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JAL-3070 use ArgumentI in all public constructors, convert to service specific argume...
author
Jim Procter
<jprocter@issues.jalview.org>
Thu, 26 Jul 2018 13:36:40 +0000
(14:36 +0100)
committer
Jim Procter
<jprocter@issues.jalview.org>
Thu, 26 Jul 2018 13:36:40 +0000
(14:36 +0100)
src/jalview/ws/jws2/AAConClient.java
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src/jalview/ws/jws2/AADisorderClient.java
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src/jalview/ws/jws2/AbstractJabaCalcWorker.java
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src/jalview/ws/jws2/JabawsCalcWorker.java
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src/jalview/ws/jws2/JabawsMsaInterfaceAlignCalcWorker.java
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src/jalview/ws/jws2/Jws2Client.java
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src/jalview/ws/jws2/MsaWSClient.java
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src/jalview/ws/jws2/MsaWSThread.java
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src/jalview/ws/jws2/RNAalifoldClient.java
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src/jalview/ws/jws2/SequenceAnnotationWSClient.java
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test/jalview/ws/jabaws/RNAStructExportImport.java
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diff --git
a/src/jalview/ws/jws2/AAConClient.java
b/src/jalview/ws/jws2/AAConClient.java
index
327864a
..
ddd69a7
100644
(file)
--- a/
src/jalview/ws/jws2/AAConClient.java
+++ b/
src/jalview/ws/jws2/AAConClient.java
@@
-24,6
+24,7
@@
import jalview.datamodel.AlignmentAnnotation;
import jalview.gui.AlignFrame;
import jalview.util.MessageManager;
import jalview.ws.jws2.jabaws2.Jws2Instance;
import jalview.gui.AlignFrame;
import jalview.util.MessageManager;
import jalview.ws.jws2.jabaws2.Jws2Instance;
+import jalview.ws.params.ArgumentI;
import jalview.ws.params.WsParamSetI;
import jalview.ws.uimodel.AlignAnalysisUIText;
import jalview.ws.params.WsParamSetI;
import jalview.ws.uimodel.AlignAnalysisUIText;
@@
-35,13
+36,12
@@
import java.util.TreeSet;
import compbio.data.sequence.FastaSequence;
import compbio.data.sequence.Score;
import compbio.data.sequence.FastaSequence;
import compbio.data.sequence.Score;
-import compbio.metadata.Argument;
public class AAConClient extends JabawsCalcWorker
{
public AAConClient(Jws2Instance service, AlignFrame alignFrame,
public class AAConClient extends JabawsCalcWorker
{
public AAConClient(Jws2Instance service, AlignFrame alignFrame,
- WsParamSetI preset, List<Argument> paramset)
+ WsParamSetI preset, List<ArgumentI> paramset)
{
super(service, alignFrame, preset, paramset);
submitGaps = true;
{
super(service, alignFrame, preset, paramset);
submitGaps = true;
diff --git
a/src/jalview/ws/jws2/AADisorderClient.java
b/src/jalview/ws/jws2/AADisorderClient.java
index
bd4e0ea
..
9cec97b
100644
(file)
--- a/
src/jalview/ws/jws2/AADisorderClient.java
+++ b/
src/jalview/ws/jws2/AADisorderClient.java
@@
-30,6
+30,7
@@
import jalview.gui.AlignFrame;
import jalview.schemes.FeatureColour;
import jalview.util.ColorUtils;
import jalview.ws.jws2.jabaws2.Jws2Instance;
import jalview.schemes.FeatureColour;
import jalview.util.ColorUtils;
import jalview.ws.jws2.jabaws2.Jws2Instance;
+import jalview.ws.params.ArgumentI;
import jalview.ws.params.WsParamSetI;
import java.awt.Color;
import jalview.ws.params.WsParamSetI;
import java.awt.Color;
@@
-44,7
+45,6
@@
import compbio.data.sequence.FastaSequence;
import compbio.data.sequence.Range;
import compbio.data.sequence.Score;
import compbio.data.sequence.ScoreManager.ScoreHolder;
import compbio.data.sequence.Range;
import compbio.data.sequence.Score;
import compbio.data.sequence.ScoreManager.ScoreHolder;
-import compbio.metadata.Argument;
public class AADisorderClient extends JabawsCalcWorker
{
public class AADisorderClient extends JabawsCalcWorker
{
@@
-62,7
+62,7
@@
public class AADisorderClient extends JabawsCalcWorker
AlignFrame af;
public AADisorderClient(Jws2Instance sh, AlignFrame alignFrame,
AlignFrame af;
public AADisorderClient(Jws2Instance sh, AlignFrame alignFrame,
- WsParamSetI thePreset, List<Argument> paramset)
+ WsParamSetI thePreset, List<ArgumentI> paramset)
{
super(sh, alignFrame, thePreset, paramset);
af = alignFrame;
{
super(sh, alignFrame, thePreset, paramset);
af = alignFrame;
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;
diff --git
a/src/jalview/ws/jws2/JabawsCalcWorker.java
b/src/jalview/ws/jws2/JabawsCalcWorker.java
index
fc36205
..
