adjust start and end of intersecting group relative to selected region

[jalview.git] / src / jalview / datamodel / AlignmentView.java

diff --git a/src/jalview/datamodel/AlignmentView.java b/src/jalview/datamodel/AlignmentView.java
index 325fc45..21b5e7f 100644 (file)
--- a/src/jalview/datamodel/AlignmentView.java
+++ b/src/jalview/datamodel/AlignmentView.java
@@ -134,7 +134,7 @@ public class AlignmentView
         // visible and selected region\r
         int ssel = selection.getStartRes(), esel = selection.getEndRes();\r
         Vector isg = new Vector();\r
-        Enumeration<?> en = grps.elements();\r
+        Enumeration en = grps.elements();\r
         while (en.hasMoreElements())\r
         {\r
           sg = (SequenceGroup) en.nextElement();\r
@@ -150,6 +150,9 @@ public class AlignmentView
             {\r
               sg.setEndRes(esel);\r
             }\r
+            sg.setStartRes(sg.getStartRes()-ssel+1);\r
+            sg.setEndRes(sg.getEndRes()-ssel+1);\r
+            \r
             isg.addElement(sg);\r
           }\r
         }\r
@@ -332,7 +335,7 @@ public class AlignmentView
        * prune any groups to the visible coordinates of the alignment.\r
        */\r
       {\r
-        int nvg = scGroups != null ? scGroups.size() : 0;\r
+        int nvg = (scGroups != null) ? scGroups.size() : 0;\r
         if (nvg > 0)\r
         {\r
           SequenceGroup[] nsg = new SequenceGroup[nvg];\r
@@ -989,9 +992,13 @@ public class AlignmentView
   public static void summariseAlignmentView(AlignmentView view,\r
           PrintStream os)\r
   {\r
-    os.println("View has " + view.sequences.length + " of which "\r
-            + (view.selected == null ? "None" : view.selected.size())\r
-            + " are selected.");\r
+    os.print("View has " + view.sequences.length + " of which ");\r
+    if (view.selected == null) {\r
+      os.print("None");\r
+    } else {\r
+      os.print(" "+view.selected.size());\r
+    }\r
+    os.println(" are selected.");\r
     os.print("View is " + view.getWidth() + " columns wide");\r
     int viswid = 0;\r
     int[] contigs = view.getContigs();\r