Examples with NexusParser babel.util.NexusParser used on opensource projects

Example 1 with NexusParser

use of babel.util.NexusParser in project Babel by rbouckaert.

the class CharsetlabelsToCharsets method run.

@Override
public void run() throws Exception {
    if (nexusInput.get() == null || nexusInput.get().getName().equals("[[none]]")) {
        throw new IllegalArgumentException("A valid nexus file must be specified");
    }
    NexusParser parser = new NexusParser();
    parser.parseFile(nexusInput.get());
    if (parser.charstatelabels == null || parser.charstatelabels.length == 0) {
        throw new IllegalArgumentException("Charsetlabels in nesus file must be specified (but could not find any)");
    }
    // process
    StringBuilder buf = new StringBuilder();
    int start = 0;
    String prevName = sanitise(parser.charstatelabels[0]);
    int k = 0;
    for (int i = 0; i < parser.charstatelabels.length; i++) {
        String name = sanitise(parser.charstatelabels[i]);
        if (!name.equals(prevName)) {
            buf.append("charset " + prevName + " = " + (start + 1) + "-" + i + ";\n");
            start = i;
            prevName = name;
            k++;
        }
    }
    buf.append("charset " + prevName + " = " + (start + 1) + "-" + parser.charstatelabels.length + ";\n");
    // output
    PrintStream out = System.out;
    if (outputInput.get() != null && !outputInput.get().getName().equals("[[none]]")) {
        Log.warning("Writing to file " + outputInput.get().getName());
        out = new PrintStream(outputInput.get());
    }
    String old = BeautiDoc.load(nexusInput.get());
    out.println(old);
    out.println("begin assumptions;");
    out.print(buf.toString());
    out.println("end;");
    Log.warning(k + " charsets");
    Log.warning("Done!");
}

Example 2 with NexusParser

use of babel.util.NexusParser in project Babel by rbouckaert.

the class DolloAnnotator method getAlignment.

private Alignment getAlignment() throws IOException {
    if (nexusFileInput.get() != null && !outputInput.get().getName().equals("[[none]]")) {
        NexusParser nexus = new NexusParser();
        nexus.parseFile(nexusFileInput.get());
        Alignment data = nexus.m_alignment;
        if (data == null || !data.getDataType().getTypeDescription().equals("binary")) {
            throw new IllegalArgumentException("Expected a binary alignment in the NEXUS file");
        }
        if (filterInput.get() != null) {
            FilteredAlignment filtered = new FilteredAlignment();
            filtered.initByName("data", data, "filter", filterInput.get());
            data = filtered;
        }
        return data;
    }
    return null;
}

Example 3 with NexusParser

use of babel.util.NexusParser in project Babel by rbouckaert.

the class CognateStats method run.

@Override
public void run() throws Exception {
    Log.warning.println("Languages (language, # columns, # states):");
    NexusParser parser = new NexusParser();
    parser.parseFile(nexusFileInput.get());
    Alignment data = parser.m_alignment;
    if (data == null) {
        throw new IOException("No alignment found in nexus file");
    }
    String[] cognates = parser.charstatelabels;
    if (cognates != null && cognates.length != data.getSiteCount()) {
        throw new IOException("Found " + cognates.length + " cognate labels, but the alignment contains " + data.getSiteCount() + " sites.");
    }
    Log.warning.println(" ");
    Log.warning.println("Singletons (language, column):");
    List<String> taxaNames = data.getTaxaNames();
    int[] cognateCounts = new int[taxaNames.size() + 1];
    for (int i = 0; i < data.getSiteCount(); i++) {
        int[] pattern = data.getPattern(data.getPatternIndex(i));
        int oneCount = 0;
        int taxonNr = -1;
        for (int k = 0; k < pattern.length; k++) {
            if (pattern[k] == 1) {
                oneCount++;
                taxonNr = k;
            }
        }
        if (oneCount == 1) {
            Log.info.println(taxaNames.get(taxonNr) + " " + (cognates == null ? i : cognates[i]));
        }
        cognateCounts[oneCount]++;
    }
    Log.info.println(cognateCounts[1] + " singletons in total.\n");
    Log.warning.println(" \nCognate distribution (number of cognates contained in N languages, where N is the first column):");
    for (int i = 0; i < cognateCounts.length; i++) {
        Log.info.println(i + " " + cognateCounts[i]);
    }
    Log.warning.println(" \nDuplicates:");
    int dupCount = 0;
    for (Alignment d : parser.filteredAlignments) {
        for (int i = 0; i < d.getSiteCount(); i++) {
            int[] pattern1 = d.getPattern(d.getPatternIndex(i));
            for (int j = i + 1; j < d.getSiteCount(); j++) {
                int[] pattern2 = d.getPattern(d.getPatternIndex(j));
                if (equals(pattern1, pattern2)) {
                    dupCount++;
                }
            }
        }
    }
    Log.info.println(dupCount + " duplicates in total.\n");
}

Example 4 with NexusParser

use of babel.util.NexusParser in project Babel by rbouckaert.

the class NexusToCharsets method run.

