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();
public char getResidueAt( int row, int col );
+ 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;
}