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JWS-112 Bumping version of Mafft to version 7.310.
[jabaws.git] / binaries / src / mafft / core / Falign.c
diff --git a/binaries/src/mafft/core/Falign.c b/binaries/src/mafft/core/Falign.c
index 250a0fa..71fd84c 100644 (file)
--- a/binaries/src/mafft/core/Falign.c
+++ b/binaries/src/mafft/core/Falign.c
@@ -159,7 +159,9 @@ static void mymergesort( int first, int last, Segment **seg )
 
        if( seg == NULL )
        {
-               free( work ); work = NULL;
+               if( work ) free( work ); 
+               work = NULL;
+               allo = 0;
                return;
        }
 
@@ -190,7 +192,9 @@ static void mymergesort( int first, int last, Segment **seg )
 }
 
 
-double Fgetlag( char  **seq1, char  **seq2, 
+double Fgetlag( 
+                               double **n_dynamicmtx, 
+                               char  **seq1, char  **seq2, 
                            double *eff1, double *eff2, 
                            int    clus1, int    clus2,
                            int alloclen )
@@ -231,7 +235,7 @@ double Fgetlag( char  **seq1, char  **seq2,
        int count, count0;
        int len1, len2;
        int totallen;
-       float dumfl = 0.0;
+       double dumdb = 0.0;
        int headgp, tailgp;
 
        len1 = strlen( seq1[0] );
@@ -704,25 +708,13 @@ system( "/usr/bin/gnuplot list.plot" );
                                Aalign( tmpres1, tmpres2, eff1, eff2, clus1, clus2, alloclen );
                                break;
                        case( 'M' ):
-                                       MSalignmm( tmpres1, tmpres2, eff1, eff2, clus1, clus2, alloclen, NULL, NULL, NULL, NULL, NULL, 0, NULL, headgp, tailgp );
+                                       MSalignmm( n_dynamicmtx, tmpres1, tmpres2, eff1, eff2, clus1, clus2, alloclen, NULL, NULL, NULL, NULL, NULL, 0, NULL, headgp, tailgp );
                                break;
                        case( 'A' ):
                                if( clus1 == 1 && clus2 == 1 )
-                                       G__align11( tmpres1, tmpres2, alloclen, headgp, tailgp );
+                                       G__align11( n_dynamicmtx, tmpres1, tmpres2, alloclen, headgp, tailgp );
                                else
-                                       A__align( tmpres1, tmpres2, eff1, eff2, clus1, clus2, alloclen, NULL, &dumfl, NULL, NULL, NULL, NULL, NULL, 0, NULL, headgp, tailgp );
-                               break;
-                       case( 'H' ):
-                               if( clus1 == 1 && clus2 == 1 )
-                                       G__align11( tmpres1, tmpres2, alloclen, headgp, tailgp );
-                               else
-                                       H__align( tmpres1, tmpres2, eff1, eff2, clus1, clus2, alloclen, NULL, &dumfl, NULL, NULL, NULL, NULL );
-                               break;
-                       case( 'Q' ):
-                               if( clus1 == 1 && clus2 == 1 )
-                                       G__align11( tmpres1, tmpres2, alloclen, headgp, tailgp );
-                               else
-                                       Q__align( tmpres1, tmpres2, eff1, eff2, clus1, clus2, alloclen, NULL, &dumfl, NULL, NULL, NULL, NULL );
+                                       A__align( n_dynamicmtx, tmpres1, tmpres2, eff1, eff2, clus1, clus2, alloclen, NULL, &dumdb, NULL, NULL, NULL, NULL, NULL, 0, NULL, headgp, tailgp, -1, -1 );
                                break;
                        default:
                                fprintf( stderr, "alg = %c\n", alg );
@@ -771,8 +763,10 @@ system( "/usr/bin/gnuplot list.plot" );
 
 
 
