*.swp
/bin
/doc/building.html
+/.j2s
+/template.html
+
+++ /dev/null
-j2s.compiler.status=enable
-
-#a semicolon-separated list of package-level file paths to be excluded
-j2s.excluded.paths=test;testng;util
-
-#a semicolon-separated list of package (foo.) or class (foo.bar) replacements to be made
-j2s.class.replacements=org.apache.log4j.->jalview.javascript.log4j.
-
-#output file name for logging methods declared - delete the file to regenerate a listing
-#j2s.log.methods.declared=swingjs/methodsDeclared.csv
-
-#output file name for logging methods called - delete the file to regenerate a listing
-#j2s.log.methods.called=swingjs/methodsCalled.csv
-
-#if set, every instance of methods called will be logged
-#otherwise, only the first call to a method will be logged
-#output will be comma-separated: called method,caller class
-#j2s.log.all.calls=true
-
-
--- /dev/null
+Last updated: 2019-10-09
+
+# TRANSPILING USING ECLIPSE AS AN EXTERNAL CLI TOOL:
+
+Download and install a clean eclipse-jee-2019-06 (or eclipse-jee-2019-09)
+
+In gradle.properties edit `jalviewjs_eclipse_root` to point to the root dir.
+If you're on a mac, DO NOT include the `Eclipse.app` folder in the path (use the path up to this point, but not the .app folder itself).
+You can use a '~' as the first character which will get replaced with `System.getProperty("user.home")`.
+
+Note that the gradle tasks (`jalviewjsEclipseCopyDropins`) will take care of copying `net.sf.j2s.core.jar` and the `com.seeq.eclipse.importprojects.jar` into the `dropins` and `plugins` dir (on either unix or mac -- not tested on windows yet).
+
+Note that the logs from the transpile go into `build/jalviewjs/` as `j2s-transpile.out` and `j2s-transpile.err`
+
+gradle tasks possibly of interest to you:
+
+
+
+```
+gradle jalviewjs # (should build the build/jalviewjs/site dir)
+
+gradle jalviewjsSiteTar # will produce build/distribution/site.tar.gz
+
+gradle jalviewjsTranspile # should run a new eclipse compile+transpile
+
+gradle jalviewjsServerStart # will run a localhost http server to allow you to test the site in a browser. Just use the URL given in the output. To stop the server you have to do gradle --stop or you can just leave it running until the gradle daemon dies.
+```
+
+If it's working okay, you just need to to
+
+```
+gradle jalviewjs
+gradle jalviewjsServer
+```
+
+and go to the localhost URL in the output of the jalviewjsServer task in your web browser (on a mac, just right clicking on the URL in terminal window gives an "Open URL" option which is nice and easy).
+
+
+++ /dev/null
-<?xml version="1.0"?>
-<!--
- * just a crude zip up of non-Jalview classes for development purposes -BH 2018
- *
- * external JAR class treatment for JavaScript: see src2/README_SWINGJS.txt
- *
- -->
-
-<project name="jalviewX" default="zipall" basedir="."
- xmlns:if="ant:if"
- xmlns:unless="ant:unless">
-
- <!-- inputs directories -->
- <property name="resource.dir" value="resources" />
- <property name="swingjs.dir" value="swingjs"/>
- <!-- output directories -->
- <property name="site.dir" value="site"/>
- <property name="j2s.dir" value="${site.dir}/swingjs/j2s"/>
- <property name="libjs.dir" value="libjs"/>
-
- <target name="zipall" depends="zipvarna,zipmig,zipintervalstore">
-
-
- </target>
-
- <target name="zipvarna">
- <!-- VARNA -->
- <property name="varna.zip" value="${libjs.dir}/VARNA-site.zip" />
- <echo> Zipping up ${varna.zip} </echo>
- <zip destfile="${varna.zip}" basedir="${site.dir}" includes="fr_*.html,swingjs/j2s/fr/**" />
- </target>
-
- <target name="zipmig">
- <!-- net.miginfo.com MiGLayout -->
- <property name="mig.zip" value="${libjs.dir}/MiGLayout-site.zip" />
- <echo> Zipping up ${mig.zip} </echo>
- <zip destfile="${mig.zip}" basedir="${site.dir}" includes="swingjs/j2s/net/miginfocom/**" />
- </target>
-
- <target name="zipintervalstore">
- <!-- intervalstore.impl NCList implementation -->
- <property name="intervalstore.zip" value="${libjs.dir}/intervalstore-site.zip" />
- <echo> Zipping up ${intervalstore.zip} </echo>
- <zip destfile="${intervalstore.zip}" basedir="${site.dir}" includes="swingjs/j2s/intervalstore/**" />
- </target>
-
- <!-- already in SwingJS
- <target name="zipjson" already in SwingJS>
- <property name="json.zip" value="${libjs.dir}/json-site.zip" />
- <echo> Zipping up ${json.zip} </echo>
- <zip destfile="${json.zip}" basedir="${site.dir}" includes="swingjs/j2s/org/json/**" />
- </target>
- -->
-
- <!-- log4j minimal implementation is already in jalview/javascript
- and is mapped from org.apache.log4j by the following .j2s line:
-
- j2s.class.replacements=org.apache.log4j.->jalview.javascript.log4j.
-
- <target name="ziplog4j">
- <!- org.apache.log4j ->
- <property name="log4j.zip" value="${libjs.dir}/log4j-site.zip" />
- <echo> Zipping up ${log4j.zip} </echo>
- <zip destfile="${log4j.zip}" basedir="${site.dir}" includes="swingjs/j2s/org/apache/log4j/**" />
- </target>
- -->
-</project>
+++ /dev/null
-<?xml version="1.0"?>
-<!--
- BH 2018.08.12
-
- - requires tools/ant-contrib.jar
-
- - creates the site/ directory if it does not exist
- - unzip libjs/*.zip into site/swingjs/j2s
- - unzips swingjs/SwingJS-site.zip into site/
- - copies non-java resources from resources/ into site/swingjs/j2s
-
--->
-
-<project name="swingjs-project" default="tosite" basedir="."
- xmlns:if="ant:if"
- xmlns:unless="ant:unless">
-
- <target name="tosite">
-
- <!-- input directories -->
-
- <!-- location of ant-contrib.jar -->
- <property name="tools.dir" value = "tools" />
-
- <!-- SwingjS_site zip file (could be varied if versioning is needed) -->
- <property name="swingjs.zip" value="swingjs/SwingJS-site.zip" />
-
- <!-- location of third-party jar contents as precompiled zipped .js files to copy to site/ -->
- <property name="libjs.dir" value="libjs" />
-
- <!-- non-Java resources to copy to site/swingjs/j2s -->
- <property name="resource.dir" value="resources" />
-
- <!-- build_properties datastamp file to copy to site/swingjs/j2s -->
- <property name="build_properties" value="classes/.build_properties" />
-
- <!-- non-Java resources to copy to site/ -->
- <property name="site-resource.dir" value="site-resources" />
-
- <!-- output directories -->
-
- <property name="site.dir" value="site" />
- <property name="j2s.dir" value="${site.dir}/swingjs/j2s" />
-
- <!-- <for ...> construct needs ant-contrib.jar -->
- <taskdef resource="net/sf/antcontrib/antlib.xml">
- <classpath>
- <pathelement location="${tools.dir}/ant-contrib.jar" />
- </classpath>
- </taskdef>
-
- <!-- unzip all libjs zip files into site
-
- all zip files placed in libjs will be processed
-
- -->
-
- <for param="file.zip">
- <path>
- <fileset dir="${libjs.dir}" includes="*.zip"/>
- </path>
- <sequential>
- <unzip src="@{file.zip}" dest="${site.dir}" overwrite="true"/>
- </sequential>
- </for>
-
- <!-- unzip SwingJS-site.zip
-
- we do this separately, as we want it done last
-
- -->
-
- <unzip src="${swingjs.zip}" dest="${site.dir}/" overwrite="true"/>
-
- <!-- transfer resources -->
-
- <echo> Copying ${resource.dir} files into ${j2s.dir} </echo>
- <copy todir="${j2s.dir}">
- <fileset dir="${resource.dir}">
- <include name="**"/>
- </fileset>
- <fileset file="${build_properties}"/>
- </copy>
-
- <echo> Copying ${site-resource.dir} files into ${site.dir} </echo>
- <copy todir="${site.dir}">
- <fileset dir="${site-resource.dir}">
- <include name="**"/>
- </fileset>
- </copy>
-
-</target>
-
-
-</project>
import org.apache.tools.ant.filters.ReplaceTokens
-//import org.apache.tools.ant.filters.ReplaceRegexp
import org.gradle.internal.os.OperatingSystem
-import org.gradle.plugins.ide.eclipse.model.*
-
+import org.gradle.plugins.ide.eclipse.model.Output
+import org.gradle.plugins.ide.eclipse.model.Library
import groovy.transform.ExternalizeMethods
buildscript {
dependencies {
classpath 'org.openclover:clover:4.3.1'
- classpath 'org.apache.commons:commons-compress:1.18'
}
}
}
}
+dependencies {
+ compile 'org.apache.commons:commons-compress:1.18'
+}
+
mainClassName = launcherClass
def cloverInstrDir = file("$buildDir/$cloverSourcesInstrDir")
def classes = "$jalviewDir/$classesDir"
*/
gitHash = ""
gitBranch = ""
+
+ jalviewjsServer = ""
}
def JAVA_INTEGER_VERSION
runtimeClasspath = compileClasspath
}
+
clover {
java {
srcDirs = [ cloverInstrDir ]
compileClasspath += files(sourceSets.main.java.outputDir)
}
- compileClasspath += fileTree(dir: "$jalviewDir/$utilsDir", include: ["**/*.jar"])
compileClasspath += fileTree(dir: "$jalviewDir/$libDir", include: ["*.jar"])
+ compileClasspath += fileTree(dir: "$jalviewDir/$utilsDir/testnglibs", include: ["**/*.jar"])
+ compileClasspath += fileTree(dir: "$jalviewDir/$utilsDir/testlibs", include: ["**/*.jar"])
runtimeClasspath = compileClasspath
}
classpath {
//defaultOutputDir = sourceSets.main.java.outputDir
def removeThese = []
- configurations.each{ if (it.isCanBeResolved()) {
- removeThese += it
+ configurations.each{
+ if (it.isCanBeResolved()) {
+ removeThese += it
+ }
}
- }
- minusConfigurations += removeThese
- plusConfigurations = [ ]
- file {
-
- whenMerged { cp ->
- def removeTheseToo = []
- HashMap<String, Boolean> addedSrcPath = new HashMap<>();
- cp.entries.each { entry ->
- if (entry.kind == 'src') {
- if (addedSrcPath.getAt(entry.path) || !(entry.path == "src" || entry.path == "test")) {
- removeTheseToo += entry
- } else {
- addedSrcPath.putAt(entry.path, true)
+ minusConfigurations += removeThese
+ plusConfigurations = [ ]
+ file {
+
+ whenMerged { cp ->
+ def removeTheseToo = []
+ HashMap<String, Boolean> alreadyAddedSrcPath = new HashMap<>();
+ cp.entries.each { entry ->
+ if (entry.kind == 'src') {
+ if (alreadyAddedSrcPath.getAt(entry.path) || !(entry.path == "src" || entry.path == "test")) {
+ removeTheseToo += entry
+ } else {
+ alreadyAddedSrcPath.putAt(entry.path, true)
+ }
}
}
- }
- cp.entries.removeAll(removeTheseToo)
-
- print ("CP="+cp.inspect())
-
- cp.entries += new Output("bin/main")
- cp.entries += new Library(fileReference(helpParentDir))
- cp.entries += new Library(fileReference(resourceDir))
-
- HashMap<String, Boolean> addedLibPath = new HashMap<>();
+ cp.entries.removeAll(removeTheseToo)
- // changing from sourcesets.main.classpath to specific Java version lib
- //sourceSets.main.compileClasspath.each{
- fileTree("$jalviewDir/$libDistDir").include("**/*.jar").include("*.jar").each {
- //don't want to add outputDir as eclipse is using its own output dir in bin/main
- if (it.isDirectory() || ! it.exists()) {
- // don't add dirs to classpath
- return
+ if (file(eclipse_bin_dir+"/main").isDirectory()) {
+ cp.entries += new Output(eclipse_bin_dir+"/main")
}
- def itPath = it.toString()
- if (itPath.startsWith(jalviewDirAbsolutePath+"/")) {
- itPath = itPath.substring(jalviewDirAbsolutePath.length()+1)
+ if (file(helpParentDir).isDirectory()) {
+ cp.entries += new Library(fileReference(helpParentDir))
}
- if (addedLibPath.get(itPath)) {
- //println("Not adding duplicate entry "+itPath)
- } else {
- //println("Adding entry "+itPath)
- cp.entries += new Library(fileReference(itPath))
- addedLibPath.put(itPath, true)
+ if (file(resourceDir).isDirectory()) {
+ cp.entries += new Library(fileReference(resourceDir))
}
- }
- // changing from sourcesets.main.classpath to specific Java version lib
- //sourceSets.test.compileClasspath.each{
- fileTree(dir: "$jalviewDir/$utilsDir", include: ["**/*.jar"]).each {
- //if ((it.isDirectory() || ! it.exists()) && ! (it.equals(sourceSets.main.java.outputDir))) {
- //no longer want to add outputDir as eclipse is using its own output dir in bin/main
- if (it.isDirectory() || ! it.exists()) {
- // don't add dirs to classpath
- return false // groovy "break" in .each loop
- }
- def itPath = it.toString()
