Run a FASTA or SSEARCH sequence similarity search using the EBI's WSFasta service (see http://www.ebi.ac.uk/Tools/webservices/services/fasta).
Submit the FASTA/SSEARCH job.
http://www.ebi.ac.uk/Tools/webservices/wsdl/WSFasta.wsdl
runFasta
Check for job completion.
org.embl.ebi.escience.scuflworkers.java.FailIfFalse
if(job_status.equals("DONE")) {
is_done = "true";
} else {
is_done = "false";
}
job_status
is_done
http://www.ebi.ac.uk/Tools/webservices/wsdl/WSFasta.wsdl
checkStatus
Wrap the input sequence in a list.
org.embl.ebi.escience.scuflworkers.java.XMLInputSplitter
Input data structure, adds a type to the input sequence.
sequence
org.embl.ebi.escience.scuflworkers.java.XMLInputSplitter
Parameters for the FASTA/SSEARCH job.
50
50
1.0
0.0
1
org.embl.ebi.escience.scuflworkers.java.XMLInputSplitter
Get the hit identifers.
http://www.ebi.ac.uk/Tools/webservices/wsdl/WSFasta.wsdl
getIds
Get the FASTA report as text.
tooloutput
http://www.ebi.ac.uk/Tools/webservices/wsdl/WSFasta.wsdl
poll
Get the FASTA report as XML.
toolxml
http://www.ebi.ac.uk/Tools/webservices/wsdl/WSFasta.wsdl
poll
Unpack plain text FASTA report from byte[] into string.
org.embl.ebi.escience.scuflworkers.java.ByteArrayToString
Unpack XML FASTA report from byte[] into string.
org.embl.ebi.escience.scuflworkers.java.ByteArrayToString
Query sequence (fasta format recommended) or sequence identifer in database:identifer format (e.g. uniprot:wap_rat).
The database to search (e.g. uniprot).
Your e-mail address.
The FASTA program to run (e.g. fasta3, fastf3, fasts3, fastx3, fasty3, tfastx, tfasty).
FASTA program output as plain text. Note the exact format of the output depends on the chosen FASTA program.
FASTA output in an XML format.
List of the identifiers of the hits found.
The identifier of the job at EBI.
Completed
Poll_FASTA_Job
getIds
Scheduled
Running
Completed
Poll_FASTA_Job
Get_Text_Result
Scheduled
Running
Completed
Poll_FASTA_Job
Get_XML_Result
Scheduled
Running