--- /dev/null
+#include "mltaln.h"
+#include "dp.h"
+
+#define DEBUG 0
+#define XXXXXXX 0
+#define USE_PENALTY_EX 1
+
+
+#if 1
+static void match_calc( float *match, char **s1, char **s2, int i1, int lgth2 )
+{
+ char *seq2 = s2[0];
+ int *intptr = amino_dis[(int)s1[0][i1]];
+
+ while( lgth2-- )
+ *match++ = intptr[(int)*seq2++];
+}
+#else
+static void match_calc( float *match, char **s1, char **s2, int i1, int lgth2 )
+{
+ int j;
+
+ for( j=0; j<lgth2; j++ )
+ match[j] = amino_dis[(*s1)[i1]][(*s2)[j]];
+}
+#endif
+
+static float genGtracking( float *lasthorizontalw, float *lastverticalw,
+ char **seq1, char **seq2,
+ char **mseq1, char **mseq2,
+ float **cpmx1, float **cpmx2,
+ int **ijpi, int **ijpj )
+{
+ 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++ )
+ {
+ ijpi[i][0] = -1;
+ ijpj[i][0] = -1; // ???
+ }
+ for( j=0; j<lgth2+1; j++ )
+ {
+ ijpi[0][j] = -1; // ???
+ ijpj[0][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++ )
+ {
+ ifi = ( ijpi[iin][jin] );
+ jfi = ( ijpj[iin][jin] );
+ 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];
+
+// fprintf( stdout, "mseq1 = %s\n", mseq1[0] );
+// fprintf( stdout, "mseq2 = %s\n", mseq2[0] );
+
+ k++;
+ iin = ifi; jin = jfi;
+ }
+ return( 0.0 );
+}
+
+
+float genG__align11( 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; /* outgap == 0 -> lgth1, outgap == 1 -> lgth1+1 */
+ int lgth1, lgth2;
+ int resultlen;
+ float wm; /* int ?????? */
+ float g;
+ float *currentw, *previousw;
+ float fpenalty = (float)penalty;
+ float fpenalty_OP = (float)penalty_OP;
+#if USE_PENALTY_EX
+ float fpenalty_ex = (float)penalty_ex;
+#endif
+#if 1
+ float *wtmp;
+ int *ijpipt;
+ int *ijpjpt;
+ float *mjpt, *Mjpt, *prept, *curpt;
+ int *mpjpt, *Mpjpt;
+#endif
+ static float mi, *m;
+ static float Mi, *largeM;
+ static int **ijpi;
+ static int **ijpj;
+ static int mpi, *mp;
+ 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 **floatwork;
+ static int orlgth1 = 0, orlgth2 = 0;
+ float tbk;
+ int tbki, tbkj;
+
+ wm = 0.0;
+
+ if( orlgth1 == 0 )
+ {
+ mseq1 = AllocateCharMtx( njob, 0 );
+ mseq2 = AllocateCharMtx( njob, 0 );
+ }
+
+
+ lgth1 = strlen( seq1[0] );
+ lgth2 = strlen( seq2[0] );
+
+
+
+ if( lgth1 <= 0 || lgth2 <= 0 )
+ {
+ fprintf( stderr, "WARNING (g11): lgth1=%d, lgth2=%d\n", lgth1, lgth2 );
+ }
+
+ if( lgth1 > orlgth1 || lgth2 > orlgth2 )
+ {
+ int ll1, ll2;
+
+ if( orlgth1 > 0 && orlgth2 > 0 )
+ {
+ FreeFloatVec( w1 );
+ FreeFloatVec( w2 );
+ FreeFloatVec( match );
+ FreeFloatVec( initverticalw );
+ FreeFloatVec( lastverticalw );
+
+ FreeFloatVec( m );
+ FreeIntVec( mp );
+ FreeFloatVec( largeM );
+ 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 );
+
+ m = AllocateFloatVec( ll2+2 );
+ mp = AllocateIntVec( ll2+2 );
+ largeM = 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 );
+
+#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 );
+ FreeIntMtx( commonJP );
+ }
+
+ 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 );
+ commonJP = AllocateIntMtx( ll1+10, ll2+10 );
+
+#if DEBUG
+ fprintf( stderr, "succeeded\n\n" );
+#endif
+
+ commonAlloc1 = ll1;
+ commonAlloc2 = ll2;
+ }
+ ijpi = commonIP;
+ ijpj = commonJP;
+
+
+#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 );
+
+ if( outgap == 1 )
+ {
+ for( i=1; i<lgth1+1; i++ )
+ {
+ initverticalw[i] += fpenalty;
+ }
+ for( j=1; j<lgth2+1; j++ )
+ {
+ currentw[j] += fpenalty;
+ }
+ }
+
+ for( j=1; j<lgth2+1; ++j )
+ {
+ m[j] = currentw[j-1]; mp[j] = 0;
