Clean up exception reporting + bug fixes

Bug: ribose run output not directed to file specified on command line

- fix up @throws for javadoc
- remove exceptions declared but not thrown per method
- bug fixes
  - delete jar files in clean-ribose target in build.xml
  - Model.java @ line 360 (fix array length growth factor)
  - ModelLoader.java @ line 164 (direct transductor output)
  - send InputStack log output to runtime log instead of compile log

Signed-off-by: jrte <jrte.project@gmail.com>

build.xml

@@ -76,21 +76,19 @@
 		<pathelement location="${jars.dir}/${ribose.version}.jar"/>
 	</path>
 
-	<target name="clean" depends="clean-ribose,clean-test">
+	<target name="clean" depends="clean-ribose,clean-test,clean-javadoc">
   	<delete failonerror="false" dir="build"/>
-		<delete failonerror="false" verbose="true">
-			<fileset dir="." includes="ribose-*.log*"/>
-		</delete>
+		<delete failonerror="false" dir="." includes="ribose-*.log*"/>
 	</target>
 
-	<target name="clean-ribose" depends="clean-javadoc">
+	<target name="clean-ribose">
+		<delete failonerror="false" dir="${jars.dir}" includes="*"/>
 		<delete failonerror="false" dir="${build.java.classes}/com"/>
 		<delete failonerror="false" dir="${build.compiler.model}"/>
 		<delete failonerror="false" dir="/tmp" includes="*.ginrout,*.ginrerr"/>
 	</target>
 
 	<target name="clean-javadoc">
-  	<delete failonerror="false" file="${jars.dir}/${ribose.version}-api.jar"/>
   	<delete failonerror="false" dir="javadoc" includes="**/*"/>
 	</target>
 

src/com/characterforming/jrte/engine/Base.java

@@ -144,7 +144,7 @@ public static int getOutBufferSize() {
 	 * @param bytes  The UTF-8 byte array
 	 * @param length The number of bytes to decode, starting from 0
 	 * @return the decoded integer
-	 * @throws NumberFormatException on error
+	 * @throws NumberFormatException if things don't work out
 	 */
 	public static int decodeInt(final byte[] bytes, int length) throws NumberFormatException {
 		int value = 0;

src/com/characterforming/jrte/engine/InputStack.java

@@ -54,7 +54,7 @@ final class FreeStack extends LinkedList<byte[]> {
 	}
 
 	InputStack(final int initialSize) {
-		this.logger = Base.getCompileLogger();
+		this.logger = Base.getRuntimeLogger();
 		this.stack = Input.stack(initialSize);
 		this.markList = Input.stack(initialSize);
 		this.markState = InputStack.CLEAR;

src/com/characterforming/jrte/engine/Model.java

@@ -47,6 +47,7 @@
 import com.characterforming.ribose.base.Bytes;
 import com.characterforming.ribose.base.CompilationException;
 import com.characterforming.ribose.base.ModelException;
+import com.characterforming.ribose.base.Signal;
 
 /**
  * @author Kim Briggs
@@ -351,17 +352,16 @@ protected int addSignal(Bytes signalName) {
 
 	protected int addTransducer(Bytes transducerName) {
 		Integer ordinal = this.transducerOrdinalMap.get(transducerName);
+		assert ordinal == null || transducerName.equals(this.transducerNameIndex[ordinal]);
 		if (ordinal == null) {
 			ordinal = this.transducerOrdinalMap.size();
 			this.transducerOrdinalMap.put(transducerName, ordinal);
 			if (ordinal >= this.transducerNameIndex.length) {
-				int length = ordinal + (ordinal << 1);
+				int length = ordinal + (Math.max(ordinal, 4) >> 1);
 				this.transducerNameIndex = Arrays.copyOf(this.transducerNameIndex, length);
 				this.transducerOffsetIndex = Arrays.copyOf(this.transducerOffsetIndex, length);
 			}
 			this.transducerNameIndex[ordinal] = transducerName;
-		} else {
-			assert this.transducerNameIndex[ordinal].equals(transducerName);
 		}
 		return ordinal;
 	}
@@ -510,7 +510,7 @@ protected long[] readTransitionMatrix() throws ModelException {
 			final int nStates = this.io.readInt();
 			final int nInputs = this.io.readInt();
 			matrix = new long[nStates * nInputs];
-			// preset all cells to invoke nul() effector on domain error
+			// preset all cells to signal NUL without changing state
 			for (int state = 0; state < nStates; state++) {
 				final int toState = state * nInputs;
 				final long nul = Transducer.transition(toState, 0);

src/com/characterforming/jrte/engine/ModelLoader.java

@@ -67,7 +67,7 @@ private ModelLoader(final File modelPath)
 	 *
 	 * @param modelFile the model file
 	 * @return the loaded model instance
-	 * @throws ModelException on error
+	 * @throws ModelException if things don't work out
 	 */
 	public static ModelLoader loadModel(File modelPath)
 	throws ModelException {
@@ -161,6 +161,7 @@ public boolean stream(Bytes transducer, ITarget target, Signal prologue, InputSt
 			int position = read;
 			if (read > 0) {
 				ITransductor trex = transductor(target);
+				trex.output(out);
 				if (prologue != null)
 					trex.signal(prologue);
 				if (trex.push(bytes, read).start(transducer).status().isRunnable()) {

