+++ /dev/null
-#include "mltaln.h"
-#include "dp.h"
-
-#define DEBUG 0
-
-static void match_calc( float *match, float **cpmx1, float **cpmx2, int i1, int lgth2, float **floatwork, int **intwork, int initialize )
-{
- int j, k, l;
- float scarr[26];
- float **cpmxpd = floatwork;
- int **cpmxpdn = intwork;
- int count = 0;
-
- if( initialize )
- {
- for( j=0; j<lgth2; j++ )
- {
- count = 0;
- for( l=0; l<26; l++ )
- {
- if( cpmx2[l][j] )
- {
- cpmxpd[count][j] = cpmx2[l][j];
- cpmxpdn[count][j] = l;
- count++;
- }
- }
- cpmxpdn[count][j] = -1;
- }
- }
-
- for( l=0; l<26; l++ )
- {
- scarr[l] = 0.0;
- for( k=0; k<26; k++ )
- scarr[l] += n_dis[k][l] * cpmx1[k][i1];
- }
- for( j=0; j<lgth2; j++ )
- {
- match[j] = 0;
- for( k=0; cpmxpdn[k][j] > -1; k++ )
- match[j] += scarr[cpmxpdn[k][j]] * cpmxpd[k][j];
- }
-}
-
-static float Atracking( float *lasthorizontalw, float *lastverticalw,
- char **seq1, char **seq2,
- char **mseq1, char **mseq2,
- float **cpmx1, float **cpmx2,
- int **ijp, int icyc, int jcyc )
-{
- int i, j, k, l, iin, jin, ifi, jfi, lgth1, lgth2;
-// char gap[] = "-";
- char *gap;
- float wm;
- gap = newgapstr;
- lgth1 = strlen( seq1[0] );
- lgth2 = strlen( seq2[0] );
-
-#if DEBUG
- for( i=0; i<lgth1; i++ )
- {
- fprintf( stderr, "lastverticalw[%d] = %f\n", i, lastverticalw[i] );
- }
-#endif
-
- if( outgap == 1 )
- ;
- else
- {
- wm = lastverticalw[0];
- for( i=0; i<lgth1; i++ )
- {
- if( lastverticalw[i] >= wm )
- {
- wm = lastverticalw[i];
- iin = i; jin = lgth2-1;
- ijp[lgth1][lgth2] = +( lgth1 - i );
- }
- }
- for( j=0; j<lgth2; j++ )
- {
- if( lasthorizontalw[j] >= wm )
- {
- wm = lasthorizontalw[j];
- iin = lgth1-1; jin = j;
- ijp[lgth1][lgth2] = -( lgth2 - j );
- }
- }
- }
-
- for( i=0; i<lgth1+1; i++ )
- {
- ijp[i][0] = i + 1;
- }
- for( j=0; j<lgth2+1; j++ )
- {
- ijp[0][j] = -( j + 1 );
- }
-
- for( i=0; i<icyc; i++ )
- {
- mseq1[i] += lgth1+lgth2;
- *mseq1[i] = 0;
- }
- for( j=0; j<jcyc; j++ )
- {
- mseq2[j] += lgth1+lgth2;
- *mseq2[j] = 0;
- }
- iin = lgth1; jin = lgth2;
- for( k=0; k<=lgth1+lgth2; k++ )
- {
- if( ijp[iin][jin] < 0 )
- {
- ifi = iin-1; jfi = jin+ijp[iin][jin];
- }
- else if( ijp[iin][jin] > 0 )
- {
- ifi = iin-ijp[iin][jin]; jfi = jin-1;
- }
- else
- {
- ifi = iin-1; jfi = jin-1;
- }
- l = iin - ifi;
- while( --l )
- {
- for( i=0; i<icyc; i++ )
- *--mseq1[i] = seq1[i][ifi+l];
- for( j=0; j<jcyc; j++ )
- *--mseq2[j] = *gap;
- k++;
- }
- l= jin - jfi;
- while( --l )
- {
- for( i=0; i<icyc; i++ )
- *--mseq1[i] = *gap;
- for( j=0; j<jcyc; j++ )
- *--mseq2[j] = seq2[j][jfi+l];
- k++;
- }
- if( iin <= 0 || jin <= 0 ) break;
- for( i=0; i<icyc; i++ )
- *--mseq1[i] = seq1[i][ifi];
- for( j=0; j<jcyc; j++ )
- *--mseq2[j] = seq2[j][jfi];
