PUBLIC int
move_standard(char *seq,
char *struc,
enum MOVE_TYPE type,
int verbosity_level,
int shifts,
int noLP){
make_pair_matrix();
short int *s0 = encode_sequence(seq, 0);
short int *s1 = encode_sequence(seq, 1);
short int *str = vrna_ptable(struc);
int energy = 0;
switch (type){
case GRADIENT: energy = move_gradient(seq, str, s0, s1, verbosity_level, shifts, noLP); break;
case FIRST: energy = move_first(seq, str, s0, s1, verbosity_level, shifts, noLP); break;
case ADAPTIVE: energy = move_adaptive(seq, str, s0, s1, verbosity_level); break;
}
int i=1;
for (; i<=str[0]; i++) {
if (str[i]==0) struc[i-1]='.';
else if (str[i]>str[str[i]]) struc[i-1]='(';
else struc[i-1]=')';
}
free(s0);
free(s1);
free(str);
return energy;
}
int main(int argc, char *argv[]){
char sequence[MAXSIZE], structure[MAXSIZE];
int i, j;
if (argc == 9) {
i = 1;
while (i < argc) {
if (!strcmp(argv[i], "-s")) {
sequence[0] = '@';
strncpy(sequence + 1, argv[i + 1], strlen(argv[i + 1])); // The sequence starts from index 1
sequence[strlen(argv[i + 1]) + 1] = '\0'; // Remember to end the sequence
i += 2;
} else if (!strcmp(argv[i], "-r")) {
strncpy(structure, argv[i + 1], strlen(argv[i + 1])); // The structure starts from index 0
structure[strlen(argv[i + 1])] = '\0'; // Remember to end the structure
i += 2;
} else if (!strcmp(argv[i], "-c")) {
SCALING_FACTOR = atof(argv[i + 1]);
i += 2;
} else if (!strcmp(argv[i], "-p")) {
PRECISION = atoi(argv[i + 1]);
i += 2;
} else {
printf("Error: Unrecognizable Flag!\n");
printf("Usage:");
printf("%s -s SEQUENCE -r STRUCTURE -c SCALING -p PRECISION\n", argv[0]);
printf("SEQUENCE is the RNA sequence.\n");
printf("STRUCTURE is the RNA structure.\n");
printf("SCALING is used internally as the scaling factor for the recursions.\n");
printf("PRECISION dictates the number of signigicant digits in the resulting distribution.\n");
printf("The length of RNA sequence should be less than %d and larger than or equal to 5.\n", MAXSIZE);
exit(1);
}
}
CheckSequenceAndStructure(sequence, structure);
S0 = encode_seq(sequence + 1);
seqlen = strlen(sequence) - 1;
Initialize_Params();
make_pair_matrix(); // Needed for pair matching.
kT = (temperature + K0) * GASCONST / 1000.0;
ML_base = (double)P -> MLbase / 100;
ML_close = (double)P -> MLclosing / 100;
std::complex<double>** McCaskillZ;
McCaskillZ = runMcCaskill(sequence, structure);
} else {
printf("Usage:");
printf("%s -s SEQUENCE -r STRUCTURE -c SCALING -p PRECISION\n", argv[0]);
printf("SEQUENCE is the RNA sequence.\n");
printf("STRUCTURE is the RNA structure.\n");
printf("SCALING is used internally as the scaling factor for the recursions.\n");
printf("PRECISION dictates the number of signigicant digits in the resulting distribution.\n");
printf("The length of RNA sequence should be less than %d and larger than or equal to 5.\n", MAXSIZE);
exit(1);
}
return 0;
}
PRIVATE void update_dfold_params(void){
vrna_md_t md;
if(P)
free(P);
set_model_details(&md);
P = vrna_params(&md);
make_pair_matrix();
}
PUBLIC void
init_maxmat(int length, int minls, int minss)
{
if ( minls > -1 ) minimum_loopsize = minls;
if ( minss > -1 ) minimum_stacksize = minss;
make_pair_matrix();
get_mm_arrays(length);
}
/* unsafe function that will be replaced by a threadsafe companion in the future */