c70e721
100644
(file)
--- a/
src/jalview/ws/jws2/JabawsCalcWorker.java
+++ b/
src/jalview/ws/jws2/JabawsCalcWorker.java
@@
-26,6
+26,7
@@
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.util.MessageManager;
import jalview.ws.jws2.jabaws2.Jws2Instance;
import jalview.gui.AlignFrame;
import jalview.util.MessageManager;
import jalview.ws.jws2.jabaws2.Jws2Instance;
+import jalview.ws.params.ArgumentI;
import jalview.ws.params.WsParamSetI;
import java.util.Iterator;
import jalview.ws.params.WsParamSetI;
import java.util.Iterator;
@@
-34,7
+35,6
@@
import java.util.List;
import compbio.data.msa.SequenceAnnotation;
import compbio.data.sequence.Score;
import compbio.data.sequence.ScoreManager;
import compbio.data.msa.SequenceAnnotation;
import compbio.data.sequence.Score;
import compbio.data.sequence.ScoreManager;
-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;
@@
-50,7
+50,7
@@
public abstract class JabawsCalcWorker extends AbstractJabaCalcWorker
protected ScoreManager scoremanager;
public JabawsCalcWorker(Jws2Instance service, AlignFrame alignFrame,
protected ScoreManager scoremanager;
public JabawsCalcWorker(Jws2Instance service, AlignFrame alignFrame,
- WsParamSetI preset, List<Argument> paramset)
+ WsParamSetI preset, List<ArgumentI> paramset)
{
super(service, alignFrame, preset, paramset);
aaservice = (SequenceAnnotation) service.service;
{
super(service, alignFrame, preset, paramset);
aaservice = (SequenceAnnotation) service.service;
diff --git
a/src/jalview/ws/jws2/JabawsMsaInterfaceAlignCalcWorker.java
b/src/jalview/ws/jws2/JabawsMsaInterfaceAlignCalcWorker.java
index
ee36d4a
..
5ccef8a
100644
(file)
--- a/
src/jalview/ws/jws2/JabawsMsaInterfaceAlignCalcWorker.java
+++ b/
src/jalview/ws/jws2/JabawsMsaInterfaceAlignCalcWorker.java
@@
-28,6
+28,7
@@
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.util.MessageManager;
import jalview.ws.jws2.jabaws2.Jws2Instance;
import jalview.gui.AlignFrame;
import jalview.util.MessageManager;
import jalview.ws.jws2.jabaws2.Jws2Instance;
+import jalview.ws.params.ArgumentI;
import jalview.ws.params.WsParamSetI;
import java.util.Iterator;
import jalview.ws.params.WsParamSetI;
import java.util.Iterator;
@@
-36,7
+37,6
@@
import java.util.List;
import compbio.data.msa.MsaWS;
import compbio.data.sequence.Alignment;
import compbio.data.sequence.Score;
import compbio.data.msa.MsaWS;
import compbio.data.sequence.Alignment;
import compbio.data.sequence.Score;
-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;
@@
-60,7
+60,7
@@
public abstract class JabawsMsaInterfaceAlignCalcWorker
public JabawsMsaInterfaceAlignCalcWorker(Jws2Instance service,
AlignFrame alignFrame, WsParamSetI preset,
public JabawsMsaInterfaceAlignCalcWorker(Jws2Instance service,
AlignFrame alignFrame, WsParamSetI preset,
- List<Argument> paramset)
+ List<ArgumentI> paramset)
{
this(alignFrame.getCurrentView(), alignFrame.alignPanel);
this.guiProgress = alignFrame;
{
this(alignFrame.getCurrentView(), alignFrame.alignPanel);
this.guiProgress = alignFrame;
diff --git
a/src/jalview/ws/jws2/Jws2Client.java
b/src/jalview/ws/jws2/Jws2Client.java
index
f233030
..
