in progress

[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 790b674..ed73cd4 100644 (file)
--- a/forester/java/src/org/forester/msa/Msa.java
+++ b/forester/java/src/org/forester/msa/Msa.java
@@ -21,7 +21,7 @@
 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
 //
 // Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/forester
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
 
 package org.forester.msa;
 
@@ -35,7 +35,7 @@ import org.forester.sequence.Sequence.TYPE;
 public interface Msa {
 
     public static enum MSA_FORMAT {
-        FASTA, PHYLIP;
+        FASTA, PHYLIP, NEXUS;
     }
 
     public String getIdentifier( int row );
@@ -48,6 +48,8 @@ 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 );