JWS-112 Bumping version of Mafft to version 7.310.

[jabaws.git] / binaries / src / mafft / core / mafft-profile.c

diff --git a/binaries/src/mafft/core/mafft-profile.c b/binaries/src/mafft/core/mafft-profile.c
index 1eb479c..7ec7440 100644 (file)
--- a/binaries/src/mafft/core/mafft-profile.c
+++ b/binaries/src/mafft/core/mafft-profile.c
@@ -87,9 +87,6 @@ char **arguments( int argc, char *argv[] )
                                case 'Q':
                                        alg = 'Q';
                                        break;
-                               case 'H':
-                                       alg = 'H';
-                                       break;
                                case 'A':
                                        alg = 'A';
                                        break;
@@ -109,11 +106,11 @@ char **arguments( int argc, char *argv[] )
                                        tbrweight = 0;
                                        break;
                                case 'z':
-                                       fftThreshold = atoi( *++argv );
+                                       fftThreshold = myatoi( *++argv );
                                        --argc;
                                        goto nextoption;
                                case 'w':
-                                       fftWinSize = atoi( *++argv );
+                                       fftWinSize = myatoi( *++argv );
                                        --argc;
                                        goto nextoption;
                                case 'Z':
@@ -135,25 +132,25 @@ char **arguments( int argc, char *argv[] )
                     --argc;
                     goto nextoption;
                 case 'k':
-                    kimuraR = atoi( *++argv );
+                    kimuraR = myatoi( *++argv );
                     fprintf( stderr, "kappa = %d\n", kimuraR );
                     --argc;
                     goto nextoption;
                                case 'b':
-                                       nblosum = atoi( *++argv );
+                                       nblosum = myatoi( *++argv );
                                        scoremtx = 1;
                                        fprintf( stderr, "blosum %d\n", nblosum );
                                        --argc;
                                        goto nextoption;
                                case 'j':
-                                       pamN = atoi( *++argv );
+                                       pamN = myatoi( *++argv );
                                        scoremtx = 0;
                                        TMorJTT = JTT;
                                        fprintf( stderr, "jtt %d\n", pamN );
                                        --argc;
                                        goto nextoption;
                                case 'm':
-                                       pamN = atoi( *++argv );
+                                       pamN = myatoi( *++argv );
                                        scoremtx = 0;
                                        TMorJTT = TM;
                                        fprintf( stderr, "tm %d\n", pamN );
@@ -184,13 +181,14 @@ void GroupAlign( int nseq1, int nseq2, char **name, int *nlen, char **seq, char
        int i;
        int clus1, clus2;
        int s1, s2;
-       float pscore;
+       double pscore;
        static char **name1, **name2;
        double *effarr = eff;
        double *effarr1 = NULL;
        double *effarr2 = NULL;
        static char *indication1, *indication2;
-       float dumfl = 0.0;
+//     double dumfl = 0.0;
+       double dumdb = 0.0;
        int intdum;
 #if DEBUG
        double time1, time2;
@@ -237,11 +235,6 @@ void GroupAlign( int nseq1, int nseq2, char **name, int *nlen, char **seq, char
        fprintf( stderr, "\n" );
 */
 
-       if( alg == 'Q' )
-               fprintf( stderr, "before realignment, score = %f\n", naiveQpairscore( nseq1, nseq2, mseq1, mseq2, effarr1, effarr2, penalty ) );
-       else if( alg == 'H' )
-               fprintf( stderr, "before realignment, score = %f\n", naivepairscore( nseq1, nseq2, mseq1, mseq2, effarr1, effarr2, penalty ) );
-
        commongappick( nseq1, mseq1 );
        commongappick( nseq2, mseq2 );
 
@@ -253,20 +246,16 @@ void GroupAlign( int nseq1, int nseq2, char **name, int *nlen, char **seq, char
        if( use_fft )
        {
                if( alg == 'M' )
-                       pscore = Falign_udpari_long( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, &intdum );
+                       pscore = Falign_udpari_long( NULL, NULL, n_dis_consweight_multi, mseq1, mseq2, effarr1, effarr2, NULL, NULL, clus1, clus2, alloclen, &intdum );
                else
-                       pscore = Falign( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, &intdum, NULL, 0, NULL );
+                       pscore = Falign( NULL, NULL, n_dis_consweight_multi, mseq1, mseq2, effarr1, effarr2, NULL, NULL, clus1, clus2, alloclen, &intdum, NULL, 0, NULL );
        }
        else
        {
                if( alg == 'M' )
-                       pscore = MSalignmm( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, NULL, NULL, NULL, NULL, NULL, 0, NULL, outgap, outgap );
-               else if( alg == 'H' )
-                       pscore = H__align( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, NULL, &dumfl, NULL, NULL, NULL, NULL );
-               else if( alg == 'Q' )
-                       pscore = Q__align( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, NULL, &dumfl, NULL, NULL, NULL, NULL );
+                       pscore = MSalignmm( n_dis_consweight_multi, mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, NULL, NULL, NULL, NULL, NULL, 0, NULL, outgap, outgap );
                else
-                       pscore = A__align( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, NULL, &dumfl, NULL, NULL, NULL, NULL, NULL, 0, NULL, outgap, outgap );
+                       pscore = A__align( n_dis_consweight_multi, mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, NULL, &dumdb, NULL, NULL, NULL, NULL, NULL, 0, NULL, outgap, outgap, -1, -1 );
        }
 #if DEBUG
                time2 = getrusage_sec();
@@ -274,11 +263,6 @@ void GroupAlign( int nseq1, int nseq2, char **name, int *nlen, char **seq, char
                fflush( stdout );
 #endif
 
-       if( alg == 'H' )
-               fprintf( stderr, "before realignment, score = %f\n", naivepairscore( nseq1, nseq2, mseq1, mseq2, effarr1, effarr2, penalty ) );
-       else if( alg == 'Q' )
-               fprintf( stderr, "after realignment, score = %f\n", naiveQpairscore( nseq1, nseq2, mseq1, mseq2, effarr1, effarr2, penalty ) );
-
        
 /*
        fprintf( stderr, "after align 1 %s \n", indication1 );