PRIVATE void init_alifold(int length){
unsigned int n;
if (length<1) nrerror("initialize_fold: argument must be greater 0");
if (init_length>0) free_alifold_arrays();
get_arrays((unsigned) length);
make_pair_matrix();
init_length=length;
for (n = 1; n <= (unsigned) length; n++)
indx[n] = (n*(n-1)) >> 1; /* n(n-1)/2 */
update_fold_params();
}
PUBLIC int find_saddle(const char *sequence, const char *struc1, const char *struc2, int max) {
int maxl, maxE, i;
const char *tmp;
move_t *bestpath=NULL;
int dir;
path_fwd = 0;
maxE = INT_MAX - 1;
seq = sequence;
update_fold_params();
make_pair_matrix();
/* nummerically encode sequence */
S = encode_sequence(seq, 0);
S1 = encode_sequence(seq, 1);
maxl=1;
do {
int saddleE;
path_fwd = !path_fwd;
if (maxl>max) maxl=max;
if(path) free(path);
saddleE = find_path_once(struc1, struc2, maxE, maxl);
if (saddleE<maxE) {
maxE = saddleE;
if (bestpath) free(bestpath);
bestpath = path;
path = NULL;
dir = path_fwd;
} else{
free(path);path=NULL;
}
tmp=struc1;
struc1=struc2;
struc2=tmp;
maxl *=2;
} while (maxl<2*max);
free(S); free(S1);
/* (re)set some globals */
path=bestpath;
path_fwd = dir;
return maxE;
}
int find_saddle(char *sequence, char *struc1, char *struc2, int max) {
int maxl, maxE, i;
char *tmp;
move_t *bestpath=NULL;
int dir;
maxE = INT_MAX - 1;
seq = sequence;
update_fold_params();
make_pair_matrix();
/* nummerically encode sequence */
S = (short *) space(sizeof(short)*(strlen(seq)+1));
S1 = (short *) space(sizeof(short)*(strlen(seq)+1));
S[0] = S1[0] = (short) strlen(seq);
for (i=0; i< strlen(seq); i++) {
S[i+1] = encode_char(seq[i]);
S1[i+1] = alias[S[i+1]];
}
maxl=1;
do {
int saddleE;
path_fwd = !path_fwd;
if (maxl>max) maxl=max;
saddleE = find_path_once(struc1, struc2, maxE, maxl);
if (saddleE<maxE) {
maxE = saddleE;
if (bestpath) free(bestpath);
bestpath = path;
dir = path_fwd;
} else
free(path);
tmp=struc1; struc1=struc2; struc2=tmp;
maxl *=2;
} while (maxl<2*max);
free(S); free(S1);
path=bestpath;
path_fwd = dir;
return maxE;
}
PRIVATE void make_pairset(void)
{
int i,j;
int sym[MAXALPHA];
make_pair_matrix();
base = strlen(symbolset);
for (i=0; i< base; i++) sym[i] = encode_char(symbolset[i]);
for (i=npairs=0; i< base; i++)
for (j=0; j<base; j++)
if (pair[sym[i]][sym[j]]) {
pairset[npairs++] = symbolset[i];
pairset[npairs++] = symbolset[j];
}
npairs /= 2;
if (npairs==0) nrerror("No pairs in this alphabet!");
}
PRIVATE char *annote(const char *structure, const char *AS[]) {
char *ps;
int i, n, s, maxl;
short *ptable;
make_pair_matrix();
n = strlen(AS[0]);
maxl = 1024;
ps = (char *) space(maxl);
ptable = make_pair_table(structure);
for (i=1; i<=n; i++) {
char pps[64], ci='\0', cj='\0';
int j, type, pfreq[8] = {0,0,0,0,0,0,0,0}, vi=0, vj=0;
if ((j=ptable[i])<i) continue;
for (s=0; AS[s]!=NULL; s++) {
type = pair[encode_char(AS[s][i-1])][encode_char(AS[s][j-1])];
pfreq[type]++;
if (type) {
if (AS[s][i-1] != ci) { ci = AS[s][i-1]; vi++;}
if (AS[s][j-1] != cj) { cj = AS[s][j-1]; vj++;}
}
}
if (maxl - strlen(ps) < 128) {
maxl *= 2;
ps = realloc(ps, maxl);
if (ps==NULL) nrerror("out of memory in realloc");
}
if (pfreq[0]>0) {
snprintf(pps, 64, "%d %d %d gmark\n", i, j, pfreq[0]);
strcat(ps, pps);
}
if (vi>1) {
