Description: Use automake
Author: Andreas Tille <tille@debian.org>
Last-Update: Wed, 12 Aug 2020 22:30:00 +0200

--- /dev/null
+++ b/Makefile.am
@@ -0,0 +1,155 @@
+lib_LTLIBRARIES  = libsquid.la
+
+libsquiddir=$(includedir)/biosquid
+libsquid_HEADERS =	dirichlet.h\
+	rk.h\
+	sqfuncs.h\
+	gki.h\
+	msa.h\
+	sre_random.h\
+	sre_stack.h\
+	ssi.h\
+	stopwatch.h\
+	vectorops.h
+
+COMMON_OBJS = \
+	a2m.c\
+	alignio.c\
+	clustal.c\
+	file.c\
+	getopt.c\
+	gki.c\
+	hsregex.c\
+	msa.c\
+	msf.c\
+	phylip.c\
+	selex.c\
+	sqerror.c\
+	sqio.c\
+	squidcore.c\
+	sre_ctype.c\
+	sre_random.c\
+	sre_string.c\
+	ssi.c\
+	stockholm.c\
+	types.c\
+	vectorops.c
+
+libsquid_la_SOURCES = $(COMMON_OBJS)\
+	aligneval.c\
+	cluster.c\
+	dayhoff.c\
+	dirichlet.c\
+	eps.c\
+	iupac.c\
+	revcomp.c\
+	rk.c\
+	seqencode.c\
+	shuffle.c\
+	sre_math.c\
+	sre_stack.c\
+	stopwatch.c\
+	translate.c\
+	weight.c\
+	wuss.c
+
+libsquid_la_LDFLAGS = -version-info @LIB_VERSION@
+libsquid_la_LIBADD = @PVMLIBS@
+
+libsquid_la_CPPFLAGS = $(INCLUDES)
+
+bin_PROGRAMS =	afetch\
+	alistat\
+	compalign\
+	compstruct\
+	revcomp\
+	seqsplit\
+	seqstat\
+	sfetch\
+	shuffle\
+	sindex\
+	sreformat\
+	translate\
+	weight
+
+LDADD = -lsquid -lm
+
+bin_MANS =  afetch\
+	alistat\
+	compstruct\
+	seqstat\
+	sfetch\
+	shuffle\
+	sindex\
+	sreformat
+
+READMES = 00README INSTALL
+
+PRECONFHDRS = \
+	squid.h.in\
+	squidconf.h.in
+
+POSTCONFHDRS = \
+	squid.h\
+	squidconf.h
+
+afetch_SOURCES = afetch_main.c
+
+alistat_SOURCES = alistat_main.c\
+                  aligneval.c\
+                  cluster.c\
+                  sre_math.c\
+                  sre_stack.c
+
+compalign_SOURCES = compalign_main.c\
+                    aligneval.c
+
+compstruct_SOURCES = compstruct_main.c\
+                     sre_math.c\
+                     sre_stack.c\
+                     wuss.c
+
+revcomp_SOURCES = revcomp_main.c\
+                  revcomp.c\
+                  shuffle.c
+
+seqsplit_SOURCES = seqsplit_main.c
+
+seqstat_SOURCES = seqstat_main.c
+
+sfetch_SOURCES = sfetch_main.c\
+                 revcomp.c\
+                 shuffle.c
+
+shuffle_SOURCES = shuffle_main.c\
+                  iupac.c\
+                  shuffle.c
+
+sindex_SOURCES = sindex_main.c
+
+sreformat_SOURCES = sreformat_main.c\
+                    eps.c\
+                    shuffle.c\
+                    sre_stack.c\
+                    wuss.c
+
+translate_SOURCES = translate_main.c\
+                    iupac.c\
+                    revcomp.c\
+                    shuffle.c\
+                    sre_stack.c\
+                    translate.c
+
+weight_SOURCES = weight_main.c\
+                 aligneval.c\
+                 cluster.c\
+                 iupac.c\
+                 sre_math.c\
+                 sre_stack.c\
+                 weight.c
+
+
+check:	libsquid.a 
+	(cd Testsuite; make CC="$(CC)" CFLAGS="$(CFLAGS)")
+	(cd Testsuite; make check)
+
--- a/configure.ac
+++ b/configure.ac
@@ -36,8 +36,16 @@
 #
 AC_PREREQ(2.57)
 AC_INIT(SQUID, 1.9g, eddy@genetics.wustl.edu, squid)
+
+AM_INIT_AUTOMAKE([1.6 foreign dist-zip tar-ustar filename-length-max=299])
+LIB_VERSION=1:0
+AC_SUBST([LIB_VERSION])
+
 AC_MSG_NOTICE([configuring the SQUID library for your system.])
 
