[Git][java-team/jalview][master] 8 commits: Adding Mime types in d/jalview.desktop and d/jalview-mime.xml
Pierre Gruet
gitlab at salsa.debian.org
Sat Feb 6 21:24:46 GMT 2021
Pierre Gruet pushed to branch master at Debian Java Maintainers / jalview
Commits:
32f5bb5a by Pierre Gruet at 2021-01-30T21:51:32+01:00
Adding Mime types in d/jalview.desktop and d/jalview-mime.xml
- - - - -
d69ca843 by Pierre Gruet at 2021-02-04T21:48:55+01:00
Setting the packaged example file as not executable
- - - - -
1e81a085 by Pierre Gruet at 2021-02-04T22:23:04+01:00
Removing useless files with very long lines from source
- - - - -
beb69435 by Pierre Gruet at 2021-02-04T22:23:17+01:00
New upstream version 2.11.1.3+dfsg2
- - - - -
128799d8 by Pierre Gruet at 2021-02-04T22:23:42+01:00
Update upstream source from tag 'upstream/2.11.1.3+dfsg2'
Update to upstream version '2.11.1.3+dfsg2'
with Debian dir aa45f731f902c286eebe6ee3c13b28fb90c421a7
- - - - -
62eb2c50 by Pierre Gruet at 2021-02-06T21:51:37+01:00
Integrating the patch of upstream to control the way the web services are launched
- - - - -
c07fe595 by Pierre Gruet at 2021-02-06T21:53:03+01:00
Forwarding patches
- - - - -
f55cce83 by Pierre Gruet at 2021-02-06T21:57:49+01:00
Polishing changelog
- - - - -
16 changed files:
- debian/changelog
- debian/copyright
- + debian/jalview-mime.xml
- debian/jalview.desktop
- debian/jalview.install
- debian/manpages/jalview.1
- debian/patches/change_package_jfree.patch
- + debian/patches/controlling_web_services.patch
- debian/patches/java8-compatibility.patch
- debian/patches/newer-mime4j-api.diff
- debian/patches/series
- debian/patches/using_right_json_simple_package.patch
- debian/rules
- − examples/embeddedWJmol.html
- − examples/index.html
- − examples/jmol/Jmol2.js
Changes:
=====================================
debian/changelog
=====================================
@@ -1,31 +1,29 @@
-jalview (2.11.1.3+dfsg1-1) UNRELEASED; urgency=medium
+jalview (2.11.1.3+dfsg2-1) UNRELEASED; urgency=medium
[ Pierre Gruet ]
- * New upstream version 2.11.1.3+dfsg (Closes: #849025)
+ * New upstream version (Closes: #849025)
* New uploader (Closes: #897294)
* Using version 4 in d/watch to remove files
* Using secure URI in d/watch
+ * Switching from cdbs to dh
* Depending on debhelper-compat 13
- * Upstream has switched from ant to gradle
- * Correcting invocation of org.jfree
- * Get rid of quaqua, which cannot be distributed on a non-Mac platform
- * Calling JSONObject correctly
- * Deactivating getdown, which is used to update software while running
+ * Making the build with Maven instead of upstream's gradle
* Removing call to classgraph, not needed for a Debian run
* Updating build-dependencies list and d/jalview.classpath
- * Switching from cdbs to dh
- * Making the build with Maven instead of upstream's gradle
+ * Modifying the jar launcher by setting properly the jar manifest
* Updating Vcs-* and Homepage fields in d/control
* Refreshing d/copyright
* Bump Standards version to 4.5.1:
- Providing a FreeDesktop entry instead of former menu entry
- Rules-Requires-Root: no
- Using the https form of the copyright-format URL
- * Modifying the jar launcher by setting properly the jar manifest
- * Putting the documentation in the resources tm embed it into the jar
* Updating manpage
- * Deactivating Google Analytics, using a non-packaged and improperly licensed software
+ * Deactivating Google Analytics, using a non-packaged and improperly
