void FreeDoubleMtx( double **mtx )
{
int i;
for( i=0; mtx[i]; i++ )
FreeDoubleVec( mtx[i] );
free( mtx );
}
void blockAlign3( int *cut1, int *cut2, Segment **seg1, Segment **seg2, double **ocrossscore, int *ncut )
// memory complexity = O(n^3), time complexity = O(n^2)
{
int i, j, shift, cur1, cur2, count;
static TLS int crossscoresize = 0;
static TLS int jumpposi, *jumppos;
static TLS double jumpscorei, *jumpscore;
static TLS int *result1 = NULL;
static TLS int *result2 = NULL;
static TLS int *ocut1 = NULL;
static TLS int *ocut2 = NULL;
double maximum;
static TLS double **crossscore = NULL;
static TLS int **track = NULL;
if( result1 == NULL )
{
result1 = AllocateIntVec( MAXSEG );
result2 = AllocateIntVec( MAXSEG );
ocut1 = AllocateIntVec( MAXSEG );
ocut2 = AllocateIntVec( MAXSEG );
}
if( crossscoresize < *ncut+2 )
{
crossscoresize = *ncut+2;
if( fftkeika ) fprintf( stderr, "allocating crossscore and track, size = %d\n", crossscoresize );
if( track ) FreeIntMtx( track );
if( crossscore ) FreeDoubleMtx( crossscore );
if( jumppos ) FreeIntVec( jumppos );
if( jumpscore ) FreeDoubleVec( jumpscore );
track = AllocateIntMtx( crossscoresize, crossscoresize );
crossscore = AllocateDoubleMtx( crossscoresize, crossscoresize );
jumppos = AllocateIntVec( crossscoresize );
jumpscore = AllocateDoubleVec( crossscoresize );
}
#if 0
for( i=0; i<*ncut-2; i++ )
fprintf( stderr, "%d.start = %d, score = %f\n", i, seg1[i]->start, seg1[i]->score );
for( i=0; i<*ncut; i++ )
fprintf( stderr, "i=%d, cut1 = %d, cut2 = %d\n", i, cut1[i], cut2[i] );
for( i=0; i<*ncut; i++ )
{
for( j=0; j<*ncut; j++ )
fprintf( stderr, "%#4.0f ", ocrossscore[i][j] );
fprintf( stderr, "\n" );
}
#endif
for( i=0; i<*ncut; i++ ) for( j=0; j<*ncut; j++ ) /* mudadanaa */
crossscore[i][j] = ocrossscore[i][j];
for( i=0; i<*ncut; i++ )
{
ocut1[i] = cut1[i];
ocut2[i] = cut2[i];
}
for( j=0; j<*ncut; j++ )
{
jumpscore[j] = -999.999;
jumppos[j] = -1;
}
for( i=1; i<*ncut; i++ )
{
jumpscorei = -999.999;
jumpposi = -1;
for( j=1; j<*ncut; j++ )
{
#if 1
fprintf( stderr, "in blockalign3, ### i=%d, j=%d\n", i, j );
#endif
#if 0
for( k=0; k<j-2; k++ )
{
/*
fprintf( stderr, "k=%d, i=%d\n", k, i );
*/
if( k && k<*ncut-1 && j<*ncut-1 && !permit( seg1[k-1], seg1[j-1] ) ) continue;
if( crossscore[i-1][k] > maxj )
{
pointi = k;
maxi = crossscore[i-1][k];
}
}
pointj = 0; maxj = 0.0;
for( k=0; k<i-2; k++ )
{
if( k && k<*ncut-1 && i<*ncut-1 && !permit( seg2[k-1], seg2[i-1] ) ) continue;
if( crossscore[k][j-1] > maxj )
{
pointj = k;
maxj = crossscore[k][j-1];
}
}
maxi += penalty;
maxj += penalty;
#endif
maximum = crossscore[i-1][j-1];
track[i][j] = 0;
if( maximum < jumpscorei && permit( seg1[jumpposi], seg1[i] ) )
{
maximum = jumpscorei;
track[i][j] = j - jumpposi;
}
if( maximum < jumpscore[j] && permit( seg2[jumppos[j]], seg2[j] ) )
{
maximum = jumpscore[j];
track[i][j] = jumpscore[j] - i;
}
crossscore[i][j] += maximum;
