Examples with Taxon dr.evolution.util.Taxon used on opensource projects

Example 11 with Taxon

use of dr.evolution.util.Taxon in project beast-mcmc by beast-dev.

the class XMLExporter method exportAlignment.

// END: Constructor
public String exportAlignment(SimpleAlignment alignment) throws IOException {
    StringWriter sw = new StringWriter();
    XMLWriter writer = new XMLWriter(sw);
    //		TODO: if we keep the taxa element than lets also write dates		
    //		writer.writeOpenTag(TaxaParser.TAXA, // tagname
    //				new Attribute[] { // attributes[]
    //				new Attribute.Default<String>(XMLParser.ID, TaxaParser.TAXA) });
    //		
    //		for (int i = 0; i < alignment.getTaxonCount(); i++) {
    //
    //			Taxon taxon = alignment.getTaxon(i);
    //
    //			writer.writeTag(
    //					TaxonParser.TAXON, // tagname
    //					new Attribute[] { // attributes[]
    //					new Attribute.Default<String>(XMLParser.ID, taxon.getId()) },
    //					true // close
    //			);
    //
    ////			System.out.println(taxon.getAttribute(Utils.ABSOLUTE_HEIGHT));
    //			
    ////			writer.writeCloseTag(TaxonParser.TAXON);
    //			
    //		}// END: taxon loop
    //		
    //		writer.writeCloseTag(TaxaParser.TAXA);
    //		
    //		writer.writeBlankLine();
    // tagname
    writer.writeOpenTag(// tagname
    AlignmentParser.ALIGNMENT, new Attribute[] { // attributes[]
    new Attribute.Default<String>(XMLParser.ID, AlignmentParser.ALIGNMENT), new Attribute.Default<String>(DataType.DATA_TYPE, alignment.getDataType().getDescription()) });
    for (int i = 0; i < alignment.getSequenceCount(); i++) {
        Taxon taxon = alignment.getTaxon(i);
        writer.writeOpenTag(SequenceParser.SEQUENCE);
        writer.writeIDref(TaxonParser.TAXON, taxon.getId());
        writer.writeText(alignment.getSequence(i).getSequenceString());
        writer.writeCloseTag(SequenceParser.SEQUENCE);
    }
    //END: sequences loop
    writer.writeCloseTag(AlignmentParser.ALIGNMENT);
    writer.close();
    return sw.toString();
}

Example 12 with Taxon

use of dr.evolution.util.Taxon in project beast-mcmc by beast-dev.

the class TreesTableModel method applyTaxa.

// END: setRow
public void applyTaxa(Tree tree) {
    // set attributes to be parsed later in Taxa panel
    Taxa taxa = new Taxa();
    for (Taxon taxon : tree.asList()) {
        double absoluteHeight = Utils.getAbsoluteTaxonHeight(taxon, tree);
        taxon.setAttribute(Utils.ABSOLUTE_HEIGHT, absoluteHeight);
        taxon.setAttribute(Utils.TREE_FILENAME, tree.getId());
        taxa.addTaxon(taxon);
        dataList.allTaxa.addTaxon(taxon);
    }
// END: taxon loop
}

Example 13 with Taxon

use of dr.evolution.util.Taxon in project beast-mcmc by beast-dev.

the class Utils method printTaxaSet.

// END: printDataType
public static void printTaxaSet(Taxa taxa) {
    for (int i = 0; i < taxa.getTaxonCount(); i++) {
        Taxon taxon = taxa.getTaxon(i);
        System.out.print("\t\t " + taxonToString(taxon, false) + ("\n"));
    }
}

Example 14 with Taxon

use of dr.evolution.util.Taxon in project beast-mcmc by beast-dev.

the class Utils method printHashMap.

// END: printMap
public static void printHashMap(ConcurrentHashMap<?, ?> hashMap) {
    Iterator<?> iterator = hashMap.entrySet().iterator();
    while (iterator.hasNext()) {
        Entry<?, ?> pairs = (Entry<?, ?>) iterator.next();
        Taxon taxon = (Taxon) pairs.getKey();
        int[] sequence = (int[]) pairs.getValue();
        System.out.println(taxon.toString());
        Utils.printArray(sequence);
    }
// END: while has next
}

Example 15 with Taxon

use of dr.evolution.util.Taxon in project beast-mcmc by beast-dev.

the class Utils method getAbsoluteTaxonHeight.

// END: taxonExists
// private boolean isFileInList(File file) {
// boolean exists = false;
//
// for (File file2 : dataList.treesList) {
//
// if (file.getName().equalsIgnoreCase(file2.getName())) {
// exists = true;
// break;
// }
//
// }
//
// return exists;
// }// END: isFileInList
public static double getAbsoluteTaxonHeight(Taxon taxon, Tree tree) {
    double height = 0.0;
    for (int i = 0; i < tree.getExternalNodeCount(); i++) {
        NodeRef externalNode = tree.getExternalNode(i);
        Taxon externalNodeTaxon = tree.getNodeTaxon(externalNode);
        if (externalNodeTaxon.equals(taxon)) {
            height = tree.getNodeHeight(externalNode);
        }
    }
    return height;
}