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 */
021
022package org.biojava.bio.program.ssbind;
023
024import org.biojava.bio.search.SearchContentHandler;
025import org.biojava.utils.stax.DelegationManager;
026import org.biojava.utils.stax.StAXContentHandler;
027import org.biojava.utils.stax.StAXContentHandlerBase;
028import org.xml.sax.Attributes;
029import org.xml.sax.SAXException;
030
031/**
032 * <code>SeqSimilarityStAXAdapter</code> is a handler for XML
033 * conforming to the BioJava BlastLike DTD. Together with its modular
034 * delegate handlers it converts XML into calls on a
035 * <code>SearchContentHandler</code> interface. Implementations of the
036 * at interface create various types of Java object from the XML data.
037 *
038 * @author Keith James
039 * @since 1.3
040 */
041public class SeqSimilarityStAXAdapter extends StAXContentHandlerBase
042{
043    public static final String NAMESPACE = "http://www.biojava.org";
044
045    // Incremented on startElement, decremented on endElement. Used to
046    // identify which method calls to handle here and which to
047    // delegate.
048    private int depth;
049
050    // The target handler
051    private SearchContentHandler scHandler;
052    // The name of the program which generated the results
053    private String program = "unknown";
054
055    public void startElement(String            nsURI,
056                             String            localName,
057                             String            qName,
058                             Attributes        attrs,
059                             DelegationManager dm)
060        throws SAXException
061    {
062        depth++;
063
064        if (! nsURI.equals(NAMESPACE))
065            throw new SAXException("Failed to handle Element " + localName
066                                   + " in namespace " + nsURI);
067
068        if (depth == 1)
069        {
070            if (localName.equals("BlastLikeDataSetCollection"))
071            {
072                scHandler.setMoreSearches(true);
073            }
074        }
075        else
076        {
077            if (localName.equals("BlastLikeDataSet"))
078            {
079                scHandler.startSearch();
080                program = attrs.getValue("program");
081                scHandler.addSearchProperty("program", program);
082                scHandler.addSearchProperty("version", attrs.getValue("version"));
083                return;
084            }
085            else if (localName.equals("Header"))
086            {
087                // Capture Header element and subtree
088                dm.delegate(HeaderStAXHandler.HEADER_HANDLER_FACTORY.getHandler(this));
089                return;
090            }
091            else if (localName.equals("Hit"))
092            {
093                // Drop through the Detail element to the Hit elements
094                // and their subtrees
095                dm.delegate(HitStAXHandler.HIT_HANDLER_FACTORY.getHandler(this));
096            }
097        }
098    }
099
100    public void endElement(String             nsURI,
101                           String             localName,
102                           String             qName,
103                           StAXContentHandler handler)
104        throws SAXException
105    {
106        depth--;
107
108        if (depth == 0)
109        {
110            if (localName.equals("BlastLikeDataSetCollection"))
111            {
112                scHandler.setMoreSearches(false);
113            }
114        }
115        else
116        {
117            if (localName.equals("BlastLikeDataSet"))
118            {
119                scHandler.endSearch();
120            }
121        }
122    }
123
124    /**
125     * <code>getSearchContentHandler</code> gets the handler which
126     * will receive the method calls generated by the adapter.
127     *
128     * @return a <code>SearchContentHandler</code>.
129     */
130    public SearchContentHandler getSearchContentHandler()
131    {
132        return scHandler;
133    }
134
135    /**
136     * <code>setSearchContentHandler</code> sets the handler which
137     * will recieve the method calls generated by the adapter.
138     *
139     * @param scHandler a <code>SearchContentHandler</code>.
140     */
141    public void setSearchContentHandler(SearchContentHandler scHandler)
142    {
143        this.scHandler = scHandler;
144    }
145
146    /**
147     * <code>getProgram</code> returns the program type which
148     * generated the results.
149     *
150     * @return a <code>String</code> indicating the progam
151     * name.
152     */
153    String getProgram()
154    {
155        return program;
156    }
157
158    /**
159     * <code>setProgram</code> informs the adapter which program type
160     * it is working on.
161     *
162     * @param program a <code>String</code> indicating the progam
163     * name.
164     */
165    void setProgram(String program)
166    {
167        this.program = program;
168    }
169}