if( jumpscorei < crossscore[i-1][j] )
{
jumpscorei = crossscore[i-1][j];
jumpposi = j;
}
if( jumpscore[j] < crossscore[i][j-1] )
{
jumpscore[j] = crossscore[i][j-1];
jumppos[j] = i;
}
}
}
#if 0
for( i=0; i<*ncut; i++ )
{
for( j=0; j<*ncut; j++ )
fprintf( stderr, "%3d ", track[i][j] );
fprintf( stderr, "\n" );
}
#endif
result1[MAXSEG-1] = *ncut-1;
result2[MAXSEG-1] = *ncut-1;
for( i=MAXSEG-1; i>=1; i-- )
{
cur1 = result1[i];
cur2 = result2[i];
if( cur1 == 0 || cur2 == 0 ) break;
shift = track[cur1][cur2];
if( shift == 0 )
{
result1[i-1] = cur1 - 1;
result2[i-1] = cur2 - 1;
continue;
}
else if( shift > 0 )
{
result1[i-1] = cur1 - 1;
result2[i-1] = cur2 - shift;
}
else if( shift < 0 )
{
result1[i-1] = cur1 + shift;
result2[i-1] = cur2 - 1;
}
}
count = 0;
for( j=i; j<MAXSEG; j++ )
{
if( ocrossscore[result1[j]][result2[j]] == 0.0 ) continue;
if( result1[j] == result1[j-1] || result2[j] == result2[j-1] )
if( ocrossscore[result1[j]][result2[j]] > ocrossscore[result1[j-1]][result2[j-1]] )
count--;
cut1[count] = ocut1[result1[j]];
cut2[count] = ocut2[result2[j]];
count++;
}
*ncut = count;
#if 0
for( i=0; i<*ncut; i++ )
fprintf( stderr, "i=%d, cut1 = %d, cut2 = %d\n", i, cut1[i], cut2[i] );
#endif
}
int alignableReagion( int clus1, int clus2,
char **seq1, char **seq2,
double *eff1, double *eff2,
Segment *seg )
{
int i, j, k;
int status, starttmp = 0; // by D.Mathog, a gess
double score;
int value = 0;
int len, maxlen;
int length = 0; // by D.Mathog, a gess
static TLS double *stra = NULL;
static TLS int alloclen = 0;
double totaleff;
double cumscore;
static TLS double threshold;
static TLS double *prf1 = NULL;
static TLS double *prf2 = NULL;
static TLS int *hat1 = NULL;
static TLS int *hat2 = NULL;
int pre1, pre2;
#if 0
char **seq1pt;
char **seq2pt;
double *eff1pt;
double *eff2pt;
#endif
#if 0
fprintf( stderr, "### In alignableRegion, clus1=%d, clus2=%d \n", clus1, clus2 );
fprintf( stderr, "seq1[0] = %s\n", seq1[0] );
fprintf( stderr, "seq2[0] = %s\n", seq2[0] );
fprintf( stderr, "eff1[0] = %f\n", eff1[0] );
fprintf( stderr, "eff2[0] = %f\n", eff2[0] );
#endif
if( clus1 == 0 )
{
if( stra ) FreeDoubleVec( stra ); stra = NULL;
if( prf1 ) FreeDoubleVec( prf1 ); prf1 = NULL;
if( prf2 ) FreeDoubleVec( prf2 ); prf2 = NULL;
if( hat1 ) FreeIntVec( hat1 ); hat1 = NULL;
if( hat2 ) FreeIntVec( hat2 ); hat2 = NULL;
alloclen = 0;
return( 0 );
}
if( prf1 == NULL )
{
prf1 = AllocateDoubleVec( nalphabets );
prf2 = AllocateDoubleVec( nalphabets );
hat1 = AllocateIntVec( nalphabets+1 );
hat2 = AllocateIntVec( nalphabets+1 );
}
len = MIN( strlen( seq1[0] ), strlen( seq2[0] ) );
maxlen = MAX( strlen( seq1[0] ), strlen( seq2[0] ) ) + fftWinSize;
if( alloclen < maxlen )
{
if( alloclen )
{
FreeDoubleVec( stra );
}
else
{
threshold = (int)fftThreshold / 100.0 * 600.0 * fftWinSize;
}
stra = AllocateDoubleVec( maxlen );
alloclen = maxlen;
}
totaleff = 0.0;
