X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FGrouping.java;h=066814e626b390897a812565b1262958f61aadc8;hb=refs%2Fheads%2Fbug%2FJAL-4214_system_freeze_when_opening_file_using_gui_in_linux;hp=88d3525ce175c71b3b1c3f6400b774d149b2208c;hpb=038cb9c86641c3de91d8f330c5e3267507c46643;p=jalview.git

diff --git a/src/jalview/analysis/Grouping.java b/src/jalview/analysis/Grouping.java
index 88d3525..066814e 100644
--- a/src/jalview/analysis/Grouping.java
+++ b/src/jalview/analysis/Grouping.java
@@ -21,7 +21,6 @@
 package jalview.analysis;
 
 import jalview.datamodel.ColumnSelection;
-import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 
@@ -110,12 +109,10 @@ public class Grouping
    * @param sequences
    * @param columnSelection
    * @param list
-   * @param hiddenColumns
    * @return
    */
   public static SequenceGroup[] makeGroupsFromCols(SequenceI[] sequences,
-          ColumnSelection cs, List<SequenceGroup> list,
-          HiddenColumns hiddenColumns)
+          ColumnSelection cs, List<SequenceGroup> list)
   {
     // TODO: determine how to get/recover input data for group generation
     Map<String, List<SequenceI>> gps = new HashMap<String, List<SequenceI>>();
@@ -140,17 +137,9 @@ public class Grouping
     int i = 0;
     for (Integer pos : cs.getSelected())
     {
-      if (hiddenColumns == null || hiddenColumns.isVisible(pos.intValue()))
-      {
-        spos[i++] = pos.intValue();
-      }
-    }
-    if (i < spos.length)
-    {
-      // mark end of visible column position
-      spos[i] = -1;
+      spos[i++] = pos.intValue();
     }
-    // actual number of visible columns
+
     for (i = 0; i < sequences.length; i++)
     {
       int slen = sequences[i].getLength();
@@ -167,10 +156,6 @@ public class Grouping
       }
       for (int p : spos)
       {
-        if (p < 0)
-        {
-          break;
-        }
         if (p >= slen)
         {
           schar.append("~");