MessageManager.getString("label.colourScheme_hydrophobic"));
MenuItem helix = new MenuItem(
- MessageManager.getString("label.colourScheme_helix_propensity"));
+ MessageManager.getString("label.colourScheme_helixpropensity"));
MenuItem strand = new MenuItem(
- MessageManager.getString("label.colourScheme_strand_propensity"));
+ MessageManager.getString("label.colourScheme_strandpropensity"));
MenuItem turn = new MenuItem(
- MessageManager.getString("label.colourScheme_turn_propensity"));
+ MessageManager.getString("label.colourScheme_turnpropensity"));
MenuItem buried = new MenuItem(
- MessageManager.getString("label.colourScheme_buried_index"));
+ MessageManager.getString("label.colourScheme_buriedindex"));
MenuItem purinepyrimidine = new MenuItem(
MessageManager.getString("label.colourScheme_purine/pyrimidine"));
AlignmentPanel ap;
List<AlignmentPanel> _aps = new ArrayList<>(); // remove? never
- // added to
+ // added to
String fileLoadingError;
"-applet", scriptWindow, null);
} catch (Exception e)
{
- System.err.println(
+ jalview.bin.Console.errPrintln(
"Couldn't create a jmol viewer. Args to allocate viewer were:\nDocumentBase="
+ ap.av.applet.getDocumentBase() + "\nCodebase="
+ ap.av.applet.getCodeBase());
{
if (jalview.bin.JalviewLite.debug)
{
- System.err.println(
+ jalview.bin.Console.errPrintln(
"AppletJmol:Trying to reuse existing PDBfile IO parser.");
}
// re-use the one we opened earlier
{
if (jalview.bin.JalviewLite.debug)
{
- System.err.println(
+ jalview.bin.Console.errPrintln(
"AppletJmol:Creating new PDBfile IO parser.");
}
FileParse fp = new FileParse(pdbentry.getFile(), protocol);
fp.mark();
- // reader = new MCview.PDBfile(fp);
+ // reader = new mc_view.PDBfile(fp);
// could set ID, etc.
// if (!reader.isValid())
// {
} catch (Exception e)
{
// give up!
- System.err.println("Couldn't access pdbentry id="
+ jalview.bin.Console.errPrintln("Couldn't access pdbentry id="
+ pdbentry.getId() + " and file=" + pdbentry.getFile()
+ " using protocol=" + protocol);
e.printStackTrace();
} catch (OutOfMemoryError ex)
{
frame.dispose();
- System.err.println(
+ jalview.bin.Console.errPrintln(
"Out of memory when trying to create dialog box with sequence-structure mapping.");
return;
}