src/com/characterforming/jrte/engine/Transductor.java

@@ -147,7 +147,7 @@ public final class Transductor implements ITransductor, IOutput {
 	 *  Constructor
 	 *
 	 * @param model The runtime model
-	 * @throws ModelException on error
+	 * @throws ModelException if things don't work out
 	 */
 	Transductor(final Model model) {
 		super();

src/com/characterforming/jrte/test/FileRunner.java

@@ -24,7 +24,6 @@
 import java.io.BufferedOutputStream;
 import java.io.File;
 import java.io.FileInputStream;
-import java.io.IOException;
 import java.nio.ByteBuffer;
 import java.nio.CharBuffer;
 import java.nio.charset.CharsetDecoder;
@@ -40,18 +39,16 @@
 import com.characterforming.ribose.ITransductor;
 import com.characterforming.ribose.ITransductor.Metrics;
 import com.characterforming.ribose.base.Bytes;
-import com.characterforming.ribose.base.RiboseException;
 import com.characterforming.ribose.base.Signal;
 
 public class FileRunner {
 
 	/**
-	 * @param args
-	 * @throws InterruptedException on error
-	 * @throws RiboseException on error
-	 * @throws IOException on error
+	 * Shell interface.
+	 * 
+	 * @param args arguments from the shell
 	 */
-	public static void main(final String[] args) throws InterruptedException, RiboseException, IOException {
+	public static void main(final String[] args) {
 		final boolean nil = args[0].compareTo("--nil") == 0;
 		int arg = nil ? 1 : 0;
 		if ((args.length - arg) < 3) {

src/com/characterforming/jrte/test/TestRunner.java

@@ -20,7 +20,6 @@
 package com.characterforming.jrte.test;
 
 import java.io.File;
-import java.io.IOException;
 import java.nio.CharBuffer;
 import java.nio.charset.CharsetEncoder;
 import java.util.logging.Level;
@@ -33,19 +32,16 @@
 import com.characterforming.ribose.ITransductor;
 import com.characterforming.ribose.ITransductor.Status;
 import com.characterforming.ribose.base.Bytes;
-import com.characterforming.ribose.base.RiboseException;
 import com.characterforming.ribose.base.Signal;
 
 public class TestRunner {
 
 	/**
-	 * @param args
-	 * @throws InterruptedException on error
-	 * @throws RiboseException on error
-	 * @throws IOException on error
-	 * @throws SecurityException on error
+	 * Shell interface.
+	 * 
+	 * @param args arguments from the shell
 	 */
-	public static void main(final String[] args) throws InterruptedException, RiboseException, SecurityException, IOException {
+	public static void main(final String[] args) {
 		if (args.length == 0) {
 			System.out.println(String.format("Usage: java -cp <classpath> %1$s <model-path> [wait-ms]", TestRunner.class.getName()));
 			System.exit(1);

src/com/characterforming/ribose/IEffector.java

@@ -80,7 +80,7 @@ public interface IEffector<T extends ITarget> {
 	 * This method is invoked at runtime when triggered by an input transition.
 	 *
 	 * @return user-defined effectors should return {@code IEffector.RTX_NONE}
-	 * @throws EffectorException on error
+	 * @throws EffectorException if things don't work out
 	 */
 	int invoke() throws EffectorException;
 

src/com/characterforming/ribose/IModel.java

@@ -63,7 +63,7 @@ public interface IModel extends AutoCloseable {
  * @param riboseModelFile path indicating where to create the model file
  * @return true if the model was created successfully
  * @throws ClassNotFoundException if {@code targetClassname} not found
- * @throws ModelException if compilation 
+ * @throws ModelException if compilation fails
  */
 	public static boolean compileRiboseModel(String targetClassname, File ginrAutomataDirectory, File riboseModelFile)
 	throws ClassNotFoundException, ModelException {
@@ -94,7 +94,7 @@ public static IModel loadRiboseModel(File riboseModelFile)
 	 *
 	 * @param target the target instance to bind to the transductor
 	 * @return a new transductor
-	 * @throws ModelException on error
+	 * @throws ModelException if things don't work out
 	 * @see ITransductor
 	 */
 	ITransductor transductor(ITarget target)
@@ -123,7 +123,7 @@ ITransductor transductor(ITarget target)
 	 * @param in the input stream to transduce (eg, {@code System.in})
 	 * @param out the output stream to render output to (eg, {@code System.out})
 	 * @return true if transduction is complete, otherwise false
-	 * @throws RiboseException on error
+	 * @throws RiboseException if things don't work out
 	 */
 	boolean stream(Bytes transducer, Signal prologue, InputStream in, OutputStream out)
 	throws RiboseException;
@@ -139,7 +139,7 @@ boolean stream(Bytes transducer, Signal prologue, InputStream in, OutputStream o
 	 * @param in the input stream to transduce (eg, {@code System.in})
 	 * @param out the output stream to render output to (eg, {@code System.out})
 	 * @return true if target is an instance of the model target class and transduction is complete
-	 * @throws RiboseException on error
+	 * @throws RiboseException if things don't work out
 	 */
 	boolean stream(Bytes transducer, ITarget target, Signal prologue, InputStream in, OutputStream out)
 	throws RiboseException;
@@ -148,7 +148,7 @@ boolean stream(Bytes transducer, ITarget target, Signal prologue, InputStream in
 	 * Decompile a transducer to System.out
 	 * 
 	 * @param transducerName the transducer name as aUnicode string
-	 * @throws ModelException on error
+	 * @throws ModelException if things don't work out
 	 */
 	void decompile(String transducerName)
 	throws ModelException;
@@ -163,7 +163,7 @@ void decompile(String transducerName)
 	/**
 	 * Close the runtime model and file.
 	 *
-	 * @throws ModelException on error
+	 * @throws ModelException if things don't work out
 	 */
 	@Override
 	void close()