- k++;
- iin = ifi; jin = jfi;
- }
- return( 0.0 );
-}
-
-
-float Aalign( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen )
-/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
-{
- register int i, j;
- int lasti; /* outgap == 0 -> lgth1, outgap == 1 -> lgth1+1 */
- int lgth1, lgth2;
- int resultlen;
- float wm = 0.0; /* int ?????? */
- float g;
- float x;
- static TLS float mi, *m;
- static TLS int **ijp;
- static TLS int mpi, *mp;
- static TLS float *currentw;
- static TLS float *previousw;
- static TLS float *match;
- static TLS float *initverticalw; /* kufuu sureba iranai */
- static TLS float *lastverticalw; /* kufuu sureba iranai */
- static TLS char **mseq1;
- static TLS char **mseq2;
- static TLS char **mseq;
- static TLS float **cpmx1;
- static TLS float **cpmx2;
- static TLS int **intwork;
- static TLS float **floatwork;
- static TLS int orlgth1 = 0, orlgth2 = 0;
-
-#if DEBUG
- fprintf( stderr, "eff in SA+++align\n" );
- for( i=0; i<icyc; i++ ) fprintf( stderr, "eff1[%d] = %f\n", i, eff1[i] );
-#endif
- if( orlgth1 == 0 )
- {
- mseq1 = AllocateCharMtx( njob, 1 );
- mseq2 = AllocateCharMtx( njob, 1 ); /* by J. Thompson */
- }
-
- lgth1 = strlen( seq1[0] );
- lgth2 = strlen( seq2[0] );
-
- if( lgth1 > orlgth1 || lgth2 > orlgth2 )
- {
- int ll1, ll2;
-
- if( orlgth1 > 0 && orlgth2 > 0 )
- {
- FreeFloatVec( currentw );
- FreeFloatVec( previousw );
- FreeFloatVec( match );
- FreeFloatVec( initverticalw );
- FreeFloatVec( lastverticalw );
-
- FreeFloatVec( m );
- FreeIntVec( mp );
-
- FreeCharMtx( mseq );
-
- FreeFloatMtx( cpmx1 );
- FreeFloatMtx( cpmx2 );
-
- FreeFloatMtx( floatwork );
- FreeIntMtx( intwork );
- }
-
- ll1 = MAX( (int)(1.1*lgth1), orlgth1 ) + 100;
- ll2 = MAX( (int)(1.1*lgth2), orlgth2 ) + 100;
-
- fprintf( stderr, "\ntrying to allocate (%d+%d)xn matrices ... ", ll1, ll2 );
-
- currentw = AllocateFloatVec( ll2+2 );
- previousw = AllocateFloatVec( ll2+2 );
- match = AllocateFloatVec( ll2+2 );
-
- initverticalw = AllocateFloatVec( ll1+2 );
- lastverticalw = AllocateFloatVec( ll1+2 );
-
- m = AllocateFloatVec( ll2+2 );
- mp = AllocateIntVec( ll2+2 );
-
- mseq = AllocateCharMtx( njob, ll1+ll2 );
-
- cpmx1 = AllocateFloatMtx( 26, ll1+2 );
- cpmx2 = AllocateFloatMtx( 26, ll2+2 );
-
- floatwork = AllocateFloatMtx( 26, MAX( ll1, ll2 )+2 );
- intwork = AllocateIntMtx( 26, MAX( ll1, ll2 )+2 );
-
- fprintf( stderr, "succeeded\n" );
-
- orlgth1 = ll1;
- orlgth2 = ll2;
- }
-
- for( i=0; i<icyc; i++ ) mseq1[i] = mseq[i];
- for( j=0; j<jcyc; j++ ) mseq2[j] = mseq[icyc+j];
-
-
- if( orlgth1 > commonAlloc1 || orlgth2 > commonAlloc2 )
- {
- int ll1, ll2;
-
- if( commonAlloc1 && commonAlloc2 )
- {
- FreeIntMtx( commonIP );
- }
-
- ll1 = MAX( orlgth1, commonAlloc1 );
