2 // FORESTER -- software libraries and applications
3 // for evolutionary biology research and applications.
5 // Copyright (C) 2008-2009 Christian M. Zmasek
6 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
9 // This library is free software; you can redistribute it and/or
10 // modify it under the terms of the GNU Lesser General Public
11 // License as published by the Free Software Foundation; either
12 // version 2.1 of the License, or (at your option) any later version.
14 // This library is distributed in the hope that it will be useful,
15 // but WITHOUT ANY WARRANTY; without even the implied warranty of
16 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
17 // Lesser General Public License for more details.
19 // You should have received a copy of the GNU Lesser General Public
20 // License along with this library; if not, write to the Free Software
21 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
23 // Contact: phylosoft @ gmail . com
24 // WWW: https://sites.google.com/site/cmzmasek/home/software/forester
26 package org.forester.io.parsers.phyloxml.data;
28 import java.util.ArrayList;
29 import java.util.List;
31 import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;
32 import org.forester.io.parsers.phyloxml.PhyloXmlMapping;
33 import org.forester.io.parsers.phyloxml.XmlElement;
34 import org.forester.phylogeny.data.Distribution;
35 import org.forester.phylogeny.data.PhylogenyData;
36 import org.forester.phylogeny.data.Point;
37 import org.forester.phylogeny.data.Polygon;
39 public class DistributionParser implements PhylogenyDataPhyloXmlParser {
41 private static final PhylogenyDataPhyloXmlParser _instance;
44 _instance = new DistributionParser();
46 catch ( final Throwable e ) {
47 throw new RuntimeException( e.getMessage() );
51 private DistributionParser() {
55 public PhylogenyData parse( final XmlElement element ) throws PhyloXmlDataFormatException {
57 List<Point> points = null;
58 List<Polygon> polygons = null;
59 for( int i = 0; i < element.getNumberOfChildElements(); ++i ) {
60 final XmlElement child_element = element.getChildElement( i );
61 if ( child_element.getQualifiedName().equals( PhyloXmlMapping.DISTRIBUTION_DESC ) ) {
62 desc = child_element.getValueAsString();
64 else if ( child_element.getQualifiedName().equals( PhyloXmlMapping.POINT ) ) {
65 if ( points == null ) {
66 points = new ArrayList<Point>();
68 points.add( ( Point ) PointParser.getInstance().parse( child_element ) );
70 else if ( child_element.getQualifiedName().equals( PhyloXmlMapping.POLYGON ) ) {
71 if ( polygons == null ) {
72 polygons = new ArrayList<Polygon>();
74 polygons.add( ( Polygon ) PolygonParser.getInstance().parse( child_element ) );
77 return new Distribution( desc, points, polygons );
80 public static PhylogenyDataPhyloXmlParser getInstance() {