X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignmentUtils.java;h=37f225c02aa70867c3041652349bc6914a2dc797;hb=2c2992b8822b686f7f12022a66aa41f6969d06d0;hp=17aab155d78b2d468971df9f39389319b648d9d3;hpb=d2b08d9048af25114cff8deabbd320471119d88d;p=jalview.git

diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java
index 17aab15..37f225c 100644
--- a/src/jalview/analysis/AlignmentUtils.java
+++ b/src/jalview/analysis/AlignmentUtils.java
@@ -2558,7 +2558,8 @@ public class AlignmentUtils
       if (!unmapped.contains(seq))
       {
         char[] newSeq = new char[width];
-        Arrays.fill(newSeq, gap);
+        Arrays.fill(newSeq, gap); // JBPComment - doubt this is faster than the
+                                  // Integer iteration below
         int newCol = 0;
         int lastCol = 0;
 
@@ -2590,6 +2591,7 @@ public class AlignmentUtils
           System.arraycopy(newSeq, 0, tmp, 0, lastCol + 1);
           newSeq = tmp;
         }
+        // TODO: optimise SequenceI to avoid char[]->String->char[]
         seq.setSequence(String.valueOf(newSeq));
         realignedCount++;
       }
@@ -2639,6 +2641,8 @@ public class AlignmentUtils
     {
       SequenceI alignedSequence = alignedDatasets.get(seq
               .getDatasetSequence());
+      // TODO: getSequenceAsString() will be deprecated in the future
+      // TODO: need to leave to SequenceI implementor to update gaps
       seq.setSequence(alignedSequence.getSequenceAsString());
     }