+ largeM[j] = currentw[j-1]; Mp[j] = 0;
+ }
+
+ if( lgth2 == 0 )
+ lastverticalw[0] = 0.0; // lgth2==0 no toki error
+ else
+ lastverticalw[0] = currentw[lgth2-1]; // lgth2==0 no toki error
+
+ if( outgap ) lasti = lgth1+1; else lasti = lgth1;
+
+#if XXXXXXX
+fprintf( stderr, "currentw = \n" );
+for( i=0; i<lgth1+1; i++ )
+{
+ fprintf( stderr, "%5.2f ", currentw[i] );
+}
+fprintf( stderr, "\n" );
+fprintf( stderr, "initverticalw = \n" );
+for( i=0; i<lgth2+1; i++ )
+{
+ fprintf( stderr, "%5.2f ", initverticalw[i] );
+}
+fprintf( stderr, "\n" );
+#endif
+
+ for( i=1; i<lasti; i++ )
+ {
+ wtmp = previousw;
+ previousw = currentw;
+ currentw = wtmp;
+
+ previousw[0] = initverticalw[i-1];
+
+ match_calc( currentw, seq1, seq2, i, lgth2 );
+#if XXXXXXX
+fprintf( stderr, "\n" );
+fprintf( stderr, "i=%d\n", i );
+fprintf( stderr, "currentw = \n" );
+for( j=0; j<lgth2; j++ )
+{
+ fprintf( stderr, "%5.2f ", currentw[j] );
+}
+fprintf( stderr, "\n" );
+#endif
+#if XXXXXXX
+fprintf( stderr, "\n" );
+fprintf( stderr, "i=%d\n", i );
+fprintf( stderr, "currentw = \n" );
+for( j=0; j<lgth2; j++ )
+{
+ fprintf( stderr, "%5.2f ", currentw[j] );
+}
+fprintf( stderr, "\n" );
+#endif
+ currentw[0] = initverticalw[i];
+
+ mi = previousw[0]; mpi = 0;
+ Mi = previousw[0]; Mpi = 0;
+
+ ijpipt = ijpi[i] + 1;
+ ijpjpt = ijpj[i] + 1;
+ mjpt = m + 1;
+ Mjpt = largeM + 1;
+ prept = previousw;
+ curpt = currentw + 1;
+ mpjpt = mp + 1;
+ Mpjpt = Mp + 1;
+ tbk = -9999999.9;
+ tbki = 0;
+ tbkj = 0;
+ for( j=1; j<lgth2+1; j++ )
+ {
+ wm = *prept;
+ *ijpipt = i-1;
+ *ijpjpt = j-1;
+
+#if 0
+ fprintf( stderr, "%5.0f->", wm );
+#endif
+#if 0
+ fprintf( stderr, "%5.0f?", g );
+#endif
+ if( (g=mi+fpenalty) > wm )
+ {
+ wm = g;
+// *ijpipt = i - 1; // iranai
+ *ijpjpt = mpi;
+ }
+ if( (g=*prept) >= mi )
+ {
+ mi = g;
+ mpi = j-1;
+ }
+#if USE_PENALTY_EX
+ mi += fpenalty_ex;
+#endif
+
+#if 0
+ fprintf( stderr, "%5.0f?", g );
+#endif
+ if( (g=*mjpt + fpenalty) > wm )
+ {
+ wm = g;
+ *ijpipt = *mpjpt;
+ *ijpjpt = j - 1; //IRU!
+ }
+ if( (g=*prept) >= *mjpt )
+ {
+ *mjpt = g;
+ *mpjpt = i-1;
+ }
+#if USE_PENALTY_EX
+ m[j] += fpenalty_ex;
+#endif
+
+#if 1
+ g = tbk + fpenalty_OP;
+ if( g > wm )
+ {
+ wm = g;
+ *ijpipt = tbki;
+ *ijpjpt = tbkj;
+// fprintf( stderr, "hit! i%d, j%d, ijpi = %d, ijpj = %d\n", i, j, *ijpipt, *ijpjpt );
+ }
+ if( Mi > tbk )
+ {
+ tbk = Mi; //error desu.
+ tbki = i-1;
+ tbkj = Mpi;
+ }
+ if( *Mjpt > tbk )
+ {
+ tbk = *Mjpt;
+ tbki = *Mpjpt;
+ tbkj = j-1;
+ }
+
+ if( *prept > *Mjpt )
+ {
+ *Mjpt = *prept;
+ *Mpjpt = i-1;
+ }
+ if( *prept > Mi )
+ {
+ Mi = *prept;
+ Mpi = j-1;
+ }
+
+#endif
+
+
+#if 0
+ fprintf( stderr, "%5.0f ", wm );
+#endif
+ *curpt++ += wm;
+ ijpipt++;
+ ijpjpt++;
+ mjpt++;
+ Mjpt++;
+ prept++;
+ mpjpt++;
+ Mpjpt++;
+ }
+ lastverticalw[i] = currentw[lgth2-1]; // lgth2==0 no toki error
+ }
+#if 0
+ for( i=0; i<lgth1; i++ )
+ {
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stdout, "i,j=%d,%d - ijpi,ijpj=%d,%d\n", i, j, ijpi[i][j], ijpj[i][j] );
+ }
+ }
+ fflush( stdout );
+#endif
+
+ genGtracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijpi, ijpj );
+
+ 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 0
+ fprintf( stderr, "\n" );
+ fprintf( stderr, ">\n%s\n", mseq1[0] );
+ fprintf( stderr, ">\n%s\n", mseq2[0] );
+ fprintf( stderr, "wm = %f\n", wm );
+#endif
+
+ return( wm );
+}
+
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