Examples with XMLWriter dr.app.beauti.util.XMLWriter used on opensource projects

Example 6 with XMLWriter

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

the class GetDateFromTree method writeHeadAndTaxa.

private static XMLWriter writeHeadAndTaxa(String curD, int index, double[][] tips) throws IOException {
    String f = path + curD + "/T_" + Integer.toString(index) + ".xml";
    System.out.println("Creating xml : " + f);
    XMLWriter w = new XMLWriter(new BufferedWriter(new FileWriter(new File(f))));
    w.writeText("<?xml version=\"1.0\" standalone=\"yes\"?>\n" + "\n" + "<!-- Generated by BEAUTi v1.7.0 Prerelease r3910                             -->\n" + "<!--       by Alexei J. Drummond and Andrew Rambaut                          -->\n" + "<!--       Department of Computer Science, University of Auckland and        -->\n" + "<!--       Institute of Evolutionary Biology, University of Edinburgh        -->\n" + "<!--       http://beast.bio.ed.ac.uk/                                        -->\n" + "<beast>\n" + "\n" + "\t<!-- The list of taxa to be analysed (can also include dates/ages).          -->\n" + "\t<!-- ntax=" + tips[0].length + "                                                                -->\n" + "\t<taxa id=\"taxa\">\n");
    for (int n = 1; n < tips[0].length; n++) {
        w.writeText("\t<taxon id=\"" + n + "\">\n" + "\t\t<date value=\"" + tips[0][n] + "\" direction=\"backwards\" units=\"years\" />\n" + "\t</taxon>\n");
    }
    w.writeText("\t</taxa>\n");
    for (int tree = 2; tree <= combiTrees; tree++) {
        w.writeText("\t<taxa id=\"taxa" + tree + "\">\n");
        for (int n = 1; n < tips[tree - 1].length; n++) {
            w.writeText("\t<taxon id=\"" + n + "t" + tree + "\">\n" + "\t\t<date value=\"" + tips[tree - 1][n] + "\" direction=\"backwards\" units=\"years\" />\n" + "\t</taxon>\n");
        }
        w.writeText("\t</taxa>\n");
    }
    return w;
}

Example 7 with XMLWriter

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

the class GenerateRelaxedClockXMLByData method main.

public static void main(String[] args) {
    int taxonNum = 14;
    for (int c = 1; c <= 100; c++) {
        String inputFileName = "geneRRNP" + c + ".phy";
        String[][] data = new String[taxonNum][2];
        try {
            System.out.println("Input data from " + path + inputFileName + "\n\n");
            FileReader fileReader = new FileReader(path + inputFileName);
            LineNumberReader lineNumberReader = new LineNumberReader(fileReader);
            String line = "";
            int lineNum = 0;
            while ((line = lineNumberReader.readLine()) != null) {
                lineNum = lineNumberReader.getLineNumber();
                System.out.println("Line:  " + lineNum + ": " + line);
                if (lineNumberReader.getLineNumber() > 1) {
                    // not need 1st row
                    String[] d = line.split("\\s+");
                    if (d.length != 2)
                        throw new IOException("d " + d.length);
                    // taxon name
                    data[lineNum - 2][0] = d[0];
                    // alignment
                    data[lineNum - 2][1] = d[1];
                }
            }
            if (lineNum != 15)
                throw new IOException("not have 15 line " + lineNum);
            fileReader.close();
            String outputFileName = "geneRRNP" + c + ".xml";
            System.out.println("\n\nCreating xml : " + path + outputFileName);
            XMLWriter w = new XMLWriter(new BufferedWriter(new FileWriter(new File(path + outputFileName))));
            writeData(w, data);
            writeRestXML(w, outputFileName);
            w.close();
            System.out.println("+++++++++++++++++++++++++++++++++++++++++++++++\n\n");
        } catch (FileNotFoundException e) {
            //To change body of catch statement use File | Settings | File Templates.
            e.printStackTrace();
        } catch (IOException e) {
            //To change body of catch statement use File | Settings | File Templates.
            e.printStackTrace();
        }
    }
}