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more test for isDuplication() and isSpecation() added (phyloXML encoded
[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
1eb9533
..
066b10f
100644
(file)
--- a/
forester/java/src/org/forester/msa/Msa.java
+++ b/
forester/java/src/org/forester/msa/Msa.java
@@
-29,13
+29,13
@@
import java.io.IOException;
import java.io.Writer;
import java.util.List;
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 {
public interface Msa {
public static enum MSA_FORMAT {
- FASTA, PHYLIP;
+ FASTA, PHYLIP, NEXUS;
}
public String getIdentifier( int row );
}
public String getIdentifier( int row );
@@
-48,13
+48,15
@@
public interface Msa {
public char getResidueAt( int row, int col );
public char getResidueAt( int row, int col );
+ public boolean isGapAt( int row, int col );
+
public List<Character> getColumnAt( 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 );
public StringBuffer getSequenceAsString( int row );