# =============================================================== #
#                                                                 #
#   File      : Makefile                                          #
#   Time-stamp: <Tue Jul/08/2008 12:39 MET Coder@ReallySoft.de>   #
#                                                                 #
#   Institute of Microbiology (Technical University Munich)       #
#   http://www.arb-home.de/                                       #
#                                                                 #
# =============================================================== #

# -----------------------------------------------------
# The ARB Makefile is aware of the following defines:
#
# BUILDHOST_64=0/1      1=>compile on 64 bit platform (defaults to ARB_64)
# DEVELOPER=name	special compilation (values: ANY,RELEASE,your name)
# OPENGL=0/1            whether OPENGL is available
#
# -----------------------------------------------------
# ARB Makefile and ARB source code are aware of the following defines:
#
# $(MACH)               name of the machine (LINUX,SUN4,SUN5,HP,SGI or DIGITAL; see config.makefile)
# DEBUG                 compiles the DEBUG sections
# DEBUG_GRAPHICS        all X-graphics are flushed immediately (for debugging)
# ARB_64=0/1            1=>compile 64 bit version
#
# -----------------------------------------------------
# The ARB source code is aware of the following defines:
#
# HAVE_BOOL             should be true if compiler supports the type 'bool'
# NO_REGEXPR            for machines w/o regular expression library
# NDEBUG                doesnt compile the DEBUG sections
# DEVEL_$(DEVELOPER)    developer-dependent flag (enables you to have private sections in code)
#                       DEVELOPER='ANY' (default setting) will be ignored
#                       configurable in config.makefile
#
# -----------------------------------------------------
# Read configuration 
include config.makefile

FORCEMASK = umask 002

# ---------------------- [unconditionally used options]

GCC:=gcc
GPP:=g++ -fmessage-length=0
CPPreal:=cpp

ifdef DARWIN
	GCC:=gcc2
	GPP:=g++2
endif

# ---------------------- compiler version detection

# supported compiler versions:

ALLOWED_GCC_3xx_VERSIONS=3.2 3.3.1 3.3.3 3.3.4 3.3.5 3.3.6 3.4.0 3.4.2 3.4.3
ALLOWED_GCC_4xx_VERSIONS=4.0.0 4.0.2 4.0.3 4.1.1 4.1.2 4.1.3 4.2.0 4.2.1 4.2.3 4.3.1
ALLOWED_GCC_VERSIONS=$(ALLOWED_GCC_3xx_VERSIONS) $(ALLOWED_GCC_4xx_VERSIONS)

GCC_VERSION_FOUND=$(shell $(GCC) -dumpversion)
GCC_VERSION_ALLOWED=$(strip $(subst ___,,$(foreach version,$(ALLOWED_GCC_VERSIONS),$(findstring ___$(version)___,___$(GCC_VERSION_FOUND)___))))

USING_GCC_3XX=$(strip $(foreach version,$(ALLOWED_GCC_3xx_VERSIONS),$(findstring $(version),$(GCC_VERSION_ALLOWED))))
USING_GCC_4XX=$(strip $(foreach version,$(ALLOWED_GCC_4xx_VERSIONS),$(findstring $(version),$(GCC_VERSION_ALLOWED))))

#----------------------

shared_cflags :=# flags for shared lib compilation

ifeq ($(DEBUG),0)
	dflags := -DNDEBUG# defines
	cflags := -O4# compiler flags (C and C++)
	lflags := -O99 --strip-all# linker flags
endif

ifeq ($(DEBUG),1)
	dflags := -DDEBUG
	cflags := -O0 -g -g3 -ggdb -ggdb3
	lflags := -g

	POST_COMPILE := 2>&1 | $(ARBHOME)/SOURCE_TOOLS/postcompile.pl

# Enable several warnings
	extended_warnings     := -Wwrite-strings -Wunused -Wno-aggregate-return -Wshadow
	extended_cpp_warnings := -Wnon-virtual-dtor -Wreorder -Wpointer-arith 
 ifneq ('$(USING_GCC_3XX)','')
		extended_cpp_warnings += -Wdisabled-optimization -Wmissing-format-attribute
		extended_cpp_warnings += -Wmissing-noreturn # -Wfloat-equal 
 endif
 ifneq ('$(USING_GCC_4XX)','')
# 		extended_cpp_warnings += -Wwhatever
 endif

 ifeq ($(DEBUG_GRAPHICS),1)
		dflags += -DDEBUG_GRAPHICS
 endif
endif

#---------------------- developer 

ifneq ($(DEVELOPER),ANY) # ANY=default setting (skip all developer specific code)
ifdef dflags
	dflags += -DDEVEL_$(DEVELOPER)# activate developer/release specific code
endif
endif

#---------------------- 32 or 64 bit

ifndef ARB_64
	ARB_64=0#default to 32bit
endif
ifndef BUILDHOST_64
	BUILDHOST_64:=$(ARB_64)# assume build host is same as version (see config.makefile)
endif

ifeq ($(ARB_64),1)
	dflags += -DARB_64 #-fPIC 
	lflags +=
	shared_cflags += -fPIC

	ifeq ($(BUILDHOST_64),1)
#		build 64-bit ARB version on 64-bit host
		CROSS_LIB:=# empty = autodetect below
	else
#		build 64-bit ARB version on 32-bit host
		CROSS_LIB:=/lib64
		cflags += -m64
		lflags += -m64 -m elf_x86_64
	endif
else
	ifeq ($(BUILDHOST_64),1)
#		build 32-bit ARB version on 64-bit host
		CROSS_LIB:=# empty = autodetect below
		cflags += -m32
		lflags += -m32 -m elf_i386 
	else
#		build 32-bit ARB version on 32-bit host
		CROSS_LIB:=/lib
	endif
endif

ifeq ('$(CROSS_LIB)','')
# autodetect libdir
	ifeq ($(ARB_64),1)
		CROSS_LIB:=`(test -d /lib64 && echo lib64) || echo lib`
	else
		CROSS_LIB:=`(test -d /lib32 && echo lib32) || echo lib`
	endif
endif

#---------------------- other flags

dflags += -D$(MACH) # define machine
dflags += -DHAVE_BOOL # all have bool [@@@ TODO: remove dependent code from ARB source]
dflags += -DNO_REGEXPR # for machines w/o regular expression library

ifdef DARWIN
	cflags += -no-cpp-precomp 
	shared_cflags += -fno-common
	dflags +=
	lflags += $(LDFLAGS) -force_flat_namespace -Wl,-stack_size -Wl,10000000 -Wl,-stack_addr -Wl,c0000000
endif

cflags += -pipe

#---------------------- X11 location

X11R6=1# we use X11R6

ifeq ($(X11R6),1)
	XHOME:=/usr/X11R6
	XINCLUDES:=-I$(XHOME)/include
else
	XHOME:=/usr/X11
	XINCLUDES:=-I$(XHOME)/include -I$(XHOME)/include/Xm
endif

