// this menu defines windows for two FastTree interfaces: nucleotide and protein
// (depending on whether FASTTREE_NUC is defined or not)

#ifdef FASTTREE_NUC
# define SEQTYPE_NAME nucleotide
# define SEQTYPE_SHRT NUC
# define ST_FLAG -nt
#else
# define SEQTYPE_NAME protein
# define SEQTYPE_SHRT PRO
# define ST_FLAG
#endif

#define CLEANUP_INPUT \
        arb_sed 's/#/>/' | \
        arb_sed 's/%/>/' | \
        arb_sed 's/"/>/' | \
        arb_sed 's/@/>/' | \
        arb_sed '/^[^>]/ y/./-/'

#ifdef USE_OPENMP
// depends on GUI
# define FASTTREE_BINARY $ARBHOME/bin/$FASTTREE
#else
# define FASTTREE_BINARY $ARBHOME/bin/FastTree
#endif

#define FASTTREE_CODE \
        (GOTO_LOCAL_DIR; \
         <TmpInputFile CLEANUP_INPUT >fasttree_in; \
         RUN_IN_WINDOW(( (FASTTREE_BINARY $NJMODE $NJ_OPT $MLMODEL -cat '$CAT' $SUPPORT ST_FLAG fasttree_in > fasttree_out || STOP_ON_FAILURE($FASTTREE)) && \
                         $DISPLAY_FUNC));)&

item:FastTree2 (SEQTYPE_NAME)
#ifdef FASTTREE_NUC
       itemmeta:F
       seqtype:N
#else
       itemmeta:p
       seqtype:A
#endif
itemmethod: FASTTREE_CODE
itemhelp: fasttree.help

arg:DISPLAY_FUNC
argtype:choice_menu
arglabel:What to do with the tree?
argchoice:Load into ARB ('tree_fasttree_//'):$ARBHOME/bin/arb_read_tree tree_fasttree_$$ fasttree_out "PRG=$FASTTREE$NJMODE FILTER=$FILTER MODEL=!$MLMODEL STYPE=SEQTYPE_SHRT"
argchoice:Treetool:treetool fasttree_out

#ifdef USE_OPENMP
       arg:FASTTREE
       argtype:choice_menu
       arglabel:Use multiprocessor?
       argchoice:No:FastTree
       argchoice:Yes:FastTreeMP
#endif

arg:NJMODE
argtype:choice_menu
arglabel:Neighbor joining phase
argchoice:default:
argchoice:fastest (recommended >50k species):-fastest
argchoice:slow (really):-slow

arg:NJ_OPT
argtype:choice_menu
arglabel:Weighted neighbor joining?
argchoice:No:
argchoice:Yes, as in BIONJ:-bionj

arg:MLMODEL
argtype:choice_menu
arglabel:ML Model
#ifdef FASTTREE_NUC
       argchoice:Jukes-Cantor:
       argchoice:GTR:-gtr
#else
       argchoice:JTT:
       argchoice:WAG:-wag
       argchoice:LG:-lg
#endif

arg:CAT
argtype:text
arglabel:Number of rate categories\n(Range [1..n]; default: 20)
argtext:20

arg:SUPPORT
argtype:choice_menu
arglabel:Support values
argchoice:1000xresample + Shimodaira Hasegawa test:
argchoice:Minimum-evolution bootstrap:-nome
argchoice:None:-nosupport

in:TmpInputFile
informat:flat
insave: