+++ /dev/null
-#include "mltaln.h"
-
-#define DEBUG 0
-
-#if 0
-void mdfymtx( char pair[njob][njob], int s1, double **partialmtx, double **mtx )
-#else
-void mdfymtx( char **pair, int s1, double **partialmtx, double **mtx )
-#endif
-{
- int i, j;
- int icount, jcount;
-#if DEBUG
- FILE *fp;
- static char name[M][B];
-
- for( i=0; i<M; i++ ) name[i][0] = 0;
- fprintf( stdout, "s1 = %d\n", s1 );
- for( i=0; i<njob; i++ )
- {
- for( j=0; j<njob; j++ )
- {
- printf( "%#2d", pair[i][j] );
- }
- printf( "\n" );
- }
-#endif
-
- for( i=0, icount=0; i<njob-1; i++ )
- {
- if( !pair[s1][i] ) continue;
- for( j=i+1, jcount=icount+1; j<njob; j++ )
- {
- if( !pair[s1][j] ) continue;
- partialmtx[icount][jcount] = mtx[i][j];
- jcount++;
- }
- icount++;
- }
-#if DEBUG
- fp = fopen( "hat2.org", "w" );
- WriteHat2( fp, njob, name, mtx );
- fclose( fp );
- fp = fopen( "hat2.mdf", "w" );
- WriteHat2( fp, icount, name, partialmtx );
- fclose( fp );
-#endif
-
-}
-
-
-float score_calc( char **seq, int s ) /* method 3 */
-{
- int i, j, k, c;
- int len = strlen( seq[0] );
- float score;
- int tmpscore;
- char *mseq1, *mseq2;
-
- score = 0.0;
- for( i=0; i<s-1; i++ )
- {
- for( j=i+1; j<s; j++ )
- {
- mseq1 = seq[i];
- mseq2 = seq[j];
- tmpscore = 0;
- c = 0;
- for( k=0; k<len; k++ )
- {
- if( mseq1[k] == '-' && mseq2[k] == '-' ) continue;
- c++;
- tmpscore += amino_dis[(int)mseq1[k]][(int)mseq2[k]];
- if( mseq1[k] == '-' )
- {
- tmpscore += penalty;
- while( mseq1[++k] == '-' )
- ;
- k--;
- if( k > len-2 ) break;
- continue;
- }
- if( mseq2[k] == '-' )
- {
- tmpscore += penalty;
- while( mseq2[++k] == '-' )
- ;
- k--;
- if( k > len-2 ) break;
- continue;
- }
- }
- /*
- if( mseq1[0] == '-' || mseq2[0] == '-' )
- {
- for( k=0; k<len; k++ )
- {
- if( mseq1[k] == '-' && mseq2[k] == '-' ) continue;
- if( !( mseq1[k] != '-' && mseq2[k] != '-' ) )
- {
- c--;
- tmpscore -= penalty;
- break;
- }
- else break;
- }
- }
- if( mseq1[len-1] == '-' || mseq2[len-1] == '-' )
- {
- for( k=0; k<len; k++ )
- {
- if( mseq1[k] == '-' && mseq2[k] == '-' ) continue;
- if( !( mseq1[k] != '-' && mseq2[k] != '-' ) )
- {
- c--;
- tmpscore -= penalty;
- break;
- }
- else break;
- }
- }
- */
- score += (double)tmpscore / (double)c;
- }
- }
- score = (float)score / ( ( (double)s * ((double)s-1.0) ) / 2.0 );
- fprintf( stderr, "score in score_calc = %f\n", score );
- return( score );
-}
-
-void cpmx_calc( char **seq, float **cpmx, double *eff, int lgth, int clus )
-{
- int i, j, k;
- double totaleff = 0.0;
-
- for( i=0; i<clus; i++ ) totaleff += eff[i];
- for( i=0; i<26; i++ ) for( j=0; j<lgth; j++ ) cpmx[i][j] = 0.0;
