# Makefile
#
# Makefile for Mac OS X for PHYLIP 3.6.

PACKAGE=phylip
VERSION=3.69

# We use GNU's version of the make utility. It may be called "gmake" on
# your system.
#
# If you're using a Mac OS X system with default locations for 
# gcc libraries, you probably don't need to change anything. You might
# might change the first noncomment statement below to redefine $(EXEDIR)
# if you'd like your executables installed in a different location than
# our default.
#
# Users with systems that differ substantially from ours may need to set
# the following variables: $(CC) $(CFLAGS) $(DFLAGS) $(LIBS) $(DLIBS)
#
# When uncompressed and extracted, the tar archive phylip-3.6x.tar.gz 
# produces the following directory structure:
#
#   phylip-3.6x/src -- the source code, including this file, Makefile.osx
#   phylip-3.6x/exe -- executables, changed by changing $(EXEDIR) value
#   phylip-3.6x/doc -- html documentation
#
#  To use the PHYLIP v3.6 Makefile, type from the phylip-3.6x/src directory:
#      cp Makefile Makefile.unix
#      cp Makefile.osx Makefile
#  and then do one of the following. (You can skip the copying steps
#  above and use "make -f Makefile.osx ..." instead if you like.)
#
#      make install         to compile the whole package and install
#                           the executables in $(EXEDIR), and then
#                           remove the object files to save space
#
#      make all             to compile the whole package but not install it
#                           or remove the object files. 
#
#      make put             to move the executables into $(EXEDIR)
#
#      make clean           to remove all object files and executables from the
#                           current directory
#
#      make dnaml.app       to compile, link, and make a clickable executable
#                           for one program. The executables will stay
#                           in the src directory.
#
#      make dnaml.install   to compile, link, make a clickable executable, 
#                           for one program and move the executable to the
#                           executables directory
#
# ----------------------------------------------------------------------------
#  (Starting here is the section where you may want to change things)
# ----------------------------------------------------------------------------
#
# the following specifies the directory where the executables will be placed
EXEDIR  = ../exe
#
# ----------------------------------------------------------------------------
#
# The following statements set these variables:
#
#    CC     -- the name (and, optionally, location) of your C compiler
#    CFLAGS -- compiler directives needed to compile most programs
#    DFLAGS -- compiler directives needed to compile draw programs
#    LIBS   -- non-default system libraries needed to compile most programs
#    DLIBS  -- non-default system libraries needed to compile draw programs
#
# We've provided a set of possible values for each variable.
#
# The value used is the one without a "#" at the beginning of the line.
#
# To try an alternate value, make sure the one you want has no "#"
# as its first character and that all other possibilities have "#" for
# their first character.
#
# Advanced users may need to further edit one of the alternatives in
# order to correctly compile on their system.
#
# ----------------------------------------------------------------------------
#
# The next two assignments are the invocations of the compiler
#
# This one specifies the "cc" C compiler
CC        = cc
#
#  To use GCC instead:
#CC        = gcc
#
# ----------------------------------------------------------------------------
#
# This is the CFLAGS statement. It specifies compiler behavior.
#
# Here are some possible CFLAGS statements:
#
#
#A minimal one
#CFLAGS =
#
# A basic one for debugging
#CFLAGS  = -g 
#
# An optimized one for gcc
#CFLAGS  = -O3 -fomit-frame-pointer
#
# For some serious debugging using Gnu gcc
#
#CFLAGS=-g -Wall -Wmain -Wmissing-prototypes -Wreturn-type -Wstrict-prototypes  -Wunused -Werror -Wredundant-decls -Waggregate-return -Wcast-align -Wcomment
#
# For making universal binaries
# theoretically this could also include "-arch ppc64", but that didn't
# work for us
# CFLAGS = -O3 -Wall -arch ppc -arch i386 -mmacosx-version-min=10.1

