jalview.release=releases/Release_2_11_1_Branch
-jalview.version=2.11.1.3
+jalview.version=2.11.1.4
task sourceDist(type: Tar) {
+ dependsOn createBuildProperties
def VERSION_UNDERSCORES = JALVIEW_VERSION.replaceAll("\\.", "_")
def outputFileName = "${project.name}_${VERSION_UNDERSCORES}.tar.gz"
// exclude(EXCLUDE_FILES)
// exclude(PROCESS_FILES)
// }
+
+ from(file(buildProperties).getParent()) {
+ include(file(buildProperties).getName())
+ rename(file(buildProperties).getName(), "build_properties")
+ filter({ line ->
+ line.replaceAll("^INSTALLATION=.*\$","INSTALLATION=Source Release"+" git-commit\\\\:"+gitHash+" ["+gitBranch+"]")
+ })
+ }
+
}
<meta charset="utf-8" />
<meta name="generator" content="pandoc" />
<meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes" />
- <title>Building Jalview from Source</title>
- <style type="text/css">
- code{white-space: pre-wrap;}
- span.smallcaps{font-variant: small-caps;}
- span.underline{text-decoration: underline;}
- div.column{display: inline-block; vertical-align: top; width: 50%;}
- </style>
- <style type="text/css">
-a.sourceLine { display: inline-block; line-height: 1.25; }
-a.sourceLine { pointer-events: none; color: inherit; text-decoration: inherit; }
-a.sourceLine:empty { height: 1.2em; }
-.sourceCode { overflow: visible; }
-code.sourceCode { white-space: pre; position: relative; }
-div.sourceCode { margin: 1em 0; }
-pre.sourceCode { margin: 0; }
-@media screen {
-div.sourceCode { overflow: auto; }
-}
-@media print {
-code.sourceCode { white-space: pre-wrap; }
-a.sourceLine { text-indent: -1em; padding-left: 1em; }
-}
-pre.numberSource a.sourceLine
- { position: relative; left: -4em; }
-pre.numberSource a.sourceLine::before
- { content: attr(title);
- position: relative; left: -1em; text-align: right; vertical-align: baseline;
- border: none; pointer-events: all; display: inline-block;
- -webkit-touch-callout: none; -webkit-user-select: none;
- -khtml-user-select: none; -moz-user-select: none;
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-div.sourceCode
- { }
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-code span.vs { color: #4070a0; } /* VerbatimString */
-code span.wa { color: #60a0b0; font-weight: bold; font-style: italic; } /* Warning */
+ <title>"Building Jalview from Source"</title>
+ <style>
+ code{white-space: pre-wrap;}
+ span.smallcaps{font-variant: small-caps;}
+ span.underline{text-decoration: underline;}
+ div.column{display: inline-block; vertical-align: top; width: 50%;}
+ div.hanging-indent{margin-left: 1.5em; text-indent: -1.5em;}
+ ul.task-list{list-style: none;}
+ pre > code.sourceCode { white-space: pre; position: relative; }
+ pre > code.sourceCode > span { display: inline-block; line-height: 1.25; }
+ pre > code.sourceCode > span:empty { height: 1.2em; }
+ code.sourceCode > span { color: inherit; text-decoration: inherit; }
+ div.sourceCode { margin: 1em 0; }
+ pre.sourceCode { margin: 0; }
+ @media screen {
+ div.sourceCode { overflow: auto; }
+ }
+ @media print {
+ pre > code.sourceCode { white-space: pre-wrap; }
+ pre > code.sourceCode > span { text-indent: -5em; padding-left: 5em; }
+ }
+ pre.numberSource code
+ { counter-reset: source-line 0; }
+ pre.numberSource code > span
+ { position: relative; left: -4em; counter-increment: source-line; }
+ pre.numberSource code > span > a:first-child::before
+ { content: counter(source-line);
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+ border: none; display: inline-block;
+ -webkit-touch-callout: none; -webkit-user-select: none;
+ -khtml-user-select: none; -moz-user-select: none;
+ -ms-user-select: none; user-select: none;
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+ pre.numberSource { margin-left: 3em; border-left: 1px solid #aaaaaa; padding-left: 4px; }
+ div.sourceCode
+ { }
+ @media screen {
+ pre > code.sourceCode > span > a:first-child::before { text-decoration: underline; }
+ }
+ code span.al { color: #ff0000; font-weight: bold; } /* Alert */
+ code span.an { color: #60a0b0; font-weight: bold; font-style: italic; } /* Annotation */
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+ code span.bn { color: #40a070; } /* BaseN */
+ code span.bu { } /* BuiltIn */
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+ code span.ch { color: #4070a0; } /* Char */
+ code span.cn { color: #880000; } /* Constant */
+ code span.co { color: #60a0b0; font-style: italic; } /* Comment */
+ code span.cv { color: #60a0b0; font-weight: bold; font-style: italic; } /* CommentVar */
+ code span.do { color: #ba2121; font-style: italic; } /* Documentation */
+ code span.dt { color: #902000; } /* DataType */
+ code span.dv { color: #40a070; } /* DecVal */
+ code span.er { color: #ff0000; font-weight: bold; } /* Error */
+ code span.ex { } /* Extension */
+ code span.fl { color: #40a070; } /* Float */
+ code span.fu { color: #06287e; } /* Function */
+ code span.im { } /* Import */
+ code span.in { color: #60a0b0; font-weight: bold; font-style: italic; } /* Information */
+ code span.kw { color: #007020; font-weight: bold; } /* Keyword */
+ code span.op { color: #666666; } /* Operator */
+ code span.ot { color: #007020; } /* Other */
+ code span.pp { color: #bc7a00; } /* Preprocessor */
+ code span.sc { color: #4070a0; } /* SpecialChar */
+ code span.ss { color: #bb6688; } /* SpecialString */
+ code span.st { color: #4070a0; } /* String */
+ code span.va { color: #19177c; } /* Variable */
+ code span.vs { color: #4070a0; } /* VerbatimString */
+ code span.wa { color: #60a0b0; font-weight: bold; font-style: italic; } /* Warning */
</style>
+ <!--[if lt IE 9]>
+ <script src="//cdnjs.cloudflare.com/ajax/libs/html5shiv/3.7.3/html5shiv-printshiv.min.js"></script>
+ <![endif]-->
<style>
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text-size-adjust: 100%;
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body a:hover {
outline: 0;
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font-weight: bold;
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body h1 {
font-size: 2em;
margin: 0.67em 0;
}
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border: 0;
}
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body hr {
box-sizing: content-box;
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overflow: auto;
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body kbd,
body pre {
font-family: monospace, monospace;
font-size: 1em;
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body input {
color: inherit;
font: inherit;
margin: 0;
}
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body html input[disabled] {
