mapping bug fixes

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

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index b3a5266..c474142 100755 (executable)
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -108,6 +108,8 @@ public class Alignment
 
   public SequenceI[] getSequencesArray()
   {
+    if (sequences==null)
+      return null;
     SequenceI[] reply = new SequenceI[sequences.size()];
     for (int i = 0; i < sequences.size(); i++)
     {
@@ -740,7 +742,7 @@ public class Alignment
     }
     AlignedCodonFrame[] t = new AlignedCodonFrame[codonFrameList.length+1];
     System.arraycopy(codonFrameList, 0, t, 0, codonFrameList.length);
-    t[codonFrameList.length+1] = codons;
+    t[codonFrameList.length] = codons;
     codonFrameList = t;
   }
 
@@ -763,7 +765,7 @@ public class Alignment
     for (int f=0;f<codonFrameList.length; f++)
     {
       if (codonFrameList[f].involvesSequence(seq))
-        cframes.add(codonFrameList[f]);
+        cframes.addElement(codonFrameList[f]);
     }
     if (cframes.size()==0)
       return null;