Java Code Examples for com.martiansoftware.jsap.JSAPResult#getBoolean()

public static void main(String[] args) throws IOException, JSAPException {

	SimpleJSAP jsap = new SimpleJSAP(GZIPArchiveReader.class.getName(), "Writes some random records on disk.",
		new Parameter[] {
			new Switch("fully", 'f', "fully",
				"Whether to read fully the record (and do a minimal cosnsistency check)."),
			new UnflaggedOption("path", JSAP.STRING_PARSER, JSAP.NO_DEFAULT, JSAP.REQUIRED, JSAP.NOT_GREEDY,
				"The path to read from."), });

	JSAPResult jsapResult = jsap.parse(args);
	if (jsap.messagePrinted())
	    System.exit(1);

	final boolean fully = jsapResult.getBoolean("fully");
	GZIPArchiveReader gzar = new GZIPArchiveReader(new FileInputStream(jsapResult.getString("path")));
	for (;;) {
	    ReadEntry e = gzar.getEntry();
	    if (e == null)
		break;
	    InputStream inflater = e.lazyInflater.get();
	    if (fully)
		ByteStreams.toByteArray(inflater);
	    e.lazyInflater.consume();
	    System.out.println(e);
	}
    }
 

public static void main( final String[] arg ) throws IOException, JSAPException, NoSuchMethodException {
	
	final SimpleJSAP jsap = new SimpleJSAP( FrontCodedStringList.class.getName(), "Builds a front-coded string list reading from standard input a newline-separated ordered list of terms.",
			new Parameter[] {
				new FlaggedOption( "bufferSize", IntSizeStringParser.getParser(), "64Ki", JSAP.NOT_REQUIRED, 'b',  "buffer-size", "The size of the I/O buffer used to read terms." ),
				new FlaggedOption( "encoding", ForNameStringParser.getParser( Charset.class ), "UTF-8", JSAP.NOT_REQUIRED, 'e', "encoding", "The term file encoding." ),
				new FlaggedOption( "ratio", IntSizeStringParser.getParser(), "4", JSAP.NOT_REQUIRED, 'r',  "ratio", "The compression ratio." ),
				new Switch( "utf8", 'u', "utf8", "Store the strings as UTF-8 byte arrays." ),
				new Switch( "zipped", 'z', "zipped", "The term list is compressed in gzip format." ),
				new UnflaggedOption( "frontCodedList", JSAP.STRING_PARSER, JSAP.NO_DEFAULT, JSAP.REQUIRED, JSAP.NOT_GREEDY, "The filename for the serialised front-coded list." )
	});
	
	JSAPResult jsapResult = jsap.parse( arg );
	if ( jsap.messagePrinted() ) return;
	
	final int bufferSize = jsapResult.getInt( "bufferSize" );
	final int ratio = jsapResult.getInt( "ratio" );
	final boolean utf8 = jsapResult.getBoolean( "utf8" );
	final boolean zipped = jsapResult.getBoolean( "zipped" );
	final String listName = jsapResult.getString( "frontCodedList" );
	final Charset encoding = (Charset)jsapResult.getObject( "encoding" );
	
	final ProgressLogger pl = new ProgressLogger();
	pl.itemsName = "words";
	pl.start( "Reading words..." );
	final FrontCodedStringList frontCodedStringList = new FrontCodedStringList( new LineIterator( new FastBufferedReader( 
			new InputStreamReader( zipped ? new GZIPInputStream( System.in ) : System.in, encoding ), bufferSize ), pl ), ratio, utf8 );
	pl.done();

