/*
* CSVExporterParser.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.inference.model.Parameter;
import dr.util.FileHelpers;
import dr.util.TabularData;
import dr.xml.*;
import java.io.File;
import java.io.FileWriter;
import java.io.IOException;
import java.io.PrintWriter;
import java.util.ArrayList;
import java.util.List;
/**
* @author Joseph Heled
* <p/>
* Very lame so far. need checks for possible qouting of elements.
*/
public class CSVExporterParser extends AbstractXMLObjectParser {
final static public String CSV_EXPORT = "CSVexport";
public String getParserName() {
return CSV_EXPORT;
}
public String getParserDescription() {
return "Write tabular data as an CSV file.";
}
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
final String fileName = xo.getStringAttribute(FILE_NAME);
final PrintWriter writer = XMLParser.getFilePrintWriter(xo, fileName);
final String sep = xo.getAttribute(SEPARATOR, "\t");
for (int k = 0; k < xo.getChildCount(); ++k) {
final XMLObject columns = (XMLObject) xo.getChild(k);
if (columns.getName().equals(COLUMNS)) {
TabularData source = (TabularData) columns.getChild(TabularData.class);
// look for columns
List<Integer> iColumns = new ArrayList<Integer>();
List<Parameter[]> adds = new ArrayList<Parameter[]>();
int maxAdds = 0;
for (int nc = 0; nc < columns.getChildCount(); ++nc) {
final Object child = columns.getChild(nc);
if (child instanceof XMLObject) {
final XMLObject column = (XMLObject) child;
if (column.getName().equals(COLUMN)) {
final String name = column.getStringAttribute(COLUMN_NAME);
final int n = source.getColumn(name);
if (n < 0) {
throw new XMLParseException("column '" + name + "' not found in log.");
}
iColumns.add(n);
final int nAddtional = column.getChildCount();
Parameter[] additionals = nAddtional > 0 ? new Parameter[nAddtional] : null;
for (int nc1 = 0; nc1 < nAddtional; ++nc1) {
additionals[nc1] = (Parameter) column.getChild(nc1);
}
maxAdds = Math.max(maxAdds, nAddtional);
adds.add(additionals);
}
}
}
final boolean hasAllAttribute = columns.hasAttribute(ALL_COLUMNS);
if (iColumns.size() == 0) {
// when no columns specified - default is all
if (!hasAllAttribute || columns.getBooleanAttribute(ALL_COLUMNS)) {
for (int nc = 0; nc < source.nColumns(); ++nc) {
iColumns.add(nc);
adds.add(null);
}
}
} else {
// some column specification
if (hasAllAttribute && columns.getBooleanAttribute(ALL_COLUMNS)) {
for (int nc = 0; nc < source.nColumns(); ++nc) {
if (!iColumns.contains(nc)) {
iColumns.add(nc);
adds.add(null);
}
}
}
}
if (columns.hasAttribute(AS_ROWS) && columns.getBooleanAttribute(AS_ROWS)) {
for (int nc = 0; nc < iColumns.size(); ++nc) {
writer.print(source.columnName(iColumns.get(nc)));
for (int nr = 0; nr < source.nRows(); ++nr) {
final Object value = source.data(nr, iColumns.get(nc));
writer.print(sep);
writer.print(value);
}
for (int nr = 0; nr < maxAdds; ++nr) {
final Parameter[] addsnc = adds.get(nc);
if (addsnc != null && nr < addsnc.length) {
final Object value = addsnc[nr].getParameterValues()[0];
writer.print(sep);
writer.print(value);
}
}
writer.println();
}
} else {
for (int nc = 0; nc < iColumns.size(); ++nc) {
if (nc > 0) {
writer.print(sep);
}
writer.print(source.columnName(iColumns.get(nc)));
}
writer.println();
for (int nr = 0; nr < source.nRows(); ++nr) {
for (int nc = 0; nc < iColumns.size(); ++nc) {
if (nc > 0) {
writer.print(sep);
}
final Object value = source.data(nr, iColumns.get(nc));
writer.print(value);
}
writer.println();
}
for (int nr = 0; nr < maxAdds; ++nr) {
for (int nc = 0; nc < iColumns.size(); ++nc) {
if (nc > 0) {
writer.print(sep);
}
final Parameter[] addsnc = adds.get(nc);
if (addsnc != null && nr < addsnc.length) {
final Object value = addsnc[nr].getParameterValues()[0];
writer.print(value);
}
}
writer.println();
}
}
}
}
writer.close();
return null;
}
public static final String FILE_NAME = "fileName";
public static final String SEPARATOR = "separator";
public static final String COLUMNS = "columns";
public static final String ALL_COLUMNS = "all";
public static final String AS_ROWS = "rows";
public static final String COLUMN = "CSVcolumn";
public static final String COLUMN_NAME = "name";
public XMLSyntaxRule[] getSyntaxRules() {
return new XMLSyntaxRule[]{
new StringAttributeRule(FILE_NAME,
"The name of a BEAST log file (can not include trees, which should be logged separately"),
new StringAttributeRule(SEPARATOR, "Values separator (default is tab)", true),
new ElementRule(COLUMNS, new XMLSyntaxRule[]{
AttributeRule.newBooleanRule(ALL_COLUMNS, true,
"Dump all columns. default is TRUE when no columns are specified, FALSE otherwise"),
AttributeRule.newBooleanRule(AS_ROWS, true,
"Write data in rows (default is columns)"),
new ElementRule(TabularData.class),
new ElementRule(COLUMN, new XMLSyntaxRule[]{
AttributeRule.newStringArrayRule(COLUMN_NAME),
new ElementRule(Parameter.class)
}, "column name", 0, Integer.MAX_VALUE)
}, "A subset of columns from one source", 1, Integer.MAX_VALUE)
};
}
public Class getReturnType() {
return CSVExporterParser.class; //TODO write CSVExporter
}
}