/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
*/
package jalview.appletgui;
-import java.awt.Font;
-
import jalview.analysis.NJTree;
import jalview.api.AlignViewportI;
-import jalview.api.FeatureRenderer;
import jalview.bin.JalviewLite;
import jalview.commands.CommandI;
import jalview.datamodel.AlignmentI;
import jalview.structure.VamsasSource;
import jalview.viewmodel.AlignmentViewport;
+import java.awt.Font;
+
public class AlignViewport extends AlignmentViewport implements
SelectionSource, VamsasSource, CommandListener
{
private AnnotationColumnChooser annotationColumnSelectionState;
- private FeatureRenderer featureRenderer;
-
- private boolean includeHiddenRegion = true;
-
public void finalize()
{
applet = null;
if (applet != null)
{
- String colour = applet.getParameter("defaultColour");
-
+ String colour = al.isNucleotide() ? applet
+ .getParameter("defaultColourNuc") : applet
+ .getParameter("defaultColourProt");
+ if (colour == null)
+ {
+ colour = applet.getParameter("defaultColour");
+ }
if (colour == null)
{
colour = applet.getParameter("userDefinedColour");
return font;
}
-
public void resetSeqLimits(int height)
{
setEndSeq(height / getCharHeight());
return currentTree;
}
-
boolean centreColumnLabels;
public boolean getCentreColumnLabels()
public void sendSelection()
{
getStructureSelectionManager().sendSelection(
- new SequenceGroup(getSelectionGroup()),
- new ColumnSelection(getColumnSelection()), this);
+ new SequenceGroup(getSelectionGroup()),
+ new ColumnSelection(getColumnSelection()), this);
}
/**
}
}
- @Override
- public FeatureRenderer getFeatureRenderer()
- {
- return featureRenderer;
- }
-
- @Override
- public void setFeatureRenderer(FeatureRenderer featureRenderer)
- {
- this.featureRenderer = featureRenderer;
-
- }
-
- public boolean isIncludeHiddenRegion()
- {
- return includeHiddenRegion;
- }
-
- public void setIncludeHiddenRegion(boolean includeHiddenRegion)
- {
- this.includeHiddenRegion = includeHiddenRegion;
- }
-
}