/site
/.gradle
/build
-/utils/HelpLinksChecker.out
+/utils/HelpLinksChecker.touch
/getdown/website
/getdown/full_app
/getdown/files
+2019-07-01 (pre 2.11.0 release)
+Notes below are out of date, but might be useful for future development with Java 11
+
+Presently the Java 11 build of Jalview treats all libraries as libraries on the classpath, and does not use them as modules. The Java 11 JRE prepped for future release is a standard AdoptOpenJDK release (possibly repackaged for getdown/install4j to use).
+
+At time of writing, the JRE cannot be updated over the air on macOS platform due to a limitation of getdown's unpackaging system only using jars and hence cannot work with symbolic links. There is a symbolic link that is essential (as a symbolic link) in the macOS distribution (Contents/MacOS/libjli.dylib -> ../Home/lib/jli/libjli.dylib). Without this, the install4j launcher will not work. Some work has started on incorporating tar capabilities in getdown using the apache-commons-compress library, though this is not complete.
+
+Future releases might incorporate Java 11 modules into a bespoke Java 11 JRE that can be updated over the air via getdown.This could reduce the size of the distribution but will absolutely need the bespoke JRE. This would mean Jalview being restricted to platforms that we (can) support, or distributing the modules as libraries in a second distribution (the shadowJar distribution).
+
+build.gradle is written to support compilation of either Java 1.8 or Java 11 compatible bytecode. Please note that the compilation (and therefore build) process REQUIRES a Java 11 (or above) JDK. This is because there is Java 11 specific code in some Jalview classes (devolved into separate classes which fail "gracefully" when read by a Java 1.8 JRE).
+Java 11 is therefore the default build target, but can be changed simply by specifying the property JAVA_VERSION=1.8 (e.g.
+
+gradle compileJava -PJAVA_VERSION=1.8
+
+). Some different versions of supporting libraries are used between Java 1.8 and 11 builds, and can be found in j8lib and j11lib folders respectively. Note that there are a number of extra libraries used in the Java 11 distribution which are present in the Java 1.8 JRE but not distributed with the Java 11 JRE.
+
+Also see doc/building.md or doc/building.html
+
+
+
+
+Old notes:
+
Java 11 module replacements
As Java 11 no longer ships with Java EE libraries, which were standard in Java 8, and available (modularised, through the --add-modules CLI mechanism) in Java 9 and 10, third party replacement libraries for these libraries/modules have to be found.
To create a Java 11 JRE in j11jre/openjdk11_platform (or whatever you wish to call it).
You can point JAVA_HOME at the JDK11 of a different platform, so long as the jlink in your path is to the jlink for the platform you're running on.
-
Licensing information for each library is given below:
-JGoogleAnalytics_0.3.jar APL 2.0 License - http://code.google.com/p/jgoogleanalytics/
-Jmol-14.6.4_2016.10.26.jar GPL/LGPLv2 http://sourceforge.net/projects/jmol/files/
-VARNAv3-93.jar GPL licenced software by K�vin Darty, Alain Denise and Yann Ponty. http://varna.lri.fr
+j8lib:
+
activation.jar
apache-mime4j-0.6.jar
axis.jar
-castor-1.1-cycle-xml.jar
+biojava-core-4.1.0.jar LGPLv2.1 - latest license at https://github.com/biojava/biojava/blob/master/LICENSE
+biojava-ontology-4.1.0.jar LGPLv2.1 - latest license at https://github.com/biojava/biojava/blob/master/LICENSE
commons-codec-1.3.jar
-commons-discovery.jar
+commons-compress-1.18.jar
commons-logging-1.1.1.jar
-commons-logging.jar
-commons-net-3.3.jar
-groovy-all-2.4.6-indy.jar APL 2.0 License - downloaded and extracted from https://dl.bintray.com/groovy/maven/apache-groovy-binary-2.4.6.zip
+getdown-core.jar Getdown license - https://github.com/threerings/getdown/blob/master/LICENSE
+groovy-all-2.4.12-indy.jar APL 2.0 License - downloaded and extracted from https://dl.bintray.com/groovy/maven/apache-groovy-binary-2.4.6.zip
+htsjdk-2.12.0.jar built from maven master at https://github.com/samtools/htsjdk MIT License to Broad Institute
httpclient-4.0.3.jar
httpcore-4.0.1.jar
httpmime-4.0.3.jar
+intervalstore-v1.0.jar
+jabaws-min-client-2.2.0.jar
+java-json.jar
jaxrpc.jar
+jersey-client-1.19.4.jar CDDL 1.1 + GPL2 w/ CPE - http://glassfish.java.net/public/CDDL+GPL_1_1.html
+jersey-core-1.19.4.jar CDDL 1.1 + GPL2 w/ CPE - http://glassfish.java.net/public/CDDL+GPL_1_1.html
+jersey-json-1.19.4.jar CDDL 1.1 + GPL2 w/ CPE - http://glassfish.java.net/public/CDDL+GPL_1_1.html
+jetty-http-9.2.10.v20150310.jar
+jetty-io-9.2.10.v20150310.jar
+jetty-server-9.2.10.v20150310.jar
+jetty-util-9.2.10.v20150310.jar
+jfreesvg-2.1.jar GPL v3 licensed library from the JFree suite - http://www.jfree.org/jfreesvg/
+JGoogleAnalytics_0.3.jar APL 2.0 License - http://code.google.com/p/jgoogleanalytics/
jhall.jar
-jswingreader-0.3.jar : Apache license - built from http://jswingreader.sourceforge.net/ svn/trunk v12
+Jmol-14.6.4_2016.10.26.jar GPL/LGPLv2 http://sourceforge.net/projects/jmol/files/
+json_simple-1.1.jar Apache 2.0 license - downloaded from https://code.google.com/p/json-simple/downloads/list (will move to 1.1.1 version when jalview is mavenised and osgi-ised)
+jsoup-1.8.1.jar
+jsr311-api-1.1.1.jar
+jswingreader-0.3.jar Apache license - built from http://jswingreader.sourceforge.net/ svn/trunk v12
+libquaqua64-8.0.jnilib.jar quaqua: v.8.0 (latest stable) by Randel S Hofer. LGPL and BSD Modified license: downloaded from http://www.randelshofer.ch/quaqua/
+libquaqua-8.0.jnilib.jar quaqua: v.8.0 (latest stable) by Randel S Hofer. LGPL and BSD Modified license: downloaded from http://www.randelshofer.ch/quaqua/
log4j-1.2.8.jar
mail.jar
-miglayout-4.0-swing.jar BSD http://www.migcalendar.com/miglayout/versions/4.0/license.txt
-min-jaba-client.jar
+miglayout-4.0-swing.jar BSD - http://www.migcalendar.com/miglayout/versions/4.0/license.txt
+quaqua-filechooser-only-8.0.jar quaqua: v.8.0 (latest stable) by Randel S Hofer. LGPL and BSD Modified license: downloaded from http://www.randelshofer.ch/quaqua/
regex.jar
saaj.jar
+servlet-api-3.1.jar
+slf4j-api-1.7.7.jar
+slf4j-log4j12-1.7.7.jar
vamsas-client.jar
+VAqua5-patch.jar This is a patched version of VAqua v5 (latest stable) by Alan Snyder et al. GPLv3 with Classpath exception, also includes contributions from Quaqua: http://violetlib.org/vaqua/overview.html - see doc/patching-vaqua.txt for patch details, and http://issues.jalview.org/browse/JAL-2988 for details of the bug that the patch addresses.
+VARNAv3-93.jar GPL licenced software by K�vin Darty, Alain Denise and Yann Ponty - http://varna.lri.fr
wsdl4j.jar
xercesImpl.jar
xml-apis.jar
-json_simple-1.1.jar : Apache 2.0 license : downloaded from https://code.google.com/p/json-simple/downloads/list (will move to 1.1.1 version when jalview is mavenised and osgi-ised)
-jfreesvg-2.1.jar : GPL v3 licensed library from the JFree suite: http://www.jfree.org/jfreesvg/
-
-quaqua: v.8.0 (latest stable) by Randel S Hofer. LGPL and BSD Modified license: downloaded from http://www.randelshofer.ch/quaqua/
-
-vaqua5-patch: This is a patched version of VAqua v5 (latest stable) by Alan Snyder et al. GPLv3 with Classpath exception, also includes contributions from Quaqua: http://violetlib.org/vaqua/overview.html - see doc/patching-vaqua.txt for patch details, and http://issues.jalview.org/browse/JAL-2988 for details of the bug that the patch addresses.
-
-lib/htsjdk-2.12.jar: built from maven master at https://github.com/samtools/htsjdk MIT License to Broad Institute
-
-lib/biojava-core-4.1.0.jar LGPLv2.1 - latest license at https://github.com/biojava/biojava/blob/master/LICENSE
-
-lib/biojava-ontology-4.1.0.jar LGPLv2.1 - latest license at https://github.com/biojava/biojava/blob/master/LICENSE
Libraries for Test Suite
-utils/classgraph-4.1.6.jar: BSD License - allows recovery of classpath for programmatic construction of a Java command line to launch Jalview
- version 4.1.6 downloaded from https://mvnrepository.com/artifact/io.github.classgraph/classgraph/4.1.6
+utils/axis-ant.jar
+utils/ant-contrib-1.0b3.jar
+utils/hamcrest-core-1.3.jar
+utils/roxes-ant-tasks-1.2-2004-01-30.jar
+utils/proguard_5.3.3.jar
+utils/jhindexer.jar
+utils/junit-4.12.jar
+utils/jhall.jar
+utils/classgraph-4.1.6.jar BSD License - allows recovery of classpath for programmatic construction of a Java command line to launch Jalview version 4.1.6 downloaded from https://mvnrepository.com/artifact/io.github.classgraph/classgraph/4.1.6
+utils/testnglibs/guava-base-r03.jar
+utils/testnglibs/guava-collections-r03.jar
+utils/testnglibs/bsh-2.0b4.jar
+utils/testnglibs/snakeyaml.jar
+utils/testnglibs/testng-sources.jar
+utils/testnglibs/testng.jar
+utils/testnglibs/junit-4.12.jar
+utils/testnglibs/jcommander.jar
+utils/wsdl4j.jar
Additional dependencies
examples/javascript/jshashtable-2.1.js : Apache License
examples/javascript/facebox-1.3.js : MTI License - http://www.opensource.org/licenses/mit-license.php
+
+New in j11lib:
+
+FastInfoset.jar CDDL Version 1.1 - https://javaee.github.io/metro-fi/LICENSE
+getdown-core.jar Getdown license - https://github.com/threerings/getdown/blob/master/LICENSE
+groovy-*2.5.7.jar Apache License, Version 2.0 - http://www.apache.org/licenses/LICENSE-2.0.html
+istack-commons-runtime.jar CDDL Version 1.1 - https://glassfish.java.net/public/CDDL+GPL_1_1.html
+javax.activation-api-1.2.0.jar CDDL/GPLv2+CE - https://github.com/javaee/activation/blob/master/LICENSE.txt
+javax.annotation-api-1.3.2.jar CDDL + GPLv2 with classpath exception - https://github.com/javaee/javax.annotation/blob/master/LICENSE
+javax.jws-api-1.1.jar CDDL + GPLv2 with classpath exception - https://glassfish.dev.java.net/nonav/public/CDDL+GPL.html
+javax.servlet-api-4.0.1.jar CDDL + GPLv2 with classpath exception - https://oss.oracle.com/licenses/CDDL+GPL-1.1
+javax.xml.rpc-api-1.1.2.jar CDDL + GPLv2 with classpath exception - https://oss.oracle.com/licenses/CDDL+GPL-1.1
+javax.xml.soap-api.jar CDDL + GPLv2 with classpath exception - https://github.com/javaee/javax.xml.soap/blob/master/LICENSE
+jaxb-api-2.3.1.jar CDDL 1.1 + GPL2 w/ CPE - https://oss.oracle.com/licenses/CDDL+GPL-1.1
+jaxb-runtime-2.3.2.jar Eclipse Distribution License - v 1.0 - http://www.eclipse.org/org/documents/edl-v10.php
+jaxws-api-2.3.1.jar CDDL + GPLv2 with classpath exception - https://github.com/javaee/jax-ws-spec/blob/master/LICENSE.md
+Jmol-14.6.4_2016.10.26-no_netscape.jar GPL/LGPLv2 http://sourceforge.net/projects/jmol/files/
+jsr311-api-1.1.1.jar CDDL License - http://www.opensource.org/licenses/cddl1.php
+mimepull-1.9.11.jar Eclipse Distribution License - v 1.0 - http://www.eclipse.org/org/documents/edl-v10.php
+policy-2.7.6.jar Eclipse Distribution License - v 1.0 - http://www.eclipse.org/org/documents/edl-v10.php
+slf4j-api-1.7.26.jar MIT License - https://opensource.org/licenses/mit-license.php
+slf4j-log4j12-1.7.26.jar MIT License - https://opensource.org/licenses/mit-license.php
+stax-ex-1.8.1.jar Eclipse Distribution License - v 1.0 - http://www.eclipse.org/org/documents/edl-v10.php
+stax2-api-4.2.jar The BSD License - http://www.opensource.org/licenses/bsd-license.php
+streambuffer-1.5.7.jar Eclipse Distribution License - v 1.0 - http://www.eclipse.org/org/documents/edl-v10.php
+txw2-2.3.2.jar Eclipse Distribution License - v 1.0 - http://www.eclipse.org/org/documents/edl-v10.php
+wsdl4j-1.6.3.jar CPL - http://www.opensource.org/licenses/cpl1.0.txt
+
def compile_target_compatibility
ext {
- // where the getdown channel will be built.
- // TODO: consider allowing this expression to be overridden by -P arg
getdownWebsiteDir = jalviewDir + '/' + getdown_website_dir + '/' + JAVA_VERSION
+ getdownDir = ""
+ reportRsyncCmd = false
+ buildDist = true
+ buildProperties = buildPropertiesFile
+ getdownLauncher = jalviewDir + '/' + getdown_lib_dir + '/' + getdown_launcher
+ switch (CHANNEL) {
+
+ case "BUILD":
+ // TODO: get bamboo build artifact URL for getdown artifacts
+ getdown_app_dir = getdown_app_dir_alt
+ buildProperties = jalviewDir + "/" + classesDir +"/" + buildPropertiesFile
+ break
+
+ case "RELEASE":
+ getdown_channel_name = CHANNEL.toLowerCase()
+ getdownDir = getdown_channel_name + "/" + JAVA_VERSION
+ getdown_app_base = getdown_channel_base + "/" + getdownDir
+ getdown_app_dir = getdown_app_dir_release
+ buildProperties = jalviewDir + "/" + classesDir +"/" + buildPropertiesFile
+ reportRsyncCommand = true
+ break
+
+ case "ARCHIVE":
+ getdown_channel_name = CHANNEL.toLowerCase()+"/"+JALVIEW_VERSION
+ getdownDir = getdown_channel_name + "/" + JAVA_VERSION
+ getdown_app_base = getdown_channel_base + "/" + getdownDir
+ getdown_app_dir = getdown_app_dir_alt
+ if (!file(ARCHIVEDIR+"/"+packageDir).exists()) {
+ print "Must provide an ARCHIVEDIR value to produce an archive distribution"
+ exit
+ } else {
+ packageDir = ARCHIVEDIR + "/" + packageDir
+ buildProperties = ARCHIVEDIR +"/" + classesDir + "/" + buildPropertiesFile
+ buildDist = false
+ }
+ reportRsyncCommand = true
+ break
+
+ case "ARCHIVELOCAL":
+ getdown_channel_name = "archive" + "/" + JALVIEW_VERSION
+ getdownDir = getdown_channel_name + "/" + JAVA_VERSION
+ getdown_app_base = file(getdownWebsiteDir).toURI().toString()
+ getdown_app_dir = getdown_app_dir_alt
+ if (!file(ARCHIVEDIR+"/"+packageDir).exists()) {
+ print "Must provide an ARCHIVEDIR value to produce an archive distribution"
+ exit
+ } else {
+ packageDir = ARCHIVEDIR + "/" + packageDir
+ buildProperties = ARCHIVEDIR +"/" + classesDir + "/" + buildPropertiesFile
+ buildDist = false
+ }
+ reportRsyncCommand = true
+ getdownLauncher = jalviewDir + '/' + getdown_lib_dir + '/' + getdown_launcher_local
+ break
+
+ case "DEVELOP":
+ getdown_channel_name = CHANNEL.toLowerCase()
+ getdownDir = getdown_channel_name + "/" + JAVA_VERSION
+ getdown_app_base = getdown_channel_base + "/" + getdownDir
+ getdown_app_dir = getdown_app_dir_alt
+ buildProperties = jalviewDir + "/" + classesDir +"/" + buildPropertiesFile
+ reportRsyncCommand = true
+ break
+
+ case "TEST-RELEASE":
+ getdown_channel_name = CHANNEL.toLowerCase()
+ getdownDir = getdown_channel_name + "/" + JAVA_VERSION
+ getdown_app_base = getdown_channel_base + "/" + getdownDir
+ getdown_app_dir = getdown_app_dir_alt
+ buildProperties = jalviewDir + "/" + classesDir +"/" + buildPropertiesFile
+ reportRsyncCommand = true
+ break
+
+ case ~/^SCRATCH(|-[-\w]*)$/:
+ getdown_channel_name = CHANNEL
+ getdownDir = getdown_channel_name + "/" + JAVA_VERSION
+ getdown_app_base = getdown_channel_base + "/" + getdownDir
+ getdown_app_dir = getdown_app_dir_alt
+ buildProperties = jalviewDir + "/" + classesDir +"/" + buildPropertiesFile
+ reportRsyncCommand = true
+ break
+
+ case "LOCAL":
+ getdown_app_base = file(getdownWebsiteDir).toURI().toString()
+ getdown_app_dir = getdown_app_dir_alt
+ buildProperties = jalviewDir + "/" + classesDir +"/" + buildPropertiesFile
+ getdownLauncher = jalviewDir + '/' + getdown_lib_dir + '/' + getdown_launcher_local
+ break
+
+ default: // something wrong specified
+ print("CHANNEL must be one of BUILD, RELEASE, ARCHIVE, DEVELOP, TEST-RELEASE, SCRATCH-..., LOCAL [default]")
+ exit
+ break
+
+ }
+
+ println("Using a "+CHANNEL+" profile. appbase="+getdown_app_base)
getdownAppDir = getdownWebsiteDir + '/' + getdown_app_dir
- getdownJ11libDir = getdownWebsiteDir + '/' + getdown_j11lib_dir
+ //getdownJ11libDir = getdownWebsiteDir + '/' + getdown_j11lib_dir
getdownResourceDir = getdownWebsiteDir + '/' + getdown_resource_dir
- getdownLauncher = jalviewDir + '/' + getdown_launcher
+ getdownInstallDir = getdownWebsiteDir + '/' + getdown_install_dir
getdownFilesDir = jalviewDir + '/' + getdown_files_dir + '/' + JAVA_VERSION + '/'
- getdown_app_base = getdown_channel_base+"/"+getdown_channel_name+"/"+JAVA_VERSION+"/"
+ getdownFilesInstallDir = getdownFilesDir+"/"+getdown_install_dir
+ /* compile without modules -- using classpath libraries
modules_compileClasspath = fileTree(dir: "$jalviewDir/$j11modDir", include: ["*.jar"])
modules_runtimeClasspath = modules_compileClasspath
+ */
gitHash = ""
gitBranch = ""
}
def additional_compiler_args = []
// these are getdown.txt properties defined dependent on the JAVA_VERSION
def getdown_alt_java_min_version
+def getdown_alt_java_max_version
// this property is assigned below and expanded to multiple lines in the getdown task
def getdown_alt_multi_java_location
+// this property is for the Java library used in eclipse
+def eclipse_java_runtime_name
if (JAVA_VERSION.equals("1.8")) {
JAVA_INTEGER_VERSION = "8"
+ //libDir = j8libDir
libDir = j11libDir
libDistDir = j8libDir
compile_source_compatibility = 1.8
compile_target_compatibility = 1.8
getdown_alt_java_min_version = getdown_alt_java8_min_version
+ getdown_alt_java_max_version = getdown_alt_java8_max_version
getdown_alt_multi_java_location = getdown_alt_java8_txt_multi_java_location
+ eclipse_java_runtime_name = "JavaSE-1.8"
} else if (JAVA_VERSION.equals("11")) {
JAVA_INTEGER_VERSION = "11"
libDir = j11libDir
compile_source_compatibility = 11
compile_target_compatibility = 11
getdown_alt_java_min_version = getdown_alt_java11_min_version
+ getdown_alt_java_max_version = getdown_alt_java11_max_version
+ getdown_alt_multi_java_location = getdown_alt_java11_txt_multi_java_location
+ eclipse_java_runtime_name = "JavaSE-11"
+ /* compile without modules -- using classpath libraries
+ additional_compiler_args += [
+ '--module-path', ext.modules_compileClasspath.asPath,
+ '--add-modules', j11modules
+ ]
+ */
+} else if (JAVA_VERSION.equals("12") || JAVA_VERSION.equals("13")) {
+ JAVA_INTEGER_VERSION = JAVA_VERSION
+ libDir = j11libDir
+ libDistDir = j11libDir
+ compile_source_compatibility = JAVA_VERSION
+ compile_target_compatibility = JAVA_VERSION
+ getdown_alt_java_min_version = getdown_alt_java11_min_version
+ getdown_alt_java_max_version = getdown_alt_java11_max_version
getdown_alt_multi_java_location = getdown_alt_java11_txt_multi_java_location
+ eclipse_java_runtime_name = "JavaSE-11"
+ /* compile without modules -- using classpath libraries
additional_compiler_args += [
- '--module-path', ext.modules_compileClasspath.asPath,
- '--add-modules', j11modules
+ '--module-path', ext.modules_compileClasspath.asPath,
+ '--add-modules', j11modules
]
+ */
} else {
throw new GradleException("JAVA_VERSION=$JAVA_VERSION not currently supported by Jalview")
}
resources {
srcDirs "$jalviewDir/$resourceDir"
- srcDirs "$jalviewDir/$libDistDir"
}
jar.destinationDir = file("$jalviewDir/$packageDir")
} else {
compileClasspath += files(sourceSets.main.java.outputDir)
}
- //compileClasspath += sourceSets.main.compileClasspath
- //compileClasspath += files( sourceSets.main.resources.srcDirs)
+
compileClasspath += fileTree(dir: "$jalviewDir/$utilsDir", include: ["**/*.jar"])
compileClasspath += fileTree(dir: "$jalviewDir/$libDir", include: ["*.jar"])
name = "Jalview with gradle build"
natures 'org.eclipse.jdt.core.javanature',
- 'org.eclipse.jdt.groovy.core.groovyNature',
- 'org.eclipse.buildship.core.gradleprojectnature'
+ 'org.eclipse.jdt.groovy.core.groovyNature',
+ 'org.eclipse.buildship.core.gradleprojectnature'
buildCommand 'org.eclipse.jdt.core.javabuilder'
buildCommand 'org.eclipse.buildship.core.gradleprojectbuilder'
//defaultOutputDir = sourceSets.main.java.outputDir
def removeThese = []
configurations.each{ if (it.isCanBeResolved()) {
- removeThese += it
- }
+ removeThese += it
}
+ }
- minusConfigurations += removeThese
- plusConfigurations = [ ]
- file {
-
- whenMerged { cp ->
- def removeTheseToo = []
- HashMap<String, Boolean> addedSrcPath = new HashMap<>();
- cp.entries.each { entry ->
- if (entry.kind == 'src') {
- if (addedSrcPath.getAt(entry.path) || !(entry.path == "src" || entry.path == "test")) {
- removeTheseToo += entry
- } else {
- addedSrcPath.putAt(entry.path, true)
- }
- }
- }
- cp.entries.removeAll(removeTheseToo)
-
- cp.entries += new Output("bin/main")
- cp.entries += new Library(fileReference(helpParentDir))
- cp.entries += new Library(fileReference(resourceDir))
-
- HashMap<String, Boolean> addedLibPath = new HashMap<>();
- def allPaths = sourceSets.test.compileClasspath + sourceSets.main.compileClasspath
- sourceSets.main.compileClasspath.each{
- //if ((it.isDirectory() || ! it.exists()) && ! (it.equals(sourceSets.main.java.outputDir))) {
- //no longer want to add outputDir as eclipse is using its own output dir in bin/main
- if (it.isDirectory() || ! it.exists()) {
- // don't add dirs to classpath
- return
- }
- def itPath = it.toString()
- if (itPath.startsWith(jalviewDirAbsolutePath+"/")) {
- itPath = itPath.substring(jalviewDirAbsolutePath.length()+1)
- }
- if (addedLibPath.get(itPath)) {
- //println("Not adding duplicate entry "+itPath)
+ minusConfigurations += removeThese
+ plusConfigurations = [ ]
+ file {
+
+ whenMerged { cp ->
+ def removeTheseToo = []
+ HashMap<String, Boolean> addedSrcPath = new HashMap<>();
+ cp.entries.each { entry ->
+ if (entry.kind == 'src') {
+ if (addedSrcPath.getAt(entry.path) || !(entry.path == "src" || entry.path == "test")) {
+ removeTheseToo += entry
} else {
- //println("Adding entry "+itPath)
- cp.entries += new Library(fileReference(itPath))
- addedLibPath.put(itPath, true)
+ addedSrcPath.putAt(entry.path, true)
}
}
+ }
+ cp.entries.removeAll(removeTheseToo)
- sourceSets.test.compileClasspath.each{
- //if ((it.isDirectory() || ! it.exists()) && ! (it.equals(sourceSets.main.java.outputDir))) {
- //no longer want to add outputDir as eclipse is using its own output dir in bin/main
- if (it.isDirectory() || ! it.exists()) {
- // don't add dirs to classpath
- return false // groovy "break" in .each loop
- }
- def itPath = it.toString()
- if (itPath.startsWith(jalviewDirAbsolutePath+"/")) {
- itPath = itPath.substring(jalviewDirAbsolutePath.length()+1)
- }
- if (addedLibPath.get(itPath)) {
- // don't duplicate
- } else {
- def lib = new Library(fileReference(itPath))
- // this doesn't work... yet. Adding test=true attribute using withXml below
- //def attrs = new Node(null, 'attributes', ["test":"true"])
- //lib.appendNode(attrs) //
- cp.entries += lib
- addedLibPath.put(itPath, true)
- }
+ print ("CP="+cp.inspect())
+
+ cp.entries += new Output("bin/main")
+ cp.entries += new Library(fileReference(helpParentDir))
+ cp.entries += new Library(fileReference(resourceDir))
+
+ HashMap<String, Boolean> addedLibPath = new HashMap<>();
+
+ // changing from sourcesets.main.classpath to specific Java version lib
+ //sourceSets.main.compileClasspath.each{
+ fileTree("$jalviewDir/$libDistDir").include("**/*.jar").include("*.jar").each {
+ //don't want to add outputDir as eclipse is using its own output dir in bin/main
+ if (it.isDirectory() || ! it.exists()) {
+ // don't add dirs to classpath
+ return
+ }
+ def itPath = it.toString()
+ if (itPath.startsWith(jalviewDirAbsolutePath+"/")) {
+ itPath = itPath.substring(jalviewDirAbsolutePath.length()+1)
+ }
+ if (addedLibPath.get(itPath)) {
+ //println("Not adding duplicate entry "+itPath)
+ } else {
+ //println("Adding entry "+itPath)
+ cp.entries += new Library(fileReference(itPath))
+ addedLibPath.put(itPath, true)
}
- }
+ }
+
+ // changing from sourcesets.main.classpath to specific Java version lib
+ //sourceSets.test.compileClasspath.each{
+ fileTree(dir: "$jalviewDir/$utilsDir", include: ["**/*.jar"]).each {
+ //if ((it.isDirectory() || ! it.exists()) && ! (it.equals(sourceSets.main.java.outputDir))) {
+ //no longer want to add outputDir as eclipse is using its own output dir in bin/main
+ if (it.isDirectory() || ! it.exists()) {
+ // don't add dirs to classpath
+ return false // groovy "break" in .each loop
+ }
+ def itPath = it.toString()
+ if (itPath.startsWith(jalviewDirAbsolutePath+"/")) {
+ itPath = itPath.substring(jalviewDirAbsolutePath.length()+1)
+ }
+ if (addedLibPath.get(itPath)) {
+ // don't duplicate
+ } else {
+ def lib = new Library(fileReference(itPath))
+ // this doesn't work... yet. Adding test=true attribute using withXml below
+ //def attrs = new Node(null, 'attributes', ["test":"true"])
+ //lib.appendNode(attrs) //
+ cp.entries += lib
+ addedLibPath.put(itPath, true)
+ }
+ }
+ }
// withXml changes ignored by buildship, these add the "test=true" attribute
withXml {
def node = it.asNode()
-
+
def srcTestAttributes
node.children().each{ cpe ->
def attributes = cpe.attributes()
def attributes = cpe.attributes()
if (attributes.get("kind") == "lib" && attributes.get("path").startsWith("utils/")) {
cpe.appendNode('attributes')
- .appendNode('attribute', [name:"test", value:"true"])
+ .appendNode('attribute', [name:"test", value:"true"])
}
}
} // withXML
jdt {
// for the IDE, use java 11 compatibility
- sourceCompatibility = 11
- targetCompatibility = 11
- javaRuntimeName = "JavaSE-11"
+ sourceCompatibility = compile_source_compatibility
+ targetCompatibility = compile_target_compatibility
+ javaRuntimeName = eclipse_java_runtime_name
file {
withProperties { props ->
}
}
}
-
+
//synchronizationTasks eclipseClasspath
//autoBuildTasks eclipseClasspath
-}
+}
task cloverInstr() {
// only instrument source, we build test classes as normal
doFirst {
delete cloverInstrDir
def argsList = ["--initstring", "${buildDir}/clover/clover.db",
- "-d", "${buildDir}/${cloverSourcesInstrDir}"]
+ "-d", "${buildDir}/${cloverSourcesInstrDir}"]
argsList.addAll(inputs.files.files.collect({ file ->
file.absolutePath
}))
com.atlassian.clover.CloverInstr.mainImpl(args)
}
}
-
+
task cloverReport {
group = "Verification"
- description = "Createst the Clover report"
- inputs.dir "${buildDir}/clover"
- outputs.dir "${reportsDir}/clover"
- onlyIf {
- file("${buildDir}/clover/clover.db").exists()
- }
+ description = "Createst the Clover report"
+ inputs.dir "${buildDir}/clover"
+ outputs.dir "${reportsDir}/clover"
+ onlyIf {
+ file("${buildDir}/clover/clover.db").exists()
+ }
doFirst {
def argsList = ["--initstring", "${buildDir}/clover/clover.db",
- "-o", "${reportsDir}/clover"]
+ "-o", "${reportsDir}/clover"]
String[] args = argsList.toArray()
com.atlassian.clover.reporters.html.HtmlReporter.runReport(args)
// and generate ${reportsDir}/clover/clover.xml
args = ["--initstring", "${buildDir}/clover/clover.db",
- "-o", "${reportsDir}/clover/clover.xml"].toArray()
+ "-o", "${reportsDir}/clover/clover.xml"].toArray()
com.atlassian.clover.reporters.xml.XMLReporter.runReport(args)
}
}
delete cloverInstrDir
}
+// format is a string like date.format("dd MMMM yyyy")
def getDate(format) {
def date = new Date()
- //return date.format("dd MMMM yyyy")
return date.format(format)
}
-task setGitHash(type: Exec) {
- workingDir = jalviewDir
- commandLine "git", "rev-parse", "--short", "HEAD"
- standardOutput = new ByteArrayOutputStream()
- project.ext.gitHash = {
- return standardOutput.toString().trim()
+task setGitVals {
+ def hashStdOut = new ByteArrayOutputStream()
+ exec {
+ commandLine "git", "rev-parse", "--short", "HEAD"
+ standardOutput = hashStdOut
+ ignoreExitValue true
}
-}
-task setGitBranch(type: Exec) {
- workingDir = jalviewDir
- commandLine "git", "rev-parse", "--abbrev-ref", "HEAD"
- standardOutput = new ByteArrayOutputStream()
- project.ext.gitBranch = {
- return standardOutput.toString().trim()
+ def branchStdOut = new ByteArrayOutputStream()
+ exec {
+ commandLine "git", "rev-parse", "--abbrev-ref", "HEAD"
+ standardOutput = branchStdOut
+ ignoreExitValue true
}
-}
-task setGitVals {
- dependsOn setGitHash
- dependsOn setGitBranch
+ project.ext.gitHash = hashStdOut.toString().trim()
+ project.ext.gitBranch = branchStdOut.toString().trim()
+
+ outputs.upToDateWhen { false }
}
task createBuildProperties(type: WriteProperties) {
dependsOn setGitVals
inputs.dir("$jalviewDir/$sourceDir")
+ inputs.dir("$classes")
inputs.dir("$jalviewDir/$resourceDir")
- outputFile "$classes/$buildPropertiesFile"
+ outputFile (buildProperties)
// taking time specific comment out to allow better incremental builds
- //comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd HH:mm:ss")
- comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd")
- property "BUILD_DATE", getDate("dd MMMM yyyy")
+ comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd HH:mm:ss")
+ //comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd")
+ property "BUILD_DATE", getDate("HH:mm:ss dd MMMM yyyy")
property "VERSION", JALVIEW_VERSION
property "INSTALLATION", INSTALLATION+" git-commit:"+project.ext.gitHash+" ["+project.ext.gitBranch+"]"
outputs.file(outputFile)
- outputs.dir("$classes")
}
def buildingHTML = "$jalviewDir/$docDir/building.html"
def buildingMD = "$jalviewDir/$docDir/building.md"
def css = "$jalviewDir/$docDir/github.css"
- def pandoc = pandoc_exec
+ def pandoc = null
+ pandoc_exec.split(",").each {
+ if (file(it.trim()).exists()) {
+ pandoc = it.trim()
+ return true
+ }
+ }
+
def hostname = "hostname".execute().text.trim()
- if (! file(pandoc).exists() && hostname.equals("jv-bamboo")) {
+ if ((pandoc == null || ! file(pandoc).exists()) && hostname.equals("jv-bamboo")) {
pandoc = System.getProperty("user.home")+"/buildtools/pandoc/bin/pandoc"
}
- if (file(pandoc).exists()) {
- commandLine pandoc, '-s', '-o', buildingHTML, '--metadata', 'pagetitle="Building Jalview from Source"', '--toc', '-H', css, buildingMD
- } else {
- commandLine "true"
+ doFirst {
+ if (pandoc != null && file(pandoc).exists()) {
+ commandLine pandoc, '-s', '-o', buildingHTML, '--metadata', 'pagetitle="Building Jalview from Source"', '--toc', '-H', css, buildingMD
+ } else {
+ println("Cannot find pandoc. Skipping convert building.md to HTML")
+ throw new StopExecutionException()
+ }
}
ignoreExitValue true
def outputDir = "$classes/$helpDir"
from(inputDir) {
exclude '**/*.gif'
- exclude '**/*.jpg'
- exclude '**/*.png'
- filter(ReplaceTokens, beginToken: '$$', endToken: '$$', tokens: ['Version-Rel': JALVIEW_VERSION])
+ exclude '**/*.jpg'
+ exclude '**/*.png'
+ filter(ReplaceTokens, beginToken: '$$', endToken: '$$', tokens: ['Version-Rel': JALVIEW_VERSION])
}
from(inputDir) {
include '**/*.gif'
- include '**/*.jpg'
- include '**/*.png'
+ include '**/*.jpg'
+ include '**/*.png'
}
into outputDir
dependsOn cloverInstr
}
- print("Running tests " + (use_clover?"WITH":"WITHOUT") + " clover [clover="+use_clover+"]\n")
+ if (use_clover) {
+ print("Running tests " + (use_clover?"WITH":"WITHOUT") + " clover [clover="+use_clover+"]\n")
+ }
useTestNG() {
includeGroups testngGroups
outputs.file("$jalviewDir/$utilsDir/BufferedLineReader.class")
}
-def helplinkscheckeroutputfile = file("$jalviewDir/$utilsDir/HelpLinksChecker.out")
+def helplinkscheckertouchfile = file("$jalviewDir/$utilsDir/HelpLinksChecker.touch")
task linkCheck(type: JavaExec) {
dependsOn prepare, compileLinkCheck
classpath = files("$jalviewDir/$utilsDir")
def help = "$classes/$helpDir"
args = [ "$classes/$helpDir", "-nointernet" ]
- doFirst {
- helplinkscheckeroutputfile.createNewFile()
- standardOutput new FileOutputStream(helplinkscheckeroutputfile, false)
+ doLast {
+ helplinkscheckertouchfile.createNewFile()
}
- outputs.file(helplinkscheckeroutputfile)
+ inputs.dir("$classes/$helpDir")
+ outputs.file(helplinkscheckertouchfile)
}
+// import the pubhtmlhelp target
+ant.properties.basedir = "$jalviewDir"
+ant.properties.helpBuildDir = jalviewDirAbsolutePath+"/$classes/$helpDir"
+ant.importBuild "$utilsDir/publishHelp.xml"
+
+
task cleanPackageDir(type: Delete) {
delete fileTree("$jalviewDir/$packageDir").include("*.jar")
}
shadowJar {
group = "distribution"
- dependsOn makeDist
+ if (buildDist) {
+ dependsOn makeDist
+ }
from ("$jalviewDir/$libDistDir") {
include("*.jar")
}
+ manifest {
+ attributes 'Implementation-Version': JALVIEW_VERSION
+ }
mainClassName = shadowJarMainClass
mergeServiceFiles()
- classifier = "all-"+JAVA_VERSION
+ classifier = "all-"+JALVIEW_VERSION+"-j"+JAVA_VERSION
minimize()
}
task getdownWebsite() {
group = "distribution"
description = "Create the getdown minimal app folder, and website folder for this version of jalview. Website folder also used for offline app installer"
- dependsOn makeDist
+ if (buildDist) {
+ dependsOn makeDist
+ }
+
+ // clean the getdown website and files dir before creating getdown folders
+ delete project.ext.getdownWebsiteDir
+ delete project.ext.getdownFilesDir
+
def getdownWebsiteResourceFilenames = []
def getdownTextString = ""
def getdownResourceDir = project.ext.getdownResourceDir
def getdownAppDir = project.ext.getdownAppDir
def getdownResourceFilenames = []
+
doFirst {
+ copy {
+ from buildProperties
+ rename(buildPropertiesFile, getdown_build_properties)
+ into project.ext.getdownAppDir
+ }
+ getdownWebsiteResourceFilenames += getdown_app_dir+"/"+getdown_build_properties
+
// go through properties looking for getdown_txt_...
def props = project.properties.sort { it.key }
- props.put("getdown_txt_java_min_version", getdown_alt_java_min_version)
- props.put("getdown_txt_multi_java_location", getdown_alt_multi_java_location)
+ if (getdown_alt_java_min_version.length() > 0) {
+ props.put("getdown_txt_java_min_version", getdown_alt_java_min_version)
+ }
+ if (getdown_alt_java_max_version.length() > 0) {
+ props.put("getdown_txt_java_max_version", getdown_alt_java_max_version)
+ }
+ props.put("getdown_txt_multi_java_location", getdown_alt_multi_java_location)
- if (getdown_local == "true") {
- getdown_app_base = file(getdownWebsiteDir).toURI().toString()
- }
props.put("getdown_txt_appbase", getdown_app_base)
props.each{ prop, val ->
if (prop.startsWith("getdown_txt_") && val != null) {
}
} else {
// file values rationalised
- if (val.indexOf('/') > -1) {
+ if (val.indexOf('/') > -1 || prop.startsWith("getdown_txt_resource")) {
def r = null
if (val.indexOf('/') == 0) {
// absolute path
getdownResourceFilenames += r.getPath()
}
}
- def line = prop.substring(12) + " = " + val + "\n"
- getdownTextString += line
+ if (! prop.startsWith("getdown_txt_resource")) {
+ def line = prop.substring(12) + " = " + val + "\n"
+ getdownTextString += line
+ }
}
}
}
}
def codeFiles = []
- makeDist.outputs.files.each{ f ->
+ fileTree(file(packageDir)).each{ f ->
if (f.isDirectory()) {
def files = fileTree(dir: f, include: ["*"]).getFiles()
codeFiles += files
// NOT USING MODULES YET, EVERYTHING SHOULD BE IN dist
/*
- if (JAVA_VERSION.equals("11")) {
- def j11libFiles = fileTree(dir: "$jalviewDir/$j11libDir", include: ["*.jar"]).getFiles()
- j11libFiles.sort().each{f ->
- def line = "code = " + getdown_j11lib_dir + '/' + f.getName() + "\n"
- getdownTextString += line
- copy {
- from f.getPath()
- into project.ext.getdownJ11libDir
- }
- }
- }
+ if (JAVA_VERSION.equals("11")) {
+ def j11libFiles = fileTree(dir: "$jalviewDir/$j11libDir", include: ["*.jar"]).getFiles()
+ j11libFiles.sort().each{f ->
+ def line = "code = " + getdown_j11lib_dir + '/' + f.getName() + "\n"
+ getdownTextString += line
+ copy {
+ from f.getPath()
+ into project.ext.getdownJ11libDir
+ }
+ }
+ }
*/
// getdown-launcher.jar should not be in main application class path so the main application can move it when updated. Listed as a resource so it gets updated.