@Override
public void run() throws Exception {
    if (nexusInput.get() == null || nexusInput.get().getName().equals("[[none]]")) {
        throw new IllegalArgumentException("A valid nexus file must be specified");
    }
    NexusParser parser = new NexusParser();
    parser.parseFile(nexusInput.get());
    Alignment data = parser.m_alignment;
    List<String> taxa = data.getTaxaNames();
    String seq = data.getSequenceAsString(taxa.get(0));
    char[][] seqs = new char[seq.length()][data.getTaxonCount()];
    for (int i = 0; i < taxa.size(); i++) {
        seq = data.getSequenceAsString(taxa.get(i));
        for (int j = 0; j < seq.length(); j++) {
            seqs[j][i] = seq.charAt(j);
        }
    }
    if (sortInput.get()) {
        Arrays.sort(seqs, (o1, o2) -> {
            for (int i = 0; i < o1.length; i++) {
                if (o1[i] == '?' && o2[i] != '?') {
                    return -1;
                } else if (o2[i] == '?' && o1[i] != '?') {
                    return 1;
                }
            }
            return 0;
        });
    }
    int n = seqs.length;
    // process
    StringBuilder buf = new StringBuilder();
    int start = 0;
    int k = 0;
    boolean strip = stripZeroColumnsInput.get();
    if (strip) {
        buf.append("charset concept" + k + " = 1,");
    }
    for (int i = 1; i < n; i++) {
        if (!matches(seqs, i, i - 1)) {
            if (!strip) {
                buf.append("charset concept" + k + " = " + (start + 1) + "-" + i + ";\n");
            } else {
                buf.deleteCharAt(buf.length() - 1);
                buf.append(";\n");
                buf.append("charset concept" + (k + 1) + " = ");
            }
            start = i;
            k++;
        }
        if (strip && has1(seqs, i)) {
            buf.append((i + 1) + ",");
        }
    }
    if (!strip) {
        buf.append("charset concept" + k + " = " + (start + 1) + "-" + n + ";\n");
    } else {
        buf.deleteCharAt(buf.length() - 1);
        buf.append(";\n");
    }
    // output
    PrintStream out = System.out;
    if (outputInput.get() != null && !outputInput.get().getName().equals("[[none]]")) {
        Log.warning("Writing to file " + outputInput.get().getName());
        out = new PrintStream(outputInput.get());
    }
    if (sortInput.get()) {
        out.print("#NEXUS\n");
        out.print("BEGIN DATA;\n");
        out.print("DIMENSIONS NTAX=" + taxa.size() + " NCHAR=" + n + ";\n");
        out.print("FORMAT DATATYPE=STANDARD MISSING=? GAP=-  SYMBOLS=\"01\";\n");
        out.print("MATRIX\n");
        for (int i = 0; i < taxa.size(); i++) {
            out.print(data.getTaxaNames().get(i) + " ");
            for (int j = 0; j < n; j++) {
                out.print(seqs[j][i]);
            }
            out.println();
        }
        out.println(";\nEND;\n");
    } else {
        String old = BeautiDoc.load(nexusInput.get());
        out.println(old);
    }
    out.println("begin assumptions;");
    out.print(buf.toString());
    out.println("end;");
    Log.warning(k + " charsets");
    Log.warning("Done!");
}

Example 5 with NexusParser

use of babel.util.NexusParser in project Babel by rbouckaert.

the class FrechetMeanCentroid method MCCTree.

private Tree MCCTree() {
    try {
        String output = outputInput.get().getAbsolutePath();
        TreeAnnotator.main(new String[] { "-b", burnInPercentageInput.get() + "", treeFileInput.get().getPath(), output });
        NexusParser parser = new NexusParser();
        parser.parseFile(outputInput.get());
        return parser.trees.get(0);
    } catch (IOException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }
    return null;
}