X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=build.gradle;h=7cdadc1015bd2b67c1e871408e37e6b279279ad5;hb=2d28597b643c287eee1f495e56c3529be05bbc5d;hp=ec665dcc5be9db474d6ae1226ba3eaa415249dc1;hpb=acc9f3f5965575e9ccc7fc854544d97d5ca0425a;p=jalview.git

diff --git a/build.gradle b/build.gradle
index ec665dc..7cdadc1 100644
--- a/build.gradle
+++ b/build.gradle
@@ -2,6 +2,7 @@ import org.apache.tools.ant.filters.ReplaceTokens
 import org.gradle.internal.os.OperatingSystem
 import org.gradle.plugins.ide.eclipse.model.Output
 import org.gradle.plugins.ide.eclipse.model.Library
+import java.security.MessageDigest
 
 import groovy.transform.ExternalizeMethods
 
@@ -42,6 +43,7 @@ def string(Object o) {
 
 ext {
   jalviewDirAbsolutePath = file(jalviewDir).getAbsolutePath()
+  jalviewDirRelativePath = jalviewDir
 
   // local build environment properties
   def localProps = "${jalviewDirAbsolutePath}/local.properties"
@@ -64,7 +66,6 @@ ext {
     }
   }
 
-
   // this property set when running Eclipse headlessly
   j2sHeadlessBuildProperty = string("net.sf.j2s.core.headlessbuild")
   // this property set by Eclipse
@@ -82,22 +83,36 @@ ext {
   } else {
     println("HEADLESS BUILD")
   }
-  /*
+  /* *-/
   System.properties.sort { it.key }.each {
     key, val -> println("SYSTEM PROPERTY ${key}='${val}'")
   }
+  /-* *-/
+  if (false && IN_ECLIPSE) {
+    jalviewDir = jalviewDirAbsolutePath
+  }
   */
 
+  // essentials
+  bareSourceDir = string(source_dir)
+  sourceDir = string("${jalviewDir}/${bareSourceDir}")
+  resourceDir = string("${jalviewDir}/${resource_dir}")
+  bareTestSourceDir = string(test_source_dir)
+  testSourceDir = string("${jalviewDir}/${bareTestSourceDir}")
+
+  // clover
   cloverInstrDir = file("${buildDir}/${cloverSourcesInstrDir}")
-  classes = string("${jalviewDir}/${classesDir}")
+  classesDir = string("${jalviewDir}/${classes_dir}")
   if (clover.equals("true")) {
     use_clover = true
-    classes = string("${buildDir}/${cloverClassesDir}")
+    classesDir = string("${buildDir}/${cloverClassesDir}")
   } else {
     use_clover = false
-    classes = string("${jalviewDir}/${classesDir}")
+    classesDir = string("${jalviewDir}/${classes_dir}")
   }
 
+  classes = classesDir
+
   getdownWebsiteDir = string("${jalviewDir}/${getdown_website_dir}/${JAVA_VERSION}")
   getdownDir = string("")
   reportRsyncCmd = false
@@ -112,7 +127,7 @@ ext {
     getdown_channel_name = string("${bamboo_planKey}/${JAVA_VERSION}")
     getdown_app_base = string("${bamboo_channelbase}/${bamboo_planKey}${bamboo_getdown_channel_suffix}/${JAVA_VERSION}")
     getdown_app_dir = getdown_app_dir_alt
-    buildProperties = string("${jalviewDir}/${classesDir}/${build_properties_file}")
+    buildProperties = string("${classesDir}/${build_properties_file}")
     break
 
     case "RELEASE":
@@ -120,7 +135,7 @@ ext {
     getdownDir = string("${getdown_channel_name}/${JAVA_VERSION}")
     getdown_app_base = string("${getdown_channel_base}/${getdownDir}")
     getdown_app_dir = getdown_app_dir_release
-    buildProperties = string("${jalviewDir}/${classesDir}/${build_properties_file}")
+    buildProperties = string("${classesDir}/${build_properties_file}")
     reportRsyncCommand = true
     break
 
