From: Ben Soares <bsoares@dundee.ac.uk>
Date: Thu, 17 Oct 2019 10:36:30 +0000 (+0100)
Subject: JAL-3210 changed classes for net.sf.j2s.core
X-Git-Tag: Release_2_11_4_0~45^2~18^2~112
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=41ba5838e9920dbc3609dbabe04df91f733c4f85;p=jalview.git

JAL-3210 changed classes for net.sf.j2s.core
---

diff --git a/utils/jalviewjs/Java2ScriptCompilationParticipant.java b/utils/jalviewjs/Java2ScriptCompilationParticipant.java
new file mode 100644
index 0000000..9c7aeb9
--- /dev/null
+++ b/utils/jalviewjs/Java2ScriptCompilationParticipant.java
@@ -0,0 +1,185 @@
+package net.sf.j2s.core;
+
+import java.util.Arrays;
+import java.util.Properties;
+
+import org.eclipse.jdt.core.IJavaProject;
+import org.eclipse.jdt.core.compiler.BuildContext;
+import org.eclipse.jdt.core.compiler.ReconcileContext;
+
+/**
+ * New Java2Script compiler uses org.eclipse.jdt.core.compiler.CompilationParticipant instead of builder
+ * 
+ * source: https://github.com/eclipse/org.aspectj.shadows/blob/master/org.eclipse.jdt.core/model/org/eclipse/jdt/core/compiler/CompilationParticipant.java
+ * 
+ * @author hansonr
+ *
+ */
+public class Java2ScriptCompilationParticipant extends org.eclipse.jdt.core.compiler.CompilationParticipant {
+	private BuildContext[] javaFiles;
+	private boolean isCleanBuild;
+
+	public Java2ScriptCompilationParticipant() {
+		System.out.println("CompilationParticipant started");
+	}
+
+	/**
+	 * Returns whether this participant is active for a given project.
+	 * <p>
+	 * Default is to return <code>false</code>.
+	 * </p>
+	 * <p>
+	 * For efficiency, participants that are not interested in the given project
+	 * should return <code>false</code> for that project.
+	 * </p>
+	 * 
+	 * @param project
+	 *            the project to participate in
+	 * @return whether this participant is active for a given project
+	 */
+	public boolean isActive(IJavaProject project) {
+ 		boolean isj2s = Java2ScriptCompiler.isActive(project);
+		System.out.println("isActive " + isj2s + " " + project.getProject().getLocation());
+		return isj2s;
+	}
+
+	/**
+	 * Notifies this participant that a build is about to start and provides it
+	 * the opportunity to create missing source folders for generated source
+	 * files. Additional source folders should be marked as optional so the
+	 * project can be built when the folders do not exist. Only sent to
+	 * participants interested in the project.
+	 * <p>
+	 * Default is to return <code>READY_FOR_BUILD</code>.
+	 * </p>
+	 * 
+	 * @see #buildFinished(IJavaProject project)
+	 * @param project
+	 *            the project about to build
+	 * @return READY_FOR_BUILD or NEEDS_FULL_BUILD
+	 */
+	public int aboutToBuild(IJavaProject project) {
+		System.out.println("aboutToBuild " + project.getProject().getLocation());
+		return READY_FOR_BUILD;
+	}
+
+	/**
+	 * Notifies this participant that a clean is about to start and provides it
+	 * the opportunity to delete generated source files. Only sent to
+	 * participants interested in the project.
+	 * 
+	 * @param project
+	 *            the project about to be cleaned
+	 */
+	public void cleanStarting(IJavaProject project) {
+		System.out.println("cleanStarting " + project.getProject().getLocation());
+		isCleanBuild = true;
+	}
+
+	/**
+	 * Notifies this participant that a compile operation is about to start and
+	 * provides it the opportunity to generate source files based on the source
+	 * files about to be compiled. When isBatchBuild is true, then files
+	 * contains all source files in the project. Only sent to participants
+	 * interested in the current build project.
