// special conventions:
//
// * each external command ('itemmethod') runs in its separate directory under ~/.arb_tmp
// * if sequences are exported ARB writes them in GenBank format into a tmpfile (e.g. sth like '/tmp/gde3170_0')
//   In 'itemmethod' every occurrence of 'TmpInputFile' (as specified at entry 'in:') is replaced by the name of that tempfile.
//   Some macros defined below expect that placeholder, i.e. always use 'TmpInputFile' for 'in:'!
// * if sequences are (re-)imported, ARB prepares a temporary output-file. itemmethod shall use the placeholder 'TmpOutputFile'
//   to generate its content. Always use 'TmpOutputFile' for 'out:'.
//   Do not remove TmpOutputFile using RM_LOCAL_FILES. It is expected and will be removed by ARB_GDE (after command termination).
// * 'arg:DISPLAY_FUNC' shall be a single command (to be chainable with && in itemmethod)

// GOTO_LOCAL_DIR and RM_LOCAL_FILES need to be used on top-script level
// (opening sub-shells might change value of $$)

#define GOTO_LOCAL_DIR          mkdir -p ~/.arb_tmp/$$; cd ~/.arb_tmp/$$
#define RM_LOCAL_FILES(FILES)   GOTO_LOCAL_DIR ; cd .. ; rm -rf $$

#define GENERATE(OUTFILE,FORMAT) arb_convert_aln --arb-notify -GenBank TmpInputFile -FORMAT OUTFILE

#define GEN_PHYLIP(OUTFILE)     GENERATE(OUTFILE,phylip)
#define GEN_FASTDNAML(OUTFILE)  GENERATE(OUTFILE,fastdnaml)
#define GEN_NEXUS(OUTFILE)      GENERATE(OUTFILE,NEXUS)

#define TEE_TO(cmd,log)            ( cmd 2>&1 ) | tee log

#define RUN_IN_WINDOW_TO_LOG(cmd,log)  ${ARB_XCMD} bash -x -c @@LD_LIBRARY_PATH="${ARB_LIBRARY_PATH:-/usr/arb/lib}";export LD_LIBRARY_PATH; TEE_TO(cmd,log); arb_wait@@
#define RUN_IN_WINDOW(cmd)             RUN_IN_WINDOW_TO_LOG(cmd,win_$AGDE_JOBID.log); arb_catlog win_$AGDE_JOBID.log
// Note: @@ will result in a single quote. see ../ARB_GDE/GDE_ParseMenu.cxx@WHY_USE_DOUBLE_AT
// $AGDE_JOBID differs between calls and gets derived from item-entry

#define STOP_ON_FAILURE(WHAT_FAILED) (arb_message "Error running WHAT_FAILED (inspect console for details)";false)
// intended use '( command || STOP_ON_FAILURE(command-description)) && ( dependent-command || STOP_ON_FAILURE(dependent-command-description) && ...)'

#include <warning.genmenu>

// ----------------------------------------
menu:Export
menumeta: E
#include <export.genmenu>

// ----------------------------------------
menu:Print
menumeta: r
#include <pretty_print.genmenu>

#include <sativa.genmenu>

// ----------------------------------------
menu:Import
menumeta:I
#include <import.genmenu>

// ----------------------------------------
menu:Align
menumeta:A
#include <align.genmenu>

// ----------------------------------------
menu:SAI
menumeta:S
#include <dnamlrates.genmenu>

// ----------------------------------------
menu:Incremental phylogeny
menumeta:c
#include <inc_fastdnaml.genmenu>

// ----------------------------------------
menu:Phylogeny Distance Matrix
menumeta:D
#include <phylip_dist_org.genmenu>
#include <phylip_dist.genmenu>

// ----------------------------------------
menu:Phylogeny max. parsimony
menumeta:p
#include <phylip_pars.genmenu>

// ----------------------------------------
menu:Phylogeny max. Likelihood EXP
menumeta:X
#include <fastdnaml.genmenu>

// ----------------------------------------
menu:Phylogeny max. Likelihood
menumeta:L

#define RAXML_NUC
#include <raxml7.genmenu>
#undef RAXML_NUC
#include <raxml7.genmenu>

#define PHYML_NUC
#include <phyml_20130708.genmenu>
#undef PHYML_NUC
#include <phyml_20130708.genmenu>

#include <phyml.genmenu>
#include <phylip_ml.genmenu>

#include <raxml8.genmenu>

// ----------------------------------------
menu:Phylogeny (Other)
menumeta:O

#define FASTTREE_NUC
#include <fasttree.genmenu>
#undef FASTTREE_NUC
#include <fasttree.genmenu>

#include <mrbayes.genmenu>
#include <puzzle.genmenu>
#include <desoete.genmenu>

// ----------------------------------------
// custom menu 'User' is loaded into 'Tools'-menu
// (has no members by default; meant to be used from custom .menu definitions)
menu:User
menumeta:U