jalview.release=releases/Release_2_11_1_Branch
-jalview.version=2.11.1.1
+jalview.version=2.11.1.3
}
////
// Set JALVIEW_VERSION if it is not already set
- if (findProperty(JALVIEW_VERSION)==null || "".equals(JALVIEW_VERSION)) {
+ if (findProperty("JALVIEW_VERSION")==null || "".equals(JALVIEW_VERSION)) {
JALVIEW_VERSION = releaseProps.get("jalview.version")
}
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<body>
-<div id="TOC">
+<nav id="TOC">
<ul>
<li><a href="#building-jalview-from-source">Building Jalview from Source</a><ul>
<li><a href="#tldr">tl;dr</a></li>
<li><a href="#gradle-and-git">gradle and git</a></li>
</ul></li>
<li><a href="#downloading-the-jalview-source-tree">Downloading the Jalview source tree</a><ul>
-<li><a href="#whats-in-the-source-tree">What's in the source tree?</a></li>
+<li><a href="#whats-in-the-source-tree">What’s in the source tree?</a></li>
</ul></li>
<li><a href="#building-jalview">Building Jalview</a><ul>
<li><a href="#minimal-jalview-build">Minimal Jalview Build</a></li>
</ul></li>
</ul></li>
</ul>
-</div>
+</nav>
<h1 id="building-jalview-from-source">Building Jalview from Source</h1>
<h2 id="tldr">tl;dr</h2>
<pre><code># download
cd jalview
gradle shadowJar
# run
-java -jar build/libs/jalview-all-11.jar
+java -jar build/libs/jalview-all-*-j11.jar
# and/or create launcher
gradle getdown
<p>The method here is described in terms of using a command line. You can easily do this on linux or in a Terminal window in macOS. You can do it in Windows.</p>
<ul>
<li>Java 11 compliant JDK</li>
-<li>gradle 5.2 or above</li>
+<li>gradle 5.2 or above <em>(NB gradle 6.6 and above currently produces NullPointerExceptions during the build. This is non-fatal and does not affect the build. Use gradle 6.5.1 to avoid this)</em></li>
<li>git</li>
</ul>
<blockquote>
-<p>The versions and installation methods here are just suggestions (which we have tested so are known to work). If you need or wish to use different implementations (particularly you might need a bespoke JDK if you are on an exotic architecture) then the general build instructions should work with any gradle 5+. You should be able to compile the bytecode with any JDK Java 11+. The resulting bytecode (in particular the shadow jar) should be runnable in any JRE Java 1.8+. Remember that because Jalview and the getdown launcher are Java bytecode you can build on one system where you might have gradle, and run on another where you don't (JRE 1.8+ required).</p>
+<p>The versions and installation methods here are just suggestions (which we have tested so are known to work). If you need or wish to use different implementations (particularly you might need a bespoke JDK if you are on an exotic architecture) then the general build instructions should work with any gradle 5+. You should be able to compile the bytecode with any JDK Java 11+. The resulting bytecode (in particular the shadow jar) should be runnable in any JRE Java 1.8+. Remember that because Jalview and the getdown launcher are Java bytecode you can build on one system where you might have gradle, and run on another where you don’t (JRE 1.8+ required).</p>
</blockquote>
<h3 id="java-11-compliant-jdk">Java 11 compliant JDK</h3>
<h4 id="all-platforms">All platforms</h4>
-<p>We recommend obtaining an OpenJDK JDK 11 (since 11 is the long term support release) from AdoptOpenJDK: <a href="https://adoptopenjdk.net/?variant=openjdk11&jvmVariant=hotspot" class="uri">https://adoptopenjdk.net/?variant=openjdk11&jvmVariant=hotspot</a>, either the <em>Installer</em> or <code>.zip</code>/<code>.tar.gz</code> variants whichever you prefer (if you're not sure, choose the <em>Installer</em>).</p>
+<p>We recommend obtaining an OpenJDK JDK 11 (since 11 is the long term support release) from AdoptOpenJDK: <a href="https://adoptopenjdk.net/?variant=openjdk11&jvmVariant=hotspot" class="uri">https://adoptopenjdk.net/?variant=openjdk11&jvmVariant=hotspot</a>, either the <em>Installer</em> or <code>.zip</code>/<code>.tar.gz</code> variants whichever you prefer (if you’re not sure, choose the <em>Installer</em>).</p>
<blockquote>
<h5 id="alternativecli-install-of-adoptopenjdk-11">Alternative/CLI install of AdoptOpenJDK 11</h5>
<p>You can also install adoptopenjdk11 using either <code>brew</code> (macOS), <code>choco</code> (Windows) (see the section on <code>gradle</code> and <code>git</code> for more informaiton on <code>brew</code> and <code>choco</code>) or <code>yum</code> or <code>apt</code> (Linux):</p>
<p>You should be able to install the latest (or sufficiently recent) versions of gradle and git using your OS package manager.</p>
<h4 id="macos">MacOS</h4>
<p>we recommend using <code>brew</code>, which can be installed following the instructions at <a href="https://brew.sh/" class="uri">https://brew.sh/</a>. After installing <code>brew</code>, open a Terminal window and type in (using an Administrator privileged user):</p>
-<div class="sourceCode"><pre class="sourceCode bash"><code class="sourceCode bash"><span class="ex">brew</span> install gradle git</code></pre></div>
+<div class="sourceCode" id="cb4"><pre class="sourceCode bash"><code class="sourceCode bash"><a class="sourceLine" id="cb4-1" title="1"><span class="ex">brew</span> install gradle git</a></code></pre></div>
<p>or if you aready have them installed but need to upgrade the version:</p>
-<div class="sourceCode"><pre class="sourceCode bash"><code class="sourceCode bash"><span class="ex">brew</span> upgrade gradle git</code></pre></div>
+<div class="sourceCode" id="cb5"><pre class="sourceCode bash"><code class="sourceCode bash"><a class="sourceLine" id="cb5-1" title="1"><span class="ex">brew</span> upgrade gradle git</a></code></pre></div>
<h4 id="windows">Windows</h4>
<p>we suggest using the <strong>Chocolatey</strong> package manager. See install instructions at <a href="https://chocolatey.org/" class="uri">https://chocolatey.org/</a>, and you will just need</p>
-<div class="sourceCode"><pre class="sourceCode bash"><code class="sourceCode bash"><span class="ex">choco</span> install gradle
-<span class="ex">choco</span> install git</code></pre></div>
+<div class="sourceCode" id="cb6"><pre class="sourceCode bash"><code class="sourceCode bash"><a class="sourceLine" id="cb6-1" title="1"><span class="ex">choco</span> install gradle</a>
+<a class="sourceLine" id="cb6-2" title="2"><span class="ex">choco</span> install git</a></code></pre></div>
<p>Alternatively, you could install a real <code>bash</code> shell and install both <code>gradle</code> and <code>git</code> through <code>apt-get</code>. See <a href="https://devblogs.microsoft.com/commandline/bash-on-ubuntu-on-windows-download-now-3/" class="uri">https://devblogs.microsoft.com/commandline/bash-on-ubuntu-on-windows-download-now-3/</a> for how to install the ubuntu bash shell in Windows 10.</p>
<p>Another alternative would be to install them separately. For <code>gradle</code> follow the instructions at <a href="https://gradle.org/install/" class="uri">https://gradle.org/install/</a>, and for <code>git</code> here are a couple of suggestions: Git for Windows <a href="https://gitforwindows.org/" class="uri">https://gitforwindows.org/</a>. Getting the individual installs working together on the command line will be trickier so we recommend using Chocolatey or bash.</p>
<h4 id="linux">Linux</h4>
-<p>this will depend on which distribution you're using.</p>
-<h5 id="for-debian-based-distributions-e.g.-mint-ubuntu-debian">For <em>Debian</em> based distributions (e.g. Mint, Ubuntu, Debian)</h5>
+<p>this will depend on which distribution you’re using.</p>
+<h5 id="for-debian-based-distributions-e.g.-mint-ubuntu-debian">For <em>Debian</em> based distributions (e.g. Mint, Ubuntu, Debian)</h5>
<p>run</p>
-<div class="sourceCode"><pre class="sourceCode bash"><code class="sourceCode bash"> <span class="fu">sudo</span> apt-get install gradle git</code></pre></div>
-<h5 id="for-rpm-based-distributions-e.g.-fedora-centos-redhat">for RPM-based distributions (e.g. Fedora, CentOS, RedHat)</h5>
+<div class="sourceCode" id="cb7"><pre class="sourceCode bash"><code class="sourceCode bash"><a class="sourceLine" id="cb7-1" title="1"> <span class="fu">sudo</span> apt-get install gradle git</a></code></pre></div>
+<h5 id="for-rpm-based-distributions-e.g.-fedora-centos-redhat">for RPM-based distributions (e.g. Fedora, CentOS, RedHat)</h5>
<p>run</p>
-<div class="sourceCode"><pre class="sourceCode bash"><code class="sourceCode bash"><span class="fu">sudo</span> yum install gradle git</code></pre></div>
-<p>If you have some other version of linux you'll probably be able to work it out!</p>
+<div class="sourceCode" id="cb8"><pre class="sourceCode bash"><code class="sourceCode bash"><a class="sourceLine" id="cb8-1" title="1"><span class="fu">sudo</span> yum install gradle git</a></code></pre></div>
+<p>If you have some other version of linux you’ll probably be able to work it out!</p>
<h2 id="downloading-the-jalview-source-tree">Downloading the Jalview source tree</h2>
-<p>This can be done with <code>git</code>. On the command line, change directory to where you want to download Jalview's build-tree top level directory. Then run</p>
-<div class="sourceCode"><pre class="sourceCode bash"><code class="sourceCode bash"><span class="fu">git</span> clone http://source.jalview.org/git/jalview.git</code></pre></div>
-<p>You'll get some progress output and after a minute or two you should have the full Jalview build-tree in the folder <code>jalview</code>.</p>
-<h3 id="whats-in-the-source-tree">What's in the source tree?</h3>
-<p>Jalview is a mature product with its codebase going back many years. As such it doesn't have a folder structure that most new gradle projects would have, so you might not find everything in the place you might expect. Here's a brief description of what you might find in the main folders under the <code>jalview</code> tree.</p>
+<p>This can be done with <code>git</code>. On the command line, change directory to where you want to download Jalview’s build-tree top level directory. Then run</p>
+<div class="sourceCode" id="cb9"><pre class="sourceCode bash"><code class="sourceCode bash"><a class="sourceLine" id="cb9-1" title="1"><span class="fu">git</span> clone http://source.jalview.org/git/jalview.git</a></code></pre></div>
+<p>You’ll get some progress output and after a minute or two you should have the full Jalview build-tree in the folder <code>jalview</code>.</p>
+<h3 id="whats-in-the-source-tree">What’s in the source tree?</h3>
+<p>Jalview is a mature product with its codebase going back many years. As such it doesn’t have a folder structure that most new gradle projects would have, so you might not find everything in the place you might expect. Here’s a brief description of what you might find in the main folders under the <code>jalview</code> tree.</p>
<p>Within the <code>jalview</code> folder you will find (of possible interest):</p>
<table>
<colgroup>
-<col width="16%" />
-<col width="83%" />
+<col style="width: 15%" />
+<col style="width: 84%" />
</colgroup>
<thead>
<tr class="header">
<tbody>
<tr class="odd">
<td><code>bin/</code></td>
-<td>used by eclipse for compiled classes -- no need to touch this</td>