XLIBS:=-L$(XHOME)/$(CROSS_LIB) -lXm -lXpm -lXp -lXt -lXext -lX11

#---------------------- open GL

ifeq ($(OPENGL),1) 
	cflags += -DARB_OPENGL # activate OPENGL code
endif

ifeq ($(OPENGL),1)
GL:=gl # this is the name of the OPENGL base target
ifdef DEBIAN
GL_LIB:=-lGL -lpthread
else
GL_LIB:=-lGL
endif
GL_PNGLIBS:= -L$(ARBHOME)/GL/glpng -lglpng_arb -lpng
GLLIBS:=-lGLEW -lGLw -lglut $(GL_PNGLIBS)
endif

XLIBS += $(GL_LIB)

#---------------------- basic libs:

SYSLIBS := -lm
ifdef DARWIN
SYSLIBS += -lstdc++
endif

ifdef SEER
    SEERLIB = SEER/SEER.a # @@@ not compiled for very long time. Dunno what SEER is.. 
else
    SEERLIB =
endif

# ------------------------------------------------------------------------- 
#	Don't put any machine/version/etc conditionals below!
#	(instead define variables above)
# -------------------------------------------------------------------------

cflags += -W -Wall $(dflags) $(extended_warnings)
cppflags := $(extended_cpp_warnings)

# compiler settings:

ACC := $(GCC)# compile C
CPP := $(GPP) $(cppflags)# compile C++
ACCLIB := $(ACC) $(shared_cflags)# compile C (shared libs)
CCPLIB := $(CPP) $(shared_cflags)# compile C++ (shared libs)

PP := $(CPPreal)# preprocessor

SHARED_LIB_SUFFIX = so# shared lib suffix (can be set to 'a' to link statically)

LINK_STATIC_LIB := ld $(lflags) -r -o# link static lib
LINK_SHARED_LIB := $(GPP) $(lflags) -shared -o# link shared lib
LINK_EXECUTABLE := $(GPP) $(lflags) -o# link executable (c++)

# other used tools

CTAGS := etags
XMKMF := /usr/bin/X11/xmkmf
MAKEDEPEND = $(FORCEMASK);makedepend

SEP=--------------------------------------------------------------------------------

# delete variables unused below

lflags:=

# ------------------------- 
#     Main arb targets:     
# ------------------------- 

first_target:
		$(MAKE) checks
		@echo $(SEP)
		@echo 'Main targets:'
		@echo ''
		@echo ' all         - Compile ARB + TOOLs + and copy shared libs + link foreign software'
		@echo '               (That is most likely the target you want)'
		@echo ''
		@echo ' clean       - remove generated files ("SUBDIR/SUBDIR.clean" to clean only SUBDIR)'
		@echo ' rebuild     - clean + all'
		@echo ' relink      - remove all binaries and relink them from objects'
		@echo ''
		@echo 'Some often used sub targets (make all makes them all):'
		@echo ''
		@echo ' arb         - Just compile ARB (but none of the integrated tools)'
		@echo ' menus       - create GDEHELP/ARB_GDEmenus from GDEHELP/ARB_GDEmenus.source'
		@echo ' perl        - Compile the PERL XSUBS into lib/ARB.so  and create links in lib to perl'
		@echo ' binlink     - Create all links in the bin directory'
		@echo ''
		@echo 'Development targets:'
		@echo ''
		@echo ' depends      - create or update dependencies ("SUBDIR/SUBDIR.depends" to update only SUBDIR)'
		@echo ' proto        - create or update prototypes ("SUBDIR/SUBDIR.proto" to update only SUBDIR)'
		@echo ' tags         - create tags for xemacs'
		@echo ' rmbak        - remove all "*%" and cores'
		@echo ' show         - show available shortcuts (AKA subtargets)'
		@echo ' up           - shortcut for depends+proto+tags'
		@echo ''
		@echo 'Internal maintainance:'
		@echo ''
		@echo ' release     - make tarfile + make save ("release_quick" to skip rebuild)'
		@echo ' tarfile     - make rebuild and create arb version tarfile ("tarfile_quick" to skip rebuild)'
#		@echo ' tarale      - compress emacs and ale lisp files int arb_ale.tar.gz'
		@echo ' save        - save all basic ARB sources into arbsrc_DATE'
#		@echo ' savedepot   - save all extended ARB source (DEPOT2 subdir) into arbdepot_DATE.cpio.gz'
		@echo ' rtc_patch   - create LIBLINK/libRTC8M.so (SOLARIS ONLY)'
		@echo ' source_doc  - create doxygen documentation'
		@echo ''
		@echo $(SEP)
		@echo ''


# auto-generate config.makefile:

CONFIG_MAKEFILE_FOUND=$(wildcard config.makefile)

config.makefile : config.makefile.template
		@echo --------------------------------------------------------------------------------
ifeq ($(strip $(CONFIG_MAKEFILE_FOUND)),)
		@cp $< $@
		@echo '$@:1: has been generated.'
		@echo 'Please edit $@ to configure your system!'
		@echo '(not needed for linux systems - simply type "make all")'
else
		@echo '$<:1: is more recent than'
		@echo '$@:1:'
		@ls -al config.makefile*
		@echo "you may either:"
		@echo "- ignore it and touch $@"
		@echo "- merge difference between $@ and $< (recommended)"
		@echo "- remove $@, run make again and edit the freshly generated $@"
endif
		@echo --------------------------------------------------------------------------------
		@false

# check if everything is configured correctly

check_DEVELOPER:
ifndef DEVELOPER
		@echo 'config.makefile:1: DEVELOPER not defined'
		@false
endif

check_DEBUG:
ifndef dflags
		@echo 'config.makefile:1: DEBUG has to be defined. Valid values are 0 and 1'
		@false
endif

check_ARB_64:
ifndef ARB_64
		@echo 'config.makefile:1: ARB_64 has to be defined. Valid values are 0 and 1'
		@false
endif

