--- /dev/null
+#include "mltaln.h"
+#include "dp.h"
+
+#define DEBUG 0
+#define XXXXXXX 0
+#define USE_PENALTY_EX 0
+
+static void extendmseq( char **mseq1, char **mseq2, char **seq1, char **seq2, int i, int j, int prevhiti, int prevhitj )
+{
+// char gap[] = "-";
+ char *gap;
+ gap = newgapstr;
+ int l;
+
+ fprintf( stderr, "i=%d, prevhiti=%d\n", i, prevhiti );
+ fprintf( stderr, "j=%d, prevhitj=%d\n", j, prevhitj );
+ l = prevhiti - i - 1;
+ fprintf( stderr, "l=%d\n", l );
+ while( l>0 )
+ {
+ *--mseq1[0] = seq1[0][i+l--];
+ *--mseq2[0] = *gap;
+ }
+ l= prevhitj - j - 1;
+ fprintf( stderr, "l=%d\n", l );
+ while( l>0 )
+ {
+ *--mseq1[0] = *gap;
+ *--mseq2[0] = seq2[0][j+l--];
+ }
+ if( i < 0 || j < 0 ) return;
+ *--mseq1[0] = seq1[0][i];
+ *--mseq2[0] = seq2[0][j];
+ fprintf( stderr, "added %c to mseq1, mseq1 = %s \n", seq1[0][i], mseq1[0] );
+ fprintf( stderr, "added %c to mseq2, mseq2 = %s \n", seq2[0][j], mseq2[0] );
+}
+
+static void match_calc( float *match, char **s1, char **s2, int i1, int lgth2 )
+{
+ char tmpc = s1[0][i1];
+ char *seq2 = s2[0];
+
+ while( lgth2-- )
+ *match++ = amino_dis[(int)tmpc][(int)*seq2++];
+}
+
+static float Atracking( float *lasthorizontalw, float *lastverticalw,
+ char **seq1, char **seq2,
+ char **mseq1, char **mseq2,
+ float **cpmx1, float **cpmx2,
+ int **ijp )
+{
+ int i, j, l, iin, jin, ifi, jfi, lgth1, lgth2, k, limk;
+// char gap[] = "-";
+ char *gap;
+ gap = newgapstr;
+ lgth1 = strlen( seq1[0] );
+ lgth2 = strlen( seq2[0] );
+
+
+#if 0
+ for( i=0; i<lgth1; i++ )
+ {
+ fprintf( stderr, "lastverticalw[%d] = %f\n", i, lastverticalw[i] );
+ }
+#endif
+
+ for( i=0; i<lgth1+1; i++ )
+ {
+ ijp[i][0] = i + 1;
+ }
+ for( j=0; j<lgth2+1; j++ )
+ {
+ ijp[0][j] = -( j + 1 );
+ }
+
+
+ mseq1[0] += lgth1+lgth2;
+ *mseq1[0] = 0;
+ mseq2[0] += lgth1+lgth2;
+ *mseq2[0] = 0;
+ iin = lgth1; jin = lgth2;
+ limk = lgth1+lgth2 + 1;
+ for( k=0; k<limk; 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 )
+ {
+ *--mseq1[0] = seq1[0][ifi+l];
+ *--mseq2[0] = *gap;
+ k++;
+ }
+ l= jin - jfi;
+ while( --l )
+ {
+ *--mseq1[0] = *gap;
+ *--mseq2[0] = seq2[0][jfi+l];
+ k++;
+ }
+ if( iin <= 0 || jin <= 0 ) break;
+ *--mseq1[0] = seq1[0][ifi];
+ *--mseq2[0] = seq2[0][jfi];
+ k++;
+ iin = ifi; jin = jfi;
+ }
+ return( 0.0 );
+}
+
+void backdp( float **WMMTX, float wmmax, float *maxinw, float *maxinh, int lgth1, int lgth2, int alloclen, float *w1, float *w2, float *initverticalw, float *m, int *mp, int iin, int jin, char **seq1, char **seq2, char **mseq1, char **mseq2 )
+{
+ register int i, j;
+ int prevhiti, prevhitj;
