JAL-3070 use ArgumentI in all public constructors, convert to service specific argume...

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.ws.params.ArgumentI;
 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.metadata.Argument;
 
 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;

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.ws.params.ArgumentI;
 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.metadata.Argument;
 
 public class AADisorderClient extends JabawsCalcWorker
 {
@@ -62,7 +62,7 @@ public class AADisorderClient extends JabawsCalcWorker
   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;

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.params.ArgumentI;
 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 compbio.metadata.Argument;
 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 List<Argument> arguments;
+  protected List<ArgumentI> arguments;
 
   protected IProgressIndicator guiProgress;
 
@@ -78,10 +78,7 @@ public abstract class AbstractJabaCalcWorker extends AlignCalcWorker
     {
       ((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);
     }
   }
@@ -98,7 +95,7 @@ public abstract class AbstractJabaCalcWorker extends AlignCalcWorker
     return preset;
   }
 
-  public List<Argument> getArguments()
+  public List<ArgumentI> getArguments()
   {
     return arguments;
   }
@@ -112,7 +109,7 @@ public abstract class AbstractJabaCalcWorker extends AlignCalcWorker
    * @param newarguments
    */
   public void updateParameters(final WsParamSetI newpreset,
-          final List<Argument> newarguments)
+          final List<ArgumentI> newarguments)
   {
     preset = newpreset;
     arguments = newarguments;
@@ -129,7 +126,7 @@ public abstract class AbstractJabaCalcWorker extends AlignCalcWorker
     }
     if (arguments != null && arguments.size() > 0)
     {
-      for (Argument rg : arguments)
+      for (Object rg : JabaParamStore.getJabafromJwsArgs(arguments))
       {
         if (Option.class.isAssignableFrom(rg.getClass()))
         {
@@ -168,7 +165,7 @@ public abstract class AbstractJabaCalcWorker extends AlignCalcWorker
   }
 
   public AbstractJabaCalcWorker(Jws2Instance service, AlignFrame alignFrame,
-          WsParamSetI preset, List<Argument> paramset)
+          WsParamSetI preset, List<ArgumentI> paramset)
   {
     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.ws.params.ArgumentI;
 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.metadata.Argument;
 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,
-          WsParamSetI preset, List<Argument> paramset)
+          WsParamSetI preset, List<ArgumentI> paramset)
   {
     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.ws.params.ArgumentI;
 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.metadata.Argument;
 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,
-          List<Argument> paramset)
+          List<ArgumentI> paramset)
   {
     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 compbio.metadata.Argument;
-
 /**
  * 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 List<Argument> paramset;
+  protected List<ArgumentI> paramset;
 
   public Jws2Client(AlignFrame _alignFrame, WsParamSetI preset,
-          List<Argument> arguments)
+          List<ArgumentI> arguments)
   {
     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.ws.params.ArgumentI;
 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 compbio.metadata.Argument;
 
 /**
  * DOCUMENT ME!
@@ -93,7 +93,7 @@ public class MsaWSClient extends Jws2Client
    */
 
   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)

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.params.ArgumentI;
 import jalview.ws.params.WsParamSetI;
 
 import java.util.ArrayList;
@@ -70,7 +71,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI
 
     WsParamSetI preset = null;
 
-    List<Argument> arguments = null;
+    List<ArgumentI> arguments = null;
 
     /**
      * input
@@ -385,7 +386,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI
       }
       if (arguments != null && arguments.size() > 0)
       {
-        newargs.addAll(arguments);
+        newargs.addAll(JabaParamStore.getJabafromJwsArgs(arguments));
       }
       return newargs;
     }
@@ -402,7 +403,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI
                 + "Preset: " + preset.getName());
         if (preset instanceof JabaWsParamSet)
         {
-          for (Argument opt : ((JabaWsParamSet) preset).getjabaArguments())
+          for (Argument opt : getJabaArguments())
           {
             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.
-        for (Argument opt : arguments)
+        for (Argument opt : getJabaArguments())
         {
           jobProgress.append(
                   opt.getName() + " " + opt.getDefaultValue() + "\n");
@@ -474,7 +475,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI
    * @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,

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.ws.params.ArgumentI;
 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.metadata.Argument;
 
 /**
  * Client for the JABA RNA Alifold Service
@@ -61,7 +61,7 @@ public class RNAalifoldClient extends JabawsCalcWorker
   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;

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)
   {
-    super(alignFrame, fave.getPreset(), fave.getJobArgset());
+    super(alignFrame, fave.getPreset(), fave.getArgumentSet());
     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.ws.jws2.JabaParamStore;
 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);
       }
     }
-    alifoldClient = new RNAalifoldClient(rnaalifoldws, af, null, opts);
+    alifoldClient = new RNAalifoldClient(rnaalifoldws, af, null,
+            JabaParamStore.getJwsArgsfromJaba(opts));
 
     af.getViewport().getCalcManager().startWorker(alifoldClient);