+<td>used by eclipse for compiled classes – no need to touch this</td>
</tr>
<tr class="even">
<td><code>build/</code></td>
</tr>
<tr class="even">
<td><code>getdown/website/</code></td>
-<td>the assembled "download" folder used by getdown for downloads/upgrades</td>
+<td>the assembled “download” folder used by getdown for downloads/upgrades</td>
</tr>
<tr class="odd">
<td><code>getdown/files/</code></td>
<td><code>gradle.properties</code></td>
<td>configurable properties for the build process</td>
</tr>
+<tr class="even">
+<td><code>RELEASE</code></td>
+<td>propertyfile configuring JALVIEW_VERSION (from jalview.version) and the release branch (from jalview.release). An alternative file can be specified via JALVIEW_RELEASE_FILE property</td>
+</tr>
</tbody>
</table>
<p>Note that you need a Java 11 JDK to compile Jalview whether your target build is Java 1.8 or Java 11.</p>
</blockquote>
<h3 id="minimal-jalview-build">Minimal Jalview Build</h3>
<p>To compile the necessary class files, just run</p>
-<div class="sourceCode"><pre class="sourceCode bash"><code class="sourceCode bash"><span class="ex">gradle</span> compileJava</code></pre></div>
+<div class="sourceCode" id="cb11"><pre class="sourceCode bash"><code class="sourceCode bash"><a class="sourceLine" id="cb11-1" title="1"><span class="ex">gradle</span> compileJava</a></code></pre></div>
<p>to compile the classes into the <code>classes</code> folder. You should now be able to run the Jalview application directly with</p>
-<div class="sourceCode"><pre class="sourceCode bash"><code class="sourceCode bash"><span class="ex">java</span> -cp <span class="st">"classes:resources:help:j11lib/*"</span> jalview.bin.Jalview</code></pre></div>
+<div class="sourceCode" id="cb12"><pre class="sourceCode bash"><code class="sourceCode bash"><a class="sourceLine" id="cb12-1" title="1"><span class="ex">java</span> -cp <span class="st">"classes:resources:help:j11lib/*"</span> jalview.bin.Jalview</a></code></pre></div>
<p>You can also run with an automatic large memory setting (which will set the maximum memory heap of the Jalview JVM to 90% of your local physical memory) and docked icon setting (if possible in your OS) with</p>
-<div class="sourceCode"><pre class="sourceCode bash"><code class="sourceCode bash"><span class="ex">java</span> -cp <span class="st">"classes:resources:help:j11lib/*"</span> jalview.bin.Launcher</code></pre></div>
+<div class="sourceCode" id="cb13"><pre class="sourceCode bash"><code class="sourceCode bash"><a class="sourceLine" id="cb13-1" title="1"><span class="ex">java</span> -cp <span class="st">"classes:resources:help:j11lib/*"</span> jalview.bin.Launcher</a></code></pre></div>
<blockquote>
-<p><em>You must use just "<code>j11lib/*</code>" and not "<code>j11lib/*.jar</code>" as this is a special Java classpath argument wildcard interpreted by <code>java</code>, <strong>not</strong> a shell expansion wildcard interpreted by the shell.</em></p>
+<p><em>You must use just “<code>j11lib/*</code>” and not “<code>j11lib/*.jar</code>” as this is a special Java classpath argument wildcard interpreted by <code>java</code>, <strong>not</strong> a shell expansion wildcard interpreted by the shell.</em></p>
</blockquote>
-<p>Note that <code>jalview.bin.Launcher</code> is a simplified launcher class that re-launches <code>jalview.bin.Jalview</code> with the same JRE (<em>not</em> the same JVM instance), classpath and arguments, but with an automatically determined <code>-Xmx...</code> memory setting if one hasn't been provided.</p>
+<p>Note that <code>jalview.bin.Launcher</code> is a simplified launcher class that re-launches <code>jalview.bin.Jalview</code> with the same JRE (<em>not</em> the same JVM instance), classpath and arguments, but with an automatically determined <code>-Xmx...</code> memory setting if one hasn’t been provided.</p>
<h3 id="jalview-in-a-jar-file">Jalview in a Jar File</h3>
<p>To package the <code>classes</code>, <code>resources</code>, and <code>help</code> into one jar, you can run</p>
-<div class="sourceCode"><pre class="sourceCode bash"><code class="sourceCode bash"><span class="ex">gradle</span> jar</code></pre></div>
+<div class="sourceCode" id="cb14"><pre class="sourceCode bash"><code class="sourceCode bash"><a class="sourceLine" id="cb14-1" title="1"><span class="ex">gradle</span> jar</a></code></pre></div>
<p>which assembles the Jalview classes and resources into <code>dist/jalview.jar</code></p>
<p>To run this, use</p>
-<div class="sourceCode"><pre class="sourceCode bash"><code class="sourceCode bash"><span class="ex">java</span> -cp <span class="st">"dist/jalview.jar:j11lib/*"</span> jalview.bin.Jalview</code></pre></div>
+<div class="sourceCode" id="cb15"><pre class="sourceCode bash"><code class="sourceCode bash"><a class="sourceLine" id="cb15-1" title="1"><span class="ex">java</span> -cp <span class="st">"dist/jalview.jar:j11lib/*"</span> jalview.bin.Jalview</a></code></pre></div>
<h3 id="distributed-jar-files">Distributed Jar Files</h3>
<p>To simplify this, all required <code>.jar</code> files can be assembled into the <code>dist</code> folder using</p>
-<div class="sourceCode"><pre class="sourceCode bash"><code class="sourceCode bash"><span class="ex">gradle</span> makeDist</code></pre></div>
+<div class="sourceCode" id="cb16"><pre class="sourceCode bash"><code class="sourceCode bash"><a class="sourceLine" id="cb16-1" title="1"><span class="ex">gradle</span> makeDist</a></code></pre></div>
<p>which puts all required jar files into <code>dist</code> so you can run with</p>
-<div class="sourceCode"><pre class="sourceCode bash"><code class="sourceCode bash"><span class="ex">java</span> -cp <span class="st">"dist/*"</span> jalview.bin.Jalview</code></pre></div>
+<div class="sourceCode" id="cb17"><pre class="sourceCode bash"><code class="sourceCode bash"><a class="sourceLine" id="cb17-1" title="1"><span class="ex">java</span> -cp <span class="st">"dist/*"</span> jalview.bin.Jalview</a></code></pre></div>
<h3 id="single-shadow-jar-file">Single <em>shadow</em> Jar File</h3>
-<p>The shadow jar file is a single <code>.jar</code> that contains all required classes and resources from <code>jalview.jar</code> and all of the supporting libraries in <code>j11lib/*.jar</code> merged into one <code>.jar</code> archive file. A default launching class (<code>MAIN-CLASS: jalview.bin.Launcher</code>) is specified in the <code>.jar</code> manifest file (<code>META/MANIFEST.MF</code>) so a start class doesn't need to be specified.</p>
-<p>Build the shadow jar file in <code>build/lib/jalview-all-11.jar</code> with</p>
-<div class="sourceCode"><pre class="sourceCode bash"><code class="sourceCode bash"><span class="ex">gradle</span> shadowJar</code></pre></div>
-<p>and run it with</p>
-<div class="sourceCode"><pre class="sourceCode bash"><code class="sourceCode bash"><span class="ex">java</span> -jar build/lib/jalview-all-11.jar</code></pre></div>
-<p>Because no arguments are required, most OSes will associate a <code>.jar</code> file with the <code>java</code> application (if this has been installed through the OS and not just a local unzip) as a <code>-jar</code> argument so you may find you can launch <code>jalview-all-11.jar</code> just by double-clicking on it)!</p>
+<p>The shadow jar file is a single <code>.jar</code> that contains all required classes and resources from <code>jalview.jar</code> and all of the supporting libraries in <code>j11lib/*.jar</code> merged into one <code>.jar</code> archive file. A default launching class (<code>MAIN-CLASS: jalview.bin.Launcher</code>) is specified in the <code>.jar</code> manifest file (<code>META/MANIFEST.MF</code>) so a start class doesn’t need to be specified.</p>
+<p>Build the shadow jar file in <code>build/libs/jalview-all-VERSION-j11.jar</code> with</p>
+<div class="sourceCode" id="cb18"><pre class="sourceCode bash"><code class="sourceCode bash"><a class="sourceLine" id="cb18-1" title="1"><span class="ex">gradle</span> shadowJar</a></code></pre></div>
+<p><strong>NB</strong> <code>VERSION</code> will be replaced with a version number or “<code>DEVELOPMENT</code>” depending on how the branch is set up.</p>
+<p>Run it with</p>
+<div class="sourceCode" id="cb19"><pre class="sourceCode bash"><code class="sourceCode bash"><a class="sourceLine" id="cb19-1" title="1"><span class="ex">java</span> -jar build/libs/jalview-all-VERSION-j11.jar</a></code></pre></div>
+<p>Because no arguments are required, most OSes will associate a <code>.jar</code> file with the <code>java</code> application (if this has been installed through the OS and not just a local unzip) as a <code>-jar</code> argument so you may find you can launch <code>jalview-all-VERSION-j11.jar</code> just by double-clicking on it)!</p>
<blockquote>
<p>The <code>shadowJar</code> task is not a requirement for any other task, so to build the shadow jar file you must specify the <code>shadowJar</code> task.</p>
</blockquote>
<h3 id="building-the-getdown-launcher">Building the <code>getdown</code> launcher</h3>
<p>We have made significant customisations to the <code>getdown</code> launcher which you can find in <code>getdown/src/getdown</code>.</p>
<blockquote>
-<p>You don't need to build this afresh as the required <code>gradle-core.jar</code> and <code>gradle-launcher.jar</code> files are already distributed in <code>j11lib</code> and <code>getdown/lib</code> but if you want to, then you'll need a working Maven and also a Java 8 JDK. Ensure the Java 8 <code>javac</code> is forefront in your path and do</p>
-<div class="sourceCode"><pre class="sourceCode bash"><code class="sourceCode bash"><span class="bu">cd</span> getdown/src/getdown
-<span class="ex">mvn</span> clean package -Dgetdown.host.whitelist=<span class="st">"jalview.org,*.jalview.org"</span></code></pre></div>
-<p>and you will find the required <code>.jar</code> files in <code>core/target/gradle-core-XXX.jar</code> and <code>launcher/target/gradle-launcher-XXX.jar</code>. The <code>gradle-core.jar</code> should then be copied to all three of the <code>j8lib</code>, <code>j11lib</code> and <code>getdown/lib</code> folders, whilst the <code>gradle-launcher.jar</code> only needs to be copied to <code>getdown/lib</code>.</p>
+<p>You don’t need to build this afresh as the required <code>getdown-core.jar</code> and <code>getdown-launcher.jar</code> files are already distributed in <code>j11lib</code> and <code>getdown/lib</code> but if you want to, then you’ll need a working Maven and also a Java 8 JDK. Ensure the Java 8 <code>javac</code> is forefront in your path and do</p>
+<div class="sourceCode" id="cb20"><pre class="sourceCode bash"><code class="sourceCode bash"><a class="sourceLine" id="cb20-1" title="1"><span class="bu">cd</span> getdown/src/getdown</a>
+<a class="sourceLine" id="cb20-2" title="2"><span class="ex">mvn</span> clean package -Dgetdown.host.whitelist=<span class="st">"jalview.org,*.jalview.org"</span></a></code></pre></div>
+<p>and you will find the required <code>.jar</code> files in <code>core/target/getdown-core-XXX.jar</code> and <code>launcher/target/getdown-launcher-XXX.jar</code>. The <code>getdown-core.jar</code> should then be copied to all three of the <code>j8lib</code>, <code>j11lib</code> and <code>getdown/lib</code> folders, whilst the <code>getdown-launcher.jar</code> only needs to be copied to <code>getdown/lib</code>.</p>