@@ -134,7 +149,7 @@ ext {
       exit
     } else {
       packageDir = string("${ARCHIVEDIR}/${packageDir}")
-      buildProperties = string("${ARCHIVEDIR}/${classesDir}/${build_properties_file}")
+      buildProperties = string("${ARCHIVEDIR}/${classes_dir}/${build_properties_file}")
       buildDist = false
     }
     reportRsyncCommand = true
@@ -150,7 +165,7 @@ ext {
       exit
     } else {
       packageDir = string("${ARCHIVEDIR}/${packageDir}")
-      buildProperties = string("${ARCHIVEDIR}/${classesDir}/${build_properties_file}")
+      buildProperties = string("${ARCHIVEDIR}/${classes_dir}/${build_properties_file}")
       buildDist = false
     }
     reportRsyncCommand = true
@@ -162,7 +177,7 @@ ext {
     getdownDir = string("${getdown_channel_name}/${JAVA_VERSION}")
     getdown_app_base = string("${getdown_channel_base}/${getdownDir}")
     getdown_app_dir = getdown_app_dir_alt
-    buildProperties = string("${jalviewDir}/${classesDir}/${build_properties_file}")
+    buildProperties = string("${classesDir}/${build_properties_file}")
     reportRsyncCommand = true
     break
 
@@ -171,7 +186,7 @@ ext {
     getdownDir = string("${getdown_channel_name}/${JAVA_VERSION}")
     getdown_app_base = string("${getdown_channel_base}/${getdownDir}")
     getdown_app_dir = getdown_app_dir_alt
-    buildProperties = string("${jalviewDir}/${classesDir}/${build_properties_file}")
+    buildProperties = string("${classesDir}/${build_properties_file}")
     reportRsyncCommand = true
     break
 
@@ -180,14 +195,14 @@ ext {
     getdownDir = string("${getdown_channel_name}/${JAVA_VERSION}")
     getdown_app_base = string("${getdown_channel_base}/${getdownDir}")
     getdown_app_dir = getdown_app_dir_alt
-    buildProperties = string("${jalviewDir}/${classesDir}/${build_properties_file}")
+    buildProperties = string("${classesDir}/${build_properties_file}")
     reportRsyncCommand = true
     break
 
     case "LOCAL":
     getdown_app_base = file(getdownWebsiteDir).toURI().toString()
     getdown_app_dir = getdown_app_dir_alt
-    buildProperties = string("${jalviewDir}/${classesDir}/${build_properties_file}")
+    buildProperties = string("${classesDir}/${build_properties_file}")
     getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
     break
 
@@ -277,7 +292,10 @@ ext {
 
 
   buildingHTML = string("${jalviewDir}/${docDir}/building.html")
-  helpFile = string("${classes}/${helpDir}/help.jhm")
+  helpFile = string("${classesDir}/${help_dir}/help.jhm")
+  helpParentDir = string("${jalviewDir}/${help_parent_dir}")
+  helpDir = string("${help_dir}")
+  helpSourceDir = string("${helpParentDir}/${helpDir}")
 
 
   relativeBuildDir = file(jalviewDirAbsolutePath).toPath().relativize(buildDir.toPath())
@@ -293,7 +311,10 @@ ext {
   jalviewjsTransferSiteCoreDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_core")
   jalviewjsJalviewCoreHtmlFile = string("")
   jalviewjsJalviewCoreName = string(jalviewjs_core_name)
+  jalviewjsCoreClasslists = []
   jalviewjsJalviewTemplateName = string(jalviewjs_name)
+  jalviewjsJ2sSettingsFileName = string("${jalviewDir}/${jalviewjs_j2s_settings}")
+  jalviewjsJ2sProps = null
 
   eclipseWorkspace = null
   eclipseBinary = string("")
@@ -306,12 +327,12 @@ ext {
 sourceSets {
   main {
     java {
-      srcDirs "${jalviewDir}/${sourceDir}"
-      outputDir = file(project.classes)
+      srcDirs sourceDir
+      outputDir = file(classesDir)
     }
 
     resources {
-      srcDirs "${jalviewDir}/${resourceDir}"
+      srcDirs resourceDir
     }
 
     jar.destinationDir = file("${jalviewDir}/${packageDir}")
@@ -342,7 +363,7 @@ sourceSets {
 
   test {
     java {
-      srcDirs "${jalviewDir}/${testSourceDir}"
+      srcDirs testSourceDir
       outputDir = file("${jalviewDir}/${testOutputDir}")
     }
 
