If you've a closer look at the
WSDL file describing the RNAfold
webservice, you can see two methods belonging together.
request and response
request_orig and
response_orig
Bioinformatic 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 RNAfold WebService we use a
technique called
Request and Reply with polling based on
BiBiWS. First the client side (e.g. your program) requests a
RNAfold 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
RNAfold 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).
Currently the RNAfold WebService support two different pairs of
request/response methods, request/response using
sequenceML as Input and
RNAStructML as Outputformat. Both formats
are supported by
BioDOM. The
request_orig/response_orig pair deals with the original data
formats (Fasta as input and a DotBracket notation as output).
request/request_orig
The request method get two parameter as input - a parameter
array with key/value pairs as described in the following table
and a valid sequenceML document (request) or one or more
sequences in FASTA format (request_orig) - and returns either a
unique id or in case of an error a fault message. (see table
below for an example param array - default values in bold) and
returns either a unique id or in case of an error a fault
message.
| key |
value |
description |
| t |
0 ≤ 37 ≤ 100 |
folding temperature in degree Celsius |
note:
all parameters are optional
response/response_orig
The response/response_orig methods gets the id returned by the
request method as input parameter and returns the calculated
result as
RNAStructML or in DotBraket notation (vienna format).
We offer two slightly different clients written in Java
programming language.
rnafoldCOrig.java uses
request_orig/response_orig functions of pknotsRG WebService.
rnafoldC.java handles with
sequenceML as input and
RNAStructML as output and is using request/response. The
Java programs needs at least Java 1.5 and the following
libraries to run/compile:
