Additional changes during vectorconf upgrade of HMMER, Infernal.

Removed all @license@ sedition tags from code files. Removed all "Copyright and license" sections from code, and toc's. Removed all SVN $Id$ and $URL$ tags. Updated copyright dates. eslDEBUGLEVEL is an integer, 0 if off; tests must be #if, not #ifdef.
EddyRivasLab · Jan 31, 2017 · 08d9df6 · 08d9df6
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commit 08d9df6
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diff --git a/LICENSE b/LICENSE
@@ -1,18 +1,18 @@
 Easel - a library of C functions for biological sequence analysis
 
 @EASEL_COPYRIGHT@
-Copyright (C) 2004-2016 Sean R. Eddy
+Copyright (C) 2004-2017 Sean R. Eddy
-Copyright (C) 2004-2016 Howard Hughes Medical Institute
+Copyright (C) 2004-2017 Howard Hughes Medical Institute
-Copyright (C) 2015-2016 President and Fellows of Harvard College
+Copyright (C) 2015-2017 President and Fellows of Harvard College
 Copyright (C) 2004-2006 Washington University School of Medicine
 
 Easel's code includes contributions from members of the Eddy/Rivas
 laboratory at Harvard University, the HMMER and Infernal development
-teams, and others, including:
+teams, and other colleagues, including:
 
    Tyler Camp        University of Texas, Austin
    Nick Carter       HHMI | Harvard University
-   Michael Farrar    deceased, 2010
+   Michael Farrar    Deceased, 2010
    Graeme Mitchison  Cambridge University
    Eric Nawrocki     National Center for Biotechnology Information (NCBI)
    Elena Rivas       Harvard University
@@ -24,14 +24,12 @@ appropriate places in individual files. Copyright holders and
 contributors include:
 
    Free Software Foundation, Inc.    configure	
-   Matteo Frigo                      aclocal.m4
+   (various authors)                 autoconf macros in m4/
-   Steven G. Johnson                 aclocal.m4
    Stephen Moshier                   esl_sse.c,esl_vmx.c   
    Julien Pommier                    esl_sse.c,esl_vmx.c   
    Sun Microsystems, Inc.            esl_stats.c::esl_erfc()
-   David Robert Nadeau               esl_stopwatch.c
+   David Robert Nadeau               espl_stopwatch.c
    Henry Spencer, U. of Toronto      esl_regexp.c
-   Christophe Tournayre              aclocal.m4
    David Wheeler                     easel.c::esl_tmpfile()
 
 

diff --git a/Makefile.in b/Makefile.in
@@ -61,7 +61,7 @@ SSE_CFLAGS     = @SSE_CFLAGS@
 AVX_CFLAGS     = @AVX_CFLAGS@
 AVX512_CFLAGS  = @AVX512_CFLAGS@
 NEON_CFLAGS    = @NEON_CFLAGS@
-ALTIVEC_CFLAGS = @ALTIVEC_CFLAGS@
+VMX_CFLAGS     = @VMX_CFLAGS@
 CPPFLAGS       = @CPPFLAGS@
 LDFLAGS        = @LDFLAGS@
 LIBGSL         = @LIBGSL@
@@ -95,7 +95,7 @@ endif
 #
 HDRS = 	easel.h\
 	esl_alphabet.h\
-	esl_altivec.h\
+	esl_vmx.h\
 	esl_avx.h\
 	esl_avx512.h\
 	esl_buffer.h\
@@ -236,15 +236,15 @@ SSE_OBJS     = esl_sse.o
 AVX_OBJS     = esl_avx.o
 AVX512_OBJS  = esl_avx512.o
 NEON_OBJS    = esl_neon.o
-ALTIVEC_OBJS = esl_altivec.o
+VMX_OBJS     = esl_vmx.o
-ALL_OBJS     = ${OBJS} ${SSE_OBJS} ${AVX_OBJS} ${AVX512_OBJS} ${NEON_OBJS} ${ALTIVEC_OBJS}
+ALL_OBJS     = ${OBJS} ${SSE_OBJS} ${AVX_OBJS} ${AVX512_OBJS} ${NEON_OBJS} ${VMX_OBJS}
 