- if (itPath.startsWith(jalviewDirAbsolutePath+"/")) {
- itPath = itPath.substring(jalviewDirAbsolutePath.length()+1)
- }
- if (addedLibPath.get(itPath)) {
- // don't duplicate
- } else {
- def lib = new Library(fileReference(itPath))
- // this doesn't work... yet. Adding test=true attribute using withXml below
- //def attrs = new Node(null, 'attributes', ["test":"true"])
- //lib.appendNode(attrs) //
- cp.entries += lib
- addedLibPath.put(itPath, true)
+ HashMap<String, Boolean> alreadyAddedLibPath = new HashMap<>();
+
+ sourceSets.main.compileClasspath.findAll { it.name.endsWith(".jar") }.each {
+ //don't want to add outputDir as eclipse is using its own output dir in bin/main
+ if (it.isDirectory() || ! it.exists()) {
+ // don't add dirs to classpath
+ return
+ }
+ def itPath = it.toString()
+ if (itPath.startsWith(jalviewDirAbsolutePath+"/")) {
+ // make relative path
+ itPath = itPath.substring(jalviewDirAbsolutePath.length()+1)
+ }
+ if (alreadyAddedLibPath.get(itPath)) {
+ //println("Not adding duplicate entry "+itPath)
+ } else {
+ //println("Adding entry "+itPath)
+ cp.entries += new Library(fileReference(itPath))
+ alreadyAddedLibPath.put(itPath, true)
+ }
}
+
+ //fileTree(dir: "$jalviewDir/$utilsDir", include: ["test*/*.jar"]).each {
+ sourceSets.test.compileClasspath.findAll { it.name.endsWith(".jar") }.each {
+ //no longer want to add outputDir as eclipse is using its own output dir in bin/main
+ if (it.isDirectory() || ! it.exists()) {
+ // don't add dirs to classpath
+ return false // groovy "break" in .each closure
+ }
+ def itPath = it.toString()
+ if (itPath.startsWith(jalviewDirAbsolutePath+"/")) {
+ itPath = itPath.substring(jalviewDirAbsolutePath.length()+1)
+ }
+ if (alreadyAddedLibPath.get(itPath)) {
+ // don't duplicate
+ } else {
+ def lib = new Library(fileReference(itPath))
+ /* this doesn't work... yet. Adding test=true attribute using withXml below
+ def attrs = new Node(null, 'attributes')
+ attrs.appendNode('attribute', ["name":"test","value":"true"])
+ lib.appendNode(attrs)
+ /**/
+ cp.entries += lib
+ alreadyAddedLibPath.put(itPath, true)
+ }
}
- }
+
+ } // whenMerged
// withXml changes ignored by buildship, these add the "test=true" attribute
withXml {
}
}
} // withXML
+
+
} // file
containers 'org.eclipse.buildship.core.gradleclasspathcontainer'
+
} // classpath
jdt {
targetCompatibility = compile_target_compatibility
javaRuntimeName = eclipse_java_runtime_name
+ // add in jalview project specific properties/preferences into eclipse core preferences
file {
withProperties { props ->
def jalview_prefs = new Properties()
}
}
}
- }
- //synchronizationTasks eclipseClasspath
- //autoBuildTasks eclipseClasspath
+ } // jdt
+
}
task cloverInstr() {
inputs.dir("$classes/$helpDir")
outputs.dir("$helpOutputDir")
}
+
+def eclipseWorkspace
+task jalviewjsSetEclipseWorkspace {
+ def eclipseWsDir = jalviewjs_eclipse_workspace
+ eclipseWorkspace = file(eclipseWsDir)
+ if (!eclipseWorkspace.exists()) {
+ eclipseWorkspace = file("${buildDir}/../tmp/eclipse-workspace")
+ //eclipseWorkspace.deleteOnExit()
+ }
+ println("ECLIPSE WORKSPACE: "+eclipseWorkspace.getPath())
+}
+
+def jalviewjsBuildDir
+def jalviewjsSiteDir
+task jalviewjsSitePath {
+ if (jalviewjs_site_dir.startsWith("/")) {
+ jalviewjsSiteDir = jalviewjs_site_dir
+ } else {
+ def relativeBuildDir = file(jalviewDirAbsolutePath).toPath().relativize(buildDir.toPath())
+ jalviewjsBuildDir = "${relativeBuildDir}/jalviewjs"
+ jalviewjsSiteDir = jalviewjsBuildDir + "/" + jalviewjs_site_dir
+ }
+}
+
+
+
+task jalviewjsUnzipFiles {
+ dependsOn jalviewjsSitePath
+
+ def zipFiles = fileTree(dir: jalviewjs_utils_dir+"/"+jalviewjs_libjs_dir).include("*.zip")
+ zipFiles += jalviewjs_utils_dir+"/"+jalviewjs_swingjs_zip
+
+ doLast {
+ zipFiles.each { file_zip ->
+ copy {
+ from zipTree(file_zip)
+ into jalviewjsSiteDir
+ }
+ }
+ }
+
+ inputs.files zipFiles
+ outputs.dir jalviewjsSiteDir
+}
+
+def eclipseDropinsDir
+def eclipseBinary
+task jalviewjsEclipsePaths {
+ def eclipseRoot
+ eclipseRoot = jalviewjs_eclipse_root
+ if (eclipseRoot.startsWith("~")) {
+ eclipseRoot = System.getProperty("user.home") + eclipseRoot.substring(1)
+ }
+ if (OperatingSystem.current().isMacOsX()) {
+ eclipseRoot += "/Eclipse.app"
+ eclipseDropinsDir = eclipseRoot+"/Contents/Eclipse/dropins"
+ eclipseBinary = eclipseRoot+"/Contents/MacOS/eclipse"
+ } else if (OperatingSystem.current().isWindows()) { // check these paths!!
+ eclipseDropinsDir = eclipseRoot+"/dropins"
+ eclipseBinary = eclipseRoot+"/eclipse"
+ } else { // linux or unix
+ eclipseDropinsDir = eclipseRoot+"/dropins"
+ eclipseBinary = eclipseRoot+"/eclipse"
+ }
+}
+
+task jalviewjsEclipseCopyDropins {
+ dependsOn jalviewjsEclipsePaths
+ def inputFiles = fileTree(dir: jalviewjs_utils_dir+"/"+jalviewjs_eclipse_dropins_dir, include: "*.jar")
+ def outputDir = eclipseDropinsDir
+
+ inputs.files inputFiles
+ inputFiles.each { file ->
+ outputs.file(outputDir+"/"+file.name)
+ }
+
+ doLast {
+ def outputFiles = []
+ inputFiles.each { file ->
+ copy {
+ from file
+ into outputDir
+ }
+ }
+ }
+}
+
+task jalviewjsCreateJ2sSettings(type: WriteProperties) {
+ dependsOn jalviewjsSitePath
+ outputFile (jalviewDir+"/"+jalviewjs_j2s_settings)
+ def props = project.properties.sort { it.key }
+ def siteDirProperty = "j2s.site.directory"
+ def setSiteDir = false
+ props.each { prop, val ->
+ if (prop.startsWith("j2s.") && val != null) {
+ if (prop == siteDirProperty) {
+ if (!(val.startsWith("/") || val.startsWith("file://") )) {
+ val = jalviewjsSiteDir+"/"+val
+ }
+ setSiteDir = true
+ }
+ property(prop,val)
+ }
+ if (!setSiteDir) {
+ property(siteDirProperty,"${jalviewjsSiteDir}")
+ }
+ }
+ outputs.file(outputFile)
+}
+
+task jalviewjsEclipseSetup {
+ dependsOn jalviewjsEclipseCopyDropins
+ dependsOn jalviewjsSetEclipseWorkspace
+ dependsOn jalviewjsCreateJ2sSettings
+}
+
+task jalviewjsCopyResources (type: Copy) {
+ dependsOn jalviewjsSitePath
+ def inputFiles = fileTree(dir: jalviewjs_resource_dir)
+ def outputDir = jalviewjsSiteDir+"/"+jalviewjs_j2s_subdir
+
+ from inputFiles
+ into outputDir
+ def outputFiles = []
+ rename { filename ->
+ outputFiles += outputDir+"/"+filename
+ null
+ }
+ outputs.files outputFiles
+ inputs.files inputFiles
+}
+
+task jalviewjsCopySiteResources (type: Copy) {
+ dependsOn jalviewjsSitePath
+ def inputFiles = fileTree(dir: jalviewjs_utils_dir+"/"+jalviewjs_site_resource_dir)
+ def outputDir = jalviewjsSiteDir
+
+ from inputFiles
+ into outputDir
+ def outputFiles = []
+ rename { filename ->
+ outputFiles += outputDir+"/"+filename
+ null
+ }
+ outputs.files outputFiles
+ inputs.files inputFiles
+}
+
+task cleanJalviewjs {
+ //delete jalviewjsBuildDir
+ //delete jalviewDir+"/"+eclipse_bin_dir
+ //delete file(eclipseWorkspace.getAbsolutePath()+"/.metadata")
+ //delete jalviewDir+"/"+jalviewjs_j2s_settings
+}
+
+task jalviewjsProjectImport(type: Exec) {
+ // work out how to do this!
+ dependsOn eclipseProject
+ dependsOn eclipseClasspath
+ dependsOn eclipseJdt
+ dependsOn jalviewjsEclipsePaths
+ dependsOn jalviewjsEclipseSetup
+ executable(eclipseBinary)
+ args(["-nosplash", "--launcher.suppressErrors", "-application", "com.seeq.eclipse.importprojects.headlessimport", "-data", eclipseWorkspace.getPath(), "-import", jalviewDirAbsolutePath])
+
+ def projdir = eclipseWorkspace.getPath()+"/.metadata/.plugins/org.eclipse.core.resources/.projects/jalview/org.eclipse.jdt.core"
+ inputs.file(jalviewDir+"/.project")
+ outputs.dir(projdir)
+ outputs.upToDateWhen { file(projdir).exists() }
+}
+
+task jalviewjsTranspile(type: Exec) {
+ dependsOn jalviewjsEclipseSetup
+ dependsOn jalviewjsProjectImport
+ dependsOn jalviewjsEclipsePaths
+ executable(eclipseBinary)
+ args(["-nosplash", "--launcher.suppressErrors", "-application", "org.eclipse.jdt.apt.core.aptBuild", "-data", eclipseWorkspace, "-"+jalviewjs_eclipseBuildArg, eclipse_project_name ])
+
+ def stdout
+ def stderr
+ doFirst {
+ stdout = new ByteArrayOutputStream()
+ stderr = new ByteArrayOutputStream()
+
+ if (jalviewjs_j2s_to_console.equals("true")) {
+ standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
+ new org.apache.tools.ant.util.TeeOutputStream(
+ new FileOutputStream("${jalviewjsBuildDir}/${jalviewjs_j2s_stdout}"),
+ stdout),
+ standardOutput)
+ errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
+ new org.apache.tools.ant.util.TeeOutputStream(
+ new FileOutputStream("${jalviewjsBuildDir}/${jalviewjs_j2s_stderr}"),
+ stderr),
+ errorOutput)
+ } else {
+ standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
+ new FileOutputStream("${jalviewjsBuildDir}/${jalviewjs_j2s_stdout}"),
+ stdout)
+ errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
+ new FileOutputStream("${jalviewjsBuildDir}/${jalviewjs_j2s_stderr}"),
+ stderr)
+ }
+ }
+ doLast {
+ if (stdout.toString().contains("Error processing ")) {
+ // j2s did not complete transpile
+ throw new GradleException("Error during transpilation:\n${stderr}\nSee eclipse transpile log files '${jalviewjsBuildDir}/${jalviewjs_j2s_stdout}' and '${jalviewjsBuildDir}/${jalviewjs_j2s_stderr}'\n")
+ }
+ }
+
+ inputs.dir(sourceDir)
+ outputs.dir(eclipse_bin_dir+"/main")
+ outputs.files(
+ fileTree(
+ dir: jalviewjsSiteDir+"/"+jalviewjs_j2s_subdir,
+ includes: [ "**/*.js" ],
+ excludes: [
+ //jalviewjsSiteDir+"/"+jalviewjs_j2s_subdir+"/intervalstore/**",
+ //jalviewjsSiteDir+"/"+jalviewjs_j2s_subdir+"/org/json/**",
+ "intervalstore/**",
+ "org/json/**",
+ ]
+ ).files
+ )
+ outputs.file(jalviewjsSiteDir+jalviewjs_server_resource)
+
+}
+
+jalviewjsUnzipFiles.mustRunAfter jalviewjsTranspile
+jalviewjsTranspile.mustRunAfter jalviewjsCopyResources
+jalviewjsTranspile.mustRunAfter jalviewjsCopySiteResources
+
+task jalviewjsPrepareSite {
+ group "JalviewJS"
+ description "Prepares the website folder including unzipping files and copying resources"
+ dependsOn jalviewjsSitePath
+ dependsOn jalviewjsUnzipFiles
+ dependsOn jalviewjsCopyResources
+ dependsOn jalviewjsCopySiteResources
+}
+
+task jalviewjsBuildSite {
+ group "JalviewJS"
+ description "Builds the whole website including transpiled code"
+ dependsOn jalviewjsPrepareSite
+ dependsOn jalviewjsTranspile
+}
+
+task jalviewjsSiteTar(type: Tar) {
+ group "JalviewJS"
+ description "Creates a tar.gz file for the website"
+ dependsOn jalviewjsBuildSite
+ def outputFilename = "jalviewjs-site-${JALVIEW_VERSION}.tar.gz"
+ try {
+ archiveFileName = outputFilename
+ } catch (Exception e) {
+ archiveName = outputFilename
+ }
+
+ compression Compression.GZIP
+
+ from jalviewjsSiteDir
+ into jalviewjs_site_dir // this is inside the tar file
+
+ inputs.dir(jalviewjsSiteDir)
+}
+
+task jalviewjsServer {
+ group "JalviewJS"
+ description "Starts a webserver on localhost to test the website"
+ dependsOn jalviewjsSitePath
+ doLast {
+
+ SimpleHttpFileServerFactory factory = new SimpleHttpFileServerFactory()
+ def port = Integer.valueOf(jalviewjs_server_port)
+ def start = port
+ def running = false
+ while(port < start+1000 && !running) {
+ try {
+ def doc_root = new File(jalviewDirAbsolutePath +"/"+ jalviewjsSiteDir)
+ jalviewjsServer = factory.start(doc_root, port)
+ running = true
+ println("SERVER STARTED with document root ${doc_root}.")
+ println("Go to "+jalviewjsServer.getResourceUrl(jalviewjs_server_resource)+" . Run gradle --stop to stop (kills all gradle daemons).")
+ println("For debug: "+jalviewjsServer.getResourceUrl(jalviewjs_server_resource)+"?j2sdebug")
+ } catch (Exception e) {
+ port++;
+ }
+ }
+
+ }
+
+}
+
+task jalviewjs {
+ dependsOn jalviewjsBuildSite
+}
+
+
+++ /dev/null
-<?xml version="1.0"?>
-<!--
- * 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.
--->
-<project name="jalviewX" default="usage" basedir="."