+ licensed software
+ * Adding Mime types in d/jalview.desktop and d/jalview-mime.xml
* Adding autopkgtests
+ * Integrating the patch of upstream to control the way the web services are
+ launched
[ Steffen Moeller ]
* Reintroduced debian/upstream/edam file
@@ -39,7 +37,7 @@ jalview (2.11.1.3+dfsg1-1) UNRELEASED; urgency=medium
[ Andreas Tille ]
* d/rules: enforce LC_ALL=C.UTF-8 to cope with UTF-8 characters
- -- Pierre Gruet <pgtdebian at free.fr> Tue, 15 Dec 2020 23:02:10 +0100
+ -- Pierre Gruet <pgtdebian at free.fr> Sat, 06 Feb 2021 21:53:09 +0100
jalview (2.7.dfsg-5) unstable; urgency=medium
=====================================
debian/copyright
=====================================
@@ -7,14 +7,18 @@ Files-Excluded: jalview/j11lib
jalview/j8digestonly
jalview/examples/biojson-doc
jalview/examples/javascript
+ jalview/examples/jmol
jalview/examples/example_biojs.html
+ jalview/examples/embeddedWJmol.html
+ jalview/examples/index.html
jalview/utils
jalview/getdown
Source: The tarball is made by deleting the jars in the j8* and j11* dirs,
the utils directory as we will rely on the Debian-packaged tools, and
some folders in the examples directory, of which copyright is a bit
- confusing. getdown is a tool to update the software at runtime, which
- we don't want to enable.
+ confusing. We also delete some files with very long lines in the
+ examples/ folder. getdown is a tool to update the software at runtime,
+ which we don't want to enable.
Files: *
Copyright: 2014-2020 The Jalview Authors
=====================================
debian/jalview-mime.xml
=====================================
@@ -0,0 +1,121 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<mime-info xmlns="http://www.freedesktop.org/standards/shared-mime-info">
+
+ <mime-type type="application/x-jalview+xml+zip">
+ <comment>Jalview File</comment>
+ <glob pattern="*.jvp" weight="100"/>
+ </mime-type>
+
+ <mime-type type="chemical/x-cif">
+ <comment>CIF File</comment>
+ <glob pattern="*.cif" weight="40"/>
+ </mime-type>
+
+ <mime-type type="chemical/x-mmcif">
+ <comment>mmCIF File</comment>
+ <glob pattern="*.mcif" weight="40"/>
+ <glob pattern="*.mmcif" weight="40"/>
+ </mime-type>
+
+ <mime-type type="chemical/x-pdb">
+ <comment>PDB File</comment>
+ <glob pattern="*.pdb" weight="40"/>
+ <glob pattern="*.ent" weight="40"/>
+ </mime-type>
+
+ <mime-type type="application/x-amsa+txt">
+ <comment>AMSA File</comment>
+ <glob pattern="*.amsa" weight="90"/>
+ </mime-type>
+
+ <mime-type type="application/x-jalview-annotations+text">
+ <comment>Jalview Annotations File</comment>
+ <glob pattern="*.annotations" weight="100"/>
+ <glob pattern="*.jvannotations" weight="100"/>
+ </mime-type>
+
+ <mime-type type="application/x-jalview-biojson+json">
+ <comment>BioJSON File</comment>
+ <glob pattern="*.biojson" weight="100"/>
+ </mime-type>
+
+ <mime-type type="application/x-blc+txt">
+ <comment>BLC File</comment>
+ <glob pattern="*.blc" weight="90"/>
+ </mime-type>
+
+ <mime-type type="application/x-clustal+txt">
+ <comment>Clustal File</comment>
+ <glob pattern="*.aln" weight="90"/>
+ </mime-type>
+
+ <mime-type type="application/x-fasta+txt">
+ <comment>Fasta File</comment>
+ <glob pattern="*.fa" weight="90"/>
+ <glob pattern="*.fasta" weight="90"/>
+ </mime-type>
+
+ <mime-type type="application/x-jalview-features+text">
+ <comment>Jalview Features File</comment>
+ <glob pattern="*.features" weight="100"/>
