Examples with Arguments dr.app.util.Arguments used on opensource projects

Example 31 with Arguments

use of dr.app.util.Arguments in project beast-mcmc by beast-dev.

the class AncestralSequenceAnnotator method main.

//Main method
public static void main(String[] args) throws IOException {
    String targetTreeFileName = null;
    String inputFileName = null;
    String outputFileName = null;
    printTitle();
    Arguments arguments = new Arguments(new Arguments.Option[] { //new Arguments.StringOption("target", new String[] { "maxclade", "maxtree" }, false, "an option of 'maxclade' or 'maxtree'"),
    new Arguments.StringOption("heights", new String[] { "keep", "median", "mean" }, false, "an option of 'keep', 'median' or 'mean'"), new Arguments.IntegerOption("burnin", "the number of states to be considered as 'burn-in'"), new Arguments.StringOption("beastInput", new String[] { "true", "false" }, false, "If the input is taken from BEAST rather than BAli-Phy"), new Arguments.RealOption("limit", "the minimum posterior probability for a node to be annotated"), new Arguments.StringOption("target", "target_file_name", "specifies a user target tree to be annotated"), new Arguments.Option("help", "option to print this message"), new Arguments.StringOption("kalign", "full_path_to_kalign", "specifies full path to the kalign executable file") });
    try {
        arguments.parseArguments(args);
    } catch (Arguments.ArgumentException ae) {
        System.out.println(ae);
        printUsage(arguments);
        System.exit(1);
    }
    if (arguments.hasOption("help")) {
        printUsage(arguments);
        System.exit(0);
    }
    int heights = KEEP_HEIGHTS;
    if (arguments.hasOption("heights")) {
        String value = arguments.getStringOption("heights");
        if (value.equalsIgnoreCase("mean")) {
            heights = MEAN_HEIGHTS;
        } else if (value.equalsIgnoreCase("median")) {
            heights = MEDIAN_HEIGHTS;
        }
    }
    int burnin = -1;
    if (arguments.hasOption("burnin")) {
        burnin = arguments.getIntegerOption("burnin");
    }
    double posteriorLimit = 0.0;
    if (arguments.hasOption("limit")) {
        posteriorLimit = arguments.getRealOption("limit");
    }
    boolean beastInput = false;
    if (arguments.hasOption("beastInput") && arguments.getStringOption("beastInput").equals("true")) {
        SEQ_STRING = "states";
    }
    int target = MAX_CLADE_CREDIBILITY;
    if (arguments.hasOption("target")) {
        target = USER_TARGET_TREE;
        targetTreeFileName = arguments.getStringOption("target");
    }
    // String kalignExecutable = "/usr/local/bin/clustalw";
    String kalignExecutable = "/usr/local/bin/kalign";
    if (arguments.hasOption("kalign")) {
        kalignExecutable = arguments.getStringOption("kalign");
    }
    String[] args2 = arguments.getLeftoverArguments();
    if (args2.length > 2) {
        System.err.println("Unknown option: " + args2[2]);
        System.err.println();
        printUsage(arguments);
        System.exit(1);
    }
    if (args2.length == 2) {
        targetTreeFileName = null;
        inputFileName = args2[0];
        outputFileName = args2[1];
    } else {
        if (inputFileName == null) {
            // No input file name was given so throw up a dialog box...
            inputFileName = Utils.getLoadFileName("AncestralSequenceAnnotator " + version.getVersionString() + " - Select input file file to analyse");
        }
        if (outputFileName == null) {
            outputFileName = Utils.getSaveFileName("AncestralSequenceAnnotator " + version.getVersionString() + " - Select output file");
        }
    }
    if (inputFileName == null || outputFileName == null) {
        System.err.println("Missing input or output file name");
        printUsage(arguments);
        System.exit(1);
    }
    new AncestralSequenceAnnotator(burnin, heights, posteriorLimit, target, targetTreeFileName, inputFileName, outputFileName, kalignExecutable);
    System.exit(0);
}

Example 32 with Arguments

use of dr.app.util.Arguments in project beast-mcmc by beast-dev.

the class RootToTip method main.

