Alignment * interactive_domain_extraction ( Constraint_list *CL)
{
int LEN=0;
int START=1;
int SCALE=2;
int GOPP=3;
int iteration=0;
char *choice;
int a,b, c;
int index;
char *s;
char last_start[100];
char out_format[100];
Alignment *RESULT=NULL;
Alignment *PREVIOUS=NULL;
Alignment *C=NULL;
Alignment *EA=NULL;
int **parameters;
choice=(char*)vcalloc ( 100, sizeof (char));
parameters=declare_int (10000, 4);
parameters[0][START]=(CL->moca)->moca_start;
parameters[0][LEN]= (CL->moca)->moca_len;
parameters[0][SCALE]=(CL->moca)->moca_scale;
parameters[0][GOPP]=CL->gop;
iteration=0;
sprintf ( last_start, "%d", (CL->moca)->moca_start);
sprintf ( out_format, "mocca_aln");
print_moca_interactive_choices ();
while ( !strm4 (choice, "Q","X", "q", "x" ))
{
c=choice[0];
if (c=='b' || c=='B')
{
iteration-=atoi(choice+1)+1;
if (iteration<0)iteration=1;
}
else
{
iteration++;
parameters[iteration][START]=parameters[iteration-1][START];
parameters[iteration][LEN]=parameters[iteration-1][LEN];
parameters[iteration][SCALE]=parameters[iteration-1][SCALE];
parameters[iteration][GOPP]=parameters[iteration-1][GOPP];
if ( c=='>')parameters[iteration][LEN]=atoi(choice+1);
else if ( c=='|')
{
sprintf ( last_start, "%s", choice);
parameters[iteration][START]=0;
s=strrchr(choice, ':');
if (s==NULL)
{
parameters[iteration][START]=atoi(choice+1);
}
else
{
s[0]='\0';
if((index=name_is_in_list (choice+1,(CL->S)->name,(CL->S)->nseq,100))==-1)
{
fprintf ( stderr, "\n\tERROR: %s NOT in Sequence Set",choice+1);
continue;
}
for ( a=0; a< index; a++)
{
parameters[iteration][START]+=(CL->S)->len[a]+1;
}
parameters[iteration][START]+=atoi(s+1)-1;
}
}
else if ( c=='C'||c=='c')parameters[iteration][SCALE]=atoi(choice+1);
else if ( c=='G'||c=='g')
{
parameters[iteration][GOPP]=atoi(choice+1);
CL->gop=parameters[iteration][GOPP];
}
else if ( c=='F'||c=='f')
{
sprintf ( out_format, "%s", choice+1);
}
else if ( c=='S'||c=='s')
{
if (choice[1]=='\0')sprintf ( choice, "default.domain_aln.%d", iteration);
output_format_aln (out_format,RESULT,EA=fast_coffee_evaluate_output(RESULT, CL),choice+1);
fprintf (stderr, "\tOutput file [%15s] in [%10s] format\n",choice+1,out_format);
free_aln (EA);
}
else if (c=='\0')
{
if ( parameters[iteration][SCALE]>0)
{
fprintf ( stderr, "\nWARNING: THRESHOLD RESET to 0");
parameters[iteration][SCALE]=0;
}
(CL->moca)->moca_scale=parameters[iteration][SCALE];
CL->gop=parameters[iteration][GOPP];
C=extract_domain_with_coordinates (C,parameters[iteration][START],parameters[iteration][LEN],CL);
if ( C==NULL)
{
fprintf ( stderr, "\nERROR: ILLEGAL COORDINATES! SEQUENCE BOUNDARY CROSSED\n");
for ( b=1,a=0; a< (CL->S)->nseq-1; a++)
{
fprintf ( stderr, "\n\t%15s=> Abs:[%d %d] Rel:[0 %d]", (CL->S)->name[a],b, b+(CL->S)->len[a]-1,(CL->S)->len[a]);