@@ -411,7 +432,7 @@ eclipse {
         HashMap<String, Boolean> alreadyAddedSrcPath = new HashMap<>();
         cp.entries.each { entry ->
           if (entry.kind == 'src') {
-            if (alreadyAddedSrcPath.getAt(entry.path) || !(entry.path == sourceDir || entry.path == testSourceDir)) {
+            if (alreadyAddedSrcPath.getAt(entry.path) || !(entry.path == bareSourceDir || entry.path == bareTestSourceDir)) {
               removeTheseToo += entry
             } else {
               alreadyAddedSrcPath.putAt(entry.path, true)
@@ -420,11 +441,9 @@ eclipse {
         }
         cp.entries.removeAll(removeTheseToo)
 
-        if (file("${jalviewDir}/${eclipse_bin_dir}/main").isDirectory()) {
-          cp.entries += new Output("${eclipse_bin_dir}/main")
-        }
-        if (file(helpParentDir).isDirectory()) {
-          cp.entries += new Library(fileReference(helpParentDir))
+        cp.entries += new Output("${eclipse_bin_dir}/main")
+        if (file(helpSourceDir).isDirectory()) {
+          cp.entries += new Library(fileReference(helpSourceDir))
         }
         if (file(resourceDir).isDirectory()) {
           cp.entries += new Library(fileReference(resourceDir))
@@ -507,7 +526,7 @@ eclipse {
 
   if (IN_ECLIPSE) {
     // Don't want these to be activated if in headless build
-    //synchronizationTasks "eclipseConfiguration"
+    synchronizationTasks "eclipseSynchronizationTask"
     autoBuildTasks "eclipseAutoBuildTask"
   }
 }
@@ -515,7 +534,7 @@ eclipse {
 
 task cloverInstr() {
   // only instrument source, we build test classes as normal
-  inputs.files files (sourceSets.main.allJava) // , fileTree(dir:"$jalviewDir/$testSourceDir", include: ["**/*.java"]))
+  inputs.files files (sourceSets.main.allJava) // , fileTree(dir: testSourceDir, include: ["**/*.java"]))
   outputs.dir cloverInstrDir
 
   doFirst {
@@ -641,8 +660,8 @@ task setGitVals {
 
 task createBuildProperties(type: WriteProperties) {
   dependsOn setGitVals
-  inputs.dir("${jalviewDir}/${sourceDir}")
-  inputs.dir("${jalviewDir}/${resourceDir}")
+  inputs.dir(sourceDir)
+  inputs.dir(resourceDir)
   file(buildProperties).getParentFile().mkdirs()
   outputFile (buildProperties)
   // taking time specific comment out to allow better incremental builds
@@ -685,7 +704,7 @@ task convertBuildingMD(type: Exec) {
         commandLine pandoc, '-s', '-o', buildingHTML, '--metadata', 'pagetitle="Building Jalview from Source"', '--toc', '-H', css, buildingMD
     } else {
         println("Cannot find pandoc. Skipping convert building.md to HTML")
-        throw new StopExecutionException()
+        throw new StopExecutionException("Cannot find pandoc. Skipping convert building.md to HTML")
     }
   }
 
@@ -706,7 +725,7 @@ clean {
 
 task syncDocs(type: Sync) {
   dependsOn convertBuildingMD
-  def syncDir = "${classes}/${docDir}"
+  def syncDir = "${classesDir}/${docDir}"
   from fileTree("${jalviewDir}/${docDir}")
   into syncDir
 
