- groups[i] = new JGroup();
-
- jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup) jal.getGroups()
- .elementAt(i);
- groups[i].setStart(sg.getStartRes());
- groups[i].setEnd(sg.getEndRes());
- groups[i].setName(sg.getName());
- if(sg.cs!=null)
- {
- if (sg.cs.conservationApplied())
- {
- groups[i].setConsThreshold(sg.cs.getConservationInc());
-
- if (sg.cs instanceof jalview.schemes.UserColourScheme)
- {
- groups[i].setColour(SetUserColourScheme(sg.cs,
- userColours,
- jms));
- }
- else
- {
- groups[i].setColour(ColourSchemeProperty.getColourName(sg.
- cs));
- }
- }
- else if(sg.cs instanceof jalview.schemes.AnnotationColourGradient)
- {
- groups[i].setColour(
- ColourSchemeProperty.getColourName(
- ( (jalview.schemes.AnnotationColourGradient) sg.cs).getBaseColour()));
- }
- else if (sg.cs instanceof jalview.schemes.UserColourScheme)
- {
- groups[i].setColour(SetUserColourScheme(sg.cs, userColours,
- jms));
- }
- else
- {
- groups[i].setColour(ColourSchemeProperty.getColourName(
- sg.cs));
- }
-
- groups[i].setPidThreshold(sg.cs.getThreshold());
- }
-
- groups[i].setOutlineColour(sg.getOutlineColour().getRGB());
- groups[i].setDisplayBoxes(sg.getDisplayBoxes());
- groups[i].setDisplayText(sg.getDisplayText());
- groups[i].setColourText(sg.getColourText());
-
- for (int s = 0; s < sg.getSize(false); s++)
- {
- jalview.datamodel.Sequence seq =
- (jalview.datamodel.Sequence) sg.getSequenceAt(s);
- groups[i].addSeq(seq.hashCode());
- }
+ Tree tree = new Tree();
+ tree.setTitle(tp.getTitle());
+ tree.setCurrentTree( (av.currentTree == tp.getTree()));
+ tree.setNewick(tp.getTree().toString());
+ tree.setThreshold(tp.treeCanvas.threshold);
+
+ tree.setFitToWindow(tp.fitToWindow.getState());
+ tree.setFontName(tp.getTreeFont().getName());
+ tree.setFontSize(tp.getTreeFont().getSize());
+ tree.setFontStyle(tp.getTreeFont().getStyle());
+ tree.setMarkUnlinked(tp.placeholdersMenu.getState());
+
+ tree.setShowBootstrap(tp.bootstrapMenu.getState());
+ tree.setShowDistances(tp.distanceMenu.getState());
+
+ tree.setHeight(tp.getHeight());
+ tree.setWidth(tp.getWidth());
+ tree.setXpos(tp.getX());
+ tree.setYpos(tp.getY());
+
+ jms.addTree(tree);