- for( j=0; j<lgth; j++ ) for( k=0; k<clus; k++ )
- cpmx[(int)amino_n[(int)seq[k][j]]][j] += (float)eff[k] / totaleff;
-}
-
-
-void cpmx_calc_new_bk( char **seq, float **cpmx, double *eff, int lgth, int clus ) // summ eff must be 1.0
-{
- int i, j, k;
- float feff;
-
- for( i=0; i<26; i++ ) for( j=0; j<lgth; j++ ) cpmx[i][j] = 0.0;
- for( k=0; k<clus; k++ )
- {
- feff = (float)eff[k];
- for( j=0; j<lgth; j++ )
- {
- cpmx[(int)amino_n[(int)seq[k][j]]][j] += feff;
- }
- }
-}
-
-void cpmx_calc_new( char **seq, float **cpmx, double *eff, int lgth, int clus ) // summ eff must be 1.0
-{
- int i, j, k;
- float feff;
- float *cpmxpt, **cpmxptpt;
- char *seqpt;
-
- j = 26;
- cpmxptpt = cpmx;
- while( j-- )
- {
- cpmxpt = *cpmxptpt++;
- i = lgth;
- while( i-- )
- *cpmxpt++ = 0.0;
- }
- for( k=0; k<clus; k++ )
- {
- feff = (float)eff[k];
- seqpt = seq[k];
-// fprintf( stderr, "seqpt = %s, lgth=%d\n", seqpt, lgth );
- for( j=0; j<lgth; j++ )
- {
- cpmx[(int)amino_n[(int)*seqpt++]][j] += feff;
- }
- }
-}
-void MScpmx_calc_new( char **seq, float **cpmx, double *eff, int lgth, int clus ) // summ eff must be 1.0
-{
- int i, j, k;
- float feff;
- float **cpmxptpt, *cpmxpt;
- char *seqpt;
-
- j = lgth;
- cpmxptpt = cpmx;
- while( j-- )
- {
- cpmxpt = *cpmxptpt++;
- i = 26;
- while( i-- )
- *cpmxpt++ = 0.0;
- }
- for( k=0; k<clus; k++ )
- {
- feff = (float)eff[k];
- seqpt = seq[k];
- cpmxptpt = cpmx;
- j = lgth;
- while( j-- )
- (*cpmxptpt++)[(int)amino_n[(int)*seqpt++]] += feff;
- }
-#if 0
- for( j=0; j<lgth; j++ ) for( i=0; i<26; i++ ) cpmx[j][i] = 0.0;
- for( k=0; k<clus; k++ )
- {
- feff = (float)eff[k];
- for( j=0; j<lgth; j++ )
- cpmx[j][(int)amino_n[(int)seq[k][j]]] += feff;
- }
-#endif
-}
-
-void cpmx_ribosum( char **seq, char **seqr, char *dir, float **cpmx, double *eff, int lgth, int clus ) // summ eff must be 1.0
-{
- int i, j, k;
- float feff;
- float **cpmxptpt, *cpmxpt;
- char *seqpt, *seqrpt, *dirpt;
- int code, code1, code2;
-
- j = lgth;
- cpmxptpt = cpmx;
- while( j-- )
- {
- cpmxpt = *cpmxptpt++;
- i = 37;
- while( i-- )
- *cpmxpt++ = 0.0;
- }
- for( k=0; k<clus; k++ )
- {
- feff = (float)eff[k];
- seqpt = seq[k];
- seqrpt = seqr[k];
- dirpt = dir;
- cpmxptpt = cpmx;
- j = lgth;
- while( j-- )
- {
-#if 0
- code1 = amino_n[(int)*seqpt];
- if( code1 > 3 ) code = 36;
- else
- code = code1;
-#else
- code1 = amino_n[(int)*seqpt];
- code2 = amino_n[(int)*seqrpt];
- if( code1 > 3 )
- {
- code = 36;
- }
- else if( code2 > 3 )
- {
- code = code1;
- }
- else if( *dirpt == '5' )
- {
- code = 4 + code2 * 4 + code1;
- }
- else if( *dirpt == '3' )
- {
- code = 20 + code2 * 4 + code1;
- }
- else // if( *dirpt == 'o' ) // nai
