reportRsyncCmd = false
buildDist = true
buildProperties = buildPropertiesFile
+ getdownLauncher = jalviewDir + '/' + getdown_lib_dir + '/' + getdown_launcher
switch (CHANNEL) {
case "BUILD":
buildDist = false
}
reportRsyncCommand = true
+ getdownLauncher = jalviewDir + '/' + getdown_lib_dir + '/' + getdown_launcher_local
break
case "DEVELOP":
getdown_app_base = file(getdownWebsiteDir).toURI().toString()
getdown_app_dir = getdown_app_dir_alt
buildProperties = jalviewDir + "/" + classesDir +"/" + buildPropertiesFile
+ getdownLauncher = jalviewDir + '/' + getdown_lib_dir + '/' + getdown_launcher_local
break
default: // something wrong specified
//getdownJ11libDir = getdownWebsiteDir + '/' + getdown_j11lib_dir
getdownResourceDir = getdownWebsiteDir + '/' + getdown_resource_dir
getdownInstallDir = getdownWebsiteDir + '/' + getdown_install_dir
- getdownLauncher = jalviewDir + '/' + getdown_launcher
getdownFilesDir = jalviewDir + '/' + getdown_files_dir + '/' + JAVA_VERSION + '/'
getdownFilesInstallDir = getdownFilesDir+"/"+getdown_install_dir
/* compile without modules -- using classpath libraries
exclude '**/*.gif'
exclude '**/*.jpg'
exclude '**/*.png'
- filter(ReplaceTokens, beginToken: '$$', endToken: '$$', tokens: ['Version-Rel': JALVIEW_VERSION])
+ filter(ReplaceTokens, beginToken: '$$', endToken: '$$', tokens: ['Version-Rel': JALVIEW_VERSION,'Year-Rel': getDate("yyyy")])
}
from(inputDir) {
include '**/*.gif'
copy {
from getdownLauncher
+ if (file(getdownLauncher).getName() != getdown_launcher) {
+ rename(file(getdownLauncher).getName(), getdown_launcher)
+ }
into project.ext.getdownWebsiteDir
}
from getdown_txt
from getdownLauncher
from getdownWebsiteDir+"/"+getdown_build_properties
+ if (file(getdownLauncher).getName() != getdown_launcher) {
+ rename(file(getdownLauncher).getName(), getdown_launcher)
+ }
into getdownInstallDir
}
from launch_jvl
from getdownLauncher
from getdownWebsiteDir+"/"+getdown_build_properties
+ if (file(getdownLauncher).getName() != getdown_launcher) {
+ rename(file(getdownLauncher).getName(), getdown_launcher)
+ }
into getdownFilesDir
}
group = "distribution"
description = "Digest the getdown website folder"
dependsOn getdownWebsite
- classpath = files(jalviewDir + '/' + getdown_core, jalviewDir+'/'+getdown_launcher)
+ doFirst {
+ classpath = files(getdownWebsiteDir + '/' + getdown_launcher)
+ }
main = "com.threerings.getdown.tools.Digester"
args project.ext.getdownWebsiteDir
inputs.dir(project.ext.getdownWebsiteDir)
task sourceDist (type: Tar) {
def VERSION_UNDERSCORES = JALVIEW_VERSION.replaceAll("\\.", "_")
- archiveFileName = project.name + "_" + VERSION_UNDERSCORES + ".tar.gz"
+ def outputFileName = project.name + "_" + VERSION_UNDERSCORES + ".tar.gz"
+ // cater for buildship < 3.1 [3.0.1 is max version in eclipse 2018-09]
+ try {
+ archiveFileName = outputFileName
+ } catch (Exception e) {
+ archiveName = outputFileName
+ }
compression Compression.GZIP
- from jalviewDir
into project.name
-
-
- exclude (".*")
- exclude ("**/.*")
- exclude ("*.class")
- exclude ("**/*.class")
- include (eclipse_extra_jdt_prefs_file)
- include ("AUTHORS")
- include ("CITATION")
- include ("FEATURETODO")
- include ("JAVA-11-README")
- include ("FEATURETODO")
- include ("LICENSE")
- include ("README")
- include ("RELEASE")
- include ("THIRDPARTYLIBS")
- include ("build.gradle")
- include ("gradle.properties")
- include ("$sourceDir/*.java")
- include ("$sourceDir/**/*.java")
- include ("$sourceDir/**/*.cdr")
- include ("$j8libDir/**/*.jar")
- include ("$j11libDir/**/*.jar")
- include ("$resourceDir/**/*")
- include ("$helpDir/**/*")
- include ("$schemaDir/**/*")
- include ("$utilsDir/**/*")
- include ("$docDir/**/*")
- include ("$examplesDir/**/*")
- include ("getdown/**/*")
- //include ("jalview-jalopy.xml")
- //include ("JalviewApplet.jpx")
- //include ("JalviewX.jpx")
- //include ("nbbuild.xml")
- //include ("nbproject/genfiles.properties")
