<parent>
<groupId>com.threerings.getdown</groupId>
<artifactId>getdown</artifactId>
- <version>1.8.3-1.1.4_JVL</version>
+ <version>1.8.3_1.1.7_JVL</version>
</parent>
<artifactId>getdown-ant</artifactId>
<parent>
<groupId>com.threerings.getdown</groupId>
<artifactId>getdown</artifactId>
- <version>1.8.3-1.1.4_JVL</version>
+ <version>1.8.3_1.1.7_JVL</version>
</parent>
<artifactId>getdown-core</artifactId>
_envc = envc;
_config = getLocalPath(envc.appDir, CONFIG_FILE);
_backupConfig = getLocalPath(envc.appDir, BACKUP_CONFIG_DIR+File.separator+CONFIG_FILE);
- log.warning("Backup config file now", "_backupConfig", _backupConfig, "exists", _backupConfig.exists(), "isReadable", _backupConfig.canRead());
}
/**
ARG: for (int i = 0; i < _jvmargs.size(); i++) {
if (_jvmargs.get(i) instanceof java.lang.String && _jvmargs.get(i).startsWith("-Xmx")) {
_jvmargs.remove(i);
+ break ARG;
}
}
addAll(maxMemHeapArg, _jvmargs);
+ log.info("Max memory set", "maxMemHeapArg", maxMemHeapArg[0]);
}
} else if (jvmmempc != -1) {
- System.out.println("'jvmmempc' value must be in range 0 to 100 (read as '"+Integer.toString(jvmmempc)+"')");
+ log.warning("'jvmmempc' value must be in range 0 to 100 (read as '"+Integer.toString(jvmmempc)+"')");
}
// get the set of optimum JVM arguments
if (j > -1) {
ext = filename.substring(j+1);
}
- if (LOCATOR_FILE_EXTENSION.equals(ext.toLowerCase())) {
+ if (ext != null && LOCATOR_FILE_EXTENSION.equals(ext.toLowerCase())) {
// this file extension should have been dealt with in Getdown class
} else {
_appargs.add(0, "-open");
private final Map<String, Object> _data;
- public static final List<String> allowedReplaceKeys = Arrays.asList("appbase","apparg","jvmarg"); // these are the ones we might use
+ public static final List<String> allowedReplaceKeys = Arrays.asList("appbase","apparg","jvmarg","jvmmempc"); // these are the ones we might use
public static final List<String> allowedMergeKeys = Arrays.asList("apparg","jvmarg"); // these are the ones we might use
//private final List<String> allowedMergeKeys = Arrays.asList("apparg","jvmarg","resource","code","java_location"); // (not exhaustive list here)
}
<parent>
<groupId>com.threerings.getdown</groupId>
<artifactId>getdown</artifactId>
- <version>1.8.3-1.1.4_JVL</version>
+ <version>1.8.3_1.1.7_JVL</version>
</parent>
<artifactId>getdown-launcher</artifactId>
<groupId>com.threerings.getdown</groupId>
<artifactId>getdown</artifactId>
<packaging>pom</packaging>
- <version>1.8.3-1.1.4_JVL</version>
+ <version>1.8.3_1.1.7_JVL</version>
<name>getdown</name>
<description>An application installer and updater.</description>
<mapID target="strucprefs" url="html/features/preferences.html#structure"/>
<mapID target="commandline" url="html/features/commandline.html"/>
<mapID target="clarguments" url="html/features/clarguments.html"/>
+ <mapID target="jvlfiles" url="html/features/jvlfiles.html"/>
<mapID target="io" url="html/io/index.html"/>
<mapID target="io.modellerpir" url="html/io/modellerpir.html"/>
<mapID target="io.seqreport" url="html/io/exportseqreport.html"/>
</tocitem>
</tocitem>
<tocitem text="Preferences" target="preferences" />
- <tocitem text="Memory Settings" target="memory" expand="false"/>
<tocitem text="Scripting with Groovy" target="groovy">
<tocitem text="Groovy Features Counter example" target="groovy.featurescounter"/>
</tocitem>
<tocitem text="Command Line" target="commandline" expand="false">
<tocitem text="Command Line Arguments" target="clarguments" />
- </tocitem>
+ <tocitem text="Memory Settings" target="memory" expand="false"/>
+ <tocitem text="Jalview Launch Files" target="jvlfiles" expand="false"/>
+ </tocitem>
<tocitem text="Privacy" target="privacy" />
</tocitem>
<tocitem text="Useful information" expand="true">
See
<a href="commandline.html">running Jalview from the command line</a>
for more information.