cursor: default;
}
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body input {
line-height: normal;
}
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body input[type="checkbox"] {
box-sizing: border-box;
padding: 0;
}
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body table {
border-collapse: collapse;
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body th {
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font: 13px / 1.4 Helvetica, arial, nimbussansl, liberationsans, freesans, clean, sans-serif, "Apple Color Emoji", "Segoe UI Emoji", "Segoe UI Symbol";
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body a:active {
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body h3 .octicon-link,
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body blockquote,
body ul,
margin-top: 0;
margin-bottom: 16px;
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height: 4px;
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</head>
<body>
-<nav id="TOC">
+<nav id="TOC" role="doc-toc">
+<ul>
+<li><a href="#building-jalview-from-source">Building Jalview from Source</a>
<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="#setting-up">Setting up</a><ul>
+<li><a href="#setting-up">Setting up</a>
+<ul>
<li><a href="#java-11-compliant-jdk">Java 11 compliant JDK</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="#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>
</ul></li>
-<li><a href="#building-jalview">Building Jalview</a><ul>
+<li><a href="#building-jalview">Building Jalview</a>
+<ul>
<li><a href="#minimal-jalview-build">Minimal Jalview Build</a></li>
<li><a href="#jalview-in-a-jar-file">Jalview in a Jar File</a></li>
<li><a href="#distributed-jar-files">Distributed Jar Files</a></li>
</ul></li>
<li><a href="#gradle-properties">Gradle properties</a></li>
<li><a href="#enabling-code-coverage-with-openclover">Enabling Code Coverage with OpenClover</a></li>
-<li><a href="#setting-up-in-eclipse-ide">Setting up in Eclipse IDE</a><ul>
+<li><a href="#setting-up-in-eclipse-ide">Setting up in Eclipse IDE</a>
+<ul>
<li><a href="#installing-eclipse-ide">Installing Eclipse IDE</a></li>
<li><a href="#importing-jalview-as-an-eclipse-project">Importing Jalview as an Eclipse project</a></li>
</ul></li>
<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" 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>
+<div class="sourceCode" id="cb4"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb4-1"><a href="#cb4-1"></a><span class="ex">brew</span> install gradle git</span></code></pre></div>
<p>or if you aready have them installed but need to upgrade the version:</p>
-<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>
+<div class="sourceCode" id="cb5"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb5-1"><a href="#cb5-1"></a><span class="ex">brew</span> upgrade gradle git</span></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" 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>
+<div class="sourceCode" id="cb6"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb6-1"><a href="#cb6-1"></a><span class="ex">choco</span> install gradle</span>
+<span id="cb6-2"><a href="#cb6-2"></a><span class="ex">choco</span> install git</span></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>run</p>
-<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>
+<div class="sourceCode" id="cb7"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb7-1"><a href="#cb7-1"></a> <span class="fu">sudo</span> apt-get install gradle git</span></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" 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>
+<div class="sourceCode" id="cb8"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb8-1"><a href="#cb8-1"></a><span class="fu">sudo</span> yum install gradle git</span></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" 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>
+<div class="sourceCode" id="cb9"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb9-1"><a href="#cb9-1"></a><span class="fu">git</span> clone http://source.jalview.org/git/jalview.git</span></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>
</blockquote>
<h3 id="minimal-jalview-build">Minimal Jalview Build</h3>
<p>To compile the necessary class files, just run</p>
-<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>
+<div class="sourceCode" id="cb11"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb11-1"><a href="#cb11-1"></a><span class="ex">gradle</span> compileJava</span></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" 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>
+<div class="sourceCode" id="cb12"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb12-1"><a href="#cb12-1"></a><span class="ex">java</span> -cp <span class="st">"classes:resources:help:j11lib/*"</span> jalview.bin.Jalview</span></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" 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>
+<div class="sourceCode" id="cb13"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb13-1"><a href="#cb13-1"></a><span class="ex">java</span> -cp <span class="st">"classes:resources:help:j11lib/*"</span> jalview.bin.Launcher</span></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>
</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>
<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" 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>
+<div class="sourceCode" id="cb14"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb14-1"><a href="#cb14-1"></a><span class="ex">gradle</span> jar</span></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" 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>
+<div class="sourceCode" id="cb15"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb15-1"><a href="#cb15-1"></a><span class="ex">java</span> -cp <span class="st">"dist/jalview.jar:j11lib/*"</span> jalview.bin.Jalview</span></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" 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>
+<div class="sourceCode" id="cb16"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb16-1"><a href="#cb16-1"></a><span class="ex">gradle</span> makeDist</span></code></pre></div>
<p>which puts all required jar files into <code>dist</code> so you can run with</p>
-<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>
+<div class="sourceCode" id="cb17"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb17-1"><a href="#cb17-1"></a><span class="ex">java</span> -cp <span class="st">"dist/*"</span> jalview.bin.Jalview</span></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/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>
