Adding javadoc and increasing unit test coverage.

core/pom.xml

@@ -37,6 +37,11 @@
   </build>
 
   <dependencies>
+    <dependency>
+      <groupId>junit</groupId>
+      <artifactId>junit</artifactId>
+      <scope>test</scope>
+    </dependency>
     <dependency>
       <groupId>org.apache.spark</groupId>
       <artifactId>spark-core_${scala.version.prefix}</artifactId>

core/src/main/java/org/bdgenomics/cannoli/util/CommandBuilder.java

@@ -57,20 +57,44 @@ abstract class CommandBuilder<C extends CommandBuilder> {
     private final List<String> arguments = new ArrayList<String>();
 
 
+    /**
+     * Add one or more arguments to the list of command arguments for this command builder.
+     *
+     * @param arguments variable number of arguments to add, must not be null
+     * @return this command builder
+     */
     public final C add(final String... arguments) {
         return addArguments(arguments);
     }
 
+    /**
+     * Add one or more arguments to the list of command arguments for this command builder.
+     *
+     * @param arguments arguments to add, must not be null
+     * @return this command builder
+     */
     public final C add(final Iterable<String> arguments) {
         return addArguments(arguments);
     }
 
+    /**
+     * Add an argument to the list of command arguments for this command builder.
+     *
+     * @param argument argument to add, must not be null
+     * @return this command builder
+     */
     public final C addArgument(final String argument) {
         checkNotNull(argument);
         arguments.add(argument);
         return (C) this;
     }
 
+    /**
+     * Add one or more arguments to the list of command arguments for this command builder.
+     *
+     * @param arguments variable number of arguments to add, must not be null
+     * @return this command builder
+     */
     public final C addArguments(final String... arguments) {
         checkNotNull(arguments);
         for (String argument : arguments) {
@@ -79,6 +103,12 @@ public final C addArguments(final String... arguments) {
         return (C) this;
     }
 
+    /**
+     * Add one or more arguments to the list of command arguments for this command builder.
+     *
+     * @param arguments arguments to add, must not be null
+     * @return this command builder
+     */
     public final C addArguments(final Iterable<String> arguments) {
         checkNotNull(arguments);
         for (String argument : arguments) {
@@ -87,25 +117,50 @@ public final C addArguments(final Iterable<String> arguments) {
         return (C) this;
     }
 
+    /**
+     * Add an environment variable to the map of environment variables for this command builder.
+     *
+     * @param variable environment variable to add, must not be null
+     * @param value environment variable value to add, must not be null
+     * @return this command builder
+     */
     public final C addEnvironment(final String variable, final String value) {
         checkNotNull(variable);
         checkNotNull(value);
         environment.put(variable, value);
         return (C) this;
     }
 
+    /**
+     * Add environment variables to the map of environment variables for this command builder.
+     *
+     * @param environment environment variables to add, must not be null
+     * @return this command builder
+     */
     public final C addEnvironment(final Map<String, String> environment) {
         checkNotNull(environment);
         this.environment.putAll(environment);
         return (C) this;
     }
 
+    /**
+     * Add a file to the list of files to make available locally for this command builder.
+     *
+     * @param file file to add, must not be null
+     * @return this command builder
+     */
     public final C addFile(final String file) {
         checkNotNull(file);
         files.add(file);
         return (C) this;
     }
 
+    /**
+     * Add zero or more files to the list of files to make available locally for this command builder.
+     *
+     * @param files variable number of files to add, must not be null
+     * @return this command builder
+     */
     public final C addFiles(final String... files) {
         checkNotNull(files);
         for (String file : files) {
@@ -114,6 +169,12 @@ public final C addFiles(final String... files) {
         return (C) this;
     }
 
+    /**
+     * Add files to the list of files to make available locally for this command builder.
+     *
+     * @param files files to add, must not be null
+     * @return this command builder
+     */
     public final C addFiles(final Iterable<String> files) {
         checkNotNull(files);
         for (String file : files) {
@@ -122,60 +183,128 @@ public final C addFiles(final Iterable<String> files) {
         return (C) this;
     }
 
