001/*
002 *                    BioJava development code
003 *
004 * This code may be freely distributed and modified under the
005 * terms of the GNU Lesser General Public Licence.  This should
006 * be distributed with the code.  If you do not have a copy,
007 * see:
008 *
009 *      http://www.gnu.org/copyleft/lesser.html
010 *
011 * Copyright for this code is held jointly by the individual
012 * authors.  These should be listed in @author doc comments.
013 *
014 * For more information on the BioJava project and its aims,
015 * or to join the biojava-l mailing list, visit the home page
016 * at:
017 *
018 *      http://www.biojava.org/
019 *
020 * Created on May 10, 2010
021 * Author: Andreas Prlic
022 *
023 */
024
025package org.biojava.nbio.structure.align.xml;
026
027import org.biojava.nbio.core.util.PrettyXMLWriter;
028import org.w3c.dom.Document;
029import org.w3c.dom.NamedNodeMap;
030import org.w3c.dom.Node;
031import org.w3c.dom.NodeList;
032import org.xml.sax.InputSource;
033import org.xml.sax.SAXException;
034import org.xml.sax.SAXParseException;
035
036import javax.xml.parsers.DocumentBuilder;
037import javax.xml.parsers.DocumentBuilderFactory;
038import java.io.IOException;
039import java.io.PrintWriter;
040import java.io.StringReader;
041import java.io.StringWriter;
042
043public class HasResultXMLConverter
044{
045
046
047
048
049        /** return flag if the server has a result
050         *
051         * @param hasResult
052         * @return flag if there is a result
053         */
054        public String toXML(boolean hasResult) throws IOException{
055                StringWriter swriter = new StringWriter();
056
057                PrintWriter writer = new PrintWriter(swriter);
058                PrettyXMLWriter xml = new PrettyXMLWriter(writer);
059
060                xml.openTag("alignment");
061                xml.attribute("hasResult", String.valueOf(hasResult));
062                xml.closeTag("alignment");
063                xml.close();
064                return swriter.toString();
065        }
066
067        public boolean fromXML(String xml) {
068
069                boolean hasResult = false;
070
071                try
072                {
073                        //Convert string to XML document
074                        DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
075                        DocumentBuilder db = factory.newDocumentBuilder();
076                        InputSource inStream = new InputSource();
077                        inStream.setCharacterStream(new StringReader(xml));
078                        Document doc = db.parse(inStream);
079
080                        // normalize text representation
081                        doc.getDocumentElement().normalize();
082
083
084                        //Element rootElement = doc.getDocumentElement();
085
086                        NodeList listOfAlignments = doc.getElementsByTagName("alignment");
087                        //int numArrays = listOfAlignments.getLength();
088                        //System.out.println("got " + numArrays + " alignment results.");
089                        // go over the blocks
090
091
092                        for(int afpPos=0; afpPos<listOfAlignments.getLength() ; afpPos++)
093                        {
094
095                                Node rootElement       = listOfAlignments.item(afpPos);
096
097                                String flag = getAttribute(rootElement,"hasResult");
098                                //System.out.println("got flag from server:" + flag);
099                                if (flag.equals("true"))
100                                        hasResult = true;
101
102                        }
103                }
104                catch (SAXParseException err)
105                {
106                        System.out.println ("** Parsing error" + ", line "
107                                        + err.getLineNumber () + ", uri " + err.getSystemId ());
108                        System.out.println(" " + err.getMessage ());
109                }
110                catch (SAXException e)
111                {
112                        Exception x = e.getException ();
113                        ((x == null) ? e : x).printStackTrace ();
114                }
115                catch (Throwable t)
116                {
117                        t.printStackTrace ();
118                }
119
120                return hasResult;
121        }
122
123
124        private static String getAttribute(Node node, String attr){
125                if( ! node.hasAttributes())
126                        return null;
127
128                NamedNodeMap atts = node.getAttributes();
129
130                if ( atts == null)
131                        return null;
132
133                Node att = atts.getNamedItem(attr);
134                if ( att == null)
135                        return null;
136
137                String value = att.getTextContent();
138
139                return value;
140
141        }
142}