+<div class="sourceCode" id="cb18"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb18-1"><a href="#cb18-1"></a><span class="ex">gradle</span> shadowJar</span></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>
+<div class="sourceCode" id="cb19"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb19-1"><a href="#cb19-1"></a><span class="ex">java</span> -jar build/libs/jalview-all-VERSION-j11.jar</span></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>
<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>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>
+<div class="sourceCode" id="cb20"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb20-1"><a href="#cb20-1"></a><span class="bu">cd</span> getdown/src/getdown</span>
+<span id="cb20-2"><a href="#cb20-2"></a><span class="ex">mvn</span> clean package -Dgetdown.host.whitelist=<span class="st">"jalview.org,*.jalview.org"</span></span></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" 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>
+<div class="sourceCode" id="cb21"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb21-1"><a href="#cb21-1"></a><span class="ex">gradle</span> getdown</span></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" 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>
+<div class="sourceCode" id="cb22"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb22-1"><a href="#cb22-1"></a><span class="ex">java</span> -jar getdown/files/11/getdown-launcher.jar getdown/files/11/ jalview</span></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>
</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" 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>
+<div class="sourceCode" id="cb23"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb23-1"><a href="#cb23-1"></a><span class="ex">gradle</span> test</span></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" 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>
+<div class="sourceCode" id="cb24"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb24-1"><a href="#cb24-1"></a><span class="ex">gradle</span> test -PtestngGroups=Network</span></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>To exclude one or more groups of tests, add them as a comma separated list in testngExcludedGroups.</p>
-<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>
+<div class="sourceCode" id="cb25"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb25-1"><a href="#cb25-1"></a><span class="ex">gradle</span> test -PtestngExcludedGroups=Not-bamboo</span></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" 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>
+<div class="sourceCode" id="cb26"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb26-1"><a href="#cb26-1"></a><span class="ex">gradle</span> installers</span></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" 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>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" 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>
+<div class="sourceCode" id="cb27"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb27-1"><a href="#cb27-1"></a><span class="ex">gradle</span> shadowJar -PJAVA_VERSION=1.8</span></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>
</ul></li>
</ul>
<p>e.g.</p>
-<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>
+<div class="sourceCode" id="cb28"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb28-1"><a href="#cb28-1"></a><span class="ex">gradle</span> getdown -PCHANNEL=SCRATCH-my_test_version</span></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>
<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" 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>
+<div class="sourceCode" id="cb29"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb29-1"><a href="#cb29-1"></a><span class="ex">gradle</span> installers -PJAVA_VERSION=1.8 -Pinstall4jMediaTypes=macosArchive</span></code></pre></div>
<p>To get an up-to-date list of possible values, you can run</p>
-<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>
+<div class="sourceCode" id="cb30"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb30-1"><a href="#cb30-1"></a><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</span></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>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>
<figure>
-<img src="./images/eclipse_egit_connection.png" alt="Eclipse eGit connection configuration" /><figcaption>Eclipse eGit connection configuration</figcaption>
+<img src="./images/eclipse_egit_connection.png" alt="" /><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>
<figure>
-<img src="./images/eclipse_egit_import.png" alt="Eclipse eGit import choice" /><figcaption>Eclipse eGit import choice</figcaption>
+<img src="./images/eclipse_egit_import.png" alt="" /><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 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>
<figure>
-<img src="./images/eclipse_add_gradle_nature.png" alt="Eclipse Add Gradle Nature" /><figcaption>Eclipse Add Gradle Nature</figcaption>
+<img src="./images/eclipse_add_gradle_nature.png" alt="" /><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>
<th><em>New Features</em></th>
<th><em>Issues Resolved</em></th>
</tr>
+ <td width="60" align="center" nowrap><strong><a
+ id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.4">.4</a><br />
+ <em>26/02/2021</em></strong></td>
+ <td align="left" valign="top"><em>Improved control of
+ Jalview's use of network services via jalview_properties</em>
+ <ul>
+ <li>
+ <!-- JAL-3814 -->New .jalview_properties token controlling
+ launch of the news browser (like -nonews argument)
+ </li>
+ <li>
+ <!-- JAL-3813 -->New .jalview_properties token controlling
+ download of linkout URLs from
+ www.jalview.org/services/identifiers
+ </li>
+ <li>
+ <!-- JAL-3812 -->New .jalview_properties token controlling
+ download of BIOJSHTML templates
+ </li>
+ <li>
+ <!-- JAL-3811 -->New 'Discover Web Services' option to trigger
+ a one off JABAWS discovery if autodiscovery was disabled
+ </li>
+ </ul></td>
+ <td align="left" valign="top">
+ <ul>
+ <li><!-- JAL-3818 -->Intermittent deadlock opening structure in Jmol</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.2.11.1.3">.3</a><br />
* <li>FOLLOW_SELECTIONS (true) Controls whether a new alignment view should
* respond to selections made in other alignments containing the same sequences.
