X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignViewport.java;h=7369c3cc91fc8836cbe8b8b2700ba94c10f7b68f;hb=d043ce47fc710d3eb2629ba926a8a7417bd67d8c;hp=c83f93f85621184a8a849fbe3c6d47709be5ba86;hpb=173f77ac7161e8866ddfe6b5689d61a83f459cfc;p=jalview.git

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index c83f93f..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.
  * 
@@ -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;
@@ -55,23 +52,18 @@ public class AlignViewport extends AlignmentViewport
 
   public jalview.bin.JalviewLite applet;
 
-  boolean MAC = false;
-
   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)
   {
     super(al);
-    calculator = new jalview.workers.AlignCalcManager();
+    calculator = new jalview.workers.AlignCalcManager2();
     this.applet = applet;
 
     // we always pad gaps
@@ -85,7 +77,7 @@ public class AlignViewport extends AlignmentViewport
       {
         try
         {
-          widthScale = new Float(param).floatValue();
+          widthScale = Float.valueOf(param).floatValue();
         } catch (Exception e)
         {
         }
@@ -108,7 +100,7 @@ public class AlignViewport extends AlignmentViewport
       {
         try
         {
-          heightScale = new Float(param).floatValue();
+          heightScale = Float.valueOf(param).floatValue();
         } catch (Exception e)
         {
         }
@@ -129,8 +121,6 @@ public class AlignViewport extends AlignmentViewport
     }
     setFont(font, true);
 
-    MAC = new jalview.util.Platform().isAMac();
-
     if (applet != null)
     {
       setShowJVSuffix(
@@ -208,11 +198,11 @@ public class AlignViewport extends AlignmentViewport
 
       if (colour != null)
       {
-        residueShading = new ResidueShader(
-                ColourSchemeProperty.getColourScheme(alignment, colour));
+        residueShading = new ResidueShader(ColourSchemeProperty
+                .getColourScheme(this, alignment, colour));
         if (residueShading != null)
         {
-          residueShading.setConsensus(hconsensus);
+          residueShading.setConsensus(consensusProfiles);
         }
       }
 
@@ -223,15 +213,8 @@ public class AlignViewport extends AlignmentViewport
       }
     }
     initAutoAnnotation();
-
   }
 
-  java.awt.Frame nullFrame;
-
-  protected FeatureSettings featureSettings = null;
-
-  private float heightScale = 1, widthScale = 1;
-
   /**
    * {@inheritDoc}
    */
@@ -268,7 +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;
@@ -311,17 +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
@@ -367,7 +339,7 @@ public class AlignViewport extends AlignmentViewport
     if (mappedCommand != null)
     {
       mappedCommand.doCommand(null);
-      firePropertyChange("alignment", null, getAlignment().getSequences());
+      notifyAlignment();
 
       // ap.scalePanelHolder.repaint();
       // ap.repaint();
@@ -410,7 +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
    */
@@ -420,4 +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
+
+  }
 }