	System.err.print( "Writing to file..." );
	BinIO.storeObject( frontCodedStringList, listName );
	System.err.println( " done." );
}
 

public static void main(String[] args) throws JSAPException, IOException, InterruptedException {
	final SimpleJSAP jsap = new SimpleJSAP(RandomReadWritesTest.class.getName(), "Writes some random records on disk.",
		new Parameter[] {
			new FlaggedOption("random", JSAP.INTEGER_PARSER, "100", JSAP.NOT_REQUIRED, 'r', "random", "The number of random record to sample from."),
			new FlaggedOption("body", JSAP.INTSIZE_PARSER, "4K", JSAP.NOT_REQUIRED, 'b', "body", "The maximum size of the random generated body (in bytes)."),
			new Switch("fully", 'f', "fully", "Whether to read fully the record (and do a minimal sequential cosnsistency check)."),
			new Switch("writeonly", 'w', "writeonly", "Whether to skip the read part (if present, 'fully' will be ignored."),
			new UnflaggedOption("path", JSAP.STRING_PARSER, JSAP.NO_DEFAULT, JSAP.REQUIRED, JSAP.NOT_GREEDY, "The path to write to."),
			new UnflaggedOption("records", JSAP.INTSIZE_PARSER, JSAP.NO_DEFAULT, JSAP.REQUIRED, JSAP.NOT_GREEDY, "The numer of records to write."),
	});

	final JSAPResult jsapResult = jsap.parse(args);
	if (jsap.messagePrinted()) System.exit(1);

	final String path = jsapResult.getString("path");
	final boolean compress = path.endsWith(".gz");
	final boolean fully = jsapResult.getBoolean("fully");
	final int parallel = compress ? 1 : 0;

	final int body = jsapResult.getInt("body");

	final WarcRecord[] rnd = prepareRndRecords(jsapResult.getInt("random"), RESPONSE_PROBABILITY, MAX_NUMBER_OF_HEADERS, MAX_LENGTH_OF_HEADER, body);
	final int[] sequence = writeRecords(path, jsapResult.getInt("records"), rnd, parallel);
	if (! jsapResult.getBoolean("writeonly"))
		readRecords(path, sequence, body, fully, compress);

}
 

@SuppressWarnings("unchecked")
public static void main( final String[] arg ) throws NoSuchMethodException, IOException, JSAPException, ClassNotFoundException {

	final SimpleJSAP jsap = new SimpleJSAP( ShiftAddXorSignedStringMap.class.getName(), "Builds a shift-add-xor signed string map by reading a newline-separated list of strings and a function built on the same list of strings.",
			new Parameter[] {
		new FlaggedOption( "bufferSize", JSAP.INTSIZE_PARSER, "64Ki", JSAP.NOT_REQUIRED, 'b',  "buffer-size", "The size of the I/O buffer used to read strings." ),
		new FlaggedOption( "encoding", ForNameStringParser.getParser( Charset.class ), "UTF-8", JSAP.NOT_REQUIRED, 'e', "encoding", "The string file encoding." ),
		new Switch( "zipped", 'z', "zipped", "The string list is compressed in gzip format." ),
		new FlaggedOption( "width", JSAP.INTEGER_PARSER, Integer.toString( Integer.SIZE ), JSAP.NOT_REQUIRED, 'w', "width", "The signature width in bits." ),
		new UnflaggedOption( "function", JSAP.STRING_PARSER, JSAP.NO_DEFAULT, JSAP.REQUIRED, JSAP.NOT_GREEDY, "The filename of the function to be signed." ),
		new UnflaggedOption( "map", JSAP.STRING_PARSER, JSAP.NO_DEFAULT, JSAP.REQUIRED, JSAP.NOT_GREEDY, "The filename of the resulting serialised signed string map." ),
		new UnflaggedOption( "stringFile", JSAP.STRING_PARSER, JSAP.NO_DEFAULT, JSAP.NOT_REQUIRED, JSAP.NOT_GREEDY, "Read strings from this file instead of standard input." ),
	});