+# Write out squidconf.h header
+AC_CONFIG_HEADER(squidconf.h)
+
 SQUID_RELCODE="squid1_9g"
 SQUID_DATE="January 2003"
 SQUID_COPYRIGHT="Copyright (C) 1992-2003 HHMI/Washington University School of Medicine"
@@ -53,51 +61,28 @@ AC_SUBST(SQUID_LICENSE)
 AC_SUBST(SQUID_LICENSETAG)
 AC_SUBST(SQUID_VERSION)
 
+
 # Make preprocessor symbols.
-AC_DEFINE_UNQUOTED(SQUID_DATE, "$SQUID_DATE")
-AC_DEFINE_UNQUOTED(SQUID_COPYRIGHT, "$SQUID_COPYRIGHT")
-AC_DEFINE_UNQUOTED(SQUID_LICENSE, "$SQUID_LICENSE")
-AC_DEFINE_UNQUOTED(SQUID_VERSION, "$SQUID_VERSION")
+AC_DEFINE_UNQUOTED(SQUID_DATE, "$SQUID_DATE", "Release date")
+AC_DEFINE_UNQUOTED(SQUID_COPYRIGHT, "$SQUID_COPYRIGHT", "copyright info")
+AC_DEFINE_UNQUOTED(SQUID_LICENSE, "$SQUID_LICENSE", "Short license info")
+AC_DEFINE_UNQUOTED(SQUID_VERSION, "$SQUID_VERSION", "Version")
+
 
 
 # Checks for programs.
 #
 AC_PROG_CC
 AC_PROG_RANLIB
+AC_PROG_LIBTOOL
 AC_PATH_PROG([AR], [ar], [:], [$PATH:/usr/ccs/bin:/usr/xpg4/bin])
 
-# GNU make check; format of makefile dependency lines for executables.
-# original from John Darrington <j.darrington@elvis.murdoch.edu.au> 
-# w/ heavy modifications.
-#
-# We need this because GNU make and SYSV make use different systems
-# specifying variables for dependencies: $$@ in sysv, %: %.o in GNU.
-# Would love to hear a better way of doing this.
-# 
-# I use two different conventions in my Makefiles. Sometimes 
-# executable "foo" has a file "foo.c" - this is the HMMER convention.
-# Sometimes executable "foo" has a file "foo_main.c" - this is
-# the SQUID convention. The configure script sets the
-# EXEC_DEPENDENCY appropriately: here, HMMER style.
-#
-# This creates a function CHECK_GNU_MAKE, which we immediately call.
-# It sets an output variable EXEC_DEPENDENCY. 
-# This is used in the src/Makefile.in.
-#
-AC_DEFUN(CHECK_GNU_MAKE,[ 
-  AC_MSG_CHECKING(whether your make is GNU make)
-  foundGNUmake='nope, assuming sysv make.' ;
-  EXEC_DEPENDENCY=[\$\$\@_main.o] ;
-  if ( make --version nothing 2> /dev/null | grep GNU > /dev/null ) ;  then
-     foundGNUmake='yes, it is.' ;
-     EXEC_DEPENDENCY='%: %_main.o' ;
-  fi
-  AC_MSG_RESULT($foundGNUmake)
-  AC_SUBST(EXEC_DEPENDENCY)
-])
-CHECK_GNU_MAKE
+# We know we use GNU make, but we require this EXEC_DEPENDENCY
+
+EXEC_DEPENDENCY='%: %_main.o'
+AC_SUBST(EXEC_DEPENDENCY)
+
 
-	
 # ================================================================
 # Provide for unsigned integers of known size
 # Sets SQD_UINT16, 32, and 64.
@@ -162,11 +147,14 @@ AC_DEFUN(SQ_ARITHMETIC_FPOS_T, [
    fpos_arithmetic="no."
    AC_TRY_COMPILE([#include <stdio.h>],
       [int main(void) { fpos_t f1, f2; if (f1 == f2) f1 = 0;}],
-      [AC_DEFINE(ARITHMETIC_FPOS_T) 
-       fpos_arithmetic="yes."])
+      [ARITHMETIC_FPOS_T=1
+      fpos_arithmetic="yes."])
    AC_MSG_RESULT($fpos_arithmetic)
 ])
 SQ_ARITHMETIC_FPOS_T()
+
+AC_DEFINE(ARITHMETIC_FPOS_T, [], "have fpos_t")
+AC_SUBST(ARITHMETIC_FPOS_T)
 # %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
 # ================================================================
@@ -177,6 +165,7 @@ AC_CHECK_FUNCS(strtoull)
 AC_CHECK_FUNCS(ftello fseeko)
 AC_CHECK_FUNCS(ftello64 fseeko64)
 AC_CHECK_FUNCS(ftell64 fseek64)
+
 AC_CHECK_FUNC(stat64, 
    [AC_MSG_CHECKING(for struct stat64)
     stat64_struct="no!"	    
@@ -184,10 +173,12 @@ AC_CHECK_FUNC(stat64,
                     #include <sys/stat.h>
                     #include <unistd.h>],
                    [int main(void) { struct stat64 s1;} ],
-	           [AC_DEFINE(HAVE_STAT64)
+	           [HAVE_STAT64=1
                     stat64_struct="yes."])
     AC_MSG_RESULT($stat64_struct)]
 )
+AC_DEFINE(HAVE_STAT64, 0, "have struct stat64")
+AC_SUBST(HAVE_STAT64)
 AC_CHECK_SIZEOF(off_t)
 AC_CHECK_SIZEOF(off64_t)
 AC_CHECK_SIZEOF(fpos_t)
@@ -218,6 +209,7 @@ esac])
 
