Merge branch 'develop' into features/JAL-4134_use_annotation_row_for_colours_and_groups

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

diff --git a/src/jalview/renderer/ContactMapRenderer.java b/src/jalview/renderer/ContactMapRenderer.java
index cbc4af9..a8f6c1b 100644 (file)
--- a/src/jalview/renderer/ContactMapRenderer.java
+++ b/src/jalview/renderer/ContactMapRenderer.java
@@ -35,12 +35,10 @@ public abstract class ContactMapRenderer implements AnnotationRowRendererI
      * 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
      */
@@ -150,14 +148,20 @@ public abstract class ContactMapRenderer implements AnnotationRowRendererI
         x++;
         continue;
       }
+      // ContactListI from viewport can map column -> group
       Color gpcol = (cm == null) ? Color.white
-              : cm.getColourForGroup(cm.getGroupsFor(column));
+              : 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);
 
@@ -174,29 +178,8 @@ 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)
@@ -231,7 +214,6 @@ public abstract class ContactMapRenderer implements AnnotationRowRendererI
                   (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);