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commit 20c547a7b8e437fe7702eafcd463cbb45f9744f4 Author: Andreas Tille <[email protected]> Date: Tue Sep 12 14:37:05 2017 +0200 New upstream version 7.310 --- core/Salignmm.c | 16 ++++++++-------- core/mafft.tmpl | 27 ++++++++++++++------------- core/mltaln.h | 2 +- core/mtxutl.c | 5 ++--- core/mtxutl.h | 2 ++ core/pairlocalalign.c | 3 ++- core/partSalignmm.c | 16 ++++++++-------- core/version.c | 2 +- readme | 2 +- 9 files changed, 39 insertions(+), 36 deletions(-) diff --git a/core/Salignmm.c b/core/Salignmm.c index 3fd40a2..a7ce530 100644 --- a/core/Salignmm.c +++ b/core/Salignmm.c @@ -1650,8 +1650,8 @@ double A__align_variousdist( int **which, double ***matrices, double **n_dynamic if( c != which[i][j] ) { - masklist1[c] = realloc( masklist1[c], sizeof( int ) * nmask[c]+1 ); - masklist2[c] = realloc( masklist2[c], sizeof( int ) * nmask[c]+1 ); + masklist1[c] = realloc( masklist1[c], sizeof( int ) * (nmask[c]+1) ); + masklist2[c] = realloc( masklist2[c], sizeof( int ) * (nmask[c]+1) ); masklist1[c][nmask[c]] = i; masklist2[c][nmask[c]] = j; @@ -2071,8 +2071,8 @@ for( i=0; i<lgth2; i++ ) if( chudanpt && *chudanpt != chudanref ) { // fprintf( stderr, "\n\n## CHUUDAN!!! S\n" ); - if( masklist1 ) FreeIntMtx( masklist1 ); masklist1 = NULL; - if( masklist2 ) FreeIntMtx( masklist2 ); masklist2 = NULL; + if( masklist1 ) freeintmtx( masklist1, maxdistclass ); masklist1 = NULL; + if( masklist2 ) freeintmtx( masklist2, maxdistclass ); masklist2 = NULL; if( nmask ) free( nmask ); nmask = NULL; *chudanres = 1; return( -1.0 ); @@ -2175,8 +2175,8 @@ fprintf( stderr, "\n" ); if( chudanpt && *chudanpt != chudanref ) { // fprintf( stderr, "\n\n## CHUUDAN!!! S\n" ); - if( masklist1 ) FreeIntMtx( masklist1 ); masklist1 = NULL; - if( masklist2 ) FreeIntMtx( masklist2 ); masklist2 = NULL; + if( masklist1 ) freeintmtx( masklist1, maxdistclass ); masklist1 = NULL; + if( masklist2 ) freeintmtx( masklist2, maxdistclass ); masklist2 = NULL; if( nmask ) free( nmask ); nmask = NULL; *chudanres = 1; return( -1.0 ); @@ -2353,8 +2353,8 @@ fprintf( stderr, "\n" ); // fprintf( stderr, "wm = %f\n", wm ); - if( masklist1 ) FreeIntMtx( masklist1 ); masklist1 = NULL; - if( masklist2 ) FreeIntMtx( masklist2 ); masklist2 = NULL; + if( masklist1 ) freeintmtx( masklist1, maxdistclass ); masklist1 = NULL; + if( masklist2 ) freeintmtx( masklist2, maxdistclass ); masklist2 = NULL; if( nmask ) free( nmask ); nmask = NULL; return( wm ); diff --git a/core/mafft.tmpl b/core/mafft.tmpl index 545526f..8607652 100644 --- a/core/mafft.tmpl +++ b/core/mafft.tmpl @@ -1,8 +1,8 @@ -#! /bin/sh +#! /bin/bash er=0; myself=`dirname "$0"`/`basename "$0"`; export myself -version="v7.307 (2017/Jan/6)"; export version +version="v7.310 (2017/Mar/17)"; export version LANG=C; export LANG os=`uname` progname=`basename "$0"` @@ -36,7 +36,7 @@ if [ $# -gt 0 ]; then fi if [ -x "$prefix/version" ]; then - versionbin=`"$prefix/version" | awk '{print $1}'` # for cygwin + versionbin=`"$prefix/version"` # for