*/
package jalview.io.packed;
+import jalview.analysis.NJTree;
+import jalview.analysis.SeqsetUtils;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
import jalview.io.NewickFile;
{
public AlignmentI al;
- public List<jalview.io.NewickFile> trees;
+ public List<NewickFile> trees;
AlignmentSet(AlignmentI a)
{
al = a;
- trees = new ArrayList<jalview.io.NewickFile>();
+ trees = new ArrayList<NewickFile>();
}
/**
// jalview.analysis.SeqsetUtils.deuniquifyAndMerge(parentDataset,
// seqDetails, al,true);
- jalview.analysis.SeqsetUtils.deuniquify(seqDetails,
- al.getSequencesArray(), true);
+ SeqsetUtils.deuniquify(seqDetails, al.getSequencesArray(), true);
// 2. Update names of associated nodes in any trees
for (NewickFile nf : trees)
{
// the following works because all trees are already had node/SequenceI
// associations created.
- jalview.analysis.NJTree njt = new jalview.analysis.NJTree(
- al.getSequencesArray(), nf);
+ NJTree njt = new NJTree(al.getSequencesArray(), nf);
// this just updates the displayed leaf name on the tree according to
// the SequenceIs.
njt.renameAssociatedNodes();