links to jars for example:
    jalviewApplet.jar and JmolApplet.jar + +

    +

    Quick Links to jars for example:
    jalviewApplet.jar and JmolApplet.jar

    @@ -258,7 +113,7 @@ function startJalview(aligURL,title,alwvar) {
    +archive="jalviewApplet.jar,JmolApplet-14.2.14_2015.06.11.jar" width="0" height="0"> @@ -269,28 +124,3 @@ archive="jalviewApplet.jar,JmolApplet-12.2.4.jar" width="0" height="0"> onClick="startJalview('plantfdx.fa','Button1.alignment','alwvar')"/>
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    Embedded viewing of Alignments

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    Structure and Alignment

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    This demo shows how JalviewLite and Jmol can be integrated with the JalviewLite javascript library.

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    JalviewLite API Demo

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    Using the Javascript API to fill out forms using data from JalviewLite -
    Click the Javascript buttons below to interact with the Applet -instance on the page.

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    Javascript Launch Button

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    JalviewLite Linked Applets Demo

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