Merge branch 'develop' into trialMerge

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

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index 73cd9e9..d10591e 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;
@@ -30,9 +29,7 @@ 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;
@@ -44,8 +41,8 @@ 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;
 
@@ -53,23 +50,10 @@ 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);
@@ -93,15 +77,15 @@ 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);
         }
       }
@@ -116,27 +100,25 @@ 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);
         }
       }
     }
     setFont(font, true);
 
-    MAC = new jalview.util.Platform().isAMac();
-
     if (applet != null)
     {
-      setShowJVSuffix(applet.getDefaultParameter("showFullId",
-              getShowJVSuffix()));
+      setShowJVSuffix(
+              applet.getDefaultParameter("showFullId", getShowJVSuffix()));
 
       setShowAnnotation(applet.getDefaultParameter("showAnnotation",
               isShowAnnotation()));
@@ -155,8 +137,8 @@ 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)
@@ -192,9 +174,9 @@ 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");
@@ -211,7 +193,8 @@ public class AlignViewport extends AlignmentViewport implements
       if (colour != null)
       {
         residueShading = new ResidueShader(
-                ColourSchemeProperty.getColourScheme(alignment, colour));
+                ColourSchemeProperty.getColourScheme(this, alignment,
+                        colour));
         if (residueShading != null)
         {
           residueShading.setConsensus(hconsensus);
@@ -220,52 +203,14 @@ 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();
 
   }
 
-  /**
-   * get the consensus sequence as displayed under the PID consensus annotation
-   * row.
-   * 
-   * @return consensus sequence as a new sequence object
-   */
-  public SequenceI getConsensusSeq()
-  {
-    if (consensus == null)
-    {
-      updateConsensus(null);
-    }
-    if (consensus == null)
-    {
-      return null;
-    }
-    StringBuilder seqs = new StringBuilder(consensus.annotations.length);
-    for (int i = 0; i < consensus.annotations.length; i++)
-    {
-      if (consensus.annotations[i] != null)
-      {
-        if (consensus.annotations[i].description.charAt(0) == '[')
-        {
-          seqs.append(consensus.annotations[i].description.charAt(1));
-        }
-        else
-        {
-          seqs.append(consensus.annotations[i].displayCharacter);
-        }
-      }
-    }
-    SequenceI sq = new Sequence("Consensus", seqs.toString());
-    sq.setDescription("Percentage Identity Consensus "
-            + ((ignoreGapsInConsensusCalculation) ? " without gaps" : ""));
-    return sq;
-  }
-
   java.awt.Frame nullFrame;
 
   protected FeatureSettings featureSettings = null;
@@ -296,7 +241,8 @@ 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)));
     }
   }
 
@@ -310,16 +256,6 @@ 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()