- xmlns:if="ant:if"
- xmlns:unless="ant:unless">
- <taskdef classpath="${clover.jar}" resource="cloverlib.xml" if:set="clover.jar"/>
- <clover-env if:set="clover.jar"/>
-
- <target name="help" depends="usage" />
- <target name="usage" depends="init">
- <echo message="~~~Jalview Ant build.xml Usage~~~~" />
- <echo message="Targets include:" />
- <echo message="usage - default target, displays this message" />
- <echo message="buildindices - generates JavaHelpSearch from the help files" />
- <echo message="build - compiles all necessary files for Application" />
- <echo message="makedist - compiles and places all necessary jar files into directory dist" />
- <echo message="makefulldist - signs all jar files and builds jnlp file for full distribution" />
- <echo message=" this needs a keystore and key."/>
- <echo message=" Add -Dtimestamp to timestamp signed jars"/>
- <echo message=" -Djalview.keyalg and -Djalview.keydig are SHA1/SHA1withRSA"/>
- <echo message=" See docs/building.html for more information." />
- <echo message="compileApplet - compiles all necessary files for Applet" />
- <echo message="makeApplet - compiles, then packages and obfuscates the Applet" />
- <echo message="testng - run jalview's tests via testNG. Default group is '${testng-groups}'" />
- <echo message=" you can specify particular test groups as a list via -Dtestng-groups=" />
- <echo message="See docs/building.html and the comments in build file for other targets." />
- <echo message="note: compile and makeApplet optionally compile/obfuscate applet against a different Java version by specifying -Djava118.home=PathtoJDK/lib which is the lib directory in the JDK install that contains rt.jar " />
- <echo message="Useful -D flags: -Ddonotobfuscate will prevent applet obfuscation" />
- <echo message="Useful -D flags: -Dclover.jar to specify path to openclover for testng coverage report" />
- </target>
-
-
- <!-- utils is a class path to additional utilities needed for
- building docs, jars and webstart stuff -->
- <!--
- Userdefined build property defaults
-
- wsdl.server list (plus namespace mapping info ???) - also want
- ... to make this a dynamically generatable property
- WebStart Location
- Build location - provide a temporary root for speed
- jarsigner keystore and info
- Jakarta and axis classpath ?
- Default argument for starting Jalview (if it exists).
-
--->
-
- <target name="init">
- <path id="axis.classpath">
- <!-->
- <fileset dir="/usr/local/axis/lib">
- <include name="**/*.jar" />
- </fileset>
- <fileset dir="/usr/local/jakarta-tomcat-5/webapps/axis/WEB-INF/lib">
- <include name="**/*.jar"/>
- <include name="*.jar"/>
- </fileset> -->
- </path>
-
- <!-- Jalview Version String displayed by application on startup and used to check for updates -->
- <property name="JALVIEW_VERSION" value="DEVELOPMENT" />
-
- <property name="INSTALLATION" value="Source" />
-
- <!-- 2.4 (VAMSAS)" -->
- <!-- Include debugging information in javac true or false -->
- <property name="javac.debug" value="true" />
-
- <!-- JarSigner Key Store for Webstart Distribution -->
- <property name="jalview.keystore" value="./keys/.keystore" />
- <!-- Keystore Password -->
- <property name="jalview.keystore.pass" value="alignmentisfun" />
- <!-- Key Name -->
- <property name="jalview.key" value="jalview" />
- <!-- Key Password -->
- <property name="jalview.key.pass" value="alignmentisfun" />
- <!-- time stamp server URL -->
- <property name="jalview.tsaurl" value="" />
- <!-- locally valid proxy for signing with external time server -->
- <property name="proxyPort" value="80"/>
- <property name="proxyHost" value="sqid"/>
- <!-- key sign/digest algorithms -->
- <property name="jalview.keyalg" value="SHA1withRSA" description="key algorithm for signing"/>
- <property name="jalview.keydig" value="SHA1" description="algorithm for jar digest"/>
-
- <!-- default TestNG groups to run -->
- <property name="testng-groups" value="Functional" />
- <!-- Java 9 JVM args -->
- <condition property="java9">
- <equals arg1="${ant.java.version}" arg2="9"/>
- </condition>
-
- <!-- Don't change anything below here unless you know what you are doing! -->
- <!-- Url path for WebStart in JNLP file -->
- <property name="WebStartLocation" value="http://www.jalview.org/webstart" />
- <!-- Webstart Image - looked for in resources/images -->
- <property name="WebStartImage" value="JalviewLogo_big.png" />
- <!-- J2SE version needed for webstart launch -->
- <!-- Anne's version needs 1.7 - should rebuild VARNA to java 1.6 for release -->
- <property name="j2sev" value="1.7+" />
- <!-- Java Compilation settings - source and target javac version -->
- <property name="javac.source" value="1.8" />
- <property name="javac.target" value="1.8" />
-
- <!-- Permissions for running Java applets and applications. -->
- <!-- Defaults are those suitable for deploying jalview webstart www.jalview.org -->
- <property name="application.codebase" value="*.jalview.org" />
- <!-- and allowing the applet to be deployed from any URL -->
- <!-- note - if you want to make sure LiveConnect works without any warnings, please rebuild and sign your applet jar with your own domain included in the codebase/allowable-codebase properties -->
- <property name="applet.codebase" value="*.jalview.org *.dundee.ac.uk *" />
- <property name="applet.caller-codebase" value="${applet.codebase}" />
-
- <!-- build directory configuration -->
- <property name="libDir" value="lib" />
- <property name="resourceDir" value="resources" />
- <property name="helpDir" value="help" />
- <property name="docDir" value="doc" />
- <property name="sourceDir" value="src" />
- <property name="schemaDir" value="schemas" />
- <property name="outputDir" value="classes" unless:set="clover.jar"/>
- <property name="outputDir" value="cloverclasses" if:set="clover.jar"/>
- <property name="packageDir" value="dist" />
- <property name="outputJar" value="jalview.jar" />
- <!-- Jalview Applet JMol Jar Dependency -->
- <property name="jmolJar" value="JmolApplet-14.6.4_2016.10.26.jar" />
- <property name="varnaJar" value="VARNAv3-93.jar" />
- <property name="jsoup" value="jsoup-1.8.1.jar" />
- <property name="jsonSimple" value="json_simple-1.1.jar" />
- <property name="javaJson" value="java-json.jar" />
- <property name="jalviewLiteJar" value="jalviewApplet.jar" />
- <property name="reportDir" value="test-reports" />
- <property name="testDir" value="test" />
- <property name="testOutputDir" value="tests" />
- <property name="cloverOutputDir" value="clover" if:set="clover.jar" />
- <!-- switch to indicate if we should obfuscate jalviewLite -->
- <!-- <property name="donotobfuscate" value="true"/> -->
- <!-- switch to exclude associations from generated jnlp files -->
- <!-- <property name="nojnlpfileassocs" value="true"/> -->
-
- <!-- Jalview Web Service Clients - see the comments in 'buildextclients' for details -->
- <property name="wsdl.File" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred?wsdl" />
- <property name="wsdl.Files" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/vamsas?wsdlFiles" />
- <property name="wsdl.MsaWS" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS?wsdl" />
- <property name="wsdl.MsaWS2" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS?wsdl" />
- <property name="WSInterf" value="MsaWS" />
- <property name="wsdl.Namespace" value="vamsas" />
- <property name="wsdl.ClientNS" value="ext.vamsas" />
- <!-- the class path for building the application -->
- <path id="build.classpath">
- <fileset dir="utils">
- <include name="*.jar" />
- <include name="**/*.jar" />
- </fileset>
- <fileset dir="${libDir}">
- <include name="*.jar" />
- <include name="**/*.jar" />
- </fileset>
- <fileset dir="${java.home}/lib">
- <include name="plugin.jar" />
- </fileset>
- <fileset dir="appletlib">
- <!-- the JmolApplet includes the JmolApplet console and the application javac seems to always try and build all packages
- -->
- <include name="${jmolJar}" />
- <include name="${varnaJar}" />
- </fileset>
- </path>
- <path id="test.classpath">
- <pathelement path="${outputDir}" />
- <path refid="build.classpath" />
- </path>
- <property name="source.dist.name" value="${basedir}/jalview-src.tar.gz" />
- <!-- The Location of the java 1.1.8 jdk -->
- <property name="java118.home" value="${java.home}" />
- <!-- jre for 1.4 version -->
- <property name="applet.jre.tools" value="${java118.home}/lib/rt.jar" />
-
- <!-- the classpath for building the 1.1 applet -->
- <path id="jalviewlite.deps">
- <fileset dir="${java118.home}">
- <include name="lib/rt.jar" />
- </fileset>
- <fileset dir="${java.home}/lib">
- <include name="plugin.jar" />
- </fileset>
- <pathelement location="appletlib/${jmolJar}" />
- <pathelement location="lib/${varnaJar}" />
- <pathelement location="appletlib/${jsoup}" />
- <pathelement location="appletlib/${jsonSimple}" />
- <pathelement location="appletlib/${javaJson}" />
-
- </path>
- <!-- default location for outputting javadoc -->
- <property name="javadocDir" value="${packageDir}/javadoc" />
- </target>
-
-
- <taskdef classpath="utils/roxes-ant-tasks-1.2-2004-01-30.jar" resource="com/roxes/tools/ant/taskdefs.properties" />
- <target name="buildPropertiesFile" depends="init">
- <tstamp prefix="build">
- <format property="date" pattern="dd MMMM yyyy" />
- </tstamp>
- <exec executable="/usr/bin/git" outputproperty="git.commit" failifexecutionfails="false">
- <arg value="rev-parse" />
- <arg value="--short" />
- <arg value="HEAD" />
- </exec>
- <exec executable="/usr/bin/git" outputproperty="git.branch" failifexecutionfails="false">
- <arg value="rev-parse" />
- <arg value="--abbrev-ref" />
- <arg value="HEAD" />
- </exec>
- <properties file="${outputDir}/.build_properties">
- <header>
- ---Jalview Build Details---
- </header>
- <property name="VERSION" value="${JALVIEW_VERSION}" />
- <property name="INSTALLATION" value="${INSTALLATION} git-commit:${git.commit} [${git.branch}]" />
- <property name="BUILD_DATE" value="${build.date}" />
- </properties>
- </target>
-
-
- <target name="clean" depends="init">
- <!-- not efficient yet. -->
- <delete dir="${outputDir}" includes="*,**/*" />
- </target>
-
- <target name="distclean" depends="init, clean">
-
- <echo message="REMOVING ALL BACKUP/AUTOSAVES!" />
- <delete>
- <fileset dir=".">
- <include name="${outputJar}" />
- <include name="#*#" />
- <include name="#*.*#" />
- <include name="**/#*#" />
- <include name="**/#*.*#" />
- <include name="*~" />
- <include name="*.*~" />
- <include name="**/*~" />
- <include name="**/*.*~" />
- </fileset>
- </delete>
- </target>
-
- <target name="prepare" depends="init">
- <mkdir dir="${outputDir}" />
- <copy todir="${outputDir}">
- <fileset dir=".">
- <include name="${docDir}/**/*.*" />
- <include name="${helpDir}/**/*.*" />
- <include name="${libDir}/*.jar" />
- </fileset>
- <fileset dir="${resourceDir}">
- <include name="**/*.*" />
- </fileset>
- </copy>
- <mkdir dir="${cloverOutputDir}" if:set="clover.jar"/>
- </target>
-
- <target name="build" depends="prepare">
- <!-- not efficient yet. -->
- <javac source="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="build.classpath">
- <exclude name="jalview/*applet*" />
- <exclude name="jalview/appletgui/**" />
- <exclude name="com/stevesoft/**" />
- </javac>
- </target>
-
-
- <target name="testclean" depends="init">
- <delete dir="${testOutputDir}" includes="*,**/*" />
- </target>
-
- <target name="prepareTests" depends="init,testclean">
- <mkdir dir="${testOutputDir}" />
- </target>
-
- <target name="buildTests" depends="build,buildindices,prepareTests">
- <javac source="${javac.source}" target="${javac.target}" srcdir="${testDir}" destdir="${testOutputDir}" debug="${javac.debug}" classpathref="test.classpath" includeantruntime="false">
- </javac>
- </target>
-
- <taskdef resource="testngtasks" classpath="utils/testnglibs/testng.jar" />
-
- <target name="testng" depends="buildTests">
- <testng outputDir="${reportDir}" haltOnFailure="false" groups="${testng-groups}" mode="testng"
- verbose="2">
- <classpath>
- <pathelement location="${testOutputDir}" />
- <pathelement location="${clover.jar}" if:set="clover.jar"/>
- <path refid="test.classpath" />
- </classpath>
- <jvmarg value="--add-modules=java.se.ee" if:set="java9"/>
- <jvmarg value="--illegal-access=warn" if:set="java9"/>
- <classfileset dir="${testOutputDir}" includes="**/*.class" />
- </testng>
- </target>
-
- <target name="buildindices" depends="init, prepare, buildPropertiesFile" unless="help.uptodate">
- <replace value="${JALVIEW_VERSION}">
- <replacetoken>
