--- /dev/null
+#include "mltaln.h"
+#include "miyata.h"
+#include "miyata5.h"
+#include "DNA.h"
+
+#include "JTT.c"
+#include "blosum.c"
+
+#define DEBUG 0
+#define TEST 0
+
+#define NORMALIZE1 1
+
+static int shishagonyuu( double in )
+{
+ int out;
+ if ( in > 0.0 ) out = ( (int)( in + 0.5 ) );
+ else if( in == 0.0 ) out = ( 0 );
+ else if( in < 0.0 ) out = ( (int)( in - 0.5 ) );
+ else out = 0;
+ return( out );
+}
+
+static void calcfreq_nuc( int nseq, char **seq, double *datafreq )
+{
+ int i, j, l;
+ int aan;
+ double total;
+ for( i=0; i<4; i++ )
+ datafreq[i] = 0.0;
+ total = 0.0;
+ for( i=0; i<nseq; i++ )
+ {
+ l = strlen( seq[i] );
+ for( j=0; j<l; j++ )
+ {
+ aan = amino_n[(int)seq[i][j]];
+ if( aan == 4 ) aan = 3;
+ if( aan >= 0 && aan < 4 )
+ {
+ datafreq[aan] += 1.0;
+ total += 1.0;
+ }
+ }
+ }
+ for( i=0; i<4; i++ )
+ if( datafreq[i] < 0.0001 ) datafreq[i] = 0.0001;
+
+
+ total = 0.0; for( i=0; i<4; i++ ) total += datafreq[i];
+// fprintf( stderr, "total = %f\n", total );
+ for( i=0; i<4; i++ ) datafreq[i] /= (double)total;
+
+#if 0
+ fprintf( stderr, "\ndatafreq = " );
+ for( i=0; i<4; i++ )
+ fprintf( stderr, "%10.5f ", datafreq[i] );
+ fprintf( stderr, "\n" );
+ exit( 1 );
+#endif
+}
+
+static void calcfreq( int nseq, char **seq, double *datafreq )
+{
+ int i, j, l;
+ int aan;
+ double total;
+ for( i=0; i<20; i++ )
+ datafreq[i] = 0.0;
+ total = 0.0;
+ for( i=0; i<nseq; i++ )
+ {
+ l = strlen( seq[i] );
+ for( j=0; j<l; j++ )
+ {
+ aan = amino_n[(int)seq[i][j]];
+ if( aan >= 0 && aan < 20 )
+ {
+ datafreq[aan] += 1.0;
+ total += 1.0;
+ }
+ }
+ }
+ for( i=0; i<20; i++ )
+ if( datafreq[i] < 0.0001 ) datafreq[i] = 0.0001;
+
+ fprintf( stderr, "datafreq = \n" );
+ for( i=0; i<20; i++ )
+ fprintf( stderr, "%f\n", datafreq[i] );
+
+ total = 0.0; for( i=0; i<20; i++ ) total += datafreq[i];
+ fprintf( stderr, "total = %f\n", total );
+ for( i=0; i<20; i++ ) datafreq[i] /= (double)total;
+}
+
+void constants( int nseq, char **seq )
+{
+ int i, j, x;
+// double tmp;
+
+ if( dorp == 'd' ) /* DNA */
+ {
+ int k, m;
+ double average;
+ double **pamx = AllocateDoubleMtx( 11,11 );
+ double **pam1 = AllocateDoubleMtx( 4, 4 );
+ double *freq = AllocateDoubleVec( 4 );
+
+
+ scoremtx = -1;
+ if( RNAppenalty == NOTSPECIFIED ) RNAppenalty = DEFAULTRNAGOP_N;
+ if( RNAppenalty_ex == NOTSPECIFIED ) RNAppenalty_ex = DEFAULTRNAGEP_N;
+ if( ppenalty == NOTSPECIFIED ) ppenalty = DEFAULTGOP_N;
+ if( ppenalty_OP == NOTSPECIFIED ) ppenalty_OP = DEFAULTGOP_N;
+ if( ppenalty_ex == NOTSPECIFIED ) ppenalty_ex = DEFAULTGEP_N;
+ if( ppenalty_EX == NOTSPECIFIED ) ppenalty_EX = DEFAULTGEP_N;
+ if( poffset == NOTSPECIFIED ) poffset = DEFAULTOFS_N;
+ if( RNApthr == NOTSPECIFIED ) RNApthr = DEFAULTRNATHR_N;
+ if( pamN == NOTSPECIFIED ) pamN = DEFAULTPAMN;
+ if( kimuraR == NOTSPECIFIED ) kimuraR = 2;
+
+ RNApenalty = (int)( 3 * 600.0 / 1000.0 * RNAppenalty + 0.5 );
+ RNApenalty_ex = (int)( 3 * 600.0 / 1000.0 * RNAppenalty_ex + 0.5 );
+// fprintf( stderr, "DEFAULTRNAGOP_N = %d\n", DEFAULTRNAGOP_N );
+// fprintf( stderr, "RNAppenalty = %d\n", RNAppenalty );
+// fprintf( stderr, "RNApenalty = %d\n", RNApenalty );
+
+
+ RNAthr = (int)( 3 * 600.0 / 1000.0 * RNApthr + 0.5 );
+ penalty = (int)( 3 * 600.0 / 1000.0 * ppenalty + 0.5);
+ penalty_OP = (int)( 3 * 600.0 / 1000.0 * ppenalty_OP + 0.5);
+ penalty_ex = (int)( 3 * 600.0 / 1000.0 * ppenalty_ex + 0.5);
+ penalty_EX = (int)( 3 * 600.0 / 1000.0 * ppenalty_EX + 0.5);
+ offset = (int)( 3 * 600.0 / 1000.0 * poffset + 0.5);
