+<pre><code class="language-bash">gradle test
+</code></pre>
+<p>These normally take around 5 - 10 minutes to complete and outputs its full results into
+the <code>tests/</code> folder. A summary of results should appear in your console.</p>
+<p>You can run different defined groups of tests with</p>
+<pre><code class="language-bash">gradle test -PtestngGroups=Network
+</code></pre>
+<p>Available groups include Functional (default), Network, External.</p>
+<h4 id="excluding-some-tests"><a href="#excluding-some-tests" name="excluding-some-tests" class="anchor"><span class="octicon octicon-link"></span>Excluding some tests</a></h4>
+<p>Some of Jalview's Functional tests don't pass reliably in all environments. We tag these tests with a group like 'Not-bamboo' to mark them for exclusion when we run tests as part of continuous integration.</p>
+<p>To exclude one or more groups of tests, add them as a comma separated list in testngExcludedGroups.</p>
+<pre><code class="language-bash">gradle test -PtestngExcludedGroups=Not-bamboo
+</code></pre>
+<h3 id="installer-packaging-with-install4j"><a href="#installer-packaging-with-install4j" name="installer-packaging-with-install4j" class="anchor"><span class="octicon octicon-link"></span>Installer packaging with <em>install4j</em></a></h3>
+<p>Jalview is currently using <em>install4j</em> <a href="https://www.ej-technologies.com/products/install4j/overview.html">https://www.ej-technologies.com/products/install4j/overview.html</a>
+as its installer packaging tool.</p>
+<p>If you have a licensed installation of <em>install4j</em> you can build Jalview installers
+by running</p>
+<pre><code class="language-bash">gradle installers
+</code></pre>
+<p>though you may need to fiddle with the <code>install4j</code> and <code>copyInstall4jTemplate</code> tasks
+in <code>build.gradle</code> file to point to your installation of <em>install4j</em> and also to bundled
+JREs if you want to bundle those into the installers.</p>
+<p>If you want more details, get in touch on our development mailing list <a href="mailto:jalview-dev@jalview.org">jalview-dev@jalview.org</a>.
+Sign up at <a href="http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev">http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev</a>.</p>
+<h2 id="gradle-properties"><a href="#gradle-properties" name="gradle-properties" class="anchor"><span class="octicon octicon-link"></span>Gradle properties</a></h2>
+<p>There are a lot of properties configured in <code>gradle.properties</code> which we strongly recommend
+being left as they are unless you have a specific problem with the build process.</p>
+<p>There are a few gradle properties you might want to set on the command line with the
+<code>-P</code> flag when building a version of Jalview with specific requirements:</p>
+<h4 id="java-version"><a href="#java-version" name="java-version" class="anchor"><span class="octicon octicon-link"></span><code>JAVA_VERSION</code></a></h4>
+<p>This changes the <em>target</em> java bytecode version</p>
+<blockquote>
+<p>NOTE that you will need to use a Java 11 (or greater) JDK Java compiler to build
+Jalview for any byte-code target version.</p>
+</blockquote>
+<p>Valid values are <code>11</code> and <code>1.8</code>.</p>
+<p>e.g.</p>
+<pre><code class="language-bash">gradle shadowJar -PJAVA_VERSION=1.8
+</code></pre>
+<p>When using <code>-PJAVA_VERSION=1.8</code> the libraries from <code>j8lib</code> (instead of <code>j11lib</code>) will be used in the compile<br />
+and runtime classpath and also used in the <code>makeDist</code> build step. Where a Java version of <code>11</code> is used in folder and file names, it will
+instead use <code>1.8</code>. Also if you are building installer packages with <em>install4j</em> the
+package builder will look for JRE 1.8 bundles to package in the installers.</p>
+<blockquote>
+<p>Note that continued development of Jalview will assume a Java 11+ runtime environment,
+the 2.11.0 release will run under a Java 1.8 JRE with a few minor features disabled.</p>
+</blockquote>
+<h4 id="channel"><a href="#channel" name="channel" class="anchor"><span class="octicon octicon-link"></span><code>CHANNEL</code></a></h4>
+<p>This changes the <code>appbase</code> setting in <code>getdown.txt</code> (<code>appbase</code> is where the getdown launcher
+looks to see if there's an updated file) to point to a particular Jalview channel or some other appropriate
+place to look for required files. If the selected channel type requires the getdown <code>appbase</code> to be a local
+directory on the filesystem (instead of a website URL) then a modified version of the <code>getdown-launcher.jar</code> will
+be used to allow this. The two versions of the <code>getdown-launcher.jar</code> can be found in <code>getdown/lib</code>.
