From 54dfce251873f378d86ae2c937c6dadd32226671 Mon Sep 17 00:00:00 2001 From: Ben Soares Date: Mon, 11 Nov 2019 01:05:27 +0000 Subject: [PATCH] Revert "JAL-3210 merging in Jalview-JS/develop" This reverts commit 9499aed89323b8f53689d6428ffc9b32250eae6c, reversing changes made to fb616bbaa70ca0f8bbae7e076f3c403a737205a9. Still not working right in Eclipse --- build.gradle | 515 ++---------- .../classlists => classlists}/jalview.txt | 0 .../classlists => classlists}/jvexamplefile.txt | 0 gradle.properties | 12 +- utils/jalviewjs/_j2sclasslist.txt | 885 ++++---------------- utils/jalviewjs/_j2sclasslist_jmol.txt | 233 ------ 6 files changed, 232 insertions(+), 1413 deletions(-) rename {utils/jalviewjs/classlists => classlists}/jalview.txt (100%) rename {utils/jalviewjs/classlists => classlists}/jvexamplefile.txt (100%) delete mode 100644 utils/jalviewjs/_j2sclasslist_jmol.txt diff --git a/build.gradle b/build.gradle index 9798062..535f3b9 100644 --- a/build.gradle +++ b/build.gradle @@ -246,7 +246,6 @@ if (JAVA_VERSION.equals("1.8")) { throw new GradleException("JAVA_VERSION=${JAVA_VERSION} not currently supported by Jalview") } - sourceSets { main { @@ -311,7 +310,6 @@ sourceSets { } } - // clover bits dependencies { if (use_clover) { @@ -320,13 +318,11 @@ dependencies { } } - configurations { cloverRuntime cloverRuntime.extendsFrom cloverCompile } - eclipse { project { name = eclipse_project_name @@ -399,13 +395,12 @@ eclipse { } //fileTree(dir: "$jalviewDir/$utilsDir", include: ["test*/*.jar"]).each { - sourceSets.test.compileClasspath.findAll { it.name.endsWith(".jar") }.any { + sourceSets.test.compileClasspath.findAll { it.name.endsWith(".jar") }.each { //no longer want to add outputDir as eclipse is using its own output dir in bin/main if (it.isDirectory() || ! it.exists()) { // don't add dirs to classpath - return false // groovy "continue" in .any closure + return false // groovy "break" in .each closure } - def itPath = it.toString() if (itPath.startsWith("${jalviewDirAbsolutePath}/")) { itPath = itPath.substring(jalviewDirAbsolutePath.length()+1) @@ -456,7 +451,6 @@ eclipse { } - task cloverInstr() { // only instrument source, we build test classes as normal inputs.files files (sourceSets.main.allJava) // , fileTree(dir:"$jalviewDir/$testSourceDir", include: ["**/*.java"])) @@ -496,6 +490,7 @@ task cloverReport { com.atlassian.clover.reporters.xml.XMLReporter.runReport(args) } } + // end clover bits @@ -510,7 +505,6 @@ compileJava { } - compileTestJava { if (use_clover) { dependsOn compileCloverJava @@ -538,14 +532,12 @@ compileCloverJava { classpath += configurations.cloverRuntime } - clean { doFirst { delete sourceSets.main.java.outputDir } } - cleanTest { doFirst { delete sourceSets.test.java.outputDir @@ -553,14 +545,12 @@ cleanTest { } } - // format is a string like date.format("dd MMMM yyyy") def getDate(format) { def date = new Date() return date.format(format) } - task setGitVals { def hashStdOut = new ByteArrayOutputStream() exec { @@ -582,7 +572,6 @@ task setGitVals { outputs.upToDateWhen { false } } - task createBuildProperties(type: WriteProperties) { dependsOn setGitVals inputs.dir("${jalviewDir}/${sourceDir}") @@ -598,7 +587,6 @@ task createBuildProperties(type: WriteProperties) { outputs.file(outputFile) } - def buildingHTML = "${jalviewDir}/${docDir}/building.html" task cleanBuildingHTML(type: Delete) { doFirst { @@ -606,7 +594,6 @@ task cleanBuildingHTML(type: Delete) { } } - task convertBuildingMD(type: Exec) { dependsOn cleanBuildingHTML def buildingMD = "${jalviewDir}/${docDir}/building.md" @@ -641,14 +628,12 @@ task convertBuildingMD(type: Exec) { outputs.file(buildingHTML) } - clean { doFirst { delete buildingHTML } } - task syncDocs(type: Sync) { dependsOn convertBuildingMD def syncDir = "${classes}/${docDir}" @@ -657,8 +642,8 @@ task syncDocs(type: Sync) { } - def helpFile = "${classes}/${helpDir}/help.jhm" + task copyHelp(type: Copy) { def inputDir = "${jalviewDir}/${helpParentDir}/${helpDir}" def outputDir = "${classes}/${helpDir}" @@ -680,14 +665,12 @@ task copyHelp(type: Copy) { outputs.dir(outputDir) } - task syncLib(type: Sync) { def syncDir = "${classes}/${libDistDir}" from fileTree("${jalviewDir}/${libDistDir}") into syncDir } - task syncResources(type: Sync) { from "${jalviewDir}/${resourceDir}" include "**/*.*" @@ -697,7 +680,6 @@ task syncResources(type: Sync) { } } - task prepare { dependsOn syncResources dependsOn syncDocs @@ -731,7 +713,6 @@ test { } - task buildIndices(type: JavaExec) { dependsOn copyHelp classpath = sourceSets.main.compileClasspath @@ -751,7 +732,6 @@ task buildIndices(type: JavaExec) { outputs.file("${workingDir}/JavaHelpSearch/TMAP") } - task compileLinkCheck(type: JavaCompile) { options.fork = true classpath = files("${jalviewDir}/${utilsDir}") @@ -764,7 +744,6 @@ task compileLinkCheck(type: JavaCompile) { outputs.file("${jalviewDir}/${utilsDir}/BufferedLineReader.class") } - task linkCheck(type: JavaExec) { dependsOn prepare, compileLinkCheck @@ -825,13 +804,11 @@ jar { outputs.file("${jalviewDir}/${packageDir}/${archiveName}") } - task copyJars(type: Copy) { from fileTree(dir: "${classes}", include: "**/*.jar").files into "${jalviewDir}/${packageDir}" } - // doing a Sync instead of Copy as Copy doesn't deal with "outputs" very well task syncJars(type: Sync) { from fileTree(dir: "${jalviewDir}/${libDistDir}", include: "**/*.jar").files @@ -841,7 +818,6 @@ task syncJars(type: Sync) { } } - task makeDist { group = "build" description = "Put all required libraries in dist" @@ -854,7 +830,6 @@ task makeDist { outputs.dir("${jalviewDir}/${packageDir}") } - task cleanDist { dependsOn cleanPackageDir dependsOn cleanTest @@ -878,7 +853,6 @@ shadowJar { minimize() } - task getdownWebsite() { group = "distribution" description = "Create the getdown minimal app folder, and website folder for this version of jalview. Website folder also used for offline app installer" @@ -1059,7 +1033,6 @@ task getdownWebsite() { outputs.dir(project.ext.getdownFilesDir) } - task getdownDigest(type: JavaExec) { group = "distribution" description = "Digest the getdown website folder" @@ -1073,7 +1046,6 @@ task getdownDigest(type: JavaExec) { outputs.file("${project.ext.getdownWebsiteDir}/digest2.txt") } - task getdown() { group = "distribution" description = "Create the minimal and full getdown app folder for installers and website and create digest file" @@ -1096,7 +1068,6 @@ task getdown() { } } - clean { doFirst { delete project.ext.getdownWebsiteDir @@ -1104,7 +1075,6 @@ clean { } } - install4j { def install4jHomeDir = "/opt/install4j" def hostname = "hostname".execute().text.trim() @@ -1125,7 +1095,6 @@ install4j { } } - def install4jConf def macosJavaVMDir def macosJavaVMTgz @@ -1194,7 +1163,6 @@ task copyInstall4jTemplate(type: Copy) { } } - task installers(type: com.install4j.gradle.Install4jTask) { group = "distribution" description = "Create the install4j installers" @@ -1220,14 +1188,12 @@ task installers(type: com.install4j.gradle.Install4jTask) { outputs.dir("${jalviewDir}/${install4jBuildDir}/${JAVA_VERSION}") } - clean { doFirst { delete install4jConf } } - task sourceDist (type: Tar) { def VERSION_UNDERSCORES = JALVIEW_VERSION.replaceAll("\\.", "_") @@ -1298,7 +1264,6 @@ task sourceDist (type: Tar) { // } } - task helppages { dependsOn copyHelp dependsOn pubhtmlhelp @@ -1307,24 +1272,18 @@ task helppages { outputs.dir("${helpOutputDir}") } - def jalviewjsBuildDir def jalviewjsSiteDir -def jalviewjsTransferSiteJsDir +def jalviewjsTransferSiteJSDir def