package jalview.appletgui;
import jalview.analysis.NJTree;
-import jalview.api.AlignExportSettingI;
import jalview.api.AlignViewportI;
-import jalview.api.FeatureRenderer;
import jalview.bin.JalviewLite;
import jalview.commands.CommandI;
import jalview.datamodel.AlignmentI;
private AnnotationColumnChooser annotationColumnSelectionState;
- private FeatureRenderer featureRenderer;
-
- private AlignExportSettingI exportSettings;
-
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);
}
/**
}
}
-
}