<p>The <code>mvn</code> command should ideally include the <code>-Dgetdown.host.whitelist=*.jalview.org</code> setting. This, and the necessary file copying commands, can be found in <code>getdown/src/getdown/mvn_cmd</code>.</p>
</blockquote>
<p>To assemble Jalview with <code>getdown</code> use the following gradle task:</p>
-<div class="sourceCode"><pre class="sourceCode bash"><code class="sourceCode bash"><span class="ex">gradle</span> getdown</code></pre></div>
-<p>This puts all the necessary files to launch Jalview with <code>getdown</code> into <code>getdown/website/11/</code>. This could be treated as the reference folder for <code>getdown</code>, which is where a getdown launcher will check to see if the Jalview application files it has are up to date, and download if they aren't or it simply doesn't have them.</p>
+<div class="sourceCode" id="cb21"><pre class="sourceCode bash"><code class="sourceCode bash"><a class="sourceLine" id="cb21-1" title="1"><span class="ex">gradle</span> getdown</a></code></pre></div>
+<p>This puts all the necessary files to launch Jalview with <code>getdown</code> into <code>getdown/website/11/</code>. This could be treated as the reference folder for <code>getdown</code>, which is where a getdown launcher will check to see if the Jalview application files it has are up to date, and download if they aren’t or it simply doesn’t have them.</p>
<p>A minimal getdown-launcher can be found in <code>getdown/files/11/</code> which checks its up-to-date status with (the absolute path to) <code>getdown/website/11/</code>.</p>
<p>This can be launched with</p>
-<div class="sourceCode"><pre class="sourceCode bash"><code class="sourceCode bash"><span class="ex">java</span> -jar getdown/files/11/getdown-launcher.jar getdown/files/11/ jalview</code></pre></div>
+<div class="sourceCode" id="cb22"><pre class="sourceCode bash"><code class="sourceCode bash"><a class="sourceLine" id="cb22-1" title="1"><span class="ex">java</span> -jar getdown/files/11/getdown-launcher.jar getdown/files/11/ jalview</a></code></pre></div>
<blockquote>
-<p>We've already met the <code>-jar file.jar</code> arguments. The next argument is the working folder for getdown, and the final argument, "<code>jalview</code>", is a getdown application id (only "<code>jalview</code>" is defined here).</p>
+<p>We’ve already met the <code>-jar file.jar</code> arguments. The next argument is the working folder for getdown, and the final argument, “<code>jalview</code>”, is a getdown application id (only “<code>jalview</code>” is defined here).</p>
</blockquote>
+<p>The command line sequence for building and relocating the getdown artifacts can be executed as a script via <code>getdown/src/getdown/mvn_cmd</code>. Please make sure this script is kept up to date should the getdown build instructions change.</p>
<h3 id="running-tests">Running tests</h3>
<p>There are substantial tests written for Jalview that use TestNG, which you can run with</p>
-<div class="sourceCode"><pre class="sourceCode bash"><code class="sourceCode bash"><span class="ex">gradle</span> test</code></pre></div>
+<div class="sourceCode" id="cb23"><pre class="sourceCode bash"><code class="sourceCode bash"><a class="sourceLine" id="cb23-1" title="1"><span class="ex">gradle</span> test</a></code></pre></div>
<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>
-<div class="sourceCode"><pre class="sourceCode bash"><code class="sourceCode bash"><span class="ex">gradle</span> test -PtestngGroups=Network</code></pre></div>
+<div class="sourceCode" id="cb24"><pre class="sourceCode bash"><code class="sourceCode bash"><a class="sourceLine" id="cb24-1" title="1"><span class="ex">gradle</span> test -PtestngGroups=Network</a></code></pre></div>
<p>Available groups include Functional (default), Network, External.</p>
<h4 id="excluding-some-tests">Excluding some tests</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>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>
-<div class="sourceCode"><pre class="sourceCode bash"><code class="sourceCode bash"><span class="ex">gradle</span> test -PtestngExcludedGroups=Not-bamboo</code></pre></div>
+<div class="sourceCode" id="cb25"><pre class="sourceCode bash"><code class="sourceCode bash"><a class="sourceLine" id="cb25-1" title="1"><span class="ex">gradle</span> test -PtestngExcludedGroups=Not-bamboo</a></code></pre></div>
<h3 id="installer-packaging-with-install4j">Installer packaging with <em>install4j</em></h3>
<p>Jalview is currently using <em>install4j</em> <a href="https://www.ej-technologies.com/products/install4j/overview.html" class="uri">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>
-<div class="sourceCode"><pre class="sourceCode bash"><code class="sourceCode bash"><span class="ex">gradle</span> installers</code></pre></div>
+<div class="sourceCode" id="cb26"><pre class="sourceCode bash"><code class="sourceCode bash"><a class="sourceLine" id="cb26-1" title="1"><span class="ex">gradle</span> installers</a></code></pre></div>
<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" class="uri">http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev</a>.</p>
+<p>If you want more details, get in touch on our development mailing list <a href="mailto:jalview-dev@jalview.org" class="email">jalview-dev@jalview.org</a>. Sign up at <a href="http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev" class="uri">http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev</a>.</p>
<h2 id="gradle-properties">Gradle properties</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>
<p>This changes the <em>target</em> java bytecode version > 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>
<p>Valid values are <code>11</code> and <code>1.8</code>.</p>
<p>e.g.</p>
-<div class="sourceCode"><pre class="sourceCode bash"><code class="sourceCode bash"><span class="ex">gradle</span> shadowJar -PJAVA_VERSION=1.8</code></pre></div>
+<div class="sourceCode" id="cb27"><pre class="sourceCode bash"><code class="sourceCode bash"><a class="sourceLine" id="cb27-1" title="1"><span class="ex">gradle</span> shadowJar -PJAVA_VERSION=1.8</a></code></pre></div>
<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"><code>CHANNEL</code></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>
+<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><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>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
+<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
+<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
+<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
+<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
+<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
+<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>
</ul></li>
</ul>
<p>e.g.</p>
-<div class="sourceCode"><pre class="sourceCode bash"><code class="sourceCode bash"><span class="ex">gradle</span> getdown -PCHANNEL=SCRATCH-my_test_version</code></pre></div>
+<div class="sourceCode" id="cb28"><pre class="sourceCode bash"><code class="sourceCode bash"><a class="sourceLine" id="cb28-1" title="1"><span class="ex">gradle</span> getdown -PCHANNEL=SCRATCH-my_test_version</a></code></pre></div>
+<h4 id="jalview_version-and-the-release-file">JALVIEW_VERSION and the RELEASE file</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: - <code>CHANNEL=RELEASE</code> will set version to jalview.version - <code>CHANNEL=TEST or DEVELOP</code> will append ‘-test’ or ‘-develop’ to jalview.version</p>
+<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"><code>install4jMediaTypes</code></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>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>
-<div class="sourceCode"><pre class="sourceCode bash"><code class="sourceCode bash"><span class="ex">gradle</span> installers -PJAVA_VERSION=1.8 -Pinstall4jMediaTypes=macosArchive</code></pre></div>
+<div class="sourceCode" id="cb29"><pre class="sourceCode bash"><code class="sourceCode bash"><a class="sourceLine" id="cb29-1" title="1"><span class="ex">gradle</span> installers -PJAVA_VERSION=1.8 -Pinstall4jMediaTypes=macosArchive</a></code></pre></div>
<p>To get an up-to-date list of possible values, you can run</p>
-<div class="sourceCode"><pre class="sourceCode bash"><code class="sourceCode bash"><span class="fu">perl</span> -n -e <span class="st">'m/^\s*<(\w+)[^>]*\bmediaFileName=/ && print "$1\n";'</span> utils/install4j/install4j_template.install4j <span class="kw">|</span> <span class="fu">sort</span> -u</code></pre></div>
+<div class="sourceCode" id="cb30"><pre class="sourceCode bash"><code class="sourceCode bash"><a class="sourceLine" id="cb30-1" title="1"><span class="fu">perl</span> -n -e <span class="st">'m/^\s*<(\w+)[^>]*\bmediaFileName=/ && print "$1\n";'</span> utils/install4j/install4j_template.install4j <span class="kw">|</span> <span class="fu">sort</span> -u</a></code></pre></div>
<p>in the <code>jalview</code> root folder.</p>
<h2 id="enabling-code-coverage-with-openclover">Enabling Code Coverage with OpenClover</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>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">Troubleshooting report generation</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>
<h2 id="setting-up-in-eclipse-ide">Setting up in Eclipse IDE</h2>
<h3 id="installing-eclipse-ide">Installing Eclipse IDE</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/" class="uri">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>
-<div class="figure">
-<img src="./images/eclipse_installer.png" title="Eclipse Installer screenshot" />
-
-</div>
+<p>To get Jalview set up as a project in Eclipse, we recommend using at least the 2020-03 version of Eclipse IDE for Java Developers which you can download from the Eclipse website: <a href="https://www.eclipse.org/downloads/" class="uri">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" 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 style="list-style-type: decimal">
+<ol type="1">
<li>Buildship Gradle Integration 3.0 (or greater)</li>
<li>EclEmma Java Code Coverage</li>
<li>Egit - Git Integration for Eclipse</li>
</ol>
-<p>To install the others, launch Eclipse, and go to Help->Eclipse Marketplace...</p>
+<p>To install the others, launch Eclipse, and go to Help->Eclipse Marketplace…</p>
<p>Search for and install:</p>
-<ol style="list-style-type: decimal">
+<ol type="1">
<li>Groovy Development Tools 3.4.0 (or greater)</li>
<li>Checkstyle Plug-in (optional)</li>
-<li>TestNG for Eclipse (optional -- only needed if you want to run tests from Eclipse)</li>
+<li>TestNG for Eclipse (optional – only needed if you want to run tests from Eclipse)</li>
</ol>
<blockquote>
-<p>At time of writing, TestNG for Eclipse does not show up in the Eclipse Marketplace as the latest released version does not install in Eclipse 2019-03. However, you can install a working release of TestNG for Eclipse by going to</p>
-<p>Help->Install New Software...</p>
+<p>At time of writing, TestNG for Eclipse does not show up in the Eclipse Marketplace as the latest released version does not install in Eclipse 2020-03. However, you can install a working release of TestNG for Eclipse by going to</p>