334f3c3
100644
(file)
--- a/
src/jalview/ws/jws2/Jws2Client.java
+++ b/
src/jalview/ws/jws2/Jws2Client.java
@@
-45,8
+45,6
@@
import javax.swing.JMenuItem;
import javax.swing.event.MenuEvent;
import javax.swing.event.MenuListener;
import javax.swing.event.MenuEvent;
import javax.swing.event.MenuListener;
-import compbio.metadata.Argument;
-
/**
* provides metadata for a jabaws2 service instance - resolves names, etc.
*
/**
* provides metadata for a jabaws2 service instance - resolves names, etc.
*
@@
-57,10
+55,10
@@
public abstract class Jws2Client extends jalview.ws.WSClient
{
protected WsParamSetI preset;
{
protected WsParamSetI preset;
- protected List<Argument> paramset;
+ protected List<ArgumentI> paramset;
public Jws2Client(AlignFrame _alignFrame, WsParamSetI preset,
public Jws2Client(AlignFrame _alignFrame, WsParamSetI preset,
- List<Argument> arguments)
+ List<ArgumentI> arguments)
{
alignFrame = _alignFrame;
this.preset = preset;
{
alignFrame = _alignFrame;
this.preset = preset;
diff --git
a/src/jalview/ws/jws2/MsaWSClient.java
b/src/jalview/ws/jws2/MsaWSClient.java
index
bbeefc6
..
dccdcea
100644
(file)
--- a/
src/jalview/ws/jws2/MsaWSClient.java
+++ b/
src/jalview/ws/jws2/MsaWSClient.java
@@
-28,6
+28,7
@@
import jalview.gui.JvOptionPane;
import jalview.gui.JvSwingUtils;
import jalview.util.MessageManager;
import jalview.ws.jws2.jabaws2.Jws2Instance;
import jalview.gui.JvSwingUtils;
import jalview.util.MessageManager;
import jalview.ws.jws2.jabaws2.Jws2Instance;
+import jalview.ws.params.ArgumentI;
import jalview.ws.params.WsParamSetI;
import java.awt.event.ActionEvent;
import jalview.ws.params.WsParamSetI;
import java.awt.event.ActionEvent;
@@
-41,7
+42,6
@@
import javax.swing.JMenuItem;
import javax.swing.ToolTipManager;
import compbio.data.msa.MsaWS;
import javax.swing.ToolTipManager;
import compbio.data.msa.MsaWS;
-import compbio.metadata.Argument;
/**
* DOCUMENT ME!
/**
* DOCUMENT ME!
@@
-93,7
+93,7
@@
public class MsaWSClient extends Jws2Client
*/
public MsaWSClient(Jws2Instance sh, WsParamSetI preset,
*/
public MsaWSClient(Jws2Instance sh, WsParamSetI preset,
- List<Argument> arguments, boolean editParams, String altitle,
+ List<ArgumentI> arguments, boolean editParams, String altitle,
jalview.datamodel.AlignmentView msa, boolean submitGaps,
boolean preserveOrder, AlignmentI seqdataset,
AlignFrame _alignFrame)
jalview.datamodel.AlignmentView msa, boolean submitGaps,
boolean preserveOrder, AlignmentI seqdataset,
AlignFrame _alignFrame)
diff --git
a/src/jalview/ws/jws2/MsaWSThread.java
b/src/jalview/ws/jws2/MsaWSThread.java
index
c4fc66b
..