-float Falign( char  **seq1, char  **seq2, 
+double Falign( int **whichmtx, double ***scoringmatrices, double **n_dynamicmtx,
+                         char  **seq1, char  **seq2, 
                          double *eff1, double *eff2, 
+                         double **eff1s, double **eff2s,
                          int    clus1, int    clus2,
                          int alloclen, int *fftlog,
                          int *chudanpt, int chudanref, int *chudanres )
@@ -815,8 +809,8 @@ float Falign( char  **seq1, char  **seq2,
        int count, count0;
        int len1, len2;
        int totallen;
-       float totalscore;
-       float dumfl = 0.0;
+       double totalscore;
+       double dumdb = 0.0;
        int headgp, tailgp;
 
 
@@ -826,14 +820,20 @@ float Falign( char  **seq1, char  **seq2,
                {
 //                     fprintf( stderr, "Freeing localarrays in Falign\n" );
                        localalloclen = 0;
+                       prevalloclen = 0;
+                       crossscoresize = 0;
                        mymergesort( 0, 0, NULL );
                        alignableReagion( 0, 0, NULL, NULL, NULL, NULL, NULL );
                        fft( 0, NULL, 1 );
-                       A__align( NULL, NULL, NULL, NULL, 0, 0, 0, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0, NULL, 0, 0 );
-                       G__align11( NULL, NULL, 0, 0, 0 );
+                       A__align( NULL, NULL, NULL, NULL, NULL, 0, 0, 0, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0, NULL, 0, 0, -1, -1 );
+                       D__align( NULL, NULL, NULL, NULL, NULL, 0, 0, 0, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0, NULL, 0, 0 );
+                       A__align_variousdist( NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0, 0, 0, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0, NULL, 0, 0 );
+                       D__align_variousdist( NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0, 0, 0, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0, NULL, 0, 0 );
+                       G__align11( NULL, NULL, NULL, 0, 0, 0 );
                        blockAlign2( NULL, NULL, NULL, NULL, NULL, NULL );
                        if( crossscore ) FreeDoubleMtx( crossscore );
-                       FreeCharMtx( result1 );
+                       crossscore = NULL;
+                       FreeCharMtx( result1 ); result1 = NULL;
                        FreeCharMtx( result2 );
                        FreeCharMtx( tmpres1 );
                        FreeCharMtx( tmpres2 );
@@ -1167,6 +1167,7 @@ system( "less seqVec2 < /dev/tty > /dev/tty" );
 
 
 