+	 *
+	 * @param files
+	 *            is an array of BuildContext
+	 * @param isBatch
+	 *            identifies when the build is a batch build
+	 */
+	public void buildStarting(BuildContext[] files, boolean isBatch) {
+		if (javaFiles != null) {
+			BuildContext[] concat = Arrays.copyOf(javaFiles, javaFiles.length + files.length);
+			System.arraycopy(files, 0, concat , javaFiles.length, files.length);
+			javaFiles = concat;
+		} else {
+			javaFiles = files;
+		}
+		System.out.println("buildStarting " + files.length + " files, isBatch=" + isBatch);
+	}
+
+	/**
+	 * Notifies this participant that a build has finished for the project. This
+	 * will be sent, even if buildStarting() was not sent when no source files
+	 * needed to be compiled or the build failed. Only sent to participants
+	 * interested in the project.
+	 * 
+	 * @param project
+	 *            the project about to build
+	 * @since 3.4
+	 */
+	public void buildFinished(IJavaProject project) {
+		if (javaFiles != null) {
+			Java2ScriptCompiler j2sCompiler = new Java2ScriptCompiler();
+			j2sCompiler.startBuild(isCleanBuild);
+			if (!j2sCompiler.initializeProject(project, true)) {
+				System.out.println(".j2s disabled");
+				return;
+			}
+			System.out.println("building JavaScript " + project.getProject().getLocation());
+			for (int i = 0; i < javaFiles.length; i++) {
+				System.out.println("[" + (i+1) + "/" + javaFiles.length + "] transpiling " + javaFiles[i]);
+// trying to keep the progess monitor running - didn't work
+//				try {
+//					Thread.currentThread().sleep(1);
+//				} catch (InterruptedException e) {
+//					// ignore
+//				}
+				if (!j2sCompiler.compileToJavaScript(javaFiles[i].getFile())) {
+					System.out.println("Error processing " + javaFiles[i].getFile());
+					break;
+				}
+			}
+			javaFiles = null;
+			System.out.println("build finished " + project.getProject().getLocation());
+		}
+		isCleanBuild = false;
+	}
+
+	/**
+	 * Returns whether this participant is interested in only Annotations.
+	 * <p>
+	 * Default is to return <code>false</code>.
+	 * </p>
+	 * 
+	 * @return whether this participant is interested in only Annotations.
+	 */
+	public boolean isAnnotationProcessor() {
+		return false;
+	}
+
+	/**
+	 * Notifies this participant that a compile operation has found source files
+	 * using Annotations. Only sent to participants interested in the current
+	 * build project that answer true to isAnnotationProcessor(). Each
+	 * BuildContext was informed whether its source file currently
+	 * hasAnnotations().
+	 *
+	 * @param files
+	 *            is an array of BuildContext
+	 */
+	public void processAnnotations(BuildContext[] files) {
+		// nothing to do
+	}
+
+	/**
+	 * Notifies this participant that a reconcile operation is happening. The
+	 * participant can act on this reconcile operation by using the given
+	 * context. Other participant can then see the result of this participation
+	 * on this context.
+	 * <p>
+	 * Note that a participant should not modify the buffer of the working copy
+	 * that is being reconciled.
+	 * </p>
+	 * <p>
+	 * Default is to do nothing.
+	 * </p>
+	 * 
+	 * @param context
+	 *            the reconcile context to act on
+	 */
+	public void reconcile(ReconcileContext context) {
+		// fired whenever a source file is changed -- before it is saved
+	}
+}
\ No newline at end of file
diff --git a/utils/jalviewjs/Java2ScriptCompiler.java b/utils/jalviewjs/Java2ScriptCompiler.java
new file mode 100644
index 0000000..ce31b52
--- /dev/null
+++ b/utils/jalviewjs/Java2ScriptCompiler.java
@@ -0,0 +1,586 @@
+package net.sf.j2s.core;
+
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileFilter;
+import java.io.FileInputStream;
+import java.io.FileNotFoundException;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.nio.file.Files;
+import java.nio.file.StandardCopyOption;
+import java.util.ArrayList;
+import java.util.Date;
+import java.util.Enumeration;
+import java.util.HashSet;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Map;
+import java.util.Properties;
+
+import org.eclipse.core.resources.IFile;
+import org.eclipse.core.resources.IProject;
+import org.eclipse.core.runtime.IProduct;
+import org.eclipse.jdt.core.IJavaProject;
+import org.eclipse.jdt.core.JavaCore;
+import org.eclipse.jdt.core.dom.AST;
+import org.eclipse.jdt.core.dom.ASTParser;
+import org.eclipse.jdt.core.dom.CompilationUnit;
+
+/**
+ * The main (and currently only operational) Java2Script compiler.