a0cd0f4
100644
(file)
--- a/
src/jalview/ws/jws2/MsaWSThread.java
+++ b/
src/jalview/ws/jws2/MsaWSThread.java
@@
-38,6
+38,7
@@
import jalview.ws.AWsJob;
import jalview.ws.JobStateSummary;
import jalview.ws.WSClientI;
import jalview.ws.jws2.dm.JabaWsParamSet;
import jalview.ws.JobStateSummary;
import jalview.ws.WSClientI;
import jalview.ws.jws2.dm.JabaWsParamSet;
+import jalview.ws.params.ArgumentI;
import jalview.ws.params.WsParamSetI;
import java.util.ArrayList;
import jalview.ws.params.WsParamSetI;
import java.util.ArrayList;
@@
-70,7
+71,7
@@
class MsaWSThread extends AWS2Thread implements WSClientI
WsParamSetI preset = null;
WsParamSetI preset = null;
- List<Argument> arguments = null;
+ List<ArgumentI> arguments = null;
/**
* input
/**
* input
@@
-385,7
+386,7
@@
class MsaWSThread extends AWS2Thread implements WSClientI
}
if (arguments != null && arguments.size() > 0)
{
}
if (arguments != null && arguments.size() > 0)
{
- newargs.addAll(arguments);
+ newargs.addAll(JabaParamStore.getJabafromJwsArgs(arguments));
}
return newargs;
}
}
return newargs;
}
@@
-402,7
+403,7
@@
class MsaWSThread extends AWS2Thread implements WSClientI
+ "Preset: " + preset.getName());
if (preset instanceof JabaWsParamSet)
{
+ "Preset: " + preset.getName());
if (preset instanceof JabaWsParamSet)
{
- for (Argument opt : ((JabaWsParamSet) preset).getjabaArguments())
+ for (Argument opt : getJabaArguments())
{
jobProgress.append(
opt.getName() + " " + opt.getDefaultValue() + "\n");
{
jobProgress.append(
opt.getName() + " " + opt.getDefaultValue() + "\n");
@@
-413,7
+414,7
@@
class MsaWSThread extends AWS2Thread implements WSClientI
{
jobProgress.append("With custom parameters : \n");
// merge arguments with preset's own arguments.
{
jobProgress.append("With custom parameters : \n");
// merge arguments with preset's own arguments.
- for (Argument opt : arguments)
+ for (Argument opt : getJabaArguments())
{
jobProgress.append(
opt.getName() + " " + opt.getDefaultValue() + "\n");
{
jobProgress.append(
opt.getName() + " " + opt.getDefaultValue() + "\n");
@@
-474,7
+475,7
@@
class MsaWSThread extends AWS2Thread implements WSClientI
* @param seqset
* Alignment
*/
* @param seqset
* Alignment
*/
- MsaWSThread(MsaWS server2, WsParamSetI preset, List<Argument> paramset,
+ MsaWSThread(MsaWS server2, WsParamSetI preset, List<ArgumentI> paramset,
String wsUrl, WebserviceInfo wsinfo,
jalview.gui.AlignFrame alFrame, String wsname, String title,
AlignmentView _msa, boolean subgaps, boolean presorder,
String wsUrl, WebserviceInfo wsinfo,
jalview.gui.AlignFrame alFrame, String wsname, String title,
AlignmentView _msa, boolean subgaps, boolean presorder,
diff --git
a/src/jalview/ws/jws2/RNAalifoldClient.java
b/src/jalview/ws/jws2/RNAalifoldClient.java
index
32ae38f
..