# For making non-universal binaries for your processor
CFLAGS = -O3 -Wall -mmacosx-version-min=10.1
#
# ----------------------------------------------------------------------------
#
# This is the DFLAGS statement. It specifies compiler behavior for the
# programs drawgram and drawtree. It adds additional information to
# the $(CFLAGS) value so these programs can use graphics.
#
# A minimal one -- drawing programs will run, but will not use graphics.
# If you use this one, you must also use the minimal value for $(DLIBS)
#DFLAGS  = $(CFLAGS) -DX
#
# to use Mac Carbon graphics (use only for Intel).
# You should also use the Carbon version of DLIBS
DFLAGS =  -O3 -Wall -arch i386 -mmacosx-version-min=10.1 -DMAC -DOSX_CARBON
#
# to use Mac Carbon graphics (use only for PPC).  Uses 32 bit PPC code only.
# You should also use the Carbon version of DLIBS
#DFLAGS =  -O3 -Wall -arch ppc -mmacosx-version-min=10.1 -DMAC -DOSX_CARBON
#
# Compiling universal binaries for draw programs using Carbon for PPC
# need to specify 32 bit for the PPC part
#DFLAGS =  -O3 -Wall -arch ppc -arch i386 -mmacosx-version-min=10.1 -DMAC -DOSX_CARBON
#
# ----------------------------------------------------------------------------
#
# Most of the programs need only the math libraries, specified like this;
#
LIBS    = -lm
#
# The drawing programs also need access to the X windowing system. This is
# specified with the DLIBS variable.
#
# A minimal one -- drawing programs will run, but will not use graphics.
# you must also set DFLAGS to the minimal value
#DLIBS  = $(CLIBS)
#
# to use Mac Carbon graphics. You should also use the Carbon version
# of DFLAGS
DLIBS=-framework Carbon # -framework AppKit -framework ApplicationServices

# ----------------------------------------------------------------------------
#  (After this point there should not be any reason to change anything
#  except for the commands at the bottom which add the icons in Mac OS X)
# ----------------------------------------------------------------------------
#
#
# the list of programs
# draw programs are listed last since they are the most likely to cause
# compilation or linking problems

PROGS   =		clique \
				consense \
				contml \
				contrast \
				dnacomp \
				dnadist \
				dnainvar \
				dnaml \
				dnamlk \
				dnamove \
				dnapars \
				dnapenny \
				dolmove \
				dollop \
				dolpenny \
				factor \
				fitch \
				gendist \
				kitsch \
				mix \
				move \
				neighbor \
				pars \
				penny \
				proml \
				promlk \
				protdist \
				protpars \
				restdist \
				restml \
				retree \
				seqboot \
				treedist \
				drawgram \
				drawtree

APPS    =          clique.app consense.app contml.app contrast.app dnacomp.app \
                   dnadist.app dnainvar.app dnaml.app dnamlk.app dnamove.app \
                   dnapars.app dnapenny.app dollop.app dolmove.app dolpenny.app \
                   drawgram.app drawtree.app factor.app fitch.app gendist.app \
                   kitsch.app mix.app move.app neighbor.app pars.app penny.app \
                   proml.app promlk.app protdist.app protpars.app restdist.app \
                   restml.app retree.app seqboot.app treedist.app 

#
# general commands
#

#  The first target it executed if you just type "make".  It tells you how to
#  use the Makefile.
#
help:
	@echo ""
	@echo " To use the PHYLIP v3.6 Makefile, type"
	@echo "     make install       to compile the whole package and install"
	@echo "                          the executables in $(EXEDIR), and then"
	@echo "                          remove the object files to save space"
	@echo "     make all           to compile the whole package but not install it"
	@echo "                          or remove the object files"
	@echo "     make put           to move the executables into $(EXEDIR)"
	@echo "     make clean         to remove all object files and executables from the"
	@echo "                          current directory"
	@echo "     make dnaml.app        to compile, link, and make a clickable executable"
	@echo "                            for one program (in this example, dnaml)."
	@echo "                            The executables will stay in the src directory."
	@echo "     make dnaml.install    to compile, link, make a clickable executable,"
	@echo "                            for one program and move the executable"
	@echo "                            to the executables directory"
	@echo " "

introduce:
	@echo "Building PHYLIP version $(VERSION)"

all:        introduce $(PROGS)
	@echo "Finished compiling."
	@echo ""

install:        pre-clean apps put clean
	@echo "Done."
	@echo ""

