motiejus/turbonss
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This commit is contained in:
Davi Reis 2009-07-04 20:17:36 -07:00
parent cbb817ddef
commit 250afcb75f
6 changed files with 146 additions and 159 deletions
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39
cdb/cdb.h
View File

@ -1,39 +0,0 @@
#ifndef __CMPH_CDB_H__
#define __CMPH_CDB_H__
#ifdef __cplusplus
extern "C"
{
#endif
typedef struct
{
int fd;
void *data;
} cdb;
int cdb_init(struct cdb *cdbp, int fd);
void cdb_free(struct cdb *cdbp);
int cdb_read(const struct cdb *cdbp, void *buf, cmph_uint32 len, cmph_uint32 pos);
int cdb_find(const struct cdb *cdbp, const void *key, cmph_uint32 keylen);
int cdb_read(const struct cdb *cdbp, void *buf, cmph_uint32 len, cmph_uint32 pos);
typedef struct
{
int fd;
void *data;
} cdb_make;
int cdb_make_start(struct cdb_make *cdbmp, int fd);
int cdb_make_add(struct cdb_make *cdbmp, const void *key, cmph_uint32 keylen, const void *val, cmph_uint32 vallen);
int cdb_make_exists(struct cdb_make *cdbmp, const void *key, cmph_uint32 klen);
int cdb_make_find(struct cdb_make *cdbmp, const void *key, cmph_uint32 klen, enum cdb_put_mode mode);
int cdb_make_put(struct cdb_make *cdbmp, const void *key, cmph_uint32 klen, const void *val, cmph_uint32 vlen, enum cdb_put_mode mode);
int cdb_make_finish(struct cdb_make *cdbmp);
#ifdef __cplusplus
}
#endif
#endif

2
cmph.pc.in
View File

@ -4,7 +4,7 @@ exec_prefix=@exec_prefix@
libdir=@libdir@ libdir=@libdir@
includedir=@includedir@ includedir=@includedir@
Name: alsa Name: cmph
Description: minimal perfect hashing library Description: minimal perfect hashing library
Version: @VERSION@ Version: @VERSION@
Libs: -L${libdir} -lcmph Libs: -L${libdir} -lcmph

150
src/Makefile
View File

@ -1,8 +1,8 @@
# Makefile.in generated by automake 1.10.1 from Makefile.am. # Makefile.in generated by automake 1.10 from Makefile.am.
# src/Makefile. Generated from Makefile.in by configure. # src/Makefile. Generated from Makefile.in by configure.
# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002, # Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
# 2003, 2004, 2005, 2006, 2007, 2008 Free Software Foundation, Inc. # 2003, 2004, 2005, 2006 Free Software Foundation, Inc.
# This Makefile.in is free software; the Free Software Foundation # This Makefile.in is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it, # gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved. # with or without modifications, as long as this notice is preserved.
@ -32,8 +32,8 @@ POST_INSTALL = :
NORMAL_UNINSTALL = : NORMAL_UNINSTALL = :
PRE_UNINSTALL = : PRE_UNINSTALL = :
POST_UNINSTALL = : POST_UNINSTALL = :
build_triplet = x86_64-unknown-linux-gnu build_triplet = i386-apple-darwin9.6.0
host_triplet = x86_64-unknown-linux-gnu host_triplet = i386-apple-darwin9.6.0
bin_PROGRAMS = cmph$(EXEEXT) bin_PROGRAMS = cmph$(EXEEXT)
subdir = src subdir = src
DIST_COMMON = $(include_HEADERS) $(srcdir)/Makefile.am \ DIST_COMMON = $(include_HEADERS) $(srcdir)/Makefile.am \
@ -59,9 +59,9 @@ LTLIBRARIES = $(lib_LTLIBRARIES)
libcmph_la_LIBADD = libcmph_la_LIBADD =
am_libcmph_la_OBJECTS = hash.lo jenkins_hash.lo vstack.lo vqueue.lo \ am_libcmph_la_OBJECTS = hash.lo jenkins_hash.lo vstack.lo vqueue.lo \
graph.lo cmph.lo cmph_structs.lo chm.lo bmz.lo bmz8.lo bdz.lo \ graph.lo cmph.lo cmph_structs.lo chm.lo bmz.lo bmz8.lo bdz.lo \
bdz_ph.lo buffer_manager.lo buffer_entry.lo brz.lo fch.lo \ bdz_ph.lo brz.lo fch.lo fch_buckets.lo chd.lo chd_ph.lo \
fch_buckets.lo select.lo compressed_seq.lo chd_ph.lo \ miller_rabin.lo buffer_manager.lo buffer_entry.lo select.lo \
miller_rabin.lo compressed_seq.lo compressed_rank.lo
