Alignment* shrink_aln ( Alignment *A, int nseq, int *list)
{
Alignment *B=NULL;
int a,seq;
B=copy_aln (A, B);
for ( a=0; a< nseq; a++)
{
seq=list[a];
sprintf ( A->seq_comment[a], "%s",B->seq_comment[seq]);
sprintf ( A->aln_comment[a], "%s",B->aln_comment[seq]);
sprintf ( A->seq_al [a], "%s",B->seq_al [seq]);
A->order[a][0]=B->order[seq][0];
A->order[a][1]=B->order[seq][1];
A->order[a][2]=B->order[seq][2];
A->order[a][3]=B->order[seq][3];
A->order[a][4]=B->order[seq][4];
A->score_seq[a]=B->score_seq[seq];
A->len[a]=B->len[seq];
}
A->nseq=nseq;
A->len_aln=strlen (A->seq_al[0]);
free_aln (B);
return A;
}
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=declare_int (2, 2);tns=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 measure_domain_length ( Constraint_list *CL,Alignment *IN, int start, int min_len, int max_len, int step)
{
Alignment *C=NULL;
int score, best_score,best_len,a, b, l;
int *score_matrix, *len_matrix;
int n_val, best_val;
score_matrix=(int*)vcalloc ( max_len, sizeof (int));
len_matrix=(int*)vcalloc ( max_len, sizeof (int));
l=strlen ( (CL->S)->seq[0]);
min_len=MAX(0, min_len);
min_len=MIN(l-start, min_len);
if ( !IN)C=extract_domain_with_coordinates (C,start,min_len, CL);
else
{
C=copy_aln (IN, C);
C->len_aln=min_len;
for ( a=0; a< C->nseq; a++)C->seq_al[a][min_len]='\0';
C=add_seq2aln (CL,C, CL->S);
}
best_score= score=((CL->moca)->evaluate_domain)(C, CL);
min_len=MAX(0, min_len);
for ( best_len=best_val=n_val=0,b=min_len; b<max_len && (start+b)<l; b+=step, n_val++)
{
if ( !IN)C=extract_domain_with_coordinates (C,start, b, CL);
else
{
C=copy_aln (IN, C);
C->len_aln=min_len;
for ( a=0; a< C->nseq; a++)C->seq_al[a][b]='\0';
C=add_seq2aln (CL,C, CL->S);
}
if ( C->len_aln>0 )score=((CL->moca)->evaluate_domain)(C, CL);
else score=-1;
if ( score< -3000)break;
fprintf ( stderr, "\n\t%d %d=>%d (%d, %d)[%d]",start, b, score, C->nseq, C->len_aln, step);
score_matrix[n_val]=score;
len_matrix [n_val]=b;
if ( score>best_score)
{
best_score=score;
best_len=b;
best_val=n_val;
}
}
free_aln(C);
for ( a=best_val; a<n_val; a++)
{
if (score_matrix[a]>best_score/2)best_len=len_matrix[a];
else break;
}
vfree ( score_matrix);
vfree ( len_matrix);
return best_len;
}
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;
}
Alignment * extract_domain ( Constraint_list *CL)
{
/*
function documentation: start
Alignment * extract_domain ( Constraint_list *CL)
given a CL, this function extracts the next best scoring local multiple alignment
It returns a CL where the aligned residues have been indicated in (CL->moca)->forbiden_residues;
the local alignment is extracted with the dp function indicated by
CL->dp_mode: (gotoh_sw_pair_wise)
Evaluation:
CL->get_dp_cost=slow_get_dp_cost;
CL->evaluate_residue_pair=sw_residue_pair_extended_list;
Continuation:
(CL->moca)->evaluate_domain=evaluate_moca_domain;
Cache of CL:
(CL->moca)->cache_cl_with_domain=cache_cl_with_moca_domain;
Domain post processing:
(CL->moca)->make_nol_aln=make_moca_nol_aln;
function documentation: end
*/
int min_start, max_start, start,min_len, max_len, len, score;
int step;
Alignment *C=NULL;
Alignment *RESULT=NULL;
Alignment *EA=NULL;