+ * 
+ * @author Bob Hanson
+ *
+ */
+class Java2ScriptCompiler {
+	/**
+	 * The name of the J2S options file, aka as the "Dot-j2s" file.
+	 */
+	private static final String J2S_OPTIONS_FILE_NAME = ".j2s";
+	
+	// BH: added "true".equals(getProperty(props,
+	// "j2s.compiler.allow.compression")) to ensure compression only occurs when
+	// desired
+	private static final int JSL_LEVEL = AST.JLS8; // deprecation just because Java has moved on
+	private boolean showJ2SSettings = true;
+
+	// We copy all non .java files from any directory from which we loaded a
+	// java file into the site directory
+	private final HashSet<String> copyResources = new HashSet<String>();
+	private Map<String, String> htMethodsCalled;
+	private List<String> lstMethodsDeclared;
+
+	private Properties props;
+	private String htmlTemplate = null;
+
+	private String projectFolder;
+
+	private String j2sPath;
+
+	private String logDeclared;
+
+	private boolean logAllCalls;
+
+	private String logCalled;
+
+	private String excludedPaths;
+
+	private String siteFolder;
+
+	private boolean testing;
+	
+	private List<String> lstExcludedPaths;
+
+	private boolean isCleanBuild;
+
+	boolean isCompilationParticipant;
+
+	private ASTParser astParser;
+
+	private IJavaProject project;
+
+	private boolean isDebugging;
+
+	static boolean isActive(IJavaProject project) {
+		try {
+			return new File(project.getProject().getLocation().toOSString(), J2S_OPTIONS_FILE_NAME).exists();
+		} catch (@SuppressWarnings("unused") Exception e) {
+			return false;
+		}
+	}
+
+	Java2ScriptCompiler() {
+		// initialized only once using CompilationParticipant; every time using
+		// older Builder idea
+	}
+
+	/**
+	 * only for CompilationParticipant
+	 * @param isClean
+	 */
+	void startBuild(boolean isClean) {
+		// at the beginning of a clean build, clear data
+		isCleanBuild = isClean;
+		htmlTemplate = null;
+		if (isClean) {
+			copyResources.clear();
+			lstMethodsDeclared = null;
+			htMethodsCalled = null;
+		}
+
+	}
+
+ 	/**
+	 * from Java2ScriptCompilationParticipant.java
+	 * 
+	 * get all necessary .j2s params for a build
+	 * 
+	 * @param project
+	 * @param isCompilationParticipant
+	 * @return true if this is a j2s project and is enabled
+	 * 
+	 */
+	boolean initializeProject(IJavaProject project, boolean isCompilationParticipant) {
+		this.project = project;
+		this.isCompilationParticipant = isCompilationParticipant;
+		if (!isActive(project)) {
+			// the file .j2s does not exist in the project directory -- skip this project
+			return false;
+		}
+		projectFolder = project.getProject().getLocation().toOSString();
+		props = new Properties();
+		try {
+			File j2sFile = new File(projectFolder, J2S_OPTIONS_FILE_NAME);
+			props.load(new FileInputStream(j2sFile));
+			String status = getProperty("j2s.compiler.status");
+			if (!"enable".equals(status) && !"enabled".equals(status)) {
+				if (getFileContents(j2sFile).trim().length() == 0) {
+				  writeToFile(j2sFile, getDefaultJ2SFile());
+				} else {
+				 // not enabled
+				return false;
+				}
+			}
+		} catch (FileNotFoundException e1) {
+			e1.printStackTrace();
+		} catch (IOException e1) {
+			e1.printStackTrace();
+		}
+
+		File file;
+		siteFolder = getProperty("j2s.site.directory");
+		if (siteFolder == null)
+			siteFolder = "site";
+		siteFolder = projectFolder + "/" + siteFolder;
+		j2sPath = siteFolder + "/swingjs/j2s";
+
+		if (isDebugging)
+			System.out.println("Java2ScriptCompiler writing to " + j2sPath);
+		// method declarations and invocations are only logged
+		// when the designated files are deleted prior to building
+
+		logDeclared = (isCompilationParticipant && !isCleanBuild ? null : getProperty("j2s.log.methods.declared"));
