X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignViewport.java;h=e2c8d277bf2fc91d003bffe97eebc02e688e38e1;hb=80238b0ded8d29f9f50399c51bc550bc1df9c426;hp=c83f93f85621184a8a849fbe3c6d47709be5ba86;hpb=173f77ac7161e8866ddfe6b5689d61a83f459cfc;p=jalview.git

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index c83f93f..e2c8d27 100644
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
  * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
  * 
  * This file is part of Jalview.
  * 
@@ -25,14 +25,11 @@ import jalview.api.FeatureSettingsModelI;
 import jalview.bin.JalviewLite;
 import jalview.commands.CommandI;
 import jalview.datamodel.AlignmentI;
-import jalview.datamodel.Annotation;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.SearchResults;
 import jalview.datamodel.SearchResultsI;
-import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceGroup;
-import jalview.datamodel.SequenceI;
 import jalview.renderer.ResidueShader;
 import jalview.schemes.ColourSchemeProperty;
 import jalview.schemes.UserColourScheme;
@@ -59,14 +56,11 @@ public class AlignViewport extends AlignmentViewport
 
   private AnnotationColumnChooser annotationColumnSelectionState;
 
-  @Override
-  public void finalize()
-  {
-    applet = null;
-    quality = null;
-    alignment = null;
-    colSel = null;
-  }
+  java.awt.Frame nullFrame;
+
+  protected FeatureSettings featureSettings = null;
+
+  private float heightScale = 1, widthScale = 1;
 
   public AlignViewport(AlignmentI al, JalviewLite applet)
   {
@@ -85,7 +79,7 @@ public class AlignViewport extends AlignmentViewport
       {
         try
         {
-          widthScale = new Float(param).floatValue();
+          widthScale = Float.valueOf(param).floatValue();
         } catch (Exception e)
         {
         }
@@ -108,7 +102,7 @@ public class AlignViewport extends AlignmentViewport
       {
         try
         {
-          heightScale = new Float(param).floatValue();
+          heightScale = Float.valueOf(param).floatValue();
         } catch (Exception e)
         {
         }
@@ -209,10 +203,11 @@ public class AlignViewport extends AlignmentViewport
       if (colour != null)
       {
         residueShading = new ResidueShader(
-                ColourSchemeProperty.getColourScheme(alignment, colour));
+                ColourSchemeProperty.getColourScheme(this, alignment,
+                        colour));
         if (residueShading != null)
         {
-          residueShading.setConsensus(hconsensus);
+          residueShading.setConsensus(consensusProfiles);
         }
       }
 
@@ -223,15 +218,8 @@ public class AlignViewport extends AlignmentViewport
       }
     }
     initAutoAnnotation();
-
   }
 
-  java.awt.Frame nullFrame;
-
-  protected FeatureSettings featureSettings = null;
-
-  private float heightScale = 1, widthScale = 1;
-
   /**
    * {@inheritDoc}
    */
@@ -311,17 +299,6 @@ public class AlignViewport extends AlignmentViewport
             .getStructureSelectionManager(applet);
   }
 
-  @Override
-  public boolean isNormaliseSequenceLogo()
-  {
-    return normaliseSequenceLogo;
-  }
-
-  public void setNormaliseSequenceLogo(boolean state)
-  {
-    normaliseSequenceLogo = state;
-  }
-
   /**
    * 
    * @return true if alignment characters should be displayed
@@ -407,10 +384,10 @@ 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. NOT IMPLEMENTED FOR APPLET
    * 
    * @param featureSettings
    */
@@ -420,4 +397,18 @@ public class AlignViewport extends AlignmentViewport
     // TODO implement for applet
   }
 
+  /**
+   * Merges the supplied feature settings descriptor with existing feature styles.
+   * 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. NOT IMPLEMENTED FOR APPLET
+   * 
+   * @param featureSettings
+   */
+  @Override
+  public void mergeFeaturesStyle(FeatureSettingsModelI featureSettings)
+  {
+    // TODO Auto-generated method stub
+
+  }
 }