Java Sequence.initByName方法代码示例

import beast.evolution.alignment.Sequence; //导入方法依赖的package包/类
static public Alignment getUncertainAlignment(boolean duplicate) throws Exception {
     
      String seq1Probs = new String("0.7,0.0,0.3,0.0; 0.0,0.3,0.0,0.7; 0.0,0.0,0.0,1.0;");
      String seq2Probs = new String("0.7,0.0,0.3,0.0; 0.0,0.3,0.0,0.7; 0.0,1.0,0.0,0.0;");
      String seq3Probs = new String("0.4,0.0,0.6,0.0; 0.0,0.6,0.0,0.4; 0.0,1.0,0.0,0.0;");
      
      if (duplicate) {
      	seq1Probs += seq1Probs;
      	seq2Probs += seq2Probs;
      	seq3Probs += seq3Probs;
      }
      Sequence seq1 = new Sequence();
seq1.initByName("taxon","seq1","value",seq1Probs,"uncertain",true);
Sequence seq2 = new Sequence();
seq2.initByName("taxon","seq2","value",seq2Probs,"uncertain",true);
Sequence seq3 = new Sequence();
seq3.initByName("taxon","seq3","value",seq3Probs,"uncertain",true);
              
      Alignment data = new Alignment();
      
      data.initByName("sequence", seq1, "sequence", seq2, "sequence", seq3,
              "dataType", "nucleotide"                
      );

  	DataType dataType = data.getDataType();
      System.out.println("Most probable sequences:");
  	for (List<Integer> seq : data.getCounts()) {
  		System.out.println(dataType.state2string(seq));    		
  	}
  	
      return data;
  }
 

import beast.evolution.alignment.Sequence; //导入方法依赖的package包/类
@Test
public void testMascotStructured(){
	
	//build alignment
	Sequence sequence1 = new Sequence();
	Sequence sequence2 = new Sequence();
	Sequence sequence3 = new Sequence();
	Sequence sequence4 = new Sequence();
	Sequence sequence5 = new Sequence();
	sequence1.initByName("taxon", "a1", "value", "???");
	sequence2.initByName("taxon", "a2", "value", "???");
	sequence3.initByName("taxon", "a3", "value", "???");
	sequence4.initByName("taxon", "b1", "value", "???");
	sequence5.initByName("taxon", "b2", "value", "???");
	
	
	Alignment alignment = new Alignment();
	alignment.initByName("sequence", sequence1,"sequence", sequence2,"sequence", sequence3,"sequence", sequence4, "sequence", sequence5);
	
	TaxonSet taxa = new TaxonSet();
	taxa.initByName("alignment", alignment);
	
	//build trait set
	TraitSet traitSet = new TraitSet();
	traitSet.initByName("value", "a1=a,a2=a,a3=a,b1=b,b2=b", "traitname", "type", "taxa", taxa);
	
	Tree tree = new TreeParser("(((a1:1,a2:2):1,(b1:1,b2:1.5):2):1,a3:1)");
	Tree traitTree = new Tree();
	tree.initByName("taxonset", taxa, "trait", traitSet);
	StructuredTreeIntervals st = new StructuredTreeIntervals();
	st.initByName("tree",tree);
	
	// build constant dynamics
	RealParameter Ne = new RealParameter("1 2");
	RealParameter backwardsMigration = new RealParameter("0.3 2");
	int dim = 2;
	Constant constant = new Constant();
	constant.initByName("backwardsMigration", backwardsMigration, "Ne", Ne, "dimension", dim, "typeTrait", traitSet);

	
	Mascot mascot = new Mascot();
	
	mascot.initByName("structuredTreeIntervals", st, "dynamics", constant);
	
	
	Assert.assertTrue(mascot.calculateLogP()==-6.870390751933608);
	

}
 

import beast.evolution.alignment.Sequence; //导入方法依赖的package包/类
@Test
public void testMascotUnstructured(){
	
	//build alignment
	Sequence sequence1 = new Sequence();
	Sequence sequence2 = new Sequence();
	Sequence sequence3 = new Sequence();
	Sequence sequence4 = new Sequence();
	Sequence sequence5 = new Sequence();
	sequence1.initByName("taxon", "a1", "value", "???");
	sequence2.initByName("taxon", "a2", "value", "???");
	sequence3.initByName("taxon", "a3", "value", "???");
	sequence4.initByName("taxon", "b1", "value", "???");
	sequence5.initByName("taxon", "b2", "value", "???");
	