+		if (logDeclared != null) {
+			if (!(file = new File(projectFolder, logDeclared)).exists()) {
+				lstMethodsDeclared = new ArrayList<String>();
+				System.err.println("logging methods declared to " + file);
+			}
+			logDeclared = projectFolder + "/" + logDeclared;
+		}
+		logAllCalls = false;
+
+		logCalled = (isCompilationParticipant && !isCleanBuild ? null : getProperty("j2s.log.methods.called"));
+		if (logCalled != null) {
+			if (!(file = new File(projectFolder, logCalled)).exists()) {
+				htMethodsCalled = new Hashtable<String, String>();
+				System.err.println("logging methods called to " + file);
+			}
+			logCalled = projectFolder + "/" + logCalled;
+			logAllCalls = "true".equals(getProperty("j2s.log.all.calls"));
+		}
+
+		excludedPaths = getProperty("j2s.excluded.paths");
+
+		lstExcludedPaths = null;
+
+		if (excludedPaths != null) {
+			lstExcludedPaths = new ArrayList<String>();
+			String[] paths = excludedPaths.split(";");
+			for (int i = 0; i < paths.length; i++)
+				if (paths[i].trim().length() > 0)
+					lstExcludedPaths.add(paths[i].trim() + "/");
+			if (lstExcludedPaths.size() == 0)
+				lstExcludedPaths = null;
+		}
+
+		testing = "true".equals(getProperty("j2s.testing"));
+		
+		String prop = getProperty("j2s.compiler.nonqualified.packages");
+		// older version of the name
+		String nonqualifiedPackages = getProperty("j2s.compiler.nonqualified.classes");
+		nonqualifiedPackages = (prop == null ? "" : prop)
+			+ (nonqualifiedPackages == null ? "" : (prop == null ? "" : ";") + nonqualifiedPackages);
+	    if (nonqualifiedPackages.length() == 0)
+	    	nonqualifiedPackages = null;
+		// includes @j2sDebug blocks
+		isDebugging = "debug".equals(getProperty("j2s.compiler.mode"));
+
+		String classReplacements = getProperty("j2s.class.replacements");
+
+		String htmlTemplateFile = getProperty("j2s.template.html");
+		if (htmlTemplateFile == null)
+			htmlTemplateFile = "template.html";
+
+		if (htmlTemplate == null) {
+			file = new File(projectFolder, htmlTemplateFile);
+			if (!file.exists()) {
+				String html = getDefaultHTMLTemplate();
+				System.err.println("creating new htmltemplate\n" + html);
+				writeToFile(file, html);
+			}
+			htmlTemplate = getFileContents(file);
+			if (showJ2SSettings)
+				System.err.println("using HTML template " + file);
+		}
+
+		Java2ScriptVisitor.setDebugging(isDebugging);
+		Java2ScriptVisitor.setLogging(lstMethodsDeclared, htMethodsCalled, logAllCalls);
+
+		Java2ScriptVisitor.NameMapper.setNonQualifiedNamePackages(nonqualifiedPackages);
+		Java2ScriptVisitor.NameMapper.setClassReplacements(classReplacements);
+		
+		astParser = ASTParser.newParser(JSL_LEVEL);
+	
+		return true;
+	}
+
+	/**
+	 * from Java2ScriptCompilationParticipant.java
+	 * 
+	 * process the source file into JavaScript using the JDT abstract syntax
+	 * tree parser and visitor
+	 * 
+	 * @param javaSource
+	 */
+	boolean compileToJavaScript(IFile javaSource) {
+		String fileName = new String(javaSource.getFullPath().removeFirstSegments(1).toPortableString());
+		if (lstExcludedPaths != null) {
+			for (int i = lstExcludedPaths.size(); --i >= 0;)
+				if (fileName.startsWith(lstExcludedPaths.get(i))) {
+					return true;
+				}
+		}
+		org.eclipse.jdt.core.ICompilationUnit createdUnit = JavaCore.createCompilationUnitFrom(javaSource);
+		astParser.setSource(createdUnit);
+		// note: next call must come before each createAST call
+		astParser.setResolveBindings(true); 
+		CompilationUnit root = (CompilationUnit) astParser.createAST(null);
+		// If the Java2ScriptVisitor is ever extended, it is important to set the project.
+		// Java2ScriptVisitor#addClassOrInterface uses getClass().newInstance().setproject(project). 