libcmph_la_OBJECTS = $(am_libcmph_la_OBJECTS) libcmph_la_OBJECTS = $(am_libcmph_la_OBJECTS)
libcmph_la_LINK = $(LIBTOOL) --tag=CC $(AM_LIBTOOLFLAGS) \ libcmph_la_LINK = $(LIBTOOL) --tag=CC $(AM_LIBTOOLFLAGS) \
$(LIBTOOLFLAGS) --mode=link $(CCLD) $(AM_CFLAGS) $(CFLAGS) \ $(LIBTOOLFLAGS) --mode=link $(CCLD) $(AM_CFLAGS) $(CFLAGS) \
@ -90,52 +90,49 @@ HEADERS = $(include_HEADERS)
ETAGS = etags ETAGS = etags
CTAGS = ctags CTAGS = ctags
DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST) DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
ACLOCAL = ${SHELL} /home/fbotelho/papers/conferences/djamel/cmph/missing --run aclocal-1.10 ACLOCAL = ${SHELL} /Users/davi/vc/cmph/missing --run aclocal-1.10
AMTAR = ${SHELL} /home/fbotelho/papers/conferences/djamel/cmph/missing --run tar AMTAR = ${SHELL} /Users/davi/vc/cmph/missing --run tar
AR = ar AR = ar
AUTOCONF = ${SHELL} /home/fbotelho/papers/conferences/djamel/cmph/missing --run autoconf AUTOCONF = ${SHELL} /Users/davi/vc/cmph/missing --run autoconf
AUTOHEADER = ${SHELL} /home/fbotelho/papers/conferences/djamel/cmph/missing --run autoheader AUTOHEADER = ${SHELL} /Users/davi/vc/cmph/missing --run autoheader
AUTOMAKE = ${SHELL} /home/fbotelho/papers/conferences/djamel/cmph/missing --run automake-1.10 AUTOMAKE = ${SHELL} /Users/davi/vc/cmph/missing --run automake-1.10
AWK = gawk AWK = awk
CC = gcc CC = gcc
CCDEPMODE = depmode=gcc3 CCDEPMODE = depmode=gcc3
CFLAGS = -O3 -Wall -Werror -lm CFLAGS = -g -O2
CPP = gcc -E CPP = gcc -E
CPPFLAGS = CPPFLAGS =
CXX = g++
CXXCPP = g++ -E
CXXDEPMODE = depmode=gcc3
CXXFLAGS = -g -O2
CYGPATH_W = echo CYGPATH_W = echo
DEFS = -DHAVE_CONFIG_H DEFS = -DHAVE_CONFIG_H
DEPDIR = .deps DEPDIR = .deps
DSYMUTIL = ECHO = echo
DUMPBIN =
ECHO_C = ECHO_C =
ECHO_N = -n ECHO_N = -n
ECHO_T = ECHO_T =
EGREP = /bin/grep -E EGREP = /usr/bin/grep -E
EXEEXT = EXEEXT =
FGREP = /bin/grep -F F77 =
FFLAGS =
GETCONF = getconf GETCONF = getconf
GREP = /bin/grep GREP = /usr/bin/grep
INSTALL = /usr/bin/install -c INSTALL = /usr/bin/install -c
INSTALL_DATA = ${INSTALL} -m 644 INSTALL_DATA = ${INSTALL} -m 644
INSTALL_PROGRAM = ${INSTALL} INSTALL_PROGRAM = ${INSTALL}
INSTALL_SCRIPT = ${INSTALL} INSTALL_SCRIPT = ${INSTALL}
INSTALL_STRIP_PROGRAM = $(install_sh) -c -s INSTALL_STRIP_PROGRAM = $(install_sh) -c -s
LD = /usr/bin/ld -m elf_x86_64
LDFLAGS = LDFLAGS =
LIBM =
LIBOBJS = LIBOBJS =
LIBS = LIBS =
LIBTOOL = $(SHELL) $(top_builddir)/libtool LIBTOOL = $(SHELL) $(top_builddir)/libtool
LIPO =
LN_S = ln -s LN_S = ln -s
LTLIBOBJS = LTLIBOBJS =
MAKEINFO = ${SHELL} /home/fbotelho/papers/conferences/djamel/cmph/missing --run makeinfo MAKEINFO = ${SHELL} /Users/davi/vc/cmph/missing --run makeinfo
MKDIR_P = /bin/mkdir -p MKDIR_P = .././install-sh -c -d
NM = /usr/bin/nm -B
NMEDIT =
OBJEXT = o OBJEXT = o
OTOOL =
OTOOL64 =
PACKAGE = cmph PACKAGE = cmph
PACKAGE_BUGREPORT = PACKAGE_BUGREPORT =
PACKAGE_NAME = PACKAGE_NAME =
@ -144,50 +141,49 @@ PACKAGE_TARNAME =
PACKAGE_VERSION = PACKAGE_VERSION =
PATH_SEPARATOR = : PATH_SEPARATOR = :
RANLIB = ranlib RANLIB = ranlib
SED = /bin/sed
SET_MAKE = SET_MAKE =
SHELL = /bin/bash SHELL = /bin/sh
STRIP = strip STRIP = strip
VERSION = 0.8 VERSION = 0.9
abs_builddir = /home/fbotelho/papers/conferences/djamel/cmph/src abs_builddir = /Users/davi/vc/cmph/src
abs_srcdir = /home/fbotelho/papers/conferences/djamel/cmph/src abs_srcdir = /Users/davi/vc/cmph/src
abs_top_builddir = /home/fbotelho/papers/conferences/djamel/cmph abs_top_builddir = /Users/davi/vc/cmph
abs_top_srcdir = /home/fbotelho/papers/conferences/djamel/cmph abs_top_srcdir = /Users/davi/vc/cmph
ac_ct_CC = gcc ac_ct_CC = gcc
ac_ct_DUMPBIN = ac_ct_CXX = g++
ac_ct_F77 =
am__include = include am__include = include
am__leading_dot = . am__leading_dot = .