* </li>
+ * <li>SHOW_JWS2_SERVICES (true) when set to false, jalview will not
+ * auto-discover JABAWS services</li>
* <li>JWS2HOSTURLS comma-separated list of URLs to try for JABAWS services</li>
* <li>SHOW_WSDISCOVERY_ERRORS (true) Controls if the web service URL discovery
* warning dialog box is displayed.</li>
* <li>CHIMERA_PATH specify full path to Chimera program (if non-standard)</li>
* <li>ID_ORG_HOSTURL location of jalview service providing identifiers.org urls
* </li>
- *
+ * <li>NONEWS - when set disables Jalview News from automatically appearing</li>
+ * <li>NOHTMLTEMPLATES - when set, the
+ * https://github.com/jalview/exporter-templates/tree/master/biojs repository is
+ * not downloaded automatically</li>
+ * <li>NOIDENTIFIERSSERVICE - when set, jalview won't automatically download
+ * available URL linkouts via www.jalview.org/services/identifiers</li>
+ * <li>
* </ul>
* Deprecated settings:
* <ul>
System.err.println("CMD [-noquestionnaire] executed successfully!");
}
- if (!aparser.contains("nonews"))
+ if (!aparser.contains("nonews")
+ || Cache.getProperty("NONEWS") == null)
{
desktop.checkForNews();
}
- BioJsHTMLOutput.updateBioJS();
+ if (!aparser.contains("nohtmltemplates")
+ || Cache.getProperty("NOHTMLTEMPLATES") == null)
+ {
+ BioJsHTMLOutput.updateBioJS();
+ }
}
// Move any new getdown-launcher-new.jar into place over old
*/
package jalview.ext.jmol;
-import jalview.api.AlignmentViewPanel;
-import jalview.api.FeatureRenderer;
-import jalview.api.FeatureSettingsModelI;
-import jalview.api.SequenceRenderer;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.HiddenColumns;
-import jalview.datamodel.PDBEntry;
-import jalview.datamodel.SequenceI;
-import jalview.gui.AppJmol;
-import jalview.gui.IProgressIndicator;
-import jalview.io.DataSourceType;
-import jalview.io.StructureFile;
-import jalview.schemes.ColourSchemeI;
-import jalview.schemes.ResidueProperties;
-import jalview.structure.AtomSpec;
-import jalview.structure.StructureMappingcommandSet;
-import jalview.structure.StructureSelectionManager;
-import jalview.structures.models.AAStructureBindingModel;
-import jalview.util.MessageManager;
-import jalview.ws.dbsources.Pdb;
-
import java.awt.Color;
import java.awt.Container;
import java.awt.event.ComponentEvent;
import java.util.StringTokenizer;
import java.util.Vector;
+import javax.swing.SwingUtilities;
+
import org.jmol.adapter.smarter.SmarterJmolAdapter;
import org.jmol.api.JmolAppConsoleInterface;
import org.jmol.api.JmolSelectionListener;
import org.jmol.script.T;
import org.jmol.viewer.Viewer;
+import jalview.api.AlignmentViewPanel;
+import jalview.api.FeatureRenderer;
+import jalview.api.FeatureSettingsModelI;
+import jalview.api.SequenceRenderer;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AppJmol;
+import jalview.gui.IProgressIndicator;
+import jalview.io.DataSourceType;
+import jalview.io.StructureFile;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ResidueProperties;
+import jalview.structure.AtomSpec;
+import jalview.structure.StructureMappingcommandSet;
+import jalview.structure.StructureSelectionManager;
+import jalview.structures.models.AAStructureBindingModel;
+import jalview.util.MessageManager;
+import jalview.ws.dbsources.Pdb;
+
public abstract class JalviewJmolBinding extends AAStructureBindingModel
implements JmolStatusListener, JmolSelectionListener,
ComponentListener
}
Thread colourby = null;
+
/**
* Sends a set of colour commands to the structure viewer
*
@Override
public void notifyCallback(CBK type, Object[] data)
{
+ /*
+ * ensure processed in AWT thread to avoid risk of deadlocks
+ */
+ SwingUtilities.invokeLater(new Runnable()
+ {
+
+ @Override
+ public void run()
+ {
+ processCallback(type, data);
+ }
+ });
+ }
+
+ /**
+ * Processes one callback notification from Jmol
+ *
+ * @param type
+ * @param data
+ */
+ protected void processCallback(CBK type, Object[] data)
+ {
try
{
switch (type)
// see JAL-623 - need method of matching pasted data up
{
pdb = getSsm().setMapping(getSequence()[pe], getChains()[pe],
- pdbfile, DataSourceType.PASTE,
- getIProgressIndicator());
+ pdbfile, DataSourceType.PASTE, getIProgressIndicator());
getPdbEntry(modelnum).setFile("INLINE" + pdb.getId());
matches = true;
foundEntry = true;
webService.add(me.webServiceNoServices);
}
// TODO: move into separate menu builder class.
