*/
package jalview.io.packed;
+import jalview.analysis.TreeModel;
+import jalview.api.FeatureColourI;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
import jalview.io.NewickFile;
import java.util.ArrayList;
+import java.util.HashMap;
import java.util.Hashtable;
import java.util.List;
+import java.util.Map;
public class JalviewDataset
{
/**
* @return the featureColours
*/
- public Hashtable getFeatureColours()
+ public Map<String, FeatureColourI> getFeatureColours()
{
return featureColours;
}
* @param featureColours
* the featureColours to set
*/
- public void setFeatureColours(Hashtable featureColours)
+ public void setFeatureColours(Map<String, FeatureColourI> featureColours)
{
this.featureColours = featureColours;
}
{
// the following works because all trees are already had node/SequenceI
// associations created.
- jalview.analysis.NJTree njt = new jalview.analysis.NJTree(
- al.getSequencesArray(), nf);
+ TreeModel njt = new TreeModel(al.getSequencesArray(), null, nf);
// this just updates the displayed leaf name on the tree according to
// the SequenceIs.
njt.renameAssociatedNodes();
/**
* current set of feature colours
*/
- Hashtable featureColours;
+ Map<String, FeatureColourI> featureColours;
/**
* original identity of each sequence in results
seqDetails = new Hashtable();
al = new ArrayList<AlignmentSet>();
parentDataset = null;
- featureColours = new Hashtable();
+ featureColours = new HashMap<String, FeatureColourI>();
}
/**
*
* @param parentAlignment
*/
- public JalviewDataset(AlignmentI aldataset, Hashtable fc,
- Hashtable seqDets)
+ public JalviewDataset(AlignmentI aldataset,
+ Map<String, FeatureColourI> fc, Hashtable seqDets)
{
+ // TODO not used - remove?
this(aldataset, fc, seqDets, null);
}
* (may be null) alignment to associate new annotation and trees
* with.
*/
- public JalviewDataset(AlignmentI aldataset, Hashtable fc,
- Hashtable seqDets, AlignmentI parentAlignment)
+ public JalviewDataset(AlignmentI aldataset,
+ Map<String, FeatureColourI> fc, Hashtable seqDets,
+ AlignmentI parentAlignment)
{
this();
parentDataset = aldataset;