void TKeyboard::Start(String banner, uint8_t set= KBMAJ)
{
dbgprintln("TKeyboard Start");
state = false;
Caption = "";
Banner = banner;
switch(set){
case KBMAJ: Set1();break;
case KBNUM: Set2();break;
case KBMIN: Set3();break;
case KBPHONE: Set4();break;
default:break;
}
}
void TKeyboard::SetMn()
{
if (Key[0][0]->Caption == "Q")
Set3();
else Set1();
}
static constexpr uint64_t Set1(const uint32_t aBits) {
return aBits == 0 ? 0 : 1 | (Set1(aBits - 1) << 1);
}
//------------------------------------------------------------
//Function merges two data sets fast. Storages it in "const char *set_mereged". This function is performed form R code.
void fast_merge_C_(char *set1, int *num_ids1_, int *num_snps1_,
char *set2, int *num_ids2_, int *num_snps2_,
unsigned *num_ids_intersected, unsigned *num_snps_intersected, unsigned *snp_intersected, unsigned *ids_intersected,
bool *replace_na_,
char *strand_set1, char *strand_set2,
char *coding_set1, char *coding_set2,
char *alleleID, char **alleleID_names, unsigned *alleleID_amount,
char *alleleID_reverse_array,
unsigned *error_amount_,
unsigned *found_error_amount_snp,
unsigned *found_error_amount_id,
unsigned *id_position_error, unsigned *id_snpposition_error, char *val_set1_error, char *val_set2_error,
unsigned *snp_position_error, char* snp_set1_codding_error, char* snp_set2_codding_error,
bool *user_want_to_look_at_strand_,
char *set_mereged)
{
bool user_want_to_look_at_strand = *user_want_to_look_at_strand_;
bool replace_na = *replace_na_;
std::map<std::string, std::string> complemetntary;
complemetntary["AT"];
complemetntary["at"];
complemetntary["TA"];
complemetntary["ta"];
complemetntary["CG"];
complemetntary["cg"];
complemetntary["GC"];
complemetntary["gc"];
//---------------------------------
std::map<char, char*> coding_polymorphism_map;
unsigned alleleID_amount_ = *alleleID_amount;
unsigned error_amount = *error_amount_;
int error_amount_tmp = *error_amount_;
unsigned snp_error_counter=0; //this is counter for function recoding_snp_data_under_coding_and_strand
for(unsigned i=0 ; i<alleleID_amount_ ; i++)
{
coding_polymorphism_map[alleleID[i]] = alleleID_names[i];
}
//---------------------------------
//---------------------------------
std::map<char, char> alleleID_reverse;
for(unsigned i=0 ; i<*alleleID_amount ; i++)
{
alleleID_reverse[alleleID[i]] = alleleID_reverse_array[i];
}
//---------------------------------
Search search(snp_intersected, ids_intersected, *num_snps_intersected, *num_ids_intersected);
unsigned shift_i=0;
unsigned num_ids1 = *num_ids1_,
num_snps1 = *num_snps1_,
num_ids2 = *num_ids2_,
num_snps2 = *num_snps2_;
const unsigned snps_sum = num_snps1 + num_snps2;
unsigned num_ids_total_in_new_set = num_ids1 + num_ids2 - *num_ids_intersected; // total amount of IDs
unsigned num_snps_total_in_new_set = snps_sum - *num_snps_intersected; // total amount of SNPs
gtps_container Set1(set1, strand_set1, coding_set1, num_ids1, num_snps1); //creat object to facilitate working with set1
gtps_container Set2(set2, strand_set2, coding_set2, num_ids2, num_snps2); //creat object to facilitate working with set2
gtps_container Set_merged(set_mereged, num_ids_total_in_new_set, num_snps_total_in_new_set); //Here we will storage our merged set
char set1_val, set2_val;
unsigned errors_counter_id=0;
//Start to merge. The mearged set will in the end
for(unsigned i=1 ; i<=snps_sum ; i++)
{
if(i <= num_snps1)
{
for(unsigned k=1 ; k<=num_ids1 ; k++)
{
Set_merged.set(k, i, Set1.get(k, i));
}//all data from current snp of set1 is copied to new set. Congratulations!!!
