Merge branch 'features/JAL-2349_matrixvis' into features/JAL-2349_matrixvis_2112

[jalview.git] / src / jalview / renderer / ContactMapRenderer.java

diff --git a/src/jalview/renderer/ContactMapRenderer.java b/src/jalview/renderer/ContactMapRenderer.java
index bd59315..7413e65 100644 (file)
--- a/src/jalview/renderer/ContactMapRenderer.java
+++ b/src/jalview/renderer/ContactMapRenderer.java
@@ -48,7 +48,7 @@ public class ContactMapRenderer implements AnnotationRowRendererI
       column = sRes + x;
       if (hasHiddenColumns)
       {
-        column = hiddenColumns.adjustForHiddenColumns(column);
+        column = hiddenColumns.visibleToAbsoluteColumn(column);
       }
 
       if (column > aaMax)
@@ -65,8 +65,6 @@ public class ContactMapRenderer implements AnnotationRowRendererI
        * {profile type, #values, total count, char1, pct1, char2, pct2...}
        */
       ContactListI contacts = viewport.getContactList(_aa, column);
-      min = _aa.graphMin;
-      max = _aa.graphMax;
       if (contacts == null)
       {
         return;
@@ -74,17 +72,17 @@ public class ContactMapRenderer implements AnnotationRowRendererI
 
       // cell height to render
       double scale = (_aa.graphHeight < contacts.getContactHeight()) ? 1
-              : (((double) _aa.graphHeight) / (double) contacts
-                      .getContactHeight());
+              : ((double) _aa.graphHeight)
+                      / (double) contacts.getContactHeight();
       int cstart, cend = -1;
       for (int ht = y2, eht = y2 - _aa.graphHeight; ht >= eht; ht -= scale)
       {
         cstart = cend + 1;
-        cend = -1
-                + (contacts.getContactHeight() * (ht - eht) / _aa.graphHeight);
+        cend = Math.max(cstart + 1, contacts.getContactHeight()
+                * ((ht - y2) / _aa.graphHeight));
         // TODO show maximum colour for range - sort of done
         // also need a 'getMaxPosForRange(start,end)'
-        g.setColor(getColorForRange(contacts, cstart, cend));
+        g.setColor(getColorForRange(min, max, contacts, cstart, cend));
 
         if (scale > 1)
         {
@@ -102,19 +100,19 @@ public class ContactMapRenderer implements AnnotationRowRendererI
 
   Color minColor = Color.white, maxColor = Color.magenta;
 
-  float min, max;
 
-  Color shadeFor(float value)
+  Color shadeFor(float min, float max, float value)
   {
     return jalview.util.ColorUtils.getGraduatedColour(value, 0, minColor,
             max, maxColor);
   }
 
-  public Color getColorForRange(ContactListI cl, int i, int j)
+  public Color getColorForRange(float min, float max, ContactListI cl,
+          int i, int j)
   {
     ContactRange cr = cl.getRangeFor(i, j);
     // average for moment - probably more interested in maxIntProj though
-    return shadeFor((float) cr.getMean());
+    return shadeFor(min, max, (float) cr.getMean());
   }
 
 }