X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FFeatureRenderer.java;h=3f875493bb4dad398e8a349cba1f8ac62a3ec5bb;hb=44cbaf5e4c094d90ef1294dd47c75a652e5f2509;hp=03d4ce60d71b153d8bc4069665dfd29719f5daa7;hpb=303e2fff7dd24d9e17a603512702a087a9cc3337;p=jalview.git

diff --git a/src/jalview/appletgui/FeatureRenderer.java b/src/jalview/appletgui/FeatureRenderer.java
index 03d4ce6..3f87549 100644
--- a/src/jalview/appletgui/FeatureRenderer.java
+++ b/src/jalview/appletgui/FeatureRenderer.java
@@ -20,11 +20,13 @@
  */
 package jalview.appletgui;
 
+import jalview.api.FeatureColourI;
 import jalview.datamodel.SearchResults;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
-import jalview.schemes.AnnotationColourGradient;
-import jalview.schemes.GraduatedColor;
+import jalview.io.FeaturesFile;
+import jalview.schemes.FeatureColour;
+import jalview.schemes.UserColourScheme;
 import jalview.util.MessageManager;
 import jalview.viewmodel.AlignmentViewport;
 
@@ -43,6 +45,9 @@ import java.awt.TextArea;
 import java.awt.TextField;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+import java.util.Hashtable;
 
 /**
  * DOCUMENT ME!
@@ -53,11 +58,15 @@ import java.awt.event.ActionListener;
 public class FeatureRenderer extends
         jalview.renderer.seqfeatures.FeatureRenderer
 {
+
+  // Holds web links for feature groups and feature types
+  // in the form label|link
+  Hashtable featureLinks = null;
+
   /**
    * Creates a new FeatureRenderer object.
    * 
    * @param av
-   *          DOCUMENT ME!
    */
   public FeatureRenderer(AlignmentViewport av)
   {
@@ -88,51 +97,35 @@ public class FeatureRenderer extends
     /**
      * render a feature style in the amend feature dialog box
      */
-    public void updateColor(Object newcol)
+    public void updateColor(FeatureColourI newcol)
     {
-
-      Color bg, col = null;
-      GraduatedColor gcol = null;
+      Color bg = null;
       String vlabel = "";
-      if (newcol instanceof Color)
-      {
-        isGcol = false;
-        col = (Color) newcol;
-        gcol = null;
-      }
-      else if (newcol instanceof GraduatedColor)
+      if (newcol.isSimpleColour())
       {
-        isGcol = true;
-        gcol = (GraduatedColor) newcol;
-        col = null;
+        bg = newcol.getColour();
+        setBackground(bg);
       }
       else
       {
-        throw new Error(
-                MessageManager
-                        .getString("error.invalid_colour_for_mycheckbox"));
-      }
-      if (col != null)
-      {
-        setBackground(bg = col);
-      }
-      else
-      {
-        if (gcol.getThreshType() != AnnotationColourGradient.NO_THRESHOLD)
+        if (newcol.isAboveThreshold())
         {
-          vlabel += " "
-                  + ((gcol.getThreshType() == AnnotationColourGradient.ABOVE_THRESHOLD) ? "(>)"
-                          : "(<)");
+          vlabel += " (>)";
         }
-        if (isColourByLabel = gcol.isColourByLabel())
+        else if (newcol.isBelowThreshold())
+        {
+          vlabel += " (<)";
+        }
+
+        if (isColourByLabel = newcol.isColourByLabel())
         {
           setBackground(bg = Color.white);
           vlabel += " (by Label)";
         }
         else
         {
-          setBackground(bg = gcol.getMinColor());
-          maxCol = gcol.getMaxColor();
+          setBackground(bg = newcol.getMinColour());
+          maxCol = newcol.getMaxColour();
         }
       }
       label = vlabel;
@@ -239,11 +232,12 @@ public class FeatureRenderer extends
             ap.seqPanel.seqCanvas.highlightSearchResults(highlight);
 
           }
-          Object col = getFeatureStyle(name.getText());
+          FeatureColourI col = getFeatureStyle(name.getText());
           if (col == null)
           {
-            col = new jalview.schemes.UserColourScheme()
+            Color generatedColour = UserColourScheme
                     .createColourFromName(name.getText());
+            col = new FeatureColour(generatedColour);
           }
 
           colourPanel.updateColor(col);
@@ -351,21 +345,16 @@ public class FeatureRenderer extends
     start.setText(features[0].getBegin() + "");
     end.setText(features[0].getEnd() + "");
     description.setText(features[0].getDescription());
-    Color col = getColour(name.getText());
-    if (col == null)
-    {
-      col = new jalview.schemes.UserColourScheme()
-              .createColourFromName(name.getText());
-    }
-    Object fcol = getFeatureStyle(name.getText());
+    // lookup (or generate) the feature colour
+    FeatureColourI fcol = getFeatureStyle(name.getText());
     // simply display the feature color in a box
     colourPanel.updateColor(fcol);
     dialog.setResizable(true);
     // TODO: render the graduated color in the box.
-    colourPanel.addMouseListener(new java.awt.event.MouseAdapter()
+    colourPanel.addMouseListener(new MouseAdapter()
     {
       @Override
-      public void mousePressed(java.awt.event.MouseEvent evt)
+      public void mousePressed(MouseEvent evt)
       {
         if (!colourPanel.isGcol)
         {
@@ -373,15 +362,14 @@ public class FeatureRenderer extends
         }
         else
         {
-          FeatureColourChooser fcc = new FeatureColourChooser(
-                  ap.alignFrame, name.getText());
+          new FeatureColourChooser(ap.alignFrame, name.getText());
           dialog.transferFocus();
         }
       }
     });
     dialog.setVisible(true);
 
-    jalview.io.FeaturesFile ffile = new jalview.io.FeaturesFile();
+    FeaturesFile ffile = new FeaturesFile();
 
     if (dialog.accept)
     {
@@ -410,7 +398,7 @@ public class FeatureRenderer extends
         if (!colourPanel.isGcol)
         {
           // update colour - otherwise its already done.
-          setColour(sf.type, colourPanel.getBackground());
+          setColour(sf.type, new FeatureColour(colourPanel.getBackground()));
         }
         try
         {
@@ -450,7 +438,7 @@ public class FeatureRenderer extends
         {
           setGroupVisibility(lastFeatureGroupAdded, true);
         }
-        setColour(lastFeatureAdded, newColour); // was fcol
+        setColour(lastFeatureAdded, new FeatureColour(newColour)); // was fcol
         setVisible(lastFeatureAdded);
         findAllFeatures(false); // different to original applet behaviour ?
         // findAllFeatures();