/utils/install4j/jalview-installers-*.install4j
*.swp
/bin
+/doc/building.html
import org.apache.tools.ant.filters.ReplaceTokens
//import org.apache.tools.ant.filters.ReplaceRegexp
import org.gradle.internal.os.OperatingSystem
+import org.gradle.plugins.ide.eclipse.model.*
+
+
+import groovy.transform.ExternalizeMethods
buildscript {
dependencies {
ext {
// where the getdown channel will be built.
- // TODO: consider allowing this expression to be overrriden by -P arg
- getdownWebsiteDir = jalviewDir + '/' + getdown_website_dir + '/' + JAVA_VERSION + '/'
+ // TODO: consider allowing this expression to be overridden by -P arg
+ getdownWebsiteDir = jalviewDir + '/' + getdown_website_dir + '/' + JAVA_VERSION
getdownAppDir = getdownWebsiteDir + '/' + getdown_app_dir
- getdownJ11libDir = getdownWebsiteDir + '/' + getdown_j11lib_dir
+ //getdownJ11libDir = getdownWebsiteDir + '/' + getdown_j11lib_dir
getdownResourceDir = getdownWebsiteDir + '/' + getdown_resource_dir
getdownLauncher = jalviewDir + '/' + getdown_launcher
getdownFilesDir = jalviewDir + '/' + getdown_files_dir + '/' + JAVA_VERSION + '/'
- def getdownChannel = getdown_channel_name
- if (getdown_channel_name.equals("COMMIT")) {
- getdownChannel = getGitHash()
- }
- getdown_app_base = getdown_channel_base+"/"+getdownChannel+"/"+JAVA_VERSION+"/"
+ getdown_app_base = getdown_channel_base+"/"+getdown_channel_name+"/"+JAVA_VERSION+"/"
modules_compileClasspath = fileTree(dir: "$jalviewDir/$j11modDir", include: ["*.jar"])
modules_runtimeClasspath = modules_compileClasspath
+ gitHash = ""
+ gitBranch = ""
}
def JAVA_INTEGER_VERSION
def getdown_alt_java_min_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_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_target_compatibility = 11
getdown_alt_java_min_version = getdown_alt_java11_min_version
getdown_alt_multi_java_location = getdown_alt_java11_txt_multi_java_location
+ eclipse_java_runtime_name = "JavaSE-11"
additional_compiler_args += [
'--module-path', ext.modules_compileClasspath.asPath,
'--add-modules', j11modules
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"])
removeThese += it
}
}
- containers 'org.eclipse.buildship.core.gradleclasspathcontainer'
minusConfigurations += removeThese
plusConfigurations = [ ]
}
}
cp.entries.removeAll(removeTheseToo)
- }
-
- withXml {
- def node = it.asNode()
- def srcTestAttributes
- node.children().each{ cpe ->
- def attributes = cpe.attributes()
- if (attributes.get("kind") == "src" && attributes.get("path") == "test") {
- srcTestAttributes = cpe.find { a -> a.name() == "attributes" }
- return
- }
- }
- def addTestAttribute = true
- srcTestAttributes.each{a ->
- if (a.name() == "attribute" && a.attributes().getAt("name") == "test") {
- addTestAttribute = false
- }
- }
- if (addTestAttribute) {
- srcTestAttributes.append(new Node(null, "attribute", [name:"test", value:"true"]))
- }
-
- node.appendNode('classpathentry', [kind:"output", path:"bin/main"])
- node.appendNode('classpathentry', [kind:"lib", path:helpParentDir])
- node.appendNode('classpathentry', [kind:"lib", path:resourceDir])
+
+ 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<>();
- 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
+
+ // 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
- //println("Not adding directory "+it)
return
}
def itPath = it.toString()
//println("Not adding duplicate entry "+itPath)
} else {
//println("Adding entry "+itPath)
- node.appendNode('classpathentry', [kind:"lib", path:itPath])
+ cp.entries += new Library(fileReference(itPath))
addedLibPath.put(itPath, true)
}
}
- sourceSets.test.compileClasspath.each{
+
+ // 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
- //println("Not adding directory "+it)
- return
+ 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)) {
- //println("Not adding duplicate entry "+itPath)
+ // don't duplicate
} else {
- //println("Adding entry "+itPath)
- node.appendNode('classpathentry', [kind:"lib", path:itPath])
- .appendNode('attributes')
- .appendNode('attribute', [name:"test", value:"true"])
+ 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()
+ if (attributes.get("kind") == "src" && attributes.get("path") == "test") {
+ srcTestAttributes = cpe.find { a -> a.name() == "attributes" }
+ return
+ }
+ }
+ def addTestAttribute = true
+ srcTestAttributes.each{a ->
+ if (a.name() == "attribute" && a.attributes().getAt("name") == "test") {
+ addTestAttribute = false
+ }
+ }
+ if (addTestAttribute) {
+ srcTestAttributes.append(new Node(null, "attribute", [name:"test", value:"true"]))
+ }
+
+ node.children().each{ cpe ->
+ def attributes = cpe.attributes()
+ if (attributes.get("kind") == "lib" && attributes.get("path").startsWith("utils/")) {
+ cpe.appendNode('attributes')
+ .appendNode('attribute', [name:"test", value:"true"])
+ }
+ }
+ } // withXML
+ } // file
+
+ containers 'org.eclipse.buildship.core.gradleclasspathcontainer'
+ } // classpath
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 ->
def jalview_prefs = new Properties()
- def ins = new FileInputStream(eclipse_extra_jdt_prefs_file)
+ def ins = new FileInputStream(jalviewDirAbsolutePath+"/"+eclipse_extra_jdt_prefs_file)
jalview_prefs.load(ins)
ins.close()
jalview_prefs.forEach { t, v ->
}
}
}
-
-}
+
+ //synchronizationTasks eclipseClasspath
+ //autoBuildTasks eclipseClasspath
+}
task cloverInstr() {
// only instrument source, we build test classes as normal
com.atlassian.clover.CloverInstr.mainImpl(args)
}
}
-
+
task cloverReport {
group = "Verification"
return date.format(format)
}
-def getGitHash() {
- def stdout = new ByteArrayOutputStream()
+task setGitVals {
+ def hashStdOut = new ByteArrayOutputStream()
exec {
commandLine "git", "rev-parse", "--short", "HEAD"
- standardOutput = stdout
- workingDir = jalviewDir
+ standardOutput = hashStdOut
+ ignoreExitValue true
}
- return stdout.toString().trim()
-}
-def getGitBranch() {
- def stdout = new ByteArrayOutputStream()
+ def branchStdOut = new ByteArrayOutputStream()
exec {
commandLine "git", "rev-parse", "--abbrev-ref", "HEAD"
- standardOutput = stdout
- workingDir = jalviewDir
+ standardOutput = branchStdOut
+ ignoreExitValue true
}
- return stdout.toString().trim()
+
+ 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/$buildPropertiesFile"
- /* taking time/date specific comment out to allow better incremental builds */
+ // taking time specific comment out to allow better incremental builds
//comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd HH:mm:ss")
comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd")
property "BUILD_DATE", getDate("dd MMMM yyyy")
property "VERSION", JALVIEW_VERSION
- property "INSTALLATION", INSTALLATION+" git-commit:"+getGitHash()+" ["+getGitBranch()+"]"
+ property "INSTALLATION", INSTALLATION+" git-commit:"+project.ext.gitHash+" ["+project.ext.gitBranch+"]"
outputs.file(outputFile)
- outputs.dir("$classes")
+}
+
+def buildingHTML = "$jalviewDir/$docDir/building.html"
+task deleteBuildingHTML(type: Delete) {
+ delete buildingHTML
+}
+
+task convertBuildingMD(type: Exec) {
+ dependsOn deleteBuildingHTML
+ def buildingMD = "$jalviewDir/$docDir/building.md"
+ def css = "$jalviewDir/$docDir/github.css"
+
+ def pandoc = pandoc_exec
+ def hostname = "hostname".execute().text.trim()
+ if (! 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"
+ }
+
+ ignoreExitValue true
+
+ inputs.file(buildingMD)
+ inputs.file(css)
+ outputs.file(buildingHTML)
+}
+clean {
+ delete buildingHTML
}
task syncDocs(type: Sync) {
+ dependsOn convertBuildingMD
def syncDir = "$classes/$docDir"
from fileTree("$jalviewDir/$docDir")
into syncDir
destinationDir = file("$jalviewDir/$utilsDir")
source = fileTree(dir: "$jalviewDir/$utilsDir", include: ["HelpLinksChecker.java", "BufferedLineReader.java"])
+ inputs.file("$jalviewDir/$utilsDir/HelpLinksChecker.java")
+ inputs.file("$jalviewDir/$utilsDir/HelpLinksChecker.java")
outputs.file("$jalviewDir/$utilsDir/HelpLinksChecker.class")
outputs.file("$jalviewDir/$utilsDir/BufferedLineReader.class")
}
workingDir = jalviewDir
def help = "$classes/$helpDir"
args = [ "$classes/$helpDir", "-nointernet" ]
- //args = [ "$classesDir/$helpDir", "-nointernet" ]
doFirst {
helplinkscheckeroutputfile.createNewFile()
}
shadowJar {
+ group = "distribution"
dependsOn makeDist
from ("$jalviewDir/$libDistDir") {
include("*.jar")
props.put("getdown_txt_multi_java_location", getdown_alt_multi_java_location)
if (getdown_local == "true") {
- getdown_app_base = "file://"+file(getdownWebsiteDir).getAbsolutePath()
+ getdown_app_base = file(getdownWebsiteDir).toURI().toString()
}
props.put("getdown_txt_appbase", getdown_app_base)
props.each{ prop, val ->
outputs.files(install4jConf)
doLast {
+ // include file associations in installer
def installerFileAssociationsXml = file("$install4jDir/$install4jInstallerFileAssociations").text
ant.replaceregexp(
byline: false,
flags: "s",
match: '<action name="EXTENSIONS_REPLACED_BY_GRADLE".*?</action>',
- //match: '<action.*?EXTENSIONS_REPLACED_BY_GRADLE.*?</action>',
replace: installerFileAssociationsXml,
file: install4jConf
)
+ /*
+ // 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
+ )
+ */
}
}
+++ /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>Building Jalview from Source</title>
-</head>
-<body>
-<h1>Building Jalview from Source</h1>
-<p/>
-
-<p>
-You will need the following:<br/>
-<ul>
- <li> Obtain: git</li>
- <li> Build/run: Java Development Kit (JDK). JDK11 is now the recommended platform for developing with Jalview. You can obtain a pre-compiled JDK11 for many platforms from https://adoptopenjdk.net/</li>
- <li> Build: Gradle 5.1 or later. On linux you can obtain this with your package manager (e.g. <code>sudo yum install gradle</code> or <code>sudo apt install gradle</code> or on macOS with brew with <code>brew install gradle</code></li>
-</ul>
-With any luck, once you check out the Jalview source from git and set your JAVA_HOME and PATH correctly, you just need to change to the <code>jalview</code> directory and run <code>gradle getdown</code>.
-</p>
-
-<h2>Obtaining Jalview</h2>
-<p>This is easiest achieved with git:
-<pre>git clone http://www.jalview.org/git/jalview.git</pre>
-Then you can <code>cd jalview</code> to get into the top level jalview dir.
-
-
-<p>
-<h2>Minimal Jalview build</h2>
-<p>To run Jalview, you just need the jalview classes and the .jar libraries that Jalview depends on.</p>
-
-
-<!--
-<p>
-You will need the following (hopefully):<br>
-<ul>
-<li>Java development kit (JDK1.8 is now the recommended platform for developing with Jalview.</li>
-<li>Ant (1.7 or later will be needed for some of the jarsigning tools).</li>
-</ul>
-With any luck, after setting your paths and JAVA_HOME correctly, you
-just need to change to the Jalview directory and run ant (this works
-from eclipse too, but NetBeans is a bit trickier).
-<pre>
- ant
-</pre>
-
-</p>
-<p><strong>Building a webstart version of jalview</strong></p>
-Jalview depends on several libraries contained in the libs directory
-of the distribution. In order to access them, they must all be signed
-jars - using the same jarsigner key as jalview itself. There is a
-build target in ant to make the signed jar files in a directory called
-dist. But first you need to make your own key:
-<p><strong>Making your own key</strong></p>
-
- <p>The ant 'makefulldist' target assumes that a keystore exists in
- a directory 'keys'. To make a key accessible using the default
- settings in the build.xml file then make the keys directory and add
- the jarsigner key with the following :</p>
- <pre>mkdir keys</pre>
- <pre>keytool -genkey -keystore keys/.keystore -keypass alignmentisfun
- -storepass alignmentisfun -sigalg SHA1withRSA -keyalg RSA -alias jalview</pre>
- <em>(you will have to answer some personal questions here)</em>
- <pre>ant makedist -DWebStartLocation="file://.pathtojalviewsource./dist" -Dapplication.codebase="*"</pre>
- <p>This should eventually generate a jalview.jnlp file in ./dist
- along with a set of signed jars using the jalview key). In order to
- test locally via webstart you'll now need to add 'file:/' to your
- java webstart security exception list. Then:</p>
- <pre>javaws file://.pathtojalviewsource./dist/jalview.jnlp</pre>
- <p>Please remember to remove that entry afterwards, since it will leave
- your system vulnerable to malicious code.
- </p>
- <p>
- <strong>Building the JalviewLite applet<br>
- </strong> The JalviewLite applet is compiled using a subset of the packages in
- the src directory (specifically: MCView, and jalview.{datamodel,
- analysis, appletgui, utils, schemes, api, structure}, and
- com.stevesoft.*). Once compiled, these class files are obfuscated to
- make the code run efficiently. To compile the applet Jar, use the
- makeApplet task - optionally passing in a 'donotobfuscate' property to
- the ant build (e.g. -Ddonotobfuscate=true) to disable obfuscation. </p><p>
- The ant target 'pubapplet' can be used to compile install the
- jalviewApplet.jar and any dependent jars (under appletlib) into a copy
- of the examples directory created under the <em>outputDir</em> build
- property (which defaults to the 'dist' directory).
- </p>
- <p>
-<h1>using IDEs to build Jalview</h1>
- <p>The Jalview source distribution includes project definitions for
- Eclipse, Netbeans and some rather ancient Borland JBuilder .jpx
- project files. These files should be sufficient to set up basic source
- folders and build paths, but you will need to ensure that all .jar
- files in the lib and appletlib directories are added to the build path
- for your IDE project, and that the 'buildindices' target in Jalview's
- build.xml is executed with the 'outputDir' ant property set to the
- directory where the IDE expects to place compiled classes ('classes'
- directory for eclipse, 'build/classes' for netbeans).</p>
- <p>Note: It is generally not recommended that you distribute build
- artefacts that were generated automatically via an IDE's own packaging
- mechanism (e.g. Netbeans' executable Jar and dependent lib directory).
- The hand-crafted ant build.xml is (currently) the only officially
- supported method of building distributable versions of Jalview.</p>
- -->
-<address>
-<a href="mailto:help@jalview.org">Jalview development team</a>
-</address>
-</body>
-</html>
--- /dev/null
+# Building Jalview from Source
+
+## tl;dr
+
+```
+# download
+git clone http://source.jalview.org/git/jalview.git
+# compile
+cd jalview
+gradle shadowJar
+# run
+java -jar build/libs/jalview-all-11.jar
+
+# and/or create launcher
+gradle getdown
+# use launcher
+cd getdown/files
+java -jar getdown-launcher.jar . jalview
+```
+
+
+## Setting up
+
+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
+* git
+
+> The versions and installation methods here are just suggestions (which we have tested
+so are known to work). If you need or wish to use different implementations (particularly
+you might need a bespoke JDK if you are on an exotic architecture) then the general
+build instructions should work with any gradle 5+. You should be able to compile the
+bytecode with any JDK Java 11+. The resulting bytecode (in particular the shadow jar)
+should be runnable in any JRE Java 1.8+. Remember that because Jalview and the getdown launcher
+are Java bytecode you can build on one system where you might have gradle, and run
+on another where you don't (JRE 1.8+ required).
+
+### Java 11 compliant JDK
+
+#### All platforms
+We recommend obtaining an OpenJDK JDK 11 (since 11 is the long term support release) from AdoptOpenJDK: <https://adoptopenjdk.net/?variant=openjdk11&jvmVariant=hotspot>, either the *Installer* or `.zip`/`.tar.gz` variants whichever you prefer (if you're not sure, choose the *Installer*).
+
+>##### Alternative/CLI install of AdoptOpenJDK 11
+>
+>You can also install adoptopenjdk11 using either `brew` (macOS), `choco` (Windows)
+(see the section on `gradle` and `git` for more informaiton on `brew` and `choco`)
+or `yum` or `apt` (Linux):
+>
+>###### alternative for MacOS and Homebrew
+>```
+>brew tap adoptopenjdk/openjdk
+>brew cask install adoptopenjdk11
+>```
+>
+>###### alternative for Windows and Chocolatey
+>```
+>choco install adoptopenjdk11
+>```
+>
+>###### alternative for Linux with yum/apt
+>
+>see <https://adoptopenjdk.net/installation.html#linux-pkg>
+
+
+### gradle and git
+You should be able to install the latest (or sufficiently recent) versions of gradle and git using your OS package manager.
+
+#### MacOS
+we recommend using `brew`, which can be installed following the instructions at <https://brew.sh/>.
+After installing `brew`, open a Terminal window and type in (using an Administrator privileged user):
+
+```bash
+brew install gradle git
+```
+
+or if you aready have them installed but need to upgrade the version:
+
+```bash
+brew upgrade gradle git
+```
+
+#### Windows
+
+we suggest using the **Chocolatey** package manager. See install instructions at <https://chocolatey.org/>, and you will just need
+
+```bash
+choco install gradle
+choco install git
+```
+
+Alternatively, you could install a real `bash` shell and install both `gradle` and `git` through `apt-get`.
+See <https://devblogs.microsoft.com/commandline/bash-on-ubuntu-on-windows-download-now-3/>
+for how to install the ubuntu bash shell in Windows 10.
+
+Another alternative would be to install them separately. For `gradle` follow the instructions at <https://gradle.org/install/>, and for `git` here are a couple of suggestions: Git for Windows <https://gitforwindows.org/>.
+Getting the individual installs working together on the command line will be trickier
+so we recommend using Chocolatey or bash.
+
+
+#### Linux
+this will depend on which distribution you're using.
+
+##### For *Debian* based distributions (e.g. Mint, Ubuntu, Debian)
+run
+
+```bash
+ sudo apt-get install gradle git
+```
+
+##### for RPM-based distributions (e.g. Fedora, CentOS, RedHat)
+run
+
+```bash
+sudo yum install gradle git
+```
+
+If you have some other version of linux you'll probably be able to work it out!
+
+
+
+
+## Downloading the Jalview source tree
+
+This can be done with `git`.
+On the command line, change directory to where you want to download Jalview's build-tree
+top level directory. Then run
+
+```bash
+git clone http://source.jalview.org/git/jalview.git
+```
+
+You'll get some progress output and after a minute or two you should have the full
+Jalview build-tree in the folder `jalview`.
+
+### What's in the source tree?
+
+Jalview is a mature product with its codebase going back many years. As such it doesn't
+have a folder structure that most new gradle projects would have, so you might not
+find everything in the place you might expect. Here's a brief description of what
+you might find in the main folders under the `jalview` tree.
+
+Within the `jalview` folder you will find (of possible interest):
+
+ dir/ or file | contains
+---------------------|----------------------------------------------------------------------------------------------------------------
+ `bin/` | used by eclipse for compiled classes -- no need to touch this
+ `build/` | the gradle build dir
+ `classes/` | contains the compiled Java classes for the Jalview application
+ `dist/` | assembled `.jar` files needed to run Jalview application
+ `examples/` | example input files usable by Jalview
+ `getdown/` | the libraries used by the Javliew launcher (getdown)
+ `getdown/src/` | our modified source for `getdown`
+ `getdown/website/` | the assembled "download" folder used by getdown for downloads/upgrades
+ `getdown/files/` | the minimal fileset to launch the Jalview launcher, which can then download the rest of the Jalview application
+ `help/` | the help documents
+ `j8lib/` | libraries needed to run Jalview under Java 1.8
+ `j11lib/` | libraries needed to run Jalivew under Java 11
+ `resource/` | non-java resources used in the Jalview application
+ `src/` | the Jalview application source `.java` files
+ `test/` | Test class source files
+ `utils/` | helper applications used in the build process
+ `utils/install4j/` | files used by the packaging tool, install4j
+ `build.gradle` | the build file used by gradle
+ `gradle.properties` | configurable properties for the build process
+
+Note that you need a Java 11 JDK to compile Jalview whether your target build is Java 1.8 or Java 11.
+
+
+## Building Jalview
+
+You will need to have the Java 11 `javac` in your path, or alternatively you can configure
+gradle to know where this is by putting
+
+```
+org.gradle.java.home=/path_to_jdk_directory
+```
+in the `gradle.properties` file.
+
+> *You may want to see some of the other properties you can change at the end of this document.*
+
+### Minimal Jalview Build
+
+To compile the necessary class files, just run
+
+```bash
+gradle compileJava
+```
+to compile the classes into the `classes` folder.
+You should now be able to run the Jalview application directly with
+
+```bash
+java -cp "classes:resources:help:j11lib/*" jalview.bin.Jalview
+```
+
+You can also run with an automatic large memory setting (which will set the maximum
+memory heap of the Jalview JVM to 90% of your local physical memory) and docked icon setting
+(if possible in your OS) with
+
+```bash
+java -cp "classes:resources:help:j11lib/*" jalview.bin.Launcher
+```
+
+>*You must use just "`j11lib/*`" and not "`j11lib/*.jar`" as this is a special Java
+classpath argument wildcard interpreted by `java`, **not** a shell expansion wildcard interpreted
+by the shell.*
+
+Note that `jalview.bin.Launcher` is a simplified launcher class that re-launches `jalview.bin.Jalview`
+with the same JRE (*not* the same JVM instance), classpath and arguments, but with an automatically determined `-Xmx...`
+memory setting if one hasn't been provided.