- //include ("nbproject/project.properties")
- //include ("nbproject/project.xml")
-
+
+ def EXCLUDE_FILES=["build/*","bin/*","test-output/","test-reports","tests","clover*/*"
+ ,".*"
+ ,"benchmarking/*"
+ ,"**/.*"
+ ,"*.class"
+ ,"**/*.class","$j11modDir/**/*.jar","appletlib","**/*locales"
+ ,"*locales/**",
+ ,"utils/InstallAnywhere"]
+ def PROCESS_FILES=[ "AUTHORS",
+ "CITATION",
+ "FEATURETODO",
+ "JAVA-11-README",
+ "FEATURETODO",
+ "LICENSE",
+ "**/README",
+ "RELEASE",
+ "THIRDPARTYLIBS","TESTNG",
+ "build.gradle",
+ "gradle.properties",
+ "**/*.java",
+ "**/*.html",
+ "**/*.xml",
+ "**/*.gradle",
+ "**/*.groovy",
+ "**/*.properties",
+ "**/*.perl",
+ "**/*.sh"]
+
+ from(jalviewDir) {
+ exclude (EXCLUDE_FILES)
+ include (PROCESS_FILES)
+ filter(ReplaceTokens, beginToken: '$$', endToken: '$$', tokens: ['Version-Rel': JALVIEW_VERSION,'Year-Rel': getDate("yyyy")])
+ }
+ from(jalviewDir) {
+ exclude (EXCLUDE_FILES)
+ exclude (PROCESS_FILES)
exclude ("appletlib")
exclude ("**/*locales")
exclude ("*locales/**")
exclude ("utils/InstallAnywhere")
- exclude (libDir)
- exclude (getdown_files_dir)
+
+ exclude (getdown_files_dir)
exclude (getdown_website_dir)
// exluding these as not using jars as modules yet
exclude ("$j11modDir/**/*.jar")
-
+}
+// from (jalviewDir) {
+// // explicit includes for stuff that seemed to not get included
+// include(fileTree("test/**/*."))
+// exclude(EXCLUDE_FILES)
+// exclude(PROCESS_FILES)
+// }
}
task helppages {
dependsOn pubhtmlhelp
inputs.dir("$classes/$helpDir")
- outputs.file("build/distribution/help/helpTOC.html")
+ outputs.dir("$helpOutputDir")
}
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 5.1 or above
+* gradle 5.2 or above
* git
> The versions and installation methods here are just suggestions (which we have tested
<parent>
<groupId>com.threerings.getdown</groupId>
<artifactId>getdown</artifactId>
- <version>1.8.3-1.1.4_JVL</version>
+ <version>1.8.3-1.1.8_FJVL</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>1.8.3-1.1.8_FJVL</version>
</parent>
<artifactId>getdown-core</artifactId>
<getdown.host.whitelist>jalview.org,*.jalview.org</getdown.host.whitelist>
<connect_timeout>8</connect_timeout>
<read_timeout>15</read_timeout>
+ <allow_file_protocol>false</allow_file_protocol>
</properties>
<build>
<filter token="host_whitelist" value="${getdown.host.whitelist}" />
<filter token="connect_timeout" value="${connect_timeout}" />
<filter token="read_timeout" value="${read_timeout}" />
+ <filter token="allow_file_protocol" value="${allow_file_protocol}" />
</filterset>
</copy>
</target>
_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");
return 30;
}
}
+
+ /*
+ * <p>Whether to allow the local "file://" scheme for appbase
+ */
+ public static boolean allowLocatorFileProtocol() {
+ try {
+ return Boolean.valueOf("@allow_file_protocol@");
+ } catch (Exception e) {
+ return false;
+ }
+ }
}
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)
}
throw new MalformedURLException(
"The host for the specified URL (" + url + ") is not in the host whitelist: " + hosts);
}
- private static boolean ALLOW_LOCATOR_FILE_PROTOCOL = true;
+ private static final boolean ALLOW_LOCATOR_FILE_PROTOCOL = Build.allowLocatorFileProtocol();
}
<parent>
<groupId>com.threerings.getdown</groupId>
<artifactId>getdown</artifactId>
- <version>1.8.3-1.1.4_JVL</version>
+ <version>1.8.3-1.1.8_FJVL</version>
</parent>
<artifactId>getdown-launcher</artifactId>
if [ x$JVLVERSION != x ]; then
export VERSION=$JVLVERSION
else
- export VERSION=1.8.3-1.1.4_JVL
+ export VERSION=1.8.3-1.1.8_JVL
fi
if [ x${VERSION%_JVL} = x$VERSION ]; then
fi
echo "Setting VERSION to '$VERSION'"
-
perl -p -i -e 's|(<version>)[^<]*JVL[^<]*(</version>)|${1}$ENV{VERSION}${2}|;' pom.xml */pom.xml
+mvn package -Dgetdown.host.whitelist="jalview.org,*.jalview.org" -Dallow_file_protocol=false -Dconnect_timeout=8 -Dread_timeout=15
+RET=$?
