JAL-2446 merged to spike branch

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

diff --git a/src/jalview/datamodel/SeqCigar.java b/src/jalview/datamodel/SeqCigar.java
index 98b0de5..9cc7b4a 100644 (file)
--- a/src/jalview/datamodel/SeqCigar.java
+++ b/src/jalview/datamodel/SeqCigar.java
@@ -494,18 +494,18 @@ public class SeqCigar extends CigarSimple
   /**
    * create an alignment from the given array of cigar sequences and gap
    * character, and marking the given segments as visible in the given
-   * columselection.
+   * hiddenColumns.
    * 
    * @param alseqs
    * @param gapCharacter
-   * @param colsel
-   *          - columnSelection where hidden regions are marked
+   * @param hidden
+   *          - hiddenColumns where hidden regions are marked
    * @param segments
    *          - visible regions of alignment
    * @return SequenceI[]
    */
   public static SequenceI[] createAlignmentSequences(SeqCigar[] alseqs,
-          char gapCharacter, ColumnSelection colsel, int[] segments)
+          char gapCharacter, HiddenColumns hidden, int[] segments)
   {
     SequenceI[] seqs = new SequenceI[alseqs.length];
     StringBuffer[] g_seqs = new StringBuffer[alseqs.length];
@@ -577,7 +577,7 @@ public class SeqCigar extends CigarSimple
           if (segments == null)
           {
             // add a hidden column for this deletion
-            colsel.hideColumns(inspos, inspos + insert.length - 1);
+            hidden.hideColumns(inspos, inspos + insert.length - 1);
           }
         }
       }
@@ -598,7 +598,7 @@ public class SeqCigar extends CigarSimple
       {
         // int start=shifts.shift(segments[i]-1)+1;
         // int end=shifts.shift(segments[i]+segments[i+1]-1)-1;
-        colsel.hideColumns(segments[i + 1], segments[i + 1]
+        hidden.hideColumns(segments[i + 1], segments[i + 1]
                 + segments[i + 2] - 1);
       }
     }