X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=11321eba1b1f91c37fa36065fb6add400ec681c2;hb=9201765247470c08d366abef2713c1c736adf2cb;hp=d0a0f11e28a5cc9f93d5f54991a2c879ee08c816;hpb=73baa0375a39ebef99c0232dba982d51a5fb48f9;p=jalview.git

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index d0a0f11..11321eb 100644
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -37,17 +37,21 @@ import jalview.datamodel.AlignmentI;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.PDBEntry;
 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.ColourSchemeI;
 import jalview.schemes.ColourSchemeProperty;
+import jalview.schemes.ResidueColourScheme;
 import jalview.schemes.UserColourScheme;
-import jalview.structure.CommandListener;
 import jalview.structure.SelectionSource;
 import jalview.structure.StructureSelectionManager;
 import jalview.structure.VamsasSource;
 import jalview.util.MessageManager;
 import jalview.viewmodel.AlignmentViewport;
+import jalview.viewmodel.ViewportRanges;
 import jalview.ws.params.AutoCalcSetting;
 
 import java.awt.Container;
@@ -60,7 +64,6 @@ import java.util.List;
 import java.util.Vector;
 
 import javax.swing.JInternalFrame;
-import javax.swing.JOptionPane;
 
 /**
  * DOCUMENT ME!
@@ -69,7 +72,7 @@ import javax.swing.JOptionPane;
  * @version $Revision: 1.141 $
  */
 public class AlignViewport extends AlignmentViewport implements
-        SelectionSource, CommandListener
+        SelectionSource
 {
   Font font;
 
@@ -235,10 +238,7 @@ public class AlignViewport extends AlignmentViewport implements
 
   void init()
   {
-    this.startRes = 0;
-    this.endRes = alignment.getWidth() - 1;
-    this.startSeq = 0;
-    this.endSeq = alignment.getHeight() - 1;
+    ranges = new ViewportRanges(this.alignment);
     applyViewProperties();
 
     String fontName = Cache.getDefault("FONT_NAME", "SansSerif");
@@ -283,28 +283,27 @@ public class AlignViewport extends AlignmentViewport implements
     initAutoAnnotation();
     String colourProperty = alignment.isNucleotide() ? Preferences.DEFAULT_COLOUR_NUC
             : Preferences.DEFAULT_COLOUR_PROT;
-    String propertyValue = Cache.getProperty(colourProperty);
-    if (propertyValue == null)
+    String schemeName = Cache.getProperty(colourProperty);
+    if (schemeName == null)
     {
-      // fall back on this property for backwards compatibility
-      propertyValue = Cache.getProperty(Preferences.DEFAULT_COLOUR);
+      // only DEFAULT_COLOUR available in Jalview before 2.9
+      schemeName = Cache.getDefault(Preferences.DEFAULT_COLOUR,
+              ResidueColourScheme.NONE);
     }
-    if (propertyValue != null)
-    {
-      globalColourScheme = ColourSchemeProperty.getColour(alignment,
-              propertyValue);
+    ColourSchemeI colourScheme = ColourSchemeProperty.getColourScheme(
+            alignment, schemeName);
+    residueShading = new ResidueShader(colourScheme);
 
-      if (globalColourScheme instanceof UserColourScheme)
-      {
-        globalColourScheme = UserDefinedColours.loadDefaultColours();
-        ((UserColourScheme) globalColourScheme).setThreshold(0,
-                isIgnoreGapsConsensus());
-      }
+    if (colourScheme instanceof UserColourScheme)
+    {
+      residueShading = new ResidueShader(
+              UserDefinedColours.loadDefaultColours());
+      residueShading.setThreshold(0, isIgnoreGapsConsensus());
+    }
 
-      if (globalColourScheme != null)
-      {
-        globalColourScheme.setConsensus(hconsensus);
-      }
+    if (residueShading != null)
+    {
+      residueShading.setConsensus(hconsensus);
     }
   }
 
@@ -382,7 +381,6 @@ public class AlignViewport extends AlignmentViewport implements
     super.setViewStyle(settingsForView);
     setFont(new Font(viewStyle.getFontName(), viewStyle.getFontStyle(),
             viewStyle.getFontSize()), false);
-
   }
 
   /**
@@ -875,9 +873,9 @@ public class AlignViewport extends AlignmentViewport implements
         MessageManager.getString("label.new_window"), };
     final String question = JvSwingUtils.wrapTooltip(true,
             MessageManager.getString("label.open_split_window?"));
-    int response = JOptionPane.showOptionDialog(Desktop.desktop, question,
+    int response = JvOptionPane.showOptionDialog(Desktop.desktop, question,
             MessageManager.getString("label.open_split_window"),
-            JOptionPane.DEFAULT_OPTION, JOptionPane.PLAIN_MESSAGE, null,
+            JvOptionPane.DEFAULT_OPTION, JvOptionPane.PLAIN_MESSAGE, null,
             options, options[0]);
 
     if (response != 1 && response != 2)
@@ -917,7 +915,7 @@ public class AlignViewport extends AlignmentViewport implements
 
     // TODO if we want this (e.g. to enable reload of the alignment from file),
     // we will need to add parameters to the stack.
-    // if (!protocol.equals(AppletFormatAdapter.PASTE))
+    // if (!protocol.equals(DataSourceType.PASTE))
     // {
     // alignFrame.setFileName(file, format);
     // }
@@ -1042,7 +1040,7 @@ 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 verticalOffset = findComplementScrollTarget(sr);
     if (!sr.isEmpty())
     {