# ---------------------------------------- check gcc version

check_same_GCC_VERSION:
		$(ARBHOME)/SOURCE_TOOLS/check_same_gcc_version.pl $(GCC_VERSION_ALLOWED)

check_GCC_VERSION:
		@echo 'GCC version check:'
		@echo "  - Your version is '$(GCC_VERSION_FOUND)'"
ifeq ('$(GCC_VERSION_ALLOWED)', '')
		@echo '  - This version is not in the list of supported gcc-versions:'
		@$(foreach version,$(ALLOWED_GCC_VERSIONS),echo '    * $(version)';)
		@echo '  - You may either ..'
		@echo '    - add your version to ALLOWED_GCC_VERSIONS in the Makefile and try it out or'
		@echo '    - switch to one of the allowed versions (see arb_README_gcc.txt for installing'
		@echo '      a different version of gcc)'
		@echo ''
		@/bin/false
else
		@echo "  - Supported gcc version '$(GCC_VERSION_ALLOWED)' detected - fine!"
		@echo ''
		$(MAKE) check_same_GCC_VERSION

endif

GCC_WITH_VTABLE_AFTER_CLASS=$(ALLOWED_GCC_295_VERSIONS)
HAVE_GCC_WITH_VTABLE_AFTER_CLASS=$(strip $(foreach version,$(GCC_WITH_VTABLE_AFTER_CLASS),$(findstring $(version),$(GCC_VERSION_ALLOWED))))

# depending on the version of gcc the location of the vtable pointer differs.
ifeq ('$(HAVE_GCC_WITH_VTABLE_AFTER_CLASS)', '')
VTABLE_INFRONTOF_CLASS=1
else
VTABLE_INFRONTOF_CLASS=0
endif

#---------------------- check ARBHOME

# use arb_INSTALL.txt to determine whether ARBHOME points to correct directory
ARB_INSTALL_FOUND=$(wildcard $(ARBHOME)/arb_INSTALL.txt)

check_ARBHOME:
ifeq ($(strip $(ARB_INSTALL_FOUND)),)
		@echo ------------------------------------------------------------
		@echo "ARBHOME is set to '$(ARBHOME)'"
		@echo "The environment variable ARBHOME has to point to the top arb source directory."
		@echo "If you use bash enter:"
		@echo "          export ARBHOME='`pwd`'"
		@echo ------------------------------------------------------------
		@false
endif

ARB_PATH_SET=$(findstring $(ARBHOME)/bin,$(PATH))

check_PATH: check_ARBHOME
ifeq ($(strip $(ARB_PATH_SET)),)
		@echo ------------------------------------------------------------
		@echo "The environment variable PATH has to contain $(ARBHOME)/bin"
		@echo "If you use bash enter:"
		@echo '			export PATH=$$ARBHOME/bin:$$PATH'
		@echo ------------------------------------------------------------
		@false
endif

check_ENVIRONMENT : check_PATH

check_tabs: check_setup
ifeq ($(DEBUG),1)
	@SOURCE_TOOLS/tabBrake.pl
endif

force_tab_check:
	touch -t 198001010000 SOURCE_TOOLS/tabBrake.stamp
	$(MAKE) check_tabs


# ---------------------

check_setup: check_ENVIRONMENT check_DEBUG check_ARB_64 check_DEVELOPER check_GCC_VERSION 
		@echo Your setup seems to be ok.

checks: check_setup check_tabs


# end test section ------------------------------

ARBDB_LIB=-lARBDB
ARBDBPP_LIB=-lARBDBPP

LIBS = $(ARBDB_LIB) $(SYSLIBS)
GUI_LIBS = $(LIBS) -lAW -lAWT $(RTC) $(XLIBS)

LIBPATH = -L$(ARBHOME)/LIBLINK

DEST_LIB = lib
DEST_BIN = bin

AINCLUDES = 	-I. -I$(ARBHOME)/INCLUDE $(XINCLUDES)
CPPINCLUDES =	-I. -I$(ARBHOME)/INCLUDE $(XINCLUDES)
MAKEDEPENDFLAGS = -- $(cflags) -DARB_OPENGL -I. -Y$(ARBHOME)/INCLUDE --

ifeq ($(VTABLE_INFRONTOF_CLASS),1)
# Some code in ARB depends on the location of the vtable pointer
# (it does a cast from class AP_tree to struct GBT_TREE). In order to
# work around that hack properly, we define FAKE_VTAB_PTR
# if the vtable is located at the beginning of class.
# We are really sorry for that hack.
cflags:=$(cflags) -DFAKE_VTAB_PTR=char
endif

#*****		List of all Directories

#			ALEIO/ALEIO.a \

ARCHS = \
			AISC/dummy.a \
			AISC_MKPTPS/dummy.a \
			ALIV3/ALIV3.a \
			ARBDB/libARBDB.a \
			ARBDB2/libARBDB.a \
			ARBDBPP/libARBDBPP.a \
			ARBDBS/libARBDB.a \
			ARBDB_COMPRESS/ARBDB_COMPRESS.a \
			ARB_GDE/ARB_GDE.a \
			AWDEMO/AWDEMO.a \
			AWT/libAWT.a \
			AWTC/AWTC.a \
			AWTI/AWTI.a \
			CAT/CAT.a \
			CONSENSUS_TREE/CONSENSUS_TREE.a \
			CONVERTALN/CONVERTALN.a \
			DBSERVER/DBSERVER.a \
			DIST/DIST.a \
			EDIT/EDIT.a \
			EDIT4/EDIT4.a \
			EISPACK/EISPACK.a \
			GDE/GDE.a \
			GENOM/GENOM.a \
			GENOM_IMPORT/GENOM_IMPORT.a \
			GL/GL.a \
			ISLAND_HOPPING/ISLAND_HOPPING.a \
			MERGE/MERGE.a \
			MULTI_PROBE/MULTI_PROBE.a \
			NALIGNER/NALIGNER.a \
			NAMES/NAMES.a \
			NAMES_COM/server.a \
			NTREE/NTREE.a \
			PARSIMONY/PARSIMONY.a \
			PGT/PGT.a \
			PHYLO/PHYLO.a \
			PRIMER_DESIGN/PRIMER_DESIGN.a \
			PROBE/PROBE.a \
			PROBE_COM/server.a \
			PROBE_DESIGN/PROBE_DESIGN.a \
			PROBE_SERVER/PROBE_SERVER.a \
			PROBE_SET/PROBE_SET.a \
			READSEQ/READSEQ.a \
			RNA3D/RNA3D.a \
			SECEDIT/SECEDIT.a \
			SEER/SEER.a \
			SEQ_QUALITY/SEQ_QUALITY.a \
			SERVERCNTRL/SERVERCNTRL.a \
			SL/SL.a \
			STAT/STAT.a \
			TEST/TEST.a \
			TOOLS/TOOLS.a \
			TREEGEN/TREEGEN.a \
			TRS/TRS.a \
			WETC/WETC.a \
			WINDOW/libAW.a \
			XML/XML.a \