@@ -714,8 +733,8 @@ task syncDocs(type: Sync) {
 
 
 task copyHelp(type: Copy) {
-  def inputDir = "${jalviewDir}/${helpParentDir}/${helpDir}"
-  def outputDir = "${classes}/${helpDir}"
+  def inputDir = helpSourceDir
+  def outputDir = "${classesDir}/${helpDir}"
   from(inputDir) {
     exclude '**/*.gif'
     exclude '**/*.jpg'
@@ -743,16 +762,16 @@ task copyHelp(type: Copy) {
 
 
 task syncLib(type: Sync) {
-  def syncDir = "${classes}/${libDistDir}"
+  def syncDir = "${classesDir}/${libDistDir}"
   from fileTree("${jalviewDir}/${libDistDir}")
   into syncDir
 }
 
 
 task syncResources(type: Sync) {
-  from "${jalviewDir}/${resourceDir}"
+  from resourceDir
   include "**/*.*"
-  into "${classes}"
+  into "${classesDir}"
   preserve {
     include "**"
   }
@@ -797,13 +816,13 @@ task buildIndices(type: JavaExec) {
   dependsOn copyHelp
   classpath = sourceSets.main.compileClasspath
   main = "com.sun.java.help.search.Indexer"
-  workingDir = "${classes}/${helpDir}"
+  workingDir = "${classesDir}/${helpDir}"
   def argDir = "html"
   args = [ argDir ]
   inputs.dir("${workingDir}/${argDir}")
 
-  outputs.dir("${classes}/doc")
-  outputs.dir("${classes}/help")
+  outputs.dir("${classesDir}/doc")
+  outputs.dir("${classesDir}/help")
   outputs.file("${workingDir}/JavaHelpSearch/DOCS")
   outputs.file("${workingDir}/JavaHelpSearch/DOCS.TAB")
   outputs.file("${workingDir}/JavaHelpSearch/OFFSETS")
@@ -833,8 +852,8 @@ task linkCheck(type: JavaExec) {
   classpath = files("${jalviewDir}/${utilsDir}")
   main = "HelpLinksChecker"
   workingDir = jalviewDir
-  def help = "${classes}/${helpDir}"
-  args = [ "${classes}/${helpDir}", "-nointernet" ]
+  def help = "${classesDir}/${helpDir}"
+  args = [ "${classesDir}/${helpDir}", "-nointernet" ]
 
   def outFOS = new FileOutputStream(helpLinksCheckerOutFile, false) // false == don't append
   def errFOS = outFOS
@@ -845,13 +864,13 @@ task linkCheck(type: JavaExec) {
     outFOS,
     errorOutput)
 
-  inputs.dir("${classes}/${helpDir}")
+  inputs.dir("${classesDir}/${helpDir}")
   outputs.file(helpLinksCheckerOutFile)
 }
 
 // import the pubhtmlhelp target
 ant.properties.basedir = "${jalviewDir}"
-ant.properties.helpBuildDir = "${jalviewDirAbsolutePath}/${classes}/${helpDir}"
+ant.properties.helpBuildDir = "${jalviewDirAbsolutePath}/${classes_dir}/${helpDir}"
 ant.importBuild "${utilsDir}/publishHelp.xml"
 
 
@@ -882,13 +901,13 @@ jar {
   exclude "**/*.jar"
   exclude "**/*.jar.*"
 
-  inputs.dir("${classes}")
+  inputs.dir(classesDir)
   outputs.file("${jalviewDir}/${packageDir}/${archiveName}")
 }
 
 
 task copyJars(type: Copy) {
-  from fileTree(dir: "${classes}", include: "**/*.jar").files
+  from fileTree(dir: classesDir, include: "**/*.jar").files
   into "${jalviewDir}/${packageDir}"
 }
 
@@ -1296,13 +1315,6 @@ task installers(type: com.install4j.gradle.Install4jTask) {
 }
 
 
-clean {
-  doFirst {
-    delete install4jConfFile
-  }
-}
-
-
 task sourceDist (type: Tar) {
   
   def VERSION_UNDERSCORES = JALVIEW_VERSION.replaceAll("\\.", "_")
@@ -1385,8 +1397,8 @@ task helppages  {
   dependsOn copyHelp
   dependsOn pubhtmlhelp
   
-  inputs.dir("${classes}/${helpDir}")
-  outputs.dir("${helpOutputDir}")
+  inputs.dir("${classesDir}/${helpDir}")
+  outputs.dir("${buildDir}/distributions/${helpDir}")
 }
 