b+=(CL->S)->len[a];
}
fprintf ( stderr, "\n");
}
else if (parameters[iteration][START]==0 && parameters[iteration][LEN]==0)
{
fprintf ( stderr, "\n\tEnter the following parameters:\n\n\t\tSTART value: |x [Return]\n\t\tLENgth value: >y [Return]\n\t\ttype [Return]\n\n");
fprintf ( stderr, "\n\n\tSTART is measured on the total length of the concatenated sequences\n\tx and y are positive integers\n\n");
}
else if ( C->nseq==0)
{
fprintf ( stderr, "\nNO MATCH FOUND: LOWER THE SCALE (C)\n");
}
else
{
RESULT=copy_aln ( C, RESULT);
unpack_seq_aln (RESULT, CL);
RESULT->output_res_num=1;
output_format_aln (out_format,RESULT,EA=fast_coffee_evaluate_output(RESULT, CL),"stdout");
free_aln(EA);
PREVIOUS=copy_aln ( RESULT, PREVIOUS);
free_aln (C);
print_moca_interactive_choices ();
}
}
fprintf ( stderr, "\t[ITERATION %3d][START=%s][LEN=%3d][GOPP=%3d][SCALE=%4d]\t",iteration,last_start,parameters[iteration][LEN],parameters[iteration][GOPP],parameters[iteration][SCALE]);
a=0;
fprintf ( stderr, "Your Choice: ");
while ( (c=fgetc(stdin))!='\n')choice[a++]=c;
choice[a]=0;
}
}
if (!RESULT)myexit(EXIT_SUCCESS);
if ( RESULT)RESULT->output_res_num=0;
return RESULT;
}
int make_fasta_cdna_pair_wise (Alignment *B,Alignment *A,int*in_ns, int **l_s,Constraint_list *CL, int *diag)
{
int a,c,p,k;
Dp_Result *DPR;
static Dp_Model *M;
int l0, l1;
int len_i, len_j;
int f0=0, f1=0;
int deltaf0, deltaf1, delta;
int nr1, nr2;
int ala, alb, aa0, aa1;
int type;
char **al;
int **tl_s;
int *tns;
/*DEBUG*/
int debug_cdna_fasta=0;
Alignment *DA;
int score;
int state,prev_state;
int t, e;
int a1, a2;
l0=strlen ( B->seq_al[l_s[0][0]]);
l1=strlen ( B->seq_al[l_s[1][0]]);
al=declare_char (2, l0+l1+1);
B=realloc_aln2 (B,B->nseq,l0+l1+1);
free_int (B->cdna_cache, -1);
B->cdna_cache=declare_int(1, l0+l1+1);
if ( !M)M=initialize_dna_dp_model (CL);
M->diag=diag;
tl_s=(int**)declare_int (2, 2);tns=(int*)vcalloc(2, sizeof(int));tl_s[0][0]=0;tl_s[1][0]=3;tns[0]=tns[1]=1;
DPR=make_fast_dp_pair_wise (A,tns, tl_s,CL,M);
vfree(tns);free_int(tl_s, -1);
/*new_trace_back*/
a=p=0;
aa0=aa1=ala=alb=0;
while ( (k=DPR->traceback[a++])!=M->START);
while ( (k=DPR->traceback[a++])!=M->END)
{
f0=M->model_properties[k][M->F0];
f1=M->model_properties[k][M->F1];
len_i=M->model_properties[k][M->LEN_I];
len_j=M->model_properties[k][M->LEN_J];
type=M->model_properties[k][M->TYPE];
if (type==M->CODING0)
{
deltaf0=(aa0*3+f0)-ala;
deltaf1=(aa1*3+f1)-alb;
delta=MAX(deltaf0, deltaf1);
for (nr1=0, nr2=0,c=0; c<delta; c++, nr1++, nr2++,p++)
{
if (nr1<deltaf0 && ala<l0)al[0][p]=B->seq_al[l_s[0][0]][ala++];
else al[0][p]='-';
if (nr2<deltaf1 && alb<l1)al[1][p]=B->seq_al[l_s[1][0]][alb++];
else al[1][p]='-';
B->cdna_cache[0][p]=M->NON_CODING;