am__quote = am__quote =
am__tar = ${AMTAR} chof - "$$tardir" am__tar = ${AMTAR} chof - "$$tardir"
am__untar = ${AMTAR} xf - am__untar = ${AMTAR} xf -
bindir = ${exec_prefix}/bin bindir = ${exec_prefix}/bin
build = x86_64-unknown-linux-gnu build = i386-apple-darwin9.6.0
build_alias = build_alias =
build_cpu = x86_64 build_cpu = i386
build_os = linux-gnu build_os = darwin9.6.0
build_vendor = unknown build_vendor = apple
builddir = . builddir = .
datadir = ${datarootdir} datadir = ${datarootdir}
datarootdir = ${prefix}/share datarootdir = ${prefix}/share
docdir = ${datarootdir}/doc/${PACKAGE} docdir = ${datarootdir}/doc/${PACKAGE}
dvidir = ${docdir} dvidir = ${docdir}
exec_prefix = ${prefix} exec_prefix = ${prefix}
host = x86_64-unknown-linux-gnu host = i386-apple-darwin9.6.0
host_alias = host_alias =
host_cpu = x86_64 host_cpu = i386
host_os = linux-gnu host_os = darwin9.6.0
host_vendor = unknown host_vendor = apple
htmldir = ${docdir} htmldir = ${docdir}
includedir = ${prefix}/include includedir = ${prefix}/include
infodir = ${datarootdir}/info infodir = ${datarootdir}/info
install_sh = $(SHELL) /home/fbotelho/papers/conferences/djamel/cmph/install-sh install_sh = $(SHELL) /Users/davi/vc/cmph/install-sh
libdir = ${exec_prefix}/lib libdir = ${exec_prefix}/lib
libexecdir = ${exec_prefix}/libexec libexecdir = ${exec_prefix}/libexec
localedir = ${datarootdir}/locale localedir = ${datarootdir}/locale
localstatedir = ${prefix}/var localstatedir = ${prefix}/var
lt_ECHO = echo
mandir = ${datarootdir}/man mandir = ${datarootdir}/man
mkdir_p = /bin/mkdir -p mkdir_p = $(top_builddir)/./install-sh -c -d
oldincludedir = /usr/include oldincludedir = /usr/include
pdfdir = ${docdir} pdfdir = ${docdir}
prefix = /usr/local prefix = /usr/local
@ -201,15 +197,30 @@ target_alias =
top_builddir = .. top_builddir = ..
top_srcdir = .. top_srcdir = ..
lib_LTLIBRARIES = libcmph.la lib_LTLIBRARIES = libcmph.la
include_HEADERS = cmph.h cmph_types.h include_HEADERS = cmph.h cmph_types.h cmph_time.h
libcmph_la_SOURCES = hash.c jenkins_hash.c\ libcmph_la_SOURCES = hash.h hash.c \
vstack.c vqueue.c\ jenkins_hash.h jenkins_hash.c\
graph.c cmph.c cmph_structs.c\ hash_state.h debug.h \
chm.c bmz.c bmz8.c bdz.c bdz_ph.c\ vstack.h vstack.c vqueue.h vqueue.c\
buffer_manager.c buffer_entry.c\ graph.h graph.c bitbool.h \
brz.c fch.c fch_buckets.c \ cmph.h cmph.c cmph_structs.h cmph_structs.c\
select.c compressed_seq.c \ chm.h chm.c chm_structs.h \
chd_ph.c miller_rabin.c bmz.h bmz.c bmz_structs.h \
bmz8.h bmz8.c bmz8_structs.h \
bdz.h bdz.c bdz_structs.h \
bdz_ph.h bdz_ph.c bdz_structs_ph.h \
brz.h brz.c brz_structs.h \
fch.h fch.c fch_structs.h \
fch_buckets.h fch_buckets.c \
chd.h chd.c chd_structs.h \
chd_ph.h chd_ph.c chd_structs_ph.h \
miller_rabin.h miller_rabin.c \
buffer_manager.h buffer_manager.c \
buffer_entry.h buffer_entry.c\
select.h select.c select_lookup_tables.h \
compressed_seq.h compressed_seq.c \
compressed_rank.h compressed_rank.c \
cmph_time.h
libcmph_la_LDFLAGS = -version-info 0:0:0 libcmph_la_LDFLAGS = -version-info 0:0:0
cmph_SOURCES = main.c wingetopt.h wingetopt.c cmph_SOURCES = main.c wingetopt.h wingetopt.c
@ -253,8 +264,8 @@ install-libLTLIBRARIES: $(lib_LTLIBRARIES)
@list='$(lib_LTLIBRARIES)'; for p in $$list; do \ @list='$(lib_LTLIBRARIES)'; for p in $$list; do \
if test -f $$p; then \ if test -f $$p; then \
f=$(am__strip_dir) \ f=$(am__strip_dir) \