for( i=0; i<clus1; i++ ) for( j=0; j<clus2; j++ ) totaleff += eff1[i] * eff2[j];
for( i=0; i<len; i++ )
{
/* make prfs */
for( j=0; j<nalphabets; j++ )
{
prf1[j] = 0.0;
prf2[j] = 0.0;
}
#if 0
seq1pt = seq1;
eff1pt = eff1;
j = clus1;
while( j-- ) prf1[amino_n[(*seq1pt++)[i]]] += *eff1pt++;
#else
for( j=0; j<clus1; j++ ) prf1[amino_n[(int)seq1[j][i]]] += eff1[j];
#endif
for( j=0; j<clus2; j++ ) prf2[amino_n[(int)seq2[j][i]]] += eff2[j];
/* make hats */
pre1 = pre2 = nalphabets;
for( j=25; j>=0; j-- )
{
if( prf1[j] )
{
hat1[pre1] = j;
pre1 = j;
}
if( prf2[j] )
{
hat2[pre2] = j;
pre2 = j;
}
}
hat1[pre1] = -1;
hat2[pre2] = -1;
/* make site score */
stra[i] = 0.0;
for( k=hat1[nalphabets]; k!=-1; k=hat1[k] )
for( j=hat2[nalphabets]; j!=-1; j=hat2[j] )
// stra[i] += n_dis[k][j] * prf1[k] * prf2[j];
stra[i] += n_disFFT[k][j] * prf1[k] * prf2[j];
stra[i] /= totaleff;
}
(seg+0)->skipForeward = 0;
(seg+1)->skipBackward = 0;
status = 0;
cumscore = 0.0;
score = 0.0;
for( j=0; j<fftWinSize; j++ ) score += stra[j];
for( i=1; i<len-fftWinSize; i++ )
{
score = score - stra[i-1] + stra[i+fftWinSize-1];
#if TMPTMPTMP
fprintf( stderr, "%d %10.0f ? %10.0f\n", i, score, threshold );
#endif
if( score > threshold )
{
#if 0
seg->start = i;
seg->end = i;
seg->center = ( seg->start + seg->end + fftWinSize ) / 2 ;
seg->score = score;
status = 0;
value++;
#else
if( !status )
{
status = 1;
starttmp = i;
length = 0;
cumscore = 0.0;
}
length++;
cumscore += score;
#endif
}
if( score <= threshold || length > SEGMENTSIZE )
{
if( status )
{
if( length > fftWinSize )
{
seg->start = starttmp;
seg->end = i;
seg->center = ( seg->start + seg->end + fftWinSize ) / 2 ;
seg->score = cumscore;
#if 0
fprintf( stderr, "%d-%d length = %d, score = %f, value = %d\n", seg->start, seg->end, length, cumscore, value );
#endif
if( length > SEGMENTSIZE )
{
(seg+0)->skipForeward = 1;
(seg+1)->skipBackward = 1;
}
else
{
(seg+0)->skipForeward = 0;
(seg+1)->skipBackward = 0;
}
value++;
seg++;
}
length = 0;
cumscore = 0.0;
status = 0;
starttmp = i;
if( value > MAXSEG - 3 ) ErrorExit( "TOO MANY SEGMENTS!");
}
}
}
if( status && length > fftWinSize )
{
seg->end = i;
seg->start = starttmp;
seg->center = ( starttmp + i + fftWinSize ) / 2 ;
seg->score = cumscore;
#if 0
fprintf( stderr, "%d-%d length = %d\n", seg->start, seg->end, length );
#endif
value++;
}
#if TMPTMPTMP
exit( 0 );
#endif
// fprintf( stderr, "returning %d\n", value );
return( value );
}
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
/* 注意 ！！！！！！！！！！ */
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
/* 注意 ！！！！！！！！！！ */
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
}
}
float Falign_localhom( char **seq1, char **seq2,
double *eff1, double *eff2,
int clus1, int clus2,
int alloclen,
LocalHom ***localhom, float *totalimpmatch,
int *gapmap1, int *gapmap2,
int *chudanpt, int chudanref, int *chudanres )
{
// tditeration.c deha alloclen ha huhen nanode
// prevalloclen ha iranai.
