+++ /dev/null
-#include "mltaln.h"
-
-#define DEBUG 0
-
-#if 0
-int seqlen( char *seq )
-{
- int val = 0;
- while( *seq )
- if( *seq++ != '-' ) val++;
- return( val );
-}
-#else
-int seqlen( char *seq )
-{
- int val = 0;
- if( *newgapstr == '-' )
- {
- while( *seq )
- if( *seq++ != '-' ) val++;
- }
- else
- {
- while( *seq )
- {
- if( *seq != '-' && *seq != *newgapstr ) val++;
- seq++;
- }
- }
- return( val );
-}
-#endif
-
-int intlen( int *num )
-{
- int value = 0;
- while( *num++ != -1 ) value++;
- return( value );
-}
-
-char seqcheck( char **seq )
-{
- int i, len;
- char **seqbk = seq;
- while( *seq )
- {
- len = strlen( *seq );
- for( i=0; i<len; i++ )
- {
- if( amino_n[(int)(*seq)[i]] == -1 )
- {
-
- fprintf( stderr, "========================================================================= \n" );
- fprintf( stderr, "========================================================================= \n" );
- fprintf( stderr, "=== \n" );
- fprintf( stderr, "=== Alphabet '%c' is unknown.\n", (*seq)[i] );
- fprintf( stderr, "=== Please check site %d in sequence %d.\n", i+1, (int)(seq-seqbk+1) );
- fprintf( stderr, "=== \n" );
- fprintf( stderr, "=== To make an alignment having unusual characters (U, @, #, etc), try\n" );
- fprintf( stderr, "=== %% mafft --anysymbol input > output\n" );
- fprintf( stderr, "=== \n" );
- fprintf( stderr, "========================================================================= \n" );
- fprintf( stderr, "========================================================================= \n" );
- return( (int)(*seq)[i] );
- }
- }
- seq++;
- }
- return( 0 );
-}
-
-void scmx_calc( int icyc, char **aseq, double *effarr, float **scmx )
-{
- int i, j, lgth;
-
- lgth = strlen( aseq[0] );
- for( j=0; j<lgth; j++ )
- {
- for( i=0; i<26; i++ )
- {
- scmx[i][j] = 0;
- }
- }
- for( i=0; i<icyc+1; i++ )
- {
- int id;
- id = amino_n[(int)aseq[i][0]];
- scmx[id][0] += (float)effarr[i];
- }
- for( j=1; j<lgth-1; j++ )
- {
- for( i=0; i<icyc+1; i++ )
- {
- int id;
- id = amino_n[(int)aseq[i][j]];
- scmx[id][j] += (float)effarr[i];
- }
- }
- for( i=0; i<icyc+1; i++ )
- {
- int id;
- id = amino_n[(int)aseq[i][lgth-1]];
- scmx[id][lgth-1] += (float)effarr[i];
- }
-}
-
-void exitall( char arr[] )
-{
- fprintf( stderr, "%s\n", arr );
- exit( 1 );
-}
-
-void display( char **seq, int nseq )
-{
- int i, imax;
- char b[121];
-
- if( !disp ) return;
- if( nseq > DISPSEQF ) imax = DISPSEQF;
- else imax = nseq;
- fprintf( stderr, " ....,....+....,....+....,....+....,....+....,....+....,....+....,....+....,....+....,....+....,....+....,....+....,....+\n" );
- for( i=0; i<+imax; i++ )
- {
- strncpy( b, seq[i]+DISPSITEI, 120 );
- b[120] = 0;
- fprintf( stderr, "%3d %s\n", i+1, b );
- }
-}
-#if 0
-double intergroup_score( char **seq1, char **seq2, double *eff1, double *eff2, int clus1, int clus2, int len )
-{
- int i, j, k;
- double score;
- double tmpscore;
- char *mseq1, *mseq2;
- double efficient;
- char xxx[100];
-
-// totaleff1 = 0.0; for( i=0; i<clus1; i++ ) totaleff1 += eff1[i];
-// totaleff2 = 0.0; for( i=0; i<clus2; i++ ) totaleff2 += eff2[i];
-
- score = 0.0;
- for( i=0; i<clus1; i++ ) for( j=0; j<clus2; j++ )
- {
- efficient = eff1[i] * eff2[j];
- mseq1 = seq1[i];
- mseq2 = seq2[j];
- tmpscore = 0.0;
- for( k=0; k<len; k++ )
- {
- if( mseq1[k] == '-' && mseq2[k] == '-' ) continue;
- tmpscore += amino_dis[(int)mseq1[k]][(int)mseq2[k]];
-
- if( mseq1[k] == '-' )
- {
- tmpscore += penalty;
- tmpscore += amino_dis[(int)mseq1[k]][(int)mseq2[k]];
- while( mseq1[++k] == '-' )
- tmpscore += amino_dis[(int)mseq1[k]][(int)mseq2[k]];
- k--;
- if( k >len-2 ) break;
- continue;
- }
- if( mseq2[k] == '-' )
- {
- tmpscore += penalty;
- tmpscore += amino_dis[(int)mseq1[k]][(int)mseq2[k]];
- while( mseq2[++k] == '-' )
- tmpscore += amino_dis[(int)mseq1[k]][(int)mseq2[k]];
- k--;
- if( k > len-2 ) break;
- continue;
- }
- }
- score += (double)tmpscore * efficient;
-#if 1
- sprintf( xxx, "%f", score );
-// fprintf( stderr, "## score in intergroup_score = %f\n", score );
-#endif
- }
-#if 0
- fprintf( stderr, "###score = %f\n", score );
-#endif
-#if 0
- fprintf( stderr, "## score in intergroup_score = %f\n", score );
-#endif
- return( score );
-}
-#endif
-
-void intergroup_score_consweight( char **seq1, char **seq2, double *eff1, double *eff2, int clus1, int clus2, int len, double *value )
-{
- int i, j, k;
- int len2 = len - 2;
- int ms1, ms2;
- double tmpscore;
- char *mseq1, *mseq2;
- double efficient;
-
-// totaleff1 = 0.0; for( i=0; i<clus1; i++ ) totaleff1 += eff1[i];
-// totaleff2 = 0.0; for( i=0; i<clus2; i++ ) totaleff2 += eff2[i];
-
-
-
- *value = 0.0;
- for( i=0; i<clus1; i++ )
- {
- for( j=0; j<clus2; j++ )
- {
- efficient = eff1[i] * eff2[j]; /* \e$B$J$<$+G[Ns$r;H$o$J$$$H$*$+$7$/$J$k\e(B, \e$BB?J,%P%0\e(B */
- mseq1 = seq1[i];
- mseq2 = seq2[j];
- tmpscore = 0.0;
- for( k=0; k<len; k++ )
- {
- ms1 = (int)mseq1[k];
- ms2 = (int)mseq2[k];
- if( ms1 == (int)'-' && ms2 == (int)'-' ) continue;
- tmpscore += (double)amino_dis_consweight_multi[ms1][ms2];
-
- if( ms1 == (int)'-' )
- {
- tmpscore += (double)penalty;
- tmpscore += (double)amino_dis_consweight_multi[ms1][ms2];
- while( (ms1=(int)mseq1[++k]) == (int)'-' )
- ;
-// tmpscore += (double)amino_dis_consweight_multi[ms1][ms2];
- k--;
- if( k >len2 ) break;
- continue;
- }
- if( ms2 == (int)'-' )
- {
- tmpscore += (double)penalty;
- tmpscore += (double)amino_dis_consweight_multi[ms1][ms2];
- while( (ms2=(int)mseq2[++k]) == (int)'-' )
- ;
-// tmpscore += (double)amino_dis_consweight_multi[ms1][ms2];
- k--;
- if( k > len2 ) break;
- continue;
- }
- }
- *value += (double)tmpscore * (double)efficient;
-// fprintf( stderr, "val in _gapnomi = %f\n", *value );
- }
- }
-#if 0
- fprintf( stdout, "###score = %f\n", score );
-#endif
-#if DEBUG
- fprintf( stderr, "score in intergroup_score = %f\n", score );
-#endif
-// return( score );
-}
-void intergroup_score_gapnomi( char **seq1, char **seq2, double *eff1, double *eff2, int clus1, int clus2, int len, double *value )
-{
- int i, j, k;
- int len2 = len - 2;
- int ms1, ms2;
- double tmpscore;
- char *mseq1, *mseq2;
- double efficient;
-
-// totaleff1 = 0.0; for( i=0; i<clus1; i++ ) totaleff1 += eff1[i];
-// totaleff2 = 0.0; for( i=0; i<clus2; i++ ) totaleff2 += eff2[i];
-
-
-
- *value = 0.0;
- for( i=0; i<clus1; i++ )
- {
- for( j=0; j<clus2; j++ )
- {
- efficient = eff1[i] * eff2[j]; /* \e$B$J$<$+G[Ns$r;H$o$J$$$H$*$+$7$/$J$k\e(B, \e$BB?J,%P%0\e(B */
- mseq1 = seq1[i];
- mseq2 = seq2[j];
- tmpscore = 0.0;
- for( k=0; k<len; k++ )
- {
- ms1 = (int)mseq1[k];
- ms2 = (int)mseq2[k];
- if( ms1 == (int)'-' && ms2 == (int)'-' ) continue;
-// tmpscore += (double)amino_dis[ms1][ms2];
-
- if( ms1 == (int)'-' )
- {
- tmpscore += (double)penalty;
-// tmpscore += (double)amino_dis[ms1][ms2];
- while( (ms1=(int)mseq1[++k]) == (int)'-' )
- ;
-// tmpscore += (double)amino_dis[ms1][ms2];
- k--;
- if( k >len2 ) break;
- continue;
- }
- if( ms2 == (int)'-' )
- {
- tmpscore += (double)penalty;
-// tmpscore += (double)amino_dis[ms1][ms2];
- while( (ms2=(int)mseq2[++k]) == (int)'-' )
- ;
-// tmpscore += (double)amino_dis[ms1][ms2];
- k--;
- if( k > len2 ) break;
- continue;
- }
- }
- *value += (double)tmpscore * (double)efficient;
-// fprintf( stderr, "val in _gapnomi = %f\n", *value );
- }
- }
-#if 0
- fprintf( stdout, "###score = %f\n", score );
-#endif
-#if DEBUG
- fprintf( stderr, "score in intergroup_score = %f\n", score );
-#endif
-// return( score );
-}
-
-void intergroup_score( char **seq1, char **seq2, double *eff1, double *eff2, int clus1, int clus2, int len, double *value )
-{
- int i, j, k;
- int len2 = len - 2;
- int ms1, ms2;
- double tmpscore;
- char *mseq1, *mseq2;
- double efficient;
-
- double gaptmpscore;
- double gapscore = 0.0;
-
-// fprintf( stderr, "#### in intergroup_score\n" );
-
-// totaleff1 = 0.0; for( i=0; i<clus1; i++ ) totaleff1 += eff1[i];
-// totaleff2 = 0.0; for( i=0; i<clus2; i++ ) totaleff2 += eff2[i];
-
- *value = 0.0;
- for( i=0; i<clus1; i++ )
- {
- for( j=0; j<clus2; j++ )
- {
- efficient = eff1[i] * eff2[j]; /* \e$B$J$<$+G[Ns$r;H$o$J$$$H$*$+$7$/$J$k\e(B, \e$BB?J,%P%0\e(B */
- mseq1 = seq1[i];
- mseq2 = seq2[j];
- tmpscore = 0.0;
- gaptmpscore = 0.0;
- for( k=0; k<len; k++ )
- {
- ms1 = (int)mseq1[k];
- ms2 = (int)mseq2[k];
- if( ms1 == (int)'-' && ms2 == (int)'-' ) continue;
-// tmpscore += (double)amino_dis[ms1][ms2];
- tmpscore += (double)amino_dis_consweight_multi[ms1][ms2];
-
- if( ms1 == (int)'-' )
- {
- tmpscore += (double)penalty;
- gaptmpscore += (double)penalty;
-// tmpscore += (double)amino_dis[ms1][ms2];
- tmpscore += (double)amino_dis_consweight_multi[ms1][ms2];
- while( (ms1=(int)mseq1[++k]) == (int)'-' )
-// tmpscore += (double)amino_dis[ms1][ms2];
- tmpscore += (double)amino_dis_consweight_multi[ms1][ms2];
- k--;
- if( k >len2 ) break;
- continue;
- }
- if( ms2 == (int)'-' )
- {
- tmpscore += (double)penalty;
- gaptmpscore += (double)penalty;
-// tmpscore += (double)amino_dis[ms1][ms2];
- tmpscore += (double)amino_dis_consweight_multi[ms1][ms2];
- while( (ms2=(int)mseq2[++k]) == (int)'-' )
-// tmpscore += (double)amino_dis[ms1][ms2];
- tmpscore += (double)amino_dis_consweight_multi[ms1][ms2];
- k--;
- if( k > len2 ) break;
- continue;
- }
- }
- *value += (double)tmpscore * (double)efficient;
- gapscore += (double)gaptmpscore * (double)efficient;
- }
- }
-#if 0
- fprintf( stderr, "###gapscore = %f\n", gapscore );
-#endif
-#if DEBUG
- fprintf( stderr, "score in intergroup_score = %f\n", score );
-#endif
-// return( score );
-}
-void intergroup_score_new( char **seq1, char **seq2, double *eff1, double *eff2, int clus1, int clus2, int len, double *value )
-{
- int i, j, k;
- int len2 = len - 2;
- int ms1, ms2;
- double tmpscore;
- char *mseq1, *mseq2;
- static double efficient[1];
-
-// totaleff1 = 0.0; for( i=0; i<clus1; i++ ) totaleff1 += eff1[i];
-// totaleff2 = 0.0; for( i=0; i<clus2; i++ ) totaleff2 += eff2[i];
-
- *value = 0.0;
- for( i=0; i<clus1; i++ )
- {
- for( j=0; j<clus2; j++ )
- {
- *efficient = eff1[i] * eff2[j]; /* \e$B$J$<$+G[Ns$r;H$o$J$$$H$*$+$7$/$J$k\e(B, \e$BB?J,%P%0\e(B */
- mseq1 = seq1[i];
- mseq2 = seq2[j];
- tmpscore = 0.0;
- for( k=0; k<len; k++ )
- {
- ms1 = (int)mseq1[k];
- ms2 = (int)mseq2[k];
- if( ms1 == (int)'-' && ms2 == (int)'-' ) continue;
- tmpscore += (double)amino_dis[ms1][ms2];
-
- if( ms1 == (int)'-' )
- {
- tmpscore += (double)penalty;
- tmpscore += (double)amino_dis[ms1][ms2];
- while( (ms1=(int)mseq1[++k]) == (int)'-' )
- tmpscore += (double)amino_dis[ms1][ms2];
- k--;
- if( k >len2 ) break;
- continue;
- }
- if( ms2 == (int)'-' )
- {
- tmpscore += (double)penalty;
- tmpscore += (double)amino_dis[ms1][ms2];
- while( (ms2=(int)mseq2[++k]) == (int)'-' )
- tmpscore += (double)amino_dis[ms1][ms2];
- k--;
- if( k > len2 ) break;
- continue;
- }
- }
- *value += (double)tmpscore * (double)*efficient;
- }
- }
-#if 0
- fprintf( stdout, "###score = %f\n", score );
-#endif
-#if DEBUG
- fprintf( stderr, "score in intergroup_score = %f\n", score );
-#endif
-// return( score );
-}
-
-
-double score_calc5( char **seq, int s, double **eff, int ex ) /* method 3 deha nai */
-{
- int i, j, k;
- double c;
- int len = strlen( seq[0] );
- double score;
- double tmpscore;
- char *mseq1, *mseq2;
- double efficient;
-#if DEBUG
- FILE *fp;
-#endif
-
- score = 0.0;
- c = 0.0;
-
- for( i=0; i<s; i++ )
- {
-
- if( i == ex ) continue;
- efficient = eff[i][ex];
- mseq1 = seq[i];
- mseq2 = seq[ex];
- tmpscore = 0.0;
- for( k=0; k<len; k++ )
- {
- if( mseq1[k] == '-' && mseq2[k] == '-' ) continue;
- tmpscore += amino_dis[(int)mseq1[k]][(int)mseq2[k]];
-
- if( mseq1[k] == '-' )
- {
- tmpscore += penalty;
- while( mseq1[++k] == '-' )
- tmpscore += amino_dis[(int)mseq1[k]][(int)mseq2[k]];
- k--;
- if( k > len-2 ) break;
- continue;
- }
- if( mseq2[k] == '-' )
- {
- tmpscore += penalty;
- while( mseq2[++k] == '-' )
- tmpscore += amino_dis[(int)mseq1[k]][(int)mseq2[k]];
- k--;
- if( k > len-2 ) break;
- continue;
- }
- }
- score += (double)tmpscore * efficient;
-/*
- fprintf( stdout, "%d-%d tmpscore = %f, eff = %f, tmpscore*eff = %f\n", i, ex, tmpscore, efficient, tmpscore*efficient );
-*/
- }
- /*
- fprintf( stdout, "total score = %f\n", score );
- */
-
- for( i=0; i<s-1; i++ )
- {
- for( j=i+1; j<s; j++ )
- {
- if( i == ex || j == ex ) continue;
-
- efficient = eff[i][j];
- mseq1 = seq[i];
- mseq2 = seq[j];
- tmpscore = 0.0;
- for( k=0; k<len; k++ )
- {
- if( mseq1[k] == '-' && mseq2[k] == '-' ) continue;
- tmpscore += amino_dis[(int)mseq1[k]][(int)mseq2[k]];
-
- if( mseq1[k] == '-' )
- {
- tmpscore += penalty;
- while( mseq1[++k] == '-' )
- tmpscore += amino_dis[(int)mseq1[k]][(int)mseq2[k]];
- k--;
- if( k > len-2 ) break;
- continue;
- }
- if( mseq2[k] == '-' )
- {
- tmpscore += penalty;
- while( mseq2[++k] == '-' )
- tmpscore += amino_dis[(int)mseq1[k]][(int)mseq2[k]];
- k--;
- if( k > len-2 ) break;
- continue;
- }
- }
- score += (double)tmpscore * efficient;
- }
- }
-/*
- fprintf( stderr, "score in score_calc5 = %f\n", score );
-*/
- return( (double)score );
-/*
-
-fprintf( trap_g, "score by fast = %f\n", (float)score );
-
-tmpscore = score = 0.0;
- for( i=0; i<s; i++ )
- {
- if( i == ex ) continue;
- tmpscore = Cscore_m_1( seq, i, eff );
- fprintf( stdout, "%d %f\n", i, tmpscore );
-
- score += tmpscore;
- }
- tmpscore = Cscore_m_1( seq, ex, eff );
- fprintf( stdout, "ex%d %f\n", i, tmpscore );
- score += tmpscore;
-
- return( score );
-*/
-}
-
-
-
-double score_calc4( char **seq, int s, double **eff, int ex ) /* method 3 deha nai */
-{
- int i, j, k;
- double c;
- int len = strlen( seq[0] );
- double score;
- long tmpscore;
- char *mseq1, *mseq2;
- double efficient;
-
- score = 0.0;
- c = 0.0;
-/*
- printf( "in score_calc4\n" );
- for( i=0; i<s; i++ )
- {
- for( j=0; j<s; j++ )
- {
- printf( "% 5.3f", eff[i][j] );
- }
- printf( "\n" );
-
- }
-*/
- for( i=0; i<s-1; i++ )
- {
- for( j=i+1; j<s; j++ )
- {
- efficient = eff[i][j];
- if( mix == 1 ) efficient = 1.0;
- /*
- printf( "weight for %d v.s. %d = %f\n", i, j, efficient );
- */
- mseq1 = seq[i];
- mseq2 = seq[j];
- tmpscore = 0;
- for( k=0; k<len; k++ )
- {
- if( mseq1[k] == '-' && mseq2[k] == '-' ) continue;
- tmpscore += amino_dis[(int)mseq1[k]][(int)mseq2[k]] + 400 * !scoremtx ;
-
- c += efficient;
-
- if( mseq1[k] == '-' )
- {
- tmpscore += penalty - n_dis[24][0];
- while( mseq1[++k] == '-' )
- ;
- k--;
- if( k > len-2 ) break;
- continue;
- }
- if( mseq2[k] == '-' )
- {
- tmpscore += penalty - n_dis[24][0];
- while( mseq2[++k] == '-' )
- ;
- k--;
- if( k > len-2 ) break;
- continue;
- }
- }
- /*
- if( x == 65 ) printf( "i=%d j=%d tmpscore=%d l=%d\n", i, j, tmpscore, len );
- */
- score += (double)tmpscore * efficient;
- }
- }
- score /= c;
- return( (double)score );
-}
-
-
-
-void upg2( int nseq, double **eff, int ***topol, double **len )
-{
- int i, j, k;
- double tmplen[M];
-
- static char **pair = NULL;
-
- if( !pair )
- {
- pair = AllocateCharMtx( njob, njob );
- }
-
- for( i=0; i<nseq; i++ ) tmplen[i] = 0.0;
- for( i=0; i<nseq; i++ ) for( j=0; j<nseq; j++ ) pair[i][j] = 0;
- for( i=0; i<nseq; i++ ) pair[i][i] = 1;
-
- for( k=0; k<nseq-1; k++ )
- {
- float minscore = 9999.0;
- int im = -1, jm = -1;
- int count;
-
- for( i=0; i<nseq-1; i++ ) for( j=i+1; j<nseq; j++ )
- {
- if( eff[i][j] < minscore )
- {
- minscore = eff[i][j];
- im = i; jm = j;
- }
- }
- for( i=0, count=0; i<nseq; i++ )
- if( pair[im][i] > 0 )
- {
- topol[k][0][count] = i;
- count++;
- }
- topol[k][0][count] = -1;
- for( i=0, count=0; i<nseq; i++ )
- if( pair[jm][i] > 0 )
- {
- topol[k][1][count] = i;
- count++;
- }
- topol[k][1][count] = -1;
-
- len[k][0] = minscore / 2.0 - tmplen[im];
- len[k][1] = minscore / 2.0 - tmplen[jm];
-
- tmplen[im] = minscore / 2.0;
-
- for( i=0; i<nseq; i++ ) pair[im][i] += ( pair[jm][i] > 0 );
- for( i=0; i<nseq; i++ ) pair[jm][i] = 0;
-
- for( i=0; i<nseq; i++ )
- {
- if( i != im && i != jm )
- {
- eff[MIN(i,im)][MAX(i,im)] =
- ( eff[MIN(i,im)][MAX(i,im)] + eff[MIN(i,jm)][MAX(i,jm)] ) / 2.0;
- eff[MIN(i,jm)][MAX(i,jm)] = 9999.0;
- }
- eff[im][jm] = 9999.0;
- }
-#if DEBUG
- printf( "STEP-%03d:\n", k+1 );
- printf( "len0 = %f\n", len[k][0] );
- for( i=0; topol[k][0][i]>-1; i++ ) printf( " %03d", topol[k][0][i] );
- printf( "\n" );
- printf( "len1 = %f\n", len[k][1] );
- for( i=0; topol[k][1][i]>-1; i++ ) printf( " %03d", topol[k][1][i] );
- printf( "\n" );
-#endif
- }
-}
-
-static void setnearest( int nseq, Bchain *acpt, float **eff, float *mindisfrompt, int *nearestpt, int pos )
-{
- int j;
- float tmpfloat;
- float **effptpt;
- Bchain *acptj;
-
- *mindisfrompt = 999.9;
- *nearestpt = -1;
-
-// if( (acpt+pos)->next ) effpt = eff[pos]+(acpt+pos)->next->pos-pos;
-
-// for( j=pos+1; j<nseq; j++ )
- for( acptj=(acpt+pos)->next; acptj!=NULL; acptj=acptj->next )
- {
- j = acptj->pos;
-// if( (tmpfloat=*effpt++) < *mindisfrompt )
- if( (tmpfloat=eff[pos][j-pos]) < *mindisfrompt )
- {
- *mindisfrompt = tmpfloat;
- *nearestpt = j;
- }
- }
- effptpt = eff;
-// for( j=0; j<pos; j++ )
- for( acptj=acpt; (acptj&&acptj->pos!=pos); acptj=acptj->next )
- {
- j = acptj->pos;
-// if( (tmpfloat=(*effptpt++)[pos-j]) < *mindisfrompt )
- if( (tmpfloat=eff[j][pos-j]) < *mindisfrompt )
- {
- *mindisfrompt = tmpfloat;
- *nearestpt = j;
- }
- }
-}
-
-static void setnearest_double_fullmtx( int nseq, Bchain *acpt, double **eff, double *mindisfrompt, int *nearestpt, int pos )
-{
- int j;
- double tmpfloat;
- double **effptpt;
- Bchain *acptj;
-
- *mindisfrompt = 999.9;
- *nearestpt = -1;
-
-// if( (acpt+pos)->next ) effpt = eff[pos]+(acpt+pos)->next->pos-pos;
-
-// for( j=pos+1; j<nseq; j++ )
- for( acptj=(acpt+pos)->next; acptj!=NULL; acptj=acptj->next )
- {
- j = acptj->pos;
-// if( (tmpfloat=*effpt++) < *mindisfrompt )
- if( (tmpfloat=eff[pos][j]) < *mindisfrompt )
- {
- *mindisfrompt = tmpfloat;
- *nearestpt = j;
- }
- }
- effptpt = eff;
-// for( j=0; j<pos; j++ )
- for( acptj=acpt; (acptj&&acptj->pos!=pos); acptj=acptj->next )
- {
- j = acptj->pos;
-// if( (tmpfloat=(*effptpt++)[pos-j]) < *mindisfrompt )
- if( (tmpfloat=eff[j][pos]) < *mindisfrompt )
- {
- *mindisfrompt = tmpfloat;
- *nearestpt = j;
- }
- }
-}
-
-
-
-static void loadtreeoneline( int *ar, float *len, FILE *fp )
-{
- static char gett[1000];
-
- fgets( gett, 999, fp );
-
-// fprintf( stderr, "gett=%s\n", gett );
-
-
- sscanf( gett, "%d %d %f %f", ar, ar+1, len, len+1 );
-
- ar[0]--;
- ar[1]--;
-
- if( ar[0] >= ar[1] )
- {
- fprintf( stderr, "Incorrect guide tree\n" );
- exit( 1 );
- }
-
-
-// fprintf( stderr, "ar[0] = %d, ar[1] = %d\n", ar[0], ar[1] );
-// fprintf( stderr, "len[0] = %f, len[1] = %f\n", len[0], len[1] );
-}
-
-void loadtree( int nseq, int ***topol, float **len, char **name, int *nlen, Treedep *dep )
-{
- int i, j, k, miniim, maxiim, minijm, maxijm;
- int *intpt, *intpt2;
- static int *hist = NULL;
- static Bchain *ac = NULL;
- int im = -1, jm = -1;
- Bchain *acjmnext, *acjmprev;
- int prevnode;
- Bchain *acpti;
- int *pt1, *pt2, *pt11, *pt22;
- static int *nmemar;
- int nmemim, nmemjm;
- float minscore;
- int *nearest = NULL; // by D.Mathog, a guess
- float *mindisfrom = NULL; // by D.Mathog, a guess
- static char **tree;
- static char *treetmp;
- static char *nametmp;
- FILE *fp;
- int node[2];
-
- fp = fopen( "_guidetree", "r" );
- if( !fp )
- {
- fprintf( stderr, "cannot open _guidetree\n" );
- exit( 1 );
- }
-
- if( !hist )
- {
- hist = AllocateIntVec( njob );
- ac = (Bchain *)malloc( njob * sizeof( Bchain ) );
- nmemar = AllocateIntVec( njob );
- mindisfrom = AllocateFloatVec( njob );
- nearest = AllocateIntVec( njob );
- treetmp = AllocateCharVec( njob*50 );
- nametmp = AllocateCharVec( 31 );
- tree = AllocateCharMtx( njob, njob*50 );
- }
-
-
- for( i=0; i<nseq; i++ )
- {
- for( j=0; j<30; j++ ) nametmp[j] = 0;
- for( j=0; j<30; j++ )
- {
- if( isalnum( name[i][j] ) )
- nametmp[j] = name[i][j];
- else
- nametmp[j] = '_';
- }
- nametmp[30] = 0;
-// sprintf( tree[i], "%d_l=%d_%.20s", i+1, nlen[i], nametmp+1 );
- sprintf( tree[i], "%d_%.20s", i+1, nametmp+1 );
- }
- for( i=0; i<nseq; i++ )
- {
- ac[i].next = ac+i+1;
- ac[i].prev = ac+i-1;
- ac[i].pos = i;
- }
- ac[nseq-1].next = NULL;
-
-
- for( i=0; i<nseq; i++ )
- {
- hist[i] = -1;
- nmemar[i] = 1;
- }
-
- fprintf( stderr, "\n" );
- for( k=0; k<nseq-1; k++ )
- {
- if( k % 10 == 0 ) fprintf( stderr, "\r% 5d / %d", k, nseq );
-#if 0
- minscore = 999.9;
- for( acpti=ac; acpti->next!=NULL; acpti=acpti->next )
- {
- i = acpti->pos;
-// fprintf( stderr, "k=%d i=%d\n", k, i );
- if( mindisfrom[i] < minscore ) // muscle
- {
- im = i;
- minscore = mindisfrom[i];
- }
- }
- jm = nearest[im];
- if( jm < im )
- {
- j=jm; jm=im; im=j;
- }
-#else
- minscore = 0.0;
- len[k][0] = len[k][1] = -1.0;
- loadtreeoneline( node, len[k], fp );
- im = node[0];
- jm = node[1];
-
- if( len[k][0] == -1.0 || len[k][1] == -1.0 )
- {
- fprintf( stderr, "\n\nERROR: Branch length is not given.\n" );
- exit( 1 );
- }
-
- if( len[k][0] < 0.0 ) len[k][0] = 0.0;
- if( len[k][1] < 0.0 ) len[k][1] = 0.0;
-
-#endif
-
- prevnode = hist[im];
- if( dep ) dep[k].child0 = prevnode;
- nmemim = nmemar[im];
-
-// fprintf( stderr, "prevnode = %d, nmemim = %d\n", prevnode, nmemim );
-
- intpt = topol[k][0] = (int *)realloc( topol[k][0], ( nmemim + 1 ) * sizeof( int ) );
- if( prevnode == -1 )
- {
- *intpt++ = im;
- *intpt = -1;
- }
- else
- {
- pt1 = topol[prevnode][0];
- pt2 = topol[prevnode][1];
- if( *pt1 > *pt2 )
- {
- pt11 = pt2;
- pt22 = pt1;
- }
- else
- {
- pt11 = pt1;
- pt22 = pt2;
- }
- for( intpt2=pt11; *intpt2!=-1; )
- *intpt++ = *intpt2++;
- for( intpt2=pt22; *intpt2!=-1; )
- *intpt++ = *intpt2++;
- *intpt = -1;
- }
-
-
- nmemjm = nmemar[jm];
- prevnode = hist[jm];
- if( dep ) dep[k].child1 = prevnode;
-
-// fprintf( stderr, "prevnode = %d, nmemjm = %d\n", prevnode, nmemjm );
-
- intpt = topol[k][1] = (int *)realloc( topol[k][1], ( nmemjm + 1 ) * sizeof( int ) );
- if( !intpt )
- {
- fprintf( stderr, "Cannot reallocate topol\n" );
- exit( 1 );
- }
- if( prevnode == -1 )
- {
- *intpt++ = jm;
- *intpt = -1;
- }
- else
- {
- pt1 = topol[prevnode][0];
- pt2 = topol[prevnode][1];
- if( *pt1 > *pt2 )
- {
- pt11 = pt2;
- pt22 = pt1;
- }
- else
- {
- pt11 = pt1;
- pt22 = pt2;
- }
- for( intpt2=pt11; *intpt2!=-1; )
- *intpt++ = *intpt2++;
- for( intpt2=pt22; *intpt2!=-1; )
- *intpt++ = *intpt2++;
- *intpt = -1;
- }
-
- minscore *= 0.5;
-
-// len[k][0] = ( minscore - tmptmplen[im] );
-// len[k][1] = ( minscore - tmptmplen[jm] );
-// len[k][0] = -1;
-// len[k][1] = -1;
-
-
- hist[im] = k;
- nmemar[im] = nmemim + nmemjm;
-
- mindisfrom[im] = 999.9;
- for( acpti=ac; acpti!=NULL; acpti=acpti->next )
- {
- i = acpti->pos;
- if( i != im && i != jm )
- {
- if( i < im )
- {
- miniim = i;
- maxiim = im;
- minijm = i;
- maxijm = jm;
- }
- else if( i < jm )
- {
- miniim = im;
- maxiim = i;
- minijm = i;
- maxijm = jm;
- }
- else
- {
- miniim = im;
- maxiim = i;
- minijm = jm;
- maxijm = i;
- }
- }
- }
-
- sprintf( treetmp, "(%s:%7.5f,%s:%7.5f)", tree[im], len[k][0], tree[jm], len[k][1] );
- strcpy( tree[im], treetmp );
-
-// fprintf( stderr, "im,jm=%d,%d\n", im, jm );
- acjmprev = ac[jm].prev;
- acjmnext = ac[jm].next;
- acjmprev->next = acjmnext;
- if( acjmnext != NULL )
- acjmnext->prev = acjmprev;
-// free( (void *)eff[jm] ); eff[jm] = NULL;
-
-#if 0 // muscle seems to miss this.
- for( acpti=ac; acpti!=NULL; acpti=acpti->next )
- {
- i = acpti->pos;
- if( nearest[i] == im )
- {
-// fprintf( stderr, "calling setnearest\n" );
-// setnearest( nseq, ac, eff, mindisfrom+i, nearest+i, i );
- }
- }
-#endif
-
-
-#if 0
- fprintf( stdout, "vSTEP-%03d:\n", k+1 );
- fprintf( stdout, "len0 = %f\n", len[k][0] );
- for( i=0; topol[k][0][i]>-1; i++ ) fprintf( stdout, " %03d", topol[k][0][i]+1 );
- fprintf( stdout, "\n" );
- fprintf( stdout, "len1 = %f\n", len[k][1] );
- for( i=0; topol[k][1][i]>-1; i++ ) fprintf( stdout, " %03d", topol[k][1][i]+1 );
- fprintf( stdout, "\n" );
-#endif
- }
- fclose( fp );
- fp = fopen( "infile.tree", "w" );
- fprintf( fp, "%s\n", treetmp );
- fprintf( fp, "#by loadtree\n" );
- fclose( fp );
-
- FreeCharMtx( tree );
- free( treetmp );
- free( nametmp );
- free( hist ); hist = NULL;
- free( (char *)ac ); ac = NULL;
- free( (void *)nmemar ); nmemar = NULL;
- free( mindisfrom );
- free( nearest );
-
-
-}
-
-static float sueff1, sueff05;
-static double sueff1_double, sueff05_double;
-
-static float cluster_mix_float( float d1, float d2 )
-{
- return( MIN( d1, d2 ) * sueff1 + ( d1 + d2 ) * sueff05 );
-}
-static float cluster_average_float( float d1, float d2 )
-{
- return( ( d1 + d2 ) * 0.5 );
-}
-static float cluster_minimum_float( float d1, float d2 )
-{
- return( MIN( d1, d2 ) );
-}
-static double cluster_mix_double( double d1, double d2 )
-{
- return( MIN( d1, d2 ) * sueff1_double + ( d1 + d2 ) * sueff05_double );
-}
-static double cluster_average_double( double d1, double d2 )
-{
- return( ( d1 + d2 ) * 0.5 );
-}
-static double cluster_minimum_double( double d1, double d2 )
-{
- return( MIN( d1, d2 ) );
-}
-
-void loadtop( int nseq, float **eff, int ***topol, float **len ) // computes branch length BUG!!
-{
- int i, k, miniim, maxiim, minijm, maxijm;
- int *intpt, *intpt2;
- static Bchain *ac = NULL;
- float eff1, eff0;
- static float *tmptmplen = NULL;
- static int *hist = NULL;
- int im = -1, jm = -1;
- Bchain *acjmnext, *acjmprev;
- int prevnode;
- Bchain *acpti;
- int *pt1, *pt2, *pt11, *pt22;
- static int *nmemar;
- int nmemim, nmemjm;
- float minscore;
- static char **tree;
- static char *treetmp;
- FILE *fp;
- int node[2];
- float dumfl[2];
- float (*clusterfuncpt[1])(float,float);
-
-
- sueff1 = 1 - SUEFF;
- sueff05 = SUEFF * 0.5;
- if ( treemethod == 'X' )
- clusterfuncpt[0] = cluster_mix_float;
- else if ( treemethod == 'E' )
- clusterfuncpt[0] = cluster_average_float;
- else if ( treemethod == 'q' )
- clusterfuncpt[0] = cluster_minimum_float;
- else
- {
- fprintf( stderr, "Unknown treemethod, %c\n", treemethod );
- exit( 1 );
- }
-
- fp = fopen( "_guidetree", "r" );
- if( !fp )
- {
- fprintf( stderr, "cannot open _guidetree\n" );
- exit( 1 );
- }
-
- if( !hist )
- {
- treetmp = AllocateCharVec( njob*50 );
- tree = AllocateCharMtx( njob, njob*50 );
- hist = AllocateIntVec( njob );
- tmptmplen = AllocateFloatVec( njob );
- ac = (Bchain *)malloc( njob * sizeof( Bchain ) );
- nmemar = AllocateIntVec( njob );
- }
-
- for( i=0; i<nseq; i++ ) sprintf( tree[i], "%d", i+1 );
- for( i=0; i<nseq; i++ )
- {
- ac[i].next = ac+i+1;
- ac[i].prev = ac+i-1;
- ac[i].pos = i;
- }
- ac[nseq-1].next = NULL;
-
- for( i=0; i<nseq; i++ ) tmptmplen[i] = 0.0;
- for( i=0; i<nseq; i++ )
- {
- hist[i] = -1;
- nmemar[i] = 1;
- }
-
- fprintf( stderr, "\n" );
- for( k=0; k<nseq-1; k++ )
- {
- if( k % 10 == 0 ) fprintf( stderr, "\r% 5d / %d", k, nseq );
-
-#if 0
- minscore = 99999.9;
- for( acpti=ac; acpti->next!=NULL; acpti=acpti->next )
- {
- effpt = eff[i=acpti->pos];
-// i = acpti->pos;
- for( acptj=acpti->next; acptj!=NULL; acptj=acptj->next )
- {
-// j=acptj->pos;
-// tmpfloat = eff[i][j-i];
-// if( tmpfloat < minscore )
- if( (tmpfloat= effpt[(j=acptj->pos)-i]) < minscore )
- {
- minscore = tmpfloat;
- im = i; jm = j;
- }
- }
- }
-
-// fprintf( stderr, "im=%d, jm=%d, minscore = %f\n", im, jm, minscore );
-#else
- dumfl[0] = dumfl[1] = -1.0;
- loadtreeoneline( node, dumfl, fp );
- im = node[0];
- jm = node[1];
- minscore = eff[im][jm-im];
-
-// fprintf( stderr, "im=%d, jm=%d, minscore = %f\n", im, jm, minscore );
-
-
- if( dumfl[0] != -1.0 || dumfl[1] != -1.0 )
- {
- fprintf( stderr, "\n\nERROR: Branch length should not be given.\n" );
- exit( 1 );
- }
-
-#endif
-
-
- prevnode = hist[im];
- nmemim = nmemar[im];
- intpt = topol[k][0] = (int *)realloc( topol[k][0], ( nmemim + 1 ) * sizeof( int ) );
- if( prevnode == -1 )
- {
- *intpt++ = im;
- *intpt = -1;
- }
- else
- {
- pt1 = topol[prevnode][0];
- pt2 = topol[prevnode][1];
- if( *pt1 > *pt2 )
- {
- pt11 = pt2;
- pt22 = pt1;
- }
- else
- {
- pt11 = pt1;
- pt22 = pt2;
- }
- for( intpt2=pt11; *intpt2!=-1; )
- *intpt++ = *intpt2++;
- for( intpt2=pt22; *intpt2!=-1; )
- *intpt++ = *intpt2++;
- *intpt = -1;
- }
-
- prevnode = hist[jm];
- nmemjm = nmemar[jm];
- intpt = topol[k][1] = (int *)realloc( topol[k][1], ( nmemjm + 1 ) * sizeof( int ) );
- if( !intpt )
- {
- fprintf( stderr, "Cannot reallocate topol\n" );
- exit( 1 );
- }
- if( prevnode == -1 )
- {
- *intpt++ = jm;
- *intpt = -1;
- }
- else
- {
- pt1 = topol[prevnode][0];
- pt2 = topol[prevnode][1];
- if( *pt1 > *pt2 )
- {
- pt11 = pt2;
- pt22 = pt1;
- }
- else
- {
- pt11 = pt1;
- pt22 = pt2;
- }
- for( intpt2=pt11; *intpt2!=-1; )
- *intpt++ = *intpt2++;
- for( intpt2=pt22; *intpt2!=-1; )
- *intpt++ = *intpt2++;
- *intpt = -1;
- }
-
- minscore *= 0.5;
-
- len[k][0] = ( minscore - tmptmplen[im] );
- len[k][1] = ( minscore - tmptmplen[jm] );
-
- if( len[k][0] < 0.0 ) len[k][0] = 0.0;
- if( len[k][1] < 0.0 ) len[k][1] = 0.0;
-
- tmptmplen[im] = minscore;
-
- hist[im] = k;
- nmemar[im] = nmemim + nmemjm;
-
- for( acpti=ac; acpti!=NULL; acpti=acpti->next )
- {
- i = acpti->pos;
- if( i != im && i != jm )
- {
- if( i < im )
- {
- miniim = i;
- maxiim = im;
- minijm = i;
- maxijm = jm;
- }
- else if( i < jm )
- {
- miniim = im;
- maxiim = i;
- minijm = i;
- maxijm = jm;
- }
- else
- {
- miniim = im;
- maxiim = i;
- minijm = jm;
- maxijm = i;
- }
- eff0 = eff[miniim][maxiim-miniim];
- eff1 = eff[minijm][maxijm-minijm];
-#if 0
- eff[miniim][maxiim-miniim] =
- MIN( eff0, eff1 ) * sueff1 + ( eff0 + eff1 ) * sueff05;
-#else
- eff[miniim][maxiim-miniim] =
- (clusterfuncpt[0])( eff0, eff1 );
-#endif
- }
- }
-// sprintf( treetmp, "(%s,%s)", tree[im], tree[jm] );
- sprintf( treetmp, "(%s:%7.5f,%s:%7.5f)", tree[im], len[k][0], tree[jm], len[k][1] );
- strcpy( tree[im], treetmp );
-
- acjmprev = ac[jm].prev;
- acjmnext = ac[jm].next;
- acjmprev->next = acjmnext;
- if( acjmnext != NULL )
- acjmnext->prev = acjmprev;
- free( (void *)eff[jm] ); eff[jm] = NULL;
-#if 0
- fprintf( stdout, "vSTEP-%03d:\n", k+1 );
- fprintf( stdout, "len0 = %f\n", len[k][0] );
- for( i=0; topol[k][0][i]>-1; i++ ) fprintf( stdout, " %03d", topol[k][0][i]+1 );
- fprintf( stdout, "\n" );
- fprintf( stdout, "len1 = %f\n", len[k][1] );
- for( i=0; topol[k][1][i]>-1; i++ ) fprintf( stdout, " %03d", topol[k][1][i]+1 );
- fprintf( stdout, "\n" );
-#endif
- }
-#if 1
- fclose( fp );
- fp = fopen( "infile.tree", "w" );
- fprintf( fp, "%s\n", treetmp );
- fprintf( fp, "by loadtop\n" );
- fclose( fp );
-#endif
- free( (void *)tmptmplen ); tmptmplen = NULL;
- free( hist ); hist = NULL;
- free( (char *)ac ); ac = NULL;
- free( (void *)nmemar ); nmemar = NULL;
-
-}
-
-
-void fixed_musclesupg_float_realloc_nobk_halfmtx_treeout( int nseq, float **eff, int ***topol, float **len, char **name, int *nlen, Treedep *dep )
-{
- int i, j, k, miniim, maxiim, minijm, maxijm;
- int *intpt, *intpt2;
- float tmpfloat;
- float eff1, eff0;
- static float *tmptmplen = NULL;
- static int *hist = NULL;
- static Bchain *ac = NULL;
- int im = -1, jm = -1;
- Bchain *acjmnext, *acjmprev;
- int prevnode;
- Bchain *acpti;
- int *pt1, *pt2, *pt11, *pt22;
- static int *nmemar;
- int nmemim, nmemjm;
- float minscore;
- int *nearest = NULL; // by D.Mathog, a guess
- float *mindisfrom = NULL; // by D.Mathog, a guess
- static char **tree;
- static char *treetmp;
- static char *nametmp, *nameptr, *tmpptr;
- FILE *fp;
- float (*clusterfuncpt[1])(float,float);
-
-
- sueff1 = 1 - SUEFF;
- sueff05 = SUEFF * 0.5;
- if ( treemethod == 'X' )
- clusterfuncpt[0] = cluster_mix_float;
- else if ( treemethod == 'E' )
- clusterfuncpt[0] = cluster_average_float;
- else if ( treemethod == 'q' )
- clusterfuncpt[0] = cluster_minimum_float;
- else
- {
- fprintf( stderr, "Unknown treemethod, %c\n", treemethod );
- exit( 1 );
- }
-
- if( !hist )
- {
- hist = AllocateIntVec( njob );
- tmptmplen = AllocateFloatVec( njob );
- ac = (Bchain *)malloc( njob * sizeof( Bchain ) );
- nmemar = AllocateIntVec( njob );
- mindisfrom = AllocateFloatVec( njob );
- nearest = AllocateIntVec( njob );
- treetmp = AllocateCharVec( njob*150 );
- nametmp = AllocateCharVec( 130 );
- tree = AllocateCharMtx( njob, njob*150 );
- }
-
-
- for( i=0; i<nseq; i++ )
- {
- for( j=0; j<130; j++ ) nametmp[j] = 0;
- for( j=0; j<130; j++ )
- {
- if( name[i][j] == 0 )
- break;
- else if( isalnum( name[i][j] ) )
- nametmp[j] = name[i][j];
- else
- nametmp[j] = '_';
- }
- nametmp[129] = 0;
-// sprintf( tree[i], "%d_l=%d_%.20s", i+1, nlen[i], nametmp+1 );
- if( outnumber )
- nameptr = strstr( nametmp, "_numo_e" ) + 8;
- else
- nameptr = nametmp + 1;
-
- if( (tmpptr=strstr( nameptr, "_oripos__" )) ) nameptr = tmpptr + 9; // = -> _ no tame
-
- sprintf( tree[i], "%d_%.60s", i+1, nameptr );
- }
- for( i=0; i<nseq; i++ )
- {
- ac[i].next = ac+i+1;
- ac[i].prev = ac+i-1;
- ac[i].pos = i;
- }
- ac[nseq-1].next = NULL;
-
- for( i=0; i<nseq; i++ ) setnearest( nseq, ac, eff, mindisfrom+i, nearest+i, i ); // muscle
-
- for( i=0; i<nseq; i++ ) tmptmplen[i] = 0.0;
- for( i=0; i<nseq; i++ )
- {
- hist[i] = -1;
- nmemar[i] = 1;
- }
-
- fprintf( stderr, "\n" );
- for( k=0; k<nseq-1; k++ )
- {
- if( k % 10 == 0 ) fprintf( stderr, "\r% 5d / %d", k, nseq );
-
- minscore = 999.9;
- for( acpti=ac; acpti->next!=NULL; acpti=acpti->next )
- {
- i = acpti->pos;
-// fprintf( stderr, "k=%d i=%d\n", k, i );
- if( mindisfrom[i] < minscore ) // muscle
- {
- im = i;
- minscore = mindisfrom[i];
- }
- }
- jm = nearest[im];
- if( jm < im )
- {
- j=jm; jm=im; im=j;
- }
-
-
- prevnode = hist[im];
- if( dep ) dep[k].child0 = prevnode;
- nmemim = nmemar[im];
- intpt = topol[k][0] = (int *)realloc( topol[k][0], ( nmemim + 1 ) * sizeof( int ) );
- if( prevnode == -1 )
- {
- *intpt++ = im;
- *intpt = -1;
- }
- else
- {
- pt1 = topol[prevnode][0];
- pt2 = topol[prevnode][1];
- if( *pt1 > *pt2 )
- {
- pt11 = pt2;
- pt22 = pt1;
- }
- else
- {
- pt11 = pt1;
- pt22 = pt2;
- }
- for( intpt2=pt11; *intpt2!=-1; )
- *intpt++ = *intpt2++;
- for( intpt2=pt22; *intpt2!=-1; )
- *intpt++ = *intpt2++;
- *intpt = -1;
- }
-
- prevnode = hist[jm];
- if( dep ) dep[k].child1 = prevnode;
- nmemjm = nmemar[jm];
- intpt = topol[k][1] = (int *)realloc( topol[k][1], ( nmemjm + 1 ) * sizeof( int ) );
- if( !intpt )
- {
- fprintf( stderr, "Cannot reallocate topol\n" );
- exit( 1 );
- }
- if( prevnode == -1 )
- {
- *intpt++ = jm;
- *intpt = -1;
- }
- else
- {
- pt1 = topol[prevnode][0];
- pt2 = topol[prevnode][1];
- if( *pt1 > *pt2 )
- {
- pt11 = pt2;
- pt22 = pt1;
- }
- else
- {
- pt11 = pt1;
- pt22 = pt2;
- }
- for( intpt2=pt11; *intpt2!=-1; )
- *intpt++ = *intpt2++;
- for( intpt2=pt22; *intpt2!=-1; )
- *intpt++ = *intpt2++;
- *intpt = -1;
- }
-
- minscore *= 0.5;
-
- len[k][0] = ( minscore - tmptmplen[im] );
- len[k][1] = ( minscore - tmptmplen[jm] );
-
- tmptmplen[im] = minscore;
-
- hist[im] = k;
- nmemar[im] = nmemim + nmemjm;
-
- mindisfrom[im] = 999.9;
- for( acpti=ac; acpti!=NULL; acpti=acpti->next )
- {
- i = acpti->pos;
- if( i != im && i != jm )
- {
- if( i < im )
- {
- miniim = i;
- maxiim = im;
- minijm = i;
- maxijm = jm;
- }
- else if( i < jm )
- {
- miniim = im;
- maxiim = i;
- minijm = i;
- maxijm = jm;
- }
- else
- {
- miniim = im;
- maxiim = i;
- minijm = jm;
- maxijm = i;
- }
- eff0 = eff[miniim][maxiim-miniim];
- eff1 = eff[minijm][maxijm-minijm];
-#if 0
- tmpfloat = eff[miniim][maxiim-miniim] =
- MIN( eff0, eff1 ) * sueff1 + ( eff0 + eff1 ) * sueff05;
-#else
- tmpfloat = eff[miniim][maxiim-miniim] =
- (clusterfuncpt[0])( eff0, eff1 );
-#endif
- if( tmpfloat < mindisfrom[i] )
- {
- mindisfrom[i] = tmpfloat;
- nearest[i] = im;
- }
- if( tmpfloat < mindisfrom[im] )
- {
- mindisfrom[im] = tmpfloat;
- nearest[im] = i;
- }
- if( nearest[i] == jm )
- {
- nearest[i] = im;
- }
- }
- }
-
- sprintf( treetmp, "(%s:%7.5f,%s:%7.5f)", tree[im], len[k][0], tree[jm], len[k][1] );
- strcpy( tree[im], treetmp );
-
- acjmprev = ac[jm].prev;
- acjmnext = ac[jm].next;
- acjmprev->next = acjmnext;
- if( acjmnext != NULL )
- acjmnext->prev = acjmprev;
- free( (void *)eff[jm] ); eff[jm] = NULL;
-
-#if 1 // muscle seems to miss this.