//getdownTextString += "class = " + file(getdownLauncher).getName() + "\n"
- getdownTextString += "resource = " + file(getdownLauncher).getName() + "\n"
+ getdownTextString += "resource = " + getdown_launcher_new + "\n"
getdownTextString += "class = " + mainClass + "\n"
def getdown_txt = file(project.ext.getdownWebsiteDir + "/getdown.txt")
getdown_txt.write(getdownTextString)
+ def launch_jvl = file(project.ext.getdownWebsiteDir + "/" + getdown_launch_jvl)
+ launch_jvl.write("appbase="+props.get("getdown_txt_appbase"))
+
copy {
- from getdown_txt
- into project.ext.getdownFilesDir
+ from getdownLauncher
+ rename(file(getdownLauncher).getName(), getdown_launcher_new)
+ into project.ext.getdownWebsiteDir
}
copy {
from getdownLauncher
- into project.ext.getdownFilesDir
+ if (file(getdownLauncher).getName() != getdown_launcher) {
+ rename(file(getdownLauncher).getName(), getdown_launcher)
+ }
+ into project.ext.getdownWebsiteDir
+ }
+
+ if (! (CHANNEL.startsWith("ARCHIVE") || CHANNEL.startsWith("DEVELOP"))) {
+ copy {
+ from getdown_txt
+ from getdownLauncher
+ from getdownWebsiteDir+"/"+getdown_build_properties
+ if (file(getdownLauncher).getName() != getdown_launcher) {
+ rename(file(getdownLauncher).getName(), getdown_launcher)
+ }
+ into getdownInstallDir
+ }
+
+ copy {
+ from getdownInstallDir
+ into getdownFilesInstallDir
+ }
}
copy {
+ from getdown_txt
+ from launch_jvl
from getdownLauncher
- into project.ext.getdownWebsiteDir
+ from getdownWebsiteDir+"/"+getdown_build_properties
+ if (file(getdownLauncher).getName() != getdown_launcher) {
+ rename(file(getdownLauncher).getName(), getdown_launcher)
+ }
+ into getdownFilesDir
}
copy {
- from jalviewDir + '/' + project.getProperty('getdown_txt_ui.background_image')
- from jalviewDir + '/' + project.getProperty('getdown_txt_ui.error_background')
- from jalviewDir + '/' + project.getProperty('getdown_txt_ui.progress_image')
- from jalviewDir + '/' + project.getProperty('getdown_txt_ui.icon')
- from jalviewDir + '/' + project.getProperty('getdown_txt_ui.mac_dock_icon')
+ from getdownResourceDir
into project.ext.getdownFilesDir + '/' + getdown_resource_dir
}
}
- inputs.dir(jalviewDir + '/' + packageDir)
+ if (buildDist) {
+ inputs.dir(jalviewDir + '/' + packageDir)
+ }
outputs.dir(project.ext.getdownWebsiteDir)
outputs.dir(project.ext.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)
group = "distribution"
description = "Create the minimal and full getdown app folder for installers and website and create digest file"
dependsOn getdownDigest
+ doLast {
+ if (reportRsyncCommand) {
+ def fromDir = getdownWebsiteDir + (getdownWebsiteDir.endsWith("/")?"":"/")
+ def toDir = getdown_rsync_dest + "/" + getdownDir + (getdownDir.endsWith("/")?"":"/")
+ println "LIKELY RSYNC COMMAND:"
+ println "mkdir -p '$toDir'\nrsync -avh --delete '$fromDir' '$toDir'"
+ if (RUNRSYNC == "true") {
+ exec {
+ commandLine "mkdir", "-p", toDir
+ }
+ exec {
+ commandLine "rsync", "-avh", "--delete", fromDir, toDir
+ }
+ }
+ }
+ }
}
clean {
rename (install4jTemplate, install4jConfFile)
filter(ReplaceTokens, beginToken: '', endToken: '', tokens: ['9999999999': JAVA_VERSION])
filter(ReplaceTokens, beginToken: '$$', endToken: '$$',
- tokens: [
- 'JAVA_VERSION': JAVA_VERSION,
- 'JAVA_INTEGER_VERSION': JAVA_INTEGER_VERSION,
- 'VERSION': JALVIEW_VERSION,
- 'MACOS_JAVA_VM_DIR': macosJavaVMDir,
- 'MACOS_JAVA_VM_TGZ': macosJavaVMTgz,
- 'WINDOWS_JAVA_VM_DIR': windowsJavaVMDir,
- 'WINDOWS_JAVA_VM_TGZ': windowsJavaVMTgz,
- 'INSTALL4JINFOPLISTFILEASSOCIATIONS': install4jInfoPlistFileAssociations,
- 'COPYRIGHT_MESSAGE': install4jCopyrightMessage,
- 'MACOS_BUNDLE_ID': install4jMacOSBundleId
- ]
+ tokens: [
+ 'JAVA_VERSION': JAVA_VERSION,
+ 'JAVA_INTEGER_VERSION': JAVA_INTEGER_VERSION,
+ 'VERSION': JALVIEW_VERSION,
+ 'MACOS_JAVA_VM_DIR': macosJavaVMDir,
+ 'MACOS_JAVA_VM_TGZ': macosJavaVMTgz,
+ 'WINDOWS_JAVA_VM_DIR': windowsJavaVMDir,
+ 'WINDOWS_JAVA_VM_TGZ': windowsJavaVMTgz,
+ 'INSTALL4JINFOPLISTFILEASSOCIATIONS': install4jInfoPlistFileAssociations,
+ 'COPYRIGHT_MESSAGE': install4jCopyrightMessage,
+ 'MACOS_BUNDLE_ID': install4jMacOSBundleId,
+ 'GETDOWN_RESOURCE_DIR': getdown_resource_dir,
+ 'GETDOWN_DIST_DIR': getdown_app_dir,
+ 'GETDOWN_ALT_DIR': getdown_app_dir_alt,
+ 'GETDOWN_INSTALL_DIR': getdown_install_dir
+ ]
)
if (OSX_KEYPASS=="") {
filter(ReplaceTokens, beginToken: 'codeSigning macEnabled="', endToken: '"', tokens: ['true':'codeSigning macEnabled="false"'])
// include uninstaller applescript app files in dmg
def installerDMGUninstallerXml = file("$install4jDir/$install4jDMGUninstallerAppFiles").text
ant.replaceregexp(
- byline: false,
- flags: "s",
- match: '<file name="UNINSTALL_OLD_JALVIEW_APP_REPLACED_IN_GRADLE" file=.*?>',
- replace: installerDMGUninstallerXml,
- file: install4jConf
+ byline: false,
+ flags: "s",
+ match: '<file name="UNINSTALL_OLD_JALVIEW_APP_REPLACED_IN_GRADLE" file=.*?>',
+ replace: installerDMGUninstallerXml,
+ file: install4jConf
)
- */
+ */
}
}
if (OSX_KEYPASS) {
macKeystorePassword=OSX_KEYPASS
-
+
}
-
+
inputs.dir(project.ext.getdownWebsiteDir)
inputs.file(install4jConf)
inputs.dir(macosJavaVMDir)
inputs.dir(windowsJavaVMDir)
outputs.dir("$jalviewDir/$install4jBuildDir/$JAVA_VERSION")
+
}
clean {
delete install4jConf
}
+
+task sourceDist (type: Tar) {
+
+ def VERSION_UNDERSCORES = JALVIEW_VERSION.replaceAll("\\.", "_")
+ def outputFileName = project.name + "_" + VERSION_UNDERSCORES + ".tar.gz"
+ // cater for buildship < 3.1 [3.0.1 is max version in eclipse 2018-09]
+ try {
+ archiveFileName = outputFileName
+ } catch (Exception e) {
+ archiveName = outputFileName
+ }
+
+ compression Compression.GZIP
+
+ from jalviewDir
+ into project.name
+
+
+ exclude (".*")
+ exclude ("**/.*")
+ exclude ("*.class")
+ exclude ("**/*.class")
+ include (eclipse_extra_jdt_prefs_file)
+ include ("AUTHORS")
+ include ("CITATION")
+ include ("FEATURETODO")
+ include ("JAVA-11-README")
+ include ("FEATURETODO")
+ include ("LICENSE")
+ include ("README")
+ include ("RELEASE")
+ include ("THIRDPARTYLIBS")
+ include ("build.gradle")
+ include ("gradle.properties")
+ include ("$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")
+
+ exclude ("appletlib")
+ exclude ("**/*locales")
+ exclude ("*locales/**")
+ exclude ("utils/InstallAnywhere")
+ exclude (libDir)
+ exclude (getdown_files_dir)
+ exclude (getdown_website_dir)
+
+ // exluding these as not using jars as modules yet
+ exclude ("$j11modDir/**/*.jar")
+
+}
+
+task helppages {
+ dependsOn copyHelp
+ dependsOn pubhtmlhelp
+
+ inputs.dir("$classes/$helpDir")
+ outputs.file("build/distribution/help/helpTOC.html")
+}
--- /dev/null
+## this command gets a list of jars in j11lib/ that are not present or different content in lib/. The output is below.
+#for y in j11lib/*.jar; do x=${y##*/}; if [ \! -e ./lib/$x ] || ! diff ./lib/$x $y; then echo $y; fi; done
+#
+j11lib/FastInfoset.jar
+j11lib/getdown-core.jar
+j11lib/groovy-2.5.7.jar
+j11lib/groovy-ant-2.5.7.jar
+j11lib/groovy-bsf-2.5.7.jar
+j11lib/groovy-cli-commons-2.5.7.jar
+j11lib/groovy-cli-picocli-2.5.7.jar
+j11lib/groovy-console-2.5.7.jar
+j11lib/groovy-datetime-2.5.7.jar
+j11lib/groovy-dateutil-2.5.7.jar
+j11lib/groovy-docgenerator-2.5.7.jar
+j11lib/groovy-groovydoc-2.5.7.jar
+j11lib/groovy-groovysh-2.5.7.jar
+j11lib/groovy-jaxb-2.5.7.jar
+j11lib/groovy-jmx-2.5.7.jar
+j11lib/groovy-json-2.5.7.jar
+j11lib/groovy-json-direct-2.5.7.jar
+j11lib/groovy-jsr223-2.5.7.jar
+j11lib/groovy-macro-2.5.7.jar
+j11lib/groovy-nio-2.5.7.jar
+j11lib/groovy-servlet-2.5.7.jar
+j11lib/groovy-sql-2.5.7.jar
+j11lib/groovy-swing-2.5.7.jar
+j11lib/groovy-templates-2.5.7.jar
+j11lib/groovy-test-2.5.7.jar
+j11lib/groovy-test-junit5-2.5.7.jar
+j11lib/groovy-testng-2.5.7.jar
+j11lib/groovy-xml-2.5.7.jar
+j11lib/istack-commons-runtime.jar
+j11lib/javax.activation-MODULE.jar
+j11lib/javax.annotation-api-MODULE.jar
+j11lib/javax.jws-api-1.1.jar
+j11lib/javax.servlet-api-MODULE.jar
+j11lib/javax.xml.rpc-api-1.1.2.jar
+j11lib/javax.xml.soap-api.jar
+j11lib/jaxb-api-java9.jar
+j11lib/jaxb-runtime.jar
+j11lib/jaxws-api.jar
+j11lib/jersey-client-1.19.1.jar
+j11lib/jersey-core-1.19.1.jar
+j11lib/jersey-json-1.19.1.jar
+j11lib/jsr311-api-1.1.1.jar
+j11lib/mimepull.jar
+j11lib/policy.jar
+j11lib/stax-ex.jar
+j11lib/stax2-api-MODULE.jar
+j11lib/streambuffer.jar
+j11lib/txw2.jar
+j11lib/wsdl4j-MODULE.jar
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
These normally take around 5 - 10 minutes to complete and outputs its full results into
the `tests/` folder. A summary of results should appear in your console.
+You can run different defined groups of tests with
+
+```bash
+gradle test -PtestngGroups=Network
+```
+
+Available groups are Functional (default), Network, External.
+
### Installer packaging with *install4j*
---
-[Jalview Development Team](mailto:help@jalview.org)
\ No newline at end of file
+[Jalview Development Team](mailto:help@jalview.org)
+++ /dev/null
-<?xml version="1.0" encoding="UTF-8"?>
-<projectDescription>
- <name>getdown</name>
- <comment></comment>
- <projects>
- </projects>
- <buildSpec>
- <buildCommand>
- <name>org.eclipse.m2e.core.maven2Builder</name>
- <arguments>
- </arguments>
- </buildCommand>
- </buildSpec>
- <natures>
- <nature>org.eclipse.m2e.core.maven2Nature</nature>
- </natures>
-</projectDescription>
+++ /dev/null
-eclipse.preferences.version=1
-encoding/<project>=UTF-8
+++ /dev/null
-activeProfiles=
-eclipse.preferences.version=1
-resolveWorkspaceProjects=true
-version=1
+++ /dev/null
-language: java
-sudo: false
-script: "mvn -B clean verify"
-
-cache:
- directories:
- - '$HOME/.m2/repository'
-
-jdk:
- - openjdk7
- - oraclejdk8
<parent>
<groupId>com.threerings.getdown</groupId>
<artifactId>getdown</artifactId>
- <version>1.8.3-SNAPSHOT</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-SNAPSHOT</version>
+ <version>1.8.3-1.1.8_FJVL</version>
</parent>
<artifactId>getdown-core</artifactId>
separated by commas (app1.foo.com,app2.bar.com,app3.baz.com). -->
<properties>
<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="build_time" value="${getdown.build.time}" />
<filter token="build_version" value="${project.version}" />
<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>
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import java.util.zip.GZIPInputStream;
-import com.sun.management.OperatingSystemMXBean;
-import java.lang.management.ManagementFactory;
import jalview.bin.MemorySetting;
{
/** The name of our configuration file. */
public static final String CONFIG_FILE = "getdown.txt";
+
+ /** Dir where a backup config file might reside */
+ public static final String BACKUP_CONFIG_DIR = "install";
/** The name of our target version file. */
public static final String VERSION_FILE = "version.txt";
*/
public enum Step
{
- UPDATE_JAVA(10),
- VERIFY_METADATA(15, 65, 95),
- DOWNLOAD(40),
+ //UPDATE_JAVA(10),
+ UPDATE_JAVA(20),
+ //VERIFY_METADATA(15, 65, 95),
+ VERIFY_METADATA(15, 45, 90),
+ DOWNLOAD(60),
PATCH(60),
- VERIFY_RESOURCES(70, 97),
- REDOWNLOAD_RESOURCES(90),
- UNPACK(98),
- LAUNCH(99);
+ //VERIFY_RESOURCES(70, 97),
+ VERIFY_RESOURCES(40, 90),
+ //REDOWNLOAD_RESOURCES(90),
+ REDOWNLOAD_RESOURCES(80),
+ //UNPACK(98),
+ UNPACK(95),
+ //LAUNCH(99);
+ LAUNCH(100);
/** What is the final percent value for this step? */
public final List<Integer> defaultPercents;
/** The paths (relative to the appdir) of images for the window icon. */
public final List<String> iconImages;
+ /** The path (relative to the appdir) to a single background image to appear first. */
+ public final String instantBackgroundImage;
+
/** The path (relative to the appdir) to a single background image. */
public final String backgroundImage;
/** Whether progress text should be hidden or not. */
public final boolean hideProgressText;
+ /** Whether the splash screen should update non-asynchronously before being shown. */
+ public final boolean progressSync;
+
+ /** Whether the splash screen should update non-asynchronously after being shown. */
+ public final boolean progressSyncAfterShown;
+
+ /** Whether the splash screen should retain focus. */
+ public final boolean keepOnTop;
+
+ /** Whether to display the appbase. */
+ public final boolean displayAppbase;
+
+ /** Whether to display the version. */
+ public final boolean displayVersion;
+
/** The minimum number of seconds to display the GUI. This is to prevent the GUI from
* flashing up on the screen and immediately disappearing, which can be confusing to the
* user. */
@Override
public String toString ()
{
- return "[name=" + name + ", bg=" + background + ", bg=" + backgroundImage +
+ return "[name=" + name + ", bg=" + background + ", bg=" + backgroundImage + ", instant_bg=" + instantBackgroundImage +
", pi=" + progressImage + ", prect=" + progress + ", pt=" + progressText +
", pb=" + progressBar + ", srect=" + status + ", st=" + statusText +
", shadow=" + textShadow + ", err=" + installError + ", nrect=" + patchNotes +
", notes=" + patchNotesUrl + ", stepPercentages=" + stepPercentages +
- ", hideProgressText" + hideProgressText + ", minShow=" + minShowSeconds + "]";
+ ", hideProgressText=" + hideProgressText + ", keepOnTop=" + keepOnTop + ", progressSync=" + progressSync +
+ ", progressSyncAfterShown=" + progressSyncAfterShown + ", minShow=" + minShowSeconds +
+ ", displayAppbase=" + displayAppbase + ", displayVersion=" + displayVersion + "]";
}
public UpdateInterface (Config config)
this.name = config.getString("ui.name");
this.progress = config.getRect("ui.progress", new Rectangle(5, 5, 300, 15));
this.progressText = config.getColor("ui.progress_text", Color.BLACK);
- this.hideProgressText = config.getBoolean("ui.hide_progress_text");
+ this.hideProgressText = config.getBoolean("ui.hide_progress_text");
+ this.progressSync = config.getBoolean("ui.progress_sync_before_shown");
+ this.progressSyncAfterShown = config.getBoolean("ui.progress_sync_after_shown");
+ this.keepOnTop = config.getBoolean("ui.keep_on_top");
+ this.displayAppbase = config.getBoolean("ui.display_appbase");
+ this.displayVersion = config.getBoolean("ui.display_version");
this.minShowSeconds = config.getInt("ui.min_show_seconds", 5);
this.progressBar = config.getColor("ui.progress_bar", 0x6699CC);
this.status = config.getRect("ui.status", new Rectangle(5, 25, 500, 100));
this.textShadow = config.getColor("ui.text_shadow", Color.CLEAR);
this.hideDecorations = config.getBoolean("ui.hide_decorations");
this.backgroundImage = config.getString("ui.background_image");
+ this.instantBackgroundImage = config.getString("ui.instant_background_image");
// default to black or white bg color, depending on the brightness of the progressText
int defaultBackground = (0.5f < Color.brightness(this.progressText)) ?
Color.BLACK : Color.WHITE;
*
*/
public Application (EnvConfig envc) {
- _envc = envc;
- _config = getLocalPath(envc.appDir, CONFIG_FILE);
+ _envc = envc;
+ _config = getLocalPath(envc.appDir, CONFIG_FILE);
+ _backupConfig = getLocalPath(envc.appDir, BACKUP_CONFIG_DIR+File.separator+CONFIG_FILE);
}
/**
* Returns the configured application directory.
*/
public File getAppDir () {
- return _envc.appDir;
+ return _envc.appDir;
}
/**
*/
public boolean useCodeCache ()
{
- return _useCodeCache;
+ return _useCodeCache;
}
/**
*/
public int getCodeCacheRetentionDays ()
{
- return _codeCacheRetentionDays;
+ return _codeCacheRetentionDays;
}
/**
* app files from its hosting server.
*/
public int maxConcurrentDownloads () {
- return _maxConcDownloads;
+ return _maxConcDownloads;
}
/**
*/
public Resource getConfigResource ()
{
- try {
- return createResource(CONFIG_FILE, Resource.NORMAL);
- } catch (Exception e) {
- throw new RuntimeException("Invalid appbase '" + _vappbase + "'.", e);
- }
+ try {
+ return createResource(CONFIG_FILE, Resource.NORMAL);
+ } catch (Exception e) {
+ throw new RuntimeException("Invalid appbase '" + _vappbase + "'.", e);
+ }
}
/**
*/
public List<Resource> getCodeResources ()
{
- return _codes;
+ return _codes;
}
/**
} catch (Exception e) {
log.warning("Failure reading config file", "file", _config, e);
}
+ if (config == null || config.getString("appbase") == null || config.getString("appbase").isEmpty()) {
+ try {
+ Config backupConfig = Config.parseConfig(_backupConfig, opts);
+ config = backupConfig;
+ log.warning("Using backup config file", "appdir", getAppDir(), "backupConfig", _backupConfig.getAbsoluteFile());
+ } catch (Exception e) {
+ log.warning("Failure reading backup config file", "file", _backupConfig, e);
+ }
+ }
// see if there's an override config from locator file
Config locatorConfig = createLocatorConfig(opts);
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");
try {
Config tmpConfig = null;
+ Map<String, Object> tmpData = new HashMap<>();
if (_locatorFile.exists()) {
tmpConfig = Config.parseConfig(_locatorFile, opts);
+ // appbase is sanitised in HostWhitelist
+ Map<String, Object> tmpConfigData = tmpConfig.getData();
+ if (tmpConfig != null) {
+ for (Map.Entry<String, Object> entry : tmpConfigData.entrySet()) {
+ String key = entry.getKey();
+ Object value = entry.getValue();
+ String mkey = key.indexOf('.') > -1 ? key.substring(key.indexOf('.') + 1) : key;
+ if (Config.allowedReplaceKeys.contains(mkey) || Config.allowedMergeKeys.contains(mkey)) {
+ tmpData.put(key, value);
+ }
+ }
+ } else {
+ log.warning("Error occurred reading config file", "file", _locatorFile);
+ }
} else {
log.warning("Given locator file does not exist", "file", _locatorFile);
}
- // appbase is sanitised in HostWhitelist
- Map<String, Object> tmpData = new HashMap<>();
- for (Map.Entry<String, Object> entry : tmpConfig.getData().entrySet()) {
- String key = entry.getKey();
- Object value = entry.getValue();
- String mkey = key.indexOf('.') > -1 ? key.substring(key.indexOf('.') + 1) : key;
- if (Config.allowedReplaceKeys.contains(mkey) || Config.allowedMergeKeys.contains(mkey)) {
- tmpData.put(key, value);
- }
- }
locatorConfig = new Config(tmpData);
} catch (Exception e) {
log.warning("Failure reading locator file", "file", _locatorFile, e);
}
- log.info("Returning locatorConfig", locatorConfig);
-
return locatorConfig;
}
+ public String getAppbase() {
+ return _appbase;
+ }
+
protected final EnvConfig _envc;
protected File _config;
+ protected File _backupConfig;
protected Digest _digest;
protected long _version = -1;
public static List<String> hostWhitelist () {
return Arrays.asList(StringUtil.parseStringArray("@host_whitelist@"));
}
+
+ /*
+ * <p>The default connect_timeout to use. Overridden by system property of the same name at runtime
+ */
+ public static int defaultConnectTimeout () {
+ try {
+ return Integer.valueOf("@connect_timeout@");
+ } catch (Exception e) {
+ return 0;
+ }
+ }
+
+ /*
+ * <p>The default read_timeout to use. Overridden by system property of the same name at runtime
+ */
+ public static int defaultReadTimeout () {
+ try {
+ return Integer.valueOf("@read_timeout@");
+ } catch (Exception e) {
+ 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;
+ }
+ }
}
import java.util.regex.Pattern;
import com.threerings.getdown.util.VersionUtil;
+import com.threerings.getdown.data.Build;
/**
* This class encapsulates all system properties that are read and processed by Getdown. Don't
* to more quickly timeout its startup update check if the server with which it is
* communicating is not available. Usage: {@code -Dconnect_timeout=N}. */
public static int connectTimeout () {
- return Integer.getInteger("connect_timeout", 0);
+ return Integer.getInteger("connect_timeout", Build.defaultConnectTimeout());
}
/** Specifies the read timeout (in seconds) to use when downloading all files from the server.
* update process wil fail. Setting the timeout to zero (or a negative value) will disable it.
* Usage: {@code -Dread_timeout=N}. */
public static int readTimeout () {
- return Integer.getInteger("read_timeout", 30);
+ return Integer.getInteger("read_timeout", Build.defaultReadTimeout());
}
/** Returns the number of threads used to perform digesting and verifying operations in
} else if (allowedReplaceKeys.contains(mkey)){
// replace value
-
_data.put(key, nvalue);
+
} else {
log.warning("Not merging key '"+key+"' into config");
}
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();
}
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.PrintStream;
+import java.nio.file.Files;
+import java.nio.file.Paths;
import java.util.Locale;
+import javax.xml.bind.DatatypeConverter;
+
+import java.security.MessageDigest;
+
import static com.threerings.getdown.Log.log;
/**
return vmpath;
}
+ private static String _getMD5FileChecksum (File file) {
+ // check md5 digest
+ String algo = "MD5";
+ String checksum = "";
+ try {
+ MessageDigest md = MessageDigest.getInstance(algo);
+ md.update(Files.readAllBytes(Paths.get(file.getAbsolutePath())));
+ byte[] digest = md.digest();
+ checksum = DatatypeConverter.printHexBinary(digest).toUpperCase();
+ } catch (Exception e) {
+ System.out.println("Couldn't create "+algo+" digest of "+file.getPath());
+ }
+ return checksum;
+ }
+
/**
* Upgrades Getdown by moving an installation managed copy of the Getdown jar file over the
* non-managed copy (which would be used to run Getdown itself).
// we assume getdown's jar file size changes with every upgrade, this is not guaranteed,
// but in reality it will, and it allows us to avoid pointlessly upgrading getdown every
// time the client is updated which is unnecessarily flirting with danger
- if (!newgd.exists() || newgd.length() == curgd.length()) {
+ if (!newgd.exists())
+ {
return;
}
+
+ if (newgd.length() == curgd.length()) {
+ if (_getMD5FileChecksum(newgd).equals(_getMD5FileChecksum(curgd)))
+ {
+ return;
+ }
+ }
log.info("Updating Getdown with " + newgd + "...");
} catch (NoClassDefFoundError e)
{
// com.sun.management.OperatingSystemMXBean doesn't exist in this JVM
- System.out.println("No com.sun.management.OperatingSystemMXBean");
+ System.err.println("No com.sun.management.OperatingSystemMXBean");
}
// We didn't get a com.sun.management.OperatingSystemMXBean.
<parent>
<groupId>com.threerings.getdown</groupId>
<artifactId>getdown</artifactId>
- <version>1.8.3-SNAPSHOT</version>
+ <version>1.8.3-1.1.8_FJVL</version>
</parent>
<artifactId>getdown-launcher</artifactId>
<build>
<plugins>
+ <!--
<plugin>
<groupId>com.github.wvengen</groupId>
<artifactId>proguard-maven-plugin</artifactId>
<addMavenDescriptor>false</addMavenDescriptor>
</configuration>
</plugin>
-
+ -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<goals>
<goal>shade</goal>
</goals>
+ <!--
+ <configuration>
+ <minimizeJar>true</minimizeJar>
+ <filters>
+ <filter>
+ <artifact>install4j-runtime</artifact>
+ <includes>
+ <include>**</include>
+ </includes>
+ </filter>
+ </filters>
+ </configuration>
+ -->
</execution>
</executions>
</plugin>
import java.awt.Container;
import java.awt.Dimension;
import java.awt.EventQueue;
+import java.awt.Graphics;
import java.awt.GraphicsEnvironment;
import java.awt.Image;
import java.awt.event.ActionEvent;
import javax.swing.JButton;
import javax.swing.JFrame;
import javax.swing.JLayeredPane;
+import javax.swing.JPanel;
import com.samskivert.swing.util.SwingUtil;
import com.threerings.getdown.data.*;
Config config = _app.init(true);
if (preloads) doPredownloads(_app.getResources());
_ifc = new Application.UpdateInterface(config);
+ if (_status != null) {
+ _status.setAppbase(_app.getAppbase());
+ }
}
/**
throw new IOException("m.java_download_failed");
}
+ // on Windows, if the local JVM is in use, we will not be able to replace it with an
+ // updated JVM; we detect this by attempting to rename the java.dll to its same name, which
+ // will fail on Windows for in use files; hackery!
+ File javaLocalDir = new File(_app.getAppDir(), LaunchUtil.LOCAL_JAVA_DIR+File.separator);
+ File javaDll = new File(javaLocalDir, "bin" + File.separator + "java.dll");
+ if (javaDll.exists()) {
+ if (!javaDll.renameTo(javaDll)) {
+ log.info("Cannot update local Java VM as it is in use.");
+ return;
+ }
+ log.info("Can update local Java VM as it is not in use.");
+ }
+
reportTrackingEvent("jvm_start", -1);
updateStatus("m.downloading_java");
// show the patch notes button, if applicable
if (!StringUtil.isBlank(_ifc.patchNotesUrl)) {
createInterfaceAsync(false);
- EventQueue.invokeLater(new Runnable() {
+ EQinvoke(new Runnable() {
public void run () {
_patchNotes.setVisible(true);
}
} else {
proc = _app.createProcess(false);
}
-
+
// close standard in to avoid choking standard out of the launched process
proc.getInputStream().close();
// close standard out, since we're not going to write to anything to it anyway
}
}
+ //_container.setVisible(true);
+ //_container.validate();
+
// if we have a UI open and we haven't been around for at least 5 seconds (the default
// for min_show_seconds), don't stick a fork in ourselves straight away but give our
// lovely user a chance to see what we're doing
if (_silent || (_container != null && !reinit)) {
return;
}
-
- EventQueue.invokeLater(new Runnable() {
+
+ EQinvoke (new Runnable() {
public void run () {
+
if (_container == null || reinit) {
if (_container == null) {
_container = createContainer();
}
configureContainer();
_layers = new JLayeredPane();
+
+
+
+ // added in the instant display of a splashscreen
+ try {
+ readConfig(false);
+ Graphics g = _container.getGraphics();
+ BufferedImage iBgImage = loadImage(_ifc.instantBackgroundImage);
+ boolean ibg = true;
+ if (iBgImage == null) {
+ iBgImage = loadImage(_ifc.backgroundImage);
+ ibg = false;
+ }
+ if (iBgImage != null) {
+ final BufferedImage bgImage = iBgImage;
+ int bwidth = bgImage.getWidth();
+ int bheight = bgImage.getHeight();
+
+ log.info("Displaying instant background image", ibg?"instant_background_image":"background_image");
+
+ instantSplashPane = new JPanel() {
+ @Override
+ protected void paintComponent(Graphics g)
+ {
+ super.paintComponent(g);
+ // attempt to draw a background image...
