JAL-2847 needed methods made public

[jalview.git] / forester / java / src / org / forester / msa / Msa.java

diff --git a/forester/java/src/org/forester/msa/Msa.java b/forester/java/src/org/forester/msa/Msa.java
index 648006a..066b10f 100644 (file)
--- a/forester/java/src/org/forester/msa/Msa.java
+++ b/forester/java/src/org/forester/msa/Msa.java
@@ -29,13 +29,13 @@ import java.io.IOException;
 import java.io.Writer;
 import java.util.List;
 
-import org.forester.sequence.Sequence;
-import org.forester.sequence.Sequence.TYPE;
+import org.forester.sequence.MolecularSequence;
+import org.forester.sequence.MolecularSequence.TYPE;
 
 public interface Msa {
 
     public static enum MSA_FORMAT {
-        FASTA, PHYLIP;
+        FASTA, PHYLIP, NEXUS;
     }
 
     public String getIdentifier( int row );
@@ -52,11 +52,11 @@ public interface Msa {
 
     public List<Character> getColumnAt( int col );
 
-    public Sequence getSequence( final String id );
+    public MolecularSequence getSequence( final String id );
 
-    public Sequence getSequence( final int row );
+    public MolecularSequence getSequence( final int row );
 
-    public List<Sequence> asSequenceList();
+    public List<MolecularSequence> asSequenceList();
 
     public StringBuffer getSequenceAsString( int row );