- {
- code = code1;
- }
-#endif
-
-// fprintf( stderr, "%c -> code=%d toa=%d, tog=%d, toc=%d, tot=%d, ton=%d, efee=%f\n", *seqpt, code%4, ribosumdis[code][4+0], ribosumdis[code][4+1], ribosumdis[code][4+2], ribosumdis[code][20+3], ribosumdis[code][36], feff );
-
- seqpt++;
- seqrpt++;
- dirpt++;
-
- (*cpmxptpt++)[code] += feff;
- }
- }
-}
-
-void mseqcat( char **seq1, char **seq2, double **eff, double *effarr1, double *effarr2, char name1[M][B], char name2[M][B], int clus1, int clus2 )
-{
- int i, j;
- for( i=0; i<clus2; i++ )
- seq1[clus1+i] = seq2[i];
- for( i=0; i<clus2; i++ ) strcpy( name1[clus1+i], name2[i] );
-
- for( i=0; i<clus1; i++ ) for( j=0; j<clus1; j++ ) eff[i][j] = effarr1[i]* effarr1[j];
- for( i=0; i<clus1; i++ ) for( j=clus1; j<clus1+clus2; j++ ) eff[i][j] = effarr1[i]* effarr2[j-clus1];
- for( i=clus1; i<clus1+clus2; i++ ) for( j=0; j<clus1; j++ ) eff[i][j] = effarr2[i-clus1] * effarr1[j];
- for( i=clus1; i<clus1+clus2; i++ ) for( j=clus1; j<clus1+clus2; j++ ) eff[i][j] = effarr2[i-clus1] * effarr2[j-clus1];
-}
-
-
-
-#if 0
-int conjuction( char pair[njob][njob], int s, char **seq, char **aseq, double *peff, double *eff, char name[M][B], char aname[M][B], char *d )
-#else
-int conjuctionforgaln( int s0, int s1, char **seq, char **aseq, double *peff, double *eff, char **name, char **aname, char *d )
-#endif
-{
- int m, k;
- char b[B];
- double total;
-
-#if 0
- fprintf( stderr, "s0 = %d, s1 = %d\n", s0, s1 );
-#endif
-
- total = 0.0;
- d[0] = 0;
- for( m=s0, k=0; m<s1; m++ )
- {
- {
- sprintf( b, " %d", m+1 );
-#if 1
- if( strlen( d ) < 100 ) strcat( d, b );
-#else
- strcat( d, b );
-#endif
- aseq[k] = seq[m];
- peff[k] = eff[m];
- total += peff[k];
-#if 0
- strcpy( aname[k], name[m] );
-#endif
- k++;
- }
- }
-#if 1
- for( m=0; m<k; m++ )
- {
- peff[m] /= total;
-// fprintf( stderr, "peff[%d] = %f\n", m, peff[m] );
- }
-#endif
- return( k );
-}
-
-void makegrouprna( RNApair ***group, RNApair ***all, int *memlist )
-{
- int k, m;
- for( k=0; (m=*memlist)!=-1; memlist++, k++ )
- {
- group[k] = all[m];
- }
-}
-
-void makegrouprnait( RNApair ***group, RNApair ***all, char **pair, int s )
-{
- int k, m;
- for( m=s, k=0; m<njob; m++ )
- {
- if( pair[s][m] != 0 )
- {
- group[k++] = all[m];
- }
- }
-}
-
-int fastconjuction_noweight( int *memlist, char **seq, char **aseq, double *peff, char *d )
-{
- int m, k, dln;
- char b[B];
- double total;
-
-#if DEBUG
- fprintf( stderr, "s = %d\n", s );
-#endif
-
- total = 0.0;
- d[0] = 0;
- dln = 0;
- for( k=0; *memlist!=-1; memlist++, k++ )
- {
- m = *memlist;
- dln += sprintf( b, " %d", m+1 );
-#if 1
- if( dln < 100 ) strcat( d, b );