+<p>Help->Install New Software…</p>
<p>and entering</p>
<p><code>TestNG Release - https://dl.bintray.com/testng-team/testng-eclipse-release</code></p>
-<p>into the <em>Work with</em> box and click on the <em>Add...</em> button.</p>
+<p>into the <em>Work with</em> box and click on the <em>Add…</em> button.</p>
<p>Eclipse might pause for a bit with the word <em>Pending</em> in the table below at this point, but it will eventually list TestNG with a selection box under the <em>Name</em> column.</p>
<p>Select <em>TestNG</em> and carry on through the install process to install the TestNG plugin.</p>
</blockquote>
<p>Java -> Installed JREs</p>
<p>If your Java 11 installation is not listed, click on</p>
<p><em>Add</em> -> Standard VM -> <em>Next</em></p>
-<p>and enter the JRE home. You can browse to where it is installed. Give it a name (like "AdoptOpenJDK 11"). Select this JDK as the default JRE and click on <em>Apply and Close</em>.</p>
+<p>and enter the JRE home. You can browse to where it is installed. Give it a name (like “AdoptOpenJDK 11”). Select this JDK as the default JRE and click on <em>Apply and Close</em>.</p>
<p>You can now import Jalview.</p>
<h3 id="importing-jalview-as-an-eclipse-project">Importing Jalview as an Eclipse project</h3>
<h4 id="importing-an-already-downloaded-git-repo">Importing an already downloaded git repo</h4>
<p>If you have already downloaded Jalview using <code>git clone</code> then you can import this folder into Eclipse directly.</p>
+<p><strong>Before importing the cloned git repo you must create the Eclipse project files.</strong> You can do this by either running</p>
+<p><code>gradle eclipse</code></p>
+<p>or</p>
+<p>Unzipping the file <code>utils/eclipse/eclipse_startup_files.zip</code> in the base repo directory (<code>jalview</code>)</p>
<p>It is important to import Jalview as a Gradle project (not as a Java project), so go to</p>
-<p>File->Import...</p>
+<p>File->Import…</p>
<p>find and select</p>
<p>Gradle->Existing Gradle Project</p>
<p>and then click on the <em>Next</em> button.</p>
<p>In the following options, it is the <strong>Project Root Directory</strong> you should set to be the <code>jalview</code> folder that git downloaded. Then you can click on the <em>Finish</em> button.</p>
<h4 id="using-eclipse-ide-to-download-the-git-repo">Using Eclipse IDE to download the git repo</h4>
-<p>If you don't have git as a command line tool or would prefer to work entirely within Eclipse IDE then Eclipse's eGit plugin can set up a git repo of the jalview source. Go to</p>
-<p>File->Import...</p>
+<p>If you don’t have git as a command line tool or would prefer to work entirely within Eclipse IDE then Eclipse’s eGit plugin can set up a git repo of the jalview source. Go to</p>
+<p>File->Import…</p>
<p>Find and select</p>
<p>Git->Projects from Git</p>
<p>and then click on the <em>Next</em> button.</p>
<p>Then select Clone URI and click on <em>Next</em>.</p>
<p>In the next window (Source Git Repository) you should put the <code>git clone</code> URL in the text box labelled <code>URI</code>. If you have a Jalview developer account (with a username and password for the Jalview git repository) then you should enter <code>https://source.jalview.org/git/jalview.git</code>. If you do not have a Jalview developer account then you should enter <code>http://source.jalview.org/git/jalview.git</code>. You will not be able to push any of your changes back to the Jalview git repository. However you can still pull all branches of the Jalview source code to your computer and develop the code there. > You can sign up for a Jalview developer account at <a href="https://source.jalview.org/crucible/" class="uri">https://source.jalview.org/crucible/</a></p>
-<p>If you have a Jalview developer account, enter the username and password and decide if you want to use Eclipse's secure storage. If you don't have an account you can leave the Authentication section blank.</p>
-<div class="figure">
-<img src="./images/eclipse_egit_connection.png" alt="Eclipse eGit connection configuration" />
-<p class="caption">Eclipse eGit connection configuration</p>
-</div>
+<p>If you have a Jalview developer account, enter the username and password and decide if you want to use Eclipse’s secure storage. If you don’t have an account you can leave the Authentication section blank.</p>
+<figure>
+<img src="./images/eclipse_egit_connection.png" alt="Eclipse eGit connection configuration" /><figcaption>Eclipse eGit connection configuration</figcaption>
+</figure>
<p>Click on the <em>Next</em> button.</p>
<p>The next window (Branch Selection) gives a list of the many Jalview branches, which by default will be all checked. You probably only want to download one branch (you can always download others at a later time). This is likely to be the <code>develop</code> branch so you can click on the <em>Deselect All</em> button, find the <code>develop</code> branch (the filter text helps), select that, and then click on the <em>Next</em> button.</p>
<p>Choose a directory to your copy of the git repo in, and leave the other options as they are and click on the <em>Next</em> button. The next stage may take a minute or two as it checks out the selected branch(es) from the Jalview git repository.</p>
-<p>When it has finished it is important to select <strong>Import as general project</strong> and then click on <em>Next</em>. > Ideally there would be an <em>Import as gradle project</em> here but there isn't -- we'll sort that out later.</p>
-<div class="figure">
-<img src="./images/eclipse_egit_import.png" alt="Eclipse eGit import choice" />
-<p class="caption">Eclipse eGit import choice</p>
-</div>
+<p>When it has finished it is important to select <strong>Import as general project</strong> and then click on <em>Next</em>. > Ideally there would be an <em>Import as gradle project</em> here but there isn’t – we’ll sort that out later.</p>
+<figure>
+<img src="./images/eclipse_egit_import.png" alt="Eclipse eGit import choice" /><figcaption>Eclipse eGit import choice</figcaption>
+</figure>
<p>Click on the <em>Next</em> button.</p>
-<p>You can change the project name here. By default it will show as <strong>jalview</strong> which is fine unless you have another instance of the a Jalview project also called jalview, in which case you could change this project's name now to avoid a conflict within Eclipse.</p>
+<p>You can change the project name here. By default it will show as <strong>jalview</strong> which is fine unless you have another instance of the a Jalview project also called jalview, in which case you could change this project’s name now to avoid a conflict within Eclipse.</p>
<p>Click on <em>Finish</em>!</p>
-<p>However, we haven't finished...</p>
+<p>However, we haven’t finished…</p>
<p>You should now see, and be able to expand, the jalview project in the Project Explorer. We need to tell eclipse that this is a Gradle project, which will then allow the Eclipse Buildship plugin to automatically configure almost everything else!</p>
<p>Right click on the project name (jalview) in the Project Explorer and find Configure towards the bottom of this long context menu, then choose Add Gradle Nature.</p>
-<div class="figure">
-<img src="./images/eclipse_add_gradle_nature.png" alt="Eclipse Add Gradle Nature" />
-<p class="caption">Eclipse Add Gradle Nature</p>
-</div>
+<figure>
+<img src="./images/eclipse_add_gradle_nature.png" alt="Eclipse Add Gradle Nature" /><figcaption>Eclipse Add Gradle Nature</figcaption>
+</figure>
<p>The project should now reconfigure itself using the <code>build.gradle</code> file to dynamically set various aspects of the project including classpath.</p>
<h4 id="additional-views">Additional views</h4>
-<p>Some views that are automatically added when Importing a Gradle Project are not added when simply Adding a Gradle Nature, but we can add these manually by clicking on Window->Show View->Console and Window->Show View->Other... Filter with the word "gradle" and choose both <strong>Gradle Executions</strong> and <strong>Gradle Tasks</strong> and then click on the <em>Open</em> button.</p>
+<p>Some views that are automatically added when Importing a Gradle Project are not added when simply Adding a Gradle Nature, but we can add these manually by clicking on Window->Show View->Console and Window->Show View->Other… Filter with the word “gradle” and choose both <strong>Gradle Executions</strong> and <strong>Gradle Tasks</strong> and then click on the <em>Open</em> button.</p>
<p>Okay, ready to code! Use of Eclipse is beyond the scope of this document, but you can find more information about developing jalview and our developer workflow in the google doc <a href="https://docs.google.com/document/d/1lZo_pZRkazDBJGNachXr6qCVlw8ByuMYG6e9SZlPUlQ/edit?usp=sharing" class="uri">https://docs.google.com/document/d/1lZo_pZRkazDBJGNachXr6qCVlw8ByuMYG6e9SZlPUlQ/edit?usp=sharing</a></p>
<hr />
<p><a href="mailto:help@jalview.org">Jalview Development Team</a></p>
cd jalview
gradle shadowJar
# run
-java -jar build/libs/jalview-all-11.jar
+java -jar build/libs/jalview-all-*-j11.jar
# and/or create launcher
gradle getdown
The method here is described in terms of using a command line. You can easily do this on linux or in a Terminal window in macOS. You can do it in Windows.
* Java 11 compliant JDK
-* gradle 5.2 or above
+* gradle 5.2 or above *(NB gradle 6.6 and above currently produces NullPointerExceptions during the build. This is non-fatal and does not affect the build. Use gradle 6.5.1 to avoid this)*
* git
> The versions and installation methods here are just suggestions (which we have tested
file. A default launching class (`MAIN-CLASS: jalview.bin.Launcher`) is specified in the `.jar`
manifest file (`META/MANIFEST.MF`) so a start class doesn't need to be specified.
-Build the shadow jar file in `build/lib/jalview-all-11.jar` with
+Build the shadow jar file in `build/libs/jalview-all-VERSION-j11.jar` with
```bash
gradle shadowJar
```
-and run it with
+
+__NB__ `VERSION` will be replaced with a version number or "`DEVELOPMENT`" depending on how the branch is set up.
+
+Run it with
```bash
-java -jar build/lib/jalview-all-11.jar
+java -jar build/libs/jalview-all-VERSION-j11.jar
```
Because no arguments are required, most OSes will associate a `.jar` file with the
`java` application (if this has been installed through the OS and not just a local
-unzip) as a `-jar` argument so you may find you can launch `jalview-all-11.jar`
+unzip) as a `-jar` argument so you may find you can launch `jalview-all-VERSION-j11.jar`
just by double-clicking on it)!
> The `shadowJar` task is not a requirement for any other task, so to build the shadow
in our preferred style. We also support running the Jalview application, debugging
and running tests with TestNG from within Eclipse.
-To get Jalview set up as a project in Eclipse, we recommend using at least the 2019-12
+To get Jalview set up as a project in Eclipse, we recommend using at least the 2020-03
version of Eclipse IDE for Java Developers which you can download from the Eclipse
website: <https://www.eclipse.org/downloads/>. 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.