 
@@ -1411,16 +1423,17 @@ task jalviewjsSetEclipseWorkspace {
   def eclipseWsDir = propVal
   def props = new Properties()
 
+  def writeProps = true
   if (( eclipseWsDir == null || !file(eclipseWsDir).exists() ) && propsFile.exists()) {
     def ins = new FileInputStream(propsFileName)
     props.load(ins)
     ins.close()
     if (props.getProperty(propKey, null) != null) {
       eclipseWsDir = props.getProperty(propKey)
+      writeProps = false
     }
   }
 
-  def writeProps = false
   if (eclipseWsDir == null || !file(eclipseWsDir).exists()) {
     def tempDir = File.createTempDir()
     eclipseWsDir = tempDir.getAbsolutePath()
@@ -1444,6 +1457,9 @@ task jalviewjsSetEclipseWorkspace {
       props.store(bytes, null)
       def propertiesString = bytes.toString()
       propsFile.text = propertiesString
+      print("NEW ")
+    } else {
+      print("EXISTING ")
     }
 
     println("ECLIPSE WORKSPACE: "+eclipseWorkspace.getPath())
@@ -1451,7 +1467,7 @@ task jalviewjsSetEclipseWorkspace {
 
   //inputs.property(propKey, eclipseWsDir) // eclipseWsDir only gets set once this task runs, so will be out-of-date
   outputs.file(propsFileName)
-  outputs.upToDateWhen { eclipseWorkspace.exists() }
+  outputs.upToDateWhen { eclipseWorkspace.exists() && propsFile.exists() }
 }
 
 
@@ -1597,11 +1613,10 @@ task jalviewjsCreateJ2sSettings(type: WriteProperties) {
   group "JalviewJS"
   description "Create the .j2s file from the j2s.* properties"
 
-  outputFile ("${jalviewDir}/${jalviewjs_j2s_settings}")
-  def j2s_props = project.properties.findAll { it.key.startsWith("j2s.") }.sort { it.key }
+  jalviewjsJ2sProps = project.properties.findAll { it.key.startsWith("j2s.") }.sort { it.key }
   def siteDirProperty = "j2s.site.directory"
   def setSiteDir = false
-  j2s_props.each { prop, val ->
+  jalviewjsJ2sProps.each { prop, val ->
     if (val != null) {
       if (prop == siteDirProperty) {
         if (!(val.startsWith('/') || val.startsWith("file://") )) {
@@ -1612,11 +1627,15 @@ task jalviewjsCreateJ2sSettings(type: WriteProperties) {
       property(prop,val)
     }
     if (!setSiteDir) { // default site location, don't override specifically set property
-      property(siteDirProperty,"${jalviewDir}/${jalviewjsTransferSiteJsDir}")
+      property(siteDirProperty,"${jalviewDirRelativePath}/${jalviewjsTransferSiteJsDir}")
     }
   }
-  inputs.properties(j2s_props)
-  outputs.file(outputFile)
+  outputFile = jalviewjsJ2sSettingsFileName
+
+  if (! IN_ECLIPSE) {
+    inputs.properties(jalviewjsJ2sProps)
+    outputs.file(jalviewjsJ2sSettingsFileName)
+  }
 }
 
 
@@ -1649,7 +1668,7 @@ task jalviewjsSyncAllLibs (type: Sync) {
 
 
 task jalviewjsSyncResources (type: Sync) {
-  def inputFiles = fileTree(dir: "${jalviewDir}/${resourceDir}")
+  def inputFiles = fileTree(dir: resourceDir)
   def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
 
