comparison NGSrich_0.5.5/src/middlewares/XMLSummaryFileBuilder.java @ 0:89ad0a9cca52 default tip

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0:89ad0a9cca52

package middlewares;

import java.util.*;
import java.io.*;
import org.jdom.*;
import org.jdom.input.*;
import org.jdom.output.*;

/**
 * Used to construct the summary file based on the computation of an 
 * EnrichmentStatsComputer object. It uses a file pattern to generate this file
 * dynamically.
 * 
 * @author Ali Abdallah
 * @version 20.07.2011
 * @since Java 1.6
 */

public class XMLSummaryFileBuilder {
	
	/**
	 * The pattern file containing the structure of the summary without real
	 * data.
	 */
	static String xmlPatternFile;
	
	/**
	 * The summary file containing the computed data.
	 */
	static String xmlOutputFile;
	
	/**
	 * An object with an abstract representation on an xml-file.
	 */
	static Document doc;
	
	/**
	 * The leaf-tags containing data as text.
	 */
	List<Element> leafs;
	
	/**
	 * The name of the current sample.  
	 */
	static String currSample;
	
	/**
	 * Creates and initializes a XMLSummaryFileBuilder object.
	 * 
	 * @param xmlPatternFile the pattern file.
	 * @param xmlOutputFile the output file.
	 * @param currSample the current read alignment sample name without 
	 * the extension.
	 */
	public XMLSummaryFileBuilder(String xmlPatternFile, String xmlOutputFile,
			String currSample) {

		leafs = new ArrayList<Element>();
		XMLSummaryFileBuilder.xmlPatternFile = xmlPatternFile;
		XMLSummaryFileBuilder.xmlOutputFile = xmlOutputFile;
		XMLSummaryFileBuilder.currSample = currSample;
		SAXBuilder builder = new SAXBuilder();
		try {
			doc = builder.build(xmlPatternFile);
		} catch (JDOMException e) {
			e.printStackTrace();
		} catch (IOException e) {
			e.printStackTrace();
		}
	}
	
	/**
	 * Same as the constructor above but the pattern file is internally 
	 * specified.
	 * 
	 * @param xmlOutputFile the output file.
	 * @param currSample the current read alignment sample name without 
	 * the extension.
	 */
	public XMLSummaryFileBuilder(String xmlOutputFile,
			String currSample) {
		this(Misc.binDir()+"/xmlFilePattern.xml", xmlOutputFile, currSample);
	}

	/**
	 * Computes all the leafs of the subtree with root e.
	 * 
	 * @param e an Element.
	 * @return all the leafs of the subtree with root e.
	 */
	public Element[] getLeafs(Element e){
		@SuppressWarnings("unchecked")
		List<Element> children = e.getChildren();
		for(int i = 0; i < children.size(); i++){
			Element child = children.get(i);
			if(child.getChildren().size() == 0)
				leafs.add(child);
			else
				getLeafs(child);
		}
		
		Object[] oleafs = leafs.toArray();
		Element[] eleafs = new Element[oleafs.length];
		for(int i = 0; i < eleafs.length; i++)
			eleafs[i] = (Element)oleafs[i];
		
		return eleafs;
	}
	
	/**
	 * Same as the above method but the element is internally specified as the
	 * root of the document.
	 * 
	 * @return an array with all leaf elements of the document. 
	 */
	public Element[] getLeafs(){
		return getLeafs(doc.getRootElement());
	}

	/**
	 * Write the summary file created.
	 * @param name the name of the file.
	 */
	public void writeXMLFile(String name) {
		XMLOutputter outp = new XMLOutputter();
		outp.setFormat(Format.getPrettyFormat());
		try {
			outp.output(doc, new FileOutputStream(name));
		} catch (FileNotFoundException e) {
			e.printStackTrace();
		} catch (IOException e) {
			e.printStackTrace();
		}
	}
	
}