+    /**
+     * Set the executable for this command builder.
+     *
+     * @param executable executable, must not be null
+     * @return this command builder
+     */
     public final C setExecutable(final String executable) {
         checkNotNull(executable);
         this.executable = executable;
         return (C) this;
     }
 
-    public final C setTimeout(@Nullable final Integer seconds) {
+    /**
+     * Set how long to let a single partition run for, in seconds, for this builder.
+     *
+     * @param timeout how long to let a single partition run for, in seconds
+     * @return this command builder
+     */
+    public final C setTimeout(@Nullable final Long timeout) {
         this.timeout = timeout;
         return (C) this;
     }
 
+    /**
+     * Set how long to let a single partition run for, in the specified time unit, for this builder.
+     *
+     * @param duration duration
+     * @param timeUnit time unit, must not be null
+     * @return this command builder
+     */
     public final C setTimeout(final long duration, final TimeUnit timeUnit) {
         checkNotNull(timeUnit);
         this.timeout = timeUnit.toSeconds(duration);
         return (C) this;
     }
 
+    /**
+     * Set the number of bases to flank each command invocation by for this builder.
+     *
+     * @param flankSize number of bases to flank each command invocation by
+     * @return this command builder
+     */
     public final C setFlankSize(@Nullable final Integer flankSize) {
         this.flankSize = flankSize;
         return (C) this;
     }
 
+    /**
+     * Return an immutable map of environment variables for this command builder.
+     *
+     * @return an immutable map of environment variables for this command builder
+     */
     public final Map<String, String> getEnvironment() {
         return ImmutableMap.copyOf(environment);
     }
 
+    /**
+     * Return an immutable list of files to make available locally for this command builder.
+     *
+     * @return an immutable list of files to make available locally for this command builder
+     */
     public final List<String> getFiles() {
         return ImmutableList.copyOf(files);
     }
 
+    /**
+     * Return how long to let a single partition run for, in seconds, for this builder.  May be null.
+     *
+     * @return how long to let a single partition run for, in seconds, for this builder
+     */
     public final Long getTimeout() {
         return timeout;
     }
 
+    /**
+     * Return how long to let a single partition run for, in seconds, for this builder, as an optional.
+     *
+     * @return how long to let a single partition run for, in seconds, for this builder, as an optional
+     */
     public final Optional<Long> getOptTimeout() {
         return Optional.ofNullable(timeout);
     }
 
+    /**
+     * Return the number of bases to flank each command invocation by for this builder.  May be null.
+     *
+     * @return the number of bases to flank each command invocation by for this builder
+     */
     public final Integer getFlankSize() {
         return flankSize;
     }
 
+    /**
+     * Return the number of bases to flank each command invocation by for this builder, as an optional.
+     *
+     * @return the number of bases to flank each command invocation by for this builder, as an optional
+     */
     public final Optional<Integer> getOptFlankSize() {
         return Optional.ofNullable(flankSize);
     }
 
+    /**
+     * Return the executable for this command builder.
+     *
+     * @return the executable for this command builder
+     */
     public final String getExecutable() {
         return executable;
     }
 
+    /**
+     * Return an immutable list of command arguments for this command builder.
+     *
+     * @return an immutable list of command arguments for this command builder
+     */
     public final List<String> getArguments() {
         return ImmutableList.copyOf(arguments);
     }
 
+    /**
+     * Reset the values in this command builder.  Call this method in <code>reset()</code> in subclasses.
+     */
     protected final void resetCommandBuilder() {
         environment.clear();
         files.clear();
@@ -185,6 +314,19 @@ protected final void resetCommandBuilder() {
         arguments.clear();
     }
 
+    /**
+     * Reset this command builder.
+     *
+     * @return this command builder
+     */
     public abstract C reset();
+
+    /**
+     * Build and return the command for this command builder as a list of strings.
+     *
+     * @return the command for this command builder as a list of strings.
+     * @throws IllegalStateException if this builder is in an illegal state, e.g.
+     *    if required values are not set
+     */
     public abstract List<String> build();
 }