From 46b81f2033652dcd018e895ed8d2c6450cfbf511 Mon Sep 17 00:00:00 2001 From: "Akifumi S. Tanabe" Date: Wed, 28 Nov 2018 05:23:52 +0900 Subject: [PATCH 1/2] Fix compilation problem on MinGW-w64 --- src/msa/pll_msa.c | 94 +++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 94 insertions(+) diff --git a/src/msa/pll_msa.c b/src/msa/pll_msa.c index 2edb225..e6d93a6 100644 --- a/src/msa/pll_msa.c +++ b/src/msa/pll_msa.c @@ -28,7 +28,9 @@ * @author Alexey Kozlov */ +#ifndef __MINGW32__ #include +#endif #include "pll_msa.h" #include "../util/pllmod_util.h" @@ -305,6 +307,97 @@ PLL_EXPORT double pllmod_msa_empirical_invariant_sites(pll_partition_t *partitio return empirical_pinv; } +#if defined __MINGW32__ +static int find_duplicate_strings_htable(char ** const strings, + unsigned long string_count, + unsigned long ** duplicates, + unsigned long * duplicate_count) +{ + if (!strings) + return PLL_FAILURE; + + unsigned long * tmpdup = (unsigned long *)malloc(string_count * 2 * + sizeof(unsigned long)); + + unsigned long * hash = (unsigned long *)calloc(string_count, + sizeof(unsigned long)); + + unsigned char * dupflag = (unsigned char *)calloc(string_count, + sizeof(unsigned char)); + + if (!hash || !tmpdup || !dupflag) + { + if (hash) + free(hash); + if (tmpdup) + free(tmpdup); + if (dupflag) + free(dupflag); + pllmod_set_error(PLL_ERROR_MEM_ALLOC, + "Cannot allocate memory for duplicates array"); + return PLL_FAILURE; + } + + *duplicate_count = 0; + + unsigned long i; + unsigned long j; + + for (i = 0; i < string_count; ++i) + { + for (j = 0; j < strlen(strings[i]); ++j) + hash[i] = hash[i] + (j+1) * (unsigned long) strings[i][j]; + } + + int coll = 0; + + for (i = 0; i < string_count; ++i) + { + if (dupflag[i]) + continue; + for (j = i+1; j < string_count; ++j) + { + if (hash[i] == hash[j]) + { + coll++; + if (strcmp(strings[i], strings[j]) == 0) + { + /* duplicate found, save it */ + tmpdup[(*duplicate_count)*2] = i; + tmpdup[(*duplicate_count)*2+1] = j; + (*duplicate_count)++; + dupflag[j] = 1; + } + } + } + } + +// printf("Collisions: %d, duplicates: %lu\n", coll, *duplicate_count); + + free(hash); + free(dupflag); + + if (*duplicate_count > 0) + { + *duplicates = (unsigned long *) realloc(tmpdup, (*duplicate_count) * 2 * + sizeof(unsigned long)); + + if (!(*duplicates)) + { + pllmod_set_error(PLL_ERROR_MEM_ALLOC, + "Cannot allocate memory for duplicates array"); + return PLL_FAILURE; + } + } + else + { + free(tmpdup); + *duplicates = NULL; + } + + return PLL_SUCCESS; +} +#else /* Find duplicates using hash table from search.h. This works best for short * strings, so we use this method for checking taxa names */ static int find_duplicate_strings_htable(char ** const strings, @@ -376,6 +469,7 @@ static int find_duplicate_strings_htable(char ** const strings, return PLL_SUCCESS; } +#endif /* Find duplicates using custom hash function optimized for long low-variance * strings - this method is used for detecting identical sequences */ From d9e982a338e8bad6037accfa26216a7dde075921 Mon Sep 17 00:00:00 2001 From: "Akifumi S. Tanabe" Date: Sat, 8 Aug 2020 16:45:53 +0900 Subject: [PATCH 2/2] Merge latest pll-modules --- .gitignore | 77 -------------------- .gitmodules | 4 - CMakeLists.txt | 0 ChangeLog.md | 0 LICENSE.txt | 0 Makefile.am | 0 README.md | 0 configure.ac | 0 doxy.cfg | 0 examples/consensus/Makefile | 0 examples/consensus/consensus.c | 0 examples/rf-distance/Makefile | 0 examples/rf-distance/rf-distance.c | 0 examples/spr-round/Makefile | 0 examples/spr-round/spr-round.c | 0 examples/weight-consensus/Makefile | 0 examples/weight-consensus/weight-consensus.c | 0 m4/ax_check_compile_flag.m4 | 0 m4/ax_ext.m4 | 0 m4/ax_gcc_x86_avx_xgetbv.m4 | 0 m4/ax_gcc_x86_cpuid.m4 | 0 src/CMakeLists.txt | 0 src/Makefile.am | 0 src/algorithm/CMakeLists.txt | 0 src/algorithm/Makefile.am | 0 src/algorithm/README.md | 0 src/algorithm/algo_callback.c | 0 src/algorithm/algo_callback.h | 0 src/algorithm/algo_search.c | 0 src/algorithm/pllmod_algorithm.c | 0 src/algorithm/pllmod_algorithm.h | 0 src/binary/CMakeLists.txt | 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Windows DLLs) -*.dll -*.so -*.so.* -*.dylib - -# Executables -*.exe -*.app -*.i*86 -*.x86_64 -*.hex - -# Debug files -*.dSYM/ - -# Autotools -config.* -configure -Makefile -Makefile.in -autom4te.cache/ -libtool -compile -missing -aclocal.m4 -depcomp -ltmain.sh -install-sh -stamp-h1 -ylwrap - -m4/libtool.m4 -m4/ltoptions.m4 -m4/ltsugar.m4 -m4/ltversion.m4 -m4/lt~obsolete.m4 -m4/pkg.m4 - -# Build files -.deps -.lib -.libs/ -.dirstamp - -# eclipse project files -.cproject -.project -.settings/ - -# binaries -examples/spr-round/spr-round -examples/rf-distance/rf-distance -examples/consensus/consensus - -# bison/flex generated -src/tree/lex_split.c -src/tree/split_utree.c -src/tree/split_utree.h - - diff --git a/.gitmodules b/.gitmodules deleted file mode 100644 index 245032b..0000000 --- a/.gitmodules +++ /dev/null @@ -1,4 +0,0 @@ -[submodule "libpll"] - path = libs/libpll - url = https://github.com/xflouris/libpll-2.git - branch = dev diff --git a/CMakeLists.txt b/CMakeLists.txt old mode 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