Merge branch 'bug/JAL-4214_system_freeze_when_opening_file_using_gui_in_linux' into...

[jalview.git] / src / jalview / analysis / Grouping.java

diff --git a/src/jalview/analysis/Grouping.java b/src/jalview/analysis/Grouping.java
index 88d3525..def5d5a 100644 (file)
--- 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("~");
@@ -284,7 +269,7 @@ public class Grouping
      * seqs.length) { for (int i = 0; i < seqs.length; i++) { if (!hasScore[i])
      * { scores[i] = (max + i); } else { int nf=(feats[i]==null) ? 0
      * :((SequenceFeature[]) feats[i]).length;
-     * System.err.println("Sorting on Score: seq "+seqs[i].getName()+
+     * jalview.bin.Console.errPrintln("Sorting on Score: seq "+seqs[i].getName()+
      * " Feats: "+nf+" Score : "+scores[i]); } } }
      * 
      * jalview.util.QuickSort.sort(scores, seqs); } else if
@@ -295,7 +280,7 @@ public class Grouping
      * (int i=0;i<seqs.length; i++) { double nf; scores[i] =
      * (0.05+fr*i)+(nf=((feats[i]==null) ? 0.0 :1.0*((SequenceFeature[])
      * feats[i]).length));
-     * System.err.println("Sorting on Density: seq "+seqs[i].getName()+
+     * jalview.bin.Console.errPrintln("Sorting on Density: seq "+seqs[i].getName()+
      * " Feats: "+nf+" Score : "+scores[i]); }
      * jalview.util.QuickSort.sort(scores, seqs); } else { if
      * (method==FEATURE_LABEL) { throw new Error("Not yet implemented."); } } if