- for( acpti=ac; acpti!=NULL; acpti=acpti->next )
- {
- i = acpti->pos;
- if( nearest[i] == im )
- {
-// fprintf( stderr, "calling setnearest\n" );
- setnearest( nseq, ac, eff, mindisfrom+i, nearest+i, i );
- }
- }
-#endif
-
-
-#if 0
- fprintf( stdout, "vSTEP-%03d:\n", k+1 );
- fprintf( stdout, "len0 = %f\n", len[k][0] );
- for( i=0; topol[k][0][i]>-1; i++ ) fprintf( stdout, " %03d", topol[k][0][i]+1 );
- fprintf( stdout, "\n" );
- fprintf( stdout, "len1 = %f\n", len[k][1] );
- for( i=0; topol[k][1][i]>-1; i++ ) fprintf( stdout, " %03d", topol[k][1][i]+1 );
- fprintf( stdout, "\n" );
-#endif
- }
- fp = fopen( "infile.tree", "w" );
- fprintf( fp, "%s\n", treetmp );
- fclose( fp );
-
- FreeCharMtx( tree );
- free( treetmp );
- free( nametmp );
- free( (void *)tmptmplen ); tmptmplen = NULL;
- free( hist ); hist = NULL;
- free( (char *)ac ); ac = NULL;
- free( (void *)nmemar ); nmemar = NULL;
- free( mindisfrom );
- free( nearest );
-
-}
-
-//void veryfastsupg_double_outtree( int nseq, double **eff, int ***topol, double **len, char **name )
-void fixed_musclesupg_double_treeout( int nseq, double **eff, int ***topol, double **len, char **name )
-{
- int i, j, k, miniim, maxiim, minijm, maxijm;
- int *intpt, *intpt2;
- double tmpfloat;
- double eff1, eff0;
- static double *tmptmplen = NULL;
- static int *hist = NULL;
- static Bchain *ac = NULL;
- int im = -1, jm = -1;
- Bchain *acjmnext, *acjmprev;
- int prevnode;
- Bchain *acpti;
- int *pt1, *pt2, *pt11, *pt22;
- static int *nmemar;
- int nmemim, nmemjm;
- double minscore;
- int *nearest = NULL; // by D.Mathog, a guess
- double *mindisfrom = NULL; // by D.Mathog, a guess
- static char **tree;
- static char *treetmp;
- static char *nametmp, *nameptr, *tmpptr;
- FILE *fp;
- double (*clusterfuncpt[1])(double,double);
-
-
- sueff1_double = 1 - SUEFF;
- sueff05_double = SUEFF * 0.5;
- if ( treemethod == 'X' )
- clusterfuncpt[0] = cluster_mix_double;
- else if ( treemethod == 'E' )
- clusterfuncpt[0] = cluster_average_double;
- else if ( treemethod == 'q' )
- clusterfuncpt[0] = cluster_minimum_double;
- else
- {
- fprintf( stderr, "Unknown treemethod, %c\n", treemethod );
- exit( 1 );
- }
-
- if( !hist )
- {
- hist = AllocateIntVec( njob );
- tmptmplen = AllocateDoubleVec( njob );
- ac = (Bchain *)malloc( njob * sizeof( Bchain ) );
- nmemar = AllocateIntVec( njob );
- mindisfrom = AllocateDoubleVec( njob );
- nearest = AllocateIntVec( njob );
- treetmp = AllocateCharVec( njob*150 );
- nametmp = AllocateCharVec( 91 );
- tree = AllocateCharMtx( njob, njob*150 );
- }
-
-
- for( i=0; i<nseq; i++ )
- {
- for( j=0; j<90; j++ ) nametmp[j] = 0;
- for( j=0; j<90; j++ )
- {
- if( name[i][j] == 0 )
- break;
- else if( isalnum( name[i][j] ) )
- nametmp[j] = name[i][j];
- else
- nametmp[j] = '_';
- }
- nametmp[90] = 0;
-// sprintf( tree[i], "%d_%.60s", i+1, nametmp+1 );
- if( outnumber )
- nameptr = strstr( nametmp, "_numo_e" ) + 8;
- else
- nameptr = nametmp + 1;
-
- if( (tmpptr=strstr( nameptr, "_oripos__" )) ) nameptr = tmpptr + 9; // = -> _ no tame
-
- sprintf( tree[i], "%d_%.60s", i+1, nameptr );
- }
- for( i=0; i<nseq; i++ )
- {
- ac[i].next = ac+i+1;
- ac[i].prev = ac+i-1;
- ac[i].pos = i;
- }
- ac[nseq-1].next = NULL;
-
- for( i=0; i<nseq; i++ ) setnearest_double_fullmtx( nseq, ac, eff, mindisfrom+i, nearest+i, i ); // muscle
-
- for( i=0; i<nseq; i++ ) tmptmplen[i] = 0.0;
- for( i=0; i<nseq; i++ )
- {
- hist[i] = -1;
- nmemar[i] = 1;
- }
-
- fprintf( stderr, "\n" );
- for( k=0; k<nseq-1; k++ )
- {
- if( k % 10 == 0 ) fprintf( stderr, "\r% 5d / %d", k, nseq );
-
- minscore = 999.9;
- for( acpti=ac; acpti->next!=NULL; acpti=acpti->next )
- {
- i = acpti->pos;
-// fprintf( stderr, "k=%d i=%d\n", k, i );
- if( mindisfrom[i] < minscore ) // muscle
- {
- im = i;
- minscore = mindisfrom[i];
- }
- }
- jm = nearest[im];
- if( jm < im )
- {
- j=jm; jm=im; im=j;
- }
-
-
- prevnode = hist[im];
- nmemim = nmemar[im];
-// intpt = topol[k][0] = (int *)realloc( topol[k][0], ( nmemim + 1 ) * sizeof( int ) );
- intpt = topol[k][0];
- if( prevnode == -1 )
- {
- *intpt++ = im;
- *intpt = -1;
- }
- else
- {
- pt1 = topol[prevnode][0];
- pt2 = topol[prevnode][1];
- if( *pt1 > *pt2 )
- {
- pt11 = pt2;
- pt22 = pt1;
- }
- else
- {
- pt11 = pt1;
- pt22 = pt2;
- }
- for( intpt2=pt11; *intpt2!=-1; )
- *intpt++ = *intpt2++;
- for( intpt2=pt22; *intpt2!=-1; )
- *intpt++ = *intpt2++;
- *intpt = -1;
- }
-
- prevnode = hist[jm];
- nmemjm = nmemar[jm];
-// intpt = topol[k][1] = (int *)realloc( topol[k][1], ( nmemjm + 1 ) * sizeof( int ) );
- intpt = topol[k][1];
- if( prevnode == -1 )
- {
- *intpt++ = jm;
- *intpt = -1;
- }
- else
- {
- pt1 = topol[prevnode][0];
- pt2 = topol[prevnode][1];
- if( *pt1 > *pt2 )
- {
- pt11 = pt2;
- pt22 = pt1;
- }
- else
- {
- pt11 = pt1;
- pt22 = pt2;
- }
- for( intpt2=pt11; *intpt2!=-1; )
- *intpt++ = *intpt2++;
- for( intpt2=pt22; *intpt2!=-1; )
- *intpt++ = *intpt2++;
- *intpt = -1;
- }
-
- minscore *= 0.5;
-
- len[k][0] = ( minscore - tmptmplen[im] );
- len[k][1] = ( minscore - tmptmplen[jm] );
-
-
- tmptmplen[im] = minscore;
-
- hist[im] = k;
- nmemar[im] = nmemim + nmemjm;
-
- mindisfrom[im] = 999.9;
- for( acpti=ac; acpti!=NULL; acpti=acpti->next )
- {
- i = acpti->pos;
- if( i != im && i != jm )
- {
- if( i < im )
- {
- miniim = i;
- maxiim = im;
- minijm = i;
- maxijm = jm;
- }
- else if( i < jm )
- {
- miniim = im;
- maxiim = i;
- minijm = i;
- maxijm = jm;
- }
- else
- {
- miniim = im;
- maxiim = i;
- minijm = jm;
- maxijm = i;
- }
- eff0 = eff[miniim][maxiim];
- eff1 = eff[minijm][maxijm];
-#if 0
- tmpfloat = eff[miniim][maxiim] =
- MIN( eff0, eff1 ) * sueff1 + ( eff0 + eff1 ) * sueff05;
-#else
- tmpfloat = eff[miniim][maxiim] =
- (clusterfuncpt[0])( eff0, eff1 );
-#endif
- if( tmpfloat < mindisfrom[i] )
- {
- mindisfrom[i] = tmpfloat;
- nearest[i] = im;
- }
- if( tmpfloat < mindisfrom[im] )
- {
- mindisfrom[im] = tmpfloat;
- nearest[im] = i;
- }
- if( nearest[i] == jm )
- {
- nearest[i] = im;
- }
- }
- }
-
- sprintf( treetmp, "(%s:%7.5f,%s:%7.5f)", tree[im], len[k][0], tree[jm], len[k][1] );
- strcpy( tree[im], treetmp );
-
- acjmprev = ac[jm].prev;
- acjmnext = ac[jm].next;
- acjmprev->next = acjmnext;
- if( acjmnext != NULL )
- acjmnext->prev = acjmprev;
-// free( (void *)eff[jm] ); eff[jm] = NULL;
-
-#if 1 // muscle seems to miss this.
- for( acpti=ac; acpti!=NULL; acpti=acpti->next )
- {
- i = acpti->pos;
- if( nearest[i] == im )
- {
-// fprintf( stderr, "calling setnearest\n" );
- setnearest_double_fullmtx( nseq, ac, eff, mindisfrom+i, nearest+i, i );
- }
- }
-#endif
-
-
-#if 0
- fprintf( stdout, "vSTEP-%03d:\n", k+1 );
- fprintf( stdout, "len0 = %f\n", len[k][0] );
- for( i=0; topol[k][0][i]>-1; i++ ) fprintf( stdout, " %03d", topol[k][0][i]+1 );
- fprintf( stdout, "\n" );
- fprintf( stdout, "len1 = %f\n", len[k][1] );
- for( i=0; topol[k][1][i]>-1; i++ ) fprintf( stdout, " %03d", topol[k][1][i]+1 );
- fprintf( stdout, "\n" );
-#endif
- }
- fp = fopen( "infile.tree", "w" );
- fprintf( fp, "%s\n", treetmp );
- fclose( fp );
-
- FreeCharMtx( tree );
- free( treetmp );
- free( nametmp );
- free( (void *)tmptmplen ); tmptmplen = NULL;
- free( hist ); hist = NULL;
- free( (char *)ac ); ac = NULL;
- free( (void *)nmemar ); nmemar = NULL;
- free( mindisfrom );
- free( nearest );
-}
-
-
-void fixed_musclesupg_float_realloc_nobk_halfmtx( int nseq, float **eff, int ***topol, float **len, Treedep *dep )
-{
- int i, j, k, miniim, maxiim, minijm, maxijm;
- int *intpt, *intpt2;
- float tmpfloat;
- float eff1, eff0;
- static float *tmptmplen = NULL;
- static int *hist = NULL;
- static Bchain *ac = NULL;
- int im = -1, jm = -1;
- Bchain *acjmnext, *acjmprev;
- int prevnode;
- Bchain *acpti;
- int *pt1, *pt2, *pt11, *pt22;
- static int *nmemar;
- int nmemim, nmemjm;
- float minscore;
-// float sueff1 = 1 - SUEFF;
-// float sueff05 = SUEFF * 0.5;
- int *nearest = NULL; // by Mathog, a guess
- float *mindisfrom = NULL; // by Mathog, a guess
- float (*clusterfuncpt[1])(float,float);
-
-
- sueff1 = 1 - SUEFF;
- sueff05 = SUEFF * 0.5;
- if ( treemethod == 'X' )
- clusterfuncpt[0] = cluster_mix_float;
- else if ( treemethod == 'E' )
- clusterfuncpt[0] = cluster_average_float;
- else if ( treemethod == 'q' )
- clusterfuncpt[0] = cluster_minimum_float;
- else
- {
- fprintf( stderr, "Unknown treemethod, %c\n", treemethod );
- exit( 1 );
- }
-
- if( !hist )
- {
- hist = AllocateIntVec( njob );
- tmptmplen = AllocateFloatVec( njob );
- ac = (Bchain *)malloc( njob * sizeof( Bchain ) );
- nmemar = AllocateIntVec( njob );
- mindisfrom = AllocateFloatVec( njob );
- nearest = AllocateIntVec( njob );
- }
-
-
- for( i=0; i<nseq; i++ )
- {
- ac[i].next = ac+i+1;
- ac[i].prev = ac+i-1;
- ac[i].pos = i;
- }
- ac[nseq-1].next = NULL;
-
- for( i=0; i<nseq; i++ ) setnearest( nseq, ac, eff, mindisfrom+i, nearest+i, i ); // muscle
-
- for( i=0; i<nseq; i++ ) tmptmplen[i] = 0.0;
- for( i=0; i<nseq; i++ )
- {
- hist[i] = -1;
- nmemar[i] = 1;
- }
-
- fprintf( stderr, "\n" );
- for( k=0; k<nseq-1; k++ )
- {
- if( k % 10 == 0 ) fprintf( stderr, "\r% 5d / %d", k, nseq );
-
- minscore = 999.9;
- for( acpti=ac; acpti->next!=NULL; acpti=acpti->next )
- {
- i = acpti->pos;
-// fprintf( stderr, "k=%d i=%d\n", k, i );
- if( mindisfrom[i] < minscore ) // muscle
- {
- im = i;
- minscore = mindisfrom[i];
- }
- }
- jm = nearest[im];
- if( jm < im )
- {
- j=jm; jm=im; im=j;
- }
-
-
- prevnode = hist[im];
- if( dep ) dep[k].child0 = prevnode;
- nmemim = nmemar[im];
- intpt = topol[k][0] = (int *)realloc( topol[k][0], ( nmemim + 1 ) * sizeof( int ) );
- if( prevnode == -1 )
- {
- *intpt++ = im;
- *intpt = -1;
- }
- else
- {
- pt1 = topol[prevnode][0];
- pt2 = topol[prevnode][1];
- if( *pt1 > *pt2 )
- {
- pt11 = pt2;
- pt22 = pt1;
- }
- else
- {
- pt11 = pt1;
- pt22 = pt2;
- }
- for( intpt2=pt11; *intpt2!=-1; )
- *intpt++ = *intpt2++;
- for( intpt2=pt22; *intpt2!=-1; )
- *intpt++ = *intpt2++;
- *intpt = -1;
- }
-
- prevnode = hist[jm];
- if( dep ) dep[k].child1 = prevnode;
- nmemjm = nmemar[jm];
- intpt = topol[k][1] = (int *)realloc( topol[k][1], ( nmemjm + 1 ) * sizeof( int ) );
- if( !intpt )
- {
- fprintf( stderr, "Cannot reallocate topol\n" );
- exit( 1 );
- }
- if( prevnode == -1 )
- {
- *intpt++ = jm;
- *intpt = -1;
- }
- else
- {
- pt1 = topol[prevnode][0];
- pt2 = topol[prevnode][1];
- if( *pt1 > *pt2 )
- {
- pt11 = pt2;
- pt22 = pt1;
- }
- else
- {
- pt11 = pt1;
- pt22 = pt2;
- }
- for( intpt2=pt11; *intpt2!=-1; )
- *intpt++ = *intpt2++;
- for( intpt2=pt22; *intpt2!=-1; )
- *intpt++ = *intpt2++;
- *intpt = -1;
- }
-
- minscore *= 0.5;
-
- len[k][0] = ( minscore - tmptmplen[im] );
- len[k][1] = ( minscore - tmptmplen[jm] );
-
- tmptmplen[im] = minscore;
-
- hist[im] = k;
- nmemar[im] = nmemim + nmemjm;
-
- mindisfrom[im] = 999.9;
- for( acpti=ac; acpti!=NULL; acpti=acpti->next )
- {
- i = acpti->pos;
- if( i != im && i != jm )
- {
- if( i < im )
- {
- miniim = i;
- maxiim = im;
- minijm = i;
- maxijm = jm;
- }
- else if( i < jm )
- {
- miniim = im;
- maxiim = i;
- minijm = i;
- maxijm = jm;
- }
- else
- {
- miniim = im;
- maxiim = i;
- minijm = jm;
- maxijm = i;
- }
- eff0 = eff[miniim][maxiim-miniim];
- eff1 = eff[minijm][maxijm-minijm];
- tmpfloat = eff[miniim][maxiim-miniim] =
-#if 0
- MIN( eff0, eff1 ) * sueff1 + ( eff0 + eff1 ) * sueff05;
-#else
- (clusterfuncpt[0])( eff0, eff1 );
-#endif
- if( tmpfloat < mindisfrom[i] )
- {
- mindisfrom[i] = tmpfloat;
- nearest[i] = im;
- }
- if( tmpfloat < mindisfrom[im] )
- {
- mindisfrom[im] = tmpfloat;
- nearest[im] = i;
- }
- if( nearest[i] == jm )
- {
- nearest[i] = im;
- }
- }
- }
-
-// fprintf( stderr, "im,jm=%d,%d\n", im, jm );
- acjmprev = ac[jm].prev;
- acjmnext = ac[jm].next;
- acjmprev->next = acjmnext;
- if( acjmnext != NULL )
- acjmnext->prev = acjmprev;
- free( (void *)eff[jm] ); eff[jm] = NULL;
-
-#if 1 // muscle seems to miss this.
- for( acpti=ac; acpti!=NULL; acpti=acpti->next )
- {
- i = acpti->pos;
- if( nearest[i] == im )
- {
-// fprintf( stderr, "calling setnearest\n" );
- setnearest( nseq, ac, eff, mindisfrom+i, nearest+i, i );
- }
- }
-#endif
-
-
-#if 0
- fprintf( stdout, "vSTEP-%03d:\n", k+1 );
- fprintf( stdout, "len0 = %f\n", len[k][0] );
- for( i=0; topol[k][0][i]>-1; i++ ) fprintf( stdout, " %03d", topol[k][0][i]+1 );
- fprintf( stdout, "\n" );
- fprintf( stdout, "len1 = %f\n", len[k][1] );
- for( i=0; topol[k][1][i]>-1; i++ ) fprintf( stdout, " %03d", topol[k][1][i]+1 );
- fprintf( stdout, "\n" );
-#endif
- }
- free( (void *)tmptmplen ); tmptmplen = NULL;
- free( hist ); hist = NULL;
- free( (char *)ac ); ac = NULL;
- free( (void *)nmemar ); nmemar = NULL;
- free( mindisfrom );
- free( nearest );
-}
-
-
-
-
-
-
-
-
-void veryfastsupg_double_loadtop( int nseq, double **eff, int ***topol, double **len ) // BUG!!!
-{
- int i, k, miniim, maxiim, minijm, maxijm;
- int *intpt, *intpt2;
- double eff1, eff0;
- static double *tmptmplen = NULL;
- static int *hist = NULL;
- static Achain *ac = NULL;
- double minscore;
- static char **tree;
- static char *treetmp;
- int im = -1, jm = -1;
- int prevnode, acjmnext, acjmprev;
- int *pt1, *pt2, *pt11, *pt22;
- FILE *fp;
- int node[2];
- float dumfl[2];
-
- fp = fopen( "_guidetree", "r" );
- if( !fp )
- {
- fprintf( stderr, "cannot open _guidetree\n" );
- exit( 1 );
- }
-
- if( !hist )
- {
- treetmp = AllocateCharVec( njob*50 );
- tree = AllocateCharMtx( njob, njob*50 );
- hist = AllocateIntVec( njob );
- tmptmplen = (double *)malloc( njob * sizeof( double ) );
- ac = (Achain *)malloc( njob * sizeof( Achain ) );
- }
- for( i=0; i<nseq; i++ ) sprintf( tree[i], "%d", i+1 );
-
- for( i=0; i<nseq; i++ )
- {
- ac[i].next = i+1;
- ac[i].prev = i-1;
-// ac[i].curr = i;
- }
- ac[nseq-1].next = -1;
-
- for( i=0; i<nseq; i++ ) tmptmplen[i] = 0.0;
- for( i=0; i<nseq; i++ ) hist[i] = -1;
-
- fprintf( stderr, "\n" );
- for( k=0; k<nseq-1; k++ )
- {
- if( k % 10 == 0 ) fprintf( stderr, "%d / %d\r", k, nseq );
-
-#if 0
- minscore = 99999.9;
- for( i=0; ac[i].next!=-1; i=ac[i].next )
- {
- for( j=ac[i].next; j!=-1; j=ac[j].next )
- {
- tmpdouble = eff[i][j];
- if( tmpdouble < minscore )
- {
- minscore = tmpdouble;
- im = i; jm = j;
- }
- }
- }
-#else
- dumfl[0] = dumfl[1] = -1.0;
- loadtreeoneline( node, dumfl, fp );
- im = node[0];
- jm = node[1];
- minscore = eff[im][jm];
-
-// fprintf( stderr, "im=%d, jm=%d, minscore = %f\n", im, jm, minscore );
-
-
- if( dumfl[0] != -1.0 || dumfl[1] != -1.0 )
- {
- fprintf( stderr, "\n\nBranch length should not given.\n" );
- exit( 1 );
- }
-#endif
-
-// fprintf( stderr, "im=%d, jm=%d\n", im, jm );
-
- intpt = topol[k][0];
- prevnode = hist[im];
- if( prevnode == -1 )
- {
- *intpt++ = im;
- *intpt = -1;
- }
- else
- {
- pt1 = topol[prevnode][0];
- pt2 = topol[prevnode][1];
- if( *pt1 > *pt2 )
- {
- pt11 = pt2;
- pt22 = pt1;
- }
- else
- {
- pt11 = pt1;
- pt22 = pt2;
- }
- for( intpt2=pt11; *intpt2!=-1; )
- *intpt++ = *intpt2++;
- for( intpt2=pt22; *intpt2!=-1; )
- *intpt++ = *intpt2++;
- *intpt = -1;
- }
-
- intpt = topol[k][1];
- prevnode = hist[jm];
- if( prevnode == -1 )
- {
- *intpt++ = jm;
- *intpt = -1;
- }
- else
- {
- pt1 = topol[prevnode][0];
- pt2 = topol[prevnode][1];
- if( *pt1 > *pt2 )
- {
- pt11 = pt2;
- pt22 = pt1;
- }
- else
- {
- pt11 = pt1;
- pt22 = pt2;
- }
- for( intpt2=pt11; *intpt2!=-1; )
- *intpt++ = *intpt2++;
- for( intpt2=pt22; *intpt2!=-1; )
- *intpt++ = *intpt2++;
- *intpt = -1;
- }
-
- minscore *= 0.5;
-
- len[k][0] = minscore - tmptmplen[im];
- len[k][1] = minscore - tmptmplen[jm];
-
- if( len[k][0] < 0.0 ) len[k][0] = 0.0;
- if( len[k][1] < 0.0 ) len[k][1] = 0.0;
-
- tmptmplen[im] = minscore;
-
- hist[im] = k;
-
- for( i=0; i!=-1; i=ac[i].next )
- {
- if( i != im && i != jm )
- {
- if( i < im )
- {
- miniim = i;
- maxiim = im;
- minijm = i;
- maxijm = jm;
- }
- else if( i < jm )
- {
- miniim = im;
- maxiim = i;
- minijm = i;
- maxijm = jm;
- }
- else
- {
- miniim = im;
- maxiim = i;
- minijm = jm;
- maxijm = i;
- }
- eff0 = eff[miniim][maxiim];
- eff1 = eff[minijm][maxijm];
- eff[miniim][maxiim] =
- MIN( eff0, eff1 ) * ( 1.0 - SUEFF ) +
- ( eff0 + eff1 ) * 0.5 * SUEFF;
- }
- }
- acjmprev = ac[jm].prev;
- acjmnext = ac[jm].next;
- ac[acjmprev].next = acjmnext;
- if( acjmnext != -1 )
- ac[acjmnext].prev = acjmprev;
-
- sprintf( treetmp, "(%s:%7.5f,%s:%7.5f)", tree[im], len[k][0], tree[jm], len[k][1] );
- strcpy( tree[im], treetmp );
-#if 0
- fprintf( stdout, "STEP-%03d:\n", k+1 );
- fprintf( stdout, "len0 = %f\n", len[k][0] );
- for( i=0; topol[k][0][i]>-1; i++ ) fprintf( stdout, " %03d", topol[k][0][i] );
- fprintf( stdout, "\n" );
- fprintf( stdout, "len1 = %f\n", len[k][1] );
- for( i=0; topol[k][1][i]>-1; i++ ) fprintf( stdout, " %03d", topol[k][1][i] );
- fprintf( stdout, "\n" );
-#endif
- }
- fclose( fp );
-
- fp = fopen( "infile.tree", "w" );
- fprintf( fp, "%s\n", treetmp );
-// fprintf( fp, "by veryfastsupg_double_loadtop\n" );
- fclose( fp );
-
-#if 1
- fprintf( stderr, "\n" );
- free( (void *)tmptmplen ); tmptmplen = NULL;
- free( hist ); hist = NULL;
- free( (char *)ac ); ac = NULL;
- FreeCharMtx( tree );
- free( treetmp );
-#endif
-}
-
-void veryfastsupg_double_loadtree( int nseq, double **eff, int ***topol, double **len )
-{
- int i, k, miniim, maxiim, minijm, maxijm;
- int *intpt, *intpt2;
- double eff1, eff0;
- static double *tmptmplen = NULL;
- static int *hist = NULL;
- static Achain *ac = NULL;
- double minscore;
- static char **tree;
- static char *treetmp;
- int im = -1, jm = -1;
- int prevnode, acjmnext, acjmprev;
- int *pt1, *pt2, *pt11, *pt22;
- FILE *fp;
- int node[2];
- float lenfl[2];
-
- fp = fopen( "_guidetree", "r" );
- if( !fp )
- {
- fprintf( stderr, "cannot open _guidetree\n" );
- exit( 1 );
- }
-
- if( !hist )
- {
- treetmp = AllocateCharVec( njob*50 );
- tree = AllocateCharMtx( njob, njob*50 );
- hist = AllocateIntVec( njob );
- tmptmplen = (double *)malloc( njob * sizeof( double ) );
- ac = (Achain *)malloc( njob * sizeof( Achain ) );
- }
-
- for( i=0; i<nseq; i++ ) sprintf( tree[i], "%d", i+1 );
-
- for( i=0; i<nseq; i++ )
- {
- ac[i].next = i+1;
- ac[i].prev = i-1;
-// ac[i].curr = i;
- }
- ac[nseq-1].next = -1;
-
- for( i=0; i<nseq; i++ ) tmptmplen[i] = 0.0;
- for( i=0; i<nseq; i++ ) hist[i] = -1;
-
- fprintf( stderr, "\n" );
- for( k=0; k<nseq-1; k++ )
- {
- if( k % 10 == 0 ) fprintf( stderr, "%d / %d\r", k, nseq );
-
-#if 0
- minscore = 99999.9;
- for( i=0; ac[i].next!=-1; i=ac[i].next )
- {
- for( j=ac[i].next; j!=-1; j=ac[j].next )
- {
- tmpdouble = eff[i][j];
- if( tmpdouble < minscore )
- {
- minscore = tmpdouble;
- im = i; jm = j;
- }
- }
- }
-#else
- lenfl[0] = lenfl[1] = -1.0;
- loadtreeoneline( node, lenfl, fp );
- im = node[0];
- jm = node[1];
- minscore = eff[im][jm];
-
-// fprintf( stderr, "im=%d, jm=%d, minscore = %f\n", im, jm, minscore );
-
-
- if( lenfl[0] == -1.0 || lenfl[1] == -1.0 )
- {
- fprintf( stderr, "\n\nWARNING: Branch length is not given.\n" );
- exit( 1 );
- }
-
- if( lenfl[0] < 0.0 ) lenfl[0] = 0.0;
- if( lenfl[1] < 0.0 ) lenfl[1] = 0.0;
-#endif
-
-// fprintf( stderr, "im=%d, jm=%d\n", im, jm );
-
- intpt = topol[k][0];
- prevnode = hist[im];
- if( prevnode == -1 )
- {
- *intpt++ = im;
- *intpt = -1;
- }