jalviewjsTransferSiteLibDir -def jalviewjsTransferSiteSwingJsDir -def jalviewjsTransferSiteCoreDir task jalviewjsSitePath { def relativeBuildDir = file(jalviewDirAbsolutePath).toPath().relativize(buildDir.toPath()) jalviewjsBuildDir = "${relativeBuildDir}/jalviewjs" jalviewjsSiteDir = "${jalviewjsBuildDir}/${jalviewjs_site_dir}" - jalviewjsTransferSiteJsDir = "${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_js" + jalviewjsTransferSiteJSDir = "${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_js" jalviewjsTransferSiteLibDir = "${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_lib" - jalviewjsTransferSiteSwingJsDir = "${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_swingjs" - jalviewjsTransferSiteCoreDir = "${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_core" } - def eclipseWorkspace task jalviewjsSetEclipseWorkspace { def propKey = "jalviewjs_eclipse_workspace" @@ -1370,9 +1329,8 @@ task jalviewjsSetEclipseWorkspace { println("ECLIPSE WORKSPACE: "+eclipseWorkspace.getPath()) } - //inputs.property(propKey, eclipseWsDir) // eclipseWsDir only gets set once this task runs, so will be out-of-date + inputs.property(propKey, eclipseWsDir) outputs.file(propsFileName) - outputs.upToDateWhen { eclipseWorkspace.exists() } } @@ -1393,7 +1351,7 @@ task jalviewjsEclipsePaths { eclipseProduct = "${eclipseRoot}/Contents/Eclipse/.eclipseproduct" } else if (OperatingSystem.current().isWindows()) { // check these paths!! if (file("${eclipseRoot}/eclipse").isDirectory() && file("${eclipseRoot}/eclipse/.eclipseproduct").exists()) { - eclipseRoot += "/eclipse.exe" + eclipseRoot += "/eclipse" } eclipseBinary = "${eclipseRoot}/eclipse" eclipseProduct = "${eclipseRoot}/.eclipseproduct" @@ -1405,7 +1363,7 @@ task jalviewjsEclipsePaths { eclipseProduct = "${eclipseRoot}/.eclipseproduct" } - eclipseVersion = "4.13" // default + eclipseVersion = "4.12" // default def assumedVersion = true if (file(eclipseProduct).exists()) { def fis = new FileInputStream(eclipseProduct) @@ -1415,6 +1373,17 @@ task jalviewjsEclipsePaths { fis.close() assumedVersion = false } + /* + String[] v = eclipseVersion.split("\\.") + def v0 = Integer.valueOf(v[0]) + def v1 = Integer.valueOf(v[1]) + if (v0 < 4 || ( v0 == 4 && v1 < 13 )) { + eclipseVersionSuffix = "_4.12" + } else { + eclipseVersionSuffix = "_4.13" + } + */ + def propKey = "eclipse_debug" eclipseDebug = (project.hasProperty(propKey) && project.getProperty(propKey).equals("true")) @@ -1426,13 +1395,35 @@ task jalviewjsEclipsePaths { } } - task eclipseSetup { dependsOn eclipseProject dependsOn eclipseClasspath dependsOn eclipseJdt } +/* using the Copy task below +task OLDjalviewjsEclipseCopyDropins { + dependsOn jalviewjsEclipsePaths + dependsOn jalviewjsCleanEclipse + def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_eclipse_dropins_dir}", include: "*.jar") + inputFiles += file(jalviewjs_j2s_plugin) + def outputDir = "${buildDir}/jalviewjs + + inputs.files inputFiles + inputFiles.each { file -> + outputs.file("${outputDir}/${file.name}") + } + + doLast { + inputFiles.each { file -> + copy { + from file + into outputDir + } + } + } +} +*/ // this version (type: Copy) will delete anything in the eclipse dropins folder that isn't in fromDropinsDir task jalviewjsEclipseCopyDropins(type: Copy) { @@ -1446,7 +1437,6 @@ task jalviewjsEclipseCopyDropins(type: Copy) { into outputDir } - // this eclipse -clean doesn't actually work task jalviewjsCleanEclipse(type: Exec) { dependsOn eclipseSetup @@ -1466,33 +1456,16 @@ y def inputByteStream = new ByteArrayInputStream(inputString.getBytes()) standardInput = inputByteStream } - /* not really working yet jalviewjsEclipseCopyDropins.finalizedBy jalviewjsCleanEclipse */ - -task jalviewjsTransferUnzipSwingJs { - dependsOn jalviewjsSitePath - - def file_zip = "${jalviewDir}/${jalviewjs_swingjs_zip}" - - doLast { - copy { - from zipTree(file_zip) - into "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}" - } - } - - inputs.file file_zip - outputs.dir "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}" -} - - +def jalviewjsTransferSiteUnzipDir task jalviewjsTransferUnzipLib { dependsOn jalviewjsSitePath def zipFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_libjs_dir}", include: "*.zip") + zipFiles += "${jalviewDir}/${jalviewjs_swingjs_zip}" doLast { zipFiles.each { file_zip -> @@ -1507,13 +1480,6 @@ task jalviewjsTransferUnzipLib { outputs.dir "${jalviewDir}/${jalviewjsTransferSiteLibDir}" } - -task jalviewjsTransferUnzipAllLibs { - dependsOn jalviewjsTransferUnzipSwingJs - dependsOn jalviewjsTransferUnzipLib -} - - task jalviewjsCreateJ2sSettings(type: WriteProperties) { group "JalviewJS" description "Create the .j2s file from the j2s.* properties" @@ -1528,33 +1494,30 @@ task jalviewjsCreateJ2sSettings(type: WriteProperties) { if (val != null) { if (prop == siteDirProperty) { if (!(val.startsWith('/') || val.startsWith("file://") )) { - val = "${jalviewDir}/${jalviewjsTransferSiteJsDir}/${val}" + val = "${jalviewDir}/${jalviewjsTransferSiteJSDir}/${val}" } setSiteDir = true } property(prop,val) } if (!setSiteDir) { // default site location, don't override specifically set property - property(siteDirProperty,"${jalviewDir}/${jalviewjsTransferSiteJsDir}") + property(siteDirProperty,"${jalviewDir}/${jalviewjsTransferSiteJSDir}") } } inputs.properties(j2s_props) outputs.file(outputFile) } - task jalviewjsEclipseSetup { dependsOn jalviewjsEclipseCopyDropins dependsOn jalviewjsSetEclipseWorkspace dependsOn jalviewjsCreateJ2sSettings } - -task jalviewjsSyncAllLibs (type: Sync) { +task jalviewjsSyncLib (type: Sync) { dependsOn jalviewjsSitePath - dependsOn jalviewjsTransferUnzipAllLibs + dependsOn jalviewjsTransferUnzipLib def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteLibDir}") - inputFiles += fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}") def outputDir = "${jalviewDir}/${jalviewjsSiteDir}" from inputFiles @@ -1571,7 +1534,6 @@ task jalviewjsSyncAllLibs (type: Sync) { inputs.files inputFiles } - task jalviewjsSyncResources (type: Sync) { dependsOn jalviewjsSitePath def inputFiles = fileTree(dir: "${jalviewDir}/${resourceDir}") @@ -1591,7 +1553,6 @@ task jalviewjsSyncResources (type: Sync) { inputs.files inputFiles } - task jalviewjsSyncSiteResources (type: Sync) { dependsOn jalviewjsSitePath def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_site_resource_dir}") @@ -1611,7 +1572,6 @@ task jalviewjsSyncSiteResources (type: Sync) { inputs.files inputFiles } - task jalviewjsSyncBuildProperties (type: Sync) { dependsOn jalviewjsSitePath dependsOn createBuildProperties @@ -1632,21 +1592,12 @@ task jalviewjsSyncBuildProperties (type: Sync) { inputs.files inputFiles } - task jalviewjsProjectImport(type: Exec) { dependsOn eclipseSetup dependsOn jalviewjsEclipsePaths dependsOn jalviewjsEclipseSetup - doFirst { - // do not run a headless import when we claim to be in Eclipse - if (ECLIPSE_IDE_DEVELOPER.equals("true")) { - throw new StopExecutionException("Not running headless import whilst ECLIPSE_IDE_DEVELOPER is '"+ECLIPSE_IDE_DEVELOPER+"'") - } - } - - //def projdir = eclipseWorkspace.getPath()+"/.metadata/.plugins/org.eclipse.core.resources/.projects/jalview/org.eclipse.jdt.core" - def projdir = eclipseWorkspace.getPath()+"/.metadata/.plugins/org.eclipse.core.resources/.projects/jalview" + def projdir = eclipseWorkspace.getPath()+"/.metadata/.plugins/org.eclipse.core.resources/.projects/jalview/org.eclipse.jdt.core" executable(eclipseBinary) args(["-nosplash", "--launcher.suppressErrors", "-application", "com.seeq.eclipse.importprojects.headlessimport", "-data", eclipseWorkspace.getPath(), "-import", jalviewDirAbsolutePath]) if (eclipseDebug) { @@ -1655,24 +1606,14 @@ task jalviewjsProjectImport(type: Exec) { args += [ "--launcher.appendVmargs", "-vmargs", "-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}" ] inputs.file("${jalviewDir}/.project") - outputs.upToDateWhen { - file(projdir).exists() - } + outputs.upToDateWhen { file(projdir).exists() } } - task jalviewjsTranspile(type: Exec) { dependsOn jalviewjsEclipseSetup dependsOn jalviewjsProjectImport dependsOn jalviewjsEclipsePaths - doFirst { - // do not run a headless transpile when we claim to be in Eclipse - if (ECLIPSE_IDE_DEVELOPER.equals("true")) { - throw new StopExecutionException("Not running headless transpile whilst ECLIPSE_IDE_DEVELOPER is '"+ECLIPSE_IDE_DEVELOPER+"'") - } - } - executable(eclipseBinary) args(["-nosplash", "--launcher.suppressErrors", "-application", "org.eclipse.jdt.apt.core.aptBuild", "-data", eclipseWorkspace, "-${jalviewjs_eclipse_build_arg}", eclipse_project_name ]) if (eclipseDebug) { @@ -1686,7 +1627,7 @@ task jalviewjsTranspile(type: Exec) { stdout = new ByteArrayOutputStream() stderr = new ByteArrayOutputStream() - def logOutFileName = "${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}" + def logOutFileName = "${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_j2s_stdout}" def logOutFile = file(logOutFileName) logOutFile.createNewFile() logOutFile.text = """ROOT: ${jalviewjs_eclipse_root} @@ -1697,6 +1638,10 @@ DEBUG: ${eclipseDebug} ---- """ def logOutFOS = new FileOutputStream(logOutFile, true) // true == append + //def logErrFileName = "${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_stderr}" + //def logErrFile = file(logFileName) + //logErrFile.createNewFile() + //def logErrFOS = new FileErrputStream(logErrFile, false) // combine stdout and stderr def logErrFOS = logOutFOS @@ -1724,261 +1669,25 @@ DEBUG: ${eclipseDebug} doLast { if (stdout.toString().contains("Error processing ")) { // j2s did not complete transpile - //throw new TaskExecutionException("Error during transpilation:\n${stderr}\nSee eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'") - throw new GradleException("Error during transpilation:\n${stderr}\nSee eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'") + throw new GradleException("Error during transpilation:\n${stderr}\nSee eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_stdout}'") } } inputs.dir("${jalviewDir}/${sourceDir}") - outputs.dir("${jalviewDir}/${jalviewjsTransferSiteJsDir}") - outputs.upToDateWhen( { file("${jalviewDir}/${jalviewjsTransferSiteJsDir}${jalviewjs_server_resource}").exists() } ) -} - - -def jalviewjsCallCore(FileCollection list, String prefixFile, String suffixFile, String jsfile, String zjsfile, File logOutFile, Boolean logOutConsole) { - - def stdout = new ByteArrayOutputStream() - def stderr = new ByteArrayOutputStream() - - def coreFile = file(jsfile) - def msg = "" - msg = "Generating ${jsfile}" - println(msg) - logOutFile.createNewFile() - logOutFile.append(msg+"\n") - - def coreTop = file(prefixFile) - def coreBottom = file(suffixFile) - coreFile.getParentFile().mkdirs() - coreFile.createNewFile() - coreFile.write( coreTop.text ) - list.each { - f -> - if (f.exists()) { - def t = f.text - t.replaceAll("Clazz\\.","Clazz_") - t.replaceAll("Class__","Clazz._") - coreFile.append( t ) - } else { - msg = "...file '"+f.getPath()+"' does not exist, skipping" - println(msg) - logOutFile.append(msg+"\n") - } - } - coreFile.append( coreBottom.text ) - - msg = "Generating ${zjsfile}" - println(msg) - logOutFile.append(msg+"\n") - def logOutFOS = new FileOutputStream(logOutFile, true) // true == append - def logErrFOS = logOutFOS - - javaexec { - classpath = files(["${jalviewDir}/tools/closure_compiler.jar"]) - args = [ "--js", jsfile, "--js_output_file", zjsfile ] - - msg = "\nRunning '"+commandLine.join(' ')+"'\n" - println(msg) - logOutFile.append(msg+"\n") - - if (logOutConsole) { - standardOutput = new org.apache.tools.ant.util.TeeOutputStream( - new org.apache.tools.ant.util.TeeOutputStream( - logOutFOS, - stdout), - standardOutput) - errorOutput = new org.apache.tools.ant.util.TeeOutputStream( - new org.apache.tools.ant.util.TeeOutputStream( - logErrFOS, - stderr), - errorOutput) - } else { - standardOutput = new org.apache.tools.ant.util.TeeOutputStream( - logOutFOS, - stdout) - errorOutput = new org.apache.tools.ant.util.TeeOutputStream( - logErrFOS, - stderr) - } - } - msg = "--" - println(msg) - logOutFile.append(msg+"\n") -} - - -def jalviewjsJalviewTemplateName = "JalviewJS" -def jalviewjsJalviewCoreName = "_jalview" -task jalviewjsNoTranspileBuildAllCores { - dependsOn jalviewjsSitePath - dependsOn jalviewjsTransferUnzipSwingJs - - def j2sDir = "${jalviewDir}/${jalviewjsTransferSiteJsDir}/${jalviewjs_j2s_subdir}" - def jsDir = "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}/${jalviewjs_js_subdir}" - def outputDir = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}/${jalviewjs_j2s_subdir}/core" - def prefixFile = "${jsDir}/core/coretop2.js" - def suffixFile = "${jsDir}/core/corebottom2.js" - - inputs.file prefixFile - inputs.file suffixFile - - def classlistFiles = [] - // add the classlists found int the jalviewjs_classlists_dir - fileTree(dir: "${jalviewDir}/${jalviewjs_classlists_dir}", include: "*.txt").each { - file -> - def name = file.getName() - ".txt" - classlistFiles += [ - 'file': file, - 'name': name - ] - } - - // _jmol and _jalview cores. Add any other peculiar classlist.txt files here - classlistFiles += [ 'file': file("${jalviewDir}/${jalviewjs_classlist_jmol}"), 'name': "_jvjmol" ] - classlistFiles += [ 'file': file("${jalviewDir}/${jalviewjs_classlist_jalview}"), 'name': jalviewjsJalviewCoreName ] - - def classlists = [] - - classlistFiles.each { - hash -> - - def file = hash['file'] - if (! file.exists()) { - println("...classlist file '"+file.getPath()+"' does not exist, skipping") - return false // this is a "continue" in groovy .each closure - } - def name = hash['name'] - if (name == null) { - name = file.getName() - ".txt" - } - - def filelist = [] - file.eachLine { - line -> - filelist += line - } - def list = fileTree(dir: j2sDir, includes: filelist) - - def jsfile = "${outputDir}/core${name}.js" - def zjsfile = "${outputDir}/core${name}.z.js" - - classlists += [ - 'jsfile': jsfile, - 'zjsfile': zjsfile, - 'list': list - ] - - inputs.file(file) - inputs.files(list) - outputs.file(jsfile) - outputs.file(zjsfile) - } - - // _stevesoft core. add any cores without a classlist here (and the inputs and outputs) - def stevesoftClasslist = [ - 'jsfile': "${outputDir}/core_stevesoft.js", - 'zjsfile': "${outputDir}/core_stevesoft.z.js", - 'list': fileTree(dir: j2sDir, include: "com/stevesoft/pat/**/*.js") - ] - classlists += stevesoftClasslist - inputs.files(stevesoftClasslist['list']) - outputs.file(stevesoftClasslist['jsfile']) - outputs.file(stevesoftClasslist['zjsfile']) - - doFirst { - def logOutFile = file("${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_j2s_closure_stdout}") - logOutFile.getParentFile().mkdirs() - logOutFile.createNewFile() - logOutFile.write(getDate("yyyy-MM-dd HH:mm:ss")+" jalviewjsNoTranspileBuildAllCores\n----\n") - - classlists.each { - jalviewjsCallCore(it.list, prefixFile, suffixFile, it.jsfile, it.zjsfile, logOutFile, jalviewjs_j2s_to_console.equals("true")) - } - } - -} - - -jalviewjsNoTranspileBuildAllCores.mustRunAfter jalviewjsTranspile - - -task jalviewjsBuildAllCores { - group "JalviewJS" - description "Build the core js lib closures listed in the classlists dir" - dependsOn jalviewjsTranspile - dependsOn jalviewjsNoTranspileBuildAllCores -} - - -def jalviewjsJalviewCoreHtmlFile -task jalviewjsPublishCoreTemplate(type: Sync) { - dependsOn jalviewjsSitePath - dependsOn jalviewjsBuildAllCores - - def inputFile = file("${jalviewDir}/${j2s_template_html}") - def outputDir = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}" - - from inputFile - into outputDir - def outputFiles = [] - jalviewjsJalviewCoreHtmlFile = "${jalviewjsJalviewTemplateName}_${jalviewjsJalviewCoreName}.html" - rename { filename -> - outputFiles += "${outputDir}/${filename}" - if (filename.equals(inputFile.getName())) { - return jalviewjsJalviewCoreHtmlFile - } - return null - } - filter(ReplaceTokens, beginToken: '_', endToken: '_', tokens: ['MAIN': '"'+mainClass+'"', 'CODE': "null", 'NAME': jalviewjsJalviewTemplateName]) - filter(ReplaceTokens, beginToken: '', endToken: '', tokens: ['NONE': jalviewjsJalviewCoreName]) - preserve { - include "**" - } - outputs.files outputFiles - inputs.files inputFile -} - - -task jalviewjsNoTranspileSyncCore (type: Sync) { - dependsOn jalviewjsSitePath - dependsOn jalviewjsNoTranspileBuildAllCores - dependsOn jalviewjsPublishCoreTemplate - def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteCoreDir}") - def outputDir = "${jalviewDir}/${jalviewjsSiteDir}" - - from inputFiles - into outputDir - def outputFiles = [] - rename { filename -> - outputFiles += "${outputDir}/${filename}" - null - } - preserve { - include "**" - } - outputs.files outputFiles - inputs.files inputFiles + outputs.dir("${jalviewDir}/${jalviewjsTransferSiteJSDir}") + outputs.upToDateWhen( { file("${jalviewDir}/${jalviewjsTransferSiteJSDir}${jalviewjs_server_resource}").exists() } ) } - -task jalviewjsSyncCore (type: Sync) { - dependsOn jalviewjsTranspile - dependsOn jalviewjsNoTranspileSyncCore - dependsOn "jalviewjsBuildAllCores" -} - - -// this Copy version of TransferSiteJs will delete anything else in the target dir -task jalviewjsCopyTransferSiteJs(type: Copy) { +// this Copy version of TransferSite will delete anything else in the target dir +task jalviewjsCopyTransferSite(type: Copy) { dependsOn jalviewjsTranspile - from "${jalviewDir}/${jalviewjsTransferSiteJsDir}" + from "${jalviewDir}/${jalviewjsTransferSiteJSDir}" into "${jalviewDir}/${jalviewjsSiteDir}" } - // this Sync version of TransferSite is used by buildship to keep the website automatically up to date when a file changes -task jalviewjsNoTranspileSyncTransferSiteJs(type: Sync) { - from "${jalviewDir}/${jalviewjsTransferSiteJsDir}" +task jalviewjsSyncTransferSite(type: Sync) { + from "${jalviewDir}/${jalviewjsTransferSiteJSDir}" include "**/*.*" into "${jalviewDir}/${jalviewjsSiteDir}" preserve { @@ -1986,56 +1695,39 @@ task jalviewjsNoTranspileSyncTransferSiteJs(type: Sync) { } } -jalviewjsSyncAllLibs.mustRunAfter jalviewjsCopyTransferSiteJs -jalviewjsSyncResources.mustRunAfter jalviewjsCopyTransferSiteJs -jalviewjsSyncSiteResources.mustRunAfter jalviewjsCopyTransferSiteJs -jalviewjsSyncBuildProperties.mustRunAfter jalviewjsCopyTransferSiteJs - -jalviewjsSyncAllLibs.mustRunAfter jalviewjsNoTranspileSyncTransferSiteJs -jalviewjsSyncResources.mustRunAfter jalviewjsNoTranspileSyncTransferSiteJs -jalviewjsSyncSiteResources.mustRunAfter jalviewjsNoTranspileSyncTransferSiteJs -jalviewjsSyncBuildProperties.mustRunAfter jalviewjsNoTranspileSyncTransferSiteJs - - -task jalviewjsNoTranspilePrepareSite { - dependsOn jalviewjsSyncAllLibs - dependsOn jalviewjsSyncResources - dependsOn jalviewjsSyncSiteResources - dependsOn jalviewjsSyncBuildProperties - dependsOn jalviewjsNoTranspileSyncCore -} +jalviewjsSyncLib.mustRunAfter jalviewjsCopyTransferSite +jalviewjsSyncResources.mustRunAfter jalviewjsCopyTransferSite +jalviewjsSyncSiteResources.mustRunAfter jalviewjsCopyTransferSite +jalviewjsSyncBuildProperties.mustRunAfter jalviewjsCopyTransferSite +jalviewjsSyncLib.mustRunAfter jalviewjsSyncTransferSite +jalviewjsSyncResources.mustRunAfter jalviewjsSyncTransferSite +jalviewjsSyncSiteResources.mustRunAfter jalviewjsSyncTransferSite +jalviewjsSyncBuildProperties.mustRunAfter jalviewjsSyncTransferSite task jalviewjsPrepareSite { group "JalviewJS" description "Prepares the website folder including unzipping files and copying resources" - dependsOn jalviewjsSyncAllLibs + dependsOn jalviewjsSyncLib dependsOn jalviewjsSyncResources dependsOn jalviewjsSyncSiteResources dependsOn jalviewjsSyncBuildProperties - dependsOn jalviewjsSyncCore } - task jalviewjsBuildSite { group "JalviewJS" description "Builds the whole website including transpiled code" - dependsOn jalviewjsCopyTransferSiteJs + dependsOn jalviewjsCopyTransferSite dependsOn jalviewjsPrepareSite } - task cleanJalviewjsSite { doFirst { - delete "${jalviewDir}/${jalviewjsTransferSiteJsDir}" - delete "${jalviewDir}/${jalviewjsTransferSiteLibDir}" - delete "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}" - delete "${jalviewDir}/${jalviewjsTransferSiteCoreDir}" + delete "${jalviewDir}/${jalviewjsTransferSiteJSDir}" delete "${jalviewDir}/${jalviewjsSiteDir}" } } - task jalviewjsSiteTar(type: Tar) { group "JalviewJS" description "Creates a tar.gz file for the website" @@ -2055,7 +1747,6 @@ task jalviewjsSiteTar(type: Tar) { inputs.dir("${jalviewDir}/${jalviewjsSiteDir}") } - task jalviewjsServer { group "JalviewJS" def filename = "jalviewjsTest.html" @@ -2069,23 +1760,19 @@ task jalviewjsServer { def start = port def running = false def url - def urlcore while(port < start+1000 && !running) { try { def doc_root = new File("${jalviewDirAbsolutePath}/${jalviewjsSiteDir}") def jalviewjsServer = factory.start(doc_root, port) running = true url = jalviewjsServer.getResourceUrl(jalviewjs_server_resource) - urlcore = jalviewjsServer.getResourceUrl(jalviewjsJalviewCoreHtmlFile) println("SERVER STARTED with document root ${doc_root}.") println("Go to "+url+" . Run gradle --stop to stop (kills all gradle daemons).") println("For debug: "+url+"?j2sdebug") - println("For core: "+urlcore) file(htmlFile).text = """ -

JalviewJS Test. <${url}>

-

JalviewJS Test with debug. <${url}?j2sdebug<

-

${jalviewjsJalviewTemplateName} Core Test. <${urlcore}>

+

Jalview JS Test. <${url}>

+

Jalview JS Test with debug. <${url}?j2sdebug<

""" } catch (Exception e) { @@ -2099,7 +1786,6 @@ task jalviewjsServer { outputs.upToDateWhen({false}) } - task cleanJalviewjsAll { group "JalviewJS" description "Delete all configuration and build artifacts to do with JalviewJS build" @@ -2118,72 +1804,51 @@ task cleanJalviewjsAll { outputs.upToDateWhen( { false } ) } +task jalviewjs { + group "JalviewJS" + description "Build the site" + dependsOn jalviewjsBuildSite +} -task jalviewjsIDE_CopyTransferSiteJs(type: Copy) { - from "${jalviewDir}/${jalviewjsTransferSiteJsDir}" +task jalviewjsIDE_CopyTransferSite(type: Copy) { + from "${jalviewDir}/${jalviewjsTransferSiteJSDir}" into "${jalviewDir}/${jalviewjsSiteDir}" } - -task jalviewjsIDE_j2sFile { +task jalviewjsIDE_j2s { group "00 JalviewJS in Eclipse" description "Creates the .j2s file" dependsOn jalviewjsCreateJ2sSettings } - -task jalviewjsIDE_BuildAllCores { - group "00 JalviewJS in Eclipse" - description "Build the core js lib closures listed in the classlists dir" - dependsOn jalviewjsNoTranspileBuildAllCores -} - - task jalviewjsIDE_AssembleSite { group "00 JalviewJS in Eclipse" description "Assembles the Eclipse transpiled