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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.
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cryptogenomicon committed Jan 31, 2017
1 parent c5830fa commit 08d9df616ecc25d9d2a00b0a16f04f5dac241199
Showing with 239 additions and 1,087 deletions.
  1. +7 −9 LICENSE
  2. +18 −18 Makefile.in
  3. +50 −64 configure.ac
  4. +0 −1 demotic/00README
  5. +0 −1 demotic/demotic_blast.pm
  6. +0 −1 demotic/demotic_fasta.pm
  7. +0 −1 demotic/demotic_h2.pm
  8. +0 −1 demotic/demotic_hmmer.pm
  9. +0 −1 devkit/rmanprocess.pl
  10. +0 −49 documentation/codestyle.tex
  11. +1 −1 documentation/copyright.tex
  12. +0 −1 easel.c
  13. +0 −6 easel.h
  14. +0 −1 esl_alphabet.c
  15. +0 −3 esl_alphabet.h
  16. +1 −1 esl_avx.c
  17. +2 −3 esl_avx.h
  18. +1 −1 esl_avx512.h
  19. +0 −7 esl_buffer.c
  20. +0 −3 esl_buffer.h
  21. +2 −8 esl_cluster.c
  22. +0 −5 esl_cluster.h
  23. +1 −1 esl_config.h.in
  24. +1 −7 esl_dirichlet.c
  25. +0 −5 esl_dirichlet.h
  26. +0 −6 esl_distance.c
  27. +1 −5 esl_distance.h
  28. +1 −7 esl_dmatrix.c
  29. +0 −6 esl_dmatrix.h
  30. +0 −8 esl_exponential.c
  31. +0 −5 esl_exponential.h
  32. +0 −11 esl_fileparser.c
  33. +1 −3 esl_fileparser.h
  34. +0 −8 esl_gamma.c
  35. +1 −5 esl_gamma.h
  36. +0 −8 esl_gencode.c
  37. +0 −3 esl_gencode.h
  38. +0 −6 esl_getopts.c
  39. +0 −7 esl_getopts.h
  40. +0 −8 esl_gev.c
  41. +1 −5 esl_gev.h
  42. +0 −8 esl_gumbel.c
  43. +0 −5 esl_gumbel.h
  44. +0 −8 esl_heap.c
  45. +0 −6 esl_heap.h
  46. +0 −6 esl_histogram.c
  47. +0 −5 esl_histogram.h
  48. +0 −9 esl_hmm.c
  49. +0 −5 esl_hmm.h
  50. +0 −8 esl_hyperexp.c
  51. +1 −7 esl_hyperexp.h
  52. +0 −10 esl_keyhash.c
  53. +1 −3 esl_keyhash.h
  54. +0 −1 esl_mem.c
  55. +0 −3 esl_mem.h
  56. +0 −12 esl_minimizer.c
  57. +0 −5 esl_minimizer.h
  58. +0 −9 esl_mixgev.c
  59. +1 −5 esl_mixgev.h
  60. +0 −4 esl_mpi.c
  61. +0 −9 esl_mpi.h
  62. +0 −4 esl_msa.c
  63. +0 −7 esl_msa.h
  64. +0 −9 esl_msacluster.c
  65. +0 −7 esl_msacluster.h
  66. +0 −6 esl_msafile.c
  67. +0 −6 esl_msafile.h
  68. +0 −7 esl_msafile2.c
  69. +1 −3 esl_msafile2.h
  70. +0 −6 esl_msafile_a2m.c
  71. +0 −3 esl_msafile_a2m.h
  72. +0 −8 esl_msafile_afa.c
  73. +0 −3 esl_msafile_afa.h
  74. +0 −4 esl_msafile_clustal.c
  75. +0 −3 esl_msafile_clustal.h
  76. +0 −7 esl_msafile_phylip.c
  77. +1 −3 esl_msafile_phylip.h
  78. +0 −7 esl_msafile_psiblast.c
  79. +1 −3 esl_msafile_psiblast.h
  80. +0 −9 esl_msafile_selex.c
  81. +0 −3 esl_msafile_selex.h
  82. +0 −6 esl_msafile_stockholm.c
  83. +0 −3 esl_msafile_stockholm.h
  84. +0 −3 esl_msashuffle.c
  85. +0 −5 esl_msashuffle.h
  86. +0 −7 esl_msaweight.c
  87. +0 −5 esl_msaweight.h
  88. +0 −8 esl_normal.c
  89. +0 −5 esl_normal.h
  90. +1 −11 esl_paml.c
  91. +0 −5 esl_paml.h
  92. +0 −8 esl_random.c
  93. +0 −3 esl_random.h
  94. +0 −8 esl_randomseq.c
  95. +0 −6 esl_randomseq.h
  96. +0 −16 esl_ratematrix.c
  97. +1 −5 esl_ratematrix.h
  98. +0 −8 esl_recorder.c
  99. +0 −6 esl_recorder.h
  100. +0 −11 esl_regexp.c
  101. +1 −5 esl_regexp.h
  102. +0 −11 esl_rootfinder.c
  103. +0 −6 esl_rootfinder.h
  104. +0 −9 esl_scorematrix.c
  105. +1 −3 esl_scorematrix.h
  106. +1 −3 esl_sq.h
  107. +0 −1 esl_sqio.c
  108. +1 −9 esl_sqio.h
  109. +0 −6 esl_sqio_ascii.c
  110. +0 −7 esl_sqio_ascii.h
  111. +0 −9 esl_sqio_ncbi.c
  112. +1 −7 esl_sqio_ncbi.h
  113. +0 −8 esl_ssi.c
  114. +0 −3 esl_ssi.h
  115. +0 −11 esl_stack.c
  116. +0 −6 esl_stack.h
  117. +0 −11 esl_stats.c
  118. +1 −6 esl_stats.h
  119. +0 −6 esl_stopwatch.c
  120. +0 −5 esl_stopwatch.h
  121. +0 −7 esl_stretchexp.c
  122. +0 −5 esl_stretchexp.h
  123. +0 −6 esl_swat.c
  124. +0 −7 esl_threads.c
  125. +0 −6 esl_threads.h