	JSAPResult jsapResult = jsap.parse( arg );
	if ( jsap.messagePrinted() ) return;

	final int bufferSize = jsapResult.getInt( "bufferSize" );
	final String functionName = jsapResult.getString( "function" );
	final String mapName = jsapResult.getString( "map" );
	final String stringFile = jsapResult.getString( "stringFile" );
	final Charset encoding = (Charset)jsapResult.getObject( "encoding" );
	final int width = jsapResult.getInt( "width" );
	final boolean zipped = jsapResult.getBoolean( "zipped" );

	final InputStream inputStream = stringFile != null ? new FileInputStream( stringFile ) : System.in;
	final Iterator<MutableString> iterator = new LineIterator( new FastBufferedReader( new InputStreamReader( zipped ? new GZIPInputStream( inputStream ) : inputStream, encoding ), bufferSize ) );
	final Object2LongFunction<CharSequence> function = (Object2LongFunction<CharSequence>)BinIO.loadObject( functionName );
	LOGGER.info( "Signing..." );
	BinIO.storeObject( new ShiftAddXorSignedStringMap( iterator, function, width ), mapName );
	LOGGER.info( "Completed." );
}
 

public static void main( final String[] arg ) throws IOException, ClassNotFoundException, JSAPException {

		SimpleJSAP jsap = new SimpleJSAP( PermutedFrontCodedStringList.class.getName(), "Builds a permuted front-coded list of strings using a given front-coded string list and permutation",  
				new Parameter[] {
					new Switch( "invert", 'i', "invert", "Invert permutation before creating the permuted list." ),
					new UnflaggedOption( "list", JSAP.STRING_PARSER, JSAP.REQUIRED, "A front-coded string list." ),
					new UnflaggedOption( "permutation", JSAP.STRING_PARSER, JSAP.REQUIRED, "A permutation for the indices of the list." ),
					new UnflaggedOption( "permutedList", JSAP.STRING_PARSER, JSAP.REQUIRED, "A the filename for the resulting permuted list." ),
			} );

		JSAPResult jsapResult = jsap.parse( arg ); 
		if ( jsap.messagePrinted() ) return;
		
		int[] basePermutation =  BinIO.loadInts( jsapResult.getString( "permutation" ) ), permutation;
		if ( jsapResult.getBoolean( "invert" ) ) {
			int i = basePermutation.length;
			permutation = new int[ i ];
			while( i-- != 0 ) permutation[ basePermutation[ i ] ] = i;
		}
		else permutation = basePermutation;
		
		basePermutation = null;
		
		BinIO.storeObject( 
				new PermutedFrontCodedStringList( (FrontCodedStringList)BinIO.loadObject( jsapResult.getString( "list" ) ), permutation ), 
				jsapResult.getString( "permutedList" ) 
		);
	}
 

@SuppressWarnings("unchecked")
public static void main( final String[] arg ) throws IOException, JSAPException, ClassNotFoundException, SecurityException, NoSuchMethodException {

	final SimpleJSAP jsap = new SimpleJSAP( LiterallySignedStringMap.class.getName(), "Builds a shift-add-xor signed string map by reading a newline-separated list of strings and a function built on the same list of strings.",
			new Parameter[] {
		new FlaggedOption( "encoding", ForNameStringParser.getParser( Charset.class ), "UTF-8", JSAP.NOT_REQUIRED, 'e', "encoding", "The string file encoding." ),
		new Switch( "zipped", 'z', "zipped", "The string list is compressed in gzip format." ),
		new Switch( "text", 't', "text", "The string list actually a text file, with one string per line." ),
		new UnflaggedOption( "function", JSAP.STRING_PARSER, JSAP.NO_DEFAULT, JSAP.REQUIRED, JSAP.NOT_GREEDY, "The filename of the function to be signed." ),
		new UnflaggedOption( "list", JSAP.STRING_PARSER, JSAP.NO_DEFAULT, JSAP.REQUIRED, JSAP.NOT_GREEDY, "The filename of the serialised list of strings, or of a text file containing a list of strings, if -t is specified." ),
		new UnflaggedOption( "map", JSAP.STRING_PARSER, JSAP.NO_DEFAULT, JSAP.REQUIRED, JSAP.NOT_GREEDY, "The filename of the resulting map." ),
	});

	JSAPResult jsapResult = jsap.parse( arg );
	if ( jsap.messagePrinted() ) return;

	final String functionName = jsapResult.getString( "function" );
	final String listName = jsapResult.getString( "list" );
	final String mapName = jsapResult.getString( "map" );

	
	final Charset encoding = (Charset)jsapResult.getObject( "encoding" );
	final boolean zipped = jsapResult.getBoolean( "zipped" );
	final boolean text = jsapResult.getBoolean( "text" );
	