+		Java2ScriptVisitor visitor = new Java2ScriptVisitor().setProject(project, testing);
+
+		try {
+
+			// transpile the code
+
+			root.accept(visitor);
+
+			// generate the .js file(s) in the site directory
+
+			outputJavaScript(visitor, j2sPath);
+
+			logMethods(logCalled, logDeclared, logAllCalls);
+
+			// add the HTML files in the site directory
+
+			addHTML(visitor.getAppList(true), siteFolder, htmlTemplate, true);
+			addHTML(visitor.getAppList(false), siteFolder, htmlTemplate, false);
+		} catch (Throwable e) {
+			e.printStackTrace();
+			e.printStackTrace(System.out);
+			// find the file and delete it.
+			String filePath = j2sPath;
+			String rootName = root.getJavaElement().getElementName();
+			rootName = rootName.substring(0, rootName.lastIndexOf('.'));
+			String packageName = visitor.getMyPackageName();
+			if (packageName != null) {
+				File folder = new File(filePath, packageName.replace('.', File.separatorChar));
+				filePath = folder.getAbsolutePath();
+				File jsFile = new File(filePath, rootName + ".js"); //$NON-NLS-1$
+				if (jsFile.exists()) {
+					System.out.println("Java2ScriptCompiler deleting " + jsFile);
+					jsFile.delete();
+				}
+			}
+			return false;
+		}
+		String packageName = visitor.getMyPackageName();
+		if (packageName != null) {
+			int pt = packageName.indexOf(".");
+			if (pt >= 0)
+				packageName = packageName.substring(0, pt);
+			if (!copyResources.contains(packageName)) {
+				copyResources.add(packageName);
+				File src = new File(projectFolder + "/src", packageName);
+				File dest = new File(j2sPath, packageName);
+				copySiteResources(src, dest);
+			}
+		}
+		return true;
+	}
+
+	//// private methods ////
+	
+	
+	private void logMethods(String logCalled, String logDeclared, boolean doAppend) {
+		if (htMethodsCalled != null)
+			try {
+				File file = new File(logCalled);
+				file.createNewFile();
+				FileOutputStream fos = new FileOutputStream(file, doAppend);
+				for (String key : htMethodsCalled.keySet()) {
+					String val = htMethodsCalled.get(key);
+					fos.write(key.getBytes());
+					if (!val.equals("-")) {
+						fos.write(',');
+						fos.write(val.getBytes());
+					}
+					fos.write('\n');
+				}
+				fos.close();
+			} catch (Exception e) {
+				System.err.println("Cannot log to " + logCalled + " " + e.getMessage());
+			}
+		if (lstMethodsDeclared != null)
+			try {
+				File file = new File(logDeclared);
+				file.createNewFile();
+				FileOutputStream fos = new FileOutputStream(file, true);
+				for (int i = 0, n = lstMethodsDeclared.size(); i < n; i++) {
+					fos.write(lstMethodsDeclared.get(i).getBytes());
+					fos.write('\n');
+				}
+				fos.close();
+			} catch (Exception e) {
+				System.err.println("Cannot log to " + logDeclared + " " + e.getMessage());
+			}
+	}
+
+	private String getProperty(String key) {
+		String val = props.getProperty(key);
+		if (showJ2SSettings)
+			System.err.println(key + " = " + val);
+		return val;
+	}
+
+	private void outputJavaScript(Java2ScriptVisitor visitor, String j2sPath) {
+
+		// fragments[0] is package]
+		List<String> elements = visitor.getElementList();
+
+		// BH all compression is deprecated --- use Google Closure Compiler
+
+		String packageName = visitor.getMyPackageName();
+		for (int i = 0; i < elements.size();) {
+			String elementName = elements.get(i++);
+			String element = elements.get(i++);
+			createJSFile(j2sPath, packageName, elementName, element);
+		}
+		showJ2SSettings = false; // just once per compilation run
+	}
+
+	private void createJSFile(String j2sPath, String packageName, String elementName, String js) {
+		if (packageName != null) {
+			File folder = new File(j2sPath, packageName.replace('.', File.separatorChar));
+			j2sPath = folder.getAbsolutePath();
+			if (!folder.exists() || !folder.isDirectory()) {
+				if (!folder.mkdirs()) {
+					throw new RuntimeException("Failed to create folder " + j2sPath); //$NON-NLS-1$
+				}
+			}
+		}
+		File f = new File(j2sPath, elementName + ".js");
+		if (isDebugging)
+			System.out.println("Java2ScriptCompiler creating " + f);
+		writeToFile(f, js);
+	}
+
+	private String getFileContents(File file) {
+		try {
+			StringBuilder sb = new StringBuilder();
+			FileInputStream is = new FileInputStream(file);
+			BufferedReader reader = new BufferedReader(new InputStreamReader(is));
+			String line = null;
+			while ((line = reader.readLine()) != null) {
+				sb.append(line).append("\n");
+			}
+			reader.close();
+			return sb.toString();
+		} catch (@SuppressWarnings("unused") IOException e) {
+			//
+		}
+		return null;
+	}
+
+	private void writeToFile(File file, String data) {
+		if (data == null)
+			return;
+		try {
+			FileOutputStream os = new FileOutputStream(file);
+			os.write(data.getBytes("UTF-8"));
+			os.close();
+		} catch (IOException e) {
+			e.printStackTrace();
+		}
+    }
+
+	/**
+	 * The default .j2s file. Replaces .j2s only if it is found but is empty.