+// int lasti, lastj;
+ float g;
+ float fpenalty = (float)penalty;
+#if USE_PENALTY_EX
+ float fpenalty_ex = (float)penalty_ex;
+#endif
+ float *currentw, *previousw, *wtmp;
+ float mi;
+ int mpi;
+ int *mpjpt;
+ float *mjpt, *prept, *curpt;
+ float wm = 0.0;
+ float forwwm;
+
+ currentw = w1;
+ previousw = w2;
+
+ match_calc( initverticalw, seq2, seq1, lgth2-1, lgth1 );
+ match_calc( currentw, seq1, seq2, lgth1-1, lgth2 );
+
+
+ prevhiti = iin;
+ prevhitj = jin;
+ fprintf( stderr, "prevhiti = %d, lgth1 = %d\n", prevhiti, lgth1 );
+ fprintf( stderr, "prevhitj = %d, lgth2 = %d\n", prevhitj, lgth2 );
+ extendmseq( mseq1, mseq2, seq1, seq2, prevhiti, prevhitj, lgth1, lgth2 );
+
+ for( i=0; i<lgth1-1; i++ )
+ {
+ initverticalw[i] += fpenalty;
+ WMMTX[i][lgth2-1] += fpenalty;
+ }
+ for( j=0; j<lgth2-1; j++ )
+ {
+ currentw[j] += fpenalty;
+ WMMTX[lgth1-1][j] += fpenalty;
+ }
+
+
+#if 0
+ fprintf( stderr, "initverticalw = \n" );
+ for( i=0; i<lgth1; i++ )
+ fprintf( stderr, "% 8.2f", initverticalw[i] );
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "currentw = \n" );
+ for( i=0; i<lgth2; i++ )
+ fprintf( stderr, "% 8.2f", currentw[i] );
+ fprintf( stderr, "\n" );
+#endif
+
+ for( j=lgth2-1; j>0; --j )
+ {
+ m[j-1] = currentw[j];
+ mp[j] = 0; // iranai
+ }
+
+ for( j=0; j<lgth2; j++ ) m[j] = 0.0;
+ //m[lgth2-1] ga, irunoka iranainoka irahai.
+
+ for( i=lgth1-2; i>-1; i-- )
+ {
+ wtmp = previousw;
+ previousw = currentw;
+ currentw = wtmp;
+
+ previousw[lgth2-1] = initverticalw[i+1];
+
+ match_calc( currentw, seq1, seq2, i, lgth2 );
+
+#if 0
+ fprintf( stderr, "i=%d, currentw = \n", i );
+ for( j=0; j<lgth2; j++ ) fprintf( stderr, "% 8.2f", currentw[j] );
+ fprintf( stderr, "\n" );
+#endif
+
+ currentw[lgth2-1] = initverticalw[i];
+
+ mi = previousw[lgth2-1];
+ mpi = lgth2-1; //iranai
+
+
+ mjpt = m + lgth2 - 2;
+ prept = previousw + lgth2 - 1;
+ curpt = currentw + lgth2 - 2;
+ mpjpt = mp + lgth2 - 2;
+
+ for( j=lgth2-2; j>-1; j-- )
+ {
+
+// fprintf( stderr, "i,j=%d,%d %c-%c ", i, j, seq1[0][i], seq2[0][j] );
+ wm = *prept;
+ g = mi + fpenalty;
+#if 0
+ fprintf( stderr, "%5.0f?", g );
+#endif
+ if( g > wm )
+ {
+ wm = g;
+ }
+ g = *prept;
+ if( g >= mi )
+ {
+ mi = g;
+ mpi = j+1; //iranai
+ }
+#if USE_PENALTY_EX
+ mi += fpenalty_ex;
+#endif
+
+ g = *mjpt + fpenalty;
+#if 0
+ fprintf( stderr, "%5.0f?", g );
+#endif
+ if( g > wm )
+ {
+ wm = g;
+ }
+ g = *prept;
+ if( g >= *mjpt )
+ {
+ *mjpt = g;
+ *mpjpt = i-1; //iranai
+ }
+#if USE_PENALTY_EX
+ m[j] += fpenalty_ex;
+#endif
+
+#if 0
+ fprintf( stderr, "*curpt = %5.0f \n", *curpt );
+#endif
+