   from inputFiles
@@ -1820,14 +1839,14 @@ DEBUG: ${eclipseDebug}
 }
 
 
-def jalviewjsCallCore(FileCollection list, String prefixFile, String suffixFile, String jsfile, String zjsfile, File logOutFile, Boolean logOutConsole) {
+def jalviewjsCallCore(String name, 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}"
+  msg = "Creating core for ${name}...\nGenerating ${jsfile}"
   println(msg)
   logOutFile.createNewFile()
   logOutFile.append(msg+"\n")
@@ -1841,8 +1860,7 @@ def jalviewjsCallCore(FileCollection list, String prefixFile, String suffixFile,
     f ->
     if (f.exists()) {
       def t = f.text
-      t.replaceAll("Clazz\\.","Clazz_")
-      t.replaceAll("Class__","Clazz._")
+      t.replaceAll("Clazz\\.([^_])","Clazz_${1}")
       coreFile.append( t )
     } else {
       msg = "...file '"+f.getPath()+"' does not exist, skipping"
@@ -1861,6 +1879,7 @@ def jalviewjsCallCore(FileCollection list, String prefixFile, String suffixFile,
   javaexec {
     classpath = files(["${jalviewDir}/tools/closure_compiler.jar"])
     args = [ "--js", jsfile, "--js_output_file", zjsfile ]
+    maxHeapSize = "2g"
 
     msg = "\nRunning '"+commandLine.join(' ')+"'\n"
     println(msg)
@@ -1899,6 +1918,8 @@ task jalviewjsBuildAllCores {
   dependsOn jalviewjsTransferUnzipSwingJs
 
   def j2sDir = "${jalviewDir}/${jalviewjsTransferSiteJsDir}/${jalviewjs_j2s_subdir}"
+  def swingJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}/${jalviewjs_j2s_subdir}"
+  def libJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteLibDir}/${jalviewjs_j2s_subdir}"
   def jsDir = "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}/${jalviewjs_js_subdir}"
   def outputDir = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}/${jalviewjs_j2s_subdir}/core"
   def prefixFile = "${jsDir}/core/coretop2.js"
@@ -1919,10 +1940,10 @@ task jalviewjsBuildAllCores {
   }
 
   // _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_jmol}"), 'name': "_jvjmol" ]
   classlistFiles += [ 'file': file("${jalviewDir}/${jalviewjs_classlist_jalview}"), 'name': jalviewjsJalviewCoreName ]
 
-  def classlists = []
+  jalviewjsCoreClasslists = []
 
   classlistFiles.each {
     hash ->
@@ -1947,10 +1968,11 @@ task jalviewjsBuildAllCores {
     def jsfile = "${outputDir}/core${name}.js"
     def zjsfile = "${outputDir}/core${name}.z.js"
 
-    classlists += [
-    'jsfile': jsfile,
-    'zjsfile': zjsfile,
-    'list': list
+    jalviewjsCoreClasslists += [
+      'jsfile': jsfile,
+      'zjsfile': zjsfile,
+      'list': list,
+      'name': name
     ]
 
     inputs.file(file)
@@ -1960,74 +1982,117 @@ task jalviewjsBuildAllCores {
   }
   
   // _stevesoft core. add any cores without a classlist here (and the inputs and outputs)
+  def stevesoftClasslistName = "_stevesoft"
   def stevesoftClasslist = [
-    'jsfile': "${outputDir}/core_stevesoft.js",
-    'zjsfile': "${outputDir}/core_stevesoft.z.js",
-    'list': fileTree(dir: j2sDir, include: "com/stevesoft/pat/**/*.js")
+    'jsfile': "${outputDir}/core${stevesoftClasslistName}.js",
+    'zjsfile': "${outputDir}/core${stevesoftClasslistName}.z.js",
+    'list': fileTree(dir: j2sDir, include: "com/stevesoft/pat/**/*.js"),
+    'name': stevesoftClasslistName
   ]
-  classlists += stevesoftClasslist
+  jalviewjsCoreClasslists += stevesoftClasslist
   inputs.files(stevesoftClasslist['list'])
   outputs.file(stevesoftClasslist['jsfile'])
   outputs.file(stevesoftClasslist['zjsfile'])
 
