G-language Genome Analysis Environment - Basic sequence manipulations

None

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;

Name	Type	Description
codon_usage	wsdl	Wsdl http://soap.g-language.org/g-language.wsdl Wsdl Operation codon_usage
getImage0	localworker	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;
gcskew	wsdl	Wsdl http://soap.g-language.org/g-language.wsdl Wsdl Operation gcskew
getImage1	localworker	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;
genomicskew	wsdl	Wsdl http://soap.g-language.org/g-language.wsdl Wsdl Operation genomicskew
getImage2	localworker	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;
view_cds	wsdl	Wsdl http://soap.g-language.org/g-language.wsdl Wsdl Operation view_cds
getImage3	localworker	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;
cai	wsdl	Wsdl http://soap.g-language.org/g-language.wsdl Wsdl Operation cai
gcwin	wsdl	Wsdl http://soap.g-language.org/g-language.wsdl Wsdl Operation gcwin
gcskew_cumulative	wsdl	Wsdl http://soap.g-language.org/g-language.wsdl Wsdl Operation gcskew
gcskew_cumulative_params	xmlsplitter
String_Constant	stringconstant	Value 1
getImage6	localworker	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;
getImage5	localworker	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;
getImage4	localworker	Script BufferedReader getReader (String fileUrl) throws IOException { InputStreamReader reader; try { reader = new FileReader(fileUrl); } catch (FileNotFoundException e) { // try a real URL instead URL url = new URL(fileUrl); reader = new InputStreamReader (url.openStream()); } return new BufferedReader(reader); } StringBuffer sb = new StringBuffer(4000); BufferedReader in = getReader(fileurl); String str; String lineEnding = System.getProperty("line.separator"); while ((str = in.readLine()) != null) { sb.append(str); sb.append(lineEnding); } in.close(); filecontents = sb.toString();
gcsi	wsdl	Wsdl http://soap.g-language.org/g-language.wsdl Wsdl Operation gcsi
gcsi_result	xmlsplitter
find_ori_ter	wsdl	Wsdl http://soap.g-language.org/g-language.wsdl Wsdl Operation find_ori_ter
find_ori_ter_result	xmlsplitter
sequence	stringconstant	Value mgen
base_information_content	wsdl	Wsdl http://soap.g-language.org/g-language.wsdl Wsdl Operation base_information_content
base_entropy	wsdl	Wsdl http://soap.g-language.org/g-language.wsdl Wsdl Operation base_entropy
base_relative_entropy	wsdl	Wsdl http://soap.g-language.org/g-language.wsdl Wsdl Operation base_relative_entropy

Name	Description
codon_usage
gcskew
genomicskew
view_cds
cai
gcsi
find_ori_ter
gcwin
gcskew_cumulative
base_information_content
base_entropy
base_relative_entropy

Source	Sink
sequence:value	codon_usage:in0
sequence:value	codon_usage:sequence
codon_usage:result	getImage0:url
sequence:value	gcskew:in0
sequence:value	gcskew:sequence
gcskew:result	getImage1:url
sequence:value	genomicskew:in0
sequence:value	genomicskew:sequence
genomicskew:result	getImage2:url
sequence:value	view_cds:in0
sequence:value	view_cds:sequence
view_cds:result	getImage3:url
sequence:value	cai:in0
sequence:value	cai:sequence
sequence:value	gcwin:in0
sequence:value	gcwin:sequence
gcskew_cumulative_params:output	gcskew_cumulative:params
sequence:value	gcskew_cumulative:in0
sequence:value	gcskew_cumulative:sequence
String_Constant:value	gcskew_cumulative_params:cumulative
gcskew_cumulative:result	getImage6:url
gcwin:result	getImage5:url
cai:result	getImage4:fileurl
sequence:value	gcsi:in0
sequence:value	gcsi:sequence
gcsi:result	gcsi_result:input
sequence:value	find_ori_ter:in0
sequence:value	find_ori_ter:sequence
find_ori_ter:result	find_ori_ter_result:input
sequence:value	base_information_content:in0
sequence:value	base_information_content:sequence
sequence:value	base_entropy:in0
sequence:value	base_entropy:sequence
sequence:value	base_relative_entropy:in0
sequence:value	base_relative_entropy:sequence
getImage0:image	codon_usage
getImage1:image	gcskew
getImage2:image	genomicskew
getImage3:image	view_cds
getImage4:filecontents	cai
gcsi_result:result	gcsi
find_ori_ter_result:result	find_ori_ter
getImage5:image	gcwin
getImage6:image	gcskew_cumulative
base_information_content:result	base_information_content
base_entropy:result	base_entropy
base_relative_entropy:result	base_relative_entropy

G-language Genome Analysis Environment - Basic sequence manipulations

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