+ offsetFFT = (int)( 3 * 600.0 / 1000.0 * (-0) + 0.5);
+ offsetLN = (int)( 3 * 600.0 / 1000.0 * 100 + 0.5);
+ penaltyLN = (int)( 3 * 600.0 / 1000.0 * -2000 + 0.5);
+ penalty_exLN = (int)( 3 * 600.0 / 1000.0 * -100 + 0.5);
+ sprintf( modelname, "%s%d (%d), %6.3f (%6.3f), %6.3f (%6.3f)", rnakozo?"RNA":"DNA", pamN, kimuraR,
+ -(double)ppenalty*0.001, -(double)ppenalty*0.003, -(double)poffset*0.001, -(double)poffset*0.003 );
+
+ if( kimuraR == 9999 )
+ {
+ for( i=0; i<4; i++ ) for( j=0; j<4; j++ )
+ pamx[i][j] = (double)locn_disn[i][j];
+#if NORMALIZE1
+ average = 0.0;
+ for( i=0; i<4; i++ ) for( j=0; j<4; j++ )
+ average += pamx[i][j];
+ average /= 16.0;
+
+ if( disp )
+ fprintf( stderr, "average = %f\n", average );
+
+ for( i=0; i<4; i++ ) for( j=0; j<4; j++ )
+ pamx[i][j] -= average;
+
+ for( i=0; i<4; i++ ) for( j=0; j<4; j++ )
+ pamx[i][j] *= 600.0 / average;
+
+ for( i=0; i<4; i++ ) for( j=0; j<4; j++ )
+ pamx[i][j] -= offset;
+#endif
+ }
+ else
+ {
+ double f = 0.99;
+ double s = (double)kimuraR / ( 2 + kimuraR ) * 0.01;
+ double v = (double)1 / ( 2 + kimuraR ) * 0.01;
+ pam1[0][0] = f; pam1[0][1] = s; pam1[0][2] = v; pam1[0][3] = v;
+ pam1[1][0] = s; pam1[1][1] = f; pam1[1][2] = v; pam1[1][3] = v;
+ pam1[2][0] = v; pam1[2][1] = v; pam1[2][2] = f; pam1[2][3] = s;
+ pam1[3][0] = v; pam1[3][1] = v; pam1[3][2] = s; pam1[3][3] = f;
+
+ fprintf( stderr, "generating %dPAM scoring matrix for nucleotides ... ", pamN );
+
+ if( disp )
+ {
+ fprintf( stderr, " TPM \n" );
+ for( i=0; i<4; i++ )
+ {
+ for( j=0; j<4; j++ )
+ fprintf( stderr, "%+#6.10f", pam1[i][j] );
+ fprintf( stderr, "\n" );
+ }
+ fprintf( stderr, "\n" );
+ }
+
+
+ MtxuntDouble( pamx, 4 );
+ for( x=0; x < pamN; x++ ) MtxmltDouble( pamx, pam1, 4 );
+ for( i=0; i<4; i++ ) for( j=0; j<4; j++ )
+ pamx[i][j] /= 1.0 / 4.0;
+
+ for( i=0; i<4; i++ ) for( j=0; j<4; j++ )
+ {
+ if( pamx[i][j] == 0.0 )
+ {
+ fprintf( stderr, "WARNING: pamx[i][j] = 0.0 ?\n" );
+ pamx[i][j] = 0.00001; /* by J. Thompson */
+ }
+ pamx[i][j] = log10( pamx[i][j] ) * 1000.0;
+ }
+
+ if( disp )
+ {
+ fprintf( stderr, " after log\n" );
+ for( i=0; i<4; i++ )
+ {
+ for( j=0; j<4; j++ )
+ fprintf( stderr, "%+#6.10f", pamx[i][j] );
+ fprintf( stderr, "\n" );
+ }
+ fprintf( stderr, "\n" );
+ }
+
+
+// ?????
+ for( i=0; i<26; i++ ) amino[i] = locaminon[i];
+ for( i=0; i<0x80; i++ ) amino_n[i] = -1;
+ for( i=0; i<26; i++ ) amino_n[(int)amino[i]] = i;
+ if( fmodel == 1 )
+ calcfreq_nuc( nseq, seq, freq );
+ else
+ {
+ freq[0] = 0.25;
+ freq[1] = 0.25;
+ freq[2] = 0.25;
+ freq[3] = 0.25;
+ }
+// fprintf( stderr, "a, freq[0] = %f\n", freq[0] );
+// fprintf( stderr, "g, freq[1] = %f\n", freq[1] );
+// fprintf( stderr, "c, freq[2] = %f\n", freq[2] );
+// fprintf( stderr, "t, freq[3] = %f\n", freq[3] );
+
+
+ average = 0.0;
+ for( i=0; i<4; i++ ) for( j=0; j<4; j++ )
+ average += pamx[i][j] * freq[i] * freq[j];
+ for( i=0; i<4; i++ ) for( j=0; j<4; j++ )
+ pamx[i][j] -= average;
+
+ average = 0.0;
+ for( i=0; i<4; i++ )
+ average += pamx[i][i] * 1.0 / 4.0;
+
+ for( i=0; i<4; i++ ) for( j=0; j<4; j++ )
+ pamx[i][j] *= 600.0 / average;
+
+
+ for( i=0; i<4; i++ ) for( j=0; j<4; j++ )
+ pamx[i][j] -= offset; /* extending gap cost */
+
+ for( i=0; i<4; i++ ) for( j=0; j<4; j++ )
+ pamx[i][j] = shishagonyuu( pamx[i][j] );
+
+ if( disp )
+ {
+ fprintf( stderr, " after shishagonyuu\n" );
+ for( i=0; i<4; i++ )
+ {
+ for( j=0; j<4; j++ )
+ fprintf( stderr, "%+#6.10f", pamx[i][j] );