- <![CDATA[$$Version-Rel$$]]>
- </replacetoken>
- <fileset dir="${outputDir}/${helpDir}">
- <include name="help.jhm" />
- </fileset>
- </replace>
-
- <java classname="com.sun.java.help.search.Indexer" classpathref="build.classpath" fork="true" dir="${outputDir}/${helpDir}">
- <arg line="html" />
- </java>
- </target>
-
- <target name="preparejnlp" depends="makedist">
- <copy todir="${packageDir}">
- <fileset dir="${resourceDir}/images">
- <include name="${WebStartImage}" />
- </fileset>
- </copy>
-
- <taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties" />
-
- <!-- create a dummy jar which will eventually contain the jnlp template -->
- <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
- <fileset dir="${packageDir}">
- <include name="jalview.jar" />
- </fileset>
- </jar>
-
- <mkdir dir="${packageDir}/JNLP-INF" />
- <antcall target="writejnlpf">
- <param name="jnlpFile" value="${packageDir}/JNLP-INF/APPLICATION-TEMPLATE.JNLP" />
- <param name="inih" value="*" />
- <param name="maxh" value="*" />
- </antcall>
-
- <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
- <fileset dir="${packageDir}">
- <include name="JNLP-INF/APPLICATION-TEMPLATE.JNLP" />
- </fileset>
- </jar>
-
- <antcall target="writejnlpf">
- <param name="jnlpFile" value="${packageDir}/jalview_256M.jnlp" />
- <param name="inih" value="10M" />
- <param name="maxh" value="256M" />
- </antcall>
- <antcall target="writejnlpf">
- <param name="jnlpFile" value="${packageDir}/jalview.jnlp" />
- <param name="inih" value="800M" />
- <param name="maxh" value="1024M" />
- </antcall>
-
- <antcall target="writejnlpf">
- <param name="jnlpFile" value="${packageDir}/jalview_1G.jnlp" />
- <param name="inih" value="128M" />
- <param name="maxh" value="512M" />
- </antcall>
-
- <antcall target="writejnlpf">
- <param name="jnlpFile" value="${packageDir}/jalview_2G.jnlp" />
- <param name="inih" value="800M" />
- <param name="maxh" value="1024M" />
- </antcall>
-
- <!-- finally, need to postprocess to add in associations at end of 'information' element
-
- <xslt in="${packageDir}/jalview_noa_1G.jnlp" out="${packageDir}/jalview_1G.jnlp">
-
- </xslt>
-
-
- -->
- <!--
- <association mime-type="application-x/ext-file" extensions="fa"/>
- <association mime-type="application-x/ext-file" extensions="fasta"/>
- <association mime-type="application-x/ext-file" extensions="mfa"/>
- <association mime-type="application-x/ext-file" extensions="fastq"/>
- <association mime-type="application-x/ext-file" extensions="blc"/>
- <association mime-type="application-x/ext-file" extensions="msf"/>
- <association mime-type="application-x/ext-file" extensions="pfam"/>
- <association mime-type="application-x/ext-file" extensions="aln"/>
- <association mime-type="application-x/ext-file" extensions="pir"/>
- <association mime-type="application-x/ext-file" extensions="amsa"/>
- <association mime-type="application-x/ext-file" extensions="stk"/>
- <association mime-type="application-x/ext-file" extensions="jar"/>-->
- </target>
-
- <target name="-jarsignwithtsa" depends="makedist,preparejnlp" if="timestamp" unless="nosign">
- <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="${jalview.keyalg}" digestalg="${jalview.keydig}"
- tsaproxyhost="${proxyHost}" tsaproxyport="${proxyPort}" tsaurl="${jalview.tsaurl}">
- <fileset dir="${packageDir}">
- <include name="*.jar" />
- </fileset>
- </signjar>
- </target>
- <target name="-jarsignnotsa" depends="makedist,preparejnlp" if:blank="timestamp" unless="nosign">
- <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="${jalview.keyalg}" digestalg="${jalview.keydig}">
- <fileset dir="${packageDir}">
- <include name="*.jar" />
- </fileset>
- </signjar>
- </target>
-
- <target name="makefulldist" depends="makedist,preparejnlp,-jarsignwithtsa,-jarsignnotsa">
- <!-- and sign the jars -->
- <!-- the default keystore details might need to be edited here -->
- </target>
-
- <target name="runenv" depends="init">
- <path id="run.classpath">
- <pathelement location="${outputDir}" />
- <fileset dir="${outputDir}">
- <include name="${libDir}/*.jar" />
- </fileset>
- </path>
- <pathconvert targetos="unix" refid="run.classpath" property="run.classpath" />
-
- <echo>java -classpath ${run.classpath} jalview.bin.Jalview
- </echo>
- </target>
-
- <target name="-generatejnlpf">
- <presetdef name="jnlpf">
- <jnlp codebase="${WebStartLocation}">
- <information>
- <title>Jalview</title>
- <vendor>The Barton Group</vendor>
- <homepage href="http://www.jalview.org" />
- <description>Jalview Multiple Alignment Editor</description>
- <description kind="short">Jalview</description>
- <icon href="${WebStartImage}" />
- <offline_allowed />
- </information>
- <resources>
- <j2se version="1.8+" />
- <jar main="true" href="jalview.jar"/>
- <fileset dir="${packageDir}">
- <exclude name="jalview.jar" />
- <include name="*.jar" />
- <include name="*_*.jar" />
- <exclude name="*quaqua*.jar" />
- </fileset>
- <property name="jalview.version" value="${JALVIEW_VERSION}" />
- </resources>
- <resources os="Mac OS X">
- <fileset dir="${packageDir}">
- <include name="quaqua-filechooser-only-8.0.jar"/>
- <include name="*quaqua64*.jnilib.jar" />
- </fileset>
- </resources>
-
- <application_desc main_class="jalview.bin.Jalview">
- </application_desc>
- <security>
- <all_permissions />
- </security>
- </jnlp>
- </presetdef>
-
- <jnlpf toFile="${jnlpFile}" />
- <!-- add the add-modules j2se attribute for java 9 -->
- <replace file="${jnlpFile}" value="j2se version="1.8+" initial-heap-size="${inih}" max-heap-size="${maxh}" java-vm-args="--add-modules=java.se.ee --illegal-access=warn"">
- <replacetoken>j2se version="1.8+"</replacetoken>
- </replace>
- </target>
-
- <target name="-dofakejnlpfileassoc" depends="-generatejnlpf" if="nojnlpfileassocs">
- <echo message="Not adding JNLP File Associations" />
- </target>
-
- <target name="-dojnlpfileassoc" depends="-generatejnlpf" unless="nojnlpfileassocs">
- <replace file="${jnlpFile}">
- <replacetoken>
- <![CDATA[</information>]]></replacetoken>
- <replacevalue>
- <![CDATA[
- <association mime-type="application-x/ext-file" extensions="fa" />
- <association mime-type="application-x/ext-file" extensions="fasta" />
- <association mime-type="application-x/ext-file" extensions="mfa" />
- <association mime-type="application-x/ext-file" extensions="fastq" />
- <association mime-type="application-x/ext-file" extensions="blc" />
- <association mime-type="application-x/ext-file" extensions="msf" />
- <association mime-type="application-x/ext-file" extensions="pfam" />
- <association mime-type="application-x/ext-file" extensions="aln"/>
- <association mime-type="application-x/ext-file" extensions="pir"/>
- <association mime-type="application-x/ext-file" extensions="amsa"/>
- <association mime-type="application-x/ext-file" extensions="stk"/>
- <association mime-type="application-x/ext-file" extensions="jvp"/>
- </information>]]></replacevalue>
- </replace>
- <echo message="Added file associations to JNLP file" />
-</target>
-<target name="writejnlpf" depends="-dojnlpfileassoc,-dofakejnlpfileassoc">
-</target>
-
-<target name="buildextclients" depends="init">
- <input message="Building external client source from WSDLs - Do you really want to do this ? (Yy/Nn)" validargs="Y,y,n,N" defaultvalue="N" addproperty="doextbuild.response" />
- <condition property="dontextbuild">
- <equals arg1="n" arg2="${doextbuild.response}" />
- </condition>
- <condition property="dontextbuild">
- <equals arg1="N" arg2="${doextbuild.response}" />
- </condition>
- <fail if="dontextbuild">
- Build External Client Code process aborted by user. Jalview source is unchanged.
- </fail>
- <!-- Currently, this doesn't happen automatically.
- 1. Run WSDL2Java as below, which generates an ext.vamsas +
- vamsas.<datapackages> fileset.
- 2. refactor ext.vamsas.SpecificserviceWS* to
- ext.vamsas.ServiceclassWS* that implements the ServiceclassWSI interface.
- 3. Update the jalview.ws.*WServices classes to reflect the
- interface type, and all locations of this wsdl type that Jalview
- might be using.
-
--->
- <path id="axisbuild">
- <path refid="build.classpath" />
- </path>
- <taskdef resource="axis-tasks.properties" classpathref="axisbuild" />
- <move todir="./bak">
- <fileset dir="${sourceDir}" id="client">
- <include name="${wsdl.ClientNS}/*.*" />
- </fileset>
- </move>
-
- <axis-wsdl2java output="${sourceDir}" verbose="true" url="${wsdl.MsaWS2}" serverside="false" deployscope="Request" debug="false" helpergen="true" all="true">
- <mappingSet>
- <mapping namespace="${wsdl.Namespace}" package="${wsdl.ClientNS}" />
- <mapping namespace="http://dataTypes.vamsas" package="${wsdl.ClientNS}" />
- </mappingSet>
- </axis-wsdl2java>
-</target>
-
-<target name="makedist" depends="build, buildPropertiesFile, linkcheck, buildindices">
- <fail if="clover.jar">
- Ignoring request to build jalview distribution with clover-instrumented classes
- </fail>
- <!-- make the package jar if not already existing -->
- <mkdir dir="${packageDir}" />
- <!-- clean dir if it already existed -->
- <delete>
- <fileset dir="${packageDir}">
- <include name="*.jar" />
- </fileset>
- </delete>
- <jar destfile="${packageDir}/${outputJar}" index="true">
- <manifest>
- <attribute name="Main-Class" value="jalview.bin.Jalview" />
- <attribute name="Permissions" value="all-permissions" />
- <attribute name="Application-Name" value="Jalview Desktop" />
- <attribute name="Codebase" value="${application.codebase}" />
- </manifest>
- <fileset dir="${outputDir}/">
- <exclude name="cache*/**" />
- <exclude name="*.jar" />
- <exclude name="*.jar.*" />
- <exclude name="**/*.jar" />
- <exclude name="**/*.jar.*" />
- </fileset>
- </jar>
-
- <copy toDir="${packageDir}" flatten="true">
- <fileset dir="${outputDir}">
- <include name="*.jar" />
- <include name="**/*.jar" />
- </fileset>
- </copy>
-</target>
-
-
-<!-- jalopy code reformatter -->
-<target name="sourcescrub" depends="init,build">
- <jalopy destdir="jsrc" classpathref="run.classpath" convention="jalview-jalopy.xml">
- <fileset dir="${sourceDir}">
- <include name="*.java" />
- <include name="**/*.java" />
- <include name="**/**/*.java" />
- </fileset>
- </jalopy>
-</target>
-
-
-
-<!-- Compile, package and obfuscate Jalview Applet -->
-<target name="makeApplet" depends="obfuscate" description="assemble the final jalviewLite applet jar with or without obfuscation" />
-
-<target name="compileApplet" depends="init,clean">
- <mkdir dir="${outputDir}" />
- <javac source="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="jalviewlite.deps" includes="jalview/appletgui/**" excludes="ext/**,gui/**,jbgui/**,MCview/**,org/**,vamsas/**,jalview/ext/rbvi/**,jalview/ext/paradise/**,jalview/ext/ensembl/**,jalview/ext/so/**" />
-</target>
-
-<target name="packageApplet" depends="compileApplet, buildPropertiesFile">
- <copy file="${resourceDir}/images/link.gif" toFile="${outputDir}/images/link.gif" />
- <copy todir="${outputDir}/lang">
- <fileset dir="${resourceDir}/lang">
- <include name="**.*" />
- </fileset>
- </copy>
- <jar destfile="in.jar" index="true">
- <manifest>
- <attribute name="Main-Class" value="jalview.bin.JalviewLite" />
- <attribute name="Application-Name" value="JalviewLite" />
- <attribute name="Codebase" value="${applet.codebase}" />
- </manifest>
- <fileset dir="${outputDir}">
- <include name="com/**" />
- <include name="MCview/**" />
- <include name="jalview/**" />
- <include name=".build_properties" />
- <include name="images/link.gif" />
- <include name="lang/**" />
- </fileset>
- </jar>
-</target>
-<target name="obfuscate" depends="-obfuscatefake,-obfuscatereally">
-</target>
-<target name="-obfuscatefake" depends="packageApplet" if="donotobfuscate">
- <copy file="in.jar" tofile="${jalviewLiteJar}" overwrite="true" />
- <delete file="in.jar" />
-</target>
-<target name="-obfuscatereally" unless="donotobfuscate">
-
- <path id="obfuscateDeps.path">
- <pathelement location="${applet.jre.tools}" />
- <pathelement location="appletlib/${jmolJar}" />
- <pathelement location="lib/${varnaJar}" />
- <pathelement location="appletlib/${jsoup}" />
- <pathelement location="appletlib/${jsonSimple}" />
- <pathelement location="appletlib/${javaJson}" />
- <fileset dir="${java.home}/lib">
- <include name="plugin.jar" />
- </fileset>
- </path>
- <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard_5.3.3.jar" />
-
- <proguard verbose="true" >
- <injar file="in.jar" />
- <outjar file="${jalviewLiteJar}" />
- <libraryjar refid="obfuscateDeps.path" />
- <dontwarn />
- <keep access="public" type="class" name="jalview.bin.JalviewLite">
