Merge branch 'feature/JAL-4159_pasimap' into spike/JAL-4159_pasimap_2113_series

[jalview.git] / src / jalview / gui / Desktop.java

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index 35c7818..0de6b17 100644 (file)
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -680,22 +680,7 @@ public class Desktop extends jalview.jbgui.GDesktop
     // configure services
     StructureSelectionManager ssm = StructureSelectionManager
             .getStructureSelectionManager(this);
-    if (Cache.getDefault(Preferences.ADD_SS_ANN, true))
-    {
-      ssm.setAddTempFacAnnot(
-              Cache.getDefault(Preferences.ADD_TEMPFACT_ANN, true));
-      ssm.setProcessSecondaryStructure(
-              Cache.getDefault(Preferences.STRUCT_FROM_PDB, true));
-      // JAL-3915 - RNAView is no longer an option so this has no effect
-      ssm.setSecStructServices(
-              Cache.getDefault(Preferences.USE_RNAVIEW, false));
-    }
-    else
-    {
-      ssm.setAddTempFacAnnot(false);
-      ssm.setProcessSecondaryStructure(false);
-      ssm.setSecStructServices(false);
-    }
+    StructureSelectionManager.doConfigureStructurePrefs(ssm);
   }
 
   public void checkForNews()
@@ -2824,6 +2809,23 @@ public class Desktop extends jalview.jbgui.GDesktop
     }
   }
 
+  @Override
+  public JProgressBar getProgressBar(long id)
+  {
+    if (progressBars == null)
+      return null;
+
+    if (progressBars.get(Long.valueOf(id)) == null)
+      return null;
+ 
+    for (Component c : progressBars.get(Long.valueOf(id)).getComponents())
+    {
+      if (c.getClass() == JProgressBar.class)
+       return (JProgressBar) c;
+    }
+    return null;
+  }
+
   /*
    * (non-Javadoc)
    *