+ <glob pattern="*.jvfeatures" weight="100"/>
+ </mime-type>
+
+ <mime-type type="application/x-gff2+txt">
+ <comment>Generic Features Format v2 File</comment>
+ <glob pattern="*.gff2" weight="90"/>
+ </mime-type>
+
+ <mime-type type="application/x-gff3+txt">
+ <comment>Generic Features Format v3 File</comment>
+ <glob pattern="*.gff3" weight="90"/>
+ </mime-type>
+
+ <mime-type type="application/x-jalview-jnet+text">
+ <comment>JnetFile File</comment>
+ <glob pattern="*.concise" weight="100"/>
+ <glob pattern="*.jnet" weight="100"/>
+ </mime-type>
+
+ <mime-type type="application/x-msf+txt">
+ <comment>MSF File</comment>
+ <glob pattern="*.msf" weight="90"/>
+ </mime-type>
+
+ <mime-type type="application/x-pfam+txt">
+ <comment>PFAM File</comment>
+ <glob pattern="*.pfam" weight="90"/>
+ </mime-type>
+
+ <mime-type type="application/x-phylip+txt">
+ <comment>PHYLIP File</comment>
+ <glob pattern="*.phy" weight="90"/>
+ </mime-type>
+
+ <mime-type type="application/x-pileup+txt">
+ <comment>PileUp File</comment>
+ <glob pattern="*.pileup" weight="90"/>
+ </mime-type>
+
+ <mime-type type="application/x-pir+txt">
+ <comment>PIR File</comment>
+ <glob pattern="*.pir" weight="90"/>
+ </mime-type>
+
+ <mime-type type="application/rnaml+xml">
+ <comment>RNAML File</comment>
+ <glob pattern="*.rnaml" weight="90"/>
+ </mime-type>
+
+ <mime-type type="application/x-jalview-scorematrix+text">
+ <comment>Substitution Matrix File</comment>
+ <glob pattern="*.mat" weight="100"/>
+ </mime-type>
+
+ <mime-type type="application/x-stockholm+txt">
+ <comment>Stockholm File</comment>
+ <glob pattern="*.sto" weight="90"/>
+ <glob pattern="*.stk" weight="90"/>
+ </mime-type>
+
+</mime-info>
=====================================
debian/jalview.desktop
=====================================
@@ -1,11 +1,12 @@
[Desktop Entry]
-Type=Application
Version=1.1
+Type=Application
Name=Jalview
-Comment=Multiple alignment editor
+Comment=Multiple Sequence Alignment Editor
Icon=jalview-icon
TryExec=jalview
-Exec=jalview %U
+Exec=jalview -open %u
Terminal=false
-Categories=Science;Biology
-Keywords=alignment;sequence
+Categories=Science;Biology;
+Keywords=alignment;sequence;
+MimeType=application/x-jalview+xml+zip;chemical/x-cif;chemical/x-mmcif;chemical/x-pdb;application/x-amsa+txt;application/x-jalview-annotations+text;application/x-jalview-biojson+json;application/x-blc+txt;application/x-clustal+txt;application/x-fasta+txt;application/x-jalview-features+text;application/x-gff2+txt;application/x-gff3+txt;application/x-jalview-jnet+text;application/x-msf+txt;application/x-pfam+txt;application/x-phylip+txt;application/x-pileup+txt;application/x-pir+txt;application/rnaml+xml;application/x-jalview-scorematrix+text;application/x-stockholm+txt
=====================================
debian/jalview.install
=====================================
@@ -1,2 +1,3 @@
debian/wrappers/jalview usr/bin
debian/jalview.desktop usr/share/applications
+debian/jalview-mime.xml usr/share/mime/packages
=====================================
debian/manpages/jalview.1
=====================================
@@ -3,7 +3,7 @@
.\" Copyright 2011 by Vincent Fourmond
.\" Can be modified and distributed under the terms of the GNU General
.\" public license, version 3 or any later version at your option.
-.TH JALVIEW 1 "21-11-2020"
+.TH JALVIEW 1 "06-02-2021"
.SH NAME
jalview \- Multiple alignment editor
.SH SYNOPSIS
@@ -97,6 +97,9 @@ Turn off questionnaire check.
