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JAL-3070 use ArgumentI in all public constructors, convert to service specific argume...
[jalview.git]
/
src
/
jalview
/
ws
/
jws2
/
AbstractJabaCalcWorker.java
diff --git
a/src/jalview/ws/jws2/AbstractJabaCalcWorker.java
b/src/jalview/ws/jws2/AbstractJabaCalcWorker.java
index
dd64e77
..
1a361c4
100644
(file)
--- a/
src/jalview/ws/jws2/AbstractJabaCalcWorker.java
+++ b/
src/jalview/ws/jws2/AbstractJabaCalcWorker.java
@@
-36,6
+36,7
@@
import jalview.workers.AlignCalcWorker;
import jalview.ws.jws2.dm.AAConSettings;
import jalview.ws.jws2.dm.JabaWsParamSet;
import jalview.ws.jws2.jabaws2.Jws2Instance;
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 jalview.ws.params.WsParamSetI;
import java.util.ArrayList;
@@
-44,7
+45,6
@@
import java.util.List;
import java.util.Map;
import compbio.data.sequence.FastaSequence;
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;
import compbio.metadata.ChunkHolder;
import compbio.metadata.JobStatus;
import compbio.metadata.JobSubmissionException;
@@
-58,7
+58,7
@@
public abstract class AbstractJabaCalcWorker extends AlignCalcWorker
protected WsParamSetI preset;
protected WsParamSetI preset;
- protected List<Argument> arguments;
+ protected List<ArgumentI> arguments;
protected IProgressIndicator guiProgress;
protected IProgressIndicator guiProgress;
@@
-78,10
+78,7
@@
public abstract class AbstractJabaCalcWorker extends AlignCalcWorker
{
((jalview.gui.AlignViewport) alignViewport).setCalcIdSettingsFor(
getCalcId(),
{
((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);
}
}
true);
}
}
@@
-98,7
+95,7
@@
public abstract class AbstractJabaCalcWorker extends AlignCalcWorker
return preset;
}
return preset;
}
- public List<Argument> getArguments()
+ public List<ArgumentI> getArguments()
{
return arguments;
}
{
return arguments;
}
@@
-112,7
+109,7
@@
public abstract class AbstractJabaCalcWorker extends AlignCalcWorker
* @param newarguments
*/
public void updateParameters(final WsParamSetI newpreset,
* @param newarguments
*/
public void updateParameters(final WsParamSetI newpreset,
- final List<Argument> newarguments)
+ final List<ArgumentI> newarguments)
{
preset = newpreset;
arguments = newarguments;
{
preset = newpreset;
arguments = newarguments;
@@
-129,7
+126,7
@@
public abstract class AbstractJabaCalcWorker extends AlignCalcWorker
}
if (arguments != null && arguments.size() > 0)
{
}
if (arguments != null && arguments.size() > 0)
{
- for (Argument rg : arguments)
+ for (Object rg : JabaParamStore.getJabafromJwsArgs(arguments))
{
if (Option.class.isAssignableFrom(rg.getClass()))
{
{
if (Option.class.isAssignableFrom(rg.getClass()))
{
@@
-168,7
+165,7
@@
public abstract class AbstractJabaCalcWorker extends AlignCalcWorker
}
public AbstractJabaCalcWorker(Jws2Instance service, AlignFrame alignFrame,
}
public AbstractJabaCalcWorker(Jws2Instance service, AlignFrame alignFrame,
- WsParamSetI preset, List<Argument> paramset)
+ WsParamSetI preset, List<ArgumentI> paramset)
{
this(alignFrame.getCurrentView(), alignFrame.alignPanel);
this.guiProgress = alignFrame;
{
this(alignFrame.getCurrentView(), alignFrame.alignPanel);
this.guiProgress = alignFrame;