+
+### Jalview in a Jar File
+
+To package the `classes`, `resources`, and `help` into one jar, you can run
+
+```bash
+gradle jar
+```
+which assembles the Jalview classes and resources into `dist/jalview.jar`
+
+To run this, use
+
+```bash
+java -cp "dist/jalview.jar:j11lib/*" jalview.bin.Jalview
+```
+
+### Distributed Jar Files
+
+To simplify this, all required `.jar` files can be assembled into the `dist` folder
+using
+
+```bash
+gradle makeDist
+```
+which puts all required jar files into `dist` so you can run with
+
+```bash
+java -cp "dist/*" jalview.bin.Jalview
+```
+
+### Single *shadow* Jar File
+
+The shadow jar file is a single `.jar` that contains all required classes and resources from `jalview.jar`
+and all of the supporting libraries in `j11lib/*.jar` merged into one `.jar` archive
+file. A default launching class (`MAIN-CLASS: jalview.bin.Launcher`) is specified in the `.jar`
+manifest file (`META/MANIFEST.MF`) so a start class doesn't need to be specified.
+
+Build the shadow jar file in `build/lib/jalview-all-11.jar` with
+
+```bash
+gradle shadowJar
+```
+and run it with
+
+```bash
+java -jar build/lib/jalview-all-11.jar
+```
+
+Because no arguments are required, most OSes will associate a `.jar` file with the
+`java` application (if this has been installed through the OS and not just a local
+unzip) as a `-jar` argument so you may find you can launch `jalview-all-11.jar`
+just by double-clicking on it)!
+
+> The `shadowJar` task is not a requirement for any other task, so to build the shadow
+jar file you must specify the `shadowJar` task.
+
+> The shadow jar file represents probably the simplest way to distribute the Jalview application to machines that already have a Java 11 installed,
+although without the many and compelling benefits of the `getdown` launcher.
+
+
+### Building the `getdown` launcher
+
+We have made significant customisations to the `getdown` launcher which you can find
+in `getdown/src/getdown`.
+
+> You don't need to build this afresh as the required `gradle-core.jar`
+and `gradle-launcher.jar` files are already distributed in `j11lib` and `getdown/lib` but if you want to, then
+you'll need a working Maven and also a Java 8 JDK. Ensure the Java 8 `javac` is forefront
+in your path and do
+>
+>```bash
+>cd getdown/src/getdown
+>mvn clean package -Dgetdown.host.whitelist="jalview.org,*.jalview.org"
+>```
+> and you will find the required `.jar` files in `core/target/gradle-core-XXX.jar`
+and `launcher/target/gradle-launcher-XXX.jar`. The `gradle-core.jar` should then be copied
+to all three of the `j8lib`, `j11lib` and `getdown/lib` folders, whilst the `gradle-launcher.jar` only
+needs to be copied to `getdown/lib`.
+>
+>The `mvn` command should ideally include the `-Dgetdown.host.whitelist=*.jalview.org` setting.
+ This, and the necessary file copying commands, can be found in `getdown/src/getdown/mvn_cmd`.
+
+To assemble Jalview with `getdown` use the following gradle task:
+
+```bash
+gradle getdown
+```
+
+This puts all the necessary files to launch Jalview with `getdown`
+into `getdown/website/11/`. This could be treated as the reference folder
+for `getdown`, which is where a getdown launcher will check to see if the Jalview application
+files it has are up to date, and download if they aren't or it simply doesn't have
+them.
+
+A minimal getdown-launcher can be found in `getdown/files/11/` which checks its up-to-date
+status with (the absolute path to) `getdown/website/11/`.
+
+This can be launched with
+
+```bash
+java -jar getdown/files/11/getdown-launcher.jar getdown/files/11/ jalview
+```
+
+> We've already met the `-jar file.jar` arguments. The next argument is the working folder for
+getdown, and the final argument, "`jalview`", is a getdown application id (only "`jalview`"
+is defined here).
+
+
+### Running tests
+
+There are substantial tests written for Jalview that use TestNG, which you can run with
+
+```bash
+gradle test
+```
+
+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.
+
+
+### Installer packaging with *install4j*
+
+Jalview is currently using *install4j* <https://www.ej-technologies.com/products/install4j/overview.html>
+as its installer packaging tool.
+
+If you have a licensed installation of *install4j* you can build Jalview installers
+by running
+
+```bash
+gradle installers
+```
+
+though you may need to fiddle with the `install4j` and `copyInstall4jTemplate` tasks
+in `build.gradle` file to point to your installation of *install4j* and also to bundled
+JREs if you want to bundle those into the installers.
+
+If you want more details, get in touch on our development mailing list <jalview-dev@jalview.org>.
+Sign up at <http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev>.
+
+
+## Building in Eclipse
+
+We develop in Eclipse, and support settings to develop and save Jalview source code
+in our preferred style. We also support running the Jalview application, debugging
+and running tests with TestNG from within Eclipse.
+
+To get Jalview set up as a project in Eclipse, we recommend using at least the 2019-03
+version of Eclipse IDE for Java Developers which you can download from the Eclipse
+website: <https://www.eclipse.org/downloads/>
+
+Once installed, we also recommend installing several plugins from the Eclipse Marketplace.
+
+To do so, launch Eclipse, and go to Help->Eclipse Marketplace...
+
+Search for and install:
+
+1. Buildship Gradle Integration 3.0 (or greater)
+1. Groovy Development Tools 3.4.0 (or greater)
+1. TestNG for Eclipse (optional -- only needed if you want to run tests from Eclipse)
+
+> At time of writing, TestNG for Eclipse does not show up in the Eclipse Marketplace
+as the latest released version does not install in Eclipse 2019-03.
+However, you can install a working beta of TestNG for Eclipse by going to
+>
+Help->Install New Software...
+>
+and entering
+>
+`TestNG Eclipse Composite P2 Repo - http://beust.com/eclipse-beta`
+>
+into the *Work with* box and click on the *Add...* button.
+>
+Eclipse might pause for a bit with the word *Pending* in the table below at this point, but it will eventually list TestNG with
+a selection box under the *Name* column.
+>
+Select *TestNG* and carry on through the
+install process to install the TestNG plugin.
+
+After installing the plugins, it is a good to get Java 11 set up in Eclipse as the default JRE.
+
+To do this go to Preferences (Eclipse->Preferences in macOS, File->Preferences
+on Windows or Window->Preferences on Linux) and find
+
+Java -> Installed JREs
+
+If your Java 11 installation is not listed, click on
+
+*Add* -> Standard VM -> *Next*
+
+and enter the JRE home. You can browse to where it was installed. Give it a name (like "AdoptOpenJDK 11"). Select this JDK
+as the default JRE and click on *Apply and Close*.
+
+
+You can now import Jalview. It is important to import
+Jalview as a Gradle project (not as a Java project), so go to
+
+File->Import...
+
+find and select
+
+Gradle->Existing Gradle Project
+
+and then click on the *Next >* button.
+
+In the following options, it is the *Project Root Directory* you should set to be the
+`jalview` folder that git downloaded. Then you can click on the *Finish* button.
+
+
+## Gradle properties
+
+There are a lot of properties configured in `gradle.properties` which we strongly recommend
+being left as they are unless you have a specific problem with the build process.
+
+There are a few gradle properties you might want to set on the command line with the
+`-P` flag when building a version of Jalview with specific requirements:
+
+#### `JAVA_VERSION`
+This changes the *target* java bytecode version
+> NOTE that you will need to use a Java 11 (or greater) JDK Java compiler to build
+Jalview for any byte-code target version.
+
+Valid values are `11` and `1.8`.
+
+e.g.
+
+```bash
+gradle shadowJar -PJAVA_VERSION=1.8
+```
+
+When using `-PJAVA_VERSION=1.8` the libraries from `j8lib` (instead of `j11lib`) will be used in the compile
+and runtime classpath and also used in the `makeDist` build step. Where a Java version of `11` is used in folder and file names, it will
+instead use `1.8`. Also if you are building installer packages with *install4j* the
+package builder will look for JRE 1.8 bundles to package in the installers.
+
+> Note that continued development of Jalview will assume a Java 11+ runtime environment,
+the 2.11.0 release will run under a Java 1.8 JRE with a few minor features disabled.
+
+#### `CHANNEL`
+This changes the `appbase` setting in `getdown.txt` (`appbase` is where the getdown launcher
+looks to see if there's an updated file) to point to a particular Jalview
+channel. Expected values are `FILE`, `STABLE`, `DEVELOPMENT`, or a specific version
+of Jalview like `2.11` or `2.10.5`.
+
+A value of `FILE` behaves differently to the other expected values and will use a local
+file-system scheme URI instead of a Jalview release channel. This `file:` scheme URI
+uses an absolute path to the `getdown/website/<JAVA_VERSION>`
+
+On a regular development machine, this property will default to `LOCAL`.
+
+e.g.
+```bash
+gradle getdown -PCHANNEL=DEVELOPMENT
+```
+
+#### `MEDIA_TYPES`
+If you are building *install4j* installers (requires *install4j* to be installed) then this property specifies a comma-separated
+list of media types (i.e. platform specific installers) *install4j* should actually build.
+
+Currently the valid values are
+`linuxDeb`,
+`linuxRPM`,
+`macosArchive`,
+`unixArchive`,
+`unixInstaller`,
+`windows`
+
+The default value is all of them.
+
+e.g.
+```bash
+gradle installers -PJAVA_VERSION=1.8 -PMEDA_TYPE=macosArchive
+```
+
+To get an up-to-date list of possible values, you can run
+
+```bash
+perl -n -e 'm/^\s*<(\w+)[^>]*\bmediaFileName=/ && print "$1\n";' utils/install4j/install4j_template.install4j | sort -u
+```
+in the `jalview` root folder.
+
+
+---
+[Jalview Development Team](mailto:help@jalview.org)
\ No newline at end of file
--- /dev/null
+#!/usr/bin/env bash
+pandoc -s -o building.html building.md --metadata pagetitle="Building Jalview from Source" --toc -H github.css
--- /dev/null
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+ line-height: 1.2;
+}
+
+body h1 .anchor {
+ line-height: 1;
+}
+
+body h2 {
+ padding-bottom: 0.3em;
+ font-size: 1.5em;
+ line-height: 1.225;
+}
+
+body h2 .anchor {
+ line-height: 1;
+}
+
+body h3 {
+ font-size: 1.25em;
+ line-height: 1.43;
+}
+
+body h3 .anchor {
+ line-height: 1.2;
+}
+
+body h4 {
+ font-size: 1em;
+}
+
+body h4 .anchor {
+ line-height: 1.2;
+}
+
+body h5 {
+ font-size: 1em;
+}
+
+body h5 .anchor {
+ line-height: 1.1;
+}
+
+body h6 {
+ font-size: 1em;
+ color: #777;
+}
+
+body h6 .anchor {
+ line-height: 1.1;
+}
+
+body p,
+body blockquote,
+body ul,
+body ol,
+body dl,
+body table,
+body pre {
+ margin-top: 0;
+ margin-bottom: 16px;
+}
+
+body hr {
+ height: 4px;
+ padding: 0;
+ margin: 16px 0;
+ background-color: #e7e7e7;
+ border: 0 none;
+}
+
+body ul,
+body ol {
+ padding-left: 2em;
+}
+
+body ul ul,
+body ul ol,
+body ol ol,
+body ol ul {
+ margin-top: 0;
+ margin-bottom: 0;
+}
+
+body li>p {
+ margin-top: 16px;
+}
+
+body dl {
+ padding: 0;
+}
+
+body dl dt {
+ padding: 0;
+ margin-top: 16px;
+ font-size: 1em;
+ font-style: italic;
+ font-weight: bold;
+}
+
+body dl dd {
+ padding: 0 16px;
+ margin-bottom: 16px;
+}
+
+body blockquote {
+ padding: 0 15px;
+ color: #777;
+ border-left: 4px solid #ddd;
+}
+
+body blockquote>:first-child {
+ margin-top: 0;
+}
+
+body blockquote>:last-child {
+ margin-bottom: 0;
+}
+
+body table {
+ display: block;
+ width: 100%;
+ overflow: auto;
+ word-break: normal;
+ word-break: keep-all;
+}
+
+body table th {
+ font-weight: bold;
+}
+
+body table th,
+body table td {
+ padding: 6px 13px;
+ border: 1px solid #ddd;
+}
+
+body table tr {
+ background-color: #fff;
+ border-top: 1px solid #ccc;
+}
+
+body table tr:nth-child(2n) {
+ background-color: #f8f8f8;
+}
+
+body img {
+ max-width: 100%;
+ box-sizing: content-box;
+ background-color: #fff;
+}
+
+body code {
+ padding: 0;
+ padding-top: 0;
+ padding-bottom: 0;
+ margin: 0;
+ font-size: 85%;
+ background-color: rgba(0,0,0,0.04);
+ border-radius: 3px;
+}
+
+body code:before,
+body code:after {
+ letter-spacing: -0.2em;
+ content: "\00a0";
+}
+
+body pre>code {
+ padding: 0;
+ margin: 0;
+ font-size: 100%;
+ word-break: normal;
+ white-space: pre;
+ background: transparent;
+ border: 0;
+}
+
+body .highlight {
+ margin-bottom: 16px;
+}
+
+body .highlight pre,
+body pre {
+ padding: 16px;
+ overflow: auto;
+ font-size: 85%;
+ line-height: 1.45;
+ background-color: #f7f7f7;
+ border-radius: 3px;
+}
+
+body .highlight pre {
+ margin-bottom: 0;
+ word-break: normal;
+}
+
+body pre {
+ word-wrap: normal;
+}
+
+body pre code {
+ display: inline;
+ max-width: initial;
+ padding: 0;
+ margin: 0;
+ overflow: initial;
+ line-height: inherit;
+ word-wrap: normal;
+ background-color: transparent;
+ border: 0;
+}
+
+body pre code:before,
+body pre code:after {
+ content: normal;
+}
+
+body kbd {
+ display: inline-block;
+ padding: 3px 5px;
+ font-size: 11px;
+ line-height: 10px;
+ color: #555;
+ vertical-align: middle;
+ background-color: #fcfcfc;
+ border: solid 1px #ccc;
+ border-bottom-color: #bbb;
+ border-radius: 3px;
+ box-shadow: inset 0 -1px 0 #bbb;
+}
+
+body .pl-c {
+ color: #969896;
+}
+
+body .pl-c1,
+body .pl-s .pl-v {
+ color: #0086b3;
+}
+
+body .pl-e,
+body .pl-en {
+ color: #795da3;
+}
+
+body .pl-s .pl-s1,
+body .pl-smi {
+ color: #333;
+}
+
+body .pl-ent {
+ color: #63a35c;
+}
+
+body .pl-k {
+ color: #a71d5d;
+}
+
+body .pl-pds,
+body .pl-s,
+body .pl-s .pl-pse .pl-s1,
+body .pl-sr,
+body .pl-sr .pl-cce,
+body .pl-sr .pl-sra,
+body .pl-sr .pl-sre {
+ color: #183691;
+}
+
+body .pl-v {
+ color: #ed6a43;
+}
+
+body .pl-id {
+ color: #b52a1d;
+}
+
+body .pl-ii {
+ background-color: #b52a1d;
+ color: #f8f8f8;
+}
+
+body .pl-sr .pl-cce {
+ color: #63a35c;
+ font-weight: bold;
+}
+
+body .pl-ml {
+ color: #693a17;
+}
+
+body .pl-mh,
+body .pl-mh .pl-en,
+body .pl-ms {
+ color: #1d3e81;
+ font-weight: bold;
+}
+
+body .pl-mq {
+ color: #008080;
+}
+
+body .pl-mi {
+ color: #333;
+ font-style: italic;
+}
+
+body .pl-mb {
+ color: #333;
+ font-weight: bold;
+}
+
+body .pl-md {
+ background-color: #ffecec;
+ color: #bd2c00;
+}
+
+body .pl-mi1 {
+ background-color: #eaffea;
+ color: #55a532;
+}
+
+body .pl-mdr {
+ color: #795da3;
+ font-weight: bold;
+}
+
+body .pl-mo {
+ color: #1d3e81;
+}
+
+body kbd {
+ display: inline-block;
+ padding: 3px 5px;
+ font: 11px Consolas, "Liberation Mono", Menlo, Courier, monospace;
+ line-height: 10px;
+ color: #555;
+ vertical-align: middle;
+ background-color: #fcfcfc;
+ border: solid 1px #ccc;
+ border-bottom-color: #bbb;
+ border-radius: 3px;
+ box-shadow: inset 0 -1px 0 #bbb;
+}
+
+body .task-list-item {
+ list-style-type: none;
+}
+
+body .task-list-item+.task-list-item {
+ margin-top: 3px;
+}
+
+body .task-list-item input {
+ margin: 0 0.35em 0.25em -1.6em;
+ vertical-align: middle;
+}
+
+body :checked+.radio-label {
+ z-index: 1;
+ position: relative;
+ border-color: #4078c0;
+}
+</style>
import com.sun.management.OperatingSystemMXBean;
import java.lang.management.ManagementFactory;
+import jalview.bin.MemorySetting;
import com.threerings.getdown.util.*;
// avoid ambiguity with java.util.Base64 which we can't use as it's 1.8+
jvmmempc = config.getInt(appPrefix + "jvmmempc", jvmmempc);
}
if (0 <= jvmmempc && jvmmempc <= 100) {
- final Object o = ManagementFactory.getOperatingSystemMXBean();
-
- try {
- if (o instanceof OperatingSystemMXBean) {
- final OperatingSystemMXBean osb = (OperatingSystemMXBean) o;
- long physicalMem = osb.getTotalPhysicalMemorySize();
- long requestedMem = physicalMem*jvmmempc/100;
- String[] maxMemHeapArg = new String[]{"-Xmx"+Long.toString(requestedMem)};
- // remove other max heap size arg
- 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);
- }
- }
- addAll(maxMemHeapArg, _jvmargs);
+
+ long maxMemLong = -1;
+
+ try
+ {
+ maxMemLong = MemorySetting.memPercent(jvmmempc);
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ } catch (Throwable t)
+ {
+ t.printStackTrace();
+ }
- }
- }
- catch (NoClassDefFoundError e) {
- // com.sun.management.OperatingSystemMXBean doesn't exist in this JVM
- System.out.println("No com.sun.management.OperatingSystemMXBean. Cannot use 'jvmmempc'.");
+ if (maxMemLong > 0)
+ {
+
+ String[] maxMemHeapArg = new String[]{"-Xmx"+Long.toString(maxMemLong)};
+ // remove other max heap size arg
+ 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);
+ }
}
+ addAll(maxMemHeapArg, _jvmargs);
+
+ }
+
} else if (jvmmempc != -1) {
System.out.println("'jvmmempc' value must be in range 0 to 100 (read as '"+Integer.toString(jvmmempc)+"')");
}
--- /dev/null
+package jalview.bin;
+
+import java.lang.management.ManagementFactory;
+import java.lang.management.OperatingSystemMXBean;
+
+public class MemorySetting
+{
+ public static final long leaveFreeMinMemory = 536870912; // 0.5 GB
+
+ public static final long applicationMinMemory = 536870912; // 0.5 GB
+
+ protected static long getPhysicalMemory()
+ {
+ final OperatingSystemMXBean o = ManagementFactory
+ .getOperatingSystemMXBean();
+
+ try
+ {
+ if (o instanceof com.sun.management.OperatingSystemMXBean)
+ {
+ final com.sun.management.OperatingSystemMXBean osb = (com.sun.management.OperatingSystemMXBean) o;
+ return osb.getTotalPhysicalMemorySize();
+ }
+ } catch (NoClassDefFoundError e)
+ {
+ // com.sun.management.OperatingSystemMXBean doesn't exist in this JVM
+ System.out.println("No com.sun.management.OperatingSystemMXBean");
+ }
+
+ // We didn't get a com.sun.management.OperatingSystemMXBean.