 # ... and add those flags, using gnu make's target-specific variable setting:
 ${SSE_OBJS}:     SIMD_CFLAGS = ${SSE_CFLAGS}
 ${AVX_OBJS}:     SIMD_CFLAGS = ${AVX_CFLAGS}
 ${AVX512_OBJS}:  SIMD_CFLAGS = ${AVX512_CFLAGS}
 ${NEON_OBJS}:    SIMD_CFLAGS = ${NEON_CFLAGS}
-${ALTIVEC_OBJS}: SIMD_CFLAGS = ${ALTIVEC_CFLAGS}
+${VMX_OBJS}:     SIMD_CFLAGS = ${VMX_CFLAGS}
 
 
 
@@ -313,14 +313,14 @@ SSE_UTESTS     = esl_sse_utest
 AVX_UTESTS     =
 AVX512_UTESTS  = 
 NEON_UTESTS    = esl_neon_utest
-ALTIVEC_UTESTS = esl_altivec_utest
+VMX_UTESTS     = esl_vmx_utest
-ALL_UTESTS     = ${UTESTS} ${SSE_UTESTS} ${AVX_UTESTS} ${NEON_UTESTS} ${ALTIVEC_UTESTS}
+ALL_UTESTS     = ${UTESTS} ${SSE_UTESTS} ${AVX_UTESTS} ${NEON_UTESTS} ${VMX_UTESTS}
 
 ${SSE_UTESTS}:     SIMD_CFLAGS= ${SSE_CFLAGS}
 ${AVX_UTESTS}:     SIMD_CFLAGS= ${AVX_CFLAGS}
 ${AVX512_UTESTS}:  SIMD_CFLAGS= ${AVX512_CFLAGS}
 ${NEON_UTESTS}:    SIMD_CFLAGS= ${NEON_CFLAGS}
-${ALTIVEC_UTESTS}: SIMD_CFLAGS= ${ALTIVEC_CFLAGS}
+${VMX_UTESTS}:     SIMD_CFLAGS= ${VMX_CFLAGS}
 
 
 
@@ -334,14 +334,14 @@ SSE_EXPERIMENTS     =
 AVX_EXPERIMENTS     = 
 AVX512_EXPERIMENTS  = 
 NEON_EXPERIMENTS    =
-ALTIVEC_EXPERIMENTS =
+VMX_EXPERIMENTS     =
-ALL_EXPERIMENTS     = ${EXPERIMENTS} ${SSE_EXPERIMENTS} ${AVX_EXPERIMENTS} ${AVX512_EXPERIMENTS} ${NEON_EXPERIMENTS} ${ALTIVEC_EXPERIMENTS}
+ALL_EXPERIMENTS     = ${EXPERIMENTS} ${SSE_EXPERIMENTS} ${AVX_EXPERIMENTS} ${AVX512_EXPERIMENTS} ${NEON_EXPERIMENTS} ${VMX_EXPERIMENTS}
 
 ${SSE_EXPERIMENTS}:     SIMD_CFLAGS= ${SSE_CFLAGS}
 ${AVX_EXPERIMENTS}:     SIMD_CFLAGS= ${AVX_CFLAGS}
 ${AVX512_EXPERIMENTS}:  SIMD_CFLAGS= ${AVX512_CFLAGS}
 ${NEON_EXPERIMENTS}:    SIMD_CFLAGS= ${NEON_CFLAGS}
-${ALTIVEC_EXPERIMENTS}: SIMD_CFLAGS= ${ALTIVEC_CFLAGS}
+${VMX_EXPERIMENTS}:     SIMD_CFLAGS= ${VMX_CFLAGS}
 
 
 
