BLAST workflow

Script

String url = "http://xml.ddbj.nig.ac.jp/rest/Invoke?";
url += "service=GetEntry&method=getFASTA_DDBJEntry&accession="+accession;

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();

Value

Script

String service = "Blast";
String method = "searchParam";
String program ="blastn";
String database ="ddbjbct";
String encode = "UTF8";

String blastQuery = "service=" + service
		+ "&method=" + method
		+ "&program=" + program
		+ "&database=" + database 
		+ "&query="+ URLEncoder.encode(query,encode)
		+ "¶m="+ URLEncoder.encode(param,encode);

Script

String service = "Blast";
String method = "searchParam";
String program  ="blastx";
String database ="SWISS";
String encode = "UTF8";

String blastQuery = "service=" + service
		+ "&method=" + method
		+ "&program=" + program
		+ "&database=" + database 
		+ "&query="+ URLEncoder.encode(query,encode)
		+ "¶m="+ URLEncoder.encode(param,encode);

Script

String service = "Blast";
String method = "searchParam";
String program  ="blastx";
String database ="PDB";
String encode = "UTF8";

String blastQuery = "service=" + service
		+ "&method=" + method
		+ "&program=" + program
		+ "&database=" + database 
		+ "&query="+ URLEncoder.encode(query,encode)
		+ "¶m="+ URLEncoder.encode(param,encode);

Script

URL url = new URL("http://xml.nig.ac.jp/rest/Invoke");

URLConnection urlc = url.openConnection();

urlc.setDoOutput(true);
urlc.setAllowUserInteraction(false);

PrintStream ps = new PrintStream(urlc.getOutputStream());
ps.print(query);
ps.close();

BufferedReader br = new BufferedReader(new InputStreamReader(urlc.getInputStream()));
StringBuffer sb = new StringBuffer();
String line = null;
while ((line = br.readLine()) != null) {
	sb.append(line + "\n");
}
String contents = sb.toString();
br.close();

Script

URL url = new URL("http://xml.nig.ac.jp/rest/Invoke");

URLConnection urlc = url.openConnection();

urlc.setDoOutput(true);
urlc.setAllowUserInteraction(false);

PrintStream ps = new PrintStream(urlc.getOutputStream());
ps.print(query);
ps.close();

BufferedReader br = new BufferedReader(new InputStreamReader(urlc.getInputStream()));
StringBuffer sb = new StringBuffer();
String line = null;
while ((line = br.readLine()) != null) {
	sb.append(line + "\n");
}
String contents = sb.toString();
br.close();

Script

URL url = new URL("http://xml.nig.ac.jp/rest/Invoke");

URLConnection urlc = url.openConnection();

urlc.setDoOutput(true);
urlc.setAllowUserInteraction(false);

PrintStream ps = new PrintStream(urlc.getOutputStream());
ps.print(query);
ps.close();

BufferedReader br = new BufferedReader(new InputStreamReader(urlc.getInputStream()));
StringBuffer sb = new StringBuffer();
String line = null;
while ((line = br.readLine()) != null) {
	sb.append(line + "\n");
}
String contents = sb.toString();
br.close();