X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignViewport.java;h=b379c2d30afcea042c86949c0b3b45b5b1f0b882;hb=47d3ff9c908b646ea2ee659b8328976d20c3dd11;hp=36cb1859829fe51aad63e4a8b93db4e0ed18c4fa;hpb=82b053436b1d354d5b09ab419cac65ca032aea94;p=jalview.git

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index 36cb185..b379c2d 100644
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -20,20 +20,16 @@
  */
 package jalview.appletgui;
 
-import jalview.analysis.TreeModel;
 import jalview.api.AlignViewportI;
 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;
@@ -54,12 +50,8 @@ public class AlignViewport extends AlignmentViewport
 
   boolean validCharWidth = true;
 
-  TreeModel currentTree = null;
-
   public jalview.bin.JalviewLite applet;
 
-  boolean MAC = false;
-
   private AnnotationColumnChooser annotationColumnSelectionState;
 
   public AlignViewport(AlignmentI al, JalviewLite applet)
@@ -79,7 +71,7 @@ public class AlignViewport extends AlignmentViewport
       {
         try
         {
-          widthScale = new Float(param).floatValue();
+          widthScale = Float.valueOf(param).floatValue();
         } catch (Exception e)
         {
         }
@@ -102,7 +94,7 @@ public class AlignViewport extends AlignmentViewport
       {
         try
         {
-          heightScale = new Float(param).floatValue();
+          heightScale = Float.valueOf(param).floatValue();
         } catch (Exception e)
         {
         }
@@ -123,8 +115,6 @@ public class AlignViewport extends AlignmentViewport
     }
     setFont(font, true);
 
-    MAC = new jalview.util.Platform().isAMac();
-
     if (applet != null)
     {
       setShowJVSuffix(
@@ -203,7 +193,8 @@ 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);
@@ -262,17 +253,7 @@ public class AlignViewport extends AlignmentViewport
 
   public void resetSeqLimits(int height)
   {
-    ranges.setEndSeq(height / getCharHeight());
-  }
-
-  public void setCurrentTree(TreeModel tree)
-  {
-    currentTree = tree;
-  }
-
-  public TreeModel getCurrentTree()
-  {
-    return currentTree;
+    ranges.setEndSeq(height / getCharHeight() - 1); // BH 2019.04.18
   }
 
   boolean centreColumnLabels;
@@ -371,7 +352,7 @@ public class AlignViewport extends AlignmentViewport
     if (mappedCommand != null)
     {
       mappedCommand.doCommand(null);
-      firePropertyChange("alignment", null, getAlignment().getSequences());
+      notifyAlignment();
 
       // ap.scalePanelHolder.repaint();
       // ap.repaint();
@@ -411,10 +392,10 @@ 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
    */
@@ -424,4 +405,18 @@ 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
+
+  }
 }