- boolean new_sspred = false;
- if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
{
+ // logic for 2.11.1.4 is
+ // always look to see if there is a discover. if there isn't
+ // we can't show any Jws2 services
+ // if there are services available, show them - regardless of
+ // the 'show JWS2 preference'
+ // if the discoverer is running then say so
+ // otherwise offer to trigger discovery if 'show JWS2' is not
+ // enabled
Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
if (jws2servs != null)
{
}
}
}
-
}
+
if (jws2servs.isRunning())
{
JMenuItem tm = new JMenuItem(
tm.setEnabled(false);
webService.add(tm);
}
+ else if (!Cache.getDefault("SHOW_JWS2_SERVICES", true))
+ {
+ JMenuItem enableJws2 = new JMenuItem(
+ "Discover Web Services");
+ enableJws2.setToolTipText(
+ "Select to start JABA Web Service discovery (or enable option in Web Service preferences)");
+ enableJws2.setEnabled(true);
+ enableJws2.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ // start service discoverer, but ignore preference
+ Desktop.instance.startServiceDiscovery(false,
+ true);
+ }
+ });
+ webService.add(enableJws2);
+ }
}
}
build_urlServiceMenu(me.webService);
initItems(chan);
updating = false;
- boolean setvisible = checkForNew(chan, true);
-
- if (setvisible)
+ if (!Cache.getDefault("NONEWS", false))
{
+ boolean setvisible = checkForNew(chan, true);
+
+ if (setvisible)
+ {
- Cache.log.debug("Will show jalview news automatically");
- showNews();
+ Cache.log.debug("Will show jalview news automatically");
+ showNews();
+ }
}
Cache.log.debug("Completed construction of reader.");
*/
package jalview.gui;
-import jalview.api.AlignViewportI;
-import jalview.api.AlignmentViewPanel;
-import jalview.bin.Cache;
-import jalview.bin.Jalview;
-import jalview.io.BackupFiles;
-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.FormatAdapter;
-import jalview.io.IdentifyFile;
-import jalview.io.JalviewFileChooser;
-import jalview.io.JalviewFileView;
-import jalview.jbgui.GSplitFrame;
-import jalview.jbgui.GStructureViewer;
-import jalview.project.Jalview2XML;
-import jalview.structure.StructureSelectionManager;
-import jalview.urls.IdOrgSettings;
-import jalview.util.ImageMaker;
-import jalview.util.MessageManager;
-import jalview.util.Platform;
-import jalview.util.UrlConstants;
-import jalview.viewmodel.AlignmentViewport;
-import jalview.ws.params.ParamManager;
-import jalview.ws.utils.UrlDownloadClient;
-
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Dimension;
import java.io.File;
import java.io.FileWriter;
import java.io.IOException;
+import java.lang.reflect.Field;
import java.net.URL;
import java.util.ArrayList;
import java.util.HashMap;
import org.stackoverflowusers.file.WindowsShortcut;
+import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
+import jalview.bin.Cache;
+import jalview.bin.Jalview;
+import jalview.io.BackupFiles;
+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.FormatAdapter;
+import jalview.io.IdentifyFile;
+import jalview.io.JalviewFileChooser;
+import jalview.io.JalviewFileView;
+import jalview.jbgui.GSplitFrame;
+import jalview.jbgui.GStructureViewer;
+import jalview.project.Jalview2XML;
+import jalview.structure.StructureSelectionManager;
+import jalview.urls.IdOrgSettings;
+import jalview.util.ImageMaker;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+import jalview.util.UrlConstants;
+import jalview.viewmodel.AlignmentViewport;
+import jalview.ws.params.ParamManager;
+import jalview.ws.utils.UrlDownloadClient;
+
/**
* Jalview Desktop
*
instance = this;
doConfigureStructurePrefs();
- setTitle("Jalview " + jalview.bin.Cache.getProperty("VERSION"));
+ String title = "Jalview " + Cache.getProperty("VERSION");
+ setTitle(title);
/*
if (!Platform.isAMac())
{
// t.printStackTrace();
}
+ if (Platform.isLinux())
+ {
+ try
+ {
+ Toolkit xToolkit = Toolkit.getDefaultToolkit();
+ Field awtAppClassNameField = xToolkit.getClass()
+ .getDeclaredField("awtAppClassName");
+ awtAppClassNameField.setAccessible(true);
+ awtAppClassNameField.set(xToolkit, "Jalview");
+ } catch (Exception e)
+ {
+ Cache.log.debug("Could not set awtAppClassName");
+ }
+ }
addWindowListener(new WindowAdapter()
{
public void getIdentifiersOrgData()
{
- // Thread off the identifiers fetcher
- new Thread(new Runnable()
- {
- @Override
- public void run()
+ if (Cache.getProperty("NOIDENTIFIERSSERVICE") == null)
+ {// Thread off the identifiers fetcher