# For making clickable executables.
apps:   $(APPS)

put:
	@echo "Installing PHYLIP v3.6 binaries in $(EXEDIR)"
	@mkdir -p '$(EXEDIR)'
	@for i in $(APPS) ; do \
         rm -rf "$(EXEDIR)/$$i" ; \
         done
	@mv $(APPS) '$(EXEDIR)'
	@cp linkmac '$(EXEDIR)'
	@echo "Installing font files in $(EXEDIR)"
	@cp font* '$(EXEDIR)'
	@echo "Finished installation."
	@echo ""

pre-clean:
	@echo "Removing preexisting executables"
	@for i in $(APPS) ; do \
    rm -rf "$(EXEDIR)/$$i" ; \
  done
	@echo "Ready for new executables"
	@echo ""

clean:
	@echo "Removing object files to save space"
	@rm -f *.o
	@echo "Finished removing object files.  Now will remove"
	@echo "executable files from the current directory, but not from the"
	@echo "executables directory.  (If some are not here, the makefile"
	@echo "will terminate with an error message but this is not a problem)"
	@echo ""
	@echo "Removing executables from this directory"
	@rm -f $(PROGS)
	@rm -rf $(APPS)
	@echo "Finished cleanup."
	@echo ""

#
# compile object files shared between programs
# (make's implicit rule for %.o will take care of these)
#

phylip.o:     phylip.h
seq.o:        phylip.h seq.h
disc.o:       phylip.h disc.h
discrete.o:   phylip.h discrete.h
dollo.o:      phylip.h dollo.h
wagner.o:     phylip.h wagner.h
dist.o:       phylip.h dist.h
cont.o:       phylip.h cont.h
mlclock.o:    phylip.h mlclock.h
moves.o:      phylip.h moves.h
printree.o:   phylip.h printree.h

#
# compile the individual programs
#

clique.o:       clique.c disc.h phylip.h

clique:         clique.o disc.o phylip.o
	$(CC) $(CFLAGS) clique.o disc.o phylip.o $(LIBS) -o clique

cons.o:         cons.c cons.h phylip.h 

consense.o:     consense.c cons.h phylip.h

consense:       consense.o phylip.o cons.o
	$(CC) $(CFLAGS) consense.o phylip.o cons.o $(LIBS) -o consense

contml.o:       contml.c cont.h phylip.h

contml:       contml.o cont.o phylip.o
	$(CC) $(CFLAGS) contml.o cont.o phylip.o $(LIBS) -o contml

contrast.o:       contrast.c cont.h phylip.h

contrast:       contrast.o cont.o phylip.o
	$(CC) $(CFLAGS) contrast.o cont.o phylip.o $(LIBS) -o contrast

dnacomp.o:      dnacomp.c seq.h phylip.h

dnacomp:      dnacomp.o seq.o phylip.o
	$(CC) $(CFLAGS) dnacomp.o seq.o phylip.o $(LIBS) -o dnacomp

dnadist.o:      dnadist.c seq.h phylip.h

dnadist:      dnadist.o seq.o phylip.o
	$(CC) $(CFLAGS) dnadist.o seq.o phylip.o $(LIBS) -o dnadist

dnainvar.o:      dnainvar.c seq.h phylip.h

dnainvar:      dnainvar.o seq.o phylip.o
	$(CC) $(CFLAGS) dnainvar.o seq.o phylip.o $(LIBS) -o dnainvar

dnaml.o:      dnaml.c seq.h phylip.h

dnaml:      dnaml.o seq.o phylip.o
	$(CC) $(CFLAGS) dnaml.o seq.o phylip.o $(LIBS) -o dnaml

