/*
* TreeTraceAnalysisParser.java
*
* Copyright (c) 2002-2015 Alexei Drummond, Andrew Rambaut and Marc Suchard
*
* This file is part of BEAST.
* See the NOTICE file distributed with this work for additional
* information regarding copyright ownership and licensing.
*
* BEAST is free software; you can redistribute it and/or modify
* it under the terms of the GNU Lesser General Public License as
* published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
*
* BEAST is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU Lesser General Public License for more details.
*
* You should have received a copy of the GNU Lesser General Public
* License along with BEAST; if not, write to the
* Free Software Foundation, Inc., 51 Franklin St, Fifth Floor,
* Boston, MA 02110-1301 USA
*/
package dr.evomodelxml;
import dr.evolution.io.Importer;
import dr.evolution.io.NewickImporter;
import dr.evolution.tree.Tree;
import dr.evomodel.tree.TreeTraceAnalysis;
import dr.xml.*;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.FileReader;
import java.io.Reader;
/**
* @author Alexei Drummond
* @version $Id: TreeTraceAnalysisParser.java,v 1.6 2005/05/24 20:25:58 rambaut Exp $
*/
public class TreeTraceAnalysisParser extends AbstractXMLObjectParser {
public final static String TREE_TRACE_ANALYSIS = "treeTraceAnalysis";
public final static String BURN_IN = "burnIn";
public final static String MIN_CLADE_PROBABILITY = "minCladeProbability";
public final static String CRED_SET_PROBABILITY = "credSetProbability";
public static final String FILE_NAME = "fileName";
public final static String REFERENCE_TREE = "referenceTree";
public final static String SHORT_REPORT = "shortReport";
public String getParserName() {
return TREE_TRACE_ANALYSIS;
}
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
try {
Reader reader;
String fileName = xo.getStringAttribute(FILE_NAME);
String name;
try {
File file = new File(fileName);
name = file.getName();
String parent = file.getParent();
if (!file.isAbsolute()) {
parent = System.getProperty("user.dir");
}
// System.out.println("Writing log file to "+parent+System.getProperty("path.separator")+name);
reader = new FileReader(new File(parent, name));
} catch (FileNotFoundException fnfe) {
throw new XMLParseException("File '" + fileName + "' can not be opened for " + getParserName() + " element.");
}
// leaving the burnin attribute off will result in 10% being used
int burnin = xo.getAttribute(BURN_IN, -1);
double minCladeProbability = xo.getAttribute(MIN_CLADE_PROBABILITY, 0.5);
double credSetProbability = xo.getAttribute(CRED_SET_PROBABILITY, 0.95);
Tree referenceTree = null;
Reader refReader;
if (xo.hasAttribute(REFERENCE_TREE)) {
String referenceName = xo.getStringAttribute(REFERENCE_TREE);
try {
File refFile = new File(referenceName);
String refName = refFile.getName();
String parent = refFile.getParent();
if (!refFile.isAbsolute()) {
parent = System.getProperty("user.dir");
}
refReader = new FileReader(new File(parent, refName));
} catch (FileNotFoundException fnfe) {
throw new XMLParseException("File '" + fileName + "' can not be opened for " + getParserName() + " element.");
}
try {
NewickImporter importTree = new NewickImporter(refReader);
if (importTree.hasTree()) {
referenceTree = importTree.importNextTree();
}
} catch (Importer.ImportException iee) {
throw new XMLParseException("Reference file '" + referenceName + "' is empty.");
}
}
boolean shortReport = xo.getAttribute(SHORT_REPORT, false);
TreeTraceAnalysis analysis = TreeTraceAnalysis.analyzeLogFile(new Reader[]{reader}, burnin, true);
if (shortReport) {
analysis.shortReport(name, referenceTree, true, credSetProbability);
} else {
analysis.report(minCladeProbability, credSetProbability, 0);
}
System.out.println();
System.out.flush();
return analysis;
} catch (java.io.IOException ioe) {
throw new XMLParseException(ioe.getMessage());
}
}
//************************************************************************
// AbstractXMLObjectParser implementation
//************************************************************************
public String getParserDescription() {
return "Analyses and reports on a trace consisting of trees.";
}
public Class getReturnType() {
return TreeTraceAnalysis.class;
}
public XMLSyntaxRule[] getSyntaxRules() {
return rules;
}
private final XMLSyntaxRule[] rules = {
new StringAttributeRule(FILE_NAME, "name of a tree log file", "trees.log"),
AttributeRule.newIntegerRule(BURN_IN, true),
AttributeRule.newDoubleRule(MIN_CLADE_PROBABILITY, true),
AttributeRule.newDoubleRule(CRED_SET_PROBABILITY, true),
AttributeRule.newBooleanRule(SHORT_REPORT, true),
AttributeRule.newStringRule(REFERENCE_TREE, true)
};
}