int i, j, k, l, m, maxk;
int nlen, nlen2, nlen4;
static TLS int crossscoresize = 0;
static TLS char **tmpseq1 = NULL;
static TLS char **tmpseq2 = NULL;
static TLS char **tmpptr1 = NULL;
static TLS char **tmpptr2 = NULL;
static TLS char **tmpres1 = NULL;
static TLS char **tmpres2 = NULL;
static TLS char **result1 = NULL;
static TLS char **result2 = NULL;
#if RND
static TLS char **rndseq1 = NULL;
static TLS char **rndseq2 = NULL;
#endif
static TLS Fukusosuu **seqVector1 = NULL;
static TLS Fukusosuu **seqVector2 = NULL;
static TLS Fukusosuu **naiseki = NULL;
static TLS Fukusosuu *naisekiNoWa = NULL;
static TLS double *soukan = NULL;
static TLS double **crossscore = NULL;
int nlentmp;
static TLS int *kouho = NULL;
static TLS Segment *segment = NULL;
static TLS Segment *segment1 = NULL;
static TLS Segment *segment2 = NULL;
static TLS Segment **sortedseg1 = NULL;
static TLS Segment **sortedseg2 = NULL;
static TLS int *cut1 = NULL;
static TLS int *cut2 = NULL;
static TLS char *sgap1, *egap1, *sgap2, *egap2;
static TLS int localalloclen = 0;
int lag;
int tmpint;
int count, count0;
int len1, len2;
int totallen;
float totalscore;
float impmatch;
extern Fukusosuu *AllocateFukusosuuVec();
extern Fukusosuu **AllocateFukusosuuMtx();
if( seq1 == NULL )
{
if( result1 )
{
// fprintf( stderr, "Freeing localarrays in Falign\n" );
localalloclen = 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 );
partA__align( NULL, NULL, NULL, NULL, 0, 0, 0, NULL, NULL, 0, 0, 0, 0, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0, NULL );
blockAlign2( NULL, NULL, NULL, NULL, NULL, NULL );
if( crossscore ) FreeDoubleMtx( crossscore );
FreeCharMtx( result1 );
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 );
}
len1 = strlen( seq1[0] );
len2 = strlen( seq2[0] );
nlentmp = MAX( len1, len2 );
nlen = 1;
while( nlentmp >= nlen ) nlen <<= 1;
#if 0
fprintf( stderr, "### nlen = %d\n", nlen );
#endif
nlen2 = nlen/2; nlen4 = nlen2 / 2;
#if DEBUG
fprintf( stderr, "len1 = %d, len2 = %d\n", len1, len2 );
fprintf( stderr, "nlentmp = %d, nlen = %d\n", nlentmp, nlen );
#endif
if( !localalloclen )
{
sgap1 = AllocateCharVec( njob );
egap1 = AllocateCharVec( njob );
sgap2 = AllocateCharVec( njob );
egap2 = AllocateCharVec( njob );
kouho = AllocateIntVec( NKOUHO );
cut1 = AllocateIntVec( MAXSEG );
cut2 = AllocateIntVec( MAXSEG );
tmpptr1 = AllocateCharMtx( njob, 0 );
tmpptr2 = AllocateCharMtx( njob, 0 );
result1 = AllocateCharMtx( njob, alloclen );
result2 = AllocateCharMtx( njob, alloclen );
tmpres1 = AllocateCharMtx( njob, alloclen );
tmpres2 = AllocateCharMtx( njob, alloclen );
// crossscore = AllocateDoubleMtx( MAXSEG, MAXSEG );
segment = (Segment *)calloc( MAXSEG, sizeof( Segment ) );
segment1 = (Segment *)calloc( MAXSEG, sizeof( Segment ) );
segment2 = (Segment *)calloc( MAXSEG, sizeof( Segment ) );
sortedseg1 = (Segment **)calloc( MAXSEG, sizeof( Segment * ) );
sortedseg2 = (Segment **)calloc( MAXSEG, sizeof( Segment * ) );
if( !( segment && segment1 && segment2 && sortedseg1 && sortedseg2 ) )
ErrorExit( "Allocation error\n" );
if ( scoremtx == -1 ) n20or4or2 = 4;
else if( fftscore == 1 ) n20or4or2 = 2;
else n20or4or2 = 20;
}
if( localalloclen < nlen )
{
if( localalloclen )
{
#if 1
if( !kobetsubunkatsu )
{
FreeFukusosuuMtx ( seqVector1 );
