[med-svn] [Git][med-team/mafft][upstream] New upstream version 7.490
Nilesh Patra (@nilesh)
gitlab at salsa.debian.org
Tue Nov 2 13:35:06 GMT 2021
Nilesh Patra pushed to branch upstream at Debian Med / mafft
Commits:
e63b54a2 by Nilesh Patra at 2021-11-02T18:59:26+05:30
New upstream version 7.490
- - - - -
8 changed files:
- core/Salignmm.c
- core/dvtditr.c
- core/mafft.tmpl
- core/mltaln.h
- core/mltaln9.c
- core/tditeration.c
- core/treeOperation.c
- readme
Changes:
=====================================
core/Salignmm.c
=====================================
@@ -1208,7 +1208,6 @@ double A__align( double **n_dynamicmtx, int penalty_l, int penalty_ex_l, char **
FreeFloatMtx( doublework );
FreeIntMtx( intwork );
-
}
else
{
@@ -1817,6 +1816,9 @@ for( i=0; i<lgth2; i++ )
{
// fprintf( stderr, "\n\n## CHUUDAN!!! S\n" );
*chudanres = 1;
+ free( mseq1 ); // 2021/Sep
+ free( mseq2 ); // 2021/Sep
+ FreeCharMtx( mseq ); // 2021/Sep
return( -1.0 );
}
#endif
@@ -1900,6 +1902,9 @@ fprintf( stderr, "\n" );
if( chudanpt && *chudanpt != chudanref )
{
// fprintf( stderr, "\n\n## CHUUDAN!!! S\n" );
+ free( mseq1 ); // 2021/Sep
+ free( mseq2 ); // 2021/Sep
+ FreeCharMtx( mseq ); // 2021/Sep
*chudanres = 1;
return( -1.0 );
}
=====================================
core/dvtditr.c
=====================================
@@ -1139,15 +1139,27 @@ exit( 1 );
fprintf( stderr, "done\n" );
fprintf( trap_g, "done\n" );
- fclose( trap_g );
+// fclose( trap_g ); // -> closeFiles()
freeconstants();
+
devide = 0;
writePre( njob, name, nlen, res_g, 1 );
#if 0
writeData( stdout, njob, name, nlen, res_g, 1 );
#endif
+// 2021/Sep
+ FreeCharMtx( nogap1seq );
+ FreeCharMtx( seq );
+ FreeCharMtx( name );
+ free( seq_g ); // seq_g_bk de free sareteirunode
+ FreeCharMtx( res_g );
+ FreeCharMtx( aseq );
+ FreeCharMtx( bseq );
+ free( segment );
+ closeFiles();
+// 2021/Sep
if( spscoreout ) reporterr( "Unweighted sum-of-pairs score = %10.5f\n", sumofpairsscore( njob, res_g ) );
=====================================
core/mafft.tmpl
=====================================
@@ -1,7 +1,7 @@
#! /bin/bash
er=0;
myself=`dirname "$0"`/`basename "$0"`; export myself
-version="v7.487 (2021/Jul/25)"; export version
+version="v7.490 (2021/Oct/30)"; export version
LANG=C; export LANG
os=`uname`
progname=`basename "$0"`
@@ -951,8 +951,12 @@ if [ $# -gt 0 ]; then
# seektarget="-str"
elif [ "$1" = "--dash" ]; then
newdash=1
- distance="global" # can be override
- iterate=3 # can be override
+ if [ "$distance" != "local" -a "$distance" != "localgenaf" ]; then # 2021/Oct
+ distance="global"
+ fi
+ if [ "$iterate" -eq 0 ]; then # 2021/Oct
+ iterate=3
+ fi
elif [ "$1" = "--dashserver" ]; then
shift
dashserver="$1"
@@ -2358,7 +2362,8 @@ $ownlist"
if [ $anysymbol -eq 1 ]; then
mv orig infile # replaceu wo mukouka
fi
- sed 's/-//g' infile > dashin # gap nozoku
+# sed 's/-//g' infile > dashin # gap nozoku
+ awk '{if(/^>/)print; else {gsub( /-/,"" ); print;}}' infile > dashin
if [ ! -x "$prefix/dash_client" -o ! -x "$prefix/dash_client" ]; then
echo "" 1>&2
=====================================
core/mltaln.h
=====================================
@@ -36,7 +36,7 @@
-#define VERSION "7.487"
+#define VERSION "7.490"
#define SHOWVERSION reporterr( "%s (%s) Version " VERSION "\nalg=%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
=====================================
core/mltaln9.c
=====================================
@@ -11278,6 +11278,7 @@ double DSPscore( int s, char **seq ) /* method 3 deha nai */
#define SEGMENTSIZE 150
+
int searchAnchors( int nseq, char **seq, Segment *seg )
{
int i, j, k, kcyc;
@@ -11286,25 +11287,14 @@ int searchAnchors( int nseq, char **seq, Segment *seg )
int value = 0;
int len;
int length;
- static double *stra = NULL;
- static int alloclen = 0;
+ double *stra = NULL;
+ int alloclen = 0;
+ double threshold;
double cumscore;
- static double threshold;
len = strlen( seq[0] );
- if( alloclen < len )
- {