+
 #define CAND 0
 #if CAND
        fftfp = fopen( "cand", "w" );
@@ -1510,31 +1511,41 @@ system( "less seqVec2 < /dev/tty > /dev/tty" );
                                totalscore += Aalign( tmpres1, tmpres2, eff1, eff2, clus1, clus2, alloclen );
                                break;
                        case( 'M' ):
-                                       totalscore += MSalignmm( tmpres1, tmpres2, eff1, eff2, clus1, clus2, alloclen, sgap1, sgap2, egap1, egap2, chudanpt, chudanref, chudanres, headgp, tailgp );
+                                       if( scoringmatrices ) // called by tditeration.c
+                                               totalscore += MSalignmm_variousdist( NULL, scoringmatrices, NULL, tmpres1, tmpres2, eff1, eff2, eff1s, eff2s, clus1, clus2, alloclen, sgap1, sgap2, egap1, egap2, chudanpt, chudanref, chudanres, headgp, tailgp );
+                                       else
+                                               totalscore += MSalignmm( n_dynamicmtx, tmpres1, tmpres2, eff1, eff2, clus1, clus2, alloclen, sgap1, sgap2, egap1, egap2, chudanpt, chudanref, chudanres, headgp, tailgp );
+//                                             totalscore += MSalignmm( n_dis_consweight_multi, tmpres1, tmpres2, eff1, eff2, clus1, clus2, alloclen, sgap1, sgap2, egap1, egap2, chudanpt, chudanref, chudanres, headgp, tailgp );
                                break;
-                       case( 'A' ):
+                       case( 'd' ):
                                if( clus1 == 1 && clus2 == 1 )
                                {
-                                       totalscore += G__align11( tmpres1, tmpres2, alloclen, headgp, tailgp );
+                                       totalscore += G__align11( n_dynamicmtx, tmpres1, tmpres2, alloclen, headgp, tailgp );
                                }
                                else
-                                       totalscore += A__align( tmpres1, tmpres2, eff1, eff2, clus1, clus2, alloclen, NULL, &dumfl, sgap1, sgap2, egap1, egap2, chudanpt, chudanref, chudanres, headgp, tailgp );
-                               break;
-                       case( 'H' ):
-                               if( clus1 == 1 && clus2 == 1 )
                                {
-                                       totalscore += G__align11( tmpres1, tmpres2, alloclen, headgp, tailgp );
+                                       if( scoringmatrices ) // called by tditeration.c
+                                       {
+                                               totalscore += D__align_variousdist( whichmtx, scoringmatrices, NULL, tmpres1, tmpres2, eff1, eff2, eff1s, eff2s, clus1, clus2, alloclen, NULL, &dumdb, sgap1, sgap2, egap1, egap2, chudanpt, chudanref, chudanres, headgp, tailgp );
+                                       }
+                                       else
+                                       totalscore += D__align( n_dynamicmtx, tmpres1, tmpres2, eff1, eff2, clus1, clus2, alloclen, NULL, &dumdb, sgap1, sgap2, egap1, egap2, chudanpt, chudanref, chudanres, headgp, tailgp );
                                }
-                               else
-                                       totalscore += H__align( tmpres1, tmpres2, eff1, eff2, clus1, clus2, alloclen, NULL, &dumfl, sgap1, sgap2, egap1, egap2 );
                                break;
-                       case( 'Q' ):
+                       case( 'A' ):
                                if( clus1 == 1 && clus2 == 1 )
                                {
-                                       totalscore += G__align11( tmpres1, tmpres2, alloclen, headgp, tailgp );
+                                       totalscore += G__align11( n_dynamicmtx, tmpres1, tmpres2, alloclen, headgp, tailgp );
                                }
                                else
-                                       totalscore += Q__align( tmpres1, tmpres2, eff1, eff2, clus1, clus2, alloclen, NULL, &dumfl, sgap1, sgap2, egap1, egap2 );
+                               {
+                                       if( scoringmatrices ) // called by tditeration.c
+                                       {
+                                               totalscore += A__align_variousdist( whichmtx, scoringmatrices, NULL, tmpres1, tmpres2, eff1, eff2, eff1s, eff2s, clus1, clus2, alloclen, NULL, &dumdb, sgap1, sgap2, egap1, egap2, chudanpt, chudanref, chudanres, headgp, tailgp );
+                                       }
+                                       else
+                                               totalscore += A__align( n_dynamicmtx, tmpres1, tmpres2, eff1, eff2, clus1, clus2, alloclen, NULL, &dumdb, sgap1, sgap2, egap1, egap2, chudanpt, chudanref, chudanres, headgp, tailgp, -1, -1 );
+                               }
                                break;
                        default:
                                fprintf( stderr, "alg = %c\n", alg );
@@ -1560,7 +1571,7 @@ system( "less seqVec2 < /dev/tty > /dev/tty" );
                for( j=0; j<clus2; j++ ) strcat( result2[j], tmpres2[j] );
                totallen += nlen;
 #if 0
-               fprintf( stderr, "i=%d", i );
+               fprintf( stderr, "$#####$$$$ i=%d", i );
                fprintf( stderr, "%4d\n", totallen );