//Main method
public static void main(String[] args) throws IOException {
    String inputFileName = null;
    String outputFileName = null;
    printTitle();
    Arguments arguments = new Arguments(new Arguments.Option[] { new Arguments.IntegerOption("burnin", "the number of trees to be ignored as 'burn-in' [default = 0]"), new Arguments.StringOption("dateorder", "date_order", "order of date field in taxon name: first, last, 1, 2 etc. [default = last]"), //                        new Arguments.StringOption("outgroup", "{taxon list}", "one or more taxa that will be used to root the tree(s) [default = find root]"),
    new Arguments.Option("keeproot", "keep the existing root of the input trees [default = estimate root]"), new Arguments.Option("writetree", "Write the optimally rooted tree to the output file"), new Arguments.Option("help", "option to print this message") });
    try {
        arguments.parseArguments(args);
    } catch (Arguments.ArgumentException ae) {
        System.out.println(ae);
        printUsage(arguments);
        System.exit(1);
    }
    if (arguments.hasOption("help")) {
        printUsage(arguments);
        System.exit(0);
    }
    int burnin = 0;
    if (arguments.hasOption("burnin")) {
        burnin = arguments.getIntegerOption("burnin");
    }
    String dateOrder = "LAST";
    if (arguments.hasOption("dateorder")) {
        dateOrder = arguments.getStringOption("dateorder").toUpperCase();
    }
    String outgroup = null;
    if (arguments.hasOption("outgroup")) {
        outgroup = arguments.getStringOption("dateorder").toUpperCase();
    }
    boolean keepRoot = arguments.hasOption("keeproot");
    boolean writeTree = arguments.hasOption("writetree");
    String[] args2 = arguments.getLeftoverArguments();
    if (args2.length > 2) {
        System.err.println("Unknown option: " + args2[2]);
        System.err.println();
        printUsage(arguments);
        System.exit(1);
    }
    if (args2.length == 0) {
        System.err.println("Missing input file name");
        printUsage(arguments);
        System.exit(1);
    }
    inputFileName = args2[0];
    if (args2.length == 2) {
        outputFileName = args2[1];
    }
    new RootToTip(burnin, dateOrder, keepRoot, outgroup, writeTree, inputFileName, outputFileName);
    System.exit(0);
}

Example 33 with Arguments

use of dr.app.util.Arguments in project beast-mcmc by beast-dev.

the class CheckPointUpdaterApp method main.

public static void main(String[] args) throws java.io.IOException {
    // There is a major issue with languages that use the comma as a decimal separator.
    // To ensure compatibility between programs in the package, enforce the US locale.
    Locale.setDefault(Locale.US);
    Arguments arguments = new Arguments(new Arguments.Option[] { new Arguments.StringOption("BEAST_XML", "FILENAME", "Specify a BEAST XML file"), new Arguments.StringOption("load_dump", "FILENAME", "Specify a filename to load a dumped state from"), new Arguments.StringOption("output_file", "FILENAME", "Specify a filename for the output file"), new Arguments.StringOption("update_choice", "UPDATECHOICE", "Specify a function by which to update the tree"), new Arguments.Option("help", "Print this information and stop") });
    try {
        arguments.parseArguments(args);
    } catch (Arguments.ArgumentException ae) {
        System.out.println();
        System.out.println(ae.getMessage());
        System.out.println();
        //printUsage(arguments);
        System.exit(1);
    }
    String inputFile = null;
    if (arguments.hasOption("BEAST_XML")) {
        inputFile = arguments.getStringOption("BEAST_XML");
    } else {
        throw new RuntimeException("No BEAST XML file specified.");
    }
    String debugStateFile;
    if (arguments.hasOption("load_dump")) {
        debugStateFile = arguments.getStringOption("load_dump");
        //pass on as argument
        System.setProperty(BeastCheckpointer.LOAD_STATE_FILE, debugStateFile);
    } else {
        throw new RuntimeException("No dump file specified.");
    }
    String choice = "";
    if (arguments.hasOption("update_choice")) {
        choice = arguments.getStringOption("update_choice");
    } else {
        throw new RuntimeException("Update mechanism needs to be specified.");
    }
    UpdateChoice chosen = null;
    for (UpdateChoice ch : UpdateChoice.values()) {
        if (choice.equals(ch.getName())) {
            chosen = ch;
            break;
        }
    }
    if (chosen == null) {
        throw new RuntimeException("Incorrect update mechanism specified.");
    }
    if (arguments.hasOption("output_file")) {
        String outputStateFile = arguments.getStringOption("output_file");
        //pass on as argument
        System.setProperty(BeastCheckpointer.SAVE_STATE_FILE, outputStateFile);
    } else {
        throw new RuntimeException("No output file specified.");
    }
    new CheckPointUpdaterApp(inputFile, debugStateFile, chosen);
    System.exit(0);
}