snprintf(pps, 64, "%d cmark\n", i);
strcat(ps, pps);
}
if (vj>1) {
snprintf(pps, 64, "%d cmark\n", j);
strcat(ps, pps);
}
}
free(ptable);
return ps;
}
// create encoded structure
encoded *encode_seq(const char* seq)
{
encoded *res;
res = (encoded*) space(sizeof(encoded));
// inicialize encode_sequence
make_pair_matrix();
res->seq = seq;
res->pt = NULL;
res->s0 = encode_sequence(seq, 0);
res->s1 = encode_sequence(seq, 1);
res->bp_left = 0;
res->bp_right = 0;
res->bp_left2 = 0;
res->bp_right2 = 0;
return res;
}
PUBLIC int
browse_neighs(char *seq,
char *struc,
int verbosity_level,
int shifts,
int noLP,
int (*funct) (struct_en*, struct_en*)){
make_pair_matrix();
short int *s0 = encode_sequence(seq, 0);
short int *s1 = encode_sequence(seq, 1);
short int *str = vrna_ptable(struc);
int res = browse_neighs_pt(seq, str, s0, s1, verbosity_level, shifts, noLP, funct);
free(s0);
free(s1);
free(str);
return res;
}
PUBLIC void
update_mm_params(void)
{
make_pair_matrix();
}
/*--------------------------------------------------------------------------*/
int main(int argc, char *argv[]){
struct RNAalifold_args_info args_info;
unsigned int input_type;
char ffname[FILENAME_MAX_LENGTH], gfname[FILENAME_MAX_LENGTH], fname[FILENAME_MAX_LENGTH];
char *input_string, *string, *structure, *cstruc, *ParamFile, *ns_bases, *c;
int n_seq, i, length, sym, r, noPS, with_sci;
int endgaps, mis, circular, doAlnPS, doColor, doMEA, n_back, eval_energy, pf, istty;
double min_en, real_en, sfact, MEAgamma, bppmThreshold, betaScale;
char *AS[MAX_NUM_NAMES]; /* aligned sequences */
char *names[MAX_NUM_NAMES]; /* sequence names */
FILE *clust_file = stdin;
pf_paramT *pf_parameters;
model_detailsT md;
fname[0] = ffname[0] = gfname[0] = '\0';
string = structure = cstruc = ParamFile = ns_bases = NULL;
pf_parameters = NULL;
endgaps = mis = pf = circular = doAlnPS = doColor = n_back = eval_energy = oldAliEn = doMEA = ribo = noPS = 0;
do_backtrack = 1;
dangles = 2;
gquad = 0;
sfact = 1.07;
bppmThreshold = 1e-6;
MEAgamma = 1.0;
betaScale = 1.;
with_sci = 0;
set_model_details(&md);
/*
#############################################
# check the command line prameters
#############################################
*/
if(RNAalifold_cmdline_parser (argc, argv, &args_info) != 0) exit(1);
/* temperature */
if(args_info.temp_given) temperature = args_info.temp_arg;
/* structure constraint */
if(args_info.constraint_given) fold_constrained=1;
/* do not take special tetra loop energies into account */
if(args_info.noTetra_given) md.special_hp = tetra_loop=0;
/* set dangle model */
if(args_info.dangles_given){
if((args_info.dangles_arg != 0) && (args_info.dangles_arg != 2))
warn_user("required dangle model not implemented, falling back to default dangles=2");
else
md.dangles = dangles=args_info.dangles_arg;
}
/* do not allow weak pairs */
if(args_info.noLP_given) md.noLP = noLonelyPairs = 1;
/* do not allow wobble pairs (GU) */
if(args_info.noGU_given) md.noGU = noGU = 1;
/* do not allow weak closing pairs (AU,GU) */
if(args_info.noClosingGU_given) md.noGUclosure = no_closingGU = 1;
/* gquadruplex support */
if(args_info.gquad_given) md.gquad = gquad = 1;
/* sci computation */
if(args_info.sci_given) with_sci = 1;