@@ -357,14 +357,14 @@ SSE_BENCHMARKS     = esl_sse_benchmark
 AVX_BENCHMARKS     =
 AVX512_BENCHMARKS  =
 NEON_BENCHMARKS    = esl_neon_benchmark
-ALTIVEC_BENCHMARKS =
+VMX_BENCHMARKS     =
-ALL_BENCHMARKS     = ${BENCHMARKS} ${SSE_BENCHMARKS} ${AVX_BENCHMARKS} ${AVX512_BENCHMARKS} ${NEON_BENCHMARKS} ${ALTIVEC_BENCHMARKS}
+ALL_BENCHMARKS     = ${BENCHMARKS} ${SSE_BENCHMARKS} ${AVX_BENCHMARKS} ${AVX512_BENCHMARKS} ${NEON_BENCHMARKS} ${VMX_BENCHMARKS}
 
 ${SSE_BENCHMARKS}:     SIMD_CFLAGS= ${SSE_CFLAGS}
 ${AVX_BENCHMARKS}:     SIMD_CFLAGS= ${AVX_CFLAGS}
 ${AVX512_BENCHMARKS}:  SIMD_CFLAGS= ${AVX512_CFLAGS}
 ${NEON_BENCHMARKS}:    SIMD_CFLAGS= ${NEON_CFLAGS}
-${ALTIVEC_BENCHMARKS}: SIMD_CFLAGS= ${ALTIVEC_CFLAGS}
+${VMX_BENCHMARKS}:     SIMD_CFLAGS= ${VMX_CFLAGS}
 
 
 
@@ -462,14 +462,14 @@ SSE_EXAMPLES     = esl_sse_example
 AVX_EXAMPLES     =
 AVX512_EXAMPLES  = 
 NEON_EXAMPLES    = esl_neon_example
-ALTIVEC_EXAMPLES = esl_altivec_example
+VMX_EXAMPLES     = esl_vmx_example
-ALL_EXAMPLES     = ${EXAMPLES} ${SSE_EXAMPLES} ${AVX_EXAMPLES} ${AVX512_EXAMPLES} ${NEON_EXAMPLES} ${ALTIVEC_EXAMPLES} 
+ALL_EXAMPLES     = ${EXAMPLES} ${SSE_EXAMPLES} ${AVX_EXAMPLES} ${AVX512_EXAMPLES} ${NEON_EXAMPLES} ${VMX_EXAMPLES} 
 
 ${SSE_EXAMPLES}:     SIMD_CFLAGS= ${SSE_CFLAGS}
 ${AVX_EXAMPLES}:     SIMD_CFLAGS= ${AVX_CFLAGS}
 ${AVX512_EXAMPLES}:  SIMD_CFLAGS= ${AVX512_CFLAGS}
 ${NEON_EXAMPLES}:    SIMD_CFLAGS= ${NEON_CFLAGS}
-${ALTIVEC_EXAMPLES}: SIMD_CFLAGS= ${ALTIVEC_CFLAGS}
+${VMX_EXAMPLES}:     SIMD_CFLAGS= ${VMX_CFLAGS}
 
 
 
@@ -494,7 +494,7 @@ pdf:
 	${QUIET_SUBDIR0}documentation ${QUIET_SUBDIR1} pdf
 
 libeasel.a:  ${ALL_OBJS} 
-	${QUIET_AR}${AR} -r libeasel.a $(OBJS) $(SSE_OBJS) $(AVX_OBJS) $(AVX512_OBJS) $(NEON_OBJS) ${ALTIVEC_OBJS} > /dev/null 2>&1
+	${QUIET_AR}${AR} -r libeasel.a $(ALL_OBJS) > /dev/null 2>&1
 	@${RANLIB} libeasel.a
 
