import jalview.analysis.AlignmentUtils;
import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
-import jalview.analysis.NJTree;
+import jalview.analysis.TreeModel;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureColourI;
import jalview.schemes.ColourSchemeProperty;
import jalview.schemes.ResidueColourScheme;
import jalview.schemes.UserColourScheme;
-import jalview.structure.CommandListener;
import jalview.structure.SelectionSource;
import jalview.structure.StructureSelectionManager;
import jalview.structure.VamsasSource;
import jalview.util.MessageManager;
import jalview.viewmodel.AlignmentViewport;
+import jalview.viewmodel.ViewportRanges;
import jalview.ws.params.AutoCalcSetting;
import java.awt.Container;
* @version $Revision: 1.141 $
*/
public class AlignViewport extends AlignmentViewport implements
- SelectionSource, CommandListener
+ SelectionSource
{
Font font;
- NJTree currentTree = null;
+ TreeModel currentTree = null;
boolean cursorMode = false;
void init()
{
- this.startRes = 0;
- this.endRes = alignment.getWidth() - 1;
- this.startSeq = 0;
- this.endSeq = alignment.getHeight() - 1;
+ ranges = new ViewportRanges(this.alignment);
applyViewProperties();
String fontName = Cache.getDefault("FONT_NAME", "SansSerif");
super.setViewStyle(settingsForView);
setFont(new Font(viewStyle.getFontName(), viewStyle.getFontStyle(),
viewStyle.getFontSize()), false);
- if (residueShading != null)
- {
- residueShading.setConservationApplied(settingsForView
- .isConservationColourSelected());
- }
}
/**
* @param tree
* DOCUMENT ME!
*/
- public void setCurrentTree(NJTree tree)
+ public void setCurrentTree(TreeModel tree)
{
currentTree = tree;
}
*
* @return DOCUMENT ME!
*/
- public NJTree getCurrentTree()
+ public TreeModel getCurrentTree()
{
return currentTree;
}
}
}
- setEndSeq(getAlignment().getHeight());
+ ranges.setEndSeq(getAlignment().getHeight());
firePropertyChange("alignment", null, getAlignment().getSequences());
}