+ new Thread(new Runnable()
{
- Cache.log.debug("Downloading data from identifiers.org");
- UrlDownloadClient client = new UrlDownloadClient();
- try
- {
- client.download(IdOrgSettings.getUrl(),
- IdOrgSettings.getDownloadLocation());
- } catch (IOException e)
+ @Override
+ public void run()
{
- Cache.log.debug("Exception downloading identifiers.org data"
- + e.getMessage());
+ Cache.log.debug("Downloading data from identifiers.org");
+ try
+ {
+ UrlDownloadClient.download(IdOrgSettings.getUrl(),
+ IdOrgSettings.getDownloadLocation());
+ } catch (IOException e)
+ {
+ Cache.log.debug("Exception downloading identifiers.org data"
+ + e.getMessage());
+ }
}
- }
- }).start();
- ;
+ }).start();
+ ;
+ }
}
@Override
KeyStroke ctrlWKey = KeyStroke.getKeyStroke(KeyEvent.VK_W,
InputEvent.CTRL_DOWN_MASK);
KeyStroke cmdWKey = KeyStroke.getKeyStroke(KeyEvent.VK_W,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx());
+ jalview.util.ShortcutKeyMaskExWrapper
+ .getMenuShortcutKeyMaskEx());
InputMap inputMap = frame
.getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW);
public void inputLocalFileMenuItem_actionPerformed(AlignViewport viewport)
{
String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
- JalviewFileChooser chooser = JalviewFileChooser
- .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat, BackupFiles.getEnabled());
+ JalviewFileChooser chooser = JalviewFileChooser.forRead(
+ Cache.getProperty("LAST_DIRECTORY"), fileFormat,
+ BackupFiles.getEnabled());
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(
"Jalview Project (old)" };
JalviewFileChooser chooser = new JalviewFileChooser(
Cache.getProperty("LAST_DIRECTORY"), suffix, desc,
- "Jalview Project", true, BackupFiles.getEnabled()); // last two booleans: allFiles,
- // allowBackupFiles
+ "Jalview Project", true, BackupFiles.getEnabled()); // last two
+ // booleans:
+ // allFiles,
+ // allowBackupFiles
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(MessageManager.getString("label.restore_state"));
// FIXME: ideally should use UI interface API
FeatureSettings viewFeatureSettings = (af.featureSettings != null
- && af.featureSettings.isOpen())
- ? af.featureSettings
- : null;
+ && af.featureSettings.isOpen()) ? af.featureSettings : null;
Rectangle fsBounds = af.getFeatureSettingsGeometry();
for (int i = 0; i < size; i++)
{
addInternalFrame(newaf, af.getTitle(), AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
- // and materialise a new feature settings dialog instance for the new alignframe
+ // and materialise a new feature settings dialog instance for the new
+ // alignframe
// (closes the old as if 'OK' was pressed)
if (ap == af.alignPanel && newaf.featureSettings != null
&& newaf.featureSettings.isOpen()
}
}
// refresh the feature setting UI for the source frame if it exists
- if (source.featureSettings != null
- && source.featureSettings.isOpen())
+ if (source.featureSettings != null && source.featureSettings.isOpen())
{
source.showFeatureSettingsUI();
}
*/
protected void addQuitHandler()
{
- getRootPane().getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW)
- .put(KeyStroke.getKeyStroke(KeyEvent.VK_Q,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()),
+ getRootPane()
+ .getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW).put(
+ KeyStroke
+ .getKeyStroke(KeyEvent.VK_Q,
+ jalview.util.ShortcutKeyMaskExWrapper
+ .getMenuShortcutKeyMaskEx()),
"Quit");
getRootPane().getActionMap().put("Quit", new AbstractAction()
{
this.inBatchMode = inBatchMode;
}
+ /**
+ * start service discovery and wait till it is done
+ */
public void startServiceDiscovery()
{
startServiceDiscovery(false);
}
+ /**
+ * start service discovery threads - blocking or non-blocking
+ *
+ * @param blocking
+ */
public void startServiceDiscovery(boolean blocking)
{
+ startServiceDiscovery(blocking, false);
+ }
+
+ /**
+ * start service discovery threads
+ *
+ * @param blocking
+ * - false means call returns immediately
+ * @param ignore_SHOW_JWS2_SERVICES_preference
+ * - when true JABA services are discovered regardless of user's JWS2
+ * discovery preference setting
+ */
+ public void startServiceDiscovery(boolean blocking,
+ boolean ignore_SHOW_JWS2_SERVICES_preference)
+ {
boolean alive = true;
Thread t0 = null, t1 = null, t2 = null;
// JAL-940 - JALVIEW 1 services are now being EOLed as of JABA 2.1 release
(t0 = new Thread(discoverer)).start();
}
- if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
