KEIO Bioinformatics Web Service - a generating sequence logo image for a set of sequence retrieval via homology search

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
ID	stringconstant	Value FOXP2_HUMAN
togoWS	wsdl	Wsdl http://soap.g-language.org/g-language.wsdl Wsdl Operation togoWS
togoWS_params	xmlsplitter
seq_format1	stringconstant	Value fasta
database	stringconstant	Value swissprot
BLAST_format	stringconstant	Value k2
Get_Image_From_URL	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;
togoWS_2	wsdl	Wsdl http://soap.g-language.org/g-language.wsdl Wsdl Operation togoWS
togoWS_2_params	xmlsplitter
seq_format2	stringconstant	Value fasta
extractalign	soaplab	Endpoint http://www.ebi.ac.uk/soaplab/services/edit.extractalign
Ragion	stringconstant	Value 420-430
checkStatus_BLAST	wsdl	Wsdl http://soap.g-language.org/kbws.wsdl Wsdl Operation checkStatus_retJobid
get_BLAST_Result	wsdl	Wsdl http://soap.g-language.org/kbws.wsdl Wsdl Operation getResult
checkStatus_MUSCLE	wsdl	Wsdl http://soap.g-language.org/kbws.wsdl Wsdl Operation checkStatus_retJobid
get_MUSCLE_Result	wsdl	Wsdl http://soap.g-language.org/kbws.wsdl Wsdl Operation getResult
runWeblogo	wsdl	Wsdl http://soap.g-language.org/kbws.wsdl Wsdl Operation runWeblogo
checkStatus_WebLogo	wsdl	Wsdl http://soap.g-language.org/kbws.wsdl Wsdl Operation checkStatus_retJobid
get_WebLogo_Result	wsdl	Wsdl http://soap.g-language.org/kbws.wsdl Wsdl Operation getResult
E_Value	stringconstant	Value 1e-50
runBlast	wsdl	Wsdl http://soap.g-language.org/kbws.wsdl Wsdl Operation runBlast
runBlast_params	xmlsplitter
runMuscle	wsdl	Wsdl http://soap.g-language.org/kbws.wsdl Wsdl Operation runMuscle

Source	Sink
ID:value	togoWS:query
togoWS_params:output	togoWS:params
seq_format1:value	togoWS_params:format
get_WebLogo_Result:result	Get_Image_From_URL:url
togoWS_2_params:output	togoWS_2:params
get_BLAST_Result:result	togoWS_2:query
seq_format2:value	togoWS_2_params:format
Ragion:value	extractalign:regions
get_MUSCLE_Result:result	extractalign:sequence_direct_data
runBlast:jobid	checkStatus_BLAST:jobid_in
checkStatus_BLAST:jobid_out	get_BLAST_Result:jobid
runMuscle:jobid	checkStatus_MUSCLE:jobid_in
checkStatus_MUSCLE:jobid_out	get_MUSCLE_Result:jobid
extractalign:outseq	runWeblogo:in0
runWeblogo:jobid	checkStatus_WebLogo:jobid
runWeblogo:jobid	checkStatus_WebLogo:jobid_in
checkStatus_WebLogo:jobid_out	get_WebLogo_Result:jobid
togoWS:result	runBlast:in0
runBlast_params:output	runBlast:params
E_Value:value	runBlast_params:e
BLAST_format:value	runBlast_params:m
database:value	runBlast_params:d
togoWS_2:result	runMuscle:in0
Get_Image_From_URL:image	Result

KEIO Bioinformatics Web Service - a generating sequence logo image for a set of sequence retrieval via homology search

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