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