site and unzips supporting zipfiles" - dependsOn jalviewjsIDE_CopyTransferSiteJs - dependsOn jalviewjsNoTranspilePrepareSite + dependsOn jalviewjsIDE_CopyTransferSite + dependsOn jalviewjsPrepareSite } - task jalviewjsIDE_SiteClean { group "00 JalviewJS in Eclipse" description "Deletes the Eclipse transpiled site" dependsOn cleanJalviewjsSite } - task jalviewjsIDE_Server { group "00 JalviewJS in Eclipse" description "Starts a webserver on localhost to test the website" dependsOn jalviewjsServer } - // buildship runs this at import task eclipseSynchronizationTask { dependsOn eclipseSetup - dependsOn jalviewjsIDE_j2sFile + dependsOn jalviewjsIDE_j2s } - // buildship runs this at build time task eclipseAutoBuildTask { - dependsOn jalviewjsNoTranspileSyncTransferSiteJs - dependsOn jalviewjsNoTranspilePrepareSite -} - - - - - - - - -task jalviewjs { - group "JalviewJS" - description "Build the site" - dependsOn jalviewjsBuildSite + dependsOn jalviewjsSyncTransferSite + dependsOn jalviewjsPrepareSite } diff --git a/utils/jalviewjs/classlists/jalview.txt b/classlists/jalview.txt similarity index 100% rename from utils/jalviewjs/classlists/jalview.txt rename to classlists/jalview.txt diff --git a/utils/jalviewjs/classlists/jvexamplefile.txt b/classlists/jvexamplefile.txt similarity index 100% rename from utils/jalviewjs/classlists/jvexamplefile.txt rename to classlists/jvexamplefile.txt diff --git a/gradle.properties b/gradle.properties index 710e942..fe03c9c 100644 --- a/gradle.properties +++ b/gradle.properties @@ -3,8 +3,6 @@ jalviewDir = . #JAVA_VERSION = 1.8 JAVA_VERSION = 11 -ECLIPSE_IDE_DEVELOPER = false - sourceDir = src #sourceDir = utils/jalviewjs/test/src @@ -157,19 +155,13 @@ jalviewjs_swingjs_zip = swingjs/SwingJS-site.zip jalviewjs_j2s_plugin = swingjs/net.sf.j2s.core.jar jalviewjs_libjs_dir = utils/jalviewjs/libjs jalviewjs_site_resource_dir = utils/jalviewjs/site-resources -jalviewjs_classlists_dir = utils/jalviewjs/classlists -jalviewjs_classlist_jmol = utils/jalviewjs/_j2sclasslist_jmol.txt -jalviewjs_classlist_jalview = utils/jalviewjs/_j2sclasslist.txt jalviewjs_j2s_settings = .j2s #jalviewjs_eclipse_workspace = ~/tmp/eclipse-workspace # these 3 files/dirs found in build/jalviewjs jalviewjs_eclipse_tmp_dropins_dir = eclipse_dropins jalviewjs_eclipse_workspace_location_file = eclipse_workspace_location jalviewjs_site_dir = site -# these dirs are subdirs of the site dir -jalviewjs_swingjs_subdir = swingjs jalviewjs_j2s_subdir = swingjs/j2s -jalviewjs_js_subdir = swingjs/js #jalviewjs_eclipseBuildArg = build jalviewjs_eclipse_build_arg = cleanBuild jalviewjs_server_port = 9001 @@ -190,7 +182,6 @@ 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. j2s.template.html = utils/jalviewjs/template.html -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 @@ -200,10 +191,9 @@ j2s_template_html = utils/jalviewjs/template.html #output will be comma-separated: called method,caller class #j2s.prop.j2s.log.all.calls=true -jalviewjs_j2s_transpile_stdout = j2s-transpile.out +jalviewjs_j2s_stdout = j2s-transpile.out #jalviewjs_j2s_stderr = j2s-transpile.err # all going into out jalviewjs_j2s_to_console = true -jalviewjs_j2s_closure_stdout = j2s-closure.out testp=gradle.properties diff --git a/utils/jalviewjs/_j2sclasslist.txt b/utils/jalviewjs/_j2sclasslist.txt index 425e51f..e35111e 100644 --- a/utils/jalviewjs/_j2sclasslist.txt +++ b/utils/jalviewjs/_j2sclasslist.txt @@ -1,328 +1,35 @@ -jalview/analysis/AAFrequency.js -jalview/analysis/AlignSeq.js -jalview/analysis/AlignmentAnnotationUtils.js -jalview/analysis/AlignmentUtils.js -jalview/analysis/AlignmentSorter.js -jalview/analysis/AnnotationSorter.js -jalview/analysis/Conservation.js -jalview/analysis/CrossRef.js -jalview/analysis/NJTree.js -jalview/analysis/SeqsetUtils.js -jalview/analysis/SequenceIdMatcher.js -jalview/analysis/TreeBuilder.js -jalview/analysis/TreeModel.js -jalview/analysis/scoremodels/DistanceScoreModel.js -jalview/analysis/scoremodels/FeatureDistanceModel.js -jalview/analysis/scoremodels/PIDModel.js -jalview/analysis/scoremodels/ScoreMatrix.js -jalview/analysis/scoremodels/ScoreModels.js -jalview/analysis/scoremodels/SimilarityParams.js -jalview/analysis/scoremodels/SimilarityScoreModel.js -jalview/api/AlignCalcManagerI.js -jalview/api/AlignCalcWorkerI.js -jalview/api/AlignViewControllerGuiI.js -jalview/api/AlignViewControllerI.js -jalview/api/AlignFrameI.js -jalview/api/AlignViewportI.js -jalview/api/AlignmentViewPanel.js -jalview/api/BuildDetailsI.js -jalview/api/FeatureColourI.js -jalview/api/FeatureRenderer.js -jalview/api/FeaturesDisplayedI.js -jalview/api/JalviewApp.js -jalview/api/OOMHandlerI.js -jalview/api/SequenceRenderer.js -jalview/api/StructureSelectionManagerProvider.js -jalview/api/ViewStyleI.js -jalview/api/analysis/PairwiseScoreModelI.js -jalview/api/analysis/ScoreModelI.js -jalview/api/analysis/SimilarityParamsI.js -jalview/bin/AppletParams.js -jalview/bin/ApplicationSingletonProvider.js -jalview/bin/ArgsParser.js -jalview/bin/BuildDetails.js -jalview/bin/Cache.js -jalview/bin/Jalview.js -jalview/bin/JalviewAppLoader.js -jalview/commands/CommandI.js -jalview/commands/OrderCommand.js -jalview/controller/AlignViewController.js -jalview/datamodel/ASequence.js -jalview/datamodel/ASequenceI.js -jalview/datamodel/Alignment.js -jalview/datamodel/AlignmentAnnotation.js -jalview/datamodel/AlignmentI.js -jalview/datamodel/AlignmentView.js -jalview/datamodel/AnnotatedCollectionI.js -jalview/datamodel/Annotation.js -jalview/datamodel/BinaryNode.js -jalview/datamodel/CigarArray.js -jalview/datamodel/CigarBase.js -jalview/datamodel/CigarSimple.js -jalview/datamodel/ColumnSelection.js -jalview/datamodel/ContiguousI.js -jalview/datamodel/DBRefSource.js -jalview/datamodel/HiddenColumns.js -jalview/datamodel/HiddenColumnsCursor.js -jalview/datamodel/HiddenCursorPosition.js -jalview/datamodel/HiddenSequences.js -jalview/datamodel/PDBEntry.js -jalview/datamodel/Profile.js -jalview/datamodel/ProfileI.js -jalview/datamodel/Profiles.js -jalview/datamodel/ProfilesI.js -jalview/datamodel/Range.js -jalview/datamodel/RangeIterator.js -jalview/datamodel/ResidueCount.js -jalview/datamodel/SearchResults.js -jalview/datamodel/SearchResultsI.js -jalview/datamodel/SeqCigar.js -jalview/datamodel/Sequence.js -jalview/datamodel/SequenceCollectionI.js -jalview/datamodel/SequenceCursor.js -jalview/datamodel/SequenceFeature.js -jalview/datamodel/SequenceGroup.js -jalview/datamodel/SequenceI.js -jalview/datamodel/SequenceNode.js -jalview/datamodel/features/FeatureLocationI.js -jalview/datamodel/features/FeatureMatcher.js -jalview/datamodel/features/FeatureMatcherI.js -jalview/datamodel/features/FeatureMatcherSet.js -jalview/datamodel/features/FeatureMatcherSetI.js -jalview/datamodel/features/FeatureStore.js -jalview/datamodel/features/FeatureStoreI.js -jalview/datamodel/features/FeatureStoreJS.js - -jalview/datamodel/features/SequenceFeatures.js -jalview/datamodel/features/SequenceFeaturesI.js -jalview/gui/AlignFrame.js -jalview/gui/AlignViewport.js -jalview/gui/AlignmentPanel.js -jalview/gui/AnnotationLabels.js -jalview/gui/AnnotationPanel.js -jalview/gui/CalculationChooser.js -jalview/gui/ColourMenuHelper.js -jalview/gui/ComboBoxTooltipRenderer.js -jalview/gui/Desktop.js -jalview/gui/FeatureRenderer.js -jalview/gui/IProgressIndicator.js -jalview/gui/IdCanvas.js -jalview/gui/IdPanel.js -jalview/gui/IdwidthAdjuster.js -jalview/gui/JalviewChangeSupport.js -jalview/gui/JvSwingUtils.js -jalview/gui/PaintRefresher.js -jalview/gui/PopupMenu.js -jalview/gui/Preferences.js -jalview/gui/ProgressBar.js -jalview/gui/ScalePanel.js -jalview/gui/SeqCanvas.js -jalview/gui/SeqPanel.js -jalview/gui/SequenceRenderer.js -jalview/gui/TreeCanvas.js -jalview/gui/TreePanel.js -jalview/gui/ViewSelectionMenu.js -jalview/io/AlignFile.js -jalview/io/AlignmentFileReaderI.js -jalview/io/AlignmentFileWriterI.js -jalview/io/AppletFormatAdapter.js -jalview/io/DataSourceType.js -jalview/io/FileFormat.js -jalview/io/FileFormatI.js -jalview/io/FileFormats.js -jalview/io/FileLoader.js -jalview/io/FileParse.js -jalview/io/IdentifyFile.js -jalview/io/NewickFile.js -jalview/io/PIRFile.js -jalview/io/ScoreMatrixFile.js -jalview/io/SequenceAnnotationReport.js -jalview/javascript/JalviewLiteJSApi.js -jalview/javascript/log4j/ConsoleAppender.js -jalview/javascript/log4j/Layout.js -jalview/javascript/log4j/Level.js -jalview/javascript/log4j/Logger.js -jalview/javascript/log4j/Priority.js -jalview/javascript/log4j/SimpleLayout.js -jalview/javascript/log4j/spi/OptionHandler.js -jalview/jbgui/GAlignFrame.js -jalview/jbgui/GAlignmentPanel.js -jalview/jbgui/GDesktop.js -jalview/jbgui/GPreferences.js -jalview/jbgui/GTreePanel.js -jalview/math/Matrix.js -jalview/math/MatrixI.js -jalview/project/Jalview2XML.js -jalview/renderer/AnnotationRenderer.js -jalview/renderer/AwtRenderPanelI.js -jalview/renderer/ResidueColourFinder.js -jalview/renderer/ResidueShader.js -jalview/renderer/ResidueShaderI.js -jalview/renderer/ScaleRenderer.js -jalview/renderer/seqfeatures/FeatureRenderer.js -jalview/schemes/Blosum62ColourScheme.js -jalview/schemes/BuriedColourScheme.js -jalview/schemes/ClustalxColourScheme.js -jalview/schemes/ColourSchemeI.js -jalview/schemes/ColourSchemeProperty.js -jalview/schemes/ColourSchemes.js -jalview/schemes/ColourSchemeLoader.js -jalview/schemes/UserColourScheme.js -jalview/schemes/Consensus.js -jalview/schemes/FeatureColour.js -jalview/schemes/HelixColourScheme.js -jalview/schemes/HydrophobicColourScheme.js -jalview/schemes/JalviewColourScheme.js -jalview/schemes/NucleotideColourScheme.js -jalview/schemes/PIDColourScheme.js -jalview/schemes/PurinePyrimidineColourScheme.js -jalview/schemes/RNAHelicesColour.js -jalview/schemes/ResidueColourScheme.js -jalview/schemes/ResidueProperties.js -jalview/schemes/ScoreColourScheme.js -jalview/schemes/StrandColourScheme.js -jalview/schemes/TCoffeeColourScheme.js -jalview/schemes/TaylorColourScheme.js -jalview/schemes/TurnColourScheme.js -jalview/schemes/UserColourScheme.js -jalview/schemes/ZappoColourScheme.js -jalview/structure/CommandListener.js -jalview/structure/SelectionListener.js -jalview/structure/SelectionSource.js -jalview/structure/SequenceListener.js -jalview/structure/StructureImportSettings.js -jalview/structure/StructureSelectionManager.js -jalview/structure/VamsasSource.js -jalview/urls/CustomUrlProvider.js -jalview/urls/IdOrgSettings.js -jalview/urls/IdentifiersUrlProvider.js -jalview/urls/UrlLinkDisplay.js -jalview/urls/UrlLinkTableModel.js -jalview/urls/UrlProvider.js -jalview/urls/UrlProviderImpl.js -jalview/urls/api/UrlProviderFactoryI.js -jalview/urls/api/UrlProviderI.js -jalview/urls/desktop/DesktopUrlProviderFactory.js -jalview/util/ColorUtils.js -jalview/util/Comparison.js -jalview/util/DBRefUtils.js -jalview/util/Format.js -jalview/util/MessageManager.js -jalview/util/Platform.js -jalview/util/QuickSort.js -jalview/util/StringUtils.js -jalview/util/UrlLink.js -jalview/util/jarInputStreamProvider.js -jalview/util/matcher/Condition.js -jalview/util/matcher/Matcher.js -jalview/util/matcher/MatcherI.js -jalview/viewmodel/AlignmentViewport.js -jalview/viewmodel/ViewportListenerI.js -jalview/viewmodel/ViewportProperties.js -jalview/viewmodel/ViewportRanges.js -jalview/viewmodel/seqfeatures/FeatureRendererModel.js -jalview/viewmodel/seqfeatures/FeatureRendererSettings.js -jalview/viewmodel/seqfeatures/FeaturesDisplayed.js -jalview/viewmodel/styles/ViewStyle.js -jalview/workers/AlignCalcManager.js -jalview/workers/AlignCalcWorker.js -jalview/workers/ConsensusThread.js -jalview/workers/ConservationThread.js -jalview/ws/sifts/SiftsSettings.js -jalview/xml/binding/jalview/Annotation.js -jalview/xml/binding/jalview/AnnotationElement.js -jalview/xml/binding/jalview/Feature.js -jalview/xml/binding/jalview/FeatureMatcher.js -jalview/xml/binding/jalview/FeatureMatcherSet.js -jalview/xml/binding/jalview/FilterBy.js -jalview/xml/binding/jalview/JalviewModel.js -jalview/xml/binding/jalview/NoValueColour.js -jalview/xml/binding/jalview/Pdbentry.js -jalview/xml/binding/jalview/Sequence.js -jalview/xml/binding/jalview/SequenceSet.js -jalview/xml/binding/jalview/SequenceType.js -jalview/xml/binding/jalview/VAMSAS.js -jalview/xml/binding/jalview/WebServiceParameterSet.js +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/ActiveEvent.js -java/awt/Adjustable.js -java/awt/AlphaComposite.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/Composite.js -java/awt/Container.js java/awt/ContainerOrderFocusTraversalPolicy.js +java/awt/Container.js java/awt/Cursor.js java/awt/DefaultFocusTraversalPolicy.js java/awt/DefaultKeyboardFocusManager.js java/awt/Dialog.js java/awt/Dimension.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/FontMetrics.js -java/awt/GraphicsCallback.js -java/awt/GraphicsConfiguration.js -java/awt/GraphicsDevice.js -java/awt/GraphicsEnvironment.js -java/awt/GridLayout.js -java/awt/Image.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/KeyEventDispatcher.js -java/awt/KeyEventPostProcessor.js -java/awt/KeyboardFocusManager.js -java/awt/LayoutManager.js -java/awt/LayoutManager2.js -java/awt/LightweightDispatcher.js -java/awt/Paint.js -java/awt/Point.js -java/awt/Queue.js -java/awt/Rectangle.js -java/awt/RenderingHints.js -java/awt/SentEvent.js -java/awt/Shape.js -java/awt/Stroke.js -java/awt/Toolkit.js -java/awt/Transparency.js -java/awt/VKCollection.js -java/awt/Window.js -java/awt/color/ColorSpace.js -java/awt/datatransfer/ClipboardOwner.js -java/awt/datatransfer/FlavorMap.js -java/awt/datatransfer/FlavorTable.js -java/awt/datatransfer/SystemFlavorMap.js -java/awt/dnd/DropTarget.js -java/awt/dnd/DropTargetContext.js -java/awt/dnd/DropTargetListener.js java/awt/dnd/peer/DropTargetPeer.js -java/awt/event/AWTEventListener.js -java/awt/event/ActionEvent.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/ContainerEvent.js java/awt/event/ContainerListener.js -java/awt/event/FocusAdapter.js java/awt/event/FocusEvent.js java/awt/event/FocusListener.js java/awt/event/HierarchyBoundsListener.js @@ -332,13 +39,9 @@ java/awt/event/InputMethodListener.js java/awt/event/InvocationEvent.js java/awt/event/ItemEvent.js java/awt/event/ItemListener.js -java/awt/event/KeyAdapter.js -java/awt/event/KeyEvent.js java/awt/event/KeyListener.js -java/awt/event/MouseAdapter.js java/awt/event/MouseEvent.js java/awt/event/MouseListener.js -java/awt/event/MouseMotionAdapter.js java/awt/event/MouseMotionListener.js java/awt/event/MouseWheelListener.js java/awt/event/TextListener.js @@ -347,124 +50,103 @@ 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/RectIterator.js java/awt/geom/Rectangle2D.js java/awt/geom/RectangularShape.js -java/awt/image/BufferedImage.js -java/awt/image/ColorModel.js -java/awt/image/DataBuffer.js -java/awt/image/DataBufferInt.js -java/awt/image/DirectColorModel.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/image/PackedColorModel.js -java/awt/image/Raster.js -java/awt/image/RenderedImage.js -java/awt/image/SampleModel.js -java/awt/image/SinglePixelPackedSampleModel.js -java/awt/image/WritableRaster.