+Some other variables used in the build process might also be set differently depending on the value of <code>CHANNEL</code>
+to allow smooth operation of getdown in the given context.</p>
+<p>There are several values of <code>CHANNEL</code> that can be chosen, with a default of <code>LOCAL</code>. Here's what they're for and what they do:</p>
+<ul>
+<li><code>LOCAL</code>: This is for running the compiled application from the development directory.
+It will set
+<ul>
+<li><code>appbase</code> as <code>file://PATH/TO/YOUR/DEVELOPMENT/getdown/files/JAVA_VERSION</code>
+(e.g. <code>file://home/user/git/jalview/getdown/files/11</code>)</li>
+<li>application subdir as <code>alt</code></li>
+<li>Getdown launcher can use a <code>file://</code> scheme appbase.</li>
+</ul>
+</li>
+<li><code>BUILD</code>: This is for creating an appbase channel on the build server by an automatic or manually started build.
+It will set
+<ul>
+<li><code>appbase</code> as <code>https://builds.jalview.org/browse/${bamboo_planKey}/latest/artifact/shared/getdown-channel/JAVA_VERSION</code>
+Note that bamboo_planKey should be set by the build plan with <code>-Pbamboo_planKey=${bamboo.planKey}</code></li>
+<li>application subdir as <code>alt</code></li>
+<li>Getdown launcher cannot use a <code>file://</code> scheme appbase.</li>
+</ul>
+</li>
+<li><code>DEVELOP</code>: This is for creating a <code>develop</code> appbase channel on the main web server. This won't become live until the actual getdown artefact is synced to the web server.
+It will set
+<ul>
+<li><code>appbase</code> as <code>http://www.jalview.org/getdown/develop/JAVA_VERSION</code></li>
+<li>application subdir as <code>alt</code></li>
+<li>Getdown launcher cannot use a <code>file://</code> scheme appbase.</li>
+</ul>
+</li>
+<li><code>SCRATCH-NAME</code>: This is for creating a temporary scratch appbase channel on the main web server. This won't become live until the actual getdown artefact is synced to the web server. This is meant for testing an over-the-air update without interfering with the live <code>release</code> or <code>develop</code> channels. The value of <code>NAME</code> can be any "word-character" [A-Za-z0-9_]
+It will set
+<ul>
+<li><code>appbase</code> as <code>http://www.jalview.org/getdown/SCRATCH-NAME/JAVA_VERSION</code></li>
+<li>application subdir as <code>alt</code></li>
+<li>Getdown launcher cannot use a <code>file://</code> scheme appbase.</li>
+</ul>
+</li>
+<li><code>TEST-LOCAL</code>: Like <code>SCRATCH</code> but with a specific <code>test-local</code> channel name and a local filesystem appbase. This is meant for testing an over-the-air update on the local filesystem. An extra property <code>LOCALDIR</code> must be given (e.g. <code>-PLOCALDIR=/home/user/tmp/test</code>)
+It will set
+<ul>
+<li><code>appbase</code> as <code>file://${LOCALDIR}</code></li>
+<li>application subdir as <code>alt</code></li>
+<li>Getdown launcher can use a <code>file://</code> scheme appbase.</li>
+</ul>
+</li>
+<li><code>TEST-RELEASE</code>: Like <code>SCRATCH</code> but with a specific <code>test-release</code> channel name. This won't become live until the actual getdown artefact is synced to the web server. This is meant for testing an over-the-air update without interfering with the live <code>release</code> or <code>develop</code> channels.
+It will set
+<ul>
+<li><code>appbase</code> as <code>http://www.jalview.org/getdown/test-release/JAVA_VERSION</code></li>
+<li>application subdir as <code>alt</code></li>
+<li>Getdown launcher cannot use a <code>file://</code> scheme appbase.</li>
+</ul>
+</li>
+<li><code>RELEASE</code>: This is for an actual release build, and will use an appbase on the main web server with the main <code>release</code> channel name. This won't become live until the actual getdown artefact is synced to the web server.