+ return -1;
+ }
+
+ public static long memPercent(int percent)
+ {
+ long memPercent = -1;
+
+ long physicalMem = getPhysicalMemory();
+ if (physicalMem > applicationMinMemory)
+ {
+ // try and set at least applicationMinMemory and thereafter ensure
+ // leaveFreeMinMemory is left for the OS
+ memPercent = Math.max(applicationMinMemory,
+ physicalMem - Math.max(physicalMem * (100 - percent) / 100,
+ leaveFreeMinMemory));
+ }
+
+ return memPercent;
+ }
+
+}
if (_ifc.rotatingBackgrounds != null) {
if (_ifc.backgroundImage != null) {
log.warning("ui.background_image and ui.rotating_background were both specified. " +
- "The rotating images are being used.");
+ "The background image is being used.");
}
- return new RotatingBackgrounds(_ifc.rotatingBackgrounds, _ifc.errorBackground,
- Getdown.this);
+ return new RotatingBackgrounds(loadImage(_ifc.backgroundImage));
+ //return new RotatingBackgrounds(_ifc.rotatingBackgrounds, _ifc.errorBackground, Getdown.this);
} else if (_ifc.backgroundImage != null) {
return new RotatingBackgrounds(loadImage(_ifc.backgroundImage));
} else {
-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
+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
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
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_channel_base = http://www.jalview.org/getdown/jalview
getdown_channel_name = TEST
getdown_txt_allow_offline = true
-getdown_txt_jvmmempc = 95
+getdown_txt_jalview.jvmmempc = 90
getdown_txt_multi_jvmarg = -Dgetdownappdir="%APPDIR%"
getdown_txt_strict_comments = true
getdown_txt_title = Jalview
install4jTemplate = install4j_template.install4j
install4jInfoPlistFileAssociations = file_associations_auto-Info_plist.xml
install4jInstallerFileAssociations = file_associations_auto-install4j.xml
+install4jDMGUninstallerAppFiles = uninstall_old_jalview_files.xml
install4jBuildDir = build/install4j
-install4jMediaTypes = windows,macosArchive,linuxRPM,linuxDeb,unixArchive
install4jMediaTypes = windows,macosArchive,linuxRPM,linuxDeb,unixArchive,unixInstaller
install4jFaster = false
eclipse_extra_jdt_prefs_file = .settings/org.eclipse.jdt.core.jalview.prefs
+pandoc_exec = /usr/local/bin/pandoc
dev = false
<tr>
<td width="60" align="center" nowrap>
<strong><a name="Jalview.2.11">2.11</a><br />
- <em>14/05/2019 (final due date !)</em></strong>
+ <em>tbc/06/2019</em></strong>
</td>
<td align="left" valign="top">
<ul>
<li>
<!-- JAL-2975 -->Can use shift + arrow keys to rotate PCA image incrementally</li>
<li>
- <!-- JAL-2965 -->PCA depth queuing with graduated colours</li>
+ <!-- JAL-2965 -->PCA depth cueing with graduated colours</li>
</ul>
<em>Deprecations</em>
<ul>
label.append_to_filename_tooltip = %n in the text will be replaced by the backup number. The text will appear after the filename. See the summary box above.
label.index_digits = Number of digits to use for the backup number (%n)
label.summary_of_backups_scheme = Summary of backup scheme
+label.scheme_examples = Scheme examples
label.increment_index = Increase appended text numbers - newest file has largest number.
label.reverse_roll = "Roll" appended text numbers - newest backup file is always number 1.
label.keep_files = Deleting old backup files
label.keep_all_backup_files = Do not delete old backup files
label.keep_only_this_number_of_backup_files = Keep only this number of most recent backup files
-label.autodelete_old_backup_files = Autodelete old backup files:
+label.autodelete_old_backup_files = Auto-delete old backup files:
label.always_ask = Always ask
label.auto_delete = Automatically delete
label.filename = filename
label.configure_feature_tooltip = Click to configure variable colour or filters
label.schemes = Schemes
label.customise = Customise
+label.custom = Custom
label.default = Default
label.single_file = Single backup
label.keep_all_versions = Keep all versions
label.rolled_backups = Rolled backup files
+label.customise_description = Select Customise, make changes, and click on OK to save your own custom scheme
+label.custom_description = Your own saved scheme
+label.default_description = Keep the last three versions of the file
+label.single_file_description = Keep the last version of the file
+label.keep_all_versions_description = Keep all previous versions of the file
+label.rolled_backups_description = Keep the last nine versions of the file from _bak.1 (newest) to _bak.9 (oldest)
+label.cancel_changes_description = Cancel changes made to your last saved Custom scheme
label.previously_saved_scheme = Previously saved scheme
label.no_backup_files = NO BACKUP FILES
label.include_backup_files = Include backup files
action.save_project = Guardar proyecto
action.save_project_as = Guardar proyecto como...
action.quit = Salir
-label.quit_jalview = Salir Javliew?
+label.quit_jalview = Salir de Jalview?
action.expand_views = Expandir vistas
action.gather_views = Capturar vistas
action.page_setup = Configuración de la página
label.append_to_filename_tooltip = %n en el texto será reemplazado por el número de respaldo. El texto será después del nombre del archivo. Vea el cuadro de resumen arriba.
label.index_digits = Número de dígitos a utilizar para el número de respaldo.
label.summary_of_backups_scheme = Resumen del esquema de copias de seguridad
+label.scheme_examples = Ejemplos de esquema
label.increment_index = Aumente los números de texto adjuntos: el archivo más nuevo tiene el número más grande
label.reverse_roll = Ciclos de texto adjuntos: el respaldo más reciente es siempre el número 1
label.keep_files = Borrando los respaldos antiguos
label.configuration = Configuración
label.configure_feature_tooltip = Haga clic para configurar el color o los filtros
label.schemes = Esquemas
-label.customise = Personalizado
+label.customise = Personalizar
+label.custom = Personal
label.default = Defecto
label.single_file = Solo uno respaldo
label.keep_all_versions = Mantener todas las versiones
label.rolled_backups = Ciclos respaldos
+label.customise_description = Seleccione Personalizar, haga cambios y haga clic en OK para guardar su propio esquema personalizado
+label.custom_description = Tu propio esquema guardado
+label.default_description = Conserve las últimas tres versiones del archivo
+label.single_file_description = Conserve la última versión del archivo
+label.keep_all_versions_description = Mantener todas las versiones anteriores del archivo
+label.rolled_backups_description = Mantenga las últimas nueve versiones del archivo desde _bak.1 (más reciente) a _bak.9 (más antigua)
+label.cancel_changes_description = Cancelar los cambios realizados en su último esquema personalizado guardado
label.previously_saved_scheme = Esquema previamente guardado
label.no_backup_files = NO ARCHIVOS DE RESPALDOS
label.include_backup_files = Incluir archivos de respaldos
</xs:documentation>
</xs:annotation>
</xs:attribute>
+ <xs:attribute name="showComplementFeatures" type="xs:boolean" use="optional" default="false" />
+ <xs:attribute name="showComplementFeaturesOnTop" type="xs:boolean" use="optional" default="false" />
</xs:complexType>
</xs:element>
<xs:element name="UserColours" minOccurs="0" maxOccurs="unbounded">
</xs:element>
</xs:choice>
</xs:sequence>
+ <xs:attribute name="mappingType" type="xs:string" use="optional">
+ <xs:annotation>
+ <xs:documentation>Biotype of the mapping e.g. CdsToPeptide</xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
</xs:extension>
</xs:complexContent>
</xs:complexType>
<xs:attribute name="source" type="xs:string"/>
<xs:attribute name="version" type="xs:string"/>
<xs:attribute name="accessionId" type="xs:string"/>
+ <xs:attribute name="locus" type="xs:boolean" default="false">
+ <xs:annotation>
+ <xs:documentation>
+ true for gene locus mapping, source=species, version=assembly, accession=chromosome
+ </xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
</xs:complexType>
</xs:element>
</xs:sequence>
</xs:documentation>
</xs:annotation>
</xs:attribute>
+ <xs:attribute name="biotype" type="xs:string" use="optional">
+ <xs:annotation>
+ <xs:documentation>
+ Biotype of the sequence (if known)
+ </xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
</xs:extension>
</xs:complexContent>
</xs:complexType>
return;
}
- MapList newMap = targetToFrom.traverse(fromLoci.getMap());
+ MapList newMap = targetToFrom.traverse(fromLoci.getMapping());
if (newMap != null)
{
JalviewTaskbar.setTaskbar(this);
} catch (Exception e)
{
- e.printStackTrace();
+ System.out.println("Cannot set Taskbar");
+ // e.printStackTrace();
} catch (Throwable t)
{
- t.printStackTrace();
+ System.out.println("Cannot set Taskbar");
+ // t.printStackTrace();
}
desktop.setVisible(true);
}
} catch (Exception e)
{
- e.printStackTrace();
+ System.out.println("Unable to setIconImage()");
}
}
}
package jalview.bin;
import java.io.File;
+import java.io.IOException;
import java.lang.management.ManagementFactory;
-import java.lang.management.OperatingSystemMXBean;
import java.util.ArrayList;
public class Launcher
private final static String startClass = "jalview.bin.Jalview";
- private final static int maxHeapSizePerCent = 95;
+ private final static int maxHeapSizePerCent = 90;
+
+ private final static String maxHeapSizePerCentProperty = "jvmmempc";
private final static String dockIconPath = "JalviewLogo_Huge.png";
ArrayList<String> command = new ArrayList<>();
command.add(javaBin);
+ String memSetting = null;
+
boolean isAMac = System.getProperty("os.name").indexOf("Mac") > -1;
for (String jvmArg : ManagementFactory.getRuntimeMXBean()
// add memory setting if not specified
boolean memSet = false;
boolean dockIcon = false;
+ boolean dockName = false;
ARG: for (int i = 0; i < command.size(); i++)
{
String arg = command.get(i);
if (arg.startsWith("-Xmx"))
{
+ memSetting = arg;
memSet = true;
}
else if (arg.startsWith("-Xdock:icon"))
{
dockIcon = true;
}
+ else if (arg.startsWith("-Xdock:name"))
+ {
+ dockName = true;
+ }
}
if (!memSet)
{
long maxMemLong = -1;
- long physicalMem = getPhysicalMemory();
- if (physicalMem > 0)
+ int percent = maxHeapSizePerCent;
+ String jvmmempc = System.getProperty(maxHeapSizePerCentProperty);
+ try
+ {
+ if (jvmmempc != null)
+ {
+ int trypercent = Integer.parseInt(jvmmempc);
+ if (0 < trypercent && trypercent <= 100)
+ {
+ percent = trypercent;
+ }
+ else
+ {
+ System.out.println("Property '" + maxHeapSizePerCentProperty
+ + "' should be in range 1..100");
+ }
+ }
+ } catch (Exception e)
+ {
+ System.out.println("Error parsing " + maxHeapSizePerCentProperty
+ + " '" + jvmmempc + "'");
+ }
+
+ try
{
- maxMemLong = physicalMem * maxHeapSizePerCent / 100;
+ maxMemLong = MemorySetting.memPercent(percent);
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ } catch (Throwable t)
+ {
+ t.printStackTrace();
}
+
if (maxMemLong > 0)
{
- command.add("-Xmx" + Long.toString(maxMemLong));
+ memSetting = "-Xmx" + Long.toString(maxMemLong);
+ command.add(memSetting);
}
}
- if (!dockIcon && isAMac)
+ if (isAMac)
{
- command.add("-Xdock:icon=" + dockIconPath);
- // -Xdock:name=... doesn't actually work :(
- // Leaving it in in case it gets fixed
- command.add("-Xdock:name=" + "Jalview");
+ if (!dockIcon)
+ {
+ command.add("-Xdock:icon=" + dockIconPath);
+ }
+ if (!dockName)
+ {
+ // -Xdock:name=... doesn't actually work :(
+ // Leaving it in in case it gets fixed
+ command.add("-Xdock:name=" + "Jalview");
+ }
}
command.add(startClass);
final ProcessBuilder builder = new ProcessBuilder(command);
- System.out.println("COMMAND: " + String.join(" ", builder.command()));
+ // System.out.println("COMMAND: " + String.join(" ", builder.command()));
+ System.out.println("Running " + startClass + " with "
+ + (memSetting == null ? "no memSetting" : memSetting));
try
{
builder.inheritIO();
Process process = builder.start();
process.waitFor();
- } catch (Exception e)
+ } catch (IOException e)
{
- e.printStackTrace();
- }
- // System.exit(0);
-
- }
-
- public static long getPhysicalMemory()
- {
- final OperatingSystemMXBean o = ManagementFactory
- .getOperatingSystemMXBean();
-
- try
- {
- if (o instanceof com.sun.management.OperatingSystemMXBean)
+ if (e.getMessage().toLowerCase().contains("memory"))
+ {
+ System.out.println("Caught a memory exception: " + e.getMessage());
+ // Probably the "Cannot allocate memory" error, try without the memory setting
+ ArrayList<String> commandNoMem = new ArrayList<>();
+ for (int i = 0; i < command.size(); i++)
+ {
+ if (!command.get(i).startsWith("-Xmx"))
+ {
+ commandNoMem.add(command.get(i));
+ }
+ }
+ final ProcessBuilder builderNoMem = new ProcessBuilder(
+ commandNoMem);
+ System.out.println("NO MEM COMMAND: "
+ + String.join(" ", builderNoMem.command()));
+ try
+ {
+ builderNoMem.inheritIO();
+ Process processNoMem = builderNoMem.start();
+ processNoMem.waitFor();
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+ else
{
- final com.sun.management.OperatingSystemMXBean osb = (com.sun.management.OperatingSystemMXBean) o;
- return osb.getTotalPhysicalMemorySize();
+ e.printStackTrace();
}
- } catch (NoClassDefFoundError e)
+ } catch (Exception e)
{
- // com.sun.management.OperatingSystemMXBean doesn't exist in this JVM
- System.out.println("No com.sun.management.OperatingSystemMXBean");
+ e.printStackTrace();
}
+ // System.exit(0);
- // We didn't get a com.sun.management.OperatingSystemMXBean.
- return -1;
}
}
--- /dev/null
+package jalview.bin;
+
+import java.lang.management.ManagementFactory;
+import java.lang.management.OperatingSystemMXBean;
+
+public class MemorySetting
+{
+ public static final long leaveFreeMinMemory = 536870912; // 0.5 GB
+
+ public static final long applicationMinMemory = 536870912; // 0.5 GB
+
+ protected static long getPhysicalMemory()
+ {
+ final OperatingSystemMXBean o = ManagementFactory
+ .getOperatingSystemMXBean();
+
+ try
+ {
+ if (o instanceof com.sun.management.OperatingSystemMXBean)
+ {
+ final com.sun.management.OperatingSystemMXBean osb = (com.sun.management.OperatingSystemMXBean) o;
+ return osb.getTotalPhysicalMemorySize();
+ }
+ } catch (NoClassDefFoundError e)
+ {
+ // com.sun.management.OperatingSystemMXBean doesn't exist in this JVM
+ System.out.println("No com.sun.management.OperatingSystemMXBean");
+ }
+
+ // We didn't get a com.sun.management.OperatingSystemMXBean.
+ return -1;
+ }
+
+ public static long memPercent(int percent)
+ {
+ long memPercent = -1;
+
+ long physicalMem = getPhysicalMemory();
+ if (physicalMem > applicationMinMemory)
+ {
+ // try and set at least applicationMinMemory and thereafter ensure
+ // leaveFreeMinMemory is left for the OS
+ memPercent = Math.max(applicationMinMemory,
+ physicalMem - Math.max(physicalMem * (100 - percent) / 100,
+ leaveFreeMinMemory));
+ }
+
+ return memPercent;
+ }
+
+}
public class DBRefEntry implements DBRefEntryI
{
- /*
- * the mapping to chromosome (genome) is held as an instance with
- * source = speciesId
- * version = assemblyId
- * accessionId = "chromosome:" + chromosomeId
- * map = mapping from sequence to reference assembly
- */
- public static final String CHROMOSOME = "chromosome";
-
String source = "";
String version = "";
}
return true;
}
-
- /**
- * Mappings to chromosome are held with accessionId as "chromosome:id"
- *
- * @return
- */
- public boolean isChromosome()
- {
- return accessionId != null && accessionId.startsWith(CHROMOSOME + ":");
- }
}
*
* @return
*/
- MapList getMap();
+ MapList getMapping();
}
--- /dev/null
+package jalview.datamodel;
+
+import jalview.util.MapList;
+
+/**
+ * A specialisation of DBRefEntry used to hold the chromosomal coordinates for a
+ * (typically gene) sequence
+ * <ul>
+ * <li>field <code>source</code> is used to hold a species id e.g. human</li>
+ * <li>field <code>version</code> is used to hold assembly id e.g GRCh38</li>
+ * <li>field <code>accession</code> is used to hold the chromosome id</li>
+ * <li>field <code>map</code> is used to hold the mapping from sequence to
+ * chromosome coordinates</li>
+ * </ul>
+ *
+ * @author gmcarstairs
+ *
+ */
+public class GeneLocus extends DBRefEntry implements GeneLociI
+{
+ /**
+ * Constructor adapts species, assembly, chromosome to DBRefEntry source,
+ * version, accession, respectively, and saves the mapping of sequence to
+ * chromosomal coordinates
+ *
+ * @param speciesId
+ * @param assemblyId
+ * @param chromosomeId
+ * @param mapping
+ */
+ public GeneLocus(String speciesId, String assemblyId, String chromosomeId,
+ Mapping mapping)
+ {
+ super(speciesId, assemblyId, chromosomeId, mapping);
+ }
+
+ /**
+ * Constructor
+ *
+ * @param speciesId
+ * @param assemblyId
+ * @param chromosomeId
+ */
+ public GeneLocus(String speciesId, String assemblyId, String chromosomeId)
+ {
+ this(speciesId, assemblyId, chromosomeId, null);
+ }
+
+ @Override
+ public boolean equals(Object o)
+ {
+ return o instanceof GeneLocus && super.equals(o);
+ }
+
+ @Override
+ public MapList getMapping()
+ {
+ return map == null ? null : map.getMap();
+ }
+
+ /**
+ * Answers the species identifier e.g. "human", stored as field <code>source</code> of
+ * DBRefEntry
+ */
+ @Override
+ public String getSpeciesId()
+ {
+ return getSource();
+ }
+
+ /**
+ * Answers the genome assembly id e.g. "GRCh38", stored as field
+ * <code>version</code> of DBRefEntry
+ */
+ @Override
+ public String getAssemblyId()
+ {
+ return getVersion();
+ }
+
+ /**
+ * Answers the chromosome identifier e.g. "X", stored as field
+ * <code>accession</code> of DBRefEntry
+ */
+ @Override
+ public String getChromosomeId()
+ {
+ return getAccessionId();
+ }
+
+}
public void setGeneLoci(String speciesId, String assemblyId,
String chromosomeId, MapList map)
{
- addDBRef(new DBRefEntry(speciesId, assemblyId, DBRefEntry.CHROMOSOME
- + ":" + chromosomeId, new Mapping(map)));
+ addDBRef(new GeneLocus(speciesId, assemblyId, chromosomeId,
+ new Mapping(map)));
}
/**
{
for (final DBRefEntry ref : refs)
{
- if (ref.isChromosome())
+ if (ref instanceof GeneLociI)
{
- return new GeneLociI()
- {
- @Override
- public String getSpeciesId()
- {
- return ref.getSource();
- }
-
- @Override
- public String getAssemblyId()
- {
- return ref.getVersion();
- }
-
- @Override
- public String getChromosomeId()
- {
- // strip off "chromosome:" prefix to chrId
- return ref.getAccessionId().substring(
- DBRefEntry.CHROMOSOME.length() + 1);
- }
-
- @Override
- public MapList getMap()
- {
- return ref.getMap().getMap();
- }
- };
+ return (GeneLociI) ref;
}
}
}
int end = Integer.parseInt(obj.get("end").toString());
String source = obj.get("source").toString();
String strand = obj.get("strand").toString();
+ Object phase = obj.get("phase");
String alleles = JSONUtils
.arrayToList((JSONArray) obj.get("alleles"));
String clinSig = JSONUtils
SequenceFeature sf = new SequenceFeature(type, desc, start, end,
source);
sf.setStrand("1".equals(strand) ? "+" : "-");
+ if (phase != null)
+ {
+ sf.setPhase(phase.toString());
+ }
setFeatureAttribute(sf, obj, "id");
setFeatureAttribute(sf, obj, "Parent");
setFeatureAttribute(sf, obj, "consequence_type");
import jalview.api.FeatureColourI;
import jalview.api.FeatureSettingsModelI;
import jalview.datamodel.AlignmentI;
-import jalview.datamodel.DBRefEntry;
import jalview.datamodel.GeneLociI;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
EnsemblFeatureType.exon, EnsemblFeatureType.cds,
EnsemblFeatureType.variation };
+ private static final String CHROMOSOME = "chromosome";
+
/**
* Default constructor (to use rest.ensembl.org)
*/
if (geneLoci != null)
{
seq.setGeneLoci(geneLoci.getSpeciesId(), geneLoci.getAssemblyId(),
- geneLoci.getChromosomeId(), geneLoci.getMap());
+ geneLoci.getChromosomeId(), geneLoci.getMapping());
}
else
{
return false;
}
String[] tokens = description.split(":");
- if (tokens.length == 6 && tokens[0].startsWith(DBRefEntry.CHROMOSOME))
+ if (tokens.length == 6 && tokens[0].startsWith(CHROMOSOME))
{
String ref = tokens[1];
String chrom = tokens[2];
return;
}
- MapList geneMapping = loci.getMap();
+ MapList geneMapping = loci.getMapping();
List<int[]> exons = mapping.getFromRanges();
List<int[]> transcriptLoci = new ArrayList<>();
import jalview.bin.Cache;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.GeneLociI;
+import jalview.datamodel.GeneLocus;
+import jalview.datamodel.Mapping;
import jalview.util.MapList;
import java.io.BufferedReader;
fromEnd });
List<int[]> toRange = Collections.singletonList(new int[] { toStart,
toEnd });
- final MapList map = new MapList(fromRange, toRange, 1, 1);
- return new GeneLociI()
- {
-
- @Override
- public String getSpeciesId()
- {
- return species == null ? "" : species;
- }
-
- @Override
- public String getAssemblyId()
- {
- return assembly;
- }
-
- @Override
- public String getChromosomeId()
- {
- return chromosome;
- }
-
- @Override
- public MapList getMap()
- {
- return map;
- }
- };
+ final Mapping map = new Mapping(
+ new MapList(fromRange, toRange, 1, 1));
+ return new GeneLocus(species == null ? "" : species, assembly,
+ chromosome, map);
} catch (NullPointerException | NumberFormatException e)
{
Cache.log.error("Error looking up gene loci: " + e.getMessage());
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefSource;
import jalview.datamodel.GeneLociI;
+import jalview.datamodel.GeneLocus;
+import jalview.datamodel.Mapping;
import jalview.util.MapList;
import java.io.BufferedReader;
final String chr = chromosome;
List<int[]> fromRange = Collections.singletonList(new int[] { 1,
fromEnd });
- final MapList map = new MapList(fromRange, regions, 1, 1);
- return new GeneLociI()
- {
-
- @Override
- public String getSpeciesId()
- {
- return species == null ? "" : species;
- }
-
- @Override
- public String getAssemblyId()
- {
- return as;
- }
-
- @Override
- public String getChromosomeId()
- {
- return chr;
- }
-
- @Override
- public MapList getMap()
- {
- return map;
- }
- };
+ Mapping mapping = new Mapping(new MapList(fromRange, regions, 1, 1));
+ return new GeneLocus(species == null ? "" : species, as, chr,
+ mapping);
} catch (IOException | ParseException | NumberFormatException e)
{
// ignore
package jalview.ext.htsjdk;
+import jalview.bin.Cache;
+
import java.io.Closeable;
import java.io.File;
import java.io.IOException;
private static final String TBI_EXTENSION = ".tbi";
+ private static final String CSI_EXTENSION = ".csi";
+
private boolean indexed;
private VCFFileReader reader;
/**
- * Constructor given a raw or compressed VCF file or a (tabix) index file
+ * Constructor given a raw or compressed VCF file or a (csi or tabix) index file
* <p>
- * For now, file type is inferred from its suffix: .gz or .bgz for compressed
- * data, .tbi for an index file, anything else is assumed to be plain text
- * VCF.
