JAL-3210 multiple core templates. work in progress

diff --git a/build.gradle b/build.gradle
index ec665dc..fc4d9ca 100644 (file)
--- a/build.gradle
+++ b/build.gradle
@@ -293,6 +293,8 @@ ext {
   jalviewjsTransferSiteCoreDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_core")
   jalviewjsJalviewCoreHtmlFile = string("")
   jalviewjsJalviewCoreName = string(jalviewjs_core_name)
+  jalviewjsDefaultCoreName = string(jalviewjs_default_core)
+  jalviewjsCoreClasslists = []
   jalviewjsJalviewTemplateName = string(jalviewjs_name)
 
   eclipseWorkspace = null
@@ -1296,13 +1298,6 @@ task installers(type: com.install4j.gradle.Install4jTask) {
 }
 
 
-clean {
-  doFirst {
-    delete install4jConfFile
-  }
-}
-
-
 task sourceDist (type: Tar) {
   
   def VERSION_UNDERSCORES = JALVIEW_VERSION.replaceAll("\\.", "_")
@@ -1820,14 +1815,14 @@ 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 ${jsfile}"
   println(msg)
   logOutFile.createNewFile()
   logOutFile.append(msg+"\n")
@@ -1841,8 +1836,7 @@ def jalviewjsCallCore(FileCollection list, String prefixFile, String suffixFile,
     f ->
     if (f.exists()) {
       def t = f.text
-      t.replaceAll("Clazz\\.","Clazz_")
-      t.replaceAll("Class__","Clazz._")
+      t.replaceAll("Clazz\\.([^_])","Clazz_${1}")
       coreFile.append( t )
     } else {
       msg = "...file '"+f.getPath()+"' does not exist, skipping"
@@ -1922,7 +1916,7 @@ task jalviewjsBuildAllCores {
   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 +1941,11 @@ 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 +1955,96 @@ 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 allClasslist = [
+    'jsfile': "${outputDir}/core${allClasslistName}.js",
+    'zjsfile': "${outputDir}/core${allClasslistName}.z.js",
+    'list': fileTree(dir: j2sDir, include: "**/*.js"),
+    '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 
+  jalviewjsCoreClasslists.each { cl ->
+    def outputFile = "${outputDir}/${jalviewjsJalviewTemplateName}_${cl.name}.html"
+    cl['outputfile'] = outputFile
+    outputFiles += outputFile
+  }
+
+  doFirst {
+    jalviewjsCoreClasslists.each { cl ->
+      jalviewjsPublishCoreTemplate(cl.name, jalviewjsJalviewTemplateName, inputFile, cl.outputfile)
     }
-    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
+  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}"
 
@@ -2138,26 +2155,32 @@ 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 = """
+        htmlText = """
         <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;${urlcore}&gt;</a></p>
         """
+        jalviewjsCoreClasslists.each { cl ->
+          urlcore = jalviewjsServer.getResourceUrl(file(cl.outputfile).getName())
+          htmlText += """
+          <p><a href="${urlcore}">${jalviewjsJalviewTemplateName} [core ${cl.name}]. &lt;${urlcore}&gt;</a></p>
+          """
+        }
+
+        file(htmlFile).text = htmlText
 
       } catch (Exception e) {
+        e.printStackTrace()
         port++;
       }
     }

diff --git a/gradle.properties b/gradle.properties
index e4ee8b9..aaf403d 100644 (file)
--- a/gradle.properties
+++ b/gradle.properties
@@ -173,8 +173,10 @@ jalviewjs_eclipse_build_arg = cleanBuild
 jalviewjs_server_port = 9001
 jalviewjs_server_wait = 30
 jalviewjs_server_resource = /jalview_bin_Jalview.html
-jalviewjs_core_name = _jalview
+jalviewjs_core_name = _all
 jalviewjs_name = JalviewJS
+#jalviewjs_core_key = core
+jalviewjs_core_key = preloadCore
 jalviewjs_default_core = all
 