+	 * 
+	 * OK, I know this should be a resource.
+	 * 
+	 * 
+	 * 
+	 */
+	
+	private String getDefaultJ2SFile() {
+
+		return "#j2s default configuration file created by net.sf.java2script_" 
+        + CorePlugin.VERSION + " " + new Date() + "\n\n" +
+        "#enable the Java2Script transpiler -- comment out to disable\n" + 
+		"j2s.compiler.status=enable\n" + 
+		"\n" + 
+		"\n" + 
+		"# destination directory for all JavaScript\n" + 
+		"j2s.site.directory=site\n" + 
+		"\n" + 
+		"# uncomment j2s.* lines to process:\n" + 
+		"\n" + 
+		"# a semicolon-separated list of package-level file paths to be excluded\n" + 
+		"#j2s.excluded.paths=test;testng\n" + 
+		"\n" + 
+		"# output file name for logging methods declared - delete the file to regenerate a listing \n" + 
+		"#j2s.log.methods.declared=methodsDeclared.csv\n" + 
+		"\n" + 
+		"#output file name for logging methods called - delete the file to regenerate a listing\n" + 
+		"#j2s.log.methods.called=methodsCalled.csv\n" + 
+		"\n" + 
+		"#if set, every instance of methods called will be logged\n" + 
+		"#otherwise, only the first call to a method will be logged \n" + 
+		"#output will be comma-separated: called method,caller class \n" + 
+		"#j2s.log.all.calls=true\n" + 
+		"\n" + 
+		"# a semicolon-separated list of packages that contain classes for which the method names\n" + 
+		"# in their classes should not be \"qualified\" to indicate their parameter types. \n" + 
+		"# This option is useful if you have an API interface in Java that refers to JavaScript \n" + 
+		"# methods such as calling window or jQuery functions or the methods in Clazz or J2S. \n" + 
+		"# The classes must not have any methods that are overloaded - with the\n" + 
+		"# same name but different paramater type, as JavaScript will only see the last one.\n" + 
+		"#j2s.compiler.nonqualified.packages=org.jmol.api.js;jspecview.api.js\n" + 
+		"\n" + 
+		"# uncomment to add debugging output. Start eclipse with the -consoleLog option to see output.\n" + 
+		"#j2s.compiler.mode=debug\n" + 
+		"\n" + 
+		"# a semicolon-separated list of from->to listings of package (foo.) or class (foo.bar) \n" + 
+		"# replacements to be made. This option allows for having one class or package used in Java\n" + 
+		"# and another used in JavaScript. Take care with this. All methods in both packages must\n" + 
+		"# have exactly the same parameter signature. We use it in Jalview to provide a minimal\n" + 
+		"# JavaScript implementation of a large third-party library while still using that library's\n" + 
+		"# jar file in Java.\n" + 
+		"#j2s.class.replacements=org.apache.log4j.->jalview.javascript.log4j.\n" + 
+		"\n" + 
+		"# uncomment and change if you do not want to use the template.html file created for you\n" + 
+		"# in your project directory. A default template file will be created by the transpiler \n" + 
+		"# directory if there is none there already.\n" + 
+		"#j2s.template.html=template.html\n";
+	}
+	/**
+	 * The default template file. The user can specify another in the .j2s file
+	 * using template.html=.....
+	 * 
+	 * @return default template with _NAME_, _CODE_, and _MAIN_ to fill in.
