JAL-857 updated examples directory web pages to be dynamicaly decorated with jalview...
[jalview.git] / examples / includes / header_jv.html
diff --git a/examples/includes/header_jv.html b/examples/includes/header_jv.html
new file mode 100644 (file)
index 0000000..d5af784
--- /dev/null
@@ -0,0 +1,355 @@
+<!--
+ * 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+-->
+
+
+<body
+       class="html not-front not-logged-in page-node page-node- page-node-18 node-type-basic-page context-about">
+       <div id="skip-link">
+               <a href="#main-content" class="element-invisible element-focusable">Skip
+                       to main content</a>
+       </div>
+       <div class="page clearfix" id="page">
+               <header id="section-header" class="section section-header">
+               <div id="zone-branding-wrapper"
+                       class="zone-wrapper zone-branding-wrapper clearfix">
+                       <div id="zone-branding"
+                               class="zone zone-branding clearfix container-12">
+                               <div class="grid-6 region region-branding" id="region-branding">
+                                       <div class="region-inner region-branding-inner">
+                                               <div
+                                                       class="block block-views block-main-logo-block block-views-main-logo-block odd block-without-title"
+                                                       id="block-views-main-logo-block">
+                                                       <div class="block-inner clearfix">
+                                                               <div class="content clearfix">
+                                                                       <div
+                                                                               class="view view-main-logo view-id-main_logo view-display-id-block view-dom-id-1828f18ab2b5b41781dad3bdfec6156b">
+                                                                               <div class="view-content">
+                                                                                       <div class="item-list">
+                                                                                               <ul>
+                                                                                                       <li
+                                                                                                               class="views-row views-row-1 views-row-odd views-row-first views-row-last">
+                                                                                                               <div class="views-field views-field-field-logo-image">
+                                                                                                                       <div class="field-content">
+                                                                                                                               <a href="http://www.jalview.org/"><img
+                                                                                                                                       class="adaptive-image" typeof="foaf:Image"
+                                                                                                                                       src="http://www.jalview.org/sites/jalview.aegir-prod-6.lifesci.dundee.ac.uk/files/styles/adaptive/adaptive-image/public/jalviewHome_0.jpg?itok=xoZsVtTd"
+                                                                                                                                       alt="" /></a>
+                                                                                                                       </div>
+                                                                                                               </div>
+                                                                                                       </li>
+                                                                                               </ul>
+                                                                                       </div>
+                                                                               </div>
+                                                                       </div>
+                                                               </div>
+                                                       </div>
+                                               </div>
+                                       </div>
+                               </div>
+                               <div class="grid-6 region region-launch-buttons"
+                                       id="region-launch-buttons">
+                                       <div class="region-inner region-launch-buttons-inner">
+                                               <div
+                                                       class="block block-views block-launch-buttons-block block-views-launch-buttons-block odd block-without-title"
+                                                       id="block-views-launch-buttons-block">
+                                                       <div class="block-inner clearfix">
+                                                               <div class="content clearfix">
+                                                                       <div
+                                                                               class="view view-launch-buttons view-id-launch_buttons view-display-id-block view-dom-id-be0b33b57f9a461aaaf77cdeab66e60c">
+                                                                               <div class="view-content">
+                                                                                       <div class="item-list">
+                                                                                               <ul>
+                                                                                                       <li
+                                                                                                               class="views-row views-row-1 views-row-odd views-row-first">
+                                                                                                               <div class="views-field views-field-field-button-image">
+                                                                                                                       <div class="field-content">
+                                                                                                                               <a href="http://www.jalview.org/webstart/jalview.jnlp"><img
+                                                                                                                                       typeof="foaf:Image"
+                                                                                                                                       src="http://www.jalview.org/sites/jalview.aegir-prod-6.lifesci.dundee.ac.uk/files/desk.jpg"
+                                                                                                                                       width="250" height="40" alt="" /></a>
+                                                                                                                       </div>
+                                                                                                               </div>
+                                                                                                       </li>
+                                                                                                       <li
+                                                                                                               class="views-row views-row-2 views-row-even views-row-last">
+                                                                                                               <div class="views-field views-field-field-button-image">
+                                                                                                                       <div class="field-content">
+                                                                                                                               <a href="http://www.jalview.org/examples/applets.html"><img
+                                                                                                                                       typeof="foaf:Image"
+                                                                                                                                       src="http://www.jalview.org/sites/jalview.aegir-prod-6.lifesci.dundee.ac.uk/files/applet.jpg"
+                                                                                                                                       width="250" height="40" alt="" /></a>
+                                                                                                                       </div>
+                                                                                                               </div>
+                                                                                                       </li>
+                                                                                               </ul>
+                                                                                       </div>
+                                                                               </div>
+                                                                       </div>
+                                                               </div>
