int main(int argc, char **argv)
{
ros::init(argc, argv, "lwrcontroller");
ros::NodeHandle n("~");
is_running = true;
LWRController lwr(n);
ros::spin();
std::cout << "About to exit...\n";
is_running = false;
usleep(2000000);
return 0;
}
void GetReady::addTF(GeneIM temp_gene_IM[],string TF_Gene_address)
{
ifstream data(TF_Gene_address.c_str());
char ch;
int i=gene_amount;
data.get(ch);
char STRING1[TFScale][10];
char *Name;
for(;i<TFScale;)
{
int num=0;
while(ch=='#')
{
string noUse;
getline(data,noUse);
data.get(ch);
}
while(ch!=' ')
{
STRING1[i][num]=ch;
data.get(ch);
num++;
}
STRING1[i][num]='\0';
Name=STRING1[i];
int j;
for(j=0;j<i;j++)
{
lwr(Name);
if(cmp(temp_gene_IM[j].gene_name,Name)==0)
{
j=i+1;
}
}
if(j==i)
{
temp_gene_IM[i].name=Name;
temp_gene_IM[i].putName();
temp_gene_IM[i].gene_number=i;
i++;
gene_amount++;
}
string noUse;
getline(data,noUse);
num=0;
if(!data.get(ch))
{
i=TFScale;
}
}
}
map<string,string> GetReady::mapPromoter(string promoters_address)
{
map<string,string> dictPromoter;
ifstream data(promoters_address.c_str());
char ch;
for(;data.get(ch);)
{
while(ch=='#')
{
string noUse;
getline(data,noUse);
data.get(ch);
}
string line;
char nameLine[20];
getline(data,line);
int j,i;
for(j=0;line[j]!=' ';j++){}
j++;
for(i=0;line[j]!=' ';i++)
{
nameLine[i]=line[j];
j++;
}
nameLine[i]='\0';
lwr(nameLine);
j++;
for(;line[j]!=' ';j++){}
j++;
for(;line[j]!=' ';j++){}
j++;
for(;line[j]!=' ';j++){}
j++;
char tempSequence[100];
for(i=0;line[j]!=' ';i++)
{
tempSequence[i]=line[j];
j++;
}
tempSequence[i]='\0';
upr(tempSequence);
string name=nameLine;
dictPromoter[name]=tempSequence;
}
return dictPromoter;
}
static int parse_month(const char *buf, int i, int len, int *val_return)
{
int j, k, l;
j = skip_word(buf, i, len);
if (j != i + 3)
return -1;
for (k = 0; k < 12; k++) {
for (l = 0; l < 3; l++) {
if (lwr(buf[i + l]) != month_names[k][l])
break;
}
if (l == 3)
break;
}
if (k >= 12)
return -1;
*val_return = k;
return j;
}
void GetReady::readTUPosition(string TU_position_address)
{
ifstream data(TU_position_address.c_str());
char ch;
for(;data.get(ch);)
{
while(ch=='#')
{
string noUse;
getline(data,noUse);
data.get(ch);
}
string line;
getline(data,line);
int i;
for(i=0;line[i]!=' ';i++){}
i++;
for(;line[i]!=' ';i++){}
i++;
char ProName[10];
int j;
for(j=0;line[i]!=' ';j++)
{
ProName[j]=line[i];
i++;
}
i++;
ProName[j]='\0';
lwr(ProName);
char TUPos[10];
for(j=0;line[i]!=' ';j++)
{
TUPos[j]=line[i];
i++;
}
TUPos[j]='\0';
string tempTUPos=TUPos;
promoter_name_dict.push_back(ProName);
TU_position.push_back(atoi(tempTUPos.c_str()));
}
}
map<string,string> GetReady::mapTFIM(string Gene_IM_address)
{
map<string,string> dictTFIM;
ifstream data(Gene_IM_address.c_str());
char ch;
int i;
for(i=1;data.get(ch);i++)
{
while(ch=='#')
{
string noUse;
getline(data,noUse);
data.get(ch);
}
string line;
char sline[30];
getline(data,line);
int j;
for(j=0;line[j]!='(';j++)
{
sline[j]=line[j];
}
sline[j]='\0';
lwr(sline);
int p;
for(p=0;sline[p]!=' ';p++)
{
}
char tempName[20];
string name;
for(int q=0;p<j;q++)
{
p++;
tempName[q]=sline[p];
}
name=tempName;
dictTFIM[name]=line;
}
return dictTFIM;
}
void GetReady::readTFGene(GeneIM temp_gene_IM[],double **old_GRN,string TF_Gene_address)
{
ifstream data(TF_Gene_address.c_str());
char ch;
int i,num=0;
char *Name;
char STRING1[GENEAM][10];
data.get(ch);
for(i=gene_amount;i<GENEAM;)
{
int a,b;
while(ch=='#')
{
string noUse;
getline(data,noUse);
data.get(ch);
}
while(ch!=' ')
{
STRING1[i][num]=ch;
data.get(ch);
num++;
}
STRING1[i][num]='\0';
Name=STRING1[i];
int j;
for(j=0;j<i;j++)
{
lwr(Name);
if(cmp(temp_gene_IM[j].gene_name,Name)==0)
{
a=j;
j=i+1;
}
}
if(j==i)
{
temp_gene_IM[i].name=Name;
temp_gene_IM[i].putName();
temp_gene_IM[i].gene_number=i;
a=i;
i++;
}
data.get(ch);
num=0;
while(ch!=' ')
{
STRING1[i][num]=ch;
data.get(ch);
num++;
}
STRING1[i][num]='\0';
Name=STRING1[i];
for(j=0;j<i;j++)
{
lwr(Name);
if(cmp(temp_gene_IM[j].gene_name,Name)==0)
{
b=j;
j=i+1;
}
}
if(j==i)
{
temp_gene_IM[i].name=Name;
temp_gene_IM[i].putName();
temp_gene_IM[i].gene_number=i;
b=i;
i++;
}
data.get(ch);
if(ch=='-')
{
if(old_GRN[b][a]==1||old_GRN[b][a]==2)
{
if(old_GRN[b][a]!=2)
uncertain<<"?\t"<<temp_gene_IM[b].getGeneName()<<"->"<<temp_gene_IM[a].getGeneName()<<endl;
old_GRN[b][a]=2;
uncertain_row.push_back(b);
uncertain_column.push_back(a);
unknow++;
}
else
old_GRN[b][a]=-1;
}
else if(ch=='+')
{
data.get(ch);
if(ch=='-')
{
old_GRN[b][a]=2;
uncertain_row.push_back(b);
uncertain_column.push_back(a);
uncertain<<"?\t"<<temp_gene_IM[b].getGeneName()<<"->"<<temp_gene_IM[a].getGeneName()<<endl;
unknow++;
}
else
old_GRN[b][a]=1;
}
else
old_GRN[b][a]=0;
string noUse;
getline(data,noUse);
num=0;
if(!data.get(ch))
{
gene_amount=i;
i=GENEAM;
}
}
}
