--- /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