+  // _all core
+  def allClasslistName = "_all"
+  def allJsFiles = fileTree(dir: j2sDir, include: "**/*.js")
+  allJsFiles += fileTree(
+    dir: libJ2sDir,
+    include: "**/*.js",
+    excludes: [
+      // these exlusions are files that the closure-compiler produces errors for. Should fix them
+      "**/org/jmol/jvxl/readers/IsoIntersectFileReader.js",
+      "**/org/jmol/export/JSExporter.js"
+    ]
+  )
+  allJsFiles += fileTree(
+    dir: swingJ2sDir,
+    include: "**/*.js",
+    excludes: [
+      // these exlusions are files that the closure-compiler produces errors for. Should fix them
+      "**/sun/misc/Unsafe.js",
+      "**/swingjs/jquery/jquery-editable-select.js",
+      "**/swingjs/jquery/j2sComboBox.js",
+      "**/sun/misc/FloatingDecimal.js"
+    ]
+  )
+  def allClasslist = [
+    'jsfile': "${outputDir}/core${allClasslistName}.js",
+    'zjsfile': "${outputDir}/core${allClasslistName}.z.js",
+    'list': allJsFiles,
+    'name': allClasslistName
+  ]
+  jalviewjsCoreClasslists += allClasslist
+  inputs.files(allClasslist['list'])
+  outputs.file(allClasslist['jsfile'])
+  outputs.file(allClasslist['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")+" jalviewjsBuildAllCores\n----\n")
 
-    classlists.each {
-      jalviewjsCallCore(it.list, prefixFile, suffixFile, it.jsfile, it.zjsfile, logOutFile, jalviewjs_j2s_to_console.equals("true"))
+    jalviewjsCoreClasslists.each {
+      jalviewjsCallCore(it.name, it.list, prefixFile, suffixFile, it.jsfile, it.zjsfile, logOutFile, jalviewjs_j2s_to_console.equals("true"))
     }
   }
 
 }
 
 
-task jalviewjsPublishCoreTemplate(type: Sync) {
-  dependsOn jalviewjsBuildAllCores
+def jalviewjsPublishCoreTemplate(String coreName, String templateName, File inputFile, String outputFile) {
+  copy {
+    from inputFile
+    into file(outputFile).getParentFile()
+    rename { filename ->
+      if (filename.equals(inputFile.getName())) {
+        return file(outputFile).getName()
+      }
+      return null
+    }
+    filter(ReplaceTokens,
+      beginToken: '_',
+      endToken: '_',
+      tokens: [
+        'MAIN': '"'+mainClass+'"',
+        'CODE': "null",
+        'NAME': jalviewjsJalviewTemplateName+" [core ${coreName}]",
+        'COREKEY': jalviewjs_core_key,
+        'CORENAME': coreName
+      ]
+    )
+  }
+}
+
 
-  def inputFile = file("${jalviewDir}/${j2s_template_html}")
+task jalviewjsPublishCoreTemplates {
+  dependsOn jalviewjsBuildAllCores
+  def inputFileName = "${jalviewDir}/${j2s_coretemplate_html}"
+  def inputFile = file(inputFileName)
   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 "**"
+  jalviewjsCoreClasslists.each { cl ->
+    def outputFile = "${outputDir}/${jalviewjsJalviewTemplateName}_${cl.name}.html"
+    cl['outputfile'] = outputFile
+    outputFiles += outputFile
   }
-  outputs.files outputFiles
-  inputs.files inputFile
+
+  doFirst {
+    jalviewjsCoreClasslists.each { cl ->
+      jalviewjsPublishCoreTemplate(cl.name, jalviewjsJalviewTemplateName, inputFile, cl.outputfile)
+    }
+  }
+  inputs.file(inputFile)
+  outputs.files(outputFiles)
 }
 
 
 task jalviewjsSyncCore (type: Sync) {
   dependsOn jalviewjsBuildAllCores
-  dependsOn jalviewjsPublishCoreTemplate
+  dependsOn jalviewjsPublishCoreTemplates
   def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteCoreDir}")
   def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
 
