X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignViewport.java;h=2e76e1aece976095f614ed165759c257d98c1240;hb=8e1be43e250107a4d86898bd554cf03098fa5957;hp=1ed45832e84c3c78b8dd396d6f9d76bbf6b97c87;hpb=882adcab8cf6f9c72a7e946223f817878c5ee444;p=jalview.git

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index 1ed4583..2e76e1a 100644
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -20,18 +20,19 @@
  */
 package jalview.appletgui;
 
-import java.awt.Font;
-
 import jalview.analysis.NJTree;
 import jalview.api.AlignViewportI;
+import jalview.api.FeatureSettingsModelI;
 import jalview.bin.JalviewLite;
 import jalview.commands.CommandI;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.SearchResults;
+import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
+import jalview.schemes.CollectionColourScheme;
 import jalview.schemes.ColourSchemeProperty;
 import jalview.schemes.UserColourScheme;
 import jalview.structure.CommandListener;
@@ -40,6 +41,8 @@ import jalview.structure.StructureSelectionManager;
 import jalview.structure.VamsasSource;
 import jalview.viewmodel.AlignmentViewport;
 
+import java.awt.Font;
+
 public class AlignViewport extends AlignmentViewport implements
         SelectionSource, VamsasSource, CommandListener
 {
@@ -57,6 +60,7 @@ public class AlignViewport extends AlignmentViewport implements
 
   private AnnotationColumnChooser annotationColumnSelectionState;
 
+  @Override
   public void finalize()
   {
     applet = null;
@@ -187,8 +191,13 @@ public class AlignViewport extends AlignmentViewport implements
 
     if (applet != null)
     {
-      String colour = applet.getParameter("defaultColour");
-
+      String colour = al.isNucleotide() ? applet
+              .getParameter("defaultColourNuc") : applet
+              .getParameter("defaultColourProt");
+      if (colour == null)
+      {
+        colour = applet.getParameter("defaultColour");
+      }
       if (colour == null)
       {
         colour = applet.getParameter("userDefinedColour");
@@ -200,8 +209,8 @@ public class AlignViewport extends AlignmentViewport implements
 
       if (colour != null)
       {
-        globalColourScheme = ColourSchemeProperty.getColour(alignment,
-                colour);
+        globalColourScheme = new CollectionColourScheme(
+                ColourSchemeProperty.getColourScheme(alignment, colour));
         if (globalColourScheme != null)
         {
           globalColourScheme.setConsensus(hconsensus);
@@ -210,8 +219,9 @@ public class AlignViewport extends AlignmentViewport implements
 
       if (applet.getParameter("userDefinedColour") != null)
       {
-        ((UserColourScheme) globalColourScheme).parseAppletParameter(applet
-                .getParameter("userDefinedColour"));
+        globalColourScheme = new CollectionColourScheme(
+                new UserColourScheme(
+                        applet.getParameter("userDefinedColour")));
       }
     }
     initAutoAnnotation();
@@ -287,7 +297,6 @@ public class AlignViewport extends AlignmentViewport implements
     return font;
   }
 
-
   public void resetSeqLimits(int height)
   {
     setEndSeq(height / getCharHeight());
@@ -303,7 +312,6 @@ public class AlignViewport extends AlignmentViewport implements
     return currentTree;
   }
 
-
   boolean centreColumnLabels;
 
   public boolean getCentreColumnLabels()
@@ -322,11 +330,12 @@ public class AlignViewport extends AlignmentViewport implements
     return followSelection;
   }
 
+  @Override
   public void sendSelection()
   {
     getStructureSelectionManager().sendSelection(
-                    new SequenceGroup(getSelectionGroup()),
-                    new ColumnSelection(getColumnSelection()), this);
+            new SequenceGroup(getSelectionGroup()),
+            new ColumnSelection(getColumnSelection()), this);
   }
 
   /**
@@ -342,39 +351,7 @@ public class AlignViewport extends AlignmentViewport implements
             .getStructureSelectionManager(applet);
   }
 
-  /**
-   * synthesize a column selection if none exists so it covers the given
-   * selection group. if wholewidth is false, no column selection is made if the
-   * selection group covers the whole alignment width.
-   * 
-   * @param sg
-   * @param wholewidth
-   */
-  public void expandColSelection(SequenceGroup sg, boolean wholewidth)
-  {
-    int sgs, sge;
-    if (sg != null
-            && (sgs = sg.getStartRes()) >= 0
-            && sg.getStartRes() <= (sge = sg.getEndRes())
-            && (colSel == null || colSel.getSelected() == null || colSel
-                    .getSelected().size() == 0))
-    {
-      if (!wholewidth && alignment.getWidth() == (1 + sge - sgs))
-      {
-        // do nothing
-        return;
-      }
-      if (colSel == null)
-      {
-        colSel = new ColumnSelection();
-      }
-      for (int cspos = sg.getStartRes(); cspos <= sg.getEndRes(); cspos++)
-      {
-        colSel.addElement(cspos);
-      }
-    }
-  }
-
+  @Override
   public boolean isNormaliseSequenceLogo()
   {
     return normaliseSequenceLogo;
@@ -389,6 +366,7 @@ public class AlignViewport extends AlignmentViewport implements
    * 
    * @return true if alignment characters should be displayed
    */
+  @Override
   public boolean isValidCharWidth()
   {
     return validCharWidth;
@@ -458,7 +436,7 @@ public class AlignViewport extends AlignmentViewport implements
      * there is no complement, or it is not following highlights, or no mapping
      * is found, the result will be empty.
      */
-    SearchResults sr = new SearchResults();
+    SearchResultsI sr = new SearchResults();
     int seqOffset = findComplementScrollTarget(sr);
     if (!sr.isEmpty())
     {
@@ -467,4 +445,18 @@ public class AlignViewport extends AlignmentViewport implements
     }
   }
 
+  /**
+   * 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.
+   * 
+   * @param featureSettings
+   */
+  @Override
+  public void applyFeaturesStyle(FeatureSettingsModelI featureSettings)
+  {
+    // TODO implement for applet
+  }
+
 }