.BR \-nonews
Turn off check for Jalview news.
.TP
+.BR \-nohtmltemplates
+Disable the automatic download of templates in the Github repository.
+.TP
.BR \-sortbytree " OR " \-nosortbytree
Enable or disable sorting of the given alignment by the given tree
.TP
=====================================
debian/patches/change_package_jfree.patch
=====================================
@@ -1,6 +1,6 @@
Description: change the package for org.jfree, which is not the correct one
Author: Pierre Gruet <pgtdebian at free.fr>
-Forwarded: no
+Forwarded: jalview-dev at jalview.org
Last-Update: 2020-11-12
--- a/src/jalview/gui/SequenceRenderer.java
=====================================
debian/patches/controlling_web_services.patch
=====================================
@@ -0,0 +1,243 @@
+Description: Do not run web services if not allowed by the user/administrator
+Author: Jim Procter <J.Procter at dundee.ac.uk>
+Forwarded: not-needed
+Reviewed-by: Pierre Gruet <pgtdebian at free.fr>
+Last-Update: 2021-02-06
+
+--- a/src/jalview/bin/Cache.java
++++ b/src/jalview/bin/Cache.java
+@@ -167,6 +167,8 @@
+ * <li>FOLLOW_SELECTIONS (true) Controls whether a new alignment view should
+ * respond to selections made in other alignments containing the same sequences.
+ * </li>
++ * <li>SHOW_JWS2_SERVICES (true) when set to false, jalview will not
++ * auto-discover JABAWS services</li>
+ * <li>JWS2HOSTURLS comma-separated list of URLs to try for JABAWS services</li>
+ * <li>SHOW_WSDISCOVERY_ERRORS (true) Controls if the web service URL discovery
+ * warning dialog box is displayed.</li>
+@@ -194,7 +196,13 @@
+ * <li>CHIMERA_PATH specify full path to Chimera program (if non-standard)</li>
+ * <li>ID_ORG_HOSTURL location of jalview service providing identifiers.org urls
+ * </li>
+- *
++ * <li>NONEWS - when set disables Jalview News from automatically appearing</li>
++ * <li>NOHTMLTEMPLATES - when set, the
++ * https://github.com/jalview/exporter-templates/tree/master/biojs repository is
++ * not downloaded automatically</li>
++ * <li>NOIDENTIFIERSSERVICE - when set, jalview won't automatically download
++ * available URL linkouts via www.jalview.org/services/identifiers</li>
++ * <li>
+ * </ul>
+ * Deprecated settings:
+ * <ul>
+--- a/src/jalview/bin/Jalview.java
++++ b/src/jalview/bin/Jalview.java
+@@ -366,12 +366,17 @@
+ System.err.println("CMD [-noquestionnaire] executed successfully!");
+ }
+
+- if (!aparser.contains("nonews"))
++ if (!aparser.contains("nonews")
++ || Cache.getProperty("NONEWS") == null)
+ {
+ desktop.checkForNews();
+ }
+
+- BioJsHTMLOutput.updateBioJS();
++ if (!aparser.contains("nohtmltemplates")
++ || Cache.getProperty("NOHTMLTEMPLATES") == null)
++ {
++ BioJsHTMLOutput.updateBioJS();
++ }
+ }
+
+ String file = null, data = null;
+--- a/src/jalview/gui/AlignFrame.java
++++ b/src/jalview/gui/AlignFrame.java
+@@ -4174,9 +4174,15 @@
+ webService.add(me.webServiceNoServices);
+ }
+ // TODO: move into separate menu builder class.