+// forwwm = wm + MIN( maxinw[i], maxinh[j] );
+ forwwm = wm + MIN( maxinw[i], maxinh[j] );
+ WMMTX[i][j] = forwwm;
+ if( forwwm == wmmax && i<prevhiti && j<prevhitj )
+ {
+ fprintf( stderr, "hit!\n" );
+ extendmseq( mseq1, mseq2, seq1, seq2, i, j, prevhiti, prevhitj );
+ if( forwwm == wmmax )
+ {
+ *--mseq1[0] = 'u';
+ *--mseq2[0] = 'u';
+ }
+ prevhiti = i;
+ prevhitj = j;
+ }
+ *curpt += wm;
+
+ mjpt--;
+ prept--;
+ mpjpt--;
+ curpt--;
+ }
+ }
+ extendmseq( mseq1, mseq2, seq1, seq2, -1, -1, prevhiti, prevhitj );
+}
+
+
+float MSalign11( char **seq1, char **seq2, int alloclen )
+/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
+{
+// int k;
+ register int i, j;
+ int lasti, lastj;
+ int iin = 0, jin = 0; // by Mathog, a guess
+ int lgth1, lgth2;
+ int resultlen;
+ float wm = 0.0; /* int ?????? */
+ float g;
+ float *currentw, *previousw;
+ float fpenalty = (float)penalty;
+#if USE_PENALTY_EX
+ float fpenalty_ex = (float)penalty_ex;
+#endif
+ float *maxinw = NULL, *maxinwpt = NULL; // by D.Mathog, guess
+ float *maxinh = NULL; // by D.Mathog, guess
+#if 1
+ float wmmax;
+ float *wtmp;
+ int *ijppt;
+ float *mjpt, *prept, *curpt;
+ int *mpjpt;
+#endif
+ static float mi, *m;
+ static int **ijp;
+ static int mpi, *mp;
+ static float *w1, *w2;
+ static float *match;
+ static float *initverticalw; /* kufuu sureba iranai */
+ static float *lastverticalw; /* kufuu sureba iranai */
+ static char **mseq1;
+ static char **mseq2;
+ static char **mseq;
+ static float **cpmx1;
+ static float **cpmx2;
+ static int **intwork;
+ static float **WMMTX;
+ static float **floatwork;
+ static int orlgth1 = 0, orlgth2 = 0;
+
+ if( orlgth1 == 0 )
+ {
+ mseq1 = AllocateCharMtx( njob, 0 );
+ mseq2 = AllocateCharMtx( njob, 0 );
+ }
+
+
+ lgth1 = strlen( seq1[0] );
+ lgth2 = strlen( seq2[0] );
+
+ if( lgth1 > orlgth1 || lgth2 > orlgth2 )
+ {
+ int ll1, ll2;
+
+ if( orlgth1 > 0 && orlgth2 > 0 )
+ {
+ FreeFloatVec( w1 );
+ FreeFloatVec( w2 );
+ FreeFloatVec( match );
+ FreeFloatVec( initverticalw );
+ FreeFloatVec( lastverticalw );
+ FreeFloatVec( maxinw );
+ FreeFloatVec( maxinh );
+
+ FreeFloatVec( m );
+ FreeIntVec( mp );
+
+ FreeCharMtx( mseq );
+
+
+ FreeFloatMtx( cpmx1 );
+ FreeFloatMtx( cpmx2 );
+
+ FreeFloatMtx( floatwork );
+ FreeIntMtx( intwork );
+ }
+
+ ll1 = MAX( (int)(1.3*lgth1), orlgth1 ) + 100;
+ ll2 = MAX( (int)(1.3*lgth2), orlgth2 ) + 100;
+
+#if DEBUG
+ fprintf( stderr, "\ntrying to allocate (%d+%d)xn matrices ... ", ll1, ll2 );
+#endif
+
+ w1 = AllocateFloatVec( ll2+2 );
+ w2 = AllocateFloatVec( ll2+2 );
+ match = AllocateFloatVec( ll2+2 );
+