- else
- {
- pt1 = topol[prevnode][0];
- pt2 = topol[prevnode][1];
- if( *pt1 > *pt2 )
- {
- pt11 = pt2;
- pt22 = pt1;
- }
- else
- {
- pt11 = pt1;
- pt22 = pt2;
- }
- for( intpt2=pt11; *intpt2!=-1; )
- *intpt++ = *intpt2++;
- for( intpt2=pt22; *intpt2!=-1; )
- *intpt++ = *intpt2++;
- *intpt = -1;
- }
-
- intpt = topol[k][1];
- prevnode = hist[jm];
- if( prevnode == -1 )
- {
- *intpt++ = jm;
- *intpt = -1;
- }
- else
- {
- pt1 = topol[prevnode][0];
- pt2 = topol[prevnode][1];
- if( *pt1 > *pt2 )
- {
- pt11 = pt2;
- pt22 = pt1;
- }
- else
- {
- pt11 = pt1;
- pt22 = pt2;
- }
- for( intpt2=pt11; *intpt2!=-1; )
- *intpt++ = *intpt2++;
- for( intpt2=pt22; *intpt2!=-1; )
- *intpt++ = *intpt2++;
- *intpt = -1;
- }
-
- minscore *= 0.5;
-
-#if 0
- len[k][0] = minscore - tmptmplen[im];
- len[k][1] = minscore - tmptmplen[jm];
-#else
- len[k][0] = lenfl[0];
- len[k][1] = lenfl[1];
-#endif
-
- tmptmplen[im] = minscore;
-
- hist[im] = k;
-
- for( i=0; i!=-1; i=ac[i].next )
- {
- if( i != im && i != jm )
- {
- if( i < im )
- {
- miniim = i;
- maxiim = im;
- minijm = i;
- maxijm = jm;
- }
- else if( i < jm )
- {
- miniim = im;
- maxiim = i;
- minijm = i;
- maxijm = jm;
- }
- else
- {
- miniim = im;
- maxiim = i;
- minijm = jm;
- maxijm = i;
- }
- eff0 = eff[miniim][maxiim];
- eff1 = eff[minijm][maxijm];
- eff[miniim][maxiim] =
- MIN( eff0, eff1 ) * ( 1.0 - SUEFF ) +
- ( eff0 + eff1 ) * 0.5 * SUEFF;
- }
- }
- acjmprev = ac[jm].prev;
- acjmnext = ac[jm].next;
- ac[acjmprev].next = acjmnext;
- if( acjmnext != -1 )
- ac[acjmnext].prev = acjmprev;
-
- sprintf( treetmp, "(%s:%7.5f,%s:%7.5f)", tree[im], len[k][0], tree[jm], len[k][1] );
- strcpy( tree[im], treetmp );
-
-#if 0
- fprintf( stdout, "STEP-%03d:\n", k+1 );
- fprintf( stdout, "len0 = %f\n", len[k][0] );
- for( i=0; topol[k][0][i]>-1; i++ ) fprintf( stdout, " %03d", topol[k][0][i] );
- fprintf( stdout, "\n" );
- fprintf( stdout, "len1 = %f\n", len[k][1] );
- for( i=0; topol[k][1][i]>-1; i++ ) fprintf( stdout, " %03d", topol[k][1][i] );
- fprintf( stdout, "\n" );
-#endif
- }
- fclose( fp );
-
-
- fp = fopen( "infile.tree", "w" );
- fprintf( fp, "%s\n", treetmp );
-// fprintf( fp, "by veryfastsupg_double_loadtree\n" );
- fclose( fp );
-
-#if 1
- fprintf( stderr, "\n" );
- free( (void *)tmptmplen ); tmptmplen = NULL;
- free( hist ); hist = NULL;
- free( (char *)ac ); ac = NULL;
- FreeCharMtx( tree );
- free( treetmp );
-#endif
-
-
-}
-
-#if 0
-void veryfastsupg_double( int nseq, double **eff, int ***topol, double **len )
-{
- int i, j, k, miniim, maxiim, minijm, maxijm;
- int *intpt, *intpt2;
- double tmpdouble;
- double eff1, eff0;
- static double *tmptmplen = NULL;
- static int *hist = NULL;
- static Achain *ac = NULL;
- double minscore;
- int im = -1, jm = -1;
- int prevnode, acjmnext, acjmprev;
- int *pt1, *pt2, *pt11, *pt22;
- if( !hist )
- {
- hist = AllocateIntVec( njob );
- tmptmplen = (double *)malloc( njob * sizeof( double ) );
- ac = (Achain *)malloc( njob * sizeof( Achain ) );
- }
-
- for( i=0; i<nseq; i++ )
- {
- ac[i].next = i+1;
- ac[i].prev = i-1;
-// ac[i].curr = i;
- }
- ac[nseq-1].next = -1;
-
- for( i=0; i<nseq; i++ ) tmptmplen[i] = 0.0;
- for( i=0; i<nseq; i++ ) hist[i] = -1;
-
- fprintf( stderr, "\n" );
- for( k=0; k<nseq-1; k++ )
- {
- if( k % 10 == 0 ) fprintf( stderr, "%d / %d\r", k, nseq );
-
- minscore = 99999.9;
- for( i=0; ac[i].next!=-1; i=ac[i].next )
- {
- for( j=ac[i].next; j!=-1; j=ac[j].next )
- {
- tmpdouble = eff[i][j];
- if( tmpdouble < minscore )
- {
- minscore = tmpdouble;
- im = i; jm = j;
- }
- }
- }
-
-// fprintf( stderr, "im=%d, jm=%d\n", im, jm );
-
- intpt = topol[k][0];
- prevnode = hist[im];
- if( prevnode == -1 )
- {
- *intpt++ = im;
- *intpt = -1;
- }
- else
- {
- pt1 = topol[prevnode][0];
- pt2 = topol[prevnode][1];
- if( *pt1 > *pt2 )
- {
- pt11 = pt2;
- pt22 = pt1;
- }
- else
- {
- pt11 = pt1;
- pt22 = pt2;
- }
- for( intpt2=pt11; *intpt2!=-1; )
- *intpt++ = *intpt2++;
- for( intpt2=pt22; *intpt2!=-1; )
- *intpt++ = *intpt2++;
- *intpt = -1;
- }
-
- intpt = topol[k][1];
- prevnode = hist[jm];
- if( prevnode == -1 )
- {
- *intpt++ = jm;
- *intpt = -1;
- }
- else
- {
- pt1 = topol[prevnode][0];
- pt2 = topol[prevnode][1];
- if( *pt1 > *pt2 )
- {
- pt11 = pt2;
- pt22 = pt1;
- }
- else
- {
- pt11 = pt1;
- pt22 = pt2;
- }
- for( intpt2=pt11; *intpt2!=-1; )
- *intpt++ = *intpt2++;
- for( intpt2=pt22; *intpt2!=-1; )
- *intpt++ = *intpt2++;
- *intpt = -1;
- }
-
- minscore *= 0.5;
-
- len[k][0] = minscore - tmptmplen[im];
- len[k][1] = minscore - tmptmplen[jm];
-
- tmptmplen[im] = minscore;
-
- hist[im] = k;
-
- for( i=0; i!=-1; i=ac[i].next )
- {
- if( i != im && i != jm )
- {
- if( i < im )
- {
- miniim = i;
- maxiim = im;
- minijm = i;
- maxijm = jm;
- }
- else if( i < jm )
- {
- miniim = im;
- maxiim = i;
- minijm = i;
- maxijm = jm;
- }
- else
- {
- miniim = im;
- maxiim = i;
- minijm = jm;
- maxijm = i;
- }
- eff0 = eff[miniim][maxiim];
- eff1 = eff[minijm][maxijm];
- eff[miniim][maxiim] =
- MIN( eff0, eff1 ) * ( 1.0 - SUEFF ) +
- ( eff0 + eff1 ) * 0.5 * SUEFF;
- }
- }
- acjmprev = ac[jm].prev;
- acjmnext = ac[jm].next;
- ac[acjmprev].next = acjmnext;
- if( acjmnext != -1 )
- ac[acjmnext].prev = acjmprev;
-#if 0
- fprintf( stdout, "STEP-%03d:\n", k+1 );
- fprintf( stdout, "len0 = %f\n", len[k][0] );
- for( i=0; topol[k][0][i]>-1; i++ ) fprintf( stdout, " %03d", topol[k][0][i] );
- fprintf( stdout, "\n" );
- fprintf( stdout, "len1 = %f\n", len[k][1] );
- for( i=0; topol[k][1][i]>-1; i++ ) fprintf( stdout, " %03d", topol[k][1][i] );
- fprintf( stdout, "\n" );
-#endif
- }
-#if 1
- fprintf( stderr, "\n" );
- free( (void *)tmptmplen ); tmptmplen = NULL;
- free( hist ); hist = NULL;
- free( (char *)ac ); ac = NULL;
-#endif
-}
-#endif
-
-void veryfastsupg_double_outtree( int nseq, double **eff, int ***topol, double **len, char **name )
-{
- int i, j, k, miniim, maxiim, minijm, maxijm;
- int *intpt, *intpt2;
- double tmpdouble;
- double eff1, eff0;
- static double *tmptmplen = NULL;
- static int *hist = NULL;
- static Achain *ac = NULL;
- double minscore;
- static char **tree;
- static char *treetmp;
- static char *nametmp;
- FILE *fpout;
- int im = -1, jm = -1;
- int prevnode, acjmnext, acjmprev;
- int *pt1, *pt2, *pt11, *pt22;
- double (*clusterfuncpt[1])(double,double);
-
-
- sueff1_double = 1 - SUEFF;
- sueff05_double = SUEFF * 0.5;
- if ( treemethod == 'X' )
- clusterfuncpt[0] = cluster_mix_double;
- else if ( treemethod == 'E' )
- clusterfuncpt[0] = cluster_average_double;
- else if ( treemethod == 'q' )
- clusterfuncpt[0] = cluster_minimum_double;
- else
- {
- fprintf( stderr, "Unknown treemethod, %c\n", treemethod );
- exit( 1 );
- }
-
- if( !hist )
- {
- treetmp = AllocateCharVec( njob*50 );
- tree = AllocateCharMtx( njob, njob*50 );
- hist = AllocateIntVec( njob );
- tmptmplen = (double *)malloc( njob * sizeof( double ) );
- ac = (Achain *)malloc( njob * sizeof( Achain ) );
- nametmp = AllocateCharVec( 31 );
- }
-
-// for( i=0; i<nseq; i++ ) sprintf( tree[i], "%d", i+1 );
- for( i=0; i<nseq; i++ )
- {
- for( j=0; j<30; j++ ) nametmp[j] = 0;
- for( j=0; j<30; j++ )
- {
- if( isalnum( name[i][j] ) )
- nametmp[j] = name[i][j];
- else
- nametmp[j] = '_';
- }
- nametmp[30] = 0;
- sprintf( tree[i], "%d_%.20s", i+1, nametmp+1 );
- }
-
- for( i=0; i<nseq; i++ )
- {
- ac[i].next = i+1;
- ac[i].prev = i-1;
-// ac[i].curr = i;
- }
- ac[nseq-1].next = -1;
-
- for( i=0; i<nseq; i++ ) tmptmplen[i] = 0.0;
- for( i=0; i<nseq; i++ ) hist[i] = -1;
-
- fprintf( stderr, "\n" );
- for( k=0; k<nseq-1; k++ )
- {
- if( k % 10 == 0 ) fprintf( stderr, "%d / %d\r", k, nseq );
-
- minscore = 99999.9;
- for( i=0; ac[i].next!=-1; i=ac[i].next )
- {
- for( j=ac[i].next; j!=-1; j=ac[j].next )
- {
- tmpdouble = eff[i][j];
- if( tmpdouble < minscore )
- {
- minscore = tmpdouble;
- im = i; jm = j;
- }
- }
- }
-
-// fprintf( stderr, "im=%d, jm=%d\n", im, jm );
-
- intpt = topol[k][0];
- prevnode = hist[im];
- if( prevnode == -1 )
- {
- *intpt++ = im;
- *intpt = -1;
- }
- else
- {
- pt1 = topol[prevnode][0];
- pt2 = topol[prevnode][1];
- if( *pt1 > *pt2 )
- {
- pt11 = pt2;
- pt22 = pt1;
- }
- else
- {
- pt11 = pt1;
- pt22 = pt2;
- }
- for( intpt2=pt11; *intpt2!=-1; )
- *intpt++ = *intpt2++;
- for( intpt2=pt22; *intpt2!=-1; )
- *intpt++ = *intpt2++;
- *intpt = -1;
- }
-
- intpt = topol[k][1];
- prevnode = hist[jm];
- if( prevnode == -1 )
- {
- *intpt++ = jm;
- *intpt = -1;
- }
- else
- {
- pt1 = topol[prevnode][0];
- pt2 = topol[prevnode][1];
- if( *pt1 > *pt2 )
- {
- pt11 = pt2;
- pt22 = pt1;
- }
- else
- {
- pt11 = pt1;
- pt22 = pt2;
- }
- for( intpt2=pt11; *intpt2!=-1; )
- *intpt++ = *intpt2++;
- for( intpt2=pt22; *intpt2!=-1; )
- *intpt++ = *intpt2++;
- *intpt = -1;
- }
-
- minscore *= 0.5;
-
- len[k][0] = minscore - tmptmplen[im];
- len[k][1] = minscore - tmptmplen[jm];
-
- tmptmplen[im] = minscore;
-
- hist[im] = k;
-
- for( i=0; i!=-1; i=ac[i].next )
- {
- if( i != im && i != jm )
- {
- if( i < im )
- {
- miniim = i;
- maxiim = im;
- minijm = i;
- maxijm = jm;
- }
- else if( i < jm )
- {
- miniim = im;
- maxiim = i;
- minijm = i;
- maxijm = jm;
- }
- else
- {
- miniim = im;
- maxiim = i;
- minijm = jm;
- maxijm = i;
- }
- eff0 = eff[miniim][maxiim];
- eff1 = eff[minijm][maxijm];
-#if 0
- eff[miniim][maxiim] =
- MIN( eff0, eff1 ) * ( 1.0 - SUEFF ) +
- ( eff0 + eff1 ) * 0.5 * SUEFF;
-#else
- eff[miniim][maxiim] =
- (clusterfuncpt[0])( eff0, eff1 );
-#endif
- }
- }
- acjmprev = ac[jm].prev;
- acjmnext = ac[jm].next;
- ac[acjmprev].next = acjmnext;
- if( acjmnext != -1 )
- ac[acjmnext].prev = acjmprev;
-
- sprintf( treetmp, "(%s:%7.5f,%s:%7.5f)", tree[im], len[k][0], tree[jm], len[k][1] );
- strcpy( tree[im], treetmp );
-#if 0
- fprintf( stdout, "STEP-%03d:\n", k+1 );
- fprintf( stdout, "len0 = %f\n", len[k][0] );
- for( i=0; topol[k][0][i]>-1; i++ ) fprintf( stdout, " %03d", topol[k][0][i] );
- fprintf( stdout, "\n" );
- fprintf( stdout, "len1 = %f\n", len[k][1] );
- for( i=0; topol[k][1][i]>-1; i++ ) fprintf( stdout, " %03d", topol[k][1][i] );
- fprintf( stdout, "\n" );
-#endif
- }
- fpout = fopen( "infile.tree", "w" );
- fprintf( fpout, "%s\n", treetmp );
-// fprintf( fpout, "by veryfastsupg_double_outtree\n" );
- fclose( fpout );
-#if 1
- fprintf( stderr, "\n" );
- free( (void *)tmptmplen ); tmptmplen = NULL;
- free( hist ); hist = NULL;
- free( (char *)ac ); ac = NULL;
- FreeCharMtx( tree );
- free( treetmp );
- free( nametmp );
-#endif
-}
-
-void veryfastsupg( int nseq, double **oeff, int ***topol, double **len )
-{
- int i, j, k, miniim, maxiim, minijm, maxijm;
- int *intpt, *intpt2;
- int tmpint;
- int eff1, eff0;
- static double *tmptmplen = NULL;
- static int **eff = NULL;
- static int *hist = NULL;
- static Achain *ac = NULL;
- int minscore;
- double minscoref;
- int im = -1, jm = -1;
- int prevnode, acjmnext, acjmprev;
- int *pt1, *pt2, *pt11, *pt22;
- if( !eff )
- {
- eff = AllocateIntMtx( njob, njob );
- hist = AllocateIntVec( njob );
- tmptmplen = (double *)malloc( njob * sizeof( double ) );
- ac = (Achain *)malloc( njob * sizeof( Achain ) );
- }
-
- for( i=0; i<nseq; i++ )
- {
- for( j=0; j<nseq; j++ )
- {
- eff[i][j] = (int)( oeff[i][j] * INTMTXSCALE + 0.5 );
- }
- }
-
- for( i=0; i<nseq; i++ )
- {
- ac[i].next = i+1;
- ac[i].prev = i-1;
-// ac[i].curr = i;
- }
- ac[nseq-1].next = -1;
-
- for( i=0; i<nseq; i++ ) tmptmplen[i] = 0.0;
- for( i=0; i<nseq; i++ ) hist[i] = -1;
-
- fprintf( stderr, "\n" );
- for( k=0; k<nseq-1; k++ )
- {
- if( k % 10 == 0 ) fprintf( stderr, "%d / %d\r", k, nseq );
-
- minscore = INTMTXSCALE*4;
- for( i=0; ac[i].next!=-1; i=ac[i].next )
- {
- for( j=ac[i].next; j!=-1; j=ac[j].next )
- {
- tmpint = eff[i][j];
- if( tmpint < minscore )
- {
- minscore = tmpint;
- im = i; jm = j;
- }
- }
- }
- minscoref = (double)minscore * 0.5 / ( INTMTXSCALE );
-
-// fprintf( stderr, "im=%d, jm=%d\n", im, jm );
-
-#if 1
- intpt = topol[k][0];
- prevnode = hist[im];
- if( prevnode == -1 )
- {
- *intpt++ = im;
- *intpt = -1;
- }
- else
- {
- pt1 = topol[prevnode][0];
- pt2 = topol[prevnode][1];
- if( *pt1 > *pt2 )
- {
- pt11 = pt2;
- pt22 = pt1;
- }
- else
- {
- pt11 = pt1;
- pt22 = pt2;
- }
- for( intpt2=pt11; *intpt2!=-1; )
- *intpt++ = *intpt2++;
- for( intpt2=pt22; *intpt2!=-1; )
- *intpt++ = *intpt2++;
- *intpt = -1;
- }
-
- intpt = topol[k][1];
- prevnode = hist[jm];
- if( prevnode == -1 )
- {
- *intpt++ = jm;
- *intpt = -1;
- }
- else
- {
- pt1 = topol[prevnode][0];
- pt2 = topol[prevnode][1];
- if( *pt1 > *pt2 )
- {
- pt11 = pt2;
- pt22 = pt1;
- }
- else
- {
- pt11 = pt1;
- pt22 = pt2;
- }
- for( intpt2=pt11; *intpt2!=-1; )
- *intpt++ = *intpt2++;
- for( intpt2=pt22; *intpt2!=-1; )
- *intpt++ = *intpt2++;
- *intpt = -1;
- }
-#else
- intpt = topol[k][0];
- for( i=0; i<nseq; i++ )
- if( pair[im][i] > -2 )
- *intpt++ = i;
- *intpt = -1;
-
- intpt = topol[k][1];
- for( i=0; i<nseq; i++ )
- if( pair[jm][i] > -2 )
- *intpt++ = i;
- *intpt = -1;
-#endif
-
- len[k][0] = minscoref - tmptmplen[im];
- len[k][1] = minscoref - tmptmplen[jm];
-
- tmptmplen[im] = minscoref;
-
- hist[im] = k;
-
- for( i=0; i!=-1; i=ac[i].next )
- {
- if( i != im && i != jm )
- {
- if( i < im )
- {
- miniim = i;
- maxiim = im;
- minijm = i;
- maxijm = jm;
- }
- else if( i < jm )
- {
- miniim = im;
- maxiim = i;
- minijm = i;
- maxijm = jm;
- }
- else
- {
- miniim = im;
- maxiim = i;
- minijm = jm;
- maxijm = i;
- }
- eff0 = eff[miniim][maxiim];
- eff1 = eff[minijm][maxijm];
- eff[miniim][maxiim] =
- MIN( eff0, eff1 ) * ( 1.0 - SUEFF ) +
- ( eff0 + eff1 ) * 0.5 * SUEFF;
- }
- }
- acjmprev = ac[jm].prev;
- acjmnext = ac[jm].next;
- ac[acjmprev].next = acjmnext;
- if( acjmnext != -1 )
- ac[acjmnext].prev = acjmprev;
-#if 0
- fprintf( stdout, "STEP-%03d:\n", k+1 );
- fprintf( stdout, "len0 = %f\n", len[k][0] );
- for( i=0; topol[k][0][i]>-1; i++ ) fprintf( stdout, " %03d", topol[k][0][i] );
- fprintf( stdout, "\n" );
- fprintf( stdout, "len1 = %f\n", len[k][1] );
- for( i=0; topol[k][1][i]>-1; i++ ) fprintf( stdout, " %03d", topol[k][1][i] );
- fprintf( stdout, "\n" );
-#endif
- }
-#if 1
- FreeIntMtx( eff ); eff = NULL;
- free( (void *)tmptmplen ); tmptmplen = NULL;
- free( hist ); hist = NULL;
- free( (char *)ac ); ac = NULL;
-#endif
-}
-void veryfastsupg_int( int nseq, int **oeff, int ***topol, double **len )
-/* len\e$B$O!"\e(B oeff\e$B$,@0?t!#\e(Blen\e$B$b<B$O@0?t!#\e(B
- \e$BI,MW$K1~$8$F3d$C$F;H$&!#\e(B */
-{
- int i, j, k, miniim, maxiim, minijm, maxijm;
- int *intpt, *intpt2;
- int tmpint;
- int eff1, eff0;
- static int *tmptmplen = NULL;
- static int **eff = NULL;
- static int *hist = NULL;
- static Achain *ac = NULL;
- int minscore;
- int im = -1, jm = -1;
- int prevnode, acjmnext, acjmprev;
- int *pt1, *pt2, *pt11, *pt22;
-
-
- if( !eff )
- {
- eff = AllocateIntMtx( njob, njob );
- hist = AllocateIntVec( njob );
- tmptmplen = AllocateIntVec( njob );
- ac = (Achain *)malloc( njob * sizeof( Achain ) );
- }
-
- for( i=0; i<nseq; i++ )
- {
- for( j=0; j<nseq; j++ )
- {
- eff[i][j] = ( oeff[i][j] );
- }
- }
-
- for( i=0; i<nseq; i++ )
- {
- ac[i].next = i+1;
- ac[i].prev = i-1;
-// ac[i].curr = i;
- }
- ac[nseq-1].next = -1;
-
- for( i=0; i<nseq; i++ ) tmptmplen[i] = 0;
- for( i=0; i<nseq; i++ ) hist[i] = -1;
-
- fprintf( stderr, "\n" );
- for( k=0; k<nseq-1; k++ )
- {
- if( k % 10 == 0 ) fprintf( stderr, "%d / %d\r", k, nseq );
-
- minscore = INTMTXSCALE*4;
- for( i=0; ac[i].next!=-1; i=ac[i].next )
- {
- for( j=ac[i].next; j!=-1; j=ac[j].next )
- {
- tmpint = eff[i][j];
- if( tmpint < minscore )
- {
- minscore = tmpint;
- im = i; jm = j;
- }
- }
- }
-
-// fprintf( stderr, "im=%d, jm=%d\n", im, jm );
-
- intpt = topol[k][0];
- prevnode = hist[im];
- if( prevnode == -1 )
- {
- *intpt++ = im;
- *intpt = -1;
- }
- else
- {
- pt1 = topol[prevnode][0];
- pt2 = topol[prevnode][1];
- if( *pt1 > *pt2 )
- {
- pt11 = pt2;
- pt22 = pt1;
- }
- else
- {
- pt11 = pt1;
- pt22 = pt2;
- }
- for( intpt2=pt11; *intpt2!=-1; )
- *intpt++ = *intpt2++;
- for( intpt2=pt22; *intpt2!=-1; )
- *intpt++ = *intpt2++;
- *intpt = -1;
- }
-
- intpt = topol[k][1];
- prevnode = hist[jm];
- if( prevnode == -1 )
- {
- *intpt++ = jm;
- *intpt = -1;
- }
- else
- {
- pt1 = topol[prevnode][0];
- pt2 = topol[prevnode][1];
- if( *pt1 > *pt2 )
- {
- pt11 = pt2;
- pt22 = pt1;
- }
- else
- {
- pt11 = pt1;
- pt22 = pt2;
- }
- for( intpt2=pt11; *intpt2!=-1; )
- *intpt++ = *intpt2++;
- for( intpt2=pt22; *intpt2!=-1; )
- *intpt++ = *intpt2++;
- *intpt = -1;
- }
-
- minscore *= 0.5;
-
- len[k][0] = (double)( minscore - tmptmplen[im] );
- len[k][1] = (double)( minscore - tmptmplen[jm] );
-
- tmptmplen[im] = minscore;
-
-#if 0
- free( tmptmplen );
- tmptmplen = AllocateIntVec( nseq );
-#endif
-
-
- hist[im] = k;
-
- for( i=0; i!=-1; i=ac[i].next )
- {
- if( i != im && i != jm )
- {
- if( i < im )
- {
- miniim = i;
- maxiim = im;
- minijm = i;
- maxijm = jm;
- }
- else if( i < jm )
- {
- miniim = im;
- maxiim = i;
- minijm = i;
- maxijm = jm;
- }
- else
- {
- miniim = im;
- maxiim = i;
- minijm = jm;
- maxijm = i;
- }
- eff0 = eff[miniim][maxiim];
- eff1 = eff[minijm][maxijm];
- eff[miniim][maxiim] =
- (int) ( (float)MIN( eff0, eff1 ) * ( 1.0 - SUEFF ) + (float)( eff0 + eff1 ) * 0.5 * SUEFF );
- }
- }
- acjmprev = ac[jm].prev;
- acjmnext = ac[jm].next;
- ac[acjmprev].next = acjmnext;
- if( acjmnext != -1 )
- ac[acjmnext].prev = acjmprev;
-#if 0
- fprintf( stdout, "STEP-%03d:\n", k+1 );
- fprintf( stdout, "len0 = %f\n", len[k][0] );
- for( i=0; topol[k][0][i]>-1; i++ ) fprintf( stdout, " %03d", topol[k][0][i] );
- fprintf( stdout, "\n" );
- fprintf( stdout, "len1 = %f\n", len[k][1] );
- for( i=0; topol[k][1][i]>-1; i++ ) fprintf( stdout, " %03d", topol[k][1][i] );
- fprintf( stdout, "\n" );
-#endif
- }
- FreeIntMtx( eff ); eff = NULL;
- free( (void *)tmptmplen ); tmptmplen = NULL;
- free( hist ); hist = NULL;
- free( (char *)ac ); ac = NULL;
-}
-void fastsupg( int nseq, double **oeff, int ***topol, double **len )
-{
- int i, j, k, miniim, maxiim, minijm, maxijm;
-#if 0
- double eff[nseq][nseq];
- char pair[njob][njob];
-#else
- static float *tmplen;
- int *intpt;
- float tmpfloat;
- float eff1, eff0;
- static float **eff = NULL;
- static char **pair = NULL;
- static Achain *ac;
- float minscore;
- int im = -1, jm = -1;
- if( !eff )
- {
- eff = AllocateFloatMtx( njob, njob );
- pair = AllocateCharMtx( njob, njob );
- tmplen = AllocateFloatVec( njob );
- ac = (Achain *)calloc( njob, sizeof( Achain ) );
- }
-#endif
-
- for( i=0; i<nseq; i++ )
- {
- for( j=0; j<nseq; j++ )
- {
- eff[i][j] = (float)oeff[i][j];
- }
- }
-
- for( i=0; i<nseq; i++ )
- {
- ac[i].next = i+1;
- ac[i].prev = i-1;
-// ac[i].curr = i;
- }
- ac[nseq-1].next = -1;
-
- for( i=0; i<nseq; i++ ) tmplen[i] = 0.0;
- for( i=0; i<nseq; i++ ) for( j=0; j<nseq; j++ ) pair[i][j] = 0;
- for( i=0; i<nseq; i++ ) pair[i][i] = 1;
-
- fprintf( stderr, "\n" );
- for( k=0; k<nseq-1; k++ )
- {
- if( k % 10 == 0 ) fprintf( stderr, "%d / %d\r", k, nseq );
-
- minscore = 9999.0;
- for( i=0; ac[i].next!=-1; i=ac[i].next )
-// for( i=0; i<nseq-1; i++ )
- {
- for( j=ac[i].next; j!=-1; j=ac[j].next )
-// for( j=i+1; j<nseq; j++ )
- {
- tmpfloat = eff[i][j];
- if( tmpfloat < minscore )
- {
