import jalview.datamodel.SequenceI;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemeProperty;
-import jalview.schemes.UserColourScheme;
import jalview.util.ColorUtils;
import java.awt.Color;
value = Float.valueOf(nextToken);
} catch (NumberFormatException e)
{
- System.err.println("Threshold '" + nextToken
+ System.err.println("line " + nlinesread + ": Threshold '" + nextToken
+ "' invalid, setting to zero");
}
String label = st.hasMoreTokens() ? st.nextToken() : null;
}
else if (key.equalsIgnoreCase("colour"))
{
- sg.cs = ColourSchemeProperty.getColour(al, value);
+ sg.cs = ColourSchemeProperty.getColourScheme(al, value);
}
else if (key.equalsIgnoreCase("pidThreshold"))
{
}
else if (key.equalsIgnoreCase("idColour"))
{
- // consider warning if colour doesn't resolve to a real colour
- def = new UserColourScheme(value);
- sg.setIdColour(def.findColour());
+ Color idColour = ColorUtils.parseColourString(value);
+ sg.setIdColour(idColour == null ? Color.black : idColour);
}
else if (key.equalsIgnoreCase("hide"))
{