G-language Genome Analysis Environment - Bacteria Analysis System

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
in0	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
in0:value	codon_usage:in0
codon_usage:result	getImage0:url
in0:value	gcskew:in0
gcskew:result	getImage1:url
in0:value	genomicskew:in0
genomicskew:result	getImage2:url
in0:value	view_cds:in0
view_cds:result	getImage3:url
in0:value	cai:in0
in0:value	gcwin:in0
gcskew_cumulative_params:output	gcskew_cumulative:params
in0:value	gcskew_cumulative:in0
String_Constant:value	gcskew_cumulative_params:cumulative
gcskew_cumulative:result	getImage6:url
gcwin:result	getImage5:url
cai:result	getImage4:fileurl
in0:value	gcsi:in0
gcsi:result	gcsi_result:input
in0:value	find_ori_ter:in0
find_ori_ter:result	find_ori_ter_result:input
in0:value	base_information_content:in0
in0:value	base_entropy:in0
in0:value	base_relative_entropy:in0
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 - Bacteria Analysis System

Preview

Run

Run this Workflow in the Taverna Workbench...

Workflow Components

Wsdl

Wsdl Operation

Script

Wsdl

Wsdl Operation

Script

Wsdl

Wsdl Operation

Script

Wsdl

Wsdl Operation

Script

Wsdl

Wsdl Operation

Wsdl

Wsdl Operation

Wsdl

Wsdl Operation

Value

Script

Script

Script

Wsdl

Wsdl Operation

Wsdl

Wsdl Operation

Value

Wsdl

Wsdl Operation

Wsdl

Wsdl Operation

Wsdl

Wsdl Operation

Reviews (0)

Comments (0)

Other workflows that use similar services (10)