 ${ALL_OBJS}: %.o : %.c ${HDRS} esl_config.h

diff --git a/configure.ac b/configure.ac
@@ -14,7 +14,7 @@
 #
 #   shell variables:
 #      - defined as usual, e.g. esl_var=no
-#      - use within scope of the configure.ac script
+#      - use within scope of the configure script
 #
 # Contents:
 #   1. autoconf requirements
@@ -53,7 +53,7 @@ m4_include([m4/esl_sse.m4])
 m4_include([m4/esl_avx.m4])
 m4_include([m4/esl_avx512.m4])
 m4_include([m4/esl_neon.m4])
-m4_include([m4/esl_altivec.m4])
+m4_include([m4/esl_vmx.m4])
 
 m4_include([m4/ax_mpi.m4])
 m4_include([m4/ax_pthread.m4])
@@ -183,70 +183,35 @@ case $enable_debugging in
      *)  AC_MSG_ERROR([Unknown argument to --enable-debugging: $enable_debugging]);;
 esac
 
-# --enable-threads      Enable POSIX multithreading
-#
-# Uses ACX_PTHREAD macro from the GNU macro archive.
-# Back to my code to finish enabling pthreads...
-# Define these preprocessor variables:
-#     HAVE_PTHREAD
-#     HAVE_PTHREAD_SETCONCURRENCY
-#     HAVE_PTHREAD_ATTR_SETSCOPE
-#
-AC_ARG_ENABLE([threads],
-              [AS_HELP_STRING([--enable-threads],
-                 [enable POSIX multithreading support (default is check)])],
-	      [],
-              [enable_threads=check])
-
-case $enable_threads in 
-   yes)   check_threads=yes
-          ;;
-   no)    check_threads=no
-          ;;
-   check) check_threads=yes
-          ;;
-   *)     check_threads=no
-          AC_MSG_NOTICE([Ignoring unknown argument to --enable-threads: $enable_threads])
-          ;;
-esac
-
-AS_IF([test "x$check_threads" != xno],
-      [ACX_PTHREAD([AC_DEFINE(HAVE_PTHREAD)
-                    AC_SUBST(PTHREAD_LIBS)
-                    AC_SUBST(PTHREAD_CFLAGS)],
-                   [if test "x$enable_threads" != xcheck; then
-                      AC_MSG_FAILURE([POSIX multithreading failed])
-                    fi])])
-
 AC_ARG_ENABLE(gcov,    [AS_HELP_STRING([--enable-gcov],    [compile for code coverage testing])],       enable_gcov=$enableval,    enable_gcov=no)
 AC_ARG_ENABLE(gprof,   [AS_HELP_STRING([--enable-gprof],   [compile for gcc code profiling])],          enable_gprof=$enableval,   enable_gprof=no)
 
 AC_ARG_ENABLE(sse,     [AS_HELP_STRING([--enable-sse],     [enable our SSE vector code])],              enable_sse=$enableval,     enable_sse=check)
 AC_ARG_ENABLE(avx,     [AS_HELP_STRING([--enable-avx],     [enable our AVX vector code])],              enable_avx=$enableval,     enable_avx=check)
 AC_ARG_ENABLE(avx512,  [AS_HELP_STRING([--enable-avx512],  [enable our AVX-512 vector code])],          enable_avx512=$enableval,  enable_avx512=check)
 AC_ARG_ENABLE(neon,    [AS_HELP_STRING([--enable-neon],    [enable our NEON vector code])] ,            enable_neon=$enableval,    enable_neon=check)
-AC_ARG_ENABLE(altivec, [AS_HELP_STRING([--enable-altivec], [enable our Altivec/VMX vector code])],      enable_altivec=$enableval, enable_altivec=check)
+AC_ARG_ENABLE(vmx,     [AS_HELP_STRING([--enable-vmx],     [enable our Altivec/VMX vector code])],      enable_vmx=$enableval,     enable_vmx=check)
 
 AC_ARG_ENABLE(threads, [AS_HELP_STRING([--enable-threads], [enable POSIX threads parallelization])],    enable_threads=$enableval, enable_threads=check)
 AC_ARG_ENABLE(mpi,     [AS_HELP_STRING([--enable-mpi],     [enable MPI parallelization])],              enable_mpi=$enableval,     enable_mpi=no)
 