/* do not convert DNA nucleotide "T" to appropriate RNA "U" */
/* set energy model */
if(args_info.energyModel_given) energy_set = args_info.energyModel_arg;
/* take another energy parameter set */
if(args_info.paramFile_given) ParamFile = strdup(args_info.paramFile_arg);
/* Allow other pairs in addition to the usual AU,GC,and GU pairs */
if(args_info.nsp_given) ns_bases = strdup(args_info.nsp_arg);
/* set pf scaling factor */
if(args_info.pfScale_given) sfact = args_info.pfScale_arg;
/* assume RNA sequence to be circular */
if(args_info.circ_given) circular=1;
/* do not produce postscript output */
if(args_info.noPS_given) noPS = 1;
/* partition function settings */
if(args_info.partfunc_given){
pf = 1;
if(args_info.partfunc_arg != -1)
do_backtrack = args_info.partfunc_arg;
}
/* MEA (maximum expected accuracy) settings */
if(args_info.MEA_given){
pf = doMEA = 1;
if(args_info.MEA_arg != -1)
MEAgamma = args_info.MEA_arg;
}
if(args_info.betaScale_given) betaScale = args_info.betaScale_arg;
/* set the bppm threshold for the dotplot */
if(args_info.bppmThreshold_given)
bppmThreshold = MIN2(1., MAX2(0.,args_info.bppmThreshold_arg));
/* set cfactor */
if(args_info.cfactor_given) cv_fact = args_info.cfactor_arg;
/* set nfactor */
if(args_info.nfactor_given) nc_fact = args_info.nfactor_arg;
if(args_info.endgaps_given) endgaps = 1;
if(args_info.mis_given) mis = 1;
if(args_info.color_given) doColor=1;
if(args_info.aln_given) doAlnPS=1;
if(args_info.old_given) oldAliEn = 1;
if(args_info.stochBT_given){
n_back = args_info.stochBT_arg;
do_backtrack = 0;
pf = 1;
init_rand();
}
if(args_info.stochBT_en_given){
n_back = args_info.stochBT_en_arg;
do_backtrack = 0;
pf = 1;
eval_energy = 1;
init_rand();
}
if(args_info.ribosum_file_given){
RibosumFile = strdup(args_info.ribosum_file_arg);
ribo = 1;
}
if(args_info.ribosum_scoring_given){
RibosumFile = NULL;
ribo = 1;
}
if(args_info.layout_type_given)
rna_plot_type = args_info.layout_type_arg;
/* alignment file name given as unnamed option? */
if(args_info.inputs_num == 1){
clust_file = fopen(args_info.inputs[0], "r");
if (clust_file == NULL) {
fprintf(stderr, "can't open %s\n", args_info.inputs[0]);
}
}
/* free allocated memory of command line data structure */
RNAalifold_cmdline_parser_free (&args_info);
/*
#############################################
# begin initializing
#############################################
*/
if(circular && gquad){
nrerror("G-Quadruplex support is currently not available for circular RNA structures");
}
make_pair_matrix();
if (circular && noLonelyPairs)
warn_user("depending on the origin of the circular sequence, "
"some structures may be missed when using --noLP\n"
"Try rotating your sequence a few times\n");
if (ParamFile != NULL) read_parameter_file(ParamFile);
if (ns_bases != NULL) {
nonstandards = space(33);
c=ns_bases;
i=sym=0;
if (*c=='-') {
sym=1; c++;
}
while (*c!='\0') {
if (*c!=',') {
nonstandards[i++]=*c++;
nonstandards[i++]=*c;
if ((sym)&&(*c!=*(c-1))) {
nonstandards[i++]=*c;
nonstandards[i++]=*(c-1);
}
}
c++;
}
}
istty = isatty(fileno(stdout))&&isatty(fileno(stdin));
/*
########################################################
# handle user input from 'stdin' if necessary
########################################################
