JAL-2349 JAL-3855 highlight residues associated with elements under mouse - Jmol...

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

diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index 615fbdd..d31e52d 100755 (executable)
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -1019,15 +1019,14 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
   static int[] getRowIndexAndOffset(int yPos, AlignmentAnnotation[] aa)
   {
     int[] res = new int[2];
+    res[0] = -1;
+    res[1] = 0;
     if (aa == null)
     {
-      res[0] = -1;
-      res[1] = 0;
       return res;
     }
     int row = -1;
     int height = 0, lheight = 0;
-
     for (int i = 0; i < aa.length; i++)
     {
       if (aa[i].visible)
@@ -1098,14 +1097,16 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
       if (clist != null)
       {
         ContactGeometry cgeom = new ContactGeometry(clist, ann.graphHeight);
-        ContactGeometry.contactInterval ci = cgeom.mapFor(rowAndOffset,
-                rowAndOffset);
+        ContactGeometry.contactInterval ci = cgeom.mapFor(rowAndOffset);
         ContactRange cr = clist.getRangeFor(ci.cStart, ci.cEnd);
         tooltip = "Contact from " + clist.getPosition() + ", [" + ci.cStart
                 + " - " + ci.cEnd + "]" + "<br/>Mean:" + cr.getMean();
-
-        // ap.getStructureSelectionManager().mouseOverSequence(ann.sequenceRef,
-        // new int[] {column, ci.cStart,ci.cEnd}, -1, null)
+        int col = ann.sequenceRef.findPosition(column);
+        ap.getStructureSelectionManager()
+                .highlightPositionsOn(ann.sequenceRef, new int[][]
+                { new int[] { col, col },
+                    new int[]
+                    { ci.cStart, ci.cEnd } }, null);
       }
     }
     return tooltip;