if ( is_gap(al[1][p]) && is_gap(al[0][p]))p--;
else if ( debug_cdna_fasta)fprintf (stderr, "\nUM: %c %c", al[0][p], al[1][p]);
}
for ( c=0; c< 3; c++, p++)
{
if ( c==0)B->cdna_cache[0][p]=M->CODING0;
else if ( c==1)B->cdna_cache[0][p]=M->CODING1;
else if ( c==2)B->cdna_cache[0][p]=M->CODING2;
if (ala<l0)al[0][p]=B->seq_al[l_s[0][0]][ala++];
else al[0][p]='-';
if (alb<l1)al[1][p]=B->seq_al[l_s[1][0]][alb++];
else al[1][p]='-';
if ( is_gap(al[1][p]) && is_gap(al[0][p]))p--;
else if ( debug_cdna_fasta)fprintf (stderr, "\n%d: %c %c",k, al[0][p], al[1][p]);
}
}
aa0+=len_i;
aa1+=len_j;
}
deltaf0=(aa0*3+f0)-ala;
deltaf1=(aa1*3+f1)-alb;
delta=MAX(deltaf0, deltaf1);
for (nr1=0, nr2=0,c=0; c<delta; c++, nr1++, nr2++,p++)
{
if (nr1<deltaf0 && ala<l0)al[0][p]=B->seq_al[l_s[0][0]][ala++];
else al[0][p]='-';
if (nr2<deltaf1 && alb<l1)al[1][p]=B->seq_al[l_s[1][0]][alb++];
else al[1][p]='-';
B->cdna_cache[0][p]=M->NON_CODING;
if ( is_gap(al[1][p]) && is_gap(al[0][p]))p--;
else if ( debug_cdna_fasta)fprintf (stderr, "\nUM: %c %c", al[0][p], al[1][p]);
}
/*End New traceback*/
al[0][p]='\0';
al[1][p]='\0';
sprintf( B->seq_al[l_s[0][0]], "%s", al[0]);
sprintf( B->seq_al[l_s[1][0]], "%s", al[1]);
B->len_aln=strlen (al[0]);
B->nseq=2;
if ( debug_cdna_fasta)
{
fprintf ( stderr, "\nA-A=%d, %d", CL->M['a'-'A']['a'-'A'], CL->M['a'-'A']['a'-'A'] *SCORE_K);
for ( a=1; a<diag[0]; a++)
{
fprintf ( stderr, "\nchosen diag: %d", diag[a]);
}
fprintf ( stderr, "\n GOP=%d GEP=%d TG_MODE=%d", M->gop, M->gep, M->TG_MODE);
fprintf ( stderr, "\nF_GOP=%d F_GEP=%d F_TG_MODE=%d", M->gop, M->gep, M->F_TG_MODE);
DA=copy_aln (B, NULL);
DA=realloc_aln2 (DA,6,(DA->len_aln+1));
for ( a=0; a<B->len_aln; a++)
{
fprintf ( stderr, "\n%d", DA->cdna_cache[0][a]);
if (DA->cdna_cache[0][a]>=M->CODING0)DA->seq_al[DA->nseq][a]=DA->cdna_cache[0][a]-M->nstate+'0';
else DA->seq_al[DA->nseq][a]=DA->cdna_cache[0][a]-M->nstate+'0';
if (DA->cdna_cache[0][a]==M->CODING0)
{
DA->seq_al[DA->nseq+1][a]=translate_dna_codon (DA->seq_al[0]+a,'*');
DA->seq_al[DA->nseq+2][a]=translate_dna_codon (DA->seq_al[1]+a,'*');
}
else
{
DA->seq_al[DA->nseq+1][a]='-';
DA->seq_al[DA->nseq+2][a]='-';
}
}
DA->nseq+=3;
print_aln (DA);
free_aln(DA);
score=0;
for (prev_state=M->START,a=0; a< DA->len_aln;)
{
state=DA->cdna_cache[0][a];
t=M->model[prev_state][state];
if ( DA->cdna_cache[0][a]==M->CODING0)
{
a1=translate_dna_codon (A->seq_al[0]+a,'x');
a2=translate_dna_codon (A->seq_al[1]+a,'x');
if ( a1!='x' && a2!='x')
{
e=CL->M[a1-'A'][a2-'A']*SCORE_K;
}
}
else if ( DA->cdna_cache[0][a]>M->CODING0);
else
{
e=M->model_properties[B->cdna_cache[0][a]][M->EMISSION];
}
if ( e==UNDEFINED || t==UNDEFINED) fprintf ( stderr, "\nPROBLEM %d\n", a);
fprintf ( stderr, "\n[%c..%c: %d(e)+%d(t)=%d]", A->seq_al[0][a], A->seq_al[1][a], e,t,e+t);