+if [ x$RET = x0 ]; then
+ cp launcher/target/getdown-launcher-$VERSION.jar ../../../getdown/lib/getdown-launcher.jar && echo "Copied getdown-launcher-$VERSION.jar to getdown/lib"
+ cp core/target/getdown-core-$VERSION.jar ../../../getdown/lib/getdown-core.jar && echo "Copied getdown-core-$VERSION.jar to getdown/lib"
+ cp core/target/getdown-core-$VERSION.jar ../../../j8lib/getdown-core.jar && echo "Copied getdown-core-$VERSION.jar to j8lib"
+ cp core/target/getdown-core-$VERSION.jar ../../../j11lib/getdown-core.jar && echo "Copied getdown-core-$VERSION.jar to j11lib"
+fi
-mvn package -Dgetdown.host.whitelist="jalview.org,*.jalview.org" -Dconnect_timeout=8 -Dread_timeout=15
+VERSION=${VERSION/JVL/FJVL}
+echo "Setting VERSION to '$VERSION'"
+perl -p -i -e 's|(<version>)[^<]*JVL[^<]*(</version>)|${1}$ENV{VERSION}${2}|;' pom.xml */pom.xml
+mvn package -Dgetdown.host.whitelist="jalview.org,*.jalview.org" -Dallow_file_protocol=true -Dconnect_timeout=4 -Dread_timeout=4
RET=$?
if [ x$RET = x0 ]; then
- cp launcher/target/getdown-launcher-$VERSION.jar ../../../getdown/lib/getdown-launcher.jar && echo "Copied getdown-launcher.jar to getdown/lib"
- cp core/target/getdown-core-$VERSION.jar ../../../getdown/lib/getdown-core.jar && echo "Copied getdown-core.jar to getdown/lib"
- cp core/target/getdown-core-$VERSION.jar ../../../j8lib/getdown-core.jar && echo "Copied getdown-core.jar to j8lib"
- cp core/target/getdown-core-$VERSION.jar ../../../j11lib/getdown-core.jar && echo "Copied getdown-core.jar to j11lib"
+ cp launcher/target/getdown-launcher-$VERSION.jar ../../../getdown/lib/getdown-launcher-local.jar && echo "Copied getdown-launcher-$VERSION.jar to getdown/lib/getdown-launcher-local.jar"
fi
<groupId>com.threerings.getdown</groupId>
<artifactId>getdown</artifactId>
<packaging>pom</packaging>
- <version>1.8.3-1.1.4_JVL</version>
+ <version>1.8.3-1.1.8_FJVL</version>
<name>getdown</name>
<description>An application installer and updater.</description>
resourceDir = resources
helpParentDir = help
helpDir = help
-helpOutputDir = build/distribution/help
+helpOutputDir = build/distributions/help
docDir = doc
sourceDir = src
schemaDir = schemas
getdown_resource_dir = resource
#getdown_j11lib_dir = j11lib
getdown_files_dir = getdown/files
-getdown_launcher = getdown/lib/getdown-launcher.jar
+getdown_lib_dir = getdown/lib
+getdown_launcher = getdown-launcher.jar
+getdown_launcher_local = getdown-launcher-local.jar
getdown_launcher_new = getdown-launcher-new.jar
getdown_core = getdown/lib/getdown-core.jar
getdown_launch_jvl = channel_launch.jvl
<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>
<li><strong>Numeric</strong> - specify a threshold above, equal
to or below which a feature will be selected or ignored.</li>
<li><strong>String</strong> - select or ignore features based on
- presence, absence, equivalence, or containment of a string.</li>
