Merge branch 'develop' into develop_m2_8_1_2

diff --git a/src/jalview/gui/OptsAndParamsPage.java b/src/jalview/gui/OptsAndParamsPage.java
index 93f5ce2..eb55994 100644 (file)
--- a/src/jalview/gui/OptsAndParamsPage.java
+++ b/src/jalview/gui/OptsAndParamsPage.java
@@ -235,10 +235,11 @@ public class OptsAndParamsPage
 
     }
 
-    public void resetToDefault()
+
+    public void resetToDefault(boolean setDefaultParams)
     {
       enabled.setSelected(false);
-      if (option.isRequired())
+      if (option.isRequired() || (setDefaultParams && option.getValue()!=null))
       {
         // Apply default value
         selectOption(option, option.getValue());
@@ -258,7 +259,7 @@ public class OptsAndParamsPage
         initVal = (initEnabled) ? (String) val.getSelectedItem() : null;
       }
     }
-
+    
   }
 
   public class ParamBox extends JPanel implements ChangeListener,

diff --git a/src/jalview/gui/WsJobParameters.java b/src/jalview/gui/WsJobParameters.java
index 8abbcee..77f3155 100644 (file)
--- a/src/jalview/gui/WsJobParameters.java
+++ b/src/jalview/gui/WsJobParameters.java
@@ -566,14 +566,27 @@ public class WsJobParameters extends JPanel implements ItemListener,
   @SuppressWarnings("unchecked")
   private void updateTable(WsParamSetI p, List<ArgumentI> jobArgset)
   {
+    boolean setDefaultParams=false;
+    if (lastParmSet == null)
+    {
+      isUserPreset = false;
+      // First call - so provide Service default settings
+      setName.setSelectedItem(lastSetName = SVC_DEF);
+    }
+    if (p==null && SVC_DEF.equals(""+setName.getSelectedItem()))
+    {
+      // indicate that service defaults should be set if available
+      setDefaultParams=true;
+    }
     // populate table from default parameter set.
     List<ArgumentI> args = paramStore.getServiceParameters();
 
     // split to params and required arguments
     {
       int cw = 0;
+      boolean optset=false;
       for (ArgumentI myarg : args)
-      {
+      { 
         // Ideally, Argument would implement isRequired !
         if (myarg instanceof ParameterI)
         {
@@ -586,7 +599,7 @@ public class WsJobParameters extends JPanel implements ItemListener,
           {
             OptionI opt = (OptionI) myarg;
             OptionBox ob = opanp.addOption(opt);
-            ob.resetToDefault();
+            ob.resetToDefault(setDefaultParams);
             if (MAX_OPTWIDTH < ob.getPreferredSize().width)
             {
               MAX_OPTWIDTH = ob.getPreferredSize().width;
@@ -620,16 +633,6 @@ public class WsJobParameters extends JPanel implements ItemListener,
       // TODO: check if args should be unselected prior to resetting using the
       // preset
     }
-    else
-    {
-      if (lastParmSet == null)
-      {
-        isUserPreset = false;
-        // first call - so create a dummy name
-
-        setName.setSelectedItem(lastSetName = SVC_DEF);
-      }
-    }
 
     if (jobArgset != null)
     {

diff --git a/src/jalview/ws/DBRefFetcher.java b/src/jalview/ws/DBRefFetcher.java
index a55658b..17c1bc9 100644 (file)
--- a/src/jalview/ws/DBRefFetcher.java
+++ b/src/jalview/ws/DBRefFetcher.java
@@ -136,10 +136,13 @@ public class DBRefFetcher implements Runnable
       {
         jalviewSourceI src = en.nextElement();
         List<DbSourceProxy> sp = src.getSequenceSourceProxies();
-        selsources.addAll(sp);
-        if (sp.size() > 1)
+        if (sp != null)
         {
-          Cache.log.debug("Added many Db Sources for :" + src.getTitle());
+          selsources.addAll(sp);
+          if (sp.size() > 1)
+          {
+            Cache.log.debug("Added many Db Sources for :" + src.getTitle());
+          }
         }
       }
       // select appropriate databases based on alignFrame context.