echo " $(LIBTOOL) $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=install $(libLTLIBRARIES_INSTALL) $(INSTALL_STRIP_FLAG) '$$p' '$(DESTDIR)$(libdir)/$$f'"; \ echo " $(LIBTOOL) --mode=install $(libLTLIBRARIES_INSTALL) $(INSTALL_STRIP_FLAG) '$$p' '$(DESTDIR)$(libdir)/$$f'"; \
$(LIBTOOL) $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=install $(libLTLIBRARIES_INSTALL) $(INSTALL_STRIP_FLAG) "$$p" "$(DESTDIR)$(libdir)/$$f"; \ $(LIBTOOL) --mode=install $(libLTLIBRARIES_INSTALL) $(INSTALL_STRIP_FLAG) "$$p" "$(DESTDIR)$(libdir)/$$f"; \
else :; fi; \ else :; fi; \
done done
@ -262,8 +273,8 @@ uninstall-libLTLIBRARIES:
@$(NORMAL_UNINSTALL) @$(NORMAL_UNINSTALL)
@list='$(lib_LTLIBRARIES)'; for p in $$list; do \ @list='$(lib_LTLIBRARIES)'; for p in $$list; do \
p=$(am__strip_dir) \ p=$(am__strip_dir) \
echo " $(LIBTOOL) $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=uninstall rm -f '$(DESTDIR)$(libdir)/$$p'"; \ echo " $(LIBTOOL) --mode=uninstall rm -f '$(DESTDIR)$(libdir)/$$p'"; \
$(LIBTOOL) $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=uninstall rm -f "$(DESTDIR)$(libdir)/$$p"; \ $(LIBTOOL) --mode=uninstall rm -f "$(DESTDIR)$(libdir)/$$p"; \
done done
clean-libLTLIBRARIES: clean-libLTLIBRARIES:
@ -285,8 +296,8 @@ install-binPROGRAMS: $(bin_PROGRAMS)
|| test -f $$p1 \ || test -f $$p1 \
; then \ ; then \
f=`echo "$$p1" | sed 's,^.*/,,;$(transform);s/$$/$(EXEEXT)/'`; \ f=`echo "$$p1" | sed 's,^.*/,,;$(transform);s/$$/$(EXEEXT)/'`; \
echo " $(INSTALL_PROGRAM_ENV) $(LIBTOOL) $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=install $(binPROGRAMS_INSTALL) '$$p' '$(DESTDIR)$(bindir)/$$f'"; \ echo " $(INSTALL_PROGRAM_ENV) $(LIBTOOL) --mode=install $(binPROGRAMS_INSTALL) '$$p' '$(DESTDIR)$(bindir)/$$f'"; \
$(INSTALL_PROGRAM_ENV) $(LIBTOOL) $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=install $(binPROGRAMS_INSTALL) "$$p" "$(DESTDIR)$(bindir)/$$f" || exit 1; \ $(INSTALL_PROGRAM_ENV) $(LIBTOOL) --mode=install $(binPROGRAMS_INSTALL) "$$p" "$(DESTDIR)$(bindir)/$$f" || exit 1; \
else :; fi; \ else :; fi; \
done done
@ -321,10 +332,12 @@ include ./$(DEPDIR)/bmz8.Plo
include ./$(DEPDIR)/brz.Plo include ./$(DEPDIR)/brz.Plo
include ./$(DEPDIR)/buffer_entry.Plo include ./$(DEPDIR)/buffer_entry.Plo
include ./$(DEPDIR)/buffer_manager.Plo include ./$(DEPDIR)/buffer_manager.Plo
include ./$(DEPDIR)/chd.Plo
include ./$(DEPDIR)/chd_ph.Plo include ./$(DEPDIR)/chd_ph.Plo
include ./$(DEPDIR)/chm.Plo include ./$(DEPDIR)/chm.Plo
include ./$(DEPDIR)/cmph.Plo include ./$(DEPDIR)/cmph.Plo
include ./$(DEPDIR)/cmph_structs.Plo include ./$(DEPDIR)/cmph_structs.Plo
include ./$(DEPDIR)/compressed_rank.Plo
include ./$(DEPDIR)/compressed_seq.Plo include ./$(DEPDIR)/compressed_seq.Plo
include ./$(DEPDIR)/fch.Plo include ./$(DEPDIR)/fch.Plo
include ./$(DEPDIR)/fch_buckets.Plo include ./$(DEPDIR)/fch_buckets.Plo
@ -387,8 +400,8 @@ ID: $(HEADERS) $(SOURCES) $(LISP) $(TAGS_FILES)
unique=`for i in $$list; do \ unique=`for i in $$list; do \
if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
done | \ done | \
$(AWK) '{ files[$$0] = 1; nonemtpy = 1; } \ $(AWK) ' { files[$$0] = 1; } \
END { if (nonempty) { for (i in files) print i; }; }'`; \ END { for (i in files) print i; }'`; \
mkid -fID $$unique mkid -fID $$unique
tags: TAGS tags: TAGS
@ -400,8 +413,8 @@ TAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
unique=`for i in $$list; do \ unique=`for i in $$list; do \
if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
done | \ done | \
$(AWK) '{ files[$$0] = 1; nonempty = 1; } \ $(AWK) ' { files[$$0] = 1; } \