-#else
- strcat( d, b );
-#endif
- aseq[k] = seq[m];
- peff[k] = 1.0;
- total += peff[k];
- }
-#if 1
- for( m=0; m<k; m++ )
- peff[m] /= total;
-#endif
- return( k );
-}
-
-int fastconjuction_noname_kozo( int *memlist, char **seq, char **aseq, double *peff, double *eff, double *peff_kozo, double *eff_kozo, char *d )
-{
- int m, k, dln;
- char b[B];
- double total;
- double total_kozo;
-
-#if DEBUG
- fprintf( stderr, "s = %d\n", s );
-#endif
-
- total = 0.0;
- total_kozo = 0.0;
- d[0] = 0;
- dln = 0;
- for( k=0; *memlist!=-1; memlist++, k++ )
- {
- m = *memlist;
- dln += sprintf( b, " %d", m+1 );
-#if 1
- if( dln < 100 ) strcat( d, b );
-#else
- strcat( d, b );
-#endif
- aseq[k] = seq[m];
- peff[k] = eff[m];
- peff_kozo[k] = eff_kozo[m];
- total += peff[k];
- total_kozo += peff_kozo[k];
- }
-#if 1
- for( m=0; m<k; m++ )
- {
-// fprintf( stderr, "peff[%d] = %f\n", m, peff[m] );
- peff[m] /= total;
- }
- if( total_kozo )
- {
- for( m=0; m<k; m++ )
- {
-// fprintf( stderr, "peff[%d] = %f\n", m, peff[m] );
- peff_kozo[m] /= total_kozo;
- if( peff_kozo[m] > 0.0 ) peff_kozo[m] += peff[m];
- }
- }
- else //iranai
- {
- for( m=0; m<k; m++ )
- {
- peff_kozo[m] = 0.0;
- }
- }
-#endif
-
-// fprintf( stderr, "\n\ntbfast_total_kozo = %f\n\n", total_kozo );
- return( k );
-}
-
-
-int fastconjuction_noname( int *memlist, char **seq, char **aseq, double *peff, double *eff, char *d )
-{
- int m, k, dln;
- char b[B];
- double total;
-
-#if DEBUG
- fprintf( stderr, "s = %d\n", s );
-#endif
-
- total = 0.0;
- d[0] = 0;
- dln = 0;
- for( k=0; *memlist!=-1; memlist++, k++ )
- {
- m = *memlist;
- dln += sprintf( b, " %d", m+1 );
-#if 1
- if( dln < 100 ) strcat( d, b );
-#else
- strcat( d, b );
-#endif
- aseq[k] = seq[m];
- peff[k] = eff[m];
- total += peff[k];
- }
-#if 1
- for( m=0; m<k; m++ )
- {
-// fprintf( stderr, "peff[%d] = %f\n", m, peff[m] );
- peff[m] /= total;
- }
-#endif
- return( k );
-}
-
-int fastconjuction( int *memlist, char **seq, char **aseq, double *peff, double *eff, char name[M][B], char aname[M][B], char *d )
-{
- int m, k, dln;
- char b[B];
- double total;
-
-#if DEBUG
- fprintf( stderr, "s = %d\n", s );
-#endif
-
- total = 0.0;
- d[0] = 0;
- dln = 0;
- for( k=0; *memlist!=-1; memlist++, k++ )
- {
- m = *memlist;
- dln += sprintf( b, " %d", m+1 );
-#if 1
- if( dln < 100 ) strcat( d, b );
-#else
- strcat( d, b );
-#endif
- aseq[k] = seq[m];
- peff[k] = eff[m];
- total += peff[k];
-#if 0
- strcpy( aname[k], name[m] );
-#endif
- }
-#if 1
- for( m=0; m<k; m++ )
- peff[m] /= total;
-#endif
- return( k );
-}
-
-
