If you take a closer look at the
WSDL file describing the ClustalW
WebService, you can see two methods belonging together.
request and response
request_orig and
response_orig
Bioinformatics programs often
perform computation on large data sets and therefore require
much CPU time. This can cause problems like http connection
timeouts (usually after 5 minutes) during online usage. To
avoid such problems when using the ClustalW WebService we use a
technique called
Request and Reply with polling based on
BiBiWS. First the client side (e.g. your program) requests a
ClustalW job submitting the necessary data (parameter and data)
and gets an
id after the job is started. Afterwards the
client can request the result by calling the corresponding
response method with the
id returned earlier. If the
ClustalW job is not finished, the user gets a status code with
an enhanced description of current status back (see
HOBIT status
codes for more information).
request /
request_orig
The request / request_orig method get an parameter array (see
table below for an example param array - default values in
bold) and sequence data either as SequenceML (request) or Fasta
format (request_orig) and returns either a unique id or in case
of an error a fault message.
| key |
value |
description |
| MATRIX |
BLOSUM, PAM, GONNET or ID |
Protein weight matrix (optional) |
| GAPOPEN |
Integer value |
gap opening penalty (optional) |
| GAPEXT |
Integer value |
gap extension penalty (optional |
note:
All parameters above are optional!
response
The response method gets the id returned by the
request method as input parameter and returns the calculated
result as ...
The Example Java clients are based on
Apache Axis.
ClustalWCOrig.java deals with the
original methods of clustalW, accepting Fasta as sequence input
data and return Fasta alignment as output.
ClustalWC.java uses the XML based methods
(request and response). Both sample clients implements the
Response/Reply with polling technique through active
waiting.