+ presence, absence, equivalence, or containment of a string (not case sensitive).</li>
</ul>
<p>
The filters and colour schemes active for a particular feature type
</tr>
<tr>
<td><em>Graduated colour thresholded (less than) by
- feature Score</em></td>
+ feature Score (or other attribute)</em></td>
<td><img src="fcsltthan.gif" /></td>
</tr>
<tr>
<td><em>Graduated colour thresholded (greater than) by
- feature Score</em></td>
+ feature Score (or other attribute)</em></td>
<td><img src="fcsgtthan.gif" /></td>
</tr>
<tr>
- <td><em>Colour by Feature Label (may also be thresholded)</em></td>
+ <td><em>Colour by Feature Label</em></td>
<td><img src="fcsntlabel.gif" /></td>
</tr>
<tr>
<td align="center" colspan="2"><em> <strong>The
- current threshold and attribute is given in the icon's tooltip.</strong>
+ current threshold and attribute is shown in the icon's tooltip.</strong>
</em></td>
</tr>
</table>
<p>
Select <strong>View→Feature Settings...</strong> in an alignment
window to open the feature settings dialog box, which allows
- precise control the visibility and appearance of sequence features for
+ precise control of the visibility and appearance of sequence features for
an alignment view.
</p>
<div align="center">
<p>The top section of the dialog box lists all the sequence feature
groups, along with a tickbox for each that controls whether its
features are displayed. When many groups are present, their names may
- be truncated, but the full name be shown in a tooltip when the mouse
+ be truncated, but the full name is shown in a tooltip when the mouse
hovers over their checkbox.</p>
<p><em>Feature colour schemes and filters</em>
<p>
##reference header that define what species and assembly name the
VCF was generated against.</li>
<li>Look at ensembl.org to identify the species' short name,
- and the assembly's unique.</li>
+ and the assembly's unique id.</li>
<li>Add mappings to the <strong>VCF_SPECIES</strong> and <strong>VCF_ASSEMBLY</strong>
properties in your .jalview_properties file. For example:<pre>
VCF_SPECIES=1000genomes=homo_sapiens,c_elegans=celegans
--- /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>
<li><strong>Calculate Tree or PCA ...</strong><em> <br> Opens the
<a href="../calculations/calculations.html">calculations dialog</a> for
for calculating <a href="../calculations/tree.html">trees</a> or
- <a href="../calculations/pca.html">principle component analysis
+ <a href="../calculations/pca.html">principal component analysis
plots</a> on the alignment or the currently selected
region.
</em><br></li>
<li><strong>Calculate Tree or PCA ...</strong> <br> <em>Opens the
<a href="../calculations/calculations.html">calculations dialog</a> for
for calculating <a href="../calculations/tree.html">trees</a> or
- <a href="../calculations/pca.html">principle component analysis
+ <a href="../calculations/pca.html">principal component analysis
plots</a> on the alignment or the currently selected
region.