dnamlk.o:      dnamlk.c seq.h phylip.h mlclock.h printree.h

dnamlk:      dnamlk.o seq.o phylip.o mlclock.o printree.o
	$(CC) $(CFLAGS) dnamlk.o seq.o phylip.o mlclock.o printree.o $(LIBS) -o dnamlk

dnamove.o:      dnamove.c seq.h moves.h phylip.h

dnamove:      dnamove.o seq.o moves.o phylip.o
	$(CC) $(CFLAGS) dnamove.o seq.o moves.o phylip.o $(LIBS) -o dnamove

dnapenny.o:      dnapenny.c seq.h phylip.h

dnapenny:      dnapenny.o seq.o phylip.o
	$(CC) $(CFLAGS) dnapenny.o seq.o phylip.o $(LIBS) -o dnapenny

dnapars.o:      dnapars.c seq.h phylip.h

dnapars:      dnapars.o seq.o phylip.o
	$(CC) $(CFLAGS) dnapars.o seq.o phylip.o $(LIBS) -o dnapars

dolmove.o:       dolmove.c disc.h moves.h dollo.h phylip.h

dolmove:       dolmove.o disc.o moves.o dollo.o phylip.o
	$(CC) $(CFLAGS) dolmove.o disc.o moves.o dollo.o phylip.o $(LIBS) -o dolmove

dollop.o:       dollop.c disc.h dollo.h phylip.h

dollop:       dollop.o disc.o dollo.o phylip.o
	$(CC) $(CFLAGS) dollop.o disc.o dollo.o phylip.o $(LIBS) -o dollop

dolpenny.o:       dolpenny.c disc.h dollo.h phylip.h

dolpenny:       dolpenny.o disc.o dollo.o phylip.o
	$(CC) $(CFLAGS) dolpenny.o disc.o dollo.o phylip.o $(LIBS) -o dolpenny

draw.o:   draw.c draw.h phylip.h interface.h
	$(CC) $(DFLAGS) -c draw.c

draw2.o:   draw2.c draw.h phylip.h 
	$(CC) $(DFLAGS) -c draw2.c

drawgram.o:     drawgram.c draw.h phylip.h
	$(CC) $(DFLAGS) -c drawgram.c

drawgram:     drawgram.o draw.o draw2.o phylip.o interface.o
	$(CC) $(DFLAGS) draw.o draw2.o drawgram.o phylip.o interface.o $(DLIBS) -o drawgram

drawtree.o:     drawtree.c draw.h phylip.h
	$(CC) $(DFLAGS) -c drawtree.c

drawtree:     drawtree.o draw.o draw2.o phylip.o interface.o
	$(CC) $(DFLAGS) draw.o draw2.o drawtree.o phylip.o interface.o $(DLIBS) -o drawtree

factor.o:       factor.c phylip.h

factor:       factor.o phylip.o
	$(CC) $(CFLAGS) factor.o phylip.o $(LIBS) -o factor

fitch.o:        fitch.c dist.h phylip.h

fitch:        fitch.o dist.o phylip.o
	$(CC) $(CFLAGS) fitch.o dist.o phylip.o $(LIBS) -o fitch

gendist.o:      gendist.c phylip.h

gendist:      gendist.o phylip.o
	$(CC) $(CFLAGS) gendist.o phylip.o $(LIBS) -o gendist

interface.o:      interface.c interface.h
	$(CC) $(DFLAGS) -c interface.c

kitsch.o:        kitsch.c dist.h phylip.h

kitsch:        kitsch.o dist.o phylip.o
	$(CC) $(CFLAGS) kitsch.o dist.o phylip.o $(LIBS) -o kitsch

mix.o:        mix.c disc.h wagner.h phylip.h

mix:        mix.o disc.o wagner.o phylip.o
	$(CC) $(CFLAGS) mix.o disc.o wagner.o phylip.o $(LIBS) -o mix

move.o:        move.c disc.h moves.h wagner.h phylip.h

move:        move.o disc.o moves.o wagner.o phylip.o
	$(CC) $(CFLAGS) move.o disc.o moves.o wagner.o phylip.o $(LIBS) -o move

