--- /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++];
+}
+static void match_calc_mtx( int mtx[0x80][0x80], float *match, char **s1, char **s2, int i1, int lgth2 )
+{
+ char *seq2 = s2[0];
+ int *intptr = mtx[(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 Atracking( float *lasthorizontalw, float *lastverticalw,
+ char **seq1, char **seq2,
+ char **mseq1, char **mseq2,
+ int **ijp,
+ int tailgp )
+{
+ 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] );
+ float wm;
+
+
+#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 );
+ }
+
+ if( tailgp == 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 );
+ }
+ }
+ }
+
+
+
+ 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 );
+}
+
+
+float G__align11( char **seq1, char **seq2, int alloclen, int headgp, int tailgp )
+/* 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;
+#if USE_PENALTY_EX
+ float fpenalty_ex = (float)penalty_ex;
+#endif
+#if 1
+ float *wtmp;
+ int *ijppt;
+ float *mjpt, *prept, *curpt;
+ int *mpjpt;
+#endif
+ static TLS float mi, *m;
+ static TLS int **ijp;
+ static TLS int mpi, *mp;
+ static TLS float *w1, *w2;
+ 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 int **intwork;
+ static TLS float **floatwork;
+ static TLS int orlgth1 = 0, orlgth2 = 0;
+
+ if( seq1 == NULL )
+ {
+ if( orlgth1 > 0 && orlgth2 > 0 )
+ {
+ orlgth1 = 0;
+ orlgth2 = 0;
+ free( mseq1 );
+ free( mseq2 );
+ FreeFloatVec( w1 );
+ FreeFloatVec( w2 );
+ FreeFloatVec( match );
+ FreeFloatVec( initverticalw );
+ FreeFloatVec( lastverticalw );
+
+ FreeFloatVec( m );
+ FreeIntVec( mp );
+
+ FreeCharMtx( mseq );
+
+
+
+ FreeFloatMtx( floatwork );
+ FreeIntMtx( intwork );
+ }
+ return( 0.0 );
+ }
+
+ 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 1
+ if( lgth1 == 0 && lgth2 == 0 )
+ return( 0.0 );
+
+ if( lgth1 == 0 )
+ {
+ seq1[0][lgth2] = 0;
+ while( lgth2 ) seq1[0][--lgth2] = '-';
+// fprintf( stderr, "seq1[0] = %s\n", seq1[0] );
+ return( 0.0 );
+ }
+
+ if( lgth2 == 0 )
+ {
+ seq2[0][lgth1] = 0;
+ while( lgth1 ) seq2[0][--lgth1] = '-';
+// fprintf( stderr, "seq2[0] = %s\n", seq2[0] );
+ return( 0.0 );
+ }
+#endif
+
+
+ wm = 0.0;
+
+ if( orlgth1 == 0 )
+ {
+ mseq1 = AllocateCharMtx( njob, 0 );
+ mseq2 = AllocateCharMtx( njob, 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( m );
+ FreeIntVec( mp );
+
+ FreeCharMtx( mseq );
+
+
+
+ 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 );
+
+ mseq = AllocateCharMtx( njob, ll1+ll2 );
+
+
+ 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 );
+ }
+
+ 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 );
+
+#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 );
+
+ if( headgp == 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;
+ }
+
+ if( lgth2 == 0 )
+ lastverticalw[0] = 0.0; // lgth2==0 no toki error
+ else
+ lastverticalw[0] = currentw[lgth2-1]; // lgth2==0 no toki error
+
+ if( tailgp ) 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;
+
+ ijppt = ijp[i] + 1;
+ mjpt = m + 1;
+ prept = previousw;
+ curpt = currentw + 1;
+ mpjpt = mp + 1;
+ for( j=1; j<lgth2+1; j++ )
+ {
+ wm = *prept;
+ *ijppt = 0;
+
+#if 0
+ fprintf( stderr, "%5.0f->", wm );
+#endif
+#if 0