+ if (bgImage != null) {
+ g.drawImage(bgImage, 0, 0, this);
+ }
+ }
+ };
+
+ instantSplashPane.setSize(bwidth,bheight);
+ instantSplashPane.setPreferredSize(new Dimension(bwidth,bheight));
+
+ _layers.add(instantSplashPane, Integer.valueOf(1));
+
+ _container.setPreferredSize(new Dimension(bwidth,bheight));
+ }
+ } catch (Exception e) {
+ log.warning("Failed to set instant background image", "ibg", _ifc.instantBackgroundImage);
+ }
+
_container.add(_layers, BorderLayout.CENTER);
_patchNotes = new JButton(new AbstractAction(_msgs.getString("m.patch_notes")) {
@Override public void actionPerformed (ActionEvent event) {
_patchNotes.setFont(StatusPanel.FONT);
_layers.add(_patchNotes);
_status = new StatusPanel(_msgs);
- _layers.add(_status);
+ setStatusAsync("m.initialising", 0, -1L, true);
+ //_layers.add(_status, Integer.valueOf(2));
initInterface();
}
showContainer();
}
});
+
}
/**
_status.init(_ifc, _background, getProgressImage());
Dimension size = _status.getPreferredSize();
_status.setSize(size);
+ //_status.updateStatusLabel();
_layers.setPreferredSize(size);
_patchNotes.setBounds(_ifc.patchNotes.x, _ifc.patchNotes.y,
protected RotatingBackgrounds getBackground ()
{
- if (_ifc.rotatingBackgrounds != null) {
+ if (_ifc.rotatingBackgrounds != null && _ifc.rotatingBackgrounds.size() > 0) {
if (_ifc.backgroundImage != null) {
log.warning("ui.background_image and ui.rotating_background were both specified. " +
"The background image is being used.");
}
- return new RotatingBackgrounds(loadImage(_ifc.backgroundImage));
- //return new RotatingBackgrounds(_ifc.rotatingBackgrounds, _ifc.errorBackground, Getdown.this);
+ return new RotatingBackgrounds(_ifc.rotatingBackgrounds, _ifc.errorBackground, Getdown.this);
} else if (_ifc.backgroundImage != null) {
return new RotatingBackgrounds(loadImage(_ifc.backgroundImage));
} else {
createInterfaceAsync(false);
}
- EventQueue.invokeLater(new Runnable() {
+ EQinvoke(new Runnable() {
public void run () {
- if (_status == null) {
+
+ if (_status == null) {
if (message != null) {
log.info("Dropping status '" + message + "'.");
}
_status.setProgress(0, -1L);
} else if (percent >= 0) {
_status.setProgress(percent, remaining);
+ } else {
+ //_status.setStatus("m.initialising", false);
}
+
}
});
+
+ if (_status != null && ! _addedStatusLayer) {
+ _layers.add(_status, Integer.valueOf(2));
+ _addedStatusLayer = true;
+ initInterface();
+ }
+
}
protected void reportTrackingEvent (String event, int progress)
setStatusAsync(null, stepToGlobalPercent(percent), -1L, false);
}
};
-
+
+ // Asynchronous or synchronous progress updates
+ protected void EQinvoke(Runnable r) {
+
+ try {
+ readConfig(false);
+ } catch (Exception e) {
+ log.warning("Could't read config when invoking GUI action", "Exception", e.getMessage());
+ }
+ if (_ifc != null && (_shownContainer?_ifc.progressSyncAfterShown:_ifc.progressSync)) {
+ try {
+ EventQueue.invokeAndWait(r);
+ //r.run();
+ } catch (Exception e) {
+ log.warning("Tried to invokeAndWait but couldn't. Going to invokeLater instead", "Exception", e.getMessage());
+ EventQueue.invokeLater(r);
+ }
+ } else {
+ EventQueue.invokeLater(r);
+ //r.run();
+ }
+
+ //try { Thread.sleep(500); } catch (Exception e) {}
+
+ }
+
protected Application _app;
protected Application.UpdateInterface _ifc = new Application.UpdateInterface(Config.EMPTY);
protected ResourceBundle _msgs;
protected Container _container;
protected JLayeredPane _layers;
+ protected JPanel instantSplashPane;
protected StatusPanel _status;
protected JButton _patchNotes;
protected AbortPanel _abort;
protected RotatingBackgrounds _background;
+ protected boolean _addedStatusLayer;
protected boolean _dead;
protected boolean _silent;
protected boolean _launchInSilent;
protected boolean _noUpdate;
protected long _startup;
-
+
protected Set<Resource> _toInstallResources;
protected boolean _readyToInstall;
protected boolean _enableTracking = true;
protected int _reportedProgress = 0;
+ protected boolean _shownContainer;
+
/** Number of minutes to wait after startup before beginning any real heavy lifting. */
protected int _delay;
import java.awt.Color;
import java.awt.Container;
-import java.awt.EventQueue;
import java.awt.Image;
import java.awt.event.ActionEvent;
import java.awt.event.KeyEvent;
import javax.swing.KeyStroke;
import javax.swing.WindowConstants;
-import com.install4j.api.launcher.StartupNotification;
import com.samskivert.swing.util.SwingUtil;
import com.threerings.getdown.data.Application;
+import com.threerings.getdown.data.Build;
import com.threerings.getdown.data.EnvConfig;
import com.threerings.getdown.data.SysProps;
import com.threerings.getdown.util.LaunchUtil;
import com.threerings.getdown.util.StringUtil;
import static com.threerings.getdown.Log.log;
+import jalview.bin.StartupNotificationListener;
/**
* The main application entry point for Getdown.
}
if (abort) System.exit(-1);
+ log.info("Starting ...");
try
{
- StartupNotification.registerStartupListener(
- new StartupNotification.Listener() {
- @Override
- public void startupPerformed(String parameters)
- {
- log.warning("StartupNotification.Listener.startupPerformed: '"+parameters+"'");
- setStartupFilesParameterString(parameters);
- }
- });
+ jalview.bin.StartupNotificationListener.setListener();
} catch (Exception e)
{
e.printStackTrace();
+ } catch (NoClassDefFoundError e)
+ {
+ log.warning("Starting without install4j classes");
+ } catch (Throwable t)
+ {
+ t.printStackTrace();
}
// record a few things for posterity
log.info("-- User Name: " + System.getProperty("user.name"));
log.info("-- User Home: " + System.getProperty("user.home"));
log.info("-- Cur dir: " + System.getProperty("user.dir"));
+ log.info("-- launcher version: "+Build.version());
log.info("-- startupFilesParameterString: " + startupFilesParameterString);
log.info("---------------------------------------------");
handleWindowClose();
}
});
+
+ // keep_on_top
+ try {
+ readConfig(false);
+ } catch (Exception e) {
+ log.warning("Error reading config for keep_on_top");
+ }
+ // move window to top, always on top
+ if (_ifc.keepOnTop) {
+ log.info("Keep on top set to ", "keep_on_top", _ifc.keepOnTop);
+ _frame.setAlwaysOnTop(true);
+ }
+
// handle close on ESC
String cancelId = "Cancel"; // $NON-NLS-1$
_frame.getRootPane().getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW).put(
log.warning("Failed to set background", "bg", _ifc.background, e);
}
- if (_ifc.iconImages != null) {
+ if (_ifc.iconImages != null && _ifc.iconImages.size() > 0) {
ArrayList<Image> icons = new ArrayList<>();
for (String path : _ifc.iconImages) {
Image img = loadImage(path);
SwingUtil.centerWindow(_frame);
_frame.setVisible(true);
}
+ _shownContainer = true;
}
@Override
super.fail(message);
// super.fail causes the UI to be created (if needed) on the next UI tick, so we
// want to wait until that happens before we attempt to redecorate the window
- EventQueue.invokeLater(new Runnable() {
+ EQinvoke(new Runnable() {
@Override
public void run() {
// if the frame was set to be undecorated, make window decoration available
import com.samskivert.util.Throttle;
import com.threerings.getdown.data.Application.UpdateInterface;
+import com.threerings.getdown.data.Build;
import com.threerings.getdown.util.MessageUtil;
import com.threerings.getdown.util.Rectangle;
import com.threerings.getdown.util.StringUtil;
// maybe update the progress label
if (_progress != percent) {
_progress = percent;
- if (!_ifc.hideProgressText) {
+ if (_ifc != null && !_ifc.hideProgressText) {
String msg = MessageFormat.format(get("m.complete"), percent);
_newplab = createLabel(msg, new Color(_ifc.progressText, true));
}
}
remaining /= values;
- if (!_ifc.hideProgressText) {
+ if (_ifc != null && !_ifc.hideProgressText) {
// now compute our display value
int minutes = (int)(remaining / 60), seconds = (int)(remaining % 60);
String remstr = minutes + ":" + ((seconds < 10) ? "0" : "") + seconds;
*/
protected void updateStatusLabel ()
{
+ if (_ifc == null) {
+ return;
+ }
String status = _status;
if (!_displayError) {
for (int ii = 0; ii < _statusDots; ii++) {
status += " .";
}
}
- _newlab = createLabel(status, new Color(_ifc.statusText, true));
+
+ StringBuilder labelText = new StringBuilder();
+ if (_ifc.displayVersion) {
+ labelText.append("launcher version: "+Build.version());
+ labelText.append("\n");
+ }
+ if (_ifc.displayAppbase) {
+ labelText.append("appbase: "+_appbase);
+ labelText.append("\n");
+ }
+ labelText.append(status);
+
+ _newlab = createLabel(labelText.toString(), new Color(_ifc.statusText, true));
// set the width of the label to the width specified
int width = _ifc.status.width;
if (width == 0) {
return key;
}
}
+
+ public void setAppbase(String appbase) {
+ _appbase = appbase;
+ }
protected Image _barimg;
protected RotatingBackgrounds _bg;
protected Throttle _rthrottle = new Throttle(1, 1000L);
protected static final Font FONT = new Font("SansSerif", Font.BOLD, 12);
+
+ public String _appbase;
}
--- /dev/null
+package jalview.bin;
+
+import com.threerings.getdown.launcher.GetdownApp;
+import static com.threerings.getdown.Log.log;
+
+public class StartupNotificationListener {
+
+ public static void setListener() {
+
+
+ try {
+ com.install4j.api.launcher.StartupNotification.registerStartupListener(
+ new com.install4j.api.launcher.StartupNotification.Listener() {
+ @Override
+ public void startupPerformed(String parameters) {
+ log.info("StartupNotification.Listener.startupPerformed: '"+parameters+"'");
+ GetdownApp.setStartupFilesParameterString(parameters);
+ }
+ }
+ );
+ } catch (Exception e) {
+ e.printStackTrace();
+ } catch (NoClassDefFoundError t) {
+ log.warning("Starting without install4j classes");
+ }
+
+ }
+
+}
m.missing_class = The configuration file is missing the application class.
m.missing_code = The configuration file specifies no code resources.
m.invalid_digest_file = The digest file is invalid.
+
+# When at 0%
+m.initialising = Initialising
+m.starting = Starting
m.missing_code = Die Konfigurationsdatei enth\u00e4lt keine Codequellen.
m.invalid_digest_file = Die Hashwertedatei ist ung\u00fcltig.
+
+# When at 0%
+m.initialising = Initialising
+m.starting = Starting
m.missing_code = El archivo de configuraci\u00f3n especifica que no hay recursos de c\u00f3digo.
m.invalid_digest_file = El archivo digest no es v\u00e1lido.
+
+# When at 0%
+m.initialising = Initialising
+m.starting = Starting
m.missing_class = Le fichier de configuration ne contient pas la classe de l'application.
m.missing_code = Le fichier de configuration ne sp\u00e9cifie aucune ressource de code.
m.invalid_digest_file = Le fichier digest est invalide.
+
+# When at 0%
+m.initialising = Initialising
+m.starting = Starting
m.missing_class = Il file di configurazione non contiene la classe da eseguire (tag "class").
m.missing_code = Il file di configurazione non contiene alcuna risorsa (tag "code").
m.invalid_digest_file = Il file di digest non è valido.
+
+# When at 0%
+m.initialising = Initialising
+m.starting = Starting
m.missing_class = \u8a2d\u5b9a\u30d5\u30a1\u30a4\u30eb\u306e\u30a2\u30d7\u30ea\u30b1\u30fc\u30b7\u30e7\u30f3\u30af\u30e9\u30b9\u304c\u4e0d\u660e\u3067\u3059\u3002
m.missing_code = \u8a2d\u5b9a\u30d5\u30a1\u30a4\u30eb\u3067\u30b3\u30fc\u30c9\u30ea\u30bd\u30fc\u30b9\u304c\u6307\u5b9a\u3055\u308c\u3066\u3044\u307e\u305b\u3093\u3002
m.invalid_digest_file = \u30c0\u30a4\u30b8\u30a7\u30b9\u30c8\u30d5\u30a1\u30a4\u30eb\u304c\u7121\u52b9\u3067\u3059\u3002
+
+# When at 0%
+m.initialising = Initialising
+m.starting = Starting
m.missing_class = \uC124\uC815 \uD30C\uC77C\uC5D0 \uC5B4\uD50C\uB9AC\uCF00\uC774\uC158 \uD074\uB798\uC2A4\uAC00 \uC5C6\uC2B5\uB2C8\uB2E4.
m.missing_code = \uC124\uC815 \uD30C\uC77C\uC5D0 \uB9AC\uC18C\uC2A4\uC5D0 \uB300\uD55C \uCF54\uB4DC\uAC00 \uBA85\uC2DC\uB418\uC5B4 \uC788\uC9C0 \uC54A\uC2B5\uB2C8\uB2E4.
m.invalid_digest_file = \uB2E4\uC774\uC81C\uC2A4\uD2B8 \uD30C\uC77C\uC774 \uC798\uBABB\uB418\uC5C8\uC2B5\uB2C8\uB2E4.
+
+# When at 0%
+m.initialising = Initialising
+m.starting = Starting
m.missing_class = O arquivo de configura\u00E7\u00E3o n\u00E3o possui a classe de aplicativo.
m.missing_code = O arquivo de configura\u00E7\u00E3o n\u00E3o especifica um recurso de c\u00F3digo.
m.invalid_digest_file = O arquivo digest \u00E9 inv\u00E1lido.
+
+# When at 0%
+m.initialising = Initialising
+m.starting = Starting
m.missing_class = \u914d\u7f6e\u6587\u4ef6\u4e2d\u65e0\u6cd5\u627e\u5230\u7a0b\u5e8f\u6587\u4ef6\u3002
m.missing_code = \u914d\u7f6e\u6587\u4ef6\u4e2d\u65e0\u6cd5\u627e\u5230\u6307\u5b9a\u7684\u8d44\u6e90\u3002
m.invalid_digest_file = \u65e0\u6548\u7684\u914d\u7f6e\u6587\u4ef6\u3002
+
+# When at 0%
+m.initialising = Initialising
+m.starting = Starting
-mvn clean package -Dgetdown.host.whitelist="jalview.org,*.jalview.org" && cp launcher/target/getdown-launcher-1.8.3-SNAPSHOT.jar ../../../getdown/lib/getdown-launcher.jar && cp core/target/getdown-core-1.8.3-SNAPSHOT.jar ../../../getdown/lib/getdown-core-1.8.3-SNAPSHOT.jar && cp core/target/getdown-core-1.8.3-SNAPSHOT.jar ../../../j8lib/getdown-core.jar && cp core/target/getdown-core-1.8.3-SNAPSHOT.jar ../../../j11lib/getdown-core.jar
+#!/usr/bin/env bash
+
+if [ x$JVLVERSION != x ]; then
+ export VERSION=$JVLVERSION
+else
+ export VERSION=1.8.3-1.1.8_JVL
+fi
+
+if [ x${VERSION%_JVL} = x$VERSION ]; then
+ VERSION=${VERSION}_JVL
+fi
+
+echo "Setting VERSION to '$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-$VERSION.jar to j11lib"
+fi
+
+VERSION=${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-$VERSION.jar ../../../getdown/lib/getdown-launcher-local.jar && echo "Copied getdown-launcher-$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-SNAPSHOT</version>
+ <version>1.8.3-1.1.8_FJVL</version>
<name>getdown</name>
<description>An application installer and updater.</description>
<groupId>com.install4j</groupId>
<artifactId>install4j-runtime</artifactId>
<version>7.0.11</version>
- <!--<scope>provided</scope>-->
+ <scope>provided</scope>
</dependency>
</dependencies>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
- <version>3.7.0</version>
+ <version>3.8.1</version>
<configuration>
- <source>1.7</source>
- <target>1.7</target>
+ <source>1.8</source>
+ <target>1.8</target>
<fork>true</fork>
<showDeprecation>true</showDeprecation>
<showWarnings>true</showWarnings>
jalviewDir = .
+#JAVA_VERSION = 1.8
JAVA_VERSION = 11
JALVIEW_VERSION = DEVELOPMENT
INSTALLATION = Source
testngGroups = Functional
-javac_source = 11
-javac_target = 11
-
j8libDir = j8lib
j11libDir = j11lib
resourceDir = resources
helpParentDir = help
helpDir = help
+helpOutputDir = build/distribution/help
docDir = doc
sourceDir = src
schemaDir = schemas
classesDir = classes
+examplesDir = examples
clover = false
use_clover = false
cloverClassesDir = clover-classes
cloverSourcesInstrDir = sources-instr
packageDir = dist
+ARCHIVEDIR =
outputJar = jalview.jar
testSourceDir = test
getdown_local = false
getdown_website_dir = getdown/website
getdown_resource_dir = resource
-getdown_app_dir = dist
-getdown_j11lib_dir = j11lib
+#getdown_j11lib_dir = j11lib
getdown_files_dir = getdown/files
-getdown_launcher = getdown/lib/getdown-launcher.jar
-getdown_core = getdown/lib/getdown-core-1.8.3-SNAPSHOT.jar
-getdown_base_txt = getdown/files/getdown.txt
+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
+getdown_build_properties = build_properties
getdown_txt_title = Jalview
-getdown_channel_base = http://www.jalview.org/getdown/jalview
-getdown_channel_name = TEST
getdown_txt_allow_offline = true
+getdown_txt_max_concurrent_downloads = 10
getdown_txt_jalview.jvmmempc = 90
-getdown_txt_multi_jvmarg = -Dgetdownappdir="%APPDIR%"
+getdown_txt_multi_jvmarg = -Dgetdownappdir=%APPDIR%
getdown_txt_strict_comments = true
getdown_txt_title = Jalview
getdown_txt_ui.name = Jalview
+getdown_txt_ui.progress_sync_before_shown = true
+getdown_txt_ui.progress_sync_after_shown = false
+getdown_txt_ui.keep_on_top = true
+getdown_txt_ui.display_appbase = true
+getdown_txt_ui.display_version = true
+getdown_txt_ui.min_show_seconds = 6
getdown_txt_ui.background = FFFFFF
-getdown_txt_ui.background_image = resources/images/jalview_logo_background_getdown-640x480.png
-getdown_txt_ui.error_background = resources/images/jetset_jalview_splash.png
-getdown_txt_ui.progress_image = resources/images/jalview_logo_background_getdown-progress.png
+getdown_txt_ui.background_image = utils/getdown/jalview_logo_background_getdown-640x480.png
+getdown_txt_ui.instant_background_image = utils/getdown/jalview_logo_background_getdown_instant-640x480.png
+getdown_txt_ui.error_background = utils/getdown/jalview_logo_background_getdown_error-640x480.png
+getdown_txt_ui.progress_image = utils/getdown/jalview_logo_background_getdown-progress.png
getdown_txt_ui.icon = resources/images/JalviewLogo_Huge.png
getdown_txt_ui.progress = 20, 440, 600, 22
getdown_txt_ui.progress_bar = AAAAFF
getdown_txt_ui.progress_text = 000000
getdown_txt_ui.status = 20, 380, 600, 58
getdown_txt_ui.status_text = 000066
-getdown_txt_ui.text_shadow = EEEEFF
-getdown_txt_ui.install_error = http://www.jalview.org/download/error
+#getdown_txt_ui.text_shadow = FFFFFF
+getdown_txt_ui.install_error = http://www.jalview.org/faq/getdownerror
getdown_txt_ui.mac_dock_icon = resources/images/jalview_logos.ico
getdown_alt_java8_min_version = 01080000
+getdown_alt_java8_max_version = 01089999
getdown_alt_java11_min_version = 11000000
-getdown_alt_java11_txt_multi_java_location = [windows-amd64] /getdown/jre/windows-jre11.tgz,[linux-amd64] /getdown/jre/linux-jre11.tgz,[mac os x] /getdown/jre/macos-jre11.tgz
+getdown_alt_java11_max_version =
+getdown_alt_java11_txt_multi_java_location = [windows-amd64] /getdown/jre/windows-jre11.jar,[linux-amd64] /getdown/jre/linux-jre11.tgz,[mac os x] /getdown/jre/macos-jre11.tgz
getdown_alt_java8_txt_multi_java_location = [windows-amd64] /getdown/jre/windows-jre1.8.tgz,[linux-amd64] /getdown/jre/linux-jre1.8.tgz,[mac os x] /getdown/jre/macos-jre1.8.tgz
JRE_installs = /Users/bsoares/Java/installs
Windows_JRE8 = OpenJDK8U-jdk_x64_windows_hotspot_8u202b08/jdk8u202-b08
eclipse_extra_jdt_prefs_file = .settings/org.eclipse.jdt.core.jalview.prefs
-pandoc_exec = /usr/local/bin/pandoc
+pandoc_exec = /usr/local/bin/pandoc,/usr/bin/pandoc
dev = false
+CHANNEL=LOCAL
+getdown_channel_base = http://www.jalview.org/getdown
+getdown_channel_name = SCRATCH-DEFAULT
+getdown_app_dir_release = release
+getdown_app_dir_alt = alt
+getdown_install_dir = install
+getdown_rsync_dest = /Volumes/jalview/docroot/getdown
+reportRsyncCommand =
+RUNRSYNC=false
<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"/>
<mapID target="groovy.colours" url="html/features/groovy.html#groovyColours" />
<mapID target="groovy.featurescounter" url="html/groovy/featuresCounter.html" />
<mapID target="privacy" url="html/privacy.html" />
- <mapID target="vamsas" url="html/vamsas/index.html"/>
<mapID target="aminoAcids" url="html/misc/aminoAcids.html" />
<mapID target="aaProperties" url="html/misc/aaproperties.html" />
<mapID target="geneticCode" url="html/misc/geneticCode.html" />
<mapID target="overview" url="html/features/overview.html" />
<mapID target="overviewprefs" url="html/features/preferences.html#overview" />
+
+ <mapID target="importvcf" url="html/features/importvcf.html" />
</map>
<tocitem text="Jalview Documentation" target="home" expand="true">
<tocitem text="What's new" target="new" expand="true">
<tocitem text="Latest Release Notes" target="release"/>
- <tocitem text="Structure Chooser" target="pdbchooser"/>
- <tocitem text="Chimera Annotation Exchange" target="chimera.annotxfer"/>
+ <tocitem text="VCF Import" target="importvcf"/>
+ <tocitem text="Feature Filters and Attribute Colourschemes" target="features.featureschemes" />
+
</tocitem>
<tocitem text="Editing Alignments" target="edit" />
<tocitem text="Select Columns by Annotation" target="selectcolbyannot" />
<tocitem text="Nucleic Acid Support" target="nucleicAcids" expand="false">
+ <tocitem text="Annotating from VCF" target="importvcf" />
<tocitem text="Viewing RNA structure" target="varna" />
<tocitem text="RNA Structure Consensus" target="calcs.alstrconsensus" />
<tocitem text="RNA Helices coloring" target="colours.rnahelices" />
<tocitem text="Opening URLs from Jalview" target="urllinks" expand="true">
<tocitem text="Configuring URL Links" target="linksprefs" />
</tocitem>
- <tocitem text="VAMSAS Data Exchange" target="vamsas">
- <!-- what can Jalview share with other apps -->
- <!-- what other apps exist -->
- </tocitem>
<tocitem text="Window Menus" target="menus" expand="false">
<tocitem text="Desktop Window" target="desktopMenu" />
<tocitem text="Alignment Window" target="alMenu">
</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">
nucleotide substitution matrix</a>, or by sequence percentage identity,
or sequence feature similarity.
</p>
- <img src="pcaviewer.gif">
+ <img src="pcaviewer.png">
<p>
<strong>The PCA Viewer</strong>
</p>
towards the front of the view.</p>
<p>
The 3d view can be rotated by dragging the mouse with the <strong>left
- mouse button</strong> pressed. The view can also be zoomed in and out with
+ mouse button</strong> pressed, or with the <strong>arrow
+ keys</strong> when <strong>SHIFT</strong> is pressed. The
+ view can also be zoomed in and out with
the up and down <strong>arrow keys</strong> (and the roll bar of the
mouse if present). Labels will be shown for each sequence if the
entry in the View menu is checked, and the plot background colour
<p>
Initially, the display shows the first three components of the
similarity space, but any eigenvector can be used by changing the
- selected dimension for the x, y, or z axis through each ones menu
+ selected dimension for the x, y, or z axis through each one's menu
located below the 3d display. The <strong><em>Reset</em></strong>
button will reset axis and rotation settings to their defaults.
</p>
<em>The output of points and transformed point coordinates was
added to the Jalview desktop in v2.7.</em> <em>The Reset button
and Change Parameters menu were added in Jalview 2.8.</em> <em>Support
- for PAM250 based PCA was added in Jalview 2.8.1.</em>
+ for PAM250 based PCA was added in Jalview 2.8.1.</em><em>In Jalview 2.11, support for saving and restoring PCAs in Project files was added, and the Change parameters menu removed.</em>
</p>
<p>
<strong>Reproducing PCA calculations performed with older
alignment, such as another tree viewer.
</p>
<p>
- <strong><em><a name="partitioning">Grouping sequences by partitioning</a> the
- tree at a particular distance</em></strong><br> Clicking anywhere along
- the extent of the tree (but not on a leaf or internal node) defines
- a tree 'partition', by cutting every branch of the tree spanning the
- depth where the mouse-click occurred. Groups are created containing
- sequences at the leaves of each connected sub tree. These groups are
- each given a different colour, which are reflected in other windows
- in the same way as if the sequence IDs were selected, and can be
- edited in the same way as user defined sequence groups.
- </p>
+ <strong><em><a name="partitioning">Grouping
+ sequences by partitioning</a> the tree at a particular distance</em></strong><br>
+ Clicking anywhere along the extent of the tree (but not on a leaf or
+ internal node) defines a tree 'partition', by cutting every branch of
+ the tree spanning the depth where the mouse-click occurred. A red line
+ will be shown where the partition was made, and groups are created
+ containing sequences at the leaves of each connected sub tree. These
+ groups are each given a different colour, which are reflected in other
+ windows in the same way as if the sequence IDs were selected, and can
+ be edited in the same way as user defined sequence groups.
+ </p>
<p>
Tree partitions are useful for comparing clusters produced by
different methods and measures. They are also an effective way of
a new scheme in the Colour menu.</p>
<p>
The <strong>"Colour→<a
- href="../colourSchemes/textcolour.html">Colour Text...</a>"
+ href="textcolour.html">Colour Text...</a>"
</strong> entry opens a dialog box to set a different text colour for light
and dark background, and the intensity threshold for transition
between them.
</p>
- <p>The default colour schemes are summarised in the table below:
- <div align="center">
- <p> </p>
- <p>
- <strong>Protein Colour Schemes</strong>
- </p>
- <table border="1">
- <tr>
- <td>
- <table border="1">
- <tr>
- <td nowrap></td>
- <td>A</td>
- <td>R</td>
- <td>N</td>
- <td>D</td>
- <td>C</td>
- <td>Q</td>
- <td>E</td>
- <td>G</td>
- <td>H</td>
- <td>I</td>
- <td>L</td>
- <td>K</td>
- <td>M</td>
- <td>F</td>
- <td>P</td>
- <td>S</td>
- <td>T</td>
- <td>W</td>
- <td>Y</td>
- <td>V</td>
- <td>B</td>
- <td>X</td>
- <td>Z</td>
- </tr>
- <tr>
- <td height="24">Clustal</td>
- <td bgcolor="#80a0f0"></td>
- <td bgcolor="#f01505"></td>
- <td bgcolor="#00ff00"></td>
- <td bgcolor="#c048c0"></td>
- <td bgcolor="#f08080"></td>
- <td bgcolor="#00ff00"></td>
- <td bgcolor="#c048c0"></td>
- <td bgcolor="#f09048"></td>
- <td bgcolor="#15a4a4"></td>
- <td bgcolor="#80a0f0"></td>
- <td bgcolor="#80a0f0"></td>
- <td bgcolor="#f01505"></td>
- <td bgcolor="#80a0f0"></td>
- <td bgcolor="#80a0f0"></td>
- <td bgcolor="#ffff00"></td>
- <td bgcolor="#00ff00"></td>
- <td bgcolor="#00ff00"></td>
- <td bgcolor="#80a0f0"></td>
- <td bgcolor="#15a4a4"></td>
- <td bgcolor="#80a0f0"></td>
- <td></td>
- <td></td>
- <td></td>
- </tr>
- <tr>
- <td height="24">Zappo</td>
- <td bgcolor="#ffafaf"></td>
- <td bgcolor="#6464ff"></td>
- <td bgcolor="#00ff00"></td>
- <td bgcolor="#ff0000"></td>
- <td bgcolor="#ffff00"></td>
- <td bgcolor="#00ff00"></td>
- <td bgcolor="#ff0000"></td>
- <td bgcolor="#ff00ff"></td>
- <td bgcolor="#6464ff"></td>
- <td bgcolor="#ffafaf"></td>
- <td bgcolor="#ffafaf"></td>
- <td bgcolor="#6464ff"></td>
- <td bgcolor="#ffafaf"></td>
- <td bgcolor="#ffc800"></td>
- <td bgcolor="#ff00ff"></td>
- <td bgcolor="#00ff00"></td>
- <td bgcolor="#00ff00"></td>
- <td bgcolor="#ffc800"></td>
- <td bgcolor="#ffc800"></td>
- <td bgcolor="#ffafaf"></td>
- <td></td>
- <td></td>
- <td></td>
- </tr>
- <tr>
- <td>Taylor</td>
- <td bgcolor="#ccff00"></td>
- <td bgcolor="#0000ff"></td>
- <td bgcolor="#cc00ff"></td>
- <td bgcolor="#ff0000"></td>
- <td bgcolor="#ffff00"></td>
- <td bgcolor="#ff00cc"></td>
- <td bgcolor="#ff0066"></td>
- <td bgcolor="#ff9900"></td>
- <td bgcolor="#0066ff"></td>
- <td bgcolor="#66ff00"></td>
- <td bgcolor="#33ff00"></td>
- <td bgcolor="#6600ff"></td>
- <td bgcolor="#00ff00"></td>
- <td bgcolor="#00ff66"></td>
- <td bgcolor="#ffcc00"></td>
- <td bgcolor="#ff3300"></td>
- <td bgcolor="#ff6600"></td>
- <td bgcolor="#00ccff"></td>
- <td bgcolor="#00ffcc"></td>
- <td bgcolor="#99ff00"></td>
- <td></td>
- <td></td>
- <td></td>
- </tr>
- <tr>
- <td>Hydrophobicity</td>
- <td bgcolor="#ad0052"></td>
- <td bgcolor="#0000ff"></td>
- <td bgcolor="#0c00f3"></td>
- <td bgcolor="#0c00f3"></td>
- <td bgcolor="#c2003d"></td>
- <td bgcolor="#0c00f3"></td>
- <td bgcolor="#0c00f3"></td>
- <td bgcolor="#6a0095"></td>
- <td bgcolor="#1500ea"></td>
- <td bgcolor="#ff0000"></td>
- <td bgcolor="#ea0015"></td>
- <td bgcolor="#0000ff"></td>
- <td bgcolor="#b0004f"></td>
- <td bgcolor="#cb0034"></td>
- <td bgcolor="#4600b9"></td>
- <td bgcolor="#5e00a1"></td>
- <td bgcolor="#61009e"></td>
- <td bgcolor="#5b00a4"></td>
- <td bgcolor="#4f00b0"></td>
- <td bgcolor="#f60009"></td>
- <td bgcolor="#0c00f3"></td>
- <td bgcolor="#680097"></td>
- <td bgcolor="#0c00f3"></td>
- </tr>
- <tr>
- <td>Helix Propensity</td>
- <td bgcolor="#e718e7"></td>
- <td bgcolor="#6f906f"></td>
- <td bgcolor="#1be41b"></td>
- <td bgcolor="#778877"></td>
- <td bgcolor="#23dc23"></td>
- <td bgcolor="#926d92"></td>
- <td bgcolor="#ff00ff"></td>
- <td bgcolor="#00ff00"></td>
- <td bgcolor="#758a75"></td>
- <td bgcolor="#8a758a"></td>
- <td bgcolor="#ae51ae"></td>
- <td bgcolor="#a05fa0"></td>
- <td bgcolor="#ef10ef"></td>
- <td bgcolor="#986798"></td>
- <td bgcolor="#00ff00"></td>
- <td bgcolor="#36c936"></td>
- <td bgcolor="#47b847"></td>
- <td bgcolor="#8a758a"></td>
- <td bgcolor="#21de21"></td>
- <td bgcolor="#857a85"></td>
- <td bgcolor="#49b649"></td>
- <td bgcolor="#758a75"></td>
- <td bgcolor="#c936c9"></td>
- </tr>
- <tr>
- <td nowrap>Strand Propensity</td>
- <td bgcolor="#5858a7"></td>
- <td bgcolor="#6b6b94"></td>
- <td bgcolor="#64649b"></td>
- <td bgcolor="#2121de"></td>
- <td bgcolor="#9d9d62"></td>
- <td bgcolor="#8c8c73"></td>
- <td bgcolor="#0000ff"></td>
- <td bgcolor="#4949b6"></td>
- <td bgcolor="#60609f"></td>
- <td bgcolor="#ecec13"></td>
- <td bgcolor="#b2b24d"></td>
- <td bgcolor="#4747b8"></td>
- <td bgcolor="#82827d"></td>
- <td bgcolor="#c2c23d"></td>
- <td bgcolor="#2323dc"></td>
- <td bgcolor="#4949b6"></td>
- <td bgcolor="#9d9d62"></td>
- <td bgcolor="#c0c03f"></td>
- <td bgcolor="#d3d32c"></td>
- <td bgcolor="#ffff00"></td>
- <td bgcolor="#4343bc"></td>
- <td bgcolor="#797986"></td>
- <td bgcolor="#4747b8"></td>
- </tr>
- <tr>
- <td>Turn Propensity</td>
- <td bgcolor="#2cd3d3"></td>
- <td bgcolor="#708f8f"></td>
- <td bgcolor="#ff0000"></td>
- <td bgcolor="#e81717"></td>
- <td bgcolor="#a85757"></td>
- <td bgcolor="#3fc0c0"></td>
- <td bgcolor="#778888"></td>
- <td bgcolor="#ff0000"></td>
- <td bgcolor="#708f8f"></td>
- <td bgcolor="#00ffff"></td>
- <td bgcolor="#1ce3e3"></td>
- <td bgcolor="#7e8181"></td>
- <td bgcolor="#1ee1e1"></td>
- <td bgcolor="#1ee1e1"></td>
- <td bgcolor="#f60909"></td>
- <td bgcolor="#e11e1e"></td>
- <td bgcolor="#738c8c"></td>
- <td bgcolor="#738c8c"></td>
- <td bgcolor="#9d6262"></td>
- <td bgcolor="#07f8f8"></td>
- <td bgcolor="#f30c0c"></td>
- <td bgcolor="#7c8383"></td>
- <td bgcolor="#5ba4a4"></td>
- </tr>
- <tr>
- <td>Buried Index</td>
- <td bgcolor="#00a35c"></td>
- <td bgcolor="#00fc03"></td>
- <td bgcolor="#00eb14"></td>
- <td bgcolor="#00eb14"></td>
- <td bgcolor="#0000ff"></td>
- <td bgcolor="#00f10e"></td>
- <td bgcolor="#00f10e"></td>
- <td bgcolor="#009d62"></td>
- <td bgcolor="#00d52a"></td>
- <td bgcolor="#0054ab"></td>
- <td bgcolor="#007b84"></td>
- <td bgcolor="#00ff00"></td>
- <td bgcolor="#009768"></td>
- <td bgcolor="#008778"></td>
- <td bgcolor="#00e01f"></td>
- <td bgcolor="#00d52a"></td>
- <td bgcolor="#00db24"></td>
- <td bgcolor="#00a857"></td>
- <td bgcolor="#00e619"></td>
- <td bgcolor="#005fa0"></td>
- <td bgcolor="#00eb14"></td>
- <td bgcolor="#00b649"></td>
- <td bgcolor="#00f10e"></td>
- </tr>
- </table>
- </td>
- </tr>
- </table>
- <p> </p>
- <p>
- <strong>Nucleotide Colour Schemes</strong>
- </p>
- <table border="1">
- <tr>
- <td>
- <table border="1">
- <tr>
- <td nowrap></td>
- <td>A</td>
- <!--Adenine-->
- <td>C</td>
- <!--Cytosine-->
- <td>G</td>
- <!--Guanine-->
- <td>T</td>
- <!--Thymine-->
- <td>U</td>
- <!--Uracil-->
- <td>I</td>
- <!--Inosine-->
- <td>X</td>
- <!--Xanthine-->
- <td>R</td>
- <!--Unknown Purine-->
- <td>Y</td>
- <!--Unknown Pyrimidine-->
- <td>N</td>
- <!--Unknown-->
- <td>W</td>
- <!--Weak nucleotide (A or T)-->
- <td>S</td>
- <!--Strong nucleotide (G or C)-->
- <td>M</td>
- <!--Amino (A or C)-->
- <td>K</td>
- <!--Keto (G or T)-->
- <td>B</td>
- <!--Not A (G or C or T)-->
- <td>H</td>
- <!--Not G (A or C or T)-->
- <td>D</td>
- <!--Not C (A or G or T)-->
- <td>V</td>
- <!--Not T (A or G or C-->
- </tr>
- <tr>
- <td height="24">Nucleotide</td>
- <td bgcolor="#64F73F"></td>
- <td bgcolor="#FFB340"></td>
- <td bgcolor="#EB413C"></td>
- <td bgcolor="#3C88EE"></td>
- <td bgcolor="#3C88EE"></td>
- <td></td>
- <td></td>
- <td></td>
- <td></td>
- <td></td>
- <td></td>
- <td></td>
- <td></td>
- <td></td>
- <td></td>
- <td></td>
- <td></td>
- <td></td>
- </tr>
- <tr>
- <td height="24">Purine/Pyrimidine</td>
- <td bgcolor="#FF83FA"></td>
- <td bgcolor="#40E0D0"></td>
- <td bgcolor="#FF83FA"></td>
- <td bgcolor="#40E0D0"></td>
- <td bgcolor="#40E0D0"></td>
- <td></td>
- <td></td>
- <td bgcolor="#FF83FA"></td>
- <td bgcolor="#40E0D0"></td>
- <td></td>
- <td></td>
- <td></td>
- <td></td>
- <td></td>
- <td></td>
- <td></td>
- <td></td>
- <td></td>
- </tr>
- </table>
- </td>
- </tr>
- </table>
+ <p>
+ <strong>Dynamic colour schemes</strong>
+ </p>
+ <p>
+ Alignments and groups may be coloured according to <a
+ href="annotationColouring.html">associated sequence and alignment
+ annotation</a>. Any applied colour schemes (such as those shown in the
+ table below) can also be <a href="conservation.html">shaded by
+ amino acid physico-chemical property conservation</a> to reveal patterns
+ of variation, or applied selectively to <a href="abovePID.html">Above
+ Identity Threshold</a>.
