PDB2KEGG step 1done during BH2010

Value

Script

URL inputURL = null;
if (base != void) {
  inputURL = new URL(new URL(base), url);
}
else {
  inputURL = new URL(url);
}
URLConnection con = inputURL.openConnection();
InputStream in = con.getInputStream();

InputStreamReader isr = new InputStreamReader(in);
Reader inReader = new BufferedReader(isr);

StringBuffer buf = new StringBuffer();
int ch;
while ((ch = inReader.read()) > -1) {
  buf.append((char)ch);
}
inReader.close();
contents = buf.toString();


//String NEWLINE = System.getProperty("line.separator");
//
//URL inputURL = null;
//if (base != void) {
//	inputURL = new URL(new URL(base), url);
//} else {
//	inputURL = new URL(url);
//}
//StringBuffer result = new StringBuffer();
//BufferedReader reader = new BufferedReader(new InputStreamReader(inputURL.openStream()));
//String line = null;
//while ((line = reader.readLine()) != null) {
//	result.append(line);
//	result.append(NEWLINE);
//}
//
//contents = result.toString();

Script

List split = new ArrayList();
if (!string.equals("")) {
	String regexString = ",";
	if (regex != void) {
		regexString = regex;
	}
	String[] result = string.split(regexString);
	for (int i = 0; i < result.length; i++) {
		split.add(result[i]);
	}
}

Value

Script

import java.util.regex.*;

filteredlist = new ArrayList();
Pattern thePat = Pattern.compile(regex);
int theGroup = Integer.parseInt(group);

for (Iterator i = stringlist.iterator(); i.hasNext();) {
	String item = (String) i.next();
	Matcher matcher = thePat.matcher(item);

	if (matcher.find()) {
		filteredlist.add(matcher.group(theGroup));
	}
}

Value

Value

Script

//out0 = "http" + in0.toLowerCase();
out0 = "http" + in0;

Value

Script

import com.hp.hpl.jena.rdf.model.*;

Model model = ModelFactory.createDefaultModel();

//CONSTRUCT {?s ?p ?o . } WHERE {?s ?p ?o . FILTER (?s = )}
model.read(sparql_endpoint + "?default-graph-uri=&query=CONSTRUCT+{%3Fs+%3Fp+%3Fo+.+}+WHERE+{%3Fs+%3Fp+%3Fo+.+FILTER+(%3Fs+%3D+%3C" + bmuri + "%3E)}&format=application%2Frdf%2Bxml&debug=on&timeout=");

StringWriter writer = new StringWriter (  ) ; 
model.write( writer, "N-TRIPLE");

ntriples = writer.toString (  ) ;

Value

Value

Script

ntriples = "<"+uri+">   .";
ntriples = ntriples + "\n<"+uri+">  \"type_structure\" .";
ntriples = ntriples + "\n<"+uri+">  <"+uri.replace("http://pdbj.org/","http://bio2rdf.org/pdb:")+"> .";