Perform a multiple sequence alignment using the MAFFT tool (see http://align.bmr.kyushu-u.ac.jp/mafft/software/). The EBI's WSMafft web service (see http://www.ebi.ac.uk/Tools/webservices/services/mafft) is used to access to tool.
Submit a MAFFT analysis job (see http://www.ebi.ac.uk/Tools/webservices/services/mafft#runmafft_params_content)
http://www.ebi.ac.uk/Tools/webservices/wsdl/WSMafft.wsdl
runMafft
MAFFT parameters.
1
org.embl.ebi.escience.scuflworkers.java.XMLInputSplitter
Wrap input data in list.
org.embl.ebi.escience.scuflworkers.java.XMLInputSplitter
Add type to input data.
sequence
org.embl.ebi.escience.scuflworkers.java.XMLInputSplitter
Get the results of a job (see http://www.ebi.ac.uk/Tools/webservices/services/mafft#poll_jobid_type)
tooloutput
http://www.ebi.ac.uk/Tools/webservices/wsdl/WSMafft.wsdl
poll
Convert byte[] from service into string.
org.embl.ebi.escience.scuflworkers.java.ByteArrayToString
Check for job completion.
Fail if job not done.
org.embl.ebi.escience.scuflworkers.java.FailIfFalse
Map job status code to true/false.
if(job_status.equals("DONE")) {
is_done = "true";
} else {
is_done = "false";
}
job_status
is_done
Get the status of a submited job (see http://www.ebi.ac.uk/Tools/webservices/services/mafft#checkstatus_jobid)
http://www.ebi.ac.uk/Tools/webservices/wsdl/WSMafft.wsdl
checkStatus
EBI job ID for MAFFT job to check.
Status of the job.
User e-mail address.
Sequences to align (fasta format recommended).
EBI job identifier
MAFFT alignment of sequences. By default in fasta format.
Completed
EBI_MAFFT_poll_job
Get_alignment
Scheduled
Running