import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefEntry;
import jalview.datamodel.GraphLine;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.RnaViewerModel;
import jalview.schemabinding.version2.AnnotationColours;
import jalview.schemabinding.version2.AnnotationElement;
import jalview.schemabinding.version2.CalcIdParam;
-import jalview.schemabinding.version2.Colour;
import jalview.schemabinding.version2.CompoundMatcher;
import jalview.schemabinding.version2.DBRef;
import jalview.schemabinding.version2.Features;
{
TreePanel tp = (TreePanel) frames[t];
- if (tp.treeCanvas.av.getAlignment() == jal)
+ if (tp.getTreeCanvas().getViewport().getAlignment() == jal)
{
Tree tree = new Tree();
tree.setTitle(tp.getTitle());
tree.setCurrentTree((av.getCurrentTree() == tp.getTree()));
tree.setNewick(tp.getTree().print());
- tree.setThreshold(tp.treeCanvas.threshold);
+ tree.setThreshold(tp.getTreeCanvas().getThreshold());
tree.setFitToWindow(tp.fitToWindow.getState());
tree.setFontName(tp.getTreeFont().getName());
{
view.setComplementId(av.getCodingComplement().getViewId());
}
- view.setViewName(av.viewName);
+ view.setViewName(av.getViewName());
view.setGatheredViews(av.isGatherViewsHere());
Rectangle size = ap.av.getExplodedGeometry();
vamsasSeq.setName(jds.getName());
vamsasSeq.setSequence(jds.getSequenceAsString());
vamsasSeq.setDescription(jds.getDescription());
- jalview.datamodel.DBRefEntry[] dbrefs = null;
+ List<DBRefEntry> dbrefs = null;
if (jds.getDatasetSequence() != null)
{
vamsasSeq.setDsseqid(seqHash(jds.getDatasetSequence()));
}
if (dbrefs != null)
{
- for (int d = 0; d < dbrefs.length; d++)
+ for (int d = 0, n = dbrefs.size(); d < n; d++)
{
DBRef dbref = new DBRef();
- dbref.setSource(dbrefs[d].getSource());
- dbref.setVersion(dbrefs[d].getVersion());
- dbref.setAccessionId(dbrefs[d].getAccessionId());
- if (dbrefs[d].hasMap())
+ DBRefEntry e = dbrefs.get(d);
+ dbref.setSource(e.getSource());
+ dbref.setVersion(e.getVersion());
+ dbref.setAccessionId(e.getAccessionId());
+ if (e.hasMap())
{
- Mapping mp = createVamsasMapping(dbrefs[d].getMap(), parentseq,
+ Mapping mp = createVamsasMapping(e.getMap(), parentseq,
jds, recurse);
dbref.setMapping(mp);
}
if (errorMessage != null)
{
final String finalErrorMessage = errorMessage;
+ errorMessage = null;
if (raiseGUI)
{
javax.swing.SwingUtilities.invokeLater(new Runnable()
}
else
{
- System.err.println("Problem loading Jalview file: " + errorMessage);
+ System.err.println(
+ "Problem loading Jalview file: " + finalErrorMessage);
}
}
- errorMessage = null;
}
Map<String, String> alreadyLoadedPDB = new HashMap<>();
tp.setTitle(tree.getTitle());
tp.setBounds(new Rectangle(tree.getXpos(), tree.getYpos(),
tree.getWidth(), tree.getHeight()));
- tp.av = av; // af.viewport; // TODO: verify 'associate with all
+ tp.setViewport(av); // af.viewport; // TODO: verify 'associate with all
// views'
// works still
- tp.treeCanvas.av = av; // af.viewport;
- tp.treeCanvas.ap = ap; // af.alignPanel;
+ tp.getTreeCanvas().setViewport(av); // af.viewport;
+ tp.getTreeCanvas().setAssociatedPanel(ap); // af.alignPanel;
}
if (tp == null)
tp.showBootstrap(tree.getShowBootstrap());
tp.showDistances(tree.getShowDistances());
- tp.treeCanvas.threshold = tree.getThreshold();
+ tp.getTreeCanvas().setThreshold(tree.getThreshold());
if (tree.getCurrentTree())
{
if (view.getViewName() != null)
{
- af.viewport.viewName = view.getViewName();
+ af.viewport.setViewName(view.getViewName());
af.setInitialTabVisible();
}
af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),