cygwin 2.7 else versionbin="0.000" fi @@ -917,9 +917,9 @@ if [ $# -gt 0 ]; then TMPFILE=`mktemp -d /tmp/$progname.XXXXXXXXXX` fi - if [ $os = "cygwin" ]; then - TMPFILE=`cygpath -w $TMPFILE` - fi +# if [ $os = "cygwin" ]; then +# TMPFILE=`cygpath -w $TMPFILE` unnecessary for cygwin2.7 +# fi umask 077 # mkdir $TMPFILE || er=1 @@ -1934,8 +1934,8 @@ if [ $# -gt 0 ]; then - ( - cd $TMPFILE; +# ( # 2017/Mar/17 + pushd $TMPFILE > /dev/null; cat /dev/null > pre @@ -1969,14 +1969,14 @@ if [ $# -gt 0 ]; then fragarg="-F" # 2014/02/06, do not consider other additional sequences, even in the case of --add fi if [ $adjustdirection -eq 1 ]; then - "$prefix/makedirectionlist" $fragarg -C $numthreads -m -I $nadd -i infile -t 0.00 -r 5000 -o a > _direction + "$prefix/makedirectionlist" $fragarg -C $numthreads -m -I $nadd -i infile -t 0.00 -r 5000 -o a > _direction 2>>"$progressfile" elif [ $adjustdirection -eq 2 ]; then - "$prefix/makedirectionlist" $fragarg -C $numthreads -m -I $nadd -i infile -t 0.00 -r 100 -o a -d > _direction + "$prefix/makedirectionlist" $fragarg -C $numthreads -m -I $nadd -i infile -t 0.00 -r 100 -o a -d > _direction 2>>"$progressfile" fi - "$prefix/setdirection" $mergearg -d _direction -i infile > infiled || exit + "$prefix/setdirection" $mergearg -d _direction -i infile > infiled 2>>"$progressfile" || exit mv infiled infile if [ $anysymbol -eq 1 ]; then - "$prefix/setdirection" $mergearg -d _direction -i orig -r > origd || exit + "$prefix/setdirection" $mergearg -d _direction -i orig -r > origd 2>>"$progressfile" || exit mv origd orig fi fi @@ -2394,7 +2394,8 @@ if [ $# -gt 0 ]; then cat dasherr >>"$progressfile" fi - ) +# ) # 2017/Mar/17 + popd > /dev/null; if [ "$outputfile" = "" ]; then diff --git a/core/mltaln.h b/core/mltaln.h index 1f22778..962cea3 100644 --- a/core/mltaln.h +++ b/core/mltaln.h @@ -25,7 +25,7 @@ #include <sys/resource.h> // for setstacksize, 2016/Jun #endif -#define VERSION "7.307" +#define VERSION "7.310" #define SHOWVERSION reporterr( "%s (%s) Version " VERSION " alg=%c, model=%s, amax=%3.1f\n%d thread(s)\n\n", progName( argv[0] ), (dorp=='d')?"nuc":((nblosum==-2)?"text":"aa"), alg, modelname, specificityconsideration, nthread ) #define FFT_THRESHOLD 80 diff --git a/core/mtxutl.c b/core/mtxutl.c index 0870b9a..263176d 100644 --- a/core/mtxutl.c +++ b/core/mtxutl.c @@ -379,12 +379,11 @@ void FreeCharCub( char ***cub ) free( cub ); } -void freeintmtx( int **mtx, int ll1, int ll2 ) +void freeintmtx( int **mtx, int ll1 ) { int i; - for( i=0; i<ll1; i++ ) - free( (char *)mtx[i] ); + for( i=0; i<ll1; i++ ) free( (char *)mtx[i] ); free( (char *)mtx ); } diff --git a/core/mtxutl.h b/core/mtxutl.h index 0e6e701..b8a5e6f 100644 --- a/core/mtxutl.h +++ b/core/mtxutl.h @@ -52,3 +52,5 @@ void FreeShortVec( short * ); short **AllocateShortMtx( int, int ); void FreeShortMtx( short ** ); + +void freeintmtx( int **, int ); diff --git a/core/pairlocalalign.c b/core/pairlocalalign.c index e1e0dab..3d46fc5 100644 --- a/core/pairlocalalign.c +++ b/core/pairlocalalign.c @@ -2046,7 +2046,8 @@ static void *athread( void *arg ) // alg='R', alg='r' -> tsukawarenai. pthread_mutex_unlock( targ->mutex_counter ); - if( j == i+1 || j % 100 == 0 ) +// if( j == i+1 || j % 100 == 0 ) + if( j == i+1 && i % 10 == 0 ) { fprintf( stderr, "% 5d / %d (by thread %3d) \r", i, njob-nadd, thread_no ); // fprintf( stderr, "% 5d - %5d / %d (thread %d)\n", i, j, njob, thread_no ); diff --git a/core/partSalignmm.c b/core/partSalignmm.c index 4c16fdd..474ddb0 100644 --- a/core/partSalignmm.c +++ b/core/partSalignmm.c @@ -1492,8 +1492,8 @@ double partA__align_variousdist( int **which, double ***matrices, double **n_dyn if( c != which[i][j] ) { - masklist1[c] = realloc( masklist1[c], sizeof( int ) * nmask[c]+1 ); - masklist2[c] = realloc( masklist2[c], sizeof( int ) * nmask[c]+1 ); + masklist1[c] = realloc( masklist1[c], sizeof( int ) * (nmask[c]+1) ); + masklist2[c] = realloc( masklist2[c], sizeof( int ) * (nmask[c]+1) ); masklist1[c][nmask[c]] = i; masklist2[c][nmask[c]] = j; @@ -1843,8 +1843,8 @@ for( i=0; i<lgth2; i++ ) { // fprintf( stderr, "\n\n## CHUUDAN!!! i\n" ); *chudanres = 1; - if( masklist1 ) FreeIntMtx( masklist1 ); masklist1 = NULL; - if( masklist2 ) FreeIntMtx( masklist2 ); masklist2 = NULL; + if( masklist1 ) freeintmtx( masklist1, maxdistclass ); masklist1 = NULL; + if( masklist2 ) freeintmtx( masklist2, maxdistclass ); masklist2 = NULL; if( nmask ) free( nmask ); nmask = NULL; return( -1.0 ); } @@ -1926,8 +1926,8 @@ fprintf( stderr, "\n" ); { // fprintf( stderr, "\n\n## CHUUDAN!!! j\n" ); *chudanres = 1; - if( masklist1 ) FreeIntMtx( masklist1 ); masklist1 = NULL; - if( masklist2 ) FreeIntMtx( masklist2 ); masklist2 = NULL; + if( masklist1 ) freeintmtx( masklist1, maxdistclass ); masklist1 = NULL; + if( masklist2 ) freeintmtx( masklist2, maxdistclass ); masklist2 = NULL; if( nmask ) free( nmask ); nmask = NULL; return( -1.0 ); } @@ -2096,8 +2096,8 @@ fprintf( stderr, "\n" ); for( j=0; j<jcyc; j++ ) fprintf( stderr, "%s\n", mseq2[j] ); */ - if( masklist1 ) FreeIntMtx( masklist1 ); masklist1 = NULL; - if( masklist2 ) FreeIntMtx( masklist2 ); masklist2 = NULL; + if( masklist1 ) freeintmtx( masklist1, maxdistclass ); masklist1 = NULL; + if( masklist2 ) freeintmtx( masklist2, maxdistclass ); masklist2 = NULL; if( nmask ) free( nmask ); nmask = NULL; return( wm ); diff --git a/core/version.c b/core/version.c index e865301..64923aa 100644 --- a/core/version.c +++ b/core/version.c @@ -2,6 +2,6 @@ int main() { - fprintf( stdout, VERSION"\n" ); + fprintf( stdout, VERSION ); return( 0 ); } diff --git a/readme b/readme index 0323e79..46b3a1b 100644 --- a/readme +++ b/readme @@ -1,6 +1,6 @@ ----------------------------------------------------------------------- MAFFT: a multiple sequence alignment program - version 7.307beta, 2017/Jan/6 + version 7.310beta, 2017/Mar/17 http://mafft.cbrc.jp/alignment/software/ [email protected] -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/mafft.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