- <field access="public" />
- <method access="public" />
- <constructor access="public" />
- </keep>
- <keep access="public" type="class" name="jalview.appletgui.AlignFrame">
- <field access="public" />
- <method access="public" />
- <constructor access="public" />
- </keep>
-
- <keep name="jalview.json.binding**">
- <constructor/>
- <method name="*"/>
- </keep>
-
- <keep access="public" type="class" name="MCview.PDBfile">
- <field access="public" />
- <method access="public" />
- <constructor access="public" />
- </keep>
-
- <keep access="public" type="class" name="jalview.ws.jws1.Annotate3D">
- <field access="public" />
- <method access="public" />
- <constructor access="public" />
- </keep>
-
- <keep access="public" type="class" name="jalview.ext.jmol.JmolParser">
- <field access="public" />
- <method access="public" />
- <constructor access="public" />
- </keep>
-
-
- <!-- -libraryjars "${obfuscateDeps}"
- -injars in.jar
- -outjars jalviewApplet.jar
- -keep public class jalview.bin.JalviewLite
- { public * ; } -->
- </proguard>
- <delete file="in.jar" />
-</target>
-
-<target name="jaxb-bindings" depends="init" description="Generates JAXB bindings for supported Jalview XML models (needs xjc on the path)">
- <delete>
- <fileset dir="${sourceDir}/jalview/xml/binding/jalview">
- <include name="*.java" />
- </fileset>
- </delete>
- <exec executable="xjc">
- <arg value="${schemaDir}/jalview.xsd"/>
- <arg value="-d"/>
- <arg value="${sourceDir}"/>
- <arg value="-p"/>
- <arg value="jalview.xml.binding.jalview"/>
- </exec>
- <delete>
- <fileset dir="${sourceDir}/jalview/xml/binding/embl">
- <include name="*.java" />
- </fileset>
- </delete>
-
- <exec executable="xjc">
- <arg value="${schemaDir}/embl.xsd"/>
- <arg value="-d"/>
- <arg value="${sourceDir}"/>
- <arg value="-b"/>
- <arg value="${schemaDir}/embl_bindings.xml"/>
- <arg value="-p"/>
- <arg value="jalview.xml.binding.embl"/>
- </exec>
-
- <delete>
- <fileset dir="${sourceDir}/jalview/xml/binding/uniprot">
- <include name="*.java" />
- </fileset>
- </delete>
-
- <exec executable="xjc">
- <arg value="${schemaDir}/uniprot.xsd"/>
- <arg value="-d"/>
- <arg value="${sourceDir}"/>
- <arg value="-p"/>
- <arg value="jalview.xml.binding.uniprot"/>
- </exec>
-</target>
-
-<target name="sourcedist" description="create jalview source distribution" depends="init">
- <delete file="${source.dist.name}" />
- <!-- temporary copy of source to update timestamps -->
- <copy todir="_sourcedist">
- <fileset dir=".">
- <exclude name=".*" />
- <exclude name="**/.*" />
- <exclude name="*.class" />
- <exclude name="**/*.class" />
- <include name="LICENSE" />
- <include name="README" />
- <include name="build.xml" />
- <include name="jalview-jalopy.xml" />
- <include name="JalviewApplet.jpx" />
- <include name="JalviewX.jpx" />
- <include name="nbbuild.xml" />
- <include name="nbproject/genfiles.properties" />
- <include name="nbproject/project.properties" />
- <include name="nbproject/project.xml" />
- <include name="${sourceDir}/*.java" />
- <include name="${sourceDir}/**/*.java" />
- <include name="${sourceDir}/**/*.cdr" />
- <include name="${libDir}/**/*" />
- <include name="${resourceDir}/**/*" />
- <include name="${helpDir}/**/*" />
- <include name="appletlib/${jmolJar}" />
- <include name="appletlib/${jsonSimple}" />
- <include name="appletlib/${javaJson}" />
- <exclude name="**/*locales" />
- <exclude name="*locales/**" />
- <exclude name="utils/InstallAnywhere/**Build.iap_xml" />
- <exclude name="utils/InstallAnywhere/**Build*/**" />
- <exclude name="utils/InstallAnywhere/**Build*/**" />
- <exclude name="utils/InstallAnywhere/.build*.*/**" />
- <exclude name="utils/InstallAnywhere/**locale*" />
- <exclude name="utils/InstallAnywhere/**locale*/**" />
- <exclude name="utils/InstallAnywhere/**locale*/**" />
- <include name="${schemaDir}/**/*" />
- <include name="utils/**/*" />
- <include name="${docDir}/**/*" />
- <include name="examples/**/*" />
- </fileset>
- </copy>
-
- <tstamp prefix="build">
- <format property="year" pattern="yyyy" />
- </tstamp>
- <!-- each replacetoken CDATA body must be on one line -
- otherwise the pattern doesn't match -->
- <replace value="${JALVIEW_VERSION}">
- <replacetoken>
- <![CDATA[$$Version-Rel$$]]>
- </replacetoken>
- <fileset dir="_sourcedist">
- <include name="**/*" />
- </fileset>
- </replace>
- <replace dir="_sourcedist" value="${build.year}">
- <replacetoken>
- <![CDATA[$$Year-Rel$$]]>
- </replacetoken>
- <fileset dir="_sourcedist">
- <include name="**/*" />
- </fileset>
- </replace>
-
- <tar destfile="${source.dist.name}" compression="gzip">
- <tarfileset dir="_sourcedist/" prefix="jalview" preserveLeadingSlashes="true">
- </tarfileset>
- </tar>
-
- <delete dir="_sourcedist" />
-</target>
-<target name="prepubapplet_1" depends="makeApplet">
- <copy todir="${packageDir}/examples">
- <fileset dir="examples">
- <include name="**/*" />
- <include name="javascript/*" />
- <include name="jmol/*" />
- </fileset>
- <fileset dir=".">
- <include name="${jalviewLiteJar}" />
- </fileset>
- <fileset dir="appletlib">
- <include name="**/*" />
- </fileset>
- </copy>
- <jar update="true" index="true" jarfile="${packageDir}/examples/${jalviewLiteJar}" />
- <jar update="true" index="true" jarfile="${packageDir}/examples/${javaJson}" />
- <jar update="true" index="true" jarfile="${packageDir}/examples/${jsonSimple}" />
- <jar update="true" index="true" jarfile="${packageDir}/examples/${jmolJar}">
- <manifest>
- <attribute name="Application-Name" value="Jmol (bundled with JalviewLite)" />
- <!-- <attribute name="Permissions" value="sandbox" /> -->
- <!--<attribute name="Trusted-Lib" value="true" /> -->
- <attribute name="Codebase" value="${applet.codebase}" />
- <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
- </manifest>
- </jar>
-
- <presetdef name="ap_applet.jar">
- <!-- build a signed applet with 'all-permissions' -
- Needs 'param name="permissions' value="all-permissions"' in applet tag
- JalviewLite+JmolApplet linked sequence/structure fails
- Mixed code warnings are raised
- -->
- <jar update="true" index="true">
- <manifest>
- <attribute name="Application-Name" value="JalviewLite" />
- <attribute name="Permissions" value="all-permissions" />
- <attribute name="Codebase" value="${applet.codebase}" />
- <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
- <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
- </manifest>
- </jar>
- </presetdef>
- <presetdef name="applet.jar">
- <!-- build signed applet with sandbox permissions -
- Needs 'param name="permissions' value="sandbox"' in applet tag
- Preserves Pre-Java 1.7_u45 behavior once 'permissions' parameter added to applet tag
- -->
-
- <jar update="true" index="true">
- <manifest>
- <attribute name="Application-Name" value="JalviewLite" />
- <attribute name="Permissions" value="sandbox" />
- <attribute name="Codebase" value="${applet.codebase}" />
- <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
- <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
- </manifest>
- </jar>
- </presetdef>
- <presetdef name="tl_applet.jar">
- <!-- build signed applet with trusted library/trusted permissions -
- Needs 'param name="permissions' value="all-permissions"' in applet tag
- j1.7_45:
- No mixed code warnings raised
- Jmol/JalviewLite sequence/structure example doesn't link structures
- Raises dialog asking user to allow page to control applet via LiveConnect javascript
-
- -->
-
- <jar update="true" index="true">
- <manifest>
- <attribute name="Application-Name" value="JalviewLite" />
- <attribute name="Permissions" value="all-permissions" />
- <attribute name="Codebase" value="${applet.codebase}" />
- <attribute name="Trusted-Only" value="true" />
- <attribute name="Trusted-Library" value="true" />
- </manifest>
- </jar>
- </presetdef>
- <presetdef name="to_applet.jar">
- <!-- not fully test variant (yet) -->
- <jar update="true" index="true">
- <manifest>
- <attribute name="Application-Name" value="JalviewLite" />
- <attribute name="Permissions" value="all-permissions" />
- <attribute name="Codebase" value="${applet.codebase}" />
- <attribute name="Trusted-Only" value="true" />
- </manifest>
- </jar>
- </presetdef>
- <!-- create differently privileged artefacts -->
- <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/u_${jalviewLiteJar}" />
- <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
- <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/u_${javaJson}" overwrite="true" />
- <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/u_${jsonSimple}" overwrite="true" />
- <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/ap_${jalviewLiteJar}" />
- <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/ap_${jmolJar}" />
- <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/ap_${javaJson}" />
- <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/ap_${jsonSimple}" />
- <ap_applet.jar jarfile="${packageDir}/examples/ap_${jalviewLiteJar}" />
- <ap_applet.jar jarfile="${packageDir}/examples/ap_${jmolJar}" />
- <ap_applet.jar jarfile="${packageDir}/examples/ap_${javaJson}" />
- <ap_applet.jar jarfile="${packageDir}/examples/ap_${jsonSimple}" />
- <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/tl_${jalviewLiteJar}" />
- <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/tl_${jmolJar}" />
- <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/tl_${javaJson}" />
- <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/tl_${jsonSimple}" />
- <tl_applet.jar jarfile="${packageDir}/examples/tl_${jalviewLiteJar}" />
- <tl_applet.jar jarfile="${packageDir}/examples/tl_${jmolJar}" />
- <tl_applet.jar jarfile="${packageDir}/examples/tl_${javaJson}" />
- <tl_applet.jar jarfile="${packageDir}/examples/tl_${jsonSimple}" />
- <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/to_${jalviewLiteJar}" />
- <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/to_${jmolJar}" />
- <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/to_${javaJson}" />
- <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/to_${jsonSimple}" />
- <to_applet.jar jarfile="${packageDir}/examples/to_${jalviewLiteJar}" />
- <to_applet.jar jarfile="${packageDir}/examples/to_${jmolJar}" />
- <to_applet.jar jarfile="${packageDir}/examples/to_${javaJson}" />
- <to_applet.jar jarfile="${packageDir}/examples/to_${jsonSimple}" />
- <!-- finally, create manifest for original jars -->
- <applet.jar jarfile="${packageDir}/examples/${jalviewLiteJar}" />
- <applet.jar jarfile="${packageDir}/examples/${jmolJar}" />
- <applet.jar jarfile="${packageDir}/examples/${javaJson}" />
- <applet.jar jarfile="${packageDir}/examples/${jsonSimple}" />
-
- <!-- todo - write examples/downloads for alternate versions of the applet
- probably don't need to do this now since we don't have alternate versions anymore !-->
-</target>
-<target name="-signapplet" depends="prepubapplet_1">
- <fileset id="signappletjarset" dir="${packageDir}/examples">
- <exclude name="u_*.jar" />
- <include name="${jalviewLiteJar}" />
- <include name="${jmolJar}" />
- <include name="${javaJson}" />
- <include name="${jsonSimple}" />
- <include name="to_${jalviewLiteJar}" />
- <include name="to_${jmolJar}" />
- <include name="to_${javaJson}" />
- <include name="to_${jsonSimple}" />
- <include name="tl_${jalviewLiteJar}" />
- <include name="tl_${jmolJar}" />
- <include name="tl_${javaJson}" />
- <include name="tl_${jsonSimple}" />
- <include name="ap_${jalviewLiteJar}" />
- <include name="ap_${jmolJar}" />
- <include name="ap_${javaJson}" />
- <include name="ap_${jsonSimple}" />
- </fileset>
-</target>
-<target name="-signappletnotsa" if:blank="timestamp" depends="-signapplet" unless="nosign">
- <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
- <fileset refid="signappletjarset" />
- </signjar>
-</target>
-
-<target name="-signapplettsa" if="timestamp" depends="-signapplet" unless="nosign">
- <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" tsaproxyhost="${proxyHost}" tsaproxyport="${proxyPort}" tsaurl="${jalview.tsaurl}">
- <fileset refid="signappletjarset" />
- </signjar>
-</target>
-
-<target name="signApplet" description="internal target to sign applet" depends="-signappletnotsa,-signapplettsa" />
-<target name="pubapplet" description="Dummy target to keep legacy Jalview build system happy. We don't actually publish the applet anymore."/>
-
-<target name="_pubapplet" description="installs the jalviewLite applet and dependent jars into an applet examples directory built under ${outputDir}" depends="makeApplet, signApplet">
-
