#include "dp.h"
#define MACHIGAI 0
-#define OUTGAP0TRY 1
+#define OUTGAP0TRY 0
#define DEBUG 0
#define XXXXXXX 0
#define USE_PENALTY_EX 0
#define FASTMATCHCALC 1
-static float **impmtx = NULL;
-static int impalloclen = 0;
+static TLS float **impmtx = NULL;
+static TLS int impalloclen = 0;
float imp_match_out_sc( int i1, int j1 )
{
// fprintf( stderr, "imp+match = %f\n", impmtx[i1][j1] * fastathreshold );
float effij_kozo;
double effijx;
char *pt, *pt1, *pt2;
- static char *nocount1 = NULL;
- static char *nocount2 = NULL;
+ static TLS char *nocount1 = NULL;
+ static TLS char *nocount2 = NULL;
LocalHom *tmpptr;
+ if( seq1 == NULL )
+ {
+ if( impmtx ) FreeFloatMtx( impmtx );
+ impmtx = NULL;
+ if( nocount1 ) free( nocount1 );
+ nocount1 = NULL;
+ if( nocount2 ) free( nocount2 );
+ nocount2 = NULL;
+
+ return;
+ }
+
if( impalloclen < lgth1 + 2 || impalloclen < lgth2 + 2 )
{
if( impmtx ) FreeFloatMtx( impmtx );
void imp_match_init( float *imp, int clus1, int clus2, int lgth1, int lgth2, char **seq1, char **seq2, double *eff1, double *eff2, LocalHom ***localhom )
{
int dif, i, j, k1, k2, tmpint, start1, start2, end1, end2;
- static int impalloclen = 0;
+ static TLS int impalloclen = 0;
char *pt;
int allgap;
- static char *nocount1 = NULL;
- static char *nocount2 = NULL;
+ static TLS char *nocount1 = NULL;
+ static TLS char *nocount2 = NULL;
if( impalloclen < lgth1 + 2 || impalloclen < lgth2 + 2 )
{
char **seq1, char **seq2,
char **mseq1, char **mseq2,
float **cpmx1, float **cpmx2,
- int **ijp, int icyc, int jcyc )
+ int **ijp, int icyc, int jcyc,
+ int tailgp )
{
int i, j, l, iin, jin, ifi, jfi, lgth1, lgth2, k;
float wm;
}
#endif
- if( outgap == 1 )
+ if( tailgp == 1 )
;
else
{
return( 0.0 );
}
-float A__align( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, LocalHom ***localhom, float *impmatch, char *sgap1, char *sgap2, char *egap1, char *egap2 )
+float A__align( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, LocalHom ***localhom, float *impmatch, char *sgap1, char *sgap2, char *egap1, char *egap2, int *chudanpt, int chudanref, int *chudanres, int headgp, int tailgp )
/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
{
// int k;
float *mjpt, *prept, *curpt;
int *mpjpt;
#endif
- static float mi, *m;
- static int **ijp;
- static int mpi, *mp;
- static float *w1, *w2;
- static float *match;
- static float *initverticalw; /* kufuu sureba iranai */
- static float *lastverticalw; /* kufuu sureba iranai */
- static char **mseq1;
- static char **mseq2;
- static char **mseq;
- static float *ogcp1;
- static float *ogcp2;
- static float *fgcp1;
- static float *fgcp2;
- static float **cpmx1;
- static float **cpmx2;
- static int **intwork;
- static float **floatwork;
- static int orlgth1 = 0, orlgth2 = 0;
+ static TLS float mi, *m;
+ static TLS int **ijp;
+ static TLS int mpi, *mp;
+ static TLS float *w1, *w2;
+ static TLS float *match;
+ static TLS float *initverticalw; /* kufuu sureba iranai */
+ static TLS float *lastverticalw; /* kufuu sureba iranai */
+ static TLS char **mseq1;
+ static TLS char **mseq2;
+ static TLS char **mseq;
+ static TLS float *ogcp1;
+ static TLS float *ogcp2;
+ static TLS float *fgcp1;
+ static TLS float *fgcp2;
+ static TLS float **cpmx1;
+ static TLS float **cpmx2;
+ static TLS int **intwork;
+ static TLS float **floatwork;
+ static TLS int orlgth1 = 0, orlgth2 = 0;