- minscore = tmpfloat;
- im = i; jm = j;
- }
- }
- }
-
-// fprintf( stderr, "im=%d, jm=%d\n", im, jm );
-
- intpt = topol[k][0];
- for( i=0; i<nseq; i++ )
- if( pair[im][i] > 0 )
- *intpt++ = i;
- *intpt = -1;
-
- intpt = topol[k][1];
- for( i=0; i<nseq; i++ )
- if( pair[jm][i] > 0 )
- *intpt++ = i;
- *intpt = -1;
-
- minscore /= 2.0;
-
- len[k][0] = (double)minscore - tmplen[im];
- len[k][1] = (double)minscore - tmplen[jm];
-
- tmplen[im] = (double)minscore;
-
- for( i=0; i<nseq; i++ ) pair[im][i] += ( pair[jm][i] > 0 );
- for( i=0; i<nseq; i++ ) pair[jm][i] = 0;
-
-// for( i=0; i<nseq; i++ )
- for( i=0; i!=-1; i=ac[i].next )
- {
- if( i != im && i != jm )
- {
- if( i < im )
- {
- miniim = i;
- maxiim = im;
- minijm = i;
- maxijm = jm;
- }
- else if( i < jm )
- {
- miniim = im;
- maxiim = i;
- minijm = i;
- maxijm = jm;
- }
- else
- {
- miniim = im;
- maxiim = i;
- minijm = jm;
- maxijm = i;
- }
- eff0 = eff[miniim][maxiim];
- eff1 = eff[minijm][maxijm];
- eff[miniim][maxiim] =
- MIN( eff0, eff1 ) * ( 1.0 - SUEFF ) +
- ( eff0 + eff1 ) * 0.5 * SUEFF;
-// eff[minijm][maxijm] = 9999.0;
- }
- }
- ac[ac[jm].prev].next = ac[jm].next;
- ac[ac[jm].next].prev = ac[jm].prev;
-// eff[im][jm] = 9999.0;
-#if 0
- fprintf( stderr, "STEP-%03d:\n", k+1 );
- fprintf( stderr, "len0 = %f\n", len[k][0] );
- for( i=0; topol[k][0][i]>-1; i++ ) fprintf( stderr, " %03d", topol[k][0][i] );
- fprintf( stderr, "\n" );
- fprintf( stderr, "len1 = %f\n", len[k][1] );
- for( i=0; topol[k][1][i]>-1; i++ ) fprintf( stderr, " %03d", topol[k][1][i] );
- fprintf( stderr, "\n" );
-#endif
- }
- fprintf( stderr, "\n" );
-
-// FreeFloatMtx( eff );
-// FreeCharMtx( pair );
-// FreeFloatVec( tmplen );
-// free( ac );
-}
-void supg( int nseq, double **oeff, int ***topol, double **len )
-{
- int i, j, k, miniim, maxiim, minijm, maxijm;
-#if 0
- double eff[nseq][nseq];
- char pair[njob][njob];
-#else
- static float *tmplen;
- int *intpt;
- float **floatptpt;
- float *floatpt;
- float tmpfloat;
- float eff1, eff0;
- static float **eff = NULL;
- static char **pair = NULL;
- if( !eff )
- {
- eff = AllocateFloatMtx( njob, njob );
- pair = AllocateCharMtx( njob, njob );
- tmplen = AllocateFloatVec( njob );
- }
-#endif
-
-
- for( i=0; i<nseq; i++ )
- {
- for( j=0; j<nseq; j++ )
- {
- eff[i][j] = (float)oeff[i][j];
- }
- }
- for( i=0; i<nseq; i++ ) tmplen[i] = 0.0;
- for( i=0; i<nseq; i++ ) for( j=0; j<nseq; j++ ) pair[i][j] = 0;
- for( i=0; i<nseq; i++ ) pair[i][i] = 1;
-
- for( k=0; k<nseq-1; k++ )
- {
- float minscore = 9999.0;
- int im = -1, jm = -1;
-
-
- floatptpt = eff;
- for( i=0; i<nseq-1; i++ )
- {
- floatpt = *floatptpt++ + i + 1;
- for( j=i+1; j<nseq; j++ )
- {
- tmpfloat = *floatpt++;
- if( tmpfloat < minscore )
- {
- minscore = tmpfloat;
- im = i; jm = j;
- }
- }
- }
- intpt = topol[k][0];
- for( i=0; i<nseq; i++ )
- if( pair[im][i] > 0 )
- *intpt++ = i;
- *intpt = -1;
-
- intpt = topol[k][1];
- for( i=0; i<nseq; i++ )
- if( pair[jm][i] > 0 )
- *intpt++ = i;
- *intpt = -1;
-
- len[k][0] = (double)minscore / 2.0 - tmplen[im];
- len[k][1] = (double)minscore / 2.0 - tmplen[jm];
-
- tmplen[im] = (double)minscore / 2.0;
-
- for( i=0; i<nseq; i++ ) pair[im][i] += ( pair[jm][i] > 0 );
- for( i=0; i<nseq; i++ ) pair[jm][i] = 0;
-
- for( i=0; i<nseq; i++ )
- {
- if( i != im && i != jm )
- {
-#if 1
- if( i < im )
- {
- miniim = i;
- maxiim = im;
- minijm = i;
- maxijm = jm;
- }
- else if( i < jm )
- {
- miniim = im;
- maxiim = i;
- minijm = i;
- maxijm = jm;
- }
- else
- {
- miniim = im;
- maxiim = i;
- minijm = jm;
- maxijm = i;
- }
-#else
- miniim = MIN( i, im );
- maxiim = MAX( i, im );
- minijm = MIN( i, jm );
- maxijm = MAX( i, jm );
-#endif
-#if 1
- eff0 = eff[miniim][maxiim];
- eff1 = eff[minijm][maxijm];
- eff[miniim][maxiim] =
- MIN( eff0, eff1 ) * ( 1.0 - SUEFF ) +
- ( eff0 + eff1 ) * 0.5 * SUEFF;
-#else
- MIN( eff[miniim][maxiim], eff[minijm][maxijm] ) * ( 1.0 - SUEFF ) +
- ( eff[miniim][maxiim] + eff[minijm][maxijm] ) * 0.5 * SUEFF;
-#endif
- eff[minijm][maxijm] = 9999.0;
- eff[im][jm] = 9999.0;
- }
- }
-#if DEBUG
- printf( "STEP-%03d:\n", k+1 );
- printf( "len0 = %f\n", len[k][0] );
- for( i=0; topol[k][0][i]>-1; i++ ) printf( " %03d", topol[k][0][i] );
- printf( "\n" );
- printf( "len1 = %f\n", len[k][1] );
- for( i=0; topol[k][1][i]>-1; i++ ) printf( " %03d", topol[k][1][i] );
- printf( "\n" );
-#endif
- }
-}
-
-void spg( int nseq, double **oeff, int ***topol, double **len )
-{
- int i, j, k;
- double tmplen[M];
-#if 0
- double eff[nseq][nseq];
- char pair[njob][njob];
-#else
- double **eff = NULL;
- char **pair = NULL;
- if( !eff )
- {
- eff = AllocateDoubleMtx( njob, njob );
- pair = AllocateCharMtx( njob, njob );
- }
-#endif
-
- for( i=0; i<nseq; i++ ) for( j=0; j<nseq; j++ ) eff[i][j] = oeff[i][j];
- for( i=0; i<nseq; i++ ) tmplen[i] = 0.0;
- for( i=0; i<nseq; i++ ) for( j=0; j<nseq; j++ ) pair[i][j] = 0;
- for( i=0; i<nseq; i++ ) pair[i][i] = 1;
-
- for( k=0; k<nseq-1; k++ )
- {
- float minscore = 9999.0;
- int im = -1, jm = -1;
- int count;
-
- for( i=0; i<nseq-1; i++ ) for( j=i+1; j<nseq; j++ )
- {
- if( eff[i][j] < minscore )
- {
- minscore = eff[i][j];
- im = i; jm = j;
- }
- }
- for( i=0, count=0; i<nseq; i++ )
- if( pair[im][i] > 0 )
- {
- topol[k][0][count] = i;
- count++;
- }
- topol[k][0][count] = -1;
- for( i=0, count=0; i<nseq; i++ )
- if( pair[jm][i] > 0 )
- {
- topol[k][1][count] = i;
- count++;
- }
- topol[k][1][count] = -1;
-
- len[k][0] = minscore / 2.0 - tmplen[im];
- len[k][1] = minscore / 2.0 - tmplen[jm];
-
- tmplen[im] = minscore / 2.0;
-
- for( i=0; i<nseq; i++ ) pair[im][i] += ( pair[jm][i] > 0 );
- for( i=0; i<nseq; i++ ) pair[jm][i] = 0;
-
- for( i=0; i<nseq; i++ )
- {
- if( i != im && i != jm )
- {
- eff[MIN(i,im)][MAX(i,im)] =
- MIN( eff[MIN(i,im)][MAX(i,im)], eff[MIN(i,jm)][MAX(i,jm)] );
- eff[MIN(i,jm)][MAX(i,jm)] = 9999.0;
- }
- eff[im][jm] = 9999.0;
- }
-#if DEBUG
- printf( "STEP-%03d:\n", k+1 );
- printf( "len0 = %f\n", len[k][0] );
- for( i=0; topol[k][0][i]>-1; i++ ) printf( " %03d", topol[k][0][i] );
- printf( "\n" );
- printf( "len1 = %f\n", len[k][1] );
- for( i=0; topol[k][1][i]>-1; i++ ) printf( " %03d", topol[k][1][i] );
- printf( "\n" );
-#endif
- }
-}
-
-double ipower( double x, int n ) /* n > 0 */
-{
- double r;
-
- r = 1;
- while( n != 0 )
- {
- if( n & 1 ) r *= x;
- x *= x; n >>= 1;
- }
- return( r );
-}
-
-void countnode( int nseq, int ***topol, double **node ) /* node[j][i] != node[i][j] */
-{
- int i, j, k, s1, s2;
- static double rootnode[M];
-
- if( nseq-2 < 0 )
- {
- fprintf( stderr, "Too few sequence for countnode: nseq = %d\n", nseq );
- exit( 1 );
- }
-
- for( i=0; i<nseq; i++ ) rootnode[i] = 0;
- for( i=0; i<nseq-2; i++ )
- {
- for( j=0; topol[i][0][j]>-1; j++ )
- rootnode[topol[i][0][j]]++;
- for( j=0; topol[i][1][j]>-1; j++ )
- rootnode[topol[i][1][j]]++;
- for( j=0; topol[i][0][j]>-1; j++ )
- {
- s1 = topol[i][0][j];
- for( k=0; topol[i][1][k]>-1; k++ )
- {
- s2 = topol[i][1][k];
- node[MIN(s1,s2)][MAX(s1,s2)] = rootnode[s1] + rootnode[s2] - 1;
- }
- }
- }
- for( j=0; topol[nseq-2][0][j]>-1; j++ )
- {
- s1 = topol[nseq-2][0][j];
- for( k=0; topol[nseq-2][1][k]>-1; k++ )
- {
- s2 = topol[nseq-2][1][k];
- node[MIN(s1,s2)][MAX(s1,s2)] = rootnode[s1] + rootnode[s2];
- }
- }
-}
-
-void countnode_int( int nseq, int ***topol, int **node ) /* node[i][j] == node[j][i] */
-{
- int i, j, k, s1, s2;
- int rootnode[M];
-
- for( i=0; i<nseq; i++ ) rootnode[i] = 0;
- for( i=0; i<nseq-2; i++ )
- {
- for( j=0; topol[i][0][j]>-1; j++ )
- rootnode[topol[i][0][j]]++;
- for( j=0; topol[i][1][j]>-1; j++ )
- rootnode[topol[i][1][j]]++;
- for( j=0; topol[i][0][j]>-1; j++ )
- {
- s1 = topol[i][0][j];
- for( k=0; topol[i][1][k]>-1; k++ )
- {
- s2 = topol[i][1][k];
- node[MIN(s1,s2)][MAX(s1,s2)] = rootnode[s1] + rootnode[s2] - 1;
- }
- }
- }
- for( j=0; topol[nseq-2][0][j]>-1; j++ )
- {
- s1 = topol[nseq-2][0][j];
- for( k=0; topol[nseq-2][1][k]>-1; k++ )
- {
- s2 = topol[nseq-2][1][k];
- node[MIN(s1,s2)][MAX(s1,s2)] = rootnode[s1] + rootnode[s2];
- }
- }
- for( i=0; i<nseq-1; i++ ) for( j=i+1; j<nseq; j++ )
- node[j][i] = node[i][j];
-#if DEBUG
- fprintf( stderr, "node[][] in countnode_int" );
- for( i=0; i<nseq; i++ )
- {
- for( j=0; j<nseq; j++ )
- {
- fprintf( stderr, "%#3d", node[i][j] );
- }
- fprintf( stderr, "\n" );
- }
-#endif
-}
-
-void counteff_simple_float( int nseq, int ***topol, float **len, double *node )
-{
- int i, j, s1, s2;
- double total;
- static double rootnode[M];
- static double eff[M];
-
-#if DEBUG
- for( i=0; i<nseq; i++ ){
- fprintf( stderr, "len0 = %f\n", len[i][0] );
- fprintf( stderr, "len1 = %f\n", len[i][1] );
- }
-#endif
- for( i=0; i<nseq; i++ )
- {
- rootnode[i] = 0.0;
- eff[i] = 1.0;
-/*
- rootnode[i] = 1.0;
-*/
- }
- for( i=0; i<nseq-1; i++ )
- {
- for( j=0; (s1=topol[i][0][j]) > -1; j++ )
- {
- rootnode[s1] += (double)len[i][0] * eff[s1];
- eff[s1] *= 0.5;
-/*
- rootnode[s1] *= 0.5;
-*/
-
- }
- for( j=0; (s2=topol[i][1][j]) > -1; j++ )
- {
- rootnode[s2] += (double)len[i][1] * eff[s2];
- eff[s2] *= 0.5;
-/*
- rootnode[s2] *= 0.5;
-*/
-
- }
- }
- for( i=0; i<nseq; i++ )
- {
-#if 1 /* 97.9.29 */
- rootnode[i] += GETA3;
-#endif
-#if 0
- fprintf( stderr, "### rootnode for %d = %f\n", i, rootnode[i] );
-#endif
- }
-#if 1
- total = 0.0;
- for( i=0; i<nseq; i++ )
- {
- total += rootnode[i];
- }
-#else
- total = 1.0;
-#endif
-
- for( i=0; i<nseq; i++ )
- {
- node[i] = rootnode[i] / total;
- }
-
-#if 0
- fprintf( stderr, "weight array in counteff_simple\n" );
- for( i=0; i<nseq; i++ )
- fprintf( stderr, "%f\n", node[i] );
- printf( "\n" );
- exit( 1 );
-#endif
-}
-
-void counteff_simple( int nseq, int ***topol, double **len, double *node )
-{
- int i, j, s1, s2;
- double total;
- static double rootnode[M];
- static double eff[M];
-
-#if DEBUG
- for( i=0; i<nseq; i++ ){
- fprintf( stderr, "len0 = %f\n", len[i][0] );
- fprintf( stderr, "len1 = %f\n", len[i][1] );
- }
-#endif
- for( i=0; i<nseq; i++ )
- {
- rootnode[i] = 0.0;
- eff[i] = 1.0;
-/*
- rootnode[i] = 1.0;
-*/
- }
- for( i=0; i<nseq-1; i++ )
- {
- for( j=0; (s1=topol[i][0][j]) > -1; j++ )
- {
- rootnode[s1] += len[i][0] * eff[s1];
- eff[s1] *= 0.5;
-/*
- rootnode[s1] *= 0.5;
-*/
-
- }
- for( j=0; (s2=topol[i][1][j]) > -1; j++ )
- {
- rootnode[s2] += len[i][1] * eff[s2];
- eff[s2] *= 0.5;
-/*
- rootnode[s2] *= 0.5;
-*/
-
- }
- }
- for( i=0; i<nseq; i++ )
- {
-#if 1 /* 97.9.29 */
- rootnode[i] += GETA3;
-#endif
-#if 0
- fprintf( stderr, "### rootnode for %d = %f\n", i, rootnode[i] );
-#endif
- }
-#if 1
- total = 0.0;
- for( i=0; i<nseq; i++ )
- {
- total += rootnode[i];
- }
-#else
- total = 1.0;
-#endif
-
- for( i=0; i<nseq; i++ )
- {
- node[i] = rootnode[i] / total;
- }
-
-#if 0
- fprintf( stderr, "weight array in counteff_simple\n" );
- for( i=0; i<nseq; i++ )
- fprintf( stderr, "%f\n", node[i] );
- printf( "\n" );
- exit( 1 );
-#endif
-}
-
-
-void counteff( int nseq, int ***topol, double **len, double **node )
-{
- int i, j, k, s1, s2;
- double rootnode[M];
- double eff[M];
-
- if( mix )
- {
- switch( weight )
- {
- case( 2 ):
- weight = 3;
- break;
- case( 3 ):
- weight = 2;
- break;
- default:
- ErrorExit( "mix error" );
- break;
- }
- }
-
- if( weight == 2 )
- {
- for( i=0; i<nseq; i++ ) rootnode[i] = 0;
- for( i=0; i<nseq-2; i++ )
- {
- for( j=0; topol[i][0][j]>-1; j++ )
- rootnode[topol[i][0][j]]++;
- for( j=0; topol[i][1][j]>-1; j++ )
- rootnode[topol[i][1][j]]++;
- for( j=0; topol[i][0][j]>-1; j++ )
- {
- s1 = topol[i][0][j];
- for( k=0; topol[i][1][k]>-1; k++ )
- {
- s2 = topol[i][1][k];
- node[MIN(s1,s2)][MAX(s1,s2)] = rootnode[s1] + rootnode[s2] - 1;
- }
- }
- }
- for( j=0; topol[nseq-2][0][j]>-1; j++ )
- {
- s1 = topol[nseq-2][0][j];
- for( k=0; topol[nseq-2][1][k]>-1; k++ )
- {
- s2 = topol[nseq-2][1][k];
- node[MIN(s1,s2)][MAX(s1,s2)] = rootnode[s1] + rootnode[s2];
- }
- }
- for( i=0; i<nseq-1; i++ ) for( j=i+1; j<nseq; j++ )
- node[i][j] = ipower( 0.5, (int)node[i][j] ) + geta2;
- for( i=0; i<nseq-1; i++ ) for( j=i+1; j<nseq; j++ )
- node[j][i] = node[i][j];
- }
-
- if( weight == 3 )
- {
-#if DEBUG
- for( i=0; i<nseq; i++ ){
- fprintf( stderr, "len0 = %f\n", len[i][0] );
- fprintf( stderr, "len1 = %f\n", len[i][1] );
- }
-#endif
- for( i=0; i<nseq; i++ )
- {
- rootnode[i] = 0.0;
- eff[i] = 1.0;
-/*
- rootnode[i] = 1.0;
-*/
- }
- for( i=0; i<nseq-1; i++ )
- {
- for( j=0; (s1=topol[i][0][j]) > -1; j++ )
- {
- rootnode[s1] += len[i][0] * eff[s1];
- eff[s1] *= 0.5;
-/*
- rootnode[s1] *= 0.5;
-*/
-
- }
- for( j=0; (s2=topol[i][1][j]) > -1; j++ )
- {
- rootnode[s2] += len[i][1] * eff[s2];
- eff[s2] *= 0.5;
-/*
- rootnode[s2] *= 0.5;
-*/
-
- }
- }
- for( i=0; i<nseq; i++ )
- {
-#if 1 /* 97.9.29 */
- rootnode[i] += GETA3;
-#endif
-#if DEBUG
- fprintf( stderr, "rootnode for %d = %f\n", i, rootnode[i] );
-#endif
- }
- for( i=0; i<nseq; i++ )
- {
- for( j=0; j<nseq; j++ )
- if( j != i )
- node[i][j] = (double)rootnode[i] * rootnode[j];
- else node[i][i] = rootnode[i];
- }
- }
-
-#if 0
- printf( "weight matrix in counteff\n" );
- for( i=0; i<nseq; i++ )
- {
- for( j=0; j<nseq; j++ )
- {
- printf( "%f ", node[i][j] );
- }
- printf( "\n" );
- }
-#endif
-}
-
-float score_calcp( char *seq1, char *seq2, int len )
-{
- int k;
- int ms1, ms2;
- float tmpscore;
- int len2 = len - 2;
-
- tmpscore = 0.0;
- for( k=0; k<len; k++ )
- {
- ms1 = (int)seq1[k];
- ms2 = (int)seq2[k];
- if( ms1 == (int)'-' && ms2 == (int)'-' ) continue;
- tmpscore += (float)amino_dis[ms1][ms2];
-
- if( ms1 == (int)'-' )
- {
- tmpscore += (float)penalty;
- tmpscore += (float)amino_dis[ms1][ms2];
- while( (ms1=(int)seq1[++k]) == (int)'-' )
- tmpscore += (float)amino_dis[ms1][ms2];
- k--;
- if( k >len2 ) break;
- continue;
- }
- if( ms2 == (int)'-' )
- {
- tmpscore += (float)penalty;
- tmpscore += (float)amino_dis[ms1][ms2];
- while( (ms2=(int)seq2[++k]) == (int)'-' )
- tmpscore += (float)amino_dis[ms1][ms2];
- k--;
- if( k > len2 ) break;
- continue;
- }
- }
- return( tmpscore );
-}
-
-float score_calc1( char *seq1, char *seq2 ) /* method 1 */
-{
- int k;
- float score = 0.0;
- int count = 0;
- int len = strlen( seq1 );
-
- for( k=0; k<len; k++ )
- {
- if( seq1[k] != '-' && seq2[k] != '-' )
- {
- score += (float)amino_dis[(int)seq1[k]][(int)seq2[k]];
- count++;
- }
- }
- if( count ) score /= (float)count;
- else score = 1.0;
- return( score );
-}
-
-float substitution_nid( char *seq1, char *seq2 )
-{
- int k;
- float s12;
- int len = strlen( seq1 );
-
- s12 = 0.0;
- for( k=0; k<len; k++ )
- if( seq1[k] != '-' && seq2[k] != '-' )
- s12 += ( seq1[k] == seq2[k] );
-
-// fprintf( stdout, "s12 = %f\n", s12 );
- return( s12 );
-}
-
-float substitution_score( char *seq1, char *seq2 )
-{
- int k;
- float s12;
- int len = strlen( seq1 );
-
- s12 = 0.0;
- for( k=0; k<len; k++ )
- if( seq1[k] != '-' && seq2[k] != '-' )
- s12 += amino_dis[(int)seq1[k]][(int)seq2[k]];
-
-// fprintf( stdout, "s12 = %f\n", s12 );
- return( s12 );
-}
-
-float substitution_hosei( char *seq1, char *seq2 ) /* method 1 */
-#if 0
-{
- int k;
- float score = 0.0;
- int count = 0;
- int len = strlen( seq1 );
-
- for( k=0; k<len; k++ )
- {
- if( seq1[k] != '-' && seq2[k] != '-' )
- {
- score += (float)( seq1[k] != seq2[k] );
- count++;
- }
- }
- if( count ) score /= (float)count;
- else score = 1.0;
- if( score < 0.95 ) score = - log( 1.0 - score );
- else score = 3.0;
- return( score );
-}
-#else
-{
- int count = 0;
- float score;
- int iscore = 0;
- char s1, s2;
-
- while( (s1=*seq1++) )
- {
- s2 = *seq2++;
- if( s1 == '-' ) continue;
- if( s2 == '-' ) continue;
- iscore += ( s1 != s2 );
- count++;
- }
- if( count ) score = (float)iscore / count;
- else score = 1.0;
- if( score < 0.95 ) score = - log( 1.0 - score );
- else score = 3.0;
- return( score );
-}
-#endif
-
-float substitution( char *seq1, char *seq2 ) /* method 1 */
-{
- int k;
- float score = 0.0;
- int count = 0;
- int len = strlen( seq1 );
-
- for( k=0; k<len; k++ )
- {
- if( seq1[k] != '-' && seq2[k] != '-' )
- {
- score += (float)( seq1[k] != seq2[k] );
- count++;
- }
- }
- if( count ) score /= (float)count;
- else score = 1.0;
- return( score );
-}
-
-
-void treeconstruction( char **seq, int nseq, int ***topol, double **len, double **eff )
-{
- int i, j;
-
- if( weight > 1 )
- {
- if( utree == 0 )
- {
- for( i=0; i<nseq-1; i++ ) for( j=i+1; j<nseq; j++ )
- {
-/*
- eff[i][j] = (double)score_calc1( seq[i], seq[j] );
-*/
- eff[i][j] = (double)substitution_hosei( seq[i], seq[j] );
- /*
- fprintf( stderr, "%f\n", eff[i][j] );
- */
- }
-/*
- fprintf( stderr, "distance matrix\n" );
- for( i=0; i<nseq; i++ )
- {
- for( j=0; j<nseq; j++ )
- {
- fprintf( stderr, "%f ", eff[i][j] );
- }
- fprintf( stderr, "\n" );
- }
-*/
-/*
- upg( nseq, eff, topol, len );
- upg2( nseq, eff, topol, len );
-*/
- spg( nseq, eff, topol, len );
- counteff( nseq, topol, len, eff );
- }
- }
- else
- {
- for( i=0; i<nseq; i++ ) for( j=0; j<nseq; j++ )
- eff[i][j] = 1.0;
- }
-/*
-fprintf( stderr, "weight matrix\n" );
-for( i=0; i<nseq; i++ )
-{
- for( j=0; j<nseq; j++ )
- {
- fprintf( stderr, "%f ", eff[i][j] );
- }
- fprintf( stderr, "\n" );
-}
-*/
-}
-
-float bscore_calc( char **seq, int s, double **eff ) /* algorithm B */
-{
- int i, j, k;
- int gb1, gb2, gc1, gc2;
- int cob;
- int nglen;
- int len = strlen( seq[0] );
- long score;
-
- score = 0;
- nglen = 0;
- for( i=0; i<s-1; i++ ) for( j=i+1; j<s; j++ )
- {
- double efficient = eff[i][j];
-
- gc1 = 0;
- gc2 = 0;
- for( k=0; k<len; k++ )
- {
- gb1 = gc1;
- gb2 = gc2;
-
- gc1 = ( seq[i][k] == '-' );
- gc2 = ( seq[j][k] == '-' );
-
- cob =
- !gb1 * gc1
- * !gb2 * !gc2
-
- + !gb1 * !gc1
- * !gb2 * gc2
-
- + !gb1 * gc1
- * gb2 * !gc2
-
- + gb1 * !gc1
- * !gb2 * gc2
-
- + gb1 * !gc1
- * gb2 * gc2 *BEFF
-
- + gb1 * gc1
- * gb2 * !gc2 *BEFF
- ;
- score += (long)cob * penalty * efficient;
- score += (long)amino_dis[(int)seq[i][k]][(int)seq[j][k]] * efficient;
- nglen += ( !gc1 * !gc2 );
- }
- }
- return( (float)score / nglen + 400.0 * !scoremtx );
-}
-
-void AllocateTmpSeqs( char ***mseq2pt, char **mseq1pt, int locnlenmax )
-{
- *mseq2pt = AllocateCharMtx( njob, locnlenmax+1 );
- *mseq1pt = AllocateCharVec( locnlenmax+1 );
-}
-
-void FreeTmpSeqs( char **mseq2, char *mseq1 )
-{
- FreeCharMtx( mseq2 );
- free( (char *)mseq1 );
-}
-
-
-void gappick0( char *aseq, char *seq )
-{
- for( ; *seq != 0; seq++ )
- {
- if( *seq != '-' )
- *aseq++ = *seq;
- }
- *aseq = 0;
-
-}
-
-void gappick( int nseq, int s, char **aseq, char **mseq2,
- double **eff, double *effarr )
-{
- int i, j, count, countjob, len, allgap;
- len = strlen( aseq[0] );
- for( i=0, count=0; i<len; i++ )
- {
- allgap = 1;
- for( j=0; j<nseq; j++ ) if( j != s ) allgap *= ( aseq[j][i] == '-' );
- if( allgap == 0 )
- {
- for( j=0, countjob=0; j<nseq; j++ )
- {
- if( j != s )
- {
- mseq2[countjob][count] = aseq[j][i];
- countjob++;
- }
- }
- count++;
- }
- }
- for( i=0; i<nseq-1; i++ ) mseq2[i][count] = 0;
-
- for( i=0, countjob=0; i<nseq; i++ )
- {
- if( i != s )
- {
- effarr[countjob] = eff[s][i];
- countjob++;
- }
- }
-/*
-fprintf( stdout, "effarr in gappick s = %d\n", s+1 );
-for( i=0; i<countjob; i++ )
- fprintf( stdout, " %f", effarr[i] );
-printf( "\n" );
-*/
-}
-