+ <br />
+ <br />Jalview processes arguments on the command line sequentially. If
+ you would like to pass a <a href="jvlfiles.html">'JVL' file</a> containing
+ <a href="../memory.html">memory settings</a> or any other launch
+ parameters, then include it at the beginning of the command line to
+ ensure they are processed before any remaining arguments.
<br>
<table width="100%" border="1" cellspacing="0" cellpadding="0">
<tr>
<p>
<strong>Running Jalview from the command line</strong>
</p>
- <p>Jalview is most easily run from the command line if you have
- built it from source, or via the 'Jalview' executable created from
- the InstallAnywhere Jalview installation. Both of these mechanisms
- allow true command line execution of Jalview - allowing you to
- provide additional options.</p>
- <p>The Java Webstart version of Jalview can be executed from the
- command line using something like :
- <pre>javaws http://www.jalview.org/webstart/jalview.jnlp -open
- <em>yourFileName</em>
- </pre>
- But, this is not guaranteed to work on all versions of webstart on all
- operating systems, and doesn't let you execute Jalview with any
- additional parameters.
<p>
- <strong>Running Jalview from the InstallAnywhere
- installation</strong>
+ Jalview can be run from the command line, and provides a <a
+ href="clarguments.html">range of arguments</a>. These arguments
+ can also be passed via <strong>.JVL</strong> files, which are opened
+ automatically by the Jalview application when double-clicked in a
+ file browser on Windows and OSX.
</p>
+ The way that you launch Jalview from the command line depends on the
+ platform you are on, and how it has been installed.
+
+ <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>
+ </li>
+ <li>Standard installation on Windows:<pre>
+ \PATH_TO_JALVIEW\Jalview.exe -open %HOMEPATH%\myalignment.fa</pre>
+ </li>
+ <li>OSX Application:<pre>
+open /Applications/Jalview.app --args -open ~/myalignment.fa</pre><em>(put
+ all the Jalview arguments <em>after</em> the --args parameter)
+ </em><br />
+ <br /></li>
+ <li>Jalview standalone executable Jar<pre>
+ <Path to Java home>/bin/java -jar %lt;Path to Jalview Jar>/jalview-all-1.8.jar -open myalignment.fa</pre></li>
+ </ul>
<p>
- If you install with InstallAnywhere you can use several more
- commands. However, if you call the application with the link
- provided by InstallAnywhere any output from the application will be
- sent to output.txt, not standard out.<br> The Jalview
- application also requires a number of additional libraries on the
- class path. The command line below adds all the jar files in the
- Jalview installation's 'lib' directory to the classpath, as well as
- the Jalview application jar file:
+ If you have installed Jalview via <em>conda</em> or another package
+ manager then you most likely have a 'jalview' command available in
+ your terminal shell's default path. Alternately, if you have built
+ Jalview from source, then take a look at the doc/building.md file
+ included in the source distribution.
</p>
- <pre>java -classpath "$INSTALL_DIR$/lib/*:$INSTALL_DIR$/jalview.jar" jalview.bin.Jalview -open [FILE] </pre>
<p>
Use '-help' to get more information on the <a
- href="clarguments.html">command line arguments</a> that
- Jalview accepts.
+ href="clarguments.html">command line arguments</a> that Jalview
+ accepts.
