--- /dev/null
+#include "mltaln.h"
+#include "dp.h"
+
+#define DEBUG 0
+#define DEBUG2 0
+#define XXXXXXX 0
+#define USE_PENALTY_EX 1
+
+typedef struct _shuryoten
+{
+ int i;
+ int j;
+ float wm;
+ struct _shuryoten *next;
+ struct _shuryoten *prev;
+} Shuryoten;
+
+
+static int localstop;
+
+static int compshuryo( Shuryoten *s1_arg, Shuryoten *s2_arg )
+{
+ Shuryoten *s1 = (Shuryoten *)s1_arg;
+ Shuryoten *s2 = (Shuryoten *)s2_arg;
+ if ( s1->wm > s2->wm ) return( -1 );
+ else if ( s1->wm < s2->wm ) return( 1 );
+ else return( 0 );
+}
+
+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[(int)(*s1)[i1]][(int)(*s2)[j]];
+}
+
+static float gentracking( int **used,
+ char **seq1, char **seq2,
+ char **mseq1, char **mseq2,
+ float **cpmx1, float **cpmx2,
+ int **ijpi, int **ijpj, int *off1pt, int *off2pt, int endi, int endj )
+{
+ int l, iin, jin, lgth1, lgth2, k, limk;
+ int ifi=0, jfi=0;
+// char gap[] = "-";
+ char *gap;
+ gap = newgapstr;
+ static char *res1 = NULL, *res2 = NULL;
+ char *mspt1, *mspt2;
+ if( res1 == NULL )
+ {
+ res1 = (char *)calloc( N, sizeof( char ) );
+ res2 = (char *)calloc( N, sizeof( char ) );
+ }
+
+ lgth1 = strlen( seq1[0] );
+ lgth2 = strlen( seq2[0] );
+
+ mspt1 = res1 + lgth1+lgth2;
+ *mspt1 = 0;
+ mspt2 = res2 + lgth1+lgth2;
+ *mspt2 = 0;
+ iin = endi; jin = endj;
+
+ limk = lgth1+lgth2;
+ if( used[iin][jin] ) return( -1.0 );
+ for( k=0; k<=limk; k++ )
+ {
+ ifi = ( ijpi[iin][jin] );
+ jfi = ( ijpj[iin][jin] );
+
+ if( used[ifi][jfi] ) return( -1.0 );
+
+ l = iin - ifi;
+ while( --l )
+ {
+ *--mspt1 = seq1[0][ifi+l];
+ *--mspt2 = *gap;
+ k++;
+ }
+ l= jin - jfi;
+ while( --l )
+ {
+ *--mspt1 = *gap;
+ *--mspt2 = seq2[0][jfi+l];
+ k++;
+ }
+
+ if( iin <= 0 || jin <= 0 ) break;
+ *--mspt1 = seq1[0][ifi];
+ *--mspt2 = seq2[0][jfi];
+ if( ijpi[ifi][jfi] == localstop ) break;
+ if( ijpj[ifi][jfi] == localstop ) break;
+ k++;
+ iin = ifi; jin = jfi;
+ }
+ if( ifi == -1 ) *off1pt = 0; else *off1pt = ifi;
+ if( jfi == -1 ) *off2pt = 0; else *off2pt = jfi;
+
+// fprintf( stderr, "ifn = %d, jfn = %d\n", ifi, jfi );
+
+ iin = endi; jin = endj;
+ limk = lgth1+lgth2;
+ for( k=0; k<=limk; k++ )
+ {
+ ifi = ( ijpi[iin][jin] );
+ jfi = ( ijpj[iin][jin] );
+
+ used[ifi][jfi] = 1;
+ if( iin <= 0 || jin <= 0 ) break;
+ if( ijpi[ifi][jfi] == localstop ) break;
+ if( ijpj[ifi][jfi] == localstop ) break;
+
+ k++;
+ iin = ifi; jin = jfi;
+ }
+
+
+ strcpy( mseq1[0], mspt1 );
+ strcpy( mseq2[0], mspt2 );
+
+ fprintf( stderr, "mseq1=%s\nmseq2=%s\n", mspt1, mspt2 );
+
+ return( 0.0 );
+}
+
+
+float suboptalign11( char **seq1, char **seq2, int alloclen, int *off1pt, int *off2pt, LocalHom *lhmpt )
+/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
+{
+ int k;
+ static int **used;
+ register int i, j;
+ int lasti, lastj; /* outgap == 0 -> lgth1, outgap == 1 -> lgth1+1 */
+ int lgth1, lgth2;
+ int resultlen;
+ float wm = 0.0; // by D.Mathog,
