CC = g++
-CPPFLAGS = -Wall -O3
-OBJS = rlcsa.o rlcsa_builder.o sasamples.o bits/bitvector.o bits/deltavector.o bits/rlevector.o bits/vectors.o misc/parameters.o misc/utils.o qsufsort/qsufsort.o
+# Use 64-bit integers in a 64-bit environment.
+# SIZE_FLAGS = -DMASSIVE_DATA_RLCSA
-all: library
+# Parallelism is supported by either libstdc++ Parallel Mode or MCSTL.
+# PARALLEL_FLAGS = -DMULTITHREAD_SUPPORT -D_GLIBCXX_PARALLEL -fopenmp
+# MCSTL_ROOT = /fs-3/d/jltsiren/suds/mcstl
+# PARALLEL_FLAGS = -DMULTITHREAD_SUPPORT -I$(MCSTL_ROOT)/c++ -fopenmp
-library: $(OBJS)
- ar rc rlcsa.a $(OBJS)
+# Vectors using nibble codes instead of delta codes are faster, but they also
+# take up more space.
+# VECTOR_FLAGS = -DUSE_NIBBLE_VECTORS
+
+#CPPFLAGS = -Wall -g $(SIZE_FLAGS) $(PARALLEL_FLAGS) $(VECTOR_FLAGS)
+CPPFLAGS = -Wall -O3 $(SIZE_FLAGS) $(PARALLEL_FLAGS) $(VECTOR_FLAGS)
+OBJS = rlcsa.o rlcsa_builder.o sasamples.o lcpsamples.o bits/array.o bits/bitvector.o bits/deltavector.o bits/rlevector.o bits/nibblevector.o misc/parameters.o misc/utils.o qsufsort/qsufsort.o
+
+VPATH = bits:misc:utils
+
+
+default: rlcsa.a
+
+
+rlcsa.a: $(OBJS)
+ ar rcs rlcsa.a $(OBJS)
depend:
- g++ -MM *.cpp bits/*.cpp misc/*.cpp qsufsort/*.c > dependencies.mk
+ g++ -MM *.cpp bits/*.cpp misc/*.cpp qsufsort/*.c utils/*.cpp > dependencies.mk
+
+rlcsa_test: rlcsa_test.o rlcsa.a
+ $(CC) $(CPPFLAGS) -o rlcsa_test rlcsa_test.o rlcsa.a
+
+lcp_test: lcp_test.o rlcsa.a
+ $(CC) $(CPPFLAGS) -o lcp_test lcp_test.o rlcsa.a
+
+parallel_build: parallel_build.o rlcsa.a
+ $(CC) $(CPPFLAGS) -o parallel_build parallel_build.o rlcsa.a
+
+build_rlcsa: build_rlcsa.o rlcsa.a
+ $(CC) $(CPPFLAGS) -o build_rlcsa build_rlcsa.o rlcsa.a
+
+locate_test: locate_test.o rlcsa.a
+ $(CC) $(CPPFLAGS) -o locate_test locate_test.o rlcsa.a
+
+display_test: display_test.o rlcsa.a
+ $(CC) $(CPPFLAGS) -o display_test display_test.o rlcsa.a
+
+read_bwt: read_bwt.o rlcsa.a
+ $(CC) $(CPPFLAGS) -o read_bwt read_bwt.o rlcsa.a
+
+extract_sequence: extract_sequence.o rlcsa.a
+ $(CC) $(CPPFLAGS) -o extract_sequence extract_sequence.o rlcsa.a
+
+rlcsa_grep: rlcsa_grep.o rlcsa.a
+ $(CC) $(CPPFLAGS) -o rlcsa_grep rlcsa_grep.o rlcsa.a
+
+build_plcp: build_plcp.o rlcsa.a
+ $(CC) $(CPPFLAGS) -o build_plcp build_plcp.o rlcsa.a
+
+sample_lcp: sample_lcp.o rlcsa.a
+ $(CC) $(CPPFLAGS) -o sample_lcp sample_lcp.o rlcsa.a
+
+extract_text: extract_text.o
+ $(CC) $(CPPFLAGS) -o utils/extract_text extract_text.o
+
+convert_patterns: convert_patterns.o
+ $(CC) $(CPPFLAGS) -o utils/convert_patterns convert_patterns.o misc/utils.o
+
+split_text: split_text.o
+ $(CC) $(CPPFLAGS) -o utils/split_text split_text.o misc/utils.o
-update:
- cp ../rlcsa.* ../rlcsa_builder.* ../sasamples.* .
- cp ../bits/* bits/
- cp ../misc/* misc/
- cp ../qsufsort/* qsufsort/
+genpatterns: genpatterns.c
+ gcc -O3 -Wall -o utils/genpatterns utils/genpatterns.c
clean:
- rm -f rlcsa.a
- rm -f $(OBJS)
+ rm -f rlcsa.a rlcsa_test lcp_test parallel_build
+ rm -f build_rlcsa locate_test display_test read_bwt extract_sequence rlcsa_grep build_plcp sample_lcp
+ rm -f utils/extract_text utils/convert_patterns utils/split_text
+ rm -f *.o bits/*.o misc/*.o qsufsort/*.o utils/*.o
+package:
+ mkdir rlcsa
+ mkdir rlcsa/bits rlcsa/misc rlcsa/qsufsort rlcsa/utils
+ cp LICENSE Makefile README dependencies.mk *.cpp *.h rlcsa
+ cp bits/*.cpp bits/*.h rlcsa/bits
+ cp misc/*.cpp misc/*.h rlcsa/misc
+ cp qsufsort/*.c qsufsort/*.h rlcsa/qsufsort
+ cp utils/*.cpp utils/*.py rlcsa/utils
+ tar cfz rlcsa.tgz rlcsa
+ rm -r rlcsa/*
+ rmdir rlcsa
include dependencies.mk