*/
package jalview.io;
-import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Sequence;
*
* @param al
*/
- public void addAnnotations(Alignment al)
+ public void addAnnotations(AlignmentI al)
{
addProperties(al);
for (int i = 0; i < annotations.size(); i++)
}
+ /**
+ * register sequence groups on the alignment for **output**
+ *
+ * @param al
+ */
public void addSeqGroups(AlignmentI al)
{
this.seqGroups = al.getGroups();
* @note implicitly called by addAnnotations()
* @param al
*/
- public void addProperties(Alignment al)
+ public void addProperties(AlignmentI al)
{
if (properties != null && properties.size() > 0)
{