Clover coverage report - baseCode - 0.2.5
Coverage timestamp: Tue Apr 12 2005 11:31:58 EDT
Overview   Package   File
    FRAMES   NO FRAMES  
file stats: LOC: 208   Methods: 8
NCLOC: 155   Classes: 2
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 Source file Conditionals Statements Methods TOTAL
GOParser.java 91.3% 89.4% 87.5% 89.9%
coverage coverage
 1    
 package baseCode.xml;
 2    
 
 3    
 import java.io.IOException;
 4    
 import java.io.InputStream;
 5    
 import java.util.HashMap;
 6    
 import java.util.Iterator;
 7    
 import java.util.Map;
 8    
 
 9    
 import org.xml.sax.Attributes;
 10    
 import org.xml.sax.InputSource;
 11    
 import org.xml.sax.SAXException;
 12    
 import org.xml.sax.XMLReader;
 13    
 import org.xml.sax.helpers.DefaultHandler;
 14    
 import org.xml.sax.helpers.XMLReaderFactory;
 15    
 
 16    
 import baseCode.bio.GOEntry;
 17    
 import baseCode.dataStructure.graph.DirectedGraph;
 18    
 import baseCode.dataStructure.graph.DirectedGraphNode;
 19    
 
 20    
 /**
 21    
  * Read in the GO XML file provided by the Gene Ontology Consortium.
 22    
  * <p>
 23    
  * Copyright (c) Columbia University
 24    
  *
 25    
  * @author Paul Pavlidis
 26    
  * @version $Id: GOParser.java,v 1.14 2004/08/04 09:47:44 pavlidis Exp $
 27    
  */
 28    
 public class GOParser {
 29    
 
 30    
    private DirectedGraph m;
 31    
 
 32    
    /**
 33    
     * Get the graph that was created.
 34    
     *
 35    
     * @return a DirectedGraph. Nodes contain OntologyEntry instances.
 36    
     */
 37  1 
    public DirectedGraph getGraph() {
 38  1 
       return m;
 39    
    }
 40    
 
 41    
    /**
 42    
     * Get a simple Map that contains keys that are the GO ids, values are the names. This can replace the functionality
 43    
     * of the GONameReader in classScore.
 44    
     *
 45    
     * @return Map
 46    
     */
 47  0 
    public Map getGONameMap() {
 48  0 
       Map nodes = m.getItems();
 49  0 
       Map result = new HashMap();
 50  0 
       for ( Iterator it = nodes.keySet().iterator(); it.hasNext(); ) {
 51  0 
          DirectedGraphNode node = ( DirectedGraphNode ) nodes.get( it.next() );
 52  0 
          GOEntry e = ( GOEntry ) node.getItem();
 53  0 
          result.put( e.getId().intern(), e.getName().intern() );
 54    
       }
 55  0 
       return result;
 56    
    }
 57    
 
 58  1 
    public GOParser( InputStream i ) throws IOException, SAXException {
 59    
 
 60  1 
       if ( i.available() == 0 ) {
 61  0 
          throw new IOException( "XML stream contains no data." );
 62    
       }
 63    
 
 64  1 
       System.setProperty( "org.xml.sax.driver",
 65    
             "org.apache.xerces.parsers.SAXParser" );
 66    
 
 67  1 
       XMLReader xr = XMLReaderFactory.createXMLReader();
 68  1 
       GOHandler handler = new GOHandler();
 69  1 
       xr.setFeature( "http://xml.org/sax/features/validation", false );
 70  1 
       xr.setFeature( "http://xml.org/sax/features/external-general-entities",
 71    
             false );
 72  1 
       xr.setFeature(
 73    
             "http://apache.org/xml/features/nonvalidating/load-external-dtd",
 74    
             false );
 75  1 
       xr.setContentHandler( handler );
 76  1 
       xr.setErrorHandler( handler );
 77  1 
       xr.setEntityResolver( handler );
 78  1 
       xr.setDTDHandler( handler );
 79  1 
       xr.parse( new InputSource( i ) );
 80    
 
 81  1 
       m = handler.getResults();
 82    
    }
 83    
 
 84    
 }
 85    
 
 86    
 class GOHandler extends DefaultHandler {
 87    
 
 88    
    private DirectedGraph m;
 89    
 
 90  1 
    public DirectedGraph getResults() {
 91  1 
       return m;
 92    
    }
 93    
 
 94  1 
    public GOHandler() {
 95  1 
       super();
 96  1 
       m = new DirectedGraph();
 97    
    }
 98    
 
 99    
    private boolean inTerm = false;
 100    
    private boolean inDef = false;
 101    
    private boolean inAcc = false;
 102    
    private boolean inName = false;
 103    
    private boolean inPartOf = false;
 104    
    private boolean inIsa = false;
 105    
    private boolean inSyn = false;
 106    
 
 107    
    private String currentAspect;
 108    
    private StringBuffer nameBuf;
 109    
    private StringBuffer accBuf;
 110    
    private StringBuffer defBuf;
 111    
 