END { if (nonempty) { for (i in files) print i; }; }'`; \ END { for (i in files) print i; }'`; \
if test -z "$(ETAGS_ARGS)$$tags$$unique"; then :; else \ if test -z "$(ETAGS_ARGS)$$tags$$unique"; then :; else \
test -n "$$unique" || unique=$$empty_fix; \ test -n "$$unique" || unique=$$empty_fix; \
$(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \ $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
@ -411,12 +424,13 @@ ctags: CTAGS
CTAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \ CTAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
$(TAGS_FILES) $(LISP) $(TAGS_FILES) $(LISP)
tags=; \ tags=; \
here=`pwd`; \
list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \ list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
unique=`for i in $$list; do \ unique=`for i in $$list; do \
if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
done | \ done | \
$(AWK) '{ files[$$0] = 1; nonempty = 1; } \ $(AWK) ' { files[$$0] = 1; } \
END { if (nonempty) { for (i in files) print i; }; }'`; \ END { for (i in files) print i; }'`; \
test -z "$(CTAGS_ARGS)$$tags$$unique" \ test -z "$(CTAGS_ARGS)$$tags$$unique" \
|| $(CTAGS) $(CTAGSFLAGS) $(AM_CTAGSFLAGS) $(CTAGS_ARGS) \ || $(CTAGS) $(CTAGSFLAGS) $(AM_CTAGSFLAGS) $(CTAGS_ARGS) \
$$tags $$unique $$tags $$unique

93
src/Makefile.in
View File

@ -1,8 +1,8 @@
# Makefile.in generated by automake 1.10.1 from Makefile.am. # Makefile.in generated by automake 1.10 from Makefile.am.
# @configure_input@ # @configure_input@
# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002, # Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
# 2003, 2004, 2005, 2006, 2007, 2008 Free Software Foundation, Inc. # 2003, 2004, 2005, 2006 Free Software Foundation, Inc.
# This Makefile.in is free software; the Free Software Foundation # This Makefile.in is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it, # gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved. # with or without modifications, as long as this notice is preserved.
@ -59,9 +59,9 @@ LTLIBRARIES = $(lib_LTLIBRARIES)
libcmph_la_LIBADD = libcmph_la_LIBADD =
am_libcmph_la_OBJECTS = hash.lo jenkins_hash.lo vstack.lo vqueue.lo \ am_libcmph_la_OBJECTS = hash.lo jenkins_hash.lo vstack.lo vqueue.lo \
graph.lo cmph.lo cmph_structs.lo chm.lo bmz.lo bmz8.lo bdz.lo \ graph.lo cmph.lo cmph_structs.lo chm.lo bmz.lo bmz8.lo bdz.lo \
bdz_ph.lo buffer_manager.lo buffer_entry.lo brz.lo fch.lo \ bdz_ph.lo brz.lo fch.lo fch_buckets.lo chd.lo chd_ph.lo \
fch_buckets.lo select.lo compressed_seq.lo chd.lo chd_ph.lo \ miller_rabin.lo buffer_manager.lo buffer_entry.lo select.lo \
miller_rabin.lo compressed_rank.lo compressed_seq.lo compressed_rank.lo
libcmph_la_OBJECTS = $(am_libcmph_la_OBJECTS) libcmph_la_OBJECTS = $(am_libcmph_la_OBJECTS)
libcmph_la_LINK = $(LIBTOOL) --tag=CC $(AM_LIBTOOLFLAGS) \ libcmph_la_LINK = $(LIBTOOL) --tag=CC $(AM_LIBTOOLFLAGS) \
$(LIBTOOLFLAGS) --mode=link $(CCLD) $(AM_CFLAGS) $(CFLAGS) \ $(LIBTOOLFLAGS) --mode=link $(CCLD) $(AM_CFLAGS) $(CFLAGS) \
@ -71,7 +71,7 @@ PROGRAMS = $(bin_PROGRAMS)
am_cmph_OBJECTS = main.$(OBJEXT) wingetopt.$(OBJEXT) am_cmph_OBJECTS = main.$(OBJEXT) wingetopt.$(OBJEXT)
cmph_OBJECTS = $(am_cmph_OBJECTS) cmph_OBJECTS = $(am_cmph_OBJECTS)
cmph_DEPENDENCIES = libcmph.la cmph_DEPENDENCIES = libcmph.la
DEFAULT_INCLUDES = -I.@am__isrc@ -I$(top_builddir) DEFAULT_INCLUDES = -I. -I$(top_builddir)@am__isrc@
depcomp = $(SHELL) $(top_srcdir)/depcomp depcomp = $(SHELL) $(top_srcdir)/depcomp
am__depfiles_maybe = depfiles am__depfiles_maybe = depfiles