score+=e+t;
prev_state=state;
if (B->cdna_cache[0][a]==M->NON_CODING)a++;
else a+=3;
}
}
for ( a=0; a<B->len_aln; a++)
{
if ( B->cdna_cache[0][a]<M->CODING0)B->cdna_cache[0][a]=0;
else B->cdna_cache[0][a]=1;
}
free_char ( al, -1);
return DPR->score;
}
int make_fasta_gotoh_pair_wise (Alignment *A,int*ns, int **l_s,Constraint_list *CL, int *diag)
{
/*TREATMENT OF THE TERMINAL GAP PENALTIES*/
/*TG_MODE=0---> gop and gep*/
/*TG_MODE=1---> --- gep*/
/*TG_MODE=2---> --- ---*/
int TG_MODE, gop, l_gop, gep,l_gep, maximise;
/*VARIABLES FOR THE MULTIPLE SEQUENCE ALIGNMENT*/
int a, b,c,k, t;
int l1, l2,eg, ch, sub,score=0, last_i=0, last_j=0, i, delta_i, j, pos_j, ala, alb, LEN, n_diag, match1, match2;
int su, in, de, tr;
int **C, **D, **I, **trace, **pos0, **LD;
int lenal[2], len;
char *buffer, *char_buf;
char **aln, **al;
/********Prepare Penalties******/
gop=CL->gop*SCORE_K;
gep=CL->gep*SCORE_K;
TG_MODE=CL->TG_MODE;
maximise=CL->maximise;
/********************************/
n_diag=diag[0];
l1=lenal[0]=strlen (A->seq_al[l_s[0][0]]);
l2=lenal[1]=strlen (A->seq_al[l_s[1][0]]);
if ( getenv ("DEBUG_TCOFFEE"))fprintf ( stderr, "\n\tNdiag=%d%% ", (diag[0]*100)/(l1+l2));
/*diag:
diag[1..n_diag]--> flaged diagonal in order;
diag[0]=0--> first diagonal;
diag[n_diag+1]=l1+l2-1;
*/
/*numeration of the diagonals strats from the bottom right [1...l1+l2-1]*/
/*sequence s1 is vertical and seq s2 is horizontal*/
/*D contains the best Deletion in S2==>comes from diagonal N+1*/
/*I contains the best insertion in S2=> comes from diagonal N-1*/
C=declare_int (lenal[0]+lenal[1]+1, n_diag+2);
D=declare_int (lenal[0]+lenal[1]+1, n_diag+2);
LD=declare_int (lenal[0]+lenal[1]+1, n_diag+2);
I=declare_int (lenal[0]+lenal[1]+1, n_diag+2);
trace=declare_int (lenal[0]+lenal[1]+1, n_diag+2);
al=declare_char (2,lenal[0]+lenal[1]+lenal[1]+1);
len= MAX(lenal[0],lenal[1])+1;
buffer=(char*)vcalloc ( 2*len, sizeof (char));
char_buf=(char*) vcalloc (2*len, sizeof (char));
pos0=aln2pos_simple ( A,-1, ns, l_s);
C[0][0]=0;
t=(TG_MODE==0)?gop:0;
for ( j=1; j<= n_diag; j++)
{
l_gop=(TG_MODE==0)?gop:0;
l_gep=(TG_MODE==2)?0:gep;
if ( (diag[j]-lenal[0])<0 )
{
trace[0][j]=UNDEFINED;
continue;
}
C[0][j]=(diag[j]-lenal[0])*l_gep +l_gop;
D[0][j]=(diag[j]-lenal[0])*l_gep +l_gop+gop;
}
D[0][j]=D[0][j-1]+gep;
t=(TG_MODE==0)?gop:0;
for ( i=1; i<=lenal[0]; i++)
{
l_gop=(TG_MODE==0)?gop:0;
l_gep=(TG_MODE==2)?0:gep;
C[i][0]=C[i][n_diag+1]=t=t+l_gep;
I[i][0]=D[i][n_diag+1]=t+ gop;
for ( j=1; j<=n_diag; j++)
{
C[i][j]=C[i][0];
D[i][j]=I[i][j]=I[i][0];
}
for (eg=0, j=1; j<=n_diag; j++)
{
pos_j=diag[j]-lenal[0]+i;
if (pos_j<=0 || pos_j>l2 )
{
trace[i][j]=UNDEFINED;
continue;
}
sub=(CL->get_dp_cost) ( A, pos0, ns[0], l_s[0], i-1, pos0, ns[1], l_s[1],pos_j-1, CL );