                fprintf( stderr, "\n\n" );
                for( j=0; j<clus1; j++ ) 
@@ -1583,12 +1594,12 @@ system( "less seqVec2 < /dev/tty > /dev/tty" );
 #if 0
        for( j=0; j<clus1; j++ ) 
        {
-               fprintf( stderr, "%s\n", result1[j] );
+               fprintf( stderr, "in Falign, %s\n", result1[j] );
        }
        fprintf( stderr, "- - - - - - - - - - -\n" );
        for( j=0; j<clus2; j++ ) 
        {
-               fprintf( stderr, "%s\n", result2[j] );
+               fprintf( stderr, "in Falign, %s\n", result2[j] );
        }
 #endif
        return( totalscore );
@@ -1604,8 +1615,12 @@ system( "less seqVec2 < /dev/tty > /dev/tty" );
 /*
 sakujo wo kentou (2010/10/05)
 */
-float Falign_udpari_long( char  **seq1, char  **seq2, 
+double Falign_udpari_long( 
+                         int **whichmtx, double ***scoringmatrices, 
+                         double **n_dynamicmtx,
+                         char  **seq1, char  **seq2, 
                          double *eff1, double *eff2, 
+                         double **eff1s, double **eff2s,
                          int    clus1, int    clus2,
                          int alloclen, int *fftlog )
 {
@@ -1647,10 +1662,65 @@ float Falign_udpari_long( char  **seq1, char  **seq2,
        int count, count0;
        int len1, len2;
        int totallen;
-       float totalscore;
+       double totalscore;
        int nkouho = 0;
        int headgp, tailgp;
-//     float dumfl = 0.0;
+//     double dumfl = 0.0;
+
+       if( seq1 == NULL )
+       {
+               if( result1 ) 
+               {
+//                     fprintf( stderr, "### Freeing localarrays in Falign\n" );
+                       localalloclen = 0;
+                       prevalloclen = 0;
+                       crossscoresize = 0;
+                       mymergesort( 0, 0, NULL );
+                       alignableReagion( 0, 0, NULL, NULL, NULL, NULL, NULL );
+                       fft( 0, NULL, 1 );
+                       A__align( NULL, NULL, NULL, NULL, NULL, 0, 0, 0, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0, NULL, 0, 0, -1, -1 );
+                       A__align_variousdist( NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0, 0, 0, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0, NULL, 0, 0 );
+                       D__align_variousdist( NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0, 0, 0, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0, NULL, 0, 0 );
+                       G__align11( NULL, NULL, NULL, 0, 0, 0 );
+                       blockAlign2( NULL, NULL, NULL, NULL, NULL, NULL );
+                       if( crossscore ) FreeDoubleMtx( crossscore );
+                       crossscore = NULL; // reallocate sareru kanousei ga arunode.
+                       FreeCharMtx( result1 ); result1 = NULL;
+                       FreeCharMtx( result2 );
+                       FreeCharMtx( tmpres1 );
+                       FreeCharMtx( tmpres2 );
+                       FreeCharMtx( tmpseq1 );
+                       FreeCharMtx( tmpseq2 );
+                       free( sgap1 );
+                       free( egap1 );
+                       free( sgap2 );
+                       free( egap2 );
+                       free( kouho );
+                       free( cut1 );
+                       free( cut2 );
+                       free( tmpptr1 );
+                       free( tmpptr2 );
+                       free( segment );
+                       free( segment1 );
+                       free( segment2 );
+                       free( sortedseg1 );
+                       free( sortedseg2 );
+                       if( !kobetsubunkatsu )
+                       {
+                               FreeFukusosuuMtx ( seqVector1 );
+                               FreeFukusosuuMtx ( seqVector2 );
+                               FreeFukusosuuVec( naisekiNoWa );
+                               FreeFukusosuuMtx( naiseki );
+                               FreeDoubleVec( soukan );
+                       }
+               }
+               else
+               {
+//                     fprintf( stderr, "Did not allocate localarrays in Falign\n" );
+               }
+
+               return( 0.0 );
+       }
 
 
 
@@ -2322,7 +2392,10 @@ system( "less seqVec2 < /dev/tty > /dev/tty" );
                switch( alg )
                {
                        case( 'M' ):
-                                       totalscore += MSalignmm( tmpres1, tmpres2, eff1, eff2, clus1, clus2, alloclen, sgap1, sgap2, egap1, egap2, NULL, 0, NULL, headgp, tailgp );
+                                       if( scoringmatrices ) // called by tditeration.c
+                                               totalscore += MSalignmm_variousdist( NULL, scoringmatrices, NULL, tmpres1, tmpres2, eff1, eff2, eff1s, eff2s, clus1, clus2, alloclen, sgap1, sgap2, egap1, egap2, NULL, 0, NULL, headgp, tailgp );
+                                       else
+                                               totalscore += MSalignmm( n_dynamicmtx, tmpres1, tmpres2, eff1, eff2, clus1, clus2, alloclen, sgap1, sgap2, egap1, egap2, NULL, 0, NULL, headgp, tailgp );
                                break;
                        default:
                                fprintf( stderr, "alg = %c\n", alg );