  126. +1 −7 esl_tree.c
  127. +0 −5 esl_tree.h
  128. +1 −8 esl_vectorops.c
  129. +0 −6 esl_vectorops.h
  130. +48 −48 esl_altivec.c → esl_vmx.c
  131. +5 −10 esl_altivec.h → esl_vmx.h
  132. +1 −7 esl_weibull.c
  133. +0 −5 esl_weibull.h
  134. +1 −8 esl_workqueue.c
  135. +0 −6 esl_workqueue.h
  136. +1 −6 esl_wuss.c
  137. +1 −3 esl_wuss.h
  138. +1 −6 interface_gsl.c
  139. +0 −2 interface_gsl.h
  140. +0 −6 interface_lapack.c
  141. +0 −2 interface_lapack.h
  142. +0 −68 m4/esl_altivec.m4
  143. +68 −0 m4/esl_vmx.m4
  144. +0 −3 miniapps/esl-afetch.c
  145. +0 −1 miniapps/esl-afetch.itest.pl
  146. +0 −3 miniapps/esl-alimanip.c
  147. +0 −1 miniapps/esl-alimap.c
  148. +1 −3 miniapps/esl-alimask.c
  149. +0 −3 miniapps/esl-alipid.c
  150. +1 −3 miniapps/esl-alistat.c
  151. +0 −2 miniapps/esl-cluster.c
  152. +1 −3 miniapps/esl-compstruct.c
  153. +0 −1 miniapps/esl-construct.c
  154. +0 −1 miniapps/esl-histplot.c
  155. +0 −1 miniapps/esl-mask.c
  156. +0 −1 miniapps/esl-mask.itest.pl
  157. +1 −3 miniapps/esl-reformat.c
  158. +0 −1 miniapps/esl-seqrange.c
  159. +0 −1 miniapps/esl-seqstat.c
  160. +0 −1 miniapps/esl-sfetch.c
  161. +1 −4 miniapps/esl-shuffle.c
  162. +0 −1 miniapps/esl-shuffle.itest.pl
  163. +1 −4 miniapps/esl-ssdraw.c
  164. +0 −3 miniapps/esl-weight.c
  165. +0 −1 testsuite/coverage_report.pl
  166. +0 −1 testsuite/i1-degen-residues.pl
  167. +0 −2 testsuite/i2-ncbi-indices.pl
  168. +0 −1 testsuite/i3-blank-gf.pl
  169. +2 −5 testsuite/testsuite.sqc
  170. +0 −2 testsuite/valgrind_report.pl
16 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) 2004-2016 Howard Hughes Medical Institute
Copyright (C) 2015-2016 President and Fellows of Harvard College
Copyright (C) 2004-2017 Sean R. Eddy
Copyright (C) 2004-2017 Howard Hughes Medical Institute
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
Steven G. Johnson aclocal.m4
(various authors) autoconf macros in 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()


@@ -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
ALL_OBJS = ${OBJS} ${SSE_OBJS} ${AVX_OBJS} ${AVX512_OBJS} ${NEON_OBJS} ${ALTIVEC_OBJS}
VMX_OBJS = esl_vmx.o
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
ALL_UTESTS = ${UTESTS} ${SSE_UTESTS} ${AVX_UTESTS} ${NEON_UTESTS} ${ALTIVEC_UTESTS}
VMX_UTESTS = esl_vmx_utest
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 =
ALL_EXPERIMENTS = ${EXPERIMENTS} ${SSE_EXPERIMENTS} ${AVX_EXPERIMENTS} ${AVX512_EXPERIMENTS} ${NEON_EXPERIMENTS} ${ALTIVEC_EXPERIMENTS}
VMX_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 =
ALL_BENCHMARKS = ${BENCHMARKS} ${SSE_BENCHMARKS} ${AVX_BENCHMARKS} ${AVX512_BENCHMARKS} ${NEON_BENCHMARKS} ${ALTIVEC_BENCHMARKS}
VMX_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
ALL_EXAMPLES = ${EXAMPLES} ${SSE_EXAMPLES} ${AVX_EXAMPLES} ${AVX512_EXAMPLES} ${NEON_EXAMPLES} ${ALTIVEC_EXAMPLES}
VMX_EXAMPLES = esl_vmx_example
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
@@ -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
ESL_ALTIVEC([
AC_DEFINE(eslENABLE_ALTIVEC)
ALTIVEC_CFLAGS=$esl_altivec_cflags
AC_SUBST(ALTIVEC_CFLAGS)
enable_altivec=yes
if test "$enable_vmx" = "yes" || test "$enable_vmx" = "check"; then
ESL_VMX([
AC_DEFINE(eslENABLE_VMX)
VMX_CFLAGS=$esl_vmx_cflags
AC_SUBST(VMX_CFLAGS)
enable_vmx=yes
],[
if test "$enable_altivec" = "yes"; then
AC_MSG_ERROR([Unable to compile our Altivec/VMX implementations. Try another compiler?])
if test "$enable_vmx" = "yes"; then
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}])
@@ -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
@@ -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;
@@ -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;

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