X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Frenderer%2FContactMapRenderer.java;h=10f87b1e041ef78fc3f7efcf4fe0fc033911c643;hb=a059dd46fe149a476bd274562cd27b2dc7d390dd;hp=aaa8a6118ae3c12ffb14f1ac4610708aff932fdd;hpb=59f8f1014e5ef09bf93c8a2cabe11b846012a521;p=jalview.git

diff --git a/src/jalview/renderer/ContactMapRenderer.java b/src/jalview/renderer/ContactMapRenderer.java
index aaa8a61..10f87b1 100644
--- a/src/jalview/renderer/ContactMapRenderer.java
+++ b/src/jalview/renderer/ContactMapRenderer.java
@@ -3,6 +3,9 @@
  */
 package jalview.renderer;
 
+import java.awt.Color;
+import java.awt.Graphics;
+
 import jalview.api.AlignViewportI;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.Annotation;
@@ -12,9 +15,6 @@ import jalview.datamodel.ContactRange;
 import jalview.datamodel.HiddenColumns;
 import jalview.renderer.api.AnnotationRowRendererI;
 
-import java.awt.Color;
-import java.awt.Graphics;
-
 /**
  * @author jprocter
  *
@@ -24,10 +24,10 @@ public class ContactMapRenderer implements AnnotationRowRendererI
 
   @Override
   public void renderRow(Graphics g, int charWidth, int charHeight,
-          boolean hasHiddenColumns, AlignViewportI viewport, HiddenColumns hiddenColumns,
-          ColumnSelection columnSelection, AlignmentAnnotation _aa,
-          Annotation[] aa_annotations, int sRes, int eRes, float min,
-          float max, int y)
+          boolean hasHiddenColumns, AlignViewportI viewport,
+          HiddenColumns hiddenColumns, ColumnSelection columnSelection,
+          AlignmentAnnotation _aa, Annotation[] aa_annotations, int sRes,
+          int eRes, float min, float max, int y)
   {
     if (sRes > aa_annotations.length)
     {
@@ -50,6 +50,12 @@ public class ContactMapRenderer implements AnnotationRowRendererI
       {
         column = hiddenColumns.visibleToAbsoluteColumn(column);
       }
+      // // TODO: highlight columns selected
+      // boolean colsel = false;
+      // if (columnSelection != null)
+      // {
+      // colsel = columnSelection.contains(column);
+      // }
 
       if (column > aaMax)
       {
@@ -72,27 +78,50 @@ public class ContactMapRenderer implements AnnotationRowRendererI
         return;
       }
       int contact_height = contacts.getContactHeight();
-      // fractional pixel height to render each contact cell
-      double pixels_per_contact = ((double) _aa.graphHeight)
-                      / (double) contact_height;
       // fractional number of contacts covering each pixel
-      double contacts_per_pixel = 1d/pixels_per_contact;
-      // number of contacts to render at a time
-      int step = (pixels_per_contact<1) ? (int) Math.floor(contacts_per_pixel) : (int) Math.ceil(pixels_per_contact);
-      
-      int pixels_step = (int) Math.ceil(step*pixels_per_contact);
-      int cstart, cend = -1;
-      for (int ht = y2, eht = y2 - _aa.graphHeight; ht >= eht; ht -= pixels_step)
+      double contacts_per_pixel = ((double) contact_height)
+              / ((double) _aa.graphHeight);
+
+      int pixels_step;
+
+      if (contacts_per_pixel >= 1)
       {
-        cstart = cend + 1;
-        cend = (int) Math.min(contact_height, cstart + step);
-        // TODO show maximum colour for range - sort of done
-        // also need a 'getMaxPosForRange(start,end)'
-        g.setColor(getColorForRange(min, max, contacts, cstart, cend));
+        // many contacts rendered per pixel
+        pixels_step = 1;
+      }
+      else
+      {
+        // pixel height for each contact
+        pixels_step = (int) Math
+                .ceil(((double) _aa.graphHeight) / (double) contact_height);
+      }
+
+      int cstart = 0, cend;
+
+      for (int ht = y2,
+              eht = y2 - _aa.graphHeight; ht >= eht; ht -= pixels_step)
+      {
+        cstart = (int) Math.floor(((double) y2 - ht) * contacts_per_pixel);
+        cend = (int) Math.min(contact_height,
+                Math.ceil(cstart + contacts_per_pixel * pixels_step));
 
-        if (pixels_step>1)
+        // TODO show maximum colour for range - sort of done
+        // also need a 'getMaxPosForRange(start,end)' to accurately render
+        Color col = getColorForRange(min, max, contacts, cstart, cend);
+
+        // TODO: show selected region
+        // if (colsel || columnSelection!=null &&
+        // columnSelection.intersects(cstart,cend))
+        // {
+        // g.setColor(col.brighter());
+        // }
+        // else
+        {
+          g.setColor(col);
+        }
+        if (pixels_step > 1)
         {
-          g.fillRect(x * charWidth, ht, charWidth, 1 + (int) pixels_step);
+          g.fillRect(x * charWidth, ht, charWidth, 1 + pixels_step);
         }
         else
         {
@@ -106,7 +135,6 @@ public class ContactMapRenderer implements AnnotationRowRendererI
 
   Color minColor = Color.white, maxColor = Color.magenta;
 
-
   Color shadeFor(float min, float max, float value)
   {
     return jalview.util.ColorUtils.getGraduatedColour(value, 0, minColor,