/*1 identify the best insertion in S2:*/
l_gop=(i==lenal[0])?((TG_MODE==0)?gop:0):gop;
l_gep=(i==lenal[0])?((TG_MODE==2)?0:gep):gep;
len=(j==1)?0:(diag[j]-diag[j-1]);
if ( a_better_than_b(I[i][j-1], C[i][j-1]+l_gop, maximise))eg++;
else eg=1;
I[i][j]=best_of_a_b (I[i][j-1], C[i][j-1]+l_gop, maximise)+len*l_gep;
/*2 Identify the best deletion in S2*/
l_gop=(pos_j==lenal[1])?((TG_MODE==0)?gop:0):gop;
l_gep=(pos_j==lenal[1])?((TG_MODE==2)?0:gep):gep;
len=(j==n_diag)?0:(diag[j+1]-diag[j]);
delta_i=((i-len)>0)?(i-len):0;
if ( a_better_than_b(D[delta_i][j+1],C[delta_i][j+1]+l_gop, maximise)){LD[i][j]=LD[delta_i][j+1]+1;}
else {LD[i][j]=1;}
D[i][j]=best_of_a_b (D[delta_i][j+1],C[delta_i][j+1]+l_gop, maximise)+len*l_gep;
/*Identify the best way*/
/*
score=C[i][j]=best_int ( 3, maximise, &fop, I[i][j], C[i-1][j]+sub, D[i][j]);
fop-=1;
if ( fop<0)trace[i][j]=fop*eg;
else if ( fop>0 ) {trace[i][j]=fop*LD[i][j];}
else if ( fop==0) trace[i][j]=0;
*/
su=C[i-1][j]+sub;
in=I[i][j];
de=D[i][j];
/*HERE ("%d %d %d", su, in, de);*/
if (su>=in && su>=de)
{
score=su;
tr=0;
}
else if (in>=de)
{
score=in;
tr=-eg;
}
else
{
score=de;
tr=LD[i][j];
}
trace[i][j]=tr;
C[i][j]=score;
last_i=i;
last_j=j;
}
}
/*
[0][Positive]
^ ^
| /
| /
| /
| /
|/
[Neg]<-------[*]
*/
i=last_i;
j=last_j;
ala=alb=0;
match1=match2=0;
while (!(match1==l1 && match2==l2))
{
if ( match1==l1)
{
len=l2-match2;
for ( a=0; a< len; a++)
{
al[0][ala++]=0;
al[1][alb++]=1;
match2++;
}
k=0;
break;
/*k=-(j-1);*/
}
else if ( match2==l2)
{
len=l1-match1;
for ( a=0; a< len; a++)
{
al[0][ala++]=1;
al[1][alb++]=0;
match1++;
}
k=0;
break;
/*k= n_diag-j;*/
}
else
{
k=trace[i][j];
}
if ( k==0)
{
if ( match2==l2 || match1==l1);
else
{
al[0][ala++]=1;
al[1][alb++]=1;
i--;
match1++;
match2++;
}
}
else if ( k>0)
{
len=diag[j+k]-diag[j];
for ( a=0; a<len; a++)
{
if ( match1==l1)break;
al[0][ala++]=1;
al[1][alb++]=0;
match1++;
}
i-=len;
j+=k;
}
else if ( k<0)
{
k*=-1;
len=diag[j]-diag[j-k];
for ( a=0; a<len; a++)
{
if ( match2==l2)break;
al[0][ala++]=0;
al[1][alb++]=1;
match2++;
}
j-=k;
}
}
LEN=ala;
c=LEN-1;
invert_list_char ( al[0], LEN);
invert_list_char ( al[1], LEN);
if ( A->declared_len<=LEN)A=realloc_aln2 ( A,A->max_n_seq, 2*LEN);
aln=A->seq_al;
for ( c=0; c< 2; c++)
{
for ( a=0; a< ns[c]; a++)
{
ch=0;
for ( b=0; b< LEN; b++)
{
if (al[c][b]==1)
char_buf[b]=aln[l_s[c][a]][ch++];
else
char_buf[b]='-';
}
char_buf[b]='\0';
aln[l_s[c][a]]=csprintf (aln[l_s[c][a]],"%s", char_buf);
}
}
A->len_aln=LEN;
A->nseq=ns[0]+ns[1];
free_int (pos0, -1);
free_int (C, -1);
free_int (D, -1);
free_int (I, -1);
free_int (trace, -1);
free_int (LD, -1);
free_char ( al, -1);
vfree(buffer);
vfree(char_buf);
return score;
}
