Macros

ARB_NT

Macros are used to combine a set of menu-actions. They work like a tape recorder, which records all buttons presses, every input to data fields, ...

To record a new macro, go to the directory where the new macro should be placed, enter a macro name and press <RECORD>. The button label will switch to <STOP>.

Now perform all actions you like to record, then press <STOP>.

If you like to expand an existing macro, check the 'Expand?' toggle before pressing <RECORD>. You can also check the 'Run before?' toggle to execute the existing macro before expanding it.

Press 'Interrupt' while recording, to plan a later interruption during playback. See ´Define macro interruption´ for details.

To execute an existing macro, select the macro and press <EXECUTE>.

Press <Execute with each marked species> to execute the selected macro multiple times: once for each marked species.

• this loop is performed in database order (see ´Sort Species According Database Entries´).
• before each call of the macro, one species will be marked AND selected - all other species will be unmarked.
• afterwards the original species marks will be restored.

Press <EDIT> to edit the selected macro.

Press <DELETE> to delete the selected macro.

The macro recorder only records elements like buttons, menues and values (like input fields, radio buttons, selection lists, toggles, ...). Actions in the main area (e.g. tree view) will not be recorded!

Elements of a window are unknown to the macro playback if the window was not opened before. So - if you just record some changes and clicks in an already open window, you need to open that window everytime before you run that macro.

Best practice is to CLOSE ALL SUBWINDOWS before you start recording a macro, then open them (again) and then perform your clicks. In that case your macro will run regardless whether the window has been opened before or not. Note: You can also record "closing a window".

If you want to make sure that some field or toggle is set to a specific value by your recorded macro, you need to CHANGE that value. If it already has the desired value, change it to something different and then change it back to your desired value - otherwise nothing will be recorded!

You may also use this as an feature: If you do NOT change a value during macro record, you can change it manually before calling the macro and that way perform similar, but different actions with one macro.

This may as well be helpful when using submacros (see below).

Macros can call other macros. To do this simply select the macro you like to call as submacro and press execute. That will be recorded like any other action.

Calling submacros is a good way to compose complex macros.

It offers you the possibility to change (or fix) small parts of a complex macro without the need to record it from scratch.

You can run macros automatically at startup by using:

These macros can even shut down ARB, letting you fully automate tasks. If a macro invokes shutdown, ARB will not prompt before closing. Ensure your macro saves the database to prevent data loss.

Sometimes ARB exits with an error (for example if a client like ARB_EDIT4 or ARB_PARSIMONY is still running). To avoid this, close all client processes when they're no longer needed.

If a client fails to close properly, the arb script will pause and wait for a key press before continuing. By default, this timeout is three days. In automated environments, you may want to customize this wait period by setting the environment variable ARB_SCRIPTED_SECS_WAIT_ON_ERROR to the desired number of seconds (see also ´ARB environment variables´).

You can find some examples in $ARBHOME/lib/macros (this directory is reachable in the macro selection box by pressing the ARBMACRO line).

Macros are perl scripts. So if you know perl or have someone @ your lab who does or just feel keen enough, macros can be easily extended to act more sophisticated.

Some examples:

• to create a macro that works with the CURRENTLY SELECTED alignment
  • record a macro using an explicit alignment (e.g. 'ali_16s') wherever needed
  • edit the recorded macro file:
    • above the 1st '# recording started'-line insert the following lines:

      my $ali_selected = BIO::remote_read_awar($gb_main,'ARB_NT','presets/use');
      if ((not defined $ali_selected) or ($ali_selected =~ /\?/)) {
        die "Please select a valid alignment";
      }

    • below replace all

       occurrences of         with
      'ali_16s'               $ali_selected

      Note the single quotes!
    
    
  
  
• to create a macro that works with two corresponding dna and protein alignments
  • record a macro using two explicit alignments (e.g. 'ali_dna' and 'ali_pro') wherever needed
  • edit the recorded macro file:
    • above the 1st '# recording started'-line insert the following lines:

      use lib "$ENV{'ARBHOME'}/PERL_SCRIPTS/lib";
      use ali_dnapro;
      my ($ali_dna,$ali_pro) =  get_dnapro_alignments($gb_main);

    • below replace all

       occurrences of         with
      'ali_dna'               $ali_dna
      'ali_pro'               $ali_pro

      Note the single quotes!
    
    
  • Notes:
    • works only if the alignment names contain 'dna' and 'pro' and both only differ by these terms.
    • you may select either the dna or the protein alignment before running the macro.
    
    
  
  

The method used in the first example above also works for other selected things, like

• the selected tree using

  my $tree_selected =  BIO::remote_read_awar($gb_main,'ARB_NT','focus/tree_name');

• the ´Selected species´ using

  my $species_selected =  BIO::remote_read_awar($gb_main,'ARB_NT','tmp/focus/species_name');
  die "no species selected" if not defined $species_selected; # show error in ARB message window and abort

• the current cursor position in the editor

  my $cursor_position =  BIO::remote_read_awar($gb_main,'ARB_NT','tmp/focus/cursor_position');

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