protected PdbPairsMessage getAlignmentPairsFromServer ( ) { String url = params . getServer ( ) ; int nrPairs = params . getStepSize ( ) ; if ( maxNrAlignments < nrPairs ) nrPairs = maxNrAlignments ; SortedSet < PdbPair > allPairs = new TreeSet < PdbPair > ( ) ; PdbPairsMessage msg = null ; try { if ( progressListeners != null ) notifyRequestingAlignments ( nrPairs ) ; if ( ! waitForAlignments ) { msg = JFatCatClient . getPdbPairs ( url , nrPairs , userName ) ; allPairs = msg . getPairs ( ) ; } else { while ( allPairs . isEmpty ( ) ) { msg = JFatCatClient . getPdbPairs ( url , nrPairs , userName ) ; allPairs = msg . getPairs ( ) ; if ( allPairs . isEmpty ( ) ) { randomSleep ( ) ; } } } } catch ( JobKillException k ) { logger . debug ( "Terminating job" , k ) ; terminate ( ) ; } catch ( Exception e ) { logger . error ( "Error while requesting alignment pairs" , e ) ; // an error has occured sleep 30 sec. randomSleep ( ) ; } return msg ; }
talk to centralized server and fetch all alignments to run .