From: Ben Soares Date: Wed, 16 Oct 2019 10:36:22 +0000 (+0100) Subject: Merge branch 'Jalview-JS/develop' into Jalview-JS/develop_with_gradle_build X-Git-Tag: Release_2_11_4_0~45^2~18^2~114 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=b60afa2c2d87c9730e62fe6d7835b4d642ab9ecd;hp=fe350265127bd31fd149b2a4b23e51d2d0bd9ef5;p=jalview.git Merge branch 'Jalview-JS/develop' into Jalview-JS/develop_with_gradle_build Merging in Jalview-JS/develop (should be no changes -- just checking) --- diff --git a/.gitignore b/.gitignore index 46cc0e5..c78ace4 100644 --- a/.gitignore +++ b/.gitignore @@ -30,3 +30,6 @@ TESTNG *.swp /bin /doc/building.html +/.j2s +/template.html + diff --git a/.j2s b/.j2s deleted file mode 100644 index 93fd157..0000000 --- a/.j2s +++ /dev/null @@ -1,20 +0,0 @@ -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 - - diff --git a/README_GRADLE_JALVIEWJS-2019-10-15.md b/README_GRADLE_JALVIEWJS-2019-10-15.md new file mode 100644 index 0000000..610ce9b --- /dev/null +++ b/README_GRADLE_JALVIEWJS-2019-10-15.md @@ -0,0 +1,38 @@ +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). + + diff --git a/build-libjs.xml b/build-libjs.xml deleted file mode 100644 index 3fb3cd3..0000000 --- a/build-libjs.xml +++ /dev/null @@ -1,67 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - Zipping up ${varna.zip} - - - - - - - Zipping up ${mig.zip} - - - - - - - Zipping up ${intervalstore.zip} - - - - - - - diff --git a/build-site.xml b/build-site.xml deleted file mode 100644 index 0cc062d..0000000 --- a/build-site.xml +++ /dev/null @@ -1,95 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Copying ${resource.dir} files into ${j2s.dir} - - - - - - - - Copying ${site-resource.dir} files into ${site.dir} - - - - - - - - - - diff --git a/build.gradle b/build.gradle index f02d8ad..07c744f 100644 --- a/build.gradle +++ b/build.gradle @@ -1,15 +1,13 @@ import org.apache.tools.ant.filters.ReplaceTokens -//import org.apache.tools.ant.filters.ReplaceRegexp import org.gradle.internal.os.OperatingSystem -import org.gradle.plugins.ide.eclipse.model.* - +import org.gradle.plugins.ide.eclipse.model.Output +import org.gradle.plugins.ide.eclipse.model.Library import groovy.transform.ExternalizeMethods buildscript { dependencies { classpath 'org.openclover:clover:4.3.1' - classpath 'org.apache.commons:commons-compress:1.18' } } @@ -30,6 +28,10 @@ repositories { } } +dependencies { + compile 'org.apache.commons:commons-compress:1.18' +} + mainClassName = launcherClass def cloverInstrDir = file("$buildDir/$cloverSourcesInstrDir") def classes = "$jalviewDir/$classesDir" @@ -164,6 +166,8 @@ ext { */ gitHash = "" gitBranch = "" + + jalviewjsServer = "" } def JAVA_INTEGER_VERSION @@ -241,6 +245,7 @@ sourceSets { runtimeClasspath = compileClasspath } + clover { java { srcDirs = [ cloverInstrDir ] @@ -277,8 +282,9 @@ sourceSets { compileClasspath += files(sourceSets.main.java.outputDir) } - compileClasspath += fileTree(dir: "$jalviewDir/$utilsDir", include: ["**/*.jar"]) compileClasspath += fileTree(dir: "$jalviewDir/$libDir", include: ["*.jar"]) + compileClasspath += fileTree(dir: "$jalviewDir/$utilsDir/testnglibs", include: ["**/*.jar"]) + compileClasspath += fileTree(dir: "$jalviewDir/$utilsDir/testlibs", include: ["**/*.jar"]) runtimeClasspath = compileClasspath } @@ -312,83 +318,88 @@ eclipse { classpath { //defaultOutputDir = sourceSets.main.java.outputDir def removeThese = [] - configurations.each{ if (it.isCanBeResolved()) { - removeThese += it + configurations.each{ + if (it.isCanBeResolved()) { + removeThese += it + } } - } - minusConfigurations += removeThese - plusConfigurations = [ ] - file { - - whenMerged { cp -> - def removeTheseToo = [] - HashMap addedSrcPath = new HashMap<>(); - cp.entries.each { entry -> - if (entry.kind == 'src') { - if (addedSrcPath.getAt(entry.path) || !(entry.path == "src" || entry.path == "test")) { - removeTheseToo += entry - } else { - addedSrcPath.putAt(entry.path, true) + minusConfigurations += removeThese + plusConfigurations = [ ] + file { + + whenMerged { cp -> + def removeTheseToo = [] + HashMap alreadyAddedSrcPath = new HashMap<>(); + cp.entries.each { entry -> + if (entry.kind == 'src') { + if (alreadyAddedSrcPath.getAt(entry.path) || !(entry.path == "src" || entry.path == "test")) { + removeTheseToo += entry + } else { + alreadyAddedSrcPath.putAt(entry.path, true) + } } } - } - cp.entries.removeAll(removeTheseToo) - - print ("CP="+cp.inspect()) - - cp.entries += new Output("bin/main") - cp.entries += new Library(fileReference(helpParentDir)) - cp.entries += new Library(fileReference(resourceDir)) - - HashMap addedLibPath = new HashMap<>(); + cp.entries.removeAll(removeTheseToo) - // changing from sourcesets.main.classpath to specific Java version lib - //sourceSets.main.compileClasspath.each{ - fileTree("$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/$utilsDir", include: ["**/*.jar"]).each { - //if ((it.isDirectory() || ! it.exists()) && ! (it.equals(sourceSets.main.java.outputDir))) { - //no longer want to add outputDir as eclipse is using its own output dir in bin/main - if (it.isDirectory() || ! it.exists()) { - // don't add dirs to classpath - return false // groovy "break" in .each loop - } - def itPath = it.toString() - if (itPath.startsWith(jalviewDirAbsolutePath+"/")) { - itPath = itPath.substring(jalviewDirAbsolutePath.length()+1) - } - if (addedLibPath.get(itPath)) { - // don't duplicate - } else { - def lib = new Library(fileReference(itPath)) - // this doesn't work... yet. Adding test=true attribute using withXml below - //def attrs = new Node(null, 'attributes', ["test":"true"]) - //lib.appendNode(attrs) // - cp.entries += lib - addedLibPath.put(itPath, true) + HashMap alreadyAddedLibPath = new HashMap<>(); + + sourceSets.main.compileClasspath.findAll { it.name.endsWith(".jar") }.each { + //don't want to add outputDir as eclipse is using its own output dir in bin/main + if (it.isDirectory() || ! it.exists()) { + // don't add dirs to classpath + return + } + def itPath = it.toString() + if (itPath.startsWith(jalviewDirAbsolutePath+"/")) { + // make relative path + itPath = itPath.substring(jalviewDirAbsolutePath.length()+1) + } + if (alreadyAddedLibPath.get(itPath)) { + //println("Not adding duplicate entry "+itPath) + } else { + //println("Adding entry "+itPath) + cp.entries += new Library(fileReference(itPath)) + alreadyAddedLibPath.put(itPath, true) + } } + + //fileTree(dir: "$jalviewDir/$utilsDir", include: ["test*/*.jar"]).each { + sourceSets.test.compileClasspath.findAll { it.name.endsWith(".jar") }.each { + //no longer want to add outputDir as eclipse is using its own output dir in bin/main + if (it.isDirectory() || ! it.exists()) { + // don't add dirs to classpath + return false // groovy "break" in .each closure + } + def itPath = it.toString() + if (itPath.startsWith(jalviewDirAbsolutePath+"/")) { + itPath = itPath.substring(jalviewDirAbsolutePath.length()+1) + } + if (alreadyAddedLibPath.get(itPath)) { + // don't duplicate + } else { + def lib = new Library(fileReference(itPath)) + /* this doesn't work... yet. Adding test=true attribute using withXml below + def attrs = new Node(null, 'attributes') + attrs.appendNode('attribute', ["name":"test","value":"true"]) + lib.appendNode(attrs) + /**/ + cp.entries += lib + alreadyAddedLibPath.put(itPath, true) + } } - } + + } // whenMerged // withXml changes ignored by buildship, these add the "test=true" attribute withXml { @@ -420,9 +431,12 @@ eclipse { } } } // withXML + + } // file containers 'org.eclipse.buildship.core.gradleclasspathcontainer' + } // classpath jdt { @@ -431,6 +445,7 @@ eclipse { targetCompatibility = compile_target_compatibility javaRuntimeName = eclipse_java_runtime_name + // add in jalview project specific properties/preferences into eclipse core preferences file { withProperties { props -> def jalview_prefs = new Properties() @@ -444,10 +459,9 @@ eclipse { } } } - } - //synchronizationTasks eclipseClasspath - //autoBuildTasks eclipseClasspath + } // jdt + } task cloverInstr() { @@ -1247,3 +1261,303 @@ task helppages { inputs.dir("$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 +} + + diff --git a/build.xml b/build.xml deleted file mode 100755 index 327cc33..0000000 --- a/build.xml +++ /dev/null @@ -1,1124 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - --> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
- ---Jalview Build Details--- -
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - java -classpath ${run.classpath} jalview.bin.Jalview - - - - - - - - Jalview - The Barton Group - - Jalview Multiple Alignment Editor - Jalview - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - j2se version="1.8+" - - - - - - - - - - - ]]> - - - - - - - - - - - - - - ]]> - - - - - - - - - - - - - - - - Build External Client Code process aborted by user. Jalview source is unchanged. - - - - - - - - - - - - - - - - - - - - - - - Ignoring request to build jalview distribution with clover-instrumented classes - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/buildcore.xml b/buildcore.xml deleted file mode 100644 index 3c21f43..0000000 --- a/buildcore.xml +++ /dev/null @@ -1,92 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Building core file '${core.name}' - warnings are OK; "does not exist" is trouble - Reading core class list from file ${classlist} - - - - - - - - - - - - - - - - - ......Now copying ${site}/${template.html} as ${$template.name}_${core.name}.html with core:"${core.name}", added to the Info block. - - - - - - - - ......Creating core${call-core.name}.js - - - - - - - ......Generating ${site.path}/j2s/core/core${call-core.name}.js - - - - ......Generating ${site.path}/j2s/core/core${call-core.name}.z.js - - - - - - - - - diff --git a/gradle.properties b/gradle.properties index 2dbdad3..85929f8 100644 --- a/gradle.properties +++ b/gradle.properties @@ -121,8 +121,6 @@ OSX_KEYSTORE = 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 @@ -139,4 +137,55 @@ RUNRSYNC=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 + + + diff --git a/src/org/json/simple/JSONValue.java b/src/org/json/simple/JSONValue.java index 5da3cd0..d6b2185 100644 --- a/src/org/json/simple/JSONValue.java +++ b/src/org/json/simple/JSONValue.java @@ -41,6 +41,7 @@ public class JSONValue { * {@code null}; please use {@link JSONValue#parseWithException(Reader)} * instead */ + @Deprecated public static Object parse(Reader in){ try{ JSONParser parser=new JSONParser(); @@ -71,6 +72,7 @@ public class JSONValue { * {@code null}; please use {@link JSONValue#parseWithException(String)} * instead */ + @Deprecated public static Object parse(String s){ StringReader in=new StringReader(s); return parse(in); diff --git a/swingjs/DEV_NOTES.txt b/swingjs/DEV_NOTES.txt deleted file mode 100644 index 751d81c..0000000 --- a/swingjs/DEV_NOTES.txt +++ /dev/null @@ -1,10 +0,0 @@ -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. diff --git a/swingjs/README.txt b/swingjs/README.txt deleted file mode 100644 index f45850b..0000000 --- a/swingjs/README.txt +++ /dev/null @@ -1,8 +0,0 @@ -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. - - diff --git a/swingjs/_j2sclasslist.txt b/swingjs/_j2sclasslist.txt deleted file mode 100644 index fb9da31..0000000 --- a/swingjs/_j2sclasslist.txt +++ /dev/null @@ -1,389 +0,0 @@ -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 diff --git a/swingjs/timestamp b/swingjs/timestamp deleted file mode 100644 index 0bfc11c..0000000 --- a/swingjs/timestamp +++ /dev/null @@ -1 +0,0 @@ -20190422120213 diff --git a/swingjs/ver/3.1.1/SwingJS-site.zip b/swingjs/ver/3.1.1/SwingJS-site.zip deleted file mode 100644 index 447678e..0000000 Binary files a/swingjs/ver/3.1.1/SwingJS-site.zip and /dev/null differ diff --git a/swingjs/ver/3.1.1/net.sf.j2s.core.3.1.1.jar b/swingjs/ver/3.1.1/net.sf.j2s.core.3.1.1.jar deleted file mode 100644 index 764c0b4..0000000 Binary files a/swingjs/ver/3.1.1/net.sf.j2s.core.3.1.1.jar and /dev/null differ diff --git a/swingjs/ver/3.2.1/SwingJS-site.zip b/swingjs/ver/3.2.1/SwingJS-site.zip deleted file mode 100644 index 5265f00..0000000 Binary files a/swingjs/ver/3.2.1/SwingJS-site.zip and /dev/null differ diff --git a/swingjs/ver/3.2.1/net.sf.j2s.core_3.2.1.jar b/swingjs/ver/3.2.1/net.sf.j2s.core_3.2.1.jar deleted file mode 100644 index a1657e5..0000000 Binary files a/swingjs/ver/3.2.1/net.sf.j2s.core_3.2.1.jar and /dev/null differ diff --git a/swingjs/ver/3.2.2/SwingJS-site.zip b/swingjs/ver/3.2.2/SwingJS-site.zip deleted file mode 100644 index c75a2aa..0000000 Binary files a/swingjs/ver/3.2.2/SwingJS-site.zip and /dev/null differ diff --git a/swingjs/ver/3.2.2/net.sf.j2s.core.jar b/swingjs/ver/3.2.2/net.sf.j2s.core.jar deleted file mode 100644 index aaeb3e1..0000000 Binary files a/swingjs/ver/3.2.2/net.sf.j2s.core.jar and /dev/null differ diff --git a/swingjs/ver/3.2.2/timestamp b/swingjs/ver/3.2.2/timestamp deleted file mode 100644 index a59b27a..0000000 --- a/swingjs/ver/3.2.2/timestamp +++ /dev/null @@ -1 +0,0 @@ -20180923174836 diff --git a/swingjs/ver/3.2.3/SwingJS-site.zip b/swingjs/ver/3.2.3/SwingJS-site.zip deleted file mode 100644 index 1ef655b..0000000 