/*CASE 1: Non Automatic Domain Extraction*/
if ((CL->moca)->moca_interactive)
{
return interactive_domain_extraction (CL);
}
else if ((CL->moca)->moca_len)
{
while ((C=extract_domain_with_coordinates (C,(CL->moca)->moca_start,(CL->moca)->moca_len,CL))->nseq==0)(CL->moca)->moca_scale=(CL->moca)->moca_scale*0.9;
RESULT=copy_aln ( C, RESULT);
unpack_seq_aln (RESULT, CL);
output_format_aln ("mocca_aln",RESULT,EA=fast_coffee_evaluate_output(RESULT, CL),"stdout");
free_aln(EA);
return RESULT;
}
else if ( !(CL->moca)->moca_len)
{
analyse_sequence (CL);
myexit (EXIT_FAILURE);
}
/*CASE 2: Automatic Domain Extraction: Find Coordinates*/
start=500;
step=10;
min_start=0;
max_start=strlen ((CL->S)->seq[0]);
min_len=20;
max_len=strlen ((CL->S)->seq[0]);
C=extract_domain_with_coordinates (C,13,30,CL);
C->output_res_num=1;
print_aln (C);
(CL->moca)->moca_scale=-180;
C=add_seq2aln (CL,C, CL->S);
print_aln (C);
(CL->moca)->moca_scale=-160;
C=add_seq2aln (CL,C, CL->S);
print_aln (C);
myexit (EXIT_FAILURE);
while ( step>0)
{
C=approximate_domain (min_start,max_start,step,min_len,max_len, step,&start, &len, &score, CL);
min_start=start-step;
max_start=start+step;
min_len=len-step;
max_len=len+step;
step=step/2;
}
C=extract_domain_with_coordinates (C,start-10, len+20,CL);
C->output_res_num=1;
print_aln (C);
myexit (EXIT_FAILURE);
return C;
}
Alignment* copy_aln ( Alignment *A, Alignment *B)
{
int a, b;
int nnseq;
int nlen;
/* c[100]=10;*/
if ( A==NULL){free_aln(B); return NULL;}
nnseq=MAX(A->nseq, A->max_n_seq);
nlen=A->len_aln+1;
if (B)
B=realloc_alignment2 (B, nnseq, nlen);
else
B=declare_aln2 (nnseq, nlen);
B->S=A->S;
/*SIZES*/
B->max_len=A->max_len;
B->min_len=A->min_len;
B->declared_len=nlen;
B->max_n_seq=nnseq;
B->nseq=A->nseq;
B->len_aln=A->len_aln;
/*sequence Information*/
if ( A->generic_comment)
{
vfree(B->generic_comment);
B->generic_comment=vcalloc (strlen(A->generic_comment)+1, sizeof (char));
sprintf ( B->generic_comment, "%s", A->generic_comment);
}
if ( (A->S)==NULL){vfree (B->len); B->len=vcalloc ( A->max_n_seq, sizeof (int));}
ga_memcpy_int ( A->len, B->len, B->nseq);
B->seq_comment=copy_char ( A->seq_comment, B->seq_comment, -1,-1);
B->aln_comment=copy_char ( A->aln_comment, B->aln_comment, -1,-1);
B->name=copy_char ( A->name, B->name, -1,-1);
B->file=copy_char ( A->file, B->file, -1,-1);
B->tree_order=copy_char ( A->tree_order, B->tree_order, -1,-1);
B->expanded_order=A->expanded_order;
free_char ( B->seq_al, -1);
B->seq_al=declare_char(B->max_n_seq, B->declared_len);
// HERE ("A: MAX_NSEQ=%d %d %d %d",B->nseq, B->max_n_seq, B->declared_len, B->len_aln);
// HERE ("B: MAX_NSEQ=%d %d %d %d",A->nseq, A->max_n_seq, A->declared_len, A->len_aln);
for ( a=0; a< nnseq; a++)
{
if (A->seq_al[a])
{
for ( b=0; b< A->len_aln; b++)
B->seq_al[a][b]=A->seq_al[a][b];
}
}
B->order=copy_int ( A->order, B->order, -1, -1);
B->S=A->S;
if (A->seq_cache)
{
B->seq_cache=copy_int ( A->seq_cache, B->seq_cache,-1,-1);
}
if (A->cdna_cache)
{
B->cdna_cache=copy_int ( A->cdna_cache, B->cdna_cache,-1,-1);
}
B->P=copy_profile (A->P);
B->Dp_result=A->Dp_result;
/*Score*/
if ( (A->S)==NULL){vfree (B->score_seq); B->score_seq=vcalloc ( A->max_n_seq, sizeof (int));}
