+++ /dev/null
-#include "mltaln.h"
-#include "dp.h"
-
-#define DEBUG 0
-#define DEBUG2 0
-#define XXXXXXX 0
-#define USE_PENALTY_EX 1
-
-static short localstop;
-
-#if 1
-static void match_calc( float *match, char **s1, char **s2, int i1, int lgth2 )
-{
- char *seq2 = s2[0];
- int *intptr;
-
- intptr = amino_dis[s1[0][i1]];
- while( lgth2-- )
- *match++ = intptr[*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 void match_calc_bk( float *match, float **cpmx1, float **cpmx2, int i1, int lgth2, float **floatwork, int **intwork, int initialize )
-{
- int j, k, l;
- float scarr[26];
- float **cpmxpd = floatwork;
- int **cpmxpdn = intwork;
- int count = 0;
-
- if( initialize )
- {
- for( j=0; j<lgth2; j++ )
- {
- count = 0;
- for( l=0; l<26; l++ )
- {
- if( cpmx2[l][j] )
- {
- cpmxpd[count][j] = cpmx2[l][j];
- cpmxpdn[count][j] = l;
- count++;
- }
- }
- cpmxpdn[count][j] = -1;
- }
- }
-
- for( l=0; l<26; l++ )
- {
- scarr[l] = 0.0;
- for( k=0; k<26; k++ )
- scarr[l] += n_dis[k][l] * cpmx1[k][i1];
- }
-#if 0 /* ¤³¤ì¤ò»È¤¦¤È¤\ad¤Ïfloatwork¤Î¥¢¥í¥±¡¼¥È¤òµÕ¤Ë¤¹¤ë */
- {
- float *fpt, **fptpt, *fpt2;
- int *ipt, **iptpt;
- fpt2 = match;
- iptpt = cpmxpdn;
- fptpt = cpmxpd;
- while( lgth2-- )
- {
- *fpt2 = 0.0;
- ipt=*iptpt,fpt=*fptpt;
- while( *ipt > -1 )
- *fpt2 += scarr[*ipt++] * *fpt++;
- fpt2++,iptpt++,fptpt++;
- }
- }
-#else
- for( j=0; j<lgth2; j++ )
- {
- match[j] = 0.0;
- for( k=0; cpmxpdn[k][j]>-1; k++ )
- match[j] += scarr[cpmxpdn[k][j]] * cpmxpd[k][j];
- }
-#endif
-}
-
-static float Ltracking( float *lasthorizontalw, float *lastverticalw,
- char **seq1, char **seq2,
- char **mseq1, char **mseq2,
- float **cpmx1, float **cpmx2,
- short **ijp, int *off1pt, int *off2pt, int endi, int endj )
-{
- int i, j, l, iin, jin, ifi, jfi, lgth1, lgth2, k, limk;
- char gap[] = "-";
- 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++ )
- {
- ijp[i][0] = localstop;
- }
- for( j=0; j<lgth2+1; j++ )
- {
- ijp[0][j] = localstop;
- }
-
- mseq1[0] += lgth1+lgth2;
- *mseq1[0] = 0;
- mseq2[0] += lgth1+lgth2;
- *mseq2[0] = 0;
- iin = endi; jin = endj;
- limk = lgth1+lgth2;
- 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];
- if( ijp[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 );
-
-
- return( 0.0 );
-}
-
-
-float L__align11( char **seq1, char **seq2, int alloclen, int *off1pt, int *off2pt )
-/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
-{
-// int k;
- register int i, j;
- int lasti, lastj; /* outgap == 0 -> lgth1, outgap == 1 -> lgth1+1 */
- int lgth1, lgth2;
- int resultlen;
- float wm = 0.0; /* int ?????? */
- float g;
- float *currentw, *previousw;
-#if 1
- float *wtmp;
- short *ijppt;
- float *mjpt, *prept, *curpt;
- int *mpjpt;
-#endif
- static float mi, *m;
- static short **ijp;
- 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 maxwm;
- int endali, endalj;
- float localthr = -offset;
- float localthr2 = -offset;
-// float localthr = 100;
-// float localthr2 = 100;
- float fpenalty = (float)penalty;
- float fpenalty_ex = (float)penalty_ex;
-
-
- if( orlgth1 == 0 )
- {
- mseq1 = AllocateCharMtx( njob, 0 );
- mseq2 = AllocateCharMtx( njob, 0 );
- }
-
-
- lgth1 = strlen( seq1[0] );
- lgth2 = strlen( seq2[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( 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 );
-
- 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 )
- {
- FreeShortMtx( 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 = AllocateShortMtx( 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 );
-
-
- lasti = lgth2+1;
- for( j=1; j<lasti; ++j )
- {
- m[j] = currentw[j-1]; mp[j] = 0;
-#if 0
- if( m[j] < localthr ) m[j] = localthr2;
-#endif
- }
-
- lastverticalw[0] = currentw[lgth2-1];
-
- lasti = lgth1+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; j++ )
- fprintf( stderr, "%c ", seq2[0][j] );
- fprintf( stderr, "\n" );
-#endif
-
- localstop = lgth1+lgth2+1;
- maxwm = -999.9;
-#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
-
- 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;
-
-#if 0
- if( mi < localthr ) mi = localthr2;
-#endif
-
- ijppt = ijp[i] + 1;
- mjpt = m + 1;
- prept = previousw;
- curpt = currentw + 1;
- mpjpt = mp + 1;
- lastj = lgth2+1;
- for( j=1; j<lastj; 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( *prept > mi )
- {
- mi = *prept;
- 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( *prept > *mjpt )
- {
- *mjpt = *prept;
- *mpjpt = i-1;
- }
-#if USE_PENALTY_EX
- *mjpt += fpenalty_ex;
-#endif
-
- if( maxwm < wm )
- {
- maxwm = wm;
- endali = i;
- endalj = j;
- }
-#if 1
- if( wm < localthr )
- {
-// fprintf( stderr, "stop i=%d, j=%d, curpt=%f\n", i, j, *curpt );
- *ijppt = 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;
- ijppt++;
- mjpt++;
- prept++;
- mpjpt++;
- }
-#if DEBUG2
- fprintf( stderr, "\n" );
-#endif
-
- lastverticalw[i] = currentw[lgth2-1];
- }
-
-
-#if DEBUG2
- fprintf( stderr, "maxwm = %f\n", maxwm );
- fprintf( stderr, "endali = %d\n", endali );
- fprintf( stderr, "endalj = %d\n", endalj );
-#endif
-
- Ltracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp, off1pt, off2pt, endali, endalj );
-
-
- 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, "wm=%f\n", wm );
- fprintf( stderr, ">\n%s\n", mseq1[0] );
- fprintf( stderr, ">\n%s\n", mseq2[0] );
-#endif
-
-
- return( wm );
-}
-
-float L__align11_noalign( char **seq1, char **seq2, int alloclen, int *off1pt, int *off2pt )
-/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
-{
-// int k;
- register int i, j;
- int lasti, lastj; /* outgap == 0 -> lgth1, outgap == 1 -> lgth1+1 */
- int lgth1, lgth2;
- int resultlen;
- float wm = 0.0; /* int ?????? */
- float g;
- float *currentw, *previousw;
-#if 1
- float *wtmp;
- short *ijppt;
- float *mjpt, *prept, *curpt;
- int *mpjpt;
-#endif
- static float mi, *m;
- static short **ijp;
- 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 maxwm;
- int endali, endalj;
- float localthr = -offset;
- float localthr2 = -offset;
-// float localthr = 100;
-// float localthr2 = 100;
- float fpenalty = (float)penalty;
- float fpenalty_ex = (float)penalty_ex;
-
-
- if( orlgth1 == 0 )
- {
- mseq1 = AllocateCharMtx( njob, 0 );
- mseq2 = AllocateCharMtx( njob, 0 );
- }
-
-
- lgth1 = strlen( seq1[0] );
- lgth2 = strlen( seq2[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( 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 );
-
- 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 0
- if( orlgth1 > commonAlloc1 || orlgth2 > commonAlloc2 )
- {
- int ll1, ll2;
-
- if( commonAlloc1 && commonAlloc2 )
- {
- FreeShortMtx( 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 = AllocateShortMtx( ll1+10, ll2+10 );
-
-#if DEBUG
- fprintf( stderr, "succeeded\n\n" );
-#endif
-
- commonAlloc1 = ll1;
- commonAlloc2 = ll2;
- }
-#endif
-// 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 );
-
-
- lasti = lgth2+1;
- for( j=1; j<lasti; ++j )
- {
- m[j] = currentw[j-1]; mp[j] = 0;
-#if 0
- if( m[j] < localthr ) m[j] = localthr2;
-#endif
- }
-
- lastverticalw[0] = currentw[lgth2-1];
-
- lasti = lgth1+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; j++ )
- fprintf( stderr, "%c ", seq2[0][j] );
- fprintf( stderr, "\n" );
-#endif
-
- localstop = lgth1+lgth2+1;
- maxwm = -999.9;
-#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
-
- 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;
-
-#if 0
- if( mi < localthr ) mi = localthr2;
-#endif
-
-// ijppt = ijp[i] + 1;
- mjpt = m + 1;
- prept = previousw;
- curpt = currentw + 1;
-// mpjpt = mp + 1;
- lastj = lgth2+1;
- for( j=1; j<lastj; 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( *prept > mi )
- {
- mi = *prept;
-// 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( *prept > *mjpt )
- {
- *mjpt = *prept;
-// *mpjpt = i-1;
- }
-#if USE_PENALTY_EX
- *mjpt += fpenalty_ex;
-#endif
-
- if( maxwm < wm )
- {
- maxwm = wm;
- endali = i;
- endalj = j;
- }
-#if 1
- if( wm < localthr )
- {
-// fprintf( stderr, "stop i=%d, j=%d, curpt=%f\n", i, j, *curpt );
-// *ijppt = 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;
-// ijppt++;
- mjpt++;
- prept++;
-// mpjpt++;
- }
-#if DEBUG2
- fprintf( stderr, "\n" );
-#endif
-
- lastverticalw[i] = currentw[lgth2-1];
- }
-
-
-#if DEBUG2
- fprintf( stderr, "maxwm = %f\n", maxwm );
- fprintf( stderr, "endali = %d\n", endali );
- fprintf( stderr, "endalj = %d\n", endalj );
-#endif
-
-#if 0
-
- Ltracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp, off1pt, off2pt, endali, endalj );
-
-
- 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] );
-
- fprintf( stderr, "wm=%f\n", wm );
- fprintf( stderr, ">\n%s\n", mseq1[0] );
- fprintf( stderr, ">\n%s\n", mseq2[0] );
-#endif
-
-
- return( wm );
-}
git://source.jalview.org / jabaws.git / blobdiff