FreeFukusosuuMtx ( seqVector2 );
FreeFukusosuuVec( naisekiNoWa );
FreeFukusosuuMtx( naiseki );
FreeDoubleVec( soukan );
}
FreeCharMtx( tmpseq1 );
FreeCharMtx( tmpseq2 );
#endif
#if RND
FreeCharMtx( rndseq1 );
FreeCharMtx( rndseq2 );
#endif
}
tmpseq1 = AllocateCharMtx( njob, nlen );
tmpseq2 = AllocateCharMtx( njob, nlen );
if( !kobetsubunkatsu )
{
naisekiNoWa = AllocateFukusosuuVec( nlen );
naiseki = AllocateFukusosuuMtx( n20or4or2, nlen );
seqVector1 = AllocateFukusosuuMtx( n20or4or2+1, nlen+1 );
seqVector2 = AllocateFukusosuuMtx( n20or4or2+1, nlen+1 );
soukan = AllocateDoubleVec( nlen+1 );
}
#if RND
rndseq1 = AllocateCharMtx( njob, nlen );
rndseq2 = AllocateCharMtx( njob, nlen );
for( i=0; i<njob; i++ )
{
generateRndSeq( rndseq1[i], nlen );
generateRndSeq( rndseq2[i], nlen );
}
#endif
localalloclen = nlen;
}
for( j=0; j<clus1; j++ ) strcpy( tmpseq1[j], seq1[j] );
for( j=0; j<clus2; j++ ) strcpy( tmpseq2[j], seq2[j] );
#if 0
fftfp = fopen( "input_of_Falign", "w" );
fprintf( fftfp, "nlen = %d\n", nlen );
fprintf( fftfp, "seq1: ( %d sequences ) \n", clus1 );
for( i=0; i<clus1; i++ )
fprintf( fftfp, "%s\n", seq1[i] );
fprintf( fftfp, "seq2: ( %d sequences ) \n", clus2 );
for( i=0; i<clus2; i++ )
fprintf( fftfp, "%s\n", seq2[i] );
fclose( fftfp );
system( "less input_of_Falign < /dev/tty > /dev/tty" );
#endif
if( !kobetsubunkatsu )
{
fprintf( stderr, "FFT ... " );
for( j=0; j<n20or4or2; j++ ) vec_init( seqVector1[j], nlen );
if( fftscore && scoremtx != -1 )
{
for( i=0; i<clus1; i++ )
{
seq_vec_2( seqVector1[0], polarity, eff1[i], tmpseq1[i] );
seq_vec_2( seqVector1[1], volume, eff1[i], tmpseq1[i] );
}
}
else
{
#if 0
for( i=0; i<clus1; i++ ) for( j=0; j<n20or4or2; j++ )
seq_vec( seqVector1[j], amino[j], eff1[i], tmpseq1[i] );
#else
for( i=0; i<clus1; i++ )
seq_vec_3( seqVector1, eff1[i], tmpseq1[i] );
#endif
}
#if RND
for( i=0; i<clus1; i++ )
{
vec_init2( seqVector1, rndseq1[i], eff1[i], len1, nlen );
}
#endif
#if 0
fftfp = fopen( "seqVec", "w" );
fprintf( fftfp, "before transform\n" );
for( k=0; k<n20or4or2; k++ )
{
fprintf( fftfp, "nlen=%d\n", nlen );
fprintf( fftfp, "%c\n", amino[k] );
for( l=0; l<nlen; l++ )
fprintf( fftfp, "%f %f\n", seqVector1[k][l].R, seqVector1[k][l].I );
}
fclose( fftfp );
system( "less seqVec < /dev/tty > /dev/tty" );
#endif
for( j=0; j<n20or4or2; j++ ) vec_init( seqVector2[j], nlen );
if( fftscore && scoremtx != -1 )
{
for( i=0; i<clus2; i++ )
{
seq_vec_2( seqVector2[0], polarity, eff2[i], tmpseq2[i] );
seq_vec_2( seqVector2[1], volume, eff2[i], tmpseq2[i] );
}
}
else
{
#if 0
for( i=0; i<clus2; i++ ) for( j=0; j<n20or4or2; j++ )
seq_vec( seqVector2[j], amino[j], eff2[i], tmpseq2[i] );
#else
for( i=0; i<clus2; i++ )
seq_vec_3( seqVector2, eff2[i], tmpseq2[i] );
#endif
}
#if RND
for( i=0; i<clus2; i++ )
{
vec_init2( seqVector2, rndseq2[i], eff2[i], len2, nlen );
}
#endif
#if 0
fftfp = fopen( "seqVec2", "w" );
fprintf( fftfp, "before fft\n" );
for( k=0; k<n20or4or2; k++ )
{
fprintf( fftfp, "%c\n", amino[k] );
for( l=0; l<nlen; l++ )
fprintf( fftfp, "%f %f\n", seqVector2[k][l].R, seqVector2[k][l].I );
}
fclose( fftfp );
system( "less seqVec2 < /dev/tty > /dev/tty" );
#endif
for( j=0; j<n20or4or2; j++ )
{
fft( nlen, seqVector2[j], (j==0) );
fft( nlen, seqVector1[j], 0 );
}
#if 0
fftfp = fopen( "seqVec2", "w" );