+ </p>
+ <p>
+ <strong>Passing JVM Arguments to Jalview</strong><br /> If you need
+ to modify parameters for Jalview's Java Virtual Machine, then take a
+ look at the instructions for how to <a href="../memory.html#jvm">setting
+ the JVM's maximum memory</a>.
</p>
<p> </p>
<p> </p>
--- /dev/null
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
+<title>JVL - Jalview Launch Files</title>
+<body>
+ <p>
+ <strong>Jalview Launch Files - JVL</strong>
+ </p>
+ <p>Files with a '.jvl' (or .JVL) extension can be opened by the
+ Jalview desktop application, and allow you to:</p>
+ <ul>
+ <li><strong>Switch between different Jalview Versions</strong></li>
+ <li><strong>Configure the <a href="../memory.html">proportion
+ of memory</a> allocated to Jalview
+ </strong></li>
+ <li><strong>Import data and pass <a
+ href="clarguments.html">command line arguments</a></strong></li>
+ </ul>
+ <p>
+ Some example JVL files are given below - copy and paste them into a
+ text editor and save them as a file with the extension '.jvl'. To
+ test, open your saved .jvl file via the OSX File Chooser or Windows
+ file explorer, or pass it to Jalview via the <a
+ href="../commandline.html">command line</a>
+ </p>
+ <p>
+ <strong>Passing command line arguments</strong>
+ <pre>
+# Jalview Launch File
+# Please install the Jalview Desktop from
+# http://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=-annotations
+jalview.apparg=http://www.jalview.org/examples/jpred_msa.seq.concise
+jalview.apparg=-colour
+jalview.apparg=Clustal
+</pre>
+ <p>
+ <strong>Launching a different version of Jalview</strong>
+ <pre>
+# Jalview Launch File
+# 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/old/v2_10_5/
+</pre>
+ For security, the Jalview application will only allow
+ <em>appbase</em> URLs from www.jalview.org, or your local file system.
+</body>
+</html>
<strong>Memory Usage Settings for Jalview</strong>
</center>
</h2>
+ <p>When launched as an Application, Jalview will automatically
+ configure the amount of memory allocated to the program to be 90% of
+ physical memory. You may wish to change this behaviour -
+ particularly if you are working on a machine that runs other memory
+ intensive processes.
<p>
- When launched as an Application, Jalview automatically tries to
- maximise the amount of memory allocated to it, but sometimes it may
- run out of memory. This is because of the way that Java runs on a
- computer - what is actually run is a program called a virtual
- machine (the JVM) which executes the java instructions. The JVM has
- limits on the memory that can be allocated to the java program - and
- you might need to increase them if you are working with particularly
- large datasets.<br> If Jalview has not explicitly told you that
- it has run out of memory, then a common sign is that a function that
- normally works seems to have no effect when working with a larger
- set of sequences (this might include open dialog boxes for saving
- PNG files, or when interpreting the result of a web service
- calculation).
+ <em>Signs that Jalview is Running out of Memory</em><br /> If
+ Jalview has not explicitly told you that it has run out of memory,
+ then a common sign is that a function that normally works seems to
+ have no effect when working with a larger set of sequences (this
+ might include open dialog boxes for saving PNG files, or when
+ interpreting the result of a web service calculation).
</p>
<p>
<em>Jalview Memory Usage Monitor</em>: If you are concerned about
window's background.
</p>
<p>
- <em>Increasing the memory available to Jalview</em><br>
- Since Jalview 2.11, the program automatically configures the JVM memory settings to set the maximum memory available to Jalview to be 90% of physical memory.
