JAL-3739 (combined) commits from feature/JAL-3739_useFormFieldText

diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties
index ece1dab..ada04d6 100644 (file)
--- a/resources/lang/Messages.properties
+++ b/resources/lang/Messages.properties
@@ -931,7 +931,7 @@ label.groovy_support_failed = Jalview Groovy Support Failed
 label.couldnt_create_groovy_shell = Couldn't create the groovy Shell. Check the error log for the details of what went wrong.
 error.unsupported_version_calcIdparam = Unsupported Version for calcIdparam {0}
 error.implementation_error_cant_reorder_tree = Implementation Error: Can't reorder this tree. Not DefaultMutableTreeNode.
-error.invalid_value_for_option = Invalid value {0} for option {1}
+error.invalid_value_for_option = Invalid value ''{0}'' for option ''{1}''
 error.implementation_error_cannot_import_vamsas_doc = Implementation Error - cannot import existing vamsas document into an existing session, Yet!
 label.vamsas_doc_couldnt_be_opened_as_new_session = VAMSAS Document could not be opened as a new session - please choose another
 error.setstatus_called_non_existent_job_pane = setStatus called for non-existent job pane {0}
@@ -955,7 +955,6 @@ error.implementation_error_minlen_must_be_greater_zero = Implementation error: m
 error.implementation_error_msawbjob_called = Implementation error - StartJob(MsaWSJob) called on a WSJobInstance {0}
 error.implementation_error_cannot_attach_ws_menu_entry = IMPLEMENTATION ERROR: cannot attach WS Menu Entry without service handle reference!
 error.parameter_migration_not_implemented_yet = Parameter migration not implemented yet
-error.implementation_error_cannot_set_jaba_option = Implementation error: cannot set Jaba Option to a value outside its allowed value range!
 error.implementation_error_valuetype_doesnt_support_jabaws_type = IMPLEMENTATION ERROR: jalview.ws.params.ValueConstrainI.ValueType does not support the JABAWS type : {0}
 error.cannot_create_jabaws_param_set = Cannot create a JabaWSParamSet from non-JabaWS parameters
 error.cannot_set_arguments_to_jabaws_param_set = Cannot set arguments to a JabaWSParamSet that are not JabaWS arguments

diff --git a/resources/lang/Messages_es.properties b/resources/lang/Messages_es.properties
index d61a546..cb3aba9 100644 (file)
--- a/resources/lang/Messages_es.properties
+++ b/resources/lang/Messages_es.properties
@@ -856,7 +856,7 @@ label.groovy_support_failed = El soporte Groovy de Jalview ha fallado
 label.couldnt_create_groovy_shell = No es posible crear el shell de Groovy. Compruebe el fichero de log para conocer los detalles.
 error.unsupported_version_calcIdparam = Versión no soportada de {0}
 error.implementation_error_cant_reorder_tree = Error de implementación: no es posible reordenar este árbol. No DefaultMutableTreeNode.
-error.invalid_value_for_option = Valor no válido de {0} para la opción {1}
+error.invalid_value_for_option = Valor no válido de ''{0}'' para la opción ''{1}''
 error.implementation_error_cannot_import_vamsas_doc = Error de implementación - todavía no es posible importar el documento VAMSAS existente en una sesión existente.
 label.vamsas_doc_couldnt_be_opened_as_new_session = El documento VAMSAS no ha podido abrirse como una nueva sesión. Por favor, escoja otra.
 error.setstatus_called_non_existent_job_pane = se lllamado a setStatus para el panel de trabajo {0} no existente
@@ -880,7 +880,6 @@ error.implementation_error_minlen_must_be_greater_zero = Error de implementaci
 error.implementation_error_msawbjob_called = Error de implementación - StartJob(MsaWSJob) invocado en un WSJobInstance {0}
 error.implementation_error_cannot_attach_ws_menu_entry = Error de implementación: ¡no es posible adjunto una WS Menu Entry sin una referencia a un manejador del servicio!
 error.parameter_migration_not_implemented_yet = La migración de parámetros no se ha implementado todavía
-error.implementation_error_cannot_set_jaba_option = Error de implementación: no es posible establecer el valor de Jaba Option a un valor fuera de su rango permitido
 error.implementation_error_valuetype_doesnt_support_jabaws_type = Error de implementación: jalview.ws.params.ValueConstrainI.ValueType no soporta el tipo JABAWS: {0}
 error.cannot_create_jabaws_param_set = No es posible crear un JabaWSParamSet con parámetros no JabaWS
 error.cannot_set_arguments_to_jabaws_param_set = No es posible establecer argumentos en JabaWSParamSet que no sean argumentos JabaWS 

diff --git a/src/jalview/gui/OptsAndParamsPage.java b/src/jalview/gui/OptsAndParamsPage.java
index 0f4d0e7..ba575ae 100644 (file)
--- a/src/jalview/gui/OptsAndParamsPage.java
+++ b/src/jalview/gui/OptsAndParamsPage.java
@@ -20,13 +20,6 @@
  */
 package jalview.gui;
 