+                                                       </div>
+                                               </div>
+                                       </div>
+                               </div>
+                       </div>
+               </div>
+               <div id="zone-menu-wrapper"
+                       class="zone-wrapper zone-menu-wrapper clearfix">
+                       <div id="zone-menu" class="zone zone-menu clearfix container-12">
+                               <div class="grid-12 region region-menu" id="region-menu">
+                                       <div class="region-inner region-menu-inner">
+                                               <section
+                                                       class="block block-nice-menus block-1 block-nice-menus-1 odd"
+                                                       id="block-nice-menus-1">
+                                               <div class="block-inner clearfix">
+                                                       <h2 class="block-title">
+                                                               <span class="nice-menu-hide-title">Main menu</span>
+                                                       </h2>
+                                                       <div class="content clearfix">
+                                                               <ul class="nice-menu nice-menu-down" id="nice-menu-1">
+                                                                       <li class="menu-346 menu-path-front  first   odd  "><a
+                                                                               href="/" title="">Home</a></li>
+                                                                       <li
+                                                                               class="menu-355 menuparent  menu-path-node-18 active-trail   even  "><a
+                                                                               href="/About">About</a>
+                                                                               <ul>
+                                                                                       <li class="menu-356 menu-path-node-19  first   odd  "><a
+                                                                                               href="/about/citation">Publications</a></li>
+                                                                                       <li class="menu-357 menu-path-node-20   even  "><a
+                                                                                               href="/about/credits">Credits</a></li>
+                                                                                       <li class="menu-494 menu-path-node-310   odd   last "><a
+                                                                                               href="/about/jalview-scientific-advisory-committee">Advisory
+                                                                                                       Committee</a></li>
+                                                                               </ul></li>
+                                                                       <li class="menu-437 menuparent  menu-path-node-340   odd  "><a
+                                                                               href="/Help" class="help-colour-scheme">Help</a>
+                                                                               <ul>
+                                                                                       <li class="menu-579 menu-path-node-576  first   odd  "><a
+                                                                                               href="/Help/Getting-Started"
+                                                                                               title="Getting Starting with jalview">Getting Started</a></li>
+                                                                                       <li class="menu-511 menu-path-faq   even  "><a
+                                                                                               href="/faq">FAQ</a></li>
+                                                                                       <li class="menu-513 menu-path-node-2   odd  "><a
+                                                                                               href="/about/documentation">Documentation</a></li>
+                                                                                       <li
+                                                                                               class="menu-514 menu-path-jalvieworg-mailman-listinfo-jalview-discuss   even  "><a
+                                                                                               href="http://www.jalview.org/mailman/listinfo/jalview-discuss"
+                                                                                               class="new-window" target="_blank">Discussion Mailing
+                                                                                                       List</a></li>
+                                                                                       <li class="menu-773 menu-path-node-618   odd   last "><a
+                                                                                               href="/Help/About-Jalview" title="About Jalview">Other
+                                                                                                       Resources</a></li>
+                                                                               </ul></li>
+                                                                       <li class="menu-363 menuparent  menu-path-node-25   even  "><a
+                                                                               href="/community" class="community">Community</a>
+                                                                               <ul>
+                                                                                       <li
+                                                                                               class="menu-364 menu-path-jalvieworg-mailman-listinfo-jalview-announce  first   odd  "><a
+                                                                                               href="http://www.jalview.org/mailman/listinfo/jalview-announce"
+                                                                                               class="new-window" target="_blank">News Mailing List</a></li>
+                                                                                       <li
+                                                                                               class="menu-365 menu-path-jalvieworg-mailman-listinfo-jalview-discuss   even  "><a
+                                                                                               href="http://www.jalview.org/mailman/listinfo/jalview-discuss"
+                                                                                               class="new-window" target="_blank">Discussion Mailing
+                                                                                                       List</a></li>
+                                                                                       <li class="menu-441 menu-path-community-links   odd  "><a
+                                                                                               href="/community/links">Links</a></li>
+                                                                                       <li
+                                                                                               class="menu-457 menu-path-community-community-news   even   last "><a
+                                                                                               href="/community/community-news">Community News</a></li>
+                                                                               </ul></li>
+                                                                       <li class="menu-366 menuparent  menu-path-node-26   odd  "><a
+                                                                               href="/development" class="development active">Development</a>
+                                                                               <ul>
+                                                                                       <li
+                                                                                               class="menu-436 menu-path-issuesjalvieworg-secure-Dashboardjspa  first   odd  "><a
+                                                                                               href="http://issues.jalview.org/secure/Dashboard.jspa"
+                                                                                               name="new-window" class="new-window" target="_blank">Jalview
+                                                                                                       Bug Tracker</a></li>
+                                                                                       <li class="menu-367 menu-path-node-27   even  "><a
+                                                                                               href="/development/development-builds">Development
+                                                                                                       Version</a></li>
+                                                                                       <li
+                                                                                               class="menu-453 menu-path-sourcejalvieworg-gitweb-pjalviewgit;asummary   odd  "><a