-int conjuctionfortbfast_kozo( double *tmptmptmp, char **pair, int s, char **seq, char **aseq, double *peff, double *eff, double *peff_kozo, double *eff_kozo, char *d )
-{
- int m, k;
- char b[B];
- double total;
- double total_kozo;
-
-#if DEBUG
- fprintf( stderr, "s = %d\n", s );
-#endif
-
- total = 0.0;
-// total_kozo = 0.0;
- total_kozo = *tmptmptmp; // masaka
- d[0] = 0;
- for( m=s, k=0; m<njob; m++ )
- {
- if( pair[s][m] != 0 )
- {
- sprintf( b, " %d", m+1 );
-#if 1
- if( strlen( d ) < 100 ) strcat( d, b );
-#else
- strcat( d, b );
-#endif
- aseq[k] = seq[m];
- peff[k] = eff[m];
- peff_kozo[k] = eff_kozo[m];
- total += peff[k];
- total_kozo += peff_kozo[k];
-#if 0
- strcpy( aname[k], name[m] );
-#endif
- k++;
- }
- }
-#if 1
- for( m=0; m<k; m++ )
- peff[m] /= total;
- if( total_kozo > 0.0 )
- {
- for( m=0; m<k; m++ )
- {
- peff_kozo[m] /= total_kozo;
- if( peff_kozo[m] > 0.0 ) peff_kozo[m] += peff[m];
- }
- }
- else //iranai
- {
- for( m=0; m<k; m++ ) peff_kozo[m] = 0.0;
- }
-#endif
-// fprintf( stderr, "\n\ndvtditr_total_kozo = %f\n\n", total_kozo );
- *tmptmptmp = total_kozo;
- return( k );
-}
-
-int conjuctionfortbfast( char **pair, int s, char **seq, char **aseq, double *peff, double *eff, char *d )
-{
- int m, k;
- char *b;
- double total;
-
- b = calloc( B, sizeof( char ) );
-#if DEBUG
- fprintf( stderr, "s = %d\n", s );
-#endif
-
- total = 0.0;
- d[0] = 0;
- for( m=s, k=0; m<njob; m++ )
- {
- if( pair[s][m] != 0 )
- {
- sprintf( b, " %d", m+1 );
-#if 1
- if( strlen( d ) < 100 ) strcat( d, b );
-#else
- strcat( d, b );
-#endif
- aseq[k] = seq[m];
- peff[k] = eff[m];
- total += peff[k];
-#if 0
- strcpy( aname[k], name[m] );
-#endif
- k++;
- }
- }
-#if 1
- for( m=0; m<k; m++ )
- peff[m] /= total;
-#endif
- free( b );
- return( k );
-}
-int conjuction( char **pair, int s, char **seq, char **aseq, double *peff, double *eff, char **name, char **aname, char *d )
-{
- int m, k;
- char b[B];
- double total;
-
-#if DEBUG
- fprintf( stderr, "s = %d\n", s );
-#endif
-
- total = 0.0;
- d[0] = 0;
- for( m=s, k=0; m<njob; m++ )
- {
- if( pair[s][m] != 0 )
- {
- sprintf( b, " %d", m+1 );
-#if 1
- if( strlen( d ) < 100 ) strcat( d, b );
-#else
- strcat( d, b );
-#endif
- aseq[k] = seq[m];
- peff[k] = eff[m];
- total += peff[k];
-#if 0
- strcpy( aname[k], name[m] );
-#endif
- k++;
- }
- }
-#if 0
- for( m=0; m<k; m++ )
- peff[m] /= total;
-#endif
- return( k );
-}
-
-void floatdelete( float **cpmx, int d, int len )
-{
- int i, j;
-
- for( i=d; i<len-1; i++ )
- {
- for( j=0; j<26; j++ )
- {
- cpmx[j][i] = cpmx[j][i+1];
- }
- }
-}
-
-void chardelete( char *seq, int d )
-{
- char b[N];
-
- strcpy( b, seq+d+1 );
- strcpy( seq+d, b );
-}
-
-int RootBranchNode( int nseq, int ***topol, int step, int branch )
