rio - gsdir work...

[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 50fcee9..790b674 100644 (file)
--- a/forester/java/src/org/forester/msa/Msa.java
+++ b/forester/java/src/org/forester/msa/Msa.java
@@ -29,13 +29,18 @@ import java.io.IOException;
 import java.io.Writer;
 import java.util.List;
 
+import org.forester.sequence.Sequence;
 import org.forester.sequence.Sequence.TYPE;
 
 public interface Msa {
 
-    public Object getIdentifier( int row );
+    public static enum MSA_FORMAT {
+        FASTA, PHYLIP;
+    }
 
-    public void setIdentifier( int row, Object identifier );
+    public String getIdentifier( int row );
+
+    public void setIdentifier( int row, String identifier );
 
     public int getLength();
 
@@ -45,11 +50,17 @@ public interface Msa {
 
     public List<Character> getColumnAt( int col );
 
+    public Sequence getSequence( final String id );
+
+    public Sequence getSequence( final int row );
+
+    public List<Sequence> 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;
 }