Dp_Model* initialize_dna_dp_model (Constraint_list *CL)
{
Dp_Model *M;
int a, b, c,d;
int f0, f1;
int deltaf1, deltaf0,deltatype;
int type, type1, type0;
M=(Dp_Model*)vcalloc( 1, sizeof (Dp_Model));
for (M->nstate=0,f0=0; f0<3; f0++)
for ( f1=0; f1<3; f1++)M->nstate+=3;
M->UM=M->nstate++;
M->START=M->nstate++;
M->END =M->nstate++;
M->TG_MODE=CL->TG_MODE;
M->F_TG_MODE=0;
M->gop=CL->gop*SCORE_K;
M->gep=CL->gep*SCORE_K;
M->f_gop=CL->f_gop*SCORE_K;
M->f_gep=CL->f_gep*SCORE_K;
M->bounded_model=declare_int (M->nstate+1, M->nstate+1);
M->model=declare_int (M->nstate+1, M->nstate+1);
for ( a=0; a<=M->nstate; a++)
for ( b=0; b<= M->nstate; b++)
M->model[a][b]=UNDEFINED;
M->model_properties=declare_int ( M->nstate, 10);
a=0;
M->TYPE=a++;M->F0=a++;M->F1=a++; M->LEN_I=a++; M->LEN_J=a++; M->DELTA_I=a++;M->DELTA_J=a++;M->EMISSION=a++;M->TERM_EMISSION=a++;
a=M->nstate;
M->NON_CODING=a++; M->INSERTION=a++; M->DELETION=a++; M->CODING0=a++; M->CODING1=a++;M->CODING2=a++;
for ( a=0,f0=0; f0<3; f0++)
for ( f1=0; f1<3; f1++, a+=3)
{
M->model_properties[a+0][M->TYPE]=M->CODING0;
M->model_properties[a+0][M->F0]=f0;
M->model_properties[a+0][M->F1]=f1;
M->model_properties[a+0][M->LEN_I]=1;
M->model_properties[a+0][M->LEN_J]=1;
M->model_properties[a+0][M->DELTA_I]=-1;
M->model_properties[a+0][M->DELTA_J]= 0;
M->model_properties[a+0][M->EMISSION]=0;
M->model_properties[a+0][M->TERM_EMISSION]=0;
M->model_properties[a+1][M->TYPE]=M->DELETION;
M->model_properties[a+1][M->F0]=f0;
M->model_properties[a+1][M->F1]=f1;
M->model_properties[a+1][M->LEN_I]=1;
M->model_properties[a+1][M->LEN_J]=0;
M->model_properties[a+1][M->DELTA_I]=-1;
M->model_properties[a+1][M->DELTA_J]=+1;
M->model_properties[a+1][M->EMISSION]=M->gep;
M->model_properties[a+1][M->TERM_EMISSION]=(M->TG_MODE==2)?0:M->gep;
M->model_properties[a+2][M->TYPE]=M->INSERTION;
M->model_properties[a+2][M->F0]=f0;
M->model_properties[a+2][M->F1]=f1;
M->model_properties[a+2][M->LEN_I]=0;
M->model_properties[a+2][M->LEN_J]=1;
M->model_properties[a+2][M->DELTA_I]= 0;
M->model_properties[a+2][M->DELTA_J]=-1;
M->model_properties[a+2][M->EMISSION]=M->gep;
M->model_properties[a+2][M->TERM_EMISSION]=(M->TG_MODE==2)?0:M->gep;
}
/*UM" Unmatched State*/
M->model_properties[a][M->TYPE]=M->NON_CODING;
M->model_properties[a][M->F0]=0;
M->model_properties[a][M->F1]=0;
M->model_properties[a][M->LEN_I]=1;
M->model_properties[a][M->LEN_J]=1;
M->model_properties[a][M->DELTA_I]=-1;
M->model_properties[a][M->DELTA_J]=0;
M->model_properties[a][M->EMISSION]=M->f_gep;
M->model_properties[a][M->TERM_EMISSION]=(M->F_TG_MODE==2)?0:M->f_gep;
M->model_properties[M->START][M->TYPE]=M->NON_CODING;
M->model_properties[a+1][M->F0]=0;
M->model_properties[a+1][M->F1]=0;
M->model_properties[a+1][M->LEN_I]=0;
M->model_properties[a+1][M->LEN_J]=0;