-{
- int i, j, s1, s2, value;
-
- value = 1;
- for( i=step+1; i<nseq-2; i++ )
- {
- for( j=0; (s1=topol[i][0][j])>-1; j++ )
- if( s1 == topol[step][branch][0] ) value++;
- for( j=0; (s2=topol[i][1][j])>-1; j++ )
- if( s2 == topol[step][branch][0] ) value++;
- }
- return( value );
-}
-
-void BranchLeafNode( int nseq, int ***topol, int *node, int step, int branch )
-{
- int i, j, k, s;
-
- for( i=0; i<nseq; i++ ) node[i] = 0;
- for( i=0; i<step-1; i++ )
- for( k=0; k<2; k++ )
- for( j=0; (s=topol[i][k][j])>-1; j++ )
- node[s]++;
- for( k=0; k<branch+1; k++ )
- for( j=0; (s=topol[step][k][j])>-1; j++ )
- node[s]++;
-}
-
-void RootLeafNode( int nseq, int ***topol, int *node )
-{
- int i, j, k, s;
- for( i=0; i<nseq; i++ ) node[i] = 0;
- for( i=0; i<nseq-2; i++ )
- for( k=0; k<2; k++ )
- for( j=0; (s=topol[i][k][j])>-1; j++ )
- node[s]++;
-}
-
-void nodeFromABranch( int nseq, int *result, int **pairwisenode, int ***topol, double **len, int step, int num )
-{
- int i, s, count;
- int *innergroup;
- int *outergroup1;
-#if 0
- int outergroup2[nseq];
- int table[nseq];
-#else
- static int *outergroup2 = NULL;
- static int *table = NULL;
- if( outergroup2 == NULL )
- {
- outergroup2 = AllocateIntVec( nseq );
- table = AllocateIntVec( nseq );
- }
-#endif
- innergroup = topol[step][num];
- outergroup1 = topol[step][!num];
- for( i=0; i<nseq; i++ ) table[i] = 1;
- for( i=0; (s=innergroup[i])>-1; i++ ) table[s] = 0;
- for( i=0; (s=outergroup1[i])>-1; i++ ) table[s] = 0;
- for( i=0, count=0; i<nseq; i++ )
- {
- if( table[i] )
- {
- outergroup2[count] = i;
- count++;
- }
- }
- outergroup2[count] = -1;
-
- for( i=0; (s=innergroup[i])>-1; i++ )
- {
- result[s] = pairwisenode[s][outergroup1[0]]
- + pairwisenode[s][outergroup2[0]]
- - pairwisenode[outergroup1[0]][outergroup2[0]] - 1;
- result[s] /= 2;
- }
- for( i=0; (s=outergroup1[i])>-1; i++ )
- {
- result[s] = pairwisenode[s][outergroup2[0]]
- + pairwisenode[s][innergroup[0]]
- - pairwisenode[innergroup[0]][outergroup2[0]] + 1;
- result[s] /= 2;
- }
- for( i=0; (s=outergroup2[i])>-1; i++ )
- {
- result[s] = pairwisenode[s][outergroup1[0]]
- + pairwisenode[s][innergroup[0]]
- - pairwisenode[innergroup[0]][outergroup1[0]] + 1;
- result[s] /= 2;
- }
-
-#if 0
- for( i=0; i<nseq; i++ )
- fprintf( stderr, "result[%d] = %d\n", i+1, result[i] );
-#endif
-}
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-#if 0
-void OneClusterAndTheOther( int locnjob, char pair[njob][njob], int *s1, int *s2, int ***topol, int step, int branch )
-#else
-void OneClusterAndTheOther( int locnjob, char **pair, int *s1, int *s2, int ***topol, int step, int branch )
