version 3.5

Makefile

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+###############################################################################
+# Makefile for zoe
+###############################################################################
+
+###########
+# LIBRARY #
+###########
+
+LIBRARY = lib/libzoe.a
+
+OBJECTS = \
+	src/zTools.o\
+	src/zTBTree.o\
+	src/bntree/bntree.o\
+	src/bntree/cache.o\
+	src/bntree/celllistitem.o\
+	src/bntree/intlistitem.o\
+	src/bntree/node.o\
+	src/zAlignment.o\
+	src/zAlignmentScanner.o\
+	src/zAlnFeature.o\
+	src/zBNTreeModel.o\
+	src/zConseq.o\
+	src/zDistribution.o\
+	src/zDNA.o\
+	src/zDuration.o\
+	src/zEstseq.o\
+	src/zEstseqSearch.o\
+	src/zFastaFile.o\
+	src/zFeatureFactory.o\
+	src/zGTF.o\
+	src/zHardCoding.o\
+	src/zHMM.o\
+	src/zHMM_State.o\
+	src/zMath.o\
+	src/zMathTables.o\
+	src/zModel.o\
+	src/zPhasePref.o\
+	src/zProtein.o\
+	src/zScanner.o\
+	src/zSeedUtils.o\
+	src/zSequence.o\
+	src/zSfeature.o\
+	src/zStopSeq.o\
+	src/zTransition.o\
+	src/zTrellis.o\
+	src/zViterbi.o\
+	src/zPairTransition.o\
+	src/zPairTrellis.o\
+	src/zPairViterbi.o\
+
+#################
+# TEST PROGRAMS #
+#################
+
+LFLAGS = -L. -Llib -lzoe -lm 
+
+EXE12 = bin/iscan
+SRC12 = src/iscan.c
+OBJ12 = $(SRC12:.c=.o)
+
+EXE13 = bin/zoe2gtf
+SRC13 = src/zoe2gtf.c
+OBJ13 = $(SRC13:.c=.o)
+
+EXE15 = bin/pairagon
+SRC15 = src/pairagon.c
+OBJ15 = $(SRC15:.c=.o)
+
+EXE16 = bin/pairagon2estgen
+SRC16 = src/pairagon2estgen.c
+OBJ16 = $(SRC16:.c=.o)
+
+EXECUTABLES = $(EXE12) $(EXE13)
+PAIRAGON_EXECUTABLES = $(EXE15) $(EXE16)
+
+TABLE = src/zMathTables.c
+TABLEGEN = src/zFloatwiseScoreAdd
+
+########################
+# Program Options      #
+########################
+
+BUILD = 20060720RZ
+VERSION = 3.5
+PROGRAM = Twinscan
+PAIRAGON_VERSION = 0.99
+PAIRAGON_PROGRAM = Pairagon
+GCC_FLAGS = "-W -Wall -Werror -ansi -pedantic -Wwrite-strings"
+DIST_FLAGS = "-DBUILD=\\\"$(PROGRAM)\ version\ $(VERSION)\ build\ $(BUILD)\\\" -DNDEBUG -O2"
+PAIRAGON_DIST_FLAGS = "-DBUILD=\\\"$(PAIRAGON_PROGRAM)\ version\ $(PAIRAGON_VERSION)\ build\ $(BUILD)\\\" -DNDEBUG -O2"
+
+# In order to make the include file to contain header file dependencies,
+# gcc needs a flag to construct this.  In another funny SunOS stunt, this
+# is entirely different in their cc.
+INCLUDE_FLAGS = "-MM"
+
+SPARC_INCLUDE_FLAGS= "-xM1"
+
+ALPHA_FLAGS = "-c99 -msg_enable level5"
+
+SPARC_FLAGS = "-O "
+
+MACOSX_FLAGS = "-Wall -W -O2"
+MACOSX_G5_FLAGS="-fast"
+# You might have to use -mcpu=7450 if it is not a G5 processor!
+
+############################
+# End Program Options      #
+############################
+
+################################################################################
+# TARGETS 