#ARCHS_CLIENTACC = PROBE_COM/client.a
#ARCHS_CLIENTCPP = NAMES_COM/client.a
ARCHS_CLIENT_PROBE = PROBE_COM/client.a
ARCHS_CLIENT_NAMES = NAMES_COM/client.a
#ARCHS_CLIENT = $(ARCHS_CLIENT_NAMES)
ARCHS_MAKEBIN = AISC_MKPTPS/dummy.a AISC/dummy.a

ARCHS_COMMUNICATION =	NAMES_COM/server.a \
			PROBE_COM/server.a

# communication libs need aisc and aisc_mkpts:
$(ARCHS_COMMUNICATION:.a=.dummy) : $(ARCHS_MAKEBIN:.a=.dummy)

#***************************************************************************************
#		Individual Programs Section
#***************************************************************************************

#***********************************	arb_ntree **************************************
NTREE = bin/arb_ntree
ARCHS_NTREE = \
		$(ARCHS_CLIENT_PROBE) \
		$(SEERLIB) \
		ARB_GDE/ARB_GDE.a \
		AWTC/AWTC.a \
		AWTI/AWTI.a \
		CAT/CAT.a \
		GENOM/GENOM.a \
		GENOM_IMPORT/GENOM_IMPORT.a \
		ISLAND_HOPPING/ISLAND_HOPPING.a \
		MERGE/MERGE.a \
		MULTI_PROBE/MULTI_PROBE.a \
		NTREE/NTREE.a \
		PRIMER_DESIGN/PRIMER_DESIGN.a \
		PROBE_DESIGN/PROBE_DESIGN.a \
		SEQ_QUALITY/SEQ_QUALITY.a \
		SERVERCNTRL/SERVERCNTRL.a \
		SL/AW_NAME/AW_NAME.a \
		SL/HELIX/HELIX.a \
		SL/DB_SCANNER/DB_SCANNER.a \
		SL/FILE_BUFFER/FILE_BUFFER.a \
		STAT/STAT.a \
		XML/XML.a \

$(NTREE): $(ARCHS_NTREE:.a=.dummy) NAMES_COM/server.dummy shared_libs
	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_NTREE) $(GUI_LIBS) || ( \
		echo Link $@ ; \
		echo "$(LINK_EXECUTABLE) $@ $(LIBPATH) $(ARCHS_NTREE) $(GUI_LIBS)" ; \
		$(LINK_EXECUTABLE) $@ $(LIBPATH) $(ARCHS_NTREE) $(GUI_LIBS)  \
		)

#*********************************** arb_rna3d **************************************
RNA3D = bin/arb_rna3d
ARCHS_RNA3D = \
		RNA3D/RNA3D.a \

$(RNA3D): $(ARCHS_RNA3D:.a=.dummy) shared_libs
	@echo $@ currently does not work as standalone application
	false

#***********************************	arb_edit **************************************
EDIT = bin/arb_edit
ARCHS_EDIT = \
		NAMES_COM/client.a \
		SERVERCNTRL/SERVERCNTRL.a \
		EDIT/EDIT.a \
		ARB_GDE/ARB_GDE.a \
		STAT/STAT.a \
		XML/XML.a \
		SL/HELIX/HELIX.a \
		SL/AW_HELIX/AW_HELIX.a \
		SL/AW_NAME/AW_NAME.a \

$(EDIT): $(ARCHS_EDIT:.a=.dummy) shared_libs
	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_EDIT) $(GUI_LIBS) || ( \
		echo Link $@ ; \
		echo "$(LINK_EXECUTABLE) $@ $(LIBPATH) $(ARCHS_EDIT) -lARBDBPP $(GUI_LIBS)" ; \
		$(LINK_EXECUTABLE) $@ $(LIBPATH) $(ARCHS_EDIT) -lARBDBPP $(GUI_LIBS) ; \
		)

#***********************************	arb_edit4 **************************************
EDIT4 = bin/arb_edit4

ARCHS_EDIT4 := \
		NAMES_COM/client.a \
		AWTC/AWTC.a \
		EDIT4/EDIT4.a \
		SECEDIT/SECEDIT.a \
		SERVERCNTRL/SERVERCNTRL.a \
		STAT/STAT.a \
		ARB_GDE/ARB_GDE.a \
		ISLAND_HOPPING/ISLAND_HOPPING.a \
		SL/HELIX/HELIX.a \
		SL/AW_HELIX/AW_HELIX.a \
		SL/AW_NAME/AW_NAME.a \
		SL/FILE_BUFFER/FILE_BUFFER.a \
		XML/XML.a \

ifeq ($(OPENGL),1)
ARCHS_EDIT4 += RNA3D/RNA3D.a
endif
LIBS_EDIT4 := $(GLLIBS)

$(EDIT4): $(ARCHS_EDIT4:.a=.dummy) shared_libs
	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_EDIT4) $(GUI_LIBS) || ( \
		echo Link $@ ; \
		echo "$(LINK_EXECUTABLE) $@ $(LIBPATH) $(ARCHS_EDIT4) $(GUI_LIBS) $(LIBS_EDIT4)" ; \
		$(LINK_EXECUTABLE) $@ $(LIBPATH) $(ARCHS_EDIT4) $(GUI_LIBS) $(LIBS_EDIT4) \
		)

#***********************************	arb_pgt **************************************

PGT = bin/arb_pgt
ARCHS_PGT = \
		PGT/PGT.a \

PGT_SYS_LIBS=$(XLIBS) -ltiff $(LIBS)

$(PGT) : $(ARCHS_PGT:.a=.dummy) shared_libs
	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_PGT) || ( \
		echo Link $@ ; \
		echo "$(LINK_EXECUTABLE) $@ $(LIBPATH) $(ARCHS_PGT) $(PGT_SYS_LIBS)"; \
		$(LINK_EXECUTABLE) $@ $(LIBPATH) $(ARCHS_PGT) $(PGT_SYS_LIBS); \
		)


#***********************************	arb_wetc **************************************
WETC = bin/arb_wetc
ARCHS_WETC = \
		WETC/WETC.a \
		SL/HELIX/HELIX.a \
		XML/XML.a \

$(WETC): $(ARCHS_WETC:.a=.dummy) shared_libs
	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_WETC) $(GUI_LIBS) || ( \
		echo Link $@ ; \
		echo "$(LINK_EXECUTABLE) $@ $(LIBPATH) $(ARCHS_WETC) $(GUI_LIBS)" ; \
		$(LINK_EXECUTABLE) $@ $(LIBPATH) $(ARCHS_WETC) $(GUI_LIBS) ; \
		)

