#Please insert up references in the next lines (line starts with keyword UP) UP arb.hlp UP glossary.hlp #Please insert subtopic references (line starts with keyword SUB) #SUB subtopic.hlp # Hypertext links in helptext can be added like this: LINK{ref.hlp|http://add|bla@domain} #************* Title of helpfile !! and start of real helpfile ******** TITLE Macros OCCURRENCE ARB_NT DESCRIPTION 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 . The button label will switch to . Now perform all actions you like to record, then press . If you like to expand an existing macro, check the 'Expand?' toggle before pressing . You can also check the 'Run before?' toggle to execute the existing macro before expanding it. To execute an existing macro, select the macro and press . Press to execute the selected macro multiple times: once for each marked species. * this loop is performed in database order (see LINK{sp_sort_fld.hlp}). * 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 to edit the selected macro. Press to delete the selected macro. SECTION What gets recorded? 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). SECTION Calling submacros 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. NOTES You can run macros directly on startup by calling arb by arb --execute macroname your_database.arb Such macros can even shutdown ARB, so you can use this to automate ARB. EXAMPLES You can find some examples in $ARBHOME/lib/macros (this directory is reachable in the macro selection box by pressing the ARBMACRO line). SECTION Enhanced techniques 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'); * the current cursor position in the editor my $cursor_position = BIO::remote_read_awar($gb_main,'ARB_NT','tmp/focus/cursor_position'); WARNINGS None BUGS None