void Table::AlignFields()
{
RemoveSpaces();
int l_Columns = GetColumns();
Content l_Content = GetContent();
Content l_ResultContent = l_Content;
for (int l_Itr = 0; l_Itr < l_Columns; ++l_Itr)
{
int l_FieldSize = 0;
for (Row l_Row : l_ResultContent)
l_FieldSize = l_Row[l_Itr].size() > l_FieldSize ? l_Row[l_Itr].size() : l_FieldSize;
l_FieldSize += 3;
for (Row& l_Row : l_ResultContent)
{
int l_WhitespaceNumber = l_FieldSize - l_Row[l_Itr].size();
for (int l_ThirdItr = 0; l_ThirdItr < l_WhitespaceNumber; ++l_ThirdItr)
{
if (!l_Itr && GetStructure(true) && !(l_ThirdItr < 2))
l_Row[l_Itr] = " " + l_Row[l_Itr];
else
l_Row[l_Itr] += " ";
}
}
}
SetContent(l_ResultContent);
}
//Destructor
Oligowalk_object::~Oligowalk_object() {
int i;
if (table!=NULL) {
//Table and numofsubstructures were allocated, so delete them
for (i = 0; i < GetStructure()->GetSequenceLength() - length + 2; ++i) {
delete[] table[i];
delete[] numofsubstructures[i];
}
delete[] table;
delete[] numofsubstructures;
delete prefilter;
}
}
//Get the oligo-self DG for a given nucleotide.
double Oligowalk_object::GetOligoSelfDG(const int index) {
//Perform error checking:
if (table==NULL) {
//This means that OligoWalk() was not called successfully.
ErrorCode = 100;
return 0.0;
}
else if (index<1||index>GetStructure()->GetSequenceLength() - length + 1) {
//This means an invalid index is being used
ErrorCode = 3;
return 0.0;
}
//note that the free eneergy changes are stored internally as integers, where they are multiplied by conversionfactor
return (((double) table[index][3])/conversionfactor);
}
//Write a report to disk using the OligoWalk data.
int Oligowalk_object::WriteReport(const char outputfilename[], const int oligo_length, const bool isDNA, const int option, const double oligo_concentration, const int usesub, const int start, const int stop) {
//Perform error checking:
if (table==NULL) {
//This means that OligoWalk() was not called successfully.
return 100;
}
//The last three 0's indicate this is not siRNA design
report(outputfilename, GetStructure(), table, numofsubstructures,
oligo_length, isDNA, oligo_concentration, usesub,start,stop,prefilter,0,
NULL,0,0,0,false);
//No errors:
return 0;
}
// Get the Tm for a given nucleotide.
double Oligowalk_object::GetTm(const int index) {
//Perform error checking:
if (table==NULL) {
//This means that OligoWalk() was not called successfully.
ErrorCode = 100;
return 0.0;
}
else if (index<1||index>GetStructure()->GetSequenceLength() - length + 1) {
//This means an invalid index is being used
ErrorCode = 3;
return 0.0;
}
//note that the Tm is stored as an integer, multiplied by 10.
return (((double) table[index][5])/10);
}
void Table::Shift()
{
Content l_NewContent;
for (int l_Itr = 0; l_Itr < m_Columns; ++l_Itr)
{
l_NewContent.push_back(null);
for (Row l_Row : m_Content)
{
l_NewContent[l_Itr].push_back(l_Row[l_Itr]);
}
}
m_Content = l_NewContent;
if (GetStructure(true))
{
TableStruct l_NewStruct;
l_NewStruct.first = m_Struct.second;
l_NewStruct.second = m_Struct.first;
m_Struct = l_NewStruct;
}
RemoveSpaces();
UpdateRowsAndColumns();
}
void Table::SetStructure(TableStruct p_Struct)
{
if (p_Struct.first.size() == m_Columns)
{
if (m_Struct.first.size())
m_Content.pop_front();
m_Struct.first = p_Struct.first;
m_Content.push_front(m_Struct.first);
}
if (m_Struct.first.size() ? p_Struct.second.size() + 1 == m_Content.size() : p_Struct.second.size() == m_Content.size())
{
bool l_NeedRemove = false;
if (m_Struct.second.size())
l_NeedRemove = true;
m_Struct.second = p_Struct.second;
int l_Itr = 0;
for (Row& l_row : m_Content)
{
if (l_NeedRemove)
l_row.pop_front();
if (!l_Itr)
l_row.push_front("");
else
l_row.push_front(p_Struct.second[l_Itr - 1]);
l_Itr++;
}
}
if (GetStructure(true))
{
RemoveSpaces();
AlignFields();
}
UpdateRowsAndColumns();
}
//Perform an OligoWalk calculation
//usesub = 0 -> no suboptimal; 3 -> heuristic
int Oligowalk_object::Oligowalk(const int oligo_length, const bool isDNA, const int option, const double oligo_concentration, const int usesub, const int start, const int stop ) {
datatable *enthalpy;
thermo *helixstack;
int test=-1;
char stackf[maxfil],datapath[maxfil];
int error;
datatable *dnadata;
//use a character array to turn off SHAPE:
char shapefile='\0';
int i,j,k,l;
Thermodynamics *ddata;
rddata *hybriddata,*enthalpyhybrid;
char *pointer;
//Make sure this is the first (and only allowed call of OligoWalk)
if (table!=NULL) return 101;
length = oligo_length;//save oligo_length for use in the destructor and for error checking later
if (!energyread) {
//The thermodynamic data tables have not been read and need to be read now.
if (ReadThermodynamic()!=0) return 5;//return non-zero if a problem occurs
}
//Read the enthalpy data from disk using the underlying thermodynamics class GetEnthalpyData function:
enthalpy = GetEnthalpyTable();
//make sure that the thermodynamics parameters could be read from disk
if (enthalpy==NULL) {
return 5;//5 is the error code that indicates the thermodynamic parameters were not found
}
//Although prefiltering isn't used in this version of OligoWalk, it needs to be initialized and passed to function.