+It will set
+<ul>
+<li><code>appbase</code> as <code>http://www.jalview.org/getdown/release/JAVA_VERSION</code></li>
+<li>application subdir as <code>release</code></li>
+<li>Getdown launcher cannot use a <code>file://</code> scheme appbase.</li>
+</ul>
+</li>
+<li><code>ARCHIVE</code>: This is a helper to create a channel for a specific release version, and will use an appbase on the main web server with a specific <code>archive/JALVIEW_VERSION</code> channel name. This won't become live until the actual getdown artefact is synced to the web server.
+You must also specify an <code>ARCHIVEDIR</code> property that points to an earlier version of Jalview with a <code>dist</code> directory containing the required jar files. This should create a getdown structure and digest with the older jar files.
+It will set
+<ul>
+<li><code>appbase</code> as <code>http://www.jalview.org/getdown/archive/JALVIEW_VERSION/JAVA_VERSION</code></li>
+<li>application subdir as <code>alt</code></li>
+<li>Getdown launcher cannot use a <code>file://</code> scheme appbase.</li>
+</ul>
+</li>
+<li><code>ARCHIVELOCAL</code>: Like <code>ARCHIVE</code> but with a local filesystem appbase for local testing.
+You must also specify an <code>ARCHIVEDIR</code> property that points to an earlier version of Jalview with a <code>dist</code> directory containing the required jar files. This should create a getdown structure and digest with the older jar files.
+It will set
+<ul>
+<li><code>appbase</code> as <code>file://PATH/TO/YOUR/DEVELOPMENT/getdown/website/JAVA_VERSION</code> (where the old jars will have been copied and digested)</li>
+<li>application subdir as <code>alt</code></li>
+<li>Getdown launcher can use a <code>file://</code> scheme appbase.</li>
+</ul>
+</li>
+</ul>
+<p>e.g.</p>
+<pre><code class="language-bash">gradle getdown -PCHANNEL=SCRATCH-my_test_version
+</code></pre>
+<h4 id="jalview-version-and-the-release-file"><a href="#jalview-version-and-the-release-file" name="jalview-version-and-the-release-file" class="anchor"><span class="octicon octicon-link"></span>JALVIEW_VERSION and the RELEASE file</a></h4>
+<p>Any Jalview build will include the value of JALVIEW_VERSION in various places, including the 'About' and Jalview Desktop window title, and in filenames for the stand-alone executable jar. You can specify a custom version for a build via the JALVIEW_VERSION property, but for most situations, JALVIEW_VERSION will be automatically configured according to the value of the CHANNEL property, using the <code>jalview.version</code> property specified in the RELEASE file:</p>
+<ul>
+<li><code>CHANNEL=RELEASE</code> will set version to jalview.version</li>
+<li><code>CHANNEL=TEST or DEVELOP</code> will append '-test' or '-develop' to jalview.version</li>
+</ul>
+<p>It is also possible to specify a custom location for the RELEASE file via an optional JALVIEW_RELEASE_FILE property.</p>
+<h4 id="install4jmediatypes"><a href="#install4jmediatypes" name="install4jmediatypes" class="anchor"><span class="octicon octicon-link"></span><code>install4jMediaTypes</code></a></h4>
+<p>If you are building <em>install4j</em> installers (requires <em>install4j</em> to be installed) then this property specifies a comma-separated
+list of media types (i.e. platform specific installers) <em>install4j</em> should actually build.</p>
+<p>Currently the valid values are
+<code>linuxDeb</code>,
+<code>linuxRPM</code>,
+<code>macosArchive</code>,
+<code>unixArchive</code>,
+<code>unixInstaller</code>,
+<code>windows</code></p>
+<p>The default value is all of them.</p>
+<p>e.g.</p>
+<pre><code class="language-bash">gradle installers -PJAVA_VERSION=1.8 -Pinstall4jMediaTypes=macosArchive
+</code></pre>
+<p>To get an up-to-date list of possible values, you can run</p>
+<pre><code class="language-bash">perl -n -e 'm/^\s*<(\w+)[^>]*\bmediaFileName=/ && print "$1\n";' utils/install4j/install4j_template.install4j | sort -u
+</code></pre>
+<p>in the <code>jalview</code> root folder.</p>
+<h2 id="enabling-code-coverage-with-openclover"><a href="#enabling-code-coverage-with-openclover" name="enabling-code-coverage-with-openclover" class="anchor"><span class="octicon octicon-link"></span>Enabling Code Coverage with OpenClover</a></h2>