#***********************************	arb_dist **************************************
DIST = bin/arb_dist
ARCHS_DIST = \
		$(ARCHS_CLIENT_PROBE) \
		DIST/DIST.a \
		SERVERCNTRL/SERVERCNTRL.a \
		CONSENSUS_TREE/CONSENSUS_TREE.a \
		EISPACK/EISPACK.a \
		SL/HELIX/HELIX.a \
		XML/XML.a \

$(DIST): $(ARCHS_DIST:.a=.dummy) shared_libs
	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_DIST) $(GUI_LIBS) || ( \
		echo Link $@ ; \
		echo "$(LINK_EXECUTABLE) $@ $(LIBPATH) $(ARCHS_DIST) $(GUI_LIBS)" ; \
		$(LINK_EXECUTABLE) $@ $(LIBPATH) $(ARCHS_DIST) $(GUI_LIBS) ; \
		)

#***********************************	arb_pars **************************************
PARSIMONY = bin/arb_pars
ARCHS_PARSIMONY = \
		NAMES_COM/client.a \
		SERVERCNTRL/SERVERCNTRL.a \
		PARSIMONY/PARSIMONY.a \
		SL/HELIX/HELIX.a \
		SL/AW_NAME/AW_NAME.a \
		XML/XML.a \

$(PARSIMONY): $(ARCHS_PARSIMONY:.a=.dummy) shared_libs
	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_PARSIMONY) $(GUI_LIBS) || ( \
		echo Link $@ ; \
		echo "$(LINK_EXECUTABLE) $@ $(LIBPATH) $(ARCHS_PARSIMONY) $(GUI_LIBS)" ; \
		$(LINK_EXECUTABLE) $@ $(LIBPATH) $(ARCHS_PARSIMONY) $(GUI_LIBS) ; \
		)

#*********************************** arb_treegen **************************************
TREEGEN = bin/arb_treegen
ARCHS_TREEGEN =	\
		TREEGEN/TREEGEN.a \

$(TREEGEN) :  $(ARCHS_TREEGEN:.a=.dummy)
	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_TREEGEN) || ( \
		echo Link $@ ; \
		echo "$(LINK_EXECUTABLE) $@ $(LIBPATH) $(ARCHS_TREEGEN)" ; \
		$(LINK_EXECUTABLE) $@ $(LIBPATH) $(ARCHS_TREEGEN) ; \
		)

#***********************************	arb_naligner **************************************
NALIGNER = bin/arb_naligner
ARCHS_NALIGNER = \
		$(ARCHS_CLIENT_PROBE) \
		NALIGNER/NALIGNER.a \
		SERVERCNTRL/SERVERCNTRL.a \
		SL/HELIX/HELIX.a \

$(NALIGNER): $(ARCHS_NALIGNER:.a=.dummy) shared_libs
	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_NALIGNER) || ( \
		echo Link $@ ; \
		echo "$(LINK_EXECUTABLE) $@ $(LIBPATH) $(ARCHS_NALIGNER) $(LIBS)" ; \
		$(LINK_EXECUTABLE) $@ $(LIBPATH) $(ARCHS_NALIGNER) $(LIBS) \
		)

#***********************************	arb_secedit **************************************
SECEDIT = bin/arb_secedit
ARCHS_SECEDIT = \
		SECEDIT/SECEDIT.a \
		XML/XML.a \

$(SECEDIT):	$(ARCHS_SECEDIT:.a=.dummy) shared_libs
	@echo $@ currently does not work as standalone application
	false


#***********************************	arb_phylo **************************************
PHYLO = bin/arb_phylo
ARCHS_PHYLO = \
		PHYLO/PHYLO.a \
		SL/HELIX/HELIX.a \
		XML/XML.a \

$(PHYLO): $(ARCHS_PHYLO:.a=.dummy) shared_libs
	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_PHYLO) $(GUI_LIBS) || ( \
		echo Link $@ ; \
		echo "$(LINK_EXECUTABLE) $@ $(LIBPATH) $(ARCHS_PHYLO) $(GUI_LIBS)" ; \
		$(LINK_EXECUTABLE) $@ $(LIBPATH) $(ARCHS_PHYLO) $(GUI_LIBS) ; \
		)

#***************************************************************************************
#					SERVER SECTION
#***************************************************************************************

#***********************************	arb_db_server **************************************
DBSERVER = bin/arb_db_server
ARCHS_DBSERVER = \
		DBSERVER/DBSERVER.a \
		SERVERCNTRL/SERVERCNTRL.a \

$(DBSERVER): $(ARCHS_DBSERVER:.a=.dummy) shared_libs
	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_DBSERVER) $(ARBDB_LIB) || ( \
		echo Link $@ ; \
		echo "$(LINK_EXECUTABLE) $@ $(LIBPATH) $(ARCHS_DBSERVER) $(ARBDB_LIB) $(SYSLIBS)" ; \
		$(LINK_EXECUTABLE) $@ $(LIBPATH) $(ARCHS_DBSERVER) $(ARBDB_LIB) $(SYSLIBS) ; \
		)

#***********************************	arb_pt_server **************************************
PROBE = bin/arb_pt_server
ARCHS_PROBE = \
		PROBE_COM/server.a \
		PROBE/PROBE.a \
		SERVERCNTRL/SERVERCNTRL.a \
		SL/HELIX/HELIX.a \

$(PROBE): $(ARCHS_PROBE:.a=.dummy) shared_libs
	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_PROBE) $(ARBDB_LIB) $(ARCHS_CLIENT_PROBE) || ( \
		echo Link $@ ; \
		echo "$(LINK_EXECUTABLE) $@ $(LIBPATH) $(ARCHS_PROBE) $(ARBDB_LIB) $(ARCHS_CLIENT_PROBE) $(SYSLIBS)" ; \
		$(LINK_EXECUTABLE) $@ $(LIBPATH) $(ARCHS_PROBE) $(ARBDB_LIB) $(ARCHS_CLIENT_PROBE) $(SYSLIBS) ; \
		)

#***********************************	arb_name_server **************************************
NAMES = bin/arb_name_server
ARCHS_NAMES = \
		NAMES_COM/server.a \
		NAMES/NAMES.a \
		SERVERCNTRL/SERVERCNTRL.a \

$(NAMES): $(ARCHS_NAMES:.a=.dummy) shared_libs
	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_NAMES) $(ARBDB_LIB) $(ARCHS_CLIENT_NAMES) || ( \
		echo Link $@ ; \
		echo "$(LINK_EXECUTABLE) $@ $(LIBPATH) $(ARCHS_NAMES) $(ARBDB_LIB) $(ARCHS_CLIENT_NAMES) $(SYSLIBS)" ; \
		$(LINK_EXECUTABLE) $@ $(LIBPATH) $(ARCHS_NAMES) $(ARBDB_LIB) $(ARCHS_CLIENT_NAMES) $(SYSLIBS) ; \
		)