*/
if(fold_constrained){
if(istty){
print_tty_constraint_full();
print_tty_input_seq_str("");
}
input_type = get_input_line(&input_string, VRNA_INPUT_NOSKIP_COMMENTS);
if(input_type & VRNA_INPUT_QUIT){ return 0;}
else if((input_type & VRNA_INPUT_MISC) && (strlen(input_string) > 0)){
cstruc = strdup(input_string);
free(input_string);
}
else warn_user("constraints missing");
}
if (istty && (clust_file == stdin))
print_tty_input_seq_str("Input aligned sequences in clustalw or stockholm format\n(enter a line starting with \"//\" to indicate the end of your input)");
n_seq = read_clustal(clust_file, AS, names);
if (n_seq==0) nrerror("no sequences found");
if (clust_file != stdin) fclose(clust_file);
/*
########################################################
# done with 'stdin' handling, now init everything properly
########################################################
*/
length = (int) strlen(AS[0]);
structure = (char *)space((unsigned) length+1);
if(fold_constrained && cstruc != NULL)
strncpy(structure, cstruc, length);
if (endgaps)
for (i=0; i<n_seq; i++) mark_endgaps(AS[i], '~');
/*
########################################################
# begin actual calculations
########################################################
*/
if (circular) {
int i;
double s = 0;
min_en = circalifold((const char **)AS, structure);
for (i=0; AS[i]!=NULL; i++)
s += energy_of_circ_structure(AS[i], structure, -1);
real_en = s/i;
} else {
float *ens = (float *)space(2*sizeof(float));
min_en = alifold((const char **)AS, structure);
if(md.gquad)
energy_of_ali_gquad_structure((const char **)AS, structure, n_seq, ens);
else
energy_of_alistruct((const char **)AS, structure, n_seq, ens);
real_en = ens[0];
free(ens);
}
string = (mis) ? consens_mis((const char **) AS) : consensus((const char **) AS);
printf("%s\n%s", string, structure);
if(istty){
if(with_sci){
float sci = min_en;
float e_mean = 0;
for (i=0; AS[i]!=NULL; i++){
char *seq = get_ungapped_sequence(AS[i]);
char *str = (char *)space(sizeof(char) * (strlen(seq) + 1));
e_mean += fold(seq, str);
free(seq);
free(str);
}
e_mean /= i;
sci /= e_mean;
printf( "\n minimum free energy = %6.2f kcal/mol (%6.2f + %6.2f)"
"\n SCI = %2.4f\n",
min_en, real_en, min_en-real_en, sci);
} else
printf("\n minimum free energy = %6.2f kcal/mol (%6.2f + %6.2f)\n",
min_en, real_en, min_en - real_en);
} else {
if(with_sci){
float sci = min_en;
float e_mean = 0;
for (i=0; AS[i]!=NULL; i++){
char *seq = get_ungapped_sequence(AS[i]);
char *str = (char *)space(sizeof(char) * (strlen(seq) + 1));
e_mean += fold(seq, str);
free(seq);
free(str);
}
e_mean /= i;
sci /= e_mean;
printf(" (%6.2f = %6.2f + %6.2f) [%2.4f]\n", min_en, real_en, min_en-real_en, sci);
}
else
printf(" (%6.2f = %6.2f + %6.2f) \n", min_en, real_en, min_en-real_en );
}
strcpy(ffname, "alirna.ps");
strcpy(gfname, "alirna.g");
if (!noPS) {
char **A;
A = annote(structure, (const char**) AS);
if(md.gquad){
if (doColor)
(void) PS_rna_plot_a_gquad(string, structure, ffname, A[0], A[1]);
else
(void) PS_rna_plot_a_gquad(string, structure, ffname, NULL, A[1]);
} else {
if (doColor)
(void) PS_rna_plot_a(string, structure, ffname, A[0], A[1]);
else
(void) PS_rna_plot_a(string, structure, ffname, NULL, A[1]);
}
