+++ /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 );
-}
-
git://source.jalview.org / jabaws.git / blobdiff