#
#  $Id: im3make,v 1.26 2000/04/11 12:01:57 srk Exp $
#
# Image Makefile.
#
# This software has been created by Genome Research Limited (GRL). 
# GRL hereby grants permission to use, copy, modify and distribute 
# this software and its documentation for non-commercial purposes 
# without fee at the user's own risk on the basis set out below.
# GRL neither undertakes nor accepts any duty whether contractual or 
# otherwise in connection with the software, its use or the use of 
# any derivative, and makes no representations or warranties, express
# or implied, concerning the software, its suitability, fitness for
# a particular purpose or non-infringement.
# In no event shall the authors of the software or GRL be responsible 
# or liable for any loss or damage whatsoever arising in any way 
# directly or indirectly out of the use of this software or its 
# derivatives, even if advised of the possibility of such damage.
# Our software can be freely distributed under the conditions set out 
# above, and must contain this copyright notice.

#################################################################
# Before running the make command
# setenv ACEDB_MACHINE to indicate one of the predefined
# Machine dependant option files, or write your own.
# These files are called  $(ACEDB_SRC)/wmake/$(ACEDB_MACHINE)_DEF
#

#################################################################
########## Machine dependent compiler modification ##############
############# Are included from an external file ################
#### This is equivalent to, but more portable than $($(CC)) #####
### Edit these rules to adapt the makefile to a new machine #####
#################################################################
# suppress auto SCCS extraction
.SCCS_GET:
.KEEP_STATE:
.SUFFIXES: .o .c .h .cc

###########################################################
##  Compiler and library options
## CC, LIBS, NAME are defined in $(ACEDB_MACHINE)_DEF
###########################################################
 
IDIR = -I.. -I../wh -I../im3src -I/usr/local/include
# Do not use -I/usr/include
# it prevents gcc from picking up its own includes
# (cc goes to /usr/include anyway)

## to undefine any rubbish
CCFLAGS =  
GCFLAGS =

## Different platforms use CC or COMPILE.c
CC =        $(COMPILER) $(USEROPTS) $(IDIR) -D$(NAME) -DHaveTIFF -c
COMPILE.c = $(COMPILER)  $(USEROPTS) $(IDIR) -D$(NAME) -DHaveTIFF -c

#.c.o:
#	$(COMPILER) $(CCFLAGS)  -c $< -o $@

# defaults overridable in $(ACEDB_MACHINE)_DEF
# e.g. different compiler when using purify
CCC = g++
CCCLINK = g++

.cc.o:
	$(CCC) $(IDIR) $(CCCFLAGS) $(USEROPTS) -c $< -o $@

XWIN_LIBS = `gtk-config --libs`
GRAPHXWIN_DEPEND  = libgraph.a libgex.a libgif.a
GRAPHXWIN_LIBS    = -lgraph -lgex -lgif

LIB_LDFLAGS = 

###################################################
############### do not edit below  ################
############### override the above ################
###### settings in $(ACEDB_MACHINE)_DEF ###########
############### if necessary ######################
###################################################

################ machine dependent compiler definitions ########

include deffile


# Note that you can keep different DEF files for the same machine
# setting various compiler options

#############################################################

      ALL_SRCS = imChooser.c imStep1.c imStep2.c imStep3.c imStep4.c \
		imPrefs.c imParamDialogGui.c imParamDialogSig.c imParams.c \
		imInfo.c imLanes.c imChange.c imMisc.c imBitmap.c \
		imConfig.c imExternal.c imHidump.c \
		utBandTrain.c

$(ALL_SRCS):
	ln -s ../im3src/$@ .


## as of version 3.10 Image is dependant on GTK libraries ###

      IM_OBJS = imChooser.o imStep1.o imStep2.o imStep3.o imStep4.o \
		imPrefs.o imParamDialogGui.o imParamDialogSig.o imParams.o \
		imInfo.o imLanes.o imChange.o imMisc.o imBitmap.o \
		imConfig.o imExternal.o imHidump.o

im3:	libfree.a $(GRAPHXWIN_DEPEND) $(IM_OBJS)
	$(LINKER) -o im3 $(IM_OBJS) -L. $(GRAPHXWIN_LIBS) $(XWIN_LIBS) -lfree $(LIBS)

$(IM_OBJS): ../im3src/im.h

imConfig.o: ../im3src/imconfig.h

##########################
# Band Shape Training Tool
##########################

    BSTT_OBJS = utBandTrain.o imZoom.o imHidump.o

bstt:		libfree.a libgraph.a libgex.a libgif.a $(BSTT_OBJS) imZoom.o imHidump.o
		$(LINKER) -L. -o bstt $(BSTT_OBJS) -L. $(GRAPHXWIN_LIBS) $(XWIN_LIBS) -lfree $(LIBS) 

$(BSTT_OBJS): ../im3src/bstt.h

########################
# Image-Conversion tool
# using ImageMagick
########################

  MAGICK_OBJS = cvdecode.o \
                cvquantize.o \
		cvcompress.o \
		cvimage.o \
		cvmonitor.o \
		cverror.o \
		cvutility.o \
		cvcolors.o

   IMCONV_OBJS = $(IMCONV_SRCS:.c=.o) 
   IMCONV_SRCS = cvMain.c cvReadClean.c imHidump.c imBitmap.c $(MAGICK_OBJS:.o=.c) 

im3conv:	libfree.a $(IMCONV_OBJS)
		$(LINKER) -o im3conv $(IMCONV_OBJS) -L. $(LIB_LDFLAGS) -lfree -ltiff $(LIBS)

$(MAGICK_OBJS:.o=.c) cvMain.c cvReadClean.c:
		ln -s ../im3src/$@ .