Binary files a/swingjs/ver/3.2.3/SwingJS-site.zip and /dev/null differ diff --git a/swingjs/ver/3.2.3/net.sf.j2s.core.jar b/swingjs/ver/3.2.3/net.sf.j2s.core.jar deleted file mode 100644 index 7d97750..0000000 Binary files a/swingjs/ver/3.2.3/net.sf.j2s.core.jar and /dev/null differ diff --git a/swingjs/ver/3.2.3/timestamp b/swingjs/ver/3.2.3/timestamp deleted file mode 100644 index c98902c..0000000 --- a/swingjs/ver/3.2.3/timestamp +++ /dev/null @@ -1 +0,0 @@ -20180927214151 diff --git a/swingjs/ver/3.2.4/DEV_NOTES.txt b/swingjs/ver/3.2.4/DEV_NOTES.txt deleted file mode 100644 index 751d81c..0000000 --- a/swingjs/ver/3.2.4/DEV_NOTES.txt +++ /dev/null @@ -1,10 +0,0 @@ -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. diff --git a/swingjs/ver/3.2.4/SwingJS-site.zip b/swingjs/ver/3.2.4/SwingJS-site.zip deleted file mode 100644 index 6f2893d..0000000 Binary files a/swingjs/ver/3.2.4/SwingJS-site.zip and /dev/null differ diff --git a/swingjs/ver/3.2.4/_j2sclasslist.txt b/swingjs/ver/3.2.4/_j2sclasslist.txt deleted file mode 100644 index fb9da31..0000000 --- a/swingjs/ver/3.2.4/_j2sclasslist.txt +++ /dev/null @@ -1,389 +0,0 @@ -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 diff --git a/swingjs/ver/3.2.4/net.sf.j2s.core.jar b/swingjs/ver/3.2.4/net.sf.j2s.core.jar deleted file mode 100644 index ec67d8c..0000000 Binary files a/swingjs/ver/3.2.4/net.sf.j2s.core.jar and /dev/null differ diff --git a/swingjs/ver/3.2.4/timestamp b/swingjs/ver/3.2.4/timestamp deleted file mode 100644 index 0bfc11c..0000000 --- a/swingjs/ver/3.2.4/timestamp +++ /dev/null @@ -1 +0,0 @@ -20190422120213 diff --git a/swingjs/SwingJS-site.zip b/utils/jalviewjs/SwingJS-site.zip similarity index 100% rename from swingjs/SwingJS-site.zip rename to utils/jalviewjs/SwingJS-site.zip diff --git a/utils/jalviewjs/eclipse/dropins/com.seeq.eclipse.importprojects-1.4.0.jar b/utils/jalviewjs/eclipse/dropins/com.seeq.eclipse.importprojects-1.4.0.jar new file mode 100644 index 0000000..69d7603 Binary files /dev/null and b/utils/jalviewjs/eclipse/dropins/com.seeq.eclipse.importprojects-1.4.0.jar differ diff --git a/swingjs/net.sf.j2s.core.jar b/utils/jalviewjs/eclipse/dropins/net.sf.j2s.core-3.2.4.jar similarity index 100% rename from swingjs/net.sf.j2s.core.jar rename to utils/jalviewjs/eclipse/dropins/net.sf.j2s.core-3.2.4.jar diff --git a/libjs/MiGLayout-site.zip b/utils/jalviewjs/libjs/MiGLayout-site.zip similarity index 100% rename from libjs/MiGLayout-site.zip rename to utils/jalviewjs/libjs/MiGLayout-site.zip diff --git a/libjs/VARNA-site.zip b/utils/jalviewjs/libjs/VARNA-site.zip similarity index 100% rename from libjs/VARNA-site.zip rename to utils/jalviewjs/libjs/VARNA-site.zip diff --git a/libjs/intervalstore-site.zip b/utils/jalviewjs/libjs/intervalstore-site.zip similarity index 100% rename from libjs/intervalstore-site.zip rename to utils/jalviewjs/libjs/intervalstore-site.zip diff --git a/libjs/jmol-app.zip b/utils/jalviewjs/libjs/jmol-app.zip similarity index 100% rename from libjs/jmol-app.zip rename to utils/jalviewjs/libjs/jmol-app.zip diff --git a/site-resources/examples/PF00111_seed.stk b/utils/jalviewjs/site-resources/examples/PF00111_seed.stk similarity index 100% rename from site-resources/examples/PF00111_seed.stk rename to