[Git][java-team/jalview][upstream] New upstream version 2.11.1.3+dfsg2
Pierre Gruet
gitlab at salsa.debian.org
Sat Feb 6 21:24:51 GMT 2021
Pierre Gruet pushed to branch upstream at Debian Java Maintainers / jalview
Commits:
beb69435 by Pierre Gruet at 2021-02-04T22:23:17+01:00
New upstream version 2.11.1.3+dfsg2
- - - - -
3 changed files:
- − examples/embeddedWJmol.html
- − examples/index.html
- − examples/jmol/Jmol2.js
Changes:
=====================================
examples/embeddedWJmol.html deleted
=====================================
@@ -1,356 +0,0 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD HTML+RDFa 1.1//EN">
-<!--
- * Jalview - A Sequence Alignment Editor and Viewer (2.11.1.3)
- * Copyright (C) 2020 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.
- -->
- <html lang="en" dir="ltr" version="HTML+RDFa 1.1"
- xmlns:content="http://purl.org/rss/1.0/modules/content/"
- xmlns:dc="http://purl.org/dc/terms/"
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-<link rel="shortcut icon"
- href="http://www.jalview.org/sites/all/themes/jalview/favicon.ico"
- type="image/vnd.microsoft.icon" />
-<meta name="viewport"
- content="width=device-width, initial-scale=1, maximum-scale=1, minimum-scale=1, user-scalable=no" />
-<meta content="" about="/About" property="dc:title" />
-<link rel="shortlink" href="/node/18" />
-<meta name="Generator" content="Drupal 7 (http://drupal.org)" />
-<link rel="canonical" href="/About" />
-<title>Development | jalview.org</title>
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- s.parentNode.insertBefore(ga, s);
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-<script src="javascript/jalview.js" language="javascript"></script>
-<script src="javascript/jvcontroller.js"> </script>
-
-
-
-</head>
-
-
-
-<div id="header"></div>
-<section id="section-content" class="section section-content">
- <div id="zone-content-wrapper"
- class="zone-wrapper zone-content-wrapper clearfix">
-
- <div id="zone-content" class="zone zone-content clearfix container-12">
- <!— — — — — — — — — — — side bar — — — — — — — — — — —>
- <aside class="grid-3 region region-sidebar-first"
- id="region-sidebar-first">
- <div class="region-inner region-sidebar-first-inner">
- <section
- class="block block-menu-block block-1 block-menu-block-1 odd"
- id="block-menu-block-1">
- <div class="block-inner clearfix">
- <h2 class="block-title">
- <a href="/development" class="development active-trail">Development</a>
- </h2>
- <div class="content clearfix">
- <div class="menu-block-wrapper menu-block-1 menu-name-main-menu parent-mlid-0 menu-level-2">
- <div id="nav" class="nav">nav</div>
- </div>
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- </section>
- <section
- class="block block-menu-block block-2 block-menu-block-2 even"
- id="block-menu-block-2">
- <div class="block-inner clearfix">
- <h2 class="block-title">
- <a href="/About" class="active-trail active">About</a>
- </h2>
-
- <div class="content clearfix">
- <div
- class="menu-block-wrapper menu-block-2 menu-name-main-menu parent-mlid-0 menu-level-2">
- <div id="nav" class="nav">nav</div>
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-
- <div class="grid-9 region region-content" id="region-content">
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- id="block-system-main">
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- <div id="content">
-
-
-
-
-
-
-
-<div>
-
-
-<script language="JavaScript">
-// instead of this, we use a custom JmolApplet spec
-// jmolInitialize('jmol');
-jmolInitialize("","JmolApplet-14.6.4_2016.10.26.jar");
-</script>
-<script>
- var loglevel=1;
- function dbg(lvl,string) {
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- var _lastTime=new Date();
- var _path;
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- var alignA;
- var alignB;
- var featuresA;
- var featuresB;
- var pairs;
- var atompairs;
- var structdata;
- var jmolview;
- var jvstructassoc;
- var modeltofiles = new Array();
-
- function lJvA() {
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- setConsole(document.getElementById("stdout"));
- linkJvJmol(jvfollower, "jmolView", modeltofiles);
- };
-
- var _jvA=new Object();
- _jvA.attributes = {
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- width : '500',
- height : '350',
- mayscript : 'True',
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- id : 'jvA'
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- automaticScrolling : "true",
-// <!-- defaultColour : "Strand Propensity", -->
- file : "uniref50_mz.fa",
-
- relaxedidmatch : "true",
- debug : "true",
- wrap : "false",
- // separator : "^",
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- RGB : "F2F2FF",
- linkLabel_1 : "EMBL-EBI Search",
- linkUrl_1 : "http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"
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- linkLabel_2 : "Uniprot"
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-<div style="width: 100%">
-
-</div>
-
-<!-- content template start -->
-<h2>Structure and Alignment</h2>
-<p>This demo shows how JalviewLite and Jmol can be integrated with the JalviewLite javascript library.</p>
-
-
-<div>
- <script>
- jmolApplet("500x500","zap; load FILE '1gaq.txt'; frame 0; background black; select all; wireframe off; spacefill off; cartoons; restrict; center *; set selectionhalos true;set hoverDelay 0.001; select 0","jmolView");
- </script>
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-<applet
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-<param name="externalstructureviewer" value="true"/>
-<param name="oninit" value="lJvA"/>
-<param name="automaticScrolling" value="true"/>
-<param name="file" value="uniref50_mz.fa"/>
-<param name="relaxedidmatch" value="true"/>
-<param name="debug" value="true"/>
-<param name="wrap" value="false"/>
-<param name="showAnnotation" value="false"/>
-<param name="embedded" value="true"/>
-<param name="showFullId" value="false"/>
-<param name="RGB" value="F2F2FF"/>
-<param name="linkLabel_1" value="EMBL-EBI Search"/>
-<param name="linkUrl_1" value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"/>
-<param name="linkLabel_2" value="Uniprot"/>
-<param name="linkUrl_2" value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
-<param name="APPLICATION_URL" value="http://www.jalview.org/services/launchApp"/>
-<param name="PDBfile" value="1gaq.txt FER1_MAIZE"/>
-</applet>
-
-</div>
-
-<!-- content template end -->
-
-
-</div>
-
-
-
-
-
-
-
-
-
-
-</div>
- </div>
- </div>
- </div>
- </div>
- <div class="clearfix">
- <nav class="links node-links clearfix"></nav>
- </div>
- </article>
- </div>
- </div>
- </div>
- </div>
- </div>
- </div>
- </div>
-</section>
-
-<div id="footer"></div>
-
-
=====================================
examples/index.html deleted
=====================================
@@ -1,217 +0,0 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD HTML+RDFa 1.1//EN">
-<!--
- * Jalview - A Sequence Alignment Editor and Viewer (2.11.1.3)
- * Copyright (C) 2020 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/>.
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=====================================
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=====================================
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