+ * If the file path ends in ".tbi" or ".csi", <em>or</em> appending one of these
+ * extensions gives a valid file path, open as indexed, else as unindexed.
*
* @param f
* @throws IOException
*/
public VCFReader(String filePath) throws IOException
{
- if (filePath.endsWith(GZ))
+ indexed = false;
+ if (filePath.endsWith(TBI_EXTENSION)
+ || filePath.endsWith(CSI_EXTENSION))
{
- if (new File(filePath + TBI_EXTENSION).exists())
- {
- indexed = true;
- }
+ indexed = true;
+ filePath = filePath.substring(0, filePath.length() - 4);
}
- else if (filePath.endsWith(TBI_EXTENSION))
+ else if (new File(filePath + TBI_EXTENSION).exists())
+ {
+ indexed = true;
+ }
+ else if (new File(filePath + CSI_EXTENSION).exists())
{
indexed = true;
- filePath = filePath.substring(0, filePath.length() - 4);
}
- reader = new VCFFileReader(new File(filePath), indexed);
+ /*
+ * we pass the name of the unindexed file to htsjdk,
+ * with a flag to assert whether it is indexed
+ */
+ File file = new File(filePath);
+ if (file.exists())
+ {
+ reader = new VCFFileReader(file, indexed);
+ }
+ else
+ {
+ Cache.log.error("File not found: " + filePath);
+ }
}
@Override
public CloseableIterator<VariantContext> query(final String chrom,
final int start, final int end)
{
- if (reader == null) {
- return null;
- }
+ if (reader == null)
+ {
+ return null;
+ }
if (indexed)
{
return reader.query(chrom, start, end);
{
final CloseableIterator<VariantContext> it = reader.iterator();
- return new CloseableIterator()
+ return new CloseableIterator<VariantContext>()
{
boolean atEnd = false;
QuitEvent e, QuitResponse r)
{
boolean confirmQuit = jalview.bin.Cache
- .getDefault(jalviewDesktop.CONFIRM_KEYBOARD_QUIT,
+ .getDefault(
+ jalview.gui.Desktop.CONFIRM_KEYBOARD_QUIT,
true);
int n;
if (confirmQuit)
{
System.out.println(
"Exception when looking for About, Preferences, Quit Handlers");
- e.printStackTrace();
+ // e.printStackTrace();
} catch (Throwable t)
{
System.out.println(
"Throwable when looking for About, Preferences, Quit Handlers");
- t.printStackTrace();
+ // t.printStackTrace();
}
}
PrintWriter out = new PrintWriter(
new FileWriter(backupfiles.getTempFilePath()));
- // TESTING code here
- boolean TESTING = true;
- if (TESTING)
- {
- out.print("; TESTSTART\n");
- int count = 20;
- for (int i = 0; i < count; i++)
- {
- // Thread.sleep(1000);
- out.println("; TEST: " + (count - 1 - i));
- }
- }
out.print(output);
- if (TESTING)
- {
- out.print("; TESTEND\n");
- }
out.close();
this.setTitle(file);
statusBar.setText(MessageManager.formatMessage(
seq.getLength());
if (geneLoci != null)
{
- MapList map = geneLoci.getMap();
+ MapList map = geneLoci.getMapping();
int mappedFromLength = MappingUtils.getLength(map.getFromRanges());
if (mappedFromLength == seq.getLength())
{
seq.setGeneLoci(geneLoci.getSpeciesId(), geneLoci.getAssemblyId(),
- geneLoci.getChromosomeId(), geneLoci.getMap());
+ geneLoci.getChromosomeId(), map);
retrievedLoci.put(dbref, geneLoci);
return true;
}
seq.getLength());
if (geneLoci != null)
{
- MapList map = geneLoci.getMap();
+ MapList map = geneLoci.getMapping();
int mappedFromLength = MappingUtils.getLength(map.getFromRanges());
if (mappedFromLength == seq.getLength())
{
seq.setGeneLoci(geneLoci.getSpeciesId(), geneLoci.getAssemblyId(),
- geneLoci.getChromosomeId(), geneLoci.getMap());
+ geneLoci.getChromosomeId(), map);
retrievedLoci.put(dbref, geneLoci);
return true;
}
APQHandlers.setAPQHandlers(this);
} catch (Exception e)
{
- System.out.println("Exception when trying to set APQHandlers");
- e.printStackTrace();
+ System.out.println("Cannot set APQHandlers");
+ // e.printStackTrace();
} catch (Throwable t)
{
- System.out.println("Throwable when trying to set APQHandlers");
- t.printStackTrace();
+ System.out.println("Cannot set APQHandlers");
+ // t.printStackTrace();
}
{
String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
JalviewFileChooser chooser = JalviewFileChooser
- .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat, true);
+ .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat, BackupFiles.getEnabled());
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(
@Override
public void quit()
{
- //System.out.println("********** Desktop.quit()");
- //System.out.println(savingFiles.toString());
Dimension screen = Toolkit.getDefaultToolkit().getScreenSize();
jalview.bin.Cache.setProperty("SCREENGEOMETRY_WIDTH",
screen.width + "");
"Jalview Project (old)" };
JalviewFileChooser chooser = new JalviewFileChooser(
Cache.getProperty("LAST_DIRECTORY"), suffix, desc,
- "Jalview Project", true, true); // last two booleans: allFiles,
+ "Jalview Project", true, BackupFiles.getEnabled()); // last two booleans: allFiles,
// allowBackupFiles
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(MessageManager.getString("label.restore_state"));
import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureColourI;
+import jalview.bin.Cache;
import jalview.datamodel.GraphLine;
import jalview.datamodel.features.FeatureAttributes;
import jalview.datamodel.features.FeatureAttributes.Datatype;
private JPanel maxColour = new JPanel();
- private JComboBox<String> threshold = new JComboBox<>();
+ private JComboBox<Object> threshold = new JComboBox<>();
private JSlider slider = new JSlider();
/*
* choice of option for 'colour for no value'
*/
- private JComboBox<String> noValueCombo;
+ private JComboBox<Object> noValueCombo;
/*
* choice of what to colour by text (Label or attribute)
*/
- private JComboBox<String> colourByTextCombo;
+ private JComboBox<Object> colourByTextCombo;
/*
* choice of what to colour by range (Score or attribute)
*/
- private JComboBox<String> colourByRangeCombo;
+ private JComboBox<Object> colourByRangeCombo;
private JRadioButton andFilters;
* @param withRange
* @param withText
*/
- protected JComboBox<String> populateAttributesDropdown(
+ protected JComboBox<Object> populateAttributesDropdown(
List<String[]> attNames, boolean withRange, boolean withText)
{
List<String> displayAtts = new ArrayList<>();
tooltips.add(desc == null ? "" : desc);
}
- JComboBox<String> attCombo = JvSwingUtils
- .buildComboWithTooltips(displayAtts, tooltips);
-
+ // now convert String List to Object List for buildComboWithTooltips
+ List<Object> displayAttsObjects = new ArrayList<>(displayAtts);
+ JComboBox<Object> attCombo = JvSwingUtils
+ .buildComboWithTooltips(displayAttsObjects, tooltips);
+
return attCombo;
}
* drop-down choice of attribute, with description as a tooltip
* if we can obtain it
*/
- final JComboBox<String> attCombo = populateAttributesDropdown(attNames,
+ final JComboBox<Object> attCombo = populateAttributesDropdown(attNames,
true, true);
String filterBy = setSelectedAttribute(attCombo, filter);
* @param attCombo
* @param filter
*/
- private String setSelectedAttribute(JComboBox<String> attCombo,
+ private String setSelectedAttribute(JComboBox<Object> attCombo,
FeatureMatcherI filter)
{
String item = null;
* @param valueField
* @param filterIndex
*/
- protected boolean updateFilter(JComboBox<String> attCombo,
+ protected boolean updateFilter(JComboBox<Object> attCombo,
JComboBox<Condition> condCombo, JTextField valueField,
int filterIndex)
{
- String attName = (String) attCombo.getSelectedItem();
+ String attName;
+ try
+ {
+ attName = (String) attCombo.getSelectedItem();
+ } catch (Exception e)
+ {
+ Cache.log.error("Problem casting Combo box entry to String");
+ attName = attCombo.getSelectedItem().toString();
+ }
Condition cond = (Condition) condCombo.getSelectedItem();
String pattern = valueField.getText().trim();
* @param entries
* @param tooltips
*/
- public static JComboBox<String> buildComboWithTooltips(
- List<String> entries, List<String> tooltips)
+ public static JComboBox<Object> buildComboWithTooltips(
+ List<Object> entries, List<String> tooltips)
{
- JComboBox<String> combo = new JComboBox<>();
+ JComboBox<Object> combo = new JComboBox<>();
final ComboBoxTooltipRenderer renderer = new ComboBoxTooltipRenderer();
combo.setRenderer(renderer);
- for (String attName : entries)
+ for (Object attName : entries)
{
combo.addItem(attName);
}
import jalview.gui.Help.HelpId;
import jalview.gui.StructureViewer.ViewerType;
import jalview.io.BackupFiles;
+import jalview.io.BackupFilesPresetEntry;
import jalview.io.FileFormatI;
import jalview.io.JalviewFileChooser;
import jalview.io.JalviewFileView;
/*
* Save Backups settings
*/
- Cache.applicationProperties.setProperty(BackupFiles.CONFIRM_DELETE_OLD,
- Boolean.toString(backupfilesConfirmDelete.isSelected()));
Cache.applicationProperties.setProperty(BackupFiles.ENABLED,
Boolean.toString(enableBackupFiles.isSelected()));
- Cache.applicationProperties.setProperty(BackupFiles.NO_MAX,
- Boolean.toString(backupfilesKeepAll.isSelected()));
- Cache.applicationProperties.setProperty(BackupFiles.REVERSE_ORDER,
- Boolean.toString(suffixReverse.isSelected()));
- Cache.applicationProperties.setProperty(BackupFiles.SUFFIX,
- suffixTemplate.getText());
- Cache.applicationProperties.setProperty(BackupFiles.ROLL_MAX,
- Integer.toString(getSpinnerInt(backupfilesRollMaxSpinner, 4)));
- Cache.applicationProperties.setProperty(BackupFiles.SUFFIX_DIGITS,
- Integer.toString(getSpinnerInt(suffixDigitsSpinner, 3)));
- Cache.applicationProperties.setProperty(BackupFiles.NS+"_PRESET",
- Integer.toString(getComboIntStringKey(backupfilesPresetsCombo)));
+ int preset = getComboIntStringKey(backupfilesPresetsCombo);
+ Cache.applicationProperties.setProperty(BackupFiles.NS + "_PRESET", Integer.toString(preset));
+
+ if (preset == BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM)
+ {
+ BackupFilesPresetEntry customBFPE = getBackupfilesCurrentEntry();
+ BackupFilesPresetEntry.backupfilesPresetEntriesValues.put(
+ BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM, customBFPE);
+ Cache.applicationProperties
+ .setProperty(BackupFilesPresetEntry.CUSTOMCONFIG,
+ customBFPE.toString());
+ }
+
+ BackupFilesPresetEntry savedBFPE = BackupFilesPresetEntry.backupfilesPresetEntriesValues
+ .get(preset);
+ Cache.applicationProperties.setProperty(
+ BackupFilesPresetEntry.SAVEDCONFIG, savedBFPE.toString());
Cache.saveProperties();
Desktop.instance.doConfigureStructurePrefs();
import jalview.viewmodel.AlignmentViewport;
import java.awt.Component;
-import java.awt.Toolkit;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.KeyAdapter;
import javax.swing.AbstractAction;
import javax.swing.InputMap;
import javax.swing.JComponent;
+import javax.swing.JDesktopPane;
+import javax.swing.JInternalFrame;
import javax.swing.JMenuItem;
import javax.swing.KeyStroke;
import javax.swing.event.InternalFrameAdapter;
};
overrideKeyBinding(key_cmdF, action);
}
+
+ /**
+ * Override to do nothing if triggered from one of the child frames
+ */
+ @Override
+ public void setSelected(boolean selected) throws PropertyVetoException
+ {
+ JDesktopPane desktopPane = getDesktopPane();
+ JInternalFrame fr = desktopPane == null ? null
+ : desktopPane.getSelectedFrame();
+ if (fr == getTopFrame() || fr == getBottomFrame())
+ {
+ /*
+ * patch for JAL-3288 (deselecting top/bottom frame closes popup menu);
+ * it may be possible to remove this method in future
+ * if the underlying Java behaviour changes
+ */
+ if (selected)
+ {
+ moveToFront();
+ }
+ return;
+ }
+ super.setSelected(selected);
+ }
}
package jalview.io;
-import jalview.bin.Cache;
-
import java.io.File;
public class BackupFilenameParts
String filename, String base, boolean extensionMatch)
{
BackupFilenameParts bfp = new BackupFilenameParts();
- String template = Cache.getDefault(BackupFiles.SUFFIX, null);
+ BackupFilesPresetEntry bfpe = BackupFilesPresetEntry
+ .getSavedBackupEntry();
+ String template = bfpe.suffix;
if (template == null)
{
return bfp;
int digits;
try
{
- digits = Integer
- .parseInt(Cache.getDefault(BackupFiles.SUFFIX_DIGITS, null));
+ digits = bfpe.digits;
} catch (Exception e)
{
return bfp;
* BackupFiles used for manipulating (naming rolling/deleting) backup/version files when an alignment or project file is saved.
* User configurable options are:
* BACKUPFILES_ENABLED - boolean flag as to whether to use this mechanism or act as before, including overwriting files as saved.
- * BACKUPFILES_SUFFIX - a template to insert after the file extension. Use '%n' to be replaced by a 0-led SUFFIX_DIGITS long integer.
- * BACKUPFILES_NO_MAX - flag to turn off setting a maximum number of backup files to keep.
- * BACKUPFILES_ROLL_MAX - the maximum number of backupfiles to keep for any one alignment or project file.
- * BACKUPFILES_SUFFIX_DIGITS - the number of digits to insert replace %n with (e.g. BACKUPFILES_SUFFIX_DIGITS = 3 would make "001", "002", etc)
- * BACKUPFILES_REVERSE_ORDER - if true then "logfile" style numbering and file rolling will occur. If false then ever-increasing version numbering will occur, but old files will still be deleted if there are more than ROLL_MAX backup files.
- * BACKUPFILES_CONFIRM_DELETE_OLD - if true then prompt/confirm with the user when deleting older backup/version files.
+ * The rest of the options are now saved as BACKUPFILES_PRESET, BACKUPFILES_SAVED and BACKUPFILES_CUSTOM
+ * (see BackupFilesPresetEntry)
*/
public class BackupFiles
public static final String ENABLED = NS + "_ENABLED";
- public static final String SUFFIX = NS + "_SUFFIX";
-
- public static final String NO_MAX = NS + "_NO_MAX";
-
- public static final String ROLL_MAX = NS + "_ROLL_MAX";
-
- public static final String SUFFIX_DIGITS = NS + "_SUFFIX_DIGITS";
-
public static final String NUM_PLACEHOLDER = "%n";
- public static final String REVERSE_ORDER = NS + "_REVERSE_ORDER";
-
- public static final String CONFIRM_DELETE_OLD = NS
- + "_CONFIRM_DELETE_OLD";
-
private static final String DEFAULT_TEMP_FILE = "jalview_temp_file_" + NS;
private static final String TEMP_FILE_EXT = ".tmp";
// REVERSE_ORDER
public BackupFiles(File file)
{
- this(file, ".bak" + NUM_PLACEHOLDER, false, 3, 3, false);
- }
-
- public BackupFiles(File file, String defaultSuffix, boolean defaultNoMax,
- int defaultMax, int defaultDigits, boolean defaultReverseOrder)
- {
classInit();
this.file = file;
- this.suffix = Cache.getDefault(SUFFIX, defaultSuffix);
- this.noMax = Cache.getDefault(NO_MAX, defaultNoMax);
- this.max = Cache.getDefault(ROLL_MAX, defaultMax);
- this.digits = Cache.getDefault(SUFFIX_DIGITS, defaultDigits);
- this.reverseOrder = Cache.getDefault(REVERSE_ORDER,
- defaultReverseOrder);
+ BackupFilesPresetEntry bfpe = BackupFilesPresetEntry.getSavedBackupEntry();
+ this.suffix = bfpe.suffix;
+ this.noMax = bfpe.keepAll;
+ this.max = bfpe.rollMax;
+ this.digits = bfpe.digits;
+ this.reverseOrder = bfpe.reverse;
// create a temp file to save new data in
File temp = null;
public static void classInit()
{
setEnabled(Cache.getDefault(ENABLED, true));
- setConfirmDelete(Cache.getDefault(CONFIRM_DELETE_OLD, true));
+ BackupFilesPresetEntry bfpe = BackupFilesPresetEntry
+ .getSavedBackupEntry();
+ setConfirmDelete(bfpe.confirmDelete);
}
public static void setEnabled(boolean flag)
--- /dev/null
+package jalview.io;
+
+import jalview.bin.Cache;
+import jalview.util.MessageManager;
+
+import java.util.HashMap;
+import java.util.Map;
+import java.util.StringTokenizer;
+
+public class BackupFilesPresetEntry
+{
+
+ public String suffix;
+
+ public static final int DIGITSMIN = 1;
+
+ public static final int DIGITSMAX = 6;
+
+ public int digits;
+
+ public boolean reverse;
+
+ public boolean keepAll;
+
+ public static final int ROLLMAXMIN = 1;
+
+ public static final int ROLLMAXMAX = 999;
+
+ public int rollMax;
+
+ public boolean confirmDelete;
+
+ public static final String SAVEDCONFIG = BackupFiles.NS + "_SAVED";
+
+ public static final String CUSTOMCONFIG = BackupFiles.NS + "_CUSTOM";
+
+ private static final String stringDelim = "\t";
+
+ public static final int BACKUPFILESSCHEMECUSTOM = 0;
+
+ public static final int BACKUPFILESSCHEMEDEFAULT = 1;
+
+ public BackupFilesPresetEntry(String suffix, int digits, boolean reverse,
+ boolean keepAll, int rollMax, boolean confirmDelete)
+ {
+ this.suffix = suffix == null ? "" : suffix;
+ this.digits = digits < DIGITSMIN ? DIGITSMIN
+ : (digits > DIGITSMAX ? DIGITSMAX : digits);
+ this.reverse = reverse;
+ this.keepAll = keepAll;
+ this.rollMax = rollMax < ROLLMAXMIN ? ROLLMAXMIN
+ : (rollMax > ROLLMAXMAX ? ROLLMAXMAX : rollMax);
+ this.confirmDelete = confirmDelete;
+ }
+
+ public boolean equals(BackupFilesPresetEntry compare)
+ {
+ return suffix.equals(compare.suffix) && digits == compare.digits
+ && reverse == compare.reverse && keepAll == compare.keepAll
+ && rollMax == compare.rollMax
+ && confirmDelete == compare.confirmDelete;
+ }
+
+ @Override
+ public String toString()
+ {
+ StringBuilder sb = new StringBuilder();
+ sb.append(suffix);
+ sb.append(stringDelim);
+ sb.append(digits);
+ sb.append(stringDelim);
+ sb.append(reverse);
+ sb.append(stringDelim);
+ sb.append(keepAll);
+ sb.append(stringDelim);
+ sb.append(rollMax);
+ sb.append(stringDelim);
+ sb.append(confirmDelete);
+ return sb.toString();
+ }
+
+ public static BackupFilesPresetEntry createBackupFilesPresetEntry(
+ String line)
+ {
+ if (line == null)
+ {
+ return null;
+ }
+ StringTokenizer st = new StringTokenizer(line, stringDelim);
+ String suffix = null;
+ int digits = 0;
+ boolean reverse = false;
+ boolean keepAll = false;
+ int rollMax = 0;
+ boolean confirmDelete = false;
+
+ try
+ {
+ suffix = st.nextToken();
+ digits = Integer.valueOf(st.nextToken());
+ reverse = Boolean.valueOf(st.nextToken());
+ keepAll = Boolean.valueOf(st.nextToken());
+ rollMax = Integer.valueOf(st.nextToken());
+ confirmDelete = Boolean.valueOf(st.nextToken());
+ } catch (Exception e)
+ {
+ Cache.log.error("Error parsing backupfiles scheme '" + line + "'");
+ }
+
+ return new BackupFilesPresetEntry(suffix, digits, reverse, keepAll,
+ rollMax, confirmDelete);
+ }
+
+ public static BackupFilesPresetEntry getSavedBackupEntry()
+ {
+ String savedPresetString = Cache
+ .getDefault(BackupFilesPresetEntry.SAVEDCONFIG, null);
+ BackupFilesPresetEntry savedPreset = BackupFilesPresetEntry
+ .createBackupFilesPresetEntry(savedPresetString);
+ if (savedPreset == null)
+ {
+ savedPreset = backupfilesPresetEntriesValues
+ .get(BACKUPFILESSCHEMEDEFAULT);
+ }
+ return savedPreset;
+ }
+
+ public static final IntKeyStringValueEntry[] backupfilesPresetEntries = {
+ new IntKeyStringValueEntry(BACKUPFILESSCHEMEDEFAULT,
+ MessageManager.getString("label.default")),
+ new IntKeyStringValueEntry(2,
+ MessageManager.getString("label.single_file")),
+ new IntKeyStringValueEntry(3,
+ MessageManager.getString("label.keep_all_versions")),
+ new IntKeyStringValueEntry(4,
+ MessageManager.getString("label.rolled_backups")),
+ // ...