#***********************************	TEST SECTION  **************************************
AWDEMO = tb/awdemo
ARCHS_AWDEMO = \
		AWDEMO/AWDEMO.a \

$(AWDEMO): $(ARCHS_AWDEMO:.a=.dummy) shared_libs
	@echo $(SEP) Link $@
	$(LINK_EXECUTABLE) $@ $(ARCHS_AWDEMO) $(LIBS)

TEST = tb/dbtest
ARCHS_TEST = \
		TEST/TEST.a \
		XML/XML.a \

$(TEST): $(ARCHS_TEST:.a=.dummy) shared_libs
	@echo $(SEP) Link $@
	$(LINK_EXECUTABLE) $@ $(LIBPATH) $(ARCHS_TEST)  -lAWT $(LIBS)

ALIV3 = bin/aliv3
ARCHS_ALIV3 = \
		ALIV3/ALIV3.a \
		SL/HELIX/HELIX.a \

$(ALIV3): $(ARCHS_ALIV3:.a=.dummy) shared_libs
	@echo $(SEP) Link $@
	$(LINK_EXECUTABLE) $@ $(LIBPATH) $(ARCHS_ALIV3) $(ARBDB_LIB) $(SYSLIBS) $(CCPLIBS)


ACORR = tb/acorr
ARCHS_ACORR = \
		DIST/DIST.a \
		SERVERCNTRL/SERVERCNTRL.a \
		FINDCORRASC/FINDCORRASC.a \
		FINDCORRMATH/FINDCORRMATH.a \
		FINDCORRWIN/FINDCORRWIN.a \
		XML/XML.a \

$(ACORR): $(ARCHS_ACORR:.a=.dummy) shared_libs
	@echo $(SEP) Link $@
	$(LINK_EXECUTABLE) $@ $(LIBPATH) $(ARCHS_ACORR) -lAWT $(ARBDBPP_LIB) $(LIBS)


ARBDB_COMPRESS = tb/arbdb_compress
ARCHS_ARBDB_COMPRESS = \
		ARBDB_COMPRESS/ARBDB_COMPRESS.a \

$(ARBDB_COMPRESS): $(ARCHS_ARBDB_COMPRESS:.a=.dummy) shared_libs
	@echo $(SEP) Link $@
	$(LINK_EXECUTABLE) $@ $(LIBPATH) $(ARCHS_ARBDB_COMPRESS) $(ARBDB_LIB)

#***********************************	OTHER EXECUTABLES   ********************************************


#***********************************	SHARED LIBRARIES SECTION  **************************************

shared_libs: dball aw awt
		@echo -------------------- Updating shared libraries
		$(MAKE) libs

libs:	lib/libARBDB.$(SHARED_LIB_SUFFIX) \
	lib/libARBDBPP.$(SHARED_LIB_SUFFIX) \
	lib/libARBDO.$(SHARED_LIB_SUFFIX) \
	lib/libAW.$(SHARED_LIB_SUFFIX) \
	lib/libAWT.$(SHARED_LIB_SUFFIX)

lib/lib%.$(SHARED_LIB_SUFFIX): LIBLINK/lib%.$(SHARED_LIB_SUFFIX)
	cp $< $@

# lib/$(MOTIF_LIBNAME):  $(MOTIF_LIBPATH)
# 	cp $< $@

#***************************************************************************************
#			Rekursiv calls to submakefiles
#***************************************************************************************

%.depends:
	@cp -p $(@D)/Makefile $(@D)/Makefile.old # save old Makefile
	@$(MAKE) -C $(@D) -r \
		"AUTODEPENDS=1" \
		"LD_LIBRARY_PATH  = ${LD_LIBRARY_PATH}" \
		"MAKEDEPENDFLAGS = $(MAKEDEPENDFLAGS)" \
		"MAKEDEPEND=$(MAKEDEPEND)" \
		"ARBHOME=$(ARBHOME)" \
		depends;
	@grep "^# DO NOT DELETE" $(@D)/Makefile >/dev/null
	@cat $(@D)/Makefile \
		| SOURCE_TOOLS/fix_depends.pl \
		>$(@D)/Makefile.2
	@mv $(@D)/Makefile.old $(@D)/Makefile # restore old Makefile
	@$(ARBHOME)/SOURCE_TOOLS/mv_if_diff $(@D)/Makefile.2 $(@D)/Makefile # update Makefile if changed

%.proto:
	@$(MAKE) -C $(@D) \
		"AUTODEPENDS=0" \
		proto

%.clean:
	@$(MAKE) -C $(@D) \
		"AUTODEPENDS=0" \
		"MACH=$(MACH)" \
		"OPENGL=$(OPENGL)" \
		clean

# rule to generate main target (normally a library):
%.dummy:
	@( export ID=$$$$; \
	(( \
	    echo "$(SEP) Make everything in $(@D)"; \
	    $(MAKE) -C $(@D) -r \
		"ACC = $(ACC)" \
		"ACCLIB = $(ACCLIB)" \
		"AINCLUDES = $(AINCLUDES)" \
		"ARBHOME = $(ARBHOME)" \
		"ARLIB = $(ARLIB)" \
		"AUTODEPENDS=1" \
		"CCPLIB = $(CCPLIB)" \
		"CCPLIBS = $(CCPLIBS)" \
		"CPP = $(CPP)" \
		"CPPINCLUDES = $(CPPINCLUDES)" \
		"DEBUG=$(DEBUG)" \
		"LD_LIBRARY_PATH  = $(LD_LIBRARY_PATH)" \
		"LIBPATH = $(LIBPATH)" \
		"LINK_EXECUTABLE = $(LINK_EXECUTABLE)" \
		"LINK_STATIC_LIB = $(LINK_STATIC_LIB)" \
		"LINK_SHARED_LIB = $(LINK_SHARED_LIB)" \
		"MAIN = $(@F:.dummy=.a)" \
		"OPENGL  = $(OPENGL)" \
		"POST_COMPILE = $(POST_COMPILE)" \
		"SHARED_LIB_SUFFIX = $(SHARED_LIB_SUFFIX)" \
		"STATIC = $(STATIC)"\
		"SYSLIBS = $(SYSLIBS)" \
		"XHOME = $(XHOME)" \
		"XLIBS = $(XLIBS)" \
		"cflags = $(cflags) -DIN_ARB_$(subst /,_,$(@D))" \
	) >$(@D).$$ID.log 2>&1 && (cat $(@D).$$ID.log;rm $(@D).$$ID.log)) || (cat $(@D).$$ID.log;rm $(@D).$$ID.log;false))

