propagated groups trimmed to correct region on viscontig

diff --git a/src/jalview/datamodel/AlignmentView.java b/src/jalview/datamodel/AlignmentView.java
index 21b5e7f..2a93861 100644 (file)
--- a/src/jalview/datamodel/AlignmentView.java
+++ b/src/jalview/datamodel/AlignmentView.java
@@ -351,9 +351,14 @@ public class AlignmentView
                 continue;\r
               }\r
             }\r
+\r
+            // clone group properties\r
+            nsg[g] = new SequenceGroup(sg);\r
+\r
             // may need to shift/trim start and end ?\r
             if (r && !viscontigs)\r
             {\r
+              // Not fully tested code - routine not yet called with viscontigs==false\r
               if (nsg[g].getStartRes() < gstart)\r
               {\r
                 nsg[g].setStartRes(0);\r
@@ -363,14 +368,11 @@ public class AlignmentView
                 nsg[g].setStartRes(nsg[g].getStartRes() - gstart);\r
                 nsg[g].setEndRes(nsg[g].getEndRes() - gstart);\r
               }\r
-              if (nsg[g].getEndRes() > gend)\r
+              if (nsg[g].getEndRes() > (gend-gstart))\r
               {\r
-                nsg[g].setEndRes(gend);\r
+                nsg[g].setEndRes(gend-gstart);\r
               }\r
             }\r
-\r
-            // clone group properties\r
-            nsg[g] = new SequenceGroup(sg);\r
           }\r
           if (viscontigs)\r
           {\r