Hashtable seqRefIds = null;
Vector frefedSequence = null;
+ boolean raiseGUI = true; // whether errors are raised in dialog boxes or not
+ public Jalview2XML()
+ {
+ }
+ public Jalview2XML(boolean raiseGUI)
+ {
+ this.raiseGUI = raiseGUI;
+ }
public void resolveFrefedSequences()
{
} catch (Exception ex)
{
//Is Version 1 Jar file?
- af = new Jalview2XML_V1().LoadJalviewAlign(file);
+ try {
+ af = new Jalview2XML_V1(raiseGUI).LoadJalviewAlign(file);
+ } catch (Exception ex2) {
+ System.err.println("Exception whilst loading as jalviewXMLV1:");
+ ex2.printStackTrace();
+ af = null;
+ }
+ if (Desktop.instance != null)
+ {
+ Desktop.instance.stopLoading();
+ }
if (af != null)
{
System.out.println("Successfully loaded archive file");
if (errorMessage != null)
{
final String finalErrorMessage = errorMessage;
- javax.swing.SwingUtilities.invokeLater(new Runnable()
- {
- public void run()
+ if (raiseGUI)
+ {
+ javax.swing.SwingUtilities.invokeLater(new Runnable()
+ {
+ public void run()
{
JOptionPane.showInternalMessageDialog(Desktop.desktop,
finalErrorMessage, "Error loading Jalview file",
JOptionPane.WARNING_MESSAGE);
}
});
+ } else {
+ System.err.println("Problem loading Jalview file: "+errorMessage);
+ }
}
return af;