+ fprintf( stderr, "\n" );
+ }
+ fprintf( stderr, "\n" );
+ }
+ fprintf( stderr, "done\n" );
+ }
+
+ for( i=0; i<5; i++ )
+ {
+ pamx[4][i] = pamx[3][i];
+ pamx[i][4] = pamx[i][3];
+ }
+
+ for( i=5; i<10; i++ ) for( j=5; j<10; j++ )
+ {
+ pamx[i][j] = pamx[i-5][j-5];
+ }
+
+ if( disp )
+ {
+ fprintf( stderr, " before dis\n" );
+ for( i=0; i<4; i++ )
+ {
+ for( j=0; j<4; j++ )
+ fprintf( stderr, "%+#6.10f", pamx[i][j] );
+ fprintf( stderr, "\n" );
+ }
+ fprintf( stderr, "\n" );
+ }
+
+ if( disp )
+ {
+ fprintf( stderr, " score matrix \n" );
+ for( i=0; i<4; i++ )
+ {
+ for( j=0; j<4; j++ )
+ fprintf( stderr, "%+#6.10f", pamx[i][j] );
+ fprintf( stderr, "\n" );
+ }
+ fprintf( stderr, "\n" );
+ }
+
+ for( i=0; i<26; i++ ) amino[i] = locaminon[i];
+ for( i=0; i<26; i++ ) amino_grp[(int)amino[i]] = locgrpn[i];
+ for( i=0; i<26; i++ ) for( j=0; j<26; j++ ) n_dis[i][j] = 0;
+ for( i=0; i<10; i++ ) for( j=0; j<10; j++ ) n_dis[i][j] = shishagonyuu( pamx[i][j] );
+ if( disp )
+ {
+ fprintf( stderr, " score matrix \n" );
+ for( i=0; i<26; i++ )
+ {
+ for( j=0; j<26; j++ )
+ fprintf( stderr, "%+6d", n_dis[i][j] );
+ fprintf( stderr, "\n" );
+ }
+ fprintf( stderr, "\n" );
+ }
+
+// RIBOSUM
+#if 1
+ average = 0.0;
+ for( i=0; i<4; i++ ) for( j=0; j<4; j++ )
+ average += ribosum4[i][j] * freq[i] * freq[j];
+ for( i=0; i<4; i++ ) for( j=0; j<4; j++ )
+ ribosum4[i][j] -= average;
+
+ average = 0.0;
+ for( i=0; i<4; i++ ) for( j=0; j<4; j++ ) for( k=0; k<4; k++ ) for( m=0; m<4; m++ )
+ {
+// if( i%4==0&&j%4==3 || i%4==3&&j%4==0 || i%4==1&&j%4==2 || i%4==2&&j%4==1 || i%4==1&&j%4==3 || i%4==3&&j%4==1 )
+// if( k%4==0&&m%4==3 || k%4==3&&m%4==0 || k%4==1&&m%4==2 || k%4==2&&m%4==1 || k%4==1&&m%4==3 || k%4==3&&m%4==1 )
+ average += ribosum16[i*4+j][k*4+m] * freq[i] * freq[j] * freq[k] * freq[m];
+ }
+ for( i=0; i<16; i++ ) for( j=0; j<16; j++ )
+ ribosum16[i][j] -= average;
+
+ average = 0.0;
+ for( i=0; i<4; i++ )
+ average += ribosum4[i][i] * freq[i];
+ for( i=0; i<4; i++ ) for( j=0; j<4; j++ )
+ ribosum4[i][j] *= 600.0 / average;
+
+ average = 0.0;
+ average += ribosum16[0*4+3][0*4+3] * freq[0] * freq[3]; // AU
+ average += ribosum16[3*4+0][3*4+0] * freq[3] * freq[0]; // UA
+ average += ribosum16[1*4+2][1*4+2] * freq[1] * freq[2]; // CG
+ average += ribosum16[2*4+1][2*4+1] * freq[2] * freq[1]; // GC
+ average += ribosum16[1*4+3][1*4+3] * freq[1] * freq[3]; // GU
+ average += ribosum16[3*4+1][3*4+1] * freq[3] * freq[1]; // UG
+ for( i=0; i<16; i++ ) for( j=0; j<16; j++ )
+ ribosum16[i][j] *= 600.0 / average;
+
+
+#if 1
+ for( i=0; i<4; i++ ) for( j=0; j<4; j++ )
+ ribosum4[i][j] -= offset; /* extending gap cost ?????*/
+ for( i=0; i<16; i++ ) for( j=0; j<16; j++ )
+ ribosum16[i][j] -= offset; /* extending gap cost ?????*/
+#endif
+
+ for( i=0; i<4; i++ ) for( j=0; j<4; j++ )
+ ribosum4[i][j] = shishagonyuu( ribosum4[i][j] );
+ for( i=0; i<16; i++ ) for( j=0; j<16; j++ )
+ ribosum16[i][j] = shishagonyuu( ribosum16[i][j] );
+
+ if( disp )
+ {
+ fprintf( stderr, "ribosum after shishagonyuu\n" );
+ for( i=0; i<4; i++ )
+ {
+ for( j=0; j<4; j++ )
+ fprintf( stderr, "%+#6.10f", ribosum4[i][j] );
+ fprintf( stderr, "\n" );
+ }
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "ribosum16 after shishagonyuu\n" );
+ for( i=0; i<16; i++ )
+ {
+ for( j=0; j<16; j++ )
+ fprintf( stderr, "%+#7.0f", ribosum16[i][j] );
+ fprintf( stderr, "\n" );
+ }
+ fprintf( stderr, "\n" );
+ }
+ fprintf( stderr, "done\n" );
+
+#if 1
