X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignViewport.java;h=0dcd5435597d10490726874fdff848d8710912b8;hb=567c2595554096f10feab130153f97286f3f7d80;hp=607dc05fc4d7104cde0a336b3ba00bcaf5a5f05c;hpb=ecdc53f0d45b7533878cef236fff851ea64ef9a9;p=jalview.git

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index 607dc05..0dcd543 100644
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -20,29 +20,31 @@
  */
 package jalview.appletgui;
 
-import java.awt.Font;
-
-import jalview.analysis.NJTree;
+import jalview.analysis.TreeModel;
 import jalview.api.AlignViewportI;
-import jalview.api.FeatureRenderer;
+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.ViewportRanges;
+
+import java.awt.Font;
 
 public class AlignViewport extends AlignmentViewport implements
-        SelectionSource, VamsasSource, CommandListener
+        SelectionSource
 {
   boolean cursorMode = false;
 
@@ -50,7 +52,7 @@ public class AlignViewport extends AlignmentViewport implements
 
   boolean validCharWidth = true;
 
-  NJTree currentTree = null;
+  TreeModel currentTree = null;
 
   public jalview.bin.JalviewLite applet;
 
@@ -58,10 +60,7 @@ public class AlignViewport extends AlignmentViewport implements
 
   private AnnotationColumnChooser annotationColumnSelectionState;
 
-  private FeatureRenderer featureRenderer;
-
-  private boolean includeHiddenRegion = true;
-
+  @Override
   public void finalize()
   {
     applet = null;
@@ -76,12 +75,10 @@ public class AlignViewport extends AlignmentViewport implements
     calculator = new jalview.workers.AlignCalcManager();
     this.applet = applet;
     alignment = al;
+    ranges = new ViewportRanges(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;
+
     if (applet != null)
     {
       // get the width and height scaling factors if they were specified
@@ -192,8 +189,13 @@ 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");
@@ -205,18 +207,19 @@ 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();
@@ -292,23 +295,21 @@ public class AlignViewport extends AlignmentViewport implements
     return font;
   }
 
-
   public void resetSeqLimits(int height)
   {
-    setEndSeq(height / getCharHeight());
+    ranges.setEndSeq(height / getCharHeight());
   }
 
-  public void setCurrentTree(NJTree tree)
+  public void setCurrentTree(TreeModel tree)
   {
     currentTree = tree;
   }
 
-  public NJTree getCurrentTree()
+  public TreeModel getCurrentTree()
   {
     return currentTree;
   }
 
-
   boolean centreColumnLabels;
 
   public boolean getCentreColumnLabels()
@@ -327,11 +328,12 @@ 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);
   }
 
   /**
@@ -347,39 +349,7 @@ 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;
@@ -394,6 +364,7 @@ public class AlignViewport extends AlignmentViewport implements
    * 
    * @return true if alignment characters should be displayed
    */
+  @Override
   public boolean isValidCharWidth()
   {
     return validCharWidth;
@@ -463,7 +434,7 @@ 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())
     {
@@ -472,27 +443,18 @@ 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 FeatureRenderer getFeatureRenderer()
-  {
-    return featureRenderer;
-  }
-
-  @Override
-  public void setFeatureRenderer(FeatureRenderer featureRenderer)
-  {
-    this.featureRenderer = featureRenderer;
-
-  }
-
-  public boolean isIncludeHiddenRegion()
-  {
-    return includeHiddenRegion;
-  }
-
-  public void setIncludeHiddenRegion(boolean includeHiddenRegion)
+  public void applyFeaturesStyle(FeatureSettingsModelI featureSettings)
   {
-    this.includeHiddenRegion = includeHiddenRegion;
+    // TODO implement for applet
   }
 
 }