X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fmsa%2FMsa.java;h=066b10ff2d41784c33ac77251eec5b4198439272;hb=88718609970e490e94727d12ebbca1270ba2c0a7;hp=6ffa1ea3cf27c279b3a29020cd611ea6cfa64656;hpb=b1a74bd076c917d428002284a53a2c6f390226fb;p=jalview.git

diff --git a/forester/java/src/org/forester/msa/Msa.java b/forester/java/src/org/forester/msa/Msa.java
index 6ffa1ea..066b10f 100644
--- 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;
 
@@ -29,11 +29,15 @@ 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, NEXUS;
+    }
+
     public String getIdentifier( int row );
 
     public void setIdentifier( int row, String identifier );
@@ -44,13 +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 );
 
@@ -58,5 +64,5 @@ public interface Msa {
 
     public void setResidueAt( final int row, final int col, final char residue );
 
-    public void write( Writer w ) throws IOException;
+    public void write( Writer w, MSA_FORMAT format ) throws IOException;
 }