COMPILE = $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \ COMPILE = $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \
@ -102,17 +102,21 @@ CCDEPMODE = @CCDEPMODE@
CFLAGS = @CFLAGS@ CFLAGS = @CFLAGS@
CPP = @CPP@ CPP = @CPP@
CPPFLAGS = @CPPFLAGS@ CPPFLAGS = @CPPFLAGS@
CXX = @CXX@
CXXCPP = @CXXCPP@
CXXDEPMODE = @CXXDEPMODE@
CXXFLAGS = @CXXFLAGS@
CYGPATH_W = @CYGPATH_W@ CYGPATH_W = @CYGPATH_W@
DEFS = @DEFS@ DEFS = @DEFS@
DEPDIR = @DEPDIR@ DEPDIR = @DEPDIR@
DSYMUTIL = @DSYMUTIL@ ECHO = @ECHO@
DUMPBIN = @DUMPBIN@
ECHO_C = @ECHO_C@ ECHO_C = @ECHO_C@
ECHO_N = @ECHO_N@ ECHO_N = @ECHO_N@
ECHO_T = @ECHO_T@ ECHO_T = @ECHO_T@
EGREP = @EGREP@ EGREP = @EGREP@
EXEEXT = @EXEEXT@ EXEEXT = @EXEEXT@
FGREP = @FGREP@ F77 = @F77@
FFLAGS = @FFLAGS@
GETCONF = @GETCONF@ GETCONF = @GETCONF@
GREP = @GREP@ GREP = @GREP@
INSTALL = @INSTALL@ INSTALL = @INSTALL@
@ -120,22 +124,15 @@ INSTALL_DATA = @INSTALL_DATA@
INSTALL_PROGRAM = @INSTALL_PROGRAM@ INSTALL_PROGRAM = @INSTALL_PROGRAM@
INSTALL_SCRIPT = @INSTALL_SCRIPT@ INSTALL_SCRIPT = @INSTALL_SCRIPT@
INSTALL_STRIP_PROGRAM = @INSTALL_STRIP_PROGRAM@ INSTALL_STRIP_PROGRAM = @INSTALL_STRIP_PROGRAM@
LD = @LD@
LDFLAGS = @LDFLAGS@ LDFLAGS = @LDFLAGS@
LIBM = @LIBM@
LIBOBJS = @LIBOBJS@ LIBOBJS = @LIBOBJS@
LIBS = @LIBS@ LIBS = @LIBS@
LIBTOOL = @LIBTOOL@ LIBTOOL = @LIBTOOL@
LIPO = @LIPO@
LN_S = @LN_S@ LN_S = @LN_S@
LTLIBOBJS = @LTLIBOBJS@ LTLIBOBJS = @LTLIBOBJS@
MAKEINFO = @MAKEINFO@ MAKEINFO = @MAKEINFO@
MKDIR_P = @MKDIR_P@ MKDIR_P = @MKDIR_P@
NM = @NM@
NMEDIT = @NMEDIT@
OBJEXT = @OBJEXT@ OBJEXT = @OBJEXT@
OTOOL = @OTOOL@
OTOOL64 = @OTOOL64@
PACKAGE = @PACKAGE@ PACKAGE = @PACKAGE@
PACKAGE_BUGREPORT = @PACKAGE_BUGREPORT@ PACKAGE_BUGREPORT = @PACKAGE_BUGREPORT@
PACKAGE_NAME = @PACKAGE_NAME@ PACKAGE_NAME = @PACKAGE_NAME@
@ -144,7 +141,6 @@ PACKAGE_TARNAME = @PACKAGE_TARNAME@
PACKAGE_VERSION = @PACKAGE_VERSION@ PACKAGE_VERSION = @PACKAGE_VERSION@
PATH_SEPARATOR = @PATH_SEPARATOR@ PATH_SEPARATOR = @PATH_SEPARATOR@
RANLIB = @RANLIB@ RANLIB = @RANLIB@
SED = @SED@
SET_MAKE = @SET_MAKE@ SET_MAKE = @SET_MAKE@
SHELL = @SHELL@ SHELL = @SHELL@
STRIP = @STRIP@ STRIP = @STRIP@
@ -154,7 +150,8 @@ abs_srcdir = @abs_srcdir@
abs_top_builddir = @abs_top_builddir@ abs_top_builddir = @abs_top_builddir@
abs_top_srcdir = @abs_top_srcdir@ abs_top_srcdir = @abs_top_srcdir@
ac_ct_CC = @ac_ct_CC@ ac_ct_CC = @ac_ct_CC@
ac_ct_DUMPBIN = @ac_ct_DUMPBIN@ ac_ct_CXX = @ac_ct_CXX@
ac_ct_F77 = @ac_ct_F77@
am__include = @am__include@ am__include = @am__include@
am__leading_dot = @am__leading_dot@ am__leading_dot = @am__leading_dot@
am__quote = @am__quote@ am__quote = @am__quote@
@ -185,7 +182,6 @@ libdir = @libdir@
libexecdir = @libexecdir@ libexecdir = @libexecdir@
localedir = @localedir@ localedir = @localedir@
localstatedir = @localstatedir@ localstatedir = @localstatedir@
lt_ECHO = @lt_ECHO@
mandir = @mandir@ mandir = @mandir@
mkdir_p = @mkdir_p@ mkdir_p = @mkdir_p@
oldincludedir = @oldincludedir@ oldincludedir = @oldincludedir@
@ -201,16 +197,30 @@ target_alias = @target_alias@
top_builddir = @top_builddir@ top_builddir = @top_builddir@
top_srcdir = @top_srcdir@ top_srcdir = @top_srcdir@
lib_LTLIBRARIES = libcmph.la lib_LTLIBRARIES = libcmph.la
include_HEADERS = cmph.h cmph_types.h include_HEADERS = cmph.h cmph_types.h cmph_time.h
libcmph_la_SOURCES = hash.c jenkins_hash.c\ libcmph_la_SOURCES = hash.h hash.c \
vstack.c vqueue.c\ jenkins_hash.h jenkins_hash.c\
graph.c cmph.c cmph_structs.c\ hash_state.h debug.h \
chm.c bmz.c bmz8.c bdz.c bdz_ph.c\ vstack.h vstack.c vqueue.h vqueue.c\