@@ -2138,30 +2203,35 @@ task jalviewjsServer {
     def start = port
     def running = false
     def url
-    def urlcore
+    def jalviewjsServer
     while(port < start+1000 && !running) {
       try {
         def doc_root = new File("${jalviewDirAbsolutePath}/${jalviewjsSiteDir}")
-        def jalviewjsServer = factory.start(doc_root, port)
+        jalviewjsServer = factory.start(doc_root, port)
         running = true
         url = jalviewjsServer.getResourceUrl(jalviewjs_server_resource)
-        urlcore = jalviewjsServer.getResourceUrl(jalviewjsJalviewCoreHtmlFile)
         println("SERVER STARTED with document root ${doc_root}.")
         println("Go to "+url+" . Run  gradle --stop  to stop (kills all gradle daemons).")
         println("For debug: "+url+"?j2sdebug")
-        println("For core: "+urlcore)
-
-        file(htmlFile).text = """
-        <p><a href="${url}">JalviewJS Test. &lt;${url}&gt;</a></p>
-        <p><a href="${url}?j2sdebug">JalviewJS Test with debug. &lt;${url}?j2sdebug&lt;</a></p>
-        <p><a href="${urlcore}">${jalviewjsJalviewTemplateName} Core Test. &lt;${urlcore}&gt;</a></p>
-        """
-
+        println("For verbose: "+url+"?j2sverbose")
       } catch (Exception e) {
         port++;
       }
     }
+    def htmlText = """
+      <p><a href="${url}">JalviewJS Test. &lt;${url}&gt;</a></p>
+      <p><a href="${url}?j2sdebug">JalviewJS Test with debug. &lt;${url}?j2sdebug&gt;</a></p>
+      <p><a href="${url}?j2sverbose">JalviewJS Test with verbose. &lt;${url}?j2sdebug&gt;</a></p>
+      """
+    jalviewjsCoreClasslists.each { cl ->
+      def urlcore = jalviewjsServer.getResourceUrl(file(cl.outputfile).getName())
+      htmlText += """
+      <p><a href="${urlcore}">${jalviewjsJalviewTemplateName} [core ${cl.name}]. &lt;${urlcore}&gt;</a></p>
+      """
+      println("For core ${cl.name}: "+urlcore)
+    }
 
+    file(htmlFile).text = htmlText
   }
 
   outputs.file(htmlFile)
@@ -2188,6 +2258,43 @@ task cleanJalviewjsAll {
 }
 
 
+task jalviewjsIDE_checkJ2sPlugin {
+  group "00 JalviewJS in Eclipse"
+  description "Compare the swingjs/net.sf.j2s.core.jar file with the Eclipse pluing version"
+
+  doFirst {
+    def j2sPlugin = string("${jalviewDir}/${jalviewjs_j2s_plugin}")
+    def j2sPluginFile = file(j2sPlugin)
+    def eclipseHome = System.properties["eclipse.home.location"]
+    if (eclipseHome == null || ! IN_ECLIPSE) {
+      throw new StopExecutionException("Cannot find running Eclipse home from System.properties['eclipse.home.location']. Skipping J2S Plugin Check.")
+    }
+    def eclipseJ2sPlugin = "${eclipseHome}/dropins/${j2sPluginFile.getName()}"
+    def eclipseJ2sPluginFile = file(eclipseJ2sPlugin)
+    if (!eclipseJ2sPluginFile.exists()) {
+      def msg = "Eclipse J2S Plugin is not installed"
+      println(msg)
+      throw new GradleException(msg)
+    }
+
+    def digest = MessageDigest.getInstance("MD5")
+
+    digest.update(j2sPluginFile.text.bytes)
+    def j2sPluginMd5 = new BigInteger(1, digest.digest()).toString(16).padLeft(32, '0')
+
+    digest.update(eclipseJ2sPluginFile.text.bytes)
+    def eclipseJ2sPluginMd5 = new BigInteger(1, digest.digest()).toString(16).padLeft(32, '0')
+     
+    if (j2sPluginMd5 != eclipseJ2sPluginMd5) {
+      def msg = "Eclipse J2S Plugin is different to '${j2sPlugin}'"
+      println(msg)
+      throw new GradleException(msg)
+    }
+
+    println("Eclipse J2S Plugin is same as '${j2sPlugin}'")
+  }
+}
+
 
 task jalviewjsIDE_j2sFile {
   group "00 JalviewJS in Eclipse"
@@ -2235,8 +2342,8 @@ task jalviewjsIDE_Server {
 
 
 // buildship runs this at import
-task eclipseConfiguration {
-  dependsOn eclipseSetup
+task eclipseSynchronizationTask {
+  //dependsOn eclipseSetup
   dependsOn jalviewjsIDE_j2sFile
 }