+ // IMPORTANT, keep "Custom" entry with key 0 (even though it appears last)
+ new IntKeyStringValueEntry(BACKUPFILESSCHEMECUSTOM,
+ MessageManager.getString("label.custom")) };
+
+ public static final String[] backupfilesPresetEntryDescriptions = {
+ MessageManager.getString("label.default_description"),
+ MessageManager.getString("label.single_file_description"),
+ MessageManager.getString("label.keep_all_versions_description"),
+ MessageManager.getString("label.rolled_backups_description"),
+ MessageManager.getString("label.custom_description") };
+
+ public static final Map<Integer, BackupFilesPresetEntry> backupfilesPresetEntriesValues = new HashMap<Integer, BackupFilesPresetEntry>()
+ {
+ /**
+ *
+ */
+ private static final long serialVersionUID = 125L;
+
+ {
+ put(1, new BackupFilesPresetEntry(
+ ".bak" + BackupFiles.NUM_PLACEHOLDER, 3, false, false, 3,
+ false));
+ put(2, new BackupFilesPresetEntry("~", 1, false, false, 1, false));
+ put(3, new BackupFilesPresetEntry(".v" + BackupFiles.NUM_PLACEHOLDER,
+ 3, false, true, 10, true));
+ put(4, new BackupFilesPresetEntry(
+ "_bak." + BackupFiles.NUM_PLACEHOLDER, 1, true, false, 9,
+ false));
+
+ // This gets replaced by GPreferences
+ put(BACKUPFILESSCHEMECUSTOM,
+ new BackupFilesPresetEntry("", 0, false, false, 0, false));
+ }
+ };
+
+}
--- /dev/null
+package jalview.io;
+
+public class IntKeyStringValueEntry
+{
+ public final int k;
+
+ public final String v;
+
+ public IntKeyStringValueEntry(int k, String v)
+ {
+ this.k = k;
+ this.v = v;
+ }
+
+ @Override
+ public String toString()
+ {
+ return v;
+ }
+
+}
import jalview.api.FeatureColourI;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
+import jalview.datamodel.GeneLociI;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.util.MessageManager;
@Override
public int compare(DBRefEntry ref1, DBRefEntry ref2)
{
- if (ref1.isChromosome())
+ if (ref1 instanceof GeneLociI)
{
return -1;
}
- if (ref2.isChromosome())
+ if (ref2 instanceof GeneLociI)
{
return 1;
}
{ "snRNA", "transcript" },
{ "miRNA", "transcript" },
{ "lincRNA", "transcript" },
+ { "lnc_RNA", "transcript" },
{ "rRNA", "transcript" },
{ "mRNA", "transcript" },
// there are many more sub-types of ncRNA...
*/
private static final String VCF_ASSEMBLY = "VCF_ASSEMBLY";
- private static final String DEFAULT_VCF_ASSEMBLY = "assembly19=GRCh38,hs37=GRCh37,grch37=GRCh37,grch38=GRCh38";
+ private static final String DEFAULT_VCF_ASSEMBLY = "assembly19=GRCh37,hs37=GRCh37,grch37=GRCh37,grch38=GRCh38";
private static final String VCF_SPECIES = "VCF_SPECIES"; // default is human
+ private static final String DEFAULT_REFERENCE = "grch37"; // fallback default is human GRCh37
+
/*
* keys to fields of VEP CSQ consequence data
* see https://www.ensembl.org/info/docs/tools/vep/vep_formats.html
public SequenceI loadVCFContig(String contig)
{
VCFHeaderLine headerLine = header.getOtherHeaderLine(VCFHeader.REFERENCE_KEY);
- String ref = headerLine == null ? null : headerLine.getValue();
+ if (headerLine == null)
+ {
+ Cache.log.error("VCF reference header not found");
+ return null;
+ }
+ String ref = headerLine.getValue();
if (ref.startsWith("file://"))
{
ref = ref.substring(7);
}
else
{
- System.err.println("VCF reference not found: " + ref);
+ Cache.log.error("VCF reference not found: " + ref);
}
return seq;
{
VCFHeaderLine ref = header
.getOtherHeaderLine(VCFHeader.REFERENCE_KEY);
- String reference = ref.getValue();
+ String reference = ref == null ? null : ref.getValue();
setSpeciesAndAssembly(reference);
*/
protected void setSpeciesAndAssembly(String reference)
{
+ if (reference == null)
+ {
+ Cache.log.error("No VCF ##reference found, defaulting to "
+ + DEFAULT_REFERENCE + ":" + DEFAULT_SPECIES);
+ reference = DEFAULT_REFERENCE; // default to GRCh37 if not specified
+ }
reference = reference.toLowerCase();
- vcfSpecies = DEFAULT_SPECIES;
/*
* for a non-human species, or other assembly identifier,
}
}
+ vcfSpecies = DEFAULT_SPECIES;
prop = Cache.getProperty(VCF_SPECIES);
if (prop != null)
{
String species = seqCoords.getSpeciesId();
String chromosome = seqCoords.getChromosomeId();
String seqRef = seqCoords.getAssemblyId();
- MapList map = seqCoords.getMap();
+ MapList map = seqCoords.getMapping();
// note this requires the configured species to match that
// returned with the Ensembl sequence; todo: support aliases?
FileMenu.add(inputMenu);
FileMenu.add(inputSequence);
FileMenu.addSeparator();
- FileMenu.add(saveState);
+ //FileMenu.add(saveState);
FileMenu.add(saveAsState);
FileMenu.add(loadState);
FileMenu.addSeparator();
import jalview.gui.StructureViewer.ViewerType;
import jalview.io.BackupFilenameParts;
import jalview.io.BackupFiles;
+import jalview.io.BackupFilesPresetEntry;
+import jalview.io.IntKeyStringValueEntry;
import jalview.util.MessageManager;
import java.awt.BorderLayout;
import java.awt.event.KeyListener;
import java.awt.event.MouseAdapter;
import java.awt.event.MouseEvent;
-import java.util.HashMap;
-import java.util.Map;
+import java.util.Arrays;
+import java.util.List;
import javax.swing.AbstractCellEditor;
import javax.swing.BorderFactory;
import javax.swing.JComboBox;
import javax.swing.JFileChooser;
import javax.swing.JLabel;
-import javax.swing.JList;
import javax.swing.JPanel;
import javax.swing.JRadioButton;
import javax.swing.JScrollPane;
protected JPanel presetsPanel = new JPanel();
+ protected JLabel presetsComboLabel = new JLabel();
+
+ protected JCheckBox customiseCheckbox = new JCheckBox();
+
protected JButton revertButton = new JButton();
- protected JComboBox<IntKeyStringValueEntry> backupfilesPresetsCombo = new JComboBox<>();
+ protected JComboBox<Object> backupfilesPresetsCombo = new JComboBox<>();
+
+ private int backupfilesPresetsComboLastSelected = 0;
protected JPanel suffixPanel = new JPanel();
protected void loadLastSavedBackupsOptions()
{
+ BackupFilesPresetEntry savedPreset = BackupFilesPresetEntry
+ .getSavedBackupEntry();
enableBackupFiles
.setSelected(Cache.getDefault(BackupFiles.ENABLED, true));
+
+ BackupFilesPresetEntry backupfilesCustomEntry = BackupFilesPresetEntry
+ .createBackupFilesPresetEntry(Cache
+ .getDefault(BackupFilesPresetEntry.CUSTOMCONFIG, null));
+ if (backupfilesCustomEntry == null)
+ {
+ backupfilesCustomEntry = BackupFilesPresetEntry.backupfilesPresetEntriesValues
+ .get(BackupFilesPresetEntry.BACKUPFILESSCHEMEDEFAULT);
+ }
+ BackupFilesPresetEntry.backupfilesPresetEntriesValues.put(
+ BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM,
+ backupfilesCustomEntry);
+
setComboIntStringKey(backupfilesPresetsCombo,
- Cache.getDefault(BackupFiles.NS + "_PRESET", 1));
- suffixTemplate.setText(Cache.getDefault(BackupFiles.SUFFIX,
- ".bak" + BackupFiles.NUM_PLACEHOLDER));
- suffixDigitsSpinner
- .setValue(Cache.getDefault(BackupFiles.SUFFIX_DIGITS, 3));
- suffixReverse.setSelected(
- Cache.getDefault(BackupFiles.REVERSE_ORDER, false));
- backupfilesKeepAll
- .setSelected(Cache.getDefault(BackupFiles.NO_MAX, false));
- backupfilesRollMaxSpinner
- .setValue(Cache.getDefault(BackupFiles.ROLL_MAX, 3));
- backupfilesConfirmDelete.setSelected(
- Cache.getDefault(BackupFiles.CONFIRM_DELETE_OLD, true));
+ Cache.getDefault(BackupFiles.NS + "_PRESET",
+ BackupFilesPresetEntry.BACKUPFILESSCHEMEDEFAULT));
+
+ backupsSetOptions(savedPreset);
backupsOptionsSetEnabled();
updateBackupFilesExampleLabel();
private boolean warnAboutSuffixReverseChange()
{
- boolean savedSuffixReverse = Cache.getDefault(BackupFiles.REVERSE_ORDER,
- false);
- int savedSuffixDigits = Cache.getDefault(BackupFiles.SUFFIX_DIGITS, 3);
- String savedSuffixTemplate = Cache.getDefault(BackupFiles.SUFFIX,
- ".bak" + BackupFiles.NUM_PLACEHOLDER);
+ BackupFilesPresetEntry bfpe = BackupFilesPresetEntry
+ .getSavedBackupEntry();
+ boolean savedSuffixReverse = bfpe.reverse;
+ int savedSuffixDigits = bfpe.digits;
+ String savedSuffixTemplate = bfpe.suffix;
boolean nowSuffixReverse = suffixReverse.isSelected();
int nowSuffixDigits = getSpinnerInt(suffixDigitsSpinner, 3);
gbc.gridy++; // row 1
backupsTab.add(presetsPanel, gbc);
- // gbc.anchor = GridBagConstraints.NORTHWEST;
// now using whole row
gbc.gridwidth = 2;
gbc.gridheight = 1;
return backupsTab;
}
- protected static final int BACKUPFILESSCHEMECUSTOMISE = 0;
-
- private static final IntKeyStringValueEntry[] backupfilesPresetEntries = {
- new IntKeyStringValueEntry(1,
- MessageManager.getString("label.default")),
- new IntKeyStringValueEntry(2,
- MessageManager.getString("label.single_file")),
- new IntKeyStringValueEntry(3,
- MessageManager.getString("label.keep_all_versions")),
- new IntKeyStringValueEntry(4,
- MessageManager.getString("label.rolled_backups")),
- // ...
- // IMPORTANT, keep "Custom" entry with key 0 (even though it appears last)
- new IntKeyStringValueEntry(BACKUPFILESSCHEMECUSTOMISE,
- MessageManager.getString("label.customise")) };
-
- private static final Map<Integer, BackupFilesPresetEntry> backupfilesPresetEntriesValues = new HashMap<Integer, BackupFilesPresetEntry>()
- {
- /**
- *
- */
- private static final long serialVersionUID = 125L;
-
- {
- put(1, new BackupFilesPresetEntry(
- ".bak" + BackupFiles.NUM_PLACEHOLDER, 3, false, false, 3,
- false));
- put(2, new BackupFilesPresetEntry("~", 1, false, false, 1, false));
- put(3, new BackupFilesPresetEntry(".v" + BackupFiles.NUM_PLACEHOLDER,
- 3, false, true, 10, true));
- put(4, new BackupFilesPresetEntry(
- "_bak." + BackupFiles.NUM_PLACEHOLDER, 1, true, false, 9,
- false));
- }
- };
-
private JPanel initBackupsTabPresetsPanel()
{
String title = MessageManager.getString("label.schemes");
- // TitledBorder tb = new TitledBorder(new EmptyBorder(0, 0, 0, 0), title);
- // TitledBorder tb = new TitledBorder(title);
- // tb.setTitleFont(LABEL_FONT);
- // presetsPanel.setBorder(tb);
presetsPanel.setLayout(new GridBagLayout());
// "Scheme: "
gbc.gridx = 0;
gbc.gridy = 0;
- presetsPanel.add(new JLabel(title + ":"), gbc);
- for (int i = 0; i < backupfilesPresetEntries.length; i++)
+ presetsComboLabel = new JLabel(title + ":");
+ presetsPanel.add(presetsComboLabel, gbc);
+
+ List<Object> entries = Arrays
+ .asList((Object[]) BackupFilesPresetEntry.backupfilesPresetEntries);
+ List<String> tooltips = Arrays.asList(
+ BackupFilesPresetEntry.backupfilesPresetEntryDescriptions);
+ backupfilesPresetsCombo = JvSwingUtils.buildComboWithTooltips(entries,
+ tooltips);
+ /*
+ for (int i = 0; i < BackupFilesPresetEntry.backupfilesPresetEntries.length; i++)
{
- backupfilesPresetsCombo.addItem(backupfilesPresetEntries[i]);
+ backupfilesPresetsCombo
+ .addItem(BackupFilesPresetEntry.backupfilesPresetEntries[i]);
}
+ */
- // put "Previously saved scheme" item in italics (it's not really
- // selectable, as such -- it deselects itself when selected) and
- // "Customise" in bold
- backupfilesPresetsCombo
- .setRenderer(new BackupFilesPresetsComboBoxRenderer());
backupfilesPresetsCombo.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- backupsTabUpdatePresets();
+ int key = getComboIntStringKey(backupfilesPresetsCombo);
+ if (!customiseCheckbox.isSelected())
+ {
+ backupfilesPresetsComboLastSelected = key;
+ }
+ if (key == BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM)
+ {
+ if (customiseCheckbox.isSelected())
+ {
+ // got here by clicking on customiseCheckbox so don't change the values
+ backupfilesCustomOptionsSetEnabled();
+ }
+ else
+ {
+ backupsTabUpdatePresets();
+ backupfilesCustomOptionsSetEnabled();
+ }
+ }
+ else
+ {
+ customiseCheckbox.setSelected(false);
+ backupsTabUpdatePresets();
+ backupfilesCustomOptionsSetEnabled();
+ }
}
});
presetsPanel.add(backupfilesPresetsCombo, gbc);
revertButton.setText(MessageManager.getString("label.cancel_changes"));
+ revertButton.setToolTipText(
+ MessageManager.getString("label.cancel_changes_description"));
revertButton.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- loadLastSavedBackupsOptions();
+ backupsSetOptions(
+ BackupFilesPresetEntry.backupfilesPresetEntriesValues.get(
+ BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM));
+ backupfilesCustomOptionsSetEnabled();
}
});
revertButton.setFont(LABEL_FONT);
+ customiseCheckbox.setFont(LABEL_FONT);
+ customiseCheckbox.setText(MessageManager.getString("label.customise"));
+ customiseCheckbox.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ int currently = getComboIntStringKey(backupfilesPresetsCombo);
+ if (customiseCheckbox.isSelected())
+ {
+ backupfilesPresetsComboLastSelected = currently;
+ setComboIntStringKey(backupfilesPresetsCombo,
+ BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM);
+ }
+ else
+ {
+ setComboIntStringKey(backupfilesPresetsCombo,
+ backupfilesPresetsComboLastSelected);
+
+ }
+ backupfilesCustomOptionsSetEnabled();
+ }
+ });
+ customiseCheckbox.setToolTipText(
+ MessageManager.getString("label.customise_description"));
+
+ // customise checkbox
+ gbc.gridx = 0;
+ gbc.gridy++;
+ presetsPanel.add(customiseCheckbox, gbc);
+
// "Cancel changes" button (aligned with combo box above)
gbc.gridx = 1;
- gbc.gridy++;
presetsPanel.add(revertButton, gbc);
return presetsPanel;
private JPanel initBackupsTabFilenameExamplesPanel()
{
String title = MessageManager
- .getString("label.summary_of_backups_scheme");
+ .getString("label.scheme_examples");
TitledBorder tb = new TitledBorder(title);
exampleFilesPanel.setBorder(tb);
exampleFilesPanel.setLayout(new GridBagLayout());
{
IntKeyStringValueEntry entry = (IntKeyStringValueEntry) backupfilesPresetsCombo
.getSelectedItem();
- int key = entry.getKey();
- String value = entry.getValue();
+ int key = entry.k;
+ String value = entry.v;
- // BACKUPFILESSCHEMECUSTOMISE (==0) reserved for "Custom"
- if (key != BACKUPFILESSCHEMECUSTOMISE)
+ if (BackupFilesPresetEntry.backupfilesPresetEntriesValues
+ .containsKey(key))
{
- if (backupfilesPresetEntriesValues.containsKey(key))
- {
- backupsSetOptions(backupfilesPresetEntriesValues.get(key));
- }
- else
- {
- System.out.println("Preset '" + value + "' not implemented");
- }
+ backupsSetOptions(
+ BackupFilesPresetEntry.backupfilesPresetEntriesValues
+ .get(key));
+ }
+ else
+ {
+ Cache.log.error(
+ "Preset '" + value + "' [key:" + key + "] not implemented");
}
- backupfilesCustomOptionsSetEnabled();
+ // Custom options will now be enabled when the customiseCheckbox is checked
+ // (performed above)
+ // backupfilesCustomOptionsSetEnabled();
updateBackupFilesExampleLabel();
}
- protected int getComboIntStringKey(JComboBox<IntKeyStringValueEntry> c)
+ protected int getComboIntStringKey(
+ JComboBox<Object> backupfilesPresetsCombo2)
{
- IntKeyStringValueEntry e = (IntKeyStringValueEntry) c.getSelectedItem();
- return e != null ? e.getKey() : 0;
+ IntKeyStringValueEntry e;
+ try
+ {
+ e = (IntKeyStringValueEntry) backupfilesPresetsCombo2
+ .getSelectedItem();
+ } catch (Exception ex)
+ {
+ Cache.log.error(
+ "Problem casting Combo entry to IntKeyStringValueEntry.");
+ e = null;
+ }
+ return e != null ? e.k : 0;
}
- protected void setComboIntStringKey(JComboBox<IntKeyStringValueEntry> c,
+ protected void setComboIntStringKey(
+ JComboBox<Object> backupfilesPresetsCombo2,
int key)
{
- for (int i = 0; i < c.getItemCount(); i++)
+ for (int i = 0; i < backupfilesPresetsCombo2.getItemCount(); i++)
{
- IntKeyStringValueEntry e = c.getItemAt(i);
- if (e.getKey() == key)
+ IntKeyStringValueEntry e;
+ try
{
- c.setSelectedIndex(i);
+ e = (IntKeyStringValueEntry) backupfilesPresetsCombo2.getItemAt(i);
+ } catch (Exception ex)
+ {
+ Cache.log.error(
+ "Problem casting Combo entry to IntKeyStringValueEntry. Skipping item. ");
+ continue;
+ }
+ if (e.k == key)
+ {
+ backupfilesPresetsCombo2.setSelectedIndex(i);
break;
}
}
- backupsTabUpdatePresets();
+ // backupsTabUpdatePresets();
}
private JPanel initBackupsTabSuffixPanel()
{
updateBackupFilesExampleLabel();
backupfilesCustomOptionsSetEnabled();
+ backupfilesRevertButtonSetEnabled(true);
}
});
- KeyListener kl = new KeyListener()
+ suffixTemplate.addKeyListener(new KeyListener()
{
@Override
public void keyReleased(KeyEvent e)
{
updateBackupFilesExampleLabel();
backupfilesCustomOptionsSetEnabled();
+ backupfilesRevertButtonSetEnabled(true);
}
@Override
}
}
- };
- suffixTemplate.addKeyListener(kl);
+ });
// digits spinner
suffixDigitsLabel
.setText(MessageManager.getString("label.index_digits"));
suffixDigitsLabel.setHorizontalAlignment(SwingConstants.LEFT);
suffixDigitsLabel.setFont(LABEL_FONT);
- int defaultmin = 1;
- int defaultmax = 6;
ChangeListener c = new ChangeListener()
{
@Override
public void stateChanged(ChangeEvent e)
{
+ backupfilesRevertButtonSetEnabled(true);
updateBackupFilesExampleLabel();
}
};
- setIntegerSpinner(suffixDigitsSpinner, defaultmin, defaultmax, 3, c);
+ setIntegerSpinner(suffixDigitsSpinner, BackupFilesPresetEntry.DIGITSMIN,
+ BackupFilesPresetEntry.DIGITSMAX, 3, c);
suffixReverse.setLabels(MessageManager.getString("label.reverse_roll"),
