- bamoptions.update(source);
- al = fa.readFile(file, protocol, format);
+ // configure a window
+ BamFileOptionsChooser bamoptions = new BamFileOptionsChooser(
+ source);
+ // ask the user which bit of the bam they want to load
+ int confirm = JvOptionPane.showConfirmDialog(null, bamoptions,
+ MessageManager.getString("label.bam_file_options"),
+ JvOptionPane.OK_CANCEL_OPTION,
+ JvOptionPane.PLAIN_MESSAGE);
+
+ if (confirm == JvOptionPane.CANCEL_OPTION
+ || confirm == JvOptionPane.CLOSED_OPTION)
+ {
+ Desktop.instance.stopLoading();
+ return;
+ }
+ else
+ {
+ bamoptions.update(source);
+ if (file.indexOf("#") == -1)
+ {
+ file = file + "#" + ((BamFile) source).suffix;
+ }
+ }