-void commongappick_record( int nseq, char **seq, int *map )
-{
- int i, j, count;
- int len = strlen( seq[0] );
-
-
- for( i=0, count=0; i<=len; i++ )
- {
- /*
- allgap = 1;
- for( j=0; j<nseq; j++ )
- allgap *= ( seq[j][i] == '-' );
- if( !allgap )
- */
- for( j=0; j<nseq; j++ )
- if( seq[j][i] != '-' ) break;
- if( j != nseq )
- {
- for( j=0; j<nseq; j++ )
- {
- seq[j][count] = seq[j][i];
- }
- map[count] = i;
- count++;
- }
- }
-}
-
-void commongappick( int nseq, char **seq )
-{
- int i, j, count;
- int len = strlen( seq[0] );
-
- for( i=0, count=0; i<=len; i++ )
- {
- /*
- allgap = 1;
- for( j=0; j<nseq; j++ )
- allgap *= ( seq[j][i] == '-' );
- if( !allgap )
- */
- for( j=0; j<nseq; j++ )
- if( seq[j][i] != '-' ) break;
- if( j != nseq )
- {
- for( j=0; j<nseq; j++ )
- {
- seq[j][count] = seq[j][i];
- }
- count++;
- }
- }
-}
-
-double score_calc0( char **seq, int s, double **eff, int ex )
-{
- double tmp;
-
- if( scmtd == 4 ) tmp = score_calc4( seq, s, eff, ex );
- if( scmtd == 5 ) tmp = score_calc5( seq, s, eff, ex );
- else tmp = score_calc5( seq, s, eff, ex );
-
- return( tmp );
-
-}
-
-/*
-float score_m_1( char **seq, int ex, double **eff )
-{
- int i, j, k;
- int len = strlen( seq[0] );
- int gb1, gb2, gc1, gc2;
- int cob;
- int nglen;
- double score;
-
- score = 0.0;
- nglen = 0;
- for( i=0; i<njob; i++ )
- {
- double efficient = eff[MIN(i,ex)][MAX(i,ex)];
- if( i == ex ) continue;
-
- gc1 = 0;
- gc2 = 0;
- for( k=0; k<len; k++ )
- {
- gb1 = gc1;
- gb2 = gc2;
-
- gc1 = ( seq[i][k] == '-' );
- gc2 = ( seq[ex][k] == '-' );
-
- cob =
- !gb1 * gc1
- * !gb2 * !gc2
-
- + !gb1 * !gc1
- * !gb2 * gc2
-
- + !gb1 * gc1
- * gb2 * !gc2
-
- + gb1 * !gc1
- * !gb2 * gc2
-
- + gb1 * !gc1
- * gb2 * gc2 *BEFF
-
- + gb1 * gc1
- * gb2 * !gc2 *BEFF
- ;
- score += (double)cob * penalty * efficient;
- score += (double)amino_dis[seq[i][k]][seq[ex][k]] * efficient;
- *
- nglen += ( !gc1 * !gc2 );
- *
- if( !gc1 && !gc2 ) fprintf( stdout, "%f\n", score );
- }
- }
- return( (float)score / nglen + 400.0 * !scoremtx );
-}
-*/
-
-#if 0
-void sitescore( char **seq, double **eff, char sco1[], char sco2[], char sco3[] )
-{
- int i, j, k;
- int len = strlen( seq[0] );
- double tmp;
- double count;
- int ch;
- double sco[N];
-
- for( i=0; i<len; i++ )
- {
- tmp = 0.0; count = 0;
- for( j=0; j<njob-1; j++ ) for( k=j+1; k<njob; k++ )
- {
- /*
- if( seq[j][i] != '-' && seq[k][i] != '-' )
- */
- {
- tmp += amino_dis[seq[j][i]][seq[k][i]] + 400 * !scoremtx;
- count++;
- }
- }
- if( count > 0.0 ) tmp /= count;
- else( tmp = 0.0 );
- ch = (int)( tmp/100.0 - 0.000001 );
- sprintf( sco1+i, "%c", ch+0x61 );
- }
- sco1[len] = 0;
-
- for( i=0; i<len; i++ )
- {
- tmp = 0.0; count = 0;
- for( j=0; j<njob-1; j++ ) for( k=j+1; k<njob; k++ )
- {
- /*
- if( seq[j][i] != '-' && seq[k][i] != '-' )
- */
- {
- tmp += eff[j][k] * ( amino_dis[seq[j][i]][seq[k][i]] + 400 * !scoremtx );
- count += eff[j][k];
- }
- }
- if( count > 0.0 ) tmp /= count;
- else( tmp = 0.0 );
- tmp = ( tmp - 400 * !scoremtx ) * 2;
- if( tmp < 0 ) tmp = 0;
- ch = (int)( tmp/100.0 - 0.000001 );
- sprintf( sco2+i, "%c", ch+0x61 );
- sco[i] = tmp;
- }
- sco2[len] = 0;
-
- for( i=WIN; i<len-WIN; i++ )
- {
- tmp = 0.0;
- for( j=i-WIN; j<=i+WIN; j++ )
- {
- tmp += sco[j];
- }
- for( j=0; j<njob; j++ )
- {
- if( seq[j][i] == '-' )
- {
- tmp = 0.0;
- break;
- }
- }
- tmp /= WIN * 2 + 1;
- ch = (int)( tmp/100.0 - 0.0000001 );
- sprintf( sco3+i, "%c", ch+0x61 );
- }
- for( i=0; i<WIN; i++ ) sco3[i] = '-';
- for( i=len-WIN; i<len; i++ ) sco3[i] = '-';
- sco3[len] = 0;
-}
-#endif
-
-void strins( char *str1, char *str2 )
-{
- char *bk;
- int len1 = strlen( str1 );
- int len2 = strlen( str2 );
-
- bk = str2;
- str2 += len1+len2;
- str1 += len1-1;
-
- while( str2 >= bk+len1 ) { *str2 = *(str2-len1); str2--;} // by D.Mathog
- while( str2 >= bk ) { *str2-- = *str1--; }
-}
-
-int isaligned( int nseq, char **seq )
-{
- int i;
- int len = strlen( seq[0] );
- for( i=1; i<nseq; i++ )
- {
- if( strlen( seq[i] ) != len ) return( 0 );
- }
- return( 1 );
-}
-
-double score_calc_for_score( int nseq, char **seq )
-{
- int i, j, k, c;
- int len = strlen( seq[0] );
- double score;
- double tmpscore;
- char *mseq1, *mseq2;
-
- score = 0.0;
- for( i=0; i<nseq-1; i++ )
- {
- for( j=i+1; j<nseq; j++ )
- {
- mseq1 = seq[i];
- mseq2 = seq[j];
- tmpscore = 0.0;
- c = 0;
- for( k=0; k<len; k++ )
- {
- if( mseq1[k] == '-' && mseq2[k] == '-' ) continue;
- tmpscore += amino_dis[(int)mseq1[k]][(int)mseq2[k]];
- c++;
- if( mseq1[k] == '-' )
- {
- tmpscore += penalty - n_dis[0][24];
- while( mseq1[++k] == '-' )
- ;
- k--;
- if( k > len-2 ) break;
- continue;
- }
- if( mseq2[k] == '-' )
- {
- tmpscore += penalty - n_dis[0][24];
- while( mseq2[++k] == '-' )
- ;
- k--;
- if( k > len-2 ) break;
- continue;
- }
- }
- score += (double)tmpscore / (double)c;
-#if DEBUG
- printf( "tmpscore in mltaln9.c = %f\n", tmpscore );
- printf( "tmpscore / c = %f\n", tmpscore/(double)c );
-#endif
- }
- }
- fprintf( stderr, "raw score = %f\n", score );
- score /= (double)nseq * ( nseq-1.0 ) / 2.0;
- score += 400.0;
-#if DEBUG
- printf( "score in mltaln9.c = %f\n", score );
-#endif
- return( (double)score );
-}
-
-void floatncpy( float *vec1, float *vec2, int len )
-{
- while( len-- )
- *vec1++ = *vec2++;
-}
-
-float score_calc_a( char **seq, int s, double **eff ) /* algorithm A+ */
-{
- int i, j, k;
- int gb1, gb2, gc1, gc2;
- int cob;
- int nglen;
- int len = strlen( seq[0] );
- float score;
-
- score = 0;
- nglen = 0;
- for( i=0; i<s-1; i++ ) for( j=i+1; j<s; j++ )
- {
- double efficient = eff[i][j];
-
- gc1 = 0;
- gc2 = 0;
- for( k=0; k<len; k++ )
- {
- gb1 = gc1;
- gb2 = gc2;
-
- gc1 = ( seq[i][k] == '-' );
- gc2 = ( seq[j][k] == '-' );
-
- cob =
- !gb1 * gc1
- * !gb2 * !gc2
-
- + gb1 * !gc1
- * !gb2 * !gc2
-
- + !gb1 * !gc1
- * !gb2 * gc2
-
- + !gb1 * !gc1
- * gb2 * !gc2
-
- + !gb1 * gc1
- * gb2 * !gc2
-
- + gb1 * !gc1
- * !gb2 * gc2
-
- + gb1 * !gc1
- * gb2 * gc2
-
- + gb1 * gc1
- * gb2 * !gc2
-
- + !gb1 * gc1
- * gb2 * gc2
-
- + gb1 * gc1
- * !gb2 * gc2
- ;
- score += 0.5 * (float)cob * penalty * efficient;
- score += (float)amino_dis[(int)seq[i][k]][(int)seq[j][k]] * (float)efficient;
- nglen += ( !gc1 * !gc2 );
- }
- }
- return( (float)score / nglen + 400.0 * !scoremtx );
-}
-
-
-float score_calc_s( char **seq, int s, double **eff ) /* algorithm S, not used */
-{
- int i, j, k;
- int gb1, gb2, gc1, gc2;
- int cob;
- int nglen;
- int len = strlen( seq[0] );
- float score;
-
- score = 0;
- nglen = 0;
- for( i=0; i<s-1; i++ ) for( j=i+1; j<s; j++ )
- {
- double efficient = eff[i][j];
-
- gc1 = 0;
- gc2 = 0;
- for( k=0; k<len; k++ )
- {
- gb1 = gc1;
- gb2 = gc2;
-
- gc1 = ( seq[i][k] == '-' );
- gc2 = ( seq[j][k] == '-' );
-
- cob =
- !gb1 * gc1
- * !gb2 * !gc2
-
- + gb1 * !gc1
- * !gb2 * !gc2
-
- + !gb1 * !gc1
- * !gb2 * gc2
-
- + !gb1 * !gc1
- * gb2 * !gc2
-
- + !gb1 * gc1
- * gb2 * !gc2
-
- + gb1 * !gc1
- * !gb2 * gc2
-
-#if 0
- + gb1 * !gc1
- * gb2 * gc2
-
- + gb1 * gc1
- * gb2 * !gc2
-
- + !gb1 * gc1
- * gb2 * gc2
-
- + gb1 * gc1
- * !gb2 * gc2
-#endif
- ;
- score += 0.5 * (float)cob * penalty * efficient;
- score += (float)amino_dis[(int)seq[i][k]][(int)seq[j][k]] * (float)efficient;
- nglen += ( !gc1 * !gc2 );
- }
- }
- return( (float)score / nglen + 400.0 );
-}
-
-double score_calc_for_score_s( int s, char **seq ) /* algorithm S */
-{
- int i, j, k;
- int gb1, gb2, gc1, gc2;
- int cob;
- int nglen;
- int len = strlen( seq[0] );
- float score;
-
- score = 0;
- nglen = 0;
- for( i=0; i<s-1; i++ ) for( j=i+1; j<s; j++ )
- {
-
- gc1 = 0;
- gc2 = 0;
- for( k=0; k<len; k++ )
- {
- gb1 = gc1;
- gb2 = gc2;
-
- gc1 = ( seq[i][k] == '-' );
- gc2 = ( seq[j][k] == '-' );
-
- cob =
- !gb1 * gc1
- * !gb2 * !gc2
-
- + gb1 * !gc1
- * !gb2 * !gc2
-
- + !gb1 * !gc1
- * !gb2 * gc2
-
- + !gb1 * !gc1
- * gb2 * !gc2
-
- + !gb1 * gc1
- * gb2 * !gc2
-
- + gb1 * !gc1
- * !gb2 * gc2
-
-#if 0
- + gb1 * !gc1
- * gb2 * gc2
-
- + gb1 * gc1
- * gb2 * !gc2
-
- + !gb1 * gc1
- * gb2 * gc2
-
- + gb1 * gc1
- * !gb2 * gc2
-#endif
- ;
- score += 0.5 * (float)cob * penalty;
- score += (float)amino_dis[(int)seq[i][k]][(int)seq[j][k]];
- nglen += ( !gc1 * !gc2 );
- }
-#if 0
- fprintf( stderr, "i = %d, j=%d\n", i+1, j+1 );
- fprintf( stderr, "score = %f\n", score );
-#endif
- }
- return( (double)score / nglen + 400.0 );
-}
-
-double SSPscore___( int s, char **seq, int ex ) /* algorithm S */
-{
- int i, j, k;
- int gb1, gb2, gc1, gc2;
- int cob;
- int nglen;
- int len = strlen( seq[0] );
- float score;
-
- score = 0;
- nglen = 0;
- i=ex; for( j=0; j<s; j++ )
- {
-
- if( j == ex ) continue;
-
- gc1 = 0;
- gc2 = 0;
- for( k=0; k<len; k++ )
- {
- gb1 = gc1;
- gb2 = gc2;
-
- gc1 = ( seq[i][k] == '-' );
- gc2 = ( seq[j][k] == '-' );
-
- cob =
- !gb1 * gc1
- * !gb2 * !gc2
-
- + gb1 * !gc1
- * !gb2 * !gc2
-
- + !gb1 * !gc1
- * !gb2 * gc2
-
- + !gb1 * !gc1
- * gb2 * !gc2
-
- + !gb1 * gc1
- * gb2 * !gc2 * 2.0
-
- + gb1 * !gc1
- * !gb2 * gc2 * 2.0
-
-#if 0
- + gb1 * !gc1
- * gb2 * gc2
-
- + gb1 * gc1
- * gb2 * !gc2
-
- + !gb1 * gc1
- * gb2 * gc2
-
- + gb1 * gc1
- * !gb2 * gc2
-#endif
- ;
- score += 0.5 * (float)cob * penalty;
- score += (float)amino_dis[(int)seq[i][k]][(int)seq[j][k]];
- nglen += ( !gc1 * !gc2 ); /* tsukawanai */
- }
-#if 0
- fprintf( stderr, "i = %d, j=%d\n", i+1, j+1 );
- fprintf( stderr, "score = %f\n", score );
-#endif
- }
- return( (double)score );
-}
-
-double SSPscore( int s, char **seq ) /* algorithm S */
-{
- int i, j, k;
- int gb1, gb2, gc1, gc2;
- int cob;
- int nglen;
- int len = strlen( seq[0] );
- float score;
-
- score = 0;
- nglen = 0;
- for( i=0; i<s-1; i++ ) for( j=i+1; j<s; j++ )
- {
-
- gc1 = 0;
- gc2 = 0;
- for( k=0; k<len; k++ )
- {
- gb1 = gc1;
- gb2 = gc2;
-
- gc1 = ( seq[i][k] == '-' );
- gc2 = ( seq[j][k] == '-' );
-
- cob =
- !gb1 * gc1
- * !gb2 * !gc2
-
- + gb1 * !gc1
- * !gb2 * !gc2
-
- + !gb1 * !gc1
- * !gb2 * gc2
-
- + !gb1 * !gc1
- * gb2 * !gc2
-
- + !gb1 * gc1
- * gb2 * !gc2
-
- + gb1 * !gc1
- * !gb2 * gc2
-
-#if 0
- + gb1 * !gc1
- * gb2 * gc2
-
- + gb1 * gc1
- * gb2 * !gc2
-
- + !gb1 * gc1
- * gb2 * gc2
-
- + gb1 * gc1
- * !gb2 * gc2
-#endif
- ;
- score += 0.5 * (float)cob * penalty;
- score += (float)amino_dis[(int)seq[i][k]][(int)seq[j][k]];
- nglen += ( !gc1 * !gc2 ); /* tsukawanai */
- }
-#if 0
- fprintf( stderr, "i = %d, j=%d\n", i+1, j+1 );
- fprintf( stderr, "score = %f\n", score );
-#endif
- }
- return( (double)score );
-}
-
-
-
-double DSPscore( int s, char **seq ) /* method 3 deha nai */
-{
- int i, j, k;
- double c;
- int len = strlen( seq[0] );
- double score;
- double tmpscore;
- char *mseq1, *mseq2;
-#if DEBUG
- FILE *fp;
-#endif
-
- score = 0.0;
- c = 0.0;
-
- for( i=0; i<s-1; i++ )
- {
- for( j=i+1; j<s; j++ )
- {
- mseq1 = seq[i];
- mseq2 = seq[j];
- tmpscore = 0.0;
- for( k=0; k<len; k++ )
- {
- if( mseq1[k] == '-' && mseq2[k] == '-' ) continue;
- tmpscore += amino_dis[(int)mseq1[k]][(int)mseq2[k]];
-
- if( mseq1[k] == '-' )
- {
- tmpscore += penalty;
- while( mseq1[++k] == '-' )
- tmpscore += amino_dis[(int)mseq1[k]][(int)mseq2[k]];
- k--;
- if( k > len-2 ) break;
- continue;
- }
- if( mseq2[k] == '-' )
- {
- tmpscore += penalty;
- while( mseq2[++k] == '-' )
- tmpscore += amino_dis[(int)mseq1[k]][(int)mseq2[k]];
- k--;
- if( k > len-2 ) break;
- continue;
- }
- }
- score += (double)tmpscore;
- }
- }
-
- return( score );
-}
-
-
-#define SEGMENTSIZE 150
-
-int searchAnchors( int nseq, char **seq, Segment *seg )
-{
- int i, j, k, kcyc;
- int status;
- double score;
- int value = 0;
- int len;
- int length;
- static double *stra = NULL;
- static int alloclen = 0;
- double cumscore;
- static double threshold;
-
- len = strlen( seq[0] );
- if( alloclen < len )
- {
- if( alloclen )
- {
- FreeDoubleVec( stra );
- }
- else
- {
- threshold = (int)divThreshold / 100.0 * 600.0 * divWinSize;
- }
- stra = AllocateDoubleVec( len );
- alloclen = len;
- }
-
- for( i=0; i<len; i++ )
- {
-#if 0
- /* make prf */
- for( j=0; j<26; j++ )
- {
- prf[j] = 0.0;
- }
- for( j=0; j<nseq; j++ ) prf[amino_n[seq[j][i]]] += 1.0;
-
- /* make hat */
- pre = 26;
- for( j=25; j>=0; j-- )
- {
- if( prf[j] )
- {
- hat[pre] = j;
- pre = j;
- }
- }
- hat[pre] = -1;
-
- /* make site score */
- stra[i] = 0.0;
- for( k=hat[26]; k!=-1; k=hat[k] )
- for( j=hat[26]; j!=-1; j=hat[j] )
- stra[i] += n_dis[k][j] * prf[k] * prf[j];
-#else
- stra[i] = 0.0;
- kcyc = nseq-1;
- for( k=0; k<kcyc; k++ ) for( j=k+1; j<nseq; j++ )
- stra[i] += n_dis[(int)amino_n[(int)seq[k][i]]][(int)amino_n[(int)seq[j][i]]];
- stra[i] /= (double)nseq * ( nseq-1 ) / 2;
-#endif
- }
-
- (seg+0)->skipForeward = 0;
- (seg+1)->skipBackward = 0;
- status = 0;
- cumscore = 0.0;
- score = 0.0;
- length = 0; /* modified at 01/09/11 */
- for( j=0; j<divWinSize; j++ ) score += stra[j];
- for( i=1; i<len-divWinSize; i++ )
- {
- score = score - stra[i-1] + stra[i+divWinSize-1];
-#if DEBUG
- fprintf( stderr, "%d %f ? %f", i, score, threshold );
- if( score > threshold ) fprintf( stderr, "YES\n" );
- else fprintf( stderr, "NO\n" );
-#endif
-
- if( score > threshold )
- {
- if( !status )
- {
- status = 1;
- seg->start = i;
- length = 0;
- cumscore = 0.0;
- }
- length++;
- cumscore += score;
- }
- if( score <= threshold || length > SEGMENTSIZE )
- {
- if( status )
- {
- seg->end = i;
- seg->center = ( seg->start + seg->end + divWinSize ) / 2 ;
- seg->score = cumscore;
-#if DEBUG
- fprintf( stderr, "%d-%d length = %d\n", seg->start, seg->end, length );
-#endif
- if( length > SEGMENTSIZE )
- {
- (seg+0)->skipForeward = 1;
- (seg+1)->skipBackward = 1;
- }
- else
- {
- (seg+0)->skipForeward = 0;
- (seg+1)->skipBackward = 0;
- }
- length = 0;
- cumscore = 0.0;
- status = 0;
- value++;
- seg++;
- if( value > MAXSEG - 3 ) ErrorExit( "TOO MANY SEGMENTS!");
- }
- }
- }
- if( status )
- {
- seg->end = i;
- seg->center = ( seg->start + seg->end + divWinSize ) / 2 ;
- seg->score = cumscore;
-#if DEBUG
-fprintf( stderr, "%d-%d length = %d\n", seg->start, seg->end, length );
-#endif
- value++;
- }
- return( value );
-}
-
-void dontcalcimportance( int nseq, double *eff, char **seq, LocalHom **localhom )
-{
- int i, j;
- LocalHom *ptr;
- static int *nogaplen = NULL;
-
- if( nogaplen == NULL )
- {
- nogaplen = AllocateIntVec( nseq );
- }
-
- for( i=0; i<nseq; i++ )
- {
- nogaplen[i] = seqlen( seq[i] );
-// fprintf( stderr, "nogaplen[%d] = %d\n", i, nogaplen[i] );
- }
-
- for( i=0; i<nseq; i++ )
- {
- for( j=0; j<nseq; j++ )
- {
- for( ptr=localhom[i]+j; ptr; ptr=ptr->next )
- {
-// fprintf( stderr, "i,j=%d,%d,ptr=%p\n", i, j, ptr );
-#if 1
- ptr->importance = ptr->opt / ptr->overlapaa;
- ptr->fimportance = (float)ptr->importance;
-#else
- ptr->importance = ptr->opt / MIN( nogaplen[i], nogaplen[j] );
-#endif
- }
- }
- }
-}
-
-void calcimportance( int nseq, double *eff, char **seq, LocalHom **localhom )
-{
- int i, j, pos, len;
- static double *importance;
- double tmpdouble;
- static int *nogaplen = NULL;
- LocalHom *tmpptr;
-
- if( importance == NULL )
- {
- importance = AllocateDoubleVec( nlenmax );
- nogaplen = AllocateIntVec( nseq );
- }
-
-
- for( i=0; i<nseq; i++ )
- {
- nogaplen[i] = seqlen( seq[i] );
-// fprintf( stderr, "nogaplen[] = %d\n", nogaplen[i] );
- }
-
-#if 0
- for( i=0; i<nseq; i++ ) for( j=0; j<nseq; j++ )
- {
- tmpptr = localhom[i]+j;
- fprintf( stderr, "%d-%d\n", i, j );
- do
- {
- fprintf( stderr, "reg1=%d-%d, reg2=%d-%d, opt=%f\n", tmpptr->start1, tmpptr->end1, tmpptr->start2, tmpptr->end2, tmpptr->opt );
- } while( tmpptr=tmpptr->next );
- }
-#endif
-
-
- for( i=0; i<nseq; i++ )
- {
-// fprintf( stderr, "i = %d\n", i );
- for( pos=0; pos<nlenmax; pos++ )
- importance[pos] = 0.0;
- for( j=0; j<nseq; j++ )
- {
- if( i == j ) continue;
- tmpptr = localhom[i]+j;
- for( tmpptr = localhom[i]+j; tmpptr; tmpptr=tmpptr->next )
- {
- if( tmpptr->opt == -1 ) continue;
- for( pos=tmpptr->start1; pos<=tmpptr->end1; pos++ )
-#if 1
- importance[pos] += eff[j];
-#else
- importance[pos] += eff[j] * tmpptr->opt / MIN( nogaplen[i], nogaplen[j] );
- importance[pos] += eff[j] * tmpptr->opt / tmpptr->overlapaa;
-#endif
- }
- }
-#if 0
- fprintf( stderr, "position specific importance of seq %d:\n", i );
- for( pos=0; pos<nlenmax; pos++ )
- fprintf( stderr, "%d: %f\n", pos, importance[pos] );
- fprintf( stderr, "\n" );
-#endif
- for( j=0; j<nseq; j++ )
- {
-// fprintf( stderr, "i=%d, j=%d\n", i, j );
- if( i == j ) continue;
- if( localhom[i][j].opt == -1.0 ) continue;
-#if 1
- for( tmpptr = localhom[i]+j; tmpptr; tmpptr=tmpptr->next )
- {
- if( tmpptr->opt == -1.0 ) continue;
- tmpdouble = 0.0;
- len = 0;
- for( pos=tmpptr->start1; pos<=tmpptr->end1; pos++ )
- {
- tmpdouble += importance[pos];
- len++;
- }
- tmpdouble /= (double)len;
-
- tmpptr->importance = tmpdouble * tmpptr->opt;
- tmpptr->fimportance = (float)tmpptr->importance;
- }
-#else
- tmpdouble = 0.0;
- len = 0;
- for( tmpptr = localhom[i]+j; tmpptr; tmpptr=tmpptr->next )
- {
- if( tmpptr->opt == -1.0 ) continue;
- for( pos=tmpptr->start1; pos<=tmpptr->end1; pos++ )
- {
- tmpdouble += importance[pos];
- len++;
- }
- }
-
- tmpdouble /= (double)len;
-
- for( tmpptr = localhom[i]+j; tmpptr; tmpptr=tmpptr->next )
- {
- if( tmpptr->opt == -1.0 ) continue;
- tmpptr->importance = tmpdouble * tmpptr->opt;
-// tmpptr->importance = tmpptr->opt / tmpptr->overlapaa; //\e$B$J$+$C$?$3$H$K$9$k\e(B
- }
-#endif
-
-// fprintf( stderr, "importance of match between %d - %d = %f\n", i, j, tmpdouble );
- }
- }
-
-#if 0
- fprintf( stderr, "before averaging:\n" );
-
- for( i=0; i<nseq; i++ ) for( j=0; j<nseq; j++ )
- {
- fprintf( stderr, "%d-%d\n", i, j );
- for( tmpptr = localhom[i]+j; tmpptr; tmpptr=tmpptr->next )
- {
- fprintf( stderr, "reg1=%d-%d, reg2=%d-%d, imp=%f -> %f opt=%f\n", tmpptr->start1, tmpptr->end1, tmpptr->start2, tmpptr->end2, tmpptr->opt / tmpptr->overlapaa, eff[i] * tmpptr->importance, tmpptr->opt );
- }
- }
-#endif
-
-#if 1
-// fprintf( stderr, "average?\n" );
- for( i=0; i<nseq-1; i++ ) for( j=i+1; j<nseq; j++ )
- {
- double imp;
- LocalHom *tmpptr1, *tmpptr2;
-
-// fprintf( stderr, "i=%d, j=%d\n", i, j );
-
- tmpptr1 = localhom[i]+j; tmpptr2 = localhom[j]+i;
- for( ; tmpptr1 && tmpptr2; tmpptr1 = tmpptr1->next, tmpptr2 = tmpptr2->next)
- {
- if( tmpptr1->opt == -1.0 || tmpptr2->opt == -1.0 )
- {
-// fprintf( stderr, "WARNING: i=%d, j=%d, tmpptr1->opt=%f, tmpptr2->opt=%f\n", i, j, tmpptr1->opt, tmpptr2->opt );
- continue;
- }
-// fprintf( stderr, "## importances = %f, %f\n", tmpptr1->importance, tmpptr2->importance );
- imp = 0.5 * ( tmpptr1->importance + tmpptr2->importance );
- tmpptr1->importance = tmpptr2->importance = imp;
- tmpptr1->fimportance = tmpptr2->fimportance = (float)imp;
-
-// fprintf( stderr, "## importance = %f\n", tmpptr1->importance );
-
- }
-
-#if 1
- if( ( tmpptr1 && !tmpptr2 ) || ( !tmpptr1 && tmpptr2 ) )
- {
- fprintf( stderr, "ERROR: i=%d, j=%d\n", i, j );
- exit( 1 );
- }
-#endif
- }
-#endif
-#if 0
- fprintf( stderr, "after averaging:\n" );
-
- for( i=0; i<nseq; i++ ) for( j=0; j<nseq; j++ )
- {
- fprintf( stderr, "%d-%d\n", i, j );
- for( tmpptr = localhom[i]+j; tmpptr; tmpptr=tmpptr->next )
- {