1c4e192
100644
(file)
--- a/
src/jalview/ws/jws2/RNAalifoldClient.java
+++ b/
src/jalview/ws/jws2/RNAalifoldClient.java
@@
-25,6
+25,7
@@
import jalview.datamodel.Annotation;
import jalview.gui.AlignFrame;
import jalview.util.MessageManager;
import jalview.ws.jws2.jabaws2.Jws2Instance;
import jalview.gui.AlignFrame;
import jalview.util.MessageManager;
import jalview.ws.jws2.jabaws2.Jws2Instance;
+import jalview.ws.params.ArgumentI;
import jalview.ws.params.WsParamSetI;
import jalview.ws.uimodel.AlignAnalysisUIText;
import jalview.ws.params.WsParamSetI;
import jalview.ws.uimodel.AlignAnalysisUIText;
@@
-40,7
+41,6
@@
import compbio.data.sequence.RNAStructReader.AlifoldResult;
import compbio.data.sequence.RNAStructScoreManager;
import compbio.data.sequence.Range;
import compbio.data.sequence.Score;
import compbio.data.sequence.RNAStructScoreManager;
import compbio.data.sequence.Range;
import compbio.data.sequence.Score;
-import compbio.metadata.Argument;
/**
* Client for the JABA RNA Alifold Service
/**
* Client for the JABA RNA Alifold Service
@@
-61,7
+61,7
@@
public class RNAalifoldClient extends JabawsCalcWorker
boolean bpScores;
public RNAalifoldClient(Jws2Instance sh, AlignFrame alignFrame,
boolean bpScores;
public RNAalifoldClient(Jws2Instance sh, AlignFrame alignFrame,
- WsParamSetI preset, List<Argument> paramset)
+ WsParamSetI preset, List<ArgumentI> paramset)
{
super(sh, alignFrame, preset, paramset);
af = alignFrame;
{
super(sh, alignFrame, preset, paramset);
af = alignFrame;
diff --git
a/src/jalview/ws/jws2/SequenceAnnotationWSClient.java
b/src/jalview/ws/jws2/SequenceAnnotationWSClient.java
index
8befb2a
..
eb08848
100644
(file)
--- a/
src/jalview/ws/jws2/SequenceAnnotationWSClient.java
+++ b/
src/jalview/ws/jws2/SequenceAnnotationWSClient.java
@@
-145,7
+145,7
@@
public class SequenceAnnotationWSClient extends Jws2Client
public SequenceAnnotationWSClient(AAConSettings fave,
AlignFrame alignFrame, boolean b)
{
public SequenceAnnotationWSClient(AAConSettings fave,
AlignFrame alignFrame, boolean b)
{
- super(alignFrame, fave.getPreset(), fave.getJobArgset());
+ super(alignFrame, fave.getPreset(), fave.getArgumentSet());
initSequenceAnnotationWSClient(fave.getService(), alignFrame,
fave.getPreset(), b);
}
initSequenceAnnotationWSClient(fave.getService(), alignFrame,
fave.getPreset(), b);
}
diff --git
a/test/jalview/ws/jabaws/RNAStructExportImport.java
b/test/jalview/ws/jabaws/RNAStructExportImport.java
index
ee07335
..
d5a7e99
100644
(file)
--- a/
test/jalview/ws/jabaws/RNAStructExportImport.java
+++ b/
test/jalview/ws/jabaws/RNAStructExportImport.java
@@
-33,6
+33,7
@@
import jalview.io.DataSourceType;
import jalview.io.FileFormat;
import jalview.io.FormatAdapter;
import jalview.io.StockholmFileTest;
import jalview.io.FileFormat;
import jalview.io.FormatAdapter;
import jalview.io.StockholmFileTest;
+import jalview.ws.jws2.JabaParamStore;
import jalview.ws.jws2.Jws2Discoverer;
import jalview.ws.jws2.RNAalifoldClient;
import jalview.ws.jws2.SequenceAnnotationWSClient;
import jalview.ws.jws2.Jws2Discoverer;
import jalview.ws.jws2.RNAalifoldClient;
import jalview.ws.jws2.SequenceAnnotationWSClient;
@@
-280,7
+281,8
@@
public class RNAStructExportImport
opts.add(rg);
}
}
opts.add(rg);
}
}
- alifoldClient = new RNAalifoldClient(rnaalifoldws, af, null, opts);
+ alifoldClient = new RNAalifoldClient(rnaalifoldws, af, null,
+ JabaParamStore.getJwsArgsfromJaba(opts));
af.getViewport().getCalcManager().startWorker(alifoldClient);
af.getViewport().getCalcManager().startWorker(alifoldClient);