	
	Alignment alignment = new Alignment();
	alignment.initByName("sequence", sequence1,"sequence", sequence2,"sequence", sequence3,"sequence", sequence4, "sequence", sequence5);
	
	
	TaxonSet taxa = new TaxonSet();
	taxa.initByName("alignment", alignment);
	
	//build trait set
	TraitSet traitSet = new TraitSet();
	traitSet.initByName("value", "a1=a,a2=a,a3=a,b1=a,b2=a", "traitname", "type", "taxa", taxa);
	
	Tree tree = new TreeParser("(((a1:1,a2:2):1,(b1:1,b2:1.5):2):1,a3:1)");
	Tree traitTree = new Tree();
	tree.initByName("taxonset", taxa, "trait", traitSet);
	StructuredTreeIntervals st = new StructuredTreeIntervals();
	st.initByName("tree",tree);
	
	// build constant dynamics
	RealParameter Ne = new RealParameter("1.5 2");
	RealParameter backwardsMigration = new RealParameter("0 0");
	int dim = 2;
	Constant constant = new Constant();
	constant.initByName("backwardsMigration", backwardsMigration, "Ne", Ne, "dimension", dim, "typeTrait", traitSet);

	
	Mascot mascot = new Mascot();
	
	mascot.initByName("structuredTreeIntervals", st, "dynamics", constant);
	
	// also set up the constant coalescent
	TreeIntervals ti = new TreeIntervals();
	ti.initByName("tree",tree);
	
	RealParameter Nec = new RealParameter("1.5");
	
	
	ConstantPopulation cp = new ConstantPopulation();
	cp.initByName("popSize", Nec);
	
	Coalescent coalescent = new Coalescent();
	coalescent.initByName("populationModel", cp, "treeIntervals", ti);
	
	Assert.assertTrue(Math.abs(mascot.calculateLogP()-coalescent.calculateLogP())<0.000000001);
}
 

import beast.evolution.alignment.Sequence; //导入方法依赖的package包/类
private static BEASTInterface parseBeast1XML(String ID, String xml) throws SAXException, IOException, ParserConfigurationException  {
	DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
	Document doc = factory.newDocumentBuilder().parse(new InputSource(new StringReader(xml)));
	doc.normalize();

	NodeList alignments = doc.getElementsByTagName("alignment");
	Alignment alignment = new Alignment();
	alignment.dataTypeInput.setValue("nucleotide", alignment);

	// parse first alignment
	org.w3c.dom.Node node = alignments.item(0);

	String dataTypeName = node.getAttributes().getNamedItem("dataType").getNodeValue();
	int totalCount = 4;
	if (dataTypeName == null) {
		alignment.dataTypeInput.setValue("integer", alignment);
	} else if (dataTypeName.toLowerCase().equals("dna") || dataTypeName.toLowerCase().equals("nucleotide")) {
		alignment.dataTypeInput.setValue("nucleotide", alignment);
		totalCount = 4;
	} else if (dataTypeName.toLowerCase().equals("aminoacid") || dataTypeName.toLowerCase().equals("protein")) {
		alignment.dataTypeInput.setValue("aminoacid", alignment);
		totalCount = 20;
	} else {
		alignment.dataTypeInput.setValue("integer", alignment);
	}

	NodeList children = node.getChildNodes();
	for (int i = 0; i < children.getLength(); i++) {
		org.w3c.dom.Node child = children.item(i);
		if (child.getNodeName().equals("sequence")) {
			Sequence sequence = new Sequence();
			// find the taxon
			String taxon = "";
			NodeList sequenceChildren = child.getChildNodes();
			for (int j = 0; j < sequenceChildren.getLength(); j++) {
				org.w3c.dom.Node child2 = sequenceChildren.item(j);
				if (child2.getNodeName().equals("taxon")) {
					taxon = child2.getAttributes().getNamedItem("idref").getNodeValue();
				}
			}
			String data = child.getTextContent();
			sequence.initByName("totalcount", totalCount, "taxon", taxon, "value", data);
			sequence.setID("seq_" + taxon);
			alignment.sequenceInput.setValue(sequence, alignment);

		}
	}
	alignment.setID(ID);
	alignment.initAndValidate();
	return alignment;
}