	ObjectList<MutableString> list = text ? new FileLinesCollection( listName, encoding.toString(), zipped ).allLines() : (ObjectList)BinIO.loadObject( listName );
	
	LOGGER.info( "Signing..." );
	BinIO.storeObject( new LiterallySignedStringMap( (Object2LongFunction)BinIO.loadObject( functionName ), list ), mapName );
	LOGGER.info( "Completed." );
}
 

public static boolean getArgGitRepositoryFirstCommit(JSAPResult arguments) {
    return arguments.getBoolean("gitRepositoryFirstCommit");
}
 

public static boolean getArgHelp(JSAPResult arguments) {
    return arguments.getBoolean("help");
}
 

public static boolean getArgGitRepositoryMode(JSAPResult arguments) {
    return arguments.getBoolean("gitRepo");
}
 

public static boolean getArgNotifyEndProcess(JSAPResult arguments) {
    return arguments.getBoolean("notifyEndProcess");
}
 

public static boolean getArgCreatePR(JSAPResult arguments) {
    return arguments.getBoolean("createPR");
}
 

public static boolean gerArgCheckstyleMode(JSAPResult arguments) {
    return arguments.getBoolean("checkstyle");
}
 

public static boolean gerArgBearsMode(JSAPResult arguments) {
    return arguments.getBoolean("bears");
}
 

public static boolean getArgSmtpTLS(JSAPResult arguments) {
    return arguments.getBoolean("smtpTLS");
}
 

public static boolean getArgCreateOutputDir(JSAPResult arguments) {
    return arguments.getBoolean("createOutputDir");
}
 

public static boolean getArgSkipDelete(JSAPResult arguments) {
    return arguments.getBoolean("skipDelete");
}
 

@Override
public void initConfigWithJSAP(JSAP jsap, String[] inputArgs) {
       JSAPResult arguments = jsap.parse(inputArgs);
	if (LauncherUtils.getArgDebug(arguments)) {
           getConfig().setDebug(true);
       }
       getConfig().setClean(true);
       getConfig().setRunId(LauncherUtils.getArgRunId(arguments));
       getConfig().setGithubToken(LauncherUtils.getArgGithubOAuth(arguments));
       
       if (GitRepositoryLauncherUtils.getArgGitRepositoryMode(arguments)) {
           if (GitRepositoryLauncherUtils.getArgGitRepositoryFirstCommit(arguments)) {
               getConfig().setGitRepositoryFirstCommit(true);
           }
       } else {
           System.err.println("Error: Parameter 'gitrepo' is required in GIT_REPOSITORY launcher mode.");
       }
       
       if (LauncherUtils.getArgOutput(arguments) != null) {
           getConfig().setOutputPath(LauncherUtils.getArgOutput(arguments).getPath());
       }
       getConfig().setMongodbHost(LauncherUtils.getArgMongoDBHost(arguments));
       getConfig().setMongodbName(LauncherUtils.getArgMongoDBName(arguments));
       getConfig().setSmtpServer(LauncherUtils.getArgSmtpServer(arguments));
       getConfig().setSmtpPort(LauncherUtils.getArgSmtpPort(arguments));
       getConfig().setSmtpTLS(LauncherUtils.getArgSmtpTLS(arguments));
       getConfig().setSmtpUsername(LauncherUtils.getArgSmtpUsername(arguments));
       getConfig().setSmtpPassword(LauncherUtils.getArgSmtpPassword(arguments));
       getConfig().setNotifyTo(LauncherUtils.getArgNotifyto(arguments));

       if (LauncherUtils.getArgPushUrl(arguments) != null) {
           getConfig().setPush(true);
           getConfig().setPushRemoteRepo(LauncherUtils.getArgPushUrl(arguments));
       }
       getConfig().setCreatePR(LauncherUtils.getArgCreatePR(arguments));