Example 34 with Arguments

use of dr.app.util.Arguments in project beast-mcmc by beast-dev.

the class RateIndicatorBF method main.

public static void main(String[] args) throws IOException {
    String inputFileName = null;
    String outputFileName = null;
    String locationsFileName = null;
    String[][] locations = null;
    boolean kml = false;
    boolean calculateRates = false;
    //red: 0000FF green: 00FF00 magenta: FF00FF white: FFFFFF yellow: 00FFFF cyan: FFFF00
    String lowerLinkColor = "FFFFFF";
    String upperLinkColor = "FF00FF";
    String KMLoutputFile = "KMLrates.kml";
    double branchWidthConstant = 2.5;
    double branchWidthMultiplier = 7.0;
    double altitudeFactor = 500;
    //Double width = 3.0;
    int burnin = -1;
    double meanPoissonPrior = 0.693;
    int offsetPoissonPrior = 0;
    int numberOfStates = 0;
    double cutoff = 3.0;
    // if false, we will use an indicator cut off value
    boolean bayesFactor = true;
    boolean rateSummary = false;
    String rateIndicatorString = "indicators";
    String actualRateString = "actualRates";
    String relativeRateString = "rates";
    String frequencyString = "frequencies";
    //this is for rate (dist/time) summaries
    String clockRateString = "clock.rate";
    String unitString = "year";
    Arguments arguments = new Arguments(new Arguments.Option[] { new Arguments.IntegerOption(BURNIN, "the number of states to be considered as 'burn-in' " + "[default = 0]"), new Arguments.StringOption(LOCATIONSFILE, "coordinates file", "a file with latitudes and " + "longitudes for each location (required for a kml output)"), //boolean for KML
    new Arguments.StringOption(KML, falseTrue, false, "generate a KML file including well-supported rates [default = false]"), new Arguments.StringOption(CALCULATERATES, falseTrue, false, "calculate the actual rates for well-supported transitions"), new Arguments.IntegerOption(LOCATIONSTATES, "the number of locations states used in the " + "analyses [requires a coordinates file if not provided]"), new Arguments.IntegerOption(POFFSET, "the offset of the (truncated) Poisson prior " + "[default=locations-1]"), new Arguments.RealOption(PMEAN, "the mean of the (truncated) Poisson prior  " + "[default=0.693 (log2)]"), new Arguments.RealOption(BFCUTOFF, "the Bayes Factor values above which we consider rates to " + "be well supported  [default=3.0]"), new Arguments.RealOption(ICUTOFF, "the indicator values above which we consider rates to be " + "well supported  [default uses a Bayes factor cut off of 3.0]"), new Arguments.StringOption(ISTRING, "indicator_string", "prefix string used for outputting " + "the rate indicators in the log file [default = indicators]"), new Arguments.StringOption(RSTRING, "relativeRate_string", "prefix string used for " + "outputting the relative rates in the log file [default = rates]"), new Arguments.StringOption(FSTRING, "frequencies_string", "prefix string used for outputting " + "the state frequencies in the log file [default = frequencies]"), new Arguments.StringOption(PSTRING, "rate*indicator_string", "prefix string used for " + "outputting the product statistic for rates*indicators [default = actualRates]"), new Arguments.StringOption(CSTRING, "clock_rate_string", "string used for outputting " + "the overall clock rate in the log file [default = clock.rate]"), new Arguments.StringOption(USTRING, "units_string", "string describing the time unit" + "[default = year]"), new Arguments.StringOption(KMLFILE, "KML output file", "KML output file name " + "[default=KMLrates.kml]"), new Arguments.StringOption(LOWCOLOR, "lower link strength color", "specifies an lower link " + "color for the links [default=FF00FF]"), new Arguments.StringOption(UPCOLOR, "upper link strength color", "specifies an upper link " + "color for the links [default=FFFF00]"), new Arguments.RealOption(BWC, "specifies the connection (rate) width constant [default=2.5]"), new Arguments.RealOption(BWM, "specifies the connection (rate)  width multiplier [default=7.0]"), new Arguments.RealOption(ALTITUDE, "specifies the altitude factor for the connections (rate) " + "[default=500]") });
    try {
        arguments.parseArguments(args);
    } catch (Arguments.ArgumentException ae) {
        progressStream.println(ae);
        printUsage(arguments);
        System.exit(1);
    }
    if (arguments.hasOption(HELP)) {
        printUsage(arguments);
        System.exit(0);
    }
    if (arguments.hasOption(BURNIN)) {
        burnin = arguments.getIntegerOption(BURNIN);
    }
    progressStream.println("Ignoring " + burnin + " states as burn-in");
    if (arguments.hasOption(LOCATIONSTATES)) {
        numberOfStates = arguments.getIntegerOption(LOCATIONSTATES);
    }
    locationsFileName = arguments.getStringOption(LOCATIONSFILE);
    if (locationsFileName != null) {
        int[] counts = countLinesAndTokens(locationsFileName);
        //read in locations