 j2s.compiler.status = enable
@@ -191,7 +193,7 @@ 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
+j2s_coretemplate_html = utils/jalviewjs/coretemplate.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

diff --git a/utils/jalviewjs/classlists/all.txt b/utils/jalviewjs/classlists/all.txt
deleted file mode 100644 (file)
index 8838142..0000000
--- a/utils/jalviewjs/classlists/all.txt
+++ /dev/null
@@ -1,4754 +0,0 @@
-ext/edu/ucsf/rbvi/strucviz2/ChimUtils.js
-ext/edu/ucsf/rbvi/strucviz2/ChimeraStructuralObject.js
-ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.js
-ext/edu/ucsf/rbvi/strucviz2/ChimeraResidue.js
-ext/edu/ucsf/rbvi/strucviz2/ChimeraTreeModel.js
-ext/edu/ucsf/rbvi/strucviz2/port/ListenerThreads.js
-ext/edu/ucsf/rbvi/strucviz2/ChimeraChain.js
-ext/edu/ucsf/rbvi/strucviz2/StructureManager.js
-ext/edu/ucsf/rbvi/strucviz2/ChimeraModel.js
-ext/edu/ucsf/rbvi/strucviz2/StructureSettings.js
-ext/vamsas/SeqSearchServiceSoapBindingStub.js
-ext/vamsas/MuscleWSSoapBindingStub.js
-ext/vamsas/SeqSearchI.js
-ext/vamsas/ServiceHandles.js
-ext/vamsas/MuscleWSService.js
-ext/vamsas/JpredSoapBindingStub.js
-ext/vamsas/IRegistryService.js
-ext/vamsas/IRegistryServiceLocator.js
-ext/vamsas/RegistryServiceSoapBindingStub.js
-ext/vamsas/MuscleWS.js
-ext/vamsas/JpredService.js
-ext/vamsas/ServiceHandle.js
-ext/vamsas/Jpred.js
-ext/vamsas/JpredServiceLocator.js
-ext/vamsas/SeqSearchServiceService.js
-ext/vamsas/SeqSearchServiceLocator.js
-ext/vamsas/IRegistry.js
-ext/vamsas/MuscleWSServiceLocator.js
-intervalstore/impl/BinarySearcher.js
-intervalstore/impl/NCList.js
-intervalstore/impl/NCNode.js
-intervalstore/impl/IntervalStore.js
-intervalstore/impl/Range.js
-intervalstore/impl/NCListBuilder.js
-intervalstore/api/IntervalStoreI.js
-intervalstore/api/IntervalI.js
-gnu/jpdf/PDFPrinterJob.js
-gnu/jpdf/TestMenuBar.js
-gnu/jpdf/PDFPage.js
-gnu/jpdf/PDFObject.js
-gnu/jpdf/TestPanel.js
-gnu/jpdf/StringTooLongException.js
-gnu/jpdf/PDFJob.js
-gnu/jpdf/BoundingBox.js
-gnu/jpdf/PDFXref.js
-gnu/jpdf/PDFGraphics.js
-gnu/jpdf/PDFTest.js
-gnu/jpdf/HelpFrame.js
-gnu/jpdf/PDFDocument.js
-gnu/jpdf/PDFInfo.js
-gnu/jpdf/PDFAnnot.js
-gnu/jpdf/PDFOutline.js
-gnu/jpdf/PDFStringHelper.js
-gnu/jpdf/PDFOutput.js
-gnu/jpdf/PDFFont.js
-gnu/jpdf/PDFPageList.js
-gnu/jpdf/PDFStream.js
-gnu/jpdf/PDFBorder.js
-gnu/jpdf/PDFImage.js
-gnu/jpdf/PDFCatalog.js
-java/applet/AppletStub.js
-java/applet/JSApplet.js
-java/applet/AppletContext.js
-java/applet/Applet.js
-java/applet/AudioClip.js
-java/security/Identity.js
-java/security/BasicPermission.js
-java/security/KeyException.js
-java/security/KeyRep.js
-java/security/Guard.js
-java/security/CodeSource.js
-java/security/PolicySpi.js
-java/security/PermissionCollection.js
-java/security/KeyStoreException.js
-java/security/interfaces/ECPrivateKey.js
-java/security/interfaces/DSAPrivateKey.js
-java/security/interfaces/RSAPrivateCrtKey.js
-java/security/interfaces/DSAParams.js
-java/security/interfaces/RSAPublicKey.js
-java/security/interfaces/DSAKeyPairGenerator.js
-java/security/interfaces/DSAPublicKey.js
-java/security/interfaces/RSAPrivateKey.js
-java/security/interfaces/ECKey.js
-java/security/interfaces/RSAKey.js
-java/security/interfaces/DSAKey.js
-java/security/interfaces/ECPublicKey.js
-java/security/interfaces/RSAMultiPrimePrivateCrtKey.js
-java/security/KeyPairGenerator.js
-java/security/AlgorithmParameterGeneratorSpi.js
-java/security/SecureRandom.js
-java/security/NoSuchAlgorithmException.js
-java/security/AccessControlException.js