1. TestNG for Eclipse (optional -- only needed if you want to run tests from Eclipse)
> At time of writing, TestNG for Eclipse does not show up in the Eclipse Marketplace
-as the latest released version does not install in Eclipse 2019-03.
+as the latest released version does not install in Eclipse 2020-03.
However, you can install a working release of TestNG for Eclipse by going to
>
Help->Install New Software...
If you have already downloaded Jalview using `git clone` then you can import this folder into Eclipse directly.
+__Before importing the cloned git repo you must create the Eclipse project files.__ You can do this by either running
+
+`gradle eclipse`
+
+or
+
+Unzipping the file `utils/eclipse/eclipse_startup_files.zip` in the base repo directory (`jalview`)
+
It is important to import
Jalview as a Gradle project (not as a Java project), so go to
test_source_dir = test
#test_source_dir = utils/jalviewjs/test/test
-JALVIEW_VERSION = DEVELOPMENT
+# JALVIEW_VERSION now being set by logic in build.gradle defaulting to looking at jalview.version property in RELEASE file
+#JALVIEW_VERSION = DEVELOPMENT
INSTALLATION = Source
jalview_keystore = keys/.keystore
jalview_keystore.pass = alignmentisfun
<ul>
<li>Standard installation on Linux/Unix:<pre>
- /PATH_TO_JALVIEW/Jalview -open http://www.jalview.org/examples/jpred_msa.fasta -annotations http://www.jalview.org/examples/jpred_msa.seq.concise -colour Clustal</pre>
+ /PATH_TO_JALVIEW/Jalview -open https://www.jalview.org/examples/jpred_msa.fasta -annotations https://www.jalview.org/examples/jpred_msa.seq.concise -colour Clustal</pre>
</li>
<li>Standard installation on Windows:<pre>
\PATH_TO_JALVIEW\Jalview.exe -open %HOMEPATH%\myalignment.fa</pre>
installation of Groovy. Just select <strong>Tools→Groovy
Console...</strong> from the Jalview Desktop's drop-down menu. After a
short pause, you should then see the <a
- href="http://groovy-lang.org/groovyconsole.html">Groovy
+ href="https://groovy-lang.org/groovyconsole.html">Groovy
Console</a> appear. This allows you to interactively execute Groovy
scripts whilst Jalview is running. We've also provided a <strong>Calculations→Execute
Groovy Script</strong> button so you can execute the currently loaded
InstallAnywhere version of Jalview, you can find additional groovy
scripts in the examples/groovy subfolder of the installation
directory. The examples are also available at <a
- href="http://www.jalview.org/examples/groovy">http://www.jalview.org/examples/groovy</a>.
+ href="https://www.jalview.org/examples/groovy">https://www.jalview.org/examples/groovy</a>.
</p>
<p>
<em>Using Groovy to add new Alignment Calculations</em><br />We've
<em>Creating custom colourschemes</em><br/>
You can create your own alignment colourschemes with a groovy script. We've provided two examples:<br/>
<ul>
- <li><a href="http://www.jalview.org/examples/groovy/colourConserved.groovy">colourConserved.groovy</a> creates an 'Conserved' colourscheme - similar to the classic <a href="http://www.nrbsc.org/old/gfx/genedoc/">GeneDOC</a> shading model.</li>
- <li><a href="http://www.jalview.org/examples/groovy/colourUnconserved.groovy">colourUnconserved.groovy</a> creates an 'Unconserved' colourscheme, where any unconserved residues are coloured pink.</li>
+ <li><a href="https://www.jalview.org/examples/groovy/colourConserved.groovy">colourConserved.groovy</a> creates an 'Conserved' colourscheme - similar to the classic <a href="http://www.nrbsc.org/old/gfx/genedoc/">GeneDOC</a> shading model.</li>
+ <li><a href="https://www.jalview.org/examples/groovy/colourUnconserved.groovy">colourUnconserved.groovy</a> creates an 'Unconserved' colourscheme, where any unconserved residues are coloured pink.</li>
</ul>
</p>
<pre>
# Jalview Launch File
# Please install the Jalview Desktop from
-# http://www.jalview.org/getdown/release
+# https://www.jalview.org/getdown/release
# and then try to open this file again
jalview.apparg=-open
-jalview.apparg=http://www.jalview.org/examples/jpred_msa.fasta
+jalview.apparg=https://www.jalview.org/examples/jpred_msa.fasta
jalview.apparg=-annotations
-jalview.apparg=http://www.jalview.org/examples/jpred_msa.seq.concise
+jalview.apparg=https://www.jalview.org/examples/jpred_msa.seq.concise
jalview.apparg=-colour
jalview.apparg=Clustal
</pre>
# Please install the Jalview Desktop from
# http://www.jalview.org/getdown/release
# and then try to open this file again
-appbase=http://www.jalview.org/getdown/archive/2_10_5/
+appbase=https://www.jalview.org/getdown/archive/2_10_5/
</pre>
For security, the Jalview application will only allow
<em>appbase</em> URLs from www.jalview.org.
</ol>
<strong>Please note: The 2.10.2 feature counting interface is not compatible with earlier versions.</strong><br/><br/>
<em><a
- href="http://www.jalview.org/examples/groovy/featuresCounter.groovy">http://www.jalview.org/examples/groovy/featuresCounter.groovy</a>
+ href="https://www.jalview.org/examples/groovy/featuresCounter.groovy">https://www.jalview.org/examples/groovy/featuresCounter.groovy</a>
- rendered with <a href="http://hilite.me">hilite.me</a></em>
<!-- HTML generated using hilite.me --><div style="background: #f8f8f8; overflow:auto;width:auto;border:solid gray;border-width:.1em .1em .1em .8em;padding:.2em .6em;"><pre style="margin: 0; line-height: 125%"><span style="color: #408080; font-style: italic">/*</span>
<span style="color: #408080; font-style: italic"> * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)</span>
<p>
For more information, you might also want to take a look at the
documentation section of the Jalview website (<a
- href="http://www.jalview.org/about/documentation">http://www.jalview.org/about/documentation</a>).
+ href="https://www.jalview.org/about/documentation">https://www.jalview.org/about/documentation</a>).
</p>
<p>
If you are using the Jalview Desktop application and are looking for
google the online version of these pages. If you don't find what you
are looking for, or want to report a bug or make a feature request,
then get in contact over at <a
- href="http://www.jalview.org/community">http://www.jalview.org/community</a>
+ href="https://www.jalview.org/community">https://www.jalview.org/community</a>
</p>
<p>
<strong>Logging, troubleshooting and reporting bugs</strong><br />If
arguments, but you must put the <em>jvl</em> file first, e.g. <pre>
/PATH_TO_JALVIEW/Jalview /path/to/file/mymemorysetting.jvl /path/to/alignments/myalignment.fa</pre> Alternatively, you can use the standard Jalview command line
arguments with or without the jvl file (first), e.g. <pre>
- /PATH_TO_JALVIEW/Jalview /path/to/file/mymemorysetting.jvl -open http://www.jalview.org/examples/jpred_msa.fasta -annotations http://www.jalview.org/examples/jpred_msa.seq.concise -colour Clustal</pre> You can use command line arguments to control memory
+ /PATH_TO_JALVIEW/Jalview /path/to/file/mymemorysetting.jvl -open https://www.jalview.org/examples/jpred_msa.fasta -annotations https://www.jalview.org/examples/jpred_msa.seq.concise -colour Clustal</pre> You can use command line arguments to control memory
settings in Windows and macOS too: <br /> In Windows you must
use, e.g. <pre>
\PATH_TO_JALVIEW\Jalview.exe %HOMEPATH%\mymemorysetting.jvl -open %HOMEPATH%\myalignment.fa</pre> In macOS you can use the macOS <em>open</em> command like this: <pre>
</tr>
<tr>
<td width="60" align="center" nowrap><strong><a
+ id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.3">.3</a><br />
+ <em>27/10/2020</em></strong></td>
+ <td align="left" valign="top">
+ <ul>
+
+ </ul>
+ </td>
+ <td align="left" valign="top">
+ <ul>
+ <li>
+ <!-- JAL-3765 -->Find doesn't always highlight all matching
+ positions in a sequence
+ </li>
+ <li>
+ <!-- JAL-3611 -->Space character in Jalview install path on
+ Windows prevents install4j launching getdown
+ </li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td width="60" align="center" nowrap><strong><a
+ id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.2">.2</a><br />
+ <em>25/09/2020</em></strong></td>
+ <td align="left" valign="top">
+ <ul>
+ </ul>
+ </td>
+ <td align="left" valign="top">
+ <ul>
+ <li>
+ <!-- JAL-3757 -->Fresh install of Jalview 2.11.1.1 reports
+ "Encountered problems opening
+ https://www.jalview.org/examples/exampleFile_2_7.jvp"
+ </li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td width="60" align="center" nowrap><strong><a
id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.1">.1</a><br />
- <em>15/09/2020</em></strong></td>
+ <em>17/09/2020</em></strong></td>
<td align="left" valign="top">
<ul>
<li>
file again, and if that fails, delete the original file and
save in place.)
</li>
+ <li>
+ <!-- JAL-3750 -->Cannot process alignments from HTTPS urls
+ via command line
+ </li>
+ <li>
+ <!-- JAL-3741 -->References to http://www.jalview.org in
+ program and documentation
+ </li>
</ul> <em>Launching Jalview</em>
<ul>
<li>
<p>
<strong>The Jalview Desktop RSS News Reader</strong><br /> The
Jalview Desktop includes a built in news reader for the <a
- href="http://www.jalview.org/feeds/desktop/rss">Jalview
+ href="https://www.jalview.org/feeds/desktop/rss">Jalview
Desktop News Channel</a>.
</p>
<br />
<p>
The <em>Jalview news reader</em> was introduced in <a
- href="http://www.jalview.org/releaseHistory.html#Jalview2.7">Jalview
+ href="https://www.jalview.org/releaseHistory.html#Jalview2.7">Jalview
version 2.7</a>. Its implementation is based on <a
- href="http://jswingreader.sourceforge.net/">JSwingReader</a>.
+ href="https://jswingreader.sourceforge.net/">JSwingReader</a>.