fprintf( fftfp, "#after fft\n" );
for( k=0; k<n20or4or2; k++ )
{
fprintf( fftfp, "#%c\n", amino[k] );
for( l=0; l<nlen; l++ )
fprintf( fftfp, "%f %f\n", seqVector2[k][l].R, seqVector2[k][l].I );
}
fclose( fftfp );
system( "less seqVec2 < /dev/tty > /dev/tty" );
#endif
for( k=0; k<n20or4or2; k++ )
{
for( l=0; l<nlen; l++ )
calcNaiseki( naiseki[k]+l, seqVector1[k]+l, seqVector2[k]+l );
}
for( l=0; l<nlen; l++ )
{
naisekiNoWa[l].R = 0.0;
naisekiNoWa[l].I = 0.0;
for( k=0; k<n20or4or2; k++ )
{
naisekiNoWa[l].R += naiseki[k][l].R;
naisekiNoWa[l].I += naiseki[k][l].I;
}
}
#if 0
fftfp = fopen( "naisekiNoWa", "w" );
fprintf( fftfp, "#Before fft\n" );
for( l=0; l<nlen; l++ )
fprintf( fftfp, "%d %f %f\n", l, naisekiNoWa[l].R, naisekiNoWa[l].I );
fclose( fftfp );
system( "less naisekiNoWa < /dev/tty > /dev/tty " );
#endif
fft( -nlen, naisekiNoWa, 0 );
for( m=0; m<=nlen2; m++ )
soukan[m] = naisekiNoWa[nlen2-m].R;
for( m=nlen2+1; m<nlen; m++ )
soukan[m] = naisekiNoWa[nlen+nlen2-m].R;
#if 0
fftfp = fopen( "naisekiNoWa", "w" );
fprintf( fftfp, "#After fft\n" );
for( l=0; l<nlen; l++ )
fprintf( fftfp, "%d %f\n", l, naisekiNoWa[l].R );
fclose( fftfp );
fftfp = fopen( "list.plot", "w" );
fprintf( fftfp, "plot 'naisekiNoWa'\npause -1" );
fclose( fftfp );
system( "/usr/bin/gnuplot list.plot &" );
#endif
#if 0
fprintf( stderr, "frt write start\n" );
fftfp = fopen( "frt", "w" );
for( l=0; l<nlen; l++ )
fprintf( fftfp, "%d %f\n", l-nlen2, soukan[l] );
fclose( fftfp );
system( "less frt < /dev/tty > /dev/tty" );
#if 0
fftfp = fopen( "list.plot", "w" );
fprintf( fftfp, "plot 'frt'\n pause +1" );
fclose( fftfp );
system( "/usr/bin/gnuplot list.plot" );
#endif
#endif
getKouho( kouho, NKOUHO, soukan, nlen );
#if 0
for( i=0; i<NKOUHO; i++ )
{
fprintf( stderr, "kouho[%d] = %d\n", i, kouho[i] );
}
#endif
}
#if KEIKA
fprintf( stderr, "Searching anchors ... " );
#endif
count = 0;
#define CAND 0
#if CAND
fftfp = fopen( "cand", "w" );
fclose( fftfp );
#endif
if( kobetsubunkatsu )
{
maxk = 1;
kouho[0] = 0;
}
else
{
maxk = NKOUHO;
}
for( k=0; k<maxk; k++ )
{
lag = kouho[k];
zurasu2( lag, clus1, clus2, seq1, seq2, tmpptr1, tmpptr2 );
#if CAND
fftfp = fopen( "cand", "a" );
fprintf( fftfp, "Candidate No.%d lag = %d\n", k+1, lag );
fprintf( fftfp, "%s\n", tmpptr1[0] );
fprintf( fftfp, "%s\n", tmpptr2[0] );
fclose( fftfp );
#endif
tmpint = alignableReagion( clus1, clus2, tmpptr1, tmpptr2, eff1, eff2, segment+count );
if( count+tmpint > MAXSEG -3 ) ErrorExit( "TOO MANY SEGMENTS.\n" );
while( tmpint-- > 0 )
{
if( lag > 0 )
{
segment1[count].start = segment[count].start ;
segment1[count].end = segment[count].end ;
segment1[count].center = segment[count].center;
segment1[count].score = segment[count].score;
segment2[count].start = segment[count].start + lag;
segment2[count].end = segment[count].end + lag;
segment2[count].center = segment[count].center + lag;
segment2[count].score = segment[count].score ;
}
else
{
segment1[count].start = segment[count].start - lag;
segment1[count].end = segment[count].end - lag;
segment1[count].center = segment[count].center - lag;
segment1[count].score = segment[count].score ;
segment2[count].start = segment[count].start ;
segment2[count].end = segment[count].end ;
segment2[count].center = segment[count].center;
