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 0ee7844..066b10f 100644 (file)
--- a/forester/java/src/org/forester/msa/Msa.java
+++ b/forester/java/src/org/forester/msa/Msa.java
@@ -21,20 +21,26 @@
 // 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;
 
 import java.io.IOException;
 import java.io.Writer;
+import java.util.List;
 
-import org.forester.sequence.Sequence.TYPE;
+import org.forester.sequence.MolecularSequence;
+import org.forester.sequence.MolecularSequence.TYPE;
 
 public interface Msa {
 
-    public Object getIdentifier( int row );
+    public static enum MSA_FORMAT {
+        FASTA, PHYLIP, NEXUS;
+    }
 
-    public void setIdentifier( int row, Object identifier );
+    public String getIdentifier( int row );
+
+    public void setIdentifier( int row, String identifier );
 
     public int getLength();
 
@@ -42,11 +48,21 @@ public interface Msa {
 
     public char getResidueAt( int row, int col );
 
+    public boolean isGapAt( int row, int col );
+
+    public List<Character> getColumnAt( int col );
+
+    public MolecularSequence getSequence( final String id );
+
+    public MolecularSequence getSequence( final int row );
+
+    public List<MolecularSequence> asSequenceList();
+
     public StringBuffer getSequenceAsString( int row );
 
     public abstract TYPE getType();
 
     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;
 }