# Additional dependencies for subtargets:

comtools: $(ARCHS_MAKEBIN:.a=.dummy)

PROBE_COM/PROBE_COM.dummy : comtools
PROBE_COM/server.dummy : comtools
PROBE_COM/client.dummy : comtools

NAMES_COM/NAMES_COM.dummy : comtools
NAMES_COM/server.dummy : comtools
NAMES_COM/client.dummy : comtools

com_probe: PROBE_COM/PROBE_COM.dummy 
com_names: NAMES_COM/NAMES_COM.dummy 

TOOLS/TOOLS.dummy : shared_libs SERVERCNTRL/SERVERCNTRL.dummy CAT/CAT.dummy com_probe

AWTC/AWTC.dummy :   			com_names com_probe

NAMES/NAMES.dummy : 			com_names
SL/AW_NAME/AW_NAME.dummy : 		com_names

PROBE/PROBE.dummy : 			com_probe
MULTI_PROBE/MULTI_PROBE.dummy : 	com_probe
PROBE_DESIGN/PROBE_DESIGN.dummy : 	com_probe
NALIGNER/NALIGNER.dummy : 		com_probe

ARB_GDE/ARB_GDE.dummy : 		proto_tools


#***************************************************************************************
#			Short aliases to make targets
#***************************************************************************************

show:
		@echo $(SEP)
		@echo 'Aliases for often needed targets:'
		@echo ''
		@echo ' executables:'
		@echo ''
		@echo '  nt     arb_ntree'
		@echo '  e4     arb_edit4 (includes secedit)'
		@echo '  di     arb_dist'
		@echo '  ph     arb_phylo'
		@echo '  pa     arb_parsimony'
		@echo '  tg     arb_treegen'
		@echo '  ds     arb_dbserver'
		@echo '  pt     arb_pt_server'
		@echo '  na     arb_name_server'
		@echo ''
		@echo ' libraries:'
		@echo ''
		@echo '  com    communication libraries'
		@echo '  dball  ARB database (all versions: db dbs and db2)'
		@echo '  aw     GUI lib'
		@echo '  awt    GUI toolkit'
		@echo '  awtc   general purpose library'
		@echo '  awti   import/export library'
		@echo '  mp     multi probe library'
		@echo '  ge     genome library'
		@echo '  pd     probe design lib'
		@echo '  prd    primer design lib'
		@echo '  ih     island hopper'
		@echo ''
		@echo ' other targets:'
		@echo ''
		@echo '  help   recompile help files'
		@echo '  test   test arbdb (needs fix)'
		@echo '  demo   GUI demo (needs fix)'
		@echo '  tools  make small tools used by arb'
		@echo ''
		@echo ' optional targets (not build by make all)'
		@echo ''
		@echo '  ps		ARB probe server'
		@echo '  pc		ARB probe client (you need java)'
		@echo ''
		@echo ' foreign targets:'
		@echo ''
		@echo '  gde    GDE'
		@echo '  agde   ARB_GDE'
		@echo ''
		@echo 'for other targets inspect $(ARBHOME)/Makefile'
		@echo ''
		@echo $(SEP)

source_doc:
		doxygen

mbin:	$(ARCHS_MAKEBIN:.a=.dummy)

com:	$(ARCHS_COMMUNICATION:.a=.dummy)

help:   HELP_SOURCE/HELP_SOURCE.dummy

HELP_SOURCE/HELP_SOURCE.dummy: xml menus# need to create some files in GDE-subtree first

dball:	db dbs db2 dp
db:	ARBDB/libARBDB.dummy
dbs:	ARBDBS/libARBDB.dummy
db2:	ARBDB2/libARBDB.dummy
dp:	ARBDBPP/libARBDBPP.dummy
aw:	WINDOW/libAW.dummy
awt:	AWT/libAWT.dummy
awtc:	AWTC/AWTC.dummy
awti:	AWTI/AWTI.dummy

ih:	ISLAND_HOPPING/ISLAND_HOPPING.dummy

mp: 	MULTI_PROBE/MULTI_PROBE.dummy
mg:	MERGE/MERGE.dummy
ge: 	GENOM/GENOM.dummy
prd: 	PRIMER_DESIGN/PRIMER_DESIGN.dummy

nt:	menus $(NTREE)
ed:	$(EDIT)

al:	$(ALIGNER)
nal:	$(NALIGNER)
a3:	$(ALIV3)

di:	$(DIST)
ph:	$(PHYLO)
pa:	$(PARSIMONY)
tg:	$(TREEGEN)

3d:	RNA3D/RNA3D.dummy
gl:	GL/GL.dummy
sl:	NAMES_COM/NAMES_COM.dummy
	$(MAKE) SL/SL.dummy

ds:	$(DBSERVER)
pt:	$(PROBE)
ps:	PROBE_SERVER/PROBE_SERVER.dummy
pc:	PROBE_WEB/PROBE_WEB.dummy
pst: 	PROBE_SET/PROBE_SET.dummy
pd:	PROBE_DESIGN/PROBE_DESIGN.dummy
na:	$(NAMES)

ac:	$(ARBDB_COMPRESS) # unused? does not compile

test:	$(TEST)
demo:	$(AWDEMO)

sec: SECEDIT/SECEDIT.dummy

e4:	$(EDIT4)
gi:	GENOM_IMPORT/GENOM_IMPORT.dummy
we:	$(WETC)
eb:	$(EDITDB)

pgt:	$(PGT)
xml:	XML/XML.dummy
templ:	TEMPLATES/TEMPLATES.dummy

#********************************************************************************

up: depends proto tags valgrind_update

#********************************************************************************

depends: $(ARCHS:.a=.depends) \
		HELP_SOURCE/HELP_SOURCE.depends \

proto_tools: AISC_MKPTPS/AISC_MKPTPS.dummy

proto: proto_tools TOOLS/TOOLS.dummy 
		$(MAKE) \
				AISC/AISC.proto \
				ARBDB/ARBDB.proto \
				ARB_GDE/ARB_GDE.proto \
				CONVERTALN/CONVERTALN.proto \
				NTREE/NTREE.proto \
				PROBE/PROBE.proto \
				SERVERCNTRL/SERVERCNTRL.proto \
				TRS/TRS.proto \
				AISC_COM/AISC_COM.proto \
				GDE/GDE.proto \

#********************************************************************************

valgrind_update:
		$(MAKE) -C SOURCE_TOOLS valgrind_update

#********************************************************************************