free(A[0]); free(A[1]); free(A);
}
if (doAlnPS)
PS_color_aln(structure, "aln.ps", (const char const **) AS, (const char const **) names);
/* free mfe arrays */
free_alifold_arrays();
if (pf) {
float energy, kT;
char * mfe_struc;
mfe_struc = strdup(structure);
kT = (betaScale*((temperature+K0)*GASCONST))/1000.; /* in Kcal */
pf_scale = exp(-(sfact*min_en)/kT/length);
if (length>2000) fprintf(stderr, "scaling factor %f\n", pf_scale);
fflush(stdout);
if (cstruc!=NULL) strncpy(structure, cstruc, length+1);
pf_parameters = get_boltzmann_factors_ali(n_seq, temperature, betaScale, md, pf_scale);
energy = alipf_fold_par((const char **)AS, structure, NULL, pf_parameters, do_backtrack, fold_constrained, circular);
if (n_back>0) {
/*stochastic sampling*/
for (i=0; i<n_back; i++) {
char *s;
double prob=1.;
s = alipbacktrack(&prob);
printf("%s ", s);
if (eval_energy ) printf("%6g %.2f ",prob, -1*(kT*log(prob)-energy));
printf("\n");
free(s);
}
}
if (do_backtrack) {
printf("%s", structure);
if (!istty) printf(" [%6.2f]\n", energy);
else printf("\n");
}
if ((istty)||(!do_backtrack))
printf(" free energy of ensemble = %6.2f kcal/mol\n", energy);
printf(" frequency of mfe structure in ensemble %g\n",
exp((energy-min_en)/kT));
if (do_backtrack) {
FILE *aliout;
cpair *cp;
char *cent;
double dist;
FLT_OR_DBL *probs = export_ali_bppm();
plist *pl, *mfel;
assign_plist_from_pr(&pl, probs, length, bppmThreshold);
assign_plist_from_db(&mfel, mfe_struc, 0.95*0.95);
if (!circular){
float *ens;
cent = get_centroid_struct_pr(length, &dist, probs);
ens=(float *)space(2*sizeof(float));
energy_of_alistruct((const char **)AS, cent, n_seq, ens);
/*cent_en = energy_of_struct(string, cent);*/ /*ali*/
printf("%s %6.2f {%6.2f + %6.2f}\n",cent,ens[0]-ens[1],ens[0],(-1)*ens[1]);
free(cent);
free(ens);
}
if(doMEA){
float mea, *ens;
plist *pl2;
assign_plist_from_pr(&pl2, probs, length, 1e-4/(1+MEAgamma));
mea = MEA(pl2, structure, MEAgamma);
ens = (float *)space(2*sizeof(float));
if(circular)
energy_of_alistruct((const char **)AS, structure, n_seq, ens);
else
ens[0] = energy_of_structure(string, structure, 0);
printf("%s {%6.2f MEA=%.2f}\n", structure, ens[0], mea);
free(ens);
free(pl2);
}
if (fname[0]!='\0') {
strcpy(ffname, fname);
strcat(ffname, "_ali.out");
} else strcpy(ffname, "alifold.out");
aliout = fopen(ffname, "w");
if (!aliout) {
fprintf(stderr, "can't open %s skipping output\n", ffname);
} else {
print_aliout(AS, pl, bppmThreshold, n_seq, mfe_struc, aliout);
}
fclose(aliout);
if (fname[0]!='\0') {
strcpy(ffname, fname);
strcat(ffname, "_dp.ps");
} else strcpy(ffname, "alidot.ps");
cp = make_color_pinfo(AS,pl, bppmThreshold, n_seq, mfel);
(void) PS_color_dot_plot(string, cp, ffname);
free(cp);
free(pl);
free(mfel);
}
free(mfe_struc);
free_alipf_arrays();
free(pf_parameters);
}
if (cstruc!=NULL) free(cstruc);
(void) fflush(stdout);
free(string);
free(structure);
for (i=0; AS[i]; i++) {
free(AS[i]); free(names[i]);
}
return 0;
}
PUBLIC void update_alifold_params(void){
if(P) free(P);
P = scale_parameters();
make_pair_matrix();
if (init_length < 0) init_length=0;
}
static void ini_ringlist(void) {
int i;
/* needed by function energy_of_struct_pt() from Vienna-RNA-1.4 */
pairList = (short *)calloc(GSV.len + 2, sizeof(short));