+ float g;
+ float *currentw, *previousw;
+#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 float **cpmx1;
+ static float **cpmx2;
+ static int **intwork;
+ static float **floatwork;
+ static int orlgth1 = 0, orlgth2 = 0;
+ float maxwm;
+ float tbk;
+ int tbki, tbkj;
+ int endali, endalj;
+// float localthr = 0.0;
+// float localthr2 = 0.0;
+ float fpenalty = (float)penalty;
+ float fpenalty_OP = (float)penalty_OP;
+ float fpenalty_ex = (float)penalty_ex;
+// float fpenalty_EX = (float)penalty_EX;
+ float foffset = (float)offset;
+ float localthr = -foffset;
+ float localthr2 = -foffset;
+ static Shuryoten *shuryo = NULL;
+ int numshuryo;
+ float minshuryowm = 0.0; // by D.Mathog
+ int minshuryopos = 0; // by D.Mathog
+ float resf;
+
+
+// fprintf( stderr, "@@@@@@@@@@@@@ penalty_OP = %f, penalty_EX = %f, pelanty = %f\n", fpenalty_OP, fpenalty_EX, fpenalty );
+
+ fprintf( stderr, "in suboptalign11\n" );
+ if( !shuryo )
+ {
+ shuryo = (Shuryoten *)calloc( 100, sizeof( Shuryoten ) );
+ }
+ for( i=0; i<100; i++ )
+ {
+ shuryo[i].i = -1;
+ shuryo[i].j = -1;
+ shuryo[i].wm = 0.0;
+ }
+ numshuryo = 0;
+
+ if( orlgth1 == 0 )
+ {
+ }
+
+
+ lgth1 = strlen( seq1[0] );
+ lgth2 = strlen( seq2[0] );
+
+ fprintf( stderr, "in suboptalign11 step 1\n" );
+
+ if( lgth1 > orlgth1 || lgth2 > orlgth2 )
+ {
+ int ll1, ll2;
+
+ fprintf( stderr, "in suboptalign11 step 1.3\n" );
+ if( orlgth1 > 0 && orlgth2 > 0 )
+ {
+ fprintf( stderr, "in suboptalign11 step 1.4\n" );
+ FreeFloatVec( w1 );
+ FreeFloatVec( w2 );
+// FreeFloatVec( match );
+ FreeFloatVec( initverticalw );
+ FreeFloatVec( lastverticalw );
+ fprintf( stderr, "in suboptalign11 step 1.5\n" );
+
+ FreeFloatVec( m );
+ FreeIntVec( mp );
+ FreeFloatVec( largeM );
+ FreeIntVec( Mp );
+ fprintf( stderr, "in suboptalign11 step 1.6\n" );
+
+
+ FreeFloatMtx( cpmx1 );
+ FreeFloatMtx( cpmx2 );
+
+ fprintf( stderr, "in suboptalign11 step 1.7\n" );
+ 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 );
+
+ cpmx1 = AllocateFloatMtx( 26, ll1+2 );
+ cpmx2 = AllocateFloatMtx( 26, ll2+2 );
+
+ floatwork = AllocateFloatMtx( 26, MAX( ll1, ll2 )+2 );
+ intwork = AllocateIntMtx( 26, MAX( ll1, ll2 )+2 );
+
+ mseq1 = AllocateCharMtx( njob, ll1+ll2 );
+ mseq2 = AllocateCharMtx( njob, ll1+ll2 );
+
+#if DEBUG
+ fprintf( stderr, "succeeded\n" );
+#endif
+
+ orlgth1 = ll1 - 100;
+ orlgth2 = ll2 - 100;
+ }
+ fprintf( stderr, "in suboptalign11 step 1.6\n" );
+
+
+
+ fprintf( stderr, "in suboptalign11 step 2\n" );
+
+ if( orlgth1 > commonAlloc1 || orlgth2 > commonAlloc2 )
+ {
+ int ll1, ll2;
+
+ if( commonAlloc1 && commonAlloc2 )
+ {
+ FreeIntMtx( commonIP );
+ FreeIntMtx( commonJP );
+ FreeIntMtx( used );
+ }
+
+ ll1 = MAX( orlgth1, commonAlloc1 );
+ ll2 = MAX( orlgth2, commonAlloc2 );
+
+#if DEBUG
+ fprintf( stderr, "\n\ntrying to allocate %dx%d matrices ... ", ll1+1, ll2+1 );
+#endif
+
+ used = AllocateIntMtx( ll1+10, ll2+10 );