+ initverticalw = AllocateFloatVec( ll1+2 );
+ lastverticalw = AllocateFloatVec( ll1+2 );
+ maxinw = AllocateFloatVec( ll1+2 );
+
+
+ m = AllocateFloatVec( ll2+2 );
+ mp = AllocateIntVec( ll2+2 );
+ maxinh = AllocateFloatVec( 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 );
+
+#if DEBUG
+ fprintf( stderr, "succeeded\n" );
+#endif
+
+ orlgth1 = ll1 - 100;
+ orlgth2 = ll2 - 100;
+ }
+
+
+ mseq1[0] = mseq[0];
+ mseq2[0] = mseq[1];
+
+
+ if( orlgth1 > commonAlloc1 || orlgth2 > commonAlloc2 )
+ {
+ int ll1, ll2;
+
+ if( commonAlloc1 && commonAlloc2 )
+ {
+ FreeIntMtx( commonIP );
+ FreeFloatMtx( WMMTX );
+ }
+
+ ll1 = MAX( orlgth1, commonAlloc1 );
+ ll2 = MAX( orlgth2, commonAlloc2 );
+
+#if DEBUG
+ fprintf( stderr, "\n\ntrying to allocate %dx%d matrices ... ", ll1+1, ll2+1 );
+#endif
+
+ commonIP = AllocateIntMtx( ll1+10, ll2+10 );
+ WMMTX = AllocateFloatMtx( ll1+10, ll2+10 );
+
+#if DEBUG
+ fprintf( stderr, "succeeded\n\n" );
+#endif
+
+ commonAlloc1 = ll1;
+ commonAlloc2 = ll2;
+ }
+ ijp = commonIP;
+
+
+#if 0
+ for( i=0; i<lgth1; i++ )
+ fprintf( stderr, "ogcp1[%d]=%f\n", i, ogcp1[i] );
+#endif
+
+ currentw = w1;
+ previousw = w2;
+
+ match_calc( initverticalw, seq2, seq1, 0, lgth1 );
+
+
+ match_calc( currentw, seq1, seq2, 0, lgth2 );
+
+ WMMTX[0][0] = initverticalw[0];
+
+ maxinh[0] = initverticalw[0];
+ for( i=1; i<lgth1+1; i++ )
+ {
+ initverticalw[i] += fpenalty;
+ WMMTX[i][0] = initverticalw[i];
+ if( maxinh[0] < initverticalw[i] ) maxinh[0] = initverticalw[i];
+ }
+ maxinw[0] = currentw[0];
+ for( j=1; j<lgth2+1; j++ )
+ {
+ currentw[j] += fpenalty;
+ WMMTX[0][j] = currentw[j];
+ if( maxinw[0] < currentw[j] ) maxinw[0] = currentw[j];
+ }
+
+ for( j=1; j<lgth2+1; ++j )
+ {
+ m[j] = currentw[j-1]; mp[j] = 0;
+ }
+
+ lastverticalw[0] = currentw[lgth2-1];
+
+ lasti = lgth1+1;
+
+ for( i=1; i<lasti; i++ )
+ {
+ wtmp = previousw;
+ previousw = currentw;
+ currentw = wtmp;
+
+ previousw[0] = initverticalw[i-1];
+
+ match_calc( currentw, seq1, seq2, i, lgth2 );
+
+ currentw[0] = initverticalw[i];
+
+ mi = previousw[0]; mpi = 0;
+
+ maxinwpt = maxinw + i;
+ *maxinwpt = currentw[0];
+
+ fprintf( stderr, "currentw[0] = %f, *maxinwpt = %f\n", currentw[0], maxinw[i] );
+
+ ijppt = ijp[i] + 1;
+ mjpt = m + 1;
+ prept = previousw;
+ curpt = currentw + 1;
+ mpjpt = mp + 1;
+ lastj = lgth2+1;
+
+ for( j=1; j<lastj; j++ )
+ {
+ wm = *prept;
+ *ijppt = 0;
+
+#if 0
+ fprintf( stderr, "%5.0f->", wm );
+#endif
+ g = mi + fpenalty;
+#if 0
+ fprintf( stderr, "%5.0f?", g );
+#endif
+ if( g > wm )
+ {
+ wm = g;
+ *ijppt = -( j - mpi );
+ }
+ g = *prept;
