spike branch updated from latest features/JAL-2446

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

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index f5e6fc7..26e8db1 100755 (executable)
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -1473,8 +1473,8 @@ public class Alignment implements AlignmentI
   {
     // TODO JAL-1270 needs test coverage
     // currently tested for use in jalview.gui.SequenceFetcher
-    boolean samegap = toappend.getGapCharacter() == getGapCharacter();
     char oldc = toappend.getGapCharacter();
+    boolean samegap = oldc == getGapCharacter();
     boolean hashidden = toappend.getHiddenSequences() != null
             && toappend.getHiddenSequences().hiddenSequences != null;
     // get all sequences including any hidden ones
@@ -1490,14 +1490,7 @@ public class Alignment implements AlignmentI
         {
           if (!samegap)
           {
-            char[] oldseq = addedsq.getSequence();
-            for (int c = 0; c < oldseq.length; c++)
-            {
-              if (oldseq[c] == oldc)
-              {
-                oldseq[c] = gapCharacter;
-              }
-            }
+            addedsq.replace(oldc, gapCharacter);
           }
           toappendsq.add(addedsq);
         }
@@ -1916,42 +1909,6 @@ public class Alignment implements AlignmentI
   }
 
   @Override
-  public int[] getVisibleStartAndEndIndex(List<int[]> hiddenCols)
-  {
-    int[] alignmentStartEnd = new int[] { 0, getWidth() - 1 };
-    int startPos = alignmentStartEnd[0];
-    int endPos = alignmentStartEnd[1];
-
-    int[] lowestRange = new int[] { -1, -1 };
-    int[] higestRange = new int[] { -1, -1 };
-
-    for (int[] hiddenCol : hiddenCols)
-    {
-      lowestRange = (hiddenCol[0] <= startPos) ? hiddenCol : lowestRange;
-      higestRange = (hiddenCol[1] >= endPos) ? hiddenCol : higestRange;
-    }
-
-    if (lowestRange[0] == -1 && lowestRange[1] == -1)
-    {
-      startPos = alignmentStartEnd[0];
-    }
-    else
-    {
-      startPos = lowestRange[1] + 1;
-    }
-
-    if (higestRange[0] == -1 && higestRange[1] == -1)
-    {
-      endPos = alignmentStartEnd[1];
-    }
-    else
-    {
-      endPos = higestRange[0] - 1;
-    }
-    return new int[] { startPos, endPos };
-  }
-
-  @Override
   public void setHiddenColumns(HiddenColumns cols)
   {
     hiddenCols = cols;