- ll2 = MAX( orlgth2, commonAlloc2 );
-
- fprintf( stderr, "\n\ntrying to allocate %dx%d matrices ... ", ll1+1, ll2+1 );
-
- commonIP = AllocateIntMtx( ll1+10, ll2+10 );
-
- fprintf( stderr, "succeeded\n\n" );
-
- commonAlloc1 = ll1;
- commonAlloc2 = ll2;
- }
- ijp = commonIP;
-
- cpmx_calc( seq1, cpmx1, eff1, strlen( seq1[0] ), icyc );
- cpmx_calc( seq2, cpmx2, eff2, strlen( seq2[0] ), jcyc );
-
- match_calc( initverticalw, cpmx2, cpmx1, 0, lgth1, floatwork, intwork, 1 );
- match_calc( currentw, cpmx1, cpmx2, 0, lgth2, floatwork, intwork, 1 );
-
- if( outgap == 1 )
- {
- for( i=1; i<lgth1+1; i++ )
- {
- initverticalw[i] += penalty * 0.5;
- }
- for( j=1; j<lgth2+1; j++ )
- {
- currentw[j] += penalty * 0.5;
- }
- }
-
- for( j=0; j<lgth2+1; ++j )
- {
- m[j] = currentw[j-1] + penalty * 0.5; mp[j] = 0;
- }
-
- lastverticalw[0] = currentw[lgth2-1];
-
- if( outgap ) lasti = lgth1+1; else lasti = lgth1;
-
- for( i=1; i<lasti; i++ )
- {
-
- floatncpy( previousw, currentw, lgth2+1 );
- previousw[0] = initverticalw[i-1];
-
- match_calc( currentw, cpmx1, cpmx2, i, lgth2, floatwork, intwork, 0 );
- currentw[0] = initverticalw[i];
-
- mi = previousw[0] + penalty * 0.5; mpi = 0;
- for( j=1; j<lgth2+1; j++ )
- {
- wm = previousw[j-1];
- ijp[i][j] = 0;
-
- g = penalty * 0.5;
- x = mi + g;
- if( x > wm )
- {
- wm = x;
- ijp[i][j] = -( j - mpi );
- }
- g = penalty * 0.5;
- x = previousw[j-1] + g;
- if( mi <= x )
- {
- mi = x;
- mpi = j-1;
- }
-
- g = penalty * 0.5;
- x = m[j] + g;
- if( x > wm )
- {
- wm = x;
- ijp[i][j] = +( i - mp[j] );
- }
- g = penalty * 0.5;
- x = previousw[j-1] + g;
- if( m[j] <= x )
- {
- m[j] = x;
- mp[j] = i-1;
- }
- currentw[j] += wm;
- }
- lastverticalw[i] = currentw[lgth2-1];
- }
- /*
- fprintf( stderr, "\n" );
- for( i=0; i<icyc; i++ ) fprintf( stderr,"%s\n", seq1[i] );
- fprintf( stderr, "#####\n" );
- for( j=0; j<jcyc; j++ ) fprintf( stderr,"%s\n", seq2[j] );
- fprintf( stderr, "====>" );
- for( i=0; i<icyc; i++ ) strcpy( mseq1[i], seq1[i] );
- for( j=0; j<jcyc; j++ ) strcpy( mseq2[j], seq2[j] );
- */
- Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp, icyc, jcyc );
-
- resultlen = strlen( mseq1[0] );
- if( alloclen < resultlen || resultlen > N )
- {
- fprintf( stderr, "alloclen=%d, resultlen=%d, N=%d\n", alloclen, resultlen, N );
- ErrorExit( "LENGTH OVER!\n" );
- }
-
- for( i=0; i<icyc; i++ ) strcpy( seq1[i], mseq1[i] );
- for( j=0; j<jcyc; j++ ) strcpy( seq2[j], mseq2[j] );
- /*
- fprintf( stderr, "\n" );
- for( i=0; i<icyc; i++ ) fprintf( stderr, "%s\n", mseq1[i] );
- fprintf( stderr, "#####\n" );
- for( j=0; j<jcyc; j++ ) fprintf( stderr, "%s\n", mseq2[j] );
- */
- return( wm );
-}
git://source.jalview.org / jabaws.git / blobdiff