X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Frenderer%2FContactMapRenderer.java;h=ca7b0c8ebc1bbcc9fa7bff2206fb2691e44d786b;hb=refs%2Fheads%2Ffeatures%2Fr2_11_2_alphafold%2FJAL-2349_JAL-3855;hp=bd59315ecfea52b24fa436d365b8987f08439b18;hpb=09cce494f72431183bd3c37e77913170a08c3ac3;p=jalview.git

diff --git a/src/jalview/renderer/ContactMapRenderer.java b/src/jalview/renderer/ContactMapRenderer.java
index bd59315..ca7b0c8 100644
--- a/src/jalview/renderer/ContactMapRenderer.java
+++ b/src/jalview/renderer/ContactMapRenderer.java
@@ -3,6 +3,10 @@
  */
 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;
@@ -12,9 +16,6 @@ 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 +25,10 @@ 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)
     {
@@ -48,7 +49,13 @@ public class ContactMapRenderer implements AnnotationRowRendererI
       column = sRes + x;
       if (hasHiddenColumns)
       {
-        column = hiddenColumns.adjustForHiddenColumns(column);
+        column = hiddenColumns.visibleToAbsoluteColumn(column);
+      }
+      // TODO: highlight columns selected
+      boolean colsel = false;
+      if (columnSelection != null)
+      {
+        colsel = columnSelection.contains(column);
       }
 
       if (column > aaMax)
@@ -61,34 +68,85 @@ public class ContactMapRenderer implements AnnotationRowRendererI
         x++;
         continue;
       }
-      /*
-       * {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;
+        x++;
+        continue;
       }
-
-      // cell height to render
-      double scale = (_aa.graphHeight < contacts.getContactHeight()) ? 1
-              : (((double) _aa.graphHeight) / (double) contacts
-                      .getContactHeight());
-      int cstart, cend = -1;
-      for (int ht = y2, eht = y2 - _aa.graphHeight; ht >= eht; ht -= scale)
+      // 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);
+
+      for (int ht = y2, eht = y2
+              - _aa.graphHeight; ht >= eht; ht -= cgeom.pixels_step)
       {
-        cstart = cend + 1;
-        cend = -1
-                + (contacts.getContactHeight() * (ht - eht) / _aa.graphHeight);
-        // TODO show maximum colour for range - sort of done
-        // also need a 'getMaxPosForRange(start,end)'
-        g.setColor(getColorForRange(contacts, cstart, cend));
-
-        if (scale > 1)
+        ContactGeometry.contactInterval ci = cgeom.mapFor(y2 - ht,
+                y2 - ht + cgeom.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));
+
+        Color col;
+        boolean rowsel = false, containsHidden = false;
+        if (columnSelection != null)
         {
-          g.fillRect(x * charWidth, ht, charWidth, 1 + (int) scale);
+          if (_aa.sequenceRef == null)
+          {
+            rowsel = columnSelection.intersects(ci.cStart, ci.cEnd);
+          }
+          else
+          {
+            // TODO check we have correctly mapped cstart to local sequence
+            // 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
+        if (colsel || rowsel)
+        {
+
+          col = getSelectedColorForRange(min, max, contacts, ci.cStart,
+                  ci.cEnd);
+          if (colsel && rowsel)
+          {
+            col = new Color(col.getBlue(), col.getGreen(), col.getRed());
+          }
+          else
+          {
+            col = new Color(col.getBlue(), col.getBlue(), col.getBlue());
+          }
+        }
+        else
+        {
+          col = getColorForRange(min, max, contacts, ci.cStart, ci.cEnd);
+        }
+        if (containsHidden)
+        {
+          col = Color.red;
+        }
+        g.setColor(col);
+        if (cgeom.pixels_step > 1)
+        {
+          g.fillRect(x * charWidth, ht, charWidth, 1 + cgeom.pixels_step);
         }
         else
         {
@@ -100,21 +158,34 @@ public class ContactMapRenderer implements AnnotationRowRendererI
 
   }
 
-  Color minColor = Color.white, maxColor = Color.magenta;
+  // 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);
 
-  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(min, max, (float) cr.getMean());
+  }
+
+  public Color getSelectedColorForRange(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 jalview.util.ColorUtils.getGraduatedColour((float) cr.getMean(),
+            0, selMinColor, max, selMaxColor);
   }
 
 }