+ </p>
+ <p>
+ Alignments and groups can also be shaded according to percentage
+ abundance of aligned residues (using <a href="pid.html">Percentage
+ Identity</a>), and for protein alignments, the <a href="blosum.html">BLOSUM
+ 62 Score</a> and <a href="clustal.html">ClustalX</a> shading schemes
+ highlight amino acid conservation.
+ </p>
+ <p>
+ The <strong>Sequence ID</strong> colour scheme shades sequences with
+ the same colour assigned to their Sequence ID. Colours are assigned
+ when groups are created by <a href="../calculations/treeviewer.html">partitioning
+ a tree</a> or subdividing the alignment by sequence with <strong>Select→Make
+ Groups For Selection</strong>.
+ </p>
+ <p>
+ <strong>Amino acid and Nucleotide based colour schemes</strong>
+ <p>The built-in colour schemes based on amino acid and nucleotide symbols are
+ summarised in the table below:
+
+ <div align="center"><p> </p>
+ <p>
+ <strong>Protein Colour Schemes</strong>
+ </p>
+ <table border="1">
+ <tr>
+ <td>
+ <table border="1">
+ <tr>
+ <td nowrap></td>
+ <td>A</td>
+ <td>R</td>
+ <td>N</td>
+ <td>D</td>
+ <td>C</td>
+ <td>Q</td>
+ <td>E</td>
+ <td>G</td>
+ <td>H</td>
+ <td>I</td>
+ <td>L</td>
+ <td>K</td>
+ <td>M</td>
+ <td>F</td>
+ <td>P</td>
+ <td>S</td>
+ <td>T</td>
+ <td>W</td>
+ <td>Y</td>
+ <td>V</td>
+ <td>B</td>
+ <td>X</td>
+ <td>Z</td>
+ </tr>
+ <tr>
+ <td height="24">Clustal</td>
+ <td bgcolor="#80a0f0"></td>
+ <td bgcolor="#f01505"></td>
+ <td bgcolor="#00ff00"></td>
+ <td bgcolor="#c048c0"></td>
+ <td bgcolor="#f08080"></td>
+ <td bgcolor="#00ff00"></td>
+ <td bgcolor="#c048c0"></td>
+ <td bgcolor="#f09048"></td>
+ <td bgcolor="#15a4a4"></td>
+ <td bgcolor="#80a0f0"></td>
+ <td bgcolor="#80a0f0"></td>
+ <td bgcolor="#f01505"></td>
+ <td bgcolor="#80a0f0"></td>
+ <td bgcolor="#80a0f0"></td>
+ <td bgcolor="#ffff00"></td>
+ <td bgcolor="#00ff00"></td>
+ <td bgcolor="#00ff00"></td>
+ <td bgcolor="#80a0f0"></td>
+ <td bgcolor="#15a4a4"></td>
+ <td bgcolor="#80a0f0"></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ </tr>
+ <tr>
+ <td height="24">Zappo</td>
+ <td bgcolor="#ffafaf"></td>
+ <td bgcolor="#6464ff"></td>
+ <td bgcolor="#00ff00"></td>
+ <td bgcolor="#ff0000"></td>
+ <td bgcolor="#ffff00"></td>
+ <td bgcolor="#00ff00"></td>
+ <td bgcolor="#ff0000"></td>
+ <td bgcolor="#ff00ff"></td>
+ <td bgcolor="#6464ff"></td>
+ <td bgcolor="#ffafaf"></td>
+ <td bgcolor="#ffafaf"></td>
+ <td bgcolor="#6464ff"></td>
+ <td bgcolor="#ffafaf"></td>
+ <td bgcolor="#ffc800"></td>
+ <td bgcolor="#ff00ff"></td>
+ <td bgcolor="#00ff00"></td>
+ <td bgcolor="#00ff00"></td>
+ <td bgcolor="#ffc800"></td>
+ <td bgcolor="#ffc800"></td>
+ <td bgcolor="#ffafaf"></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ </tr>
+ <tr>
+ <td>Taylor</td>
+ <td bgcolor="#ccff00"></td>
+ <td bgcolor="#0000ff"></td>
+ <td bgcolor="#cc00ff"></td>
+ <td bgcolor="#ff0000"></td>
+ <td bgcolor="#ffff00"></td>
+ <td bgcolor="#ff00cc"></td>
+ <td bgcolor="#ff0066"></td>
+ <td bgcolor="#ff9900"></td>
+ <td bgcolor="#0066ff"></td>
+ <td bgcolor="#66ff00"></td>
+ <td bgcolor="#33ff00"></td>
+ <td bgcolor="#6600ff"></td>
+ <td bgcolor="#00ff00"></td>
+ <td bgcolor="#00ff66"></td>
+ <td bgcolor="#ffcc00"></td>
+ <td bgcolor="#ff3300"></td>
+ <td bgcolor="#ff6600"></td>
+ <td bgcolor="#00ccff"></td>
+ <td bgcolor="#00ffcc"></td>
+ <td bgcolor="#99ff00"></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ </tr>
+ <tr>
+ <td>Hydrophobicity</td>
+ <td bgcolor="#ad0052"></td>
+ <td bgcolor="#0000ff"></td>
+ <td bgcolor="#0c00f3"></td>
+ <td bgcolor="#0c00f3"></td>
+ <td bgcolor="#c2003d"></td>
+ <td bgcolor="#0c00f3"></td>
+ <td bgcolor="#0c00f3"></td>
+ <td bgcolor="#6a0095"></td>
+ <td bgcolor="#1500ea"></td>
+ <td bgcolor="#ff0000"></td>
+ <td bgcolor="#ea0015"></td>
+ <td bgcolor="#0000ff"></td>
+ <td bgcolor="#b0004f"></td>
+ <td bgcolor="#cb0034"></td>
+ <td bgcolor="#4600b9"></td>
+ <td bgcolor="#5e00a1"></td>
+ <td bgcolor="#61009e"></td>
+ <td bgcolor="#5b00a4"></td>
+ <td bgcolor="#4f00b0"></td>
+ <td bgcolor="#f60009"></td>
+ <td bgcolor="#0c00f3"></td>
+ <td bgcolor="#680097"></td>
+ <td bgcolor="#0c00f3"></td>
+ </tr>
+ <tr>
+ <td>Helix Propensity</td>
+ <td bgcolor="#e718e7"></td>
+ <td bgcolor="#6f906f"></td>
+ <td bgcolor="#1be41b"></td>
+ <td bgcolor="#778877"></td>
+ <td bgcolor="#23dc23"></td>
+ <td bgcolor="#926d92"></td>
+ <td bgcolor="#ff00ff"></td>
+ <td bgcolor="#00ff00"></td>
+ <td bgcolor="#758a75"></td>
+ <td bgcolor="#8a758a"></td>
+ <td bgcolor="#ae51ae"></td>
+ <td bgcolor="#a05fa0"></td>
+ <td bgcolor="#ef10ef"></td>
+ <td bgcolor="#986798"></td>
+ <td bgcolor="#00ff00"></td>
+ <td bgcolor="#36c936"></td>
+ <td bgcolor="#47b847"></td>
+ <td bgcolor="#8a758a"></td>
+ <td bgcolor="#21de21"></td>
+ <td bgcolor="#857a85"></td>
+ <td bgcolor="#49b649"></td>
+ <td bgcolor="#758a75"></td>
+ <td bgcolor="#c936c9"></td>
+ </tr>
+ <tr>
+ <td nowrap>Strand Propensity</td>
+ <td bgcolor="#5858a7"></td>
+ <td bgcolor="#6b6b94"></td>
+ <td bgcolor="#64649b"></td>
+ <td bgcolor="#2121de"></td>
+ <td bgcolor="#9d9d62"></td>
+ <td bgcolor="#8c8c73"></td>
+ <td bgcolor="#0000ff"></td>
+ <td bgcolor="#4949b6"></td>
+ <td bgcolor="#60609f"></td>
+ <td bgcolor="#ecec13"></td>
+ <td bgcolor="#b2b24d"></td>
+ <td bgcolor="#4747b8"></td>
+ <td bgcolor="#82827d"></td>
+ <td bgcolor="#c2c23d"></td>
+ <td bgcolor="#2323dc"></td>
+ <td bgcolor="#4949b6"></td>
+ <td bgcolor="#9d9d62"></td>
+ <td bgcolor="#c0c03f"></td>
+ <td bgcolor="#d3d32c"></td>
+ <td bgcolor="#ffff00"></td>
+ <td bgcolor="#4343bc"></td>
+ <td bgcolor="#797986"></td>
+ <td bgcolor="#4747b8"></td>
+ </tr>
+ <tr>
+ <td>Turn Propensity</td>
+ <td bgcolor="#2cd3d3"></td>
+ <td bgcolor="#708f8f"></td>
+ <td bgcolor="#ff0000"></td>
+ <td bgcolor="#e81717"></td>
+ <td bgcolor="#a85757"></td>
+ <td bgcolor="#3fc0c0"></td>
+ <td bgcolor="#778888"></td>
+ <td bgcolor="#ff0000"></td>
+ <td bgcolor="#708f8f"></td>
+ <td bgcolor="#00ffff"></td>
+ <td bgcolor="#1ce3e3"></td>
+ <td bgcolor="#7e8181"></td>
+ <td bgcolor="#1ee1e1"></td>
+ <td bgcolor="#1ee1e1"></td>
+ <td bgcolor="#f60909"></td>
+ <td bgcolor="#e11e1e"></td>
+ <td bgcolor="#738c8c"></td>
+ <td bgcolor="#738c8c"></td>
+ <td bgcolor="#9d6262"></td>
+ <td bgcolor="#07f8f8"></td>
+ <td bgcolor="#f30c0c"></td>
+ <td bgcolor="#7c8383"></td>
+ <td bgcolor="#5ba4a4"></td>
+ </tr>
+ <tr>
+ <td>Buried Index</td>
+ <td bgcolor="#00a35c"></td>
+ <td bgcolor="#00fc03"></td>
+ <td bgcolor="#00eb14"></td>
+ <td bgcolor="#00eb14"></td>
+ <td bgcolor="#0000ff"></td>
+ <td bgcolor="#00f10e"></td>
+ <td bgcolor="#00f10e"></td>
+ <td bgcolor="#009d62"></td>
+ <td bgcolor="#00d52a"></td>
+ <td bgcolor="#0054ab"></td>
+ <td bgcolor="#007b84"></td>
+ <td bgcolor="#00ff00"></td>
+ <td bgcolor="#009768"></td>
+ <td bgcolor="#008778"></td>
+ <td bgcolor="#00e01f"></td>
+ <td bgcolor="#00d52a"></td>
+ <td bgcolor="#00db24"></td>
+ <td bgcolor="#00a857"></td>
+ <td bgcolor="#00e619"></td>
+ <td bgcolor="#005fa0"></td>
+ <td bgcolor="#00eb14"></td>
+ <td bgcolor="#00b649"></td>
+ <td bgcolor="#00f10e"></td>
+ </tr>
+ </table>
+ </td>
+ </tr>
+ </table>
+ <p> </p>
+ <p>
+ <strong>Nucleotide Colour Schemes</strong>
+ </p>
+ <table border="1">
+ <tr>
+ <td>
+ <table border="1">
+ <tr>
+ <td nowrap></td>
+ <td>A</td>
+ <!--Adenine-->
+ <td>C</td>
+ <!--Cytosine-->
+ <td>G</td>
+ <!--Guanine-->
+ <td>T</td>
+ <!--Thymine-->
+ <td>U</td>
+ <!--Uracil-->
+ <td>I</td>
+ <!--Inosine-->
+ <td>X</td>
+ <!--Xanthine-->
+ <td>R</td>
+ <!--Unknown Purine-->
+ <td>Y</td>
+ <!--Unknown Pyrimidine-->
+ <td>N</td>
+ <!--Unknown-->
+ <td>W</td>
+ <!--Weak nucleotide (A or T)-->
+ <td>S</td>
+ <!--Strong nucleotide (G or C)-->
+ <td>M</td>
+ <!--Amino (A or C)-->
+ <td>K</td>
+ <!--Keto (G or T)-->
+ <td>B</td>
+ <!--Not A (G or C or T)-->
+ <td>H</td>
+ <!--Not G (A or C or T)-->
+ <td>D</td>
+ <!--Not C (A or G or T)-->
+ <td>V</td>
+ <!--Not T (A or G or C-->
+ </tr>
+ <tr>
+ <td height="24">Nucleotide</td>
+ <td bgcolor="#64F73F"></td>
+ <td bgcolor="#FFB340"></td>
+ <td bgcolor="#EB413C"></td>
+ <td bgcolor="#3C88EE"></td>
+ <td bgcolor="#3C88EE"></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ </tr>
+ <tr>
+ <td height="24">Purine/Pyrimidine</td>
+ <td bgcolor="#FF83FA"></td>
+ <td bgcolor="#40E0D0"></td>
+ <td bgcolor="#FF83FA"></td>
+ <td bgcolor="#40E0D0"></td>
+ <td bgcolor="#40E0D0"></td>
+ <td></td>
+ <td></td>
+ <td bgcolor="#FF83FA"></td>
+ <td bgcolor="#40E0D0"></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ </tr>
+ </table>
+ </td>
+ </tr>
+ </table>
- </div>
- <p align="center"> </p>
+ </div>
+ <p align="center"> </p>
</body>
</html>
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>
</tr>
<tr>
<td>
- <div align="center">-vdoc VAMSAS DOCUMENT FILE/URL</div>
- <td>
- <div align="left">
- Import the given vamsas document into a new session.<br>
- <em>New in 2.5</em>
- </div>
- </td>
- </tr>
- <tr>
- <td>
- <div align="center">-vsess VAMSAS SESSION URL</div>
- <td>
- <div align="left">
- Join the given vamsas session<br>If a document was also
- specified, this will be imported first and then committed as
- new data from Jalview to the specified session (Experimental -
- not yet enabled!).<em>New in 2.5</em>
- </div>
- </div>
- </td>
- </tr>
- <tr>
- <td>
<div align="center">-fasta FILE</div>
</td>
<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>
<body>
<p>
<strong>Sequence Features File</strong>
+
<p>
- <p>The Sequence features file (which used to be known as the
- "Groups file" prior to version 2.08) is a simple way of getting your
- own sequence annotations into Jalview. It was introduced to allow
- sequence features to be rendered in the Jalview applet, and so is
- intentionally lightweight and minimal because the applet is often
- used in situations where data file size must be kept to a minimum,
- and no XML parser is available.</p>
+
+ <p>The Sequence features File provides a simple way of getting
+ your own sequence features into Jalview. It also allows feature
+ display styles and filters to be saved and imported to another
+ alignment. Users familiar with the earliest versions of Jalview will
+ know that features files were originally termed 'groups' files, and
+ that the format was was designed as a space efficient format to
+ allow sequence features to be rendered in the Jalview applet.</p>
<p>
Features files are imported into Jalview in the following ways:<br>
+
<ul>
<li>from the command line <pre>
<strong> -features <<em>Features filename</em>></strong>
</li>
</ul>
- </p>
-
<p>
<strong>Sequence Features File Format</strong>
</p>
<p>
A features file is a simple ASCII text file, where each line
contains tab separated text fields. <strong>No comments are
- allowed</strong>.
+ allowed</strong>. Its structure consists of three blocks:
</p>
+ <ul>
+ <li><a href="#colourdefs">Feature Colour Specifications</a>
+ define how features of a particular type are rendered.</li>
+ <li><a href="#filterdefs">Feature Filters</a> provide a way of
+ excluding features of a particular type from display and analysis.
+ (new in Jalview 2.11)</li>
+ <li><a href="#featuredef">Sequence Feature definitions</a> -
+ tab separated fields that describe groups of positional and
+ non-positional features. Data can also be provided as <a href="#gff">GFF</a></li>
+ </ul>
+
<p>
- <strong>Feature Colours</strong>
+ <strong><a name="colourdefs">Feature Colours</a></strong>
</p>
<p>The first set of lines contain feature type definitions and their colours:
<pre>
-<strong><em>Feature label</em>	<em>Feature Colour</em>
+<strong><em><Feature Type></em>	<em><Feature Style></em>
<!-- 	<em>Feature links</em> --></strong>
</pre>
- A feature type has a text label, and a colour specification. This can
- be either:
-
- <ul>
- <li>A single colour specified as either a red,green,blue 24 bit
+ Each feature type definition assigns a style to features of the given type. <Feature Style> can be either a simple colour, or a more complex <a href="featureschemes.html">Graduated Colour Scheme</a> that shades features according to their description, score, or other attributes.
+<p>
+ <em>Assigning a colour for a <Feature Type></em><br/>A single colour specified as either a red,green,blue 24 bit
triplet in hexadecimal (eg. 00ff00) or as comma separated numbers
(ranging from 0 to 255))<br>
- (For help with colour values, see <a href="https://www.w3schools.com/colors/colors_converter.asp">https://www.w3schools.com/colors/colors_converter.asp</a>.)</li>
-
- <li>A <a href="featureschemes.html">graduated colourscheme</a>
- specified as a "|" separated list of fields: <pre>
-[label <em>or</em> score<em> or</em> attribute|attName|]<mincolor>|<maxcolor>|[absolute|]<minvalue>|<maxvalue>[|<novalue>][|<thresholdtype>|[<threshold value>]]
-</pre> The fields are as follows:
-
- <ul>
- <li><em>label</em><br> Indicates that the feature
- description should be used to create a colour for features of
- this type.<br> <em>Note: if no threshold value is
- needed then only 'label' is required.<br> This
- keyword was added in Jalview 2.6
- </em></li>
-
- <li><em>score</em><br> Indicates that the feature
- score should be used to create a graduated colour for features of
- this type, in conjunction with mincolor, maxcolor.<br><em>This keyword was added in Jalview 2.11.
- It may be omitted (score is the default) if mincolor and maxcolor are specified.
- </em></li>
-
- <li><em>attribute|attName</em><br> Indicates that the value of feature
- attribute 'attName' should be used to create a colour for features of
- this type.
- <br>For example, <em>attribute|clinical_significance</em> to colour by clinical_significance.
- <br>To colour by range of a numeric attribute, include <em>mincolor</em> and <em>maxcolor</em>, or omit to colour by text (category).
- <br>(Note: the value of the attribute used for colouring will also be shown in the tooltip as you mouse over features.)
- <br>A sub-attribute should be written as, for example, CSQ:IMPACT.
- <br><em>This keyword was added in Jalview 2.11</em></li>
-
- <li><em>mincolor</em> and <em>maxcolor</em><br> Colour
- triplets specified as hexadecimal or comma separated values
- (may be left blank for a <em>label</em> style colourscheme,
- but remember to specify the remaining fields)</li>
-
- <li><em>absolute</em><br> An optional switch
- indicating that the <em>minvalue</em> and <em>maxvalue</em>
- parameters should be left as is, rather than rescaled
- according to the range of scores for this feature type.</li>
-
- <li><em>minvalue</em> and <em>maxvalue</em><br>
- Minimum and maximum values defining the range of scores for
- which the colour range will be defined over.<br>If minvalue is
- greater than maxvalue then the linear mapping will have
- negative gradient.</li>
-
- <li><em>novalue</em> <br>
- Specifies the colour to use if colouring by attribute, when the attribute is absent.
- Valid options are <em>novaluemin, novaluemax, novaluenone</em>, to use mincolor, maxcolor, or no colour.
- <br>If not specified this will default to novaluemin.</li>
-
- <li><em>thresholdtype</em><br> Either
- "none", "below", or "above". <em>below</em>
- and <em>above</em> require an additional <em>threshold
- value</em> which is used to control the display of features with
- a score either below or above the value.</li>
- </ul>
- </li>
+ (For help with colour values, see <a href="https://www.w3schools.com/colors/colors_converter.asp">https://www.w3schools.com/colors/colors_converter.asp</a>.)</p>
+ <p><em>Specifying a <a href="featureschemes.html">Graduated Colourscheme</a></em><br/>
+ Data dependent feature colourschemes are defined by a series of "|" separated fields: <pre>
+[label <em>or</em> score<em> or</em> attribute|<attName>|]<mincolor>|<maxcolor>|[absolute|]<minvalue>|<maxvalue>[|<novalue>][|<thresholdtype>|[<threshold value>]]
+</pre><br/>The fields are interpreted follows:
+
+ <ul>
+ <li><em>label</em><br> Indicates that the feature
+ description should be used to create a colour for features of this
+ type.<br> <em>Note: if no threshold value is needed then
+ only 'label' is required.<br> This keyword was added in
+ Jalview 2.6
+ </em></li>
+
+ <li><em>score</em><br> Indicates that the feature score
+ should be used to create a graduated colour for features of this
+ type, in conjunction with mincolor, maxcolor.<br>
+ <em>This keyword was added in Jalview 2.11. It may be omitted
+ (score is the default) if mincolor and maxcolor are specified. </em></li>
+
+ <li><em>attribute|<attName></em><br> Indicates that
+ the value of feature attribute 'attName' should be used to create
+ a colour for features of this type. <br>For example, <em>attribute|clinical_significance</em>
+ to colour by "clinical_significance". <br>To colour by range
+ of a numeric attribute, include <em>mincolor</em> and <em>maxcolor</em>,
+ or omit to colour by text (category). <br>(Note: the value of
+ the attribute used for colouring will also be shown in the tooltip
+ as you mouse over features.) <br>A sub-attribute should be
+ written as, for example, CSQ:IMPACT. <br>
+ <em>This keyword was added in Jalview 2.11</em></li>
+
+ <li><em>mincolor</em> and <em>maxcolor</em><br> Colour
+ triplets specified as hexadecimal or comma separated values (may
+ be left blank for a <em>label</em> style colourscheme, but
+ remember to specify the remaining fields)</li>
+
+ <li><em>absolute</em><br> An optional switch indicating
+ that the <em>minvalue</em> and <em>maxvalue</em> parameters should
+ be left as is, rather than rescaled according to the range of
+ scores for this feature type.<br /> <em>This also enables
+ the 'Threshold is Min/Max' option for this type's feature
+ shading style dialog.</em></li>
+
+ <li><em>minvalue</em> and <em>maxvalue</em><br> Minimum
+ and maximum values defining the range of scores for which the
+ colour range will be defined over.<br>If minvalue is greater
+ than maxvalue then the linear mapping will have negative gradient.</li>
+
+ <li><em>novalue</em> <br> Specifies the colour to use if
+ colouring by attribute, when the attribute is absent. Valid
+ options are <em>novaluemin, novaluemax, novaluenone</em>, to use
+ mincolor, maxcolor, or no colour. <br>If not specified this
+ will default to novaluemin.</li>
+
+ <li><em>thresholdtype</em><br> Either "none",
+ "below", or "above". <em>below</em> and <em>above</em>
+ require an additional <em>threshold value</em> which is used to
+ control the display of features with a score either below or above
+ the value.</li>
</ul>
- </p>
<p>
- <strong>Feature Filters</strong>
+ <strong><a name="filterdefs">Feature Filters</a></strong>
</p>
<p>This section is optional, and allows one or more filters to be defined for each feature type.
<br>Only features that satisfy the filter conditions will be displayed.
</p>
<p>
- <strong>Feature Instances</strong>
+ <strong><a name="featuredef">Feature Definitions</a></strong>
</p>
- <p>The remaining lines in the file are the sequence annotation
- definitions, where the now defined features are attached to regions
- on particular sequences. Each feature can optionally include some
- descriptive text which is displayed in a tooltip when the mouse is
- near the feature on that sequence (and may also be used to generate
- a colour for the feature).</p>
+ <p>The remaining lines in the file are sequence feature data.
+ Features are either non-positional - attached to a whole sequence
+ (as specified by its ID), or positional, so attached to a specific
+ range on a sequence. In addition to a type, features can also
+ include descriptive text and a score, and depending on the format
+ used, many additional attributes.</p>
+ <em><a name="gff">Importing Generalised Feature Format (GFF) feature data</a></em>
<p>
- If your sequence annotation is already available in <a href="http://gmod.org/wiki/GFF2">GFF2</a> (http://gmod.org/wiki/GFF2) or
- <a href="https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md">GFF3</a>
- (http://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md) format,
- then you can leave it as is, after first adding a line containing only
- 'GFF' after any Jalview feature colour definitions (<em>this
- mixed format capability was added in Jalview 2.6</em>). Alternately,
- you can use Jalview's own sequence feature annotation format, which
- additionally allows HTML and URLs to be directly attached to each
- piece of annotation.
+ Jalview has its own tabular format (described below) for describing
+ sequence features, which allows HTML descriptions (including URLs)
+ to be defined for each feature. However, sequence feature
+ definitions can also be provided in <a
+ href="http://gmod.org/wiki/GFF2">GFF2</a>
+ (http://gmod.org/wiki/GFF2) or <a
+ href="https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md">GFF3</a>
+ (http://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md)
+ format. To do this, a line containing only 'GFF' should precede any
+ GFF data (<em>this mixed format capability was added in Jalview
+ 2.6</em>).
</p>
<p>
- <strong>Jalview's sequence feature annotation format</strong>
+ <em>Jalview's sequence feature format</em>
</p>
<p>Each feature is specified as a tab-separated series of columns
as defined below:
<body>
<p>
- <strong>Sequence feature colour schemes</strong>
- </p>
- <p>
- Jalview can visualize annotation present on parts of a sequence by
- overlaying colours according to the annotation present at each
- position. It allows features to be colored either according to type,
- or for a particular type, according to an individual feature's
- associated label or score. The <a href="featuresettings.html">Feature
- Settings dialog box</a> controls the order and display of each
- sequence annotation type, and also allows the colour scheme used for
- the the feature to be changed <em>via</em> the 'Graduated Colour'
- option in the sequence feature pop-up menu (obtained by
- right-clicking on a sequence feature).
+ <strong>Visualisation of Sequence Features</strong>
</p>
+ <p>Jalview can visualize sequence features - the positional
+ annotation present on parts of a sequence, as colours overlaid on
+ corresponding positions in the alignment. Features may be coloured
+ either according to their type, or for a particular type, according to
+ each feature's associated label, score, or other attributes.</p>
+ <p>
+ The <a href="featuresettings.html">Feature Settings dialog box</a>
+ controls the order and display of each feature type, and
+ also allows filters and colour schemes to be configured.
+ </p>
- <center>
- <img src="featurecoloursettings.gif"><br />Graduated feature
- colour scheme settings dialog box</img>
- </center>
- <p>The Graduated Feature Colour dialog box has the following
- controls:
- <ul>
- <li><em>Colour by Label</em> - when checked this derives a
- colour for each feature based on the label text.</li>
- <li><em>Min and Max Color boxes</em> - Click on these boxes to
- set the minimum and maximum colours used to shade features by
- their associated score.</li>
- <li><em>Threshold type combo box</em> - Allows features to be
- hidden features if their score is below or above a given
- threshold.<br /> <em>Set the threshold using the slider or
- type it in to the text box. The threshold cannot be set outside
- the available range of feature scores.</em></li>
- <li><em>Threshold is Min/Max</em> - When checked, the threshold
- will be used as the upper or lower limit when shading the features
- according to their score using the Min and Max colour.</li>
- </ul>
- </p>
- <p>
- <strong>Icon styles for graduated feature styles</strong><br />
- <p>
- When a graduated colourscheme is applied to a feature, it is
- indicated in the feature settings or amend feature dialog box by the
- following types of icon:<br />
- <center>
- <table width="50%" border="1">
- <tr>
- <td><strong>Type of Colouring</strong></td>
- <td><strong>Icon</strong></td>
- </tr>
- <tr>
- <td><em>Graduated colour by Feature Score</em></td>
- <td><img src="fcsminmax.gif" /></td>
- </tr>
- <tr>
- <td><em>Graduated colour thresholded (less than) by
- feature Score</em></td>
- <td><img src="fcsltthan.gif" /></td>
- </tr>
- <tr>
- <td><em>Graduated colour thresholded (greater than) by
- feature Score</em></td>
- <td><img src="fcsgtthan.gif" /></td>
- </tr>
- <tr>
- <td><em>Colour by Feature Label (may also be
- thresholded)</em></td>
- <td><img src="fcsntlabel.gif" /></td>
- </tr>
- <tr>
- <td align="center" colspan="2"><em> <strong>The
- current threshold is given in the icon's tooltip.</strong>
- </em></td>
- </tr>
- </table>
- </center>
- </p>
- <em>Graduated feature colours were introduced in Jalview 2.5</em>
+
+ <div align="center">
+ <img src="featureDisplaySettings.png" /><br />
+ <em>Feature Display Settings dialog for 'sequence_variant'
+ features imported from VCF</em>
+ </div>
+ <p>The Feature Display Settings has the following controls:
+ <p><strong>Colour</strong></p>
+ <ul>
+ <li><em>Simple Colour</em> - select this to assign a given colour
+ to any features of this type. The assigned colour can be changed by
+ clicking on the colour box.</li>
+ <li><em>Colour by text</em> - this option derives a colour for
+ each feature based on its label, or any other attributes presented <em>via</em>
+ the drop-down menu.</li>
+ <li><em>Graduated Colour</em> - shade features according to
+ associated score, or other numeric attribute.
+ <ul>
+ <li><em>Min and Max Color boxes</em> - Click on these boxes to
+ set the minimum and maximum colours for the shading scheme.</li>
+ <li><em>Threshold type combo box</em> - Specify an exclusion
+ threshold.<br />Set the threshold using the slider or
+ type it in to the text box. The threshold cannot be set outside
+ the available range of values observed for the selected attribute.</li>
+ <li><em>Threshold is Min/Max</em> - When checked, the threshold
+ will be used as the upper or lower limit for shading using the Min
+ and Max colour.</li>
+ </ul></li>
+ </ul>
+ <p>
+ <strong><em>Filters</em></strong><br /> Any number of filter
+ conditions may be specified to select features based on one or more
+ attributes. The <strong>join</strong> condition specifies whether all
+ filters must apply (<strong><em>And</em></strong>) or whether any one
+ filter must apply (<strong><em>Or</em></strong>) for a feature to be
+ selected.
+ </p>
+ <p>The filters available depend on the type of attribute:</p>
+ <ul>
+ <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 (not case sensitive).</li>
+ </ul>
+ <p>
+ The filters and colour schemes active for a particular feature type
+ are shown in the <em>Colour</em> and <em>Configuration</em> columns in
+ the feature settings dialog. Styles and filters can be saved as a
+ Jalview Feature Colours file, and are also exported and imported via <a
+ href="featuresFormat.html">Jalview Feature files</a>.
+
+ <p>
+ <strong>Icon styles for feature rendering styles</strong><br />
+
+ <p>
+ When a graduated colour scheme is applied to a feature according to
+ the value of a particular attribute, it is indicated in the feature
+ settings or amend feature dialog box by the following types of icon:<br />
+
+ <div align="center">
+ <table width="50%" border="1">
+ <tr>
+ <td><strong>Type of Colouring</strong></td>
+ <td><strong>Icon</strong></td>
+ </tr>
+ <tr>
+ <td><em>Graduated colour by Feature Score</em></td>
+ <td><img src="fcsminmax.gif" /></td>
+ </tr>
+ <tr>
+ <td><em>Graduated colour thresholded (less than) by
+ 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 (or other attribute)</em></td>
+ <td><img src="fcsgtthan.gif" /></td>
+ </tr>
+ <tr>
+ <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 shown in the icon's tooltip.</strong>
+ </em></td>
+ </tr>
+ </table>
+ </div>
+ </p>
+ <em>Graduated feature colours were introduced in Jalview 2.5.
+ Attribute based colouring and filters were added in Jalview 2.11.</em>
</body>
</html>
<p>
<strong>Sequence Feature Settings Dialog Box</strong>
</p>
+ <p>
+ Select <strong>View→Feature Settings...</strong> in an alignment
+ window to open the feature settings dialog box, which allows
+ precise control of the visibility and appearance of sequence features for
+ an alignment view.
+ </p>
+ <div align="center">
+ <img src="featureSettings.png" width="400"> <br/>
+ Sequence Feature Settings for the Jalview Application (version 2.11)
+ </div>
+ <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 is shown in a tooltip when the mouse
+ hovers over their checkbox.</p>
+ <p><em>Feature colour schemes and filters</em>
+ <p>
+ The table in the middle lists all the feature types in the currently
+ selected groups, along with their display style, any configured
+ filters, and a tickbox indicating whether the type is enabled for
+ display.</p><p>Features may be highlighted with either a single colour or a <a
+ href="featureschemes.html">feature colourscheme</a> based on
+ either the scores associated with that feature or from the feature's
+ description (e.g. to distinguish different names associated with a
+ DOMAIN feature).The colour used for a feature can
+ be changed by clicking on its <strong><em>colour box</em></strong>. To configure the shading
+ style or filter for a feature, click its <strong><em>configuration</em></strong> box.
+ </p>
+ <p>
+ <em>Feature settings pop-up menu</em><br> <strong>Right-click</strong>
+ on a feature to open a pop-up menu that allows you to
+ <ul>
+ <li>Hide, show and select columns containing that feature</li>
+ <li>Sort the alignment or current selection according to count or score for that feature
+ type (see below)</li>
+ </ul>
+
+ <p>
+ <strong>Transparency and Feature Ordering</strong>
+ </p>
+ <p>Sequence features represent a variety of different types of
+ positional annotation, and often overlap. For example, a metal binding
+ site feature may be attached to one position along a stretch of
+ sequence marked with a secondary structure feature.</p>
+ <p>
+ The ordering of the sequence features in the dialog box list is the
+ order used by Jalview for rendering sequence features. A feature at
+ the bottom of the list is rendered <em>below</em> a feature higher
+ up in the list.<br> <em><strong>You can change
+ the order of a feature by dragging it up and down the list with
+ the mouse.</strong></em>
+ </p>
+ <p>
+ Use the <strong><em>Optimise order</em></strong> button to adjust the
+ feature render ordering to place features that on average cover shorter regions
+ of sequence above features annotating longer regions.
+ </p>
+ <p><a name="transparency"></a>
+ The <strong><em>transparency slider</em></strong> controls
+ the visibility of features rendered below other features. Reducing
+ the transparency will mean that features at the top of the list can
+ obscure features lower down, and increasing it allows the user to
+ 'see through' the upper layers of a set of features.
+ </p>
<p>
- Select <strong>View→Feature Settings...</strong> menu entry in
- an alignment window to open the feature settings dialog box, which
- allows you to precisely control the presence and appearance of
- sequence features for the current alignment.
+ <strong><em>You can save all features, with their
+ current colours and visibility in a Jalview format file. </em></strong>
</p>
- <center>
- <img src="featureSettings.gif" width="400" height="452"> <br>
- Sequence Feature Settings for the Jalview Application</img>
- </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. The table in the middle lists all the
- features in the currently selected groups, along with their display
- style and whether they are currently being displayed (only the
- ticked features and groups are displayed). <strong><em>You
- can change the colour or shading style used for a feature in the
- associated alignment by clicking on its colour box.</em></strong>
+ <a name="selectbyfeature"><strong>Selecting alignment
+ columns by feature</strong></a>
</p>
<p>
- <a name="selectbyfeature"><strong><em>Selecting
- alignment columns by feature</em></strong></a><br> <strong>Double-clicking
- a feature type</strong> in the <strong>Feature Settings</strong> dialog
- allows you to select columns in the alignment that contain (or do
- not contain) features of that type. If a region of the alignment is
- currently selected, then only features in the current selection will
- be searched. The following keys affect the way in which selections
- are made:
- <ul>
+ Double-clicking a <strong>feature type</strong> in the <strong>Feature
+ Settings</strong> dialog allows you to select columns in the
+ alignment that contain (or do not contain) features of that type that
+ are currently visible (e.g. not filtered out or otherwise excluded due
+ to an applied colour scheme threshold). If a region of the alignment
+ is currently selected, then only features in the current selection
+ will be searched. The following keys affect the way in which
+ selections are made:<ul>
<li>Hold down <strong>Alt</strong> to select columns not
containing features of a particular type.
</li>
<em>Select columns by feature was added in Jalview 2.8.1</em>
</p>
<p>
- <strong><em>Feature settings pop-up menu</em></strong><br> <strong>Right-click</strong>
- on a feature to open a pop-up menu that allows you to
- <ul>
- <li>Hide, show and select columns containing that feature</li>
- <li>Sort the alignment or current selection using that feature
- type (see below)</li>
- <li>Toggle the type of colouring used for the feature</li>
- </ul>
- <p>
- Features may be highlighted with either a single colour or a <a
- href="featureschemes.html">feature colourscheme</a> based on
- either the scores associated with that feature or from the feature's
- description (e.g. to distinguish different names associated with a
- DOMAIN feature).