</p>
<br />
<em>If you need to prevent the news-reader opening, then add the
</head>
<body>
<p>
- <strong>Jalview 2.11.1.1</strong>
+ <strong>Jalview 2.11.1.3</strong>
</p>
- <p>Jalview 2.11.1.1 is the first patch release for Jalview version
- 2.11.1. In addition to fixes for some critical bugs, it also
- contains a handful of new features suggested by the Jalview
- community.</p>
+ <p>Jalview 2.11.1.3 is the third patch release, fixing a bug
+ introduced in last weeks Jalview 2.11.1.1 release affecting display
+ of Jalview's example project for some users. Together, these
+ releases include fixes for a number of critical bugs, and also contains a
+ handful of new features suggested by the Jalview community.</p>
<ul>
<li>Shift+arrow keys navigate to next gap or residue in cursor
mode (enable with F2)</li>
* update residueIndex to next position after the start of the match
* (findIndex returns a value base 1, columnIndex is held base 0)
*/
- residueIndex += offset + 1;
+ residueIndex = searchPattern.matchedFrom()+1;
/*
* return false if the match is entirely in a hidden region
* when shading by annotation</li>
* <li>ANNOTATIONCOLOUR_MAX (red) Shade used for maximum value of annotation
* when shading by annotation</li>
- * <li>www.jalview.org (http://www.jalview.org) a property enabling all HTTP
- * requests to be redirected to a mirror of http://www.jalview.org</li>
+ * <li>www.jalview.org (https://www.jalview.org) a property enabling all HTTP
+ * requests to be redirected to a mirror of https://www.jalview.org</li>
* <li>FIGURE_AUTOIDWIDTH (false) Expand the left hand column of an exported
* alignment figure to accommodate even the longest sequence ID or annotation
* label.</li>
DEFAULT_CACHE_THRESHOLD_IN_DAYS));
IdOrgSettings.setUrl(getDefault("ID_ORG_HOSTURL",
- "http://www.jalview.org/services/identifiers"));
+ "https://www.jalview.org/services/identifiers"));
IdOrgSettings.setDownloadLocation(ID_ORG_FILE);
StructureImportSettings.setDefaultStructureFileFormat(jalview.bin.Cache
*/
package jalview.bin;
-import jalview.ext.so.SequenceOntology;
-import jalview.gui.AlignFrame;
-import jalview.gui.Desktop;
-import jalview.gui.PromptUserConfig;
-import jalview.io.AppletFormatAdapter;
-import jalview.io.BioJsHTMLOutput;
-import jalview.io.DataSourceType;
-import jalview.io.FileFormat;
-import jalview.io.FileFormatException;
-import jalview.io.FileFormatI;
-import jalview.io.FileFormats;
-import jalview.io.FileLoader;
-import jalview.io.HtmlSvgOutput;
-import jalview.io.IdentifyFile;
-import jalview.io.NewickFile;
-import jalview.io.gff.SequenceOntologyFactory;
-import jalview.schemes.ColourSchemeI;
-import jalview.schemes.ColourSchemeProperty;
-import jalview.util.MessageManager;
-import jalview.util.Platform;
-import jalview.ws.jws2.Jws2Discoverer;
-
import java.io.BufferedReader;
import java.io.File;
import java.io.FileOutputStream;
import jalview.io.FileFormat;
import jalview.io.FileFormatException;
import jalview.io.FileFormatI;
+import jalview.io.FileFormats;
import jalview.io.FileLoader;
import jalview.io.HtmlSvgOutput;
import jalview.io.IdentifyFile;
import jalview.io.gff.SequenceOntologyFactory;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemeProperty;
+import jalview.util.HttpUtils;
import jalview.util.MessageManager;
import jalview.util.Platform;
import jalview.ws.jws2.Jws2Discoverer;
// String defurl =
// "http://anaplog.compbio.dundee.ac.uk/cgi-bin/questionnaire.pl";
// //
- String defurl = "http://www.jalview.org/cgi-bin/questionnaire.pl";
+ String defurl = "https://www.jalview.org/cgi-bin/questionnaire.pl";
Cache.log.debug(
"Starting questionnaire with default url: " + defurl);
desktop.checkForQuestionnaire(defurl);
}
System.out.println("CMD [-open " + file + "] executed successfully!");
- if (!file.startsWith("http://"))
+ protocol = AppletFormatAdapter.checkProtocol(file);
+
+ if (protocol == DataSourceType.FILE)
{
if (!(new File(file)).exists())
{
}
}
- protocol = AppletFormatAdapter.checkProtocol(file);
-
try
{
format = new IdentifyFile().identify(file, protocol);
af.createEPS(outputFile);
continue;
}
- FileFormatI outFormat=null;
- try {
+ FileFormatI outFormat = null;
+ try
+ {
outFormat = FileFormats.getInstance().forName(outputFormat);
- } catch (Exception formatP) {
- System.out.println("Couldn't parse "+outFormat+" as a valid Jalview format string.");
+ } catch (Exception formatP)
+ {
+ System.out.println("Couldn't parse " + outFormat
+ + " as a valid Jalview format string.");
}
if (outFormat != null)
{
{
file = jalview.bin.Cache.getDefault("STARTUP_FILE",
jalview.bin.Cache.getDefault("www.jalview.org",
- "http://www.jalview.org")
- + "/examples/exampleFile_2_7.jar");
- if (file.equals(
- "http://www.jalview.org/examples/exampleFile_2_3.jar"))
+ "https://www.jalview.org")
+ + "/examples/exampleFile_2_7.jvp");
+ if (file.equals("http://www.jalview.org/examples/exampleFile_2_3.jar")
+ || file.equals(
+ "http://www.jalview.org/examples/exampleFile_2_7.jar"))
{
+ file.replace("http:", "https:");
// hardwire upgrade of the startup file
- file.replace("_2_3.jar", "_2_7.jar");
+ file.replace("_2_3", "_2_7");
+ file.replace("2_7.jar", "2_7.jvp");
// and remove the stale setting
jalview.bin.Cache.removeProperty("STARTUP_FILE");
}
- protocol = DataSourceType.FILE;
-
- if (file.indexOf("http:") > -1)
- {
- protocol = DataSourceType.URL;
- }
+ protocol = AppletFormatAdapter.checkProtocol(file);
if (file.endsWith(".jar"))
{
+ "-groovy FILE\tExecute groovy script in FILE, after all other arguments have been processed (if FILE is the text 'STDIN' then the file will be read from STDIN)\n"
+ "-jvmmempc=PERCENT\tOnly available with standalone executable jar or jalview.bin.Launcher. Limit maximum heap size (memory) to PERCENT% of total physical memory detected. This defaults to 90 if total physical memory can be detected. See https://www.jalview.org/help/html/memory.html for more details.\n"
+ "-jvmmemmax=MAXMEMORY\tOnly available with standalone executable jar or jalview.bin.Launcher. Limit maximum heap size (memory) to MAXMEMORY. MAXMEMORY can be specified in bytes, kilobytes(k), megabytes(m), gigabytes(g) or if you're lucky enough, terabytes(t). This defaults to 32g if total physical memory can be detected, or to 8g if total physical memory cannot be detected. See https://www.jalview.org/help/html/memory.html for more details.\n"
- + "\n~Read documentation in Application or visit http://www.jalview.org for description of Features and Annotations file~\n\n");
+ + "\n~Read documentation in Application or visit https://www.jalview.org for description of Features and Annotations file~\n\n");
}
private static void startUsageStats(final Desktop desktop)
import jalview.schemes.ColourSchemes;
import jalview.schemes.ResidueColourScheme;
import jalview.schemes.TCoffeeColourScheme;
+import jalview.util.HttpUtils;
import jalview.util.MessageManager;
import jalview.util.Platform;
import jalview.viewmodel.AlignmentViewport;
Desktop.instance.closeAssociatedWindows();
FileLoader loader = new FileLoader();
- DataSourceType protocol = fileName.startsWith("http:")
+ DataSourceType protocol = HttpUtils.startsWithHttpOrHttps(fileName)
? DataSourceType.URL
: DataSourceType.FILE;
loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
Rectangle bounds = this.getBounds();
FileLoader loader = new FileLoader();
- DataSourceType protocol = fileName.startsWith("http:")
+ DataSourceType protocol = HttpUtils.startsWithHttpOrHttps(fileName)
? DataSourceType.URL
: DataSourceType.FILE;
AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
public void save_actionPerformed(ActionEvent e)
{
if (fileName == null || (currentFileFormat == null)
- || fileName.startsWith("http"))
+ || HttpUtils.startsWithHttpOrHttps(fileName))
{
saveAs_actionPerformed(null);
}
}
/**
- * Calls AlignmentI.moveSelectedSequencesByOne with current sequence selection or the sequence under cursor in keyboard mode
+ * Calls AlignmentI.moveSelectedSequencesByOne with current sequence selection
+ * or the sequence under cursor in keyboard mode
*
* @param up
* or down (if !up)
if (sg == null)
{
- if (viewport.cursorMode)
+ if (viewport.cursorMode)
{
sg = new SequenceGroup();
- sg.addSequence(viewport.getAlignment()
- .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY),false);
- } else {
+ sg.addSequence(viewport.getAlignment().getSequenceAt(
+ alignPanel.getSeqPanel().seqCanvas.cursorY), false);
+ }
+ else
+ {
return;
}
}
-
+
if (sg.getSize() < 1)
{
- return;
+ return;
}
-
+
// TODO: JAL-3733 - add an event to the undo buffer for this !
-
+
viewport.getAlignment().moveSelectedSequencesByOne(sg,
viewport.getHiddenRepSequences(), up);
alignPanel.paintAlignment(true, false);
chan.setURL(
jalview.bin.Cache.getDefault("JALVIEW_NEWS_RSS",
jalview.bin.Cache.getDefault("www.jalview.org",
- "http://www.jalview.org")
+ "https://www.jalview.org")
+ "/feeds/desktop/rss"));
loadLastM();
_channelModel.addChannel(chan);
} catch (java.lang.ClassCastException cex)
{
Cache.log.warn(
- "Squashed a possible GUI implementation error. If you can recreate this, please look at http://issues.jalview.org/browse/JAL-869",
+ "Squashed a possible GUI implementation error. If you can recreate this, please look at https://issues.jalview.org/browse/JAL-869",
cex);
}
}
panel.add(history);
history.setPreferredSize(new Dimension(400, 20));
history.setEditable(true);
- history.addItem("http://www.");
+ history.addItem("https://www.");
String historyItems = jalview.bin.Cache.getProperty("RECENT_URL");
"..Checking..")