- if( alloclen )
- {
- FreeDoubleVec( stra );
- }
- else
- {
- threshold = (int)divThreshold / 100.0 * 600.0 * divWinSize;
- }
- stra = AllocateDoubleVec( len );
- alloclen = len;
- }
+ threshold = (int)divThreshold / 100.0 * 600.0 * divWinSize;
+ stra = AllocateDoubleVec( len );
for( i=0; i<len; i++ )
{
@@ -11382,6 +11372,8 @@ reporterr( "%d-%d length = %d\n", seg->start, seg->end, length );
#endif
value++;
}
+
+ FreeDoubleVec( stra );
return( value );
}
=====================================
core/tditeration.c
=====================================
@@ -269,11 +269,12 @@ static void freelocalarrays(
int **whichmtx
)
{
-// fprintf( stderr, "Skipping freelocalarrays\n" );
-// return;
+// fprintf( stderr, "freelocalarrays\n" );
int i;
if( commonIP ) FreeIntMtx( commonIP );
commonIP = NULL;
+ commonAlloc1 = 0;
+ commonAlloc2 = 0;
Falign( NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0, 0, 0, NULL, NULL, 0, NULL );
Falign_localhom( NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0, 0, 0, 0, NULL, NULL, NULL,NULL, 0, NULL );
D__align( NULL, NULL, NULL, NULL, NULL, 0, 0, 0, 0, NULL, NULL, NULL, NULL, NULL, NULL, 0, NULL, 0, 0 );
@@ -1330,7 +1331,7 @@ int TreeDependentIteration( int locnjob, char **name, int nlen[M],
Writeoptions( trap_g );
fflush( trap_g );
- if( effarr == NULL ) /* locnjob == njob ni kagiru */
+ if( 1 || effarr == NULL ) /* locnjob == njob ni kagiru */
{
indication1 = AllocateCharVec( 150 );
indication2 = AllocateCharVec( 150 );
@@ -2384,8 +2385,38 @@ int TreeDependentIteration( int locnjob, char **name, int nlen[M],
value = 2;
end:
- if( grouprna1 ) free( grouprna1 );
- if( grouprna2 ) free( grouprna2 );
+// if( grouprna1 ) free( grouprna1 );
+// if( grouprna2 ) free( grouprna2 );
+
+#if 1
+ freelocalarrays
+ (
+ NULL,
+ grouprna1, grouprna2,
+ rnapairboth,
+ indication1, indication2,
+ distarr,
+ effarr, effarrforlocalhom, effarr1, effarr2,
+ mseq1, mseq2,
+ NULL,
+ gapmap1, gapmap2,
+ effarr1_kozo, effarr2_kozo, effarr_kozo,
+ memlist, pairbuf,
+ localhomshrink,
+ swaplist,
+ smalldistmtx,
+ scoringmatrices,
+ eff1s, eff2s,
+ whichmtx
+ );
+ if( branchnode ) free( branchnode );
+ if( stopol) free( stopol );
+ if( mtx ) FreeDoubleMtx( mtx );
+ if( node ) FreeIntMtx( node );
+ if( branchWeight ) FreeDoubleMtx( branchWeight );
+ if( history) FreeFloatCub( history );
+ treeCnv( NULL, 0, 0, NULL, NULL ); // 2021/Sep
+#endif
// freelocalarrays
// (
// NULL,
@@ -2407,5 +2438,6 @@ int TreeDependentIteration( int locnjob, char **name, int nlen[M],
// );
// free( branchnode );
// free( stopol );
+//
return( value );
} /* int Tree... */
=====================================
core/treeOperation.c
=====================================
@@ -129,14 +129,25 @@ void stopolInit( int n, Node *stopol )
void treeCnv( Node *stopol, int locnseq, int ***topol, double **len, double **bw )
{
+ static int **tmpintvec = NULL;
+ static int numintvec = 0;
+ if( stopol == NULL )
+ {
+ while( --numintvec >= 0 )
+ {
+ free( tmpintvec[numintvec] );
+ }
+ free( tmpintvec );
+ numintvec = 0;
+ tmpintvec = NULL;
+ return;
+ }
int i;
NodeInCub parent;
int *count;
int ccount;
int rep;
int tmpint;
- static int **tmpintvec = NULL;
- static int numintvec = 0;
count = AllocateIntVec( 2 * locnseq ); /* oome */
if( !count ) ErrorExit( "Cannot allocate count.\n" );
=====================================
readme
=====================================
@@ -1,6 +1,6 @@
-----------------------------------------------------------------------
MAFFT: a multiple sequence alignment program
- version 7.487, 2021/Jul/25
+ version 7.490, 2021/Oct/30
http://mafft.cbrc.jp/alignment/software/
katoh at ifrec.osaka-u.ac.jp
View it on GitLab: https://salsa.debian.org/med-team/mafft/-/commit/e63b54a2e319f96084cd39fb0c2ed42cba90765f
--
View it on GitLab: https://salsa.debian.org/med-team/mafft/-/commit/e63b54a2e319f96084cd39fb0c2ed42cba90765f
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