FeatureRenderer takes alignmentPanel

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

diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java
index 4c0450c..96e82c1 100755 (executable)
--- a/src/jalview/gui/FeatureSettings.java
+++ b/src/jalview/gui/FeatureSettings.java
@@ -136,9 +136,9 @@ public class FeatureSettings
           fs.handlingUpdate=false;
         }
       }
-      
+
     });
-    
+
     frame = new JInternalFrame();
     frame.setContentPane(this);
     Desktop.addInternalFrame(frame, "Sequence Feature Settings", 400, 450);
@@ -157,7 +157,7 @@ public class FeatureSettings
    * true when Feature Settings are updating from feature renderer
    */
   private boolean handlingUpdate=false;
-  
+
   /**
    * contains a float[3] for each feature type string. created by setTableData
    */
@@ -212,13 +212,13 @@ public class FeatureSettings
         index++;
       }
     }
-    
+
     resetTable(null);
 
     validate();
   }
   /**
-   * 
+   *
    * @param group
    * @return true if group has been seen before and is already added to set.
    */
@@ -228,7 +228,7 @@ public class FeatureSettings
     {
       visible = ( (Boolean) fr.featureGroups.get(group)).booleanValue();
         } else {
-        visible=true; // new group is always made visible 
+        visible=true; // new group is always made visible
       }
 
       if (groupPanel == null)
@@ -250,7 +250,7 @@ public class FeatureSettings
 
       if (alreadyAdded)
       {
-        
+
         return true;
       }
 
@@ -564,16 +564,16 @@ public class FeatureSettings
     boolean sort=false;
     for (int i=0;i<width.length; i++) {
       //awidth = (float[]) typeWidth.get(data[i][0]);
-      if (width[i]==0) 
+      if (width[i]==0)
       {
         width[i] = fr.getOrder(data[i][0].toString());
         if (width[i]<0)
         {
           width[i] = fr.setOrder(data[i][0].toString(), i/data.length);
         }
-      } else { 
+      } else {
         width[i] /=max; // normalize
-        fr.setOrder(data[i][0].toString(), width[i]); // store for later 
+        fr.setOrder(data[i][0].toString(), width[i]); // store for later
       }
       if (i>0)
         sort = sort || width[i-1]>width[i];
@@ -581,7 +581,7 @@ public class FeatureSettings
     if (sort)
       jalview.util.QuickSort.sort(width, data);
     // update global priority order
-    
+
     updateFeatureRenderer(data,false);
     table.repaint();
   }
@@ -604,11 +604,6 @@ public class FeatureSettings
   {
     fr.setFeaturePriority(data, visibleNew);
     af.alignPanel.paintAlignment(true);
-
-    if (af.alignPanel.overviewPanel != null)
-    {
-      af.alignPanel.overviewPanel.updateOverviewImage();
-    }
   }
 
   int selectedRow = -1;