- </p>
- <p>
<strong><a name="sortbyfeature">Ordering alignment by
- features</a></strong><br> The 'Seq Sort by Score' and 'Seq Sort by
+ features</a></strong></p><p>The 'Seq Sort by Score' and 'Seq Sort by
Density' buttons will sort the alignment based on the average score
or total number of currently active features and groups on each
sequence. To order the alignment using a specific feature type, use
introduced in Jalview 2.5</em>
</p>
- <p>
- <strong>Transparency and Feature Ordering</strong>
- </p>
- <p>It is important to realise that sequence features are often not
- distinct and often overlap (for example, a metal binding site
- feature may be attached to one position along a stretch of sequence
- marked with a secondary structure feature).</p>
- <p>
- The ordering of the sequence features in the dialog box list is the
- order used by Jalview for rendering sequence features. A feature at
- the bottom of the list is rendered <em>below</em> a feature higher
- up in the list.<br> <em><strong>You can change
- the order of a feature by dragging it up and down the list with
- the mouse (not applet)</strong></em>.
- </p>
- <p>
- The <strong><em>Optimise order</em></strong> button (currently only
- available in the application) will re-order the feature render
- ordering based on the average length of each feature type.
- </p>
- <p><a name="transparency"></a>
- The <strong><em>transparency slider setting</em></strong> controls
- the visibility of features rendered below other features. Reducing
- the transparency will mean that features at the top of the list can
- obscure features lower down, and increasing it allows the user to
- 'see through' the upper layers of a set of features.
- </p>
- <p>
- <strong><em>You can save all features, with their
- current colours and visibility in a Jalview format file. </em></strong>
- </p>
</body>
</html>
--- /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.
+ -->
+<head>
+<title>Importing Variants from VCF</title>
+</head>
+<body>
+ <p>
+ <strong>Importing Genomic Variants from VCF</strong>
+ </p>
+
+ <p>Jalview can annotate nucleotide sequences associated with
+ genomic loci with features representing variants imported from VCF
+ files. This new feature in Jalview 2.11, is currently tuned to work
+ best with tab indexed VCF files produced by the GATK Variant
+ Annotation Pipeline (with or without annotation provided by the
+ Ensembl Variant Effect Predictor), but other sources of VCF files
+ should also work.</p>
+ <p>
+ If your sequences have genomic loci, then a <strong>Taxon
+ name</strong> and <strong>chromosome location</strong> should be shown in
+ the Sequence Details report and the Sequence ID tooltip (providing
+ you have enabled it via the submenu in the <em><strong>View</strong></em>
+ menu). Jalview matches the assembly information provided in the VCF
+ file to the taxon name, using an internal lookup table. If a match
+ is found, Jalview employs the Ensembl API's lift-over services to
+ locate your sequences' loci in the VCF file assembly's reference
+ frame. If all goes well, after loading a VCF, Jalview will report
+ the number of variants added as sequence features via the alignment
+ window's status bar. These are added by default when loci are
+ retrieved from Ensembl.
+ </p>
+ <p>
+ <strong>Working with variants from organisms other than
+ H.sapiens.</strong>
+ </p>
+ <ol>
+ <li>Look in your VCF file to identify keywords in the
+ ##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 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
+VCF_ASSEMBLY=assembly19=GRCh37,hs37=GRCh37</pre><br /> <br />These allow
+ annotations to be mapped from both Human 1000genomes VCF files and
+ C.elegans files.
+ </li>
+ </ol>
+ <strong>Work in Progress!</strong>
+ <p>VCF support in Jalview is under active development. Please get
+ in touch via our mailing list if you have any questions, problems or
+ otherwise find it useful !</p>
+</body>
+</html>
<strong>Jalview Project Archives</strong>
</p>
- <p>These are java archives of an XML file containing alignments,
- trees and Jalview display information. A data exchange standard is
- currently being developed, so there is no stable schema yet, but
- Jalview web services will soon make use of the same interchange
- format.</p>
+ <p>These are Zip archives of an XML file containing alignments,
+ trees, Principal Component Analyses (since 2.11.0), 3D structures,
+ and display information for Jalview, VARNA, Jmol and UCSF Chimera.
+ XML documents conform to a schema, and changes to the format are
+ made to ensure future versions of Jalview will be able to read old
+ Jalview project files.</p>
<p>
- For those who want to know...<br> Jalview uses java classes
- automatically created using <a href="http://www.castor.org">Castor</a>.
- Jalview 2.08 uses descriptor classes which significantly increase
- the speed of marshalling / unmarshalling java objects into XML.
- Files created prior to Jalview 2.08 can still be read in, but they
- will be saved in the new format.
+ <em>For those who want to know...</em><br> Jalview 2.11.0
+ onwards employ the JAX-B java to XML binding framework to read and
+ write Jalview project files. Earlier versions of Jalview employed <a
+ href="http://www.castor.org">Castor</a>. Jalview 2.08 used
+ descriptor classes which significantly increase the speed of
+ marshalling / unmarshalling java objects into XML. <br /> <br />
+ Files created prior to Jalview 2.08 can no longer be read by Jalview
+ 2.11.0. If you need to import old project files, then please import
+ them to Jalview 2.10.5 (available from the Jalview version archive)
+ and save the project again to convert it to the new format.
</p>
</body>
</html>
--- /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>
overview that are hidden in the alignment.
</p>
<p>
- <em>Gap Colour</em> - The default colour scheme for a new alignment
- window. If the chosen option is "User Defined" then the
- last User Defined Colour loaded or saved via the User Defined
- Colours panel will be loaded.
- </p>
- <p>
<a name="structure"><strong>"Structure"
Preferences tab</strong></a><em> added in Jalview 2.8.2</em>
</p>
here, by entering the full path to the Chimera executable program.
Double-click this field to open a file chooser dialog.
<p>
+ <p>
+ <em>PDB Fields shown in Search and Structure Summaries</em> - ticks
+ in this table indicate fields shown by default when browsing results
+ of a free text search via the PDB sequence fetcher, or 3D structures
+ offered by the 3D Structure Chooser.<p>
+ <p>
<a name="connections"><strong>"Connections"
Preferences tab</strong></a>
</p>
statement</a> for more information.
</p>
<p>
+ <a name="backups"><strong>The "Backups" Preferences Tab</strong></a>
+ </p>
+ <p>Since Jalview 2.11.0, overwriting an existing file when saving
+ or exporting data will by default trigger a backup file to be
+ created. Several options are provided to control how backup files
+ are named, and how many old versions will be kept.</p>
+ <p>
+ <em>Schemes</em> - select from three default schemes <em>Single Backup</em>, <em>Keep All Versions</em>, and <em>Rolled Backup Files</em>, or choose <em>Custom</em> to enable a previously defined custom scheme.
+ </p><p>
+ <em>Custom</em> - Check this box to adjust the parameters of the currently selected scheme. Once <em>OK</em> is selected these parameters will be saved as the <em>Custom</em> scheme in your user preferences. To revert changes hit <em>Cancel</em>.
+ </p>
+ <p><em>Scheme Examples</em> - shows how backup files will appear according to the currently selected scheme and parameters.
+ </p>
+ <p><em>Deleting Old Backup Files</em> - these settings control how many backups are kept.</p>
+ <p><em>Backup filename strategy</em> - specify the naming convention for numbered backups and how they are ordered.</p>
+ <p>
<a name="links"><strong>The "Links" Preferences
tab</strong></a>
</p>
loaded onto the alignment will automatically sort the alignment.
</p>
<p> </p>
+ <em>Web Services Preferences</em> - documentation for this tab is
+ given in the
+ <a href="../webServices/webServicesPrefs.html">Web Services
+ Preferences section</a>.
<p> </p>
</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>
- Jalview sometimes runs 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> The way
- you increase the memory settings for the JVM depends on which
- installation of Jalview you use:
+ <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">Web Start Version</font></em>
- <p>
- JavaWS sets the JVM parameters through special tags in the JNLP
- file. You can obtain a JNLP file with modified memory settings
- from our service with the following link (replace 2G with
- desired memory in G or M):<br /> <a
- href="http://www.jalview.org/services/launchApp?jvm-max-heap=2G">http://www.jalview.org/services/launchApp?jvm-max-heap=2G</a>
- </p>
- <p>
- Alternatively, if you want to create your own JNLP file then
- please download the latest JNLP file from <a
- href="http://www.jalview.org/webstart/jalview.jnlp">http://www.jalview.org/webstart/jalview.jnlp</a>
- and modify the max-heap-size parameter for the j2se tag in the
- <resources> element. e.g.
- <pre>
-<j2se version="1.7+" initial-heap-size="500M" max-heap-size="1000M"/>
-</pre> In both cases, you should save your new jnlp file somewhere and then
- either point your web browser at the file's url, launch it from
- your file browser, or from a terminal window run javaws (located
- in your Java installation's bin directory) with the file location
- as its argument. The file's url is something like :<br> <pre>
-file://<full path to file>
-</pre> If Jalview doesn't start up, see <a href="#memsetting">below</a>.
- You'll have to edit the above settings in the JNLP file using a
- text editor, save it, and try starting Jalview with it once more.
- </p></li>
- <li><em><font size="3">Install Anywhere version</font></em>
- <p>You need to change the InstallAnywhere configuration
- settings for the application. These are found in different
- places depending upon which operating system you have :
+ <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>Unix/Windows</em>
- <p>Take a look inside the Jalview program installation
- directory (this might be in C:\Program Files\Jalview on
- windows). You should find a file called 'Jalview.lax' in it
- - make a backup, and then add the following lines to the end
- of the original file :
- <pre>
-lax.nl.java.option.java.heap.size.max=1000m
-lax.nl.java.option.java.heap.size.initial=500m
-</pre> Case and (lack of) spaces are important here! Do not add any spaces
- after the m in each line, and do not put any spaces before
- 'lax'.<br> Also there MUST be a carriage return after the
- final line.
- <p></p></li>
- <li><em>Mac OSX</em>
- <p>
- The lines you need to change are in the <em>Info.plist</em>
- file inside the <em>Jalview.app/Contents</em> directory
- (which is where the installAnywhere installation was made) :
-
-
- <pre>
-<key&ht;VMOptions</key&ht;
-<array>
-! <string>-Xms2M</string>
-! <string>-Xmx64M</string>
-</array>
-</pre>Exchange the above two string tags for : <pre>
-<string>-Xms500M</string>
-<string>-Xmx1000M</string>
-</pre>
- <p></p></li>
- </ul>
- <li><font size="3"><em>In all cases</em></font><br> Save
- the file and try to start Jalview in the normal way. If it doesn't
- start, see below...</li>
+ <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>
- <p>
- <em>Please Note:</em> We do modify the default memory settings in
- Jalview from time to time, so you may find different numbers to
- those shown in the examples above.
- </p>
- <font size="3"><em>Jalview doesn't start... What do the
- memory settings mean ?<a name="memsetting"></a>
- </em></font>
- <p>The 1000m value corresponds to the maximum number of megabytes
- of space that java objects can occupy. The 500m is the initial heap
- size that java will run in - increasing this can speed up memory
- allocation if you know you will need 500 meg of memory to begin with
- (ie it should speed up loading large alignments).</p>
- <p>If, after setting the initial and maximum heap size to some
- large value, you cannot actually start Jalview, then the max and
- initial sizes are too big for your machine (there seems to be a
- physical limit related to physical RAM - email the usual address to
- enlighten us if you know better!). Our experiments found 1000m to be
- the biggest setting that could be used on a 1GB machine. Just try
- reducing the sizes until Jalview starts up properly!</p>
- <p>
- We increased the default memory in Jalview 2.10.5 to 1G. To launch
- Jalview with the pre 2.10.5 default memory allocation, use the <a
- href="http://www.jalview.org/webstart/jalview_256MB.jnlp">Jalview
- 256MB JNLP</a>.
- </p>
- <p> </p>
</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>
parsed into sequence associated annotation which can then be
used to sort the alignment via the Sort by→Score menu.
</em> <br></li>
- <li><strong>Translate as cDNA</strong><br> <em>This
+ <li><a name="transcdna"><strong>Translate as cDNA</strong></a><br> <em>This
option is visible for nucleotide alignments. Selecting this
option shows the DNA's calculated protein product in a new <a
href="../features/splitView.html">split frame</a> window. Note
annotations</a>.
</em></li>
<li><strong>Load VCF File<br>
- </strong><em>Load VCF annotations from a plain text or tab-indexed file.
- <br>This option is offered for nucleotide alignments, and requires at least one
- sequence to have known genomic coordinates.
- <br>Genomic coordinates are attached to entries retrieved from Ensembl.
- <br>Support for VCF was added in Jalview 2.11.
- </em></li>
+ </strong><em><a href="../features/importvcf.html">Load VCF annotations</a> from a plain text, or indexed file (.csi,.tsi).
+ <br>Only available for nucleotide alignments, and requires at least one
+ sequence to have known genomic coordinates.</em></li>
<li><strong>Close (Control W)</strong><br> <em>Close
the alignment window. Make sure you have saved your alignment
before you close - either as a Jalview project or by using the <strong>Save
<!-- <li><strong>Enable Experimental Features</strong> <em>Enable or disable <a href="../whatsNew.html#experimental">features still under development</a> in Jalview's user interface. This setting is remembered in your preferences.</em> -->
</ul></li>
- <li><strong>Vamsas</strong> <em>For more details, read the
- <a href="../vamsas/index.html">Jalview VAMSAS documentation</a>.<br />
- When no session is active, the menu provides options for
- initiating a new VAMSAS session:
- </em>
- <ul>
- <li><strong>Connect to<br /></strong> <em>Connect to
- one of the existing sessions available.</em></li>
- <li><strong>New VAMSAS session<br /></strong> <em>Initiates
- a new local VAMSAS session.</em></li>
- <li><strong>Load VAMSAS session...<br /></strong> <em>Opens
- a file browser allowing you to choose a VAMSAS document to
- import into a new local session.</em></li>
- </ul> <em>When Jalview is joined to a VAMSAS session, the menu
- contains the following:</em>
- <ul>
- <li><strong>Session Update<br /></strong> <em>Sends
- alignment data in the Jalview desktop to the VAMSAS session.</em></li>
- <li><strong>Save VAMSAS Session...<br /></strong> <em>Saves
- the current session to a VAMSAS document archive.</em></li>
- <li><strong>Stop VAMSAS Session<br /></strong> <em>Disconnects
- from the current session. You may be asked if you want to
- save the current session's data if no other VAMSAS clients
- are connected.</em></li>
- </ul></li>
<li><strong>Help </strong>
<ul>
<li><strong>About<br>
via the browser when downloading the application, or when the
Jalview Desktop user interface is launched.<br> <br>
<ul>
- <li><i>The JNLP file at
- www.jalview.org/webstart/jalview.jnlp is retrieved to
- determine if you are running the latest version of Jalview.</i></li>
+ <li><i>The Jalview Getdown Launcher</i> (Since 2.11.0) examines release
+ channels every time Jalview launches to determine if a new
+ release is available.</li>
<li><i>The questionnaire web service at
www.jalview.org/cgi-bin/questionnaire.pl is checked and a
unique cookie for the current questionnaire is stored in the
</tr>
<tr>
<td width="60" align="center" nowrap>
- <strong><a name="Jalview.2.11">2.11</a><br />
- <em>tbc/06/2019</em></strong>
+ <strong><a name="Jalview.2.11.0">2.11.0</a><br />
+ <em>04/07/2019</em></strong>
</td>
<td align="left" valign="top">
<ul>
<li>
- <!-- JAL-1793 -->Annotate nucleotide alignments from VCF data files</li>
- <li>
- <!-- JAL-3141 -->Optional automatic backups when saving
- Jalview project or alignment files</li>
- <li>
- <!-- JAL-1767,JAL-2647 -->Principal Components Analysis and
- Viewer state is saved in Jalview Project<br />The 'Change
- parameters' option has also been removed from the PCA viewer</li>
+ <!-- JAL-1059, JAL-3196,JAL-3007,JAL-3236 -->Jalview Native Application and
+ Installers built with <a href="https://www.ej-technologies.com/products/install4j/overview.html">install4j</a> (licensed to the Jalview open
+ source project) rather than InstallAnywhere
+ </li>
<li>
- <!-- JAL-3127 -->New 'Colour by Sequence ID' (subgroup) option</li>
+ <!-- JAL-1929 -->Jalview Launcher System to auto-configure memory
+ settings, receive over the air updates and launch specific
+ versions via (<a href="https://github.com/threerings/getdown">Three
+ Rings' GetDown</a>)
+ </li>
+ <li>
+ <!-- JAL-1839,JAL-3254,JAL-3260 -->File type associations for
+ formats supported by Jalview (including .jvp project files)
+ </li>
+ <li>
+ <!-- JAL-3260 -->Jalview launch files (.jvl) to pass command line
+ arguments and switch between different getdown channels
+ </li>
+ <li>
+ <!-- JAL-3141 -->Backup files created when saving Jalview project
+ or alignment files
+ </li>
+
+ <li>
+ <!-- JAL-1793 -->Annotate nucleotide alignments from VCF data files</li>
+ <li><!-- JAL-2753 -->Version of HTSJDK shipped with Jalview updated to version 2.12.0</li>
<li>
- <!-- JAL-2620 -->Alternative genetic code tables supported for
+ <!-- JAL-2620 -->Alternative genetic code tables for
'Translate as cDNA'</li>
<li>
- <!-- JAL-2933 -->Finder panel remembers last position in each view</li>
- <li>
- <!-- JAL-3198 -->More efficient creation of selections and
- multiple groups when working with large alignments</li>
- <li>
- <!-- JAL-3200 -->Speedier import of annotation rows when
- parsing stockholm files</li>
- <li>
<!-- JAL-3018 -->Update of Ensembl Rest Client to API v10.0</li>
- <li>
- <!-- JAL-2808,JAL-2069 -->Sequence features can be filtered and
- shaded according to any associated attributes (e.g. variant
- attributes from VCF file, or key-value pairs imported from
- column 9 of GFF file)</li>
- <li>
- <!-- JAL-2897 -->Show synonymous codon variants on peptide sequences</li>
- <li>
- <!-- JAL-2792 -->Popup report of a selected sequence feature's details</li>
- <li>
- <!-- JAL-3139,JAL-2816 -->More efficient sequence feature render
- algorithm (Z-sort/transparency and filter aware)</li>
- <li>
- <!-- JAL-2527 -->Alignment Overview now by default shows
- only visible region of alignment (this can be changed in
- user preferences)</li>
- <li>
- <!-- JAL-3169 -->File Chooser stays open after Cancel overwrite</li>
- <li>
- <!-- JAL-2420,JAL-3166 -->Better popup menu behaviour when
- all sequences are hidden</li>
- <li>
- <!-- JAL-1244 -->Status bar shows bounds when dragging a selection
- region, and gap count when inserting or deleting gaps</li>
- <li>
- <!-- JAL-3132 -->Status bar updates over sequence and annotation labels</li>
- <li>
- <!-- JAL-3093 -->Show annotation tooltips and popup menus in wrapped mode</li>
- <li>
- <!-- JAL-3073 -->Can select columns by dragging left/right in annotations</li>
- <li>
- <!-- JAL-3049,JAL-3054 -->Improved tooltips in Feature Settings dialog</li>
- <li>
- <!-- JAL-2814 -->Help button on Uniprot and PDB search panels</li>
- <li>
- <!-- JAL-2621 -->Cursor changes over draggable box in Overview panel</li>
- <li>
- <!-- JAL-3203 -->Overview panel default changed to not show hidden regions</li>
- <li>
- <!-- JAL-3181 -->Consistent ordering of links in sequence id popup menu</li>
- <li>
- <!-- JAL-3021 -->Sequence Details report opens positioned to top of report</li>
- <li>
- <!-- JAL-3218 -->Scale panel popup menu allows Hide selected columns adjacent
- to a hidden column marker</li>
- <li>
- <!-- JAL-2975 -->Can use shift + arrow keys to rotate PCA image incrementally</li>
- <li>
- <!-- JAL-2965 -->PCA depth cueing with graduated colours</li>
- </ul>
+ <li><strong>Enhanced visualisation and analysis of Sequence Features</strong>
+ <ul>
+ <li>
+ <!-- JAL-3140 JAL-2446 -->IntervalStoreJ (NCList
+ implementation that allows updates) used for Sequence Feature collections</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
+ file, or key-value pairs imported from column 9 of GFF
+ file)
+ </li>
+ <li>
+ <!-- JAL-2879 -->Feature Attributes and shading schemes
+ stored and restored from Jalview Projects
+ </li>
+ <li>
+ <!-- JAL-3334 -->Use full Sequence Ontology (via BioJava) to
+ recognise variant features
+ </li>
+ <li>
+ <!-- JAL-2897,JAL-3330 -->Show synonymous codon variants on peptide
+ sequences (also coloured red by default)
+ </li>
+ <li>
+ <!-- JAL-2792 -->Popup window to show full report for a selected sequence feature's
+ details
+ </li>
+ <li>
+ <!-- JAL-3139,JAL-2816,JAL-1117 -->More efficient sequence feature render
+ algorithm (Z-sort/transparency and filter aware)
+ </li>
+ <li>
+ <!-- JAL-3049,JAL-3054 -->Improved tooltips in Feature Settings
+ dialog
+ </li>
+ </ul>
+ </li>
+ <li>
+ <!-- JAL-3205 -->Symmetric score matrices for faster
+ tree and PCA calculations
+ </li>
+ <li><strong>Principal Components Analysis Viewer</strong>
+ <ul>
+ <li>
+ <!-- JAL-1767,JAL-2647 -->Principal Components Analysis results
+ and Viewer state saved in Jalview Project
+ </li>
+ <li><!-- JAL-2962 -->'Change parameters' option removed from viewer's
+ drop-down menus</li>
+ <li>
+ <!-- JAL-2975 -->Can use shift + arrow keys to rotate PCA image
+ incrementally
+ </li>
+ <li>
+ <!-- JAL-2965, JAL-1285 -->PCA plot is depth cued
+ </li>
+ </ul>
+ </li>
+ <li>
+ <!-- JAL-3127 -->New 'Colour by Sequence ID' option
+ </li>
+ <li><strong>Speed and Efficiency</strong>
+ <ul>
+ <li>
+ <!-- JAL-2185,JAL-3198 -->More efficient creation of selections and
+ multiple groups when working with large alignments
+ </li>
+ <li>
+ <!-- JAL-3200 -->Speedier import of annotation rows when parsing
+ Stockholm files
+ </li>
+ </ul>
+ <li><strong>User Interface</strong>
+ <ul>
+ <li>
+ <!-- JAL-2933 -->Finder panel remembers last position in each
+ view
+ </li>
+ <li>
+ <!-- JAL-2527 JAL-3203 -->Alignment Overview now WYSIWIS (What you see is
+ what is shown)<br />Only visible regions of alignment are shown by
+ default (can be changed in user preferences)
+ </li>
+ <li>
+ <!-- JAL-3169 -->File Chooser stays open after responding Cancel
+ to the Overwrite Dialog
+ </li>
+ <li>
+ <!-- JAL-2420,JAL-3166 -->Better popup menu behaviour when all
+ sequences are hidden
+ </li>
+ <li>
+ <!-- JAL-1244 -->Status bar shows bounds when dragging a
+ selection region, and gap count when inserting or deleting gaps
+ </li>
+ <li>
+ <!-- JAL-3132 -->Status bar updates over sequence and annotation
+ labels
+ </li>
+ <li>
+ <!-- JAL-3093 -->Annotation tooltips and popup menus are shown
+ when in wrapped mode
+ </li>
+ <li>
+ <!-- JAL-3073 -->Can select columns by dragging left/right in a graph or histogram
+ annotation
+ </li>
+ <li>
+ <!-- JAL-2814,JAL-437 -->Help button on Uniprot and PDB search panels
+ </li>
+ <li>
+ <!-- JAL-2621 -->Cursor changes over draggable box in Overview
+ panel
+ </li>
+ <li>
+ <!-- JAL-3181 -->Consistent ordering of links in sequence id
+ popup menu
+ </li>
+ <li>
+ <!-- JAL-3080 -->Red line indicating tree-cut position not shown if no subgroups are created</li>
+ <li>
+ <!-- JAL-3042 -->Removed ability to configure length of search history by right-clicking search box</li>
+
+
+ </ul></li>
+ <li><!-- JAL-3232 -->Jalview Groovy Scripting Console updated to Groovy v2.5</li>
+ <li><strong>Java 11 Support (not yet on general release)</strong>
+ <ul>
+ <li>
+ <!-- -->OSX GUI integrations for App menu's 'About' entry and
+ trapping CMD-Q
+ </li>
+ </ul></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>
- </ul>
- <em>Release Processes</em>
- <ul>
- <li>
- Atlassian Bamboo continuous integration server for
- unattended Test Suite execution</li>
- <li>
- <!-- JAL-2864 -->Memory test suite to detect leaks in common
- operations</li>
- <li>
- <!-- JAL-3140 -->IntervalStoreJ (new updatable NCList
- implementation) used for Sequence Feature collections</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>
- </ul>
- </td>
- <td align="left" valign="top">
+ <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
+ 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
+ </li>
+ <li>
+ <!-- JAL-1424 -->Enhanced checks for missing and duplicated keys in Message bundles</li>
+ <li>
+ <!-- JAL-3225 -->Eclipse project configuration managed with
+ gradle-eclipse
+ </li>
<li>
- <!-- JAL-3143 -->Timeouts when retrieving data from Ensembl</li>
- <li>
- <!-- JAL-3244 -->'View [Structure] Mappings' and structure superposition in Jmol fail on Windows</li>
- <li>
- <!-- JAL-3239 -->Text misaligned in EPS or SVG image export with monospaced font</li>
- <li>
- <!-- JAL-3171 -->Warning of 'Duplicate entry' when saving
- Jalview project involving multiple views</li>
- <li>
- <!-- JAL-3164 -->Overview for complementary view in a linked
- CDS/Protein alignment is not updated when Hide Columns by
- Annotation dialog hides columns</li>
- <li>
- <!-- JAL-3158 -->Selection highlighting in the complement of
- a CDS/Protein alignment stops working after making a
- selection in one view, then making another selection in the
- other view</li>
- <li>
- <!-- JAL-3161 -->Annotations tooltip changes beyond visible columns</li>
- <li>
- <!-- JAL-3154 -->Table Columns could be re-ordered in
- Feature Settings and Jalview Preferences panels</li>
- <li>
- <!-- JAL-2865 -->Jalview hangs when closing windows
- or the overview updates with large alignments</li>
- <li>
- <!-- JAL-2750 -->Tree and PCA calculation fails for selected
- region if columns were selected by dragging right-to-left
- and the mouse moved to the left of the first column</li>
- <li>
- <!-- JAL-2846 -->Error message for trying to load in invalid
- URLs doesn't tell users the invalid URL</li>
- <li>
- <!-- JAL-3178 -->Nonpositional features lose feature group
- on export as Jalview features file</li>
- <li>
- <!-- JAL-3097,JAL-3099 -->Blank extra columns drawn or
- printed when columns are hidden</li>
- <li>
- <!-- JAL-3082 -->Regular expression error for '(' in Select Columns by Annotation description</li>
- <li>
- <!-- JAL-3072 -->Scroll doesn't stop on mouse up after
- dragging out of Scale or Annotation Panel</li>
- <li>
- <!-- JAL-3075 -->Column selection incorrect after scrolling out of scale panel</li>
- <li>
- <!-- JAL-3074 -->Left/right drag in annotation can scroll alignment down</li>
- <li>
- <!-- JAL-3108 -->Error if mouse moved before clicking Reveal in scale panel</li>
- <li>
- <!-- JAL-3002 -->Column display is out by one after Page Down, Page Up in wrapped mode</li>
- <li>
- <!-- JAL-2839 -->Finder doesn't skip hidden regions</li>
- <li>
- <!-- JAL-2932 -->Finder searches in minimised alignments</li>
- <li>
- <!-- JAL-2250 -->'Apply Colour to All Groups' not always selected on
- opening an alignment</li>
- <li>
- <!-- JAL-3180 -->'Colour by Annotation' not marked selected in Colour menu</li>
- <li>
- <!-- JAL-3201 -->Per-group Clustal colour scheme changes when
- different groups in the alignment are selected</li>
- <li>
- <!-- JAL-2717 -->Internationalised colour scheme names not shown correctly in menu</li>
- <li>
- <!-- JAL-3206 -->Colour by Annotation can go black at min/max threshold limit</li>
- <li>
- <!-- JAL-3125 -->Value input for graduated feature colour threshold gets 'unrounded'</li>
- <li>
- <!-- JAL-2982 -->PCA image export doesn't respect background colour</li>
- <li>
- <!-- JAL-2963 -->PCA points don't dim when rotated about y axis</li>
- <li>
- <!-- JAL-2959 -->PCA Print dialog continues after Cancel</li>
+ <!-- JAL-3174,JAL-2886,JAL-2729,JAL-1889 -->Atlassian
+ Bamboo continuous integration for unattended Test Suite
+ execution
+ </li>
<li>
- <!-- JAL-3078 -->Cancel in Tree Font dialog resets alignment, not Tree font</li>
+ <!-- JAL-2864 -->Memory test suite to detect leaks in common
+ operations
+ </li>
<li>
- <!-- JAL-2964 -->Associate Tree with All Views not restored from project file</li>
+ <!-- JAL-2360,JAL-2416 -->More unit test coverage, and minor
+ issues resolved
+ </li>
<li>
- <!-- JAL-2915 -->Scrolling of split frame is sluggish if Overview shown in complementary view</li>
+ <!-- JAL-3248 -->Developer documentation migrated to
+ markdown (with HTML rendering)
+ </li>
<li>
- <!-- JAL-2898 -->stop_gained variants not shown correctly on peptide sequence</li>
+ <!-- JAL-3287 -->HelpLinksChecker runs on Windows
+ </li>
<li>
- <!-- JAL-914 -->Help page can be opened twice</li>
+ <!-- JAL-3289 -->New URLs for publishing development
+ versions of Jalview
+ </li>
</ul>
- <em>Editing</em>
+ </td>
+ <td align="left" valign="top">
+ <ul>
+ <li>
+ <!-- JAL-3143 -->Timeouts when retrieving data from Ensembl
+ </li>
+ <li>
+ <!-- JAL-3244 -->'View [Structure] Mappings' and structure
+ superposition in Jmol fail on Windows
+ </li>
+ <li>
+ <!-- JAL-3286 -->Blank error dialog is displayed when discovering
+ structures for sequences with lots of PDB structures
+ </li>
+ <li>
+ <!-- JAL-3239 -->Text misaligned in EPS or SVG image export with
+ monospaced font
+ </li>
+ <li>
+ <!-- JAL-3171 -->Warning of 'Duplicate entry' when saving Jalview
+ project involving multiple views
+ </li>
+ <li>
+ <!-- JAL-3164 -->Overview for complementary view in a linked
+ CDS/Protein alignment is not updated when Hide Columns by
+ Annotation dialog hides columns
+ </li>
+ <li>
+ <!-- JAL-3158 -->Selection highlighting in the complement of a
+ CDS/Protein alignment stops working after making a selection in
+ one view, then making another selection in the other view
+ </li>
+ <li>
+ <!-- JAL-3161 -->Annotations tooltip changes beyond visible
+ columns
+ </li>
+ <li>
+ <!-- JAL-3154 -->Table Columns could be re-ordered in Feature
+ Settings and Jalview Preferences panels
+ </li>
+ <li>
+ <!-- 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
+ region if columns were selected by dragging right-to-left and the
+ mouse moved to the left of the first column
+ </li>
+ <li>
+ <!-- JAL-3218 -->Couldn't hide selected columns adjacent to a
+ hidden column marker via scale popup menu
+ </li>
+ <li>
+ <!-- JAL-2846 -->Error message for trying to load in invalid URLs
+ doesn't tell users the invalid URL
+ </li>
+ <li>
+ <!-- JAL-2816 -->Tooltips displayed for features filtered by
+ score from view
+ </li>
+ <li>
+ <!-- JAL-3330 -->Sequence Variants retrieved from Ensembl during
+ show cross references or Fetch Database References are shown in
+ red in original view
+ </li>
+ <li>
+ <!-- JAL-2898,JAL-2207 -->stop_gained variants not shown correctly on
+ peptide sequence (computed variant shown as p.Res.null)
+ </li>
+ <li>
+ <!-- JAL-2060 -->'Graduated colour' option not offered for
+ manually created features (where feature score is Float.NaN)
+ </li>
+ <li>
+ <!-- JAL-3097,JAL-3099 -->Blank extra columns drawn or printed
+ when columns are hidden
+ </li>
+ <li>
+ <!-- JAL-3082 -->Regular expression error for '(' in Select
+ Columns by Annotation description
+ </li>
+ <li>
+ <!-- JAL-3072 -->Scroll doesn't stop on mouse up after dragging
+ out of Scale or Annotation Panel
+ </li>
+ <li>
+ <!-- JAL-3075 -->Column selection incorrect after scrolling out of
+ scale panel
+ </li>
+ <li>
+ <!-- JAL-3074 -->Left/right drag in annotation can scroll
+ alignment down
+ </li>
+ <li>
+ <!-- JAL-3108 -->Error if mouse moved before clicking Reveal in
+ scale panel
+ </li>
+ <li>
+ <!-- JAL-3002 -->Column display is out by one after Page Down,
+ Page Up in wrapped mode
+ </li>
+ <li>
+ <!-- JAL-2839,JAL-781 -->Finder doesn't skip hidden regions
+ </li>
+ <li>
+ <!-- JAL-2932 -->Finder searches in minimised alignments
+ </li>
+ <li>
+ <!-- JAL-2250 -->'Apply Colour to All Groups' not always selected
+ on opening an alignment
+ </li>
+ <li>
+ <!-- JAL-3180 -->'Colour by Annotation' not marked selected in
+ Colour menu
+ </li>
+ <li>
+ <!-- JAL-3201 -->Per-group Clustal colour scheme changes when
+ different groups in the alignment are selected
+ </li>
+ <li>
+ <!-- JAL-2717 -->Internationalised colour scheme names not shown
+ correctly in menu
+ </li>
+ <li>
+ <!-- JAL-3206 -->Colour by Annotation can go black at min/max
+ threshold limit
+ </li>
+ <li>
+ <!-- JAL-3125 -->Value input for graduated feature colour
+ threshold gets 'unrounded'
+ </li>
+ <li>
+ <!-- JAL-2982 -->PCA image export doesn't respect background
+ colour
+ </li>
+ <li>
+ <!-- JAL-2963 -->PCA points don't dim when rotated about y axis
+ </li>
+ <li>
+ <!-- JAL-2959 -->PCA Print dialog continues after Cancel
+ </li>
+ <li>
+ <!-- JAL-3078 -->Cancel in Tree Font dialog resets alignment, not
+ Tree font
+ </li>
+ <li>
+ <!-- JAL-2964 -->Associate Tree with All Views not restored from
+ project file
+ </li>
+ <li>
+ <!-- JAL-2915 -->Scrolling of split frame is sluggish if Overview
+ shown in complementary view
+ </li>
+ <li>
+ <!-- JAL-3313 -->Codon consensus incorrectly scaled when shown
+ without normalisation
+ </li>
+ <li>
+ <!-- JAL-3021 -->Sequence Details report should open positioned at top
+ of report
+ </li>
+ <li>
+ <!-- JAL-914 -->Help page can be opened twice
+ </li>
+ <li>
+ <!-- JAL-3333 -->Fuzzy text in web service status menu on OSX Mojave
+ </li>
+ </ul> <em>Editing</em>
+ <ul>
+ <li>
+ <!-- JAL-2822 -->Start and End should be updated when sequence
+ data at beginning or end of alignment added/removed via 'Edit'
+ sequence
+ </li>
+ <li>
+ <!-- JAL-2541,JAL-2684 (tests) -->Delete/Cut selection doesn't
+ relocate sequence features correctly when start of sequence is
+ removed (Known defect since 2.10)
+ </li>
+ <li>
+ <!-- JAL-2830 -->Inserting gap sequence via the Edit Sequence
+ dialog corrupts dataset sequence
+ </li>
+ <li>
+ <!-- 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-2822 -->Start and End should be updated when
- sequence data at beginning or end of alignment added/removed
- via 'Edit' sequence</li>
- <li>
- <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
- sequence features correctly when start of sequence is
- removed (Known defect since 2.10)</li>
- </ul>
- <em>New Known Defects</em>
+ <!-- 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-2647 -->Input Data menu entry is greyed out when PCA View is restored from a Jalview 2.11 project</li>
- <li>
- <!-- JAL-3213 -->Alignment panel height can be too small after 'New View'</li>
- <li>
- <!-- JAL-3240 -->Display is incorrect after removing gapped columns within hidden columns</li>
- </ul>
- </td>
- </tr>
+ <!-- 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
+ </li>
+ <li>
+ <!-- JAL-3313 -->Codon consensus logo incorrectly scaled in gapped
+ regions of protein alignment.
