G-language Genome Analysis Environment - GC skew analysis (basic)

Script

if ((id == void) || (id == null) || id.equals("")) {
	throw new RunTimeException("port id must have a non-empty value");
}

URL url = new URL ("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?rettype=fasta&db=nucleotide&retmode=text&id=" + id);

BufferedReader reader = new BufferedReader (new InputStreamReader(url.openStream()));
StringWriter writer = new StringWriter();

char[] buffer = new char[1024];
    while (true) {
        int r = reader.read(buffer);
        if (r <= 0) {
            break;
        }
        writer.write(buffer, 0, r);
    }
outputText = writer.toString();

Script

URL inputURL = null;
if (base != void) {
	inputURL = new URL(new URL(base), url);
} else {
	inputURL = new URL(url);
}

byte[] contents;
if (inputURL.openConnection().getContentLength() == -1) {
	// Content size unknown, must read first...
	byte[] buffer = new byte[1024];
	int bytesRead = 0;
	int totalBytesRead = 0;
	InputStream is = inputURL.openStream();
	while (bytesRead != -1) {
		totalBytesRead += bytesRead;
		bytesRead = is.read(buffer, 0, 1024);
	}
	contents = new byte[totalBytesRead];
} else {
	contents = new byte[inputURL.openConnection().getContentLength()];
}
int bytesRead = 0;
int totalBytesRead = 0;
InputStream is = inputURL.openStream();
while (bytesRead != -1) {
	bytesRead = is.read(contents, totalBytesRead, contents.length - totalBytesRead);
	totalBytesRead += bytesRead;
	if (contents.length==totalBytesRead) break;
}

image = contents;

Wsdl

Wsdl Operation

Value

Value

Value

Value

Value

Value

Value