+ for( i=0; i<37; i++ ) for( j=0; j<37; j++ ) ribosumdis[i][j] = 0.0; //iru
+ for( m=0; m<9; m++ ) for( i=0; i<4; i++ ) // loop
+ for( k=0; k<9; k++ ) for( j=0; j<4; j++ ) ribosumdis[m*4+i][k*4+j] = ribosum4[i][j]; // loop-loop
+// for( k=0; k<9; k++ ) for( j=0; j<4; j++ ) ribosumdis[m*4+i][k*4+j] = n_dis[i][j]; // loop-loop
+
+ for( i=0; i<16; i++ ) for( j=0; j<16; j++ ) ribosumdis[i+4][j+4] = ribosum16[i][j]; // stem5-stem5
+ for( i=0; i<16; i++ ) for( j=0; j<16; j++ ) ribosumdis[i+20][j+20] = ribosum16[i][j]; // stem5-stem5
+#else // do not use ribosum
+ for( i=0; i<37; i++ ) for( j=0; j<37; j++ ) ribosumdis[i][j] = 0.0; //iru
+ for( m=0; m<9; m++ ) for( i=0; i<4; i++ ) // loop
+ for( k=0; k<9; k++ ) for( j=0; j<4; j++ ) ribosumdis[m*4+i][k*4+j] = n_dis[i][j]; // loop-loop
+#endif
+
+ if( disp )
+ {
+ fprintf( stderr, "ribosumdis\n" );
+ for( i=0; i<37; i++ )
+ {
+ for( j=0; j<37; j++ )
+ fprintf( stderr, "%+5d", ribosumdis[i][j] );
+ fprintf( stderr, "\n" );
+ }
+ fprintf( stderr, "\n" );
+ }
+ fprintf( stderr, "done\n" );
+#endif
+
+ FreeDoubleMtx( pam1 );
+ FreeDoubleMtx( pamx );
+ free( freq );
+
+ }
+ else if( dorp == 'p' && scoremtx == 1 ) /* Blosum */
+ {
+ double *freq;
+ double *freq1;
+ double *datafreq;
+ double average;
+// double tmp;
+ double **n_distmp;
+
+ n_distmp = AllocateDoubleMtx( 20, 20 );
+ datafreq = AllocateDoubleVec( 20 );
+ freq = AllocateDoubleVec( 20 );
+
+ if( ppenalty == NOTSPECIFIED ) ppenalty = DEFAULTGOP_B;
+ if( ppenalty_OP == NOTSPECIFIED ) ppenalty_OP = DEFAULTGOP_B;
+ if( ppenalty_ex == NOTSPECIFIED ) ppenalty_ex = DEFAULTGEP_B;
+ if( ppenalty_EX == NOTSPECIFIED ) ppenalty_EX = DEFAULTGEP_B;
+ if( poffset == NOTSPECIFIED ) poffset = DEFAULTOFS_B;
+ if( pamN == NOTSPECIFIED ) pamN = 0;
+ if( kimuraR == NOTSPECIFIED ) kimuraR = 1;
+ penalty = (int)( 600.0 / 1000.0 * ppenalty + 0.5 );
+ penalty_OP = (int)( 600.0 / 1000.0 * ppenalty_OP + 0.5 );
+ penalty_ex = (int)( 600.0 / 1000.0 * ppenalty_ex + 0.5 );
+ penalty_EX = (int)( 600.0 / 1000.0 * ppenalty_EX + 0.5 );
+ offset = (int)( 600.0 / 1000.0 * poffset + 0.5 );
+ offsetFFT = (int)( 600.0 / 1000.0 * (-0) + 0.5);
+ offsetLN = (int)( 600.0 / 1000.0 * 100 + 0.5);
+ penaltyLN = (int)( 600.0 / 1000.0 * -2000 + 0.5);
+ penalty_exLN = (int)( 600.0 / 1000.0 * -100 + 0.5);
+
+ BLOSUMmtx( nblosum, n_distmp, freq, amino, amino_grp );
+ if( nblosum == -1 )
+ sprintf( modelname, "User-defined, %6.3f, %+6.3f, %+6.3f", -(double)ppenalty/1000, -(double)poffset/1000, -(double)ppenalty_ex/1000 );
+ else
+ sprintf( modelname, "BLOSUM%d, %6.3f, %+6.3f, %+6.3f", nblosum, -(double)ppenalty/1000, -(double)poffset/1000, -(double)ppenalty_ex/1000 );
+#if 0
+ for( i=0; i<26; i++ ) amino[i] = locaminod[i];
+ for( i=0; i<26; i++ ) amino_grp[(int)amino[i]] = locgrpd[i];
+ for( i=0; i<0x80; i++ ) amino_n[i] = 0;
+ for( i=0; i<26; i++ ) amino_n[(int)amino[i]] = i;
+#endif
+ for( i=0; i<0x80; i++ )amino_n[i] = -1;
+ for( i=0; i<26; i++) amino_n[(int)amino[i]] = i;
+ if( fmodel == 1 )
+ {
+ calcfreq( nseq, seq, datafreq );
+ freq1 = datafreq;
+ }
+ else
+ freq1 = freq;
+#if TEST
+ fprintf( stderr, "raw scoreing matrix : \n" );
+ for( i=0; i<20; i++ )
+ {
+ for( j=0; j<20; j++ )
+ {
+ fprintf( stdout, "%6.2f", n_distmp[i][j] );
+ }
+ fprintf( stdout, "\n" );
+ }
+#endif
+ if( fmodel == -1 )
+ average = 0.0;
+ else
+ {
+ for( i=0; i<20; i++ )
+#if TEST
+ fprintf( stdout, "freq[%c] = %f, datafreq[%c] = %f, freq1[] = %f\n", amino[i], freq[i], amino[i], datafreq[i], freq1[i] );
+#endif
+ average = 0.0;