float fpenalty = (float)penalty;
float *fgcp2pt;
float *ogcp2pt;
float ogcp1va;
+ if( seq1 == NULL )
+ {
+ if( orlgth1 )
+ {
+// fprintf( stderr, "## Freeing local arrays in A__align\n" );
+ orlgth1 = 0;
+ orlgth2 = 0;
+
+ imp_match_init_strict( NULL, 0, 0, 0, 0, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0 );
+
+ free( mseq1 );
+ free( mseq2 );
+ FreeFloatVec( w1 );
+ FreeFloatVec( w2 );
+ FreeFloatVec( match );
+ FreeFloatVec( initverticalw );
+ FreeFloatVec( lastverticalw );
+
+ FreeFloatVec( m );
+ FreeIntVec( mp );
+
+ FreeCharMtx( mseq );
+
+ FreeFloatVec( ogcp1 );
+ FreeFloatVec( ogcp2 );
+ FreeFloatVec( fgcp1 );
+ FreeFloatVec( fgcp2 );
+
+
+ FreeFloatMtx( cpmx1 );
+ FreeFloatMtx( cpmx2 );
+
+ FreeFloatMtx( floatwork );
+ FreeIntMtx( intwork );
+
+ }
+ else
+ {
+// fprintf( stderr, "## Not allocated\n" );
+ }
+ return( 0.0 );
+ }
+
+ lgth1 = strlen( seq1[0] );
+ lgth2 = strlen( seq2[0] );
+#if 1
+ if( lgth1 == 0 || lgth2 == 0 )
+ {
+ fprintf( stderr, "WARNING (Aalignmm): lgth1=%d, lgth2=%d\n", lgth1, lgth2 );
+ }
+ if( lgth1 == 0 && lgth2 == 0 )
+ return( 0.0 );
+
+ if( lgth1 == 0 )
+ {
+ for( i=0; i<icyc; i++ )
+ {
+ j = lgth2;
+ seq1[i][j] = 0;
+ while( j ) seq1[i][--j] = '-';
+// fprintf( stderr, "seq1[i] = %s\n", seq1[i] );
+ }
+ return( 0.0 );
+ }
+
+ if( lgth2 == 0 )
+ {
+ for( i=0; i<jcyc; i++ )
+ {
+ j = lgth1;
+ seq2[i][j] = 0;
+ while( j ) seq2[i][--j] = '-';
+// fprintf( stderr, "seq2[i] = %s\n", seq2[i] );
+ }
+ return( 0.0 );
+ }
+#endif
+
#if 0
fprintf( stderr, "#### eff in SA+++align\n" );
fprintf( stderr, "#### seq1[0] = %s\n", seq1[0] );
fprintf( stderr, "#### strlen( seq1[0] ) = %d\n", strlen( seq1[0] ) );
for( i=0; i<icyc; i++ ) fprintf( stderr, "eff1[%d] = %f\n", i, eff1[i] );
+ fprintf( stderr, "#### seq2[0] = %s\n", seq2[0] );
+ fprintf( stderr, "#### strlen( seq2[0] ) = %d\n", strlen( seq2[0] ) );
+ for( i=0; i<jcyc; i++ ) fprintf( stderr, "eff2[%d] = %f\n", i, eff2[i] );
#endif
if( orlgth1 == 0 )
{
}
- lgth1 = strlen( seq1[0] );
- lgth2 = strlen( seq2[0] );
-#if 0
- if( lgth1 == 0 || lgth2 == 0 )
- {
- fprintf( stderr, "WARNING (Aalignmm): lgth1=%d, lgth2=%d\n", lgth1, lgth2 );
- }
-#endif
if( lgth1 > orlgth1 || lgth2 > orlgth2 )
{
#endif
- if( outgap == 1 )
+ if( headgp == 1 )
{
for( i=1; i<lgth1+1; i++ )
{
else
lastverticalw[0] = currentw[lgth2-1];
- if( outgap ) lasti = lgth1+1; else lasti = lgth1;
+ if( tailgp ) lasti = lgth1+1; else lasti = lgth1;
#if XXXXXXX
fprintf( stderr, "currentw = \n" );
for( i=1; i<lasti; i++ )
{
+
+#ifdef enablemultithread
+// fprintf( stderr, "chudan = %d, %d\n", *chudanpt, chudanref );
+ if( chudanpt && *chudanpt != chudanref )
+ {
+// fprintf( stderr, "\n\n## CHUUDAN!!! S\n" );
+ *chudanres = 1;
+ return( -1.0 );
+ }
+#endif
wtmp = previousw;
previousw = currentw;
currentw = wtmp;
lastj = lgth2+1;
for( j=1; j<lastj; j++ )
{
+#ifdef xxxenablemultithread
+// fprintf( stderr, "chudan = %d, %d\n", *chudanpt, chudanref );
+ if( chudanpt && *chudanpt != chudanref )
+ {
+// fprintf( stderr, "\n\n## CHUUDAN!!! S\n" );
+ *chudanres = 1;
+ return( -1.0 );
+ }
+#endif
wm = *prept;
*ijppt = 0;
Atracking_localhom( impmatch, currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp, icyc, jcyc );
}
else
- Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp, icyc, jcyc );
+ Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp, icyc, jcyc, tailgp );