+ fprintf( stderr, "%5.0f?", g );
+#endif
+ if( (g=mi+fpenalty) > wm )
+ {
+ wm = g;
+ *ijppt = -( j - 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;
+ *ijppt = +( i - *mpjpt );
+ }
+ if( (g=*prept) >= *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;
+ ijppt++;
+ mjpt++;
+ prept++;
+ mpjpt++;
+ }
+ lastverticalw[i] = currentw[lgth2-1]; // lgth2==0 no toki error
+ }
+
+ Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, ijp, tailgp );
+
+ 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 );
+}
+
+float G__align11_noalign( int scoremtx[0x80][0x80], int penal, int penal_ex, 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)penal;
+#if USE_PENALTY_EX
+ float fpenalty_ex = (float)penal_ex;
+#endif
+#if 1
+ float *wtmp;
+ float *mjpt, *prept, *curpt;
+// int *mpjpt;
+#endif
+ static TLS float mi, *m;
+ static TLS float *w1, *w2;
+ static TLS float *match;
+ static TLS float *initverticalw; /* kufuu sureba iranai */
+ static TLS float *lastverticalw; /* kufuu sureba iranai */
+ static TLS int **intwork;
+ static TLS float **floatwork;
+ static TLS int orlgth1 = 0, orlgth2 = 0;
+
+ if( seq1 == NULL )
+ {
+ if( orlgth1 > 0 && orlgth2 > 0 )
+ {
+ orlgth1 = 0;
+ orlgth2 = 0;
+ FreeFloatVec( w1 );
+ FreeFloatVec( w2 );
+ FreeFloatVec( match );
+ FreeFloatVec( initverticalw );
+ FreeFloatVec( lastverticalw );
+ free( m );
+
+
+ FreeFloatMtx( floatwork );
+ FreeIntMtx( intwork );
+ }
+ return( 0.0 );
+ }
+
+ wm = 0.0;
+
+
+
+ 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 );
+
+
+
+
+ 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 );
+
+
+
+ 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;
+ }
+
+
+
+
+
+
+#if 0
+ for( i=0; i<lgth1; i++ )
+ fprintf( stderr, "ogcp1[%d]=%f\n", i, ogcp1[i] );
+#endif
+
+ currentw = w1;
+ previousw = w2;
+
+
+ match_calc_mtx( scoremtx, initverticalw, seq2, seq1, 0, lgth1 );
+
+
+ match_calc_mtx( scoremtx, currentw, seq1, seq2, 0, lgth2 );
+
+ if( 1 ) // tsuneni 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];
+ }
+
+ if( lgth2 == 0 )
+ lastverticalw[0] = 0.0; // lgth2==0 no toki error
+ else
+ lastverticalw[0] = currentw[lgth2-1]; // lgth2==0 no toki error
+
+ if( 1 ) lasti = lgth1+1; else lasti = lgth1; // tsuneni outgap-1
+
+#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_mtx( scoremtx, 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];
+
+ mjpt = m + 1;
+ prept = previousw;
+ curpt = currentw + 1;
+ for( j=1; j<lgth2+1; j++ )
+ {
+ wm = *prept;
+
+#if 0
+ fprintf( stderr, "%5.0f->", wm );
+#endif
+#if 0
+ fprintf( stderr, "%5.0f?", g );
+#endif
+ if( (g=mi+fpenalty) > wm )
+ {
+ wm = g;
+ }
+ if( (g=*prept) >= mi )
+ {
+ mi = g;
+ }
+#if USE_PENALTY_EX
+ mi += fpenalty_ex;
+#endif
+
+#if 0
+ fprintf( stderr, "%5.0f?", g );
+#endif
+ if( (g=*mjpt + fpenalty) > wm )
+ {
+ wm = g;
+ }
+ if( (g=*prept) >= *mjpt )
+ {
+ *mjpt = g;
+ }
+#if USE_PENALTY_EX
+ m[j] += fpenalty_ex;
+#endif
+
+#if 0
+ fprintf( stderr, "%5.0f ", wm );
+#endif
+ *curpt++ += wm;
+ mjpt++;
+ prept++;
+ }
+ lastverticalw[i] = currentw[lgth2-1]; // lgth2==0 no toki error
+ }
+
+#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 );
+}
git://source.jalview.org / jabaws.git / blobdiff