       // we fork if we need to create a PR or if we need to notify
       if ((getConfig().isCreatePR() || (getConfig().getSmtpServer() != null && !getConfig().getSmtpServer().isEmpty() && getConfig().getNotifyTo() != null && getConfig().getNotifyTo().length > 0)) && getConfig().getGithubToken() != null) {
           getConfig().setFork(true);
       }

       if (arguments.getString("gitRepositoryUrl") == null) {
           System.err.println("Error: Parameter 'gitrepourl' is required in GIT_REPOSITORY launcher mode.");
       }

       if (getConfig().isGitRepositoryFirstCommit() && arguments.getString("gitRepositoryIdCommit") != null) {
           System.err.println("Error: Parameters 'gitrepofirstcommit' and 'gitrepoidcommit' cannot be used at the same time.");
       }

       getConfig().setGitRepositoryUrl(arguments.getString("gitRepositoryUrl"));
       getConfig().setGitRepositoryBranch(arguments.getString("gitRepositoryBranch"));
       getConfig().setGitRepositoryIdCommit(arguments.getString("gitRepositoryIdCommit"));
       

       getConfig().setZ3solverPath(new File(arguments.getString("z3")).getPath());
       getConfig().setWorkspacePath(arguments.getString("workspace"));
       if (arguments.getBoolean("tmpDirAsWorkSpace")) {
           tempDir = com.google.common.io.Files.createTempDir();
           getConfig().setWorkspacePath(tempDir.getAbsolutePath());
           getConfig().setOutputPath(tempDir.getAbsolutePath());
           getConfig().setZ3solverPath(new File(tempDir.getAbsolutePath() + File.separator + "z3_for_linux").getPath());
       }

       getConfig().setGithubUserEmail(LauncherUtils.getArgGithubUserEmail(arguments));
       getConfig().setGithubUserName(LauncherUtils.getArgGithubUserName(arguments));
       getConfig().setListenerMode(arguments.getString("listenermode"));
       getConfig().setActiveMQUrl(arguments.getString("activemqurl"));
       getConfig().setActiveMQListenQueueName(arguments.getString("activemqlistenqueuename"));

       getConfig().setGitUrl(arguments.getString("giturl"));
       getConfig().setGitBranch(arguments.getString("gitbranch"));
       getConfig().setGitCommitHash(arguments.getString("gitcommithash"));
       getConfig().setMavenHome(arguments.getString("MavenHome"));

       if (arguments.getFile("projectsToIgnore") != null) {
           getConfig().setProjectsToIgnoreFilePath(arguments.getFile("projectsToIgnore").getPath());
       }

       getConfig().setRepairTools(new HashSet<>(Arrays.asList(arguments.getStringArray("repairTools"))));
       
       // Make sure that it is a multiple of three in the list
       if((arguments.getStringArray("experimentalPluginRepoList").length) % 3 == 0) {
           getConfig().setExperimentalPluginRepoList(arguments.getStringArray("experimentalPluginRepoList"));
       } else if (arguments.getStringArray("experimentalPluginRepoList").length != 0) {
           LOGGER.warn("The experimental plugin repo list is not correctly formed."
                   + " Please make sure you have provided id, name and url for all repos. "
                   + "Repairnator will continue without these repos.");
           getConfig().setExperimentalPluginRepoList(null);
       } else {
           getConfig().setExperimentalPluginRepoList(null);
       }
}
 

