+ public void registerPDBEntry(PDBEntry pdbentry)
+ {
+ if (pdbentry.getFile() != null
+ && pdbentry.getFile().trim().length() > 0)
+ {
+ registerPDBFile(pdbentry.getId(), pdbentry.getFile());
+ }
+ }
+
+ public void addCommandListener(CommandListener cl)
+ {
+ if (!commandListeners.contains(cl))
+ {
+ commandListeners.add(cl);
+ }
+ }
+
+ public boolean hasCommandListener(CommandListener cl)
+ {
+ return this.commandListeners.contains(cl);
+ }
+
+ public boolean removeCommandListener(CommandListener l)
+ {
+ return commandListeners.remove(l);
+ }
+
+ /**
+ * Forward a command to any command listeners (except for the command's
+ * source).
+ *
+ * @param command
+ * the command to be broadcast (in its form after being performed)
+ * @param undo
+ * if true, the command was being 'undone'
+ * @param source
+ */
+ public void commandPerformed(CommandI command, boolean undo,
+ VamsasSource source)
+ {
+ for (CommandListener listener : commandListeners)
+ {
+ listener.mirrorCommand(command, undo, this, source);
+ }
+ }
+
+ /**
+ * Returns a new CommandI representing the given command as mapped to the
+ * given sequences. If no mapping could be made, or the command is not of a
+ * mappable kind, returns null.
+ *
+ * @param command
+ * @param undo
+ * @param mapTo
+ * @param gapChar
+ * @return
+ */
+ public CommandI mapCommand(CommandI command, boolean undo,
+ final AlignmentI mapTo, char gapChar)
+ {
+ if (command instanceof EditCommand)
+ {
+ return MappingUtils.mapEditCommand((EditCommand) command, undo,
+ mapTo, gapChar, seqmappings);
+ }
+ else if (command instanceof OrderCommand)
+ {
+ return MappingUtils.mapOrderCommand((OrderCommand) command, undo,
+ mapTo, seqmappings);
+ }
+ return null;
+ }
+
+ public IProgressIndicator getProgressIndicator()
+ {
+ return progressIndicator;
+ }
+
+ public void setProgressIndicator(IProgressIndicator progressIndicator)
+ {
+ this.progressIndicator = progressIndicator;
+ }
+
+ public long getProgressSessionId()
+ {
+ return progressSessionId;
+ }
+
+ public void setProgressSessionId(long progressSessionId)
+ {
+ this.progressSessionId = progressSessionId;
+ }
+
+ public void setProgressBar(String message)
+ {
+ progressIndicator.setProgressBar(message, progressSessionId);
+ }
+
+ public List<AlignedCodonFrame> getSequenceMappings()
+ {
+ return seqmappings;
+ }
+