          self.icons["folder"] = ImageTk.PhotoImage(file=os.path.join(
              self.pathicons, "open_folder.png"))
          self.icons["load"] = ImageTk.PhotoImage(file=os.path.join(
              self.pathicons, "open_file.png"))
          self.icons["context"] = ImageTk.PhotoImage(file=os.path.join(
              self.pathicons, "open_file.png"))
          self.icons["save"] = ImageTk.PhotoImage(file=os.path.join(self.pathicons, "save.png"))
          self.icons["reset"] = ImageTk.PhotoImage(file=os.path.join(self.pathicons, "reset.png"))
          self.icons["clear"] = ImageTk.PhotoImage(file=os.path.join(self.pathicons, "clear.png"))
 
</s> remove         orig, ext = os.path.splitext(self.alignments.file)
        filename = "{}_merged{}".format(orig, ext)
 </s> add         folder = os.path.split(self.final_alignments.file)[0]
        ext = os.path.splitext(self.final_alignments.file)[1]
        now = datetime.now().strftime("%Y%m%d_%H%M%S")
        filename = os.path.join(folder, "alignments_merged_{}{}".format(now, ext)) </s> remove         self.alignments = AlignmentData(self.args.alignments_file, dest_format)
 </s> add         if len(self.args.alignments_file) == 1:
            retval = AlignmentData(self.args.alignments_file[0], dest_format)
        else:
            retval = [AlignmentData(a_file, dest_format) for a_file in self.args.alignments_file]
        logger.debug("Alignments: %s", retval)
        return retval </s> remove                     optval = optval.split(" ")
 </s> add                     if "\"" in optval:
                        optval = [arg[1:-1] for arg in re.findall(r"\".+?\"", optval)]
                    else:
                        optval = optval.split(" ") </s> remove         self.alignments = alignments
        self.alignments2 = AlignmentData(arguments.alignments_file2, "json")
 </s> add         self.final_alignments = alignments[0]
        self.process_alignments = alignments[1:]
        self.icons["load_multi"] = ImageTk.PhotoImage(file=os.path.join(
            self.pathicons, "open_file.png"))
          self.icons["folder"] = ImageTk.PhotoImage(file=os.path.join(
              self.pathicons, "open_folder.png"))
          self.icons["load"] = ImageTk.PhotoImage(file=os.path.join(
              self.pathicons, "open_file.png"))
        self.icons["load_multi"] = ImageTk.PhotoImage(file=os.path.join(
            self.pathicons, "open_file.png"))
          self.icons["context"] = ImageTk.PhotoImage(file=os.path.join(
              self.pathicons, "open_file.png"))
          self.icons["save"] = ImageTk.PhotoImage(file=os.path.join(self.pathicons, "save.png"))
          self.icons["reset"] = ImageTk.PhotoImage(file=os.path.join(self.pathicons, "reset.png"))
          self.icons["clear"] = ImageTk.PhotoImage(file=os.path.join(self.pathicons, "clear.png"))
keep keep keep add keep keep keep keep keep
 Alignments Tool: Allow merging of many alignments file

Adds multi select functionality to GUI, meaning multiple alignments files can now be selected for merging.

Extract: nFilter, Filter now have a file dialog in gui for selecting 1/multiple files 
lib/gui/utils.py