protected void initConfig(JSAPResult arguments) {
    if (LauncherUtils.getArgDebug(arguments)) {
        this.getConfig().setDebug(true);
    }
    this.getConfig().setClean(true);
    this.getConfig().setRunId(LauncherUtils.getArgRunId(arguments));
    this.getConfig().setGithubToken(LauncherUtils.getArgGithubOAuth(arguments));
    if (LauncherUtils.gerArgBearsMode(arguments)) {
        this.getConfig().setLauncherMode(LauncherMode.BEARS);
    } else if (LauncherUtils.gerArgCheckstyleMode(arguments)) {
        this.getConfig().setLauncherMode(LauncherMode.CHECKSTYLE);
    } else {
        this.getConfig().setLauncherMode(LauncherMode.REPAIR);
    }
    if (LauncherUtils.getArgOutput(arguments) != null) {
        this.getConfig().setOutputPath(LauncherUtils.getArgOutput(arguments).getPath());
    }
    this.getConfig().setMongodbHost(LauncherUtils.getArgMongoDBHost(arguments));
    this.getConfig().setMongodbName(LauncherUtils.getArgMongoDBName(arguments));
    this.getConfig().setSmtpServer(LauncherUtils.getArgSmtpServer(arguments));
    this.getConfig().setSmtpPort(LauncherUtils.getArgSmtpPort(arguments));
    this.getConfig().setSmtpTLS(LauncherUtils.getArgSmtpTLS(arguments));
    this.getConfig().setSmtpUsername(LauncherUtils.getArgSmtpUsername(arguments));
    this.getConfig().setSmtpPassword(LauncherUtils.getArgSmtpPassword(arguments));
    this.getConfig().setNotifyTo(LauncherUtils.getArgNotifyto(arguments));

    if (LauncherUtils.getArgPushUrl(arguments) != null) {
        this.getConfig().setPush(true);
        this.getConfig().setPushRemoteRepo(LauncherUtils.getArgPushUrl(arguments));
    }
    this.getConfig().setCreatePR(LauncherUtils.getArgCreatePR(arguments));

    // we fork if we need to create a PR or if we need to notify (but only when we have a git token)
    if (this.getConfig().isCreatePR() || (this.getConfig().getSmtpServer() != null && !this.getConfig().getSmtpServer().isEmpty() && this.getConfig().getNotifyTo() != null && this.getConfig().getNotifyTo().length > 0 && this.getConfig().getGithubToken() != null)) {
        this.getConfig().setFork(true);
    }
    this.getConfig().setBuildId(arguments.getInt("build"));
    if (this.getConfig().getLauncherMode() == LauncherMode.BEARS) {
        this.getConfig().setNextBuildId(arguments.getInt("nextBuild"));
    }
    this.getConfig().setZ3solverPath(new File(arguments.getString("z3")).getPath());
    this.getConfig().setWorkspacePath(arguments.getString("workspace"));
    if (arguments.getBoolean("tmpDirAsWorkSpace")) {
        this.tempDir = com.google.common.io.Files.createTempDir();
        this.getConfig().setWorkspacePath(this.tempDir.getAbsolutePath());
        this.getConfig().setOutputPath(this.tempDir.getAbsolutePath());
        this.getConfig().setZ3solverPath(new File(this.tempDir.getAbsolutePath() + File.separator + "z3_for_linux").getPath());
    }

    this.getConfig().setGithubUserEmail(LauncherUtils.getArgGithubUserEmail(arguments));
    this.getConfig().setGithubUserName(LauncherUtils.getArgGithubUserName(arguments));
    this.getConfig().setListenerMode(arguments.getString("listenermode"));
    this.getConfig().setActiveMQUrl(arguments.getString("activemqurl"));
    this.getConfig().setActiveMQListenQueueName(arguments.getString("activemqlistenqueuename"));
    this.getConfig().setActiveMQUsername(arguments.getString("activemqusername"));
    this.getConfig().setActiveMQPassword(arguments.getString("activemqpassword"));

    this.getConfig().setGitUrl(arguments.getString("giturl"));
    this.getConfig().setGitBranch(arguments.getString("gitbranch"));
    this.getConfig().setGitCommitHash(arguments.getString("gitcommithash"));
    this.getConfig().setMavenHome(arguments.getString("MavenHome"));

    this.getConfig().setNoTravisRepair(arguments.getBoolean("noTravisRepair"));

    if (arguments.getFile("projectsToIgnore") != null) {
        this.getConfig().setProjectsToIgnoreFilePath(arguments.getFile("projectsToIgnore").getPath());
    }

    this.getConfig().setRepairTools(new HashSet<>(Arrays.asList(arguments.getStringArray("repairTools"))));
    if (this.getConfig().getLauncherMode() == LauncherMode.REPAIR) {
        LOGGER.info("The following repair tools will be used: " + StringUtils.join(this.getConfig().getRepairTools(), ", "));
    }