+<p>Bytecode instrumentation tasks are enabled by specifying 'true' (or just a non-whitespace non-numeric word) in the 'clover' property. This adds the 'openclover' plugin to the build script's classpath, making it possible to track code execution during test which can be viewed as an HTML report published at build/reports/clover/index.html.</p>
+<p><code>gradle -Pclover=true test cloverReport</code></p>
+<h4 id="troubleshooting-report-generation"><a href="#troubleshooting-report-generation" name="troubleshooting-report-generation" class="anchor"><span class="octicon octicon-link"></span>Troubleshooting report generation</a></h4>
+<p>The build forks a new JVM process to run the clover report generation tools (both XML and HTML reports are generated by default). The following properties can be used to specify additional options or adjust JVM memory settings. Default values for these options are:</p>
+<h5 id="jvm-memory-settings---increase-if-out-of-memory-errors-are-reported"><a href="#jvm-memory-settings---increase-if-out-of-memory-errors-are-reported" name="jvm-memory-settings---increase-if-out-of-memory-errors-are-reported" class="anchor"><span class="octicon octicon-link"></span>JVM Memory settings - increase if out of memory errors are reported</a></h5>
+<p><code>cloverReportJVMHeap = 2g</code></p>
+<h5 id="-dfileencodingutf-8-is-an-essential-parameters-for-report-generation-add-additional-ones-separated-by-a-space"><a href="#-dfileencodingutf-8-is-an-essential-parameters-for-report-generation-add-additional-ones-separated-by-a-space" name="-dfileencodingutf-8-is-an-essential-parameters-for-report-generation-add-additional-ones-separated-by-a-space" class="anchor"><span class="octicon octicon-link"></span>-Dfile.encoding=UTF-8 is an essential parameters for report generation. Add additional ones separated by a space.</a></h5>
+<p><code>cloverReportJVMArgs = -Dfile.encoding=UTF-8</code></p>
+<h5 id="add--v-to-debug-velocity-html-generation-errors-or--d-to-track-more-detailed-issues-with-the-coverage-database"><a href="#add--v-to-debug-velocity-html-generation-errors-or--d-to-track-more-detailed-issues-with-the-coverage-database" name="add--v-to-debug-velocity-html-generation-errors-or--d-to-track-more-detailed-issues-with-the-coverage-database" class="anchor"><span class="octicon octicon-link"></span>Add -v to debug velocity html generation errors, or -d to track more detailed issues with the coverage database</a></h5>
+<p><code>cloverReportHTMLOptions =</code></p>
+<h5 id="-v-for-verbose--d-for-debug-level-messages-as-above"><a href="#-v-for-verbose--d-for-debug-level-messages-as-above" name="-v-for-verbose--d-for-debug-level-messages-as-above" class="anchor"><span class="octicon octicon-link"></span>-v for verbose, -d for debug level messages (as above)</a></h5>
+<p><code>cloverReportXMLOptions =</code></p>
+<p><em>Note</em> do not forget to include the -Dfile.encoding=UTF-8 option: this is essential for some platforms in order for Clover to correctly parse some Jalview source files that contain characters that are UTF-8 encoded.</p>
+<h2 id="setting-up-in-eclipse-ide"><a href="#setting-up-in-eclipse-ide" name="setting-up-in-eclipse-ide" class="anchor"><span class="octicon octicon-link"></span>Setting up in Eclipse IDE</a></h2>
+<h3 id="installing-eclipse-ide"><a href="#installing-eclipse-ide" name="installing-eclipse-ide" class="anchor"><span class="octicon octicon-link"></span>Installing Eclipse IDE</a></h3>
+<p>We develop in Eclipse, and support settings to develop and save Jalview source code
+in our preferred style. We also support running the Jalview application, debugging
+and running tests with TestNG from within Eclipse.</p>
+<p>To get Jalview set up as a project in Eclipse, we recommend using at least the 2019-12
+version of Eclipse IDE for Java Developers which you can download from the Eclipse
+website: <a href="https://www.eclipse.org/downloads/">https://www.eclipse.org/downloads/</a>. Since Eclipse 2020-03 you are encouraged to use the Eclipse Installer (see the Eclipse Downloads page).
+In the installer, when given a choice of packages for Eclipse you should choose the "Eclipse IDE for Enterprise Java Developers" package.</p>
+<p><img src="./images/eclipse_installer.png" alt="" title="Eclipse Installer screenshot" /></p>
+<p>Once Eclipse is installed, we also recommend installing several plugins from the Eclipse Marketplace.</p>
+<p>Some of these should already be installed with the Enterprise Java Developer package:</p>
+<ol>