+ " is available for download from "
+ jalview.bin.Cache.getDefault("www.jalview.org",
- "http://www.jalview.org")
+ "https://www.jalview.org")
+ " !!");
if (red)
{
"AUTHORFNAMES",
"The Jalview Authors (See AUTHORS file for current list)")
+ "<br><br>Development managed by The Barton Group, University of Dundee, Scotland, UK.<br>"
- + "<br><br>For help, see the FAQ at <a href=\"http://www.jalview.org/faq\">www.jalview.org/faq</a> and/or join the jalview-discuss@jalview.org mailing list"
+ + "<br><br>For help, see the FAQ at <a href=\"https://www.jalview.org/faq\">www.jalview.org/faq</a> and/or join the jalview-discuss@jalview.org mailing list"
+ "<br><br>If you use Jalview, please cite:"
+ "<br>Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)"
+ "<br>Jalview Version 2 - a multiple sequence alignment editor and analysis workbench"
startupCheckbox
.setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
- Cache.getDefault("www.jalview.org", "http://www.jalview.org")
- + "/examples/exampleFile_2_3.jar"));
+ Cache.getDefault("www.jalview.org", "https://www.jalview.org")
+ + "/examples/exampleFile_2_7.jvp"));
/*
* Set Colours tab defaults
{
private static String version = new BuildDetails().getVersion();
- private String webstartUrl = "http://www.jalview.org/services/launchApp";
+ private String webstartUrl = "https://www.jalview.org/services/launchApp";
private String application = "Jalview";
import static jalview.math.RotatableMatrix.Axis.Y;
import static jalview.math.RotatableMatrix.Axis.Z;
+import java.awt.Color;
+import java.awt.Font;
+import java.awt.Rectangle;
+import java.io.BufferedReader;
+import java.io.DataInputStream;
+import java.io.DataOutputStream;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.io.OutputStreamWriter;
+import java.io.PrintWriter;
+import java.lang.reflect.InvocationTargetException;
+import java.math.BigInteger;
+import java.net.MalformedURLException;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.Enumeration;
+import java.util.GregorianCalendar;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Hashtable;
+import java.util.IdentityHashMap;
+import java.util.Iterator;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.Set;
+import java.util.Vector;
+import java.util.jar.JarEntry;
+import java.util.jar.JarInputStream;
+import java.util.jar.JarOutputStream;
+
+import javax.swing.JInternalFrame;
+import javax.swing.SwingUtilities;
+import javax.xml.bind.JAXBContext;
+import javax.xml.bind.JAXBElement;
+import javax.xml.bind.Marshaller;
+import javax.xml.datatype.DatatypeConfigurationException;
+import javax.xml.datatype.DatatypeFactory;
+import javax.xml.datatype.XMLGregorianCalendar;
+import javax.xml.stream.XMLInputFactory;
+import javax.xml.stream.XMLStreamReader;
+
import jalview.analysis.Conservation;
import jalview.analysis.PCA;
import jalview.analysis.scoremodels.ScoreModels;
import jalview.structure.StructureSelectionManager;
import jalview.structures.models.AAStructureBindingModel;
import jalview.util.Format;
+import jalview.util.HttpUtils;
import jalview.util.MessageManager;
import jalview.util.Platform;
import jalview.util.StringUtils;
import jalview.xml.binding.jalview.ThresholdType;
import jalview.xml.binding.jalview.VAMSAS;
-import java.awt.Color;
-import java.awt.Font;
-import java.awt.Rectangle;
-import java.io.BufferedReader;
-import java.io.DataInputStream;
-import java.io.DataOutputStream;
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.FileOutputStream;
-import java.io.IOException;
-import java.io.InputStreamReader;
-import java.io.OutputStreamWriter;
-import java.io.PrintWriter;
-import java.lang.reflect.InvocationTargetException;
-import java.math.BigInteger;
-import java.net.MalformedURLException;
-import java.net.URL;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collections;
-import java.util.Enumeration;
-import java.util.GregorianCalendar;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.Hashtable;
-import java.util.IdentityHashMap;
-import java.util.Iterator;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Map.Entry;
-import java.util.Set;
-import java.util.Vector;
-import java.util.jar.JarEntry;
-import java.util.jar.JarInputStream;
-import java.util.jar.JarOutputStream;
-
-import javax.swing.JInternalFrame;
-import javax.swing.SwingUtilities;
-import javax.xml.bind.JAXBContext;
-import javax.xml.bind.JAXBElement;
-import javax.xml.bind.Marshaller;
-import javax.xml.datatype.DatatypeConfigurationException;
-import javax.xml.datatype.DatatypeFactory;
-import javax.xml.datatype.XMLGregorianCalendar;
-import javax.xml.stream.XMLInputFactory;
-import javax.xml.stream.XMLStreamReader;
-
/**
* Write out the current jalview desktop state as a Jalview XML stream.
*
else
{
vamsasSeq = createVamsasSequence(id, jds);
-// vamsasSet.addSequence(vamsasSeq);
+ // vamsasSet.addSequence(vamsasSeq);
vamsasSet.getSequence().add(vamsasSeq);
vamsasSetIds.put(id, vamsasSeq);
seqRefIds.put(id, jds);
if (colourScheme instanceof jalview.schemes.UserColourScheme)
{
- jGroup.setColour(
- setUserColourScheme(colourScheme, userColours,
- object));
+ jGroup.setColour(setUserColourScheme(colourScheme,
+ userColours, object));
}
else
{
}
}
- //jms.setJGroup(groups);
+ // jms.setJGroup(groups);
Object group;
for (JGroup grp : groups)
{
* save any filter for the feature type
*/
FeatureMatcherSetI filter = fr.getFeatureFilter(featureType);
- if (filter != null) {
- Iterator<FeatureMatcherI> filters = filter.getMatchers().iterator();
+ if (filter != null)
+ {
+ Iterator<FeatureMatcherI> filters = filter.getMatchers()
+ .iterator();
FeatureMatcherI firstFilter = filters.next();
- setting.setMatcherSet(Jalview2XML.marshalFilter(
- firstFilter, filters, filter.isAnded()));
+ setting.setMatcherSet(Jalview2XML.marshalFilter(firstFilter,
+ filters, filter.isAnded()));
}
/*
setting.setDisplay(
av.getFeaturesDisplayed().isVisible(featureType));
- float rorder = fr
- .getOrder(featureType);
+ float rorder = fr.getOrder(featureType);
if (rorder > -1)
{
setting.setOrder(rorder);
Group g = new Group();
g.setName(grp);
g.setDisplay(((Boolean) fr.checkGroupVisibility(grp, false))
- .booleanValue());
+ .booleanValue());
// fs.addGroup(g);
fs.getGroup().add(g);
groupsAdded.addElement(grp);
{
if (calcIdParam.getVersion().equals("1.0"))
{
- final String[] calcIds = calcIdParam.getServiceURL().toArray(new String[0]);
+ final String[] calcIds = calcIdParam.getServiceURL()
+ .toArray(new String[0]);
Jws2Instance service = Jws2Discoverer.getDiscoverer()
.getPreferredServiceFor(calcIds);
if (service != null)
return id;
}
- jalview.schemes.UserColourScheme getUserColourScheme(
- JalviewModel jm, String id)
+ jalview.schemes.UserColourScheme getUserColourScheme(JalviewModel jm,
+ String id)
{
List<UserColours> uc = jm.getUserColours();
UserColours colours = null;
-/*
+ /*
for (int i = 0; i < uc.length; i++)
{
if (uc[i].getId().equals(id))
break;
}
}
-*/
+ */
for (UserColours c : uc)
{
if (c.getId().equals(id))
newColours = new java.awt.Color[23];
for (int i = 0; i < 23; i++)
{
- newColours[i] = new java.awt.Color(Integer.parseInt(
- colours.getUserColourScheme().getColour().get(i + 24)
- .getRGB(),
- 16));
+ newColours[i] = new java.awt.Color(
+ Integer.parseInt(colours.getUserColourScheme().getColour()
+ .get(i + 24).getRGB(), 16));
}
ucs.setLowerCaseColours(newColours);
}
viewportsAdded.clear();
frefedSequence = null;
- if (file.startsWith("http://"))
+ if (HttpUtils.startsWithHttpOrHttps(file))
{
url = new URL(file);
}
XMLStreamReader streamReader = XMLInputFactory.newInstance()
.createXMLStreamReader(jin);
javax.xml.bind.Unmarshaller um = jc.createUnmarshaller();
- JAXBElement<JalviewModel> jbe = um
- .unmarshal(streamReader, JalviewModel.class);
+ JAXBElement<JalviewModel> jbe = um.unmarshal(streamReader,
+ JalviewModel.class);
JalviewModel object = jbe.getValue();
/*
AlignFrame loadFromObject(JalviewModel jalviewModel, String file,
boolean loadTreesAndStructures, jarInputStreamProvider jprovider)
{
- SequenceSet vamsasSet = jalviewModel.getVamsasModel().getSequenceSet().get(0);
+ SequenceSet vamsasSet = jalviewModel.getVamsasModel().getSequenceSet()
+ .get(0);
List<Sequence> vamsasSeqs = vamsasSet.getSequence();
// JalviewModelSequence jms = object.getJalviewModelSequence();
if (tmpSeq.getStart() != jseq.getStart()
|| tmpSeq.getEnd() != jseq.getEnd())
{
- System.err.println(
- String.format("Warning JAL-2154 regression: updating start/end for sequence %s from %d/%d to %d/%d",
- tmpSeq.getName(), tmpSeq.getStart(),
- tmpSeq.getEnd(), jseq.getStart(),
- jseq.getEnd()));
+ System.err.println(String.format(
+ "Warning JAL-2154 regression: updating start/end for sequence %s from %d/%d to %d/%d",
+ tmpSeq.getName(), tmpSeq.getStart(), tmpSeq.getEnd(),
+ jseq.getStart(), jseq.getEnd()));
}
}
else
else
{
// defer to later
- frefedSequence.add(
- newAlcodMapRef(map.getDnasq(), cf, mapping));
+ frefedSequence
+ .add(newAlcodMapRef(map.getDnasq(), cf, mapping));
}
}
}
jaa.setCalcId(annotation.getCalcId());
if (annotation.getProperty().size() > 0)
{
- for (Annotation.Property prop : annotation
- .getProperty())
+ for (Annotation.Property prop : annotation.getProperty())
{
jaa.setProperty(prop.getName(), prop.getValue());
}
sg.setShowNonconserved(safeBoolean(jGroup.isShowUnconserved()));
sg.thresholdTextColour = safeInt(jGroup.getTextColThreshold());
// attributes with a default in the schema are never null
- sg.setShowConsensusHistogram(jGroup.isShowConsensusHistogram());
- sg.setshowSequenceLogo(jGroup.isShowSequenceLogo());
- sg.setNormaliseSequenceLogo(jGroup.isNormaliseSequenceLogo());
+ sg.setShowConsensusHistogram(jGroup.isShowConsensusHistogram());
+ sg.setshowSequenceLogo(jGroup.isShowSequenceLogo());
+ sg.setNormaliseSequenceLogo(jGroup.isNormaliseSequenceLogo());
sg.setIgnoreGapsConsensus(jGroup.isIgnoreGapsinConsensus());
if (jGroup.getConsThreshold() != null
&& jGroup.getConsThreshold().intValue() != 0)
if (addAnnotSchemeGroup)
{
// reconstruct the annotation colourscheme
- sg.setColourScheme(constructAnnotationColour(
- jGroup.getAnnotationColours(), null, al, jalviewModel, false));
+ sg.setColourScheme(
+ constructAnnotationColour(jGroup.getAnnotationColours(),
+ null, al, jalviewModel, false));
}
}
}
* @param av
* @param ap
*/
- protected void loadTrees(JalviewModel jm, Viewport view,
- AlignFrame af, AlignViewport av, AlignmentPanel ap)
+ protected void loadTrees(JalviewModel jm, Viewport view, AlignFrame af,
+ AlignViewport av, AlignmentPanel ap)
{
// TODO result of automated refactoring - are all these parameters needed?
