- if (!atomsPicked.contains(picked))
- {
- viewer.select(picked);
- atomsPicked.add(picked);
- }
- else
- {
- viewer.select("not " + picked);
- atomsPicked.remove(picked);
- }
- viewerCommandHistory(true);
- // TODO: in application this happens
- //
- // if (scriptWindow != null)
- // {
- // scriptWindow.sendConsoleMessage(strInfo);
- // scriptWindow.sendConsoleMessage("\n");
- // }
-
- }
-
- // incremented every time a load notification is successfully handled -
- // lightweight mechanism for other threads to detect when they can start
- // referring to new structures.
- private long loadNotifiesHandled = 0;
-
- public long getLoadNotifiesHandled()
- {
- return loadNotifiesHandled;
- }
-
- public void notifyFileLoaded(String fullPathName, String fileName2,
- String modelName, String errorMsg, int modelParts)
- {
- if (errorMsg != null)
- {
- fileLoadingError = errorMsg;
- refreshGUI();
- return;
- }
- // TODO: deal sensibly with models loaded inLine:
- // modelName will be null, as will fullPathName.
-
- // the rest of this routine ignores the arguments, and simply interrogates
- // the Jmol view to find out what structures it contains, and adds them to
- // the structure selection manager.
- fileLoadingError = null;
- String[] oldmodels = modelFileNames;
- modelFileNames = null;
- chainNames = new ArrayList<String>();
- chainFile = new HashMap<String, String>();
- boolean notifyLoaded = false;
- String[] modelfilenames = getPdbFile();
- // first check if we've lost any structures
- if (oldmodels != null && oldmodels.length > 0)
- {
- int oldm = 0;
- for (int i = 0; i < oldmodels.length; i++)
- {
- for (int n = 0; n < modelfilenames.length; n++)
- {
- if (modelfilenames[n] == oldmodels[i])
- {
- oldmodels[i] = null;
- break;
- }
- }
- if (oldmodels[i] != null)
- {
- oldm++;
- }
- }
- if (oldm > 0)