 AC_ARG_WITH(gsl,       [AS_HELP_STRING([--with-gsl],       [use the GSL, GNU Scientific Library])],     with_gsl=$withval,         with_gsl=no)
 
 
+
+
+
+
 ################################################################
 # 5. Checks for programs, including ${CC} and its ${CFLAGS}
 ################################################################
 
 AC_PROG_CC
-AC_PROG_INSTALL
-# MPI :  set @CC@ to mpicc;
-#        set @MPILIBS@ if needed (usually not; mpicc deals w/ it);
-#        defines HAVE_MPI. 
-if test "$enable_mpi" = "yes"; then
-   ACX_MPI(,AC_MSG_ERROR([MPI library not found for --enable-mpi]))
-   CC=$MPICC
-fi
 AC_PROG_CPP
+AC_PROG_INSTALL
+AC_PROG_RANLIB
+AC_PATH_PROG([AR], [ar], [:], [$PATH:/usr/ccs/bin:/usr/xpg4/bin])
+
 
 # AC_PROG_CC_STDC wants to append -c99 to icc; icc doesn't like this.
 # To autodetect icc, we use the AX_COMPILER_VENDOR macro.
@@ -255,9 +220,6 @@ if test "$ax_cv_c_compiler_vendor" != "intel"; then
   AC_PROG_CC_STDC
 fi
 
-AC_PROG_RANLIB
-AC_PATH_PROG([AR],       [ar],       [:], [$PATH:/usr/ccs/bin:/usr/xpg4/bin])
-
 
 # Select our default optimization flags in CFLAGS.
 #  --enable-gcov, --enable-gprof, and --enable-debugging are mutually exclusive.
@@ -281,6 +243,30 @@ else
 fi
 
 
+# MPI :  set @CC@ to mpicc;
+#        set @MPILIBS@ if needed (usually not; mpicc deals w/ it);
+#        defines HAVE_MPI. 
+if test "$enable_mpi" = "yes"; then
+   AX_MPI(,AC_MSG_ERROR([MPI library not found for --enable-mpi]))
+   CC=$MPICC
+fi
+
+
+# Support for POSIX multithreading (we should generally have this)
+#
+if test "$enable_threads" != "no"; then
+  AX_PTHREAD([
+      AC_DEFINE(HAVE_PTHREAD)
+      AC_SUBST(PTHREAD_LIBS)
+      AC_SUBST(PTHREAD_CFLAGS)
+    ],[
+      if test "$enable_threads" = "yes"; then
+        AC_MSG_FAILURE([Unable to compile with POSIX multithreading.])
+      fi
+      enable_threads=no
+    ])
+fi
+
 
 # Support for vector implementations (xref SRE:H3/28)
 #
@@ -315,7 +301,7 @@ if test "$enable_sse" = "yes" || test "$enable_sse" = "check"; then
     enable_sse=yes
     ],[
     if test "$enable_sse" = "yes"; then
-      AC_MSG_ERROR([Unable to compile our SSE implementations. Try another compiler?])
+      AC_MSG_FAILURE([Unable to compile our SSE implementations. Try another compiler?])
     fi
     enable_sse=no
     ])
@@ -329,7 +315,7 @@ if test "$enable_avx" = "yes" || test "$enable_avx" = "check"; then
     enable_avx=yes
     ],[
     if test "$enable_avx" = "yes"; then
-      AC_MSG_ERROR([Unable to compile our AVX implementations. Try another compiler?])
+      AC_MSG_FAILURE([Unable to compile our AVX implementations. Try another compiler?])
     fi
     enable_avx=no
     ])
@@ -343,7 +329,7 @@ if test "$enable_avx512" = "yes" || test "$enable_avx512" = "check"; then
     enable_avx512=yes
     ],[
     if test "$enable_avx512" = "yes"; then
-      AC_MSG_ERROR([Unable to compile our AVX-512 implementations. Try another compiler?])
+      AC_MSG_FAILURE([Unable to compile our AVX-512 implementations. Try another compiler?])
     fi
     enable_avx512=no
     ])
@@ -358,23 +344,23 @@ if test "$enable_neon" = "yes" || test "$enable_neon" = "check"; then
     enable_neon=yes
     ],[
     if test "$enable_neon" = "yes"; then
-      AC_MSG_ERROR([Unable to compile our ARM NEON implementations. Try another compiler?])
+      AC_MSG_FAILURE([Unable to compile our ARM NEON implementations. Try another compiler?])
     fi
     enable_neon=no
     ])
 fi
 