+################################################################################
+
+
+all: include $(LIBRARY) $(EXECUTABLES)
+
+$(LIBRARY): $(OBJECTS)
+	rm -f $(LIBRARY)
+	ar cr $(LIBRARY) $(OBJECTS)
+	ranlib $(LIBRARY)
+
+include:
+	$(CC) $(INCLUDE_FLAGS) src/*.c > Makefile.include
+	src/get-glib-flags.sh >> Makefile.include
+
+pairagon-exe: $(LIBRARY) $(PAIRAGON_EXECUTABLES)
+
+clean:
+	rm -f src/*.o src/bntree/*.o $(LIBRARY) $(PAIRAGON_EXECUTABLES) $(EXECUTABLES) $(TABLE) $(TABLEGEN)
+
+product:
+	make all CC="gcc" CFLAGS+=$(GCC_FLAGS) CFLAGS+=-march=i686 CFLAGS+=-DNDEBUG CFLAGS+=-O2 CFLAGS+=$(DIST_FLAGS)
+
+gcc-distribution:
+	make all CC="gcc" CFLAGS+=$(GCC_FLAGS) CFLAGS+=-march=i686 CFLAGS+=-DNDEBUG CFLAGS+=-O2 CFLAGS+=$(DIST_FLAGS)
+
+linux:
+	make all CC="gcc" CFLAGS+=$(GCC_FLAGS) CFLAGS+=-march=i686 CFLAGS+=-DNDEBUG CFLAGS+=-O2 CFLAGS+=$(DIST_FLAGS)
+
+alpha:
+	make all CC="cc" CFLAGS+=$(ALPHA_FLAGS) CFLAGS+=$(DIST_FLAGS)
+
+macosx:
+	make all CC="gcc" CFLAGS+=$(MACOSX_FLAGS) CFLAGS+=$(DIST_FLAGS)
+
+macosxg5:
+	make all CC="gcc" CFLAGS+=$(MACOSX_FLAGS) CFLAGS+=$(MACOSX_G5_FLAGS) CFLAGS+=$(DIST_FLAGS)
+
+sparc:
+	make all CC="cc" INCLUDE_FLAGS=$(SPARC_INCLUDE_FLAGS) CFLAGS+=$(SPARC_FLAGS) CFLAGS+=$(DIST_FLAGS)
+
+pairagon-linux:
+	make pairagon-exe CC="gcc" CFLAGS+=$(GCC_FLAGS) CFLAGS+=$(PAIRAGON_DIST_FLAGS) $(GLIB_FLAGS)
+
+pairagon-sparc:
+	make pairagon-exe CC="cc" CFLAGS+=$(SPARC_FLAGS) CFLAGS+=$(PAIRAGON_DIST_FLAGS)
+
+pairagon-macosx:
+	make pairagon-exe CC="cc" CFLAGS+=$(MACOSX_FLAGS) CFLAGS+=$(PAIRAGON_DIST_FLAGS)
+
+pairagon-distro:
+	make pairagon-exe CC="gcc" CFLAGS+=$(GCC_FLAGS) CFLAGS+=-march=i686 CFLAGS+=$(PAIRAGON_DIST_FLAGS)
+
+.PHONY:include all pairagon-exe clean product gcc-distribution alpha macosx sparc pairagon-linux pairagon-sparc pairagon-macosx pairagon-distro
+
+#######################
+# Excecutable Section #
+#######################
+
+$(EXE12): $(OBJ12) $(LIBRARY)
+	$(CC) -o $(EXE12) $(CFLAGS) $(OBJ12) $(LFLAGS) $(GLIB_LFLAGS)
+
+$(EXE13): $(OBJ13) $(LIBRARY)
+	$(CC) -o $(EXE13) $(CFLAGS) $(OBJ13) $(LFLAGS) $(GLIB_LFLAGS)
+
+$(EXE15): $(OBJ15) $(LIBRARY)
+	$(CC) -o $(EXE15) $(CFLAGS) $(OBJ15) $(LFLAGS) $(GLIB_LFLAGS)
+
+$(EXE16): $(OBJ16) $(LIBRARY)
+	$(CC) -o $(EXE16) $(CFLAGS) $(OBJ16) $(LFLAGS) $(GLIB_LFLAGS)
+
+###################
+# Inference Rules #
+###################
+
+.SUFFIXES : .c .o
+
+.c.o:
+	$(CC) $(CFLAGS) -c -o $@ $<
+
+
+#######################
+# Source Dependencies #
+#######################
+
+$(TABLEGEN): src/zFloatwiseScoreAdd.c
+	$(CC) $(CFLAGS) -o $(TABLEGEN) src/zFloatwiseScoreAdd.c -lm
+
+$(TABLE): $(TABLEGEN)
+	./$(TABLEGEN) > $(TABLE)
+
+include Makefile.include
+

Makefile.include

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+