        if (numberOfStates > 0) {
            if (numberOfStates != counts[0]) {
                System.err.println("number of states provided (" + numberOfStates + ") does not match lines in coordinates file (" + counts[0] + ") ??");
            }
        }
        locations = new String[counts[0]][counts[1]];
        readLocationsCoordinates(locationsFileName, locations);
        if (numberOfStates == 0) {
            numberOfStates = counts[0];
        }
    } else {
        if (numberOfStates == 0) {
            System.err.println("no states provided, nor coordinates file ??");
        }
    }
    String kmlBooleanString = arguments.getStringOption(KML);
    if (kmlBooleanString != null && kmlBooleanString.compareToIgnoreCase("true") == 0) {
        kml = true;
        if (locationsFileName == null) {
            System.err.println("you want a KML file without a coordinates file??");
        }
    }
    String ratesBooleanString = arguments.getStringOption(CALCULATERATES);
    if (ratesBooleanString != null && ratesBooleanString.compareToIgnoreCase("true") == 0) {
        calculateRates = true;
    }
    String kmlFileName = arguments.getStringOption(KMLFILE);
    if (kmlFileName != null) {
        KMLoutputFile = kmlFileName;
    }
    if (arguments.hasOption(PMEAN)) {
        meanPoissonPrior = arguments.getRealOption(PMEAN);
        progressStream.println("Poisson prior with mean " + meanPoissonPrior);
    } else {
        progressStream.println("Poisson prior with mean " + meanPoissonPrior + " (default)");
    }
    if (arguments.hasOption(POFFSET)) {
        offsetPoissonPrior = arguments.getIntegerOption(POFFSET);
        progressStream.println("Poisson offset = " + offsetPoissonPrior);
    } else {
        offsetPoissonPrior = numberOfStates - 1;
        progressStream.println("Poisson offset = " + offsetPoissonPrior + " (locations - 1)");
    }
    if (arguments.hasOption(BFCUTOFF)) {
        cutoff = arguments.getRealOption(BFCUTOFF);
    }
    if (arguments.hasOption(ICUTOFF)) {
        cutoff = arguments.getRealOption(ICUTOFF);
        bayesFactor = false;
    }
    if (bayesFactor) {
        progressStream.println("Bayes factor cutoff = " + cutoff);
    } else {
        progressStream.println("indicator factor cutoff = " + cutoff);
    }
    if (arguments.hasOption(BWC)) {
        branchWidthConstant = arguments.getRealOption(BWC);
    }
    if (arguments.hasOption(BWM)) {
        branchWidthMultiplier = arguments.getRealOption(BWM);
    }
    if (arguments.hasOption(ALTITUDE)) {
        altitudeFactor = arguments.getRealOption(ALTITUDE);
    }
    String indicatorString = arguments.getStringOption(ISTRING);
    if (indicatorString != null) {
        rateIndicatorString = indicatorString;
    }
    String rateString = arguments.getStringOption(PSTRING);
    if (rateString != null) {
        actualRateString = rateString;
    }
    String freqString = arguments.getStringOption(FSTRING);
    if (freqString != null) {
        frequencyString = freqString;
    }
    String relRateString = arguments.getStringOption(RSTRING);
    if (relRateString != null) {
        relativeRateString = relRateString;
    }
    String clockString = arguments.getStringOption(CSTRING);
    if (clockString != null) {
        clockRateString = clockString;
    }
    String color1String = arguments.getStringOption(LOWCOLOR);
    if (color1String != null) {
        lowerLinkColor = color1String;
        if (locationsFileName == null) {
            System.err.print("color string but no coordinates file for KML output??");
        }
    }
    String color2String = arguments.getStringOption(UPCOLOR);
    if (color2String != null) {
        upperLinkColor = color2String;
        if (locationsFileName == null) {
            System.err.print("color string but no coordinates file for KML output??");
        }
    }
    final String[] args2 = arguments.getLeftoverArguments();
    switch(args2.length) {
        case 0:
            printUsage(arguments);
            System.exit(1);
        case 2:
            outputFileName = args2[1];
        // fall to
        case 1:
            inputFileName = args2[0];
            break;
        default:
            {
                System.err.println("Unknown option: " + args2[2]);
                System.err.println();
                printUsage(arguments);
                System.exit(1);
            }
    }
    RateIndicatorBF rateIndicatorBF = new RateIndicatorBF(inputFileName, burnin, rateIndicatorString, numberOfStates, locations, bayesFactor, cutoff, meanPoissonPrior, offsetPoissonPrior, actualRateString, relativeRateString, frequencyString, clockRateString, unitString, calculateRates);
    rateIndicatorBF.outputTextFile(outputFileName);
    if (kml) {
        rateIndicatorBF.outputKML(KMLoutputFile, lowerLinkColor, upperLinkColor, branchWidthConstant, branchWidthMultiplier, altitudeFactor);
    }
    System.exit(0);
}