MessageManager.getString("label.increment_index"));
}
if (okay)
{
+ backupfilesRevertButtonSetEnabled(true);
updateBackupFilesExampleLabel();
}
else
{
- boolean savedSuffixReverse = Cache
- .getDefault(BackupFiles.REVERSE_ORDER, false);
+ boolean savedSuffixReverse = BackupFilesPresetEntry
+ .getSavedBackupEntry().reverse;
suffixReverse.setSelected(savedSuffixReverse);
}
}
@Override
public void actionPerformed(ActionEvent e)
{
+ backupfilesRevertButtonSetEnabled(true);
updateBackupFilesExampleLabel();
}
});
@Override
public void actionPerformed(ActionEvent e)
{
+ backupfilesRevertButtonSetEnabled(true);
keepRollMaxOptionsEnabled();
updateBackupFilesExampleLabel();
}
@Override
public void stateChanged(ChangeEvent e)
{
+ backupfilesRevertButtonSetEnabled(true);
updateBackupFilesExampleLabel();
}
};
- setIntegerSpinner(backupfilesRollMaxSpinner, 1, 999, 4, true, c);
+ setIntegerSpinner(backupfilesRollMaxSpinner,
+ BackupFilesPresetEntry.ROLLMAXMIN,
+ BackupFilesPresetEntry.ROLLMAXMAX, 4, true, c);
backupfilesConfirmDelete.setLabels(
MessageManager.getString("label.always_ask"),
MessageManager.getString("label.auto_delete"));
+ backupfilesConfirmDelete.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ backupfilesRevertButtonSetEnabled(true);
+ }
+ });
// update the enabled section
keepRollMaxOptionsEnabled();
kgbc.gridwidth = GridBagConstraints.REMAINDER;
kgbc.fill = GridBagConstraints.HORIZONTAL;
kgbc.weightx = 1.0;
- /*
- keepfilesPanel.add(backupfilesConfirmDelete.getTrueButton(), kgbc);
-
- // fourth row (indented)
- kgbc.gridy = 3;
- keepfilesPanel.add(backupfilesConfirmDelete.getFalseButton(), kgbc);
- */
JPanel jp = new JPanel();
jp.setLayout(new FlowLayout());
int uppersurround = 0;
StringBuilder exampleSB = new StringBuilder();
boolean firstLine = true;
+ int lineNumber = 0;
if (reverse)
{
if (index == min + lowersurround && index < max - uppersurround - 1)
{
exampleSB.append("\n...");
+ lineNumber++;
}
else if (index > min + lowersurround && index < max - uppersurround)
{
else
{
exampleSB.append("\n");
+ lineNumber++;
}
exampleSB.append(BackupFilenameParts.getBackupFilename(index,
base, suffix, digits));
if (index == min + lowersurround && index < max - uppersurround - 1)
{
exampleSB.append("\n...");
+ lineNumber++;
}
else if (index > min + lowersurround && index < max - uppersurround)
{
else
{
exampleSB.append("\n");
+ lineNumber++;
}
exampleSB.append(BackupFilenameParts.getBackupFilename(index,
base, suffix, digits));
}
+ // add some extra empty lines to pad out the example files box. ugh, please tell
+ // me how to do this better
+ int remainingLines = lowersurround + uppersurround + 1 - lineNumber;
+ if (remainingLines > 0)
+ {
+ for (int i = 0; i < remainingLines; i++)
+ {
+ exampleSB.append("\n ");
+ lineNumber++;
+ }
+ }
+
backupfilesExampleLabel.setText(exampleSB.toString());
}
i = Integer.parseInt((String) s.getValue());
} catch (Exception e)
{
- System.out.println(
+ Cache.log.error(
"Exception casting the initial value of s.getValue()");
}
}
i = (Integer) s.getValue();
} catch (Exception e)
{
- System.out.println("Failed casting (Integer) JSpinner s.getValue()");
+ Cache.log.error("Failed casting (Integer) JSpinner s.getValue()");
}
return i;
}
private void backupfilesKeepAllSetEnabled(boolean tryEnabled)
{
boolean enabled = tryEnabled && enableBackupFiles.isSelected()
- && getComboIntStringKey(backupfilesPresetsCombo) == 0
+ && customiseCheckbox.isSelected()
&& suffixTemplate.getText()
.indexOf(BackupFiles.NUM_PLACEHOLDER) > -1;
keepfilesPanel.setEnabled(enabled);
private void backupfilesSuffixTemplateSetEnabled(boolean tryEnabled)
{
boolean enabled = tryEnabled && enableBackupFiles.isSelected()
- && getComboIntStringKey(backupfilesPresetsCombo) == 0;
+ && customiseCheckbox.isSelected();
suffixPanel.setEnabled(enabled);
suffixTemplateLabel.setEnabled(enabled);
suffixTemplate.setEnabled(enabled);
backupfilesSuffixTemplateDigitsSetEnabled();
}
+ private void backupfilesRevertButtonSetEnabled(boolean tryEnabled)
+ {
+ boolean enabled = tryEnabled && enableBackupFiles.isSelected()
+ && customiseCheckbox.isSelected() && backupfilesCustomChanged();
+ revertButton.setEnabled(enabled);
+ }
+
+ private boolean backupfilesCustomChanged()
+ {
+ BackupFilesPresetEntry custom = BackupFilesPresetEntry.backupfilesPresetEntriesValues
+ .get(BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM);
+ BackupFilesPresetEntry current = getBackupfilesCurrentEntry();
+ return !custom.equals(current);
+ }
+
+ protected BackupFilesPresetEntry getBackupfilesCurrentEntry()
+ {
+ String suffix = suffixTemplate.getText();
+ int digits = getSpinnerInt(suffixDigitsSpinner, 3);
+ boolean reverse = suffixReverse.isSelected();
+ boolean keepAll = backupfilesKeepAll.isSelected();
+ int rollMax = getSpinnerInt(backupfilesRollMaxSpinner, 3);
+ boolean confirmDelete = backupfilesConfirmDelete.isSelected();
+
+ BackupFilesPresetEntry bfpe = new BackupFilesPresetEntry(suffix, digits,
+ reverse, keepAll, rollMax, confirmDelete);
+
+ return bfpe;
+ }
+
protected void backupfilesCustomOptionsSetEnabled()
{
- int scheme = getComboIntStringKey(backupfilesPresetsCombo);
- boolean enabled = scheme == 0 && enableBackupFiles.isSelected();
+ boolean enabled = customiseCheckbox.isSelected();
+ backupfilesRevertButtonSetEnabled(enabled);
backupfilesSuffixTemplateSetEnabled(enabled);
backupfilesKeepAllSetEnabled(enabled);
}
{
boolean enabled = enableBackupFiles.isSelected();
presetsPanel.setEnabled(enabled);
+ presetsComboLabel.setEnabled(enabled);
backupfilesPresetsCombo.setEnabled(enabled);
+ customiseCheckbox.setEnabled(enabled);
+ revertButton.setEnabled(enabled);
}
protected void backupsOptionsSetEnabled()
}
}
-class IntKeyStringValueEntry
-{
- int k;
-
- String v;
-
- public IntKeyStringValueEntry(int k, String v)
- {
- this.k = k;
- this.v = v;
- }
-
- @Override
- public String toString()
- {
- return this.getValue();
- }
-
- public int getKey()
- {
- return k;
- }
-
- public String getValue()
- {
- return v;
- }
-}
-
-class BackupFilesPresetEntry
-{
- String suffix;
-
- int digits;
-
- boolean reverse;
-
- boolean keepAll;
-
- int rollMax;
-
- boolean confirmDelete;
-
- public BackupFilesPresetEntry(String suffix, int digits, boolean reverse,
- boolean keepAll, int rollMax, boolean confirmDelete)
- {
- this.suffix = suffix;
- this.digits = digits;
- this.reverse = reverse;
- this.keepAll = keepAll;
- this.rollMax = rollMax;
- this.confirmDelete = confirmDelete;
- }
-}
-
-class BackupFilesPresetsComboBoxRenderer extends DefaultListCellRenderer
-{
- /**
- *
- */
- private static final long serialVersionUID = 88L;
-
- @Override
- public Component getListCellRendererComponent(JList list, Object value,
- int index, boolean isSelected, boolean cellHasFocus)
- {
- super.getListCellRendererComponent(list, value, index, isSelected, cellHasFocus);
-
- try {
- IntKeyStringValueEntry e = (IntKeyStringValueEntry) value;
- if (e.getKey() == GPreferences.BACKUPFILESSCHEMECUSTOMISE)
- {
- // "Customise" item
- this.setFont(this.getFont().deriveFont(Font.BOLD));
- }
- } catch (Exception e) {
- return this;
- }
-
- return this;
- }
-}
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.GeneLocus;
import jalview.datamodel.GraphLine;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.Point;
parentseq = jds;
}
}
+
+ /*
+ * save any dbrefs; special subclass GeneLocus is flagged as 'locus'
+ */
if (dbrefs != null)
{
for (int d = 0; d < dbrefs.length; d++)
{
DBRef dbref = new DBRef();
- dbref.setSource(dbrefs[d].getSource());
- dbref.setVersion(dbrefs[d].getVersion());
- dbref.setAccessionId(dbrefs[d].getAccessionId());
- if (dbrefs[d].hasMap())
+ DBRefEntry dbRefEntry = dbrefs[d];
+ dbref.setSource(dbRefEntry.getSource());
+ dbref.setVersion(dbRefEntry.getVersion());
+ dbref.setAccessionId(dbRefEntry.getAccessionId());
+ if (dbRefEntry instanceof GeneLocus)
{
- Mapping mp = createVamsasMapping(dbrefs[d].getMap(), parentseq,
+ dbref.setLocus(true);
+ }
+ if (dbRefEntry.hasMap())
+ {
+ Mapping mp = createVamsasMapping(dbRefEntry.getMap(), parentseq,
jds, recurse);
dbref.setMapping(mp);
}
- // vamsasSeq.addDBRef(dbref);
vamsasSeq.getDBRef().add(dbref);
}
}
return datasetId;
}
+ /**
+ * Add any saved DBRefEntry's to the sequence. An entry flagged as 'locus' is
+ * constructed as a special subclass GeneLocus.
+ *
+ * @param datasetSequence
+ * @param sequence
+ */
private void addDBRefs(SequenceI datasetSequence, Sequence sequence)
{
for (int d = 0; d < sequence.getDBRef().size(); d++)
{
DBRef dr = sequence.getDBRef().get(d);
- jalview.datamodel.DBRefEntry entry = new jalview.datamodel.DBRefEntry(
- dr.getSource(), dr.getVersion(), dr.getAccessionId());
+ DBRefEntry entry;
+ if (dr.isLocus())
+ {
+ entry = new GeneLocus(dr.getSource(), dr.getVersion(),
+ dr.getAccessionId());
+ }
+ else
+ {
+ entry = new DBRefEntry(dr.getSource(), dr.getVersion(),
+ dr.getAccessionId());
+ }
if (dr.getMapping() != null)
{
entry.setMap(addMapping(dr.getMapping()));
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 ShortcutKeyMaskExWrapper11();
}
else
{
- SHIFT_DOWN_MASK = KeyEvent.SHIFT_DOWN_MASK;
- ALT_DOWN_MASK = KeyEvent.ALT_DOWN_MASK;
+ wrapper = new ShortcutKeyMaskExWrapper8();
}
-
- init = true;
+ SHIFT_DOWN_MASK = wrapper.SHIFT_DOWN_MASK;
+ ALT_DOWN_MASK = wrapper.ALT_DOWN_MASK;
}
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 = KeyEvent.SHIFT_DOWN_MASK;
+ public final static int 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 = KeyEvent.SHIFT_MASK;
+ public final static int 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);
+}
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2018.12.20 at 11:47:26 AM GMT
+// Generated on: 2019.06.07 at 02:21:15 PM BST
//
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2018.12.20 at 11:47:26 AM GMT
+// Generated on: 2019.06.07 at 02:21:15 PM BST
//
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2018.12.20 at 11:47:26 AM GMT
+// Generated on: 2019.06.07 at 02:21:15 PM BST
//
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2018.12.20 at 11:47:26 AM GMT
+// Generated on: 2019.06.07 at 02:21:15 PM BST
//
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2018.12.20 at 11:47:26 AM GMT
+// Generated on: 2019.06.07 at 02:21:15 PM BST
//
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2018.12.20 at 11:47:26 AM GMT
+// Generated on: 2019.06.07 at 02:21:15 PM BST
//
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2018.12.20 at 11:47:26 AM GMT
+// Generated on: 2019.06.07 at 02:21:15 PM BST
//
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2018.12.20 at 11:47:26 AM GMT
+// Generated on: 2019.06.07 at 02:21:15 PM BST
//
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2018.12.20 at 11:47:26 AM GMT
+// Generated on: 2019.06.07 at 02:21:15 PM BST
//
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2018.12.20 at 11:47:26 AM GMT
+// Generated on: 2019.06.07 at 02:21:15 PM BST
//
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2018.12.20 at 11:47:26 AM GMT
+// Generated on: 2019.06.07 at 02:21:15 PM BST
//
* <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
* <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
* <attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="showComplementFeaturesOnTop" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
* </restriction>
* </complexContent>
* </complexType>
* <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
* <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
* <attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="showComplementFeaturesOnTop" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
* </restriction>
* </complexContent>
* </complexType>
protected String id;
@XmlAttribute(name = "complementId")
protected String complementId;
+ @XmlAttribute(name = "showComplementFeatures")
+ protected Boolean showComplementFeatures;
+ @XmlAttribute(name = "showComplementFeaturesOnTop")
+ protected Boolean showComplementFeaturesOnTop;
@XmlAttribute(name = "width")
protected Integer width;
@XmlAttribute(name = "height")
}
/**
+ * Gets the value of the showComplementFeatures property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isShowComplementFeatures() {
+ if (showComplementFeatures == null) {
+ return false;
+ } else {
+ return showComplementFeatures;
+ }
+ }
+
+ /**
+ * Sets the value of the showComplementFeatures property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setShowComplementFeatures(Boolean value) {
+ this.showComplementFeatures = value;
+ }
+
+ /**
+ * Gets the value of the showComplementFeaturesOnTop property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isShowComplementFeaturesOnTop() {
+ if (showComplementFeaturesOnTop == null) {
+ return false;
+ } else {
+ return showComplementFeaturesOnTop;
+ }
+ }
+
+ /**
+ * Sets the value of the showComplementFeaturesOnTop property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setShowComplementFeaturesOnTop(Boolean value) {
+ this.showComplementFeaturesOnTop = value;
+ }
+
+ /**
* Gets the value of the width property.
*
* @return
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2018.12.20 at 11:47:26 AM GMT
+// Generated on: 2019.06.07 at 02:21:15 PM BST
//
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2018.12.20 at 11:47:26 AM GMT
+// Generated on: 2019.06.07 at 02:21:15 PM BST
//
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2018.12.20 at 11:47:26 AM GMT
+// Generated on: 2019.06.07 at 02:21:15 PM BST
//
import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlAccessorType;
+import javax.xml.bind.annotation.XmlAttribute;
import javax.xml.bind.annotation.XmlElement;
import javax.xml.bind.annotation.XmlRootElement;
import javax.xml.bind.annotation.XmlType;
* </element>
* </choice>
* </sequence>
+ * <attribute name="mappingType" type="{http://www.w3.org/2001/XMLSchema}string" />
* </extension>
* </complexContent>
* </complexType>
@XmlElement(name = "Sequence")
protected Sequence sequence;
protected String dseqFor;
+ @XmlAttribute(name = "mappingType")
+ protected String mappingType;
/**
* Gets the value of the sequence property.
this.dseqFor = value;
}
+ /**
+ * Gets the value of the mappingType property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getMappingType() {
+ return mappingType;
+ }
+
+ /**
+ * Sets the value of the mappingType property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setMappingType(String value) {
+ this.mappingType = value;
+ }
+
}
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2018.12.20 at 11:47:26 AM GMT
+// Generated on: 2019.06.07 at 02:21:15 PM BST
//
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2018.12.20 at 11:47:26 AM GMT
+// Generated on: 2019.06.07 at 02:21:15 PM BST
//
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2018.12.20 at 11:47:26 AM GMT
+// Generated on: 2019.06.07 at 02:21:15 PM BST
//
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2018.12.20 at 11:47:26 AM GMT
+// Generated on: 2019.06.07 at 02:21:15 PM BST
//
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2018.12.20 at 11:47:26 AM GMT
+// Generated on: 2019.06.07 at 02:21:15 PM BST
//
* <attribute name="source" type="{http://www.w3.org/2001/XMLSchema}string" />
* <attribute name="version" type="{http://www.w3.org/2001/XMLSchema}string" />
* <attribute name="accessionId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="locus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
* </restriction>
* </complexContent>
* </complexType>
* </element>
* </sequence>
* <attribute name="dsseqid" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="biotype" type="{http://www.w3.org/2001/XMLSchema}string" />
* </extension>
* </complexContent>
* </complexType>
protected List<Sequence.DBRef> dbRef;
@XmlAttribute(name = "dsseqid")
protected String dsseqid;
+ @XmlAttribute(name = "biotype")
+ protected String biotype;
/**
* Gets the value of the dbRef property.
this.dsseqid = value;
}
+ /**
+ * Gets the value of the biotype property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getBiotype() {
+ return biotype;
+ }
+
+ /**
+ * Sets the value of the biotype property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setBiotype(String value) {
+ this.biotype = value;
+ }
+
/**
* <p>Java class for anonymous complex type.
* <attribute name="source" type="{http://www.w3.org/2001/XMLSchema}string" />
* <attribute name="version" type="{http://www.w3.org/2001/XMLSchema}string" />
* <attribute name="accessionId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="locus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
* </restriction>
* </complexContent>
* </complexType>
protected String version;
@XmlAttribute(name = "accessionId")
protected String accessionId;
+ @XmlAttribute(name = "locus")
+ protected Boolean locus;
/**
* Gets the value of the mapping property.
