import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.datamodel.SequenceNode;
+import jalview.ext.archaeopteryx.ArchaeopteryxInit;
import jalview.io.JalviewFileChooser;
import jalview.io.JalviewFileView;
import jalview.io.NewickFile;
}
});
+
TreeLoader tl = new TreeLoader(newTree, inputData);
tl.start();
class TreeLoader extends Thread
{
- private NewickFile newtree;
+ private NewickFile newTree;
private AlignmentView odata = null;
public TreeLoader(NewickFile newickFile, AlignmentView inputData)
{
- this.newtree = newickFile;
+ this.newTree = newickFile;
this.odata = inputData;
- if (newickFile != null)
+ if (newTree != null)
{
// Must be outside run(), as Jalview2XML tries to
// update distance/bootstrap visibility at the same time
- showBootstrap(newickFile.HasBootstrap());
- showDistances(newickFile.HasDistances());
+ showBootstrap(newTree.hasBootstrap());
+ showDistances(newTree.hasDistances());
+
}
+
}
@Override
public void run()
{
- if (newtree != null)
+ if (newTree != null)
{
tree = new TreeModel(av.getAlignment().getSequencesArray(), odata,
- newtree);
+ newTree);
if (tree.getOriginalData() == null)
{
originalSeqData.setVisible(false);
}
+
+
+
}
else
{
: new AverageDistanceTree(av, sm, similarityParams);
tree = new TreeModel(njtree);
showDistances(true);
+
+
+
}
+ ArchaeopteryxInit archae = new ArchaeopteryxInit(tree);
+ archae.startArchaeopteryx();
tree.reCount(tree.getTopNode());
tree.findHeight(tree.getTopNode());
treeCanvas.setTree(tree);
treeCanvas.repaint();
+
av.setCurrentTree(tree);
if (av.getSortByTree())
{
if (treeCanvas.applyToAllViews)
{
- final ArrayList<CommandI> commands = new ArrayList<CommandI>();
+ final ArrayList<CommandI> commands = new ArrayList<>();
for (AlignmentPanel ap : PaintRefresher
.getAssociatedPanels(av.getSequenceSetId()))
{
}
if (newname == null)
{
- SequenceFeature sf[] = sq.getSequenceFeatures();
- for (int i = 0; sf != null && i < sf.length; i++)
+ List<SequenceFeature> features = sq.getFeatures()
+ .getPositionalFeatures(labelClass);
+ for (SequenceFeature feature : features)
{
- if (sf[i].getType().equals(labelClass))
+ if (newname == null)
+ {
+ newname = feature.getDescription();
+ }
+ else
{
- if (newname == null)
- {
- newname = new String(sf[i].getDescription());
- }
- else
- {
- newname = newname + "; " + sf[i].getDescription();
- }
+ newname = newname + "; " + feature.getDescription();
}
}
}