-import jalview.util.MessageManager;
-import jalview.ws.params.ArgumentI;
-import jalview.ws.params.OptionI;
-import jalview.ws.params.ParameterI;
-import jalview.ws.params.ValueConstrainI;
-import jalview.ws.params.ValueConstrainI.ValueType;
-
 import java.awt.BorderLayout;
 import java.awt.Component;
 import java.awt.Dimension;
@@ -35,6 +28,8 @@ import java.awt.GridLayout;
 import java.awt.Rectangle;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
+import java.awt.event.FocusAdapter;
+import java.awt.event.FocusEvent;
 import java.awt.event.KeyEvent;
 import java.awt.event.KeyListener;
 import java.awt.event.MouseEvent;
@@ -59,6 +54,12 @@ import javax.swing.border.TitledBorder;
 import javax.swing.event.ChangeEvent;
 import javax.swing.event.ChangeListener;
 
+import jalview.util.MessageManager;
+import jalview.ws.params.ArgumentI;
+import jalview.ws.params.OptionI;
+import jalview.ws.params.ParameterI;
+import jalview.ws.params.ValueConstrainI;
+import jalview.ws.params.ValueConstrainI.ValueType;
 import net.miginfocom.swing.MigLayout;
 
 /**
@@ -621,6 +622,15 @@ public class OptsAndParamsPage
             {
             }
           });
+          valueField.addFocusListener(new FocusAdapter() {
+
+            @Override
+            public void focusLost(FocusEvent e)
+            {
+              actionPerformed(null);
+            }
+            
+          });
           valueField.setPreferredSize(new Dimension(60, 25));
           slider = makeSlider(parm.getValidValue());
           slider.addChangeListener(this);

diff --git a/src/jalview/gui/WsJobParameters.java b/src/jalview/gui/WsJobParameters.java
index 976e551..7a139e2 100644 (file)
--- a/src/jalview/gui/WsJobParameters.java
+++ b/src/jalview/gui/WsJobParameters.java
@@ -20,19 +20,6 @@
  */
 package jalview.gui;
 
-import jalview.gui.OptsAndParamsPage.OptionBox;
-import jalview.gui.OptsAndParamsPage.ParamBox;
-import jalview.util.MessageManager;
-import jalview.ws.jws2.JabaParamStore;
-import jalview.ws.jws2.JabaPreset;
-import jalview.ws.jws2.Jws2Discoverer;
-import jalview.ws.jws2.jabaws2.Jws2Instance;
-import jalview.ws.params.ArgumentI;
-import jalview.ws.params.OptionI;
-import jalview.ws.params.ParamDatastoreI;
-import jalview.ws.params.ParameterI;
-import jalview.ws.params.WsParamSetI;
-
 import java.awt.BorderLayout;
 import java.awt.Component;
 import java.awt.Dimension;
@@ -75,6 +62,19 @@ import compbio.metadata.Parameter;
 import compbio.metadata.Preset;
 import compbio.metadata.PresetManager;
 import compbio.metadata.RunnerConfig;
+import jalview.bin.Cache;
+import jalview.gui.OptsAndParamsPage.OptionBox;
+import jalview.gui.OptsAndParamsPage.ParamBox;
+import jalview.util.MessageManager;
+import jalview.ws.jws2.JabaParamStore;
+import jalview.ws.jws2.JabaPreset;
+import jalview.ws.jws2.Jws2Discoverer;
+import jalview.ws.jws2.jabaws2.Jws2Instance;
+import jalview.ws.params.ArgumentI;
+import jalview.ws.params.OptionI;
+import jalview.ws.params.ParamDatastoreI;
+import jalview.ws.params.ParameterI;
+import jalview.ws.params.WsParamSetI;
 import net.miginfocom.swing.MigLayout;
 
