X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fmsa%2FMsa.java;h=066b10ff2d41784c33ac77251eec5b4198439272;hb=718bd74aff29f5883486fc0ab8b54e1519ab51d0;hp=1eb9533c17c278f510d6816b83576eb1f7ccb8d6;hpb=656be28debec520e0e35a8b311114398a40ea366;p=jalview.git

diff --git a/forester/java/src/org/forester/msa/Msa.java b/forester/java/src/org/forester/msa/Msa.java
index 1eb9533..066b10f 100644
--- 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 );
@@ -48,13 +48,15 @@ public interface Msa {
 
     public char getResidueAt( int row, int col );
 
+    public boolean isGapAt( int row, int col );
+
     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 );