+ if (ignore_SHOW_JWS2_SERVICES_preference
+ || Cache.getDefault("SHOW_JWS2_SERVICES", true))
{
t2 = jalview.ws.jws2.Jws2Discoverer.getDiscoverer()
.startDiscoverer(changeSupport);
public class UrlDownloadClient
{
- public UrlDownloadClient()
- {
-
- }
-
/**
* Download and save a file from a URL
*
<mime-type type="application/x-jalview+xml+zip">
<comment>Jalview File</comment>
- <icon name="jalview-file"/>
+ <generic-icon name="x-jalview-file"/>
<glob pattern="*.jvp" weight="100"/>
</mime-type>
<mime-type type="chemical/x-cif">
<comment>CIF File</comment>
- <icon name="jalview-file"/>
+ <generic-icon name="x-jalview-file"/>
<glob pattern="*.cif" weight="40"/>
</mime-type>
<mime-type type="chemical/x-mmcif">
<comment>mmCIF File</comment>
- <icon name="jalview-file"/>
+ <generic-icon name="x-jalview-file"/>
<glob pattern="*.mcif" weight="40"/>
<glob pattern="*.mmcif" weight="40"/>
</mime-type>
<mime-type type="chemical/x-pdb">
<comment>PDB File</comment>
- <icon name="jalview-file"/>
+ <generic-icon name="x-jalview-file"/>
<glob pattern="*.pdb" weight="40"/>
<glob pattern="*.ent" weight="40"/>
</mime-type>
<mime-type type="application/x-amsa+txt">
<comment>AMSA File</comment>
- <icon name="jalview-file"/>
+ <generic-icon name="x-jalview-file"/>
<glob pattern="*.amsa" weight="90"/>
</mime-type>
<mime-type type="application/x-jalview-annotations+text">
<comment>Jalview Annotations File</comment>
- <icon name="jalview-file"/>
+ <generic-icon name="x-jalview-file"/>
<glob pattern="*.annotations" weight="100"/>
<glob pattern="*.jvannotations" weight="100"/>
</mime-type>
<mime-type type="application/x-jalview-biojson+json">
<comment>BioJSON File</comment>
- <icon name="jalview-file"/>
+ <generic-icon name="x-jalview-file"/>
<glob pattern="*.biojson" weight="100"/>
</mime-type>
<mime-type type="application/x-blc+txt">
<comment>BLC File</comment>
- <icon name="jalview-file"/>
+ <generic-icon name="x-jalview-file"/>
<glob pattern="*.blc" weight="90"/>
</mime-type>
<mime-type type="application/x-clustal+txt">
<comment>Clustal File</comment>
- <icon name="jalview-file"/>
+ <generic-icon name="x-jalview-file"/>
<glob pattern="*.aln" weight="90"/>
</mime-type>
<mime-type type="application/x-fasta+txt">
<comment>Fasta File</comment>
- <icon name="jalview-file"/>
+ <generic-icon name="x-jalview-file"/>
<glob pattern="*.fa" weight="90"/>
<glob pattern="*.fasta" weight="90"/>
</mime-type>
<mime-type type="application/x-jalview-features+text">
<comment>Jalview Features File</comment>
- <icon name="jalview-file"/>
+ <generic-icon name="x-jalview-file"/>
<glob pattern="*.features" weight="100"/>
<glob pattern="*.jvfeatures" weight="100"/>
</mime-type>
<mime-type type="application/x-gff2+txt">
<comment>Generic Features Format v2 File</comment>
- <icon name="jalview-file"/>
+ <generic-icon name="x-jalview-file"/>
<glob pattern="*.gff2" weight="90"/>
</mime-type>
<mime-type type="application/x-gff3+txt">
<comment>Generic Features Format v3 File</comment>
- <icon name="jalview-file"/>
+ <generic-icon name="x-jalview-file"/>
<glob pattern="*.gff3" weight="90"/>
</mime-type>
<mime-type type="application/x-jalview-jnet+text">
<comment>JnetFile File</comment>
- <icon name="jalview-file"/>
+ <generic-icon name="x-jalview-file"/>
<glob pattern="*.concise" weight="100"/>
<glob pattern="*.jnet" weight="100"/>
</mime-type>
<mime-type type="application/x-msf+txt">
<comment>MSF File</comment>
- <icon name="jalview-file"/>
+ <generic-icon name="x-jalview-file"/>
<glob pattern="*.msf" weight="90"/>
</mime-type>
<mime-type type="application/x-pfam+txt">
<comment>PFAM File</comment>
- <icon name="jalview-file"/>
+ <generic-icon name="x-jalview-file"/>
<glob pattern="*.pfam" weight="90"/>
</mime-type>
<mime-type type="application/x-phylip+txt">
<comment>PHYLIP File</comment>
- <icon name="jalview-file"/>
+ <generic-icon name="x-jalview-file"/>
<glob pattern="*.phy" weight="90"/>
</mime-type>
<mime-type type="application/x-pileup+txt">
<comment>PileUp File</comment>
- <icon name="jalview-file"/>
+ <generic-icon name="x-jalview-file"/>
<glob pattern="*.pileup" weight="90"/>
</mime-type>
<mime-type type="application/x-pir+txt">
<comment>PIR File</comment>
- <icon name="jalview-file"/>
+ <generic-icon name="x-jalview-file"/>
<glob pattern="*.pir" weight="90"/>
</mime-type>
<mime-type type="application/rnaml+xml">
<comment>RNAML File</comment>
- <icon name="jalview-file"/>