 
 
+AC_DEFINE(DEBUGLEVEL, 0, "Debugging level")
 # --enable-debugging=x    - set debugging level to <x> (1-3)
 # 
 # At all levels, including 0, replaces CFLAGS w/ "-g -Wall" (so it assumes gcc).
@@ -229,28 +221,28 @@ AC_ARG_ENABLE(debugging,
 [ case $enable_debugging in
    yes)  AC_MSG_NOTICE([enabled debugging diagnostics level 0 (CFLAGS only, no verbosity)])
          CFLAGS="-g -Wall"
-         AC_DEFINE(DEBUGLEVEL, 0)
+         DEBUGLEVEL=0
          ;;
      1)  AC_MSG_NOTICE([enabled debugging diagnostics level 1 (low verbosity)])
          CFLAGS="-g -Wall"
-         AC_DEFINE(DEBUGLEVEL, 1)
+         DEBUGLEVEL=1
          ;;
      2)  AC_MSG_NOTICE([enabled debugging diagnostics level 2 (moderate verbosity)])
          CFLAGS="-g -Wall"
-	 AC_DEFINE(DEBUGLEVEL, 2)
+	 DEBUGLEVEL=2
          ;;
      3)  AC_MSG_NOTICE([enabled debugging diagnostics level 3 (high verbosity)])
          CFLAGS="-g -Wall"
-	 AC_DEFINE(DEBUGLEVEL, 3)
+	 DEBUGLEVEL=3
          ;;
     no)  AC_MSG_NOTICE([debugging diagnostics disabled])
-         AC_DEFINE(DEBUGLEVEL, 0)
+         DEBUGLEVEL=0
          ;;
      *)  echo "Ignoring unknown argument to --enable-debugging: $enable_debugging"
 	 ;;
 esac])
 
-
+AC_SUBST(DEBUGLEVEL) 
 
 # --enable-lfs           Large File Summit (LFS) support for >2GB files
 # See: http://ftp.sas.com/standards/large.file/x_open.20Mar96.html
@@ -259,14 +251,22 @@ AC_ARG_ENABLE(lfs,
 [  --enable-lfs            enable LFS, Large File Support],
 [case $enable_lfs in
    yes) AC_MSG_NOTICE([configured for optional LFS, large file support])
-	AC_DEFINE(_LARGEFILE_SOURCE)
-	AC_DEFINE(_LARGEFILE64_SOURCE)
-	AC_DEFINE(_FILE_OFFSET_BITS, 64)
+	_LARGEFILE_SOURCE=1
+	_LARGEFILE64_SOURCE=1
+	_FILE_OFFSET_BITS=64
         ;;
    no)  ;;
     *)  echo "Ignoring unknown argument to --enable-lfs: $enable_lfs"
         ;;
 esac])
+AC_DEFINE(_LARGEFILE_SOURCE, 0, "Source supports large files")
+AC_DEFINE(_LARGEFILE64_SOURCE, 0, "Source supports large files")
+AC_DEFINE(_FILE_OFFSET_BITS, 64, "Size of file offset bits)
+AC_SUBST(_LARGEFILE_SOURCE)
+AC_SUBST(_LARGEFILE64_SOURCE)
+AC_SUBST(_FILE_OFFSET_BITS)
+
+
 
 
 
@@ -282,21 +282,17 @@ AC_ARG_ENABLE(pvm,
  	 PVMLIBDIR="-L${PVM_ROOT}/lib/${PVM_ARCH}"
 	 PVMINCDIR="-I${PVM_ROOT}/include"
 	 PVMLIBS="-lpvm3"
-	 AC_DEFINE(SRE_ENABLE_PVM)
+	 SRE_ENABLE_PVM=1
 	 ;;
    no)   AC_MSG_NOTICE([PVM (Parallel Virtual machine) support disabled])
          ;;
    *)    echo "Ignoring unknown argument to --enable-pvm: $enable_pvm"
 	 ;;
 esac])
 AC_SUBST(PVMLIBDIR)
 AC_SUBST(PVMINCDIR)
 AC_SUBST(PVMLIBS)
 
-
-# Write out squidconf.h header
-AC_CONFIG_HEADER(squidconf.h)
-
 # Write out Makefiles, and squid.h also has some output variable substitution.
 AC_CONFIG_FILES(Makefile)
 AC_CONFIG_FILES(Testsuite/Makefile)
--- a/Testsuite/Makefile.in
+++ b/Testsuite/Makefile.in
@@ -14,7 +14,7 @@
 SHELL  = /bin/sh
 CC     = @CC@
 DEFS   = @DEFS@
-LIBS   = -lsquid @LIBS@ -lm
+LIBS   = -lsquid @PVMLIBS@ @LIBS@ -lm
 
 TESTPROGS = iospeed rndspeed