-java/security/ProviderException.js
-java/security/SecureClassLoader.js
-java/security/InvalidAlgorithmParameterException.js
-java/security/AuthProvider.js
-java/security/Provider.js
-java/security/KeyPair.js
-java/security/KeyManagementException.js
-java/security/PrivilegedExceptionAction.js
-java/security/Certificate.js
-java/security/acl/NotOwnerException.js
-java/security/acl/LastOwnerException.js
-java/security/acl/Acl.js
-java/security/acl/AclNotFoundException.js
-java/security/acl/Permission.js
-java/security/acl/Group.js
-java/security/acl/AclEntry.js
-java/security/acl/Owner.js
-java/security/AccessController.js
-java/security/Key.js
-java/security/SecureRandomSpi.js
-java/security/NoSuchProviderException.js
-java/security/DigestException.js
-java/security/PermissionsHash.js
-java/security/URIParameter.js
-java/security/DomainCombiner.js
-java/security/ProtectionDomain.js
-java/security/Security.js
-java/security/CodeSigner.js
-java/security/AlgorithmParametersSpi.js
-java/security/Timestamp.js
-java/security/KeyFactorySpi.js
-java/security/DomainLoadStoreParameter.js
-java/security/AllPermissionCollection.js
-java/security/MessageDigest.js
-java/security/CryptoPrimitive.js
-java/security/InvalidParameterException.js
-java/security/GuardedObject.js
-java/security/AlgorithmConstraints.js
-java/security/SignatureException.js
-java/security/Principal.js
-java/security/IdentityScope.js
-java/security/KeyStoreSpi.js
-java/security/UnrecoverableKeyException.js
-java/security/PrivilegedActionException.js
-java/security/Signature.js
-java/security/GeneralSecurityException.js
-java/security/spec/RSAOtherPrimeInfo.js
-java/security/spec/RSAKeyGenParameterSpec.js
-java/security/spec/InvalidParameterSpecException.js
-java/security/spec/ECParameterSpec.js
-java/security/spec/RSAPrivateKeySpec.js
-java/security/spec/DSAPrivateKeySpec.js
-java/security/spec/ECGenParameterSpec.js
-java/security/spec/ECPublicKeySpec.js
-java/security/spec/RSAMultiPrimePrivateCrtKeySpec.js
-java/security/spec/RSAPrivateCrtKeySpec.js
-java/security/spec/ECFieldFp.js
-java/security/spec/RSAPublicKeySpec.js
-java/security/spec/EncodedKeySpec.js
-java/security/spec/ECField.js
-java/security/spec/ECPoint.js
-java/security/spec/ECPrivateKeySpec.js
-java/security/spec/DSAGenParameterSpec.js
-java/security/spec/InvalidKeySpecException.js
-java/security/spec/DSAParameterSpec.js
-java/security/spec/EllipticCurve.js
-java/security/spec/PKCS8EncodedKeySpec.js
-java/security/spec/PSSParameterSpec.js
-java/security/spec/KeySpec.js
-java/security/spec/MGF1ParameterSpec.js
-java/security/spec/DSAPublicKeySpec.js
-java/security/spec/X509EncodedKeySpec.js
-java/security/spec/ECFieldF2m.js
-java/security/spec/AlgorithmParameterSpec.js
-java/security/SignatureSpi.js
-java/security/InvalidKeyException.js
-java/security/UnrecoverableEntryException.js
-java/security/UnresolvedPermission.js
-java/security/DigestInputStream.js
-java/security/cert/CertStore.js
-java/security/cert/CRLException.js
-java/security/cert/CertPathValidatorException.js
-java/security/cert/CertificateEncodingException.js
-java/security/cert/PKIXRevocationChecker.js
-java/security/cert/CertPathValidatorSpi.js
-java/security/cert/TrustAnchor.js
-java/security/cert/CertPathBuilder.js
-java/security/cert/CertificateFactory.js
-java/security/cert/Certificate.js
-java/security/cert/CertPathBuilderSpi.js
-java/security/cert/X509CertSelector.js
-java/security/cert/CertPathBuilderResult.js
-java/security/cert/X509Extension.js