Example 35 with Arguments

use of dr.app.util.Arguments in project beast-mcmc by beast-dev.

the class DiscreteTreeToKML method main.

public static void main(String[] args) throws Arguments.ArgumentException {
    String inputFileName = null;
    String outputFileName = null;
    RootedTree tree = null;
    String[][] locations = null;
    String stateAnnotation = "state";
    //in case trees are scaled in other time units
    double timeScaler = 1;
    // the width of branches will be stateProbability*branchWidthMultiplier+branchWidthConstant
    double branchWidthConstant = 2.0;
    double branchWidthMultiplier = 5.0;
    // this is to chop up the branches of the surface tree in 'divider' segments
    double divider = 100;
    // use state probabilities for branch width
    boolean useStateProbability = true;
    // branch width if posterior probabilities are not used
    double branchWidth = 10.0;
    // use posterior probabilities to color branch
    boolean usePosterior = false;
    // use heights (time) to color branches
    boolean useHeights = true;
    //red: 0000FF green: 00FF00 magenta: FF00FF white: FFFFFF yellow: 00FFFF cyan: FFFF00
    String startBranchColor = "FF00FF";
    String endBranchColor = "FFFF00";
    // branch color if color range based on rates is not used
    String branchColor = "ffffff";
    // branches are arcs with heights proportional to the distance between locations
    boolean arcBranches = true;
    // the height of the arcs is proportional to the time the branch spans, by default arch-heights are proportional to the distance between locations
    boolean arcTimeHeight = false;
    // this is the factor with which to multiply the time of the branch to get the altitude for that branch in the surface Tree
    double altitudeFactor = 100;
    boolean temporary = false;
    // required to convert heights to calendar dates
    double mostRecentDate = 2010;
    //circles
    int numberOfIntervals = 100;
    //boolean autoRadius = false;
    double radius = 0;
    String circleOpacity = "8F";
    //extra coordinates for some taxa
    boolean coordinatesForTaxa = false;
    String[][] taxaCoordinates = null;
    //tree slices for google maps, requires treeHeight in exporterString: e.g., exporterString.writeTreeToKML(0.025);
    //TODO: have this outputed to a different file (what happens now)?
    boolean makeTreeSlices = false;
    double[] sliceTimes = null;
    double treeSliceBranchWidth = 3;
    // shows complete branch for slice if time is more recent than the branch's midpoint
    boolean showBranchAtMidPoint = false;
    Arguments arguments = new Arguments(new Arguments.Option[] { new Arguments.StringOption(COORDINATES, "coordinate file", "specifies a tab-delimited file with coordinates for the locations"), new Arguments.StringOption(ANNOTATION, "location state annotation string", "specifies the string used for location state annotation [default=state]"), new Arguments.RealOption(TIMESCALER, "specifies the scaling factor by which to rescale time [default=1]"), new Arguments.RealOption(MRSD, "specifies the most recent sampling data in fractional years to rescale time [default=2010]"), new Arguments.RealOption(BWC, "specifies the branch width constant [default=2]"), new Arguments.RealOption(BWM, "specifies the branch width multiplier [default=5]"), new Arguments.StringOption(USP, falseTrue, false, "use state probabilities for branch width [default = true]"), new Arguments.StringOption(BCUSE, use, false, "use heights or posterior probabilities for branch colors [default = heights]"), new Arguments.RealOption(BW, "specifies the branch width if posterior probabilities are not used [default=10]"), new Arguments.IntegerOption(DIVIDER, "specifies in how many segments at branch should be chopped up [default=50]"), new Arguments.StringOption(BSTARTCOLOR, "branch start color", "specifies a starting color for the branches [default=FF00FF]"), new Arguments.StringOption(BENDCOLOR, "branch end color", "specifies an end color for the branches [default=FFFF00]"), new Arguments.StringOption(BCOLOR, "branch color", "specifies a branch color if color range based on rates is not used [default=ffffff]"), new