X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignViewport.java;h=f5d6ce76eedf3cd0e6f94b2764d16e652279df8e;hb=7f4da0a2b0c10f158a03dbfce8878e67e90c4a68;hp=e4e3e1777a886f3ec492a021878d43b9c6a184fc;hpb=ca431c5b3c0febeecdf541537070d5141d3b531a;p=jalview.git

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index e4e3e17..f5d6ce7 100644
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -22,26 +22,29 @@ package jalview.appletgui;
 
 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.renderer.ResidueShader;
 import jalview.schemes.ColourSchemeProperty;
 import jalview.schemes.UserColourScheme;
-import jalview.structure.CommandListener;
 import jalview.structure.SelectionSource;
 import jalview.structure.StructureSelectionManager;
 import jalview.structure.VamsasSource;
 import jalview.viewmodel.AlignmentViewport;
+import jalview.viewmodel.ViewportPositionProps;
 
 import java.awt.Font;
 
 public class AlignViewport extends AlignmentViewport implements
-        SelectionSource, VamsasSource, CommandListener
+        SelectionSource
 {
   boolean cursorMode = false;
 
@@ -57,6 +60,7 @@ public class AlignViewport extends AlignmentViewport implements
 
   private AnnotationColumnChooser annotationColumnSelectionState;
 
+  @Override
   public void finalize()
   {
     applet = null;
@@ -71,12 +75,13 @@ public class AlignViewport extends AlignmentViewport implements
     calculator = new jalview.workers.AlignCalcManager();
     this.applet = applet;
     alignment = al;
+    posProps = new ViewportPositionProps(this.alignment);
     // we always pad gaps
     this.setPadGaps(true);
-    this.startRes = 0;
-    this.endRes = al.getWidth() - 1;
-    this.startSeq = 0;
-    this.endSeq = al.getHeight() - 1;
+    this.setStartRes(0);
+    this.setEndRes(al.getWidth() - 1);
+    this.setStartSeq(0);
+    this.setEndSeq(al.getHeight() - 1);
     if (applet != null)
     {
       // get the width and height scaling factors if they were specified
@@ -187,8 +192,13 @@ 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");
@@ -200,18 +210,19 @@ public class AlignViewport extends AlignmentViewport implements
 
       if (colour != null)
       {
-        globalColourScheme = ColourSchemeProperty.getColour(alignment,
-                colour);
-        if (globalColourScheme != null)
+        residueShading = new ResidueShader(
+                ColourSchemeProperty.getColourScheme(alignment, colour));
+        if (residueShading != null)
         {
-          globalColourScheme.setConsensus(hconsensus);
+          residueShading.setConsensus(hconsensus);
         }
       }
 
       if (applet.getParameter("userDefinedColour") != null)
       {
-        ((UserColourScheme) globalColourScheme).parseAppletParameter(applet
-                .getParameter("userDefinedColour"));
+        residueShading = new ResidueShader(
+                new UserColourScheme(
+                        applet.getParameter("userDefinedColour")));
       }
     }
     initAutoAnnotation();
@@ -287,7 +298,6 @@ public class AlignViewport extends AlignmentViewport implements
     return font;
   }
 
-
   public void resetSeqLimits(int height)
   {
     setEndSeq(height / getCharHeight());
@@ -303,7 +313,6 @@ public class AlignViewport extends AlignmentViewport implements
     return currentTree;
   }
 
-
   boolean centreColumnLabels;
 
   public boolean getCentreColumnLabels()
@@ -322,11 +331,12 @@ 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 +352,7 @@ 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 +367,7 @@ public class AlignViewport extends AlignmentViewport implements
    * 
    * @return true if alignment characters should be displayed
    */
+  @Override
   public boolean isValidCharWidth()
   {
     return validCharWidth;
@@ -458,7 +437,7 @@ 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())
     {
@@ -467,5 +446,18 @@ 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
+  }
 
 }