if(unsigned snp_in_set2=search.what_snp_is_in_set2(i)) //snp_in_set2 is number of snp in set2 which is intersected with snp with number i
{
//Variable snp_in_set2 storages snp number which corresponds with snp in set1. In other words snp with number snp_in_set2 in snp2 and current snp in set1 is similar. Not clear?
//Now we need to copy data from set2. Without intersectioning IDs!
unsigned int shift_k=0;
for(unsigned k=1 ; k<=num_ids2 ; k++)
{
set2_val = Set2.get(k, snp_in_set2);
set2_val = recoding_snp_data_under_coding_and_strand(set2_val, &Set2, &Set1, snp_in_set2, i, &coding_polymorphism_map, &alleleID_reverse , snp_position_error, snp_set1_codding_error, snp_set2_codding_error, &error_amount_tmp, found_error_amount_snp, &snp_error_counter, user_want_to_look_at_strand, &complemetntary);
if(unsigned id_num_in_set1 = search.what_id_is_in_set1(k)) //This means that current id and current snp belong for both set
{
set1_val = Set1.get(id_num_in_set1, i);
// set2_val = Set2.get(k, snp_in_set2);
// set2_val = recoding_snp_data_under_coding_and_strand(set2_val, &Set2, &Set1, snp_in_set2, i, &coding_polymorphism_map, &alleleID_reverse , snp_position_error, snp_set1_codding_error, snp_set2_codding_error, &error_amount_tmp, found_error_amount_snp, &snp_error_counter, user_want_to_look_at_strand, &complemetntary);
if(error_amount_tmp == -1)
{
//Function "recoding_snp_data_under_coding_and_strand" changed it to -1 because amount of errors a lot and we have to finish merging.
return;
}
if(set1_val != set2_val)
{
// condition added by Yurii: avoid too many errors when
// merging sets with largely different # of genotyped SNPs
if (!(replace_na && (set1_val==0 || set2_val==0))) {
id_position_error[errors_counter_id]=id_num_in_set1;
id_snpposition_error[errors_counter_id]=i;
val_set1_error[errors_counter_id]=set1_val;
val_set2_error[errors_counter_id]=set2_val;
errors_counter_id++;
}
if(errors_counter_id >= error_amount)
{
*found_error_amount_id = errors_counter_id;
Rprintf("ID:Error: Too many errors while merging sets (see error table). Change error_amount value to increase error-table size.\n");
return;
}
//Replace NA if it is not forbiden by user
if(replace_na)
{
if( int(set1_val) == 0 && int(set2_val) != 0 )
{
//Set_merged.set(id_num_in_set1, i, Set2.get(k,snp_in_set2));
Set_merged.set(id_num_in_set1, i, set2_val);
}
}
}
shift_k++;
continue;
}
//Set_merged.set(k - shift_k + num_ids1, i, Set2.get(k,snp_in_set2));
Set_merged.set(k - shift_k + num_ids1, i, set2_val);
}
}
}
else
{
unsigned shift_k=0;
if(search.is_it_snp_in_set1(i-num_snps1))
{
shift_i++;
continue;
} // This snp has storaged already for both sets.
for(unsigned k=1 ; k<=num_ids2 ; k++)
{
if(unsigned num_id_in_set1 = search.what_id_is_in_set1(k))
{
Set_merged.set(num_id_in_set1, i-shift_i, Set2.get(k, i-num_snps1));
shift_k++;
}
else
{
Set_merged.set(k-shift_k+num_ids1, i-shift_i, Set2.get(k, i-num_snps1));
}
}
}
}//end of for cycle
*found_error_amount_id = errors_counter_id;
}