+- boolean new_sspred = false;
+- if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
+ {
++ // logic for 2.11.1.4 is
++ // always look to see if there is a discover. if there isn't
++ // we can't show any Jws2 services
++ // if there are services available, show them - regardless of
++ // the 'show JWS2 preference'
++ // if the discoverer is running then say so
++ // otherwise offer to trigger discovery if 'show JWS2' is not
++ // enabled
+ Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
+ if (jws2servs != null)
+ {
+@@ -4193,8 +4199,8 @@
+ }
+ }
+ }
+-
+ }
++
+ if (jws2servs.isRunning())
+ {
+ JMenuItem tm = new JMenuItem(
+@@ -4202,6 +4208,26 @@
+ tm.setEnabled(false);
+ webService.add(tm);
+ }
++ else if (!Cache.getDefault("SHOW_JWS2_SERVICES", true))
++ {
++ JMenuItem enableJws2 = new JMenuItem(
++ "Discover Web Services");
++ enableJws2.setToolTipText(
++ "Select to start JABA Web Service discovery (or enable option in Web Service preferences)");
++ enableJws2.setEnabled(true);
++ enableJws2.addActionListener(new ActionListener()
++ {
++
++ @Override
++ public void actionPerformed(ActionEvent e)
++ {
++ // start service discoverer, but ignore preference
++ Desktop.instance.startServiceDiscovery(false,
++ true);
++ }
++ });
++ webService.add(enableJws2);
++ }
+ }
+ }
+ build_urlServiceMenu(me.webService);
+--- a/src/jalview/gui/BlogReader.java
++++ b/src/jalview/gui/BlogReader.java
+@@ -272,13 +272,16 @@
+
+ initItems(chan);
+ updating = false;
+- boolean setvisible = checkForNew(chan, true);
+-
+- if (setvisible)
++ if (!Cache.getDefault("NONEWS", false))
+ {
++ boolean setvisible = checkForNew(chan, true);
++
++ if (setvisible)
++ {
+
+- Cache.log.debug("Will show jalview news automatically");
+- showNews();
++ Cache.log.debug("Will show jalview news automatically");
++ showNews();
++ }
+ }
+ Cache.log.debug("Completed construction of reader.");
+
+--- a/src/jalview/gui/Desktop.java
++++ b/src/jalview/gui/Desktop.java
+@@ -559,26 +559,27 @@
+
+ public void getIdentifiersOrgData()
+ {
+- // Thread off the identifiers fetcher
+- new Thread(new Runnable()
+- {
+- @Override
+- public void run()
++ if (Cache.getProperty("NOIDENTIFIERSSERVICE") == null)
++ {// Thread off the identifiers fetcher
++ new Thread(new Runnable()
+ {
+- Cache.log.debug("Downloading data from identifiers.org");
+- UrlDownloadClient client = new UrlDownloadClient();
+- try
+- {
+- client.download(IdOrgSettings.getUrl(),
+- IdOrgSettings.getDownloadLocation());
+- } catch (IOException e)
++ @Override
++ public void run()
+ {
+- Cache.log.debug("Exception downloading identifiers.org data"
+- + e.getMessage());
++ Cache.log.debug("Downloading data from identifiers.org");
++ try
++ {
++ UrlDownloadClient.download(IdOrgSettings.getUrl(),
++ IdOrgSettings.getDownloadLocation());
++ } catch (IOException e)
++ {
++ Cache.log.debug("Exception downloading identifiers.org data"
++ + e.getMessage());
++ }
+ }
+- }
+- }).start();
+- ;
++ }).start();
++ ;
++ }
+ }
+
+ @Override
+@@ -2571,13 +2572,36 @@
+ this.inBatchMode = inBatchMode;
+ }
+
++ /**
++ * start service discovery and wait till it is done
++ */
+ public void startServiceDiscovery()
+ {
+ startServiceDiscovery(false);
+ }
+
++ /**
++ * start service discovery threads - blocking or non-blocking
++ *
++ * @param blocking
++ */
+ public void startServiceDiscovery(boolean blocking)
+ {
++ startServiceDiscovery(blocking,false);
++ }
++
++ /**
++ * start service discovery threads
++ *
++ * @param blocking
++ * - false means call returns immediately
++ * @param ignore_SHOW_JWS2_SERVICES_preference
++ * - when true JABA services are discovered regardless of user's JWS2
++ * discovery preference setting
++ */
++ public void startServiceDiscovery(boolean blocking,
++ boolean ignore_SHOW_JWS2_SERVICES_preference)
++ {
+ boolean alive = true;
+ Thread t0 = null, t1 = null, t2 = null;
+ // JAL-940 - JALVIEW 1 services are now being EOLed as of JABA 2.1 release
+@@ -2595,7 +2619,8 @@
+ (t0 = new Thread(discoverer)).start();