+ <generic-icon name="x-jalview-file"/>
<glob pattern="*.rnaml" weight="90"/>
</mime-type>
<mime-type type="application/x-jalview-scorematrix+text">
<comment>Substitution Matrix File</comment>
- <icon name="jalview-file"/>
+ <generic-icon name="x-jalview-file"/>
<glob pattern="*.mat" weight="100"/>
</mime-type>
<mime-type type="application/x-stockholm+txt">
<comment>Stockholm File</comment>
- <icon name="jalview-file"/>
+ <generic-icon name="x-jalview-file"/>
<glob pattern="*.sto" weight="90"/>
<glob pattern="*.stk" weight="90"/>
</mime-type>
Icon=jalview-icon
Type=Application
TryExec=jalview
-Exec=jalview -open %u
+Exec=jalview %u
Terminal=false
Categories=Science;Biology;
Keywords=alignment;sequence;
--- /dev/null
+#!/usr/bin/env bash
+set -e
+ARG1=$1
+
+# copy the debian default settings if no user jalview settings file exist
+if [ -n "${HOME}" -a \! -e ${HOME}/.jalview_properties ]; then
+ /bin/cp /etc/jalview_properties ${HOME}/.jalview_properties
+fi
+
+# check to see if $1 is set and is not start of other cli set args
+OPEN=""
+if [ -n "$ARG1" -a "$ARG1" = "${ARG1#-}" ]; then
+ # first argument exists and does not start with a "-"
+ OPEN="-open"
+fi
+
+java -jar /usr/share/java/jalview.jar $OPEN "$@"
--- /dev/null
+# global template for ~/.jalview_properties for debian systems
+#
+# this file is copied into a user's home directory by
+# the jalview wrapper script when no .jalview_properties file
+# exists.
+#
+# changes to this file will not affect the jalview configuration
+# for existing users (at least not at the time of writing)
+
+# Configure the automatic display of the Jalview Example Project for new users
+# default is true
+# SHOW_STARTUP_FILE=false
+
+# Location of the file to be loaded in on startup if SHOW_STARTUP_FILE is true
+# default is https://www.jalview.org/examples/exampleFile_2_7.jvp
+# STARTUP_FILE=https://www.jalview.org/examples/exampleFile_2_7.jvp
+
+#
+# Disable Jalview's connections to various web services
+#
+
+# Connection: https://www.jalview.org/services/identifiers
+# uncomment to stop jalview retrieving a list of URL templates for
+# biological databases originally provided by identifiers.org
+#
+# NOIDENTIFIERSSERVICE=true
+
+# Connection: https://www.jalview.org/feeds/desktop/rss
+# uncomment to stop Jalview checking the www.jalview.org news feed
+# NONEWS=true
+
+# Connection: https://raw.githubusercontent.com/jalview/exporter-templates/master/biojs/package.json
+# uncomment to disable download of the latest 'BioJS' HTML export template
+# NOHTMLTEMPLATES=true
+
+# Uncomment to disable pings to google analytics
+# these provide record of launch statistics for the Jalview project
+#
+# default is to prompt user on launch.
+# Allowed values are 'true', 'false' or undefined
+# USAGESTATS=false
+
+# Uncomment to disable jalview's retrieval of https://www.jalview.org/cgi-bin/questionnaire.pl
+# this service is used to make Jalview users aware
+# of any community questionnaires currently active on www.jalview.org
+# Allowed values are true/false. Default is true.
+# NOQUESTIONNAIRES=true
+
+# Uncomment to disable jalview's retrieval of https://www.jalview.org/webstart/jalview.jnlp
+# this document contains the version number of the latest release
+# and used to notify the user if they should consider upgrading their installation.
+# Allowed values are true/false. Default is true.
+# VERSION_CHECK=false
+
+# Uncomment to prevent jalview automatically contacting
+# https://www.compbio.dundee.ac.uk/jabaws/ to discover web services
+# When disabled, users can still initiate service discovery via a button
+# in the 'Web Services' menu.
+# Allowed values are true or false. Default is true.
+# SHOW_JWS2_SERVICES=false
\ No newline at end of file
<mime-type type="$$MIMETYPE$$">
<comment>$$NAME$$ File</comment>
- <icon name="$$ICONFILE$$"/>
+ <generic-icon name="$$ICONFILE$$"/>
$$ <glob pattern="*.EXTENSIONS" weight="$$PRIORITY$$0"/>
$$ </mime-type>
$MimeType .= $mimetype;
my $iconfile = $a->{iconfile};
- $iconfile = "jalview-file" unless $iconfile;
+ $iconfile = "x-jalview-file" unless $iconfile;
my $primary = (! grep($_ eq $shortname, @non_primary));
my $primarystring = $primary?"true":"false";
Icon=jalview-icon
Type=Application
TryExec=jalview
-Exec=jalview -open %u
+Exec=jalview %u
Terminal=false
Categories=Science;Biology;
Keywords=alignment;sequence;
git://source.jalview.org / jalview.git / commitdiff
