JAL-2541 clearer comments
[jalview.git] / src / jalview / datamodel / Alignment.java
index 5d91b36..5553840 100755 (executable)
@@ -1067,21 +1067,18 @@ public class Alignment implements AlignmentI
         currentSeq = currentSeq.createDatasetSequence();
       }
     }
-    if (seqs.contains(currentSeq))
-    {
-      return;
-    }
+
     List<SequenceI> toProcess = new ArrayList<>();
     toProcess.add(currentSeq);
     while (toProcess.size() > 0)
     {
       // use a queue ?
       SequenceI curDs = toProcess.remove(0);
-      if (seqs.contains(curDs))
+
+      if (!seqs.add(curDs))
       {
         continue;
       }
-      seqs.add(curDs);
       // iterate over database references, making sure we add forward referenced
       // sequences
       if (curDs.getDBRefs() != null)
@@ -1476,8 +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
@@ -1493,14 +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);
         }