- fprintf( stderr, "reg1=%d-%d, reg2=%d-%d, imp=%f -> %f opt=%f\n", tmpptr->start1, tmpptr->end1, tmpptr->start2, tmpptr->end2, tmpptr->opt / tmpptr->overlapaa, tmpptr->importance, tmpptr->opt );
- }
- }
-#endif
-}
-
-
-#if 0
-void weightimportance( int nseq, double **eff, LocalHom **localhom )
-{
- int i, j, pos, len;
- static double *importance;
- double tmpdouble;
- LocalHom *tmpptr, *tmpptr1, *tmpptr2;
- if( importance == NULL )
- importance = AllocateDoubleVec( nlenmax );
-
-
- fprintf( stderr, "effmtx = :\n" );
- for( i=0; i<nseq; i++ )
- {
- for( j=0; j<nseq; j++ )
- {
- fprintf( stderr, "%6.3f ", eff[i][j] );
- }
- fprintf( stderr, "\n" );
- }
- for( i=0; i<nseq; i++ )
- {
- for( pos=0; pos<nlenmax; pos++ )
- importance[pos] = 0.0;
- for( j=0; j<nseq; j++ )
- {
-
- if( i == j ) continue;
- tmpptr = localhom[i]+j;
- while( 1 )
- {
- fprintf( stderr, "i=%d, j=%d\n", i, j );
- for( pos=tmpptr->start1; pos<=tmpptr->end1; pos++ )
-// importance[pos] += eff[i][j] * tmpptr->importance;
- importance[pos] += eff[i][j] / (double)nseq * tmpptr->importance / 1.0;
- fprintf( stderr, "eff[][] = %f, localhom[i][j].importance = %f \n", eff[i][j], tmpptr->importance );
- tmpptr = tmpptr->next;
- if( tmpptr == NULL ) break;
- }
-
- }
-#if 0
- fprintf( stderr, "position specific importance of seq %d:\n", i );
- for( pos=0; pos<nlenmax; pos++ )
- fprintf( stderr, "%d: %f\n", pos, importance[pos] );
- fprintf( stderr, "\n" );
-#endif
- for( j=0; j<nseq; j++ )
- {
- fprintf( stderr, "i=%d, j=%d\n", i, j );
- if( i == j ) continue;
- tmpptr = localhom[i]+j;
- do
- {
- tmpdouble = 0.0;
- len = 0;
- for( pos=tmpptr->start1; pos<=tmpptr->end1; pos++ )
- {
- tmpdouble += importance[pos];
- len++;
- }
- tmpdouble /= (double)len;
- tmpptr->importance = tmpdouble;
- fprintf( stderr, "importance of match between %d - %d = %f\n", i, j, tmpdouble );
- tmpptr = tmpptr->next;
- } while( tmpptr );
- }
- }
-#if 1
- for( i=0; i<nseq-1; i++ ) for( j=i+1; j<nseq; j++ )
- {
- fprintf( stderr, "i = %d, j=%d\n", i, j );
- tmpptr1 = localhom[i]+j;
- tmpptr2 = localhom[j]+i;
- while( tmpptr1 && tmpptr2 )
- {
- tmpptr1->importance += tmpptr2->importance;
- tmpptr1->importance *= 0.5;
- tmpptr2->importance *= tmpptr1->importance;
- fprintf( stderr, "%d-%d: s1=%d, e1=%d, s2=%d, e2=%d, importance=%f\n", i, j, tmpptr1->start1, tmpptr1->end1, tmpptr1->start2, tmpptr1->end2, tmpptr1->importance );
- tmpptr1 = tmpptr1->next;
- tmpptr2 = tmpptr2->next;
- fprintf( stderr, "tmpptr1 = %p, tmpptr2 = %p\n", tmpptr1, tmpptr2 );
- }
- }
-#endif
-}
-
-void weightimportance2( int nseq, double *eff, LocalHom **localhom )
-{
- int i, j, pos, len;
- static double *wimportance;
- double tmpdouble;
- if( wimportance == NULL )
- wimportance = AllocateDoubleVec( nlenmax );
-
-
- fprintf( stderr, "effmtx = :\n" );
- for( i=0; i<nseq; i++ )
- {
- for( j=0; j<nseq; j++ )
- {
- fprintf( stderr, "%6.3f ", eff[i] * eff[j] );
- }
- fprintf( stderr, "\n" );
- }
- for( i=0; i<nseq; i++ )
- {
- fprintf( stderr, "i = %d\n", i );
- for( pos=0; pos<nlenmax; pos++ )
- wimportance[pos] = 0.0;
- for( j=0; j<nseq; j++ )
- {
- if( i == j ) continue;
- for( pos=localhom[i][j].start1; pos<=localhom[i][j].end1; pos++ )
-// wimportance[pos] += eff[i][j];
- wimportance[pos] += eff[i] * eff[j] / (double)nseq * localhom[i][j].importance / 1.0;
- }
-#if 0
- fprintf( stderr, "position specific wimportance of seq %d:\n", i );
- for( pos=0; pos<nlenmax; pos++ )
- fprintf( stderr, "%d: %f\n", pos, wimportance[pos] );
- fprintf( stderr, "\n" );
-#endif
- for( j=0; j<nseq; j++ )
- {
- if( i == j ) continue;
- tmpdouble = 0.0;
- len = 0;
- for( pos=localhom[i][j].start1; pos<=localhom[i][j].end1; pos++ )
- {
- tmpdouble += wimportance[pos];
- len++;
- }
- tmpdouble /= (double)len;
- localhom[i][j].wimportance = tmpdouble;
- fprintf( stderr, "wimportance of match between %d - %d = %f\n", i, j, tmpdouble );
- }
- }
-#if 1
- for( i=0; i<nseq-1; i++ ) for( j=i+1; j<nseq; j++ )
- {
- localhom[i][j].wimportance += localhom[j][i].wimportance;
- localhom[i][j].wimportance = 0.5 * ( localhom[i][j].wimportance );
- }
- for( i=0; i<nseq-1; i++ ) for( j=i+1; j<nseq; j++ )
- {
- localhom[j][i].wimportance = localhom[i][j].wimportance;
- }
-#endif
-}
-
-void weightimportance4( int clus1, int clus2, double *eff1, double *eff2, LocalHom ***localhom )
-{
- int i, j, pos, len;
- static double *wimportance;
- LocalHom *tmpptr, *tmpptr1, *tmpptr2;
- if( wimportance == NULL )
- wimportance = AllocateDoubleVec( nlenmax );
-
-
-#if 0
- fprintf( stderr, "effarr1 = :\n" );
- for( i=0; i<clus1; i++ )
- fprintf( stderr, "%6.3f\n", eff1[i] );
- fprintf( stderr, "effarr2 = :\n" );
- for( i=0; i<clus2; i++ )
- fprintf( stderr, "%6.3f\n", eff2[i] );
-#endif
-
- for( i=0; i<clus1; i++ )
- {
- for( j=0; j<clus2; j++ )
- {
-// fprintf( stderr, "i=%d, j=%d\n", i, j );
- tmpptr = localhom[i][j];
- do
- {
- tmpptr->wimportance = tmpptr->importance * eff1[i] * eff2[j];
- tmpptr = tmpptr->next;
- } while( tmpptr );
- }
- }
-}
-
-static void addlocalhom_e( LocalHom *localhom, int start1, int start2, int end1, int end2, double opt )
-{
- LocalHom *tmpptr;
- tmpptr = localhom;
-
- fprintf( stderr, "adding localhom\n" );
- while( tmpptr->next )
- tmpptr = tmpptr->next;
- fprintf( stderr, "allocating localhom\n" );
- tmpptr->next = (LocalHom *)calloc( 1, sizeof( LocalHom ) );
- fprintf( stderr, "done\n" );
- tmpptr = tmpptr->next;
-
- tmpptr->start1 = start1;
- tmpptr->start2 = start2;
- tmpptr->end1 = end1;
- tmpptr->end2 = end2;
- tmpptr->opt = opt;
-
- fprintf( stderr, "start1 = %d, end1 = %d, start2 = %d, end2 = %d\n", start1, end1, start2, end2 );
-}
-
-#if 0
-#endif
-
-
-
-void extendlocalhom( int nseq, LocalHom **localhom )
-{
- int i, j, k, pos0, pos1, pos2, st;
- int start1, start2, end1, end2;
- static int *tmpint1 = NULL;
- static int *tmpint2 = NULL;
- static int *tmpdouble1 = NULL;
- static int *tmpdouble2 = NULL;
- double opt;
- LocalHom *tmpptr;
- if( tmpint1 == NULL )
- {
- tmpint1 = AllocateIntVec( nlenmax );
- tmpint2 = AllocateIntVec( nlenmax );
- tmpdouble1 = AllocateIntVec( nlenmax );
- tmpdouble2 = AllocateIntVec( nlenmax );
- }
-
-
- for( k=0; k<nseq; k++ )
- {
- for( i=0; i<nseq-1; i++ )
- {
- if( i == k ) continue;
- for( pos0=0; pos0<nlenmax; pos0++ )
- tmpint1[pos0] = -1;
-
- tmpptr=localhom[k]+i;
- do
- {
- pos0 = tmpptr->start1;
- pos1 = tmpptr->start2;
- while( pos0<=tmpptr->end1 )
- {
- tmpint1[pos0] = pos1++;
- tmpdouble1[pos0] = tmpptr->opt;
- pos0++;
- }
- } while( tmpptr = tmpptr->next );
-
-
- for( j=i+1; j<nseq; j++ )
- {
- if( j == k ) continue;
- for( pos1=0; pos1<nlenmax; pos1++ ) tmpint2[pos1] = -1;
- tmpptr=localhom[k]+j;
- do
- {
- pos0 = tmpptr->start1;
- pos2 = tmpptr->start2;
- while( pos0<=tmpptr->end1 )
- {
- tmpint2[pos0] = pos2++;
- tmpdouble2[pos0++] = tmpptr->opt;
- }
- } while( tmpptr = tmpptr->next );
-
-#if 0
-
- fprintf( stderr, "i,j=%d,%d\n", i, j );
-
- for( pos0=0; pos0<nlenmax; pos0++ )
- fprintf( stderr, "%d ", tmpint1[pos0] );
- fprintf( stderr, "\n" );
-
- for( pos0=0; pos0<nlenmax; pos0++ )
- fprintf( stderr, "%d ", tmpint2[pos0] );
- fprintf( stderr, "\n" );
-#endif
-
-
- st = 0;
- for( pos0=0; pos0<nlenmax; pos0++ )
- {
-// fprintf( stderr, "pos0 = %d/%d, st = %d, tmpint1[pos0] = %d, tmpint2[pos0] = %d\n", pos0, nlenmax, st, tmpint1[pos0], tmpint2[pos0] );
- if( tmpint1[pos0] >= 0 && tmpint2[pos0] >= 0 )
- {
- if( st == 0 )
- {
- st = 1;
- start1 = tmpint1[pos0];
- start2 = tmpint2[pos0];
- opt = MIN( tmpdouble1[pos0], tmpdouble2[pos0] );
- }
- else if( tmpint1[pos0-1] != tmpint1[pos0]-1 || tmpint2[pos0-1] != tmpint2[pos0]-1 )
- {
- addlocalhom_e( localhom[i]+j, start1, start2, tmpint1[pos0-1], tmpint2[pos0-1], opt );
- addlocalhom_e( localhom[j]+i, start2, start1, tmpint2[pos0-1], tmpint1[pos0-1], opt );
- start1 = tmpint1[pos0];
- start2 = tmpint2[pos0];
- opt = MIN( tmpdouble1[pos0], tmpdouble2[pos0] );
- }
- }
- if( tmpint1[pos0] == -1 || tmpint2[pos0] == -1 )
- {
- if( st == 1 )
- {
- st = 0;
- addlocalhom_e( localhom[i]+j, start1, start2, tmpint1[pos0-1], tmpint2[pos0-1], opt );
- addlocalhom_e( localhom[j]+i, start2, start1, tmpint2[pos0-1], tmpint1[pos0-1], opt );
- }
- }
- }
- }
- }
- }
-}
-#endif
-
-static void addlocalhom2_e( LocalHom *pt, LocalHom *lh, int sti, int stj, int eni, int enj, double opt, int overlp, int interm )
-{
-// dokka machigatteru
- if( pt != lh ) // susumeru
- {
- pt->next = (LocalHom *)calloc( 1, sizeof( LocalHom ) );
- pt = pt->next;
- pt->next = NULL;
- lh->last = pt;
- }
- else // sonomamatsukau
- {
- lh->last = pt;
- }
- lh->nokori++;
-// fprintf( stderr, "in addlocalhom2_e, pt = %p, pt->next = %p, interm=%d, sti-eni-stj-enj=%d %d %d %d\n", pt, pt->next, interm, sti, eni, stj, enj );
-
- pt->start1 = sti;
- pt->start2 = stj;
- pt->end1 = eni;
- pt->end2 = enj;
- pt->opt = opt;
- pt->extended = interm;
- pt->overlapaa = overlp;
-#if 0
- fprintf( stderr, "i: %d-%d\n", sti, eni );
- fprintf( stderr, "j: %d-%d\n", stj, enj );
- fprintf( stderr, "opt=%f\n", opt );
- fprintf( stderr, "overlp=%d\n", overlp );
-#endif
-}
-
-void extendlocalhom2( int nseq, LocalHom **localhom, double **dist )
-{
- int overlp, plim;
- int i, j, k;
- int pi, pj, pk, len;
- int status, sti, stj;
- int *ipt;
- int co;
- static int *ini = NULL;
- static int *inj = NULL;
- LocalHom *pt;
-
- sti = 0; // by D.Mathog, a guess
- stj = 0; // by D.Mathog, a guess
-
- if( ini == NULL )
- {
- ini = AllocateIntVec( nlenmax+1 );
- inj = AllocateIntVec( nlenmax+1 );
- }
-
-
- for( i=0; i<nseq-1; i++ )
- {
- for( j=i+1; j<nseq; j++ )
- {
-#if 0
- for( k=0; k<nseq; k++ ) sai[k] = 0;
- numint = ncons;
- while( 1 )
- {
- k = (int)( rnd() * nseq );
- if( k == i || k == j ) continue; // mou yatta nomo habuita hoga ii
- if( numint-- == 0 ) break;
- if( sai[k] ) continue;
- sai[k] = 1;
-#else
- for( k=0; k<nseq; k++ )
- {
-#endif
-// fprintf( stderr, "i=%d, j=%d, k=%d, dists = %f,%f,%f thrinter=%f\n", i, j, k, dist[i][j], dist[MIN(i,k)][MAX(i,k)], dist[MIN(j,k)][MAX(j,k)], thrinter );
- if( k == i || k == j ) continue; // mou yatta nomo habuita hoga ii
- if( dist[MIN(i,k)][MAX(i,k)] > dist[i][j] * thrinter || dist[MIN(j,k)][MAX(j,k)] > dist[i][j] * thrinter ) continue;
- ipt = ini; co = nlenmax+1;
- while( co-- ) *ipt++ = -1;
- ipt = inj; co = nlenmax+1;
- while( co-- ) *ipt++ = -1;
- overlp = 0;
-
- {
- for( pt=localhom[i]+k; pt; pt=pt->next )
- {
-// fprintf( stderr, "i=%d,k=%d,st1:st2=%d:%d,pt=%p,extended=%p\n", i, k, pt->start1, pt->start2, pt, pt->extended );
- if( pt->opt == -1 )
- {
- fprintf( stderr, "opt kainaide tbfast.c = %f\n", pt->opt );
- }
- if( pt->extended > -1 ) break;
- pi = pt->start1;
- pk = pt->start2;
- len = pt->end1 - pt->start1 + 1;
- ipt = ini + pk;
- while( len-- ) *ipt++ = pi++;
- }
- }
-
- {
- for( pt=localhom[j]+k; pt; pt=pt->next )
- {
- if( pt->opt == -1 )
- {
- fprintf( stderr, "opt kainaide tbfast.c = %f\n", pt->opt );
- }
- if( pt->extended > -1 ) break;
- pj = pt->start1;
- pk = pt->start2;
- len = pt->end1 - pt->start1 + 1;
- ipt = inj + pk;
- while( len-- ) *ipt++ = pj++;
- }
- }
-#if 0
- fprintf( stderr, "i=%d,j=%d,k=%d\n", i, j, k );
- overlp = 0;
- for( pk = 0; pk < nlenmax; pk++ )
- {
- if( ini[pk] != -1 && inj[pk] != -1 ) overlp++;
- fprintf( stderr, " %d", inj[pk] );
- }
- fprintf( stderr, "\n" );
-
- fprintf( stderr, "i=%d,j=%d,k=%d\n", i, j, k );
- overlp = 0;
- for( pk = 0; pk < nlenmax; pk++ )
- {
- if( ini[pk] != -1 && inj[pk] != -1 ) overlp++;
- fprintf( stderr, " %d", ini[pk] );
- }
- fprintf( stderr, "\n" );
-#endif
- overlp = 0;
- plim = nlenmax+1;
- for( pk = 0; pk < plim; pk++ )
- if( ini[pk] != -1 && inj[pk] != -1 ) overlp++;
-
-
- status = 0;
- plim = nlenmax+1;
- for( pk=0; pk<plim; pk++ )
- {
-// fprintf( stderr, "%d %d: %d-%d\n", i, j, ini[pk], inj[pk] );
- if( status )
- {
- if( ini[pk] == -1 || inj[pk] == -1 || ini[pk-1] != ini[pk] - 1 || inj[pk-1] != inj[pk] - 1 ) // saigonoshori
- {
- status = 0;
-// fprintf( stderr, "end here!\n" );
-
- pt = localhom[i][j].last;
-// fprintf( stderr, "in ex (ba), pt = %p, nokori=%d, i,j,k=%d,%d,%d\n", pt, localhom[i][j].nokori, i, j, k );
- addlocalhom2_e( pt, localhom[i]+j, sti, stj, ini[pk-1], inj[pk-1], MIN( localhom[i][k].opt, localhom[j][k].opt ) * 1.0, overlp, k );
-// fprintf( stderr, "in ex, pt = %p, pt->next = %p, pt->next->next = %p\n", pt, pt->next, pt->next->next );
-
- pt = localhom[j][i].last;
-// fprintf( stderr, "in ex (ba), pt = %p, pt->next = %p\n", pt, pt->next );
-// fprintf( stderr, "in ex (ba), pt = %p, pt->next = %p, k=%d\n", pt, pt->next, k );
- addlocalhom2_e( pt, localhom[j]+i, stj, sti, inj[pk-1], ini[pk-1], MIN( localhom[i][k].opt, localhom[j][k].opt ) * 1.0, overlp, k );
-// fprintf( stderr, "in ex, pt = %p, pt->next = %p, pt->next->next = %p\n", pt, pt->next, pt->next->next );
- }
- }
- if( !status ) // else deha arimasenn.
- {
- if( ini[pk] == -1 || inj[pk] == -1 ) continue;
- sti = ini[pk];
- stj = inj[pk];
-// fprintf( stderr, "start here!\n" );
- status = 1;
- }
- }
-// if( status ) fprintf( stderr, "end here\n" );
-
-// exit( 1 );
-// fprintf( hat3p, "%d %d %d %6.3f %d %d %d %d %p\n", i, j, tmpptr->overlapaa, tmpptr->opt, tmpptr->start1, tmpptr->end1, tmpptr->start2, tmpptr->end2, tmpptr->next );
- }
-#if 0
- for( pt=localhomtable[i]+j; pt; pt=pt->next )
- {
- if( tmpptr->opt == -1.0 ) continue;
- fprintf( hat3p, "%d %d %d %6.3f %d %d %d %d %p\n", i, j, tmpptr->overlapaa, tmpptr->opt, tmpptr->start1, tmpptr->end1, tmpptr->start2, tmpptr->end2, tmpptr->next );
- }
-#endif
- }
- }
-}
-
-int makelocal( char *s1, char *s2, int thr )
-{
- int start, maxstart, maxend;
- char *pt1, *pt2;
- double score;
- double maxscore;
-
- pt1 = s1;
- pt2 = s2;
-
- maxend = 0; // by D.Mathog, a guess
-
-// fprintf( stderr, "thr = %d, \ns1 = %s\ns2 = %s\n", thr, s1, s2 );
- maxscore = 0.0;
- score = 0.0;
- start = 0;
- maxstart = 0;
- while( *pt1 )
- {
-// fprintf( stderr, "*pt1 = %c*pt2 = %c\n", *pt1, *pt2 );
- if( *pt1 == '-' || *pt2 == '-' )
- {
-// fprintf( stderr, "penalty = %d\n", penalty );
- score += penalty;
- while( *pt1 == '-' || *pt2 == '-' )
- {
- pt1++; pt2++;
- }
- continue;
- }
-
- score += ( amino_dis[(int)*pt1++][(int)*pt2++] - thr );
-// score += ( amino_dis[(int)*pt1++][(int)*pt2++] );
- if( score > maxscore )
- {
-// fprintf( stderr, "score = %f\n", score );
- maxscore = score;
- maxstart = start;
-// fprintf( stderr, "## max! maxstart = %d, start = %d\n", maxstart, start );
- }
- if( score < 0.0 )
- {
-// fprintf( stderr, "## resetting, start = %d, maxstart = %d\n", start, maxstart );
- if( start == maxstart )
- {
- maxend = pt1 - s1;
-// fprintf( stderr, "maxend = %d\n", maxend );
- }
- score = 0.0;
- start = pt1 - s1;
- }
- }
- if( start == maxstart )
- maxend = pt1 - s1 - 1;
-
-// fprintf( stderr, "maxstart = %d, maxend = %d, maxscore = %f\n", maxstart, maxend, maxscore );
- s1[maxend+1] = 0;
- s2[maxend+1] = 0;
- return( maxstart );
-}
-
-void resetlocalhom( int nseq, LocalHom **lh )
-{
- int i, j;
- LocalHom *pt;
-
- for( i=0; i<nseq-1; i++ ) for( j=i+1; j<nseq; j++ )
- {
- for( pt=lh[i]+j; pt; pt=pt->next )
- pt->opt = 1.0;
- }
-
-}
-
-void gapireru( char *res, char *ori, char *gt )
-{
- char g;
- while( (g = *gt++) )
- {
- if( g == '-' )
- {
- *res++ = *newgapstr;
- }
- else
- {
- *res++ = *ori++;
- }
- }
- *res = 0;
-}
-
-void getkyokaigap( char *g, char **s, int pos, int n )
-{
-// char *bk = g;
-// while( n-- ) *g++ = '-';
- while( n-- ) *g++ = (*s++)[pos];
-
-// fprintf( stderr, "bk = %s\n", bk );
-}
-
-void new_OpeningGapCount( float *ogcp, int clus, char **seq, double *eff, int len, char *sgappat )
-#if 0
-{
- int i, j, gc, gb;
- float feff;
-
-
- for( i=0; i<len+1; i++ ) ogcp[i] = 0.0;
- for( j=0; j<clus; j++ )
- {
- feff = (float)eff[j];
- gc = ( sgappat[j] == '-' );
- for( i=0; i<len; i++ )
- {
- gb = gc;
- gc = ( seq[j][i] == '-' );
- if( !gb * gc ) ogcp[i] += feff;
- }
- }
-}
-#else
-{
- int i, j, gc, gb;
- float feff;
- float *fpt;
- char *spt;
-
- fpt = ogcp;
- i = len;
- while( i-- ) *fpt++ = 0.0;
- for( j=0; j<clus; j++ )
- {
- feff = (float)eff[j];
- spt = seq[j];
- fpt = ogcp;
- gc = ( sgappat[j] == '-' );
- i = len;
- while( i-- )
- {
- gb = gc;
- gc = ( *spt++ == '-' );
- {
- if( !gb * gc ) *fpt += feff;
- fpt++;
- }
- }
- }
-}
-#endif
-void new_OpeningGapCount_zure( float *ogcp, int clus, char **seq, double *eff, int len, char *sgappat, char *egappat )
-#if 0
-{
- int i, j, gc, gb;
- float feff;
-
-
- for( i=0; i<len+1; i++ ) ogcp[i] = 0.0;
- for( j=0; j<clus; j++ )
- {
- feff = (float)eff[j];
- gc = ( sgappat[j] == '-' );
- for( i=0; i<len; i++ )
- {
- gb = gc;
- gc = ( seq[j][i] == '-' );
- if( !gb * gc ) ogcp[i] += feff;
- }
- {
- gb = gc;
- gc = ( egappat[j] == '-' );
- if( !gb * gc ) ogcp[i] += feff;
- }
- }
-}
-#else
-{
- int i, j, gc, gb;
- float feff;
- float *fpt;
- char *spt;
-
- fpt = ogcp;
- i = len+2;
- while( i-- ) *fpt++ = 0.0;
- for( j=0; j<clus; j++ )
- {
- feff = (float)eff[j];
- spt = seq[j];
- fpt = ogcp;
- gc = ( sgappat[j] == '-' );
- i = len;
- while( i-- )
- {
- gb = gc;
- gc = ( *spt++ == '-' );
- {
- if( !gb * gc ) *fpt += feff;
- fpt++;
- }
- }
- {
- gb = gc;
- gc = ( egappat[j] == '-' );
- if( !gb * gc ) *fpt += feff;
- }
- }
-}
-#endif
-
-void new_FinalGapCount_zure( float *fgcp, int clus, char **seq, double *eff, int len, char *sgappat, char *egappat )
-#if 0
-{
- int i, j, gc, gb;
- float feff;
-
- for( i=0; i<len+1; i++ ) fgcp[i] = 0.0;
- for( j=0; j<clus; j++ )
- {
- feff = (float)eff[j];
- gc = ( sgappat[j] == '-' );
- for( i=0; i<len; i++ )
- {
- gb = gc;
- gc = ( seq[j][i] == '-' );
- {
- if( gb * !gc ) fgcp[i] += feff;
- }
- }
- {
- gb = gc;
- gc = ( egappat[j] == '-' );
- {
- if( gb * !gc ) fgcp[len] += feff;
- }
- }
- }
-}
-#else
-{
- int i, j, gc, gb;
- float feff;
- float *fpt;
- char *spt;
-
- fpt = fgcp;
- i = len+2;
- while( i-- ) *fpt++ = 0.0;
- for( j=0; j<clus; j++ )
- {
- feff = (float)eff[j];
- fpt = fgcp;
- spt = seq[j];
- gc = ( sgappat[j] == '-' );
- i = len;
- while( i-- )
- {
- gb = gc;
- gc = ( *spt++ == '-' );
- {
- if( gb * !gc ) *fpt += feff;
- fpt++;
- }
- }
- {
- gb = gc;
- gc = ( egappat[j] == '-' );
- {
- if( gb * !gc ) *fpt += feff;
- }
- }
- }
-}
-#endif
-void new_FinalGapCount( float *fgcp, int clus, char **seq, double *eff, int len, char *egappat )
-#if 0
-{
- int i, j, gc, gb;
- float feff;
-
- for( i=0; i<len; i++ ) fgcp[i] = 0.0;
- for( j=0; j<clus; j++ )
- {
- feff = (float)eff[j];
- gc = ( seq[j][0] == '-' );
- for( i=1; i<len; i++ )
- {
- gb = gc;
- gc = ( seq[j][i] == '-' );
- {
- if( gb * !gc ) fgcp[i-1] += feff;
- }
- }
- {
- gb = gc;
- gc = ( egappat[j] == '-' );
- {
- if( gb * !gc ) fgcp[len-1] += feff;
- }
- }
- }
-}
-#else
-{
- int i, j, gc, gb;
- float feff;
- float *fpt;
- char *spt;
-
- fpt = fgcp;
- i = len;
- while( i-- ) *fpt++ = 0.0;
- for( j=0; j<clus; j++ )
- {
- feff = (float)eff[j];
- fpt = fgcp;
- spt = seq[j];
- gc = ( *spt == '-' );
- i = len;
- while( i-- )
- {
- gb = gc;
- gc = ( *++spt == '-' );
- {
- if( gb * !gc ) *fpt += feff;
- fpt++;
- }
- }
- {
- gb = gc;
- gc = ( egappat[j] == '-' );
- {
- if( gb * !gc ) *fpt += feff;
- }
- }
- }
-}
-#endif
-
-void st_OpeningGapCount( float *ogcp, int clus, char **seq, double *eff, int len )
-{
- int i, j, gc, gb;