segment2[count].score = segment[count].score ;
}
#if 0
fftfp = fopen( "cand", "a" );
fprintf( fftfp, "Goukaku=%dko\n", tmpint );
fprintf( fftfp, "in 1 %d\n", segment1[count].center );
fprintf( fftfp, "in 2 %d\n", segment2[count].center );
fclose( fftfp );
#endif
segment1[count].pair = &segment2[count];
segment2[count].pair = &segment1[count];
count++;
#if 0
fprintf( stderr, "count=%d\n", count );
#endif
}
}
#if 1
if( !kobetsubunkatsu )
fprintf( stderr, "%d segments found\n", count );
#endif
if( !count && fftNoAnchStop )
ErrorExit( "Cannot detect anchor!" );
#if 0
fftfp = fopen( "fft", "a" );
fprintf( fftfp, "RESULT before sort:\n" );
for( l=0; l<count; l++ )
{
fprintf( fftfp, "cut[%d]=%d, ", l, segment1[l].center );
fprintf( fftfp, "%d score = %f\n", segment2[l].center, segment1[l].score );
}
fclose( fftfp );
#endif
#if KEIKA
fprintf( stderr, "Aligning anchors ... " );
#endif
for( i=0; i<count; i++ )
{
sortedseg1[i] = &segment1[i];
sortedseg2[i] = &segment2[i];
}
#if 0
tmpsort( count, sortedseg1 );
tmpsort( count, sortedseg2 );
qsort( sortedseg1, count, sizeof( Segment * ), segcmp );
qsort( sortedseg2, count, sizeof( Segment * ), segcmp );
#else
mymergesort( 0, count-1, sortedseg1 );
mymergesort( 0, count-1, sortedseg2 );
#endif
for( i=0; i<count; i++ ) sortedseg1[i]->number = i;
for( i=0; i<count; i++ ) sortedseg2[i]->number = i;
if( kobetsubunkatsu )
{
for( i=0; i<count; i++ )
{
cut1[i+1] = sortedseg1[i]->center;
cut2[i+1] = sortedseg2[i]->center;
}
cut1[0] = 0;
cut2[0] = 0;
cut1[count+1] = len1;
cut2[count+1] = len2;
count += 2;
}
else
{
if( crossscoresize < count+2 )
{
crossscoresize = count+2;
#if 1
fprintf( stderr, "######allocating crossscore, size = %d\n", crossscoresize );
#endif
if( crossscore ) FreeDoubleMtx( crossscore );
crossscore = AllocateDoubleMtx( crossscoresize, crossscoresize );
}
for( i=0; i<count+2; i++ ) for( j=0; j<count+2; j++ )
crossscore[i][j] = 0.0;
for( i=0; i<count; i++ )
{
crossscore[segment1[i].number+1][segment1[i].pair->number+1] = segment1[i].score;
cut1[i+1] = sortedseg1[i]->center;
cut2[i+1] = sortedseg2[i]->center;
}
#if DEBUG
fprintf( stderr, "AFTER SORT\n" );
for( i=0; i<count; i++ ) fprintf( stderr, "%d, %d\n", segment1[i].start, segment2[i].start );
#endif
crossscore[0][0] = 10000000.0;
cut1[0] = 0;
cut2[0] = 0;
crossscore[count+1][count+1] = 10000000.0;
cut1[count+1] = len1;
cut2[count+1] = len2;
count += 2;
count0 = count;
blockAlign2( cut1, cut2, sortedseg1, sortedseg2, crossscore, &count );
if( count0 > count )
{
#if 0
fprintf( stderr, "\7 REPEAT!? \n" );
#else
fprintf( stderr, "REPEAT!? \n" );
#endif
if( fftRepeatStop ) exit( 1 );
}
#if KEIKA
else fprintf( stderr, "done\n" );
#endif
}
#if 0
fftfp = fopen( "fft", "a" );
fprintf( fftfp, "RESULT after sort:\n" );
for( l=0; l<count; l++ )
{
fprintf( fftfp, "cut[%d]=%d, ", l, segment1[l].center );
fprintf( fftfp, "%d\n", segment2[l].center );
}
fclose( fftfp );
#endif
#if 0
fftfp = fopen( "fft", "a" );
fprintf( fftfp, "RESULT after sort:\n" );
for( l=0; l<count; l++ )
{
fprintf( fftfp, "cut : %d %d\n", cut1[l], cut2[l] );
}
fclose( fftfp );
#endif
#if KEIKA
fprintf( trap_g, "Devided to %d segments\n", count-1 );
fprintf( trap_g, "%d %d forg\n", MIN( clus1, clus2 ), count-1 );
#endif
totallen = 0;
for( j=0; j<clus1; j++ ) result1[j][0] = 0;