-java/security/cert/CertSelector.js
-java/security/cert/CertificateExpiredException.js
-java/security/cert/CertPathChecker.js
-java/security/cert/X509CRLEntry.js
-java/security/cert/Extension.js
-java/security/cert/CertPathValidator.js
-java/security/cert/PKIXBuilderParameters.js
-java/security/cert/PKIXCertPathBuilderResult.js
-java/security/cert/CertStoreSpi.js
-java/security/cert/X509CRLSelector.js
-java/security/cert/CertificateFactorySpi.js
-java/security/cert/X509CRL.js
-java/security/cert/PKIXCertPathValidatorResult.js
-java/security/cert/CertStoreParameters.js
-java/security/cert/LDAPCertStoreParameters.js
-java/security/cert/PolicyQualifierInfo.js
-java/security/cert/X509Certificate.js
-java/security/cert/CertificateNotYetValidException.js
-java/security/cert/PKIXCertPathChecker.js
-java/security/cert/PolicyNode.js
-java/security/cert/CertificateException.js
-java/security/cert/CRLReason.js
-java/security/cert/CollectionCertStoreParameters.js
-java/security/cert/CRL.js
-java/security/cert/CertificateParsingException.js
-java/security/cert/CertPathBuilderException.js
-java/security/cert/PKIXReason.js
-java/security/cert/CertPathHelperImpl.js
-java/security/cert/CertPathParameters.js
-java/security/cert/CRLSelector.js
-java/security/cert/CertPathValidatorResult.js
-java/security/cert/CertStoreException.js
-java/security/cert/CertPath.js
-java/security/cert/CertificateRevokedException.js
-java/security/cert/PKIXParameters.js
-java/security/PrivilegedAction.js
-java/security/Permission.js
-java/security/AccessControlContext.js
-java/security/AlgorithmParameterGenerator.js
-java/security/PKCS12Attribute.js
-java/security/MessageDigestSpi.js
-java/security/UnresolvedPermissionCollection.js
-java/security/KeyStore.js
-java/security/PrivateKey.js
-java/security/DigestOutputStream.js
-java/security/Permissions.js
-java/security/PublicKey.js
-java/security/BasicPermissionCollection.js
-java/security/Policy.js
-java/security/SecurityPermission.js
-java/security/PermissionsEnumerator.js
-java/security/AlgorithmParameters.js
-java/security/Signer.js
-java/security/KeyPairGeneratorSpi.js
-java/security/SignedObject.js
-java/security/AllPermission.js
-java/security/KeyFactory.js
-java/beans/PropertyChangeListener.js
-java/beans/VetoableChangeListenerProxy.js
-java/beans/PropertyChangeEvent.js
-java/beans/FeatureDescriptor.js
-java/beans/PropertyChangeListenerProxy.js
-java/beans/PropertyEditor.js
-java/beans/VetoableChangeListener.js
-java/beans/PropertyVetoException.js
-java/beans/PropertyChangeSupport.js
-java/beans/VetoableChangeSupport.js
-java/beans/PropertyDescriptor.js
-java/beans/ChangeListenerMap.js
-java/beans/PropertyEditorSupport.js
-java/beans/IndexedPropertyChangeEvent.js
-java/beans/IntrospectionException.js
-java/util/Vector.js
-java/util/HashSet.js
-java/util/JumboEnumSet.js
-java/util/HashMap.js
-java/util/IllformedLocaleException.js
-java/util/BitSet.js
-java/util/RandomAccessSubList.js
-java/util/Set.js
-java/util/UnknownFormatConversionException.js
-java/util/NavigableMap.js
-java/util/List.js
-java/util/Enumeration.js
-java/util/FormatterClosedException.js
-java/util/IllegalFormatConversionException.js
-java/util/LinkedHashSet.js
-java/util/AbstractCollection.js
-java/util/Observer.js
-java/util/Optional.js
-java/util/TimerTask.js
-java/util/GregorianCalendar.js
-java/util/RegularEnumSet.js
-java/util/Objects.js
-java/util/DualPivotQuicksort.js
-java/util/concurrent/TimeoutException.js
-java/util/concurrent/CompletionService.js