utils/jalviewjs/site-resources/examples/PF00111_seed.stk diff --git a/site-resources/examples/RF00031_folded.stk b/utils/jalviewjs/site-resources/examples/RF00031_folded.stk similarity index 100% rename from site-resources/examples/RF00031_folded.stk rename to utils/jalviewjs/site-resources/examples/RF00031_folded.stk diff --git a/site-resources/examples/exampleFeatures.txt b/utils/jalviewjs/site-resources/examples/exampleFeatures.txt similarity index 100% rename from site-resources/examples/exampleFeatures.txt rename to utils/jalviewjs/site-resources/examples/exampleFeatures.txt diff --git a/site-resources/examples/jaxbtest.jvx b/utils/jalviewjs/site-resources/examples/jaxbtest.jvx similarity index 100% rename from site-resources/examples/jaxbtest.jvx rename to utils/jalviewjs/site-resources/examples/jaxbtest.jvx diff --git a/site-resources/examples/rna_ss_test.stk b/utils/jalviewjs/site-resources/examples/rna_ss_test.stk similarity index 100% rename from site-resources/examples/rna_ss_test.stk rename to utils/jalviewjs/site-resources/examples/rna_ss_test.stk diff --git a/site-resources/examples/uniref50.fa b/utils/jalviewjs/site-resources/examples/uniref50.fa similarity index 100% rename from site-resources/examples/uniref50.fa rename to utils/jalviewjs/site-resources/examples/uniref50.fa diff --git a/site-resources/jalview_bin_JalviewJS2.html b/utils/jalviewjs/site-resources/jalview_bin_JalviewJS2.html similarity index 100% rename from site-resources/jalview_bin_JalviewJS2.html rename to utils/jalviewjs/site-resources/jalview_bin_JalviewJS2.html diff --git a/site-resources/jalview_bin_JalviewJS_core.html b/utils/jalviewjs/site-resources/jalview_bin_JalviewJS_core.html similarity index 100% rename from site-resources/jalview_bin_JalviewJS_core.html rename to utils/jalviewjs/site-resources/jalview_bin_JalviewJS_core.html diff --git a/site-resources/jalview_bin_JalviewJS_embedded.html b/utils/jalviewjs/site-resources/jalview_bin_JalviewJS_embedded.html similarity index 100% rename from site-resources/jalview_bin_JalviewJS_embedded.html rename to utils/jalviewjs/site-resources/jalview_bin_JalviewJS_embedded.html diff --git a/site-resources/jalview_bin_JalviewJS_embedded_core.html b/utils/jalviewjs/site-resources/jalview_bin_JalviewJS_embedded_core.html similarity index 100% rename from site-resources/jalview_bin_JalviewJS_embedded_core.html rename to utils/jalviewjs/site-resources/jalview_bin_JalviewJS_embedded_core.html diff --git a/template.html b/utils/jalviewjs/template.html similarity index 84% rename from template.html rename to utils/jalviewjs/template.html index e959685..7c20d44 100644 --- a/template.html +++ b/utils/jalviewjs/template.html @@ -1,8 +1,7 @@ -SwingJS test _NAME_ - +SwingJS test _NAME_
-
+
This is System.out. clear it
Add ?j2snocore to URL to see full class list; ?j2sdebug to use uncompressed j2s/core files
get _j2sClassList.txt
diff --git a/utils/jalviewjs/urls.txt b/utils/jalviewjs/urls.txt new file mode 100644 index 0000000..7a8cf0a --- /dev/null +++ b/utils/jalviewjs/urls.txt @@ -0,0 +1,11 @@ +# 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 + diff --git a/utils/classgraph-4.1.6.jar b/utils/testlibs/classgraph-4.1.6.jar similarity index 100% rename from utils/classgraph-4.1.6.jar rename to utils/testlibs/classgraph-4.1.6.jar