Examples with RootedTree jebl.evolution.trees.RootedTree used on opensource projects

Example 11 with RootedTree

use of jebl.evolution.trees.RootedTree 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;
    }
}

Example 12 with RootedTree

use of jebl.evolution.trees.RootedTree in project beast-mcmc by beast-dev.

the class LineageCountThroughTime method getLTT.

public static Variate[] getLTT(String treeFile, double minTime, double maxTime, int binCount, // number of trees to skip
int skip) throws IOException, ImportException {
    double delta = (maxTime - minTime) / (binCount - 1);
    BufferedReader reader = new BufferedReader(new FileReader(treeFile));
    String line = reader.readLine();
    TreeImporter importer;
    if (line.toUpperCase().startsWith("#NEXUS")) {
        importer = new NexusImporter(reader);
    } else {
        importer = new NewickImporter(reader, false);
    }
    int state = 0;
    while (importer.hasTree() && state < skip) {
        importer.importNextTree();
        state += 1;
    }
    // the age of the end of this group
    List<double[]> branchingTimes = new ArrayList<double[]>();
    state = 0;
    while (importer.hasTree()) {
        RootedTree tree = (RootedTree) importer.importNextTree();
        double[] bt = new double[tree.getInternalNodes().size()];
        int i = 0;
        for (Node node : tree.getInternalNodes()) {
            bt[i] = tree.getHeight(node);
            i++;
        }
        Arrays.sort(bt);
        branchingTimes.add(bt);
        state += 1;
    }
    Variate[] bins = new Variate[binCount];
    double height = 0;
    double n = branchingTimes.get(0).length;
    for (int k = 0; k < binCount; k++) {
        bins[k] = new Variate.D();
        if (height >= 0.0 && height <= maxTime) {
            for (state = 0; state < branchingTimes.size(); state++) {
                int index = 0;
                while (index < branchingTimes.get(state).length && branchingTimes.get(state)[index] < height) {
                    index += 1;
                }
                double lineageCount = 1;
                if (index < branchingTimes.get(state).length) {
                    lineageCount = n - index + 1;
                }
                bins[k].add(lineageCount);
            }
        }
        height += delta;
    }
    Variate xData = new Variate.D();
    Variate yDataMean = new Variate.D();
    Variate yDataMedian = new Variate.D();
    Variate yDataUpper = new Variate.D();
    Variate yDataLower = new Variate.D();
    double t = minTime;
    for (Variate bin : bins) {
        xData.add(t);
        if (bin.getCount() > 0) {
            yDataMean.add(bin.getMean());
            yDataMedian.add(bin.getQuantile(0.5));
            yDataLower.add(bin.getQuantile(0.025));
            yDataUpper.add(bin.getQuantile(0.975));
        } else {
            yDataMean.add(Double.NaN);
            yDataMedian.add(Double.NaN);
            yDataLower.add(Double.NaN);
            yDataUpper.add(Double.NaN);
        }
        t += delta;
    }
    return new Variate[] { xData, yDataMean };
}