JAL-1953 2.11.2 with Archeopteryx!

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

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 3c520e3..ac295a1 100644 (file)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -29,6 +29,7 @@ import jalview.api.FeatureSettingsModelI;
 import jalview.api.FeaturesDisplayedI;
 import jalview.api.ViewStyleI;
 import jalview.bin.Cache;
+import jalview.bin.Console;
 import jalview.commands.CommandI;
 import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.Alignment;
@@ -123,14 +124,14 @@ 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(
+      Console.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);
+      Console.debug("Setting viewport's view id : " + viewId);
     }
     init();
 
@@ -185,14 +186,14 @@ 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(
+      Console.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);
+      Console.debug("Setting viewport's view id : " + viewId);
     }
 
     if (hiddenColumns != null)
@@ -290,8 +291,8 @@ public class AlignViewport extends AlignmentViewport
       schemeName = Cache.getDefault(Preferences.DEFAULT_COLOUR,
               ResidueColourScheme.NONE);
     }
-    ColourSchemeI colourScheme = ColourSchemeProperty
-            .getColourScheme(this, alignment, schemeName);
+    ColourSchemeI colourScheme = ColourSchemeProperty.getColourScheme(this,
+            alignment, schemeName);
     residueShading = new ResidueShader(colourScheme);
 
     if (colourScheme instanceof UserColourScheme)
@@ -519,7 +520,6 @@ public class AlignViewport extends AlignmentViewport
    * return the alignPanel containing the given viewport. Use this to get the
    * components currently handling the given viewport.
    * 
-   * @param av
    * @return null or an alignPanel guaranteed to have non-null alignFrame
    *         reference
    */
@@ -594,7 +594,7 @@ public class AlignViewport extends AlignmentViewport
     // calculator.getRegisteredWorkersOfClass(settings.getWorkerClass())
     if (needsUpdate)
     {
-      Cache.log.debug("trigger update for " + calcId);
+      Console.debug("trigger update for " + calcId);
     }
   }
 
@@ -740,7 +740,7 @@ public class AlignViewport extends AlignmentViewport
     final String question = JvSwingUtils.wrapTooltip(true,
             MessageManager.getString("label.open_split_window?"));
     final AlignViewport us = this;
-    
+
     /*
      * options No, Split Window, New Window correspond to
      * dialog responses 0, 1, 2 (even though JOptionPane shows them
@@ -752,7 +752,7 @@ public class AlignViewport extends AlignmentViewport
               @Override
               public void run()
               {
-                  addDataToAlignment(al);
+                addDataToAlignment(al);
               }
             }).setResponseHandler(1, new Runnable()
             {
@@ -769,7 +769,7 @@ public class AlignViewport extends AlignmentViewport
                 us.openLinkedAlignmentAs(al, title, false);
               }
             });
-       dialog.showDialog(question,
+    dialog.showDialog(question,
             MessageManager.getString("label.open_split_window"),
             JvOptionPane.DEFAULT_OPTION, JvOptionPane.PLAIN_MESSAGE, null,
             options, options[0]);
@@ -777,7 +777,7 @@ public class AlignViewport extends AlignmentViewport
 
   protected void openLinkedAlignmentAs(AlignmentI al, String title,
           boolean newWindowOrSplitPane)
-    {
+  {
     /*
      * Identify protein and dna alignments. Make a copy of this one if opening
      * in a new split pane.
@@ -823,8 +823,7 @@ public class AlignViewport extends AlignmentViewport
 
     try
     {
-      newAlignFrame.setMaximum(
-              jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false));
+      newAlignFrame.setMaximum(Cache.getDefault("SHOW_FULLSCREEN", false));
     } catch (java.beans.PropertyVetoException ex)
     {
     }
@@ -990,10 +989,10 @@ public class AlignViewport extends AlignmentViewport
   }
 
   /**
-   * Applies the supplied feature settings descriptor to currently known features.
-   * This supports an 'initial configuration' of feature colouring based on a
-   * preset or user favourite. This may then be modified in the usual way using
-   * the Feature Settings dialogue.
+   * Applies the supplied feature settings descriptor to currently known
+   * features. This supports an 'initial configuration' of feature colouring
+   * based on a preset or user favourite. This may then be modified in the usual
+   * way using the Feature Settings dialogue.
    * 
    * @param featureSettings
    */
@@ -1006,8 +1005,8 @@ public class AlignViewport extends AlignmentViewport
   /**
    * when mergeOnly is set, then group and feature visibility or feature colours
    * are not modified for features and groups already known to the feature
-   * renderer. Feature ordering is always adjusted, and transparency is always set
-   * regardless.
+   * renderer. Feature ordering is always adjusted, and transparency is always
+   * set regardless.
    * 
    * @param featureSettings
    * @param mergeOnly
@@ -1019,12 +1018,13 @@ public class AlignViewport extends AlignmentViewport
     {
       return;
     }
-    
+
     FeatureRenderer fr = getAlignPanel().getSeqPanel().seqCanvas
             .getFeatureRenderer();
     List<String> origRenderOrder = new ArrayList<>();
     List<String> origGroups = new ArrayList<>();
-    // preserve original render order - allows differentiation between user configured colours and autogenerated ones
+    // preserve original render order - allows differentiation between user
+    // configured colours and autogenerated ones
     origRenderOrder.addAll(fr.getRenderOrder());
     origGroups.addAll(fr.getFeatureGroups());
 
@@ -1056,7 +1056,8 @@ public class AlignViewport extends AlignmentViewport
                       && origColour.getColour().equals(
                               ColorUtils.createColourFromName(type)))))
       {
-        // if we are merging, only update if there wasn't already a colour defined for
+        // if we are merging, only update if there wasn't already a colour
+        // defined for
         // this type
         if (preferredColour != null)
         {
@@ -1080,7 +1081,8 @@ public class AlignViewport extends AlignmentViewport
     {
       if (!mergeOnly || !origGroups.contains(group))
       {
-        // when merging, display groups only if the aren't already marked as not visible
+        // when merging, display groups only if the aren't already marked as not
+        // visible
         fr.setGroupVisibility(group,
                 featureSettings.isGroupDisplayed(group));
       }
@@ -1098,6 +1100,8 @@ public class AlignViewport extends AlignmentViewport
       fr.orderFeatures(featureSettings);
     }
     fr.setTransparency(featureSettings.getTransparency());
+
+    fr.notifyFeaturesChanged();
   }
 
   public String getViewName()