src/com/characterforming/ribose/IOutput.java

@@ -73,7 +73,7 @@ public interface IOutput {
 	 *
 	 * @param fieldName the name of the field (UTF-8 bytes, withouy `~` prefix in lead byte)
 	 * @return a field instance or null
-	 * @throws TargetBindingException on error
+	 * @throws TargetBindingException if things don't work out
 	 */
 	IField getField(Bytes fieldName) throws TargetBindingException;
 
@@ -82,7 +82,7 @@ public interface IOutput {
 	 *
 	 * @param fieldName the name of the field (UTF-8 bytes, without `~` prefix in lead byte)
 	 * @return the ordinal number of the field
-	 * @throws TargetBindingException on error
+	 * @throws TargetBindingException if things don't work out
 	 */
 	int getFieldOrdinal(Bytes fieldName) throws TargetBindingException;
 

src/com/characterforming/ribose/IParameterizedEffector.java

@@ -105,7 +105,7 @@ public interface IParameterizedEffector<T extends ITarget, P> extends IEffector<
 	 *
 	 * @param parameterIndex the index of the parameter object to be applied
 	 * @return user-defined effectors should return 0 (RTX_SI)
-	 * @throws EffectorException on error
+	 * @throws EffectorException if things don't work out
 	 */
 	int invoke(int parameterIndex) throws EffectorException;
 
@@ -124,7 +124,7 @@ public interface IParameterizedEffector<T extends ITarget, P> extends IEffector<
 	 *
 	 * @param parameterTokens an array of parameters, where each parameter is an array of bytes.
 	 * @return the compiled parameter value object
-	 * @throws TargetBindingException on error
+	 * @throws TargetBindingException if things don't work out
 	 */
 	P compileParameter(IToken[] parameterTokens) throws TargetBindingException;
 

src/com/characterforming/ribose/ITarget.java

@@ -92,7 +92,7 @@ public interface ITarget {
 	 * the interaction is driven from an effector invokation.
 	 *
 	 * @return an array of IEffector instances bound to the target instance
-	 * @throws TargetBindingException on error
+	 * @throws TargetBindingException if things don't work out
 	 */
 	IEffector<?>[] getEffectors() throws TargetBindingException;
 }

src/com/characterforming/ribose/ITransductor.java

@@ -314,7 +314,7 @@ public void update(Metrics accumulator) {
 	 *
 	 * @param transducer the name of the transducer to push
 	 * @return this ITransductor
-	 * @throws ModelException on error
+	 * @throws ModelException if things don't work out
 	 */
 	ITransductor start(Bytes transducer) throws ModelException;
 
@@ -339,8 +339,8 @@ public void update(Metrics accumulator) {
 	 * if the transduction involves backtracking with mark/reset.
 	 *
 	 * @return this ITransductor
-	 * @throws EffectorException on error
-	 * @throws DomainErrorException on error
+	 * @throws EffectorException if an effector invocation fails
+	 * @throws DomainErrorException if no transition defined for current input
 	 * @see #recycle(byte[])
 	 * @see #status()
 	 */

src/com/characterforming/ribose/Ribose.java

@@ -323,7 +323,7 @@ private static boolean execDecompile(final String[] args) {
 		} catch (ModelException e) {
 			final String format = "Failed to decompile %1$s";
 			rteLogger.log(Level.SEVERE, e, () -> String.format(format,
-					transducerName));
+				transducerName));
 		} finally {
 			Base.endLogging();
 		}

src/com/characterforming/ribose/base/BaseParameterizedEffector.java

@@ -101,7 +101,6 @@ public final void setParameters(IParameterizedEffector<?,?> proxyEffector) {
 		assert proxyEffector instanceof BaseParameterizedEffector<?,?>;
 		if (proxyEffector instanceof BaseParameterizedEffector<?,?> proxy) {
 			this.parameters = (P[])proxy.parameters;
-			this.tokens = proxy.tokens;
 		}
 	}