 /**
@@ -1339,8 +1339,11 @@ public class WsJobParameters extends JPanel implements ItemListener,
     if (e.getSource() == setName && e.getStateChange() == e.SELECTED)
     {
       final String setname = (String) setName.getSelectedItem();
-      System.out.println("Item state changed for " + setname
-              + " (handling ? " + !settingDialog + ")");
+      if (Cache.log.isDebugEnabled())
+      {
+        Cache.log.debug("Item state changed for " + setname
+                + " (handling ? " + !settingDialog + ")");
+      }
       if (settingDialog)
       {
         // ignore event

diff --git a/src/jalview/ws/jws2/Jws2Client.java b/src/jalview/ws/jws2/Jws2Client.java
index 0f1a25e..71ba1b9 100644 (file)
--- a/src/jalview/ws/jws2/Jws2Client.java
+++ b/src/jalview/ws/jws2/Jws2Client.java
@@ -20,6 +20,17 @@
  */
 package jalview.ws.jws2;
 
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.util.List;
+
+import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+import javax.swing.event.MenuEvent;
+import javax.swing.event.MenuListener;
+
+import compbio.metadata.Argument;
 import jalview.api.AlignCalcWorkerI;
 import jalview.bin.Cache;
 import jalview.gui.AlignFrame;
@@ -34,18 +45,6 @@ import jalview.ws.jws2.jabaws2.Jws2Instance;
 import jalview.ws.params.WsParamSetI;
 import jalview.ws.uimodel.AlignAnalysisUIText;
 
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.util.List;
-
-import javax.swing.JCheckBoxMenuItem;
-import javax.swing.JMenu;
-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.
  * 
@@ -122,9 +121,10 @@ public abstract class Jws2Client extends jalview.ws.WSClient
       WsParamSetI prset = jobParams.getPreset();
       if (prset == null)
       {
-        paramset = jobParams.isServiceDefaults() ? null
-                : JabaParamStore
-                        .getJabafromJwsArgs(jobParams.getJobParams());
+        paramset =
+                /* JAL-3739 always take values from input form */
+                /* jobParams.isServiceDefaults() ? null : */
+                JabaParamStore.getJabafromJwsArgs(jobParams.getJobParams());
         this.preset = null;
       }
       else

diff --git a/src/jalview/ws/jws2/MsaWSClient.java b/src/jalview/ws/jws2/MsaWSClient.java
index 23c6949..e33b4bd 100644 (file)
--- a/src/jalview/ws/jws2/MsaWSClient.java
+++ b/src/jalview/ws/jws2/MsaWSClient.java
@@ -20,16 +20,6 @@
  */
 package jalview.ws.jws2;
 
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.AlignmentView;
-import jalview.gui.AlignFrame;
-import jalview.gui.Desktop;
-import jalview.gui.JvOptionPane;
-import jalview.gui.JvSwingUtils;
-import jalview.util.MessageManager;
-import jalview.ws.jws2.jabaws2.Jws2Instance;
-import jalview.ws.params.WsParamSetI;
-
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
 import java.awt.event.MouseAdapter;
@@ -42,6 +32,15 @@ import javax.swing.ToolTipManager;
 
 import compbio.data.msa.MsaWS;
 import compbio.metadata.Argument;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AlignmentView;
+import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
+import jalview.gui.JvOptionPane;
+import jalview.gui.JvSwingUtils;
+import jalview.util.MessageManager;
+import jalview.ws.jws2.jabaws2.Jws2Instance;
+import jalview.ws.params.WsParamSetI;
 
 /**
  * DOCUMENT ME!
@@ -214,9 +213,9 @@ public class MsaWSClient extends Jws2Client
 
   @Override
   public void attachWSMenuEntry(JMenu rmsawsmenu,
-          final Jws2Instance service, final AlignFrame alignFrame)
+          final Jws2Instance service, final AlignFrame af)
   {
-    if (registerAAConWSInstance(rmsawsmenu, service, alignFrame))
+    if (registerAAConWSInstance(rmsawsmenu, service, af))
     {
       // Alignment dependent analysis calculation WS gui
       return;
@@ -264,14 +263,14 @@ public class MsaWSClient extends Jws2Client
         @Override
         public void actionPerformed(ActionEvent e)
         {
-          AlignmentView msa = alignFrame.gatherSequencesForAlignment();
+          AlignmentView msa = af.gatherSequencesForAlignment();
 
           if (msa != null)
           {
-            new MsaWSClient(service, alignFrame.getTitle(), msa, withGaps,
+            new MsaWSClient(service, af.getTitle(), msa, withGaps,
                     true,
-                    alignFrame.getViewport().getAlignment().getDataset(),
-                    alignFrame);
+                    af.getViewport().getAlignment().getDataset(),
+                    af);
           }
 