+ </li>
+ <li>
+ <!-- JAL-2647 -->Input Data menu entry is greyed out when PCA View
+ is restored from a Jalview 2.11 project
+ </li>
+ <li>
+ <!-- JAL-3213 -->Alignment panel height can be too small after
+ 'New View'
+ </li>
+ <li>
+ <!-- JAL-3240 -->Display is incorrect after removing gapped
+ columns within hidden columns
+ </li>
+ <li>
+ <!-- JAL-3314 -->Rightmost selection is lost when mouse re-enters
+ window after dragging left to select columns to left of visible
+ region
+ </li>
+ <li>
+ <!-- JAL-2876 -->Features coloured according to their description
+ string and thresholded by score in earlier versions of Jalview are
+ 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-3338 -->F2 doesn't enable/disable keyboard mode in linked CDS/Protein view
+ </li>
+ <li>
+ <!-- JAL-797 -->Closing tree windows with CMD/CTRL-W for
+ alignments with multiple views can close views unexpectedly
+ </li>
+ </ul>
+ <em>Java 11 Specific defects</em>
+ <ul>
+ <li>
+ <!-- JAL-3235 -->Jalview Properties file is not sorted
+ alphabetically when saved
+ </li>
+ </ul>
+ </td>
+ </tr>
<tr>
<td width="60" nowrap>
<div align="center">
<!-- 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
open URL in the browser can be dropped onto Jalview.</em>
</li>
</ul>
+ <em>New Known Defects</em>
+ <ul>
+ <li><!-- JAL-3083 -->Cancel option doesn't reset Colour by Annotation</li>
+ </ul>
</div></td>
</tr>
<tr>
<!-- JAL-2593 -->Improved performance when rendering lots
of features (particularly when transparency is disabled)
</li>
+ <li>
+ <!-- JAL-2296,JAL-2295 -->Experimental features in 2.10.2 for
+ exchange of Jalview features and Chimera attributes made
+ generally available
+ </li>
</ul>
</div>
</td>
Sequences' enabled) or Ensembl isoforms (Workaround in
2.10.4 is to fail back to N&W mapping)
</li>
- </ul>
+ <li>
+ <!-- JAL-2990 -->Export Annotations from File Menu with CSV
+ option gives blank output
+ </li>
+ </ul>
</div>
</td>
</tr>
<!-- JAL-2589 -->User defined gap colour not shown in
overview when features overlaid on alignment
</li>
+ <li>
+ <!-- JAL-2567 -->Feature settings for different views not
+ recovered correctly from Jalview project file
+ </li>
+ <li>
+ <!-- JAL-2256 -->Feature colours in overview when first opened
+ (automatically via preferences) are different to the main
+ alignment panel
+ </li>
</ul>
<em>Data import/export</em>
<ul>
+++ /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.
- -->
-<head>
-<title>VAMSAS Interoperation</title>
-</head>
-<body>
- <p>
- <strong>VAMSAS Interoperation</strong>
- </p>
- <p>
- Jalview can interact with other applications using "the <strong>VAMSAS
- Interoperation framework</strong>" which is an experimental model for
- interoperation between bioinformatics applications (<strong>V</strong>isualization
- and <strong>A</strong>nalysis of <strong>Molecular</strong> <strong>S</strong>equences,
- <strong>Alignements</strong> and <strong>S</strong>tructures).
- Currently, the only other VAMSAS enabled application is <a
- href="http://www.topali.org">TOPALi</a> - a user friendly
- program for phylogenetics and evolutionary analysis.
- <p>
- VAMSAS enabled applications access a shared bioinformatics dataset
- containing sequences, alignments, annotation and trees, which can be
- represented by an XML document analogous to a <a
- href="../features/jalarchive.html">Jalview Project
- Archive</a>.
- </p>
- <br>
- <strong>Connecting to a VAMSAS session</strong>
- <br> The VAMSAS functionality in Jalview is accessed through the
- Desktop's
- <strong>Vamsas</strong> menu. The options available in this menu
- depend on whether the application is currently interacting with a
- VAMSAS dataset in a
- <strong>VAMSAS session</strong>. When the application is not connected
- to a session is active, the menu options are as follows:
- <br>
- <ul>
- <li><em>Connect to an existing session</em><br> If
- visible, this submenu contains a list of existing sessions that
- the VAMSAS framework has discovered on your computer. <br>
- Choose one to connect to it.</li>
- <li><em>New VAMSAS Session</em><br> This option will
- create a new session on your computer.</li>
- <li><em>Load VAMSAS Session...</em><br> This option will
- open a file browser window allowing you to select a VAMSAS session
- archive from which a new session will be created.<br /> <em>New
- in 2.5:</em>Sessions created from an imported document inherit the
- file or URL for the document.</li>
-
- </ul>
- <br>
- <strong>VAMSAS and Firewalls</strong>: VAMSAS uses sockets to
- communicate between different programs. This means that after starting
- a session, your firewall software may ask you whether to allow the
- java executable access to the internet (port 53782). If you do not
- allow this, messages will not be exchanged with other VAMSAS
- applications.
- </br>
- <br> Once you have successfully connected to a VAMSAS session,
- any data made available by other VAMSAS applications will be
- automatically imported into Jalview. However, in order to share the
- data in Jalview with other VAMSAS applications, you must manually
- select the
- <strong>Vamsas→"Session Update"</strong> entry that is
- visible when a session is active. Selecting this option will update
- the VAMSAS session document, with the data loaded into Jalview. Any
- new alignments, trees and annotation will be written to the session,
- in addition to any edits you have made to data originally stored in
- the document.
- <br>
- <strong>Saving the current session</strong>
- <br> You can save the current session as a VAMSAS Session archive
- using the
- <strong>Vamsas→"Session Update"</strong>. The file
- contains a snapshot of the current VAMSAS session, including data from
- any other applications connected to the session.
- <strong>Leaving a VAMSAS session</strong>
- <br> A session can be disconnected from at any time using the
- <strong>Vamsas→"Stop Session"</strong> option.
- Selecting this option will only disconnect Jalview from the session -
- any other applications will remain connected to the session. If
- Jalview is the only application connected to the session and you have
- not yet saved the VAMSAS session then you will be prompted with an
- optional 'Save VAMSAS session...' dialog box, allowing the session to
- be saved and returned to at a later date.
- <br>
- <strong>VAMSAS Session Persistence</strong>
- <br> VAMSAS sessions are persistent - this means that they exist
- independently of any VAMSAS applications that are connected to them.
- This means that if something goes wrong with a VAMSAS application and
- it crashes or otherwise fails, the VAMSAS session it is connected to
- will (hopefully) be unaffected. For instance, if Jalview is killed or
- crashes whilst it is still connected to a session, that session can be
- recovered in a new Jalview instance using the
- <strong>Vamsas→"Existing session"</strong> sub menu.
- </p>
- <p>
- <strong>A quick Demo</strong> <br> Jalview can talk to itself
- through VAMSAS. Simply start two copies of the application, create a
- new vamsas session in one, and connect to the new session in the
- other. Then load your data into one of the applications, and use the
- <strong>Vamsas→"Session Update"</strong> menu entry
- to try to propagate the data to the other application. <br>
- <table>
- <tr>
- <td>Data Sharing Capability</td>
- <td>Jalview Version</td>
- </tr>
- <tr>
- <td>Alignments, sequences and annotation, trees, database
- references, cDNA/protein mappings.</td>
- <td>2.4</td>
- </tr>
- <tr>
- <td>Mouseover location across linked DNA, protein and
- structure positions.</td>
- <td>2.4</td>
- </tr>
- <tr>
- <td>Jalview project settings (Multiple views, groups, tree
- partitions, colouring, window positions)</td>
- <td>2.5</td>
- </tr>
- <tr>
- <td>Sequence region and column selections</td>
- <td>2.5</td>
- </tr>
- </table>
- <br />
- <p>
- Version 0.2 of the VAMSAS client library is used in <em>Jalview
- 2.5</em>. For further details about the VAMSAS framework, please check
- the <a href="http://www.vamsas.ac.uk">VAMSAS website</a>. The VAMSAS
- framework is implemented as a Java 1.4 Library and depends on a
- number of other open source projects. Its source is released under
- the LGPL license.
- </p>
-</body>
-</html>
</head>
<body>
<p>
- <strong>Jalview 2.11 - major and minor new features</strong>
+ <strong>Jalview 2.11 - new installer and new capabilities</strong>
</p>
<p>Jalview 2.11 introduces support for loading VCF files, and new
filters and shading models for sequence features. Under the hood,
we've addressed many bugs, and also made some important changes in
the way the Jalview desktop is installed and launched.</p>
<ul>
- <li><em>VCF Support</em>. Proteins and genomic contigs with
- chromosomal location annotation (such as protein coding genes
- retrieved from Ensembl) can be annotated with variants imported
- from a local VCF file.</li>
- <li><em>The Jalview Launcher and Update System</em><br />
+ <li><strong>The Jalview Launcher and Update System</strong>.
Jalview's new installation model means you'll only need to
download and install Jalview once. After installation, Jalview
will automatically keep itself up to date. The launcher also sets
Jalview's memory automatically, so you'll never again have to
- manually configure Java's memory settings.<br />We are grateful to
- Install4J who provided us with a free license for their
- installation system, and Jalview's over the air update system is
- via Getdown.</li>
+ manually configure Java's memory settings.<br />We are grateful
+ to ej Technologies for providing a free open source project
+ license for <a
+ href="https://www.ej-technologies.com/products/install4j/overview.html">install4j</a>,
+ and also to <a
+ href="https://en.wikipedia.org/wiki/Three_Rings_Design">Three
+ Rings Design</a> for Jalview's new over the air update system: <a
+ href="https://github.com/threerings/getdown">Getdown</a>.</li>
+ <li><strong>VCF Support</strong>. Proteins and genomic contigs with
+ chromosomal location annotation (such as protein coding genes
+ retrieved from Ensembl) can be annotated with variants <a
+ href="features/importvcf.html">imported from a local VCF file</a>.</li>
+ <li><strong>Feature filters and attribute colourschemes</strong>. A new
+ <a href="features/featureschemes.html">Feature Display
+ Settings</a> dialog allows filters and feature attribute based
+ colourschemes to be constructed, and a new <em>filters</em> column
+ added to the <a href="features/featuresettings.html">Feature
+ Settings</a> dialog. Jalview's sequence feature datamodel has also
+ been further optimised, and is now maintained as a separate
+ library <em>IntervalStoreJ</em> (available at https://github.com/bartongroup/IntervalStoreJ)</li>
+ <li><strong>Alternative tables for CDS translation</strong>. The <a
+ href="menus/alwcalculate.html">Translate as cDNA</a> option now
+ offers alternative amino acid coding schemes.</li>
+ <li><strong>PCA plots stored in Jalview Projects</strong>. The <a
+ href="calculations/pca.html">PCA viewer</a> user interface has
+ 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
+ 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
+ backup filenames to be configured.</li>
</ul>
<p>
The full list of bugs fixed in this release can be found in the <a
- href="releases.html#Jalview.2.11">2.11 Release Notes</a>.
+ href="releases.html#Jalview.2.11.0">2.11 Release Notes</a>.
</p>
<p>
- <strong>Jalview and Java 11, 13, and onwards</strong>
+ <strong>Jalview and Java 11, and onwards</strong>
+ </p>
+ <p>The Jalview application comes bundled with its own independent
+ Java installation. Version 2.11.0 includes an AdoptOpenJDK Java 1.8
+ runtime which will be kept up to date. A Java 11 based installation
+ is available from the Jalview development pages.</p>
+ <p>
+ <em>Saying goodbye...</em><br>Long time Jalview users will notice
+ that this release no longer features the
+ <em>Vamsas</em> desktop menu, or a <em>Distributed
+ Annotation System (DAS)</em> tab on the feature settings dialog.
+ DAS is no longer supported by major bioinformatics databases, and we
+ decided that it was no longer feasible to maintain either JDAS or
+ the VAMSAS client library which rely on out-dated Java XML binding
+ technologies.
+ </p>
+ <p>
+ <em>Next up...</em><br /> Keep an eye on the Jalview web site for
+ news about JalviewJS - the web based JavaScript implementation of
+ Jalview. Whilst Jalview 2.11 has been in development, we have also
+ been working with Prof. Bob Hanson (Jmol and JSmol) to enable
+ Jalview to run as both a Java application and a JavaScript app in a
+ web page. To find out more, open <em>http://www.jalview.org/jalview-js/</em>
+ in Chrome or Firefox.
</p>
- <p>Java 11 provides improved performance and better OS
- integration, so we now recommend users select our Java 11 Jalview
- distribution rather than the legacy Java 8 build.</p>
- <em>Known Issues - update for 211 </em>
- <ul>
- <li>OSX: The 'Open File' dialog for Jalview's Groovy Console
- appears with the title 'Save As', and attempting to select a file
- to load yields a FileNotFound exception.</br>The workaround is to first
- clear the 'Untitled' filename before selecting the file you wish
- to load.
- </li>
- <li>OSX: Links don't open when clicked on or via the Sequence
- or Alignment window popup menu.</li>
- <li>OSX (Webstart): Jalview only displays old news feed items</li>
- </ul>
</body>
</html>
label.structure_chooser_no_of_structures = Structure Chooser - {0} Found ({1})
info.no_pdb_entry_found_for = No PDB entry found for {0}
exception.unable_to_detect_internet_connection = Jalview is unable to detect an internet connection
-exception.fts_rest_service_no_longer_available = {0} rest services no longer available!
-exception.resource_not_be_found = The requested resource could not be found
-exception.fts_server_error = There seems to be an error from the {0} server
exception.fts_server_unreachable = Jalview is unable to reach the {0} server. \nPlease ensure that you are connected to the internet and try again.
label.nw_mapping = Needleman & Wunsch Alignment
label.sifts_mapping = SIFTs Mapping
action.prev_page= <<
label.next_page_tooltip=Next Page
label.prev_page_tooltip=Previous Page
-exception.bad_request=Bad request. There is a problem with your input.
-exception.service_not_available=Service not available. The server is being updated, try again later.
status.launching_3d_structure_viewer = Launching 3D Structure viewer...
status.fetching_3d_structures_for_selected_entries = Fetching 3D Structures for selected entries...
status.fetching_dbrefs_for_sequences_without_valid_refs = Fetching db refs for {0} sequence(s) without valid db ref required for SIFTS mapping
label.show_selected_annotations=Mostrar anotaciones seleccionadas
status.colouring_chimera=Coloreando Chimera
label.configure_displayed_columns=Configurar Columnas Mostradas
-exception.resource_not_be_found=El recurso solicitado no se ha encontrado
label.aacon_calculations=cálculos AACon
label.pdb_web-service_error=Error de servicio web PDB
exception.unable_to_detect_internet_connection=Jalview no puede detectar una conexión a Internet
exception.outofmemory_loading_mmcif_file=Sin memoria al cargar el fichero mmCIF
label.hide_columns_not_containing=Ocultar las columnas que no contengan
label.pdb_sequence_fetcher=Recuperador de secuencias PDB
-exception.fts_server_error=Parece que hay un error desde el servidor {0}
-exception.service_not_available=Servicio no disponible. El servidor se está actualizando, vuelva a intentarlo más tarde.
status.waiting_for_user_to_select_output_file=Esperando que el usuario seleccione el fichero {0}
action.prev_page=<<
status.cancelled_image_export_operation=Operación de exportación {0} cancelada
label.couldnt_run_groovy_script=No se ha podido ejecutar el script Groovy
-exception.bad_request=Solicitud incorrecta. Hay un problema con su entrada.
label.run_groovy=Ejecutar script Groovy desde la consola
action.next_page=>>
label.uniprot_sequence_fetcher=Recuperador de secuencias UniProt
label.sifts_mapping=Mapeado SIFTs
label.mapping_method=Método de mapeo de secuencia \u27F7 estructura
info.error_creating_file=Error al crear fichero {0}
-exception.fts_rest_service_no_longer_available= Servicios Rest {0} ya no están disponibles!
status.launching_3d_structure_viewer=Lanzando visualizador de estructura 3D...
status.obtaining_mapping_with_sifts=Obteniendo mapeo por SIFTS
status.fetching_3d_structures_for=Buscando la estructura 3D para {0}
for (int col = 0; col < cols; col++)
{
// todo would prefer a Java bean for consensus data
- Hashtable<String, int[]> columnHash = new Hashtable<String, int[]>();
+ Hashtable<String, int[]> columnHash = new Hashtable<>();
// #seqs, #ungapped seqs, counts indexed by (codon encoded + 1)
int[] codonCounts = new int[66];
codonCounts[0] = alignment.getSequences().size();
{
codonCounts[codonEncoded + 2]++;
ungappedCount++;
+ break;
}
}
}
*/
void setFollowHighlight(boolean b);
+ /**
+ * configure the feature renderer with predefined feature settings
+ *
+ * @param featureSettings
+ */
public void applyFeaturesStyle(FeatureSettingsModelI featureSettings);
/**
+ * Apply the given feature settings on top of existing feature settings.
+ */
+ public void mergeFeaturesStyle(FeatureSettingsModelI featureSettings);
+
+ /**
* check if current selection group is defined on the view, or is simply a
* temporary group.
*
*/
boolean isOutwithThreshold(SequenceFeature sf);
- /*
- * Answers a human-readable text description of the colour, suitable for
- * display as a tooltip, possibly internationalised for the user's locale.
+ /**
+ * Answers a human-readable text description of the colour, suitable for display
+ * as a tooltip, possibly internationalised for the user's locale.
*
* @return
*/
}
/**
- * Applies the supplied feature settings descriptor to currently known
- * features. This supports an 'initial configuration' of feature colouring
- * based on a preset or user favourite. This may then be modified in the usual
- * way using the Feature Settings dialogue.
+ * Applies the supplied feature settings descriptor to currently known features.
+ * This supports an 'initial configuration' of feature colouring based on a
+ * preset or user favourite. This may then be modified in the usual way using
+ * the Feature Settings dialogue. NOT IMPLEMENTED FOR APPLET
*
* @param featureSettings
*/
// TODO implement for applet
}
+ /**
+ * Merges the supplied feature settings descriptor with existing feature styles.
+ * This supports an 'initial configuration' of feature colouring based on a
+ * preset or user favourite. This may then be modified in the usual way using
+ * the Feature Settings dialogue. NOT IMPLEMENTED FOR APPLET
+ *
+ * @param featureSettings
+ */
+ @Override
+ public void mergeFeaturesStyle(FeatureSettingsModelI featureSettings)
+ {
+ // TODO Auto-generated method stub
+
+ }
}
}
+ /**
+ * update singleton Strings with these build details
+ *
+ * @param version
+ * @param buildDate
+ * @param installation
+ */
public BuildDetails(String version, String buildDate, String installation)
{
BuildDetails.version = version;
BuildDetails.installation = installation;
}
+ @Override
public String getBuildDate()
{
return buildDate;
BuildDetails.buildDate = buildDate;
}
+ @Override
public String getVersion()
{
return version;
BuildDetails.version = version;
}
+ @Override
public String getInstallation()
{
return installation;
applicationProperties.remove("YEAR");
}
- // FIND THE VERSION NUMBER AND BUILD DATE FROM jalview.jar
- // MUST FOLLOW READING OF LOCAL PROPERTIES FILE AS THE
- // VERSION MAY HAVE CHANGED SINCE LAST USING JALVIEW
- try
- {
- String buildDetails = "jar:".concat(Cache.class.getProtectionDomain()
- .getCodeSource().getLocation().toString()
- .concat("!/.build_properties"));
-
- java.net.URL localJarFileURL = new java.net.URL(buildDetails);
-
- InputStream in = localJarFileURL.openStream();
- applicationProperties.load(in);
- in.close();
- } catch (Exception ex)
- {
- System.out.println("Error reading build details: " + ex);
- applicationProperties.remove("VERSION");
- }
-
- String jnlpVersion = System.getProperty("jalview.version");
- String codeVersion = getProperty("VERSION");
- String codeInstallation = getProperty("INSTALLATION");
- if (codeVersion == null)
- {
- // THIS SHOULD ONLY BE THE CASE WHEN TESTING!!
- codeVersion = "Test";
- jnlpVersion = "Test";
- codeInstallation = "";
- }
- else
- {
- codeInstallation = " (" + codeInstallation + ")";
- }
- new BuildDetails(codeVersion, null, codeInstallation);
+ loadBuildProperties(false);
SiftsSettings
.setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
"http://www.jalview.org/services/identifiers"));
IdOrgSettings.setDownloadLocation(ID_ORG_FILE);
- System.out
- .println("Jalview Version: " + codeVersion + codeInstallation);
-
StructureImportSettings.setDefaultStructureFileFormat(jalview.bin.Cache
.getDefault("PDB_DOWNLOAD_FORMAT", PDB_DOWNLOAD_FORMAT));
StructureImportSettings
// StructureImportSettings
// .setDefaultPDBFileParser(jalview.bin.Cache.getDefault(
// "DEFAULT_PDB_FILE_PARSER", DEFAULT_PDB_FILE_PARSER));
- // jnlpVersion will be null if we're using InstallAnywhere
+
+ String jnlpVersion = System.getProperty("jalview.version");
+
+ // jnlpVersion will be null if a latest version check for the channel needs to
+ // be done
// Dont do this check if running in headless mode
+
if (jnlpVersion == null && getDefault("VERSION_CHECK", true)
&& (System.getProperty("java.awt.headless") == null || System
.getProperty("java.awt.headless").equals("false")))
}
}
- setProperty("VERSION", codeVersion);
-
// LOAD USERDEFINED COLOURS
jalview.bin.Cache
.initUserColourSchemes(getProperty("USER_DEFINED_COLOURS"));
false);
}
+ public static void loadBuildProperties(boolean reportVersion)
+ {
+ String codeInstallation = getProperty("INSTALLATION");
+ boolean printV = codeInstallation == null;
+
+ // FIND THE VERSION NUMBER AND BUILD DATE FROM jalview.jar
+ try
+ {
+ String buildDetails = "jar:".concat(Cache.class.getProtectionDomain()
+ .getCodeSource().getLocation().toString()
+ .concat("!/.build_properties"));
+
+ java.net.URL localJarFileURL = new java.net.URL(buildDetails);
+
+ InputStream in = localJarFileURL.openStream();
+ applicationProperties.load(in);
+ in.close();
+ } catch (Exception ex)
+ {
+ System.out.println("Error reading build details: " + ex);
+ applicationProperties.remove("VERSION");
+ }
+ String codeVersion = getProperty("VERSION");
+ codeInstallation = getProperty("INSTALLATION");
+
+ if (codeVersion == null)
+ {
+ // THIS SHOULD ONLY BE THE CASE WHEN TESTING!!
+ codeVersion = "Test";
+ codeInstallation = "";
+ }
+ else
+ {
+ codeInstallation = " (" + codeInstallation + ")";
+ }
+ setProperty("VERSION", codeVersion);
+ new BuildDetails(codeVersion, null, codeInstallation);
+ if (printV && reportVersion)
+ {
+ System.out
+ .println("Jalview Version: " + codeVersion + codeInstallation);
+ }
+ }
+
private static void deleteBuildProperties()
{
applicationProperties.remove("LATEST_VERSION");
try
{
oldValue = applicationProperties.setProperty(key, obj);
- if (!propsAreReadOnly)
+ if (propertiesFile != null && !propsAreReadOnly)
{
FileOutputStream out = new FileOutputStream(propertiesFile);
applicationProperties.store(out, "---JalviewX Properties File---");
}
}
}
+
+ /**
+ *
+ * @return Jalview version, build details and JVM platform version for console
+ */
+ public static String getVersionDetailsForConsole()
+ {
+ return "Jalview Version: "
+ + jalview.bin.Cache.getDefault("VERSION", "TEST")
+ + "\n" + "Jalview Installation: "
+ + jalview.bin.Cache.getDefault("INSTALLATION",
+ "unknown")
+ + "\n" + "Build Date: "
+ + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown")
+ + "\n" + "Java version: "
+ + System.getProperty("java.version") + "\n"
+ + System.getProperty("os.arch") + " "
+ + System.getProperty("os.name") + " "
+ + System.getProperty("os.version")
+ + (jalview.bin.Cache.getDefault("VERSION", "TEST")
+ .equals("DEVELOPMENT")
+ ? "\nGetdown appdir: " + System.getProperty("getdownappdir") + "\nJava path: "
+ + System.getProperty(
+ "java.home")
+ + File.separator + "bin"
+ + File.separator + "java"
+ : "");
+ }
+
+ /**
+ *
+ * @return build details as reported in splashscreen
+ */
+ public static String getBuildDetailsForSplash()
+ {
+ // consider returning more human friendly info
+ // eg 'built from Source' or update channel
+ return jalview.bin.Cache.getDefault("INSTALLATION", "unknown");
+ }
}
perms.add(new AllPermission());
return (perms);
}
-
+
@Override
public void refresh()
{
class FeatureFetcher
{
/*
- * TODO: generalise to track all jalview events to orchestrate batch
- * processing events.
+ * TODO: generalise to track all jalview events to orchestrate batch processing
+ * events.
*/
private int queued = 0;
* main class for Jalview application
*
* @param args
- * open <em>filename</em>
+ * open <em>filename</em>
*/
public static void main(String[] args)
{
System.out.println(System.getProperty("os.arch") + " "
+ System.getProperty("os.name") + " "
+ System.getProperty("os.version"));
+ // report Jalview version
+ Cache.loadBuildProperties(true);
- String appdirString = System.getProperty("getdownappdir");
- if (appdirString != null && appdirString.length() > 0)
- {
- final File appdir = new File(appdirString);
- new Thread()
- {
- @Override
- public void run()
- {
- LaunchUtil.upgradeGetdown(
- new File(appdir, "getdown-launcher-old.jar"),
- new File(appdir, "getdown-launcher.jar"),
- new File(appdir, "getdown-launcher-new.jar"));
- }
- }.start();
-
- }
ArgsParser aparser = new ArgsParser(args);
boolean headless = false;
"Failed to set QuaQua look and feel: " + e.toString());
}
}
- if (lookAndFeel == null || !(lookAndFeel.getClass()
- .isAssignableFrom(UIManager.getLookAndFeel().getClass()))
+ if (lookAndFeel == null
+ || !(lookAndFeel.getClass().isAssignableFrom(
+ UIManager.getLookAndFeel().getClass()))
|| !UIManager.getLookAndFeel().getClass().toString()
.toLowerCase().contains("quaqua"))
{
}
/*
- * configure 'full' SO model if preferences say to,
- * else use the default (SO Lite)
+ * configure 'full' SO model if preferences say to, else use the default (SO
+ * Lite)
*/
- if (Cache.getDefault("USE_FULL_SO", false))
+ if (Cache.getDefault("USE_FULL_SO", true))
{
SequenceOntologyFactory.setInstance(new SequenceOntology());
}
BioJsHTMLOutput.updateBioJS();
}
+ // Move any new getdown-launcher-new.jar into place over old
+ // getdown-launcher.jar
+ String appdirString = System.getProperty("getdownappdir");
+ if (appdirString != null && appdirString.length() > 0)
+ {
+ final File appdir = new File(appdirString);
+ new Thread()
+ {
+ @Override
+ public void run()
+ {
+ LaunchUtil.upgradeGetdown(
+ new File(appdir, "getdown-launcher-old.jar"),
+ new File(appdir, "getdown-launcher.jar"),
+ new File(appdir, "getdown-launcher-new.jar"));
+ }
+ }.start();
+ }
+
String file = null, data = null;
FileFormatI format = null;
DataSourceType protocol = null;
System.out.println("No files to open!");
System.exit(1);
}
- String vamsasImport = aparser.getValue("vdoc");
- String vamsasSession = aparser.getValue("vsess");
- if (vamsasImport != null || vamsasSession != null)
- {
- if (desktop == null || headless)
- {
- System.out.println(
- "Headless vamsas sessions not yet supported. Sorry.");
- System.exit(1);
- }
- // if we have a file, start a new session and import it.
- boolean inSession = false;
- if (vamsasImport != null)
- {
- try
- {
- DataSourceType viprotocol = AppletFormatAdapter
- .checkProtocol(vamsasImport);
- if (viprotocol == DataSourceType.FILE)
- {
- inSession = desktop.vamsasImport(new File(vamsasImport));
- }
- else if (viprotocol == DataSourceType.URL)
- {
- inSession = desktop.vamsasImport(new URL(vamsasImport));
- }
-
- } catch (Exception e)
- {
- System.err.println("Exeption when importing " + vamsasImport
- + " as a vamsas document.");
- e.printStackTrace();
- }
- if (!inSession)
- {
- System.err.println("Failed to import " + vamsasImport
- + " as a vamsas document.");
- }
- else
- {
- System.out.println("Imported Successfully into new session "
- + desktop.getVamsasApplication().getCurrentSession());
- }
- }
- if (vamsasSession != null)
- {
- if (vamsasImport != null)
- {
- // close the newly imported session and import the Jalview specific
- // remnants into the new session later on.
- desktop.vamsasStop_actionPerformed(null);
- }
- // now join the new session
- try
- {
- if (desktop.joinVamsasSession(vamsasSession))
- {
- System.out.println(
- "Successfully joined vamsas session " + vamsasSession);
- }
- else
- {
- System.err.println("WARNING: Failed to join vamsas session "
- + vamsasSession);
- }
- } catch (Exception e)
- {
- System.err.println(
- "ERROR: Failed to join vamsas session " + vamsasSession);
- e.printStackTrace();
- }
- if (vamsasImport != null)
- {
- // the Jalview specific remnants can now be imported into the new
- // session at the user's leisure.
- Cache.log.info(
- "Skipping Push for import of data into existing vamsas session."); // TODO:
- // enable
- // this
- // when
- // debugged
- // desktop.getVamsasApplication().push_update();
- }
- }
- }
long progress = -1;
// Finally, deal with the remaining input data.
if (file != null)
{
data.replaceAll("%20", " ");
- ColourSchemeI cs = ColourSchemeProperty
- .getColourScheme(af.getViewport(),
- af.getViewport().getAlignment(), data);
+ ColourSchemeI cs = ColourSchemeProperty.getColourScheme(
+ af.getViewport(), af.getViewport().getAlignment(), data);
if (cs != null)
{
// And the user
// ////////////////////
- if (!headless && file == null && vamsasImport == null
+ if (!headless && file == null
&& jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true))
{
file = jalview.bin.Cache.getDefault("STARTUP_FILE",
// passed in correctly)"
+ "-jabaws URL\tSpecify URL for Jabaws services (e.g. for a local installation).\n"
+ "-fetchfrom nickname\tQuery nickname for features for the alignments and display them.\n"
- // +
- // "-vdoc vamsas-document\tImport vamsas document into new
- // session or join existing session with same URN\n"
- // + "-vses vamsas-session\tJoin session with given URN\n"
+ "-groovy FILE\tExecute groovy script in FILE, after all other arguments have been processed (if FILE is the text 'STDIN' then the file will be read from STDIN)\n"
+ "\n~Read documentation in Application or visit http://www.jalview.org for description of Features and Annotations file~\n\n");
}
* Locate the given string as a file and pass it to the groovy interpreter.
*
* @param groovyscript
- * the script to execute
+ * the script to execute
* @param jalviewContext
- * the Jalview Desktop object passed in to the groovy binding as the
- * 'Jalview' object.
+ * the Jalview Desktop object passed in to the groovy
+ * binding as the 'Jalview' object.
*/
private void executeGroovyScript(String groovyscript, AlignFrame af)
{
}
/**
- * Quit method delegates to Desktop.quit - unless running in headless mode
- * when it just ends the JVM
+ * Quit method delegates to Desktop.quit - unless running in headless mode when
+ * it just ends the JVM
*/
public void quit()
{
} catch (NoClassDefFoundError e)
{
// com.sun.management.OperatingSystemMXBean doesn't exist in this JVM
- System.out.println("No com.sun.management.OperatingSystemMXBean");
+ Cache.log.error("No com.sun.management.OperatingSystemMXBean");
}
// We didn't get a com.sun.management.OperatingSystemMXBean.
// old ds and edited ds are different, so
// create the new dataset sequence
SequenceI newds = new Sequence(oldds);
- newds.setSequence(fullseq);
+ newds.setSequence(fullseq.toUpperCase());
if (command.oldds == null)
{
*/
public abstract class FTSRestClient implements FTSRestClientI
{
- protected Collection<FTSDataColumnI> dataColumns = new ArrayList<FTSDataColumnI>();
+ protected Collection<FTSDataColumnI> dataColumns = new ArrayList<>();
- protected Collection<FTSDataColumnGroupI> dataColumnGroups = new ArrayList<FTSDataColumnGroupI>();
+ protected Collection<FTSDataColumnGroupI> dataColumnGroups = new ArrayList<>();
- protected Collection<FTSDataColumnI> searchableDataColumns = new ArrayList<FTSDataColumnI>();
+ protected Collection<FTSDataColumnI> searchableDataColumns = new ArrayList<>();
- protected Collection<FTSDataColumnI> defaulDisplayedDataColumns = new ArrayList<FTSDataColumnI>();
+ protected Collection<FTSDataColumnI> defaulDisplayedDataColumns = new ArrayList<>();
protected FTSDataColumnI primaryKeyColumn;
throw new Exception("Couldn't find data column group with id : " + id);
}
- public String getMessageByHTTPStatusCode(int code, String service)
+ public static String getMessageByHTTPStatusCode(int code, String service)
{
String message = "";
switch (code)
{
case 400:
- message = MessageManager.getString("exception.bad_request");
+ message = "Bad request. There is a problem with your input.";
break;
case 410:
message = MessageManager.formatMessage(
- "exception.fts_rest_service_no_longer_available", service);
+ service + " rest services no longer available!");
break;
case 403:
case 404:
- message = MessageManager.getString("exception.resource_not_be_found");
+ message = "The requested resource could not be found";
break;
case 408:
case 409:
case 502:
case 504:
case 505:
- message = MessageManager.formatMessage("exception.fts_server_error",
- service);
+ message = "There seems to be an error from the " + service
+ + " server";
break;
case 503:
- message = MessageManager.getString("exception.service_not_available");
+ message = "Service not available. The server is being updated, try again later.";
break;
default:
break;
}
- return message;
+ return String.valueOf(code) + " " + message;
}
protected String getResourceFile(String fileName)
// System.out.println("query >>>>>>> " + pdbRestRequest.toString());
// Check the response status and report exception if one occurs
- if (clientResponse.getStatus() != 200)
+ int responseStatus = clientResponse.getStatus();
+ if (responseStatus != 200)
{
String errorMessage = "";
- if (clientResponse.getStatus() == 400)
+ if (responseStatus == 400)
{
errorMessage = parseJsonExceptionString(responseString);
throw new Exception(errorMessage);
else
{
errorMessage = getMessageByHTTPStatusCode(
- clientResponse.getStatus(), "PDB");
+ responseStatus, "PDB");
throw new Exception(errorMessage);
}
}
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureSettingsControllerI;
+import jalview.api.FeatureSettingsModelI;
import jalview.api.SplitContainerI;
import jalview.api.ViewStyleI;
import jalview.api.analysis.SimilarityParamsI;
@Override
public void finished()
{
+
+ for (FeatureSettingsModelI srcSettings : dbRefFetcher
+ .getFeatureSettingsModels())
+ {
+
+ alignPanel.av.mergeFeaturesStyle(srcSettings);
+ }
AlignFrame.this.setMenusForViewport();
}
});
@Override
public void finished()
{
+ FeatureSettingsModelI srcSettings = dassource[0]
+ .getFeatureColourScheme();
+ alignPanel.av.mergeFeaturesStyle(
+ srcSettings);
AlignFrame.this.setMenusForViewport();
}
});
import jalview.structure.SelectionSource;
import jalview.structure.StructureSelectionManager;
import jalview.structure.VamsasSource;
+import jalview.util.ColorUtils;
import jalview.util.MessageManager;
import jalview.viewmodel.AlignmentViewport;
import jalview.ws.params.AutoCalcSetting;
import java.awt.Font;
import java.awt.FontMetrics;
import java.awt.Rectangle;
+import java.util.ArrayList;
import java.util.Hashtable;
import java.util.Iterator;
import java.util.List;
@Override
public void applyFeaturesStyle(FeatureSettingsModelI featureSettings)
{
+ transferFeaturesStyles(featureSettings, false);
+ }
+
+ /**
+ * Applies the supplied feature settings descriptor to currently known features.
+ * This supports an 'initial configuration' of feature colouring based on a
+ * preset or user favourite. This may then be modified in the usual way using
+ * the Feature Settings dialogue.
