*/
package jalview.io;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Enumeration;
-import java.util.Hashtable;
-import java.util.List;
-import java.util.Vector;
-
-import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
import jalview.util.MessageManager;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Vector;
+
/**
* DOCUMENT ME!
*
*
* @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)
{
return newickStrings == null ? 0 : newickStrings.size();
}
+ public void addGroups(AlignmentI al)
+ {
+
+ for (SequenceGroup sg : getSeqGroups())
+ {
+ al.addGroup(sg);
+ }
+ }
+
}