+	 */
+	private String getDefaultHTMLTemplate() {
+		return "<!DOCTYPE html>\n" + 
+				"<html>\n" + 
+				"<head>\n" + 
+				"<title>SwingJS test _NAME_</title><meta charset=\"utf-8\" />\n" + 
+				"<script src=\"swingjs/swingjs2.js\"></script>\n" + 
+				"<script>\n" + 
+				"if (!self.SwingJS)alert('swingjs2.js was not found. It needs to be in swingjs folder in the same directory as ' + document.location.href)\n" + 
+				"Info = {\n" + 
+				"  code: _CODE_,\n" + 
+				"  main: _MAIN_,\n" + 
+				"  core: \"NONE\",\n" + 
+				"	width: 850,\n" + 
+				"	height: 550,\n" + 
+				"  readyFunction: null,\n" + 
+				"	serverURL: 'https://chemapps.stolaf.edu/jmol/jsmol/php/jsmol.php',\n" + 
+				"	j2sPath: 'swingjs/j2s',\n" + 
+				"	console:'sysoutdiv',\n" + 
+				"	allowjavascript: true\n" + 
+				"}\n" + 
+				"</script>\n" + 
+				"</head>\n" + 
+				"<body>\n" + 
+				"<script>\n" + 
+				"SwingJS.getApplet('testApplet', Info)\n" + 
+				"getClassList = function(){J2S._saveFile('_j2sclasslist.txt', Clazz.ClassFilesLoaded.sort().join('\\n'))}\n" + 
+				"</script>\n" + 
+				"<div style=\"position:absolute;left:900px;top:30px;width:600px;height:300px;\">\n" + 
+				"<div id=\"sysoutdiv\" contentEditable=\"true\" style=\"border:1px solid green;width:100%;height:95%;overflow:auto\"></div>\n" + 
+				"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>\n" + 
+				"</div>\n" + 
+				"</body>\n" + 
+				"</html>\n";
+	}
+
+	/**
+	 * Create a test HTML file for the applet or application. It will go into
+	 * <project>/site.
+	 * 
+	 * @param appList
+	 * @param siteFolder
+	 * @param template
+	 * @param isApplet
+	 */
+	private void addHTML(ArrayList<String> appList, String siteFolder, String template, boolean isApplet) {
+		if (appList == null || template == null)
+			return;
+		for (int i = appList.size(); --i >= 0;) {
+			String cl = appList.get(i);
+			String _NAME_ = cl.substring(cl.lastIndexOf(".") + 1);
+			String fname = cl.replaceAll("\\.", "_") + (isApplet ? "_applet" : "") + ".html";
+			cl = "\"" + cl + "\"";
+			String _MAIN_ = (isApplet ? "null" : cl);
+			String _CODE_ = (isApplet ? cl : "null");
+			template = template.replace("_NAME_", _NAME_).replace("_CODE_", _CODE_).replace("_MAIN_", _MAIN_);
+			System.err.println("Java2Script creating " + siteFolder + "/" + fname);
+			writeToFile(new File(siteFolder, fname), template);
+		}
+	}
+
+	private FileFilter filter = new FileFilter() {
+
+		@Override
+		public boolean accept(File pathname) {
+			return pathname.isDirectory() || !pathname.getName().endsWith(".java");
+		}
+
+	};
+
+	private void copySiteResources(File from, File dest) {
+		copyNonclassFiles(from, dest);
+	}
+
+	private void copyNonclassFiles(File dir, File target) {
+		if (dir.equals(target))
+			return;
+		File[] files = dir.listFiles(filter);
+		File f = null;
+		if (files != null) 
+			try {
+				if (!target.exists())
+					Files.createDirectories(target.toPath());
+				for (int i = 0; i < files.length; i++) {
+					f = files[i];
+					if (f == null) {
+						//
+					} else if (f.isDirectory()) {
+						copyNonclassFiles(f, new File(target, f.getName()));
+					} else {
+						Files.copy(f.toPath(), new File(target, f.getName()).toPath(),
+								StandardCopyOption.REPLACE_EXISTING);
+						System.err.println("copied to site: " + f.toPath());
+					}
+				}
+			} catch (IOException e1) {
+				// TODO Auto-generated catch block
+				System.err.println("error copying " + f + " to " + target);
+				e1.printStackTrace();
+			}
+	}
+
+}