- <!-- bizarre bug causes JmolApplet to always get signed, even if excluded from above. so copy explicitly -->
- <copy file="appletlib/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
- <copy file="appletlib/${jsonSimple}" tofile="${packageDir}/examples/u_${jsonSimple}" overwrite="true" />
- <copy file="appletlib/${javaJson}" tofile="${packageDir}/examples/u_${javaJson}" overwrite="true" />
- <!-- finally, replace any launchApp servlet tags with a version specification -->
- <replace value="http://www.jalview.org/services/launchApp?version=${JALVIEW_VERSION}"">
- <replacetoken>
- <![CDATA[http://www.jalview.org/services/launchApp"]]>
- </replacetoken>
- <fileset dir="${packageDir}/examples">
- <include name="**/*.html" />
- </fileset>
- </replace>
- <replace value="http://www.jalview.org/services/launchApp?version=${JALVIEW_VERSION}'">
- <replacetoken>
- <![CDATA[http://www.jalview.org/services/launchApp']]>
- </replacetoken>
- <fileset dir="${packageDir}/examples">
- <include name="**/*.html" />
- </fileset>
- </replace>
-
-</target>
-<target name="sourcedoc" description="Create jalview source documentation pages" depends="init">
- <javadoc destdir="${javadocDir}">
- <packageset dir="${sourceDir}" includes="jalview/*,MCView/*">
- </packageset>
- </javadoc>
-</target>
-<target name="linkcheck" depends="init,prepare">
- <javac srcdir="utils" destdir="utils" includes="HelpLinksChecker.java"/>
- <java fork="true" dir="${helpDir}" classpath="utils" classname="HelpLinksChecker" failonerror="true">
- <arg file="${helpDir}"/>
- <arg value="-nointernet" />
- </java>
-</target>
-
-<target name="eclipse-install" depends="init,prepare">
-
- <property name="eclipseTempFile" value="eclipse-jee-oxygen-R-linux-gtk-x86_64.tar.gz"/>
- <property name="eclipseInstallURL" value="http://mirror.csclub.uwaterloo.ca/eclipse/technology/epp/downloads/release/oxygen/R/eclipse-jee-oxygen-R-linux-gtk-x86_64.tar.gz"/>
- <property name="java2scriptURL" value="https://github.com/BobHanson/java2script/blob/master/sources/net.sf.j2s.core/dist/dropins/net.sf.j2s.core.jar?raw=true"/>
-
- <get url="${eclipseInstallURL}" dest="${eclipseTempFile}"/>
- <untar compression="gzip" src="${eclipseTempFile}" dest="${eclipse-inst}"/>
-
- <!-- not needed since we ship transpiler with source
- <get url="${java2scriptURL}" dest="eclipse-inst/dropins/net.sf.j2s.core.jar" /> -->
-
-</target>
-
-<target name="build-site" depends="init,prepare,compile-site,unzip-to-site,make-j2s-cores">
- <!-- tarball -->
- <tar compression="gzip" destfile="site.tar.gz">
- <tarfileset dir="site" />
- </tar>
-</target>
-<target name="prepare-site" depends="init,prepare,buildPropertiesFile">
- <property name="swingjsdir" value="swingjs"/>
- <property name="eclipse-inst" value="/home/bamboo/buildtools/eclipse/eclipse-js"/>
- <property name="eclipse-exec" value="${eclipse-inst}/eclipse"/>
- <property name="site" value="site"/>
- <!-- where the eclipse js workspace has been initialised -->
- <property name="eclipse-work" value="/home/bamboo/buildtools/eclipse/eclipse-js-workspace"/>
- <!-- git repository linked to project in workspace -->
- <property name="eclipse-workrepo" value="/home/bamboo/buildtools/eclipse/eclipse-js-workspace/jalview-js"/>
-</target>
- <target name="clean-site" depends="prepare-site">
- <delete dir="${eclipse-workrepo}/${site}"/>
- <mkdir dir="${eclipse-workrepo}/${site}"/>
- </target>
-<target name="compile-site" depends="prepare-site,clean-site">
- <!-- update transpiler -->
- <copy file="${swingjsdir}/net.sf.j2s.core.jar" todir="${eclipse-inst}/dropins" overwrite="true" failonerror="true"/>
- <!-- update the git repo linked to the eclipse workspace -->
- <exec executable="/usr/bin/git" outputproperty="git.commit" failifexecutionfails="true">
- <arg value="rev-parse" />
- <arg value="--short" />
- <arg value="HEAD" />
- </exec>
- <!-- update and checkout the same commit in the workspace project -->
- <exec executable="/usr/bin/git" failifexecutionfails="true" dir="${eclipse-workrepo}">
- <arg value="reset" />
- <arg value="--hard" />
- </exec>
- <exec executable="/usr/bin/git" failifexecutionfails="true" dir="${eclipse-workrepo}">
- <arg value="pull" />
- </exec>
- <exec executable="/usr/bin/git" failifexecutionfails="true" dir="${eclipse-workrepo}">
- <arg value="checkout" />
- <arg value="${git.commit}" />
- </exec>
- <!-- custom classpath for .js builds -->
- <copy file=".classpath.js" tofile="${eclipse-workrepo}/.classpath" overwrite="true"/>
- <!-- clean eclipse log -->
- <delete file="${eclipse-work}/.metadata/.log"/>
-
- <!-- execute the eclipse build - the build may fail but valid javascript may still be produced, so we ignore return codes -->
- <exec executable="${eclipse-exec}" failonerror="no">
- <arg value="-nosplash"/>
- <arg value="--launcher.suppressErrors"/>
- <arg value="-application"/>
- <arg value="org.eclipse.jdt.apt.core.aptBuild"/>
- <arg value="-data"/>
- <arg value="${eclipse-work}"/>
- </exec>
- <!-- report log -->
- <exec executable="/bin/cat">
- <arg value="${eclipse-work}/.metadata/.log"/>
- </exec>
- <!-- TODO: run jslint and something else here to check we have a complete set of .js files for java -->
- <!-- possibly compare timestamps between .js files and their mate in source - any newer or not present triggers a new build -->
- <!-- <mkdir dir="${packageDir}/${site}" /> -->
- <!-- <property name="swingjs.zipurl" value="https://github.com/BobHanson/java2script/blob/master/sources/net.sf.j2s.java.core/dist/SwingJS-site.zip?raw=true" /> -->
-
- <!-- and reset the .classpath -->
- <exec executable="/usr/bin/git" failifexecutionfails="true" dir="${eclipse-workrepo}">
- <arg value="checkout" />
- <arg value="${git.commit}"/>
- <arg value="--"/>
- <arg value=".classpath" />
- </exec>
-
- <!-- finally copy artefacts from eclipse project checkout to the build site -->
- <copy todir="${site}">
- <fileset dir="${eclipse-workrepo}/site"/>
- </copy>
-</target>
-<target name="unzip-to-site" depends="prepare-site">
- <ant antfile="build-site.xml"/>
-</target>
-
- <target name="make-j2s-cores" depends="">
- <ant antfile="buildcore.xml" target="build-all-cores"/>
- </target>
-</project>
+++ /dev/null
-<project name="JSmol" default="toJs" basedir=".">
-
- <taskdef resource="net/sf/antcontrib/antcontrib.properties">
- <classpath>
- <pathelement location="./utils/ant-contrib-1.0b3.jar" />
- </classpath>
- </taskdef>
-
- <target name="build-all-cores" id="build-all-cores" depends="toJs">
- <foreach target="CallToJs" param="classlist">
- <path>
- <fileset dir="./classlists/" includes="*.txt" />
- </path>
- </foreach>
- </target>
-
- <target name="CallToJs" id="CallToJs" description="Don't call this directly - used by build-all-cores to configure the toJs task for each set of classes in classlist">
- <basename property="core.name.txt" file="${classlist}"/>
- <propertyregex property="core.name" input="${core.name.txt}" replace="" regexp="\.txt"/>
- <antcall target="toJs"/>
- </target>
-
- <target name="toJs" id="toJs">
- <!-- sensible defaults for default target -->
- <property name="site" value="site"/>
- <property name="site.path" value="${site}/swingjs" />
- <property name="core.name" value="_jalview" />
- <property name="classlist"
- description="Class list .txt generated by java2script classloader to be bundled into corefile - default is _j2sclasslist.txt"
- value="_j2sclasslist.txt" />
- <!-- create a NON svn local directory only containing JS files
-
- <echo>Deleting the site directory.</echo>
- <delete quiet="true" dir="site" />
- -->
-
- <!-- make core files -->
-
- <echo>Building core file '${core.name}' - warnings are OK; "does not exist" is trouble</echo>
- <echo>Reading core class list from file ${classlist}</echo>
- <loadresource property="coreclasses">
- <file file="${classlist}"/>
- </loadresource>
-
- <antcall target="call-core">
- <param name="call-core.name" value="${core.name}" />
- <param name="call-core.list" value="
- core/coreswingjs.js
- ${coreclasses}
- " />
- </antcall>
- <antcall target="publish-core-template"/>
- </target>
-
- <target name="publish-core-template" id="publish-core-template" description="Creates a new file ${template.name}_${core.name} from ${template.html} in ${site} which include core file ${core.name} in the Info block">
- <!-- TODO: extend to process all html templates -->
- <property name="template.html" value="jalview_bin_Jalview.html"/>
- <property name="template.name" value="JalviewJS"/>
-
- <echo>......Now copying ${site}/${template.html} as ${$template.name}_${core.name}.html with core:"${core.name}", added to the Info block.</echo>
- <copy file="${site}/${template.html}" tofile="${site}/${template.name}_${core.name}.html"/>
- <replace token="NONE" value="${core.name}" file="${site}/${template.name}_${core.name}.html"/>
-
- </target>
-
-
- <target name="call-core" id="call-core">
- <echo>......Creating core${call-core.name}.js</echo>
- <concat destfile="${site.path}/js/core/tmp.js">
- <filelist dir="${site.path}/j2s" files="${call-core.list}" />
- </concat>
-
- <replace dir="${site.path}/js/core" includes="tmp.js" token="Clazz." value="Clazz_"/>
- <replace dir="${site.path}/js/core" includes="tmp.js" token="Clazz__" value="Clazz._"/>
- <echo>......Generating ${site.path}/j2s/core/core${call-core.name}.js</echo>
- <concat destfile="${site.path}/j2s/core/core${call-core.name}.js">
- <filelist dir="${site.path}/js" files="
- core/coretop2.js
- core/tmp.js
- core/corebottom2.js
- " />
- </concat>
- <echo>......Generating ${site.path}/j2s/core/core${call-core.name}.z.js</echo>
- <java jar="tools/closure_compiler.jar" fork="true" dir="${site.path}/j2s/core" failonerror="false">
- <arg line="--js core${call-core.name}.js --js_output_file core${call-core.name}.z.js" />
- </java>
- <delete quiet="true" file="${site.path}/js/core/tmp.js" />
- </target>
-
-
-
-</project>
OSX_KEYPASS =
JSIGN_SH = echo
-eclipse_extra_jdt_prefs_file = .settings/org.eclipse.jdt.core.jalview.prefs
-
pandoc_exec = /usr/local/bin/pandoc,/usr/bin/pandoc
dev = false
bamboo_channelbase = https://builds.jalview.org/browse
bamboo_planKey =
bamboo_getdown_channel_suffix = /latest/artifact/shared/getdown-channel
-
\ No newline at end of file
+
+eclipse_extra_jdt_prefs_file = .settings/org.eclipse.jdt.core.jalview.prefs
+eclipse_project_name = jalview
+eclipse_bin_dir = bin
+
+jalviewjs_eclipse_root = ~/buildtools/eclipse/eclipse-jee-2019-06
+
+jalviewjs_utils_dir = utils/jalviewjs
+jalviewjs_eclipse_dropins_dir = eclipse/dropins
+jalviewjs_swingjs_zip = SwingJS-site.zip
+jalviewjs_libjs_dir = libjs
+jalviewjs_resource_dir = resources
+jalviewjs_site_resource_dir = site-resources
+jalviewjs_site_dir = site
+jalviewjs_j2s_subdir = swingjs/j2s
+jalviewjs_j2s_settings_file = dot_j2s
+jalviewjs_j2s_settings = .j2s
+jalviewjs_eclipse_workspace = ../tmp/eclipse-workspace
+#jalviewjs_eclipseBuildArg = build
+jalviewjs_eclipseBuildArg = cleanBuild
+jalviewjs_server_port = 9001
+jalviewjs_server_wait = 30
+jalviewjs_server_resource = /jalview_bin_Jalview.html
+
+j2s.compiler.status = enable
+#j2s.site.directory = null
+#j2s.log.methods.declared = null
+#j2s.log.methods.called = null
+#a semicolon-separated list of package-level file paths to be excluded
+j2s.excluded.paths = test;testng;util
+#j2s.testing = null
+#j2s.compiler.nonqualified.packages = null
+#j2s.compiler.nonqualified.classes = null
+#j2s.compiler.mode = debug
+#a semicolon-separated list of package (foo.) or class (foo.bar) replacements to be made
+j2s.class.replacements = org.apache.log4j.->jalview.javascript.log4j.
+j2s.template.html = utils/jalviewjs/template.html
+#output file name for logging methods declared - delete the file to regenerate a listing
+#j2s.prop.j2s.log.methods.declared=swingjs/methodsDeclared_csv
+#output file name for logging methods called - delete the file to regenerate a listing
+#j2s.prop.j2s.log.methods_called=swingjs/methodsCalled_csv
+#if set, every instance of methods called will be logged
+#otherwise, only the first call to a method will be logged
+#output will be comma-separated: called method,caller class
+#j2s.prop.j2s.log.all.calls=true
+
+jalviewjs_j2s_stdout = j2s-transpile.out
+jalviewjs_j2s_stderr = j2s-transpile.err
+jalviewjs_j2s_to_console = true
+
+
+
* {@code null}; please use {@link JSONValue#parseWithException(Reader)}
* instead
*/
+ @Deprecated
public static Object parse(Reader in){
try{
JSONParser parser=new JSONParser();
* {@code null}; please use {@link JSONValue#parseWithException(String)}
* instead
*/
+ @Deprecated
public static Object parse(String s){
