X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignViewport.java;h=7369c3cc91fc8836cbe8b8b2700ba94c10f7b68f;hb=d043ce47fc710d3eb2629ba926a8a7417bd67d8c;hp=d10591e97d080d644023bb05a9c1ec3b7c33c6ac;hpb=3da878124135ff033f42d19d8733891b09e953cd;p=jalview.git

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index d10591e..7369c3c 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.
  * 
@@ -54,10 +54,16 @@ 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);
-    calculator = new jalview.workers.AlignCalcManager();
+    calculator = new jalview.workers.AlignCalcManager2();
     this.applet = applet;
 
     // we always pad gaps
@@ -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)
         {
         }
@@ -192,12 +198,11 @@ public class AlignViewport extends AlignmentViewport
 
       if (colour != null)
       {
-        residueShading = new ResidueShader(
-                ColourSchemeProperty.getColourScheme(this, alignment,
-                        colour));
+        residueShading = new ResidueShader(ColourSchemeProperty
+                .getColourScheme(this, alignment, colour));
         if (residueShading != null)
         {
-          residueShading.setConsensus(hconsensus);
+          residueShading.setConsensus(consensusProfiles);
         }
       }
 
@@ -208,15 +213,8 @@ public class AlignViewport extends AlignmentViewport
       }
     }
     initAutoAnnotation();
-
   }
 
-  java.awt.Frame nullFrame;
-
-  protected FeatureSettings featureSettings = null;
-
-  private float heightScale = 1, widthScale = 1;
-
   /**
    * {@inheritDoc}
    */
@@ -253,7 +251,7 @@ 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 +294,6 @@ 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
@@ -352,7 +339,7 @@ public class AlignViewport extends AlignmentViewport
     if (mappedCommand != null)
     {
       mappedCommand.doCommand(null);
-      firePropertyChange("alignment", null, getAlignment().getSequences());
+      notifyAlignment();
 
       // ap.scalePanelHolder.repaint();
       // ap.repaint();
@@ -395,7 +382,7 @@ 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.
+   * way using the Feature Settings dialogue. NOT IMPLEMENTED FOR APPLET
    * 
    * @param featureSettings
    */
@@ -405,4 +392,18 @@ 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
+
+  }
 }