+ for( i=0; i<20; i++ ) for( j=0; j<20; j++ )
+ average += n_distmp[i][j] * freq1[i] * freq1[j];
+ }
+#if TEST
+ fprintf( stdout, "####### average2 = %f\n", average );
+#endif
+
+ for( i=0; i<20; i++ ) for( j=0; j<20; j++ )
+ n_distmp[i][j] -= average;
+#if TEST
+ fprintf( stdout, "average2 = %f\n", average );
+ fprintf( stdout, "after average substruction : \n" );
+ for( i=0; i<20; i++ )
+ {
+ for( j=0; j<20; j++ )
+ {
+ fprintf( stdout, "%6.2f", n_distmp[i][j] );
+ }
+ fprintf( stdout, "\n" );
+ }
+#endif
+
+ average = 0.0;
+ for( i=0; i<20; i++ )
+ average += n_distmp[i][i] * freq1[i];
+#if TEST
+ fprintf( stdout, "####### average1 = %f\n", average );
+#endif
+
+ for( i=0; i<20; i++ ) for( j=0; j<20; j++ )
+ n_distmp[i][j] *= 600.0 / average;
+#if TEST
+ fprintf( stdout, "after average division : \n" );
+ for( i=0; i<20; i++ )
+ {
+ for( j=0; j<=i; j++ )
+ {
+ fprintf( stdout, "%7.1f", n_distmp[i][j] );
+ }
+ fprintf( stdout, "\n" );
+ }
+#endif
+
+ for( i=0; i<20; i++ ) for( j=0; j<20; j++ )
+ n_distmp[i][j] -= offset;
+#if TEST
+ fprintf( stdout, "after offset substruction (offset = %d): \n", offset );
+ for( i=0; i<20; i++ )
+ {
+ for( j=0; j<=i; j++ )
+ {
+ fprintf( stdout, "%7.1f", n_distmp[i][j] );
+ }
+ fprintf( stdout, "\n" );
+ }
+#endif
+#if 0
+/* Ãí°Õ ¡ª¡ª¡ª¡ª¡ª¡ª¡ª¡ª¡ª¡ª */
+ penalty -= offset;
+#endif
+
+
+ for( i=0; i<20; i++ ) for( j=0; j<20; j++ )
+ n_distmp[i][j] = shishagonyuu( n_distmp[i][j] );
+
+ if( disp )
+ {
+ fprintf( stdout, " scoring matrix \n" );
+ for( i=0; i<20; i++ )
+ {
+ fprintf( stdout, "%c ", amino[i] );
+ for( j=0; j<20; j++ )
+ fprintf( stdout, "%5.0f", n_distmp[i][j] );
+ fprintf( stdout, "\n" );
+ }
+ fprintf( stdout, " " );
+ for( i=0; i<20; i++ )
+ fprintf( stdout, " %c", amino[i] );
+
+ average = 0.0;
+ for( i=0; i<20; i++ ) for( j=0; j<20; j++ )
+ average += n_distmp[i][j] * freq1[i] * freq1[j];
+ fprintf( stdout, "average = %f\n", average );
+
+ average = 0.0;
+ for( i=0; i<20; i++ )
+ average += n_distmp[i][i] * freq1[i];
+ fprintf( stdout, "itch average = %f\n", average );
+ fprintf( stderr, "parameters: %d, %d, %d\n", penalty, penalty_ex, offset );
+
+
+ exit( 1 );
+ }
+
+ for( i=0; i<26; i++ ) for( j=0; j<26; j++ ) n_dis[i][j] = 0;
+ for( i=0; i<20; i++ ) for( j=0; j<20; j++ ) n_dis[i][j] = (int)n_distmp[i][j];
+
+ FreeDoubleMtx( n_distmp );
+ FreeDoubleVec( datafreq );
+ FreeDoubleVec( freq );
+
+ fprintf( stderr, "done.\n" );
+
+ }
+ else if( dorp == 'p' && scoremtx == 2 ) /* Miyata-Yasunaga */
+ {
+ fprintf( stderr, "Not supported\n" );
+ exit( 1 );
+ for( i=0; i<26; i++ ) for( j=0; j<26; j++ ) n_dis[i][j] = locn_dism[i][j];
+ for( i=0; i<26; i++ ) if( i != 24 ) n_dis[i][24] = n_dis[24][i] = exgpm;
+ n_dis[24][24] = 0;
+ if( ppenalty == NOTSPECIFIED ) ppenalty = locpenaltym;
+ if( poffset == NOTSPECIFIED ) poffset = -20;
+ if( pamN == NOTSPECIFIED ) pamN = 0;
+ if( kimuraR == NOTSPECIFIED ) kimuraR = 1;
+
+ penalty = ppenalty;
+ offset = poffset;
+
+ sprintf( modelname, "Miyata-Yasunaga, %6.3f, %6.3f", -(double)ppenalty/1000, -(double)poffset/1000 );
+ for( i=0; i<26; i++ ) amino[i] = locaminom[i];
+ for( i=0; i<26; i++ ) amino_grp[(int)amino[i]] = locgrpm[i];
+#if DEBUG
+ fprintf( stdout, "scoreing matrix : \n" );
+ for( i=0; i<26; i++ )
+ {
+ for( j=0; j<26; j++ )
+ {
+ fprintf( stdout, "%#5d", n_dis[i][j] );
+ }
+ fprintf( stdout, "\n" );
+ }
+#endif
+ }
+ else /* JTT */
+ {
+ double **rsr;
+ double **pam1;
+ double **pamx;
+ double *freq;
+ double *freq1;