ga_memcpy_int( A->score_seq,B->score_seq,B->nseq);
B->score_res=A->score_res;
B->score_aln=A->score_aln;
B->score=A->score;
B->ibit=A->ibit;
B->cpu=A->cpu;
B->finished=A->finished;
/*Output Options*/
B->output_res_num=A->output_res_num;
B->residue_case=A->residue_case;
B->expand=A->expand;
B->CL=A->CL;
B->random_tag=A->random_tag;
/*Make the function Recursive */
if ( A->A)
{
B->A=copy_aln (A->A, NULL);
}
else B->A=NULL;
return B;
}
Constraint_list *copy_constraint_list (Constraint_list *CL, int mode)
{
Constraint_list *NCL;
Sequence *S;
int a, b;
/*Sequences*/
S=(mode==HARD_COPY)?duplicate_sequence (CL->S):CL->S;
if (mode==HARD_COPY)
NCL=declare_constraint_list (S, NULL, NULL,0, NULL, NULL);
else
{
NCL=vcalloc ( 1, sizeof (Constraint_list));
NCL[0]=CL[0];
}
NCL->copy_mode=mode;
if (mode==SOFT_COPY)NCL->pCL=CL;
NCL->S=S;
/*master*/
if (mode==HARD_COPY && CL->master)
{NCL->master=vcalloc ( S->nseq, sizeof(int));
for ( a=0; a< S->nseq; a++)
NCL->master[a]=CL->master[a];
}
else if (mode==SOFT_COPY)
{
NCL->seq_for_quadruplet=CL->seq_for_quadruplet;
}
NCL->o2a_byte=CL->o2a_byte;
/*struc List*/
NCL->STRUC_LIST=(mode==HARD_COPY)?duplicate_sequence (CL->STRUC_LIST):CL->STRUC_LIST;
sprintf ( NCL->align_pdb_param_file, "%s", CL->align_pdb_param_file);
sprintf ( NCL->align_pdb_hasch_mode, "%s", CL->align_pdb_hasch_mode);
NCL->W=(mode==HARD_COPY)?duplicate_weights (CL->W):CL->W;
NCL->DM=(mode==HARD_COPY)?duplicate_distance_matrix (CL->DM):CL->DM;
NCL->ktupDM=(mode==HARD_COPY)?duplicate_distance_matrix (CL->ktupDM):CL->ktupDM;
NCL->RunName=CL->RunName;
if ( mode==HARD_COPY && CL->translation){NCL->translation=vcalloc ((CL->S)->nseq, sizeof (int)); for ( a=0; a< (CL->S)->nseq; a++)NCL->translation[a]=CL->translation[a];}
else{NCL->translation=CL->translation;}
NCL->out_aln_format=(mode==HARD_COPY)?duplicate_char (CL->out_aln_format, -1, -1):CL->out_aln_format;
NCL->n_out_aln_format=CL->n_out_aln_format;
/*Packing Sequence: To use with domain analysis*/
NCL->packed_seq_lu=(mode==HARD_COPY)?duplicate_int (CL->packed_seq_lu, -1, -1):CL->packed_seq_lu;
/*DATA*/
if (CL->fp)(mode==HARD_COPY)?NCL->fp=vtmpfile():CL->fp;
if ( mode==HARD_COPY)
{
NCL->residue_index=duplicate_residue_index (NCL->residue_index);
}
else NCL->residue_index=CL->residue_index;
if ( mode==HARD_COPY)
{
NCL->M=copy_int ( CL->M,NCL->M,-1, -1);
}
else
NCL->M=CL->M;
/*List Information*/
NCL->ne=CL->ne;
sprintf ( NCL->list_name, "%s", CL->list_name);
NCL->entry_len=CL->entry_len;
NCL->el_size=CL->el_size;
/*Normalisation information*/
NCL->filter_lib=CL->filter_lib;
NCL->normalise=CL->normalise;
NCL->overweight=CL->overweight;
NCL->max_ext_value=CL->max_ext_value;
NCL->max_value=CL->max_value;
/*Pair wise alignment method*/
NCL->pw_parameters_set=CL->pw_parameters_set;
NCL->gop=CL->gop;
NCL->f_gop=CL->f_gop;
NCL->gep=CL->gep;
NCL->f_gep=CL->f_gep;
NCL->nomatch=CL->nomatch;
NCL->TG_MODE=CL->TG_MODE;
NCL->F_TG_MODE=CL->F_TG_MODE;
sprintf ( NCL->dp_mode, "%s", CL->dp_mode);
NCL->maximise=CL->maximise;
sprintf ( NCL->matrix_for_aa_group, "%s", CL->matrix_for_aa_group);
sprintf ( NCL->method_matrix, "%s", CL->method_matrix);