+ 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
+
+ fprintf( stderr, "in suboptalign11 step 3\n" );
+ currentw = w1;
+ previousw = w2;
+
+ match_calc( initverticalw, seq2, seq1, 0, lgth1 );
+
+ match_calc( currentw, seq1, seq2, 0, lgth2 );
+
+
+ lasti = lgth2+1;
+ for( j=1; j<lasti; ++j )
+ {
+ m[j] = currentw[j-1]; mp[j] = 0;
+ largeM[j] = currentw[j-1]; Mp[j] = 0;
+ }
+
+ lastverticalw[0] = currentw[lgth2-1];
+
+
+#if 0
+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
+#if DEBUG2
+ fprintf( stderr, "\n" );
+ fprintf( stderr, " " );
+ for( j=0; j<lgth2+1; j++ )
+ fprintf( stderr, "%c ", seq2[0][j] );
+ fprintf( stderr, "\n" );
+#endif
+
+ localstop = lgth1+lgth2+1;
+ maxwm = -999.9;
+ endali = endalj = 0;
+#if DEBUG2
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "%c ", seq1[0][0] );
+
+ for( j=0; j<lgth2+1; j++ )
+ fprintf( stderr, "%5.0f ", currentw[j] );
+ fprintf( stderr, "\n" );
+#endif
+
+ 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 );
+#if DEBUG2
+ fprintf( stderr, "%c ", seq1[0][i] );
+ fprintf( stderr, "%5.0f ", currentw[0] );
+#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
+#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;
+
+#if 0
+ if( mi < localthr ) mi = localthr2;
+#endif
+
+ 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 = -999999.9;
+ tbki = 0;
+ tbkj = 0;
+ lastj = lgth2+1;
+ for( j=1; j<lastj; j++ )
+ {
+ wm = *prept;
+ *ijpipt = i-1;
+ *ijpjpt = j-1;
+
+
+// fprintf( stderr, "i,j=%d,%d %c-%c\n", i, j, seq1[0][i], seq2[0][j] );
+// fprintf( stderr, "wm=%f\n", wm );
+#if 0
+ fprintf( stderr, "%5.0f->", wm );
+#endif
+ g = mi + fpenalty;
+#if 0
+ fprintf( stderr, "%5.0f?", g );
+#endif
+ if( g > wm )
+ {
+ wm = g;
+// *ijpipt = i - 1;
+ *ijpjpt = mpi;
+ }
+ g = *prept;
+ if( g > mi )
+ {
+ mi = g;
+ mpi = j-1;
+ }
+
+#if USE_PENALTY_EX
+ mi += fpenalty_ex;
+#endif
+
+#if 0
+ fprintf( stderr, "%5.0f->", wm );
+#endif
+ g = *mjpt + fpenalty;
+#if 0
+ fprintf( stderr, "m%5.0f?", g );
+#endif
+ if( g > wm )
+ {
+ wm = g;
+ *ijpipt = *mpjpt;
+// *ijpjpt = j - 1;
+ }
+ g = *prept;
+ if( g > *mjpt )
+ {
+ *mjpt = g;
+ *mpjpt = i-1;
+ }
+#if USE_PENALTY_EX
+ *mjpt += fpenalty_ex;
+#endif
+
+
+ g = tbk + fpenalty_OP;
+// g = tbk;
+ 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 );
+ }
+ g = Mi;
+ if( g > tbk )
+ {
+ tbk = g;
+ tbki = i-1;
+ tbkj = Mpi;
+ }
+ g = *Mjpt;
+ if( g > tbk )
+ {
+ tbk = g;
+ tbki = *Mpjpt;
+ tbkj = j-1;
+ }
+// tbk += fpenalty_EX;// + foffset;
+
+ g = *prept;
+ if( g > *Mjpt )
+ {
+ *Mjpt = g;
+ *Mpjpt = i-1;
+ }
+// *Mjpt += fpenalty_EX;// + foffset;
+
+ g = *prept;
+ if( g > Mi )
+ {
+ Mi = g;
+ Mpi = j-1;
+ }
+// Mi += fpenalty_EX;// + foffset;
+
+
+// fprintf( stderr, "wm=%f, tbk=%f(%c-%c), mi=%f, *mjpt=%f\n", wm, tbk, seq1[0][tbki], seq2[0][tbkj], mi, *mjpt );
+// fprintf( stderr, "ijp = %c,%c\n", seq1[0][abs(*ijpipt)], seq2[0][abs(*ijpjpt)] );
+
+