for( j=0; j<clus2; j++ ) result2[j][0] = 0;
totalscore = 0.0;
*totalimpmatch = 0.0;
for( i=0; i<count-1; i++ )
{
#if DEBUG
fprintf( stderr, "DP %03d / %03d %4d to ", i+1, count-1, totallen );
#else
#if KEIKA
fprintf( stderr, "DP %03d / %03d\r", i+1, count-1 );
#endif
#endif
if( cut1[i] )
{
getkyokaigap( sgap1, seq1, cut1[i]-1, clus1 );
getkyokaigap( sgap2, seq2, cut2[i]-1, clus2 );
}
else
{
for( j=0; j<clus1; j++ ) sgap1[j] = 'o';
for( j=0; j<clus2; j++ ) sgap2[j] = 'o';
}
if( cut1[i+1] != len1 )
{
getkyokaigap( egap1, seq1, cut1[i+1], clus1 );
getkyokaigap( egap2, seq2, cut2[i+1], clus2 );
}
else
{
for( j=0; j<clus1; j++ ) egap1[j] = 'o';
for( j=0; j<clus2; j++ ) egap2[j] = 'o';
}
for( j=0; j<clus1; j++ )
{
strncpy( tmpres1[j], seq1[j]+cut1[i], cut1[i+1]-cut1[i] );
tmpres1[j][cut1[i+1]-cut1[i]] = 0;
}
if( kobetsubunkatsu ) commongappick_record( clus1, tmpres1, gapmap1 );
for( j=0; j<clus2; j++ )
{
strncpy( tmpres2[j], seq2[j]+cut2[i], cut2[i+1]-cut2[i] );
tmpres2[j][cut2[i+1]-cut2[i]] = 0;
}
if( kobetsubunkatsu ) commongappick_record( clus2, tmpres2, gapmap2 );
#if 0
fprintf( stderr, "count = %d\n", count );
fprintf( stderr, "### reg1 = %d-%d\n", cut1[i], cut1[i+1]-1 );
fprintf( stderr, "### reg2 = %d-%d\n", cut2[i], cut2[i+1]-1 );
#endif
switch( alg )
{
case( 'a' ):
totalscore += Aalign( tmpres1, tmpres2, eff1, eff2, clus1, clus2, alloclen );
break;
case( 'Q' ):
totalscore += partQ__align( tmpres1, tmpres2, eff1, eff2, clus1, clus2, alloclen, localhom, &impmatch, cut1[i], cut1[i+1]-1, cut2[i], cut2[i+1]-1, gapmap1, gapmap2, sgap1, sgap2, egap1, egap2 );
*totalimpmatch += impmatch;
// fprintf( stderr, "*totalimpmatch in Falign_localhom = %f\n", *totalimpmatch );
break;
case( 'A' ):
totalscore += partA__align( tmpres1, tmpres2, eff1, eff2, clus1, clus2, alloclen, localhom, &impmatch, cut1[i], cut1[i+1]-1, cut2[i], cut2[i+1]-1, gapmap1, gapmap2, sgap1, sgap2, egap1, egap2, chudanpt, chudanref, chudanres );
*totalimpmatch += impmatch;
// fprintf( stderr, "*totalimpmatch in Falign_localhom = %f\n", *totalimpmatch );
break;
default:
fprintf( stderr, "alg = %c\n", alg );
ErrorExit( "ERROR IN SOURCE FILE Falign.c" );
break;
}
#ifdef enablemultithread
if( chudanres && *chudanres )
{
// fprintf( stderr, "\n\n## CHUUDAN!!! at Falign_localhom\n" );
return( -1.0 );
}
#endif
nlen = strlen( tmpres1[0] );
if( totallen + nlen > alloclen )
{
fprintf( stderr, "totallen=%d + nlen=%d > alloclen = %d\n", totallen, nlen, alloclen );
ErrorExit( "LENGTH OVER in Falign\n " );
}
for( j=0; j<clus1; j++ ) strcat( result1[j], tmpres1[j] );
for( j=0; j<clus2; j++ ) strcat( result2[j], tmpres2[j] );
totallen += nlen;
#if 0
fprintf( stderr, "%4d\r", totallen );
fprintf( stderr, "\n\n" );
for( j=0; j<clus1; j++ )
{
fprintf( stderr, "%s\n", tmpres1[j] );
}
fprintf( stderr, "-------\n" );
for( j=0; j<clus2; j++ )
{
fprintf( stderr, "%s\n", tmpres2[j] );
}
#endif
}
#if KEIKA
fprintf( stderr, "DP ... done \n" );
#endif
for( j=0; j<clus1; j++ ) strcpy( seq1[j], result1[j] );
for( j=0; j<clus2; j++ ) strcpy( seq2[j], result2[j] );
#if 0
for( j=0; j<clus1; j++ )
{
fprintf( stderr, "%s\n", result1[j] );
}
fprintf( stderr, "- - - - - - - - - - -\n" );
for( j=0; j<clus2; j++ )
{
fprintf( stderr, "%s\n", result2[j] );
}
#endif
return( totalscore );
}