+ *
+ * @param featureSettings
+ */
+ @Override
+ public void mergeFeaturesStyle(FeatureSettingsModelI featureSettings)
+ {
+ transferFeaturesStyles(featureSettings, true);
+ }
+
+ /**
+ * when mergeOnly is set, then group and feature visibility or feature colours
+ * are not modified for features and groups already known to the feature
+ * renderer. Feature ordering is always adjusted, and transparency is always set
+ * regardless.
+ *
+ * @param featureSettings
+ * @param mergeOnly
+ */
+ private void transferFeaturesStyles(FeatureSettingsModelI featureSettings,
+ boolean mergeOnly)
+ {
if (featureSettings == null)
{
return;
}
-
+
FeatureRenderer fr = getAlignPanel().getSeqPanel().seqCanvas
.getFeatureRenderer();
+ List<String> origRenderOrder = new ArrayList(),
+ origGroups = new ArrayList();
+ // preserve original render order - allows differentiation between user configured colours and autogenerated ones
+ origRenderOrder.addAll(fr.getRenderOrder());
+ origGroups.addAll(fr.getFeatureGroups());
+
fr.findAllFeatures(true);
List<String> renderOrder = fr.getRenderOrder();
FeaturesDisplayedI displayed = fr.getFeaturesDisplayed();
- displayed.clear();
+ if (!mergeOnly)
+ {
+ // only clear displayed features if we are mergeing
+ displayed.clear();
+ }
// TODO this clears displayed.featuresRegistered - do we care?
-
+ //
+ // JAL-3330 - JBP - yes we do - calling applyFeatureStyle to a view where
+ // feature visibility has already been configured is not very friendly
/*
* set feature colour if specified by feature settings
* set visibility of all features
{
FeatureColourI preferredColour = featureSettings
.getFeatureColour(type);
- if (preferredColour != null)
- {
- fr.setColour(type, preferredColour);
- }
- if (featureSettings.isFeatureDisplayed(type))
+ FeatureColourI origColour = fr.getFeatureStyle(type);
+ if (!mergeOnly || (!origRenderOrder.contains(type)
+ || origColour == null
+ || (!origColour.isGraduatedColour()
+ && origColour.getColour() != null
+ && origColour.getColour().equals(
+ ColorUtils.createColourFromName(type)))))
{
- displayed.setVisible(type);
+ // if we are merging, only update if there wasn't already a colour defined for
+ // this type
+ if (preferredColour != null)
+ {
+ fr.setColour(type, preferredColour);
+ }
+ if (featureSettings.isFeatureDisplayed(type))
+ {
+ displayed.setVisible(type);
+ }
}
}
*/
for (String group : fr.getFeatureGroups())
{
- fr.setGroupVisibility(group, featureSettings.isGroupDisplayed(group));
+ if (!mergeOnly || !origGroups.contains(group))
+ {
+ // when merging, display groups only if the aren't already marked as not visible
+ fr.setGroupVisibility(group,
+ featureSettings.isGroupDisplayed(group));
+ }
}
/*
FeatureSettingsModelI featureColourScheme = new SequenceFetcher()
.getFeatureColourScheme(source);
+ if (dna && AlignmentUtils.looksLikeEnsembl(alignment))
+ {
+ // override default featureColourScheme so products have Ensembl variant colours
+ featureColourScheme = new SequenceFetcher()
+ .getFeatureColourScheme(DBRefSource.ENSEMBL);
+ }
+
AlignmentI xrefsAlignment = makeCrossReferencesAlignment(dataset,
xrefs);
if (!dna)
/*
* apply 'database source' feature configuration
- * if any was found
+ * if any - first to the new splitframe view about to be displayed
*/
- // TODO is this the feature colouring for the original
- // alignment or the fetched xrefs? either could be Ensembl
+
newFrame.getViewport().applyFeaturesStyle(featureColourScheme);
copyThis.getViewport().applyFeaturesStyle(featureColourScheme);
+ /*
+ * and for JAL-3330 also to original alignFrame view(s)
+ * this currently trashes any original settings.
+ */
+ for (AlignmentViewPanel origpanel: alignFrame.getAlignPanels()) {
+ origpanel.getAlignViewport()
+ .mergeFeaturesStyle(featureColourScheme);
+ }
+
SplitFrame sf = new SplitFrame(dna ? copyThis : newFrame,
dna ? newFrame : copyThis);
+
newFrame.setVisible(true);
copyThis.setVisible(true);
String linkedTitle = MessageManager
import java.awt.event.WindowEvent;
import java.beans.PropertyChangeEvent;
import java.beans.PropertyChangeListener;
-import java.io.BufferedInputStream;
import java.io.File;
-import java.io.FileOutputStream;
import java.io.FileWriter;
import java.io.IOException;
import java.net.URL;
import javax.swing.event.HyperlinkEvent.EventType;
import javax.swing.event.InternalFrameAdapter;
import javax.swing.event.InternalFrameEvent;
-import javax.swing.event.MenuEvent;
-import javax.swing.event.MenuListener;
import org.stackoverflowusers.file.WindowsShortcut;
* constructor.
*/
instance = this;
- doVamsasClientCheck();
doConfigureStructurePrefs();
setTitle("Jalview " + jalview.bin.Cache.getProperty("VERSION"));
}
jconsole = new Console(this, showjconsole);
// add essential build information
- jconsole.setHeader(
- "Jalview Version: " + jalview.bin.Cache.getProperty("VERSION")
- + "\n" + "Jalview Installation: "
- + jalview.bin.Cache.getDefault("INSTALLATION",
- "unknown")
- + "\n" + "Build Date: "
- + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown")
- + "\n" + "Java version: "
- + System.getProperty("java.version") + "\n"
- + System.getProperty("os.arch") + " "
- + System.getProperty("os.name") + " "
- + System.getProperty("os.version")
- + (jalview.bin.Cache.getProperty("VERSION").equals("DEVELOPMENT")
- ? "\nJava path:"
- + System.getProperty(
- "java.home")
- + File.separator + "bin"
- + File.separator + "java"
- : "")
- );
+ jconsole.setHeader(jalview.bin.Cache.getVersionDetailsForConsole());
showConsole(showjconsole);
return null;
}
- private void doVamsasClientCheck()
- {
- if (jalview.bin.Cache.vamsasJarsPresent())
- {
- setupVamsasDisconnectedGui();
- VamsasMenu.setVisible(true);
- final Desktop us = this;
- VamsasMenu.addMenuListener(new MenuListener()
- {
- // this listener remembers when the menu was first selected, and
- // doesn't rebuild the session list until it has been cleared and
- // reselected again.
- boolean refresh = true;
-
- @Override
- public void menuCanceled(MenuEvent e)
- {
- refresh = true;
- }
-
- @Override
- public void menuDeselected(MenuEvent e)
- {
- refresh = true;
- }
-
- @Override
- public void menuSelected(MenuEvent e)
- {
- if (refresh)
- {
- us.buildVamsasStMenu();
- refresh = false;
- }
- }
- });
- vamsasStart.setVisible(true);
- }
- }
-
void showPasteMenu(int x, int y)
{
JPopupMenu popup = new JPopupMenu();
message.append("<h1><strong>Version: "
+ jalview.bin.Cache.getProperty("VERSION")
+ "</strong></h1>");
- message.append("<strong>Last Updated: <em>"
+ message.append("<strong>Built: <em>"
+ jalview.bin.Cache.getDefault("BUILD_DATE", "unknown")
- + "</em></strong>");
+ + "</em> from " + jalview.bin.Cache.getBuildDetailsForSplash()
+ + "</strong>");
}
else
if (jalview.bin.Cache.getDefault("LATEST_VERSION", "Checking")
.equals("Checking"))
{
- message.append("<br>...Checking latest version...</br>");
+ // JBP removed this message for 2.11: May be reinstated in future version
+ // message.append("<br>...Checking latest version...</br>");
}
else if (!jalview.bin.Cache.getDefault("LATEST_VERSION", "Checking")
.equals(jalview.bin.Cache.getProperty("VERSION")))
}
Jalview.setCurrentAlignFrame(null);
System.out.println("ALL CLOSED");
- if (v_client != null)
- {
- // TODO clear binding to vamsas document objects on close_all
- }
/*
* reset state of singleton objects as appropriate (clear down session state
}
- jalview.gui.VamsasApplication v_client = null;
-
- @Override
- public void vamsasImport_actionPerformed(ActionEvent e)
- {
- if (v_client == null)
- {
- // Load and try to start a session.
- JalviewFileChooser chooser = new JalviewFileChooser(
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
-
- chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle(
- MessageManager.getString("label.open_saved_vamsas_session"));
- chooser.setToolTipText(MessageManager.getString(
- "label.select_vamsas_session_opened_as_new_vamsas_session"));
-
- int value = chooser.showOpenDialog(this);
-
- if (value == JalviewFileChooser.APPROVE_OPTION)
- {
- String fle = chooser.getSelectedFile().toString();
- if (!vamsasImport(chooser.getSelectedFile()))
- {
- JvOptionPane.showInternalMessageDialog(Desktop.desktop,
- MessageManager.formatMessage(
- "label.couldnt_import_as_vamsas_session",
- new Object[]
- { fle }),
- MessageManager
- .getString("label.vamsas_document_import_failed"),
- JvOptionPane.ERROR_MESSAGE);
- }
- }
- }
- else
- {
- jalview.bin.Cache.log.error(
- "Implementation error - load session from a running session is not supported.");
- }
- }
-
- /**
- * import file into a new vamsas session (uses jalview.gui.VamsasApplication)
- *
- * @param file
- * @return true if import was a success and a session was started.
- */
- public boolean vamsasImport(URL url)
- {
- // TODO: create progress bar
- if (v_client != null)
- {
-
- jalview.bin.Cache.log.error(
- "Implementation error - load session from a running session is not supported.");
- return false;
- }
-
- try
- {
- // copy the URL content to a temporary local file
- // TODO: be a bit cleverer here with nio (?!)
- File file = File.createTempFile("vdocfromurl", ".vdj");
- FileOutputStream fos = new FileOutputStream(file);
- BufferedInputStream bis = new BufferedInputStream(url.openStream());
- byte[] buffer = new byte[2048];
- int ln;
- while ((ln = bis.read(buffer)) > -1)
- {
- fos.write(buffer, 0, ln);
- }
- bis.close();
- fos.close();
- v_client = new jalview.gui.VamsasApplication(this, file,
- url.toExternalForm());
- } catch (Exception ex)
- {
- jalview.bin.Cache.log.error(
- "Failed to create new vamsas session from contents of URL "
- + url,
- ex);
- return false;
- }
- setupVamsasConnectedGui();
- v_client.initial_update(); // TODO: thread ?
- return v_client.inSession();
- }
-
- /**
- * import file into a new vamsas session (uses jalview.gui.VamsasApplication)
- *
- * @param file
- * @return true if import was a success and a session was started.
- */
- public boolean vamsasImport(File file)
- {
- if (v_client != null)
- {
-
- jalview.bin.Cache.log.error(
- "Implementation error - load session from a running session is not supported.");
- return false;
- }
-
- setProgressBar(MessageManager.formatMessage(
- "status.importing_vamsas_session_from", new Object[]
- { file.getName() }), file.hashCode());
- try
- {
- v_client = new jalview.gui.VamsasApplication(this, file, null);
- } catch (Exception ex)
- {
- setProgressBar(MessageManager.formatMessage(
- "status.importing_vamsas_session_from", new Object[]
- { file.getName() }), file.hashCode());
- jalview.bin.Cache.log.error(
- "New vamsas session from existing session file failed:", ex);
- return false;
- }
- setupVamsasConnectedGui();
- v_client.initial_update(); // TODO: thread ?
- setProgressBar(MessageManager.formatMessage(
- "status.importing_vamsas_session_from", new Object[]
- { file.getName() }), file.hashCode());
- return v_client.inSession();
- }
-
- public boolean joinVamsasSession(String mysesid)
- {
- if (v_client != null)
- {
- throw new Error(MessageManager
- .getString("error.try_join_vamsas_session_another"));
- }
- if (mysesid == null)
- {
- throw new Error(
- MessageManager.getString("error.invalid_vamsas_session_id"));
- }
- v_client = new VamsasApplication(this, mysesid);
- setupVamsasConnectedGui();
- v_client.initial_update();
- return (v_client.inSession());
- }
-
- @Override
- public void vamsasStart_actionPerformed(ActionEvent e)
- {
- if (v_client == null)
- {
- // Start a session.
- // we just start a default session for moment.
- /*
- * JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
- * getProperty("LAST_DIRECTORY"));
- *
- * chooser.setFileView(new JalviewFileView());
- * chooser.setDialogTitle("Load Vamsas file");
- * chooser.setToolTipText("Import");
- *
- * int value = chooser.showOpenDialog(this);
- *
- * if (value == JalviewFileChooser.APPROVE_OPTION) { v_client = new
- * jalview.gui.VamsasApplication(this, chooser.getSelectedFile());
- */
- v_client = new VamsasApplication(this);
- setupVamsasConnectedGui();
- v_client.initial_update(); // TODO: thread ?
- }
- else
- {
- // store current data in session.
- v_client.push_update(); // TODO: thread
- }
- }
-
- protected void setupVamsasConnectedGui()
- {
- vamsasStart.setText(MessageManager.getString("label.session_update"));
- vamsasSave.setVisible(true);
- vamsasStop.setVisible(true);
- vamsasImport.setVisible(false); // Document import to existing session is
- // not possible for vamsas-client-1.0.
- }
-
- protected void setupVamsasDisconnectedGui()
- {
- vamsasSave.setVisible(false);
- vamsasStop.setVisible(false);
- vamsasImport.setVisible(true);
- vamsasStart
- .setText(MessageManager.getString("label.new_vamsas_session"));
- }
-
- @Override
- public void vamsasStop_actionPerformed(ActionEvent e)
- {
- if (v_client != null)
- {
- v_client.end_session();
- v_client = null;
- setupVamsasDisconnectedGui();
- }
- }
-
- protected void buildVamsasStMenu()
- {
- if (v_client == null)
- {
- String[] sess = null;
- try
- {
- sess = VamsasApplication.getSessionList();
- } catch (Exception e)
- {
- jalview.bin.Cache.log.warn("Problem getting current sessions list.",
- e);
- sess = null;
- }
- if (sess != null)
- {
- jalview.bin.Cache.log.debug(
- "Got current sessions list: " + sess.length + " entries.");
- VamsasStMenu.removeAll();
- for (int i = 0; i < sess.length; i++)
- {
- JMenuItem sessit = new JMenuItem();
- sessit.setText(sess[i]);
- sessit.setToolTipText(MessageManager
- .formatMessage("label.connect_to_session", new Object[]
- { sess[i] }));
- final Desktop dsktp = this;
- final String mysesid = sess[i];
- sessit.addActionListener(new ActionListener()
- {
-
- @Override
- public void actionPerformed(ActionEvent e)
- {
- if (dsktp.v_client == null)
- {
- Thread rthr = new Thread(new Runnable()
- {
-
- @Override
- public void run()
- {
- dsktp.v_client = new VamsasApplication(dsktp, mysesid);
- dsktp.setupVamsasConnectedGui();
- dsktp.v_client.initial_update();
- }
-
- });
- rthr.start();
- }
- };
- });
- VamsasStMenu.add(sessit);
- }
- // don't show an empty menu.
- VamsasStMenu.setVisible(sess.length > 0);
-
- }
- else
- {
- jalview.bin.Cache.log.debug("No current vamsas sessions.");
- VamsasStMenu.removeAll();
- VamsasStMenu.setVisible(false);
- }
- }
- else
- {
- // Not interested in the content. Just hide ourselves.
- VamsasStMenu.setVisible(false);
- }
- }
-
- @Override
- public void vamsasSave_actionPerformed(ActionEvent e)
- {
- if (v_client != null)
- {
- // TODO: VAMSAS DOCUMENT EXTENSION is VDJ
- JalviewFileChooser chooser = new JalviewFileChooser("vdj",
- "Vamsas Document");
-
- chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle(MessageManager
- .getString("label.save_vamsas_document_archive"));
-
- int value = chooser.showSaveDialog(this);
-
- if (value == JalviewFileChooser.APPROVE_OPTION)
- {
- java.io.File choice = chooser.getSelectedFile();
- JPanel progpanel = addProgressPanel(MessageManager
- .formatMessage("label.saving_vamsas_doc", new Object[]
- { choice.getName() }));
- Cache.setProperty("LAST_DIRECTORY", choice.getParent());
- String warnmsg = null;
- String warnttl = null;
- try
- {
- v_client.vclient.storeDocument(choice);
- } catch (Error ex)
- {
- warnttl = "Serious Problem saving Vamsas Document";
- warnmsg = ex.toString();
- jalview.bin.Cache.log
- .error("Error Whilst saving document to " + choice, ex);
-
- } catch (Exception ex)
- {
- warnttl = "Problem saving Vamsas Document.";
- warnmsg = ex.toString();
- jalview.bin.Cache.log.warn(
- "Exception Whilst saving document to " + choice, ex);
-
- }
- removeProgressPanel(progpanel);
- if (warnmsg != null)
- {
- JvOptionPane.showInternalMessageDialog(Desktop.desktop,
-
- warnmsg, warnttl, JvOptionPane.ERROR_MESSAGE);
- }
- }
- }
- }
-
- JPanel vamUpdate = null;
-
- /**
- * hide vamsas user gui bits when a vamsas document event is being handled.
- *
- * @param b
- * true to hide gui, false to reveal gui
- */
- public void setVamsasUpdate(boolean b)
- {
- Cache.log.debug("Setting gui for Vamsas update "
- + (b ? "in progress" : "finished"));
-
- if (vamUpdate != null)
- {
- this.removeProgressPanel(vamUpdate);
- }
- if (b)
- {
- vamUpdate = this.addProgressPanel(
- MessageManager.getString("label.updating_vamsas_session"));
- }
- vamsasStart.setVisible(!b);
- vamsasStop.setVisible(!b);
- vamsasSave.setVisible(!b);
- }
-
public JInternalFrame[] getAllFrames()
{
return desktop.getAllFrames();
public VamsasApplication getVamsasApplication()
{
- return v_client;
+ // TODO: JAL-3311 remove remaining code from Jalview relating to VAMSAS
+ return null;
}
boolean isUniProtRefsFound = false;
StringBuilder queryBuilder = new StringBuilder();
Set<String> seqRefs = new LinkedHashSet<>();
+
+ /*
+ * note PDBs as DBRefEntry so they are not duplicated in query
+ */
+ Set<String> pdbids = new HashSet<>();
if (seq.getAllPDBEntries() != null
&& queryBuilder.length() < MAX_QLENGTH)
{
if (isValidSeqName(entry.getId()))
{
- queryBuilder.append("pdb_id:").append(entry.getId().toLowerCase())
- .append(" OR ");
+ String id = entry.getId().toLowerCase();
+ queryBuilder.append("pdb_id:").append(id).append(" OR ");
isPDBRefsFound = true;
+ pdbids.add(id);
}
}
}
else if (dbRef.getSource().equalsIgnoreCase(DBRefSource.PDB))
{
- queryBuilder.append("pdb_id:")
- .append(getDBRefId(dbRef).toLowerCase()).append(" OR ");
- isPDBRefsFound = true;
+ String id = getDBRefId(dbRef).toLowerCase();
+ if (!pdbids.contains(id))
+ {
+ queryBuilder.append("pdb_id:").append(id).append(" OR ");
+ isPDBRefsFound = true;
+ pdbids.add(id);
+ }
}
else
{
public void disableGui(boolean b)
{
- Desktop.instance.setVamsasUpdate(b);
+ // JAL-3311 TODO: remove this class!
+ // Desktop.instance.setVamsasUpdate(b);
}
Hashtable _backup_vobj2jv;
import java.awt.BorderLayout;
import java.awt.Color;
-import java.awt.Font;
+import java.awt.Dimension;
import java.awt.Graphics;
import java.awt.Graphics2D;
import java.awt.GridLayout;
import java.awt.Image;
import java.awt.MediaTracker;
+import java.awt.RenderingHints;
import java.awt.event.ActionEvent;
import java.awt.image.BufferedImage;
import java.util.Vector;
import javax.swing.JComponent;
import javax.swing.JEditorPane;
import javax.swing.JInternalFrame;
-import javax.swing.JOptionPane;
import javax.swing.JPanel;
import javax.swing.JScrollPane;
import javax.swing.JTabbedPane;
Image image;
- int angle = 0;
+ float angle = 0f;
String title = "";
setInfoText(info);
java.net.URL url = getClass()
- .getResource("/images/Jalview_Logo_small.png");
+ .getResource("/images/Jalview_Logo_small_with_border.png");
image = java.awt.Toolkit.getDefaultToolkit().createImage(url);
MediaTracker mt = new MediaTracker(this);
}
AnimatedPanel ap = new AnimatedPanel();
- titlePanel.add(ap, BorderLayout.CENTER);
+ ap.setPreferredSize(new Dimension(60, 60));
+ titlePanel.add(ap, BorderLayout.WEST);
+ titlePanel.add(titleText, BorderLayout.CENTER);
+ setStatus(currentStatus);
Thread thread = new Thread(ap);
thread.start();
frame.addInternalFrameListener(
new javax.swing.event.InternalFrameAdapter()
{
- public void internalFrameClosed(
+ @Override
+ public void internalFrameClosed(
javax.swing.event.InternalFrameEvent evt)
{
// System.out.println("Shutting down webservice client");
public void setStatus(int status)
{
currentStatus = status;
+
+ String message = null;
+ switch (currentStatus)
+ {
+ case STATE_QUEUING:
+ message = MessageManager.getString("label.state_queueing");
+ break;
+
+ case STATE_RUNNING:
+ message = MessageManager.getString("label.state_running");
+ break;
+
+ case STATE_STOPPED_OK:
+ message = MessageManager.getString("label.state_completed");
+ break;
+
+ case STATE_CANCELLED_OK:
+ message = MessageManager.getString("label.state_job_cancelled");
+ break;
+
+ case STATE_STOPPED_ERROR:
+ message = MessageManager.getString("label.state_job_error");
+ break;
+
+ case STATE_STOPPED_SERVERERROR:
+ message = MessageManager.getString("label.server_error_try_later");
+ break;
+ }
+ titleText.setText(title + (message == null ? "" : " - " + message));
+ titleText.repaint();
}
/**
* @param e
* DOCUMENT ME!
*/
- protected void cancel_actionPerformed(ActionEvent e)
+ @Override
+protected void cancel_actionPerformed(ActionEvent e)
{
if (!serviceIsCancellable)
{
{
javax.swing.SwingUtilities.invokeLater(new Runnable()
{
- public void run()
+ @Override
+ public void run()
{
JvOptionPane.showInternalMessageDialog(Desktop.desktop, message,
title, JvOptionPane.WARNING_MESSAGE);
BufferedImage offscreen;
+ @Override
public void run()
{
startTime = System.currentTimeMillis();
+ float invSpeed = 15f;
+ float factor = 1f;
while (currentStatus < STATE_STOPPED_OK)
{
+ if (currentStatus == STATE_QUEUING)
+ {
+ invSpeed = 25f;
+ factor = 1f;
+ }
+ else if (currentStatus == STATE_RUNNING)
+ {
+ invSpeed = 10f;
+ factor = (float) (0.5 + 1.5
+ * (0.5 - (0.5 * Math.sin(3.14159 / 180 * (angle + 45)))));
+ }
try
{
Thread.sleep(50);
- int units = (int) ((System.currentTimeMillis() - startTime)
- / 10f);
- angle += units;
+ float delta = (System.currentTimeMillis() - startTime) / invSpeed;
+ angle += delta * factor;
angle %= 360;
startTime = System.currentTimeMillis();
if (currentStatus >= STATE_STOPPED_OK)
{
+ park();
angle = 0;
}
cancel.setEnabled(false);
}
+ public void park()
+ {
+ startTime = System.currentTimeMillis();
+
+ while (angle < 360)
+ {
+ float invSpeed = 5f;
+ float factor = 1f;
+ try
+ {
+ Thread.sleep(25);
+
+ float delta = (System.currentTimeMillis() - startTime) / invSpeed;
+ angle += delta * factor;
+ startTime = System.currentTimeMillis();
+
+ if (angle >= 360)
+ {
+ angle = 360;
+ }
+
+ repaint();
+ } catch (Exception ex)
+ {
+ }
+ }
+
+ }
+
void drawPanel()
{
if (offscreen == null || offscreen.getWidth(this) != getWidth()
|| offscreen.getHeight(this) != getHeight())
{
offscreen = new BufferedImage(getWidth(), getHeight(),
- BufferedImage.TYPE_INT_ARGB);
+ BufferedImage.TYPE_INT_RGB);
}
Graphics2D g = (Graphics2D) offscreen.getGraphics();
+ g.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
+ RenderingHints.VALUE_ANTIALIAS_ON);
+ g.setRenderingHint(RenderingHints.KEY_INTERPOLATION,
+ RenderingHints.VALUE_INTERPOLATION_BICUBIC);
+ g.setRenderingHint(RenderingHints.KEY_RENDERING,
+ RenderingHints.VALUE_RENDER_QUALITY);
+
g.setColor(Color.white);
g.fillRect(0, 0, getWidth(), getHeight());
- g.setFont(new Font("Arial", Font.BOLD, 12));
- g.setColor(Color.black);
-
- switch (currentStatus)
- {
- case STATE_QUEUING:
- g.drawString(
- title.concat(" - ").concat(
- MessageManager.getString("label.state_queueing")),
- 60, 30);
-
- break;
-
- case STATE_RUNNING:
- g.drawString(
- title.concat(" - ").concat(
- MessageManager.getString("label.state_running")),
- 60, 30);
-
- break;
-
- case STATE_STOPPED_OK:
- g.drawString(
- title.concat(" - ").concat(
- MessageManager.getString("label.state_completed")),
- 60, 30);
-
- break;
-
- case STATE_CANCELLED_OK:
- g.drawString(
- title.concat(" - ")
- .concat(MessageManager
- .getString("label.state_job_cancelled")),
- 60, 30);
-
- break;
-
- case STATE_STOPPED_ERROR:
- g.drawString(
- title.concat(" - ").concat(
- MessageManager.getString("label.state_job_error")),
- 60, 30);
-
- break;
-
- case STATE_STOPPED_SERVERERROR:
- g.drawString(
- title.concat(" - ")
- .concat(MessageManager
- .getString("label.server_error_try_later")),
- 60, 30);
-
- break;
- }
-
if (image != null)
{
int x = image.getWidth(this) / 2, y = image.getHeight(this) / 2;
- g.rotate(Math.toRadians(angle), 10 + x, 10 + y);
- g.drawImage(image, 10, 10, this);
- g.rotate(-Math.toRadians(angle), 10 + x, 10 + y);
+ g.rotate(3.14159 / 180 * (angle), x, y);
+ g.drawImage(image, 0, 0, this);
+ g.rotate(-3.14159 / 180 * (angle), x, y);
}
}
- public void paintComponent(Graphics g1)
+ @Override
+ public void paintComponent(Graphics g1)
{
drawPanel();
renderAsHtml = b;
}
- public void hyperlinkUpdate(HyperlinkEvent e)
+ @Override
+public void hyperlinkUpdate(HyperlinkEvent e)
{
Desktop.hyperlinkUpdate(e);
}
{ "snRNA", "transcript" },
{ "miRNA", "transcript" },
{ "lincRNA", "transcript" },
+ { "lnc_RNA", "transcript" },
{ "rRNA", "transcript" },
{ "mRNA", "transcript" },
// there are many more sub-types of ncRNA...
import jalview.gui.JvSwingUtils;
import jalview.util.MessageManager;
-import jalview.util.ShortcutKeyMaskExWrapper;
import java.awt.BorderLayout;
import java.awt.Font;
});
close.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
java.awt.event.KeyEvent.VK_W,
- ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false));
+ jalview.util.ShortcutKeyMaskExWrapper
+ .getMenuShortcutKeyMaskEx(),
+ false));
selectAll.setText(MessageManager.getString("action.select_all"));
selectAll.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
java.awt.event.KeyEvent.VK_A,
- ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false));
+ jalview.util.ShortcutKeyMaskExWrapper
+ .getMenuShortcutKeyMaskEx(),
+ false));
selectAll.addActionListener(new ActionListener()
{
@Override
save.setText(MessageManager.getString("action.save"));
save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
java.awt.event.KeyEvent.VK_S,
- ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false));
+ jalview.util.ShortcutKeyMaskExWrapper
+ .getMenuShortcutKeyMaskEx(),
+ false));
save.addActionListener(new ActionListener()
{
@Override
});
copyItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
java.awt.event.KeyEvent.VK_C,
- ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false));
+ jalview.util.ShortcutKeyMaskExWrapper
+ .getMenuShortcutKeyMaskEx(),
+ false));
editMenubar.add(jMenu1);
editMenubar.add(editMenu);
JMenu HelpMenu = new JMenu();
- protected JMenu VamsasMenu = new JMenu();
-
- protected JMenu VamsasStMenu = new JMenu();
-
JMenuItem inputLocalFileMenuItem = new JMenuItem();
JMenuItem inputURLMenuItem = new JMenuItem();
JMenu inputMenu = new JMenu();
- protected JMenuItem vamsasStart = new JMenuItem();
-
- protected JMenuItem vamsasImport = new JMenuItem();
-
- protected JMenuItem vamsasSave = new JMenuItem();
-
JMenuItem inputSequence = new JMenuItem();
- protected JMenuItem vamsasStop = new JMenuItem();
-
JMenuItem closeAll = new JMenuItem();
JMenuItem raiseRelated = new JMenuItem();
{
FileMenu.setMnemonic('F');
inputLocalFileMenuItem.setMnemonic('L');
- VamsasMenu.setMnemonic('V');
inputURLMenuItem.setMnemonic('U');
inputTextboxMenuItem.setMnemonic('C');
quit.setMnemonic('Q');
FileMenu.setText(MessageManager.getString("action.file"));
HelpMenu.setText(MessageManager.getString("action.help"));
- VamsasMenu.setText("Vamsas");
- VamsasMenu.setToolTipText(MessageManager
- .getString("label.share_data_vamsas_applications"));
- VamsasStMenu.setText(MessageManager.getString("label.connect_to"));
- VamsasStMenu.setToolTipText(
- MessageManager.getString("label.join_existing_vamsas_session"));
inputLocalFileMenuItem
.setText(MessageManager.getString("label.load_tree_from_file"));
inputLocalFileMenuItem.setAccelerator(
}
});
inputMenu.setText(MessageManager.getString("label.input_alignment"));
- vamsasStart
- .setText(MessageManager.getString("label.new_vamsas_session"));
- vamsasStart.setVisible(false);
- vamsasStart.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- vamsasStart_actionPerformed(e);
- }
- });
- vamsasImport.setText(
- MessageManager.getString("action.load_vamsas_session"));
- vamsasImport.setVisible(false);
- vamsasImport.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- vamsasImport_actionPerformed(e);
- }
- });
- vamsasSave.setText(
- MessageManager.getString("action.save_vamsas_session"));
- vamsasSave.setVisible(false);
- vamsasSave.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- vamsasSave_actionPerformed(e);
- }
- });
inputSequence
.setText(MessageManager.getString("action.fetch_sequences"));
inputSequence.addActionListener(new ActionListener()
inputSequence_actionPerformed(e);
}
});
- vamsasStop
- .setText(MessageManager.getString("label.stop_vamsas_session"));
- vamsasStop.setVisible(false);
- vamsasStop.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- vamsasStop_actionPerformed(e);
- }
- });
closeAll.setText(MessageManager.getString("action.close_all"));
closeAll.addActionListener(new ActionListener()
{
desktopMenubar.add(FileMenu);
desktopMenubar.add(toolsMenu);
- VamsasMenu.setVisible(false);
- desktopMenubar.add(VamsasMenu);
desktopMenubar.add(HelpMenu);
desktopMenubar.add(windowMenu);
FileMenu.add(inputMenu);
FileMenu.add(quit);
HelpMenu.add(aboutMenuItem);
HelpMenu.add(documentationMenuItem);
- VamsasMenu.add(VamsasStMenu);
- VamsasStMenu.setVisible(false);
- VamsasMenu.add(vamsasStart);
- VamsasMenu.add(vamsasImport);
- VamsasMenu.add(vamsasSave);
- VamsasMenu.add(vamsasStop);
if (!Platform.isAMac() || specversion < 11)
{
toolsMenu.add(preferences);
GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
new Insets(0, 2, 5, 5), 70, 1));
+ versioncheck.setVisible(false);
+
// Add padding so the panel doesn't look ridiculous
JPanel spacePanel = new JPanel();
connectTab.add(spacePanel,
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Dimension;
+import java.awt.Font;
import java.awt.GridBagConstraints;
import java.awt.GridBagLayout;
import java.awt.GridLayout;
protected JPanel buttonPanel = new JPanel();
+ public JLabel titleText = new JLabel();
+
public JButton cancel = new JButton();
public JButton showResultsNewFrame = new JButton();
*/
private void jbInit() throws Exception
{
- infoText.setFont(new java.awt.Font("Verdana", 0, 10));
+ infoText.setFont(new Font("Verdana", 0, 10));
infoText.setBorder(null);
infoText.setEditable(false);
infoText.setText("");
titlePanel.setBackground(Color.white);
titlePanel.setPreferredSize(new Dimension(0, 60));
titlePanel.setLayout(borderLayout3);
+ titleText.setFont(new Font("Arial", Font.BOLD, 12));
+ titleText.setBorder(null);
+ titleText.setText("");
jScrollPane1.setBorder(null);
jScrollPane1.setPreferredSize(new Dimension(400, 70));
- cancel.setFont(new java.awt.Font("Verdana", 0, 11));
+ cancel.setFont(new Font("Verdana", 0, 11));
cancel.setText(MessageManager.getString("action.cancel"));
cancel.addActionListener(new java.awt.event.ActionListener()
{
- public void actionPerformed(ActionEvent e)
+ @Override
+ public void actionPerformed(ActionEvent e)
{
cancel_actionPerformed(e);
}
return false;
}
return (jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx() // .getMenuShortcutKeyMaskEx()
- & e.getModifiersEx()) != 0; // getModifiers()) != 0;
+ & jalview.util.ShortcutKeyMaskExWrapper
+ .getModifiersEx(e)) != 0; // getModifiers()) != 0;
}
return e.isControlDown();
}
package jalview.util;
-import java.awt.Toolkit;
-import java.awt.event.KeyEvent;
+import java.awt.event.MouseEvent;
public class ShortcutKeyMaskExWrapper
{
- private static boolean init = false;
+ private static final Float specversion;
- private static final Float specversion = Float
- .parseFloat(System.getProperty("java.specification.version"));
+ private static final float modern;
- private static final float modern = 11;
+ public static final int SHIFT_DOWN_MASK;
- public static int SHIFT_DOWN_MASK = KeyEvent.SHIFT_DOWN_MASK;
+ public static final int ALT_DOWN_MASK;
- public static int ALT_DOWN_MASK = KeyEvent.ALT_DOWN_MASK;
+ private static final ShortcutKeyMaskExWrapperI wrapper;
- public ShortcutKeyMaskExWrapper()
+ static
{
- }
+ specversion = Float
+ .parseFloat(System.getProperty("java.specification.version"));
+ modern = 11;
- private static void init()
- {
- if (init)
- {
- return;
- }
- if (specversion < modern)
+ if (specversion >= modern)
{
- SHIFT_DOWN_MASK = KeyEvent.SHIFT_MASK;
- ALT_DOWN_MASK = KeyEvent.ALT_MASK;
+ wrapper = new jalview.util.ShortcutKeyMaskExWrapper11();
+ SHIFT_DOWN_MASK = jalview.util.ShortcutKeyMaskExWrapper11.SHIFT_DOWN_MASK;
+ ALT_DOWN_MASK = jalview.util.ShortcutKeyMaskExWrapper11.ALT_DOWN_MASK;
}
else
{
- SHIFT_DOWN_MASK = KeyEvent.SHIFT_DOWN_MASK;
- ALT_DOWN_MASK = KeyEvent.ALT_DOWN_MASK;
+ wrapper = new jalview.util.ShortcutKeyMaskExWrapper8();
+ SHIFT_DOWN_MASK = jalview.util.ShortcutKeyMaskExWrapper8.SHIFT_DOWN_MASK;
+ ALT_DOWN_MASK = jalview.util.ShortcutKeyMaskExWrapper8.ALT_DOWN_MASK;
}
-
- init = true;
}
public static int getMenuShortcutKeyMaskEx()
{
- init();
- if (specversion < modern)
- {
- return Toolkit.getDefaultToolkit().getMenuShortcutKeyMask();
- }
- else
- {
- return Toolkit.getDefaultToolkit().getMenuShortcutKeyMaskEx();
- }
+ return wrapper.getMenuShortcutKeyMaskEx();
+ }
+
+ public static int getModifiersEx(MouseEvent e)
+ {
+ return wrapper.getModifiersEx(e);
}
}
--- /dev/null
+package jalview.util;
+
+import java.awt.GraphicsEnvironment;
+import java.awt.Toolkit;
+import java.awt.event.KeyEvent;
+import java.awt.event.MouseEvent;
+
+public class ShortcutKeyMaskExWrapper11 implements ShortcutKeyMaskExWrapperI
+{
+ public final static int SHIFT_DOWN_MASK;
+
+ public final static int ALT_DOWN_MASK;
+
+ static
+ {
+ SHIFT_DOWN_MASK = KeyEvent.SHIFT_DOWN_MASK;
+ ALT_DOWN_MASK = KeyEvent.ALT_DOWN_MASK;
+ }
+
+ @Override
+ public int getMenuShortcutKeyMaskEx()
+ {
+ try
+ {
+ if (!GraphicsEnvironment.isHeadless())
+ {
+ return Toolkit.getDefaultToolkit().getMenuShortcutKeyMaskEx();
+ }
+ } catch (java.lang.Throwable t)
+ {
+ }
+ return 0;
+ }
+
+ @Override
+ public int getModifiersEx(MouseEvent e)
+ {
+ return e.getModifiersEx();
+ }
+
+
+}
--- /dev/null
+package jalview.util;
+
+import java.awt.GraphicsEnvironment;
+import java.awt.Toolkit;
+import java.awt.event.KeyEvent;
+import java.awt.event.MouseEvent;
+
+public class ShortcutKeyMaskExWrapper8 implements ShortcutKeyMaskExWrapperI
+{
+ public final static int SHIFT_DOWN_MASK;
+
+ public final static int ALT_DOWN_MASK;
+
+ static
+ {
+ SHIFT_DOWN_MASK = KeyEvent.SHIFT_MASK;
+ ALT_DOWN_MASK = KeyEvent.ALT_MASK;
+ }
+
+ @Override
+ public int getMenuShortcutKeyMaskEx()
+ {
+ try
+ {
+ if (!GraphicsEnvironment.isHeadless())
+ {
+ return Toolkit.getDefaultToolkit().getMenuShortcutKeyMask();
+ }
+ } catch (java.lang.Throwable t)
+ {
+ }
+ return 0;
+ }
+
+ @Override
+ public int getModifiersEx(MouseEvent e)
+ {
+ return e.getModifiers();
+ }
+
+}
--- /dev/null
+package jalview.util;
+
+import java.awt.event.MouseEvent;
+
+public interface ShortcutKeyMaskExWrapperI
+{
+ public static int SHIFT_DOWN_MASK = 0;
+
+ public static int ALT_DOWN_MASK = 0;
+
+ public int getMenuShortcutKeyMaskEx();
+
+ public int getModifiersEx(MouseEvent e);
+}
package jalview.ws;
import jalview.analysis.AlignSeq;
+import jalview.api.FeatureSettingsModelI;
import jalview.bin.Cache;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefEntry;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Enumeration;
+import java.util.HashMap;
import java.util.Hashtable;
import java.util.List;
+import java.util.Map;
import java.util.StringTokenizer;
import java.util.Vector;
Arrays.asList(dataset));
List<String> warningMessages = new ArrayList<>();
+ // clear any old feature display settings recorded from past sessions
+ featureDisplaySettings = null;
+
int db = 0;
while (sdataset.size() > 0 && db < dbSources.length)
{
}
if (retrieved != null)
{
- transferReferences(sdataset, dbsource.getDbSource(), retrieved,
+ transferReferences(sdataset, dbsource, retrieved,
trimDsSeqs, warningMessages);
}
}
* @param warningMessages
* a list of messages to add to
*/
- boolean transferReferences(Vector<SequenceI> sdataset, String dbSource,
+ boolean transferReferences(Vector<SequenceI> sdataset,
+ DbSourceProxy dbSourceProxy,
AlignmentI retrievedAl, boolean trimDatasetSeqs,
List<String> warningMessages)
{
return false;
}
+ String dbSource = dbSourceProxy.getDbName();
boolean modified = false;
SequenceI[] retrieved = recoverDbSequences(
retrievedAl.getSequencesArray());
* seqs.elementAt(jj); if (!sequenceMatches.contains(sequence)) {
* sequenceMatches.addElement(sequence); } } } }
*/
+ if (sequenceMatches.size() > 0)
+ {
+ addFeatureSettings(dbSourceProxy);
+ }
// sequenceMatches now contains the set of all sequences associated with
// the returned db record
final String retrievedSeqString = retrievedSeq.getSequenceAsString();
return modified;
}
+ Map<String, FeatureSettingsModelI> featureDisplaySettings = null;
+
+ private void addFeatureSettings(DbSourceProxy dbSourceProxy)
+ {
+ FeatureSettingsModelI fsettings = dbSourceProxy
+ .getFeatureColourScheme();
+ if (fsettings != null)
+ {
+ if (featureDisplaySettings == null)
+ {
+ featureDisplaySettings = new HashMap<>();
+ }
+ featureDisplaySettings.put(dbSourceProxy.getDbName(), fsettings);
+ }
+ }
+
+ /**
+ *
+ * @return any feature settings associated with sources that have provided sequences
+ */
+ public List<FeatureSettingsModelI>getFeatureSettingsModels()
+ {
+ return featureDisplaySettings == null
+ ? Arrays.asList(new FeatureSettingsModelI[0])
+ : Arrays.asList(featureDisplaySettings.values()
+ .toArray(new FeatureSettingsModelI[1]));
+ }
/**
* Adds the message to the list unless it already contains it
*
int i = 0;
for (int j = sorted.length - 1; j >= 0; j--, i++)
{
- srcs[i] = sorted[j];
+ tosort[i] = sorted[j];
}
- return srcs;
+ return tosort;
}
}
testee = new EditCommand();
seqs = new SequenceI[4];
seqs[0] = new Sequence("seq0", "abcdefghjk");
- seqs[0].setDatasetSequence(new Sequence("seq0ds", "abcdefghjk"));
+ seqs[0].setDatasetSequence(new Sequence("seq0ds", "ABCDEFGHJK"));
seqs[1] = new Sequence("seq1", "fghjklmnopq");
- seqs[1].setDatasetSequence(new Sequence("seq1ds", "fghjklmnopq"));
+ seqs[1].setDatasetSequence(new Sequence("seq1ds", "FGHJKLMNOPQ"));
seqs[2] = new Sequence("seq2", "qrstuvwxyz");
- seqs[2].setDatasetSequence(new Sequence("seq2ds", "qrstuvwxyz"));
+ seqs[2].setDatasetSequence(new Sequence("seq2ds", "QRSTUVWXYZ"));
seqs[3] = new Sequence("seq3", "1234567890");
seqs[3].setDatasetSequence(new Sequence("seq3ds", "1234567890"));
al = new Alignment(seqs);
4, 8, al);
assertEquals("abcdefghjk", seqs[0].getSequenceAsString());
assertEquals("fghjZ-xYopq", seqs[1].getSequenceAsString());
- assertEquals("fghjZxYopq",
+ // Dataset Sequence should always be uppercase
+ assertEquals("fghjZxYopq".toUpperCase(),
seqs[1].getDatasetSequence().getSequenceAsString());
assertEquals("qrstuvwxyz", seqs[2].getSequenceAsString());
assertEquals("1234567890", seqs[3].getSequenceAsString());
assertEquals("ABxyZ-DEF", seq.getSequenceAsString());
assertEquals(1, seq.getStart());
assertEquals(8, seq.getEnd());
- assertEquals("ABxyZDEF",
+ // Dataset sequence always uppercase
+ assertEquals("ABxyZDEF".toUpperCase(),
seq.getDatasetSequence().getSequenceAsString());
assertEquals(8, seq.getDatasetSequence().getEnd());
assertEquals("ABxyZ-DEF", seq.getSequenceAsString());
assertEquals(1, seq.getStart());
assertEquals(8, seq.getEnd());
- assertEquals("ABxyZDEF",
+ // dataset sequence should be Uppercase
+ assertEquals("ABxyZDEF".toUpperCase(),
seq.getDatasetSequence().getSequenceAsString());
assertEquals(8, seq.getDatasetSequence().getEnd());
assertEquals("----klmnopq", seqs[1].getSequenceAsString());
// and ds is preserved
assertTrue(dsseq == seqs[1].getDatasetSequence());
- // and it is unchanged
- assertEquals("fghjklmnopq", dsseq.getSequenceAsString());
+ // and it is unchanged and UPPERCASE !