Arguments.StringOption(ARCHBRANCH, falseTrue, false, "use arcs for the branches [default = true], by default arc-heights are proportional to the distance between locations"), new Arguments.StringOption(ARCHHEIGHT, arch, false, "use time or distance for arch heights [default = no arcs]"), new Arguments.RealOption(ALTITUDE, "specifies the altitudefactor for the branches [default=1000]"), new Arguments.StringOption(TEMP, falseTrue, false, "display branches only temporary [default=false"), new Arguments.IntegerOption(CIRCLESEGMENTS, "specifies the number of segments to construct circles [default=100]"), new Arguments.IntegerOption(RADIUS, "specifies the radiusfactor for the circles [default='autoradius']"), new Arguments.StringOption(CIRCLEOP, "circle opacity", "sets the opacity of the circles [default=8F]"), new Arguments.Option(HELP, "option to print this message"), new Arguments.StringOption(COORDSFORTAXA, "file with taxa coords", "specifies a file with additional coordinates for particular taxa"), new Arguments.RealOption(SLICEBW, "specifies the branch width for tree slices [default=3]"), new Arguments.StringOption(SLICES, "time", "specifies a slice time-list [default=none]"), new Arguments.StringOption(SLICEMIDPOINT, falseTrue, false, "shows complete branch for sliced tree if time is more recent than the branch's midpoint [default=false") });
    try {
        arguments.parseArguments(args);
    } catch (Arguments.ArgumentException ae) {
        progressStream.println(ae);
        printUsage(arguments);
        System.exit(1);
    }
    if (args.length == 0 || arguments.hasOption(HELP)) {
        printUsage(arguments);
        System.exit(0);
    }
    try {
        String coordinatesFileString = arguments.getStringOption(COORDINATES);
        //System.out.println(coordinatesFileString);
        if (coordinatesFileString != null) {
            // count lines in locations file and tokens per line
            int[] counts = countLinesAndTokens(coordinatesFileString);
            //System.out.println(counts[0]+"\t"+counts[1]);
            //read in locations
            locations = new String[counts[0]][counts[1]];
            readLocationsCoordinates(coordinatesFileString, locations);
        } else {
            progressStream.println("no coordinates for taxa??");
            System.exit(1);
        }
        if (arguments.hasOption(MRSD)) {
            mostRecentDate = arguments.getRealOption(MRSD);
        }
        if (arguments.hasOption(TIMESCALER)) {
            timeScaler = arguments.getRealOption(TIMESCALER);
        }
        if (arguments.hasOption(DIVIDER)) {
            divider = arguments.getRealOption(DIVIDER);
        }
        if (arguments.hasOption(ALTITUDE)) {
            altitudeFactor = arguments.getRealOption(ALTITUDE);
        }
        String stateAnnotationString = arguments.getStringOption(ANNOTATION);
        if (stateAnnotationString != null) {
            stateAnnotation = stateAnnotationString;
        }
        String useStateProbString = arguments.getStringOption(USP);
        if (useStateProbString != null && useStateProbString.compareToIgnoreCase("posteriors") != 0)
            useStateProbability = false;
        String useColorString = arguments.getStringOption(BCUSE);
        if (useColorString != null && useColorString.compareToIgnoreCase("posteriors") == 0) {
            usePosterior = true;
            useHeights = false;
        }
        if (useColorString != null && useColorString.compareToIgnoreCase("heights") == 0) {
            useHeights = true;
            usePosterior = false;
        }
        if (arguments.hasOption(BWC)) {
            branchWidthConstant = arguments.getRealOption(BWC);
        }
        if (arguments.hasOption(BWM)) {
            branchWidthMultiplier = arguments.getRealOption(BWM);
        }
        if (arguments.hasOption(BW)) {
            branchWidth = arguments.getRealOption(BW);
        }
        String color1String = arguments.getStringOption(BSTARTCOLOR);
        if (color1String != null) {
            startBranchColor = color1String;
        }
        String color2String = arguments.getStringOption(BENDCOLOR);
        if (color2String != null) {
