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;
if (sg != null)
{
String keyValue, key, value;
- ColourSchemeI def = sg.cs;
- sg.cs = null;
+ ColourSchemeI def = sg.getColourScheme();
while (st.hasMoreTokens())
{
keyValue = st.nextToken();
}
else if (key.equalsIgnoreCase("colour"))
{
- sg.cs = ColourSchemeProperty.getColourScheme(al, value);
+ sg.cs.setColourScheme(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"))
{
}
sg.recalcConservation();
}
- if (sg.cs == null)
+ if (sg.getColourScheme() == null)
{
- sg.cs = def;
+ sg.setColourScheme(def);
}
}
}