+ assertEquals("fghjklmnopq".toUpperCase(), dsseq.getSequenceAsString());
// and that alignment sequence start has been adjusted
assertEquals(5, seqs[1].getStart());
assertEquals(11, seqs[1].getEnd());
assertEquals("----klmnopq", seqs[1].getSequenceAsString());
// and ds is preserved
assertTrue(dsseq == seqs[1].getDatasetSequence());
- // and it is unchanged
- assertEquals("fghjklmnopq", dsseq.getSequenceAsString());
+ // and it is unchanged AND UPPERCASE !
+ assertEquals("fghjklmnopq".toUpperCase(), dsseq.getSequenceAsString());
// and that alignment sequence start has been adjusted
assertEquals(5, seqs[1].getStart());
assertEquals(11, seqs[1].getEnd());
AlignFrame af;
@BeforeClass(alwaysRun = true)
- public void setUpJvOptionPane()
+ public static void setUpBeforeClass() throws Exception
+ {
+ setUpJvOptionPane();
+ /*
+ * use read-only test properties file
+ */
+ Cache.loadProperties("test/jalview/io/testProps.jvprops");
+ Jalview.main(new String[] { "-nonews" });
+ }
+
+ @AfterMethod(alwaysRun = true)
+ public void tearDown()
+ {
+ Desktop.instance.closeAll_actionPerformed(null);
+ }
+
+ /**
+ * configure (read-only) properties for test to ensure Consensus is computed for
+ * colour Above PID testing
+ */
+ @BeforeMethod(alwaysRun = true)
+ public void setUp()
+ {
+ Cache.loadProperties("test/jalview/io/testProps.jvprops");
+ Cache.applicationProperties.setProperty("SHOW_IDENTITY",
+ Boolean.TRUE.toString());
+ af = new FileLoader().LoadFileWaitTillLoaded("examples/uniref50.fa",
+ DataSourceType.FILE);
+
+ /*
+ * wait for Consensus thread to complete
+ */
+ synchronized (this)
+ {
+ while (af.getViewport().getConsensusSeq() == null)
+ {
+ try
+ {
+ wait(50);
+ } catch (InterruptedException e)
+ {
+ }
+ }
+ }
+ }
+
+ public static void setUpJvOptionPane()
{
JvOptionPane.setInteractiveMode(false);
JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
assertEquals(next[1], 8);
}
- @BeforeClass(alwaysRun = true)
- public static void setUpBeforeClass() throws Exception
- {
- /*
- * use read-only test properties file
- */
- Cache.loadProperties("test/jalview/io/testProps.jvprops");
- Jalview.main(new String[] { "-nonews" });
- }
-
- @AfterMethod(alwaysRun = true)
- public void tearDown()
- {
- Desktop.instance.closeAll_actionPerformed(null);
- }
-
- /**
- * configure (read-only) properties for test to ensure Consensus is computed
- * for colour Above PID testing
- */
- @BeforeMethod(alwaysRun = true)
- public void setUp()
- {
- Cache.loadProperties("test/jalview/io/testProps.jvprops");
- Cache.applicationProperties.setProperty("SHOW_IDENTITY",
- Boolean.TRUE.toString());
- af = new FileLoader().LoadFileWaitTillLoaded("examples/uniref50.fa",
- DataSourceType.FILE);
-
- /*
- * wait for Consensus thread to complete
- */
- synchronized (this)
- {
- while (af.getViewport().getConsensusSeq() == null)
- {
- try
- {
- wait(50);
- } catch (InterruptedException e)
- {
- }
- }
- }
- }
-
/**
* Test that changing background (alignment) colour scheme
* <ul>
assertEquals(Color.yellow, fc1.getColour());
assertEquals(10f, fc1.getMin());
assertEquals(20f, fc1.getMax());
+
+ /*
+ * modify original attribute label and check that copy doesn't change
+ */
+ fc.setAttributeName("MAF", "AF");
+ assertArrayEquals(new String[] { "AF" }, fc1.getAttributeName());
+
}
@Test(groups = { "Functional" })
import jalview.ws.seqfetcher.DbSourceProxy;
import java.util.Enumeration;
+import java.util.HashMap;
import java.util.List;
+import java.util.Map;
import java.util.Vector;
+import org.testng.Assert;
import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
public class SequenceFetcherTest
{
JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
}
+ @Test(groups = "Functional")
+ public void testNoDuplicatesInFetchDbRefs()
+ {
+ Map<String, List<DbSourceProxy>> seen = new HashMap<>();
+ jalview.ws.SequenceFetcher sfetcher = new jalview.ws.SequenceFetcher();
+ String dupes = "";
+ for (String src : sfetcher.getOrderedSupportedSources())
+ {
+ List<DbSourceProxy> seenitem = seen.get(src);
+ if (seenitem != null)
+ {
+ dupes += (dupes.length() > 0 ? "," : "") + src;
+ }
+ else
+ {
+ seen.put(src, sfetcher.getSourceProxy(src));
+ }
+ }
+ if (dupes.length() > 0)
+ {
+ Assert.fail("Duplicate sources : " + dupes);
+ }
+ }
+
/**
* simple run method to test dbsources.
*
--- /dev/null
+#!/usr/bin/env bash
+
+J8HOME=/path/to/java8/jdk
+J11HOME=/path/to/java11/jdk
+OLDBUILDDIR=/path/to/old/build/root
+JALVIEWDIR=/path/to/recent/jalview
+LOCALARCHIVEDIR=/path/to/where/to/store/archive/locally
+WEBSITEDOCROOTMOUNT=/path/to/mounted/website/docroot
+
+
+cd OLDBUILDDIR
+mkdir tar
+cd tar
+wget http://www.jalview.org/source/jalview_2_08b.tar.gz http://www.jalview.org/source/jalview_2_2_1.tar.gz http://www.jalview.org/source/jalview_2_3_buildfix.tar.gz http://www.jalview.org/source/jalview_2_4_0b2.tar.gz http://www.jalview.org/source/jalview_2_5_1.tar.gz http://www.jalview.org/source/jalview_2_6_1.tar.gz http://www.jalview.org/source/jalview_2_7.tar.gz http://www.jalview.org/source/jalview_2_8_2b1.tar.gz http://www.jalview.org/source/jalview_2_9_0b1.tar.gz http://www.jalview.org/source/jalview_2_10_5.tar.gz
+cd -
+
+export JAVA_HOME=J8HOME
+export PATH=$JAVA_HOME/bin:$PATH
+
+for x in tar/jalview_*.tar.gz
+do
+ V=${x#*jalview_}
+ V=${V%.tar.gz}
+ echo $V
+ tar --one-top-level -xvf $x
+ cd jalview_$V/jalview
+ ant makedist -DJALVIEW_VERSION="$V"
+ cd -
+done
+
+export JAVA_HOME=J11HOME
+export PATH=$JAVA_HOME/bin:$PATH
+
+cd $JALVIEWDIR
+for x in $OLDBUILDDIR/jalview_*/jalview
+do
+ V=${x##*jalview_}
+ V=${V%/jalview}
+ echo $V
+ [ -e getdown/website ] && /bin/rm -r getdown/website
+ [ -e getdown/files ] && /bin/rm -r getdown/website
+ gradle getdown -PCHANNEL=ARCHIVE -PJALVIEW_VERSION="$V" -PJAVA_VERSION=1.8 -PARCHIVEDIR=$x -Pgetdown_rsync_dest=$LOCALARCHIVEDIR -PRUNRSYNC=true
+done
+
+
+cd $LOCALARCHIVEDIR
+rsync -avh --delete $LOCALARCHIVEDIR/archive/ $WEBSITEDOCROOTMOUNT/getdown/archive/
+
<key>CFBundleIconFile</key>
<string>applet</string>
<key>CFBundleIdentifier</key>
- <string>com.apple.ScriptEditor.id.Uninstall-Old-Jalview--optional</string>
+ <string>com.apple.ScriptEditor.id.Uninstall-Old-Jalview</string>
<key>CFBundleInfoDictionaryVersion</key>
<string>6.0</string>
<key>CFBundleName</key>
- <string>Uninstall Old Jalview (optional)</string>
+ <string>Uninstall Old Jalview</string>
<key>CFBundlePackageType</key>
<string>APPL</string>
<key>CFBundleShortVersionString</key>
</dict>
<key>LSRequiresCarbon</key>
<true/>
+ <key>NSAppleEventsUsageDescription</key>
+ <string>This script needs to control other applications to run.</string>
+ <key>NSAppleMusicUsageDescription</key>
+ <string>This script needs access to your music to run.</string>
+ <key>NSCalendarsUsageDescription</key>
+ <string>This script needs access to your calendars to run.</string>
+ <key>NSCameraUsageDescription</key>
+ <string>This script needs access to your camera to run.</string>
+ <key>NSContactsUsageDescription</key>
+ <string>This script needs access to your contacts to run.</string>
+ <key>NSHomeKitUsageDescription</key>
+ <string>This script needs access to your HomeKit Home to run.</string>
+ <key>NSMicrophoneUsageDescription</key>
+ <string>This script needs access to your microphone to run.</string>
+ <key>NSPhotoLibraryUsageDescription</key>
+ <string>This script needs access to your photos to run.</string>
+ <key>NSRemindersUsageDescription</key>
+ <string>This script needs access to your reminders to run.</string>
+ <key>NSSiriUsageDescription</key>
+ <string>This script needs access to Siri to run.</string>
+ <key>NSSystemAdministrationUsageDescription</key>
+ <string>This script needs access to administer this system to run.</string>
<key>WindowState</key>
<dict>
<key>bundleDividerCollapsed</key>
<key>bundlePositionOfDivider</key>
<real>0.0</real>
<key>dividerCollapsed</key>
- <false/>
+ <true/>
<key>eventLogLevel</key>
<integer>2</integer>
<key>name</key>
<key>positionOfDivider</key>
<real>421</real>
<key>savedFrame</key>
- <string>20 1180 700 672 0 0 3360 1867 </string>
+ <string>272 342 1754 910 0 0 3360 1867 </string>
<key>selectedTab</key>
- <string>description</string>
+ <string>result</string>
</dict>
</dict>
</plist>
-{\rtf1\ansi\ansicpg1252\cocoartf1561\cocoasubrtf600
+{\rtf1\ansi\ansicpg1252\cocoartf1671\cocoasubrtf500
{\fonttbl}
{\colortbl;\red255\green255\blue255;}
{\*\expandedcolortbl;;}
--- /dev/null
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE plist PUBLIC "-//Apple//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd">
+<plist version="1.0">
+<dict>
+ <key>files</key>
+ <dict>
+ <key>Resources/Scripts/main.scpt</key>
+ <data>
+ KEuZnZPFR5wgwG/qEhXMd5yBoi4=
+ </data>
+ <key>Resources/applet.icns</key>
+ <data>
+ vIRz6m6+ZxDNfi4iTsXj5rdcZUA=
+ </data>
+ <key>Resources/applet.rsrc</key>
+ <data>
+ oLbJze+WI6mK9fT14HFV6EwFoEI=
+ </data>
+ <key>Resources/description.rtfd/TXT.rtf</key>
+ <data>
+ JdCHmFsejhMRQNi2CzUAg7xM/6Q=
+ </data>
+ </dict>
+ <key>files2</key>
+ <dict>
+ <key>Resources/Scripts/main.scpt</key>
+ <dict>
+ <key>hash</key>
+ <data>
+ KEuZnZPFR5wgwG/qEhXMd5yBoi4=
+ </data>
+ <key>hash2</key>
+ <data>
+ Y+OMztx129elZ3oX0uhaiMMNU87xhkEPVzSuhF528t0=
+ </data>
+ </dict>
+ <key>Resources/applet.icns</key>
+ <dict>
+ <key>hash</key>
+ <data>
+ vIRz6m6+ZxDNfi4iTsXj5rdcZUA=
+ </data>
+ <key>hash2</key>
+ <data>
+ D7gig1wJlOzR/Iy+y6TESLN0j/cIpjThUyO1pj5fZEc=
+ </data>
+ </dict>
+ <key>Resources/applet.rsrc</key>
+ <dict>
+ <key>hash</key>
+ <data>
+ oLbJze+WI6mK9fT14HFV6EwFoEI=
+ </data>
+ <key>hash2</key>
+ <data>
+ 6bi/D/GzKmLhXbbC8+OLEX9+44Au0XOyGRd+kfw6uzA=
+ </data>
+ </dict>
+ <key>Resources/description.rtfd/TXT.rtf</key>
+ <dict>
+ <key>hash</key>
+ <data>
+ JdCHmFsejhMRQNi2CzUAg7xM/6Q=
+ </data>
+ <key>hash2</key>
+ <data>
+ e8RCmynIiyJGwHTnWQowZeGP0OUnjjA6SQTvIzP7Hxs=
+ </data>
+ </dict>
+ </dict>
+ <key>rules</key>
+ <dict>
+ <key>^Resources/</key>
+ <true/>
+ <key>^Resources/.*\.lproj/</key>
+ <dict>
+ <key>optional</key>
+ <true/>
+ <key>weight</key>
+ <real>1000</real>
+ </dict>
+ <key>^Resources/.*\.lproj/locversion.plist$</key>
+ <dict>
+ <key>omit</key>
+ <true/>
+ <key>weight</key>
+ <real>1100</real>
+ </dict>
+ <key>^Resources/Base\.lproj/</key>
+ <dict>
+ <key>weight</key>
+ <real>1010</real>
+ </dict>
+ <key>^version.plist$</key>
+ <true/>
+ </dict>
+ <key>rules2</key>
+ <dict>
+ <key>.*\.dSYM($|/)</key>
+ <dict>
+ <key>weight</key>
+ <real>11</real>
+ </dict>
+ <key>^(.*/)?\.DS_Store$</key>
+ <dict>
+ <key>omit</key>
+ <true/>
+ <key>weight</key>
+ <real>2000</real>
+ </dict>
+ <key>^(Frameworks|SharedFrameworks|PlugIns|Plug-ins|XPCServices|Helpers|MacOS|Library/(Automator|Spotlight|LoginItems))/</key>
+ <dict>
+ <key>nested</key>
+ <true/>
+ <key>weight</key>
+ <real>10</real>
+ </dict>
+ <key>^.*</key>
+ <true/>
+ <key>^Info\.plist$</key>
+ <dict>
+ <key>omit</key>
+ <true/>
+ <key>weight</key>
+ <real>20</real>
+ </dict>
+ <key>^PkgInfo$</key>
+ <dict>
+ <key>omit</key>
+ <true/>
+ <key>weight</key>
+ <real>20</real>
+ </dict>
+ <key>^Resources/</key>
+ <dict>
+ <key>weight</key>
+ <real>20</real>
+ </dict>
+ <key>^Resources/.*\.lproj/</key>
+ <dict>
+ <key>optional</key>
+ <true/>
+ <key>weight</key>
+ <real>1000</real>
+ </dict>
+ <key>^Resources/.*\.lproj/locversion.plist$</key>
+ <dict>
+ <key>omit</key>
+ <true/>
+ <key>weight</key>
+ <real>1100</real>
+ </dict>
+ <key>^Resources/Base\.lproj/</key>
+ <dict>
+ <key>weight</key>
+ <real>1010</real>
+ </dict>
+ <key>^[^/]+$</key>
+ <dict>
+ <key>nested</key>
+ <true/>
+ <key>weight</key>
+ <real>10</real>
+ </dict>
+ <key>^embedded\.provisionprofile$</key>
+ <dict>
+ <key>weight</key>
+ <real>20</real>
+ </dict>
+ <key>^version\.plist$</key>
+ <dict>
+ <key>weight</key>
+ <real>20</real>
+ </dict>
+ </dict>
+</dict>
+</plist>
<?xml version="1.0" encoding="UTF-8"?>
-<install4j version="7.0.9" transformSequenceNumber="7">
+<install4j version="7.0.11" transformSequenceNumber="7">
<directoryPresets config="." />
<application name="Jalview" distributionSourceDir="" applicationId="6595-2347-1923-0725" mediaDir="../../build/install4j" mediaFilePattern="${compiler:sys.shortName}_${compiler:sys.platform}_${compiler:sys.version}" compression="6" lzmaCompression="true" pack200Compression="false" excludeSignedFromPacking="true" commonExternalFiles="false" createMd5Sums="true" shrinkRuntime="true" shortName="Jalview" publisher="University of Dundee" publisherWeb="http://www.jalview.org/" version="$$VERSION$$" allPathsRelative="true" backupOnSave="false" autoSave="false" convertDotsToUnderscores="true" macSignature="????" macVolumeId="5aac4968c304f65" javaMinVersion="9999999999" javaMaxVersion="" allowBetaVM="true" jdkMode="jdk" jdkName="JDK 11.0">
<languages skipLanguageSelection="false" languageSelectionInPrincipalLanguage="false">
<dirEntry mountPoint="885" file="$$WINDOWS_JAVA_VM_DIR$$" overwriteMode="4" shared="false" fileMode="755" uninstallMode="0" overrideFileMode="true" overrideOverwriteMode="false" overrideUninstallMode="true" entryMode="subdir" subDirectory="${compiler:JRE_DIR}" excludeSuffixes="" dirMode="755" overrideDirMode="false">
<exclude />
</dirEntry>
- <dirEntry mountPoint="1875" file="../../getdown/website/$$JAVA_VERSION$$/dist" overwriteMode="1" shared="false" fileMode="644" uninstallMode="2" overrideFileMode="true" overrideOverwriteMode="true" overrideUninstallMode="true" entryMode="subdir" subDirectory="dist" excludeSuffixes="" dirMode="755" overrideDirMode="true">
+ <dirEntry mountPoint="1875" file="../../getdown/website/$$JAVA_VERSION$$/$$GETDOWN_DIST_DIR$$" overwriteMode="1" shared="false" fileMode="644" uninstallMode="2" overrideFileMode="true" overrideOverwriteMode="true" overrideUninstallMode="true" entryMode="subdir" subDirectory="$$GETDOWN_DIST_DIR$$" excludeSuffixes="" dirMode="755" overrideDirMode="true">
<exclude />
</dirEntry>
<dirEntry mountPoint="2107" file="Uninstall Old Jalview.app" overwriteMode="4" shared="false" fileMode="755" uninstallMode="0" overrideFileMode="true" overrideOverwriteMode="false" overrideUninstallMode="false" entryMode="subdir" subDirectory="Uninstall Old Jalview.app" excludeSuffixes="" dirMode="755" overrideDirMode="true">
<java mainClass="com.threerings.getdown.launcher.GetdownApp" mainMode="1" vmParameters="" arguments=". jalview" allowVMPassthroughParameters="true" preferredVM="" bundleRuntime="true">
<classPath>
<archive location="getdown-launcher.jar" failOnError="true" />
+ <scanDirectory location="$$GETDOWN_INSTALL_DIR$$" failOnError="false" />
</classPath>
<modulePath />
<nativeLibraryDirectories />
<java mainClass="com.threerings.getdown.launcher.GetdownApp" mainMode="1" vmParameters="" arguments=". jalview" allowVMPassthroughParameters="true" preferredVM="" bundleRuntime="true">
<classPath>
<archive location="getdown-launcher.jar" failOnError="true" />
+ <scanDirectory location="$$GETDOWN_INSTALL_DIR$$" failOnError="false" />
</classPath>
<modulePath />
<nativeLibraryDirectories />
</splashScreen>
<java mainClass="jalview.bin.Launcher" mainMode="1" vmParameters="" arguments="" allowVMPassthroughParameters="true" preferredVM="" bundleRuntime="true">
<classPath>
- <scanDirectory location="dist" failOnError="false" />
+ <scanDirectory location="$$GETDOWN_DIST_DIR$$" failOnError="false" />
</classPath>
<modulePath />
<nativeLibraryDirectories />
<java class="java.beans.XMLDecoder">
<object class="com.install4j.runtime.beans.actions.files.DeleteFileAction">
<void property="files">
- <array class="java.io.File" length="17">
+ <array class="java.io.File" length="31">
<void index="0">
<object class="java.io.File">
<string>jre</string>
</void>
<void index="1">
<object class="java.io.File">
- <string>.install4j</string>
+ <string>jre.jar</string>
</object>
</void>
<void index="2">
<object class="java.io.File">
- <string>dist</string>
+ <string>.install4j</string>
</object>
</void>
<void index="3">
<object class="java.io.File">
- <string>resource</string>
+ <string>$$GETDOWN_DIST_DIR$$</string>
</object>
</void>
<void index="4">
<object class="java.io.File">
- <string>getdown-launcher.jar</string>
+ <string>$$GETDOWN_ALT_DIR$$</string>
</object>
</void>
<void index="5">
<object class="java.io.File">
- <string>getdown-launcher-old.jar</string>
+ <string>$$GETDOWN_RESOURCE_DIR$$</string>
</object>
</void>
<void index="6">
<object class="java.io.File">
- <string>getdown-launcher-new.jar</string>
+ <string>getdown-launcher.jar</string>
</object>
</void>
<void index="7">
<object class="java.io.File">
- <string>*.jarv</string>
+ <string>getdown-launcher-old.jar</string>
</object>
</void>
<void index="8">
<object class="java.io.File">
- <string>gettingdown.lock</string>
+ <string>getdown-launcher-new.jar</string>
</object>
</void>
<void index="9">
<object class="java.io.File">
- <string>*.log</string>
+ <string>*.jarv</string>
</object>
</void>
<void index="10">
<object class="java.io.File">
- <string>*.txt</string>
+ <string>gettingdown.lock</string>
</object>
</void>
<void index="11">
<object class="java.io.File">
- <string>*_new</string>
+ <string>*.log</string>
</object>
</void>
<void index="12">
<object class="java.io.File">
- <string>digest.txt</string>
+ <string>*.txt</string>
</object>
</void>
<void index="13">
<object class="java.io.File">
- <string>digest2.txt</string>
+ <string>*_new</string>
</object>
</void>
<void index="14">
<object class="java.io.File">
- <string>getdown-launcher.jarv</string>
+ <string>digest.txt</string>
</object>
</void>
<void index="15">
<object class="java.io.File">
- <string>launcher.log</string>
+ <string>digest2.txt</string>
</object>
</void>
<void index="16">
<object class="java.io.File">
+ <string>getdown-launcher.jarv</string>
+ </object>
+ </void>
+ <void index="17">
+ <object class="java.io.File">
+ <string>getdown-launcher-new.jarv</string>
+ </object>
+ </void>
+ <void index="18">
+ <object class="java.io.File">
+ <string>channel_launch.jvl</string>
+ </object>
+ </void>
+ <void index="19">
+ <object class="java.io.File">
+ <string>launcher.log</string>
+ </object>
+ </void>
+ <void index="20">
+ <object class="java.io.File">
<string>proxy.txt</string>
</object>
</void>
+ <void index="21">
+ <object class="java.io.File">
+ <string>META-INF</string>
+ </object>
+ </void>
+ <void index="22">
+ <object class="java.io.File">
+ <string>install/getdown-launcher.jar</string>
+ </object>
+ </void>
+ <void index="23">
+ <object class="java.io.File">
+ <string>install/getdown.txt</string>
+ </object>
+ </void>
+ <void index="24">
+ <object class="java.io.File">
+ <string>install/build_properties</string>
+ </object>
+ </void>
+ <void index="25">
+ <object class="java.io.File">
+ <string>build_properties</string>
+ </object>
+ </void>
+ <void index="26">
+ <object class="java.io.File">
+ <string>install</string>
+ </object>
+ </void>
+ <void index="27">
+ <object class="java.io.File">
+ <string>dist</string>
+ </object>
+ </void>
+ <void index="28">
+ <object class="java.io.File">
+ <string>release</string>
+ </object>
+ </void>
+ <void index="29">
+ <object class="java.io.File">
+ <string>alt</string>
+ </object>
+ </void>
+ <void index="30">
+ <object class="java.io.File">
+ <string>resource</string>
+ </object>
+ </void>
</array>
</void>
<void property="recursive">
<group name="" id="49" customizedId="" beanClass="com.install4j.runtime.beans.groups.VerticalFormComponentGroup" enabled="true" commentSet="false" comment="" actionElevationType="inherit" useExternalParametrization="true" externalParametrizationName="Customize title bar" externalParametrizationMode="include">
<serializedBean>
<java class="java.beans.XMLDecoder">
- <object class="com.install4j.runtime.beans.groups.VerticalFormComponentGroup">
+ <object class="com.install4j.runtime.beans.groups.VerticalFormComponentGroup" id="VerticalFormComponentGroup0">
<void property="backgroundColor">
<object class="java.awt.Color">
<int>255</int>
<string>icon:${installer:sys.installerApplicationMode}_header.png</string>
</object>
</void>
+ <void id="Integer0" property="cellSpacing" />
+ <void id="Integer1" property="borderWidth" />
<void property="imageInsets">
<object class="java.awt.Insets">
- <int>0</int>
+ <object idref="Integer0" />
<int>5</int>
- <int>1</int>
- <int>1</int>
+ <object idref="Integer1" />
+ <object idref="Integer1" />
</object>
</void>
<void property="insets">
<object class="java.awt.Insets">
- <int>0</int>
+ <object idref="Integer0" />
<int>20</int>
- <int>0</int>
+ <object idref="Integer0" />
<int>10</int>
</object>
</void>
<group name="" id="53" customizedId="" beanClass="com.install4j.runtime.beans.groups.HorizontalFormComponentGroup" enabled="true" commentSet="false" comment="" actionElevationType="inherit" useExternalParametrization="false" externalParametrizationName="" externalParametrizationMode="all">
<serializedBean>
<java class="java.beans.XMLDecoder">
- <object class="com.install4j.runtime.beans.groups.HorizontalFormComponentGroup">
+ <object class="com.install4j.runtime.beans.groups.HorizontalFormComponentGroup" id="HorizontalFormComponentGroup0">
<void property="alignFirstLabel">
<boolean>false</boolean>
</void>
+ <void id="Integer0" property="cellSpacing" />
<void property="insets">
<object class="java.awt.Insets">
<int>3</int>
- <int>5</int>
+ <object idref="Integer0" />
<int>8</int>
- <int>5</int>
+ <object idref="Integer0" />
</object>
</void>
</object>
--- /dev/null
+<project name="Publish Help Webpages for Jalview" default="pubhtmlhelp">
+
+<target name="pubhtmlhelp">
+ <property name="appletHelpDir" value="../build/distribution/help"/>
+ <!-- finally, publish the help files -->
+ <javac srcdir="." destdir="." includes="help2Website.java"/>
+ <java fork="true" dir="${helpBuildDir}" classpath="." classname="help2Website"/>
+ <delete dir="${appletHelpDir}"/>
+ <copy preservelastmodified="true" overwrite="true"
+ todir="${appletHelpDir}">
+ <fileset dir="${helpBuildDir}">
+ <include name="*htm*"/>
+ <include name="icons/**.*"/>
+ <include name="html/**/*.*"/>
+ <exclude name="**/CVS"/>
+ <exclude name="CVS"/>
+ </fileset>
+ </copy>
+ <replace dir="${appletHelpDir}">
+ <include name="**/*.htm*"/>
+ <replacetoken><![CDATA[</body>]]></replacetoken>
+ <replacevalue><![CDATA[
+<script type="text/javascript">
+ var gaJsHost = (("https:" == document.location.protocol) ?
+ "https://ssl." : "http://www.");
+ document.write(unescape("%3Cscript src=\'" + gaJsHost +
+ "google-analytics.com/ga.js\' type=\'text/javascript\'%3E%3C/script%3E"));
+</script>
+<script type="text/javascript">
+try{
+ var pageTracker = _gat._getTracker("'UA-9060947-1'");
+ pageTracker._trackPageview();
+} catch(err) {}
+</script>
+</body>
+]]></replacevalue>
+</replace>
+<echo file="${appletHelpDir}/help.html">
+<![CDATA[<html><head>
+<title>Jalview Documentation</title>
+</head>
+<frameset cols="300,*">
+<frame src="helpTOC.html" name=tocframe scrolling=yes >
+<frame src="html/index.html" name=bodyframe >
+<noframes><body>
+This page requires a browser that supports frames.
+<script type="text/javascript">
+ var gaJsHost = (("https:" == document.location.protocol) ?
+ "https://ssl." : "http://www.");
+ document.write(unescape("%3Cscript src=\'" + gaJsHost +
+ "google-analytics.com/ga.js\' type=\'text/javascript\'%3E%3C/script%3E"));
+</script>
+<script type="text/javascript">
+try{
+ var pageTracker = _gat._getTracker("'UA-9060947-1'");
+ pageTracker._trackPageview();
+} catch(err) {}
+</script></body>
+<noframes></frameset>
+</html>
+]]></echo>
+
+ </target>
+</project>
git://source.jalview.org / jalview.git / commitdiff
