JAL-2349 allow PAE or other contact matrices to hold a coordinate mapping allowing...

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

diff --git a/src/jalview/renderer/ContactMapRenderer.java b/src/jalview/renderer/ContactMapRenderer.java
index 0a2278b..00a6169 100644 (file)
--- a/src/jalview/renderer/ContactMapRenderer.java
+++ b/src/jalview/renderer/ContactMapRenderer.java
@@ -12,6 +12,7 @@ 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;
@@ -114,6 +115,7 @@ public abstract class ContactMapRenderer implements AnnotationRowRendererI
 
     int column;
     int aaMax = aa_annotations.length - 1;
+    ContactMatrixI cm = viewport.getContactMatrix(_aa);
     while (x < eRes - sRes)
     {
       column = sRes + x;
@@ -144,18 +146,25 @@ public abstract class ContactMapRenderer implements AnnotationRowRendererI
         x++;
         continue;
       }
+      // ContactListI from viewport can map column -> group
+      Color gpcol = (cm==null) ? Color.white: contacts.getColourForGroup(); // 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
+      // TODO: optionally pass visible column mask to the ContactGeometry object so it maps
       // only visible contacts to geometry
       // Bean holding mapping from contact list to pixels
+      // TODO: allow bracketing/limiting of range on contacts to render (like visible column mask but more flexible?)
+      
+      // COntactListI provides mapping for column -> cm-groupmapping
       final ContactGeometry cgeom = new ContactGeometry(contacts,
               _aa.graphHeight);
 
       for (int ht = y2, eht = y2
               - _aa.graphHeight; ht >= eht; ht -= cgeom.pixels_step)
       {
+        
         ContactGeometry.contactInterval ci = cgeom.mapFor(y2 - ht,
                 y2 - ht + cgeom.pixels_step);
         // cstart = (int) Math.floor(((double) y2 - ht) * contacts_per_pixel);
@@ -166,29 +175,7 @@ public abstract class ContactMapRenderer implements AnnotationRowRendererI
         boolean rowsel = false, containsHidden = false;
         if (columnSelection != null)
         {
-          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);
-            }
-
-          }
+          rowsel = cgeom.intersects(ci, columnSelection, hiddenColumns, maskHiddenCols);
         }
         // TODO: show selected region
         if (colsel || rowsel)
@@ -213,7 +200,14 @@ public abstract class ContactMapRenderer implements AnnotationRowRendererI
         {
           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);