-#endif
-{
- int i;
- int r1;
-
- *s1 = topol[step][branch][0];
- for( i=0; (r1=topol[step][branch][i])>-1; i++ )
- pair[*s1][r1] = 1;
- for( i=0; i<locnjob; i++ )
- {
- if( !pair[*s1][i] )
- {
- *s2 = i;
- break;
- }
- }
- for( i=*s2; i<locnjob; i++ )
- {
- if( !pair[*s1][i] )
- pair[*s2][i] = 1;
- }
-}
-
-void makeEffMtx( int nseq, double **mtx, double *vec )
-{
- int i, j;
- for( i=0; i<nseq; i++ ) for( j=0; j<nseq; j++ )
- mtx[i][j] = vec[i] * vec[j];
-}
-
-void node_eff( int nseq, double *eff, int *node )
-{
- int i;
- extern double ipower( double, int );
- for( i=0; i<nseq; i++ )
- eff[i] = ipower( 0.5, node[i] ) + geta2;
- /*
- eff[i] = ipower( 0.5, node[i] ) + 0;
- */
-#if DEBUG
- for( i=0; i<nseq; i++ )
-#endif
-}
-
-
-int shrinklocalhom( char **pair, int s1, int s2, LocalHom **localhom, LocalHom ***localhomshrink )
-{
- int m1, k1, m2, k2;
-
- for( m1=s1, k1=0; m1<njob; m1++ )
- {
- if( pair[s1][m1] != 0 )
- {
- for( m2=s2, k2=0; m2<njob; m2++ )
- {
- if( pair[s2][m2] != 0 )
- {
- if( localhom[m1][m2].opt == -1 )
- localhomshrink[k1][k2] = NULL;
- else
- localhomshrink[k1][k2] = localhom[m1]+m2;
- k2++;
- }
- }
- k1++;
- }
- }
- return( 0 );
-}
-int msshrinklocalhom( char **pair, int s1, int s2, LocalHom **localhom, LocalHom ***localhomshrink )
-{
- int m1, k1, n1, m2, k2, n2;
-
- for( m1=s1, k1=0; m1<njob; m1++ )
- {
- if( pair[s1][m1] != 0 )
- {
- for( m2=s2, k2=0; m2<njob; m2++ )
- {
- if( pair[s2][m2] != 0 )
- {
- n1 = MIN(m1,m2); n2=MAX(m1,m2);
- if( localhom[m1][m2].opt == -1 )
- localhomshrink[k1][k2] = NULL;
- else
- localhomshrink[k1][k2] = localhom[n1]+n2;
- k2++;
- }
- }
- k1++;
- }
- }
- return( 0 );
-}
-
-int fastshrinklocalhom( int *mem1, int *mem2, LocalHom **localhom, LocalHom ***localhomshrink )
-{
- int k1, k2;
- int *intpt1, *intpt2;
-
-
- for( intpt1=mem1, k1=0; *intpt1!=-1; intpt1++, k1++ )
- {
- for( intpt2=mem2, k2=0; *intpt2!=-1; intpt2++, k2++ )
- {
- if( localhom[*intpt1][*intpt2].opt == -1 )
- localhomshrink[k1][k2] = NULL;
- else
- localhomshrink[k1][k2] = localhom[*intpt1]+*intpt2;
- }
- }
- return( 0 );
-}
-
-int msfastshrinklocalhom( int *mem1, int *mem2, LocalHom **localhom, LocalHom ***localhomshrink )
-{
- int k1, k2;
- int *intpt1, *intpt2;
- int m1, m2;
-
- for( intpt1=mem1, k1=0; *intpt1!=-1; intpt1++, k1++ )
- {
- for( intpt2=mem2, k2=0; *intpt2!=-1; intpt2++, k2++ )
- {
- m1 = MIN(*intpt1,*intpt2); m2 = MAX(*intpt1,*intpt2);
- if( localhom[m1][m2].opt == -1 )
- localhomshrink[k1][k2] = NULL;
- else
- localhomshrink[k1][k2] = localhom[m1]+m2;
- }
- }
- return( 0 );
-}
-
git://source.jalview.org / jabaws.git / blobdiff