X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Frenderer%2FContactMapRenderer.java;h=cbc4af93dd25768be4bf548dcfd27da445411b43;hb=4b7d3640209c4434d569c746672cf9eed4250ace;hp=58e6ab15002d8bce407c61a9677e4304b2f1d2d0;hpb=c6b983048da1ba01c4edf75349de2d410b45356d;p=jalview.git

diff --git a/src/jalview/renderer/ContactMapRenderer.java b/src/jalview/renderer/ContactMapRenderer.java
index 58e6ab1..cbc4af9 100644
--- a/src/jalview/renderer/ContactMapRenderer.java
+++ b/src/jalview/renderer/ContactMapRenderer.java
@@ -5,12 +5,14 @@ package jalview.renderer;
 
 import java.awt.Color;
 import java.awt.Graphics;
+import java.util.Iterator;
 
 import jalview.api.AlignViewportI;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.Annotation;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.ContactListI;
+import jalview.datamodel.ContactMatrixI;
 import jalview.datamodel.ContactRange;
 import jalview.datamodel.HiddenColumns;
 import jalview.renderer.api.AnnotationRowRendererI;
@@ -19,8 +21,82 @@ import jalview.renderer.api.AnnotationRowRendererI;
  * @author jprocter
  *
  */
-public class ContactMapRenderer implements AnnotationRowRendererI
+public abstract class ContactMapRenderer implements AnnotationRowRendererI
 {
+  /**
+   * bean holding colours for shading
+   * 
+   * @author jprocter
+   *
+   */
+  public class Shading
+  {
+    /**
+     * shown when no data available from map
+     */
+    Color no_data;
+
+    /**
+     * shown for region not currently visible - should normally not see this
+     */
+    Color hidden;
+
+    /**
+     * linear shading scheme min/max
+     */
+    Color maxColor, minColor;
+
+    /**
+     * linear shading scheme min/max for selected region
+     */
+    Color selMinColor, selMaxColor;
+
+    public Shading(Color no_data, Color hidden, Color maxColor,
+            Color minColor, Color selMinColor, Color selMaxColor)
+    {
+      super();
+      this.no_data = no_data;
+      this.hidden = hidden;
+      this.maxColor = maxColor;
+      this.minColor = minColor;
+      this.selMinColor = selMinColor;
+      this.selMaxColor = selMaxColor;
+    }
+
+  }
+
+  final Shading shade;
+
+  /**
+   * build an EBI-AlphaFold style renderer of PAE matrices
+   * 
+   * @return
+   */
+  public static ContactMapRenderer newPAERenderer()
+  {
+    return new ContactMapRenderer()
+    {
+      @Override
+      public Shading getShade()
+      {
+        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));
+      }
+    };
+  }
+
+  /**
+   * 
+   * @return instance of Shading used to initialise the renderer
+   */
+  public abstract Shading getShade();
+
+  public ContactMapRenderer()
+  {
+    this.shade = getShade();
+  }
 
   @Override
   public void renderRow(Graphics g, int charWidth, int charHeight,
@@ -37,12 +113,13 @@ public class ContactMapRenderer implements AnnotationRowRendererI
 
     int x = 0, y2 = y;
 
-    g.setColor(Color.pink);
+    g.setColor(shade.no_data);
 
     g.drawLine(x, y2, (eRes - sRes) * charWidth, y2);
 
     int column;
     int aaMax = aa_annotations.length - 1;
+    ContactMatrixI cm = viewport.getContactMatrix(_aa);
     while (x < eRes - sRes)
     {
       column = sRes + x;
@@ -73,6 +150,13 @@ public class ContactMapRenderer implements AnnotationRowRendererI
         x++;
         continue;
       }
+      Color gpcol = (cm == null) ? Color.white
+              : cm.getColourForGroup(cm.getGroupsFor(column));
+      // feature still in development - highlight or omit regions hidden in
+      // the alignment - currently marks them as red rows
+      boolean maskHiddenCols = false;
+      // TODO: pass visible column mask to the ContactGeometry object so it maps
+      // only visible contacts to geometry
       // Bean holding mapping from contact list to pixels
       final ContactGeometry cgeom = new ContactGeometry(contacts,
               _aa.graphHeight);
@@ -86,10 +170,8 @@ public class ContactMapRenderer implements AnnotationRowRendererI
         // 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;
-        boolean rowsel = false;
+        boolean rowsel = false, containsHidden = false;
         if (columnSelection != null)
         {
           if (_aa.sequenceRef == null)
@@ -102,10 +184,18 @@ public class ContactMapRenderer implements AnnotationRowRendererI
             // numbering
             int s = _aa.sequenceRef.findIndex(ci.cStart);
             int e = _aa.sequenceRef.findIndex(ci.cEnd);
+            if (maskHiddenCols && hasHiddenColumns)
+            {
+              // TODO: turn into function and create test !!
+              Iterator<int[]> viscont = hiddenColumns
+                      .getVisContigsIterator(s, e, false);
+              containsHidden = !viscont.hasNext();
+            }
             if (s > 0 && s < _aa.sequenceRef.getLength())
             {
               rowsel = columnSelection.intersects(s, e);
             }
+
           }
         }
         // TODO: show selected region
@@ -122,13 +212,26 @@ public class ContactMapRenderer implements AnnotationRowRendererI
           {
             col = new Color(col.getBlue(), col.getBlue(), col.getBlue());
           }
-          g.setColor(col);
         }
         else
         {
           col = getColorForRange(min, max, contacts, ci.cStart, ci.cEnd);
-          g.setColor(col);
         }
+        if (containsHidden)
+        {
+          col = shade.hidden;
+        }
+        if (gpcol != null && gpcol != Color.white)
+        {
+          // todo - could overlay group as a transparent rectangle ?
+          col = new Color(
+                  (int) (((float) (col.getRed() + gpcol.getRed())) / 2f),
+                  (int) (((float) (col.getGreen() + gpcol.getGreen()))
+                          / 2f),
+                  (int) (((float) (col.getBlue() + gpcol.getBlue())) / 2f));
+        }
+        g.setColor(col);
+
         if (cgeom.pixels_step > 1)
         {
           g.fillRect(x * charWidth, ht, charWidth, 1 + cgeom.pixels_step);
@@ -143,17 +246,10 @@ public class ContactMapRenderer implements AnnotationRowRendererI
 
   }
 
-  // Shading parameters
-  // currently hardwired for alphafold
-  Color maxColor = new Color(246, 252, 243),
-          minColor = new Color(0, 60, 26),
-          selMinColor = new Color(26, 0, 60),
-          selMaxColor = new Color(243, 246, 252);
-
   Color shadeFor(float min, float max, float value)
   {
-    return jalview.util.ColorUtils.getGraduatedColour(value, 0, minColor,
-            max, maxColor);
+    return jalview.util.ColorUtils.getGraduatedColour(value, 0,
+            shade.minColor, max, shade.maxColor);
   }
 
   public Color getColorForRange(float min, float max, ContactListI cl,
@@ -170,7 +266,7 @@ public 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(),
-            0, selMinColor, max, selMaxColor);
+            0, shade.selMinColor, max, shade.selMaxColor);
   }
 
 }