########################################
# batch mode modules for image analysis
########################################


  IMAGE_AM_SRCS =	$(IMAGE_AM_OBJS:.o=.cc)

  IMAGE_AM_OBJS = amPgm.o amCli.o amInfo.o amABI.o \
		amDataStruct.o amMystring.o amILoad.o amLLoad.o \
		amStep2.o amLaneTrack.o \
		amStep3.o amTrace.o amBandCall.o \
		amStep4.o amRBLoad.o amNormGrid.o amLockOnLane.o\
		amStep5.o amBandCall2.o amBandCall2b.o \
		amBrent.o amLinmin.o amMnbrak.o \
		amPowell.o amBandModel.o  amSpline.o amSplint.o amApproxPeak.o \
		amBandModel2.o amWellFind.o  amParafit.o amLudcmp.o \
		amLubksb.o amReadTrain.o banddiff.o amBandHeight.o \
		amBGSubtract.o amMultiPrep.o general.o laneconvert.o \
		fill_ics.o write_ics.o write_ids.o


$(IMAGE_AM_SRCS):
		ln -s ../im3src/$@ .

#################
#the lanetracker

IMAGE_AM2_OBJS = amLaneTrack.o amPgm.o amStep2.o amCli.o amMystring.o \
	amABI.o amInfo.o amDataStruct.o amParafit.o amLudcmp.o \
	        amLubksb.o amReadTrain.o amILoad.o

amStep2: $(IMAGE_AM2_OBJS)
	$(CCCLINK) -g -o amStep2 $(CCFLAGS) $(IMAGE_AM2_OBJS) -lm

#############################
#lanetracing and bandcalling

IMAGE_AM3_OBJS = amPgm.o amStep3.o amCli.o amMystring.o amABI.o amInfo.o \
	amILoad.o amLLoad.o amDataStruct.o amTrace.o amBandCall.o \
	amLaneTrack.o amBandCall2.o amBandCall2b.o amBrent.o amLinmin.o amMnbrak.o \
	amPowell.o amBandModel.o amSpline.o amSplint.o amApproxPeak.o \
	amBandModel2.o amWellFind.o amParafit.o amLudcmp.o \
	amLubksb.o amReadTrain.o amBandHeight.o amBGSubtract.o amMultiPrep.o \
	general.o laneconvert.o

amStep3: $(IMAGE_AM3_OBJS)
	$(CCCLINK) -g -o amStep3 $(CCFLAGS) $(IMAGE_AM3_OBJS) -lm

###################
#the normalisation

IMAGE_AM4_OBJS = amStep4.o amCli.o amMystring.o amInfo.o \
	amRBLoad.o amNormGrid.o amLockOnLane.o amDataStruct.o \
	amLLoad.o

amStep4: $(IMAGE_AM4_OBJS)
	$(CCCLINK) -g -o amStep4 $(CCFLAGS) $(IMAGE_AM4_OBJS) -lm

###########################
#the output of the results

IMAGE_AM5_OBJS = amStep5.o amCli.o amMystring.o amInfo.o amRBLoad.o \
	amSpline.o amSplint.o fill_ics.o write_ics.o write_ids.o

amStep5: $(IMAGE_AM5_OBJS)
	$(CCCLINK) -g -o amStep5 $(CCFLAGS) $(IMAGE_AM5_OBJS) -lm

##########################################
# little tool for comparison of band files

IMAGE_BANDDIFF_OBJS = amRBLoad.o amCli.o amMystring.o amInfo.o banddiff.o

banddiff: $(IMAGE_BANDDIFF_OBJS)
	$(CCCLINK) -g -o banddiff $(CCFLAGS) $(IMAGE_BANDDIFF_OBJS) -lm


###########################################################################
# little tool to patch the built-in configurations in a im3 executable file
#

image_configure.c:
	ln -s ../im3src/$@ .

image_configure: image_configure.o
	$(LINKER) -o image_configure image_configure.o $(LIBS)


########### remove all objects created by rules in this file ########
image_clean:
	rm -f $(IM_OBJS) imHidump.o $(BSTT_OBJS) imPrefs.bstt.o \
		$(IMCONV_OBJS) $(IMAGE_AM_OBJS)

###########################################################
########### end of the image make file ####################
###########################################################
 
