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#include "gainLossAlphabet.h"
gainLossAlphabet::gainLossAlphabet() {}
int gainLossAlphabet::fromChar(const char s) const{
switch (s) {
case '0': return 0; break;
case '1': return 1; break;
case '2': return 1; break; // added to read seq with paralogs
case '3': return 1; break; // added to read seq with paralogs
case '4': return 1; break; // added to read seq with paralogs
case '5': return 1; break; // added to read seq with paralogs
case '6': return 1; break; // added to read seq with paralogs
case '7': return 1; break; // added to read seq with paralogs
case '8': return 1; break; // added to read seq with paralogs
case '9': return 1; break; // added to read seq with paralogs
case '-' : case'_' : return -2; break;
case '?' : case'*' : return -2; break;
case 'x' : case'X' : return -2; break;
default:
vector<string> err;
err.push_back(" The gainLoss sequences contained the character: ");
err[0]+=s;
err.push_back(" gainLoss was not one of the following: ");
err.push_back(" 0, 1, or for unknown '?'/'-'");
errorMsg::reportError(err);
}// end of switch
return -99; // never suppose to be here.
}// end of function
vector<int> gainLossAlphabet::fromString(const string &str) const {
vector<int> vec;
for (unsigned int i=0;i<str.size();i++)
vec.push_back(fromChar(str[i]));
return vec;
}
string gainLossAlphabet::fromInt(const int in_id) const{
char res = 0;
switch (in_id) {
case 0 : res = '0' ; break;
case 1 : res = '1' ; break;
case -2 : res = '-'; break;
default:
vector<string> err;
err.push_back("unable to print gainLoss_id. gainLossl_id was not one of the following: ");
err.push_back("0,1");
errorMsg::reportError(err);
}//end of switch
string vRes;
vRes.append(1,res);
return vRes;
}// end of function
// There are no relations here.
int gainLossAlphabet::relations(const int charInSeq, const int charToCheck) const{
if (charInSeq == charToCheck)
return 1;
if(charInSeq == -1 || charInSeq == -2)
return 1 ;// missing data
return 0;
}
int gainLossAlphabet::fromChar(const string& str, const int pos) const{
return fromChar(str[pos]);
}
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