this.accessionId = value;
}
+ /**
+ * Gets the value of the locus property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isLocus() {
+ if (locus == null) {
+ return false;
+ } else {
+ return locus;
+ }
+ }
+
+ /**
+ * Sets the value of the locus property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setLocus(Boolean value) {
+ this.locus = value;
+ }
+
}
}
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2018.12.20 at 11:47:26 AM GMT
+// Generated on: 2019.06.07 at 02:21:15 PM BST
//
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2018.12.20 at 11:47:26 AM GMT
+// Generated on: 2019.06.07 at 02:21:15 PM BST
//
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2018.12.20 at 11:47:26 AM GMT
+// Generated on: 2019.06.07 at 02:21:15 PM BST
//
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2018.12.20 at 11:47:26 AM GMT
+// Generated on: 2019.06.07 at 02:21:15 PM BST
//
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2018.12.20 at 11:47:26 AM GMT
+// Generated on: 2019.06.07 at 02:21:15 PM BST
//
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2018.12.20 at 11:47:26 AM GMT
+// Generated on: 2019.06.07 at 02:21:15 PM BST
//
@javax.xml.bind.annotation.XmlSchema(namespace = "www.vamsas.ac.uk/jalview/version2", elementFormDefault = javax.xml.bind.annotation.XmlNsForm.QUALIFIED)
* transcript 'CDS' is 10-16, 17-21
* which is 'gene' 158-164, 210-214
*/
- MapList toMap = toLoci.getMap();
+ MapList toMap = toLoci.getMapping();
assertEquals(1, toMap.getFromRanges().size());
assertEquals(2, toMap.getFromRanges().get(0).length);
assertEquals(1, toMap.getFromRanges().get(0)[0]);
AlignmentUtils.transferGeneLoci(from, map, to);
assertEquals("GRCh38", toLoci.getAssemblyId());
assertEquals("7", toLoci.getChromosomeId());
- toMap = toLoci.getMap();
+ toMap = toLoci.getMapping();
assertEquals("[ [1, 12] ] 1:1 to [ [158, 164] [210, 214] ]",
toMap.toString());
}
import jalview.io.DataSourceType;
import jalview.io.FileLoader;
import jalview.util.MessageManager;
+import jalview.viewmodel.ViewportRanges;
-import java.awt.event.InputEvent;import java.awt.EventQueue;
+import java.awt.EventQueue;
import java.awt.event.MouseEvent;
import java.lang.reflect.InvocationTargetException;
int x = 0;
final int charWidth = alignFrame.getViewport().getCharWidth();
assertTrue(charWidth > 0); // sanity check
- assertEquals(alignFrame.getViewport().getRanges().getStartRes(), 0);
+ ViewportRanges ranges = alignFrame.getViewport().getRanges();
+ assertEquals(ranges.getStartRes(), 0);
/*
* mouse at top left of unwrapped panel
false, 0);
SeqCanvas seqCanvas = alignFrame.alignPanel.getSeqPanel().seqCanvas;
int w = seqCanvas.getWidth();
- // limited to number of whole columns, base 0
- int expected = w / charWidth - 1;
+ // limited to number of whole columns, base 0,
+ // and to end of visible range
+ int expected = w / charWidth;
+ expected = Math.min(expected, ranges.getEndRes());
assertEquals(testee.findColumn(evt), expected);
/*
}
private static boolean actuallyDeleteTmpFiles = true;
- private static String testDir = "examples";
+
+ private static String testDir = "test/jalview/io";
private static String testBasename = "backupfilestest";
private static String suffix = "_BACKUPTEST-%n";
- private static int digits = 8;
+ private static int digits = 6;
private static int rollMax = 2;
}
// check 10 backup files
- HashMap correctindexmap = new HashMap();
- correctindexmap.put(1, "backupfilestestTemp.fa_BACKUPTEST-00000001");
- correctindexmap.put(2, "backupfilestestTemp.fa_BACKUPTEST-00000002");
- correctindexmap.put(3, "backupfilestestTemp.fa_BACKUPTEST-00000003");
- correctindexmap.put(4, "backupfilestestTemp.fa_BACKUPTEST-00000004");
- correctindexmap.put(5, "backupfilestestTemp.fa_BACKUPTEST-00000005");
- correctindexmap.put(6, "backupfilestestTemp.fa_BACKUPTEST-00000006");
- correctindexmap.put(7, "backupfilestestTemp.fa_BACKUPTEST-00000007");
- correctindexmap.put(8, "backupfilestestTemp.fa_BACKUPTEST-00000008");
- correctindexmap.put(9, "backupfilestestTemp.fa_BACKUPTEST-00000009");
- correctindexmap.put(10, "backupfilestestTemp.fa_BACKUPTEST-00000010");
- HashMap wrongindexmap = new HashMap();
+ HashMap<Integer, String> correctindexmap = new HashMap<>();
+ correctindexmap.put(1, "backupfilestestTemp.fa_BACKUPTEST-000001");
+ correctindexmap.put(2, "backupfilestestTemp.fa_BACKUPTEST-000002");
+ correctindexmap.put(3, "backupfilestestTemp.fa_BACKUPTEST-000003");
+ correctindexmap.put(4, "backupfilestestTemp.fa_BACKUPTEST-000004");
+ correctindexmap.put(5, "backupfilestestTemp.fa_BACKUPTEST-000005");
+ correctindexmap.put(6, "backupfilestestTemp.fa_BACKUPTEST-000006");
+ correctindexmap.put(7, "backupfilestestTemp.fa_BACKUPTEST-000007");
+ correctindexmap.put(8, "backupfilestestTemp.fa_BACKUPTEST-000008");
+ correctindexmap.put(9, "backupfilestestTemp.fa_BACKUPTEST-000009");
+ correctindexmap.put(10, "backupfilestestTemp.fa_BACKUPTEST-000010");
+ HashMap<Integer, String> wrongindexmap = new HashMap<>();
wrongindexmap.put(1, "backupfilestestTemp.fa_BACKUPTEST-1");
- wrongindexmap.put(2, "backupfilestestTemp.fa_BACKUPTEST-00000002");
- wrongindexmap.put(3, "backupfilestestTemp.fa_BACKUPTEST-00000003");
- wrongindexmap.put(4, "backupfilestestTemp.fa_BACKUPTEST-00000004");
- wrongindexmap.put(5, "backupfilestestTemp.fa_BACKUPTEST-00000005");
- wrongindexmap.put(6, "backupfilestestTemp.fa_BACKUPTEST-00000006");
- wrongindexmap.put(7, "backupfilestestTemp.fa_BACKUPTEST-00000007");
- wrongindexmap.put(8, "backupfilestestTemp.fa_BACKUPTEST-00000008");
- wrongindexmap.put(9, "backupfilestestTemp.fa_BACKUPTEST-00000009");
- wrongindexmap.put(10, "backupfilestestTemp.fa_BACKUPTEST-00000010");
+ wrongindexmap.put(2, "backupfilestestTemp.fa_BACKUPTEST-000002");
+ wrongindexmap.put(3, "backupfilestestTemp.fa_BACKUPTEST-000003");
+ wrongindexmap.put(4, "backupfilestestTemp.fa_BACKUPTEST-000004");
+ wrongindexmap.put(5, "backupfilestestTemp.fa_BACKUPTEST-000005");
+ wrongindexmap.put(6, "backupfilestestTemp.fa_BACKUPTEST-000006");
+ wrongindexmap.put(7, "backupfilestestTemp.fa_BACKUPTEST-000007");
+ wrongindexmap.put(8, "backupfilestestTemp.fa_BACKUPTEST-000008");
+ wrongindexmap.put(9, "backupfilestestTemp.fa_BACKUPTEST-000009");
+ wrongindexmap.put(10, "backupfilestestTemp.fa_BACKUPTEST-000010");
int[] indexes2 = { 3, 4, 5, 6, 7, 8, 9, 10 };
int[] indexes3 = { 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 };
Assert.assertTrue(checkBackupFiles(correctindexmap));
// check there are "rollMax" backup files and they are all saved correctly
// check 10 backup files
- HashMap correctindexmap = new HashMap();
- correctindexmap.put(9, "backupfilestestTemp.fa_BACKUPTEST-00000009");
- correctindexmap.put(10, "backupfilestestTemp.fa_BACKUPTEST-00000010");
+ HashMap<Integer, String> correctindexmap = new HashMap<>();
+ correctindexmap.put(9, "backupfilestestTemp.fa_BACKUPTEST-000009");
+ correctindexmap.put(10, "backupfilestestTemp.fa_BACKUPTEST-000010");
int[] indexes2 = { 10 };
int[] indexes3 = { 8, 9, 10 };
Assert.assertTrue(checkBackupFiles(correctindexmap));
// check there are "rollMax" backup files and they are all saved correctly
// check 10 backup files
- HashMap correctindexmap = new HashMap();
- correctindexmap.put(1, "backupfilestestTemp.fa_BACKUPTEST-00000001");
- correctindexmap.put(2, "backupfilestestTemp.fa_BACKUPTEST-00000002");
+ HashMap<Integer, String> correctindexmap = new HashMap<>();
+ correctindexmap.put(1, "backupfilestestTemp.fa_BACKUPTEST-000001");
+ correctindexmap.put(2, "backupfilestestTemp.fa_BACKUPTEST-000002");
int[] indexes2 = { 1 };
int[] indexes3 = { 1, 2, 3 };
Assert.assertTrue(checkBackupFiles(correctindexmap));
{
Cache.loadProperties("test/jalview/io/testProps.jvprops");
+ BackupFilesPresetEntry bfpe = new BackupFilesPresetEntry(suffix, digits,
+ reverse, noMax, rollMax, false);
+
+ Cache.applicationProperties.setProperty(BackupFiles.ENABLED,
+ Boolean.toString(enabled));
+ Cache.applicationProperties.setProperty(
+ BackupFilesPresetEntry.SAVEDCONFIG, bfpe.toString());
+ /*
Cache.applicationProperties.setProperty(BackupFiles.ENABLED,
Boolean.toString(enabled));
Cache.applicationProperties.setProperty(BackupFiles.SUFFIX, suffix);
Integer.toString(rollMax));
Cache.applicationProperties.setProperty(BackupFiles.CONFIRM_DELETE_OLD,
"false");
+ */
}
private void save()
#---JalviewX Properties File---
#Fri Apr 25 09:54:25 BST 2014
#
-BACKUPFILES_ROLL_MAX=2
-BACKUPFILES_REVERSE_ORDER=false
-BACKUPFILES_SUFFIX=_BACKUPFILESTESTTMP%n
-BACKUPFILES_CONFIRM_DELETE_OLD=false
-BACKUPFILES_NO_MAX=false
BACKUPFILES_ENABLED=true
-BACKUPFILES_SUFFIX_DIGITS=8
+BACKUPFILES_PRESET=0
+BACKUPFILES_SAVED=_BACKUPFILESTESTTMP%n\t6\tfalse\tfalse\t2\tfalse
+BACKUPFILES_CUSTOM=_BACKUPFILESTESTTMP%n\t6\tfalse\tfalse\t2\tfalse
SCREEN_Y=768
SCREEN_X=936
SHOW_WSDISCOVERY_ERRORS=true
import jalview.api.ViewStyleI;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.GeneLocus;
import jalview.datamodel.HiddenSequences;
+import jalview.datamodel.Mapping;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.PDBEntry.Type;
import jalview.datamodel.SequenceCollectionI;
import jalview.schemes.StrandColourScheme;
import jalview.schemes.TCoffeeColourScheme;
import jalview.structure.StructureImportSettings;
+import jalview.util.MapList;
import jalview.util.matcher.Condition;
import jalview.viewmodel.AlignmentViewport;
.getAlignViewport(),
"Didn't restore correct view association for the PCA view");
}
+
+ /**
+ * Test save and reload of DBRefEntry including GeneLocus in project
+ *
+ * @throws Exception
+ */
+ @Test(groups = { "Functional" })
+ public void testStoreAndRecoverGeneLocus() throws Exception
+ {
+ Desktop.instance.closeAll_actionPerformed(null);
+ String seqData = ">P30419\nACDE\n>X1235\nGCCTGTGACGAA";
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(seqData,
+ DataSourceType.PASTE);
+ assertNotNull(af, "Didn't read in the example file correctly.");
+
+ AlignmentViewPanel ap = Desktop.getAlignmentPanels(null)[0];
+ SequenceI pep = ap.getAlignment().getSequenceAt(0);
+ SequenceI cds = ap.getAlignment().getSequenceAt(1);
+
+ /*
+ * give 'protein' a dbref to self, a dbref with map to CDS,
+ * and a dbref with map to gene 'locus'
+ */
+ DBRefEntry dbref1 = new DBRefEntry("Uniprot", "1", "P30419", null);
+ pep.addDBRef(dbref1);
+ Mapping cdsmap = new Mapping(cds,
+ new MapList(new int[]
+ { 1, 4 }, new int[] { 1, 12 }, 1, 3));
+ DBRefEntry dbref2 = new DBRefEntry("EMBLCDS", "2", "X1235", cdsmap);
+ pep.addDBRef(dbref2);
+ Mapping locusmap = new Mapping(null,
+ new MapList(new int[]
+ { 1, 4 }, new int[] { 2674123, 2674135 }, 1, 3));
+ DBRefEntry dbref3 = new GeneLocus("human", "GRCh38", "5", locusmap);
+ pep.addDBRef(dbref3);
+
+ File tfile = File.createTempFile("testStoreAndRecoverGeneLocus",
+ ".jvp");
+ try
+ {
+ new Jalview2XML(false).saveState(tfile);
+ } catch (Throwable e)
+ {
+ Assert.fail("Didn't save the state", e);
+ }
+ Desktop.instance.closeAll_actionPerformed(null);
+
+ new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
+ DataSourceType.FILE);
+ AlignmentViewPanel rap = Desktop.getAlignmentPanels(null)[0];
+ SequenceI rpep = rap.getAlignment().getSequenceAt(0);
+ assertEquals(rpep.getName(), "P30419");
+ DBRefEntry[] dbrefs = rpep.getDBRefs();
+ assertEquals(dbrefs.length, 3);
+ DBRefEntry dbRef = dbrefs[0];
+ assertFalse(dbRef instanceof GeneLocus);
+ assertNull(dbRef.getMap());
+ assertEquals(dbRef, dbref1);
+
+ /*
+ * restored dbrefs with mapping have a different 'map to'
+ * sequence but otherwise match the original dbrefs
+ */
+ dbRef = dbrefs[1];
+ assertFalse(dbRef instanceof GeneLocus);
+ assertTrue(dbRef.equalRef(dbref2));
+ assertNotNull(dbRef.getMap());
+ SequenceI rcds = rap.getAlignment().getSequenceAt(1);
+ assertSame(dbRef.getMap().getTo(), rcds);
+ // compare MapList but not map.to
+ assertEquals(dbRef.getMap().getMap(), dbref2.getMap().getMap());
+
+ /*
+ * GeneLocus map.to is null so can compare Mapping objects
+ */
+ dbRef = dbrefs[2];
+ assertTrue(dbRef instanceof GeneLocus);
+ assertEquals(dbRef, dbref3);
+ }
}
else
{
internalHrefCount++;
+ String relFile = System.getProperty("os.name").indexOf("Win") > -1 ? href.replace("/", File.separator) : href;
File hrefFile = href.equals("") ? htmlFile : new File(htmlFolder,
href);
- if (hrefFile != htmlFile && !fileExists(hrefFile, href))
+ if (hrefFile != htmlFile && !fileExists(hrefFile, relFile))
{
badLink = true;
invalidInternalHrefCount++;
--- /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>CFBundleAllowMixedLocalizations</key>
+ <true/>
+ <key>CFBundleDevelopmentRegion</key>
+ <string>English</string>
+ <key>CFBundleExecutable</key>
+ <string>applet</string>
+ <key>CFBundleIconFile</key>
+ <string>applet</string>
+ <key>CFBundleIdentifier</key>
+ <string>com.apple.ScriptEditor.id.Uninstall-Old-Jalview--optional</string>
+ <key>CFBundleInfoDictionaryVersion</key>
+ <string>6.0</string>
+ <key>CFBundleName</key>
+ <string>Uninstall Old Jalview (optional)</string>
+ <key>CFBundlePackageType</key>
+ <string>APPL</string>
+ <key>CFBundleShortVersionString</key>
+ <string>1.0</string>
+ <key>CFBundleSignature</key>
+ <string>aplt</string>
+ <key>LSMinimumSystemVersionByArchitecture</key>
+ <dict>
+ <key>x86_64</key>
+ <string>10.6</string>
+ </dict>
+ <key>LSRequiresCarbon</key>
+ <true/>
+ <key>WindowState</key>
+ <dict>
+ <key>bundleDividerCollapsed</key>
+ <true/>
+ <key>bundlePositionOfDivider</key>
+ <real>0.0</real>
+ <key>dividerCollapsed</key>
+ <false/>
+ <key>eventLogLevel</key>
+ <integer>2</integer>
+ <key>name</key>
+ <string>ScriptWindowState</string>
+ <key>positionOfDivider</key>
+ <real>421</real>
+ <key>savedFrame</key>
+ <string>20 1180 700 672 0 0 3360 1867 </string>
+ <key>selectedTab</key>
+ <string>description</string>
+ </dict>
+</dict>
+</plist>
--- /dev/null
+APPLaplt
\ No newline at end of file
--- /dev/null
+{\rtf1\ansi\ansicpg1252\cocoartf1561\cocoasubrtf600
+{\fonttbl}
+{\colortbl;\red255\green255\blue255;}
+{\*\expandedcolortbl;;}
+}
\ No newline at end of file
<?xml version="1.0" encoding="UTF-8"?>
<install4j version="7.0.9" transformSequenceNumber="7">
- <directoryPresets config="../../../../../buildtools/jre/openjdk-java_vm/macos-jdk8u202-b08-jre" />
+ <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">
<principalLanguage id="en" customLocalizationFile="" />
</languages>
<searchSequence>
<directory location="${compiler:JRE_DIR}" />
+ <registry />
+ <envVar name="JAVA_HOME" />
</searchSequence>
<variables>
<variable name="OSX_KEYSTORE" value="" description="" category="" />
<fileset name="Full file set" id="734" customizedId="" />
<fileset name="Mac OS X JRE" id="880" customizedId="" />
<fileset name="Windows JRE" id="882" customizedId="" />
+ <fileset name="Jalview application" id="1873" customizedId="" />
+ <fileset name="MacOS Old Jalview Uninstaller" id="2105" customizedId="" />
</filesets>
<roots>
<root id="735" fileset="734" location="" />
<root id="881" fileset="880" location="" />
<root id="883" fileset="882" location="" />
+ <root id="1874" fileset="1873" location="" />
+ <root id="2106" fileset="2105" location="" />
</roots>
<mountPoints>
<mountPoint id="454" root="" location="" mode="755" />
<mountPoint id="736" root="735" location="" mode="755" />
<mountPoint id="884" root="881" location="" mode="755" />
<mountPoint id="885" root="883" location="" mode="755" />
+ <mountPoint id="1875" root="1874" location="" mode="755" />
+ <mountPoint id="2107" root="2106" location="" mode="755" />
</mountPoints>
<entries>
<dirEntry mountPoint="454" file="../../getdown/files/$$JAVA_VERSION$$" overwriteMode="4" shared="false" fileMode="644" uninstallMode="2" overrideFileMode="false" overrideOverwriteMode="true" overrideUninstallMode="true" entryMode="direct" subDirectory="files" excludeSuffixes="" dirMode="755" overrideDirMode="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">
+ <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">
+ <exclude />
+ </dirEntry>
</entries>
<components>
<component name="jalview_getdown" id="1031" customizedId="" displayDescription="false" hideHelpButton="false" selected="true" changeable="true" downloadable="false" hidden="false">
</include>
<dependencies />
</component>
+ <component name="jalview" id="1881" customizedId="" displayDescription="false" hideHelpButton="false" selected="true" changeable="true" downloadable="false" hidden="false">
+ <description />
+ <include all="false">
+ <entry location=".i4j_fileset_1873" fileType="regular" />
+ </include>
+ <dependencies />
+ </component>
+ <component name="macos_old_jalview_uninstaller" id="2110" customizedId="" displayDescription="false" hideHelpButton="false" selected="true" changeable="true" downloadable="false" hidden="false">
+ <description />
+ <include all="false">
+ <entry location=".i4j_fileset_2105" fileType="regular" />
+ </include>
+ <dependencies />
+ </component>
</components>
</files>
<launchers>
<file path="../../resources/images/JalviewLogo_Huge.png" />
</iconImageFiles>
</launcher>
+ <launcher name="Jalview package" id="1876" customizedId="" external="false" excludeFromMenu="false" unixMode="755" unixAutoStart="true" menuName="${compiler:sys.shortName} $$VERSION$$" icnsFile="" customMacBundleIdentifier="false" macBundleIdentifier="" swtApp="false" fileset="1873" macBundleBinary="JavaApplicationStub" addMacEntitlements="false" macEntitlementsFile="" useCustomMacosExecutableName="false" customMacosExecutableName="" useJavaMinVersionOverride="false" javaMinVersionOverride="" useJavaMaxVersionOverride="false" javaMaxVersionOverride="" checkUpdater="false" updateExecutionMode="unattendedProgress" unattendedUpdateTitle="${i18n:updater.WindowTitle("${compiler:sys.fullName}")}">
+ <executable name="${compiler:sys.shortName}" type="1" iconSet="true" iconFile="" executableDir="" redirectStderr="false" stderrFile="error.log" stderrMode="overwrite" redirectStdout="false" stdoutFile="output.log" stdoutMode="overwrite" failOnStderrOutput="false" executableMode="1" changeWorkingDirectory="false" workingDirectory="." singleInstance="true" serviceStartType="2" serviceDependencies="" serviceDescription="" jreLocation="" executionLevel="asInvoker" checkConsoleParameter="false" globalSingleInstance="false" singleInstanceActivate="true" dpiAware="java9+">
+ <versionInfo include="false" fileVersion="" fileDescription="" legalCopyright="" internalName="" productName="" />
+ </executable>
+ <splashScreen show="false" width="0" height="0" bitmapFile="" textOverlay="false">
+ <text>
+ <statusLine x="20" y="20" text="" fontSize="8" fontColor="0,0,0" bold="false" />
+ <versionLine x="20" y="40" text="version ${compiler:sys.version}" fontSize="8" fontColor="0,0,0" bold="false" />
+ </text>
+ </splashScreen>
+ <java mainClass="jalview.bin.Launcher" mainMode="1" vmParameters="" arguments="" allowVMPassthroughParameters="true" preferredVM="" bundleRuntime="true">
+ <classPath>
+ <scanDirectory location="dist" failOnError="false" />
+ </classPath>
+ <modulePath />
+ <nativeLibraryDirectories />
+ <vmOptions />
+ </java>
+ <includedFiles />
+ <unextractableFiles />
+ <vmOptionsFile mode="template" overwriteMode="0" fileMode="644">
+ <content />
+ </vmOptionsFile>
+ <customScript mode="1" file="">
+ <content />
+ </customScript>
+ <infoPlist mode="1" file="">
+ <content />
+ </infoPlist>
+ <iconImageFiles>
+ <file path="../../resources/images/JalviewLogo_Huge.png" />
+ </iconImageFiles>
+ </launcher>
</launchers>
<installerGui installerType="1" addOnAppId="" suggestPreviousLocations="true" autoUpdateDescriptorUrl="https://www.jalview.org/install4j/updates.xml" useAutoUpdateBaseUrl="false" autoUpdateBaseUrl="">
<staticMembers script="" />
<preActivation />
<postActivation />
<actions>
+ <action name="" id="2012" customizedId="" beanClass="com.install4j.runtime.beans.actions.desktop.CreateStartMenuEntryAction" enabled="true" commentSet="false" comment="" actionElevationType="elevated" rollbackBarrier="false" rollbackBarrierExitCode="0" multiExec="false" failureStrategy="1" errorMessage="">
+ <serializedBean>
+ <java class="java.beans.XMLDecoder">
+ <object class="com.install4j.runtime.beans.actions.desktop.CreateStartMenuEntryAction">
+ <void property="allUsers">
+ <boolean>false</boolean>
+ </void>
+ <void property="entryName">
+ <string>${compiler:sys.shortName}</string>
+ </void>
+ <void property="file">
+ <object class="java.io.File">
+ <string>${compiler:sys.shortName}</string>
+ </object>
+ </void>
+ <void property="icon">
+ <object class="com.install4j.api.beans.ExternalFile">
+ <string>../../resources/images/jalview_logos.ico</string>
+ </object>
+ </void>
+ <void property="unixIconFile">
+ <object class="com.install4j.api.beans.ExternalFile">
+ <string>../../resources/images/JalviewLogo_Huge.png</string>
+ </object>
+ </void>
+ </object>
+ </java>
+ </serializedBean>
+ <condition>!context.getBooleanVariable("sys.programGroupDisabled")</condition>
+ </action>
<action name="" id="573" customizedId="" beanClass="com.install4j.runtime.beans.actions.desktop.CreateDesktopLinkAction" enabled="true" commentSet="false" comment="" actionElevationType="elevated" rollbackBarrier="false" rollbackBarrierExitCode="0" multiExec="false" failureStrategy="1" errorMessage="Could not make desktop link">
<serializedBean>
<java class="java.beans.XMLDecoder">
</styles>
</installerGui>
<mediaSets>