</em><br>
</li>
<li>
<!-- JAL-1839,JAL-3254,JAL-3260 -->File type associations for
- formats supported by jalview (including .jvp project files)
+ formats supported by Jalview (including .jvp project files)
</li>
<li>
<!-- JAL-3260 -->Jalview launch files (.jvl) to pass command line
<!-- JAL-3140 JAL-2446 -->IntervalStoreJ (NCList
implementation that allows updates) used for Sequence Feature collections</li>
<li>
- <li>
<!-- JAL-2744, JAL-2808,JAL-2069,JAL-2820 -->Sequence
features can be filtered and shaded according to any
associated attributes (e.g. variant attributes from VCF
</li>
<li>
<!-- JAL-2527 JAL-3203 -->Alignment Overview now WYSIWIS (What you see is
- what is shown)<br />Only visible region of alignment is shown by
+ what is shown)<br />Only visible regions of alignment are shown by
default (can be changed in user preferences)
</li>
<li>
</ul>
<em>Deprecations</em>
<ul>
- <li>
- <!-- JAL-3035 -->DAS sequence retrieval and annotation
+ <li><!-- JAL-3035 -->DAS sequence retrieval and annotation
capabilities removed from the Jalview Desktop
</li>
- <li>
- <!-- JAL-3063,JAL-3116 -->Castor library for XML marshalling and
+ <li><!-- JAL-3063,JAL-3116 -->Castor library for XML marshalling and
unmarshalling has been replaced by JAXB for Jalview projects
and XML based data retrieval clients</li>
<li><!-- JAL-3311 -->Disable VAMSAS menu in preparation for removal</li>
<li><!-- -->Jalview Desktop no longer distributed via Java Web Start</li>
</ul> <em>Documentation</em>
<ul>
- <li>
- <!-- JAL-3003 -->Added remarks about transparent rendering effects
+ <li><!-- JAL-3003 -->Added remarks about transparent rendering effects
not supported in EPS figure export
</li>
<li><!-- JAL-2903 -->Typos in documentation for Preferences dialog</li>
</ul> <em>Development and Release Processes</em>
<ul>
<li>
- <!-- JAL-3196,JAL-3179.JAL-2671 -->Build system migrated from Ant to Gradle
+ <!-- JAL-3196,JAL-3179.JAL-2671 -->Build system migrated from Ant to Gradle
</li>
- <li><!-- JAL-1424 -->Enhanced checks for missing and duplicated keys in Message bundles</li>
+ <li>
+ <!-- JAL-1424 -->Enhanced checks for missing and duplicated keys in Message bundles</li>
<li>
- <!-- JAL-3225 -->Eclipse project configuration managed with
+ <!-- JAL-3225 -->Eclipse project configuration managed with
gradle-eclipse
</li>
<li>
- <!-- JAL-3174,JAL-2886,JAL-2729,JAL-1889 --> Atlassian
+ <!-- JAL-3174,JAL-2886,JAL-2729,JAL-1889 -->Atlassian
Bamboo continuous integration for unattended Test Suite
execution
</li>
<li>
- <!-- JAL-2864 -->Memory test suite to detect leaks in common
+ <!-- JAL-2864 -->Memory test suite to detect leaks in common
operations
</li>
<li>
- <!-- JAL-2360,JAL-2416 -->More unit test coverage, and minor
- issues resolved.
+ <!-- JAL-2360,JAL-2416 -->More unit test coverage, and minor
+ issues resolved
</li>
<li>
- <!-- JAL-3248 -->Developer documentation migrated to
+ <!-- JAL-3248 -->Developer documentation migrated to
markdown (with HTML rendering)
</li>
<li>
- <!-- JAL-3287 -->HelpLinksChecker runs on Windows
+ <!-- JAL-3287 -->HelpLinksChecker runs on Windows
</li>
<li>
- <!-- JAL-3289 -->New URLs for publishing development
+ <!-- JAL-3289 -->New URLs for publishing development
versions of Jalview
</li>
- <li>
- <li>
</ul>
</td>
<td align="left" valign="top">
Settings and Jalview Preferences panels
</li>
<li>
- <!-- JAL-2865 -->Jalview hangs when closing windows or the
- overview updates with large alignments
+ <!-- JAL-2865 -->Jalview hangs when closing windows, or redrawing the
+ overview with large alignments
</li>
<li>
<!-- JAL-2750 -->Tree and PCA calculation fails for selected
</li>
<li>
<!-- JAL-2060 -->'Graduated colour' option not offered for
- manually created features (where if feature score is Float.NaN)
+ manually created features (where feature score is Float.NaN)
</li>
<li>
<!-- JAL-3097,JAL-3099 -->Blank extra columns drawn or printed
<!-- JAL-868 -->Structure colours not updated when associated tree
repartitions the alignment view (Regression in 2.10.5)
</li>
- </ul>
- <em>Datamodel</em>
- <ul>
- <li>
- <!-- JAL-2986 -->Sequence.findIndex returns wrong value when
- sequence's End is greater than its length
- </li>
- <li><strong>Bugs fixed for Java 11 Support (not
- yet on general release)</strong>
- <ul>
- <li>
- <!-- JAL-3288 -->Menus work properly in split-screen
- </li>
- </ul></li>
+ </ul> <em>Datamodel</em>
+ <ul>
+ <li>
+ <!-- JAL-2986 -->Sequence.findIndex returns wrong value when
+ sequence's End is greater than its length
+ </li>
+ </ul> <em>Bugs fixed for Java 11 Support (not yet on
+ general release)</em>
+ <ul>
+ <li>
+ <!-- JAL-3288 -->Menus work properly in split-screen
+ </li>
</ul> <em>New Known Defects</em>
- <ul>
- <li><!-- JAL-3340 -->Select columns containing feature by double clicking ignores bounds of an existing selected region
+ <ul>
+ <li>
+ <!-- JAL-3340 -->Select columns containing feature by double clicking ignores bounds of an existing selected region
</li>
<li>
<!-- JAL-3313 -->Codon consensus logo incorrectly scaled in gapped
not shown as thresholded features in 2.11. To workaround please
create a Score filter instead.