 112  917 
    public void startElement( String uri, String name, String qName,
 113    
          Attributes atts ) {
 114    
 
 115  917 
       if ( name.equals( "term" ) ) {
 116  68 
          inTerm = true;
 117  849 
       } else if ( name.equals( "accession" ) ) {
 118  68 
          accBuf = new StringBuffer();
 119  68 
          inAcc = true;
 120  781 
       } else if ( name.equals( "definition" ) ) {
 121  65 
          defBuf = new StringBuffer();
 122  65 
          inDef = true;
 123  716 
       } else if ( name.equals( "is_a" ) ) {
 124  77 
          inIsa = true;
 125  77 
          String res = atts.getValue( "rdf:resource" );
 126  77 
          String parent = res.substring( res.lastIndexOf( '#' ) + 1, res
 127    
                .length() );
 128    
 
 129  77 
          if ( !m.containsKey( parent ) ) {
 130  9 
             m.addNode( parent, new GOEntry( parent, "no name yet",
 131    
                   "no definition yet", "no aspect yet" ) );
 132    
          }
 133  77 
          String currentTerm = accBuf.toString();
 134  77 
          m.addParentTo( currentTerm, parent );
 135    
 
 136  639 
       } else if ( name.equals( "part_of" ) ) {
 137  1 
          inPartOf = true;
 138  1 
          String res = atts.getValue( "rdf:resource" );
 139  1 
          String parent = res.substring( res.lastIndexOf( '#' ) + 1, res
 140    
                .length() );
 141    
 
 142  1 
          if ( !m.containsKey( parent ) ) {
 143  0 
             m.addNode( parent, new GOEntry( parent, "no name yet",
 144    
                   "no definition yet", "no aspect yet" ) );
 145    
          }
 146  1 
          String currentTerm = accBuf.toString();
 147  1 
          m.addParentTo( currentTerm, parent );
 148  638 
       } else if ( name.equals( "synonym" ) ) {
 149  29 
          inSyn = true;
 150  609 
       } else if ( name.equals( "name" ) ) {
 151  68 
          nameBuf = new StringBuffer();
 152  68 
          inName = true;
 153    
       }
 154    
    }
 155    
 
 156  917 
    public void endElement( String uri, String name, String qName ) {
 157  917 
       if ( name.equals( "term" ) ) {
 158  68 
          inTerm = false;
 159  849 
       } else if ( name.equals( "accession" ) ) {
 160  68 
          inAcc = false;
 161  68 
          String currentTerm = accBuf.toString();
 162  68 
          m.addNode( currentTerm, new GOEntry( currentTerm, "no name yet",
 163    
                "no definition yet", "no aspect yet" ) );
 164  781 
       } else if ( name.equals( "definition" ) ) {
 165  65 
          String currentTerm = accBuf.toString();
 166  65 
          ( ( GOEntry ) m.getNodeContents( currentTerm ) ).setDefinition( defBuf
 167    
                .toString().intern() );
 168  65 
          inDef = false;
 169  716 
       } else if ( name.equals( "is_a" ) ) {
 170  77 
          inIsa = false;
 171  639 
       } else if ( name.equals( "part_of" ) ) {
 172  1 
          inPartOf = false;
 173  638 
       } else if ( name.equals( "synonym" ) ) {
 174  29 
          inSyn = false;
 175  609 
       } else if ( name.equals( "name" ) ) {
 176  68 
          inName = false;
 177  68 
          String currentTerm = accBuf.toString();
 178    
 
 179  68 
          String currentName = nameBuf.toString().intern();
 180    
 
 181  68 
          ( ( GOEntry ) m.getNodeContents( currentTerm ) ).setName( currentName );
 182    
 
 183  68 
          if ( currentName.equals( "molecular_function" )
 184    
                || currentName.equals( "biological_process" )
 185    
                || currentName.equals( "cellular_component" ) ) {
 186  1 
             currentAspect = currentName;
 187    
          }
 188    
 
 189  68 
          ( ( GOEntry ) m.getNodeContents( currentTerm ) )
 190    
                .setAspect( currentAspect );
 191    
 
 192    
       }
 193    
    }
 194    
 
 195  1770 
    public void characters( char ch[], int start, int length ) {
 196    
 
 197  1770 
       if ( inTerm ) {
 198  1698 
          if ( inAcc ) {
 199  68 
             accBuf.append( ch, start, length );
 200  1630 
          } else if ( inDef ) {
 201  70 
             defBuf.append( ch, start, length );
 202  1560 
          } else if ( inName ) {
 203  69 
             nameBuf.append( ch, start, length );
 204    
          }
 205    
       }
 206    
    }
 207    
 
 208    
 }
 
CloverReport generated by Clover v1.2.3
Tue Apr 12 2005 11:31:59 EDT.		   30 day Evaluation Version distributed via the Maven Jar Repository. Clover is not free. You have 30 days to evaluate it.