-java/util/concurrent/SynchronousQueue.js
-java/util/concurrent/ConcurrentSkipListMap.js
-java/util/concurrent/LinkedBlockingDeque.js
-java/util/concurrent/RunnableScheduledFuture.js
-java/util/concurrent/DelayQueue.js
-java/util/concurrent/ConcurrentSkipListSet.js
-java/util/concurrent/ConcurrentHashMap.js
-java/util/concurrent/CopyOnWriteArraySet.js
-java/util/concurrent/ThreadFactory.js
-java/util/concurrent/Executor.js
-java/util/concurrent/ThreadPoolExecutor.js
-java/util/concurrent/RunnableFuture.js
-java/util/concurrent/Delayed.js
-java/util/concurrent/RecursiveTask.js
-java/util/concurrent/RejectedExecutionException.js
-java/util/concurrent/CompletionStage.js
-java/util/concurrent/CompletionException.js
-java/util/concurrent/ExecutorService.js
-java/util/concurrent/Phaser.js
-java/util/concurrent/ArrayBlockingQueue.js
-java/util/concurrent/ConcurrentMap.js
-java/util/concurrent/locks/AbstractOwnableSynchronizer.js
-java/util/concurrent/locks/LockSupport.js
-java/util/concurrent/locks/AbstractQueuedLongSynchronizer.js
-java/util/concurrent/locks/Lock.js
-java/util/concurrent/locks/ReentrantReadWriteLock.js
-java/util/concurrent/locks/AbstractQueuedSynchronizer.js
-java/util/concurrent/locks/ReentrantLock.js
-java/util/concurrent/locks/ReadWriteLock.js
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-javax/swing/plaf/MenuItemUI.js
-javax/swing/plaf/MenuBarUI.js
-javax/swing/plaf/ComponentInputMapUIResource.js
-javax/swing/plaf/UIResource.js
-javax/swing/plaf/ToolBarUI.js
-javax/swing/plaf/SplitPaneUI.js
-javax/swing/plaf/DesktopIconUI.js
-javax/swing/plaf/DialogUI.js
-javax/swing/plaf/ProgressBarUI.js
-javax/swing/plaf/PopupMenuUI.js
-javax/swing/plaf/basic/BasicGraphicsUtils.js
-javax/swing/plaf/basic/BasicBorders.js
-javax/swing/plaf/WindowUI.js
-javax/swing/plaf/FrameUI.js
-javax/swing/plaf/InsetsUIResource.js
-javax/swing/plaf/RootPaneUI.js
-javax/swing/plaf/LayeredPaneUI.js
-javax/swing/plaf/TextUI.js
-javax/swing/plaf/ActionMapUIResource.js
-javax/swing/plaf/FontUIResource.js
-javax/swing/plaf/BorderUIResource.js
-javax/swing/plaf/MenuUI.js
-javax/swing/plaf/SeparatorUI.js
-javax/swing/plaf/PanelUI.js
-javax/swing/plaf/InputMapUIResource.js
-javax/swing/JColorChooser.js
-javax/swing/JTabbedPane.js
-javax/swing/DefaultRowSorter.js
-javax/swing/SpinnerListModel.js
-javax/swing/JSpinner.js
-javax/swing/Autoscroller.js
-javax/swing/JSeparator.js
-javax/swing/SizeRequirements.js
-javax/swing/ButtonModel.js
-javax/swing/ColorChooserDialog.js
-javax/swing/SwingHeavyWeight.js
-javax/swing/JRadioButtonMenuItem.js
-javax/swing/AbstractCellEditor.js
-javax/swing/BoxLayout.js
-javax/swing/Icon.js
-javax/swing/JWindow.js
-javax/swing/JRadioButton.js
-javax/swing/SwingPaintEventDispatcher.js
-javax/swing/JRootPane.js
-javax/swing/ComboBoxModel.js
-javax/swing/LayoutComparator.js
-javax/swing/MutableComboBoxModel.js
-javax/swing/SortingFocusTraversalPolicy.js
-javax/swing/InputMap.js
-javax/swing/ListCellRenderer.js
-javax/swing/DefaultSingleSelectionModel.js
-javax/swing/JApplet.js
-javax/swing/AncestorNotifier.js
-javax/swing/JToolBar.js
-javax/swing/JLabel.js
-javax/swing/KeyStroke.js
-javax/swing/ScrollPaneLayout.js
-javax/swing/JButton.js
-javax/swing/GraphicsWrapper.js
-javax/swing/SingleSelectionModel.js
-javax/swing/RowSorter.js
-javax/swing/DefaultListCellRenderer.js
-javax/swing/LayoutFocusTraversalPolicy.js
-javax/swing/MenuElement.js
-javax/swing/ColorTracker.js
-javax/swing/JComboBox.js
-javax/swing/JTextPane.js
-javax/swing/WindowConstants.js
