X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Frenderer%2FContactMapRenderer.java;fp=src%2Fjalview%2Frenderer%2FContactMapRenderer.java;h=edf3ca2100011415f6159f898623b959e41878d6;hb=b122ba188c2ffcbb302809bafc02058e355643ee;hp=c5d4b14a0da11ba1eca7b57139f481b8c14be6ce;hpb=e91b3bef83f320e13c59ad5d21d69f0abf3d7507;p=jalview.git

diff --git a/src/jalview/renderer/ContactMapRenderer.java b/src/jalview/renderer/ContactMapRenderer.java
index c5d4b14..edf3ca2 100644
--- a/src/jalview/renderer/ContactMapRenderer.java
+++ b/src/jalview/renderer/ContactMapRenderer.java
@@ -49,6 +49,15 @@ public abstract class ContactMapRenderer implements AnnotationRowRendererI
      */
     Color selMinColor, selMaxColor;
 
+    /**
+     * 
+     * @param no_data - colour when no data available
+     * @param hidden - colour if this row is hidden
+     * @param maxColor - colour for maximum value of contact
+     * @param minColor - colour for minimum value of contact
+     * @param selMinColor - min colour if the contact has been selected
+     * @param selMaxColor - max colour if contact is selected
+     */
     public Shading(Color no_data, Color hidden, Color maxColor,
             Color minColor, Color selMinColor, Color selMaxColor)
     {
@@ -79,8 +88,8 @@ public abstract class ContactMapRenderer implements AnnotationRowRendererI
       {
         return new Shading(Color.pink, Color.red,
 
-                new Color(246, 252, 243), new Color(0, 60, 26),
-                new Color(26, 0, 60), new Color(243, 246, 252));
+                new Color(247, 252, 245), new Color(0, 68, 28),
+                new Color(28, 0, 68), new Color(245,247,252));
       }
     };
   }
@@ -173,14 +182,14 @@ public abstract class ContactMapRenderer implements AnnotationRowRendererI
       for (int ht = 0, botY = topY
               - _aa.height; ht < _aa.graphHeight; ht += cgeom.pixels_step)
       {
-        ContactGeometry.contactInterval ci = cgeom.mapFor(ht,
-                ht + cgeom.pixels_step);
+        ContactGeometry.contactInterval ci = cgeom.mapFor(ht);
         // cstart = (int) Math.floor(((double) y2 - ht) * contacts_per_pixel);
         // cend = (int) Math.min(contact_height,
         // Math.ceil(cstart + contacts_per_pixel * pixels_step));
 
         Color col;
-        boolean rowsel = false, containsHidden = false;
+        boolean rowsel = false;
+        boolean containsHidden = false;
         if (columnSelection != null)
         {
           rowsel = cgeom.intersects(ci, columnSelection, hiddenColumns,
@@ -221,7 +230,7 @@ public abstract class ContactMapRenderer implements AnnotationRowRendererI
         g.setColor(col);
         if (cgeom.pixels_step > 1)
         {
-          g.fillRect(x * charWidth, botY+ht, charWidth, 1 + cgeom.pixels_step);
+          g.fillRect(x * charWidth, botY+ht, charWidth, cgeom.pixels_step);
         }
         else
         {
@@ -252,7 +261,7 @@ public abstract class ContactMapRenderer implements AnnotationRowRendererI
   {
     ContactRange cr = cl.getRangeFor(i, j);
     // average for moment - probably more interested in maxIntProj though
-    return jalview.util.ColorUtils.getGraduatedColour((float) cr.getMean(),
+    return jalview.util.ColorUtils.getGraduatedColour((float) cr.getMin(),
             0, shade.selMinColor, max, shade.selMaxColor);
   }