X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignViewport.java;h=7369c3cc91fc8836cbe8b8b2700ba94c10f7b68f;hb=d043ce47fc710d3eb2629ba926a8a7417bd67d8c;hp=753e972d8eba8e9dd8dbee66d1ba36539b85765b;hpb=6c32da957091bb863e5bc70e94b13fd4bf72cf38;p=jalview.git

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index 753e972..7369c3c 100644
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -52,8 +52,6 @@ public class AlignViewport extends AlignmentViewport
 
   public jalview.bin.JalviewLite applet;
 
-  boolean MAC = false;
-
   private AnnotationColumnChooser annotationColumnSelectionState;
 
   java.awt.Frame nullFrame;
@@ -65,7 +63,7 @@ public class AlignViewport extends AlignmentViewport
   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
@@ -79,7 +77,7 @@ public class AlignViewport extends AlignmentViewport
       {
         try
         {
-          widthScale = new Float(param).floatValue();
+          widthScale = Float.valueOf(param).floatValue();
         } catch (Exception e)
         {
         }
@@ -102,7 +100,7 @@ public class AlignViewport extends AlignmentViewport
       {
         try
         {
-          heightScale = new Float(param).floatValue();
+          heightScale = Float.valueOf(param).floatValue();
         } catch (Exception e)
         {
         }
@@ -123,8 +121,6 @@ public class AlignViewport extends AlignmentViewport
     }
     setFont(font, true);
 
-    MAC = new jalview.util.Platform().isAMac();
-
     if (applet != null)
     {
       setShowJVSuffix(
@@ -202,9 +198,8 @@ public class AlignViewport extends AlignmentViewport
 
       if (colour != null)
       {
-        residueShading = new ResidueShader(
-                ColourSchemeProperty.getColourScheme(getAlignment(),
-                        colour));
+        residueShading = new ResidueShader(ColourSchemeProperty
+                .getColourScheme(this, alignment, colour));
         if (residueShading != null)
         {
           residueShading.setConsensus(consensusProfiles);
@@ -256,7 +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;
@@ -344,7 +339,7 @@ public class AlignViewport extends AlignmentViewport
     if (mappedCommand != null)
     {
       mappedCommand.doCommand(null);
-      firePropertyChange("alignment", null, getAlignment().getSequences());
+      notifyAlignment();
 
       // ap.scalePanelHolder.repaint();
       // ap.repaint();
@@ -387,7 +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
    */
@@ -397,4 +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
+
+  }
 }