//Note that the true indicates that empirical scores would be used a
prefilter = new siPREFILTER(*GetDatatable(),*enthalpy,0,true,GetStructure()->GetSequenceLength() - oligo_length + 2,isDNA);
//Allocate the tables needed for storing the results
table = new int*[GetStructure()->GetSequenceLength() - oligo_length + 2];
for (i = 0; i < GetStructure()->GetSequenceLength() - oligo_length + 2; i++) {
//DHM commented out these lines for now. They need to be restored later.
//if (siRNA) table[i] = new int[7];
//else table[i] = new int[6];
table[i] = new int[6];
}
//allocate memory of number of suboptimal structures
numofsubstructures= new int*[GetStructure()->GetSequenceLength() - oligo_length +2];
for (i = 0; i < GetStructure()->GetSequenceLength() - oligo_length + 2; i++) {
numofsubstructures[i]= new int [2];
numofsubstructures[i][0]=0;
numofsubstructures[i][1]=0;
}
//Get the path information for location of data files from $DATAPATH, if available
pointer = getenv("DATAPATH");
if (pointer!=NULL) {
strcpy(datapath,pointer);
strcat(datapath,"/");
}
else strcpy(datapath,"");
//Allocate helixstack:
helixstack = new thermo(pointer);
//Now read the DNA parameters if the oligos are DNA:
if (isDNA) {
ddata = new Thermodynamics(false);//allocate space for DNA parameters
//set the temperature for the DNA parameters
error = ddata->SetTemperature(GetTemperature());
//Check fo an error
if (error!=0) {
delete ddata;
delete prefilter;
delete helixstack;
return error;
}
//Read the dna thermodynamic parameters
error = ddata->ReadThermodynamic();
//Check fo an error
if (error!=0) {
delete ddata;
delete prefilter;
delete helixstack;
return error;
}
//Read the hybrid data as well
hybriddata = new rddata;
strcpy(stackf,datapath);
strcat (stackf,"stackdr.dat");
//Check for errors
if (readrd (hybriddata,stackf)==0) {
delete ddata;
delete prefilter;
delete helixstack;
return 5;
}
if (GetTemperature()<310||GetTemperature()>311) {
//The temperature is simgificantly different from 37 dgrees C, so read and use the enthalpy data.
strcpy(stackf,datapath);
//strcat(stackf,"/");
strcat (stackf,"stackdr.dh");
enthalpyhybrid = new rddata;
//Check for errors
if (readrd (enthalpyhybrid,stackf)==0) {
delete ddata;
delete prefilter;
delete enthalpyhybrid;
delete helixstack;
return 5;
}
for (i=0;i<5;i++) {
for (j=0;j<5;j++) {
for (k=0;k<5;k++) {
for (l=0;l<5;l++) {
hybriddata->stack[i][j][k][l]=Tscale(GetTemperature(),hybriddata->stack[i][j][k][l],enthalpyhybrid->stack[i][j][k][l]);
}
}
}
}
hybriddata->init=Tscale(GetTemperature(),hybriddata->init,enthalpyhybrid->init);
delete enthalpyhybrid;
}
strcpy(helixstack->DH,datapath);
//strcat(helixstack->DH,"\\");
strcat(helixstack->DH,"stackdr.dh");
strcpy(helixstack->DS,datapath);
//strcat(helixstack->DS,"\\");
strcat(helixstack->DS,"stackdr.ds");
strcpy(helixstack->HELIX,datapath);
//strcat(helixstack->HELIX,"\\");
strcat(helixstack->HELIX,"helixdr.dat");
dnadata = ddata->GetDatatable();
}
else {
dnadata = NULL;
}
if (helixstack->read()==0) {
//This means an error occurred reading the helixstack parameters
if (isDNA) delete ddata;
delete prefilter;
delete helixstack;
return 5;
}
//For now, siRNA is off.
//if (siRNA) {
// //mask will store whether an oligo meets siRNA design criteria
// mask = new bool [ct.numofbases - length + 2];
//}
//else mask = NULL;
//note that foldsize is temporarilly set to zero so that there is no folding size limit
//note that distance is set to zero so that there is no maximum pairping distance
//note that test is set to -1 so there is no testing
//note that write is set to FALSE to turn off writing
olig(isDNA, option, GetStructure(), oligo_length,
oligo_concentration, table, numofsubstructures, *GetDatatable(), *dnadata,
hybriddata,usesub,GetProgress(),helixstack,
start,stop,prefilter, 0, 0, &shapefile,&test,false);
//siRNA is off right now
//if (oligoobject->siRNA) {
// filterbysirna(&oligoobject->ct,oligoobject->table,oligoobject->length,&oligoobject->data,oligoobject->mask,oligoobject->asuf,oligoobject->tofe,oligoobject->fnnfe);
//}
//note that foldsize is temporarilly set to zero here.
//report(oligoobject->outputfile, &oligoobject->ct, oligoobject->table, oligoobject->numofsubstructures,
// oligoobject->length, oligoobject->isdna, oligoobject->c, oligoobject->usesub,oligoobject->start,oligoobject->stop,prefilter,0,
// oligoobject->mask,oligoobject->asuf,oligoobject->tofe,oligoobject->fnnfe);
//Clean up if this is DNA
if (isDNA) {
delete ddata;
}
delete helixstack;
return 0;
}