M->model_properties[a+1][M->DELTA_I]=0 ;
M->model_properties[a+1][M->DELTA_J]=0;
M->model_properties[a+1][M->EMISSION]=0;
M->model_properties[a+1][M->TERM_EMISSION]=0;
M->model_properties[M->END][M->TYPE]=M->NON_CODING;
M->model_properties[a+2][M->F0]=0;
M->model_properties[a+2][M->F1]=0;
M->model_properties[a+2][M->LEN_I]=0;
M->model_properties[a+2][M->LEN_J]=0;
M->model_properties[a+2][M->DELTA_I]=0 ;
M->model_properties[a+2][M->DELTA_J]=0;
M->model_properties[a+2][M->EMISSION]=0;
M->model_properties[a+2][M->TERM_EMISSION]=0;
/*1: SET THE INDEL PENALTIES*/
for ( a=0; a< M->START; a++)
{
deltaf0=M->model_properties[M->START][M->F0]-M->model_properties[a][M->F0];
deltaf1=M->model_properties[M->START][M->F1]-M->model_properties[a][M->F1];
if ( deltaf0==0 && deltaf1==0)deltatype=0;
else if ( deltaf0<=0 && deltaf1<=0)deltatype=1;
else deltatype=-1;
type=M->model_properties[a][M->TYPE];
if ( type==M->NON_CODING) M->model[a][M->END]=M->model[M->START][a]=(M->F_TG_MODE==0)?M->f_gop:0;
else if ( type==M->CODING0 && deltatype==0)M->model[a][M->END]=M->model[M->START][a]=ALLOWED;
else if ( type==M->CODING0 && deltatype==1)M->model[a][M->END]=M->model[M->START][a]=(M->F_TG_MODE==0)?M->f_gop:0;
else if ( type==M->INSERTION && deltatype==0)M->model[a][M->END]=M->model[M->START][a]=(M->TG_MODE==0)?M->gop:0;
else if ( type==M->INSERTION && deltatype==1)M->model[a][M->END]=M->model[M->START][a]=(M->TG_MODE==0)?M->gop:0+(M->F_TG_MODE==0)?M->f_gop:0;
else if ( type==M->DELETION && deltatype==0)M->model[a][M->END]=M->model[M->START][a]=(M->TG_MODE==0)?M->gop:0;
else if ( type==M->DELETION && deltatype==1)M->model[a][M->END]=M->model[M->START][a]=(M->TG_MODE==0)?M->gop:0+(M->F_TG_MODE==0)?M->f_gop:0;
else M->model[a][M->END]=M->model[M->START][a]=UNDEFINED;
/*
if (type==M->NON_CODING ||M->model_properties[a][M->F0] ||M->model_properties[a][M->F1]) M->model[M->START][a]=M->model[a][M->END]=(M->F_TG_MODE==0)?M->f_gop:0;
else if (type==M->INSERTION || type==M->DELETION)M->model[M->START][a]=M->model[a][M->END]=( M->TG_MODE==0)?M->gop:0;
else M->model[M->START][a]=M->model[a][M->END]=ALLOWED;
*/
for ( b=0; b< M->START; b++)
{
deltaf0=M->model_properties[a][M->F0]-M->model_properties[b][M->F0];
deltaf1=M->model_properties[a][M->F1]-M->model_properties[b][M->F1];
type0=M->model_properties[a][M->TYPE];
type1=M->model_properties[b][M->TYPE];
if ( deltaf0==0 && deltaf1==0)deltatype=0;
else if ( deltaf0<=0 && deltaf1<=0)deltatype=1;
else deltatype=-1;
if ( type0==M->NON_CODING && type1==M->NON_CODING )M->model[a][b]=UNDEFINED;
else if ( type0==M->NON_CODING && type1==M->CODING0 )M->model[a][b]=ALLOWED ;
else if ( type0==M->NON_CODING && type1==M->INSERTION )M->model[a][b]=M->gop;
