JAL-2598 Sequence.getSequence return a copy of the char array

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

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index a442cf0..96747e4 100755 (executable)
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -260,9 +260,8 @@ public class Sequence extends ASequence implements SequenceI
   protected void initSeqFrom(SequenceI seq,
           AlignmentAnnotation[] alAnnotation)
   {
-    char[] oseq = seq.getSequence();
-    initSeqAndName(seq.getName(), Arrays.copyOf(oseq, oseq.length),
-            seq.getStart(), seq.getEnd());
+    char[] oseq = seq.getSequence(); // returns a copy of the array
+    initSeqAndName(seq.getName(), oseq, seq.getStart(), seq.getEnd());
 
     description = seq.getDescription();
     if (seq != datasetSequence)
@@ -563,7 +562,9 @@ public class Sequence extends ASequence implements SequenceI
   @Override
   public char[] getSequence()
   {
-    return sequence;
+    // return sequence;
+    return sequence == null ? null : Arrays.copyOf(sequence,
+            sequence.length);
   }
 
   /*
@@ -1395,7 +1396,7 @@ public class Sequence extends ASequence implements SequenceI
 
   private boolean _isNa;
 
-  private long _seqhash = 0;
+  private int _seqhash = 0;
 
   /**
    * Answers false if the sequence is more than 85% nucleotide (ACGTU), else
@@ -1825,4 +1826,34 @@ public class Sequence extends ASequence implements SequenceI
   {
     changeCount++;
   }
+
+  /**
+   * {@inheritDoc}
+   */
+  @Override
+  public int replace(char c1, char c2)
+  {
+    if (c1 == c2)
+    {
+      return 0;
+    }
+    int count = 0;
+    synchronized (sequence)
+    {
+      for (int c = 0; c < sequence.length; c++)
+      {
+        if (sequence[c] == c1)
+        {
+          sequence[c] = c2;
+          count++;
+        }
+      }
+    }
+    if (count > 0)
+    {
+      sequenceChanged();
+    }
+
+    return count;
+  }
 }