+ double *mutab;
+ double *datafreq;
+ double average;
+ double tmp;
+ double delta;
+
+ rsr = AllocateDoubleMtx( 20, 20 );
+ pam1 = AllocateDoubleMtx( 20, 20 );
+ pamx = AllocateDoubleMtx( 20, 20 );
+ freq = AllocateDoubleVec( 20 );
+ mutab = AllocateDoubleVec( 20 );
+ datafreq = AllocateDoubleVec( 20 );
+
+ if( ppenalty == NOTSPECIFIED ) ppenalty = DEFAULTGOP_J;
+ if( ppenalty_OP == NOTSPECIFIED ) ppenalty_OP = DEFAULTGOP_J;
+ if( ppenalty_ex == NOTSPECIFIED ) ppenalty_ex = DEFAULTGEP_J;
+ if( ppenalty_EX == NOTSPECIFIED ) ppenalty_EX = DEFAULTGEP_J;
+ if( poffset == NOTSPECIFIED ) poffset = DEFAULTOFS_J;
+ if( pamN == NOTSPECIFIED ) pamN = DEFAULTPAMN;
+ if( kimuraR == NOTSPECIFIED ) kimuraR = 1;
+
+ penalty = (int)( 600.0 / 1000.0 * ppenalty + 0.5 );
+ penalty_OP = (int)( 600.0 / 1000.0 * ppenalty_OP + 0.5 );
+ penalty_ex = (int)( 600.0 / 1000.0 * ppenalty_ex + 0.5 );
+ penalty_EX = (int)( 600.0 / 1000.0 * ppenalty_EX + 0.5 );
+ offset = (int)( 600.0 / 1000.0 * poffset + 0.5 );
+ offsetFFT = (int)( 600.0 / 1000.0 * (-0) + 0.5 );
+ offsetLN = (int)( 600.0 / 1000.0 * 100 + 0.5);
+ penaltyLN = (int)( 600.0 / 1000.0 * -2000 + 0.5);
+ penalty_exLN = (int)( 600.0 / 1000.0 * -100 + 0.5);
+
+ sprintf( modelname, "%s %dPAM, %6.3f, %6.3f", (TMorJTT==TM)?"Transmembrane":"JTT", pamN, -(double)ppenalty/1000, -(double)poffset/1000 );
+
+ JTTmtx( rsr, freq, amino, amino_grp, (int)(TMorJTT==TM) );
+
+#if TEST
+ fprintf( stdout, "rsr = \n" );
+ for( i=0; i<20; i++ )
+ {
+ for( j=0; j<20; j++ )
+ {
+ fprintf( stdout, "%9.2f ", rsr[i][j] );
+ }
+ fprintf( stdout, "\n" );
+ }
+#endif
+
+ for( i=0; i<0x80; i++ ) amino_n[i] = -1;
+ for( i=0; i<26; i++ ) amino_n[(int)amino[i]] = i;
+
+ if( fmodel == 1 )
+ {
+ calcfreq( nseq, seq, datafreq );
+ freq1 = datafreq;
+ }
+ else
+ freq1 = freq;
+
+ fprintf( stderr, "generating %dPAM %s scoring matrix for amino acids ... ", pamN, (TMorJTT==TM)?"Transmembrane":"JTT" );
+
+ tmp = 0.0;
+ for( i=0; i<20; i++ )
+ {
+ mutab[i] = 0.0;
+ for( j=0; j<20; j++ )
+ mutab[i] += rsr[i][j] * freq[j];
+ tmp += mutab[i] * freq[i];
+ }
+#if TEST
+ fprintf( stdout, "mutability = \n" );
+ for( i=0; i<20; i++ )
+ fprintf( stdout, "%5.3f\n", mutab[i] );
+
+ fprintf( stdout, "tmp = %f\n", tmp );
+#endif
+ delta = 0.01 / tmp;
+ for( i=0; i<20; i++ )
+ {
+ for( j=0; j<20; j++ )
+ {
+ if( i != j )
+ pam1[i][j] = delta * rsr[i][j] * freq[i];
+ else
+ pam1[i][j] = 1.0 - delta * mutab[i];
+ }
+ }
+
+ if( disp )
+ {
+ fprintf( stdout, "pam1 = \n" );
+ for( i=0; i<20; i++ )
+ {
+ for( j=0; j<20; j++ )
+ {
+ fprintf( stdout, "%9.6f ", pam1[i][j] );
+ }
+ fprintf( stdout, "\n" );
+ }
+ }
+
+ MtxuntDouble( pamx, 20 );
+ for( x=0; x < pamN; x++ ) MtxmltDouble( pamx, pam1, 20 );
+
+ for( i=0; i<20; i++ ) for( j=0; j<20; j++ )
+ pamx[i][j] /= freq[j];
+
+ for( i=0; i<20; i++ ) for( j=0; j<20; j++ )
+ {
+ if( pamx[i][j] == 0.0 )
+ {
+ fprintf( stderr, "WARNING: pamx[%d][%d] = 0.0?\n", i, j );
+ pamx[i][j] = 0.00001; /* by J. Thompson */
+ }
+ pamx[i][j] = log10( pamx[i][j] ) * 1000.0;
+ }
+
+#if TEST
+ fprintf( stdout, "raw scoring matrix : \n" );
+ for( i=0; i<20; i++ )
+ {
+ for( j=0; j<20; j++ )
+ {
+ fprintf( stdout, "%5.0f", pamx[i][j] );
+ }
+ fprintf( stdout, "\n" );
+ }
+ average = tmp = 0.0;
+ for( i=0; i<20; i++ ) for( j=0; j<20; j++ )
+ {
+ average += pamx[i][j] * freq1[i] * freq1[j];
+ tmp += freq1[i] * freq1[j];
+ }
+ average /= tmp;
+ fprintf( stdout, "Zenbu average = %f, tmp = %f \n", average, tmp );