buffer_manager.c buffer_entry.c\ graph.h graph.c bitbool.h \
brz.c fch.c fch_buckets.c \ cmph.h cmph.c cmph_structs.h cmph_structs.c\
select.c compressed_seq.c \ chm.h chm.c chm_structs.h \
chd.c chd_ph.c miller_rabin.c \ bmz.h bmz.c bmz_structs.h \
compressed_rank.c bmz8.h bmz8.c bmz8_structs.h \
bdz.h bdz.c bdz_structs.h \
bdz_ph.h bdz_ph.c bdz_structs_ph.h \
brz.h brz.c brz_structs.h \
fch.h fch.c fch_structs.h \
fch_buckets.h fch_buckets.c \
chd.h chd.c chd_structs.h \
chd_ph.h chd_ph.c chd_structs_ph.h \
miller_rabin.h miller_rabin.c \
buffer_manager.h buffer_manager.c \
buffer_entry.h buffer_entry.c\
select.h select.c select_lookup_tables.h \
compressed_seq.h compressed_seq.c \
compressed_rank.h compressed_rank.c \
cmph_time.h
libcmph_la_LDFLAGS = -version-info 0:0:0 libcmph_la_LDFLAGS = -version-info 0:0:0
cmph_SOURCES = main.c wingetopt.h wingetopt.c cmph_SOURCES = main.c wingetopt.h wingetopt.c
@ -254,8 +264,8 @@ install-libLTLIBRARIES: $(lib_LTLIBRARIES)
@list='$(lib_LTLIBRARIES)'; for p in $$list; do \ @list='$(lib_LTLIBRARIES)'; for p in $$list; do \
if test -f $$p; then \ if test -f $$p; then \
f=$(am__strip_dir) \ f=$(am__strip_dir) \
echo " $(LIBTOOL) $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=install $(libLTLIBRARIES_INSTALL) $(INSTALL_STRIP_FLAG) '$$p' '$(DESTDIR)$(libdir)/$$f'"; \ echo " $(LIBTOOL) --mode=install $(libLTLIBRARIES_INSTALL) $(INSTALL_STRIP_FLAG) '$$p' '$(DESTDIR)$(libdir)/$$f'"; \
$(LIBTOOL) $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=install $(libLTLIBRARIES_INSTALL) $(INSTALL_STRIP_FLAG) "$$p" "$(DESTDIR)$(libdir)/$$f"; \ $(LIBTOOL) --mode=install $(libLTLIBRARIES_INSTALL) $(INSTALL_STRIP_FLAG) "$$p" "$(DESTDIR)$(libdir)/$$f"; \
else :; fi; \ else :; fi; \
done done
@ -263,8 +273,8 @@ uninstall-libLTLIBRARIES:
@$(NORMAL_UNINSTALL) @$(NORMAL_UNINSTALL)
@list='$(lib_LTLIBRARIES)'; for p in $$list; do \ @list='$(lib_LTLIBRARIES)'; for p in $$list; do \
p=$(am__strip_dir) \ p=$(am__strip_dir) \
echo " $(LIBTOOL) $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=uninstall rm -f '$(DESTDIR)$(libdir)/$$p'"; \ echo " $(LIBTOOL) --mode=uninstall rm -f '$(DESTDIR)$(libdir)/$$p'"; \
$(LIBTOOL) $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=uninstall rm -f "$(DESTDIR)$(libdir)/$$p"; \ $(LIBTOOL) --mode=uninstall rm -f "$(DESTDIR)$(libdir)/$$p"; \
done done
clean-libLTLIBRARIES: clean-libLTLIBRARIES:
@ -286,8 +296,8 @@ install-binPROGRAMS: $(bin_PROGRAMS)
|| test -f $$p1 \ || test -f $$p1 \
; then \ ; then \
f=`echo "$$p1" | sed 's,^.*/,,;$(transform);s/$$/$(EXEEXT)/'`; \ f=`echo "$$p1" | sed 's,^.*/,,;$(transform);s/$$/$(EXEEXT)/'`; \
echo " $(INSTALL_PROGRAM_ENV) $(LIBTOOL) $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=install $(binPROGRAMS_INSTALL) '$$p' '$(DESTDIR)$(bindir)/$$f'"; \ echo " $(INSTALL_PROGRAM_ENV) $(LIBTOOL) --mode=install $(binPROGRAMS_INSTALL) '$$p' '$(DESTDIR)$(bindir)/$$f'"; \
$(INSTALL_PROGRAM_ENV) $(LIBTOOL) $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=install $(binPROGRAMS_INSTALL) "$$p" "$(DESTDIR)$(bindir)/$$f" || exit 1; \ $(INSTALL_PROGRAM_ENV) $(LIBTOOL) --mode=install $(binPROGRAMS_INSTALL) "$$p" "$(DESTDIR)$(bindir)/$$f" || exit 1; \
else :; fi; \ else :; fi; \
done done
@ -390,8 +400,8 @@ ID: $(HEADERS) $(SOURCES) $(LISP) $(TAGS_FILES)
unique=`for i in $$list; do \ unique=`for i in $$list; do \
if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
done | \ done | \
$(AWK) '{ files[$$0] = 1; nonemtpy = 1; } \ $(AWK) ' { files[$$0] = 1; } \