            endBranchColor = color2String;
        }
        String colorString = arguments.getStringOption(BCOLOR);
        if (colorString != null) {
            branchColor = colorString;
        }
        String archString = arguments.getStringOption(ARCHBRANCH);
        if (archString != null && archString.compareToIgnoreCase("false") == 0)
            arcBranches = false;
        String archHeightString = arguments.getStringOption(ARCHHEIGHT);
        if (archHeightString != null && archHeightString.compareToIgnoreCase("time") == 0) {
            arcTimeHeight = true;
        }
        String tempString = arguments.getStringOption(TEMP);
        if (tempString != null && tempString.compareToIgnoreCase("true") == 0)
            temporary = true;
        if (arguments.hasOption(CIRCLESEGMENTS)) {
            numberOfIntervals = arguments.getIntegerOption(CIRCLESEGMENTS);
        }
        if (arguments.hasOption(RADIUS)) {
            radius = arguments.getIntegerOption(RADIUS);
        }
        String circleOpacityString = arguments.getStringOption(CIRCLEOP);
        if (circleOpacityString != null) {
            circleOpacity = circleOpacityString;
        }
        //read in extra taxon locations
        String taxaCoordinatesFileString = arguments.getStringOption(COORDSFORTAXA);
        if (taxaCoordinatesFileString != null) {
            coordinatesForTaxa = true;
            progressStream.println("\radditional taxa locations:");
            // count lines in locations file and tokens per line
            int[] counts = countLinesAndTokens(taxaCoordinatesFileString);
            //read in locations
            taxaCoordinates = new String[counts[0]][counts[1]];
            readLocationsCoordinates(taxaCoordinatesFileString, taxaCoordinates);
        }
        String sliceString = arguments.getStringOption(SLICES);
        if (sliceString != null) {
            makeTreeSlices = true;
            sliceTimes = parseVariableLengthDoubleArray(sliceString);
        }
        if (arguments.hasOption(SLICEBW)) {
            treeSliceBranchWidth = arguments.getRealOption(SLICEBW);
        }
        String midpointString = arguments.getStringOption(SLICEMIDPOINT);
        if (midpointString != null && midpointString.compareToIgnoreCase("true") == 0)
            showBranchAtMidPoint = true;
    } catch (Arguments.ArgumentException e) {
        progressStream.println(e);
        printUsage(arguments);
        System.exit(-1);
    }
    final String[] args2 = arguments.getLeftoverArguments();
    outputFileName = args2[0] + ".kml";
    switch(args2.length) {
        case 0:
            printUsage(arguments);
            System.exit(1);
        case 2:
            outputFileName = args2[1];
        // fall to
        case 1:
            inputFileName = args2[0];
            tree = readTree(inputFileName);
            break;
        default:
            {
                System.err.println("Unknown option: " + args2[2]);
                System.err.println();
                printUsage(arguments);
                System.exit(1);
            }
    }
    DiscreteKMLString exporterString = new DiscreteKMLString(tree, stateAnnotation, locations, inputFileName, mostRecentDate, timeScaler, divider, branchWidthConstant, branchWidthMultiplier, useStateProbability, branchWidth, startBranchColor, endBranchColor, branchColor, useHeights, usePosterior, arcBranches, arcTimeHeight, altitudeFactor, temporary, numberOfIntervals, radius, circleOpacity, coordinatesForTaxa, taxaCoordinates, makeTreeSlices);
    try {
        BufferedWriter out1 = new BufferedWriter(new FileWriter(outputFileName));
        StringBuffer buffer = new StringBuffer();
        if (makeTreeSlices) {
            for (int i = 0; i < sliceTimes.length; i++) exporterString.writeTreeToKML(sliceTimes[i], treeSliceBranchWidth, showBranchAtMidPoint);
        } else {
            exporterString.writeTreeToKML();
            exporterString.writeLineagesToCircles();
        }
        exporterString.writeLocationsKML();
        exporterString.compileBuffer(buffer);
        out1.write(buffer.toString());
        out1.close();
    } catch (IOException e) {
        e.printStackTrace();
        return;
    }
}