-javax/swing/filechooser/FileNameExtensionFilter.js
-javax/swing/filechooser/FileFilter.js
-javax/swing/filechooser/FileView.js
-javax/swing/ComboBoxEditor.js
-javax/swing/JEditorPane.js
-javax/swing/SwingContainerOrderFocusTraversalPolicy.js
-javax/swing/ImageIcon.js
-javax/swing/JDialog.js
-javax/swing/TimerQueue.js
-javax/swing/UIManager.js
-javax/swing/ProgressMonitor.js
-javax/swing/ComponentInputMap.js
-javax/swing/DefaultComboBoxModel.js
-javax/swing/event/TreeModelListener.js
-javax/swing/event/DocumentListener.js
-javax/swing/event/UndoableEditListener.js
-javax/swing/event/ListSelectionListener.js
-javax/swing/event/MenuKeyListener.js
-javax/swing/event/UndoableEditEvent.js
-javax/swing/event/SwingPropertyChangeSupport.js
-javax/swing/event/MenuDragMouseListener.js
-javax/swing/event/CaretEvent.js
-javax/swing/event/AncestorListener.js
-javax/swing/event/TableModelEvent.js
-javax/swing/event/RowSorterListener.js
-javax/swing/event/CaretListener.js
-javax/swing/event/EventListenerList.js
-javax/swing/event/InternalFrameAdapter.js
-javax/swing/event/ListDataListener.js
-javax/swing/event/ListDataEvent.js
-javax/swing/event/MenuKeyEvent.js
-javax/swing/event/PopupMenuEvent.js
-javax/swing/event/TreeExpansionListener.js
-javax/swing/event/RowSorterEvent.js
-javax/swing/event/DocumentEvent.js
-javax/swing/event/ListSelectionEvent.js
-javax/swing/event/TreeSelectionListener.js
-javax/swing/event/MenuDragMouseEvent.js
-javax/swing/event/InternalFrameListener.js
-javax/swing/event/ChangeEvent.js
-javax/swing/event/HyperlinkListener.js
-javax/swing/event/TableColumnModelEvent.js
-javax/swing/event/AncestorEvent.js
-javax/swing/event/MouseInputAdapter.js
-javax/swing/event/TreeExpansionEvent.js
-javax/swing/event/MenuEvent.js
-javax/swing/event/TreeSelectionEvent.js
-javax/swing/event/InternalFrameEvent.js
-javax/swing/event/HyperlinkEvent.js
-javax/swing/event/MouseInputListener.js
-javax/swing/event/ChangeListener.js
-javax/swing/event/TableColumnModelListener.js
-javax/swing/event/TreeWillExpandListener.js
-javax/swing/event/MenuListener.js
-javax/swing/event/PopupMenuListener.js
-javax/swing/event/TreeModelEvent.js
-javax/swing/event/CellEditorListener.js
-javax/swing/event/TableModelListener.js
-javax/swing/ActionPropertyChangeListener.js
-javax/swing/CellRendererPane.js
-javax/swing/UIDefaults.js
-javax/swing/DefaultDesktopManager.js
-javax/swing/RootPaneContainer.js
-javax/swing/JMenu.js
-javax/swing/LayoutStyle.js
-javax/swing/AbstractListModel.js
-javax/swing/ViewportLayout.js
-javax/swing/FocusManager.js
-javax/swing/DefaultCellEditor.js
-javax/swing/JTable.js
-javax/swing/ClientPropertyKey.js
-javax/swing/text/GlyphPainter2.js
-javax/swing/text/BoxView.js
-javax/swing/text/StyleConstants.js
-javax/swing/text/FlowView.js
-javax/swing/text/MaskFormatter.js
-javax/swing/text/View.js
-javax/swing/text/DefaultFormatter.js
-javax/swing/text/TableView.js
-javax/swing/text/TabStop.js
-javax/swing/text/WrappedPlainView.js
-javax/swing/text/DefaultFormatterFactory.js
-javax/swing/text/AttributeSet.js
-javax/swing/text/StyledEditorKit.js
-javax/swing/text/TabableView.js
-javax/swing/text/TextAction.js
-javax/swing/text/CompositeView.js
-javax/swing/text/StateInvariantError.js
-javax/swing/text/TabExpander.js
-javax/swing/text/NavigationFilter.js
-javax/swing/text/Utilities.js
-javax/swing/text/ElementIterator.js
-javax/swing/text/AbstractDocument.js
-javax/swing/text/EditorKit.js
-javax/swing/text/Keymap.js
-javax/swing/text/LayeredHighlighter.js
