JAL-4020 Added search for PyMOLWinWithConsole.bat (and PyMOLWin.exe) in likely places...

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

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index 9004457..d64cd75 100644 (file)
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -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;
@@ -74,7 +71,7 @@ public class AlignViewport extends AlignmentViewport
       {
         try
         {
-          widthScale = new Float(param).floatValue();
+          widthScale = Float.valueOf(param).floatValue();
         } catch (Exception e)
         {
         }
@@ -97,7 +94,7 @@ public class AlignViewport extends AlignmentViewport
       {
         try
         {
-          heightScale = new Float(param).floatValue();
+          heightScale = Float.valueOf(param).floatValue();
         } catch (Exception e)
         {
         }
@@ -195,8 +192,8 @@ 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);
@@ -255,7 +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;
@@ -397,7 +394,7 @@ 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
    */
@@ -407,4 +404,18 @@ 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
+
+  }
 }