import jalview.javascript.MouseOverStructureListener;
import jalview.structure.SelectionListener;
import jalview.structure.StructureSelectionManager;
+import jalview.util.ColorUtils;
import jalview.util.HttpUtils;
import jalview.util.MessageManager;
SequenceI rs = sel.getSequenceAt(0);
start = rs.findIndex(start);
end = rs.findIndex(end);
- List<Integer> cs = csel.getSelected();
+ List<Integer> cs = new ArrayList<Integer>(csel.getSelected());
csel.clear();
for (Integer selectedCol : cs)
{
{
boolean result = false;
String param = applet.getParameter("jnetfile");
+ if (param == null)
+ {
+ // jnet became jpred around 2016
+ param = applet.getParameter("jpredfile");
+ }
if (param != null)
{
try
{
return defcolour;
}
- Color col = jalview.schemes.ColourSchemeProperty
- .getAWTColorFromName(colprop);
+ Color col = ColorUtils.parseColourString(colprop);
if (col == null)
{
- try
- {
- col = new jalview.schemes.UserColourScheme(colprop).findColour('A');
- } catch (Exception ex)
- {
- System.err.println("Couldn't parse '" + colprop
- + "' as a colour for " + colparam);
- col = null;
- }
+ System.err.println("Couldn't parse '" + colprop
+ + "' as a colour for " + colparam);
}
return (col == null) ? defcolour : col;
-
}
public void openJalviewHelpUrl()