+ average = tmp = 0.0;
+ for( i=0; i<20; i++ ) for( j=i; j<20; j++ )
+ {
+ average += pamx[i][j] * freq1[i] * freq1[j];
+ tmp += freq1[i] * freq1[j];
+ }
+ average /= tmp;
+ fprintf( stdout, "Zenbu average2 = %f, tmp = %f \n", average, tmp );
+ average = tmp = 0.0;
+ for( i=0; i<20; i++ )
+ {
+ average += pamx[i][i] * freq1[i];
+ tmp += freq1[i];
+ }
+ average /= tmp;
+ fprintf( stdout, "Itch average = %f, tmp = %f \n", average, tmp );
+#endif
+
+#if NORMALIZE1
+ if( fmodel == -1 )
+ average = 0.0;
+ else
+ {
+#if TEST
+ for( i=0; i<20; i++ )
+ fprintf( stdout, "freq[%c] = %f, datafreq[%c] = %f, freq1[] = %f\n", amino[i], freq[i], amino[i], datafreq[i], freq1[i] );
+#endif
+ average = 0.0;
+ for( i=0; i<20; i++ ) for( j=0; j<20; j++ )
+ average += pamx[i][j] * freq1[i] * freq1[j];
+ }
+#if TEST
+ fprintf( stdout, "####### average2 = %f\n", average );
+#endif
+
+ for( i=0; i<20; i++ ) for( j=0; j<20; j++ )
+ pamx[i][j] -= average;
+#if TEST
+ fprintf( stdout, "average2 = %f\n", average );
+ fprintf( stdout, "after average substruction : \n" );
+ for( i=0; i<20; i++ )
+ {
+ for( j=0; j<20; j++ )
+ {
+ fprintf( stdout, "%5.0f", pamx[i][j] );
+ }
+ fprintf( stdout, "\n" );
+ }
+#endif
+
+ average = 0.0;
+ for( i=0; i<20; i++ )
+ average += pamx[i][i] * freq1[i];
+#if TEST
+ fprintf( stdout, "####### average1 = %f\n", average );
+#endif
+
+ for( i=0; i<20; i++ ) for( j=0; j<20; j++ )
+ pamx[i][j] *= 600.0 / average;
+#if TEST
+ fprintf( stdout, "after average division : \n" );
+ for( i=0; i<20; i++ )
+ {
+ for( j=0; j<=i; j++ )
+ {
+ fprintf( stdout, "%5.0f", pamx[i][j] );
+ }
+ fprintf( stdout, "\n" );
+ }
+#endif
+
+ for( i=0; i<20; i++ ) for( j=0; j<20; j++ )
+ pamx[i][j] -= offset;
+#if TEST
+ fprintf( stdout, "after offset substruction (offset = %d): \n", offset );
+ for( i=0; i<20; i++ )
+ {
+ for( j=0; j<=i; j++ )
+ {
+ fprintf( stdout, "%5.0f", pamx[i][j] );
+ }
+ fprintf( stdout, "\n" );
+ }
+#endif
+#if 0
+/* Ãí°Õ ¡ª¡ª¡ª¡ª¡ª¡ª¡ª¡ª¡ª¡ª */
+ penalty -= offset;
+#endif
+
+
+ for( i=0; i<20; i++ ) for( j=0; j<20; j++ )
+ pamx[i][j] = shishagonyuu( pamx[i][j] );
+
+#else
+
+ average = 0.0;
+ for( i=0; i<20; i++ ) for( j=0; j<20; j++ )
+ average += pamx[i][j];
+ average /= 400.0;
+
+ for( i=0; i<20; i++ ) for( j=0; j<20; j++ )
+ {
+ pamx[i][j] -= average;
+ pamx[i][j] = shishagonyuu( pamx[i][j] );
+ }
+#endif
+ if( disp )
+ {
+ fprintf( stdout, " scoring matrix \n" );
+ for( i=0; i<20; i++ )
+ {
+ fprintf( stdout, "%c ", amino[i] );
+ for( j=0; j<20; j++ )
+ fprintf( stdout, "%5.0f", pamx[i][j] );
+ fprintf( stdout, "\n" );
+ }
+ fprintf( stdout, " " );
+ for( i=0; i<20; i++ )
+ fprintf( stdout, " %c", amino[i] );
+
+ average = 0.0;
+ for( i=0; i<20; i++ ) for( j=0; j<20; j++ )
+ average += pamx[i][j] * freq1[i] * freq1[j];
+ fprintf( stdout, "average = %f\n", average );
+
+ average = 0.0;
+ for( i=0; i<20; i++ )
+ average += pamx[i][i] * freq1[i];
+ fprintf( stdout, "itch average = %f\n", average );
+ fprintf( stderr, "parameters: %d, %d, %d\n", penalty, penalty_ex, offset );
+
+
+ exit( 1 );
+ }
+
+ for( i=0; i<26; i++ ) for( j=0; j<26; j++ ) n_dis[i][j] = 0;
+ for( i=0; i<20; i++ ) for( j=0; j<20; j++ ) n_dis[i][j] = (int)pamx[i][j];
+
+ fprintf( stderr, "done.\n" );
+ FreeDoubleMtx( rsr );
+ FreeDoubleMtx( pam1 );
+ FreeDoubleMtx( pamx );
+ FreeDoubleVec( freq );
+ FreeDoubleVec( mutab );
+ FreeDoubleVec( datafreq );
+ }
+ fprintf( stderr, "scoremtx = %d\n", scoremtx );
+
+#if DEBUG
+ fprintf( stderr, "scoremtx = %d\n", scoremtx );