StringReader in=new StringReader(s);
return parse(in);
+++ /dev/null
-This is sources/net.sf.j2s.java.core/dist/DEV_NOTES.txt
-
-_j2sclasslist.txt
-
-the list of .js files concatenated into coreswingjs.js and minified to coreswingjs.z.js
-
-
-SwingJS-site.zip
-
-the full site directory for SwingJS including all files not in the test/ directory.
+++ /dev/null
-The swingjs directory contains the current transpiler (net.sf.j2s.core.jar)
-and the run-time core site files (SwingJS-site.zip)
-
-In addition are version directories -- for example, ver/3.1.1 and ver/3.2.1
-
-The second of these, ver/3.2.1, adds Java 8 functionality.
-
-
+++ /dev/null
-java/applet/Applet.js
-java/applet/AppletContext.js
-java/applet/AppletStub.js
-java/applet/JSApplet.js
-java/awt/ActiveEvent.js
-java/awt/Adjustable.js
-java/awt/AWTEvent.js
-java/awt/AWTEventMulticaster.js
-java/awt/AWTKeyStroke.js
-java/awt/BasicStroke.js
-java/awt/BorderLayout.js
-java/awt/Button.js
-java/awt/Color.js
-java/awt/color/ColorSpace.js
-java/awt/Component.js
-java/awt/ComponentOrientation.js
-java/awt/Container.js
-java/awt/ContainerOrderFocusTraversalPolicy.js
-java/awt/Cursor.js
-java/awt/DefaultFocusTraversalPolicy.js
-java/awt/DefaultKeyboardFocusManager.js
-java/awt/Dialog.js
-java/awt/Dimension.js
-java/awt/dnd/peer/DropTargetPeer.js
-java/awt/event/ActionListener.js
-java/awt/event/AdjustmentEvent.js
-java/awt/event/AdjustmentListener.js
-java/awt/event/AWTEventListener.js
-java/awt/event/ComponentAdapter.js
-java/awt/event/ComponentEvent.js
-java/awt/event/ComponentListener.js
-java/awt/event/ContainerListener.js
-java/awt/event/FocusEvent.js
-java/awt/event/FocusListener.js
-java/awt/event/HierarchyBoundsListener.js
-java/awt/event/HierarchyListener.js
-java/awt/event/InputEvent.js
-java/awt/event/InputMethodListener.js
-java/awt/event/InvocationEvent.js
-java/awt/event/ItemEvent.js
-java/awt/event/ItemListener.js
-java/awt/event/KeyListener.js
-java/awt/event/MouseEvent.js
-java/awt/event/MouseListener.js
-java/awt/event/MouseMotionListener.js
-java/awt/event/MouseWheelListener.js
-java/awt/event/TextListener.js
-java/awt/event/WindowAdapter.js
-java/awt/event/WindowEvent.js
-java/awt/event/WindowFocusListener.js
-java/awt/event/WindowListener.js
-java/awt/event/WindowStateListener.js
-java/awt/EventDispatchThread.js
-java/awt/EventFilter.js
-java/awt/EventQueue.js
-java/awt/EventQueueItem.js
-java/awt/FlowLayout.js
-java/awt/FocusTraversalPolicy.js
-java/awt/Font.js
-java/awt/font/FontRenderContext.js
-java/awt/FontMetrics.js
-java/awt/Frame.js
-java/awt/geom/AffineTransform.js
-java/awt/geom/Dimension2D.js
-java/awt/geom/Path2D.js
-java/awt/geom/PathIterator.js
-java/awt/geom/Point2D.js
-java/awt/geom/Rectangle2D.js
-java/awt/geom/RectangularShape.js
-java/awt/geom/RectIterator.js
-java/awt/GraphicsCallback.js
-java/awt/GraphicsConfiguration.js
-java/awt/GraphicsDevice.js
-java/awt/GraphicsEnvironment.js
-java/awt/image/ImageObserver.js
-java/awt/Insets.js
-java/awt/ItemSelectable.js
-java/awt/JSComponent.js
-java/awt/JSDialog.js
-java/awt/JSFrame.js
-java/awt/JSPanel.js
-java/awt/KeyboardFocusManager.js
-java/awt/KeyEventDispatcher.js
-java/awt/KeyEventPostProcessor.js
-java/awt/Label.js
-java/awt/LayoutManager.js
-java/awt/LayoutManager2.js
-java/awt/LightweightDispatcher.js
-java/awt/Paint.js
-java/awt/Panel.js
-java/awt/peer/ComponentPeer.js
-java/awt/peer/ContainerPeer.js
-java/awt/peer/FramePeer.js
-java/awt/peer/KeyboardFocusManagerPeer.js
-java/awt/peer/LightweightPeer.js
-java/awt/peer/WindowPeer.js
-java/awt/Point.js
-java/awt/Queue.js
-java/awt/Rectangle.js
-java/awt/RenderingHints.js
-java/awt/Scrollbar.js
-java/awt/ScrollPane.js
-java/awt/Shape.js
-java/awt/Stroke.js
-java/awt/TextArea.js
-java/awt/TextComponent.js
-java/awt/TextField.js
-java/awt/Toolkit.js
-java/awt/Transparency.js
-java/awt/Window.js
-java/beans/ChangeListenerMap.js
-java/beans/PropertyChangeEvent.js
-java/beans/PropertyChangeListener.js
-java/beans/PropertyChangeSupport.js
-java/lang/AbstractStringBuilder.js
-java/lang/Class.js
-java/lang/Enum.js
-java/lang/Iterable.js
-java/lang/reflect/Constructor.js
-java/lang/reflect/Method.js
-java/lang/StringBuffer.js
-java/lang/StringBuilder.js
-java/lang/Thread.js
-java/lang/ThreadGroup.js
-java/math/RoundingMode.js
-java/net/URL.js
-java/net/URLStreamHandlerFactory.js
-java/text/CharacterIterator.js
-java/text/DecimalFormat.js
-java/text/DecimalFormatSymbols.js
-java/text/DigitList.js
-java/text/FieldPosition.js
-java/text/Format.js
-java/text/NumberFormat.js
-java/util/AbstractCollection.js
-java/util/AbstractList.js
-java/util/AbstractMap.js
-java/util/AbstractSequentialList.js
-java/util/AbstractSet.js
-java/util/ArrayList.js
-java/util/Arrays.js
-java/util/Collection.js
-java/util/Collections.js
-java/util/Deque.js
-java/util/Dictionary.js
-java/util/Enumeration.js
-java/util/EventListener.js
-java/util/EventObject.js
-java/util/HashMap.js
-java/util/HashSet.js
-java/util/Hashtable.js
-java/util/IdentityHashMap.js
-java/util/Iterator.js
-java/util/LinkedHashMap.js
-java/util/LinkedList.js
-java/util/List.js
-java/util/ListResourceBundle.js
-java/util/Locale.js
-java/util/Map.js
-java/util/Objects.js
-java/util/Queue.js
-java/util/Random.js
-java/util/RandomAccess.js
-java/util/ResourceBundle.js
-java/util/Set.js
-java/util/Vector.js
-javajs/api/JSFunction.js
-javajs/util/AjaxURLConnection.js
-javajs/util/AjaxURLStreamHandlerFactory.js
-javajs/util/AU.js
-javajs/util/JSThread.js
-javajs/util/Lst.js
-javajs/util/PT.js
-javajs/util/SB.js
-javax/swing/AbstractAction.js
-javax/swing/AbstractButton.js
-javax/swing/AbstractListModel.js
-javax/swing/Action.js
-javax/swing/ActionMap.js
-javax/swing/AncestorNotifier.js
-javax/swing/ArrayTable.js
-javax/swing/border/AbstractBorder.js
-javax/swing/border/BevelBorder.js
-javax/swing/border/Border.js
-javax/swing/border/CompoundBorder.js
-javax/swing/border/EmptyBorder.js
-javax/swing/border/EtchedBorder.js
-javax/swing/border/LineBorder.js
-javax/swing/BorderFactory.js
-javax/swing/BoundedRangeModel.js
-javax/swing/BoxLayout.js
-javax/swing/ButtonGroup.js
-javax/swing/ButtonModel.js
-javax/swing/ClientPropertyKey.js
-javax/swing/ComboBoxModel.js
-javax/swing/DefaultBoundedRangeModel.js
-javax/swing/DefaultButtonModel.js
-javax/swing/DefaultComboBoxModel.js
-javax/swing/DefaultSingleSelectionModel.js
-javax/swing/DropMode.js
-javax/swing/event/AncestorEvent.js
-javax/swing/event/AncestorListener.js
-javax/swing/event/CaretEvent.js
-javax/swing/event/CaretListener.js
-javax/swing/event/ChangeEvent.js
-javax/swing/event/ChangeListener.js
-javax/swing/event/DocumentEvent.js
-javax/swing/event/DocumentListener.js
-javax/swing/event/EventListenerList.js
-javax/swing/event/ListDataEvent.js
-javax/swing/event/ListDataListener.js
-javax/swing/event/UndoableEditEvent.js
-javax/swing/event/UndoableEditListener.js
-javax/swing/InputMap.js
-javax/swing/JApplet.js
-javax/swing/JButton.js
-javax/swing/JCheckBox.js
-javax/swing/JCheckBoxMenuItem.js
-javax/swing/JComboBox.js
-javax/swing/JComponent.js
-javax/swing/JFrame.js
-javax/swing/JLabel.js
-javax/swing/JLayeredPane.js
-javax/swing/JMenu.js
-javax/swing/JMenuBar.js
-javax/swing/JMenuItem.js
-javax/swing/JPanel.js
-javax/swing/JPopupMenu.js
-javax/swing/JRadioButtonMenuItem.js
-javax/swing/JRootPane.js
-javax/swing/JScrollBar.js
-javax/swing/JScrollPane.js
-javax/swing/JSeparator.js
-javax/swing/JTextArea.js
-javax/swing/JTextField.js
-javax/swing/JToggleButton.js
-javax/swing/JViewport.js
-javax/swing/KeyboardManager.js
-javax/swing/KeyStroke.js
-javax/swing/ListModel.js
-javax/swing/LookAndFeel.js
-javax/swing/MenuElement.js
-javax/swing/MutableComboBoxModel.js
-javax/swing/plaf/ActionMapUIResource.js
-javax/swing/plaf/basic/BasicBorders.js
-javax/swing/plaf/BorderUIResource.js
-javax/swing/plaf/ColorUIResource.js
-javax/swing/plaf/ComponentUI.js
-javax/swing/plaf/DimensionUIResource.js
-javax/swing/plaf/FontUIResource.js
-javax/swing/plaf/InputMapUIResource.js
-javax/swing/plaf/InsetsUIResource.js
-javax/swing/plaf/UIResource.js
-javax/swing/RepaintManager.js
-javax/swing/RootPaneContainer.js
-javax/swing/Scrollable.js
-javax/swing/ScrollPaneConstants.js
-javax/swing/ScrollPaneLayout.js
-javax/swing/SingleSelectionModel.js
-javax/swing/SizeRequirements.js
-javax/swing/SwingConstants.js
-javax/swing/SwingPaintEventDispatcher.js
-javax/swing/SwingUtilities.js
-javax/swing/text/AbstractDocument.js
-javax/swing/text/AttributeSet.js
-javax/swing/text/Caret.js
-javax/swing/text/DefaultCaret.js
-javax/swing/text/DefaultEditorKit.js
-javax/swing/text/Document.js
-javax/swing/text/EditorKit.js
-javax/swing/text/Element.js
-javax/swing/text/GapContent.js
-javax/swing/text/GapVector.js
-javax/swing/text/JTextComponent.js
-javax/swing/text/MutableAttributeSet.js
-javax/swing/text/PlainDocument.js
-javax/swing/text/PlainView.js
-javax/swing/text/Position.js
-javax/swing/text/Segment.js
-javax/swing/text/SegmentCache.js
-javax/swing/text/SimpleAttributeSet.js
-javax/swing/text/Style.js
-javax/swing/text/StyleConstants.js
-javax/swing/text/StyleContext.js
-javax/swing/text/TabExpander.js
-javax/swing/text/TextAction.js
-javax/swing/text/Utilities.js
-javax/swing/text/View.js
-javax/swing/tree/TreeNode.js
-javax/swing/UIDefaults.js
-javax/swing/UIManager.js
-javax/swing/undo/AbstractUndoableEdit.js
-javax/swing/undo/CompoundEdit.js
-javax/swing/undo/UndoableEdit.js
-javax/swing/ViewportLayout.js
-javax/swing/WindowConstants.js
-sun/awt/AppContext.js
-sun/awt/AWTAccessor.js
-sun/awt/AWTAutoShutdown.js
-sun/awt/CausedFocusEvent.js
-sun/awt/ComponentFactory.js
-sun/awt/KeyboardFocusManagerPeerProvider.js
-sun/awt/MostRecentKeyValue.js
-sun/awt/MostRecentThreadAppContext.js
-sun/awt/PaintEventDispatcher.js
-sun/awt/PostEventQueue.js
-sun/awt/RequestFocusController.js
-sun/awt/SunToolkit.js
-sun/awt/WindowClosingListener.js
-sun/awt/WindowClosingSupport.js
-sun/font/FontDesignMetrics.js
-sun/swing/DefaultLookup.js
-sun/swing/SwingLazyValue.js
-sun/text/resources/FormatData.js
-sun/text/resources/FormatData_en.js
-sun/util/resources/LocaleData.js
-swingjs/a2s/A2SContainer.js
-swingjs/a2s/A2SEvent.js
-swingjs/a2s/A2SListener.js
-swingjs/a2s/Applet.js
-swingjs/a2s/Button.js
-swingjs/a2s/Label.js
-swingjs/a2s/Panel.js
-swingjs/a2s/Scrollbar.js
-swingjs/a2s/ScrollPane.js
-swingjs/a2s/TextArea.js
-swingjs/a2s/TextField.js
-swingjs/api/Interface.js
-swingjs/api/js/DOMNode.js
-swingjs/api/js/HTML5CanvasContext2D.js
-swingjs/api/js/JSInterface.js
-swingjs/api/JSMinimalAbstractDocument.js
-swingjs/jquery/JQueryUI.js
-swingjs/JSAbstractDocument.js
-swingjs/JSApp.js
-swingjs/JSApplet.js
-swingjs/JSAppletThread.js
-swingjs/JSAppletViewer.js
-swingjs/JSDocumentEvent.js
-swingjs/JSFocusPeer.js
-swingjs/JSFontMetrics.js
-swingjs/JSFrameViewer.js
-swingjs/JSGraphics2D.js
-swingjs/JSGraphicsConfiguration.js
-swingjs/JSGraphicsEnvironment.js
-swingjs/JSMouse.js
-swingjs/JSNullComponentPeer.js
-swingjs/JSPlainDocument.js
-swingjs/JSScreenDevice.js
-swingjs/JSThreadGroup.js
-swingjs/JSToolkit.js
-swingjs/JSUtil.js
-swingjs/plaf/ButtonListener.js
-swingjs/plaf/DefaultMenuLayout.js
-swingjs/plaf/HTML5LookAndFeel.js
-swingjs/plaf/JSAppletUI.js
-swingjs/plaf/JSButtonUI.js
-swingjs/plaf/JSCheckBoxMenuItemUI.js
-swingjs/plaf/JSCheckBoxUI.js
-swingjs/plaf/JSComboBoxUI.js
-swingjs/plaf/JSComponentUI.js
-swingjs/plaf/JSEventHandler.js
-swingjs/plaf/JSFrameUI.js
-swingjs/plaf/JSGraphicsUtils.js
-swingjs/plaf/JSLabelUI.js
-swingjs/plaf/JSLayeredPaneUI.js
-swingjs/plaf/JSLightweightUI.js
-swingjs/plaf/JSMenuBarUI.js
-swingjs/plaf/JSMenuItemUI.js
-swingjs/plaf/JSMenuUI.js
-swingjs/plaf/JSPanelUI.js
-swingjs/plaf/JSPopupMenuSeparatorUI.js
-swingjs/plaf/JSPopupMenuUI.js
-swingjs/plaf/JSRadioButtonMenuItemUI.js
-swingjs/plaf/JSRadioButtonUI.js
-swingjs/plaf/JSRootPaneUI.js
-swingjs/plaf/JSScrollBarUI.js
-swingjs/plaf/JSScrollPaneUI.js
-swingjs/plaf/JSSeparatorUI.js
-swingjs/plaf/JSSliderUI.js
-swingjs/plaf/JSTextAreaUI.js
-swingjs/plaf/JSTextFieldUI.js
-swingjs/plaf/JSTextUI.js
-swingjs/plaf/JSTextViewUI.js
-swingjs/plaf/JSViewportUI.js
-swingjs/plaf/JSWindowUI.js
-swingjs/plaf/LazyActionMap.js
-swingjs/plaf/Resizer.js
-swingjs/plaf/TextListener.js
+++ /dev/null
-20190422120213
+++ /dev/null
-20180923174836
+++ /dev/null
-20180927214151
+++ /dev/null
-This is sources/net.sf.j2s.java.core/dist/DEV_NOTES.txt
-
-_j2sclasslist.txt
-
-the list of .js files concatenated into coreswingjs.js and minified to coreswingjs.z.js
-
-
-SwingJS-site.zip
-
-the full site directory for SwingJS including all files not in the test/ directory.
