# -*-Mode: Makefile;-*-  (emacs! this is a makefile!)

.SUFFIXES: .doc .help .html

# GENHELPDEST, GENDOCDEST and HELPFILELIST are passed from 'Makefile'

HELP_NAMES=$(shell cat $(HELPFILELIST))
HELP_TARGETS=$(addprefix $(GENHELPDEST)/,$(HELP_NAMES))
HELP_PLAIN=./HELP_PLAIN
HELP_WRITTEN=./HELP_WRITTEN
HEADER=arb_help.head
SED:=$(ARBHOME)/SH/arb_sed
all: info forcedoc $(HELP_TARGETS)

info:
	@echo "----------------------------------------------------------------"
	@echo "Collecting documentation for external programs used in GDE menus"
#	@echo "HELP_TARGETS=$(HELP_TARGETS)"

# ------------------------------------------------------------
# rules to generate helpfiles
# we need rules here for each helpfile specified on an 'itemhelp' line in GDE menus.
#
# Different ways to include help are (HOWTO_ADD_GDE_HELP):
# - existing file in tool directory, e.g. .@FASTDNAML
# - multiple existing files in tool directory, e.g. .@CLUSTALW
# - single existing files in ./HELP_PLAIN or ./HELP_WRITTEN
# - files generated into ./HELP_DOC_GEN (e.g. used for html ducumentation like proml)


ARBHOME=..
GDE=$(ARBHOME)/GDE

GENHELP_DEPENDS=genhelp.sh Makefile.helpfiles
GENHELPTREE_DEPENDS=genhelptree.sh $(GENHELP_DEPENDS)

# ---------- CLUSTALW

CLUSTALW=$(GDE)/CLUSTALW
CLUSTALW_HELP=$(CLUSTALW)/clustalw_help
CLUSTALW_DOC=$(CLUSTALW)/clustalw.doc

$(GENHELPDEST)/clustalw.help: $(CLUSTALW_HELP) $(CLUSTALW_DOC) $(GENHELPTREE_DEPENDS)
	./genhelptree.sh $@ "$(subst .help,,$(notdir $@))" $(HEADER) $(CLUSTALW_HELP) $(CLUSTALW_DOC)

# ---------- AXML / FASTDNAML

AXML_HELP=$(GDE)/AxML/AxML.doc
FASTDNAML_DOC=$(GDE)/FASTDNAML/fastDNAml.doc

$(GENHELPDEST)/dnaml.help: $(AXML_HELP) $(FASTDNAML_DOC) $(GENHELPTREE_DEPENDS)
	./genhelptree.sh $@ "$(subst .help,,$(notdir $@))" $(HEADER) $(AXML_HELP) $(FASTDNAML_DOC)

# ---------- READSEQ

READSEQ=$(ARBHOME)/READSEQ
READSEQ_DOC_NAMES=Readme Formats Readseq.help
READSEQ_DOCS=$(addprefix $(READSEQ)/,$(READSEQ_DOC_NAMES))

$(GENHELPDEST)/readseq.help: $(READSEQ_DOCS) $(GENHELPTREE_DEPENDS)
	./genhelptree.sh $@ "$(subst .help,,$(notdir $@))" $(HEADER) $(READSEQ_DOCS)

# ---------- PHYLIP

PHYLIP_DISTANCE_HELP_NAMES=fitch kitsch neighbor dnadist protdist
PHYLIP_DISTANCE_HELPS=$(addsuffix .doc,$(addprefix $(GENDOCDEST)/,$(PHYLIP_DISTANCE_HELP_NAMES)))

$(GENHELPDEST)/phylip_distance.help: $(PHYLIP_DISTANCE_HELPS) $(GENHELPTREE_DEPENDS)
	./genhelptree.sh $@ "$(subst .help,,$(notdir $@))" $(HEADER) $(PHYLIP_DISTANCE_HELPS)

