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/*
Copyright (C) 2011 Tal Pupko TalP@tauex.tau.ac.il.
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
#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 '-' : case'_' : return -1; 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");
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 (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("0,1,2");
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;
return 0;
}
int gainLossAlphabet::fromChar(const string& str, const int pos) const{
return fromChar(str[pos]);
}
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