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/print/Printable.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/io/BufferedInputStream.js -java/io/BufferedReader.js -java/io/ByteArrayInputStream.js -java/io/Closeable.js -java/io/File.js -java/io/FileDescriptor.js -java/io/FileInputStream.js -java/io/FileReader.js -java/io/FileSystem.js -java/io/FilterInputStream.js -java/io/InputStream.js -java/io/InputStreamReader.js -java/io/PushbackInputStream.js -java/io/Reader.js java/lang/AbstractStringBuilder.js -java/lang/AutoCloseable.js java/lang/Class.js java/lang/Enum.js java/lang/Iterable.js -java/lang/Readable.js -java/lang/Runtime.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/lang/reflect/Constructor.js -java/lang/reflect/Method.js -java/math/BigDecimal.js -java/math/BigInteger.js -java/math/MathContext.js java/math/RoundingMode.js -java/net/HttpURLConnection.js -java/net/MalformedURLException.js java/net/URL.js -java/net/URLConnection.js -java/net/URLDecoder.js -java/net/URLStreamHandler.js java/net/URLStreamHandlerFactory.js -java/nio/Bits.js -java/nio/Buffer.js -java/nio/ByteBuffer.js -java/nio/ByteOrder.js -java/nio/CharBuffer.js -java/nio/HeapByteBuffer.js -java/nio/HeapCharBuffer.js -java/nio/charset/Charset.js -java/nio/charset/CharsetDecoder.js -java/nio/charset/CoderResult.js -java/nio/charset/CodingErrorAction.js -java/security/AccessControlContext.js -java/security/AccessController.js -java/security/PrivilegedAction.js -java/security/PrivilegedExceptionAction.js -java/text/AttributedCharacterIterator.js java/text/CharacterIterator.js -java/text/DateFormat.js -java/text/DateFormatSymbols.js java/text/DecimalFormat.js java/text/DecimalFormatSymbols.js java/text/DigitList.js java/text/FieldPosition.js java/text/Format.js -java/text/MessageFormat.js java/text/NumberFormat.js -java/text/SimpleDateFormat.js java/util/AbstractCollection.js java/util/AbstractList.js java/util/AbstractMap.js -java/util/AbstractQueue.js java/util/AbstractSequentialList.js java/util/AbstractSet.js -java/util/ArrayDeque.js java/util/ArrayList.js java/util/Arrays.js -java/util/BitSet.js -java/util/Calendar.js java/util/Collection.js java/util/Collections.js java/util/Comparator.js java/util/Deque.js java/util/Dictionary.js -java/util/DualPivotQuicksort.js java/util/Enumeration.js java/util/EventListener.js java/util/EventObject.js -java/util/GregorianCalendar.js java/util/HashMap.js java/util/HashSet.js java/util/Hashtable.js @@ -473,75 +155,26 @@ java/util/Iterator.js java/util/LinkedHashMap.js java/util/LinkedList.js java/util/List.js -java/util/ListIterator.js java/util/ListResourceBundle.js java/util/Locale.js java/util/Map.js -java/util/NavigableMap.js -java/util/NavigableSet.js java/util/Objects.js -java/util/Properties.js -java/util/PropertyResourceBundle.js java/util/Queue.js +java/util/Random.js java/util/RandomAccess.js java/util/ResourceBundle.js java/util/Set.js -java/util/SortedMap.js -java/util/SortedSet.js -java/util/StringTokenizer.js java/util/TimSort.js -java/util/TimeZone.js -java/util/TreeMap.js -java/util/TreeSet.js java/util/Vector.js -java/util/concurrent/AbstractExecutorService.js -java/util/concurrent/BlockingQueue.js -java/util/concurrent/ConcurrentHashMap.js -java/util/concurrent/ConcurrentMap.js -java/util/concurrent/Executor.js -java/util/concurrent/ExecutorService.js -java/util/concurrent/Executors.js -java/util/concurrent/LinkedBlockingQueue.js -java/util/concurrent/RejectedExecutionHandler.js -java/util/concurrent/Semaphore.js -java/util/concurrent/ThreadFactory.js -java/util/concurrent/ThreadPoolExecutor.js -java/util/concurrent/TimeUnit.js -java/util/concurrent/atomic/AtomicBoolean.js -java/util/concurrent/atomic/AtomicInteger.js -java/util/concurrent/locks/AbstractOwnableSynchronizer.js -java/util/concurrent/locks/AbstractQueuedSynchronizer.js -java/util/concurrent/locks/Condition.js -java/util/concurrent/locks/Lock.js -java/util/concurrent/locks/ReadWriteLock.js -java/util/concurrent/locks/ReentrantLock.js -java/util/concurrent/locks/ReentrantReadWriteLock.js -java/util/jar/JarEntry.js -java/util/jar/JarInputStream.js -java/util/logging/Level.js -java/util/logging/Logger.js -java/util/regex/MatchResult.js -java/util/regex/Matcher.js -java/util/regex/Pattern.js -java/util/zip/CRC32.js -java/util/zip/Inflater.js -java/util/zip/InflaterInputStream.js -java/util/zip/ZipConstants.js -java/util/zip/ZipEntry.js -java/util/zip/ZipInputStream.js -javajs/api/GenericLineReader.js javajs/api/JSFunction.js -javajs/api/JSONEncodable.js -javajs/util/AU.js javajs/util/AjaxURLConnection.js -javajs/util/AjaxURLStreamHandler.js javajs/util/AjaxURLStreamHandlerFactory.js -javajs/util/Encoding.js +javajs/util/AU.js javajs/util/JSThread.js javajs/util/Lst.js javajs/util/PT.js -javajs/util/Rdr.js javajs/util/SB.js +javax/net/ssl/HttpsUrlConnection.js javax/swing/AbstractAction.js javax/swing/AbstractButton.js javax/swing/AbstractListModel.js @@ -549,6 +182,13 @@ 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 @@ -556,14 +196,24 @@ javax/swing/ButtonGroup.js javax/swing/ButtonModel.js javax/swing/ClientPropertyKey.js javax/swing/ComboBoxModel.js -javax/swing/ComponentInputMap.js javax/swing/DefaultBoundedRangeModel.js javax/swing/DefaultButtonModel.js javax/swing/DefaultComboBoxModel.js -javax/swing/DefaultDesktopManager.js -javax/swing/DefaultListCellRenderer.js javax/swing/DefaultSingleSelectionModel.js -javax/swing/DesktopManager.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/FocusManager.js javax/swing/InternalFrameFocusTraversalPolicy.js javax/swing/LayoutComparator.js @@ -578,10 +228,7 @@ javax/swing/JCheckBox.js javax/swing/JCheckBoxMenuItem.js javax/swing/JComboBox.js javax/swing/JComponent.js -javax/swing/JDesktopPane.js -javax/swing/JDialog.js javax/swing/JFrame.js -javax/swing/JInternalFrame.js javax/swing/JLabel.js javax/swing/JLayeredPane.js javax/swing/JMenu.js @@ -589,182 +236,124 @@ javax/swing/JMenuBar.js javax/swing/JMenuItem.js javax/swing/JPanel.js javax/swing/JPopupMenu.js -javax/swing/JProgressBar.js -javax/swing/JRadioButton.js javax/swing/JRadioButtonMenuItem.js javax/swing/JRootPane.js javax/swing/JScrollBar.js javax/swing/JScrollPane.js javax/swing/JSeparator.js -javax/swing/JTabbedPane.js +javax/swing/JTextArea.js +javax/swing/JTextField.js javax/swing/JToggleButton.js -javax/swing/JToolTip.js javax/swing/JViewport.js -javax/swing/JWindow.js -javax/swing/KeyStroke.js javax/swing/KeyboardManager.js -javax/swing/ListCellRenderer.js +javax/swing/KeyStroke.js javax/swing/ListModel.js javax/swing/LookAndFeel.js javax/swing/MenuElement.js -javax/swing/MenuSelectionManager.js javax/swing/MutableComboBoxModel.js -javax/swing/Popup.js -javax/swing/PopupFactory.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/Scrollable.js javax/swing/SingleSelectionModel.js javax/swing/SizeRequirements.js javax/swing/SwingConstants.js javax/swing/SwingPaintEventDispatcher.js javax/swing/SwingUtilities.js -javax/swing/Timer.js -javax/swing/ToolTipManager.