Merge branch 'develop' into update/JAL-3949_abstracted_logging_for_jalviewjs_and_sanity

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

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 0125f0d..ea0afe1 100644 (file)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -123,14 +123,14 @@ public class AlignViewport extends AlignmentViewport
     sequenceSetID = seqsetid;
     viewId = viewid;
     // TODO remove these once 2.4.VAMSAS release finished
-    if (Cache.log != null && Cache.log.isDebugEnabled() && seqsetid != null)
+    if (seqsetid != null)
     {
-      Cache.log.debug(
+      Cache.debug(
               "Setting viewport's sequence set id : " + sequenceSetID);
     }
-    if (Cache.log != null && Cache.log.isDebugEnabled() && viewId != null)
+    if (viewId != null)
     {
-      Cache.log.debug("Setting viewport's view id : " + viewId);
+      Cache.debug("Setting viewport's view id : " + viewId);
     }
     init();
 
@@ -185,14 +185,14 @@ public class AlignViewport extends AlignmentViewport
     sequenceSetID = seqsetid;
     viewId = viewid;
     // TODO remove these once 2.4.VAMSAS release finished
-    if (Cache.log != null && Cache.log.isDebugEnabled() && seqsetid != null)
+    if (seqsetid != null)
     {
-      Cache.log.debug(
+      Cache.debug(
               "Setting viewport's sequence set id : " + sequenceSetID);
     }
-    if (Cache.log != null && Cache.log.isDebugEnabled() && viewId != null)
+    if (viewId != null)
     {
-      Cache.log.debug("Setting viewport's view id : " + viewId);
+      Cache.debug("Setting viewport's view id : " + viewId);
     }
 
     if (hiddenColumns != null)
@@ -594,7 +594,7 @@ public class AlignViewport extends AlignmentViewport
     // calculator.getRegisteredWorkersOfClass(settings.getWorkerClass())
     if (needsUpdate)
     {
-      Cache.log.debug("trigger update for " + calcId);
+      Cache.debug("trigger update for " + calcId);
     }
   }
 
@@ -824,7 +824,7 @@ public class AlignViewport extends AlignmentViewport
     try
     {
       newAlignFrame.setMaximum(
-              jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false));
+              Cache.getDefault("SHOW_FULLSCREEN", false));
     } catch (java.beans.PropertyVetoException ex)
     {
     }
@@ -1022,8 +1022,8 @@ public class AlignViewport extends AlignmentViewport
     
     FeatureRenderer fr = getAlignPanel().getSeqPanel().seqCanvas
             .getFeatureRenderer();
-    List<String> origRenderOrder = new ArrayList(),
-            origGroups = new ArrayList();
+    List<String> origRenderOrder = new ArrayList<>();
+    List<String> origGroups = new ArrayList<>();
     // preserve original render order - allows differentiation between user configured colours and autogenerated ones
     origRenderOrder.addAll(fr.getRenderOrder());
     origGroups.addAll(fr.getFeatureGroups());
@@ -1034,7 +1034,7 @@ public class AlignViewport extends AlignmentViewport
     if (!mergeOnly)
     {
       // only clear displayed features if we are mergeing
-      displayed.clear();
+      // displayed.clear();
     }
     // TODO this clears displayed.featuresRegistered - do we care?
     //
@@ -1066,6 +1066,10 @@ public class AlignViewport extends AlignmentViewport
         {
           displayed.setVisible(type);
         }
+        else if (featureSettings.isFeatureHidden(type))
+        {
+          displayed.setHidden(type);
+        }
       }
     }
 
@@ -1094,6 +1098,8 @@ public class AlignViewport extends AlignmentViewport
       fr.orderFeatures(featureSettings);
     }
     fr.setTransparency(featureSettings.getTransparency());
+
+    fr.notifyFeaturesChanged();
   }
 
   public String getViewName()