+                                                                                               href="http://source.jalview.org/gitweb/?p=jalview.git;a=summary"
+                                                                                               class="new-window" target="_blank">Jalview Git Web</a></li>
+                                                                                       <li class="menu-512 menu-path-node-341   even  "><a
+                                                                                               href="/development/Version-Archive">Version Archive</a></li>
+                                                                                       <li
+                                                                                               class="menu-462 menu-path-development-release-history   odd  "><a
+                                                                                               href="/development/release-history">Release History</a></li>
+                                                                                       <li
+                                                                                               class="menu-456 menu-path-development-development-news   even   last "><a
+                                                                                               href="/development/development-news">Development News</a></li>
+                                                                               </ul></li>
+                                                                       <li class="menu-369 menuparent  menu-path-node-29   even  "><a
+                                                                               href="/training" class="training">Training</a>
+                                                                               <ul>
+                                                                                       <li
+                                                                                               class="menu-440 menu-path-training-training-courses  first   odd  "><a
+                                                                                               href="/training/training-courses">Training Courses</a></li>
+                                                                                       <li class="menu-1374 menu-path-node-654   even  "><a
+                                                                                               href="/training/Training-Videos"
+                                                                                               title="Jalview Online Training Videos">Training Videos</a></li>
+                                                                                       <li class="menu-458 menu-path-training-training-news   odd  "><a
+                                                                                               href="/training/training-news">Training News</a></li>
+                                                                                       <li class="menu-610 menu-path-node-606   even   last "><a
+                                                                                               href="/ISMB-2014-Presentation">Jalview &amp; JABA Slides</a></li>
+                                                                               </ul></li>
+                                                                       <li class="menu-358 menu-path-node-21   odd   last "><a
+                                                                               href="/Download" class="download-right">Download</a></li>
+                                                               </ul>
+                                                       </div>
+                                               </div>
+                                               </section>
+                                       </div>
+                               </div>
+                       </div>
+               </div>
+               <div id="zone-header-wrapper"
+                       class="zone-wrapper zone-header-wrapper clearfix">
+                       <div id="zone-header" class="zone zone-header clearfix container-12">
+                               <div class="grid-12 region region-header-first"
+                                       id="region-header-first">
+                                       <div class="region-inner region-header-first-inner">
+                                               <div
+                                                       class="block block-menu-block primary-nav block-3 block-menu-block-3 odd block-without-title"
+                                                       id="block-menu-block-3">
+                                                       <div class="block-inner clearfix">
+
+                                                               <div class="content clearfix">
+                                                                       <div
+                                                                               class="menu-block-wrapper menu-block-3 menu-name-main-menu parent-mlid-0 menu-level-1">
+                                                                               <ul class="menu">
+                                                                                       <li class="first leaf menu-mlid-346"><a href="/"
+                                                                                               title="">Home</a></li>
+                                                                                       <li class="expanded active-trail active menu-mlid-355"><a
+                                                                                               href="/About" class="active-trail active">About</a>
+                                                                                               <ul class="menu">
+                                                                                                       <li class="first leaf menu-mlid-356"><a
+                                                                                                               href="/about/citation">Publications</a></li>
+                                                                                                       <li class="leaf menu-mlid-357"><a
+                                                                                                               href="/about/credits">Credits</a></li>
+                                                                                                       <li class="last leaf menu-mlid-494"><a
+                                                                                                               href="/about/jalview-scientific-advisory-committee">Advisory
+                                                                                                                       Committee</a></li>
+                                                                                               </ul></li>
+                                                                                       <li class="expanded menu-mlid-437"><a href="/Help"
+                                                                                               class="help-colour-scheme">Help</a>
+                                                                                               <ul class="menu">
+                                                                                                       <li class="first leaf menu-mlid-579"><a
+                                                                                                               href="/Help/Getting-Started"
+                                                                                                               title="Getting Starting with jalview">Getting Started</a></li>
+                                                                                                       <li class="leaf menu-mlid-511"><a href="/faq">FAQ</a></li>
+                                                                                                       <li class="leaf menu-mlid-513"><a
+                                                                                                               href="/about/documentation">Documentation</a></li>
+                                                                                                       <li class="leaf menu-mlid-514"><a
+                                                                                                               href="http://www.jalview.org/mailman/listinfo/jalview-discuss"
+                                                                                                               class="new-window" target="_blank">Discussion Mailing
+                                                                                                                       List</a></li>
+                                                                                                       <li class="last leaf menu-mlid-773"><a
+                                                                                                               href="/Help/About-Jalview" title="About Jalview">Other
+                                                                                                                       Resources</a></li>
+                                                                                               </ul></li>
+                                                                                       <li class="expanded menu-mlid-363"><a href="/community"
