Merge branch 'alpha/JAL-3362_Jalview_212_alpha' into alpha/merge_212_JalviewJS_2112

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

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index d10591e..0fa569e 100644 (file)
--- 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.
  * 
@@ -54,6 +54,12 @@ public class AlignViewport extends AlignmentViewport
 
   private AnnotationColumnChooser annotationColumnSelectionState;
 
+  java.awt.Frame nullFrame;
+
+  protected FeatureSettings featureSettings = null;
+
+  private float heightScale = 1, widthScale = 1;
+
   public AlignViewport(AlignmentI al, JalviewLite applet)
   {
     super(al);
@@ -71,7 +77,7 @@ public class AlignViewport extends AlignmentViewport
       {
         try
         {
-          widthScale = new Float(param).floatValue();
+          widthScale = Float.valueOf(param).floatValue();
         } catch (Exception e)
         {
         }
@@ -94,7 +100,7 @@ public class AlignViewport extends AlignmentViewport
       {
         try
         {
-          heightScale = new Float(param).floatValue();
+          heightScale = Float.valueOf(param).floatValue();
         } catch (Exception e)
         {
         }
@@ -197,7 +203,7 @@ public class AlignViewport extends AlignmentViewport
                         colour));
         if (residueShading != null)
         {
-          residueShading.setConsensus(hconsensus);
+          residueShading.setConsensus(consensusProfiles);
         }
       }
 
@@ -208,15 +214,8 @@ public class AlignViewport extends AlignmentViewport
       }
     }
     initAutoAnnotation();
-
   }
 
-  java.awt.Frame nullFrame;
-
-  protected FeatureSettings featureSettings = null;
-
-  private float heightScale = 1, widthScale = 1;
-
   /**
    * {@inheritDoc}
    */
@@ -253,7 +252,7 @@ public class AlignViewport extends AlignmentViewport
 
   public void resetSeqLimits(int height)
   {
-    ranges.setEndSeq(height / getCharHeight());
+    ranges.setEndSeq(height / getCharHeight() - 1); // BH 2019.04.18
   }
 
   boolean centreColumnLabels;
@@ -296,17 +295,6 @@ 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
@@ -392,10 +380,10 @@ 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
    */
@@ -405,4 +393,18 @@ 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
+
+  }
 }