+ }
+
+- if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
++ if (ignore_SHOW_JWS2_SERVICES_preference
++ || Cache.getDefault("SHOW_JWS2_SERVICES", true))
+ {
+ t2 = jalview.ws.jws2.Jws2Discoverer.getDiscoverer()
+ .startDiscoverer(changeSupport);
+--- a/src/jalview/ws/utils/UrlDownloadClient.java
++++ b/src/jalview/ws/utils/UrlDownloadClient.java
+@@ -33,11 +33,6 @@
+
+ public class UrlDownloadClient
+ {
+- public UrlDownloadClient()
+- {
+-
+- }
+-
+ /**
+ * Download and save a file from a URL
+ *
=====================================
debian/patches/java8-compatibility.patch
=====================================
@@ -1,6 +1,6 @@
Description: Fix the compilation errors with Java 8
Author: Emmanuel Bourg <ebourg at apache.org>
-Forwarded: no
+Forwarded: jalview-dev at jalview.org
--- a/src/jalview/ws/rest/InputType.java
+++ b/src/jalview/ws/rest/InputType.java
@@ -42,7 +42,6 @@
=====================================
debian/patches/newer-mime4j-api.diff
=====================================
@@ -1,6 +1,6 @@
Description: Patch to use the latest version of Apache Mime4J
Author: Emmanuel Bourg <ebourg at apache.org>
-Forwarded: no
+Forwarded: jalview-dev at jalview.org
--- a/src/jalview/ws/io/mime/JalviewMimeContentHandler.java
+++ b/src/jalview/ws/io/mime/JalviewMimeContentHandler.java
@@ -29,9 +29,9 @@
=====================================
debian/patches/series
=====================================
@@ -7,3 +7,4 @@ deactivate_getdown.patch
deactivate_classgraph.patch
correct_last_assertion_MemorySettingTest.patch
deactivate_google_analytics.patch
+controlling_web_services.patch
=====================================
debian/patches/using_right_json_simple_package.patch
=====================================
@@ -3,7 +3,7 @@ Description: JSONObject was wrongly invoked
Moreover it is called on an AlignmentPojo object, I added the getAppSettings
method in the call to get a HashMap<String, Object>.
Author: Pierre Gruet <pgtdebian at free.fr>
-Forwarded: no
+Forwarded: jalview-dev at jalview.org
Last-Update: 2020-11-15
--- a/src/jalview/io/JSONFile.java
=====================================
debian/rules
=====================================
@@ -34,3 +34,8 @@ override_dh_auto_install:
jh_installlibs
jh_manifest
jh_depends
+
+override_dh_fixperms:
+ # Setting the packaged example file as not executable.
+ chmod a-x debian/$(DEB_SOURCE)/usr/share/doc/jalview/examples/uniref50.fa
+ dh_fixperms
=====================================
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/"
- xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:og="http://ogp.me/ns#"
- xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
- xmlns:sioc="http://rdfs.org/sioc/ns#"
- xmlns:sioct="http://rdfs.org/sioc/types#"
- xmlns:skos="http://www.w3.org/2004/02/skos/core#"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema#">
-<head profile="http://www.w3.org/1999/xhtml/vocab">
-<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-<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>
-<link type="text/css" rel="stylesheet"
- href="http://www.jalview.org/sites/jalview.aegir-prod-6.lifesci.dundee.ac.uk/files/css/css_pbm0lsQQJ7A7WCCIMgxLho6mI_kBNgznNUWmTWcnfoE.css"
- media="all" />
-<link type="text/css" rel="stylesheet"
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-</section>
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-
-
=====================================
examples/index.html deleted
=====================================
@@ -1,217 +0,0 @@
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-<!--
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- * Jalview is free software: you can redistribute it and/or
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- * as published by the Free Software Foundation, either version 3
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- *
- * 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
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- -->
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