JAL-1793 spike branch updated to latest

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

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index 1d2c4bc..262948d 100644 (file)
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -20,7 +20,6 @@
  */
 package jalview.appletgui;
 
-import jalview.analysis.TreeModel;
 import jalview.api.AlignViewportI;
 import jalview.api.FeatureSettingsModelI;
 import jalview.bin.JalviewLite;
@@ -45,8 +44,8 @@ import jalview.viewmodel.AlignmentViewport;
 import java.awt.Font;
 import java.awt.FontMetrics;
 
-public class AlignViewport extends AlignmentViewport implements
-        SelectionSource
+public class AlignViewport extends AlignmentViewport
+        implements SelectionSource
 {
   boolean cursorMode = false;
 
@@ -54,23 +53,12 @@ public class AlignViewport extends AlignmentViewport implements
 
   boolean validCharWidth = true;
 
-  TreeModel currentTree = null;
-
   public jalview.bin.JalviewLite applet;
 
   boolean MAC = false;
 
   private AnnotationColumnChooser annotationColumnSelectionState;
 
-  @Override
-  public void finalize()
-  {
-    applet = null;
-    quality = null;
-    alignment = null;
-    colSel = null;
-  }
-
   public AlignViewport(AlignmentI al, JalviewLite applet)
   {
     super(al);
@@ -94,15 +82,15 @@ public class AlignViewport extends AlignmentViewport implements
         }
         if (widthScale <= 1.0)
         {
-          System.err
-                  .println("Invalid alignment character width scaling factor ("
+          System.err.println(
+                  "Invalid alignment character width scaling factor ("
                           + widthScale + "). Ignoring.");
           widthScale = 1;
         }
         if (JalviewLite.debug)
         {
-          System.err
-                  .println("Alignment character width scaling factor is now "
+          System.err.println(
+                  "Alignment character width scaling factor is now "
                           + widthScale);
         }
       }
@@ -117,15 +105,15 @@ public class AlignViewport extends AlignmentViewport implements
         }
         if (heightScale <= 1.0)
         {
-          System.err
-                  .println("Invalid alignment character height scaling factor ("
+          System.err.println(
+                  "Invalid alignment character height scaling factor ("
                           + heightScale + "). Ignoring.");
           heightScale = 1;
         }
         if (JalviewLite.debug)
         {
-          System.err
-                  .println("Alignment character height scaling factor is now "
+          System.err.println(
+                  "Alignment character height scaling factor is now "
                           + heightScale);
         }
       }
@@ -136,8 +124,8 @@ public class AlignViewport extends AlignmentViewport implements
 
     if (applet != null)
     {
-      setShowJVSuffix(applet.getDefaultParameter("showFullId",
-              getShowJVSuffix()));
+      setShowJVSuffix(
+              applet.getDefaultParameter("showFullId", getShowJVSuffix()));
 
       setShowAnnotation(applet.getDefaultParameter("showAnnotation",
               isShowAnnotation()));
@@ -156,8 +144,8 @@ public class AlignViewport extends AlignmentViewport implements
       setShowUnconserved(applet.getDefaultParameter("showUnconserved",
               getShowUnconserved()));
 
-      setScaleProteinAsCdna(applet.getDefaultParameter(
-              "scaleProteinAsCdna", isScaleProteinAsCdna()));
+      setScaleProteinAsCdna(applet.getDefaultParameter("scaleProteinAsCdna",
+              isScaleProteinAsCdna()));
 
       String param = applet.getParameter("upperCase");
       if (param != null)
@@ -193,9 +181,9 @@ public class AlignViewport extends AlignmentViewport implements
 
     if (applet != null)
     {
-      String colour = al.isNucleotide() ? applet
-              .getParameter("defaultColourNuc") : applet
-              .getParameter("defaultColourProt");
+      String colour = al.isNucleotide()
+              ? applet.getParameter("defaultColourNuc")
+              : applet.getParameter("defaultColourProt");
       if (colour == null)
       {
         colour = applet.getParameter("defaultColour");
@@ -221,9 +209,8 @@ public class AlignViewport extends AlignmentViewport implements
 
       if (applet.getParameter("userDefinedColour") != null)
       {
-        residueShading = new ResidueShader(
-                new UserColourScheme(
-                        applet.getParameter("userDefinedColour")));
+        residueShading = new ResidueShader(new UserColourScheme(
+                applet.getParameter("userDefinedColour")));
       }
     }
     initAutoAnnotation();
@@ -260,7 +247,8 @@ public class AlignViewport extends AlignmentViewport implements
     {
       Font f2 = new Font(f.getName(), Font.BOLD, f.getSize());
       FontMetrics fm = nullFrame.getGraphics().getFontMetrics(f2);
-      setCharWidth((int) (widthScale * (fm.stringWidth("MMMMMMMMMMM") / 10)));
+      setCharWidth(
+              (int) (widthScale * (fm.stringWidth("MMMMMMMMMMM") / 10)));
     }
   }
 
@@ -274,16 +262,6 @@ public class AlignViewport extends AlignmentViewport implements
     ranges.setEndSeq(height / getCharHeight());
   }
 
-  public void setCurrentTree(TreeModel tree)
-  {
-    currentTree = tree;
-  }
-
-  public TreeModel getCurrentTree()
-  {
-    return currentTree;
-  }
-
   boolean centreColumnLabels;
 
   public boolean getCentreColumnLabels()