X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fdatamodel%2FSequence.java;h=615f6703ca1dfafb36786f22c4d8f747e12a71b1;hb=d6e1bbede5adc04f34c969213ac6a4c6d9e5d34a;hp=290cdfc10dfa46ab7ba09734be35bf2e55038b8c;hpb=3da861b096b63333831a2d77a103d261814c81a1;p=jalview.git

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 290cdfc..615f670 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -33,7 +33,7 @@ public class Sequence implements SequenceI
 {
     SequenceI datasetSequence;
     String name;
-    String sequence;
+    private String sequence;
     String description;
     int start;
     int end;
@@ -146,7 +146,7 @@ public class Sequence implements SequenceI
         sequenceFeatures = features;
     }
 
-    public void addSequenceFeature(SequenceFeature sf)
+    public synchronized void addSequenceFeature(SequenceFeature sf)
     {
       if(sequenceFeatures==null)
       {
@@ -165,17 +165,9 @@ public class Sequence implements SequenceI
       System.arraycopy(sequenceFeatures, 0, temp, 0, sequenceFeatures.length);
       temp[sequenceFeatures.length] = sf;
 
-
       sequenceFeatures = temp;
     }
 
-    SequenceFeature [] sfarray;
-
-        public SequenceFeature[] getsfarray()
-        {
-          return sfarray;
-        }
-
 
     /**
      * DOCUMENT ME!
@@ -453,7 +445,7 @@ public class Sequence implements SequenceI
     public int[] gapMap()
     {
         // Returns an int array giving the position of each residue in the sequence in the alignment
-        String seq = jalview.analysis.AlignSeq.extractGaps("-. ", sequence);
+        String seq = jalview.analysis.AlignSeq.extractGaps(jalview.util.Comparison.GapChars, sequence);
         int[] map = new int[seq.length()];
         int j = 0;
         int p = 0;
@@ -632,11 +624,10 @@ public class Sequence implements SequenceI
     public void showHiddenSequence(SequenceI seq)
     {
       hiddenSequences.deleteSequence(seq, false);
-      if (hiddenSequences.getSize() < 1)
+      if (hiddenSequences.getSize(false) < 1)
       {
         hiddenSequences = null;
       }
-
     }
 
     public void changeCase(boolean toUpper, int start, int end)