- <p> </p>
+ <em>Increasing the memory available to Jalview</em><br /> The
+ amount of memory allocated is defined wheb Jalview is launched
+ because of the way that Java runs on a computer - what is actually
+ run is a program called a Java virtual machine (a JVM) which
+ executes the java program instructions. The JVM has limits on the
+ memory that can be allocated to the java program - and it is often
+ necessary to adjust them if you are working with particularly large
+ datasets, or need to make room for other processes on the machine.<br />
+ <br />Jalview 2.11 includes a launcher that automatically
+ configures the proportion of memory allocated to Jalview's JVM, and
+ its behaviour can be altered in a number of different ways:
+ </p>
+
+ <ul>
+ <li><em><font size="3">JVL file</font></em> <br /> The easiest
+ way to launch Jalview with a different percentage of physical
+ memory available is to create a text file with extension <em>.jvl</em>
+ and a single line to specify the percentage of memory you wish
+ Jalview to request: <pre>
+ jalview.jvmmempc=50</pre> In Windows and in macOS you can then launch Jalview by
+ double clicking on this file, and your memory setting will be used
+ instead of the default value. <br /> <br /> In Linux or other
+ unix variants you can launch Jalview on the command line and
+ provide your JVL file as an argument with <pre>
+ /PATH_TO_JALVIEW/Jalview /path/to/file/mymemorysetting.jvl</pre> If you want to use a memory setting like this and open a
+ file you can use both the jvl and alignment files as command line
+ 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
+ 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>
+ open /Applications/Jalview.app --args ~/mymemorysetting.jvl -open ~/myalignment.fa</pre><em>(put all the Jalview arguments <em>after</em> the --args
+ parameter)
+ </em><br/><br/></li>
+ <li><em><font size="3"><a name="jvm"/>Directly opening Jalview
+ with a JVM</font></em> <br /> Launching Jalview directly with a JVM is
+ entirely possible, but is not recommended for regular interactive
+ use because it bypasses Jalview's launcher which also handles
+ automatic updates and configuration of other aspects of Jalview
+ operation. <br /> However by launching Jalview in this way you
+ have full access to the Java command line arguments. In particular
+ you can set the maximum allowed memory with the <em>-Xmx...</em>
+ JVM argument. <br /> <em>-Xmx</em> should be immediately followed
+ (no space or equals) by the maximum amount of memory specified in
+ bytes, or in kilobytes, megabytes or gigabytes by following the
+ number with a "k", "m" or "g" respectively. <br />For example: <pre>
+ -Xmx8g</pre>Jalview binaries for Windows and macOS are distributed
+ with their own JVM which you will find in
+ <ul>
+ <li><em>Windows:</em> .../Jalview/jre/bin/java.exe</li>
+ <li><em>macOS:</em>
+ .../Jalview.app/Contents/Resources/app/jre/Contents/Home/bin/java</li>
+ </ul> For linux and other unixes you will have to install a Java 1.8
+ JRE (we recommend the ones found at <a
+ href="https://adoptopenjdk.net">https://adoptopenjdk.net/</a>) <br />
+ <br /> You will also need to reference the "appdir" release
+ folder with all of the Jalview jar files.
+ <ul>
+ <li>On Windows this will be <pre>\PATH_TO_JALVIEW\release</pre>
+ </li>
+ <li>On macOS it will be <pre>/Applications/Jalview.app/Contents/Resources/app/release</pre>
+ and on linux or unix <pre>/PATH_TO_JALVIEW/release</pre>
+ </li>
+ </ul> Assuming the <em>java</em> (or <em>java.exe</em> on Windows)
+ commands are available to you, you can run, e.g. <pre>
+ java -Xmx1500m -cp "/PATH_TO_RELEASE_DIR/*" jalview.bin.Jalview
+ </pre> Or on Windows <pre>
+ java.exe -Xmx1500m -cp "\PATH_TO_RELEASE_DIR\*" jalview.bin.Jalview
+ </pre> <em>Note:</em> for this to work the classpath argument wildcard <strong>must</strong> be simply
+ a '*' and not '*.jar'. <br /> <br />
+ You can also add other <a href="features/commandline.html">Jalview
+ command line arguments</a> as above after the <em>jalview.bin.Jalview</em>
+ class name, but <strong>you cannot use <em>jvl</em> files
+ </strong> if launching Jalview in this way.</li>
+ </ul>
</body>
</html>
git://source.jalview.org / jalview.git / commitdiff