- <linuxDeb name="Linux Deb Archive" id="153" customizedId="" mediaFileName="" installDir="/opt/${compiler:sys.shortName}" overridePrincipalLanguage="false" jreBitType="all" runPostProcessor="false" postProcessor="" failOnPostProcessorError="false" useLegacyMediaFileIds="false" legacyMediaFileIds="" downloadURL="" includeAllDownloadableComponents="true" includedJRE="" manualJREEntry="false" overwriteNeverAsConfigFiles="false" dependencies="" bzip="true" description="Jalview Desktop" maintainerEmail="help@jalview.org" architectureSet="false" architecture="">
+ <linuxDeb name="Jalview .deb Package" id="153" customizedId="" mediaFileName="jalview-$$VERSION$$" installDir="/opt/${compiler:sys.shortName}" overridePrincipalLanguage="false" jreBitType="all" runPostProcessor="false" postProcessor="" failOnPostProcessorError="false" useLegacyMediaFileIds="false" legacyMediaFileIds="" downloadURL="" includeAllDownloadableComponents="true" includedJRE="" manualJREEntry="false" overwriteNeverAsConfigFiles="false" dependencies="openjdk-8-jre" bzip="true" description="Jalview Desktop" maintainerEmail="help@jalview.org" architectureSet="false" architecture="">
<excludedComponents>
+ <component id="1031" />
<component id="1155" />
<component id="1156" />
<component id="1276" />
+ <component id="2110" />
</excludedComponents>
<includedDownloadableComponents />
<excludedLaunchers>
+ <launcher id="737" />
<launcher id="1402" />
</excludedLaunchers>
<excludedBeans />
<overriddenPrincipalLanguage id="en" customLocalizationFile="" />
<exclude>
<entry location=".i4j_fileset_" fileType="regular" />
+ <entry location=".i4j_fileset_734" fileType="regular" />
<entry location=".i4j_fileset_880" fileType="regular" />
<entry location=".i4j_fileset_882" fileType="regular" />
</exclude>
<content />
</postUninstallScript>
</linuxDeb>
- <linuxRPM name="Linux RPM" id="570" customizedId="" mediaFileName="" installDir="/opt/${compiler:sys.shortName}" overridePrincipalLanguage="false" jreBitType="all" runPostProcessor="false" postProcessor="" failOnPostProcessorError="false" useLegacyMediaFileIds="false" legacyMediaFileIds="" downloadURL="" includeAllDownloadableComponents="true" includedJRE="" manualJREEntry="false" overwriteNeverAsConfigFiles="false" dependencies="" os="linux" arch="i386">
+ <linuxRPM name="Jalview RPM Package" id="570" customizedId="" mediaFileName="jalview-$$VERSION$$" installDir="/opt/${compiler:sys.shortName}" overridePrincipalLanguage="false" jreBitType="all" runPostProcessor="false" postProcessor="" failOnPostProcessorError="false" useLegacyMediaFileIds="false" legacyMediaFileIds="" downloadURL="" includeAllDownloadableComponents="true" includedJRE="" manualJREEntry="false" overwriteNeverAsConfigFiles="false" dependencies="java-1.8.0-openjdk" os="linux" arch="noarch">
<excludedComponents>
+ <component id="1031" />
<component id="1155" />
<component id="1156" />
<component id="1276" />
+ <component id="2110" />
</excludedComponents>
<includedDownloadableComponents />
<excludedLaunchers>
+ <launcher id="737" />
<launcher id="1402" />
</excludedLaunchers>
<excludedBeans />
<overriddenPrincipalLanguage id="en" customLocalizationFile="" />
<exclude>
<entry location=".i4j_fileset_" fileType="regular" />
+ <entry location=".i4j_fileset_734" fileType="regular" />
<entry location=".i4j_fileset_880" fileType="regular" />
<entry location=".i4j_fileset_882" fileType="regular" />
</exclude>
<content />
</postUninstallScript>
</linuxRPM>
- <windows name="Offline Windows" id="743" customizedId="" mediaFileName="${compiler:sys.shortName}-OFFLINE_${compiler:sys.platform}_${compiler:sys.version}-j$$JAVA_INTEGER_VERSION$$" installDir="${compiler:sys.shortName}" overridePrincipalLanguage="false" jreBitType="64" runPostProcessor="true" postProcessor="${compiler:JSIGN_SH} $EXECUTABLE" failOnPostProcessorError="false" useLegacyMediaFileIds="false" legacyMediaFileIds="" downloadURL="" includeAllDownloadableComponents="false" includedJRE="$$WINDOWS_JAVA_VM_TGZ$$" manualJREEntry="true" bundleType="1" jreURL="" jreShared="false" directDownload="false" installOnlyIfNecessary="false" customInstallBaseDir="~/AppData/Local" contentFilesType="1" verifyIntegrity="true">
+ <windows name="Offline Windows x64 Installer" id="743" customizedId="" mediaFileName="${compiler:sys.shortName}-OFFLINE_${compiler:sys.platform}_${compiler:sys.version}-j$$JAVA_INTEGER_VERSION$$" installDir="${compiler:sys.shortName}" overridePrincipalLanguage="false" jreBitType="64" runPostProcessor="true" postProcessor="${compiler:JSIGN_SH} $EXECUTABLE" failOnPostProcessorError="false" useLegacyMediaFileIds="false" legacyMediaFileIds="" downloadURL="" includeAllDownloadableComponents="false" includedJRE="$$WINDOWS_JAVA_VM_TGZ$$" manualJREEntry="true" bundleType="1" jreURL="" jreShared="false" directDownload="false" installOnlyIfNecessary="false" customInstallBaseDir="~/AppData/Local" contentFilesType="1" verifyIntegrity="true">
<excludedComponents>
<component id="1155" />
<component id="1156" />
<component id="1276" />
+ <component id="1881" />
+ <component id="2110" />
</excludedComponents>
<includedDownloadableComponents />
<excludedLaunchers>
<exclude>
<entry location=".i4j_fileset_" fileType="regular" />
<entry location=".i4j_fileset_880" fileType="regular" />
+ <entry location=".i4j_fileset_882" fileType="regular" />
+ <entry location=".i4j_fileset_1873" fileType="regular" />
+ </exclude>
+ <variables />
+ <autoUpdate useMinUpdatableVersion="false" minUpdatableVersion="" useMaxUpdatableVersion="false" maxUpdatableVersion="">
+ <commentFiles />
+ <customAttributes />
+ </autoUpdate>
+ </windows>
+ <windows name="Network Windows x64 Installer" id="1862" customizedId="" mediaFileName="${compiler:sys.shortName}-NETWORK_${compiler:sys.platform}_${compiler:sys.version}-j$$JAVA_INTEGER_VERSION$$" installDir="${compiler:sys.shortName}" overridePrincipalLanguage="false" jreBitType="64" runPostProcessor="true" postProcessor="${compiler:JSIGN_SH} $EXECUTABLE" failOnPostProcessorError="false" useLegacyMediaFileIds="false" legacyMediaFileIds="" downloadURL="" includeAllDownloadableComponents="false" includedJRE="$$WINDOWS_JAVA_VM_TGZ$$" manualJREEntry="true" bundleType="1" jreURL="" jreShared="false" directDownload="false" installOnlyIfNecessary="false" customInstallBaseDir="~/AppData/Local" contentFilesType="1" verifyIntegrity="true">
+ <excludedComponents>
+ <component id="1031" />
+ <component id="1155" />
+ <component id="1156" />
+ <component id="1881" />
+ <component id="2110" />
+ </excludedComponents>
+ <includedDownloadableComponents />
+ <excludedLaunchers />
+ <excludedBeans />
+ <overriddenPrincipalLanguage id="en" customLocalizationFile="" />
+ <exclude>
+ <entry location=".i4j_fileset_734" fileType="regular" />
+ <entry location=".i4j_fileset_880" fileType="regular" />
+ <entry location=".i4j_fileset_1873" fileType="regular" />
</exclude>
<variables />
<autoUpdate useMinUpdatableVersion="false" minUpdatableVersion="" useMaxUpdatableVersion="false" maxUpdatableVersion="">
<customAttributes />
</autoUpdate>
</windows>
- <macosArchive name="Offline macOS Single Bundle Archive" id="878" customizedId="" mediaFileName="${compiler:sys.shortName}-OFFLINE_${compiler:sys.platform}-app_${compiler:sys.version}-j$$JAVA_INTEGER_VERSION$$" installDir="${compiler:sys.shortName}" overridePrincipalLanguage="false" jreBitType="all" runPostProcessor="false" postProcessor="" failOnPostProcessorError="false" useLegacyMediaFileIds="false" legacyMediaFileIds="" downloadURL="" includeAllDownloadableComponents="true" includedJRE="" manualJREEntry="false" archiveType="dmg" volumeName="${compiler:sys.shortName} Installer" launcherId="737">
+ <macosArchive name="Offline macOS Disk Image" id="878" customizedId="" mediaFileName="${compiler:sys.shortName}-OFFLINE_${compiler:sys.platform}-app_${compiler:sys.version}-j$$JAVA_INTEGER_VERSION$$" installDir="${compiler:sys.shortName}" overridePrincipalLanguage="false" jreBitType="all" runPostProcessor="false" postProcessor="" failOnPostProcessorError="false" useLegacyMediaFileIds="false" legacyMediaFileIds="" downloadURL="" includeAllDownloadableComponents="true" includedJRE="" manualJREEntry="false" archiveType="dmg" volumeName="${compiler:sys.shortName} Installer" launcherId="737">
<excludedComponents>
<component id="1156" />
<component id="1276" />
+ <component id="1881" />
</excludedComponents>
<includedDownloadableComponents />
<excludedBeans />
<exclude>
<entry location=".i4j_fileset_" fileType="regular" />
<entry location=".i4j_fileset_882" fileType="regular" />
+ <entry location=".i4j_fileset_1873" fileType="regular" />
</exclude>
<variables />
<autoUpdate useMinUpdatableVersion="false" minUpdatableVersion="" useMaxUpdatableVersion="false" maxUpdatableVersion="">
<symlink name="Jalview.app/Contents/Resources/app/${compiler:JRE_DIR}/Contents/MacOS/libjli.dylib" target="../Home/lib/jli/libjli.dylib" />
<file name="Jalview.app/Contents/Resources/Jalview-File.icns" file="./Jalview-File.icns" />
<file name="Jalview.app/Contents/Resources/Jalview-Version-Locator.icns" file="Jalview-Version-Locator.icns" />
+ <symlink name="Uninstall Old Jalview (optional).app" target="Jalview.app/Contents/Resources/app/Uninstall Old Jalview.app" />
</topLevelFiles>
</macosArchive>
- <macosArchive name="Network macOS Single Bundle Archive" id="1274" customizedId="" mediaFileName="${compiler:sys.shortName}-NETWORK_${compiler:sys.platform}-app_${compiler:sys.version}-j$$JAVA_INTEGER_VERSION$$" installDir="${compiler:sys.shortName}" overridePrincipalLanguage="false" jreBitType="all" runPostProcessor="false" postProcessor="" failOnPostProcessorError="false" useLegacyMediaFileIds="false" legacyMediaFileIds="" downloadURL="" includeAllDownloadableComponents="true" includedJRE="" manualJREEntry="false" archiveType="dmg" volumeName="${compiler:sys.shortName} Installer" launcherId="1402">
+ <macosArchive name="Network macOS Disk Image" id="1274" customizedId="" mediaFileName="${compiler:sys.shortName}-NETWORK_${compiler:sys.platform}-app_${compiler:sys.version}-j$$JAVA_INTEGER_VERSION$$" installDir="${compiler:sys.shortName}" overridePrincipalLanguage="false" jreBitType="all" runPostProcessor="false" postProcessor="" failOnPostProcessorError="false" useLegacyMediaFileIds="false" legacyMediaFileIds="" downloadURL="" includeAllDownloadableComponents="true" includedJRE="" manualJREEntry="false" archiveType="dmg" volumeName="${compiler:sys.shortName} Installer" launcherId="1402">
<excludedComponents>
<component id="1031" />
<component id="1156" />
+ <component id="1881" />
</excludedComponents>
<includedDownloadableComponents />
<excludedBeans />
<exclude>
<entry location=".i4j_fileset_734" fileType="regular" />
<entry location=".i4j_fileset_882" fileType="regular" />
+ <entry location=".i4j_fileset_1873" fileType="regular" />
</exclude>
<variables />
<autoUpdate useMinUpdatableVersion="false" minUpdatableVersion="" useMaxUpdatableVersion="false" maxUpdatableVersion="">
<symlink name="Jalview.app/Contents/Resources/app/${compiler:JRE_DIR}/Contents/MacOS/libjli.dylib" target="../Home/lib/jli/libjli.dylib" />
<file name="Jalview.app/Contents/Resources/Jalview-Version-Locator.icns" file="Jalview-Version-Locator.icns" />
<file name="Jalview.app/Contents/Resources/Jalview-File.icns" file="Jalview-File.icns" />
+ <symlink name="Uninstall Old Jalview (optional).app" target="Jalview.app/Contents/Resources/app/Uninstall Old Jalview.app" />
</topLevelFiles>
</macosArchive>
- <unixInstaller name="Unix Installer" id="1595" customizedId="" mediaFileName="${compiler:sys.shortName}-OFFLINE_${compiler:sys.platform}_installer_${compiler:sys.version}-j$$JAVA_INTEGER_VERSION$$" installDir="${compiler:sys.shortName}" overridePrincipalLanguage="false" jreBitType="all" runPostProcessor="false" postProcessor="" failOnPostProcessorError="false" useLegacyMediaFileIds="false" legacyMediaFileIds="" downloadURL="" includeAllDownloadableComponents="false" includedJRE="" manualJREEntry="false" bundleType="1" jreURL="" jreShared="false" directDownload="false" installOnlyIfNecessary="false" customInstallBaseDir="" contentFilesType="1">
- <excludedComponents />
+ <unixInstaller name="Offline Unix Shell Installer" id="1595" customizedId="" mediaFileName="${compiler:sys.shortName}-OFFLINE_${compiler:sys.platform}_installer_${compiler:sys.version}-j$$JAVA_INTEGER_VERSION$$" installDir="${compiler:sys.shortName}" overridePrincipalLanguage="false" jreBitType="all" runPostProcessor="false" postProcessor="" failOnPostProcessorError="false" useLegacyMediaFileIds="false" legacyMediaFileIds="" downloadURL="" includeAllDownloadableComponents="false" includedJRE="" manualJREEntry="false" bundleType="1" jreURL="" jreShared="false" directDownload="false" installOnlyIfNecessary="false" customInstallBaseDir="~/opt/" contentFilesType="1">
+ <excludedComponents>
+ <component id="1155" />
+ <component id="1156" />
+ <component id="1276" />
+ <component id="1881" />
+ <component id="2110" />
+ </excludedComponents>
<includedDownloadableComponents />
<excludedLaunchers>
<launcher id="1402" />
<excludedBeans />
<overriddenPrincipalLanguage id="en" customLocalizationFile="" />
<exclude>
- <entry location=".i4j_fileset_734" fileType="regular" />
+ <entry location=".i4j_fileset_" fileType="regular" />
<entry location=".i4j_fileset_880" fileType="regular" />
<entry location=".i4j_fileset_882" fileType="regular" />
+ <entry location=".i4j_fileset_1873" fileType="regular" />
</exclude>
<variables />
<autoUpdate useMinUpdatableVersion="false" minUpdatableVersion="" useMaxUpdatableVersion="false" maxUpdatableVersion="">
<content />
</installerScript>
</unixInstaller>
- <unixArchive name="Unix Archive" id="1596" customizedId="" mediaFileName="${compiler:sys.shortName}-OFFLINE_${compiler:sys.platform}_archive_${compiler:sys.version}-j$$JAVA_INTEGER_VERSION$$" installDir="${compiler:sys.shortName}" overridePrincipalLanguage="false" jreBitType="all" runPostProcessor="false" postProcessor="" failOnPostProcessorError="false" useLegacyMediaFileIds="false" legacyMediaFileIds="" downloadURL="" includeAllDownloadableComponents="true" includedJRE="" manualJREEntry="false">
+ <unixInstaller name="Network Unix Shell Installer" id="1867" customizedId="" mediaFileName="${compiler:sys.shortName}-NETWORK_${compiler:sys.platform}_installer_${compiler:sys.version}-j$$JAVA_INTEGER_VERSION$$" installDir="${compiler:sys.shortName}" overridePrincipalLanguage="false" jreBitType="all" runPostProcessor="false" postProcessor="" failOnPostProcessorError="false" useLegacyMediaFileIds="false" legacyMediaFileIds="" downloadURL="" includeAllDownloadableComponents="false" includedJRE="" manualJREEntry="false" bundleType="1" jreURL="" jreShared="false" directDownload="false" installOnlyIfNecessary="false" customInstallBaseDir="~/opt/" contentFilesType="1">
<excludedComponents>
<component id="1031" />
<component id="1155" />
<component id="1156" />
+ <component id="1881" />
+ <component id="2110" />
+ </excludedComponents>
+ <includedDownloadableComponents />
+ <excludedLaunchers />
+ <excludedBeans />
+ <overriddenPrincipalLanguage id="en" customLocalizationFile="" />
+ <exclude>
+ <entry location=".i4j_fileset_734" fileType="regular" />
+ <entry location=".i4j_fileset_880" fileType="regular" />
+ <entry location=".i4j_fileset_882" fileType="regular" />
+ <entry location=".i4j_fileset_1873" fileType="regular" />
+ </exclude>
+ <variables />
+ <autoUpdate useMinUpdatableVersion="false" minUpdatableVersion="" useMaxUpdatableVersion="false" maxUpdatableVersion="">
+ <commentFiles />
+ <customAttributes />
+ </autoUpdate>
+ <installerScript mode="1" file="">
+ <content />
+ </installerScript>
+ </unixInstaller>
+ <unixArchive name="Offline Unix .tar.gz Archive" id="1596" customizedId="" mediaFileName="${compiler:sys.shortName}-OFFLINE_${compiler:sys.platform}_archive_${compiler:sys.version}-j$$JAVA_INTEGER_VERSION$$" installDir="${compiler:sys.shortName}" overridePrincipalLanguage="false" jreBitType="all" runPostProcessor="false" postProcessor="" failOnPostProcessorError="false" useLegacyMediaFileIds="false" legacyMediaFileIds="" downloadURL="" includeAllDownloadableComponents="true" includedJRE="" manualJREEntry="false">
+ <excludedComponents>
+ <component id="1155" />
+ <component id="1156" />
+ <component id="1276" />
+ <component id="1881" />
+ <component id="2110" />
</excludedComponents>
<includedDownloadableComponents />
<excludedLaunchers>
</excludedLaunchers>
<excludedBeans />
<overriddenPrincipalLanguage id="en" customLocalizationFile="" />
- <exclude />
+ <exclude>
+ <entry location=".i4j_fileset_" fileType="regular" />
+ <entry location=".i4j_fileset_880" fileType="regular" />
+ <entry location=".i4j_fileset_882" fileType="regular" />
+ <entry location=".i4j_fileset_1873" fileType="regular" />
+ </exclude>
<variables />
<autoUpdate useMinUpdatableVersion="false" minUpdatableVersion="" useMaxUpdatableVersion="false" maxUpdatableVersion="">
<commentFiles />
<customAttributes />
</autoUpdate>
</unixArchive>
- <windows name="Network Windows" id="1862" customizedId="" mediaFileName="${compiler:sys.shortName}-NETWORK_${compiler:sys.platform}_${compiler:sys.version}-j$$JAVA_INTEGER_VERSION$$" installDir="${compiler:sys.shortName}" overridePrincipalLanguage="false" jreBitType="64" runPostProcessor="true" postProcessor="${compiler:JSIGN_SH} $EXECUTABLE" failOnPostProcessorError="false" useLegacyMediaFileIds="false" legacyMediaFileIds="" downloadURL="" includeAllDownloadableComponents="false" includedJRE="$$WINDOWS_JAVA_VM_TGZ$$" manualJREEntry="true" bundleType="1" jreURL="" jreShared="false" directDownload="false" installOnlyIfNecessary="false" customInstallBaseDir="~/AppData/Local" contentFilesType="1" verifyIntegrity="true">
+ <unixArchive name="Network Unix .tar.gz Archive" id="1871" customizedId="" mediaFileName="${compiler:sys.shortName}-NETWORK_${compiler:sys.platform}_archive_${compiler:sys.version}-j$$JAVA_INTEGER_VERSION$$" installDir="${compiler:sys.shortName}" overridePrincipalLanguage="false" jreBitType="all" runPostProcessor="false" postProcessor="" failOnPostProcessorError="false" useLegacyMediaFileIds="false" legacyMediaFileIds="" downloadURL="" includeAllDownloadableComponents="true" includedJRE="" manualJREEntry="false">
<excludedComponents>
<component id="1031" />
<component id="1155" />
<component id="1156" />
+ <component id="1881" />
+ <component id="2110" />
</excludedComponents>
<includedDownloadableComponents />
<excludedLaunchers />
<exclude>
<entry location=".i4j_fileset_734" fileType="regular" />
<entry location=".i4j_fileset_880" fileType="regular" />
+ <entry location=".i4j_fileset_882" fileType="regular" />
+ <entry location=".i4j_fileset_1873" fileType="regular" />
</exclude>
<variables />
<autoUpdate useMinUpdatableVersion="false" minUpdatableVersion="" useMaxUpdatableVersion="false" maxUpdatableVersion="">
<commentFiles />
<customAttributes />
</autoUpdate>
- </windows>
+ </unixArchive>
</mediaSets>
<buildIds buildAll="true">
<mediaSet refId="153" />
<mediaSet refId="1595" />
<mediaSet refId="1596" />
<mediaSet refId="1862" />
+ <mediaSet refId="1867" />
+ <mediaSet refId="1871" />
</buildIds>
<buildOptions verbose="false" faster="false" disableSigning="false" disableJreBundling="false" debug="false" />
</install4j>
--- /dev/null
+#!/usr/bin/env bash
+
+find Uninstall\ Old\ Jalview.app | perl -p -e 'chomp;$_=qq( <file name=").$_.qq(" file="./).$_.qq(" />\n);' > uninstall_old_jalview_files.xml
+
+# makes the file used to replace the line
+# <file name="UNINSTALL_OLD_JALVIEW_APP_REPLACED_IN_GRADLE" file="./Uninstall Old Jalview.app" />
+# (replacement happens in gradle)
--- /dev/null
+ <file name="Uninstall Old Jalview.app" file="./Uninstall Old Jalview.app" />
+ <file name="Uninstall Old Jalview.app/Contents" file="./Uninstall Old Jalview.app/Contents" />
+ <file name="Uninstall Old Jalview.app/Contents/MacOS" file="./Uninstall Old Jalview.app/Contents/MacOS" />
+ <file name="Uninstall Old Jalview.app/Contents/MacOS/applet" file="./Uninstall Old Jalview.app/Contents/MacOS/applet" />
+ <file name="Uninstall Old Jalview.app/Contents/Resources" file="./Uninstall Old Jalview.app/Contents/Resources" />
+ <file name="Uninstall Old Jalview.app/Contents/Resources/applet.rsrc" file="./Uninstall Old Jalview.app/Contents/Resources/applet.rsrc" />
+ <file name="Uninstall Old Jalview.app/Contents/Resources/description.rtfd" file="./Uninstall Old Jalview.app/Contents/Resources/description.rtfd" />
+ <file name="Uninstall Old Jalview.app/Contents/Resources/description.rtfd/TXT.rtf" file="./Uninstall Old Jalview.app/Contents/Resources/description.rtfd/TXT.rtf" />
+ <file name="Uninstall Old Jalview.app/Contents/Resources/Scripts" file="./Uninstall Old Jalview.app/Contents/Resources/Scripts" />
+ <file name="Uninstall Old Jalview.app/Contents/Resources/Scripts/main.scpt" file="./Uninstall Old Jalview.app/Contents/Resources/Scripts/main.scpt" />
+ <file name="Uninstall Old Jalview.app/Contents/Resources/applet.icns" file="./Uninstall Old Jalview.app/Contents/Resources/applet.icns" />
+ <file name="Uninstall Old Jalview.app/Contents/Info.plist" file="./Uninstall Old Jalview.app/Contents/Info.plist" />
+ <file name="Uninstall Old Jalview.app/Contents/PkgInfo" file="./Uninstall Old Jalview.app/Contents/PkgInfo" />
git://source.jalview.org / jalview.git / commitdiff