    // Make sure that it is a multiple of three in the list
    if((arguments.getStringArray("experimentalPluginRepoList").length) % 3 == 0) {
        this.getConfig().setExperimentalPluginRepoList(arguments.getStringArray("experimentalPluginRepoList"));
    } else if (arguments.getStringArray("experimentalPluginRepoList").length != 0) {
        LOGGER.warn("The experimental plugin repo list is not correctly formed."
                + " Please make sure you have provided id, name and url for all repos. "
                + "Repairnator will continue without these repos.");
        this.getConfig().setExperimentalPluginRepoList(null);
    } else {
        this.getConfig().setExperimentalPluginRepoList(null);
    }
}
 

@SuppressWarnings("unchecked")
public static void main( final String[] arg ) throws ClassNotFoundException, IOException, JSAPException, SecurityException, NoSuchMethodException {

	final SimpleJSAP jsap = new SimpleJSAP( ImmutableExternalPrefixMap.class.getName(), "Builds an external map reading from standard input a newline-separated list of terms or a serialised term list. If the dump stream name is not specified, the map will be self-contained.", 
			new Parameter[] {
				new FlaggedOption( "blockSize", JSAP.INTSIZE_PARSER, ( STD_BLOCK_SIZE / 1024 ) + "Ki", JSAP.NOT_REQUIRED, 'b', "block-size", "The size of a block in the dump stream." ),
				new Switch( "serialised", 's', "serialised", "The data source (file or standard input) provides a serialised java.util.List of terms." ),
				new Switch( "zipped", 'z', "zipped", "Standard input is compressed in gzip format." ),
				new FlaggedOption( "termFile", JSAP.STRING_PARSER, JSAP.NO_DEFAULT, JSAP.NOT_REQUIRED, 'o', "offline", "Read terms from this file instead of standard input." ),					
				new FlaggedOption( "encoding", ForNameStringParser.getParser( Charset.class ), "UTF-8", JSAP.NOT_REQUIRED, 'e', "encoding", "The term list encoding." ),
				new UnflaggedOption( "map", JSAP.STRING_PARSER, JSAP.NO_DEFAULT, JSAP.REQUIRED, JSAP.NOT_GREEDY, "The filename for the serialised map." ),
				new UnflaggedOption( "dump", JSAP.STRING_PARSER, JSAP.NO_DEFAULT, JSAP.NOT_REQUIRED, JSAP.NOT_GREEDY, "An optional dump stream (the resulting map will not be self-contained)." )
		}
	);

	JSAPResult jsapResult = jsap.parse( arg );
	if ( jsap.messagePrinted() ) return;
	
	Collection<? extends CharSequence> termList;
	
	final String termFile = jsapResult.getString( "termFile" );
	final Charset encoding = (Charset)jsapResult.getObject( "encoding" );
	final boolean zipped = jsapResult.getBoolean( "zipped" );
	final boolean serialised = jsapResult.getBoolean( "serialised" );

	if ( zipped && serialised ) throw new IllegalArgumentException( "The zipped and serialised options are incompatible" );

	if ( serialised ) termList = (List<? extends CharSequence>) ( termFile != null ? BinIO.loadObject( termFile ) : BinIO.loadObject( System.in ) );
	else {
		if ( termFile != null ) termList = new FileLinesCollection( termFile, encoding.name(), zipped );
		else {
			final ObjectArrayList<MutableString> list = new ObjectArrayList<MutableString>();
			termList = list;
			final FastBufferedReader terms = new FastBufferedReader( new InputStreamReader( 
					zipped ? new GZIPInputStream( System.in ) : System.in, encoding.name() ) );
			final MutableString term = new MutableString();
			while( terms.readLine( term ) != null ) list.add( term.copy() );
			terms.close();
		}
	}

	BinIO.storeObject( new ImmutableExternalPrefixMap( termList, jsapResult.getInt( "blockSize" ), jsapResult.getString( "dump" ) ), jsapResult.getString( "map" ) );
}
 

private static boolean isGeneResamplign(JSAPResult config) {
	return config.getBoolean("gene-sampling") || config.getBoolean("gene-only") ;
}