         }
@@ -291,13 +290,10 @@ public class MsaWSClient extends Jws2Client
           @Override
           public void actionPerformed(ActionEvent e)
           {
-            AlignmentView msa = alignFrame.gatherSequencesForAlignment();
+            AlignmentView msa = af.gatherSequencesForAlignment();
             if (msa != null)
             {
-              new MsaWSClient(service, null, null, true,
-                      alignFrame.getTitle(), msa, withGaps, true,
-                      alignFrame.getViewport().getAlignment().getDataset(),
-                      alignFrame);
+              startJob(service, af, withGaps, msa);
             }
 
           }
@@ -312,9 +308,9 @@ public class MsaWSClient extends Jws2Client
 
           final int showToolTipFor = ToolTipManager.sharedInstance()
                   .getDismissDelay();
-          for (final WsParamSetI preset : presets)
+          for (final WsParamSetI preSet : presets)
           {
-            final JMenuItem methodR = new JMenuItem(preset.getName());
+            final JMenuItem methodR = new JMenuItem(preSet.getName());
             final int QUICK_TOOLTIP = 1500;
             // JAL-1582 shorten tooltip display time in these menu items as
             // they can obscure other options
@@ -336,27 +332,27 @@ public class MsaWSClient extends Jws2Client
 
             });
             String tooltip = JvSwingUtils.wrapTooltip(true, "<strong>"
-                    + (preset.isModifiable()
+                    + (preSet.isModifiable()
                             ? MessageManager.getString("label.user_preset")
                             : MessageManager
                                     .getString("label.service_preset"))
-                    + "</strong><br/>" + preset.getDescription());
+                    + "</strong><br/>" + preSet.getDescription());
             methodR.setToolTipText(tooltip);
             methodR.addActionListener(new ActionListener()
             {
               @Override
               public void actionPerformed(ActionEvent e)
               {
-                AlignmentView msa = alignFrame
+                AlignmentView msa = af
                         .gatherSequencesForAlignment();
 
                 if (msa != null)
                 {
-                  MsaWSClient msac = new MsaWSClient(service, preset,
-                          alignFrame.getTitle(), msa, false, true,
-                          alignFrame.getViewport().getAlignment()
+                  MsaWSClient msac = new MsaWSClient(service, preSet,
+                          af.getTitle(), msa, false, true,
+                          af.getViewport().getAlignment()
                                   .getDataset(),
-                          alignFrame);
+                          af);
                 }
 
               }
@@ -378,4 +374,20 @@ public class MsaWSClient extends Jws2Client
       }
     } while (!finished);
   }
+
+  protected void startJob(final Jws2Instance service, final AlignFrame af,
+          final boolean withGaps, AlignmentView msa)
+  {
+    try {
+    new MsaWSClient(service, null, null, true,
+            af.getTitle(), msa, withGaps, true,
+            af.getViewport().getAlignment().getDataset(),
+            af);
+    } catch (Exception e) {
+      JvOptionPane.showMessageDialog(alignFrame, e.getMessage(),
+              MessageManager.getString("label.state_job_error"),
+              JvOptionPane.WARNING_MESSAGE);
+
+    }
+  }
 }

diff --git a/src/jalview/ws/jws2/dm/JabaOption.java b/src/jalview/ws/jws2/dm/JabaOption.java
index cbfbd3b..5a3fb35 100644 (file)
--- a/src/jalview/ws/jws2/dm/JabaOption.java
+++ b/src/jalview/ws/jws2/dm/JabaOption.java
@@ -20,15 +20,14 @@
  */
 package jalview.ws.jws2.dm;
 
-import jalview.util.MessageManager;
-import jalview.ws.jws2.ParameterUtils;
-import jalview.ws.params.OptionI;
-
 import java.net.MalformedURLException;
 import java.net.URL;
 import java.util.List;
 
 import compbio.metadata.Option;
+import jalview.util.MessageManager;
+import jalview.ws.jws2.ParameterUtils;
+import jalview.ws.params.OptionI;
 
 public class JabaOption implements jalview.ws.params.OptionI
 {
@@ -94,9 +93,9 @@ public class JabaOption implements jalview.ws.params.OptionI
       opt.setDefaultValue(selectedItem);
     } catch (Exception e)
     {
-      e.printStackTrace();
-      throw new Error(MessageManager.getString(
-              "error.implementation_error_cannot_set_jaba_option"));
+      throw new IllegalArgumentException(MessageManager
+              .formatMessage("error.invalid_value_for_option", new String[]
+              { selectedItem, opt.getName() }));
     }
   }