assert(pairList != NULL);
typeList = (short *)calloc(GSV.len + 2, sizeof(short));
assert(typeList != NULL);
aliasList = (short *)calloc(GSV.len + 2, sizeof(short));
assert(aliasList != NULL);
pairList[0] = typeList[0] = aliasList[0] = GSV.len;
ptype = (char **)calloc(GSV.len + 2, sizeof(char *));
assert(ptype != NULL);
for (i=0; i<=GSV.len; i++) {
ptype[i] = (char*)calloc(GSV.len + 2, sizeof(char));
assert(ptype[i] != NULL);
}
/* allocate virtual root */
wurzl = (baum *)calloc(1, sizeof(baum));
assert(wurzl != NULL);
/* allocate ringList */
rl = (baum *)calloc(GSV.len+1, sizeof(baum));
assert(rl != NULL);
/* allocate PostOrderList */
/* initialize virtualroot */
wurzl->typ = 'r';
wurzl->nummer = -1;
/* connect virtualroot to ringlist-tree in down direction */
wurzl->down = &rl[GSV.len];
/* initialize post-order list */
make_pair_matrix();
/* initialize rest of ringlist-tree */
for(i = 0; i < GSV.len; i++) {
int c;
GAV.currform[i] = '.';
GAV.prevform[i] = 'x';
pairList[i+1] = 0;
rl[i].typ = 'u';
/* decode base to numeric value */
c = encode_char(GAV.farbe[i]);
rl[i].base = typeList[i+1] = c;
aliasList[i+1] = alias[typeList[i+1]];
/* astablish links for node of the ringlist-tree */
rl[i].nummer = i;
rl[i].next = &rl[i+1];
rl[i].prev = ((i == 0) ? &rl[GSV.len] : &rl[i-1]);
rl[i].up = rl[i].down = NULL;
}
GAV.currform[GSV.len] = GAV.prevform[GSV.len] = '\0';
make_ptypes(aliasList);
rl[i].nummer = i;
rl[i].base = 0;
/* make ringlist circular in next, prev direction */
rl[i].next = &rl[0];
rl[i].prev = &rl[i-1];
/* make virtual basepair for virtualroot */
rl[i].up = wurzl;
rl[i].typ = 'x';
}
duplexT duplexfold(const char *s1, const char *s2) {
int i, j, l1, Emin=INF, i_min=0, j_min=0;
char *struc;
duplexT mfe;
n1 = (int) strlen(s1);
n2 = (int) strlen(s2);
if ((!P) || (fabs(P->temperature - temperature)>1e-6)) {
update_fold_params(); P = scale_parameters();
make_pair_matrix();
}
c = (int **) space(sizeof(int *) * (n1+1));
for (i=1; i<=n1; i++) c[i] = (int *) space(sizeof(int) * (n2+1));
encode_seq(s1, s2);
for (i=1; i<=n1; i++) {
for (j=n2; j>0; j--) {
int type, type2, E, k,l;
type = pair[S1[i]][S2[j]];
c[i][j] = type ? P->DuplexInit : INF;
if (!type) continue;
if (i>1) c[i][j] += P->dangle5[type][SS1[i-1]];
if (j<n2) c[i][j] += P->dangle3[type][SS2[j+1]];
if (type>2) c[i][j] += P->TerminalAU;
for (k=i-1; k>0 && k>i-MAXLOOP-2; k--) {
for (l=j+1; l<=n2; l++) {
if (i-k+l-j-2>MAXLOOP) break;
type2 = pair[S1[k]][S2[l]];
if (!type2) continue;
E = LoopEnergy(i-k-1, l-j-1, type2, rtype[type],
SS1[k+1], SS2[l-1], SS1[i-1], SS2[j+1]);
c[i][j] = MIN2(c[i][j], c[k][l]+E);
}
}
E = c[i][j];
if (i<n1) E += P->dangle3[rtype[type]][SS1[i+1]];
if (j>1) E += P->dangle5[rtype[type]][SS2[j-1]];
if (type>2) E += P->TerminalAU;
if (E<Emin) {
Emin=E; i_min=i; j_min=j;
}
}
}
struc = backtrack(i_min, j_min);
if (i_min<n1) i_min++;
if (j_min>1 ) j_min--;
l1 = strchr(struc, '&')-struc;
/*
printf("%s %3d,%-3d : %3d,%-3d (%5.2f)\n", struc, i_min+1-l1, i_min,
j_min, j_min+strlen(struc)-l1-2, Emin*0.01);
*/
mfe.i = i_min;
mfe.j = j_min;
mfe.energy = (float) Emin/100.;
mfe.structure = struc;
if (!delay_free) {
for (i=1; i<=n1; i++) free(c[i]);
free(c);
free(S1); free(S2); free(SS1); free(SS2);
}
return mfe;
}