neighbor.o:        neighbor.c dist.h phylip.h

neighbor:        neighbor.o dist.o phylip.o
	$(CC) $(CFLAGS) neighbor.o dist.o phylip.o $(LIBS) -o neighbor

pars.o:   pars.c discrete.h phylip.h

pars: pars.o discrete.o phylip.o
	$(CC) $(CFLAGS) pars.o discrete.o phylip.o $(LIBS) -o pars

penny.o:  penny.c disc.h wagner.h phylip.h

penny:  penny.o disc.o wagner.o phylip.o
	$(CC) $(CFLAGS) penny.o disc.o wagner.o  phylip.o $(LIBS) -o penny

proml.o:      proml.c seq.h phylip.h

proml:      proml.o seq.o phylip.o
	$(CC) $(CFLAGS) proml.o seq.o phylip.o $(LIBS) -o proml

promlk.o:      promlk.c seq.h phylip.h mlclock.h printree.h

promlk:      promlk.o seq.o phylip.o mlclock.o printree.o
	$(CC) $(CFLAGS) promlk.o seq.o phylip.o mlclock.o printree.o $(LIBS) -o promlk

protdist.o:      protdist.c seq.h phylip.h

protdist:      protdist.o seq.o phylip.o
	$(CC) $(CFLAGS) protdist.o seq.o phylip.o $(LIBS) -o protdist

protpars.o: protpars.c seq.h phylip.h

protpars: protpars.o seq.o phylip.o
	$(CC) $(CFLAGS) protpars.o seq.o phylip.o $(LIBS) -o protpars

restdist.o: restdist.c seq.h phylip.h

restdist: restdist.o seq.o phylip.o
	$(CC) $(CFLAGS) restdist.o seq.o phylip.o $(LIBS) -o restdist

restml.o: restml.c seq.h phylip.h

restml: restml.o seq.o phylip.o
	$(CC) $(CFLAGS) restml.o seq.o phylip.o $(LIBS) -o restml

retree.o:       retree.c moves.h phylip.h

retree:       retree.o moves.o phylip.o
	$(CC) $(CFLAGS) retree.o moves.o phylip.o $(LIBS) -o retree

seqboot.o:      seqboot.c phylip.h

seqboot:      seqboot.o seq.o phylip.o
	$(CC) $(CFLAGS) seqboot.o seq.o phylip.o $(LIBS) -o seqboot

treedist.o:     treedist.c cons.h phylip.h

treedist:     treedist.o phylip.o cons.o
	$(CC) $(CFLAGS) treedist.o cons.o phylip.o $(LIBS) -o treedist
#
# This is where the clickable executables are made for Mac OSX
#
%.app: % mac/Info.plist.in mac/command.in mac/%.icns 
	@rm -rf $@
	/Developer/Tools/Rez -d __DARWIN__ -t APPL Carbon.r -o $<
	/Developer/Tools/SetFile -a C $<
	-mkdir -p $@/Contents/MacOS
	-mkdir -p $@/Contents/Resources
	sed -e "s/IDENTIFIER/$</" \
	-e "s/COMMAND/$<.command/" \
	-e "s/EXECUTABLE/$</" \
	-e "s/ICONNAME/$</" \
	-e "s/VERSION/$(VERSION)/" \
	mac/Info.plist.in > $@/Contents/Info.plist
	sed -e "s/EXECUTABLE/$</" \
	mac/command.in > $@/Contents/MacOS/$<.command
	chmod ug+x $@/Contents/MacOS/$<.command
	echo -n "APPL????" >$@/Contents/PkgInfo
	cp $< $@/Contents/MacOS/$<
	cp -f mac/$<.icns $@/Contents/Resources/$<.icns

# Location of the lsregister command to force re-registration with LaunchServices
LSREGISTER=/System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/LaunchServices.framework/Versions/A/Support/lsregister

%.install:	%.app
	@rm -rf '$(EXEDIR)/$<'
	@mv $< '$(EXEDIR)'