import jalview.ws.jws2.dm.AAConSettings;
import jalview.ws.jws2.dm.JabaWsParamSet;
import jalview.ws.jws2.jabaws2.Jws2Instance;
+import jalview.ws.params.ArgumentI;
import jalview.ws.params.WsParamSetI;
import java.util.ArrayList;
import java.util.Map;
import compbio.data.sequence.FastaSequence;
-import compbio.metadata.Argument;
import compbio.metadata.ChunkHolder;
import compbio.metadata.JobStatus;
import compbio.metadata.JobSubmissionException;
protected WsParamSetI preset;
- protected List<Argument> arguments;
+ protected List<ArgumentI> arguments;
protected IProgressIndicator guiProgress;
{
((jalview.gui.AlignViewport) alignViewport).setCalcIdSettingsFor(
getCalcId(),
- new AAConSettings(true, service, this.preset,
- (arguments != null)
- ? JabaParamStore.getJwsArgsfromJaba(arguments)
- : null),
+ new AAConSettings(true, service, this.preset, arguments),
true);
}
}
return preset;
}
- public List<Argument> getArguments()
+ public List<ArgumentI> getArguments()
{
return arguments;
}
* @param newarguments
*/
public void updateParameters(final WsParamSetI newpreset,
- final List<Argument> newarguments)
+ final List<ArgumentI> newarguments)
{
preset = newpreset;
arguments = newarguments;
}
if (arguments != null && arguments.size() > 0)
{
- for (Argument rg : arguments)
+ for (Object rg : JabaParamStore.getJabafromJwsArgs(arguments))
{
if (Option.class.isAssignableFrom(rg.getClass()))
{
}
public AbstractJabaCalcWorker(Jws2Instance service, AlignFrame alignFrame,
- WsParamSetI preset, List<Argument> paramset)
+ WsParamSetI preset, List<ArgumentI> paramset)
{
this(alignFrame.getCurrentView(), alignFrame.alignPanel);
this.guiProgress = alignFrame;