-javax/swing/text/SegmentCache.js
-javax/swing/text/DefaultStyledDocument.js
-javax/swing/text/DateFormatter.js
-javax/swing/text/ParagraphView.js
-javax/swing/text/Position.js
-javax/swing/text/SimpleAttributeSet.js
-javax/swing/text/ChangedCharSetException.js
-javax/swing/text/Caret.js
-javax/swing/text/Segment.js
-javax/swing/text/DefaultCaret.js
-javax/swing/text/Highlighter.js
-javax/swing/text/PlainView.js
-javax/swing/text/JTextComponent.js
-javax/swing/text/AbstractWriter.js
-javax/swing/text/BadLocationException.js
-javax/swing/text/ViewFactory.js
-javax/swing/text/Element.js
-javax/swing/text/IconView.js
-javax/swing/text/LabelView.js
-javax/swing/text/PlainDocument.js
-javax/swing/text/StyleContext.js
-javax/swing/text/DefaultEditorKit.js
-javax/swing/text/ComponentView.js
-javax/swing/text/Document.js
-javax/swing/text/Style.js
-javax/swing/text/NumberFormatter.js
-javax/swing/text/StringContent.js
-javax/swing/text/DocumentFilter.js
-javax/swing/text/InternationalFormatter.js
-javax/swing/text/GapContent.js
-javax/swing/text/GlyphView.js
-javax/swing/text/MutableAttributeSet.js
-javax/swing/text/GapVector.js
-javax/swing/text/GlyphPainter1.js
-javax/swing/text/DefaultHighlighter.js
-javax/swing/text/TabSet.js
-javax/swing/text/StyledDocument.js
-javax/swing/OverlayLayout.js
-javax/swing/border/TitledBorder.js
-javax/swing/border/LineBorder.js
-javax/swing/border/BevelBorder.js
-javax/swing/border/EmptyBorder.js
-javax/swing/border/AbstractBorder.js
-javax/swing/border/CompoundBorder.js
-javax/swing/border/Border.js
-javax/swing/border/MatteBorder.js
-javax/swing/border/SoftBevelBorder.js
-javax/swing/border/EtchedBorder.js
-javax/swing/JFileChooser.js
-javax/swing/ActionMap.js
-javax/swing/JLayeredPane.js
-javax/swing/ScrollPaneConstants.js
-javax/swing/Timer.js
-javax/swing/JFrame.js
-javax/swing/SwingConstants.js
-javax/swing/JToolTip.js
-javax/swing/JPopupMenu.js
-javax/swing/JMenuItem.js
-javax/swing/CellEditor.js
-javax/swing/DefaultButtonModel.js
-javax/swing/KeyboardManager.js
-javax/sound/sampled/DataLine.js
-javax/sound/sampled/SourceDataLine.js
-javax/sound/sampled/AudioFileFormat.js
-javax/sound/sampled/LineUnavailableException.js
-javax/sound/sampled/LineListener.js
-javax/sound/sampled/AudioInputStream.js
-javax/sound/sampled/UnsupportedAudioFileException.js
-javax/sound/sampled/Control.js
-javax/sound/sampled/Line.js
-javax/sound/sampled/AudioFormat.js
-javax/sound/sampled/AudioSystem.js
-javax/sound/sampled/LineEvent.js
-javax/print/attribute/Attribute.js
-javax/print/attribute/AttributeSet.js
-javax/print/attribute/UnmodifiableSetException.js
-javax/print/attribute/standard/PageRanges.js
-javax/print/attribute/standard/Copies.js
-javax/print/attribute/standard/RequestingUserName.js
-javax/print/attribute/standard/JobName.js
-javax/print/attribute/HashAttributeSet.js
-javax/print/attribute/PrintRequestAttributeSet.js
-javax/print/attribute/AttributeSetUtilities.js
-javax/print/attribute/DocAttribute.js
-javax/print/attribute/IntegerSyntax.js
-javax/print/attribute/DocAttributeSet.js
-javax/print/attribute/PrintJobAttributeSet.js
-javax/print/attribute/HashDocAttributeSet.js
-javax/print/attribute/PrintServiceAttributeSet.js
-javax/print/attribute/HashPrintRequestAttributeSet.js
-javax/print/attribute/PrintJobAttribute.js
-javax/print/attribute/TextSyntax.js
-javax/print/attribute/PrintRequestAttribute.js
-javax/json/Json.js
-javax/json/spi/JsonProvider.js
-javax/json/JsonObject.js
-javax/json/JsonException.js
-javax/json/JsonValue.js
