/*
* BioJava development code
*
* This code may be freely distributed and modified under the
* terms of the GNU Lesser General Public Licence. This should
* be distributed with the code. If you do not have a copy,
* see:
*
* http://www.gnu.org/copyleft/lesser.html
*
* Copyright for this code is held jointly by the individual
* authors. These should be listed in @author doc comments.
*
* For more information on the BioJava project and its aims,
* or to join the biojava-l mailing list, visit the home page
* at:
*
* http://www.biojava.org/
*/
package org.biojava.bio.dist;
import java.io.BufferedWriter;
import java.io.IOException;
import java.io.OutputStream;
import java.io.OutputStreamWriter;
import java.util.Iterator;
import org.biojava.bio.BioError;
import org.biojava.bio.symbol.FiniteAlphabet;
import org.biojava.bio.symbol.IllegalSymbolException;
import org.biojava.bio.symbol.Symbol;
/**
* Writes an OrderNDistribution or simple Distribution to an XML file.
*
* @author Russell Smithies
* @author Mark Schreiber
* @since 1.3
*/
public class XMLDistributionWriter{
BufferedWriter out = null;
private void writeOND2XML(OrderNDistribution ond, OutputStream os) throws IOException{
Distribution conditionedDist = null;
FiniteAlphabet conditionedAlpha = null;
out = new BufferedWriter(new OutputStreamWriter(os));
out.write("");
out.write("");
out.write("");
for (Iterator i = ((FiniteAlphabet) ond.getConditioningAlphabet()).iterator();
i.hasNext();) {
Symbol sym = (Symbol) i.next();
out.write("");
try {
conditionedDist = ond.getDistribution(sym);
} catch (IllegalSymbolException ex) {
throw new BioError("Distribution has been built with Illegal Symbols !?", ex);
}
conditionedAlpha = (FiniteAlphabet) conditionedDist.getAlphabet();
for (Iterator it = conditionedAlpha.iterator(); it.hasNext();) {
Symbol condSym = (Symbol) it.next();
double weight = 0.0;
try {
weight = conditionedDist.getWeight(condSym);
} catch (IllegalSymbolException ex) {
throw new BioError("Distribution has been built with Illegal Symbols !?", ex);
}
out.write("");
}
out.write("");
}
out.write("");
out.flush();
} //end writeXML
private void writeDist2XML(Distribution d, OutputStream os) throws IOException{
out = new BufferedWriter(new OutputStreamWriter(os));
out.write("");
out.write("");
out.write("");
for (Iterator i = ((FiniteAlphabet) d.getAlphabet()).iterator();
i.hasNext();) {
Symbol sym = (Symbol) i.next();
double weight = 0.0;
try {
weight = d.getWeight(sym);
} catch (IllegalSymbolException ex) {
throw new BioError("Distribution has been built with Illegal Symbols !?", ex);
}
out.write("");
}
out.write("");
out.flush();
} //end writeXML
/**
* Writes an OrderNDistribution or simple Distribution to an XML file.
* @param d Distribution to write.
* @param os OutputStream to write to.
* @throws IOException if an error occurs during writing
*/
public void writeDistribution(Distribution d, OutputStream os) throws IOException{
if (d instanceof OrderNDistribution) {
writeOND2XML((OrderNDistribution) d, os);
} else {
writeDist2XML(d, os);
}
}
}