# ------------------------------------------------------------
# all help files in ./HELP_PLAIN are automatically found

$(GENHELPDEST)/%.help: $(HELP_PLAIN)/%.help $(HEADER) $(GENHELP_DEPENDS)
	./genhelp.sh $@ "$(subst .help,,$(notdir $@))" $(HEADER) $<

# all help files in ./HELP_DOC_GEN are automatically found

$(GENHELPDEST)/%.help: $(GENDOCDEST)/%.doc $(HEADER) $(GENHELP_DEPENDS)
	./genhelp.sh $@ "$(subst .help,,$(notdir $@))" $(HEADER) $<

# ------------------------------------------------------------
# rules to generate plain doc from provided html files

HELP_TREEPUZZLE=../GDE/TREEPUZZLE/doc
PHYLIP_MAIN=../GDE/PHYLIP
HELP_PHYLIP=$(PHYLIP_MAIN)/doc
HELP_PHYML=../GDE/PHYML

FORCED_DOC_NAMES=proml dnapars protpars phyml phylip
LYNX_PARA=-dump -nolist -display_charset=iso-8859-1

# - convert copyright symbol dumped by lynx
# - remove underscore lines dumped for "<HR/>" (causes paragraph-reflow to fail)
FILTER_LYNX_OUTPUT=$(SED) -e 's/©/(C)/' -e 's/^\s\s*__*$$//'

$(GENDOCDEST)/%.doc: $(HELP_PHYLIP)/%.html Makefile.helpfiles
	@(test -f $@ && chmod u+w $@) || true
	(echo "   [ generated from ../$< ]"; echo ""; lynx $(LYNX_PARA) $<) | $(FILTER_LYNX_OUTPUT) > $@
	@test -s $@ || (echo $@ not generated or empty && rm $@ && false)
	@chmod a-w $@

$(GENDOCDEST)/treepuzzle.doc: $(HELP_TREEPUZZLE)/manual.html Makefile.helpfiles
	@(test -f $@ && chmod u+w $@) || true
	(echo "   [ generated from ../$< ]"; echo ""; lynx $(LYNX_PARA) $<) | $(FILTER_LYNX_OUTPUT) > $@
	@test -s $@ || (echo $@ not generated or empty && rm $@ && false)
	@chmod a-w $@

$(GENDOCDEST)/phyml.doc: $(HELP_PHYML)/usersguide_phyliplike.html Makefile.helpfiles
	@(test -f $@ && chmod u+w $@) || true
	(echo "   [ generated from ../$< ]"; echo ""; lynx $(LYNX_PARA) $<) | $(FILTER_LYNX_OUTPUT) > $@
	@test -s $@ || (echo $@ not generated or empty && rm $@ && false)
	@chmod a-w $@

$(GENDOCDEST)/phylip.doc: $(PHYLIP_MAIN)/phylip.html Makefile.helpfiles
	@(test -f $@ && chmod u+w $@) || true
	(echo "   [ generated from ../$< ]"; echo ""; lynx $(LYNX_PARA) $<) | $(FILTER_LYNX_OUTPUT) > $@
	@test -s $@ || (echo $@ not generated or empty && rm $@ && false)
	@chmod a-w $@

FORCED_DOCS=$(addsuffix .doc,$(addprefix $(GENDOCDEST)/,$(FORCED_DOC_NAMES)))
forcedoc: $(FORCED_DOCS) Makefile

# ------------------------------------------------------------
# default rule to raise error if no rule is given to generate a helpfile.
# dont warn if there's a help file in HELP_WRITTEN
# (files there are processed by ../HELP_SOURCE/genhelp/Makefile )
#
# if you encounter an error, please read .@HOWTO_ADD_GDE_HELP

$(GENHELPDEST)/%.help:
	@( test -f $(HELP_WRITTEN)/$(notdir $@) ) \
	|| \
	( \
		echo "Makefile.helpfiles:22: Error: No rule to make $(notdir $@) (to which is referred-to inside GDE menus, see hits below)" ; \
		grep -n $(notdir $@) MENUS/*.menu ; \
		false )

clean:
	rm -rf $(GENHELPDEST) $(GENDOCDEST)