From 8359bd8f5bae0bfc1a63ba114b7a4d67fbb62efe Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 10 Nov 2005 11:04:37 +0000
Subject: [PATCH] Return accurate RGB for transparent residues

---
 src/jalview/gui/FeatureRenderer.java  |   45 +++++++++++++++++++++++++++------
 src/jalview/gui/SequenceRenderer.java |   18 +++++++++++++
 2 files changed, 55 insertions(+), 8 deletions(-)

diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java
index 829bafb..fcd952b 100755
--- a/src/jalview/gui/FeatureRenderer.java
+++ b/src/jalview/gui/FeatureRenderer.java
@@ -24,6 +24,8 @@ import java.awt.*;
 
 import java.util.*;
 
+import java.awt.image.*;
+
 
 /**
  * DOCUMENT ME!
@@ -41,6 +43,7 @@ public class FeatureRenderer
     float transparency = 1.0f;
     FontMetrics fm;
     int charOffset;
+    boolean drawText = true;
 
     // The following vector holds the features which are
     // to be added, in the correct order or rendering
@@ -58,6 +61,29 @@ public class FeatureRenderer
     }
 
     /**
+     * This is used by the Molecule Viewer to get the accurate colour
+     * of the rendered sequence
+     */
+    BufferedImage bi;
+    public Color findFeatureColour(Color initialCol, SequenceI seq, int i)
+    {
+      if(!av.showSequenceFeatures)
+        return initialCol;
+
+      if(bi==null)
+        bi = new BufferedImage(1,1,BufferedImage.TYPE_INT_RGB);
+
+      drawText = false;
+      bi.getGraphics().setColor(initialCol);
+      bi.getGraphics().fillRect(0, 0, 1, 1);
+      drawSequence(bi.getGraphics(), seq, i, i, 0, 0, 1, 1);
+      drawText = true;
+
+      return new Color(bi.getRGB(0, 0));
+    }
+
+
+    /**
      * DOCUMENT ME!
      *
      * @param g DOCUMENT ME!
@@ -74,7 +100,8 @@ public class FeatureRenderer
                              int start, int end, int x1, int y1, int width, int height)
     {
 
-      if (seq.getDatasetSequence().getSequenceFeatures() == null)
+      if (seq.getDatasetSequence().getSequenceFeatures() == null
+          || seq.getDatasetSequence().getSequenceFeatures().size()==0)
         return;
 
       fm = g.getFontMetrics();
@@ -89,7 +116,7 @@ public class FeatureRenderer
 
       String type;
       SequenceFeature sf;
-      if (featuresDisplayed == null || featuresDisplayed.size()==0)
+      if (featuresDisplayed == null)
         findAllFeatures();
 
       Enumeration e = featuresDisplayed.elements(), e2;
@@ -171,12 +198,14 @@ public class FeatureRenderer
 
             g.fillRect( (i - start) * width, y1, width, height);
 
-            g.setColor(Color.white);
-
-            charOffset = (width - fm.charWidth(s)) / 2;
-            g.drawString(String.valueOf(s),
-                         charOffset + x1 + (width * (i - start)),
-                         (y1 + height) - height/5);//pady = height / 5;
+            if(drawText)
+           {
+             g.setColor(Color.white);
+             charOffset = (width - fm.charWidth(s)) / 2;
+             g.drawString(String.valueOf(s),
+                          charOffset + x1 + (width * (i - start)),
+                          (y1 + height) - height / 5); //pady = height / 5;
+           }
           }
         }
     }
diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java
index b961b2c..c431e7c 100755
--- a/src/jalview/gui/SequenceRenderer.java
+++ b/src/jalview/gui/SequenceRenderer.java
@@ -23,6 +23,7 @@ import jalview.datamodel.*;
 import jalview.schemes.*;
 
 import java.awt.*;
+import java.awt.image.BufferedImage;
 
 
 /**
@@ -77,6 +78,23 @@ public class SequenceRenderer
         return resBoxColour;
     }
 
+    BufferedImage bi;
+    public Color findSequenceColour(Color initialCol, SequenceI seq, int i)
+    {
+      if (bi == null)
+        bi = new BufferedImage(1, 1, BufferedImage.TYPE_INT_RGB);
+
+      bi.getGraphics().setColor(initialCol);
+      bi.getGraphics().fillRect(0, 0, 1, 1);
+      allGroups = null;
+      graphics = bi.getGraphics();
+
+      drawBoxes(seq, i,i, 0, 0, 1,1);
+
+      return new Color(bi.getRGB(0, 0));
+    }
+
+
     /**
      * DOCUMENT ME!
      *
-- 
1.7.10.2