FUTURE TODO

Registry for jalview WS - gives list of web services providers
 - checks the status of the web services
 - web service providers gives list of available WS
 - synchronises with other registries
 - UI for adding new WS from third party provider
 - Jalview should include component for adding new Web service and WS registry  
 
 With Jim: 
Integration with Jalview
Jalview 
 - should use local engine to run tasks locally
 - keep sufficient information about the task to be able to re-run it on the same 
 or different service provider (task persistence)
 - Provide for configuration for choosing which registries/ws providers to use
 - be able to bypass firewalls and proxies to access WS
 
 
NOTES
1) Keep in mind that jobs could be submitted from behind the firewalls and proxies make sure to support this
2) Make sure it will be possible to distinguish between communication errors,  execution errors  
and possibly misconfiguration errors

FUTURE TASKS 
Prepare HMM profile for the user alignment and call jnet - instead of jpred. 
JPRED REWRITING Wrap Jpred
Wrap scanPS    

CBS soft: 
Transmembrane regions
Phosphorilation sites
Glycozilation sites
Signal P

They all have SOAP WS...
 
CDD domains
PFAM domains
 
JPRED IMPROVEMENTS
1) Make sure PSIBLAST does not generate large output (e.g. one approach is to stop on the first iteration
if large number of sequences is already generated, second approach is to search PFAM to see if the sequence is from the family
and if it is so, then use the family)
2) Use blast -m 7 option - generate xml output its 8 times more compact
3) Paralellize PSI blast
4) Improve unmask alignments routine 
 
/homes/ws-dev1/NOBACK/jpred3_submit_concise
/homes/ws-dev1/servers/JalviewWS/webapps/JalviewWS/WEB-INF/classes/vamsas/pl/bin/jpred3_submit_concise
/homes/ws-dev1/servers/Test/webapps/JalviewWS/WEB-INF/classes/vamsas/pl/bin/jpred3_submit_concise
/homes/ws-dev1/servers/Test/webapps/TestJWS/WEB-INF/classes/vamsas/pl/bin/jpred3_submit_concise
/homes/ws-dev1/servers/Test/webapps/JalviewWS-back/WEB-INF/classes/vamsas/pl/bin/jpred3_submit_concise


JAXB - cannot serialize Maps and instance variables in Enums!
Best replacement for Maps is a custom object for key->value pair and a HashSet for storing the pairs.
JaxB cannot serialize instances of generic classes(?)