+ fprintf( stderr, "amino[] = %s\n", amino );
+#endif
+
+ for( i=0; i<0x80; i++ )amino_n[i] = -1;
+ for( i=0; i<26; i++) amino_n[(int)amino[i]] = i;
+ for( i=0; i<0x80; i++ ) for( j=0; j<0x80; j++ ) amino_dis[i][j] = 0;
+ for( i=0; i<0x80; i++ ) for( j=0; j<0x80; j++ ) amino_disLN[i][j] = 0;
+ for( i=0; i<0x80; i++ ) for( j=0; j<0x80; j++ ) amino_dis_consweight_multi[i][j] = 0.0;
+ for( i=0; i<26; i++) for( j=0; j<26; j++ )
+ {
+ amino_dis[(int)amino[i]][(int)amino[j]] = n_dis[i][j];
+ n_dis_consweight_multi[i][j] = (float)n_dis[i][j] * consweight_multi;
+ amino_dis_consweight_multi[(int)amino[i]][(int)amino[j]] = (double)n_dis[i][j] * consweight_multi;
+ }
+
+ if( dorp == 'd' ) /* DNA */
+ {
+ for( i=0; i<5; i++) for( j=0; j<5; j++ )
+ amino_disLN[(int)amino[i]][(int)amino[j]] = n_dis[i][j] + offset - offsetLN;
+ for( i=5; i<10; i++) for( j=5; j<10; j++ )
+ amino_disLN[(int)amino[i]][(int)amino[j]] = n_dis[i][j] + offset - offsetLN;
+ for( i=0; i<5; i++) for( j=0; j<5; j++ )
+ n_disFFT[i][j] = n_dis[i][j] + offset - offsetFFT;
+ for( i=5; i<10; i++) for( j=5; j<10; j++ )
+ n_disFFT[i][j] = n_dis[i][j] + offset - offsetFFT;
+ }
+ else // protein
+ {
+ for( i=0; i<20; i++) for( j=0; j<20; j++ )
+ amino_disLN[(int)amino[i]][(int)amino[j]] = n_dis[i][j] + offset - offsetLN;
+ for( i=0; i<20; i++) for( j=0; j<20; j++ )
+ n_disFFT[i][j] = n_dis[i][j] + offset - offsetFFT;
+ }
+
+#if 0
+ fprintf( stderr, "amino_dis (offset = %d): \n", offset );
+ for( i=0; i<20; i++ )
+ {
+ for( j=0; j<20; j++ )
+ {
+ fprintf( stderr, "%5d", amino_dis[(int)amino[i]][(int)amino[j]] );
+ }
+ fprintf( stderr, "\n" );
+ }
+
+ fprintf( stderr, "amino_disLN (offsetLN = %d): \n", offsetLN );
+ for( i=0; i<20; i++ )
+ {
+ for( j=0; j<20; j++ )
+ {
+ fprintf( stderr, "%5d", amino_disLN[(int)amino[i]][(int)amino[j]] );
+ }
+ fprintf( stderr, "\n" );
+ }
+
+ fprintf( stderr, "n_dis (offset = %d): \n", offset );
+ for( i=0; i<26; i++ )
+ {
+ for( j=0; j<26; j++ )
+ {
+ fprintf( stderr, "%5d", n_dis[i][j] );
+ }
+ fprintf( stderr, "\n" );
+ }
+
+ fprintf( stderr, "n_disFFT (offsetFFT = %d): \n", offsetFFT );
+ for( i=0; i<26; i++ )
+ {
+ for( j=0; j<26; j++ )
+ {
+ fprintf( stderr, "%5d", n_disFFT[i][j] );
+ }
+ fprintf( stderr, "\n" );
+ }
+exit( 1 );
+#endif
+
+
+ ppid = 0;
+
+
+ if( fftThreshold == NOTSPECIFIED )
+ {
+ fftThreshold = FFT_THRESHOLD;
+ }
+ if( fftWinSize == NOTSPECIFIED )
+ {
+ if( dorp == 'd' )
+ fftWinSize = FFT_WINSIZE_D;
+ else
+ fftWinSize = FFT_WINSIZE_P;
+ }
+
+
+ if( fftscore )
+ {
+ double av, sd;
+
+ for( i=0; i<20; i++ ) polarity[i] = polarity_[i];
+ for( av=0.0, i=0; i<20; i++ ) av += polarity[i];
+ av /= 20.0;
+ for( sd=0.0, i=0; i<20; i++ ) sd += ( polarity[i]-av ) * ( polarity[i]-av );
+ sd /= 20.0; sd = sqrt( sd );
+ for( i=0; i<20; i++ ) polarity[i] -= av;
+ for( i=0; i<20; i++ ) polarity[i] /= sd;
+
+ for( i=0; i<20; i++ ) volume[i] = volume_[i];
+ for( av=0.0, i=0; i<20; i++ ) av += volume[i];
+ av /= 20.0;
+ for( sd=0.0, i=0; i<20; i++ ) sd += ( volume[i]-av ) * ( volume[i]-av );
+ sd /= 20.0; sd = sqrt( sd );
+ for( i=0; i<20; i++ ) volume[i] -= av;
+ for( i=0; i<20; i++ ) volume[i] /= sd;
+
+#if 0
+ for( i=0; i<20; i++ ) fprintf( stdout, "amino=%c, pol = %f<-%f, vol = %f<-%f\n", amino[i], polarity[i], polarity_[i], volume[i], volume_[i] );
+ for( i=0; i<20; i++ ) fprintf( stdout, "%c %+5.3f %+5.3f\n", amino[i], volume[i], polarity[i] );
+#endif
+ }
+}
git://source.jalview.org / jabaws.git / blobdiff