+ if( maxwm < wm )
+ {
+ maxwm = wm;
+ endali = i;
+ endalj = j;
+ }
+
+#if 1
+ if( numshuryo < 100 )
+ {
+ shuryo[numshuryo].i = i;
+ shuryo[numshuryo].j = j;
+ shuryo[numshuryo].wm = wm;
+
+ if( minshuryowm > wm )
+ {
+ minshuryowm = wm;
+ minshuryopos = numshuryo;
+ }
+ numshuryo++;
+ }
+ else
+ {
+ if( wm > minshuryowm )
+ {
+ shuryo[minshuryopos].i = i;
+ shuryo[minshuryopos].j = j;
+ shuryo[minshuryopos].wm = wm;
+ minshuryowm = wm;
+ for( k=0; k<100; k++ ) // muda
+ {
+ if( shuryo[k].wm < minshuryowm )
+ {
+ minshuryowm = shuryo[k].wm;
+ minshuryopos = k;
+ break;
+ }
+ }
+ }
+ }
+#endif
+#if 1
+ if( wm < localthr )
+ {
+// fprintf( stderr, "stop i=%d, j=%d, curpt=%f\n", i, j, *curpt );
+ *ijpipt = localstop;
+// *ijpjpt = localstop;
+ wm = localthr2;
+ }
+#endif
+#if 0
+ fprintf( stderr, "%5.0f ", *curpt );
+#endif
+#if DEBUG2
+ fprintf( stderr, "%5.0f ", wm );
+// fprintf( stderr, "%c-%c *ijppt = %d, localstop = %d\n", seq1[0][i], seq2[0][j], *ijppt, localstop );
+#endif
+
+ *curpt += wm;
+ ijpipt++;
+ ijpjpt++;
+ mjpt++;
+ Mjpt++;
+ prept++;
+ mpjpt++;
+ Mpjpt++;
+ curpt++;
+ }
+#if DEBUG2
+ fprintf( stderr, "\n" );
+#endif
+
+ lastverticalw[i] = currentw[lgth2-1];
+ }
+
+ for( k=0; k<100; k++ )
+ {
+ fprintf( stderr, "shuryo[%d].i,j,wm = %d,%d,%f\n", k, shuryo[k].i, shuryo[k].j, shuryo[k].wm );
+ }
+
+
+#if 1
+ fprintf( stderr, "maxwm = %f\n", maxwm );
+ fprintf( stderr, "endali = %d\n", endali );
+ fprintf( stderr, "endalj = %d\n", endalj );
+#endif
+
+ qsort( shuryo, 100, sizeof( Shuryoten ), (int (*)())compshuryo );
+ for( k=0; k<100; k++ )
+ {
+ fprintf( stderr, "shuryo[%d].i,j,wm = %d,%d,%f\n", k, shuryo[k].i, shuryo[k].j, shuryo[k].wm );
+ }
+
+
+ lasti = lgth1+1;
+ for( i=0; i<lasti; i++ )
+ {
+ ijpi[i][0] = localstop;
+ ijpj[i][0] = localstop;
+ }
+ lastj = lgth2+1;
+ for( j=0; j<lastj; j++ )
+ {
+ ijpi[0][j] = localstop;
+ ijpj[0][j] = localstop;
+ }
+
+ for( i=0; i<lasti; i++ ) for( j=0; j<lastj; j++ ) used[i][j] = 0;
+
+ for( k=0; k<numshuryo; k++ )
+ {
+ if( shuryo[k].wm < shuryo[0].wm * 0.3 ) break;
+ fprintf( stderr, "k=%d, shuryo[k].i,j,wm=%d,%d,%f go\n", k, shuryo[k].i, shuryo[k].j, shuryo[k].wm );
+ resf = gentracking( used, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijpi, ijpj, off1pt, off2pt, shuryo[k].i, shuryo[k].j );
+ if( resf == -1.0 ) continue;
+ putlocalhom3( mseq1[0], mseq2[0], lhmpt, *off1pt, *off2pt, (int)shuryo[k].wm, strlen( mseq1[0] ) );
+#if 0
+ fprintf( stderr, "\n" );
+ fprintf( stderr, ">\n%s\n", mseq1[0] );
+ fprintf( stderr, ">\n%s\n", mseq2[0] );
+#endif
+ }
+ for( i=0; i<20; i++ )
+ {
+ for( j=0; j<20; j++ )
+ {
+ fprintf( stderr, "%2d ", used[i][j] );
+ }
+ fprintf( stderr, "\n" );
+ }
+
+
+// fprintf( stderr, "### impmatch = %f\n", *impmatch );
+
+ 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" );
+ }
+
+
+
+
+
+ return( wm );
+}
+
git://source.jalview.org / jabaws.git / blobdiff