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 -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/border/TitledBorder.js -javax/swing/event/AncestorEvent.js -javax/swing/event/AncestorListener.js -javax/swing/event/ChangeEvent.js -javax/swing/event/ChangeListener.js -javax/swing/event/EventListenerList.js -javax/swing/event/InternalFrameAdapter.js -javax/swing/event/InternalFrameEvent.js -javax/swing/event/InternalFrameListener.js -javax/swing/event/ListDataListener.js -javax/swing/event/MenuKeyListener.js -javax/swing/event/MenuListener.js -javax/swing/event/TableModelListener.js -javax/swing/plaf/ActionMapUIResource.js -javax/swing/plaf/BorderUIResource.js -javax/swing/plaf/ColorUIResource.js -javax/swing/plaf/ComponentInputMapUIResource.js -javax/swing/plaf/ComponentUI.js -javax/swing/plaf/DimensionUIResource.js -javax/swing/plaf/FontUIResource.js -javax/swing/plaf/InsetsUIResource.js -javax/swing/plaf/UIResource.js -javax/swing/plaf/basic/BasicBorders.js -javax/swing/table/AbstractTableModel.js -javax/swing/table/TableModel.js -javax/xml/bind/ContextFinder.js -javax/xml/bind/GetPropertyAction.js -javax/xml/bind/JAXBContext.js -javax/xml/bind/JAXBContextFactory.js -javax/xml/bind/JAXBElement.js -javax/xml/bind/ModuleUtil.js -javax/xml/bind/ServiceLoaderUtil.js -javax/xml/bind/Unmarshaller.js -javax/xml/bind/ValidationEventHandler.js -javax/xml/bind/annotation/adapters/CollapsedStringAdapter.js -javax/xml/bind/annotation/adapters/XmlAdapter.js -javax/xml/bind/helpers/AbstractUnmarshallerImpl.js -javax/xml/bind/helpers/DefaultValidationEventHandler.js -javax/xml/datatype/DatatypeFactory.js -javax/xml/datatype/XMLGregorianCalendar.js -javax/xml/namespace/QName.js -javax/xml/stream/XMLInputFactory.js -javax/xml/stream/XMLStreamReader.js -org/apache/xerces/jaxp/datatype/DatatypeFactoryImpl.js -org/apache/xerces/jaxp/datatype/XMLGregorianCalendarImpl.js -org/json/simple/parser/JSONParser.js -org/json/simple/parser/ParseException.js -org/json/simple/parser/Yylex.js -org/xml/sax/AttributeList.js -org/xml/sax/Attributes.js -org/xml/sax/ContentHandler.js -org/xml/sax/InputSource.js -org/xml/sax/Parser.js -org/xml/sax/XMLReader.js -org/xml/sax/ext/Attributes2.js -sun/awt/AWTAutoShutdown.js sun/awt/AppContext.js +sun/awt/AWTAutoShutdown.js sun/awt/CausedFocusEvent.js sun/awt/ComponentFactory.js -sun/awt/EventQueueItem.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/SunGraphicsCallback.js sun/awt/SunToolkit.js sun/awt/WindowClosingListener.js sun/awt/WindowClosingSupport.js -sun/awt/image/DataStealer.js -sun/awt/image/IntegerComponentRaster.js -sun/awt/image/IntegerInterleavedRaster.js -sun/awt/image/SunWritableRaster.js sun/font/FontDesignMetrics.js -sun/java2d/StateTrackable.js -sun/java2d/StateTrackableDelegate.js -sun/nio/cs/ArrayDecoder.js -sun/nio/cs/HistoricallyNamedCharset.js -sun/nio/cs/StandardCharsets.js -sun/nio/cs/ThreadLocalCoders.js -sun/nio/cs/UTF_8.js -sun/nio/cs/Unicode.js sun/swing/DefaultLookup.js sun/swing/SwingLazyValue.js -sun/swing/UIAction.js sun/text/resources/FormatData.js sun/text/resources/FormatData_en.js -sun/util/calendar/AbstractCalendar.js -sun/util/calendar/BaseCalendar.js -sun/util/calendar/CalendarDate.js -sun/util/calendar/CalendarSystem.js -sun/util/calendar/CalendarUtils.js -sun/util/calendar/Gregorian.js -sun/util/calendar/ZoneInfo.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/jquery/JQueryUI.js swingjs/JSApp.js swingjs/JSAppletThread.js swingjs/JSAppletViewer.js -swingjs/JSCharSet.js -swingjs/JSDummyApplet.js swingjs/JSFocusPeer.js swingjs/JSFontMetrics.js swingjs/JSFrameViewer.js swingjs/JSGraphics2D.js -swingjs/JSGraphicsCompositor.js swingjs/JSGraphicsConfiguration.js swingjs/JSGraphicsEnvironment.js -swingjs/JSKeyEvent.js -swingjs/JSMenuManager.js swingjs/JSMouse.js +swingjs/JSNullComponentPeer.js swingjs/JSScreenDevice.js swingjs/JSThreadGroup.js swingjs/JSToolkit.js swingjs/JSUtil.js -swingjs/a2s/Dialog.js -swingjs/api/Interface.js -swingjs/api/js/DOMNode.js -swingjs/api/js/HTML5CanvasContext2D.js -swingjs/api/js/JSInterface.js -swingjs/jquery/JQueryUI.js -swingjs/jzlib/Adler32.js -swingjs/jzlib/CRC32.js -swingjs/jzlib/Checksum.js -swingjs/jzlib/InfBlocks.js -swingjs/jzlib/InfCodes.js -swingjs/jzlib/InfTree.js -swingjs/jzlib/Inflate.js -swingjs/jzlib/Inflater.js -swingjs/jzlib/InflaterInputStream.js -swingjs/jzlib/ZStream.js swingjs/plaf/ButtonListener.js swingjs/plaf/DefaultMenuLayout.js swingjs/plaf/HTML5LookAndFeel.js @@ -774,12 +363,9 @@ swingjs/plaf/JSCheckBoxMenuItemUI.js swingjs/plaf/JSCheckBoxUI.js swingjs/plaf/JSComboBoxUI.js swingjs/plaf/JSComponentUI.js -swingjs/plaf/JSDesktopIconUI.js -swingjs/plaf/JSDesktopPaneUI.js swingjs/plaf/JSEventHandler.js swingjs/plaf/JSFrameUI.js swingjs/plaf/JSGraphicsUtils.js -swingjs/plaf/JSInternalFrameUI.js swingjs/plaf/JSLabelUI.js swingjs/plaf/JSLayeredPaneUI.js swingjs/plaf/JSLightweightUI.js @@ -789,8 +375,6 @@ swingjs/plaf/JSMenuUI.js swingjs/plaf/JSPanelUI.js swingjs/plaf/JSPopupMenuSeparatorUI.js swingjs/plaf/JSPopupMenuUI.js -swingjs/plaf/JSPopupUI.js -swingjs/plaf/JSProgressBarUI.js swingjs/plaf/JSRadioButtonMenuItemUI.js swingjs/plaf/JSRadioButtonUI.js swingjs/plaf/JSRootPaneUI.js @@ -798,201 +382,14 @@ swingjs/plaf/JSScrollBarUI.js swingjs/plaf/JSScrollPaneUI.js swingjs/plaf/JSSeparatorUI.js swingjs/plaf/JSSliderUI.js -swingjs/plaf/JSTabbedPaneUI.js -swingjs/plaf/JSToolTipUI.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/xml/JSJAXBClass.js -swingjs/xml/JSJAXBContext.js -swingjs/xml/JSJAXBContextFactory.js -swingjs/xml/JSJAXBField.js -swingjs/xml/JSJAXBUnmarshaller.js -swingjs/xml/JSSAXAttributes.js -swingjs/xml/JSSAXParser.js -swingjs/xml/JSXMLGregorianCalendarImpl.js -swingjs/xml/JSXMLInputFactory.js -swingjs/xml/JSXMLStreamReader.js -intervalstore/api/IntervalI.js -intervalstore/api/IntervalStoreI.js -intervalstore/nonc/IntervalStore.js -jalview/analysis/GeneticCodeI.js -jalview/analysis/GeneticCodes.js -jalview/api/FeaturesSourceI.js -jalview/io/FastaFile.js -jalview/io/FeaturesFile.js -jalview/io/FormatAdapter.js -jalview/schemes/IdColourScheme.js -jalview/util/LinkedIdentityHashSet.js -jalview/util/ParseHtmlBodyAndLinks.js -java/util/function/Function.js -swingjs/a2s/A2SContainer.js - -jalview/fts/api/FTSData.js -jalview/fts/api/FTSDataColumnI.js -jalview/fts/api/FTSRestClientI.js -jalview/fts/core/DecimalFormatTableCellRenderer.js -jalview/fts/core/FTSDataColumnPreferences.js -jalview/fts/core/FTSRestClient.js -jalview/fts/core/FTSRestRequest.js -jalview/fts/core/FTSRestResponse.js -jalview/fts/service/pdb/PDBFTSRestClient.js -jalview/gui/StructureChooser.js -jalview/javascript/json/JSON.js -jalview/javascript/web/Client.js -jalview/javascript/web/ClientResponse.js -jalview/javascript/web/WebResource.js -jalview/jbgui/BackupFilesPresetEntry.js -jalview/jbgui/GStructureChooser.js -jalview/jbgui/IntKeyStringValueEntry.js -java/awt/CardLayout.js -java/awt/TextComponent.js -java/awt/image/ImageConsumer.js -java/io/ObjectStreamField.js -java/net/URI.js -java/util/ComparableTimSort.js -java/util/LinkedHashSet.js -java/util/WeakHashMap.js -javajs/util/Base64.js -javax/net/ssl/HttpsURLConnection.js -javax/swing/CellRendererPane.js -javax/swing/DefaultListSelectionModel.js -javax/swing/DefaultRowSorter.js -javax/swing/DropMode.js -javax/swing/Icon.js -javax/swing/ImageIcon.js -javax/swing/JTable.js -javax/swing/JTextField.js -javax/swing/ListSelectionModel.js -javax/swing/RowSorter.js -javax/swing/SortOrder.js -javax/swing/event/CaretEvent.js -javax/swing/event/CaretListener.js -javax/swing/event/CellEditorListener.js -javax/swing/event/DocumentListener.js -javax/swing/event/ListSelectionEvent.js -javax/swing/event/ListSelectionListener.js -javax/swing/event/MouseInputListener.js -javax/swing/event/RowSorterEvent.js -javax/swing/event/RowSorterListener.js -javax/swing/event/SwingPropertyChangeSupport.js -javax/swing/event/TableColumnModelEvent.js -javax/swing/event/TableColumnModelListener.js -javax/swing/event/TableModelEvent.js -javax/swing/plaf/InputMapUIResource.js 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