downgrade owl api and reorganised src files

1 files changed, 0 insertions, 129 deletions

diff --git a/test/uk/ac/ox/cs/data/Fragment.java b/test/uk/ac/ox/cs/data/Fragment.java
deleted file mode 100644
index 1038a33..0000000
--- a/test/uk/ac/ox/cs/data/Fragment.java
+++ /dev/null
@@ -1,129 +0,0 @@
-package uk.ac.ox.cs.data;
-
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.FileNotFoundException;
-import java.io.FileOutputStream;
-import java.util.Random;
-
-import org.openrdf.model.Statement;
-import org.openrdf.rio.RDFHandler;
-import org.openrdf.rio.RDFHandlerException;
-import org.openrdf.rio.turtle.TurtleParser;
-import org.openrdf.rio.turtle.TurtleWriter;
-
-import uk.ac.ox.cs.pagoda.util.Utility;
-
-public class Fragment {
-        
-        private TurtleWriter m_writer;
-        private FragmentRDFHandler m_handler; 
-
-        public Fragment(int fragment, String outFile) {
-                try {
-                        m_writer = new TurtleWriter(new FileOutputStream(outFile));
-                } catch (FileNotFoundException e) {
-                        e.printStackTrace();
-                }
-                m_handler = new FragmentRDFHandler(fragment, m_writer); 
-        }
-        
-        public void process(String prefix, String fileName) {
-                FileInputStream istream; 
-                try {
-                        TurtleParser parser = new TurtleParser();
-                        parser.setRDFHandler(m_handler);
-                        
-                        File f = new File(fileName);
-                        if (f.isDirectory())
-                                for (String tFileName: f.list()) {
-                                        if (tFileName.endsWith(".ttl")) {
-                                                parser.parse(istream = new FileInputStream(fileName + Utility.FILE_SEPARATOR + tFileName), prefix);
-                                                istream.close(); 
-                                        }
-                                }
-                        else {
-                                parser.parse(istream = new FileInputStream(fileName), prefix);
-                                istream.close(); 
-                        }
-                } catch (Exception e) {
-                        e.printStackTrace();
-                        Utility.logError("aoaoaoao ~~~~~");
-                        return ;
-                }
-                Utility.logInfo("DONE");
-        }
-
-        public void dispose() {
-                try {
-                        m_writer.endRDF();
-                } catch (RDFHandlerException e) {
-                        e.printStackTrace();
-                } 
-        }
-        
-        public static void main(String[] args) {
-                /**
-                 * for ChEMBL
-                 */
-                Fragment f = new Fragment(100, "data_01.ttl");
-                f.process("http://rdf.ebi.ac.uk/terms/chembl#", "/media/krr-nas-share/Yujiao/ontologies/bio2rdf/chembl/data");
-                
-                /**
-                 * for Reactome
-                 *              "http://www.biopax.org/release/biopax-level3.owl#", 
-                                "/home/scratch/yzhou/ontologies/bio2rdf/reactome"
-                                "/home/scratch/yzhou/ontologies/bio2rdf/reactome/biopaxrdf", 
-                 */
-                
-//              Fragment f = new Fragment(1000, "data_001.ttl");
-//              f.process("http://www.biopax.org/release/biopax-level3.owl#", "/media/krr-nas-share/Yujiao/ontologies/bio2rdf/reactome/data.ttl");
-                
-                f.dispose();
-        }
-        
-}
-
-
-class FragmentRDFHandler implements RDFHandler {
-        
-        int m_mod;
-        TurtleWriter m_writer; 
-        Random m_rand = new Random(); 
-        
-        public FragmentRDFHandler(int mod, TurtleWriter writer) {
-                m_mod = mod;  
-                m_writer = writer; 
-        }
-
-        @Override
-        public void endRDF() throws RDFHandlerException {
-        }
-
-        @Override
-        public void handleComment(String arg0) throws RDFHandlerException {
-                m_writer.handleComment(arg0);
-                Utility.logDebug("handling comment: " + arg0);
-        }
-
-        @Override
-        public void handleNamespace(String arg0, String arg1) throws RDFHandlerException {
-                m_writer.handleNamespace(arg0, arg1);
-        }
-
-        @Override
-        public void handleStatement(Statement arg0) throws RDFHandlerException {
-                if (m_rand.nextInt() % m_mod == 0)
-                        m_writer.handleStatement(arg0);
-        }
-        
-        boolean m_started = false; 
-
-        @Override
-        public void startRDF() throws RDFHandlerException {
-                if (m_started) return ; 
-                m_started = true; 
-                m_writer.startRDF();
-        }
-        
-}
\ No newline at end of file