else if ( type0==M->NON_CODING && type1==M->DELETION )M->model[a][b]=M->gop;
else if ( type0==M->CODING0 && type1==M->NON_CODING )M->model[a][b]=M->f_gop;
else if ( type0==M->CODING0 && type1==M->CODING0 && deltatype==0 )M->model[a][b]=ALLOWED;
else if ( type0==M->CODING0 && type1==M->CODING0 && deltatype==1 )M->model[a][b]=M->f_gop;
else if ( type0==M->CODING0 && type1==M->INSERTION && deltatype==0 )M->model[a][b]=M->gop;
else if ( type0==M->CODING0 && type1==M->INSERTION && deltatype==1 )M->model[a][b]=M->gop+M->f_gop;
else if ( type0==M->CODING0 && type1==M->DELETION && deltatype==0 )M->model[a][b]=M->gop;
else if ( type0==M->CODING0 && type1==M->DELETION && deltatype==1 )M->model[a][b]=M->gop+M->f_gop;
else if ( type0==M->INSERTION && type1==M->NON_CODING )M->model[a][b]=M->f_gop;
else if ( type0==M->INSERTION && type1==M->CODING0 && deltatype==0 )M->model[a][b]=ALLOWED;
else if ( type0==M->INSERTION && type1==M->CODING0 && deltatype==1 )M->model[a][b]=M->f_gop;
else if ( type0==M->INSERTION && type1==M->INSERTION && deltatype==0 )M->model[a][b]=ALLOWED;
else if ( type0==M->INSERTION && type1==M->INSERTION && deltatype==1 )M->model[a][b]=M->f_gop;
else if ( type0==M->INSERTION && type1==M->DELETION && deltatype==0 )M->model[a][b]=M->gop;
else if ( type0==M->INSERTION && type1==M->DELETION && deltatype==1 )M->model[a][b]=M->gop+M->f_gop;
else if ( type0==M->DELETION && type1==M->NON_CODING )M->model[a][b]=M->f_gop;
else if ( type0==M->DELETION && type1==M->CODING0 && deltatype==0 )M->model[a][b]=ALLOWED;
else if ( type0==M->DELETION && type1==M->CODING0 && deltatype==1 )M->model[a][b]=M->f_gop;
else if ( type0==M->DELETION && type1==M->INSERTION && deltatype==0 )M->model[a][b]=M->gop;
else if ( type0==M->DELETION && type1==M->INSERTION && deltatype==1 )M->model[a][b]=M->gop+M->f_gop;
else if ( type0==M->DELETION && type1==M->DELETION && deltatype==0 )M->model[a][b]=ALLOWED;
else if ( type0==M->DELETION && type1==M->DELETION && deltatype==1 )M->model[a][b]=M->f_gop;
else {M->model[a][b]=UNDEFINED;}
}
}
/*2 SET THE FRAMESHIFT PENALTIES
for ( a=0; a< M->START; a++)
{
type=M->model_properties[a][M->TYPE];
for ( b=0; b< M->START; b++)
{
deltaf0=M->model_properties[a][M->F0]-M->model_properties[b][M->F0];
deltaf1=M->model_properties[a][M->F1]-M->model_properties[b][M->F1];
if (b==M->UM) M->model[a][b]+=M->f_gop;
else if (a==M->UM) M->model[a][b]+=ALLOWED;
else if (deltaf1==0 && deltaf0==0)M->model[a][b]+=ALLOWED;
else if (deltaf1<=0 && deltaf0<=0)M->model[a][b]+=M->f_gop;
else M->model[a][b]=UNDEFINED;
}
}
M->model[M->UM][M->UM]=UNDEFINED;
*/
for (c=0,a=0, d=0; a< M->START; a++)
for ( b=0; b<M->START; b++, d++)
{
if (M->model[a][b]!=UNDEFINED)
{
M->bounded_model[b][1+M->bounded_model[b][0]++]=a;
c++;
}
}
return M;
}