-javax/json/JsonWriterFactory.js
-javax/json/JsonStructure.js
-javax/json/JsonArrayBuilder.js
-javax/json/JsonString.js
-javax/json/JsonNumber.js
-javax/json/JsonObjectBuilder.js
-javax/json/JsonReaderFactory.js
-javax/json/JsonBuilderFactory.js
-javax/json/JsonReader.js
-javax/json/stream/JsonGeneratorFactory.js
-javax/json/stream/JsonGenerationException.js
-javax/json/stream/JsonGenerator.js
-javax/json/stream/JsonParsingException.js
-javax/json/stream/JsonLocation.js
-javax/json/stream/JsonParserFactory.js
-javax/json/stream/JsonParser.js
-javax/json/JsonArray.js
-javax/json/JsonWriter.js
-javax/imageio/IIOException.js
-javax/imageio/ImageWriteParam.js
-javax/imageio/ImageIO.js
-javax/imageio/IIOParam.js
-javax/imageio/IIOImage.js
-javax/imageio/ImageWriter.js
-javax/imageio/stream/IIOByteBuffer.js
-javax/imageio/stream/FileImageOutputStream.js
-javax/imageio/stream/ImageInputStream.js
-javax/imageio/stream/ImageOutputStream.js
-javax/imageio/metadata/IIOMetadata.js
-javax/net/ssl/HttpsURLConnection.js
-mc_view/PDBfile.js
-mc_view/PDBCanvas.js
-mc_view/Residue.js
-mc_view/AppletPDBCanvas.js
-mc_view/Bond.js
-mc_view/Zsort.js
-mc_view/AppletPDBViewer.js
-mc_view/Atom.js
-mc_view/PDBChain.js
-mc_view/MCMatrix.js
-net/miginfocom/swing/SwingContainerWrapper.js
-net/miginfocom/swing/SwingComponentWrapper.js
-net/miginfocom/swing/MigLayout.js
-net/miginfocom/layout/ComponentWrapper.js
-net/miginfocom/layout/LinkHandler.js
-net/miginfocom/layout/BoundSize.js
-net/miginfocom/layout/ConstraintParser.js
-net/miginfocom/layout/AC.js
-net/miginfocom/layout/LayoutCallback.js
-net/miginfocom/layout/ContainerWrapper.js
-net/miginfocom/layout/LC.js
-net/miginfocom/layout/UnitConverter.js
-net/miginfocom/layout/AnimSpec.js
-net/miginfocom/layout/DimConstraint.js
-net/miginfocom/layout/ResizeConstraint.js
-net/miginfocom/layout/PlatformDefaults.js
-net/miginfocom/layout/UnitValue.js
-net/miginfocom/layout/LayoutUtil.js
-net/miginfocom/layout/InCellGapProvider.js
-net/miginfocom/layout/Grid.js
-net/miginfocom/layout/CC.js

diff --git a/utils/jalviewjs/coretemplate.html b/utils/jalviewjs/coretemplate.html
new file mode 100644 (file)
index 0000000..7d802f2
--- /dev/null
+++ b/utils/jalviewjs/coretemplate.html
@@ -0,0 +1,32 @@
+<!DOCTYPE html>
+<html>
+<head>
+<title>SwingJS test _NAME_</title><meta charset="utf-8" />
+<script src="swingjs/swingjs2.js"></script>
+<script>
+if (!self.SwingJS)alert('swingjs2.js was not found. It needs to be in swingjs folder in the same directory as ' + document.location.href)
+Info = {
+  code: _CODE_,
+  main: _MAIN_,
+  _COREKEY_: "_CORENAME_",
+       width: 850,
+       height: 550,
+  readyFunction: null,
+       serverURL: 'https://chemapps.stolaf.edu/jmol/jsmol/php/jsmol.php',
+       j2sPath: 'swingjs/j2s',
+       console:'sysoutdiv',
+       allowjavascript: true
+}
+</script>
+</head>
+<body>
+<script>
+SwingJS.getApplet('testApplet', Info)
+getClassList = function(){J2S._saveFile('_j2sclasslist.txt', Clazz.ClassFilesLoaded.sort().join('\n'))}
+</script>
+<div style="position:absolute;left:900px;top:30px;width:600px;height:300px;">
+<div id="sysoutdiv" contentEditable="true" style="border:1px solid green;width:100%;height:95%;overflow:auto"></div>
+This is System.out. <a href="javascript:testApplet._clearConsole()">clear it</a> <br>Add ?j2snocore to URL to see full class list; ?j2sdebug to use uncompressed j2s/core files <br><a href="javascript:getClassList()">get _j2sClassList.txt</a>
+</div>
+</body>
+</html>