+ if( g >= mi )
+ {
+ mi = g;
+ mpi = j-1;
+ }
+#if USE_PENALTY_EX
+ mi += fpenalty_ex;
+#endif
+
+ g = *mjpt + fpenalty;
+#if 0
+ fprintf( stderr, "%5.0f?", g );
+#endif
+ if( g > wm )
+ {
+ wm = g;
+ *ijppt = +( i - *mpjpt );
+ }
+ g = *prept;
+ if( g >= *mjpt )
+ {
+ *mjpt = g;
+ *mpjpt = i-1;
+ }
+#if USE_PENALTY_EX
+ m[j] += fpenalty_ex;
+#endif
+
+#if 0
+ fprintf( stderr, "%5.0f ", wm );
+#endif
+ *curpt += wm;
+
+ WMMTX[i][j] = *curpt;
+
+
+ if( j<lgth2 && *maxinwpt < *curpt ) *maxinwpt = *curpt;
+ if( j<lgth2 && maxinh[j] < *curpt ) maxinh[j] = *curpt;
+// fprintf( stderr, "maxintwpt = %f\n", *maxinwpt );
+
+ ijppt++;
+ mjpt++;
+ prept++;
+ mpjpt++;
+ curpt++;
+ }
+ lastverticalw[i] = currentw[lgth2-1];
+ }
+
+ wmmax = -999.9;
+ for( i=0; i<lgth1; i++ )
+ {
+ g = lastverticalw[i];
+ if( g > wmmax )
+ {
+ wmmax = g;
+ iin = i;
+ jin = lgth2-1;
+ }
+ }
+ for( j=0; j<lgth2; j++ )
+ {
+ g = currentw[j];
+ if( g > wmmax )
+ {
+ wmmax = g;
+ iin = lgth1-1;
+ jin = j;
+ }
+ }
+
+ for( i=0; i<lgth1; i++ )
+ fprintf( stderr, "maxinw[%d] = %f\n", i, maxinw[i] );
+ for( j=0; j<lgth2; j++ )
+ fprintf( stderr, "maxinh[%d] = %f\n", j, maxinh[j] );
+
+ fprintf( stderr, "wmmax = %f (%d,%d)\n", wmmax, iin, jin );
+ if( iin == lgth1 - 1 && jin == lgth2 - 1 )
+ ;
+ else
+ wmmax += fpenalty;
+
+ fprintf( stderr, "wmmax = %f\n", wmmax );
+
+#if 0
+ for( i=0; i<lgth1; i++ )
+ {
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 10.2f ", WMMTX[i][j] );
+ }
+ fprintf( stderr, "\n" );
+ }
+#endif
+
+ mseq1[0] += lgth1+lgth2;
+ *mseq1[0] = 0;
+ mseq2[0] += lgth1+lgth2;
+ *mseq2[0] = 0;
+
+ backdp( WMMTX, wmmax, maxinw, maxinh, lgth1, lgth2, alloclen, w1, w2, initverticalw, m, mp, iin, jin, seq1, seq2, mseq1, mseq2 );
+
+ fprintf( stderr, "\n" );
+#if 1
+ fprintf( stderr, "\n" );
+ fprintf( stderr, ">MSres\n%s\n", mseq1[0] );
+ fprintf( stderr, ">MSres\n%s\n", mseq2[0] );
+#endif
+
+#if 0
+ for( i=0; i<lgth1; i++ )
+ {
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 10.2f ", WMMTX[i][j] );
+ }
+ fprintf( stderr, "\n" );
+ }
+#endif
+
+ mseq1[0] = mseq[0];
+ mseq2[0] = mseq[1];
+ mseq1[0] += lgth1+lgth2;
+ *mseq1[0] = 0;
+ mseq2[0] += lgth1+lgth2;
+ *mseq2[0] = 0;
+
+ Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp );
+
+
+ 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" );
+ }
+
+
+ strcpy( seq1[0], mseq1[0] );
+ strcpy( seq2[0], mseq2[0] );
+#if 1
+ fprintf( stderr, "\n" );
+ fprintf( stderr, ">\n%s\n", mseq1[0] );
+ fprintf( stderr, ">\n%s\n", mseq2[0] );
+#endif
+
+
+ return( wm );
+}
+
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