END { if (nonempty) { for (i in files) print i; }; }'`; \ END { for (i in files) print i; }'`; \
mkid -fID $$unique mkid -fID $$unique
tags: TAGS tags: TAGS
@ -403,8 +413,8 @@ TAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
unique=`for i in $$list; do \ unique=`for i in $$list; do \
if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
done | \ done | \
$(AWK) '{ files[$$0] = 1; nonempty = 1; } \ $(AWK) ' { files[$$0] = 1; } \
END { if (nonempty) { for (i in files) print i; }; }'`; \ END { for (i in files) print i; }'`; \
if test -z "$(ETAGS_ARGS)$$tags$$unique"; then :; else \ if test -z "$(ETAGS_ARGS)$$tags$$unique"; then :; else \
test -n "$$unique" || unique=$$empty_fix; \ test -n "$$unique" || unique=$$empty_fix; \
$(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \ $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
@ -414,12 +424,13 @@ ctags: CTAGS
CTAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \ CTAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
$(TAGS_FILES) $(LISP) $(TAGS_FILES) $(LISP)
tags=; \ tags=; \
here=`pwd`; \
list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \ list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
unique=`for i in $$list; do \ unique=`for i in $$list; do \
if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
done | \ done | \
$(AWK) '{ files[$$0] = 1; nonempty = 1; } \ $(AWK) ' { files[$$0] = 1; } \
END { if (nonempty) { for (i in files) print i; }; }'`; \ END { for (i in files) print i; }'`; \
test -z "$(CTAGS_ARGS)$$tags$$unique" \ test -z "$(CTAGS_ARGS)$$tags$$unique" \
|| $(CTAGS) $(CTAGSFLAGS) $(AM_CTAGSFLAGS) $(CTAGS_ARGS) \ || $(CTAGS) $(CTAGSFLAGS) $(AM_CTAGSFLAGS) $(CTAGS_ARGS) \
$$tags $$unique $$tags $$unique

18
src/cmph.c
View File

@ -1,14 +1,14 @@
#include "cmph.h" #include "cmph.h"
#include "cmph_structs.h" #include "cmph_structs.h"
#include "chm.h" #include "chm.h"
#include "bmz.h" /* included -- Fabiano */ #include "bmz.h"
#include "bmz8.h" /* included -- Fabiano */ #include "bmz8.h"
#include "brz.h" /* included -- Fabiano */ #include "brz.h"
#include "fch.h" /* included -- Fabiano */ #include "fch.h"
#include "bdz.h" /* included -- Fabiano */ #include "bdz.h"
#include "bdz_ph.h" /* included -- Fabiano */ #include "bdz_ph.h"
#include "chd_ph.h" /* included -- Fabiano */ #include "chd_ph.h"
#include "chd.h" /* included -- Fabiano */ #include "chd.h"
#include <stdlib.h> #include <stdlib.h>
#include <assert.h> #include <assert.h>
@ -16,7 +16,7 @@
//#define DEBUG //#define DEBUG
#include "debug.h" #include "debug.h"
const char *cmph_names[] = {"bmz", "bmz8", "chm", "brz", "fch", "bdz", "bdz_ph", "chd_ph", "chd", NULL }; /* included -- Fabiano */ const char *cmph_names[] = {"bmz", "bmz8", "chm", "brz", "fch", "bdz", "bdz_ph", "chd_ph", "chd", NULL };
typedef struct typedef struct
{ {

3
src/cmph_types.h
View File

@ -35,7 +35,8 @@ typedef unsigned int cmph_uint32;
typedef enum { CMPH_HASH_JENKINS, CMPH_HASH_COUNT } CMPH_HASH; typedef enum { CMPH_HASH_JENKINS, CMPH_HASH_COUNT } CMPH_HASH;
extern const char *cmph_hash_names[]; extern const char *cmph_hash_names[];
typedef enum { CMPH_BMZ, CMPH_BMZ8, CMPH_CHM, CMPH_BRZ, CMPH_FCH, typedef enum { CMPH_BMZ, CMPH_BMZ8, CMPH_CHM, CMPH_BRZ, CMPH_FCH,
CMPH_BDZ, CMPH_BDZ_PH, CMPH_CHD_PH, CMPH_CHD, CMPH_COUNT } CMPH_ALGO; /* included -- Fabiano */ CMPH_BDZ, CMPH_BDZ_PH,
CMPH_CHD_PH, CMPH_CHD, CMPH_COUNT } CMPH_ALGO;
extern const char *cmph_names[]; extern const char *cmph_names[];
#endif #endif