+++ /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