CDrawDoc::CDrawDoc(const char *ctfilename, bool *Clockwise, CMainFrame *pMainFrame, CRNAstructureApp *App)
{
CString name;
clockwise = Clockwise;
pmainframe = pMainFrame;
name = ctfilename;
openct(&ct,ctfilename);
SetTitle(name);
//allocate space for the coordinates
out = new coordinates(ct.numofbases);
iscolorannotated = false;
isSHAPEannotated = false;
app = App;
}
//Run a dynalign calculation.
//Return 0 if there is no error, return 107 if the dat files aren't found,
int Dynalign_object::Dynalign(const short int maxtrace,
const short int bpwin, const short int awin, const short int percent, const short int imaxseparation, const float gap, const bool singleinsert, const char savefile[], const bool optimalonly, const short int singlefold_subopt_percent, const bool local,
const short int numProcessors,
const int maxpairs,
const short int cycles) {
bool constraints= false;
bool **allowed_alignments;//An array for storing those nucleotide pairs that can align or not.
int errormessage;
int i;
structure *ct;//have a structure pointer in case the user does template from ct
//Read the thermodynamic parameters, if necessary, and store in RNA1:
errormessage = GetRNA1()->ReadThermodynamic();
if (errormessage!=0) return 110;
//decide if there are folding or alignment constraints:
if (forcealign!=NULL) constraints=true;
else if (GetRNA1()->GetStructure()->npair>0) constraints=true;
else if (GetRNA2()->GetStructure()->npair>0) constraints=true;
else if (GetRNA1()->GetStructure()->nforbid>0) constraints=true;
else if (GetRNA2()->GetStructure()->nforbid>0) constraints=true;
else if (GetRNA1()->GetStructure()->nnopair>0) constraints=true;
else if (GetRNA2()->GetStructure()->nnopair>0) constraints=true;
else if (GetRNA1()->GetStructure()->nmod>0) constraints=true;
else if (GetRNA2()->GetStructure()->nmod>0) constraints=true;
else if (GetRNA1()->GetStructure()->ngu>0) constraints=true;
else if (GetRNA2()->GetStructure()->ngu>0) constraints=true;
//convert the gap parameter to 10*kcal/mol
short igapincrease = (int)(gap * 10.0);
//do the dynalign calculation
//This section folds thie individual sequences to find insignificant pairs to be ingnored by Dynalign.
GetRNA1()->GetStructure()->allocatetem();
GetRNA2()->GetStructure()->allocatetem();
//The default behavior is to fold the sequences to determine pair hat should be not allowed in dynalign
if(dsv_templated) {
if(templatefromdsv(GetRNA1()->GetStructure(), templatefilename, MAXDSV, maxpairs))
return 109;
}
else if (ct_templated) {
ct = new structure();
openct(ct,templatefilename);
templatefromct(ct);
delete ct;
}
else templatefromfold(GetRNA1()->GetStructure(), GetRNA1()->GetDatatable(), singlefold_subopt_percent);
templatefromfold( GetRNA2()->GetStructure(), GetRNA1()->GetDatatable(), singlefold_subopt_percent );
//This next section determined the allowed nucleotide alignments if the HMM forward-backward is used:
if (imaxseparation < 0) {
//allocate space in allowed_alignments
allowed_alignments = new bool *[GetRNA1()->GetStructure()->numofbases+1];
for (i=0;i<=GetRNA1()->GetStructure()->numofbases;i++) {
allowed_alignments[i] = new bool [GetRNA2()->GetStructure()->numofbases+1];
}
// Needed for having nucleotide sequences as c strings.
GetRNA1()->GetStructure()->nucs[GetRNA1()->GetStructure()->numofbases + 1] = 0;
GetRNA2()->GetStructure()->nucs[GetRNA2()->GetStructure()->numofbases + 1] = 0;
calculate_coinc_probs_env(GetRNA1()->GetStructure(), GetRNA2()->GetStructure(), NULL, allowed_alignments, NULL, forcealign);
}
else allowed_alignments = NULL;
//allocate space for the alignment
align = new short *[maxtrace];//maximum number of tracebacks and next line and below at delete
for (i=0;i<maxtrace;i++) align[i] = new short [GetRNA1()->GetStructure()->numofbases+1];
//also store the maxtrace for deleting later
Maxtrace = maxtrace;
//The heart of the calculation is here:
errormessage = dynalign(GetRNA1()->GetStructure(), GetRNA2()->GetStructure(), align, imaxseparation, igapincrease, GetRNA1()->GetDatatable(),
singleinsert, maxtrace, bpwin, awin, percent, forcealign, allowed_alignments, GetRNA1()->GetProgress(),
savefile, optimalonly, local,
/*force =*/ constraints, numProcessors);
if (imaxseparation < 0) {
//delete space in allowed_alignments
for (i=0;i<=GetRNA1()->GetStructure()->numofbases;i++) {
delete[] allowed_alignments[i];
}
delete[] allowed_alignments;
}
return errormessage;
}