+++ /dev/null
-java/applet/Applet.js
-java/applet/AppletContext.js
-java/applet/AppletStub.js
-java/applet/JSApplet.js
-java/awt/ActiveEvent.js
-java/awt/Adjustable.js
-java/awt/AWTEvent.js
-java/awt/AWTEventMulticaster.js
-java/awt/AWTKeyStroke.js
-java/awt/BasicStroke.js
-java/awt/BorderLayout.js
-java/awt/Button.js
-java/awt/Color.js
-java/awt/color/ColorSpace.js
-java/awt/Component.js
-java/awt/ComponentOrientation.js
-java/awt/Container.js
-java/awt/ContainerOrderFocusTraversalPolicy.js
-java/awt/Cursor.js
-java/awt/DefaultFocusTraversalPolicy.js
-java/awt/DefaultKeyboardFocusManager.js
-java/awt/Dialog.js
-java/awt/Dimension.js
-java/awt/dnd/peer/DropTargetPeer.js
-java/awt/event/ActionListener.js
-java/awt/event/AdjustmentEvent.js
-java/awt/event/AdjustmentListener.js
-java/awt/event/AWTEventListener.js
-java/awt/event/ComponentAdapter.js
-java/awt/event/ComponentEvent.js
-java/awt/event/ComponentListener.js
-java/awt/event/ContainerListener.js
-java/awt/event/FocusEvent.js
-java/awt/event/FocusListener.js
-java/awt/event/HierarchyBoundsListener.js
-java/awt/event/HierarchyListener.js
-java/awt/event/InputEvent.js
-java/awt/event/InputMethodListener.js
-java/awt/event/InvocationEvent.js
-java/awt/event/ItemEvent.js
-java/awt/event/ItemListener.js
-java/awt/event/KeyListener.js
-java/awt/event/MouseEvent.js
-java/awt/event/MouseListener.js
-java/awt/event/MouseMotionListener.js
-java/awt/event/MouseWheelListener.js
-java/awt/event/TextListener.js
-java/awt/event/WindowAdapter.js
-java/awt/event/WindowEvent.js
-java/awt/event/WindowFocusListener.js
-java/awt/event/WindowListener.js
-java/awt/event/WindowStateListener.js
-java/awt/EventDispatchThread.js
-java/awt/EventFilter.js
-java/awt/EventQueue.js
-java/awt/EventQueueItem.js
-java/awt/FlowLayout.js
-java/awt/FocusTraversalPolicy.js
-java/awt/Font.js
-java/awt/font/FontRenderContext.js
-java/awt/FontMetrics.js
-java/awt/Frame.js
-java/awt/geom/AffineTransform.js
-java/awt/geom/Dimension2D.js
-java/awt/geom/Path2D.js
-java/awt/geom/PathIterator.js
-java/awt/geom/Point2D.js
-java/awt/geom/Rectangle2D.js
-java/awt/geom/RectangularShape.js
-java/awt/geom/RectIterator.js
-java/awt/GraphicsCallback.js
-java/awt/GraphicsConfiguration.js
-java/awt/GraphicsDevice.js
-java/awt/GraphicsEnvironment.js
-java/awt/image/ImageObserver.js
-java/awt/Insets.js
-java/awt/ItemSelectable.js
-java/awt/JSComponent.js
-java/awt/JSDialog.js
-java/awt/JSFrame.js
-java/awt/JSPanel.js
-java/awt/KeyboardFocusManager.js
-java/awt/KeyEventDispatcher.js
-java/awt/KeyEventPostProcessor.js
-java/awt/Label.js
-java/awt/LayoutManager.js
-java/awt/LayoutManager2.js
-java/awt/LightweightDispatcher.js
-java/awt/Paint.js
-java/awt/Panel.js
-java/awt/peer/ComponentPeer.js
-java/awt/peer/ContainerPeer.js
-java/awt/peer/FramePeer.js
-java/awt/peer/KeyboardFocusManagerPeer.js
-java/awt/peer/LightweightPeer.js
-java/awt/peer/WindowPeer.js
-java/awt/Point.js
-java/awt/Queue.js
-java/awt/Rectangle.js
-java/awt/RenderingHints.js
-java/awt/Scrollbar.js
-java/awt/ScrollPane.js
-java/awt/Shape.js
-java/awt/Stroke.js
-java/awt/TextArea.js
-java/awt/TextComponent.js
-java/awt/TextField.js
-java/awt/Toolkit.js
-java/awt/Transparency.js
-java/awt/Window.js
-java/beans/ChangeListenerMap.js
-java/beans/PropertyChangeEvent.js
-java/beans/PropertyChangeListener.js
-java/beans/PropertyChangeSupport.js
-java/lang/AbstractStringBuilder.js
-java/lang/Class.js
-java/lang/Enum.js
-java/lang/Iterable.js
-java/lang/reflect/Constructor.js
-java/lang/reflect/Method.js
-java/lang/StringBuffer.js
-java/lang/StringBuilder.js
-java/lang/Thread.js
-java/lang/ThreadGroup.js
-java/math/RoundingMode.js
-java/net/URL.js
-java/net/URLStreamHandlerFactory.js
-java/text/CharacterIterator.js
-java/text/DecimalFormat.js
-java/text/DecimalFormatSymbols.js
-java/text/DigitList.js
-java/text/FieldPosition.js
-java/text/Format.js
-java/text/NumberFormat.js
-java/util/AbstractCollection.js
-java/util/AbstractList.js
-java/util/AbstractMap.js
-java/util/AbstractSequentialList.js
-java/util/AbstractSet.js
-java/util/ArrayList.js
-java/util/Arrays.js
-java/util/Collection.js
-java/util/Collections.js
-java/util/Deque.js
-java/util/Dictionary.js
-java/util/Enumeration.js
-java/util/EventListener.js
-java/util/EventObject.js
-java/util/HashMap.js
-java/util/HashSet.js
-java/util/Hashtable.js
-java/util/IdentityHashMap.js
-java/util/Iterator.js
-java/util/LinkedHashMap.js
-java/util/LinkedList.js
-java/util/List.js
-java/util/ListResourceBundle.js
-java/util/Locale.js
-java/util/Map.js
-java/util/Objects.js
-java/util/Queue.js
-java/util/Random.js
-java/util/RandomAccess.js
-java/util/ResourceBundle.js
-java/util/Set.js
-java/util/Vector.js
-javajs/api/JSFunction.js
-javajs/util/AjaxURLConnection.js
-javajs/util/AjaxURLStreamHandlerFactory.js
-javajs/util/AU.js
-javajs/util/JSThread.js
-javajs/util/Lst.js
-javajs/util/PT.js
-javajs/util/SB.js
-javax/swing/AbstractAction.js
-javax/swing/AbstractButton.js
-javax/swing/AbstractListModel.js
-javax/swing/Action.js
-javax/swing/ActionMap.js
-javax/swing/AncestorNotifier.js
-javax/swing/ArrayTable.js
-javax/swing/border/AbstractBorder.js
-javax/swing/border/BevelBorder.js
-javax/swing/border/Border.js
-javax/swing/border/CompoundBorder.js
-javax/swing/border/EmptyBorder.js
-javax/swing/border/EtchedBorder.js
-javax/swing/border/LineBorder.js
-javax/swing/BorderFactory.js
-javax/swing/BoundedRangeModel.js
-javax/swing/BoxLayout.js
-javax/swing/ButtonGroup.js
-javax/swing/ButtonModel.js
-javax/swing/ClientPropertyKey.js
-javax/swing/ComboBoxModel.js
-javax/swing/DefaultBoundedRangeModel.js
-javax/swing/DefaultButtonModel.js
-javax/swing/DefaultComboBoxModel.js
-javax/swing/DefaultSingleSelectionModel.js
-javax/swing/DropMode.js
-javax/swing/event/AncestorEvent.js
-javax/swing/event/AncestorListener.js
-javax/swing/event/CaretEvent.js
-javax/swing/event/CaretListener.js
-javax/swing/event/ChangeEvent.js
-javax/swing/event/ChangeListener.js
-javax/swing/event/DocumentEvent.js
-javax/swing/event/DocumentListener.js
-javax/swing/event/EventListenerList.js
-javax/swing/event/ListDataEvent.js
-javax/swing/event/ListDataListener.js
-javax/swing/event/UndoableEditEvent.js
-javax/swing/event/UndoableEditListener.js
-javax/swing/InputMap.js
-javax/swing/JApplet.js
-javax/swing/JButton.js
-javax/swing/JCheckBox.js
-javax/swing/JCheckBoxMenuItem.js
-javax/swing/JComboBox.js
-javax/swing/JComponent.js
-javax/swing/JFrame.js
-javax/swing/JLabel.js
-javax/swing/JLayeredPane.js
-javax/swing/JMenu.js
-javax/swing/JMenuBar.js
-javax/swing/JMenuItem.js
-javax/swing/JPanel.js
-javax/swing/JPopupMenu.js
-javax/swing/JRadioButtonMenuItem.js
-javax/swing/JRootPane.js
-javax/swing/JScrollBar.js
-javax/swing/JScrollPane.js
-javax/swing/JSeparator.js
-javax/swing/JTextArea.js
-javax/swing/JTextField.js
-javax/swing/JToggleButton.js
-javax/swing/JViewport.js
-javax/swing/KeyboardManager.js
-javax/swing/KeyStroke.js
-javax/swing/ListModel.js
-javax/swing/LookAndFeel.js
-javax/swing/MenuElement.js
-javax/swing/MutableComboBoxModel.js
-javax/swing/plaf/ActionMapUIResource.js
-javax/swing/plaf/basic/BasicBorders.js
-javax/swing/plaf/BorderUIResource.js
-javax/swing/plaf/ColorUIResource.js
-javax/swing/plaf/ComponentUI.js
-javax/swing/plaf/DimensionUIResource.js
-javax/swing/plaf/FontUIResource.js
-javax/swing/plaf/InputMapUIResource.js
-javax/swing/plaf/InsetsUIResource.js
-javax/swing/plaf/UIResource.js
-javax/swing/RepaintManager.js
-javax/swing/RootPaneContainer.js
-javax/swing/Scrollable.js
-javax/swing/ScrollPaneConstants.js
-javax/swing/ScrollPaneLayout.js
-javax/swing/SingleSelectionModel.js
-javax/swing/SizeRequirements.js
-javax/swing/SwingConstants.js
-javax/swing/SwingPaintEventDispatcher.js
-javax/swing/SwingUtilities.js
-javax/swing/text/AbstractDocument.js
-javax/swing/text/AttributeSet.js
-javax/swing/text/Caret.js
-javax/swing/text/DefaultCaret.js
-javax/swing/text/DefaultEditorKit.js
-javax/swing/text/Document.js
-javax/swing/text/EditorKit.js
-javax/swing/text/Element.js
-javax/swing/text/GapContent.js
-javax/swing/text/GapVector.js
-javax/swing/text/JTextComponent.js
-javax/swing/text/MutableAttributeSet.js
-javax/swing/text/PlainDocument.js
-javax/swing/text/PlainView.js
-javax/swing/text/Position.js
-javax/swing/text/Segment.js
-javax/swing/text/SegmentCache.js
-javax/swing/text/SimpleAttributeSet.js
-javax/swing/text/Style.js
-javax/swing/text/StyleConstants.js
-javax/swing/text/StyleContext.js
-javax/swing/text/TabExpander.js
-javax/swing/text/TextAction.js
-javax/swing/text/Utilities.js
-javax/swing/text/View.js
-javax/swing/tree/TreeNode.js
-javax/swing/UIDefaults.js
-javax/swing/UIManager.js
-javax/swing/undo/AbstractUndoableEdit.js
-javax/swing/undo/CompoundEdit.js
-javax/swing/undo/UndoableEdit.js
-javax/swing/ViewportLayout.js
-javax/swing/WindowConstants.js
-sun/awt/AppContext.js
-sun/awt/AWTAccessor.js
-sun/awt/AWTAutoShutdown.js
-sun/awt/CausedFocusEvent.js
-sun/awt/ComponentFactory.js
-sun/awt/KeyboardFocusManagerPeerProvider.js
-sun/awt/MostRecentKeyValue.js
-sun/awt/MostRecentThreadAppContext.js
-sun/awt/PaintEventDispatcher.js
-sun/awt/PostEventQueue.js
-sun/awt/RequestFocusController.js
-sun/awt/SunToolkit.js
-sun/awt/WindowClosingListener.js
-sun/awt/WindowClosingSupport.js
-sun/font/FontDesignMetrics.js
-sun/swing/DefaultLookup.js
-sun/swing/SwingLazyValue.js
-sun/text/resources/FormatData.js
-sun/text/resources/FormatData_en.js
-sun/util/resources/LocaleData.js
-swingjs/a2s/A2SContainer.js
-swingjs/a2s/A2SEvent.js
-swingjs/a2s/A2SListener.js
-swingjs/a2s/Applet.js
-swingjs/a2s/Button.js
-swingjs/a2s/Label.js
-swingjs/a2s/Panel.js
-swingjs/a2s/Scrollbar.js
-swingjs/a2s/ScrollPane.js
-swingjs/a2s/TextArea.js
-swingjs/a2s/TextField.js
-swingjs/api/Interface.js
-swingjs/api/js/DOMNode.js
-swingjs/api/js/HTML5CanvasContext2D.js
-swingjs/api/js/JSInterface.js
-swingjs/api/JSMinimalAbstractDocument.js
-swingjs/jquery/JQueryUI.js
-swingjs/JSAbstractDocument.js
-swingjs/JSApp.js
-swingjs/JSApplet.js
-swingjs/JSAppletThread.js
-swingjs/JSAppletViewer.js
-swingjs/JSDocumentEvent.js
-swingjs/JSFocusPeer.js
-swingjs/JSFontMetrics.js
-swingjs/JSFrameViewer.js
-swingjs/JSGraphics2D.js
-swingjs/JSGraphicsConfiguration.js
-swingjs/JSGraphicsEnvironment.js
-swingjs/JSMouse.js
-swingjs/JSNullComponentPeer.js
-swingjs/JSPlainDocument.js
-swingjs/JSScreenDevice.js
-swingjs/JSThreadGroup.js
-swingjs/JSToolkit.js
-swingjs/JSUtil.js
-swingjs/plaf/ButtonListener.js
-swingjs/plaf/DefaultMenuLayout.js
-swingjs/plaf/HTML5LookAndFeel.js
-swingjs/plaf/JSAppletUI.js
-swingjs/plaf/JSButtonUI.js
-swingjs/plaf/JSCheckBoxMenuItemUI.js
-swingjs/plaf/JSCheckBoxUI.js
-swingjs/plaf/JSComboBoxUI.js
-swingjs/plaf/JSComponentUI.js
-swingjs/plaf/JSEventHandler.js
-swingjs/plaf/JSFrameUI.js
-swingjs/plaf/JSGraphicsUtils.js
-swingjs/plaf/JSLabelUI.js
-swingjs/plaf/JSLayeredPaneUI.js
-swingjs/plaf/JSLightweightUI.js
-swingjs/plaf/JSMenuBarUI.js
-swingjs/plaf/JSMenuItemUI.js
-swingjs/plaf/JSMenuUI.js
-swingjs/plaf/JSPanelUI.js
-swingjs/plaf/JSPopupMenuSeparatorUI.js
-swingjs/plaf/JSPopupMenuUI.js
-swingjs/plaf/JSRadioButtonMenuItemUI.js
-swingjs/plaf/JSRadioButtonUI.js
-swingjs/plaf/JSRootPaneUI.js
-swingjs/plaf/JSScrollBarUI.js
-swingjs/plaf/JSScrollPaneUI.js
-swingjs/plaf/JSSeparatorUI.js
-swingjs/plaf/JSSliderUI.js
-swingjs/plaf/JSTextAreaUI.js
-swingjs/plaf/JSTextFieldUI.js
-swingjs/plaf/JSTextUI.js
-swingjs/plaf/JSTextViewUI.js
-swingjs/plaf/JSViewportUI.js
-swingjs/plaf/JSWindowUI.js
-swingjs/plaf/LazyActionMap.js
-swingjs/plaf/Resizer.js
-swingjs/plaf/TextListener.js
+++ /dev/null
-20190422120213
<!DOCTYPE html>
<html>
<head>
-<title>SwingJS test _NAME_</title>
-<meta charset="utf-8" />
+<title>SwingJS test _NAME_</title><meta charset="utf-8" />
<script src="swingjs/swingjs2.js"></script>
<script>
if (!self.SwingJS)alert('swingjs2.js was not found. It needs to be in swingjs folder in the same directory as ' + document.location.href)
getClassList = function(){J2S._saveFile('_j2sclasslist.txt', Clazz.ClassFilesLoaded.sort().join('\n'))}
</script>
<div style="position:absolute;left:900px;top:30px;width:600px;height:300px;">
-<div id="sysoutdiv" style="border:1px solid green;width:100%;height:95%;overflow:auto"></div>
+<div id="sysoutdiv" contentEditable="true" style="border:1px solid green;width:100%;height:95%;overflow:auto"></div>
This is System.out. <a href="javascript:testApplet._clearConsole()">clear it</a> <br>Add ?j2snocore to URL to see full class list; ?j2sdebug to use uncompressed j2s/core files <br><a href="javascript:getClassList()">get _j2sClassList.txt</a>
</div>
</body>
--- /dev/null
+# see https://github.com/seeq12/eclipse-import-projects-plugin
+# see https://github.com/java2script/java2script
+
+for x in \
+https://github.com/seeq12/eclipse-import-projects-plugin/raw/master/jar/com.seeq.eclipse.importprojects_1.4.0.jar \
+https://github.com/BobHanson/java2script/raw/master/sources/net.sf.j2s.core/dist/swingjs/SwingJS-site.zip \
+https://github.com/BobHanson/java2script/raw/master/sources/net.sf.j2s.core/dist/swingjs/net.sf.j2s.core.jar
+do
+ wget "$x"
+done
+
git://source.jalview.org / jalview.git / commitdiff