-if test "$enable_altivec" = "yes" || test "$enable_altivec" = "check"; then
+if test "$enable_vmx" = "yes" || test "$enable_vmx" = "check"; then
-  ESL_ALTIVEC([
+  ESL_VMX([
-    AC_DEFINE(eslENABLE_ALTIVEC)
+    AC_DEFINE(eslENABLE_VMX)
-    ALTIVEC_CFLAGS=$esl_altivec_cflags
+    VMX_CFLAGS=$esl_vmx_cflags
-    AC_SUBST(ALTIVEC_CFLAGS)
+    AC_SUBST(VMX_CFLAGS)
-    enable_altivec=yes
+    enable_vmx=yes
     ],[
-    if test "$enable_altivec" = "yes"; then
+    if test "$enable_vmx" = "yes"; then
-      AC_MSG_ERROR([Unable to compile our Altivec/VMX implementations. Try another compiler?])
+      AC_MSG_FAILURE([Unable to compile our Altivec/VMX implementations. Try another compiler?])
     fi
-    enable_altivec=no
+    enable_vmx=no
     ])
 fi
 
@@ -555,12 +541,12 @@ AC_MSG_NOTICE([    SSE_CFLAGS= $SSE_CFLAGS])
 AC_MSG_NOTICE([    AVX_CFLAGS= $AVX_CFLAGS])
 AC_MSG_NOTICE([ AVX512_CFLAGS= $AVX512_CFLAGS])
 AC_MSG_NOTICE([   NEON_CFLAGS= $NEON_CFLAGS])
-AC_MSG_NOTICE([ALTIVEC_CFLAGS= $ALTIVEC_CFLAGS])
+AC_MSG_NOTICE([    VMX_CFLAGS= $VMX_CFLAGS])
 AC_MSG_NOTICE([])
 AC_MSG_NOTICE([           sse: $esl_have_sse])
 AC_MSG_NOTICE([           avx: $esl_have_avx])
 AC_MSG_NOTICE([        avx512: $esl_have_avx512])
 AC_MSG_NOTICE([          neon: $esl_have_neon])
-AC_MSG_NOTICE([       altivec: $esl_have_altivec])
+AC_MSG_NOTICE([           vmx: $esl_have_vmx])
 AC_MSG_NOTICE([])
 AC_MSG_NOTICE([          LIBS= ${LIBS} ${LIBGSL} ${PTHREAD_LIBS}])
diff --git a/demotic/00README b/demotic/00README
@@ -3,7 +3,6 @@ output of one program with the greek input of another program.
 
 original:   SRE, Wed Oct 25 16:32:09 2000
 into Easel: SRE, Fri Apr 16 16:10:25 2010
-SVN $Id$
 
   demotic_blast.pm   NCBI blastp; NCBI blastpgp; WU blastp
   demotic_fasta.pm   fasta; ssearch

diff --git a/demotic/demotic_blast.pm b/demotic/demotic_blast.pm
@@ -5,7 +5,6 @@
 #    and for PSIBLAST runs from checkpoint files (as I use in profmark).
 #    (SRE originated, 10/2000)
 #
-# SVN $Id$
 ############################################################################
 
 package demotic_blast;

diff --git a/demotic/demotic_fasta.pm b/demotic/demotic_fasta.pm
@@ -3,7 +3,6 @@
 #    Parses fasta or ssearch output, stores extracted information in convenient vars.
 #    SRE, Wed Jun 25 13:41:41 2003
 #
-#  SVN $Id$
 ############################################################################
 
 package demotic_fasta;