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

[jalview.git] / src / jalview / gui / TreeCanvas.java

diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java
index 3a055ae..f6b842d 100755 (executable)
--- a/src/jalview/gui/TreeCanvas.java
+++ b/src/jalview/gui/TreeCanvas.java
@@ -54,6 +54,7 @@ import jalview.analysis.Conservation;
 import jalview.analysis.TreeModel;
 import jalview.api.AlignViewportI;
 import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
 import jalview.datamodel.BinaryNode;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.ContactMatrixI;
@@ -67,6 +68,7 @@ import jalview.schemes.ColourSchemeI;
 import jalview.structure.SelectionSource;
 import jalview.util.Format;
 import jalview.util.MessageManager;
+import jalview.ws.datamodel.MappableContactMatrixI;
 
 /**
  * DOCUMENT ME!
@@ -1035,6 +1037,41 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
             cm.setColorForGroup(gp, colors.get(gp));
           }
         }
+        // stash colors in linked annotation row.
+        // doesn't work yet. TESTS!
+        int sstart = aa.sequenceRef != null ? aa.sequenceRef.getStart() - 1
+                : 0;
+        Annotation ae;
+        Color gpcol = null;
+        int[] seqpos = null;
+        for (BitSet gp : colors.keySet())
+        {
+          gpcol = colors.get(gp);
+          for (int p = gp.nextSetBit(0); p >= 0
+                  && p < Integer.MAX_VALUE; p = gp.nextSetBit(p + 1))
+          {
+            if (cm instanceof MappableContactMatrixI)
+            {
+              MappableContactMatrixI mcm = (MappableContactMatrixI) cm;
+              seqpos = mcm.getMappedPositionsFor(aa.sequenceRef, p);
+              if (seqpos == null)
+              {
+                // no mapping for this column.
+                continue;
+              }
+              // TODO: handle ranges...
+              ae = aa.getAnnotationForPosition(seqpos[0]);
+            }
+            else
+            {
+              ae = aa.getAnnotationForPosition(p + sstart);
+            }
+            if (ae != null)
+            {
+              ae.colour = gpcol.brighter().darker();
+            }
+          }
+        }
       }
     }
 
@@ -1071,7 +1108,6 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
       return false;
     }
     ColumnSelection cs = av.getColumnSelection();
-
     HiddenColumns hc = av.getAlignment().getHiddenColumns();
     int offp = (rseq != null) ? rseq.findIndex(rseq.getStart() + colm)
             : colm;
@@ -1087,7 +1123,6 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
     }
     return false;
   }
-
   private BitSet createColumnGroupFor(Vector<BinaryNode> l, Color col)
   {
     BitSet gp = new BitSet();
@@ -1136,22 +1171,39 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
       {
         continue;
       }
+      // TODO - sort indices for faster lookup
       ColumnSelection cs = av.getColumnSelection();
       HiddenColumns hc = av.getAlignment().getHiddenColumns();
+      ContactMatrixI cm = av.getContactMatrix(tp.assocAnnotation);
+      MappableContactMatrixI mcm = null;
+      int offp;
+      if (cm instanceof MappableContactMatrixI)
+      {
+        mcm = (MappableContactMatrixI) cm;
+        int[] seqpos = mcm.getMappedPositionsFor(
+                tp.assocAnnotation.sequenceRef, colm);
+        if (seqpos == null)
+        {
+          // no mapping for this column.
+          continue;
+        }
+        // TODO: handle ranges...
+        offp = seqpos[0];
+      }
+      else
       {
-        int offp = (rseq != null) ? rseq.findIndex(rseq.getStart() + colm)
+        offp = (rseq != null) ? rseq.findIndex(rseq.getStart() + colm)
                 : colm;
-
-        if (!av.hasHiddenColumns() || hc.isVisible(offp - 1))
+      }
+      if (!av.hasHiddenColumns() || hc.isVisible(offp - 1))
+      {
+        if (cs.contains(offp - 1))
         {
-          if (cs.contains(offp - 1))
-          {
-            cs.removeElement(offp - 1);
-          }
-          else
-          {
-            cs.addElement(offp - 1);
-          }
+          cs.removeElement(offp - 1);
+        }
+        else
+        {
+          cs.addElement(offp - 1);
         }
       }
     }