// fprintf( stderr, "### impmatch = %f\n", *impmatch );
for( i=0; i<icyc; i++ ) strcpy( seq1[i], mseq1[i] );
for( j=0; j<jcyc; j++ ) strcpy( seq2[j], mseq2[j] );
- /*
+#if 0
fprintf( stderr, "\n" );
for( i=0; i<icyc; i++ ) fprintf( stderr, "%s\n", mseq1[i] );
fprintf( stderr, "#####\n" );
for( j=0; j<jcyc; j++ ) fprintf( stderr, "%s\n", mseq2[j] );
- */
+#endif
// fprintf( stderr, "wm = %f\n", wm );
float *mjpt, *prept, *curpt;
int *mpjpt;
#endif
- static float mi, *m;
- static int **ijp;
- static int mpi, *mp;
- static float *w1, *w2;
- static float *match;
- static float *initverticalw; /* kufuu sureba iranai */
- static float *lastverticalw; /* kufuu sureba iranai */
- static char **mseq1;
- static char **mseq2;
- static char **mseq;
- static float *ogcp1;
- static float *ogcp2;
- static float *fgcp1;
- static float *fgcp2;
- static float **cpmx1;
- static float **cpmx2;
- static int **intwork;
- static float **floatwork;
- static int orlgth1 = 0, orlgth2 = 0;
+ static TLS float mi, *m;
+ static TLS int **ijp;
+ static TLS int mpi, *mp;
+ static TLS float *w1, *w2;
+ static TLS float *match;
+ static TLS float *initverticalw; /* kufuu sureba iranai */
+ static TLS float *lastverticalw; /* kufuu sureba iranai */
+ static TLS char **mseq1;
+ static TLS char **mseq2;
+ static TLS char **mseq;
+ static TLS float *ogcp1;
+ static TLS float *ogcp2;
+ static TLS float *fgcp1;
+ static TLS float *fgcp2;
+ static TLS float **cpmx1;
+ static TLS float **cpmx2;
+ static TLS int **intwork;
+ static TLS float **floatwork;
+ static TLS int orlgth1 = 0, orlgth2 = 0;
float *fgcp2pt;
float *ogcp2pt;
float fgcp1va;
#endif
- if( outgap == 1 )
+ if( 1 ) // tsuneni outgap=1
{
for( i=1; i<lgth1+1; i++ )
{
else
lastverticalw[0] = currentw[lgth2-1];
- if( outgap ) lasti = lgth1+1; else lasti = lgth1;
+ if( 1 ) lasti = lgth1+1; else lasti = lgth1; // tsuneni outgap=1
#if XXXXXXX
fprintf( stderr, "currentw = \n" );
Atracking_localhom_gapmap( impmatch, currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp, icyc, jcyc, gapmap1, gapmap2 );
}
else
- Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp, icyc, jcyc );
+ Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp, icyc, jcyc, 1 );
// fprintf( stderr, "### impmatch = %f\n", *impmatch );
return( wm );
}
-float translate_and_Calign( char **mseq1, char **mseq2, double *effarr1, double *effarr2, int clus1, int clus2, int alloclen )
-{
- int i;
- float wm;
- char **result;
- char *seq = NULL, **aseq = NULL;
- double *effarr = NULL;
- int nseq = 0;
- int resultlen;
-
- if ( clus1 == 1 && clus2 != 1 )
- {
- seq = mseq1[0]; aseq = mseq2; effarr = effarr2; nseq = clus2+1;
-#if 0
- printf( "effarr in transl... = \n" );
- for( i=0; i<clus2; i++ ) printf( "%f ", effarr2[i] );
-#endif
- }
- else if( clus1 != 1 && clus2 == 1 )
- {
- seq = mseq2[0]; aseq = mseq1; effarr = effarr1; nseq = clus1+1;
- }
- else ErrorExit( "ERROR in translate_and_Calign" );
-
- result = Calignm1( &wm, aseq, seq, effarr, nseq-2, 0 );
-
- resultlen = strlen( result[0] );
- if( alloclen < resultlen || resultlen > N )
- {
- fprintf( stderr, "alloclen=%d, resultlen=%d, N=%d\n", alloclen, resultlen, N );
- ErrorExit( "LENGTH OVER!\n" );
- }
- for( i=0; i<nseq-1; i++ ) strcpy( aseq[i], result[i] );
- strcpy( seq, result[nseq-1] );
-
- return( 0.0 );
-}
git://source.jalview.org / jabaws.git / blobdiff