import jalview.util.MessageManager;
import jalview.workers.AlignCalcWorker;
import jalview.ws.api.CancellableI;
+import jalview.ws.api.JalviewServiceEndpointProviderI;
import jalview.ws.api.JobId;
import jalview.ws.api.SequenceAnnotationServiceI;
+import jalview.ws.api.ServiceWithParameters;
import jalview.ws.api.WSAnnotationCalcManagerI;
import jalview.ws.gui.AnnotationWsJob;
import jalview.ws.jws2.dm.AAConSettings;
-import jalview.ws.jws2.jabaws2.Jws2Instance;
import jalview.ws.params.ArgumentI;
import jalview.ws.params.WsParamSetI;
implements WSAnnotationCalcManagerI
{
- protected Jws2Instance service;
+ protected ServiceWithParameters service;
protected WsParamSetI preset;
super(alignViewport, alignPanel);
}
- public SeqAnnotationServiceCalcWorker(Jws2Instance service, AlignFrame alignFrame,
+ public SeqAnnotationServiceCalcWorker(ServiceWithParameters service,
+ AlignFrame alignFrame,
WsParamSetI preset, List<ArgumentI> paramset)
{
this(alignFrame.getCurrentView(), alignFrame.alignPanel);
this.service = service;
try
{
- annotService = (jalview.ws.api.SequenceAnnotationServiceI) service
+ annotService = (jalview.ws.api.SequenceAnnotationServiceI) ((JalviewServiceEndpointProviderI) service)
.getEndpoint();
} catch (ClassCastException cce)
{
}
// configure submission flags
- if (service.getAlignAnalysisUI() != null)
+ proteinAllowed = service.isProteinService();
+ nucleotidesAllowed = service.isNucleotideService();
+ alignedSeqs = service.isNeedsAlignedSequences();
+ bySequence = !service.isAlignmentAnalysis();
+ filterNonStandardResidues = service.isFilterSymbols();
+ min_valid_seqs = service.getMinimumInputSequences();
+
+ if (service.isInteractiveUpdate())
{
- // instantaneous calculation. Right now that's either AACons or RNAAliFold
- proteinAllowed = service.getAlignAnalysisUI().isPr();
- nucleotidesAllowed = service.getAlignAnalysisUI().isNa();
- alignedSeqs = service.getAlignAnalysisUI().isNeedsAlignedSeqs();
- bySequence = !service.getAlignAnalysisUI().isAA();
- filterNonStandardResidues = service.getAlignAnalysisUI()
- .isFilterSymbols();
- min_valid_seqs = service.getAlignAnalysisUI().getMinimumSequences();
initViewportParams();
}
- else
- {
- // assume disorder prediction : per-sequence protein only no gaps
- // analysis.
- // TODO - move configuration to UIInfo base class for all these flags !
- alignedSeqs = false;
- bySequence = true;
- filterNonStandardResidues = true;
- nucleotidesAllowed = false;
- proteinAllowed = true;
- submitGaps = false;
- min_valid_seqs = 1;
- }
}
/**