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RNAforester - WebService

This is a short introduction using RNAforester WebServices offered by BiBiServ. If you're not familiar with using webservices in general you should have a closer look to our webservice related linklist.

WSDL - methods, parameters and datatypes

If you've a closer look at the WSDL file describing the RNAforester webservice, you can see two methods belonging together.

request and response

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 RNAforester WebService we use a technique called Request and Reply with polling based on BiBiWS. First the client side (e.g. your program) requests a RNAforester 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 RNAforester 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
The request method get an parameter array (see table below for supported key/value pairs) and RNA secondary structure data (in RNAStructML format) and returns either a unique id or in case of an error a fault message.

key value description
method String matching regexp (global | local | sil) alignment method
alignment String matching regexp (pairwise | multiple) alignment mode
b_m Integer (1) base match score
b_r Integer (0) base indel score
b_d Integer ≤ -1 (-10) base match score
bp_r Integer (10) basepair(bond) match score
bp_d Integer ≤ -1 (-5) basepair bond indel score
subopt_percent 0 ≥ Integer ≤ 100 local suboptimal alignments within int% (only in conjunction with alignment method local)
ribosum Boolean RIBOSUM85-60 scoring matrix (base-pair substitutions)
cmin Double minimum basepair frequency for consensus structure
note:
Required parameter are in italic, defaults are in bold

response
The response method gets the id returned by the request method as input parameter and returns the calculated result as XMl/DOM document in RNAStructAlignmentML format.

Example Java client

The Example Java client is based on Apache Axis (≥ 1.2) and combined both methods (request and response) through active waiting.
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Thu Dec 20 16:05:25 2012