X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Frenderer%2FContactMapRenderer.java;h=7a052da6e6d6e0d07d98de38e15d2905e3280277;hb=b4940c3adf6345861921c7abdf948e0a0c9beb61;hp=c0339cca7592f40b77a85fd22b041119ea5d7323;hpb=ccf89f08f1a38a60c87be23267e27ae07bb85d13;p=jalview.git

diff --git a/src/jalview/renderer/ContactMapRenderer.java b/src/jalview/renderer/ContactMapRenderer.java
index c0339cc..7a052da 100644
--- a/src/jalview/renderer/ContactMapRenderer.java
+++ b/src/jalview/renderer/ContactMapRenderer.java
@@ -8,6 +8,8 @@ import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.Annotation;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.ContactListI;
+import jalview.datamodel.ContactRange;
+import jalview.datamodel.HiddenColumns;
 import jalview.renderer.api.AnnotationRowRendererI;
 
 import java.awt.Color;
@@ -22,7 +24,7 @@ public class ContactMapRenderer implements AnnotationRowRendererI
 
   @Override
   public void renderRow(Graphics g, int charWidth, int charHeight,
-          boolean hasHiddenColumns, AlignViewportI viewport,
+          boolean hasHiddenColumns, AlignViewportI viewport, HiddenColumns hiddenColumns,
           ColumnSelection columnSelection, AlignmentAnnotation _aa,
           Annotation[] aa_annotations, int sRes, int eRes, float min,
           float max, int y)
@@ -46,8 +48,14 @@ public class ContactMapRenderer implements AnnotationRowRendererI
       column = sRes + x;
       if (hasHiddenColumns)
       {
-        column = columnSelection.adjustForHiddenColumns(column);
+        column = hiddenColumns.visibleToAbsoluteColumn(column);
       }
+      // // TODO: highlight columns selected
+      // boolean colsel = false;
+      // if (columnSelection != null)
+      // {
+      // colsel = columnSelection.contains(column);
+      // }
 
       if (column > aaMax)
       {
@@ -59,33 +67,61 @@ public class ContactMapRenderer implements AnnotationRowRendererI
         x++;
         continue;
       }
-      /*
-       * {profile type, #values, total count, char1, pct1, char2, pct2...}
-       */
+      if (_aa.sequenceRef != null)
+      {
+        // get the sequence position for the column
+        column = _aa.sequenceRef.findPosition(column) - 1;
+      }
       ContactListI contacts = viewport.getContactList(_aa, column);
-
       if (contacts == null)
       {
         return;
       }
+      int contact_height = contacts.getContactHeight();
+      // fractional number of contacts covering each pixel
+      double contacts_per_pixel = ((double) contact_height)
+              / ((double) _aa.graphHeight);
+
+      int pixels_step;
+
+      if (contacts_per_pixel >= 1)
+      {
+        // 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);
+      }
 
-      // cell height to render
-      double scale = (_aa.graphHeight < contacts.getContactHeight()) ? 1
-              : (((double) _aa.graphHeight) / (double) contacts
-                      .getContactHeight());
-      // distance between contact map per cell
-      int step = (int) ((contacts.getContactHeight()) * scale / _aa.graphHeight);
+      int cstart = 0, cend;
 
-      // profl[1] is the number of values in the profile
-      for (int stp = 0, ht = y2, eht = y2 - _aa.graphHeight; ht > eht; ht -= scale, stp++)
+      for (int ht = y2,
+              eht = y2 - _aa.graphHeight; ht >= eht; ht -= pixels_step)
       {
-        g.setColor(contacts
-                .getColorForScore((int) (stp * step * ((double) _aa.graphHeight / (double) contacts
-                        .getContactHeight()))));
+        cstart = (int) Math.floor(((double) y2 - ht) * contacts_per_pixel);
+        cend = (int) Math.min(contact_height,
+                Math.ceil(cstart + contacts_per_pixel * pixels_step));
+
+        // 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);
 
-        if (scale > 1)
+        // TODO: show selected region
+        // if (colsel || columnSelection!=null &&
+        // columnSelection.intersects(cstart,cend))
+        // {
+        // g.setColor(col.brighter());
+        // }
+        // else
         {
-          g.fillRect(x * charWidth, ht, charWidth, 1 + (int) scale);
+          g.setColor(col);
+        }
+        if (pixels_step > 1)
+        {
+          g.fillRect(x * charWidth, ht, charWidth, 1 + pixels_step);
         }
         else
         {
@@ -96,4 +132,21 @@ 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,
+            max, maxColor);
+  }
+
+  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(min, max, (float) cr.getMean());
+  }
+
 }