+ public Sequence( final MolecularSequence mol_seq ) {
+ init();
+ setMolecularSequence( mol_seq.getMolecularSequenceAsString() );
+ setName( mol_seq.getIdentifier() );
+ String type;
+ if ( mol_seq.getType() == TYPE.AA ) {
+ type = "protein";
+ }
+ else if ( mol_seq.getType() == TYPE.DNA ) {
+ type = "dna";
+ }
+ else if ( mol_seq.getType() == TYPE.RNA ) {
+ type = "rna";
+ }
+ else {
+ throw new IllegalArgumentException( "unknown sequence type " + mol_seq.getType() );
+ }
+ try {
+ setType( type );
+ }
+ catch ( final PhyloXmlDataFormatException e ) {
+ throw new IllegalArgumentException( "don't know how to handle type " + mol_seq.getType() );
+ }
+ }
+