TAGFILE=TAGS
TAGFILE_TMP=TAGS.tmp

tags: tags_$(MACH)
	mv $(TAGFILE_TMP) $(TAGFILE)

tags_LINUX: tags2
tags_SUN5: tags1

tags1:
# first search class definitions
	$(CTAGS) -f $(TAGFILE_TMP)          --language=none "--regex=/^[ \t]*class[ \t]+\([^ \t]+\)/" `find . -name '*.[ch]xx' -type f`
	$(CTAGS) -f $(TAGFILE_TMP) --append --language=none "--regex=/\([^ \t]+\)::/" `find . -name '*.[ch]xx' -type f`
# then append normal tags (headers first)
	$(CTAGS) -f $(TAGFILE_TMP) --append --members ARBDB/*.h `find . -name '*.[h]xx' -type f`
	$(CTAGS) -f $(TAGFILE_TMP) --append ARBDB/*.c `find . -name '*.[c]xx' -type f`

# if the above tag creation does not work -> try tags2:
tags2:
	ctags -f $(TAGFILE_TMP)    -e --c-types=cdt --sort=no `find . \( -name '*.[ch]xx' -o -name "*.[ch]" \) -type f | grep -v -i perl5`
	ctags -f $(TAGFILE_TMP) -a -e --c-types=f-tvx --sort=no `find . \( -name '*.[ch]xx' -o -name "*.[ch]" \) -type f | grep -v -i perl5`

#********************************************************************************

links: SOURCE_TOOLS/generate_all_links.stamp

SOURCE_TOOLS/generate_all_links.stamp: SOURCE_TOOLS/generate_all_links.sh
	SOURCE_TOOLS/generate_all_links.sh
	touch SOURCE_TOOLS/generate_all_links.stamp

gde:		GDE/GDE.dummy
GDE:		gde
agde: 		ARB_GDE/ARB_GDE.dummy
tools:		TOOLS/TOOLS.dummy
trs:		TRS/TRS.dummy
convert:	SL/FILE_BUFFER/FILE_BUFFER.dummy
	$(MAKE) CONVERTALN/CONVERTALN.dummy

readseq:	READSEQ/READSEQ.dummy

#***************************************************************************************
#			Some user commands
#***************************************************************************************
rtc_patch:
	rtc_patch_area -so LIBLINK/libRTC8M.so

menus: binlink
	@(( \
		echo $(SEP) Make everything in GDEHELP; \
		$(MAKE) -C GDEHELP -r "PP=$(PP)" all \
	) > GDEHELP.log 2>&1 && (cat GDEHELP.log;rm GDEHELP.log)) || (cat GDEHELP.log;rm GDEHELP.log;false)

ifeq ($(DEBUG),1)
BIN_TARGET=develall
else
BIN_TARGET=all
endif


binlink:
	$(MAKE) -C bin $(BIN_TARGET)

bin/arb_%:	DEPOT2/%
	cp $< $@
bin/%:	DEPOT2/%
	cp $< $@


preplib:
	(cd lib;$(MAKE) all)

# ---------------------------------------- perl

perl: tools
	@echo $(SEP) Make everything in PERL2ARB
	@$(MAKE) -C PERL2ARB -r -f Makefile.main \
		"AUTODEPENDS=1" \
		"MACH=$(MACH)" \
		"dflags=$(dflags)" \
		"ARBHOME=$(ARBHOME)" \
		"DEBUG=$(DEBUG)" \
		"MAKEDEPEND=$(MAKEDEPEND)" \
		"MAKEDEPENDFLAGS=$(MAKEDEPENDFLAGS)" \
		all

perl_clean:
	@$(MAKE) -C PERL2ARB -r -f Makefile.main \
		"AUTODEPENDS=0" \
		"MACH=$(MACH)" \
		clean

# ----------------------------------------

wc:
	wc `find . -type f \( -name '*.[ch]' -o -name '*.[ch]xx' \) -print`

# ---------------------------------------- cleaning

rmbak:
	find . \( -name '*%' -o -name '*.bak' -o -name 'core' \
		-o -name 'infile' -o -name treefile -o -name outfile \
		-o -name 'gde*_?' -o -name '*~' \) \
	-print -exec rm {} \;

bclean:
	@echo Cleaning bin directory
	find bin -type l -exec rm {} \;
	find bin -type f \! \( -name ".cvsignore" -o -name "Makefile" -o -path "bin/CVS*" \) -exec rm {} \;
	cd bin;make all

libclean:
	rm -f `find . -type f \( -name '*.a' ! -type l \) -print`

clean2: $(ARCHS:.a=.clean) \
		GDEHELP/GDEHELP.clean \
		HELP_SOURCE/HELP_SOURCE.clean \
		SOURCE_TOOLS/SOURCE_TOOLS.clean \
		bin/bin.clean \
		perl_clean
	rm -f *.last_gcc

# links are needed for cleanup
clean: links
	$(MAKE) clean2

# -----------------------------------

rebuild: clean
	$(MAKE) all

relink: bclean libclean
	$(MAKE) all

savedepot: rmbak
	util/arb_save_depot

tarfile: rebuild
	util/arb_compress

tarfile_quick: all
	util/arb_compress

save: sourcetarfile 

# test early whether save will work 
testsave:
	@util/arb_srclst.pl >/dev/null

sourcetarfile: rmbak
	util/arb_save

save2: rmbak
		util/arb_save ignore

release: 
	@echo Making release
	@echo PATH=$(PATH)
	@echo ARBHOME=$(ARBHOME)
	-rm arb.tgz arbsrc.tgz
	$(MAKE) testsave
	$(MAKE) tarfile sourcetarfile

release_quick:
	-rm arb.tgz arbsrc.tgz
	$(MAKE) tarfile_quick sourcetarfile

# --------------------------------------------------------------------------------

# basic arb libraries
arbbasic: links preplib
		$(MAKE) arbbasic2

arbbasic2: templ mbin com ${MAKE_RTC} sl $(GL)

# shared arb libraries
arbshared: dball aw dp awt

# needed arb applications
arbapplications: nt pa ed e4 we pt na al nal di ph ds trs pgt

# optionally things (no real harm for ARB if any of them fails):
arbxtras: tg ps pc pst a3

tryxtras:
	@echo $(SEP)
	@( $(MAKE) arbxtras || ( \
		echo $(SEP) ;\
		echo "One of the optional tools failed to build (see error somewhere above)" ;\
		echo "ARB will work nevertheless!" ) )

arb: arbbasic
	$(MAKE) arbshared arbapplications help

all: checks
	$(MAKE) links
	$(MAKE) com
	$(MAKE) arb
	$(MAKE) libs
	$(MAKE) convert tools gde readseq
	$(MAKE) binlink
	$(MAKE) perl
	-$(MAKE) tryxtras
	@echo $(SEP)
	@echo "made 'all' with success."
	@echo "to start arb enter 'arb'"

# DO NOT DELETE