NCL->diagonal_threshold=CL->diagonal_threshold;
NCL->ktup=CL->ktup;
NCL->use_fragments=CL->use_fragments;
NCL->fasta_step=CL->fasta_step;
NCL->lalign_n_top=CL->lalign_n_top;
NCL->sw_min_dist=CL->sw_min_dist;
NCL->matrices_list=(mode==HARD_COPY)?duplicate_char (CL->matrices_list, -1, -1):CL->matrices_list;
NCL->n_matrices=CL->n_matrices;
sprintf (NCL->distance_matrix_mode, "%s", CL->distance_matrix_mode);
sprintf (NCL->distance_matrix_sim_mode, "%s", CL->distance_matrix_sim_mode);
sprintf (NCL->tree_mode, "%s", CL->tree_mode);
NCL->tree_aln=(mode==HARD_COPY)?copy_aln (CL->tree_aln, NULL):CL->tree_aln;
/*Functions used for dynamic programming and Evaluation*/
NCL->no_overaln=CL->no_overaln;
NCL->profile_mode=CL->profile_mode;
sprintf ( NCL->profile_comparison, "%s",CL->profile_comparison);
NCL->get_dp_cost=CL->get_dp_cost;
NCL->evaluate_residue_pair=CL->evaluate_residue_pair;
NCL->pair_wise=CL->pair_wise;
NCL->weight_field=CL->weight_field;
NCL->max_n_pair=CL->max_n_pair;
/*threading parameters*/
NCL->Prot_Blast=(mode==HARD_COPY)?duplicate_blast_param ( CL->Prot_Blast):CL->Prot_Blast;
NCL->DNA_Blast =(mode==HARD_COPY)?duplicate_blast_param ( CL->DNA_Blast):CL->DNA_Blast;
NCL->Pdb_Blast =(mode==HARD_COPY)?duplicate_blast_param ( CL->Pdb_Blast):CL->Pdb_Blast;
NCL->TC =(mode==HARD_COPY)?duplicate_TC_param ( CL->TC):CL->TC;
/*Split parameters*/
NCL->split=CL->split;
NCL->split_nseq_thres= CL->split_nseq_thres;
NCL->split_score_thres= CL->split_score_thres;
/*Structural status*/
NCL->check_pdb_status=CL->check_pdb_status;
/*log*/
sprintf ( NCL->method_log, "%s",CL->method_log);
sprintf ( NCL->evaluate_mode, "%s",CL->evaluate_mode);
/* Gene Prediction*/
sprintf ( NCL->genepred_score, "%s",CL->genepred_score);
/*Parameters for domain extraction*/
NCL->moca=(mode==HARD_COPY)?duplicate_moca ( CL->moca):CL->moca;
/*Functions for hiding forbiden pairs of residues*/
/* Copy only for soft_copy*/
if (mode==SOFT_COPY)
{
NCL->forbiden_pair_list=CL->forbiden_pair_list;
}
/*extention properties:*/
NCL->nseq_for_quadruplet=CL->nseq_for_quadruplet;
if (mode==HARD_COPY && CL->seq_for_quadruplet)
{NCL->seq_for_quadruplet=vcalloc ( S->nseq, sizeof(int));
for ( a=0; a< S->nseq; a++)
NCL->seq_for_quadruplet[a]=CL->seq_for_quadruplet[a];
}
else if (mode==SOFT_COPY)
{
NCL->seq_for_quadruplet=CL->seq_for_quadruplet;
}
/*extention properties: Do only a soft copy*/
/* Not To be copied yet */
if ( mode==SOFT_COPY)
{
NCL->extend_jit=CL->extend_jit;
NCL->extend_threshold=CL->extend_threshold;
sprintf ( NCL->extend_clean_mode, "%s", CL->extend_clean_mode);
sprintf ( NCL->extend_compact_mode, "%s", CL->extend_compact_mode);
}
/*Lookup table parameteres*/
NCL->chunk= CL->chunk;
/* Do NOT copy NCL->seq_indexed, NCL->start_index, NCL->max_L_len, NCL->chunk*/
/*
if ( mode==SOFT_COPY)
{
NCL->seq_indexed=CL->seq_indexed;
NCL->start_index=CL->start_index;
NCL->end_index=CL->start_index;
NCL->max_L_len=CL->max_L_len;
}
*/
/*PDB STRUCTURE ALIGNMENTS*/
/* Do only a soft copy */
if ( mode==SOFT_COPY)
{
NCL->T=CL->T;
}
/*MISC*/
NCL->cpu=CL->cpu;
NCL->local_stderr=CL->local_stderr;
sprintf (NCL->multi_thread, "%s", CL->multi_thread);
return NCL;
}