- float feff;
- float *fpt;
- char *spt;
-
- fpt = ogcp;
- i = len;
- while( i-- ) *fpt++ = 0.0;
- for( j=0; j<clus; j++ )
- {
- feff = (float)eff[j];
- spt = seq[j];
- fpt = ogcp;
- gc = 0;
-// gc = 1;
- i = len;
- while( i-- )
- {
- gb = gc;
- gc = ( *spt++ == '-' );
- {
- if( !gb * gc ) *fpt += feff;
- fpt++;
- }
- }
- }
- ogcp[len] = 0.0;
-}
-
-void st_FinalGapCount_zure( float *fgcp, int clus, char **seq, double *eff, int len )
-{
- int i, j, gc, gb;
- float feff;
- float *fpt;
- char *spt;
-
- fpt = fgcp;
- i = len+1;
- while( i-- ) *fpt++ = 0.0;
- for( j=0; j<clus; j++ )
- {
- feff = (float)eff[j];
- fpt = fgcp+1;
- spt = seq[j];
- gc = ( *spt == '-' );
- i = len;
-// for( i=1; i<len; i++ )
- while( i-- )
- {
- gb = gc;
- gc = ( *++spt == '-' );
- {
- if( gb * !gc ) *fpt += feff;
- fpt++;
- }
- }
- {
- gb = gc;
- gc = 0;
-// gc = 1;
- {
- if( gb * !gc ) *fpt += feff;
- }
- }
- }
-}
-
-void st_FinalGapCount( float *fgcp, int clus, char **seq, double *eff, int len )
-{
- int i, j, gc, gb;
- float feff;
- float *fpt;
- char *spt;
-
- fpt = fgcp;
- i = len;
- while( i-- ) *fpt++ = 0.0;
- for( j=0; j<clus; j++ )
- {
- feff = (float)eff[j];
- fpt = fgcp;
- spt = seq[j];
- gc = ( *spt == '-' );
- i = len;
-// for( i=1; i<len; i++ )
- while( i-- )
- {
- gb = gc;
- gc = ( *++spt == '-' );
- {
- if( gb * !gc ) *fpt += feff;
- fpt++;
- }
- }
- {
- gb = gc;
- gc = 0;
-// gc = 1;
- {
- if( gb * !gc ) *fpt += feff;
- }
- }
- }
-}
-
-void getGapPattern( float *fgcp, int clus, char **seq, double *eff, int len, char *xxx )
-{
- int i, j, gc, gb;
- float feff;
- float *fpt;
- char *spt;
-
- fpt = fgcp;
- i = len+1;
- while( i-- ) *fpt++ = 0.0;
- for( j=0; j<clus; j++ )
- {
- feff = (float)eff[j];
- fpt = fgcp;
- spt = seq[j];
- gc = ( *spt == '-' );
- i = len+1;
- while( i-- )
- {
- gb = gc;
- gc = ( *++spt == '-' );
- {
- if( gb * !gc ) *fpt += feff;
- fpt++;
- }
- }
-#if 0
- {
- gb = gc;
- gc = ( egappat[j] == '-' );
- {
- if( gb * !gc ) *fpt += feff;
- }
- }
-#endif
- }
- for( j=0; j<len; j++ )
- {
- fprintf( stderr, "%d, %f\n", j, fgcp[j] );
- }
-}
-
-void getdigapfreq_st( float *freq, int clus, char **seq, double *eff, int len )
-{
- int i, j;
- float feff;
- for( i=0; i<len+1; i++ ) freq[i] = 0.0;
- for( i=0; i<clus; i++ )
- {
- feff = eff[i];
- if( 0 && seq[i][0] == '-' ) // machigai kamo
- freq[0] += feff;
- for( j=1; j<len; j++ )
- {
- if( seq[i][j] == '-' && seq[i][j-1] == '-' )
- freq[j] += feff;
- }
- if( 0 && seq[i][len-1] == '-' )
- freq[len] += feff;
- }
-// fprintf( stderr, "\ndigapf = \n" );
-// for( i=0; i<len+1; i++ ) fprintf( stderr, "%5.3f ", freq[i] );
-}
-
-void getdiaminofreq_x( float *freq, int clus, char **seq, double *eff, int len )
-{
- int i, j;
- float feff;
- for( i=0; i<len+2; i++ ) freq[i] = 0.0;
- for( i=0; i<clus; i++ )
- {
- feff = eff[i];
- if( seq[i][0] != '-' ) // tadashii
- freq[0] += feff;
- for( j=1; j<len; j++ )
- {
- if( seq[i][j] != '-' && seq[i][j-1] != '-' )
- freq[j] += feff;
- }
- if( 1 && seq[i][len-1] != '-' ) // xxx wo tsukawanaitoki [len-1] nomi
- freq[len] += feff;
- }
-// fprintf( stderr, "\ndiaaf = \n" );
-// for( i=0; i<len+1; i++ ) fprintf( stderr, "%5.3f ", freq[i] );
-}
-
-void getdiaminofreq_st( float *freq, int clus, char **seq, double *eff, int len )
-{
- int i, j;
- float feff;
- for( i=0; i<len+1; i++ ) freq[i] = 0.0;
- for( i=0; i<clus; i++ )
- {
- feff = eff[i];
- if( seq[i][0] != '-' )
- freq[0] += feff;
- for( j=1; j<len; j++ )
- {
- if( seq[i][j] != '-' && seq[i][j-1] != '-' )
- freq[j] += feff;
- }
-// if( 1 && seq[i][len-1] != '-' ) // xxx wo tsukawanaitoki [len-1] nomi
- freq[len] += feff;
- }
-// fprintf( stderr, "\ndiaaf = \n" );
-// for( i=0; i<len+1; i++ ) fprintf( stderr, "%5.3f ", freq[i] );
-}
-
-void getdigapfreq_part( float *freq, int clus, char **seq, double *eff, int len, char *sgappat, char *egappat )
-{
- int i, j;
- float feff;
- for( i=0; i<len+2; i++ ) freq[i] = 0.0;
- for( i=0; i<clus; i++ )
- {
- feff = eff[i];
-// if( seq[i][0] == '-' )
- if( seq[i][0] == '-' && sgappat[i] == '-' )
- freq[0] += feff;
- for( j=1; j<len; j++ )
- {
- if( seq[i][j] == '-' && seq[i][j-1] == '-' )
- freq[j] += feff;
- }
-// if( seq[i][len] == '-' && seq[i][len-1] == '-' ) // xxx wo tsukawanaitoki arienai
- if( egappat[i] == '-' && seq[i][len-1] == '-' )
- freq[len] += feff;
- }
-// fprintf( stderr, "\ndigapf = \n" );
-// for( i=0; i<len+1; i++ ) fprintf( stderr, "%5.3f ", freq[i] );
-}
-
-void getdiaminofreq_part( float *freq, int clus, char **seq, double *eff, int len, char *sgappat, char *egappat )
-{
- int i, j;
- float feff;
- for( i=0; i<len+2; i++ ) freq[i] = 0.0;
- for( i=0; i<clus; i++ )
- {
- feff = eff[i];
- if( seq[i][0] != '-' && sgappat[i] != '-' )
- freq[0] += feff;
- for( j=1; j<len; j++ )
- {
- if( seq[i][j] != '-' && seq[i][j-1] != '-' )
- freq[j] += feff;
- }
-// if( 1 && seq[i][len-1] != '-' ) // xxx wo tsukawanaitoki [len-1] nomi
- if( egappat[i] != '-' && seq[i][len-1] != '-' ) // xxx wo tsukawanaitoki [len-1] nomi
- freq[len] += feff;
- }
-// fprintf( stderr, "\ndiaaf = \n" );
-// for( i=0; i<len+1; i++ ) fprintf( stderr, "%5.3f ", freq[i] );
-}
-
-void getgapfreq_zure_part( float *freq, int clus, char **seq, double *eff, int len, char *sgap )
-{
- int i, j;
- float feff;
- for( i=0; i<len+2; i++ ) freq[i] = 0.0;
- for( i=0; i<clus; i++ )
- {
- feff = eff[i];
- if( sgap[i] == '-' )
- freq[0] += feff;
- for( j=0; j<len; j++ )
- {
- if( seq[i][j] == '-' )
- freq[j+1] += feff;
- }
-// if( egap[i] == '-' )
-// freq[len+1] += feff;
- }
-// fprintf( stderr, "\ngapf = \n" );
-// for( i=0; i<len+1; i++ ) fprintf( stderr, "%5.3f ", freq[i] );
-}
-
-void getgapfreq_zure( float *freq, int clus, char **seq, double *eff, int len )
-{
- int i, j;
- float feff;
- for( i=0; i<len+1; i++ ) freq[i] = 0.0;
- for( i=0; i<clus; i++ )
- {
- feff = eff[i];
- for( j=0; j<len; j++ )
- {
- if( seq[i][j] == '-' )
- freq[j+1] += feff;
- }
- }
- freq[len+1] = 0.0;
-// fprintf( stderr, "\ngapf = \n" );
-// for( i=0; i<len+1; i++ ) fprintf( stderr, "%5.3f ", freq[i] );
-}
-
-void getgapfreq( float *freq, int clus, char **seq, double *eff, int len )
-{
- int i, j;
- float feff;
- for( i=0; i<len+1; i++ ) freq[i] = 0.0;
- for( i=0; i<clus; i++ )
- {
- feff = eff[i];
- for( j=0; j<len; j++ )
- {
- if( seq[i][j] == '-' )
- freq[j] += feff;
- }
- }
- freq[len] = 0.0;
-// fprintf( stderr, "\ngapf = \n" );
-// for( i=0; i<len+1; i++ ) fprintf( stderr, "%5.3f ", freq[i] );
-}
-
-void st_getGapPattern( Gappat **pat, int clus, char **seq, double *eff, int len )
-{
- int i, j, k, gb, gc;
- int known;
- float feff;
- Gappat **fpt;
- char *spt;
- int gaplen;
-
- fpt = pat;
- i = len+1;
- while( i-- )
- {
- if( *fpt ) free( *fpt );
- *fpt++ = NULL;
- }
-
- for( j=0; j<clus; j++ )
- {
-// fprintf( stderr, "seq[%d] = %s\n", j, seq[j] );
- feff = (float)eff[j];
-
- fpt = pat;
- *fpt = NULL; // Falign.c kara yobareru tokiha chigau.
- spt = seq[j];
- gc = 0;
- gaplen = 0;
-
- for( i=0; i<len+1; i++ )
-// while( i-- )
- {
-// fprintf( stderr, "i=%d, gaplen = %d\n", i, gaplen );
- gb = gc;
- gc = ( i != len && *spt++ == '-' );
- if( gc )
- gaplen++;
- else
- {
- if( gb && gaplen )
- {
- k = 1;
- known = 0;
- if( *fpt ) for( ; (*fpt)[k].len != -1; k++ )
- {
- if( (*fpt)[k].len == gaplen )
- {
-// fprintf( stderr, "known\n" );
- known = 1;
- break;
- }
- }
-
- if( known == 0 )
- {
- *fpt = (Gappat *)realloc( *fpt, (k+3) * sizeof( Gappat ) ); // mae1 (total), ato2 (len0), term
- if( !*fpt )
- {
- fprintf( stderr, "Cannot allocate gappattern!'n" );
- fprintf( stderr, "Use an approximate method, with the --mafft5 option.\n" );
- exit( 1 );
- }
- (*fpt)[k].freq = 0.0;
- (*fpt)[k].len = gaplen;
- (*fpt)[k+1].len = -1;
- (*fpt)[k+1].freq = 0.0; // iranai
-// fprintf( stderr, "gaplen=%d, Unknown, %f\n", gaplen, (*fpt)[k].freq );
- }
-
-// fprintf( stderr, "adding pos %d, len=%d, k=%d, freq=%f->", i, gaplen, k, (*fpt)[k].freq );
- (*fpt)[k].freq += feff;
-// fprintf( stderr, "%f\n", (*fpt)[k].freq );
- gaplen = 0;
- }
- }
- fpt++;
- }
- }
-#if 1
- for( j=0; j<len+1; j++ )
- {
- if( pat[j] )
- {
-// fprintf( stderr, "j=%d\n", j );
-// for( i=1; pat[j][i].len!=-1; i++ )
-// fprintf( stderr, "pos=%d, i=%d, len=%d, freq=%f\n", j, i, pat[j][i].len, pat[j][i].freq );
-
- pat[j][0].len = 0; // iminashi
- pat[j][0].freq = 0.0;
- for( i=1; pat[j][i].len!=-1;i++ )
- {
- pat[j][0].freq += pat[j][i].freq;
-// fprintf( stderr, "totaling, i=%d, result = %f\n", i, pat[j][0].freq );
- }
-// fprintf( stderr, "totaled, result = %f\n", pat[j][0].freq );
-
- pat[j][i].freq = 1.0 - pat[j][0].freq;
- pat[j][i].len = 0; // imiari
- pat[j][i+1].len = -1;
- }
- else
- {
- pat[j] = (Gappat *)calloc( 3, sizeof( Gappat ) );
- pat[j][0].freq = 0.0;
- pat[j][0].len = 0; // iminashi
-
- pat[j][1].freq = 1.0 - pat[j][0].freq;
- pat[j][1].len = 0; // imiari
- pat[j][2].len = -1;
- }
- }
-#endif
-}
-
-static void commongappickpair( char *r1, char *r2, char *i1, char *i2 )
-{
-// strcpy( r1, i1 );
-// strcpy( r2, i2 );
-// return; // not SP
- while( *i1 )
- {
- if( *i1 == '-' && *i2 == '-' )
- {
- i1++;
- i2++;
- }
- else
- {
- *r1++ = *i1++;
- *r2++ = *i2++;
- }
- }
- *r1 = 0;
- *r2 = 0;
-}
-
-float naiveRpairscore( int n1, int n2, char **seq1, char **seq2, double *eff1, double *eff2, int penal )
-{
-// return( 0 );
- int i, j;
- float val;
- float valf;
- int pv;
- double deff;
- char *p1, *p2, *p1p, *p2p;
- val = 0.0;
- for( i=0; i<n1; i++ ) for( j=0; j<n2; j++ )
- {
- deff = eff1[i] * eff2[j];
-// fprintf( stderr, "feff %d-%d = %f\n", i, j, feff );
-// fprintf( stderr, "i1 = %s\n", seq1[i] );
-// fprintf( stderr, "i2 = %s\n", seq2[j] );
-// fprintf( stderr, "s1 = %s\n", s1 );
-// fprintf( stderr, "s2 = %s\n", s2 );
-// fprintf( stderr, "penal = %d\n", penal );
-
- valf = 0;
- p1 = seq1[i]; p2 = seq2[j];
- pv = 0;
- if( *p1 == '-' && *p2 != '-' )
- pv = penal;
- if( *p1 != '-' && *p2 == '-' )
- pv = penal;
-// if( pv ) fprintf( stderr, "Penal!, %f, %d-%d, pos1,pos2=%d,%d\n", pv * deff * 0.5, i, j, p1-seq1[i], p2-seq2[j] );
- p1p = p1; p2p = p2;
- valf += (float)amino_dis[(int)*p1++][(int)*p2++] + 0.5 * pv;
- while( *p1p )
- {
- pv = 0;
- if( *p1p != '-' && *p2p != '-' )
- {
- if( *p1 == '-' && *p2 != '-' )
- pv = penal;
- if( *p1 != '-' && *p2 == '-' )
- pv = penal;
- if( *p1 != '-' && *p2 != '-' )
- ;
- if( *p1 == '-' && *p2 == '-' )
- ;
- }
- if( *p1p == '-' && *p2p == '-' )
- {
- if( *p1 == '-' && *p2 != '-' )
- pv = penal;
-// ;
- if( *p1 != '-' && *p2 == '-' )
- pv = penal;
-// ;
- if( *p1 != '-' && *p2 != '-' )
- ;
- if( *p1 == '-' && *p2 == '-' )
- ;
- }
- if( *p1p != '-' && *p2p == '-' )
- {
- if( *p1 == '-' && *p2 != '-' )
- pv = penal * 2; // ??
-// ;
- if( *p1 != '-' && *p2 == '-' )
- ;
- if( *p1 != '-' && *p2 != '-' )
- pv = penal;
-// ;
- if( *p1 == '-' && *p2 == '-' )
- pv = penal;
-// ;
- }
- if( *p1p == '-' && *p2p != '-' )
- {
- if( *p1 == '-' && *p2 != '-' )
- ;
- if( *p1 != '-' && *p2 == '-' )
- pv = penal * 2; // ??
-// ;
- if( *p1 != '-' && *p2 != '-' )
- pv = penal;
-// ;
- if( *p1 == '-' && *p2 == '-' )
- pv = penal;
-// ;
- }
-// fprintf( stderr, "adding %c-%c, %d\n", *p1, *p2, amino_dis[*p1][*p2] );
-// if( pv ) fprintf( stderr, "Penal!, %f, %d-%d, pos1,pos2=%d,%d\n", pv * deff * 0.5, i, j, p1-seq1[i], p2-seq2[j] );
- valf += amino_dis[(int)*p1++][(int)*p2++] + 0.5 * pv;
- p1p++; p2p++;
- }
-// fprintf( stderr, "valf = %d\n", valf );
- val += deff * ( valf );
- }
- fprintf( stderr, "val = %f\n", val );
- return( val );
-// exit( 1 );
-}
-float naiveQpairscore( int n1, int n2, char **seq1, char **seq2, double *eff1, double *eff2, int penal )
-{
- int i, j;
- float val;
- float valf;
- int pv;
- double deff;
- char *p1, *p2, *p1p, *p2p;
- return( 0 );
- val = 0.0;
- for( i=0; i<n1; i++ ) for( j=0; j<n2; j++ )
- {
- deff = eff1[i] * eff2[j];
-// fprintf( stderr, "feff %d-%d = %f\n", i, j, feff );
-// fprintf( stderr, "i1 = %s\n", seq1[i] );
-// fprintf( stderr, "i2 = %s\n", seq2[j] );
-// fprintf( stderr, "s1 = %s\n", s1 );
-// fprintf( stderr, "s2 = %s\n", s2 );
-// fprintf( stderr, "penal = %d\n", penal );
-
- valf = 0;
- p1 = seq1[i]; p2 = seq2[j];
- pv = 0;
- if( *p1 == '-' && *p2 != '-' )
- pv = penal;
- if( *p1 != '-' && *p2 == '-' )
- pv = penal;
-// if( pv ) fprintf( stderr, "Penal!, %f, %d-%d, pos1,pos2=%d,%d\n", pv * deff * 0.5, i, j, p1-seq1[i], p2-seq2[j] );
- p1p = p1; p2p = p2;
- valf += (float)amino_dis[(int)*p1++][(int)*p2++] + 0.5 * pv;
- while( *p1p )
- {
- pv = 0;
- if( *p1p != '-' && *p2p != '-' )
- {
- if( *p1 == '-' && *p2 != '-' )
- pv = penal;
- if( *p1 != '-' && *p2 == '-' )
- pv = penal;
- if( *p1 != '-' && *p2 != '-' )
- ;
- if( *p1 == '-' && *p2 == '-' )
- ;
- }
- if( *p1p == '-' && *p2p == '-' )
- {
- if( *p1 == '-' && *p2 != '-' )
-// pv = penal;
- ;
- if( *p1 != '-' && *p2 == '-' )
-// pv = penal;
- ;
- if( *p1 != '-' && *p2 != '-' )
- ;
- if( *p1 == '-' && *p2 == '-' )
- ;
- }
- if( *p1p != '-' && *p2p == '-' )
- {
- if( *p1 == '-' && *p2 != '-' )
- pv = penal * 2; // ??
-// ;
- if( *p1 != '-' && *p2 == '-' )
- ;
- if( *p1 != '-' && *p2 != '-' )
- pv = penal;
-// ;
- if( *p1 == '-' && *p2 == '-' )
-// pv = penal;
- ;
- }
- if( *p1p == '-' && *p2p != '-' )
- {
- if( *p1 == '-' && *p2 != '-' )
- ;
- if( *p1 != '-' && *p2 == '-' )
- pv = penal * 2; // ??
-// ;
- if( *p1 != '-' && *p2 != '-' )
- pv = penal;
-// ;
- if( *p1 == '-' && *p2 == '-' )
-// pv = penal;
- ;
- }
-// fprintf( stderr, "adding %c-%c, %d\n", *p1, *p2, amino_dis[*p1][*p2] );
-// if( pv ) fprintf( stderr, "Penal!, %f, %d-%d, pos1,pos2=%d,%d\n", pv * deff * 0.5, i, j, p1-seq1[i], p2-seq2[j] );
- valf += amino_dis[(int)*p1++][(int)*p2++] + 0.5 * pv;
- p1p++; p2p++;
- }
-// fprintf( stderr, "valf = %d\n", valf );
- val += deff * ( valf );
- }
- fprintf( stderr, "val = %f\n", val );
- return( val );
-// exit( 1 );
-}
-float naiveHpairscore( int n1, int n2, char **seq1, char **seq2, double *eff1, double *eff2, int penal )
-{
- int i, j;
- float val;
- float valf;
- int pv;
-// float feff = 0.0; // by D.Mathog, a guess
- double deff;
- char *p1, *p2, *p1p, *p2p;
- val = 0.0;
- for( i=0; i<n1; i++ ) for( j=0; j<n2; j++ )
- {
- deff = eff1[i] * eff2[j];
-// fprintf( stderr, "i1 = %s\n", seq1[i] );
-// fprintf( stderr, "i2 = %s\n", seq2[j] );
-// fprintf( stderr, "s1 = %s\n", s1 );
-// fprintf( stderr, "s2 = %s\n", s2 );
-// fprintf( stderr, "penal = %d\n", penal );
-
- valf = 0;
- p1 = seq1[i]; p2 = seq2[j];
- pv = 0;
- if( *p1 == '-' && *p2 != '-' )
- pv = penal;
- if( *p1 != '-' && *p2 == '-' )
- pv = penal;
- if( pv ) fprintf( stderr, "Penal!, %f, %d-%d, pos1,pos2=%d,%d\n", pv * deff * 0.5, i, j, (int)(p1-seq1[i]), (int)(p2-seq2[j]) );
- p1p = p1; p2p = p2;
- valf += (float)amino_dis[(int)*p1++][(int)*p2++] + 0.5 * pv;
- while( *p1p )
- {
- pv = 0;
- if( *p1p != '-' && *p2p != '-' )
- {
- if( *p1 == '-' && *p2 != '-' )
- pv = penal;
- if( *p1 != '-' && *p2 == '-' )
- pv = penal;
- if( *p1 != '-' && *p2 != '-' )
- ;
- if( *p1 == '-' && *p2 == '-' )
- ;
- }
- if( *p1p == '-' && *p2p == '-' )
- {
- if( *p1 == '-' && *p2 != '-' )
-// pv = penal;
- ;
- if( *p1 != '-' && *p2 == '-' )
-// pv = penal;
- ;
- if( *p1 != '-' && *p2 != '-' )
- ;
- if( *p1 == '-' && *p2 == '-' )
- ;
- }
- if( *p1p != '-' && *p2p == '-' )
- {
- if( *p1 == '-' && *p2 != '-' )
-// pv = penal;
- ;
- if( *p1 != '-' && *p2 == '-' )
- ;
- if( *p1 != '-' && *p2 != '-' )
- pv = penal;
- if( *p1 == '-' && *p2 == '-' )
-// pv = penal;
- ;
- }
- if( *p1p == '-' && *p2p != '-' )
- {
- if( *p1 == '-' && *p2 != '-' )
- ;
- if( *p1 != '-' && *p2 == '-' )
-// pv = penal;
- ;
- if( *p1 != '-' && *p2 != '-' )
- pv = penal;
- if( *p1 == '-' && *p2 == '-' )
-// pv = penal;
- ;
- }
-// fprintf( stderr, "adding %c-%c, %d\n", *p1, *p2, amino_dis[*p1][*p2] );
-// if( pv ) fprintf( stderr, "Penal!, %f, %d-%d, pos1,pos2=%d,%d\n", pv * deff * 0.5, i, j, p1-seq1[i], p2-seq2[j] );
- valf += amino_dis[(int)*p1++][(int)*p2++] + 0.5 * pv;
- p1p++; p2p++;
- }
-// fprintf( stderr, "valf = %d\n", valf );
- val += deff * ( valf );
- }
- fprintf( stderr, "val = %f\n", val );
- return( val );
-// exit( 1 );
-}
-
-float naivepairscore11( char *seq1, char *seq2, int penal )
-{
- float vali;
- int len = strlen( seq1 );
- char *s1, *s2, *p1, *p2;
- s1 = calloc( len+1, sizeof( char ) );
- s2 = calloc( len+1, sizeof( char ) );
- {
- vali = 0.0;
- commongappickpair( s1, s2, seq1, seq2 );
-// fprintf( stderr, "###i1 = %s\n", seq1 );
-// fprintf( stderr, "###i2 = %s\n", seq2 );
-// fprintf( stderr, "###penal = %d\n", penal );
-
- p1 = s1; p2 = s2;
- while( *p1 )
- {
- if( *p1 == '-' )
- {
-// fprintf( stderr, "Penal! %c-%c in %d-%d, %f\n", *(p1-1), *(p2-1), i, j, feff );
- vali += (float)penal;
-// while( *p1 == '-' || *p2 == '-' )
- while( *p1 == '-' ) // SP
- {
- p1++;
- p2++;
- }
- continue;
- }
- if( *p2 == '-' )
- {
-// fprintf( stderr, "Penal! %c-%c in %d-%d, %f\n", *(p1-1), *(p2-1), i, j, feff );
- vali += (float)penal;
-// while( *p2 == '-' || *p1 == '-' )
- while( *p2 == '-' ) // SP
- {
- p1++;
- p2++;
- }
- continue;
- }
-// fprintf( stderr, "adding %c-%c, %d\n", *p1, *p2, amino_dis[*p1][*p2] );
- vali += (float)amino_dis[(int)*p1++][(int)*p2++];
- }
- }
- free( s1 );
- free( s2 );
-// fprintf( stderr, "###vali = %d\n", vali );
- return( vali );
-}
-
-float naivepairscore( int n1, int n2, char **seq1, char **seq2, double *eff1, double *eff2, int penal )
-{
-// return( 0.0 );
- int i, j;
- float val;
- int vali;
- float feff;
- int len = strlen( seq1[0] );
- char *s1, *s2, *p1, *p2;
- s1 = calloc( len+1, sizeof( char ) );
- s2 = calloc( len+1, sizeof( char ) );
- val = 0.0;
- for( i=0; i<n1; i++ ) for( j=0; j<n2; j++ )
- {
- vali = 0;
- feff = eff1[i] * eff2[j];
-// fprintf( stderr, "feff %d-%d = %f\n", i, j, feff );
- commongappickpair( s1, s2, seq1[i], seq2[j] );
-// fprintf( stderr, "i1 = %s\n", seq1[i] );
-// fprintf( stderr, "i2 = %s\n", seq2[j] );
-// fprintf( stderr, "s1 = %s\n", s1 );
-// fprintf( stderr, "s2 = %s\n", s2 );
-// fprintf( stderr, "penal = %d\n", penal );
-
- p1 = s1; p2 = s2;
- while( *p1 )
- {
- if( *p1 == '-' )
- {
-// fprintf( stderr, "Penal! %c-%c in %d-%d, %f\n", *(p1-1), *(p2-1), i, j, feff );
- vali += penal;
-// while( *p1 == '-' || *p2 == '-' )
- while( *p1 == '-' ) // SP
- {
- p1++;
- p2++;
- }
- continue;
- }
- if( *p2 == '-' )
- {
-// fprintf( stderr, "Penal! %c-%c in %d-%d, %f\n", *(p1-1), *(p2-1), i, j, feff );
- vali += penal;
-// while( *p2 == '-' || *p1 == '-' )
- while( *p2 == '-' ) // SP
- {
- p1++;
- p2++;
- }
- continue;
- }
-// fprintf( stderr, "adding %c-%c, %d\n", *p1, *p2, amino_dis[*p1][*p2] );
- vali += amino_dis[(int)*p1++][(int)*p2++];
- }
-// fprintf( stderr, "vali = %d\n", vali );
- val += feff * vali;
- }
- free( s1 );
- free( s2 );
- fprintf( stderr, "val = %f\n", val );
- return( val );
-// exit( 1 );
-}
-
-double plainscore( int nseq, char **s )
-{
- int i, j, ilim;
- double v = 0.0;
-
- ilim = nseq-1;
- for( i=0; i<ilim; i++ ) for( j=i+1; j<nseq; j++ )
- {
- v += (double)naivepairscore11( s[i], s[j], penalty );
- }
-
- fprintf( stderr, "penalty = %d\n", penalty );
-
- return( v );
-}
-
git://source.jalview.org / jabaws.git / blobdiff