try
for (int s = 0; s < structureStateCount; s++)
{
// check to see if we haven't already created this structure view
- final StructureState structureState = pdbid
- .getStructureState().get(s);
+ final StructureState structureState = pdbid.getStructureState()
+ .get(s);
String sviewid = (structureState.getViewId() == null) ? null
: structureState.getViewId() + uniqueSetSuffix;
jalview.datamodel.PDBEntry jpdb = new jalview.datamodel.PDBEntry();
colourByViewer &= structureState.isColourByJmol();
jmoldat.setColourByViewer(colourByViewer);
- if (jmoldat.getStateData().length() < structureState
- .getValue()/*Content()*/.length())
+ if (jmoldat.getStateData().length() < structureState.getValue()
+ /*Content()*/.length())
{
jmoldat.setStateData(structureState.getValue());// Content());
}
String reformatedOldFilename = oldfilenam.replaceAll("/", "\\\\");
filedat = oldFiles.get(new File(reformatedOldFilename));
}
- newFileLoc.append(Platform.escapeBackslashes(filedat.getFilePath()));
+ newFileLoc
+ .append(Platform.escapeBackslashes(filedat.getFilePath()));
pdbfilenames.add(filedat.getFilePath());
pdbids.add(filedat.getPdbId());
seqmaps.add(filedat.getSeqList().toArray(new SequenceI[0]));
}
AlignFrame loadViewport(String file, List<JSeq> JSEQ,
- List<SequenceI> hiddenSeqs, AlignmentI al,
- JalviewModel jm, Viewport view, String uniqueSeqSetId,
- String viewId, List<JvAnnotRow> autoAlan)
+ List<SequenceI> hiddenSeqs, AlignmentI al, JalviewModel jm,
+ Viewport view, String uniqueSeqSetId, String viewId,
+ List<JvAnnotRow> autoAlan)
{
AlignFrame af = null;
af = new AlignFrame(al, safeInt(view.getWidth()),
viewport.setColourText(safeBoolean(view.isShowColourText()));
- viewport
- .setConservationSelected(
- safeBoolean(view.isConservationSelected()));
+ viewport.setConservationSelected(
+ safeBoolean(view.isConservationSelected()));
viewport.setIncrement(safeInt(view.getConsThreshold()));
viewport.setShowJVSuffix(safeBoolean(view.isShowFullId()));
viewport.setRightAlignIds(safeBoolean(view.isRightAlignIds()));
af.changeColour(cs);
viewport.setColourAppliesToAllGroups(true);
- viewport
- .setShowSequenceFeatures(
- safeBoolean(view.isShowSequenceFeatures()));
+ viewport.setShowSequenceFeatures(
+ safeBoolean(view.isShowSequenceFeatures()));
viewport.setCentreColumnLabels(view.isCentreColumnLabels());
viewport.setIgnoreGapsConsensus(view.isIgnoreGapsinConsensus(), null);
.getFeatureRenderer();
FeaturesDisplayed fdi;
viewport.setFeaturesDisplayed(fdi = new FeaturesDisplayed());
- String[] renderOrder = new String[jm.getFeatureSettings()
- .getSetting().size()];
+ String[] renderOrder = new String[jm.getFeatureSettings().getSetting()
+ .size()];
Map<String, FeatureColourI> featureColours = new Hashtable<>();
Map<String, Float> featureOrder = new Hashtable<>();
- for (int fs = 0; fs < jm.getFeatureSettings()
- .getSetting().size(); fs++)
+ for (int fs = 0; fs < jm.getFeatureSettings().getSetting()
+ .size(); fs++)
{
Setting setting = jm.getFeatureSettings().getSetting().get(fs);
String featureType = setting.getType();
.getMatcherSet();
if (filters != null)
{
- FeatureMatcherSetI filter = Jalview2XML
- .parseFilter(featureType, filters);
+ FeatureMatcherSetI filter = Jalview2XML.parseFilter(featureType,
+ filters);
if (!filter.isEmpty())
{
fr.setFeatureFilter(featureType, filter);
float max = setting.getMax() == null ? 1f
: setting.getMax().floatValue();
FeatureColourI gc = new FeatureColour(maxColour, minColour,
- maxColour,
- noValueColour, min, max);
+ maxColour, noValueColour, min, max);
if (setting.getAttributeName().size() > 0)
{
gc.setAttributeName(setting.getAttributeName().toArray(
}
else
{
- featureColours.put(featureType,
- new FeatureColour(maxColour));
+ featureColours.put(featureType, new FeatureColour(maxColour));
}
renderOrder[fs] = featureType;
if (setting.getOrder() != null)
}
}
}
+
/**
*
* @param vamsasSeq
* @param fcol
* @return
*/
- public static Colour marshalColour(
- String featureType, FeatureColourI fcol)
+ public static Colour marshalColour(String featureType,
+ FeatureColourI fcol)
{
Colour col = new Colour();
if (fcol.isSimpleColour())
boolean and)
{
jalview.xml.binding.jalview.FeatureMatcherSet result = new jalview.xml.binding.jalview.FeatureMatcherSet();
-
+
if (filters.hasNext())
{
/*
}
result.setMatchCondition(matcherModel);
}
-
+
return result;
}
* @param matcherSetModel
* @return
*/
- public static FeatureMatcherSetI parseFilter(
- String featureType,
+ public static FeatureMatcherSetI parseFilter(String featureType,
jalview.xml.binding.jalview.FeatureMatcherSet matcherSetModel)
{
FeatureMatcherSetI result = new FeatureMatcherSet();
featureType, e.getMessage()));
// return as much as was parsed up to the error
}
-
+
return result;
}
* @throws IllegalStateException
* if AND and OR conditions are mixed
*/
- protected static void parseFilterConditions(
- FeatureMatcherSetI matcherSet,
+ protected static void parseFilterConditions(FeatureMatcherSetI matcherSet,
jalview.xml.binding.jalview.FeatureMatcherSet matcherSetModel,
boolean and)
{
else if (filterBy == FilterBy.BY_SCORE)
{
matchCondition = FeatureMatcher.byScore(cond, pattern);
-
+
}
else if (filterBy == FilterBy.BY_ATTRIBUTE)
{
matchCondition = FeatureMatcher.byAttribute(cond, pattern,
attNames);
}
-
+
/*
* note this throws IllegalStateException if AND-ing to a
* previously OR-ed compound condition, or vice versa
public static FeatureColourI parseColour(Colour colourModel)
{
FeatureColourI colour = null;
-
+
if (colourModel.getMax() != null)
{
Color mincol = null;
Color maxcol = null;
Color noValueColour = null;
-
+
try
{
mincol = new Color(Integer.parseInt(colourModel.getMinRGB(), 16));
{
Cache.log.warn("Couldn't parse out graduated feature color.", e);
}
-
+
NoValueColour noCol = colourModel.getNoValueColour();
if (noCol == NoValueColour.MIN)
{
{
noValueColour = maxcol;
}
-
+
colour = new FeatureColour(maxcol, mincol, maxcol, noValueColour,
safeFloat(colourModel.getMin()),
safeFloat(colourModel.getMax()));
Color color = new Color(Integer.parseInt(colourModel.getRGB(), 16));
colour = new FeatureColour(color);
}
-
+
return colour;
}
}
*/
public static final boolean isNucleotide(SequenceI seq)
{
- return isNucleotide(new SequenceI[] { seq });
+ if (seq==null)
+ {
+ return false;
+ }
+ long ntCount = 0;
+ long aaCount = 0;
+
+ int len = seq.getLength();
+ for (int i = 0; i < len; i++)
+ {
+ char c = seq.getCharAt(i);
+ if (isNucleotide(c))
+ {
+ ntCount++;
+ }
+ else if (!isGap(c))
+ {
+ aaCount++;
+ }
+ }
+ /*
+ * Check for nucleotide count > 85% of total count (in a form that evades
+ * int / float conversion or divide by zero).
+ */
+ if (ntCount * 100 > EIGHTY_FIVE * (ntCount + aaCount))
+ {
+ return true;
+ }
+ else
+ {
+ return false;
+ }
}
/**
{
return false;
}
-
- int ntCount = 0;
- int aaCount = 0;
+ // true if we have seen a nucleotide sequence
+ boolean na=false;
for (SequenceI seq : seqs)
{
if (seq == null)
{
continue;
}
+ na=true;
// TODO could possibly make an informed guess just from the first sequence
// to save a lengthy calculation
- int len = seq.getLength();
- for (int i = 0; i < len; i++)
- {
- char c = seq.getCharAt(i);
- if (isNucleotide(c))
- {
- ntCount++;
- }
- else if (!isGap(c))
- {
- aaCount++;
- }
+ if (seq.isProtein()) {
+ // if even one looks like protein, the alignment is protein
+ return false;
}
}
-
- /*
- * Check for nucleotide count > 85% of total count (in a form that evades
- * int / float conversion or divide by zero).
- */
- if (ntCount * 100 > EIGHTY_FIVE * (ntCount + aaCount))
- {
- return true;
- }
- else
- {
- return false;
- }
-
+ return na;
}
/**
return false;
}
+ public static boolean startsWithHttpOrHttps(String file)
+ {
+ return file.startsWith("http://") || file.startsWith("https://");
+ }
+
}
assertEquals(matches.get(1).getEnd(), 6);
}
+ @Test(groups = "Functional")
+ public void testFind_findAll()
+ {
+ /*
+ * simple JAL-3765 test
+ * single symbol should find *all* matching symbols
+ */
+ Finder f = new Finder(av);
+ f.findAll("M", false,false,false);
+ SearchResultsI sr = f.getSearchResults();
+ assertEquals(sr.getCount(),5);
+
+ }
/**
* Test for (undocumented) find residue by position
*/
seq = new Sequence("DNA", "ACTugGCCAG");
SequenceI seq2 = new Sequence("Protein", "FLIMVSPTYW");
/*
- * 90% DNA:
+ * 90% DNA but one protein sequence - expect false
*/
- assertTrue(Comparison.isNucleotide(new SequenceI[] { seq, seq, seq,
+ assertFalse(Comparison.isNucleotide(new SequenceI[] { seq, seq, seq,
seq, seq, seq, seq, seq, seq, seq2 }));
- assertTrue(Comparison.isNucleotide(new SequenceI[][] {
+ assertFalse(Comparison.isNucleotide(new SequenceI[][] {
new SequenceI[] { seq }, new SequenceI[] { seq, seq, seq },
new SequenceI[] { seq, seq, seq, seq, seq, seq2 } }));
/*
- * 80% DNA:
+ * 80% DNA but one protein sequence - Expect false
*/
assertFalse(Comparison.isNucleotide(new SequenceI[] { seq, seq, seq,
seq, seq, seq, seq, seq, seq2, seq2 }));
<versionLine x="85" y="109" text="version ${compiler:sys.version}" />
</text>
</splashScreen>
- <java mainClass="com.threerings.getdown.launcher.GetdownApp" vmParameters="-Dinstaller_template_version=${compiler:INSTALLER_TEMPLATE_VERSION}" arguments="${launcher:sys.launcherDirectory} jalview">
+ <java mainClass="com.threerings.getdown.launcher.GetdownApp" vmParameters="-Dinstaller_template_version=${compiler:INSTALLER_TEMPLATE_VERSION}" arguments=""${launcher:sys.launcherDirectory}" jalview">
<classPath>
<archive location="getdown-launcher.jar" />
<archive location="${compiler:GETDOWN_INSTALL_DIR}/getdown-launcher.jar" failOnError="false" />
git://source.jalview.org / jalview.git / commitdiff