</li>
- <li><!-- JAL-3184 -->Cancel on Feature Settings dialog doesn't reset group visibility</li>
+ <li>
+ <!-- JAL-3184 -->Cancel on Feature Settings dialog doesn't reset group visibility</li>
<li>
<!-- JAL-3338 -->F2 doesn't enable/disable keyboard mode in linked CDS/Protein view
</li>
<!-- JAL-797 -->Closing tree windows with CMD/CTRL-W for
alignments with multiple views can close views unexpectedly
</li>
- <li><strong>Java 11 Specific defects</strong>
+ </ul>
+ <em>Java 11 Specific defects</em>
<ul>
<li>
<!-- JAL-3235 -->Jalview Properties file is not sorted
alphabetically when saved
</li>
- </ul>
- </li>
- </ul>
+ </ul>
</td>
</tr>
<tr>
<!-- JAL-247 -->Hidden sequence markers and representative
sequence bolding included when exporting alignment as EPS,
SVG, PNG or HTML. <em>Display is configured via the
- Format menu, or for command-line use via a jalview
+ Format menu, or for command-line use via a Jalview
properties file.</em>
</li>
<li>
</li>
<li>
<!-- JAL-3106 -->.jvp should be used as default extension
- (not .jar) when saving a jalview project file.
+ (not .jar) when saving a Jalview project file.
</li>
<li>
<!-- JAL-3105 -->Mac Users: closing a window correctly
also been improved.</li>
<li><strong>Backup files</strong>. Jalview will automatically
create backups when overwriting existing files, and - unlike with
- earlier versions, should Jalview crash during a save, the original
+ earlier versions - should Jalview crash during a save, the original
file will be unaffected. The <a
href="features/preferences.html#backups">Backups tab</a> in
Jalview's preferences dialog allows the number and format of
+++ /dev/null
-NOBACK
-XmlSchema-SNAPSHOT.jar
-annogen-0.1.0.jar
-axiom-api-1.0-RC2.jar
-axiom-dom-1.0-RC2.jar
-axiom-impl-1.0-RC2.jar
-axis-wsdl4j-1.2.jar
-axis.jar.bak
-axis.jar.commons
-axis2-adb-1.0-RC2.jar
-axis2-kernel-1.0-RC2.jar
-backport-util-concurrent-2.0_01_pd.jar
-backport-util-concurrent-2.1.jar
-castor.zip
-commons-codec-1.2.jar
-commons-codec-1.3.jar
-commons-fileupload-1.0.jar
-commons-httpclient-3.0.jar
-commons-logging-1.0.4.jar
-geronimo-spec-activation-1.0.2-rc4.jar
-geronimo-spec-javamail-1.3.1-rc5.jar
-geronimo-spec-jms-1.1-rc4.jar
-jaxen-1.1-beta-7.jar
-jhall.jar.bak
-log4j-1.2.13.jar
-maven-itest-plugin-1.0.jar
-phylip-client-axis-1.3.jar
-policy-1.0.1-RC.jar
-policy-1.0.jar
-servletapi-2.3.jar
-stax-api-1.0.jar
-wstx-asl-2.8.2.jar
-wstx-asl-2.9.2.jar
-xercesImpl.jar.bak
-xml-apis.jar.bak
<project name="Publish Help Webpages for Jalview" default="pubhtmlhelp">
<target name="pubhtmlhelp">
- <property name="appletHelpDir" value="../build/distribution/help"/>
+ <property name="appletHelpDir" value="../build/distributions/help"/>
<!-- finally, publish the help files -->
<javac srcdir="." destdir="." includes="help2Website.java"/>
<java fork="true" dir="${helpBuildDir}" classpath="." classname="help2Website"/>
git://source.jalview.org / jalview.git / commitdiff