+                                                                                               class="community">Community</a>
+                                                                                               <ul class="menu">
+                                                                                                       <li class="first leaf menu-mlid-364"><a
+                                                                                                               href="http://www.jalview.org/mailman/listinfo/jalview-announce"
+                                                                                                               class="new-window" target="_blank">News Mailing List</a></li>
+                                                                                                       <li class="leaf menu-mlid-365"><a
+                                                                                                               href="http://www.jalview.org/mailman/listinfo/jalview-discuss"
+                                                                                                               class="new-window" target="_blank">Discussion Mailing
+                                                                                                                       List</a></li>
+                                                                                                       <li class="leaf menu-mlid-441"><a
+                                                                                                               href="/community/links">Links</a></li>
+                                                                                                       <li class="last leaf menu-mlid-457"><a
+                                                                                                               href="/community/community-news">Community News</a></li>
+                                                                                               </ul></li>
+                                                                                       <li class="expanded menu-mlid-366"><a
+                                                                                               href="/development" class="development">Development</a>
+                                                                                               <ul class="menu">
+                                                                                                       <li class="first leaf menu-mlid-436"><a
+                                                                                                               href="http://issues.jalview.org/secure/Dashboard.jspa"
+                                                                                                               name="new-window" class="new-window" target="_blank">Jalview
+                                                                                                                       Bug Tracker</a></li>
+                                                                                                       <li class="leaf menu-mlid-367"><a
+                                                                                                               href="/development/development-builds">Development
+                                                                                                                       Version</a></li>
+                                                                                                       <li class="leaf menu-mlid-453"><a
+                                                                                                               href="http://source.jalview.org/gitweb/?p=jalview.git;a=summary"
+                                                                                                               class="new-window" target="_blank">Jalview Git Web</a></li>
+                                                                                                       <li class="leaf menu-mlid-512"><a
+                                                                                                               href="/development/Version-Archive">Version Archive</a></li>
+                                                                                                       <li class="leaf menu-mlid-462"><a
+                                                                                                               href="/development/release-history">Release History</a></li>
+                                                                                                       <li class="last leaf menu-mlid-456"><a
+                                                                                                               href="/development/development-news">Development News</a></li>
+                                                                                               </ul></li>
+                                                                                       <li class="expanded menu-mlid-369"><a href="/training"
+                                                                                               class="training">Training</a>
+                                                                                               <ul class="menu">
+                                                                                                       <li class="first leaf menu-mlid-440"><a
+                                                                                                               href="/training/training-courses">Training Courses</a></li>
+                                                                                                       <li class="leaf menu-mlid-1374"><a
+                                                                                                               href="/training/Training-Videos"
+                                                                                                               title="Jalview Online Training Videos">Training Videos</a></li>
+                                                                                                       <li class="leaf menu-mlid-458"><a
+                                                                                                               href="/training/training-news">Training News</a></li>
+                                                                                                       <li class="last leaf menu-mlid-610"><a
+                                                                                                               href="/ISMB-2014-Presentation">Jalview &amp; JABA
+                                                                                                                       Slides</a></li>
+                                                                                               </ul></li>
+                                                                                       <li class="last expanded menu-mlid-358"><a
+                                                                                               href="/Download" class="download-right">Download</a></li>
+                                                                               </ul>
+                                                                       </div>
+                                                               </div>
+                                                       </div>
+                                               </div>
+                                       </div>
+                               </div>
+                               <div class="grid-6 region region-header-second"
+                                       id="region-header-second">
+                                       <div class="region-inner region-header-second-inner">
+                                               <div
+                                                       class="block block-delta-blocks block-breadcrumb block-delta-blocks-breadcrumb odd block-without-title"
+                                                       id="block-delta-blocks-breadcrumb">
+                                                       <div class="block-inner clearfix">
+
+                                                               <div class="content clearfix">
+                                                                       <div id="breadcrumb" class="clearfix">
+                                                                               <ul class="breadcrumb">
+                                                                                       <li class="depth-1 odd first"><a href="/">Home</a></li>
+                                                                                       <li class="depth-2 even last"><a href="/About"
+                                                                                               class="active">About</a></li>
+                                                                               </ul>
+                                                                       </div>
+                                                               </div>
+                                                       </div>
+                                               </div>
+                                       </div>
+                               </div>
+                       </div>
+               </div>
+               </header>
+               
+               
+               <form name="custom_form" id="custom_form" action="jalview_examples.php" method="post">
+               <input type="hidden" name="target" id="target" value="APPLETS"><br>
+               </form>